******************************** BUILD PASSED ******************************** Sun Nov 12 03:46:21 EST 2006 CVS checkout Projects/Builds directory cvs [checkout aborted]: connect to cvs.concord.org(63.138.119.217):2401 failed: Connection refused build:start: scm:parse-connection: [echo] Using connection: scm:cvs:ext:maven@cvs.concord.org:/home/buildspace/CodeBank:Projects/Biologica Using SCM method: cvs Using CVSROOT: :ext:maven@cvs.concord.org:/home/buildspace/CodeBank Using module: Projects/Biologica scm:validate: scm:checkout-project: scm:cvs-checkout-project: [echo] Checking out Projects/Biologica; from CVSROOT: :ext:maven@cvs.concord.org:/home/buildspace/CodeBank [delete] Deleting directory /home/maven/buildfiles/target/checkouts/Projects/Biologica [mkdir] Created dir: /home/maven/buildfiles/target/checkouts/Projects/Biologica [cvs] Using cvs passfile: /home/maven/.cvspass [cvs] U Projects/Biologica/.classpath [cvs] U Projects/Biologica/.cvsignore [cvs] U Projects/Biologica/.project [cvs] U Projects/Biologica/LICENSE.txt [cvs] U Projects/Biologica/build.xml [cvs] U Projects/Biologica/file_catalog.xml [cvs] U Projects/Biologica/jardesc.jardesc [cvs] U Projects/Biologica/project.properties [cvs] U Projects/Biologica/project.xml [cvs] U Projects/Biologica/src/org/concord/biologica/biologica.properties [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/bodies_large.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/bodies_medium.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/bodies_small.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/bodies_xlarge.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/bodies_xsmall.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/bodies_xxsmall.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/dead_large.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/dead_medium.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/dead_small.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/dead_xlarge.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/dead_xsmall.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/dead_xxsmall.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/fire_large.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/fire_medium.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/fire_small.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/fire_xlarge.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/fire_xsmall.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/fire_xxsmall.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/heads_large.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/heads_medium.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/heads_small.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/heads_xlarge.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/heads_xsmall.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/heads_xxsmall.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/invisible_large.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/invisible_medium.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/invisible_small.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/invisible_xlarge.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/invisible_xsmall.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/invisible_xxsmall.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/plates_large.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/plates_medium.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/plates_small.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/plates_xlarge.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/plates_xsmall.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/plates_xxsmall.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/scales_large.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/scales_medium.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/scales_small.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/scales_xlarge.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/scales_xsmall.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/scales_xxsmall.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/wings_large.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/wings_medium.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/wings_small.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/wings_xlarge.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/wings_xsmall.dat [cvs] U Projects/Biologica/src/org/concord/biologica/data/dragon/wings_xxsmall.dat [cvs] U Projects/Biologica/src/org/concord/biologica/datasupport/ColorUtil.java [cvs] U Projects/Biologica/src/org/concord/biologica/datasupport/DataOrganism.java [cvs] U Projects/Biologica/src/org/concord/biologica/datasupport/ImageReader.java [cvs] U Projects/Biologica/src/org/concord/biologica/datasupport/ShortImageDescription.java [cvs] U Projects/Biologica/src/org/concord/biologica/datasupport/SpecieFileDesc.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/AlgorithmicNucleicAcid.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/AminoAcid.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/Base.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/BehaviorRules.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/BioEngine.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/BioEngineBeanInfo.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/BioLogicaRule.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/BioLogicaSpecies.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/Branch.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/Characteristic.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/ChromosomeSpecification.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/Codon.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/CrossOver.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/Debug.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/ElementContext.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/Elements.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/EngineObject.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/EngineProp.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/EngineStrings.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/Environment.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/EnvironmentUnit.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/Family.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/FoodChain.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/Gamete.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/Gene.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/GenotypeToPhenotypeRule.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/IChromosome.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/IEnvironment.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/INucleicAcid.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/INucleicAcidHolder.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/ImportContext.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/InternalEngineException.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/NotBioLogicaFileException.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/NucleicAcid.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/ObjectDeletedException.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/ObjectLockedException.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/Organism.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/OrganismAllele.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/OrganismAllelePair.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/OrganismChromosome.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/OrganismChromosomePair.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/OrganismImage.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/PathStrings.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/RawNucleicAcid.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/Rule.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/Rules.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/Species.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/SpeciesAllele.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/SpeciesChromosome.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/SpeciesImage.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/SpeciesImageColumn.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/SpeciesImageRow.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/Terrain.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/TerrainEng.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/Trait.java [cvs] U Projects/Biologica/src/org/concord/biologica/engine/World.java [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/alignment.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/arrowleft.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/arrowright.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/backend.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/backfast.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/backone.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/backslow.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/bigfish_large.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/celltool.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/celltool_hilited.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/celltool_rollover.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/celltool_selected.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/cellvw.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/centromere.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/chromosome_collapsed.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/chromosome_expanded.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/chromosomes.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/chromosomes_meiosis.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/chromotool.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/chromotool_rollover.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/chromotool_selected.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/chromovw.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/collapsed.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/copy.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/crosstool.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/crosstool_rollover.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/crosstool_selected.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/cursor.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/cut.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/dna.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/dnatool.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/dnatool_rollover.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/dnatool_selected.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/dnavw.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/empty.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/engine.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/engine2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/engine3.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/environment.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/environment2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/environment3.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/environment_collapsed.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/environment_editing.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/environment_expanded.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/expanded.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/female.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/female2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/femtool.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/femtool_rollover.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/femtool_selected.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/folder_collapsed.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/folder_expanded.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/grayvw.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/help.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/helptool.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/helptool_rollover.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/helptool_selected.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/levels.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/levels_selected.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/lock.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_allele.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_allele1.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_allele2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_allele3.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_allele4.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_allele5.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_characteristic.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_characteristic2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_chromosome.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_chromosome2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_environment2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_environment3.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_gene.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_gene2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_organism2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_rule.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_rule2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_simage_column.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_simage_row.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_species.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_species2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_species_image.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_terrain2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_terrain3.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_trait.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_trait2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_trait3.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/locked_world2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/magdnglass.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/magupglass.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/male.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/male2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/maletool.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/maletool_rollover.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/maletool_selected.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/mate.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/mountain.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/mountains.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/multiorgvw.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/new.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/nosex.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/open.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/organism.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/organism2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/orgtool.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/orgtool_rollover.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/orgtool_selected.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/orgvw.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/orgvw2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/orgvw3.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/paste.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/pedtool.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/pedtool_rollover.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/pedtool_selected.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/pedvw.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/play.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/playend.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/playfast.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/playone.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/popvw.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/print.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/printpre.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/pspbrwse.jbf [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/pushvw.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/rule.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/save.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/selectorgvw.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/seltool.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/seltool_rollover.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/seltool_selected.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/selvw.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/singleorgvw.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/sniptool.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/sniptool_rollover.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/sniptool_selected.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/species.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/species_collapsed.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/species_expanded.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/speciesvw.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/stop.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/trait.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/trait_old.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/universe_collapsed.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/universe_expanded.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_allele.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_allele1.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_allele2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_allele3.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_allele4.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_allele5.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_characteristic.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_characteristic2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_chromosome.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_chromosome2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_environment2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_environment3.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_gene.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_gene2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_organism2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_rule.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_rule2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_simage_column.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_simage_row.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_species.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_species2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_species_image.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_terrain2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_terrain3.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_trait.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_trait2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_trait3.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unlocked_world2.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/unselvw.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/valignment.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/views.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/gifs/world.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/DNAhelp.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/MinMaxhelp.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/Xchromohelp.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/alignmentbutton.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/applybuttonhelp.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/arrowtoolhelp.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/chromotool.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/crosstoolhelp.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/cuttoolhelp.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/def_DNA.html [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/def_allele.html [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/def_base.html [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/def_chromosome.html [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/def_dominant.html [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/def_fertilization.html [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/def_gamete.html [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/def_gene.html [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/def_genotype.html [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/def_heterozygous.html [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/def_homozygous.html [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/def_meiosis.html [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/def_mutate.html [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/def_pedigree.html [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/def_phenotype.html [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/def_random.html [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/def_recessive.html [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/def_segregate.html [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/def_trait.html [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/glossary.html [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/gpPracticeHelp.html [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/introPractice.html [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/meioPracticeHelp.html [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/meiosisbuttons.jpg [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/minusmagnify.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/mutaPracticeHelp.html [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/pedigreePracticeHelp.html [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/plusmagnify.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/revertbuttonhelp.gif [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/screenshot.jpg [cvs] U Projects/Biologica/src/org/concord/biologica/locked/html/traits.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/species.xml [cvs] U Projects/Biologica/src/org/concord/biologica/species/Bigfish/bigfish_large.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/Mediumfish/mediumfish_large.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/Pisum Sativum/Flowerstem_large.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/Pisum Sativum/Flowerstem_medium.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/Pisum Sativum/Flowerstem_small.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/Pisum Sativum/Flowerstem_xlarge.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/Pisum Sativum/Pod_large.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/Pisum Sativum/Pod_medium.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/Pisum Sativum/Pod_small.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/Pisum Sativum/Pod_xlarge.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/Pisum Sativum/Seed_large.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/Pisum Sativum/Seed_medium.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/Pisum Sativum/Seed_small.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/Pisum Sativum/Seed_xlarge.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/Pisum Sativum/sshape_large.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/Pisum Sativum/sshape_medium.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/Pisum Sativum/sshape_small.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/Pisum Sativum/sshape_xlarge.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/Pisum Sativum/sshape_xsmall.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/Pisum Sativum/sshape_xxsmall.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/Smallfish/smallfish_large.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/arabidopsis/dead_large.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/arabidopsis/dead_medium.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/arabidopsis/dead_small.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/arabidopsis/dead_xlarge.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/arabidopsis/dead_xsmall.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/arabidopsis/dead_xxsmall.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/arabidopsis/flowers_large.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/arabidopsis/flowers_medium.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/arabidopsis/flowers_small.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/arabidopsis/flowers_xlarge.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/arabidopsis/flowers_xsmall.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/arabidopsis/flowers_xxsmall.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/arabidopsis/invisible_large.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/arabidopsis/invisible_medium.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/arabidopsis/invisible_small.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/arabidopsis/invisible_xlarge.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/arabidopsis/invisible_xsmall.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/arabidopsis/invisible_xxsmall.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/arabidopsis/plants_large.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/arabidopsis/plants_medium.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/arabidopsis/plants_small.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/arabidopsis/plants_xlarge.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/arabidopsis/plants_xsmall.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/arabidopsis/plants_xxsmall.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/budgie/blue_large.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/budgie/blue_medium.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/budgie/green_large.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/budgie/green_medium.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/budgie/white_large.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/budgie/white_medium.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/budgie/yellow_large.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/budgie/yellow_medium.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/bodies_large.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/bodies_medium.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/bodies_small.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/bodies_xlarge.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/bodies_xsmall.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/bodies_xxsmall.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/dead_large.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/dead_medium.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/dead_small.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/dead_xlarge.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/dead_xsmall.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/dead_xxsmall.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/fire_large.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/fire_medium.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/fire_small.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/fire_xlarge.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/fire_xsmall.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/fire_xxsmall.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/heads_large.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/heads_medium.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/heads_small.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/heads_xlarge.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/heads_xsmall.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/heads_xxsmall.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/invisible_large.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/invisible_medium.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/invisible_small.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/invisible_xlarge.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/invisible_xsmall.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/invisible_xxsmall.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/plates_large.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/plates_medium.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/plates_small.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/plates_xlarge.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/plates_xsmall.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/plates_xxsmall.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/scales_large.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/scales_medium.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/scales_small.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/scales_xlarge.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/scales_xsmall.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/scales_xxsmall.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/wings_large.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/wings_medium.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/wings_small.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/wings_xlarge.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/wings_xsmall.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/dragon/wings_xxsmall.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/hamster/golden_hamster_large.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/hamster/golden_hamster_medium.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/hamster/grey_hamster_large.gif [cvs] U Projects/Biologica/src/org/concord/biologica/species/hamster/grey_hamster_medium.gif [cvs] U Projects/Biologica/src/org/concord/biologica/test/TestWindow.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/AllInOneView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/BigFertilizationView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/BigMeiosisView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/BioComboBox.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/BioComboBoxModel.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/BioDialogBox.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/BioLogicaViewManager.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/BioToolBar.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/CCDraggable.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/CellArc.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/CellLine.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/CharacteristicView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/ChromosomePracticeView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/ChromosomeView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/CursorText.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/DNAView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/EnvironmentView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/EnvironmentZoomInViewDialogBox.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/FertilizationChromosomeModel.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/FertilizationModel.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/FilledCircle.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/GifFileFilter.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/GlossaryFrame.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/LocalImageIcon.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/MeiosisChromosomeModel.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/MeiosisModel.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/MeiosisPracticeView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/MeiosisView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/MultipleOrganismView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/MutationsPracticeView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/ObjectPropertiesView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/OrganismAlleleControl.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/OrganismView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/PatchView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/PedigreeFamily.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/PedigreeLevel.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/PedigreeObject.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/PedigreeOrganism.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/PedigreeOrganismView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/PedigreePracticeView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/PedigreeView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/PracticeView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/SelectionPresenter.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/SelectionSet.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/SexOrganismView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/SexView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/SmallFertilizationView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/SmallMeiosisView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/SpeciesFileFilter.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/SpindleLine.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/StaticOrganismView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/TerrainEngView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/TerrainPatch.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/Tool.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/ToolView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/TreeView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/TreeViewCellRenderer.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/TreeViewModel.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/TreeViewNode.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/UIGraphics.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/UIProp.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/UIView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/WelcomeView.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/WorldFileFilter.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/XMLFileFilter.java [cvs] U Projects/Biologica/src/org/concord/biologica/ui/sound/pinhit.au [cvs] U Projects/Biologica/src/org/concord/biologica/ui/sound/pinhit.wav [cvs] U Projects/Biologica/src/org/concord/biologica/worlds/arabidopsis.xml [cvs] U Projects/Biologica/src/org/concord/biologica/worlds/budgie.xml [cvs] U Projects/Biologica/src/org/concord/biologica/worlds/dragon.xml [cvs] U Projects/Biologica/src/org/concord/biologica/worlds/dragonmf1.xml [cvs] U Projects/Biologica/src/org/concord/biologica/worlds/fishworld.xml [cvs] U Projects/Biologica/src/org/concord/biologica/worlds/hamster.xml [cvs] U Projects/Biologica/src/org/concord/biologica/worlds/peasimple.xml [cvs] U Projects/Biologica/src/org/concord/biologica/worlds/pisum.xml BUILD SUCCESSFUL Total time: 7 seconds Finished at: Sun Nov 12 03:32:48 EST 2006 Attempting to download framework-SNAPSHOT.jar. 16/104K 32/104K 48/104K 64/104K 80/104K 104/104K 104K downloaded Attempting to download loader-SNAPSHOT.jar. 64/172K 96/172K 144/172K 172/172K 172K downloaded build:start: ant:generate-build: [echo] Generating /home/maven/buildfiles/target/checkouts/Projects/Biologica/build.xml BUILD SUCCESSFUL Total time: 3 seconds Finished at: Sun Nov 12 03:32:53 EST 2006 Attempting to download framework-SNAPSHOT.jar. Attempting to download loader-SNAPSHOT.jar. build:start: site:deploy: site: xdoc:register-reports: maven-jdepend-plugin:register: maven-checkstyle-plugin:register: maven-changes-plugin:register: maven-changelog-plugin:register: maven-developer-activity-plugin:register: maven-file-activity-plugin:register: maven-license-plugin:register: xdoc:init: [mkdir] Created dir: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/generated-xdocs [mkdir] Created dir: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs maven-javadoc-plugin:register: [mkdir] Created dir: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/javadoc [mkdir] Created dir: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/javadoc/src maven-jxr-plugin:register: maven-junit-report-plugin:register: maven-linkcheck-plugin:register: maven-tasklist-plugin:register: site:run-reports: [echo] Generating the Metrics... maven-jdepend-plugin:report: java:prepare-filesystem: [mkdir] Created dir: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/classes java:compile: [echo] Compiling to /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/classes [echo] ========================================================== NOTE: Targetting JVM 1.5, classes will not run on earlier JVMs ========================================================== [javac] Compiling 127 source files to /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/classes /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/Tool.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1999, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/MultipleOrganismView.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/SpindleLine.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1999, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/MeiosisChromosomeModel.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeFamily.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/AllInOneView.java:29: warning: unmappable character for encoding ASCII // Copyright ? 1999, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/MeiosisModel.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/MeiosisView.java:28: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/LocalImageIcon.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/CharacteristicView.java:28: warning: unmappable character for encoding ASCII //Copyright ??? 2004, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/CharacteristicView.java:28: warning: unmappable character for encoding ASCII //Copyright ??? 2004, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/CharacteristicView.java:28: warning: unmappable character for encoding ASCII //Copyright ??? 2004, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/FertilizationModel.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/MutationsPracticeView.java:28: warning: unmappable character for encoding ASCII * Copyright ? 2000, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/OrganismAlleleControl.java:28: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/CellLine.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1999, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/DNAView.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1999, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/BioDialogBox.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1999, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/OrganismView.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/SexView.java:28: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/CellArc.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1999, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/FertilizationChromosomeModel.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/FilledCircle.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1999, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/SpeciesFileFilter.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/BioToolBar.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/UIProp.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/UIView.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/GlossaryFrame.java:28: warning: unmappable character for encoding ASCII * Copyright ? 2000, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/SelectionSet.java:30: warning: unmappable character for encoding ASCII // Copyright ? 1999, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/ToolView.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1999, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/SelectionPresenter.java:29: warning: unmappable character for encoding ASCII // Copyright ? 1999, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/TreeView.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/TreeViewModel.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/WorldFileFilter.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeOrganism.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/TreeViewCellRenderer.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/WelcomeView.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/GifFileFilter.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/SmallFertilizationView.java:28: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/MeiosisPracticeView.java:28: warning: unmappable character for encoding ASCII * Copyright ? 2000, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeOrganismView.java:30: warning: unmappable character for encoding ASCII // Copyright ? 1999, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeView.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/XMLFileFilter.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreePracticeView.java:28: warning: unmappable character for encoding ASCII * Copyright ? 2000, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeObject.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/SmallMeiosisView.java:28: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/StaticOrganismView.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/BigFertilizationView.java:28: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/ChromosomeView.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/BioLogicaViewManager.java:28: warning: unmappable character for encoding ASCII * Copyright ? 2000, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/SexOrganismView.java:28: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/TreeViewNode.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/UIGraphics.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/ChromosomePracticeView.java:27: warning: unmappable character for encoding ASCII * Copyright ? 2000, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeLevel.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PracticeView.java:28: warning: unmappable character for encoding ASCII * Copyright ? 2000, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/BigMeiosisView.java:28: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/ObjectPropertiesView.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/BioComboBox.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/test/TestWindow.java:28: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/World.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/PathStrings.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1999, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/RawNucleicAcid.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1997, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/INucleicAcid.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1997, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/OrganismAllele.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1997, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Gene.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Environment.java:30: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Base.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1997, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/AminoAcid.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1997, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/TerrainEng.java:30: warning: unmappable character for encoding ASCII //Copyright ??? 2002, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/TerrainEng.java:30: warning: unmappable character for encoding ASCII //Copyright ??? 2002, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/TerrainEng.java:30: warning: unmappable character for encoding ASCII //Copyright ??? 2002, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/ObjectDeletedException.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1997, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/OrganismAllelePair.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1999, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/OrganismChromosome.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1997, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Rules.java:29: warning: unmappable character for encoding ASCII //Copyright ? 2002, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/EngineProp.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Organism.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1997, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesImageColumn.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/EngineStrings.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1997, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/GenotypeToPhenotypeRule.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1997, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Codon.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1997, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/BioEngine.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Species.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1997, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/INucleicAcidHolder.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1997, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesChromosome.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1997, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/NucleicAcid.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1997, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/AlgorithmicNucleicAcid.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1997, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/NotBioLogicaFileException.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesAllele.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1997, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/IChromosome.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Rule.java:30: warning: unmappable character for encoding ASCII //Copyright ? 2004, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/InternalEngineException.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1997, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesImageRow.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/ElementContext.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1999, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/EngineObject.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/ObjectLockedException.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Characteristic.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1997, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Family.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/ChromosomeSpecification.java:27: warning: unmappable character for encoding ASCII // Copyright ? 1998, The Concord Consortium ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings [echo] Generating the Checkstyle... checkstyle:init: checkstyle:report: checkstyle:run: [echo] Using file:/home/maven/.maven/cache/maven-checkstyle-plugin-2.5/plugin-resources/sun_checks.xml for checkstyle ... [mkdir] Created dir: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/images [copy] Copying 1 file to /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/images [echo] Generating the Change Log... maven-changelog-plugin:report: [echo] Generating the Developer Activity... maven-developer-activity-plugin:report: [echo] Generating the File Activity... maven-file-activity-plugin:report: [echo] Generating the Project License... maven-license-plugin:report: xdoc:init: license:transfer: license: [echo] Generating the JavaDocs... xdoc:init: maven-javadoc-plugin:report: [mkdir] Created dir: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/apidocs [javadoc] Generating Javadoc [javadoc] Javadoc execution [javadoc] Loading source files for package org.concord.biologica.ui... [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/Tool.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1999, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/MultipleOrganismView.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/SpindleLine.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1999, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/MeiosisChromosomeModel.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeFamily.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/AllInOneView.java:29: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1999, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/MeiosisModel.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/MeiosisView.java:28: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/LocalImageIcon.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/CharacteristicView.java:28: warning: unmappable character for encoding ASCII [javadoc] //Copyright ??? 2004, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/CharacteristicView.java:28: warning: unmappable character for encoding ASCII [javadoc] //Copyright ??? 2004, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/CharacteristicView.java:28: warning: unmappable character for encoding ASCII [javadoc] //Copyright ??? 2004, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/FertilizationModel.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/MutationsPracticeView.java:28: warning: unmappable character for encoding ASCII [javadoc] * Copyright ? 2000, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/OrganismAlleleControl.java:28: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/CellLine.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1999, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/DNAView.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1999, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/BioDialogBox.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1999, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/OrganismView.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/SexView.java:28: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/CellArc.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1999, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/FertilizationChromosomeModel.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/FilledCircle.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1999, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/SpeciesFileFilter.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/BioToolBar.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/UIProp.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/UIView.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/GlossaryFrame.java:28: warning: unmappable character for encoding ASCII [javadoc] * Copyright ? 2000, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/SelectionSet.java:30: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1999, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/ToolView.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1999, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/SelectionPresenter.java:29: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1999, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/TreeView.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/TreeViewModel.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/WorldFileFilter.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeOrganism.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/TreeViewCellRenderer.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/WelcomeView.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/GifFileFilter.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/SmallFertilizationView.java:28: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/MeiosisPracticeView.java:28: warning: unmappable character for encoding ASCII [javadoc] * Copyright ? 2000, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeOrganismView.java:30: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1999, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeView.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/XMLFileFilter.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreePracticeView.java:28: warning: unmappable character for encoding ASCII [javadoc] * Copyright ? 2000, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeObject.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/SmallMeiosisView.java:28: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/StaticOrganismView.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/BigFertilizationView.java:28: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/ChromosomeView.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/BioLogicaViewManager.java:28: warning: unmappable character for encoding ASCII [javadoc] * Copyright ? 2000, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/SexOrganismView.java:28: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/TreeViewNode.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/UIGraphics.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/ChromosomePracticeView.java:27: warning: unmappable character for encoding ASCII [javadoc] * Copyright ? 2000, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeLevel.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PracticeView.java:28: warning: unmappable character for encoding ASCII [javadoc] * Copyright ? 2000, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/BigMeiosisView.java:28: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/ObjectPropertiesView.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] Loading source files for package org.concord.biologica.test... [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/BioComboBox.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] Loading source files for package org.concord.biologica.engine... [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/test/TestWindow.java:28: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/World.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/PathStrings.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1999, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/RawNucleicAcid.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1997, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/INucleicAcid.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1997, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/OrganismAllele.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1997, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Gene.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Environment.java:30: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Base.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1997, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/AminoAcid.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1997, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/TerrainEng.java:30: warning: unmappable character for encoding ASCII [javadoc] //Copyright ??? 2002, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/TerrainEng.java:30: warning: unmappable character for encoding ASCII [javadoc] //Copyright ??? 2002, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/TerrainEng.java:30: warning: unmappable character for encoding ASCII [javadoc] //Copyright ??? 2002, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/ObjectDeletedException.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1997, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/OrganismAllelePair.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1999, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/OrganismChromosome.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1997, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Rules.java:29: warning: unmappable character for encoding ASCII [javadoc] //Copyright ? 2002, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/EngineProp.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Organism.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1997, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesImageColumn.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/EngineStrings.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1997, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/GenotypeToPhenotypeRule.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1997, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Codon.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1997, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/BioEngine.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Species.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1997, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/INucleicAcidHolder.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1997, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesChromosome.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1997, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/NucleicAcid.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1997, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/AlgorithmicNucleicAcid.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1997, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/NotBioLogicaFileException.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesAllele.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1997, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/IChromosome.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Rule.java:30: warning: unmappable character for encoding ASCII [javadoc] //Copyright ? 2004, The Concord Consortium [javadoc] ^ [javadoc] Loading source files for package org.concord.biologica.datasupport... [javadoc] Constructing Javadoc information... [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/InternalEngineException.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1997, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesImageRow.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/ElementContext.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1999, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/EngineObject.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/ObjectLockedException.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Characteristic.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1997, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Family.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/ChromosomeSpecification.java:27: warning: unmappable character for encoding ASCII [javadoc] // Copyright ? 1998, The Concord Consortium [javadoc] ^ [javadoc] Standard Doclet version 1.5.0_07 [javadoc] Building tree for all the packages and classes... [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/BioComboBox.java:71: warning - @beaninfo is an unknown tag. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/FertilizationChromosomeModel.java:410: warning - @param argument "newEnlosingViewRectangle" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/MeiosisChromosomeModel.java:563: warning - @param argument "aChromosomeVisiblePairNumber" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/MeiosisChromosomeModel.java:881: warning - @param argument "newEnlosingViewRectangle" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/MeiosisChromosomeModel.java:1872: warning - @param argument "OrganismAllele[]" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/MeiosisChromosomeModel.java:1986: warning - @param argument "Color[]" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/MeiosisModel.java:1946: warning - @param argument "Array" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/MeiosisView.java:1310: warning - @param argument "aReplayButtonEnabled" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/MeiosisView.java:1340: warning - @param argument "aReplayButtonVisible" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/MeiosisView.java:1376: warning - @param argument "aReplayButtonEnabled" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/ObjectPropertiesView.java:1504: warning - @param argument "anEngineObject" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/OrganismAlleleControl.java:160: warning - @param argument "aFont" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeFamily.java:319: warning - @param argument "Point" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeFamily.java:319: warning - @param argument "Point" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeFamily.java:747: warning - @param argument "pedigreeOrganismView" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeFamily.java:782: warning - @param argument "pedigreeOrganismView" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeLevel.java:202: warning - @param argument "aPedigreeOrganism" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeLevel.java:588: warning - @param argument "pedigreeOrganismView" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeLevel.java:621: warning - @param argument "pedigreeOrganismView" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeObject.java:346: warning - @param argument "pedigreeOrganismView" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeOrganism.java:109: warning - @param argument "pedigreeOrganismView" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeOrganismView.java:607: warning - @ is an unknown tag. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeOrganismView.java:1383: warning - @param argument "anOffspringPulldown" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeOrganismView.java:2108: warning - @return tag cannot be used in method with void return type. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeView.java:782: warning - @param argument "aFamily" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeView.java:1242: warning - @param argument "aCrossOverEnabled" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/PedigreeView.java:2140: warning - @param argument "onlyLiveChildren" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/SelectionSet.java:363: warning - @param argument "boolean" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/SelectionSet.java:407: warning - @param argument "Enumeration" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/SexView.java:1372: warning - @param argument "aReplayButtonEnabled" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/SexView.java:1402: warning - @param argument "aReplayButtonVisible" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/SexView.java:1438: warning - @param argument "aReplayButtonEnabled" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/IEnvironment.java:74: warning - @return tag has no arguments. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/IEnvironment.java:84: warning - @return tag has no arguments. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/IEnvironment.java:64: warning - @return tag has no arguments. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/ToolView.java:141: warning - @param argument "anOrientation" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/TreeView.java:285: warning - @param argument "anEngineObject" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/TreeView.java:397: warning - @param argument "oldSelectedState" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/TreeView.java:397: warning - @param argument "newSelectedState" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/AlgorithmicNucleicAcid.java:435: warning - @param argument "int" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/BioEngineBeanInfo.java:105: warning - @param argument "iconKind" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Characteristic.java:255: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Characteristic.java:312: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/CrossOver.java:50: warning - @param argument "parentOne" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/CrossOver.java:50: warning - @param argument "parentTwo" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/CrossOver.java:50: warning - @param argument "blnCrossOver" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/CrossOver.java:91: warning - @param argument "blnCrossOver" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/CrossOver.java:166: warning - @param argument "po" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Debug.java:218: warning - @obj is an unknown tag. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/ElementContext.java:184: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Environment.java:249: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Environment.java:304: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Family.java:757: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Family.java:757: warning - @param argument "amap" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Family.java:812: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Family.java:1159: warning - @param argument "int" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Gene.java:295: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Gene.java:295: warning - @param argument "amap" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Gene.java:358: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Gene.java:746: warning - @param argument "int" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/GenotypeToPhenotypeRule.java:321: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/GenotypeToPhenotypeRule.java:321: warning - @param argument "amap" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/GenotypeToPhenotypeRule.java:377: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/GenotypeToPhenotypeRule.java:878: warning - @param argument "SpeciesAllele" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/GenotypeToPhenotypeRule.java:878: warning - @param argument "SpeciesAllele" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/IEnvironment.java:49: warning - @return tag has no arguments. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/IEnvironment.java:44: warning - @return tag has no arguments. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/INucleicAcid.java:123: warning - @param argument "locked" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/INucleicAcidHolder.java:95: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/NucleicAcid.java:493: warning - @param argument "int" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Organism.java:1479: warning - @param argument "aMother" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Organism.java:1479: warning - @param argument "aFather" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Organism.java:1785: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Organism.java:1785: warning - @param argument "amap" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Organism.java:1873: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/OrganismAllele.java:259: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/OrganismAllele.java:259: warning - @param argument "amap" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/OrganismAllele.java:319: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/OrganismAllelePair.java:191: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/OrganismAllelePair.java:191: warning - @param argument "amap" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/OrganismAllelePair.java:244: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/OrganismChromosome.java:357: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/OrganismChromosome.java:357: warning - @param argument "amap" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/OrganismChromosome.java:418: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/OrganismChromosomePair.java:243: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/OrganismChromosomePair.java:243: warning - @param argument "amap" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/OrganismChromosomePair.java:302: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/OrganismImage.java:217: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/OrganismImage.java:217: warning - @param argument "amap" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/OrganismImage.java:271: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/RawNucleicAcid.java:190: warning - @param argument "RawNucleicAcid" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/RawNucleicAcid.java:306: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/RawNucleicAcid.java:306: warning - @param argument "amap" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/RawNucleicAcid.java:360: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/RawNucleicAcid.java:634: warning - @param argument "int" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Species.java:410: warning - @param argument "anImageColumnWidth" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Species.java:410: warning - @param argument "anImageRowHeight" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Species.java:605: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Species.java:605: warning - @param argument "amap" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Species.java:705: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesAllele.java:267: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesAllele.java:267: warning - @param argument "amap" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesAllele.java:329: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesAllele.java:876: warning - @param argument "String" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesChromosome.java:384: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesChromosome.java:384: warning - @param argument "amap" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesChromosome.java:445: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesImage.java:769: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesImage.java:769: warning - @param argument "amap" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesImage.java:864: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesImageColumn.java:216: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesImageColumn.java:216: warning - @param argument "amap" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesImageColumn.java:270: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesImageColumn.java:741: warning - @param argument "Characteristic" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesImageColumn.java:741: warning - @param argument "Characteristic" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesImageRow.java:97: warning - Tag @see: can't find ROW_GENDER in org.concord.biologica.engine.EngineProp [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesImageRow.java:272: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesImageRow.java:272: warning - @param argument "amap" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesImageRow.java:332: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesImageRow.java:884: warning - @param argument "Characteristic" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/SpeciesImageRow.java:884: warning - @param argument "Characteristic" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Terrain.java:190: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Terrain.java:190: warning - @param argument "amap" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Terrain.java:243: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/TerrainEng.java:548: warning - @return tag has no arguments. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Trait.java:240: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Trait.java:240: warning - @param argument "amap" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Trait.java:300: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/World.java:319: warning - @param argument "urlString" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/World.java:1692: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/World.java:1692: warning - @param argument "amap" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/World.java:1766: warning - @param argument "anElementName" is not a parameter name. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/engine/Organism.java:4505: warning - Tag @param cannot be used in field documentation. It can only be used in the following types of documentation: class/interface, constructor, method. [javadoc] /home/maven/buildfiles/target/checkouts/Projects/Biologica/src/org/concord/biologica/ui/BigMeiosisView.java:1004: warning - Tag @param cannot be used in field documentation. It can only be used in the following types of documentation: class/interface, constructor, method. [javadoc] Generating /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/apidocs/serialized-form.html... [javadoc] Copying file /home/maven/.maven/cache/maven-javadoc-plugin-1.7/plugin-resources/stylesheet.css to file /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/apidocs/stylesheet.css... [javadoc] Building index for all the packages and classes... [javadoc] Building index for all classes... [javadoc] Generating /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/apidocs/help-doc.html... [javadoc] 234 warnings [delete] Deleting directory /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/javadoc/src [echo] Generating the Source Xref... maven-jxr-plugin:report: [mkdir] Created dir: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/xref [echo] [copy] Copying 1 file to /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/xref Scanning /home/maven/buildfiles/target/checkouts/Projects/Biologica/src [echo] Generating the Link Check Report... maven-linkcheck-plugin:report: [copy] Copying 1 file to /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/generated-xdocs [echo] Generating the Task List... xdoc:init: maven-tasklist-plugin:report: [echo] Generating tasklist ... xdoc:init: xdoc:register-reports: maven-jdepend-plugin:register: maven-checkstyle-plugin:register: maven-changes-plugin:register: maven-changelog-plugin:register: maven-developer-activity-plugin:register: maven-file-activity-plugin:register: maven-license-plugin:register: xdoc:init: maven-javadoc-plugin:register: maven-jxr-plugin:register: maven-junit-report-plugin:register: maven-linkcheck-plugin:register: maven-tasklist-plugin:register: xdoc:generate-from-pom: [echo] Generating xdocs from POM ... xdoc:transform: xdoc:init: xdoc:copy-resources: [copy] Copying 4 files to /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/style [copy] Copying 94 files to /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/images About to use JSL stylesheet file:/home/maven/.maven/cache/maven-xdoc-plugin-1.8/plugin-resources/site.jsl xdoc:init: xdoc:copy-user-resources: xdoc:init: xdoc:jelly-init: xdoc:register-reports: maven-jdepend-plugin:register: maven-checkstyle-plugin:register: maven-changes-plugin:register: maven-changelog-plugin:register: maven-developer-activity-plugin:register: maven-file-activity-plugin:register: maven-license-plugin:register: xdoc:init: maven-javadoc-plugin:register: maven-jxr-plugin:register: maven-junit-report-plugin:register: maven-linkcheck-plugin:register: maven-tasklist-plugin:register: xdoc:jelly-transform: [echo] Generating /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/dependencies.html from /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/generated-xdocs/dependencies.xml [echo] Generating /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/downloads.html from /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/generated-xdocs/downloads.xml [echo] Generating /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/maven-reports.html from /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/generated-xdocs/maven-reports.xml [echo] Generating /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/linkcheck.html from /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/generated-xdocs/linkcheck.xml [echo] Generating /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/cvs-usage.html from /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/generated-xdocs/cvs-usage.xml [echo] Generating /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/issue-tracking.html from /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/generated-xdocs/issue-tracking.xml [echo] Generating /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/task-list.html from /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/generated-xdocs/task-list.xml [echo] Generating /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/checkstyle-report.html from /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/generated-xdocs/checkstyle-report.xml [echo] Generating /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/mail-lists.html from /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/generated-xdocs/mail-lists.xml [echo] Generating /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/project-info.html from /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/generated-xdocs/project-info.xml [echo] Generating /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/javadoc.html from /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/generated-xdocs/javadoc.xml [echo] Generating /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/index.html from /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/generated-xdocs/index.xml [echo] Generating /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/license.html from /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/generated-xdocs/license.xml [echo] Generating /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/javadoc-warnings-report.html from /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/generated-xdocs/javadoc-warnings-report.xml [echo] Generating /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/team-list.html from /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/generated-xdocs/team-list.xml [echo] Generating /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/jdepend-report.html from /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/generated-xdocs/jdepend-report.xml maven-linkcheck-plugin:report-real: [mkdir] Created dir: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/linkcheck [mkdir] Created dir: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/linkcheck/docs maven-linkcheck-plugin: Not using a proxy Found 0 files so far. Memory: 282M/305M Validating downloads.html Checking link http://maven.apache.org/ Checking link http://maven.apache.org/development-process.html Checking link http://source.concord.org/ Checking link http://www.concord.org Checking link http://www.concord.org/global-images/small_trans_logo_75.gif Received: [404] for http://www.concord.org/global-images/small_trans_logo_75.gif Received: [404] for http://www.concord.org/global-images/small_trans_logo_75.gif Validating team-list.html Validating linkcheck.html Validating dependencies.html Validating javadoc-warnings-report.html Validating jdepend-report.html Checking link http://www.clarkware.com/software/JDepend.html Received: [412] for http://www.clarkware.com/software/JDepend.html Received: [412] for http://www.clarkware.com/software/JDepend.html Validating issue-tracking.html Validating checkstyle-report.html Caught java.lang.OutOfMemoryError: Java heap space processing checkstyle-report.html Exception Message: Java heap space Validating index.html Validating project-info.html Validating mail-lists.html Validating task-list.html Validating javadoc.html Validating maven-reports.html Validating apidocs/allclasses-frame.html Validating apidocs/overview-summary.html Validating apidocs/org/concord/biologica/ui/TerrainEngView.html Validating apidocs/org/concord/biologica/ui/FertilizationChromosomeModel.html Validating apidocs/org/concord/biologica/ui/Tool.html Validating apidocs/org/concord/biologica/ui/PracticeView.html Validating apidocs/org/concord/biologica/ui/SpeciesFileFilter.html Validating apidocs/org/concord/biologica/ui/MeiosisPracticeView.html Validating apidocs/org/concord/biologica/ui/EnvironmentView.html Validating apidocs/org/concord/biologica/ui/ChromosomePracticeView.html Validating apidocs/org/concord/biologica/ui/BigFertilizationView.html Validating apidocs/org/concord/biologica/ui/PedigreeFamily.html Validating apidocs/org/concord/biologica/ui/SmallFertilizationView.html Validating apidocs/org/concord/biologica/ui/PedigreeView.html Validating apidocs/org/concord/biologica/ui/ObjectPropertiesView.html Validating apidocs/org/concord/biologica/ui/OrganismView.html Validating apidocs/org/concord/biologica/ui/FilledCircle.html Validating apidocs/org/concord/biologica/ui/MeiosisModel.html Validating apidocs/org/concord/biologica/ui/AllInOneView.html Validating apidocs/org/concord/biologica/ui/CharacteristicView.html Validating apidocs/org/concord/biologica/ui/WorldFileFilter.html Validating apidocs/org/concord/biologica/ui/CellArc.html Validating apidocs/org/concord/biologica/ui/GifFileFilter.html Validating apidocs/org/concord/biologica/ui/UIGraphics.html Validating apidocs/org/concord/biologica/ui/class-use/TerrainEngView.html Validating apidocs/org/concord/biologica/ui/class-use/FertilizationChromosomeModel.html Validating apidocs/org/concord/biologica/ui/class-use/Tool.html Validating apidocs/org/concord/biologica/ui/class-use/PracticeView.html Validating apidocs/org/concord/biologica/ui/class-use/SpeciesFileFilter.html Validating apidocs/org/concord/biologica/ui/class-use/MeiosisPracticeView.html Validating apidocs/org/concord/biologica/ui/class-use/EnvironmentView.html Validating apidocs/org/concord/biologica/ui/class-use/ChromosomePracticeView.html Validating apidocs/org/concord/biologica/ui/class-use/BigFertilizationView.html Validating apidocs/org/concord/biologica/ui/class-use/PedigreeFamily.html Validating apidocs/org/concord/biologica/ui/class-use/SmallFertilizationView.html Validating apidocs/org/concord/biologica/ui/class-use/PedigreeView.html Validating apidocs/org/concord/biologica/ui/class-use/ObjectPropertiesView.html Validating apidocs/org/concord/biologica/ui/class-use/OrganismView.html Validating apidocs/org/concord/biologica/ui/class-use/FilledCircle.html Validating apidocs/org/concord/biologica/ui/class-use/MeiosisModel.html Validating apidocs/org/concord/biologica/ui/class-use/AllInOneView.html Validating apidocs/org/concord/biologica/ui/class-use/CharacteristicView.html Validating apidocs/org/concord/biologica/ui/class-use/WorldFileFilter.html Validating apidocs/org/concord/biologica/ui/class-use/CellArc.html Validating apidocs/org/concord/biologica/ui/class-use/GifFileFilter.html Validating apidocs/org/concord/biologica/ui/class-use/UIGraphics.html Validating apidocs/org/concord/biologica/ui/class-use/UIView.html Validating apidocs/org/concord/biologica/ui/class-use/OrganismAlleleControl.html Validating apidocs/org/concord/biologica/ui/class-use/TerrainPatch.html Validating apidocs/org/concord/biologica/ui/class-use/PedigreeLevel.html Validating apidocs/org/concord/biologica/ui/class-use/BioLogicaViewManager.html Validating apidocs/org/concord/biologica/ui/class-use/TreeViewCellRenderer.html Validating apidocs/org/concord/biologica/ui/class-use/FertilizationModel.html Validating apidocs/org/concord/biologica/ui/class-use/PedigreeObject.html Validating apidocs/org/concord/biologica/ui/class-use/SpindleLine.html Validating apidocs/org/concord/biologica/ui/class-use/GlossaryFrame.html Validating apidocs/org/concord/biologica/ui/class-use/BioDialogBox.html Validating apidocs/org/concord/biologica/ui/class-use/LocalImageIcon.html Validating apidocs/org/concord/biologica/ui/class-use/DNAView.html Validating apidocs/org/concord/biologica/ui/class-use/ChromosomeView.html Validating apidocs/org/concord/biologica/ui/class-use/BioComboBox.html Validating apidocs/org/concord/biologica/ui/class-use/UIProp.html Validating apidocs/org/concord/biologica/ui/class-use/StaticOrganismView.html Validating apidocs/org/concord/biologica/ui/class-use/PedigreePracticeView.html Validating apidocs/org/concord/biologica/ui/class-use/SexView.html Validating apidocs/org/concord/biologica/ui/class-use/SexOrganismView.html Validating apidocs/org/concord/biologica/ui/class-use/MutationsPracticeView.html Validating apidocs/org/concord/biologica/ui/class-use/MeiosisView.html Validating apidocs/org/concord/biologica/ui/class-use/MeiosisChromosomeModel.html Validating apidocs/org/concord/biologica/ui/class-use/CellLine.html Validating apidocs/org/concord/biologica/ui/class-use/CursorText.html Validating apidocs/org/concord/biologica/ui/class-use/TreeViewModel.html Validating apidocs/org/concord/biologica/ui/class-use/ToolView.html Validating apidocs/org/concord/biologica/ui/class-use/MultipleOrganismView.html Validating apidocs/org/concord/biologica/ui/class-use/BigMeiosisView.html Validating apidocs/org/concord/biologica/ui/class-use/TreeView.html Validating apidocs/org/concord/biologica/ui/class-use/SelectionSet.html Validating apidocs/org/concord/biologica/ui/class-use/PedigreeOrganism.html Validating apidocs/org/concord/biologica/ui/class-use/BioComboBoxModel.html Validating apidocs/org/concord/biologica/ui/class-use/PatchView.html Validating apidocs/org/concord/biologica/ui/class-use/PedigreeOrganismView.html Validating apidocs/org/concord/biologica/ui/class-use/SelectionPresenter.html Validating apidocs/org/concord/biologica/ui/class-use/CCDraggable.html Validating apidocs/org/concord/biologica/ui/class-use/EnvironmentZoomInViewDialogBox.html Validating apidocs/org/concord/biologica/ui/class-use/TreeViewNode.html Validating apidocs/org/concord/biologica/ui/class-use/WelcomeView.html Validating apidocs/org/concord/biologica/ui/class-use/BioToolBar.html Validating apidocs/org/concord/biologica/ui/class-use/XMLFileFilter.html Validating apidocs/org/concord/biologica/ui/class-use/SmallMeiosisView.html Validating apidocs/org/concord/biologica/ui/UIView.html Validating apidocs/org/concord/biologica/ui/OrganismAlleleControl.html Validating apidocs/org/concord/biologica/ui/TerrainPatch.html Validating apidocs/org/concord/biologica/ui/PedigreeLevel.html Validating apidocs/org/concord/biologica/ui/BioLogicaViewManager.html Validating apidocs/org/concord/biologica/ui/package-use.html Validating apidocs/org/concord/biologica/ui/TreeViewCellRenderer.html Validating apidocs/org/concord/biologica/ui/FertilizationModel.html Validating apidocs/org/concord/biologica/ui/PedigreeObject.html Validating apidocs/org/concord/biologica/ui/SpindleLine.html Validating apidocs/org/concord/biologica/ui/GlossaryFrame.html Validating apidocs/org/concord/biologica/ui/BioDialogBox.html Validating apidocs/org/concord/biologica/ui/LocalImageIcon.html Validating apidocs/org/concord/biologica/ui/DNAView.html Validating apidocs/org/concord/biologica/ui/ChromosomeView.html Validating apidocs/org/concord/biologica/ui/package-tree.html Validating apidocs/org/concord/biologica/ui/BioComboBox.html Validating apidocs/org/concord/biologica/ui/UIProp.html Validating apidocs/org/concord/biologica/ui/StaticOrganismView.html Validating apidocs/org/concord/biologica/ui/PedigreePracticeView.html Validating apidocs/org/concord/biologica/ui/SexView.html Validating apidocs/org/concord/biologica/ui/SexOrganismView.html Validating apidocs/org/concord/biologica/ui/MutationsPracticeView.html Validating apidocs/org/concord/biologica/ui/MeiosisView.html Validating apidocs/org/concord/biologica/ui/MeiosisChromosomeModel.html Validating apidocs/org/concord/biologica/ui/CellLine.html Validating apidocs/org/concord/biologica/ui/CursorText.html Validating apidocs/org/concord/biologica/ui/TreeViewModel.html Validating apidocs/org/concord/biologica/ui/ToolView.html Validating apidocs/org/concord/biologica/ui/MultipleOrganismView.html Validating apidocs/org/concord/biologica/ui/BigMeiosisView.html Validating apidocs/org/concord/biologica/ui/TreeView.html Validating apidocs/org/concord/biologica/ui/SelectionSet.html Validating apidocs/org/concord/biologica/ui/PedigreeOrganism.html Validating apidocs/org/concord/biologica/ui/BioComboBoxModel.html Validating apidocs/org/concord/biologica/ui/package-summary.html Validating apidocs/org/concord/biologica/ui/PatchView.html Validating apidocs/org/concord/biologica/ui/PedigreeOrganismView.html Validating apidocs/org/concord/biologica/ui/SelectionPresenter.html Validating apidocs/org/concord/biologica/ui/CCDraggable.html Validating apidocs/org/concord/biologica/ui/EnvironmentZoomInViewDialogBox.html Validating apidocs/org/concord/biologica/ui/TreeViewNode.html Validating apidocs/org/concord/biologica/ui/WelcomeView.html Validating apidocs/org/concord/biologica/ui/BioToolBar.html Validating apidocs/org/concord/biologica/ui/XMLFileFilter.html Validating apidocs/org/concord/biologica/ui/package-frame.html Validating apidocs/org/concord/biologica/ui/SmallMeiosisView.html Validating apidocs/org/concord/biologica/test/TestWindow.html Validating apidocs/org/concord/biologica/test/class-use/TestWindow.html Validating apidocs/org/concord/biologica/test/class-use/TestWindow.WindowCloser.html Validating apidocs/org/concord/biologica/test/package-use.html Validating apidocs/org/concord/biologica/test/package-tree.html Validating apidocs/org/concord/biologica/test/package-summary.html Validating apidocs/org/concord/biologica/test/package-frame.html Validating apidocs/org/concord/biologica/test/TestWindow.WindowCloser.html Validating apidocs/org/concord/biologica/engine/OrganismChromosomePair.html Validating apidocs/org/concord/biologica/engine/RawNucleicAcid.html Validating apidocs/org/concord/biologica/engine/SpeciesImage.html Validating apidocs/org/concord/biologica/engine/Species.html Validating apidocs/org/concord/biologica/engine/Base.html Validating apidocs/org/concord/biologica/engine/EngineProp.html Validating apidocs/org/concord/biologica/engine/Organism.html Validating apidocs/org/concord/biologica/engine/SpeciesChromosome.html Validating apidocs/org/concord/biologica/engine/Terrain.html Validating apidocs/org/concord/biologica/engine/ImportContext.html Validating apidocs/org/concord/biologica/engine/Gamete.html Validating apidocs/org/concord/biologica/engine/EngineObject.LocalPropertyChangeSupport.html Validating apidocs/org/concord/biologica/engine/OrganismChromosome.html Validating apidocs/org/concord/biologica/engine/Debug.html Validating apidocs/org/concord/biologica/engine/OrganismImage.html Validating apidocs/org/concord/biologica/engine/BioLogicaRule.html Validating apidocs/org/concord/biologica/engine/World.html Validating apidocs/org/concord/biologica/engine/BioEngine.html Validating apidocs/org/concord/biologica/engine/IEnvironment.html Validating apidocs/org/concord/biologica/engine/Characteristic.html Validating apidocs/org/concord/biologica/engine/ElementContext.html Validating apidocs/org/concord/biologica/engine/class-use/OrganismChromosomePair.html Validating apidocs/org/concord/biologica/engine/class-use/RawNucleicAcid.html Validating apidocs/org/concord/biologica/engine/class-use/SpeciesImage.html Validating apidocs/org/concord/biologica/engine/class-use/Species.html Validating apidocs/org/concord/biologica/engine/class-use/Base.html Validating apidocs/org/concord/biologica/engine/class-use/EngineProp.html Validating apidocs/org/concord/biologica/engine/class-use/Organism.html Validating apidocs/org/concord/biologica/engine/class-use/SpeciesChromosome.html Validating apidocs/org/concord/biologica/engine/class-use/Terrain.html Validating apidocs/org/concord/biologica/engine/class-use/ImportContext.html Validating apidocs/org/concord/biologica/engine/class-use/Gamete.html Validating apidocs/org/concord/biologica/engine/class-use/EngineObject.LocalPropertyChangeSupport.html Validating apidocs/org/concord/biologica/engine/class-use/OrganismChromosome.html Validating apidocs/org/concord/biologica/engine/class-use/Debug.html Validating apidocs/org/concord/biologica/engine/class-use/OrganismImage.html Validating apidocs/org/concord/biologica/engine/class-use/BioLogicaRule.html Validating apidocs/org/concord/biologica/engine/class-use/World.html Validating apidocs/org/concord/biologica/engine/class-use/BioEngine.html Validating apidocs/org/concord/biologica/engine/class-use/IEnvironment.html Validating apidocs/org/concord/biologica/engine/class-use/Characteristic.html Validating apidocs/org/concord/biologica/engine/class-use/ElementContext.html Validating apidocs/org/concord/biologica/engine/class-use/IChromosome.html Validating apidocs/org/concord/biologica/engine/class-use/SpeciesAllele.html Validating apidocs/org/concord/biologica/engine/class-use/PathStrings.html Validating apidocs/org/concord/biologica/engine/class-use/EnvironmentUnit.html Validating apidocs/org/concord/biologica/engine/class-use/ObjectDeletedException.html Validating apidocs/org/concord/biologica/engine/class-use/BioLogicaSpecies.html Validating apidocs/org/concord/biologica/engine/class-use/INucleicAcidHolder.html Validating apidocs/org/concord/biologica/engine/class-use/Trait.html Validating apidocs/org/concord/biologica/engine/class-use/ObjectLockedException.html Validating apidocs/org/concord/biologica/engine/class-use/Environment.html Validating apidocs/org/concord/biologica/engine/class-use/AlgorithmicNucleicAcid.html Validating apidocs/org/concord/biologica/engine/class-use/OrganismAllele.html Validating apidocs/org/concord/biologica/engine/class-use/NotBioLogicaFileException.html Validating apidocs/org/concord/biologica/engine/class-use/TerrainEng.html Validating apidocs/org/concord/biologica/engine/class-use/AminoAcid.html Validating apidocs/org/concord/biologica/engine/class-use/Rule.html Validating apidocs/org/concord/biologica/engine/class-use/Gene.html Validating apidocs/org/concord/biologica/engine/class-use/NucleicAcid.html Validating apidocs/org/concord/biologica/engine/class-use/Branch.html Validating apidocs/org/concord/biologica/engine/class-use/ChromosomeSpecification.html Validating apidocs/org/concord/biologica/engine/class-use/GenotypeToPhenotypeRule.html Validating apidocs/org/concord/biologica/engine/class-use/Family.html Validating apidocs/org/concord/biologica/engine/class-use/EngineStrings.html Validating apidocs/org/concord/biologica/engine/class-use/Elements.html Validating apidocs/org/concord/biologica/engine/class-use/INucleicAcid.html Validating apidocs/org/concord/biologica/engine/class-use/SpeciesImageRow.html Validating apidocs/org/concord/biologica/engine/class-use/FoodChain.html Validating apidocs/org/concord/biologica/engine/class-use/SpeciesImageColumn.html Validating apidocs/org/concord/biologica/engine/class-use/Rules.html Validating apidocs/org/concord/biologica/engine/class-use/InternalEngineException.html Validating apidocs/org/concord/biologica/engine/class-use/OrganismAllelePair.html Validating apidocs/org/concord/biologica/engine/class-use/Codon.html Validating apidocs/org/concord/biologica/engine/class-use/BehaviorRules.html Validating apidocs/org/concord/biologica/engine/class-use/BioEngineBeanInfo.html Validating apidocs/org/concord/biologica/engine/class-use/EngineObject.html Validating apidocs/org/concord/biologica/engine/class-use/CrossOver.html Validating apidocs/org/concord/biologica/engine/IChromosome.html Validating apidocs/org/concord/biologica/engine/SpeciesAllele.html Validating apidocs/org/concord/biologica/engine/package-use.html Validating apidocs/org/concord/biologica/engine/PathStrings.html Validating apidocs/org/concord/biologica/engine/EnvironmentUnit.html Validating apidocs/org/concord/biologica/engine/ObjectDeletedException.html Validating apidocs/org/concord/biologica/engine/package-tree.html Validating apidocs/org/concord/biologica/engine/BioLogicaSpecies.html Validating apidocs/org/concord/biologica/engine/INucleicAcidHolder.html Validating apidocs/org/concord/biologica/engine/Trait.html Validating apidocs/org/concord/biologica/engine/ObjectLockedException.html Validating apidocs/org/concord/biologica/engine/Environment.html Validating apidocs/org/concord/biologica/engine/AlgorithmicNucleicAcid.html Validating apidocs/org/concord/biologica/engine/OrganismAllele.html Validating apidocs/org/concord/biologica/engine/NotBioLogicaFileException.html Validating apidocs/org/concord/biologica/engine/TerrainEng.html Validating apidocs/org/concord/biologica/engine/AminoAcid.html Validating apidocs/org/concord/biologica/engine/Rule.html Validating apidocs/org/concord/biologica/engine/Gene.html Validating apidocs/org/concord/biologica/engine/NucleicAcid.html Validating apidocs/org/concord/biologica/engine/Branch.html Validating apidocs/org/concord/biologica/engine/ChromosomeSpecification.html Validating apidocs/org/concord/biologica/engine/GenotypeToPhenotypeRule.html Validating apidocs/org/concord/biologica/engine/Family.html Validating apidocs/org/concord/biologica/engine/EngineStrings.html Validating apidocs/org/concord/biologica/engine/Elements.html Validating apidocs/org/concord/biologica/engine/INucleicAcid.html Validating apidocs/org/concord/biologica/engine/SpeciesImageRow.html Validating apidocs/org/concord/biologica/engine/FoodChain.html Validating apidocs/org/concord/biologica/engine/package-summary.html Validating apidocs/org/concord/biologica/engine/SpeciesImageColumn.html Validating apidocs/org/concord/biologica/engine/Rules.html Validating apidocs/org/concord/biologica/engine/InternalEngineException.html Validating apidocs/org/concord/biologica/engine/OrganismAllelePair.html Validating apidocs/org/concord/biologica/engine/Codon.html Validating apidocs/org/concord/biologica/engine/BehaviorRules.html Validating apidocs/org/concord/biologica/engine/package-frame.html Validating apidocs/org/concord/biologica/engine/BioEngineBeanInfo.html Validating apidocs/org/concord/biologica/engine/EngineObject.html Validating apidocs/org/concord/biologica/engine/CrossOver.html Validating apidocs/org/concord/biologica/datasupport/ColorUtil.html Validating apidocs/org/concord/biologica/datasupport/SpecieFileDesc.html Validating apidocs/org/concord/biologica/datasupport/class-use/ColorUtil.html Validating apidocs/org/concord/biologica/datasupport/class-use/SpecieFileDesc.html Validating apidocs/org/concord/biologica/datasupport/class-use/DataOrganism.html Validating apidocs/org/concord/biologica/datasupport/class-use/ShortImageDescription.html Validating apidocs/org/concord/biologica/datasupport/class-use/ImageReader.html Validating apidocs/org/concord/biologica/datasupport/package-use.html Validating apidocs/org/concord/biologica/datasupport/DataOrganism.html Validating apidocs/org/concord/biologica/datasupport/package-tree.html Validating apidocs/org/concord/biologica/datasupport/package-summary.html Validating apidocs/org/concord/biologica/datasupport/package-frame.html Validating apidocs/org/concord/biologica/datasupport/ShortImageDescription.html Validating apidocs/org/concord/biologica/datasupport/ImageReader.html Validating apidocs/constant-values.html Validating apidocs/overview-tree.html Validating apidocs/help-doc.html Validating apidocs/overview-frame.html Validating apidocs/index.html Validating apidocs/deprecated-list.html Validating apidocs/serialized-form.html Validating apidocs/allclasses-noframe.html Validating apidocs/index-all.html Caught java.lang.StackOverflowError processing apidocs/index-all.html Exception Message: null Validating xref/allclasses-frame.html Validating xref/overview-summary.html Validating xref/org/concord/biologica/ui/TerrainEngView.html Validating xref/org/concord/biologica/ui/FertilizationChromosomeModel.html Validating xref/org/concord/biologica/ui/Tool.html Validating xref/org/concord/biologica/ui/PracticeView.html Validating xref/org/concord/biologica/ui/SpeciesFileFilter.html Validating xref/org/concord/biologica/ui/MeiosisPracticeView.html Validating xref/org/concord/biologica/ui/EnvironmentView.html Validating xref/org/concord/biologica/ui/ChromosomePracticeView.html Validating xref/org/concord/biologica/ui/BigFertilizationView.html Validating xref/org/concord/biologica/ui/PedigreeFamily.html Validating xref/org/concord/biologica/ui/SmallFertilizationView.html Validating xref/org/concord/biologica/ui/PedigreeView.html Validating xref/org/concord/biologica/ui/ObjectPropertiesView.html Validating xref/org/concord/biologica/ui/OrganismView.html Validating xref/org/concord/biologica/ui/FilledCircle.html Validating xref/org/concord/biologica/ui/MeiosisModel.html Validating xref/org/concord/biologica/ui/AllInOneView.html Validating xref/org/concord/biologica/ui/CharacteristicView.html Validating xref/org/concord/biologica/ui/WorldFileFilter.html Validating xref/org/concord/biologica/ui/CellArc.html Validating xref/org/concord/biologica/ui/GifFileFilter.html Validating xref/org/concord/biologica/ui/UIGraphics.html Validating xref/org/concord/biologica/ui/UIView.html Validating xref/org/concord/biologica/ui/OrganismAlleleControl.html Validating xref/org/concord/biologica/ui/TerrainPatch.html Validating xref/org/concord/biologica/ui/PedigreeLevel.html Validating xref/org/concord/biologica/ui/BioLogicaViewManager.html Validating xref/org/concord/biologica/ui/TreeViewCellRenderer.html Validating xref/org/concord/biologica/ui/FertilizationModel.html Validating xref/org/concord/biologica/ui/PedigreeObject.html Validating xref/org/concord/biologica/ui/SpindleLine.html Validating xref/org/concord/biologica/ui/GlossaryFrame.html Validating xref/org/concord/biologica/ui/BioDialogBox.html Validating xref/org/concord/biologica/ui/LocalImageIcon.html Validating xref/org/concord/biologica/ui/DNAView.html Validating xref/org/concord/biologica/ui/ChromosomeView.html Validating xref/org/concord/biologica/ui/BioComboBox.html Validating xref/org/concord/biologica/ui/UIProp.html Validating xref/org/concord/biologica/ui/StaticOrganismView.html Validating xref/org/concord/biologica/ui/PedigreePracticeView.html Validating xref/org/concord/biologica/ui/SexView.html Validating xref/org/concord/biologica/ui/SexOrganismView.html Validating xref/org/concord/biologica/ui/MutationsPracticeView.html Validating xref/org/concord/biologica/ui/MeiosisView.html Validating xref/org/concord/biologica/ui/MeiosisChromosomeModel.html Validating xref/org/concord/biologica/ui/CellLine.html Validating xref/org/concord/biologica/ui/CursorText.html Validating xref/org/concord/biologica/ui/TreeViewModel.html Validating xref/org/concord/biologica/ui/ToolView.html Validating xref/org/concord/biologica/ui/MultipleOrganismView.html Validating xref/org/concord/biologica/ui/BigMeiosisView.html Validating xref/org/concord/biologica/ui/TreeView.html Validating xref/org/concord/biologica/ui/SelectionSet.html Validating xref/org/concord/biologica/ui/PedigreeOrganism.html Validating xref/org/concord/biologica/ui/BioComboBoxModel.html Validating xref/org/concord/biologica/ui/package-summary.html Validating xref/org/concord/biologica/ui/PatchView.html Validating xref/org/concord/biologica/ui/PedigreeOrganismView.html Validating xref/org/concord/biologica/ui/SelectionPresenter.html Validating xref/org/concord/biologica/ui/CCDraggable.html Validating xref/org/concord/biologica/ui/EnvironmentZoomInViewDialogBox.html Validating xref/org/concord/biologica/ui/TreeViewNode.html Validating xref/org/concord/biologica/ui/WelcomeView.html Validating xref/org/concord/biologica/ui/BioToolBar.html Validating xref/org/concord/biologica/ui/XMLFileFilter.html Validating xref/org/concord/biologica/ui/package-frame.html Validating xref/org/concord/biologica/ui/SmallMeiosisView.html Validating xref/org/concord/biologica/test/TestWindow.html Validating xref/org/concord/biologica/test/package-summary.html Validating xref/org/concord/biologica/test/package-frame.html Validating xref/org/concord/biologica/engine/OrganismChromosomePair.html Validating xref/org/concord/biologica/engine/RawNucleicAcid.html Validating xref/org/concord/biologica/engine/SpeciesImage.html Validating xref/org/concord/biologica/engine/Species.html Validating xref/org/concord/biologica/engine/Base.html Validating xref/org/concord/biologica/engine/EngineProp.html Validating xref/org/concord/biologica/engine/Organism.html Validating xref/org/concord/biologica/engine/SpeciesChromosome.html Validating xref/org/concord/biologica/engine/Terrain.html Validating xref/org/concord/biologica/engine/ImportContext.html Validating xref/org/concord/biologica/engine/Gamete.html Validating xref/org/concord/biologica/engine/OrganismChromosome.html Validating xref/org/concord/biologica/engine/Debug.html Validating xref/org/concord/biologica/engine/OrganismImage.html Validating xref/org/concord/biologica/engine/BioLogicaRule.html Validating xref/org/concord/biologica/engine/World.html Validating xref/org/concord/biologica/engine/BioEngine.html Validating xref/org/concord/biologica/engine/IEnvironment.html Validating xref/org/concord/biologica/engine/Characteristic.html Validating xref/org/concord/biologica/engine/ElementContext.html Validating xref/org/concord/biologica/engine/IChromosome.html Validating xref/org/concord/biologica/engine/SpeciesAllele.html Validating xref/org/concord/biologica/engine/PathStrings.html Validating xref/org/concord/biologica/engine/EnvironmentUnit.html Validating xref/org/concord/biologica/engine/ObjectDeletedException.html Validating xref/org/concord/biologica/engine/BioLogicaSpecies.html Validating xref/org/concord/biologica/engine/INucleicAcidHolder.html Validating xref/org/concord/biologica/engine/Trait.html Validating xref/org/concord/biologica/engine/ObjectLockedException.html Validating xref/org/concord/biologica/engine/Environment.html Validating xref/org/concord/biologica/engine/AlgorithmicNucleicAcid.html Validating xref/org/concord/biologica/engine/OrganismAllele.html Validating xref/org/concord/biologica/engine/NotBioLogicaFileException.html Validating xref/org/concord/biologica/engine/TerrainEng.html Validating xref/org/concord/biologica/engine/AminoAcid.html Validating xref/org/concord/biologica/engine/Rule.html Validating xref/org/concord/biologica/engine/Gene.html Validating xref/org/concord/biologica/engine/NucleicAcid.html Validating xref/org/concord/biologica/engine/Branch.html Validating xref/org/concord/biologica/engine/ChromosomeSpecification.html Validating xref/org/concord/biologica/engine/GenotypeToPhenotypeRule.html Validating xref/org/concord/biologica/engine/Family.html Validating xref/org/concord/biologica/engine/EngineStrings.html Validating xref/org/concord/biologica/engine/Elements.html Validating xref/org/concord/biologica/engine/INucleicAcid.html Validating xref/org/concord/biologica/engine/SpeciesImageRow.html Validating xref/org/concord/biologica/engine/FoodChain.html Validating xref/org/concord/biologica/engine/package-summary.html Validating xref/org/concord/biologica/engine/SpeciesImageColumn.html Validating xref/org/concord/biologica/engine/Rules.html Validating xref/org/concord/biologica/engine/InternalEngineException.html Validating xref/org/concord/biologica/engine/OrganismAllelePair.html Validating xref/org/concord/biologica/engine/Codon.html Validating xref/org/concord/biologica/engine/BehaviorRules.html Validating xref/org/concord/biologica/engine/package-frame.html Validating xref/org/concord/biologica/engine/BioEngineBeanInfo.html Validating xref/org/concord/biologica/engine/EngineObject.html Validating xref/org/concord/biologica/engine/CrossOver.html Validating xref/org/concord/biologica/datasupport/ColorUtil.html Validating xref/org/concord/biologica/datasupport/SpecieFileDesc.html Validating xref/org/concord/biologica/datasupport/DataOrganism.html Validating xref/org/concord/biologica/datasupport/package-summary.html Validating xref/org/concord/biologica/datasupport/package-frame.html Validating xref/org/concord/biologica/datasupport/ShortImageDescription.html Validating xref/org/concord/biologica/datasupport/ImageReader.html Validating xref/overview-frame.html Validating xref/index.html Validating cvs-usage.html Validating license.html [echo] Generating /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/docs/linkcheck.html from /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/linkcheck/docs/linkcheck.xml xdoc: xdoc:init: site:init: site:sshdeploy: [echo] siteAddress = source.concord.org siteDirectory = /web/source.concord.org/html/software/biologica siteUser = maven [tar] Building tar: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/biologica-1.0-site.tar [gzip] Building: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/biologica-1.0-site.tar.gz [delete] Deleting: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/biologica-1.0-site.tar [exec] This system is for the use of authorized users only. All data and usage may be monitored. Unauthorized access will be pursued. [exec] This system is for the use of authorized users only. All data and usage may be monitored. Unauthorized access will be pursued. [exec] This system is for the use of authorized users only. All data and usage may be monitored. Unauthorized access will be pursued. [exec] tar: images: Cannot unlink: Is a directory [exec] tar: images/logos: Cannot unlink: Is a directory [exec] images/ [exec] images/logos/ [exec] style/ [exec] apidocs/ [exec] apidocs/org/ [exec] apidocs/org/concord/ [exec] apidocs/org/concord/biologica/ [exec] tar: style: Cannot unlink: Is a directory [exec] tar: apidocs: Cannot unlink: Is a directory [exec] tar: apidocs/org: Cannot unlink: Is a directory [exec] apidocs/org/concord/biologica/ui/ [exec] apidocs/org/concord/biologica/ui/class-use/ [exec] apidocs/org/concord/biologica/test/ [exec] tar: apidocs/org/concord: Cannot unlink: Is a directory [exec] tar: apidocs/org/concord/biologica: Cannot unlink: Is a directory [exec] apidocs/org/concord/biologica/test/class-use/ [exec] apidocs/org/concord/biologica/engine/ [exec] apidocs/org/concord/biologica/engine/class-use/ [exec] tar: apidocs/org/concord/biologica/ui: Cannot unlink: Is a directory [exec] tar: apidocs/org/concord/biologica/ui/class-use: Cannot unlink: Is a directory [exec] apidocs/org/concord/biologica/datasupport/ [exec] apidocs/org/concord/biologica/datasupport/class-use/ [exec] apidocs/resources/ [exec] xref/ [exec] xref/org/ [exec] xref/org/concord/ [exec] tar: apidocs/org/concord/biologica/test: Cannot unlink: Is a directory [exec] xref/org/concord/biologica/ [exec] xref/org/concord/biologica/ui/ [exec] xref/org/concord/biologica/test/ [exec] xref/org/concord/biologica/engine/ [exec] tar: apidocs/org/concord/biologica/test/class-use: Cannot unlink: Is a directory [exec] tar: apidocs/org/concord/biologica/engine: Cannot unlink: Is a directory [exec] xref/org/concord/biologica/datasupport/ [exec] downloads.html [exec] team-list.html [exec] images/icon_folder_lrg.gif [exec] images/icon_warning_sml.gif [exec] images/fix.gif [exec] tar: apidocs/org/concord/biologica/engine/class-use: Cannot unlink: Is a directory [exec] tar: apidocs/org/concord/biologica/datasupport: Cannot unlink: Is a directory [exec] images/icon_doc_lrg.gif [exec] images/icon_arrowwaste1_sml.gif [exec] images/newwindow-classic.png [exec] images/icon_info_sml.gif [exec] images/sw_min.gif [exec] tar: apidocs/org/concord/biologica/datasupport/class-use: Cannot unlink: Is a directory [exec] tar: apidocs/resources: Cannot unlink: Is a directory [exec] images/strich.gif [exec] images/icon_arrowfolderopen2_sml.gif [exec] images/nw_med_hi.gif [exec] images/icon_usergroups_sml.gif [exec] tar: xref: Cannot unlink: Is a directory [exec] tar: xref/org: Cannot unlink: Is a directory [exec] images/icon_arrowfolder1_sml.gif [exec] images/icon_arrowfolder2_sml.gif [exec] images/remove.gif [exec] images/rss.png [exec] images/icon_success_sml.gif [exec] images/icon_doc_sml.gif [exec] tar: xref/org/concord: Cannot unlink: Is a directory [exec] tar: xref/org/concord/biologica: Cannot unlink: Is a directory [exec] images/icon_confirmsml.gif [exec] images/external-classic.png [exec] images/icon_usergroups_lrg.gif [exec] images/icon_sortdown.gif [exec] images/add.gif [exec] tar: xref/org/concord/biologica/ui: Cannot unlink: Is a directory [exec] tar: xref/org/concord/biologica/test: Cannot unlink: Is a directory [exec] images/logos/maven-build-successfull.png [exec] images/logos/maven-petesucks.png [exec] images/logos/maven-button-5.png [exec] tar: xref/org/concord/biologica/engine: Cannot unlink: Is a directory [exec] tar: xref/org/concord/biologica/datasupport: Cannot unlink: Is a directory [exec] images/logos/maven-button-black.png [exec] images/logos/maven-button-copper.png [exec] images/logos/maven-button-3.png [exec] images/logos/maven-propaganda-2.png [exec] images/logos/maven-button-4.png [exec] images/logos/maven-button-pinky.png [exec] images/logos/maven-propaganda.png [exec] images/logos/maven-bulldozer.png [exec] images/logos/maven-button-green.png [exec] images/logos/maven-button-1.png [exec] images/logos/maven-button-purple.png [exec] images/logos/maven-built.png [exec] images/logos/maven-button-teal.png [exec] images/logos/maven-redgreen.png [exec] images/logos/maven-feather.png [exec] images/logos/maven-button-blue.png [exec] images/logos/maven-button-2.png [exec] images/logos/maven-bolt.png [exec] images/logos/maven-brewed.png [exec] images/logos/maven-mavenfactured.png [exec] images/logos/maven-frankenstein.png [exec] images/icon_help_lrg.gif [exec] images/icon_success_lrg.gif [exec] images/icon_arrowmembers1_sml.gif [exec] images/expanded.gif [exec] images/icon_arrowusergroups1_sml.gif [exec] images/none.png [exec] images/newwindow.png [exec] images/icon_sortright.gif [exec] images/update.gif [exec] images/nw_med_rond.gif [exec] images/nw_min.gif [exec] images/product_logo.gif [exec] images/icon_sortleft.gif [exec] images/nw_med.gif [exec] images/nw_maj.gif [exec] images/icon_waste_lrg.gif [exec] images/icon_help_sml.gif [exec] images/icon_error_lrg.gif [exec] images/se_maj_rond.gif [exec] images/icon_warning_lrg.gif [exec] images/sw_med_rond.gif [exec] images/collapsed.gif [exec] images/nw_min_hi.gif [exec] images/sw_maj_rond.gif [exec] images/nw_min_036.gif [exec] images/icon_arrowfolderclosed1_sml.gif [exec] images/poweredby_036.gif [exec] images/help_logo.gif [exec] images/icon_folder_sml.gif [exec] images/pdf.gif [exec] images/icon_members_sml.gif [exec] images/icon_members_lrg.gif [exec] images/file.gif [exec] images/icon_alert.gif [exec] images/icon_arrowusergroups2_sml.gif [exec] images/icon_waste_sml.gif [exec] images/external.png [exec] images/icon_infosml.gif [exec] images/folder-open.gif [exec] images/icon_arrowmembers2_sml.gif [exec] images/folder-closed.gif [exec] images/icon_arrowwaste2_sml.gif [exec] images/nw_maj_rond.gif [exec] images/icon_info_lrg.gif [exec] images/nw_maj_hi.gif [exec] images/icon_error_sml.gif [exec] images/icon_sortup.gif [exec] images/icon_alertsml.gif [exec] style/maven-base.css [exec] style/print.css [exec] style/maven-theme.css [exec] style/maven-classic.css [exec] linkcheck.html [exec] dependencies.html [exec] javadoc-warnings-report.html [exec] jdepend-report.html [exec] issue-tracking.html [exec] checkstyle-report.html [exec] index.html [exec] project-info.html [exec] mail-lists.html [exec] task-list.html [exec] javadoc.html [exec] maven-reports.html [exec] apidocs/allclasses-frame.html [exec] apidocs/overview-summary.html [exec] apidocs/org/concord/biologica/ui/TerrainEngView.html [exec] apidocs/org/concord/biologica/ui/FertilizationChromosomeModel.html [exec] apidocs/org/concord/biologica/ui/Tool.html [exec] apidocs/org/concord/biologica/ui/PracticeView.html [exec] apidocs/org/concord/biologica/ui/SpeciesFileFilter.html [exec] apidocs/org/concord/biologica/ui/MeiosisPracticeView.html [exec] apidocs/org/concord/biologica/ui/EnvironmentView.html [exec] apidocs/org/concord/biologica/ui/ChromosomePracticeView.html [exec] apidocs/org/concord/biologica/ui/BigFertilizationView.html [exec] apidocs/org/concord/biologica/ui/PedigreeFamily.html [exec] apidocs/org/concord/biologica/ui/SmallFertilizationView.html [exec] apidocs/org/concord/biologica/ui/PedigreeView.html [exec] apidocs/org/concord/biologica/ui/ObjectPropertiesView.html [exec] apidocs/org/concord/biologica/ui/OrganismView.html [exec] apidocs/org/concord/biologica/ui/FilledCircle.html [exec] apidocs/org/concord/biologica/ui/MeiosisModel.html [exec] apidocs/org/concord/biologica/ui/AllInOneView.html [exec] apidocs/org/concord/biologica/ui/CharacteristicView.html [exec] apidocs/org/concord/biologica/ui/WorldFileFilter.html [exec] apidocs/org/concord/biologica/ui/CellArc.html [exec] apidocs/org/concord/biologica/ui/GifFileFilter.html [exec] apidocs/org/concord/biologica/ui/UIGraphics.html [exec] apidocs/org/concord/biologica/ui/class-use/TerrainEngView.html [exec] apidocs/org/concord/biologica/ui/class-use/FertilizationChromosomeModel.html [exec] apidocs/org/concord/biologica/ui/class-use/Tool.html [exec] apidocs/org/concord/biologica/ui/class-use/PracticeView.html [exec] apidocs/org/concord/biologica/ui/class-use/SpeciesFileFilter.html [exec] apidocs/org/concord/biologica/ui/class-use/MeiosisPracticeView.html [exec] apidocs/org/concord/biologica/ui/class-use/EnvironmentView.html [exec] apidocs/org/concord/biologica/ui/class-use/ChromosomePracticeView.html [exec] apidocs/org/concord/biologica/ui/class-use/BigFertilizationView.html [exec] apidocs/org/concord/biologica/ui/class-use/PedigreeFamily.html [exec] apidocs/org/concord/biologica/ui/class-use/SmallFertilizationView.html [exec] apidocs/org/concord/biologica/ui/class-use/PedigreeView.html [exec] apidocs/org/concord/biologica/ui/class-use/ObjectPropertiesView.html [exec] apidocs/org/concord/biologica/ui/class-use/OrganismView.html [exec] apidocs/org/concord/biologica/ui/class-use/FilledCircle.html [exec] apidocs/org/concord/biologica/ui/class-use/MeiosisModel.html [exec] apidocs/org/concord/biologica/ui/class-use/AllInOneView.html [exec] apidocs/org/concord/biologica/ui/class-use/CharacteristicView.html [exec] apidocs/org/concord/biologica/ui/class-use/WorldFileFilter.html [exec] apidocs/org/concord/biologica/ui/class-use/CellArc.html [exec] apidocs/org/concord/biologica/ui/class-use/GifFileFilter.html [exec] apidocs/org/concord/biologica/ui/class-use/UIGraphics.html [exec] apidocs/org/concord/biologica/ui/class-use/UIView.html [exec] apidocs/org/concord/biologica/ui/class-use/OrganismAlleleControl.html [exec] apidocs/org/concord/biologica/ui/class-use/TerrainPatch.html [exec] apidocs/org/concord/biologica/ui/class-use/PedigreeLevel.html [exec] apidocs/org/concord/biologica/ui/class-use/BioLogicaViewManager.html [exec] apidocs/org/concord/biologica/ui/class-use/TreeViewCellRenderer.html [exec] apidocs/org/concord/biologica/ui/class-use/FertilizationModel.html [exec] apidocs/org/concord/biologica/ui/class-use/PedigreeObject.html [exec] apidocs/org/concord/biologica/ui/class-use/SpindleLine.html [exec] tar: Error exit delayed from previous errors [exec] apidocs/org/concord/biologica/ui/class-use/GlossaryFrame.html [exec] apidocs/org/concord/biologica/ui/class-use/BioDialogBox.html [exec] apidocs/org/concord/biologica/ui/class-use/LocalImageIcon.html [exec] apidocs/org/concord/biologica/ui/class-use/DNAView.html [exec] apidocs/org/concord/biologica/ui/class-use/ChromosomeView.html [exec] apidocs/org/concord/biologica/ui/class-use/BioComboBox.html [exec] apidocs/org/concord/biologica/ui/class-use/UIProp.html [exec] apidocs/org/concord/biologica/ui/class-use/StaticOrganismView.html [exec] apidocs/org/concord/biologica/ui/class-use/PedigreePracticeView.html [exec] apidocs/org/concord/biologica/ui/class-use/SexView.html [exec] apidocs/org/concord/biologica/ui/class-use/SexOrganismView.html [exec] apidocs/org/concord/biologica/ui/class-use/MutationsPracticeView.html [exec] apidocs/org/concord/biologica/ui/class-use/MeiosisView.html [exec] apidocs/org/concord/biologica/ui/class-use/MeiosisChromosomeModel.html [exec] apidocs/org/concord/biologica/ui/class-use/CellLine.html [exec] apidocs/org/concord/biologica/ui/class-use/CursorText.html [exec] apidocs/org/concord/biologica/ui/class-use/TreeViewModel.html [exec] apidocs/org/concord/biologica/ui/class-use/ToolView.html [exec] apidocs/org/concord/biologica/ui/class-use/MultipleOrganismView.html [exec] apidocs/org/concord/biologica/ui/class-use/BigMeiosisView.html [exec] apidocs/org/concord/biologica/ui/class-use/TreeView.html [exec] apidocs/org/concord/biologica/ui/class-use/SelectionSet.html [exec] apidocs/org/concord/biologica/ui/class-use/PedigreeOrganism.html [exec] apidocs/org/concord/biologica/ui/class-use/BioComboBoxModel.html [exec] apidocs/org/concord/biologica/ui/class-use/PatchView.html [exec] apidocs/org/concord/biologica/ui/class-use/PedigreeOrganismView.html [exec] apidocs/org/concord/biologica/ui/class-use/SelectionPresenter.html [exec] apidocs/org/concord/biologica/ui/class-use/CCDraggable.html [exec] apidocs/org/concord/biologica/ui/class-use/EnvironmentZoomInViewDialogBox.html [exec] apidocs/org/concord/biologica/ui/class-use/TreeViewNode.html [exec] apidocs/org/concord/biologica/ui/class-use/WelcomeView.html [exec] apidocs/org/concord/biologica/ui/class-use/BioToolBar.html [exec] apidocs/org/concord/biologica/ui/class-use/XMLFileFilter.html [exec] apidocs/org/concord/biologica/ui/class-use/SmallMeiosisView.html [exec] apidocs/org/concord/biologica/ui/UIView.html [exec] apidocs/org/concord/biologica/ui/OrganismAlleleControl.html [exec] apidocs/org/concord/biologica/ui/TerrainPatch.html [exec] apidocs/org/concord/biologica/ui/PedigreeLevel.html [exec] apidocs/org/concord/biologica/ui/BioLogicaViewManager.html [exec] apidocs/org/concord/biologica/ui/package-use.html [exec] apidocs/org/concord/biologica/ui/TreeViewCellRenderer.html [exec] apidocs/org/concord/biologica/ui/FertilizationModel.html [exec] apidocs/org/concord/biologica/ui/PedigreeObject.html [exec] apidocs/org/concord/biologica/ui/SpindleLine.html [exec] apidocs/org/concord/biologica/ui/GlossaryFrame.html [exec] apidocs/org/concord/biologica/ui/BioDialogBox.html [exec] apidocs/org/concord/biologica/ui/LocalImageIcon.html [exec] apidocs/org/concord/biologica/ui/DNAView.html [exec] apidocs/org/concord/biologica/ui/ChromosomeView.html [exec] apidocs/org/concord/biologica/ui/package-tree.html [exec] apidocs/org/concord/biologica/ui/BioComboBox.html [exec] apidocs/org/concord/biologica/ui/UIProp.html [exec] apidocs/org/concord/biologica/ui/StaticOrganismView.html [exec] apidocs/org/concord/biologica/ui/PedigreePracticeView.html [exec] apidocs/org/concord/biologica/ui/SexView.html [exec] apidocs/org/concord/biologica/ui/SexOrganismView.html [exec] apidocs/org/concord/biologica/ui/MutationsPracticeView.html [exec] apidocs/org/concord/biologica/ui/MeiosisView.html [exec] apidocs/org/concord/biologica/ui/MeiosisChromosomeModel.html [exec] apidocs/org/concord/biologica/ui/CellLine.html [exec] apidocs/org/concord/biologica/ui/CursorText.html [exec] apidocs/org/concord/biologica/ui/TreeViewModel.html [exec] apidocs/org/concord/biologica/ui/ToolView.html [exec] apidocs/org/concord/biologica/ui/MultipleOrganismView.html [exec] apidocs/org/concord/biologica/ui/BigMeiosisView.html [exec] apidocs/org/concord/biologica/ui/TreeView.html [exec] apidocs/org/concord/biologica/ui/SelectionSet.html [exec] apidocs/org/concord/biologica/ui/PedigreeOrganism.html [exec] apidocs/org/concord/biologica/ui/BioComboBoxModel.html [exec] apidocs/org/concord/biologica/ui/package-summary.html [exec] apidocs/org/concord/biologica/ui/PatchView.html [exec] apidocs/org/concord/biologica/ui/PedigreeOrganismView.html [exec] apidocs/org/concord/biologica/ui/SelectionPresenter.html [exec] apidocs/org/concord/biologica/ui/CCDraggable.html [exec] apidocs/org/concord/biologica/ui/EnvironmentZoomInViewDialogBox.html [exec] apidocs/org/concord/biologica/ui/TreeViewNode.html [exec] apidocs/org/concord/biologica/ui/WelcomeView.html [exec] apidocs/org/concord/biologica/ui/BioToolBar.html [exec] apidocs/org/concord/biologica/ui/XMLFileFilter.html [exec] apidocs/org/concord/biologica/ui/package-frame.html [exec] apidocs/org/concord/biologica/ui/SmallMeiosisView.html [exec] apidocs/org/concord/biologica/test/TestWindow.html [exec] apidocs/org/concord/biologica/test/class-use/TestWindow.html [exec] apidocs/org/concord/biologica/test/class-use/TestWindow.WindowCloser.html [exec] apidocs/org/concord/biologica/test/package-use.html [exec] apidocs/org/concord/biologica/test/package-tree.html [exec] apidocs/org/concord/biologica/test/package-summary.html [exec] apidocs/org/concord/biologica/test/package-frame.html [exec] apidocs/org/concord/biologica/test/TestWindow.WindowCloser.html [exec] apidocs/org/concord/biologica/engine/OrganismChromosomePair.html [exec] apidocs/org/concord/biologica/engine/RawNucleicAcid.html [exec] apidocs/org/concord/biologica/engine/SpeciesImage.html [exec] apidocs/org/concord/biologica/engine/Species.html [exec] apidocs/org/concord/biologica/engine/Base.html [exec] apidocs/org/concord/biologica/engine/EngineProp.html [exec] apidocs/org/concord/biologica/engine/Organism.html [exec] apidocs/org/concord/biologica/engine/SpeciesChromosome.html [exec] apidocs/org/concord/biologica/engine/Terrain.html [exec] apidocs/org/concord/biologica/engine/ImportContext.html [exec] apidocs/org/concord/biologica/engine/Gamete.html [exec] apidocs/org/concord/biologica/engine/EngineObject.LocalPropertyChangeSupport.html [exec] apidocs/org/concord/biologica/engine/OrganismChromosome.html [exec] apidocs/org/concord/biologica/engine/Debug.html [exec] apidocs/org/concord/biologica/engine/OrganismImage.html [exec] apidocs/org/concord/biologica/engine/BioLogicaRule.html [exec] apidocs/org/concord/biologica/engine/World.html [exec] apidocs/org/concord/biologica/engine/BioEngine.html [exec] apidocs/org/concord/biologica/engine/IEnvironment.html [exec] apidocs/org/concord/biologica/engine/Characteristic.html [exec] apidocs/org/concord/biologica/engine/ElementContext.html [exec] apidocs/org/concord/biologica/engine/class-use/OrganismChromosomePair.html [exec] apidocs/org/concord/biologica/engine/class-use/RawNucleicAcid.html [exec] apidocs/org/concord/biologica/engine/class-use/SpeciesImage.html [exec] apidocs/org/concord/biologica/engine/class-use/Species.html [exec] apidocs/org/concord/biologica/engine/class-use/Base.html [exec] apidocs/org/concord/biologica/engine/class-use/EngineProp.html [exec] apidocs/org/concord/biologica/engine/class-use/Organism.html [exec] apidocs/org/concord/biologica/engine/class-use/SpeciesChromosome.html [exec] apidocs/org/concord/biologica/engine/class-use/Terrain.html [exec] apidocs/org/concord/biologica/engine/class-use/ImportContext.html [exec] apidocs/org/concord/biologica/engine/class-use/Gamete.html [exec] apidocs/org/concord/biologica/engine/class-use/EngineObject.LocalPropertyChangeSupport.html [exec] apidocs/org/concord/biologica/engine/class-use/OrganismChromosome.html [exec] apidocs/org/concord/biologica/engine/class-use/Debug.html [exec] apidocs/org/concord/biologica/engine/class-use/OrganismImage.html [exec] apidocs/org/concord/biologica/engine/class-use/BioLogicaRule.html [exec] apidocs/org/concord/biologica/engine/class-use/World.html [exec] apidocs/org/concord/biologica/engine/class-use/BioEngine.html [exec] apidocs/org/concord/biologica/engine/class-use/IEnvironment.html [exec] apidocs/org/concord/biologica/engine/class-use/Characteristic.html [exec] apidocs/org/concord/biologica/engine/class-use/ElementContext.html [exec] apidocs/org/concord/biologica/engine/class-use/IChromosome.html [exec] apidocs/org/concord/biologica/engine/class-use/SpeciesAllele.html [exec] apidocs/org/concord/biologica/engine/class-use/PathStrings.html [exec] apidocs/org/concord/biologica/engine/class-use/EnvironmentUnit.html [exec] apidocs/org/concord/biologica/engine/class-use/ObjectDeletedException.html [exec] apidocs/org/concord/biologica/engine/class-use/BioLogicaSpecies.html [exec] apidocs/org/concord/biologica/engine/class-use/INucleicAcidHolder.html [exec] apidocs/org/concord/biologica/engine/class-use/Trait.html [exec] apidocs/org/concord/biologica/engine/class-use/ObjectLockedException.html [exec] apidocs/org/concord/biologica/engine/class-use/Environment.html [exec] apidocs/org/concord/biologica/engine/class-use/AlgorithmicNucleicAcid.html [exec] apidocs/org/concord/biologica/engine/class-use/OrganismAllele.html [exec] apidocs/org/concord/biologica/engine/class-use/NotBioLogicaFileException.html [exec] apidocs/org/concord/biologica/engine/class-use/TerrainEng.html [exec] apidocs/org/concord/biologica/engine/class-use/AminoAcid.html [exec] apidocs/org/concord/biologica/engine/class-use/Rule.html [exec] apidocs/org/concord/biologica/engine/class-use/Gene.html [exec] apidocs/org/concord/biologica/engine/class-use/NucleicAcid.html [exec] apidocs/org/concord/biologica/engine/class-use/Branch.html [exec] apidocs/org/concord/biologica/engine/class-use/ChromosomeSpecification.html [exec] apidocs/org/concord/biologica/engine/class-use/GenotypeToPhenotypeRule.html [exec] apidocs/org/concord/biologica/engine/class-use/Family.html [exec] apidocs/org/concord/biologica/engine/class-use/EngineStrings.html [exec] apidocs/org/concord/biologica/engine/class-use/Elements.html [exec] apidocs/org/concord/biologica/engine/class-use/INucleicAcid.html [exec] apidocs/org/concord/biologica/engine/class-use/SpeciesImageRow.html [exec] apidocs/org/concord/biologica/engine/class-use/FoodChain.html [exec] apidocs/org/concord/biologica/engine/class-use/SpeciesImageColumn.html [exec] apidocs/org/concord/biologica/engine/class-use/Rules.html [exec] apidocs/org/concord/biologica/engine/class-use/InternalEngineException.html [exec] apidocs/org/concord/biologica/engine/class-use/OrganismAllelePair.html [exec] apidocs/org/concord/biologica/engine/class-use/Codon.html [exec] apidocs/org/concord/biologica/engine/class-use/BehaviorRules.html [exec] apidocs/org/concord/biologica/engine/class-use/BioEngineBeanInfo.html [exec] apidocs/org/concord/biologica/engine/class-use/EngineObject.html [exec] apidocs/org/concord/biologica/engine/class-use/CrossOver.html [exec] apidocs/org/concord/biologica/engine/IChromosome.html [exec] apidocs/org/concord/biologica/engine/SpeciesAllele.html [exec] apidocs/org/concord/biologica/engine/package-use.html [exec] apidocs/org/concord/biologica/engine/PathStrings.html [exec] apidocs/org/concord/biologica/engine/EnvironmentUnit.html [exec] apidocs/org/concord/biologica/engine/ObjectDeletedException.html [exec] apidocs/org/concord/biologica/engine/package-tree.html [exec] apidocs/org/concord/biologica/engine/BioLogicaSpecies.html [exec] apidocs/org/concord/biologica/engine/INucleicAcidHolder.html [exec] apidocs/org/concord/biologica/engine/Trait.html [exec] apidocs/org/concord/biologica/engine/ObjectLockedException.html [exec] apidocs/org/concord/biologica/engine/Environment.html [exec] apidocs/org/concord/biologica/engine/AlgorithmicNucleicAcid.html [exec] apidocs/org/concord/biologica/engine/OrganismAllele.html [exec] apidocs/org/concord/biologica/engine/NotBioLogicaFileException.html [exec] apidocs/org/concord/biologica/engine/TerrainEng.html [exec] apidocs/org/concord/biologica/engine/AminoAcid.html [exec] apidocs/org/concord/biologica/engine/Rule.html [exec] apidocs/org/concord/biologica/engine/Gene.html [exec] apidocs/org/concord/biologica/engine/NucleicAcid.html [exec] apidocs/org/concord/biologica/engine/Branch.html [exec] apidocs/org/concord/biologica/engine/ChromosomeSpecification.html [exec] apidocs/org/concord/biologica/engine/GenotypeToPhenotypeRule.html [exec] apidocs/org/concord/biologica/engine/Family.html [exec] apidocs/org/concord/biologica/engine/EngineStrings.html [exec] apidocs/org/concord/biologica/engine/Elements.html [exec] apidocs/org/concord/biologica/engine/INucleicAcid.html [exec] apidocs/org/concord/biologica/engine/SpeciesImageRow.html [exec] apidocs/org/concord/biologica/engine/FoodChain.html [exec] apidocs/org/concord/biologica/engine/package-summary.html [exec] apidocs/org/concord/biologica/engine/SpeciesImageColumn.html [exec] apidocs/org/concord/biologica/engine/Rules.html [exec] apidocs/org/concord/biologica/engine/InternalEngineException.html [exec] apidocs/org/concord/biologica/engine/OrganismAllelePair.html [exec] apidocs/org/concord/biologica/engine/Codon.html [exec] apidocs/org/concord/biologica/engine/BehaviorRules.html [exec] apidocs/org/concord/biologica/engine/package-frame.html [exec] apidocs/org/concord/biologica/engine/BioEngineBeanInfo.html [exec] apidocs/org/concord/biologica/engine/EngineObject.html [exec] apidocs/org/concord/biologica/engine/CrossOver.html [exec] apidocs/org/concord/biologica/datasupport/ColorUtil.html [exec] apidocs/org/concord/biologica/datasupport/SpecieFileDesc.html [exec] apidocs/org/concord/biologica/datasupport/class-use/ColorUtil.html [exec] apidocs/org/concord/biologica/datasupport/class-use/SpecieFileDesc.html [exec] apidocs/org/concord/biologica/datasupport/class-use/DataOrganism.html [exec] apidocs/org/concord/biologica/datasupport/class-use/ShortImageDescription.html [exec] apidocs/org/concord/biologica/datasupport/class-use/ImageReader.html [exec] apidocs/org/concord/biologica/datasupport/package-use.html [exec] apidocs/org/concord/biologica/datasupport/DataOrganism.html [exec] apidocs/org/concord/biologica/datasupport/package-tree.html [exec] apidocs/org/concord/biologica/datasupport/package-summary.html [exec] apidocs/org/concord/biologica/datasupport/package-frame.html [exec] apidocs/org/concord/biologica/datasupport/ShortImageDescription.html [exec] apidocs/org/concord/biologica/datasupport/ImageReader.html [exec] apidocs/constant-values.html [exec] apidocs/overview-tree.html [exec] apidocs/package-list [exec] apidocs/help-doc.html [exec] apidocs/overview-frame.html [exec] apidocs/index.html [exec] apidocs/deprecated-list.html [exec] apidocs/stylesheet.css [exec] apidocs/serialized-form.html [exec] apidocs/allclasses-noframe.html [exec] apidocs/resources/inherit.gif [exec] apidocs/index-all.html [exec] xref/allclasses-frame.html [exec] xref/overview-summary.html [exec] xref/org/concord/biologica/ui/TerrainEngView.html [exec] xref/org/concord/biologica/ui/FertilizationChromosomeModel.html [exec] xref/org/concord/biologica/ui/Tool.html [exec] xref/org/concord/biologica/ui/PracticeView.html [exec] xref/org/concord/biologica/ui/SpeciesFileFilter.html [exec] xref/org/concord/biologica/ui/MeiosisPracticeView.html [exec] xref/org/concord/biologica/ui/EnvironmentView.html [exec] xref/org/concord/biologica/ui/ChromosomePracticeView.html [exec] xref/org/concord/biologica/ui/BigFertilizationView.html [exec] xref/org/concord/biologica/ui/PedigreeFamily.html [exec] xref/org/concord/biologica/ui/SmallFertilizationView.html [exec] xref/org/concord/biologica/ui/PedigreeView.html [exec] xref/org/concord/biologica/ui/ObjectPropertiesView.html [exec] xref/org/concord/biologica/ui/OrganismView.html [exec] xref/org/concord/biologica/ui/FilledCircle.html [exec] xref/org/concord/biologica/ui/MeiosisModel.html [exec] xref/org/concord/biologica/ui/AllInOneView.html [exec] xref/org/concord/biologica/ui/CharacteristicView.html [exec] xref/org/concord/biologica/ui/WorldFileFilter.html [exec] xref/org/concord/biologica/ui/CellArc.html [exec] xref/org/concord/biologica/ui/GifFileFilter.html [exec] xref/org/concord/biologica/ui/UIGraphics.html [exec] xref/org/concord/biologica/ui/UIView.html [exec] xref/org/concord/biologica/ui/OrganismAlleleControl.html [exec] xref/org/concord/biologica/ui/TerrainPatch.html [exec] xref/org/concord/biologica/ui/PedigreeLevel.html [exec] xref/org/concord/biologica/ui/BioLogicaViewManager.html [exec] xref/org/concord/biologica/ui/TreeViewCellRenderer.html [exec] xref/org/concord/biologica/ui/FertilizationModel.html [exec] xref/org/concord/biologica/ui/PedigreeObject.html [exec] xref/org/concord/biologica/ui/SpindleLine.html [exec] xref/org/concord/biologica/ui/GlossaryFrame.html [exec] xref/org/concord/biologica/ui/BioDialogBox.html [exec] xref/org/concord/biologica/ui/LocalImageIcon.html [exec] xref/org/concord/biologica/ui/DNAView.html [exec] xref/org/concord/biologica/ui/ChromosomeView.html [exec] xref/org/concord/biologica/ui/BioComboBox.html [exec] xref/org/concord/biologica/ui/UIProp.html [exec] xref/org/concord/biologica/ui/StaticOrganismView.html [exec] xref/org/concord/biologica/ui/PedigreePracticeView.html [exec] xref/org/concord/biologica/ui/SexView.html [exec] xref/org/concord/biologica/ui/SexOrganismView.html [exec] xref/org/concord/biologica/ui/MutationsPracticeView.html [exec] xref/org/concord/biologica/ui/MeiosisView.html [exec] xref/org/concord/biologica/ui/MeiosisChromosomeModel.html [exec] xref/org/concord/biologica/ui/CellLine.html [exec] xref/org/concord/biologica/ui/CursorText.html [exec] xref/org/concord/biologica/ui/TreeViewModel.html [exec] xref/org/concord/biologica/ui/ToolView.html [exec] xref/org/concord/biologica/ui/MultipleOrganismView.html [exec] xref/org/concord/biologica/ui/BigMeiosisView.html [exec] xref/org/concord/biologica/ui/TreeView.html [exec] xref/org/concord/biologica/ui/SelectionSet.html [exec] xref/org/concord/biologica/ui/PedigreeOrganism.html [exec] xref/org/concord/biologica/ui/BioComboBoxModel.html [exec] xref/org/concord/biologica/ui/package-summary.html [exec] xref/org/concord/biologica/ui/PatchView.html [exec] xref/org/concord/biologica/ui/PedigreeOrganismView.html [exec] xref/org/concord/biologica/ui/SelectionPresenter.html [exec] xref/org/concord/biologica/ui/CCDraggable.html [exec] xref/org/concord/biologica/ui/EnvironmentZoomInViewDialogBox.html [exec] xref/org/concord/biologica/ui/TreeViewNode.html [exec] xref/org/concord/biologica/ui/WelcomeView.html [exec] xref/org/concord/biologica/ui/BioToolBar.html [exec] xref/org/concord/biologica/ui/XMLFileFilter.html [exec] xref/org/concord/biologica/ui/package-frame.html [exec] xref/org/concord/biologica/ui/SmallMeiosisView.html [exec] xref/org/concord/biologica/test/TestWindow.html [exec] xref/org/concord/biologica/test/package-summary.html [exec] xref/org/concord/biologica/test/package-frame.html [exec] xref/org/concord/biologica/engine/OrganismChromosomePair.html [exec] xref/org/concord/biologica/engine/RawNucleicAcid.html [exec] xref/org/concord/biologica/engine/SpeciesImage.html [exec] xref/org/concord/biologica/engine/Species.html [exec] xref/org/concord/biologica/engine/Base.html [exec] xref/org/concord/biologica/engine/EngineProp.html [exec] xref/org/concord/biologica/engine/Organism.html [exec] xref/org/concord/biologica/engine/SpeciesChromosome.html [exec] xref/org/concord/biologica/engine/Terrain.html [exec] xref/org/concord/biologica/engine/ImportContext.html [exec] xref/org/concord/biologica/engine/Gamete.html [exec] xref/org/concord/biologica/engine/OrganismChromosome.html [exec] xref/org/concord/biologica/engine/Debug.html [exec] xref/org/concord/biologica/engine/OrganismImage.html [exec] xref/org/concord/biologica/engine/BioLogicaRule.html [exec] xref/org/concord/biologica/engine/World.html [exec] xref/org/concord/biologica/engine/BioEngine.html [exec] xref/org/concord/biologica/engine/IEnvironment.html [exec] xref/org/concord/biologica/engine/Characteristic.html [exec] xref/org/concord/biologica/engine/ElementContext.html [exec] xref/org/concord/biologica/engine/IChromosome.html [exec] xref/org/concord/biologica/engine/SpeciesAllele.html [exec] xref/org/concord/biologica/engine/PathStrings.html [exec] xref/org/concord/biologica/engine/EnvironmentUnit.html [exec] xref/org/concord/biologica/engine/ObjectDeletedException.html [exec] xref/org/concord/biologica/engine/BioLogicaSpecies.html [exec] xref/org/concord/biologica/engine/INucleicAcidHolder.html [exec] xref/org/concord/biologica/engine/Trait.html [exec] xref/org/concord/biologica/engine/ObjectLockedException.html [exec] xref/org/concord/biologica/engine/Environment.html [exec] xref/org/concord/biologica/engine/AlgorithmicNucleicAcid.html [exec] xref/org/concord/biologica/engine/OrganismAllele.html [exec] xref/org/concord/biologica/engine/NotBioLogicaFileException.html [exec] xref/org/concord/biologica/engine/TerrainEng.html [exec] xref/org/concord/biologica/engine/AminoAcid.html [exec] xref/org/concord/biologica/engine/Rule.html [exec] xref/org/concord/biologica/engine/Gene.html [exec] xref/org/concord/biologica/engine/NucleicAcid.html [exec] xref/org/concord/biologica/engine/Branch.html [exec] xref/org/concord/biologica/engine/ChromosomeSpecification.html [exec] xref/org/concord/biologica/engine/GenotypeToPhenotypeRule.html [exec] xref/org/concord/biologica/engine/Family.html [exec] xref/org/concord/biologica/engine/EngineStrings.html [exec] xref/org/concord/biologica/engine/Elements.html [exec] xref/org/concord/biologica/engine/INucleicAcid.html [exec] xref/org/concord/biologica/engine/SpeciesImageRow.html [exec] xref/org/concord/biologica/engine/FoodChain.html [exec] xref/org/concord/biologica/engine/package-summary.html [exec] xref/org/concord/biologica/engine/SpeciesImageColumn.html [exec] xref/org/concord/biologica/engine/Rules.html [exec] xref/org/concord/biologica/engine/InternalEngineException.html [exec] xref/org/concord/biologica/engine/OrganismAllelePair.html [exec] xref/org/concord/biologica/engine/Codon.html [exec] xref/org/concord/biologica/engine/BehaviorRules.html [exec] xref/org/concord/biologica/engine/package-frame.html [exec] xref/org/concord/biologica/engine/BioEngineBeanInfo.html [exec] xref/org/concord/biologica/engine/EngineObject.html [exec] xref/org/concord/biologica/engine/CrossOver.html [exec] xref/org/concord/biologica/datasupport/ColorUtil.html [exec] xref/org/concord/biologica/datasupport/SpecieFileDesc.html [exec] xref/org/concord/biologica/datasupport/DataOrganism.html [exec] xref/org/concord/biologica/datasupport/package-summary.html [exec] xref/org/concord/biologica/datasupport/package-frame.html [exec] xref/org/concord/biologica/datasupport/ShortImageDescription.html [exec] xref/org/concord/biologica/datasupport/ImageReader.html [exec] xref/overview-frame.html [exec] xref/index.html [exec] xref/stylesheet.css [exec] cvs-usage.html [exec] license.html [delete] Deleting: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/biologica-1.0-site.tar.gz java:prepare-filesystem: java:compile: [echo] Compiling to /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/classes [echo] ========================================================== NOTE: Targetting JVM 1.5, classes will not run on earlier JVMs ========================================================== java:jar-resources: Copying 381 files to /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/classes test:prepare-filesystem: [mkdir] Created dir: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/test-classes [mkdir] Created dir: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/test-reports test:test-resources: test:compile: [echo] No test source files to compile. test:test: [echo] No tests to run. jar:jar: ccmanifest:dependency: [echo] MANIFEST /home/maven/buildfiles/target/checkouts/Projects/Biologica/conf/Manifest.mf [echo] MANIFEST DIR /home/maven/buildfiles/target/checkouts/Projects/Biologica/conf [mkdir] Created dir: /home/maven/buildfiles/target/checkouts/Projects/Biologica/conf ccmanifest: [jar] Building jar: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/biologica-1.0.jar ccdist:signjar: [echo] Signing jar file... [signjar] Signing Jar : /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/biologica-1.0.jar [mkdir] Created dir: /home/maven/buildfiles/target/checkouts/Projects/Biologica/lib [copy] Copying 1 file to /home/maven/buildfiles/target/checkouts/Projects/Biologica/lib [copy] Copying 1 file to /home/maven/buildfiles/target/checkouts/Projects/Biologica/lib Copying: from '/home/maven/buildfiles/target/checkouts/Projects/Biologica/target/biologica-1.0.jar' to: '/home/maven/.maven/repository/biologica/jars/biologica-1.0.jar' Copying: from '/home/maven/buildfiles/target/checkouts/Projects/Biologica/project.xml' to: '/home/maven/.maven/repository/biologica/poms/biologica-1.0.pom' jar:install: jar:deploy-snapshot: [echo] maven.repo.list is set - using artifact deploy mode Will deploy to 1 repository(ies): LOCAL Deploying to repository: LOCAL Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/project.xml-->biologica/poms/biologica-SNAPSHOT.pom Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/project.xml.md5-->biologica/poms/biologica-SNAPSHOT.pom.md5 Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/project.xml-->biologica/poms/biologica-20061112.084528.pom Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/project.xml.md5-->biologica/poms/biologica-20061112.084528.pom.md5 Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/biologica-pom-snapshot-version-->biologica/poms/biologica-snapshot-version Will deploy to 1 repository(ies): LOCAL Deploying to repository: LOCAL Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/biologica-1.0.jar-->biologica/jars/biologica-SNAPSHOT.jar Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/biologica-1.0.jar.md5-->biologica/jars/biologica-SNAPSHOT.jar.md5 Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/biologica-1.0.jar-->biologica/jars/biologica-20061112.084528.jar Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/biologica-1.0.jar.md5-->biologica/jars/biologica-20061112.084528.jar.md5 Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/biologica-jar-snapshot-version-->biologica/jars/biologica-snapshot-version dist:build-setup: [mkdir] Created dir: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/distributions dist:prepare-src-filesystem: [mkdir] Created dir: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/biologica-1.0/src/biologica-1.0 [echo] +-------------------------------------------------------+ | C R E A T I N G S O U R C E D I S T R I B U T I O N | +-------------------------------------------------------+ [copy] Copying 3 files to /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/biologica-1.0/src/biologica-1.0 [copy] Copying 1 file to /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/biologica-1.0/src/biologica-1.0 [copy] Copying 508 files to /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/biologica-1.0/src/biologica-1.0/src dist:build-src: [tar] Building tar: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/distributions/biologica-1.0-src.tar [gzip] Building: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/distributions/biologica-1.0-src.tar.gz [delete] Deleting: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/distributions/biologica-1.0-src.tar [zip] Building zip: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/distributions/biologica-1.0-src.zip dist:deploy-src-snapshot: [echo] maven.repo.list is set - using artifact deploy mode Will deploy to 1 repository(ies): LOCAL Deploying to repository: LOCAL Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/project.xml-->biologica/poms/biologica-SNAPSHOT.pom Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/project.xml.md5-->biologica/poms/biologica-SNAPSHOT.pom.md5 Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/project.xml-->biologica/poms/biologica-20061112.084548.pom Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/project.xml.md5-->biologica/poms/biologica-20061112.084548.pom.md5 Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/biologica-pom-snapshot-version-->biologica/poms/biologica-snapshot-version Will deploy to 1 repository(ies): LOCAL Deploying to repository: LOCAL Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/distributions/biologica-1.0-src.tar.gz-->biologica/distributions/biologica-SNAPSHOT-src.tar.gz Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/distributions/biologica-1.0-src.tar.gz.md5-->biologica/distributions/biologica-SNAPSHOT-src.tar.gz.md5 Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/distributions/biologica-1.0-src.tar.gz-->biologica/distributions/biologica-20061112.084548-src.tar.gz Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/distributions/biologica-1.0-src.tar.gz.md5-->biologica/distributions/biologica-20061112.084548-src.tar.gz.md5 Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/distributions/biologica-distribution-src-targz-snapshot-version-->biologica/distributions/biologica-snapshot-version [echo] maven.repo.list is set - using artifact deploy mode Will deploy to 1 repository(ies): LOCAL Deploying to repository: LOCAL Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/project.xml-->biologica/poms/biologica-SNAPSHOT.pom Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/project.xml.md5-->biologica/poms/biologica-SNAPSHOT.pom.md5 Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/project.xml-->biologica/poms/biologica-20061112.084602.pom Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/project.xml.md5-->biologica/poms/biologica-20061112.084602.pom.md5 Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/biologica-pom-snapshot-version-->biologica/poms/biologica-snapshot-version Will deploy to 1 repository(ies): LOCAL Deploying to repository: LOCAL Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/distributions/biologica-1.0-src.zip-->biologica/distributions/biologica-SNAPSHOT-src.zip Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/distributions/biologica-1.0-src.zip.md5-->biologica/distributions/biologica-SNAPSHOT-src.zip.md5 Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/distributions/biologica-1.0-src.zip-->biologica/distributions/biologica-20061112.084602-src.zip Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/distributions/biologica-1.0-src.zip.md5-->biologica/distributions/biologica-20061112.084602-src.zip.md5 Deploying: /home/maven/buildfiles/target/checkouts/Projects/Biologica/target/distributions/biologica-distribution-src-zip-snapshot-version-->biologica/distributions/biologica-snapshot-version BUILD SUCCESSFUL Total time: 13 minutes 27 seconds Finished at: Sun Nov 12 03:46:21 EST 2006