diff --git a/.gitignore b/.gitignore index 4112f99..4db7a73 100644 --- a/.gitignore +++ b/.gitignore @@ -3,3 +3,4 @@ /.project /.classpath /.travis.yml~ +*/manifest diff --git a/GenBank/manifest b/GenBank/manifest deleted file mode 100644 index ce5001f..0000000 --- a/GenBank/manifest +++ /dev/null @@ -1,4 +0,0 @@ -sequence1.gb -sequence2.gb -sequence3.gb -sequence4.gb diff --git a/InvalidFiles/manifest b/InvalidFiles/manifest deleted file mode 100644 index c2e2a5c..0000000 --- a/InvalidFiles/manifest +++ /dev/null @@ -1,213 +0,0 @@ -sbol-10101.xml -sbol-10105.xml -sbol-10106.xml -sbol-10201.xml -sbol-10202.xml -sbol-10203.xml -sbol-10204.xml -sbol-10206.xml -sbol-10208.xml -sbol-10212.xml -sbol-10213.xml -sbol-10215.xml -sbol-10216.xml -sbol-10217.xml -sbol-10218.xml -sbol-10219.xml -sbol-10220.xml -sbol-10221.xml -sbol-10222.xml -sbol-10223.xml -sbol-10224.xml -sbol-10225.xml -sbol-10226.xml -sbol-10227.xml -sbol-10302.xml -sbol-10303.xml -sbol-10304.xml -sbol-10306.xml -sbol-10307.xml -sbol-10401.xml -sbol-10402.xml -sbol-10403.xml -sbol-10405.xml -sbol-10407.xml -sbol-10501.xml -sbol-10502.xml -sbol-10503.xml -sbol-10507.xml -sbol-10511.xml -sbol-10512.xml -sbol-10513.xml -sbol-10516.xml -sbol-10518.xml -sbol-10519.xml -sbol-10520.xml -sbol-10521.xml -sbol-10522.xml -sbol-10523.xml -sbol-10524.xml -sbol-10525.xml -sbol-10526.xml -sbol-10527.xml -sbol-10528.xml -sbol-10529.xml -sbol-10602.xml -sbol-10603.xml -sbol-10604.xml -sbol-10605.xml -sbol-10606.xml -sbol-10607.xml -sbol-10701.xml -sbol-10702.xml -sbol-10706.xml -sbol-10707.xml -sbol-10708.xml -sbol-10709.xml -sbol-10801.xml -sbol-10802.xml -sbol-10803.xml -sbol-10804.xml -sbol-10805.xml -sbol-10807.xml -sbol-10808.xml -sbol-10809.xml -sbol-10810.xml -sbol-10811.xml -sbol-10901.xml -sbol-10902.xml -sbol-10903.xml -sbol-10904.xml -sbol-10905.xml -sbol-10906.xml -sbol-10909.xml -sbol-11002.xml -sbol-11101.xml -sbol-11102.xml -sbol-11103.xml -sbol-11104.xml -sbol-11201.xml -sbol-11202.xml -sbol-11301.xml -sbol-11401.xml -sbol-11402.xml -sbol-11403.xml -sbol-11404.xml -sbol-11405.xml -sbol-11406.xml -sbol-11407.xml -sbol-11409.xml -sbol-11410.xml -sbol-11411.xml -sbol-11412.xml -sbol-11413.xml -sbol-11414.xml -sbol-11501.xml -sbol-11502.xml -sbol-11504.xml -sbol-11507.xml -sbol-11508.xml -sbol-11511.xml -sbol-11601.xml -sbol-11602.xml -sbol-11604.xml -sbol-11605.xml -sbol-11606.xml -sbol-11607.xml -sbol-11608.xml -sbol-11609.xml -sbol-11701.xml -sbol-11702.xml -sbol-11703.xml -sbol-11704.xml -sbol-11705.xml -sbol-11706.xml -sbol-11801.xml -sbol-11802.xml -sbol-11901.xml -sbol-11902.xml -sbol-11905.xml -sbol-11906.xml -sbol-11907.xml -sbol-12001.xml -sbol-12002.xml -sbol-12003.xml -sbol-12004.xml -sbol-12007.xml -sbol-12101.xml -sbol-12102.xml -sbol-12103.xml -sbol-12301.xml -sbol-12302.xml -sbol-12303.xml -sbol-12401.xml -sbol-12402.xml -sbol-12403.xml -sbol-12404.xml -sbol-12405.xml -sbol-12406.xml -sbol-12407.xml -sbol-12408.xml -sbol-12409.xml -sbol-12410.xml -sbol-12411.xml -sbol-12501.xml -sbol-12502.xml -sbol-12503.xml -sbol-12504.xml -sbol-12505.xml -sbol-12506.xml -sbol-12507.xml -sbol-12601.xml -sbol-12602.xml -sbol-12603.xml -sbol-12604.xml -sbol-12605.xml -sbol-12606.xml -sbol-12701.xml -sbol-12801.xml -sbol-12901.xml -sbol-12902.xml -sbol-12903.xml -sbol-12904.xml -sbol-12905.xml -sbol-12906.xml -sbol-12907.xml -sbol-12908.xml -sbol-12909.xml -sbol-12910.xml -sbol-12911.xml -sbol-12912.xml -sbol-12913.xml -sbol-12914.xml -sbol-13001.xml -sbol-13002.xml -sbol-13003.xml -sbol-13004.xml -sbol-13005.xml -sbol-13006.xml -sbol-13007.xml -sbol-13008.xml -sbol-13009.xml -sbol-13010.xml -sbol-13011.xml -sbol-13012.xml -sbol-13013.xml -sbol-13014.xml -sbol-13015.xml -sbol-13016.xml -sbol-13017.xml -sbol-13018.xml -sbol-13019.xml -sbol-13020.xml -sbol-13021.xml -sbol-13022.xml -sbol-13101.xml -sbol-13102.xml -sbol-13103.xml -sbol-13201.xml -sbol-13202.xml -sbol-13204.xml -sbol-13206.xml -sbol-13207.xml -sbol-13208.xml diff --git a/RDF/manifest b/RDF/manifest deleted file mode 100644 index c442594..0000000 --- a/RDF/manifest +++ /dev/null @@ -1,4 +0,0 @@ -igem1.xml -igem2.xml -igem3.xml -toggle.xml diff --git a/SBOL1/manifest b/SBOL1/manifest deleted file mode 100644 index 0dca100..0000000 --- a/SBOL1/manifest +++ /dev/null @@ -1,27 +0,0 @@ -BBa_I0462.xml -BBa_T9002.xml -labhost_All.xml -labhost_Aspergillus_nidulans.xml -labhost_Bacillus_subtilis.xml -labhost_Drosophila_melanogaster.xml -labhost_Escherichia_Coli.xml -labhost_Gram-negative_bacteria.xml -labhost_Insect_Cells.xml -labhost_Kluyveromyces_lactis.xml -labhost_Mammalian_Cells.xml -labhost_Pichia_pastoris.xml -labhost_Plant_Cells.xml -labhost_Saccharomyces_cerevisiae.xml -labhost_Schizosaccharomyces_pombe.xml -labhost_Unspecified.xml -pACPc_invF.xml -pIKE_pTAK_cassettes.xml -pIKE_pTAK_cassettes_2.xml -pIKE_pTAK_left_right_cassettes.xml -pIKE_pTAK_toggle_switches.xml -partial_pIKE_left_cassette.xml -partial_pIKE_right_casette.xml -partial_pIKE_right_cassette.xml -partial_pTAK_left_cassette.xml -partial_pTAK_right_cassette.xml -precedesTest.xml diff --git a/SBOL2/manifest b/SBOL2/manifest deleted file mode 100644 index 7a1765f..0000000 --- a/SBOL2/manifest +++ /dev/null @@ -1,91 +0,0 @@ -AnnotationOutput.xml -BBa_I0462.xml -CD_SA_Cut_Example.xml -CD_SA_Range_Example.xml -Collection.xml -ComponentDefinitionOutput.xml -ComponentDefinitionOutput_gl.xml -ComponentDefinitionOutput_gl_cd_sa_comp.xml -ComponentDefinitionOutput_gl_noRange.xml -CreateAndRemoveCollections.xml -CreateAndRemoveComponentDefinition.xml -CreateAndRemoveGenericTopLevel.xml -CreateAndRemoveModel.xml -CreateAndRemoveModuleDefinition.xml -EF587312.xml -GenericTopLevelOutput.xml -GenericTopLevelOutput_ann.xml -ModelOutput.xml -ModuleDefinitionOutput.xml -ModuleDefinitionOutput_int_md_ann.xml -Provenance_CodonOptimization.xml -Provenance_CodonOptimization_Agent_Act_CD.xml -Provenance_SpecifyCutOperation_Ag.xml -Provenance_SpecifyCutOperation_Ag_Act.xml -Provenance_SpecifyCutOperation_ag_ann.xml -Provenance_SpecifyJoinOperation_act_us.xml -Provenance_StrainDerivation.xml -RepressionModel.xml -SBOLDocumentOutput.xml -SequenceConstraintOutput.xml -SequenceOutput.xml -act_example.xml -attachment.xml -attachment_ann.xml -design_usa_act_ann.xml -eukaryotic_transcriptional_cd_sa_gl.xml -implementation_example.xml -labhost_All.xml -labhost_Aspergillus_nidulans.xml -labhost_Bacillus_subtilis.xml -labhost_Drosophila_melanogaster.xml -labhost_Escherichia_Coli.xml -labhost_Gram-negative_bacteria.xml -labhost_Insect_Cells.xml -labhost_Kluyveromyces_lactis.xml -labhost_Mammalian_Cells.xml -labhost_Pichia_pastoris.xml -labhost_Plant_Cells.xml -labhost_Saccharomyces_cerevisiae.xml -labhost_Schizosaccharomyces_pombe.xml -labhost_Unspecified.xml -memberAnnotations.xml -memberAnnotations_int_md.xml -memberAnnotations_interaction.xml -memberAnnotations_md_ann.xml -memberAnnotations_md_mod_ann.xml -multipleCollections_no_Members.xml -multipleGenericTopLevel.xml -multipleSequences.xml -pIKE_pTAK_cassettes 2.xml -pIKE_pTAK_cassettes.xml -pIKE_pTAK_cassettes_2.xml -pIKE_pTAK_left_right_cassettes.xml -pIKE_pTAK_toggle_switches.xml -partial_pIKE_left_cassette.xml -partial_pIKE_right_casette.xml -partial_pIKE_right_cassette.xml -partial_pTAK_left_cassette.xml -partial_pTAK_right_cassette.xml -sequence1.xml -sequence2.xml -sequence3.xml -sequence4.xml -sequence_ann.xml -simple_attachment_plan_ann.xml -simple_attachment_ref.xml -singleCollection.xml -singleCompDef_withSeq.xml -singleComponentDefinition.xml -singleFunctionalComponent.xml -singleGenericTopLevel.xml -singleModel.xml -singleModuleDefinition.xml -singleSequence.xml -test_Collection_remove.xml -test_ComponentDefinition_remove.xml -test_GenericTopLevel_remove.xml -test_Model_remove.xml -test_ModuleDefinition_remove.xml -test_Sequence_remove.xml -toggle.xml diff --git a/SBOL2_bp/manifest b/SBOL2_bp/manifest deleted file mode 100644 index 305dbaa..0000000 --- a/SBOL2_bp/manifest +++ /dev/null @@ -1,10 +0,0 @@ -BBa_T9002.xml -CutExample.xml -Provenance_SpecifyAmplifyOperation.xml -Provenance_SpecifyCutOperation.xml -Provenance_SpecifyCutOperation2.xml -Provenance_SpecifyCutOperation_Ag_Act_CD.xml -Provenance_SpecifyCutOperation_redone.xml -Provenance_SpecifyJoinOperation.xml -SimpleComponentDefinitionExample.xml -design-build-test-learn.xml diff --git a/SBOL2_ic/manifest b/SBOL2_ic/manifest deleted file mode 100644 index 87571da..0000000 --- a/SBOL2_ic/manifest +++ /dev/null @@ -1,71 +0,0 @@ -CollectionOutput.xml -ModuleDefinitionOutput_int_fc_md_ann.xml -ModuleDefinitionOutput_int_md_mod.xml -ModuleDefinitionOutput_int_md_mod_fc.xml -ModuleDefinitionOutput_int_md_mod_fc_ann.xml -ModuleDefinitionOutput_maps_md_fc.xml -ModuleDefinitionOutput_maps_md_mod.xml -ModuleDefinitionOutput_md_fc_ann.xml -ModuleDefinitionOutput_md_mod_fc_ann.xml -ModuleDefinitionOutput_md_mod_int.xml -ModuleDefinitionOutput_mod_fc_md.xml -ModuleDefinitionOutput_mod_fc_model_md.xml -ModuleDefinitionOutput_mod_md.xml -ModuleDefinitionOutput_pa_int_fc_md.xml -ModuleDefinitionOutput_pa_int_fc_md_ann.xml -ModuleDefinitionOutput_pa_int_md_mod_fc.xml -ModuleDefinitionOutput_pa_int_md_mod_fc_ann.xml -ModuleDefinitionOutput_pa_maps_mod_int_md.xml -ModuleDefinitionOutput_pa_maps_mod_int_md2.xml -SimpleModuleDefinition.xml -SimpleModuleDefinition_fc_md.xml -act_agent_assoc_example.xml -act_assoc_example.xml -attachment_pointers.xml -design-build-test-learn2.xml -design-build-test-learn3.xml -design-build-test-learn4.xml -design-build-test-learn5.xml -design-build-test-learn6.xml -design-build-test-learn7.xml -design-build-test-learn_imp.xml -design-build-test-learn_plan.xml -design_assoc_act_ann.xml -design_usa_assoc_act.xml -design_usa_assoc_act_ann.xml -eukaryotic_promoters.xml -eukaryotic_promoters_enumerated.xml -eukaryotic_promoters_sampled.xml -eukaryotic_transcriptional_cd_com_sa.xml -eukaryotic_transcriptional_cd_com_sa_cut.xml -eukaryotic_transcriptional_cd_com_sa_range.xml -eukaryotic_transcriptional_cd_com_sa_sc_cut.xml -eukaryotic_transcriptional_cd_com_sa_sc_cut_ann.xml -eukaryotic_transcriptional_cd_com_sa_sc_gl.xml -eukaryotic_transcriptional_cd_com_sa_sc_gl_ann.xml -eukaryotic_transcriptional_cd_com_sa_sc_ran_ann.xml -eukaryotic_transcriptional_cd_com_sa_sc_range.xml -eukaryotic_transcriptional_cd_com_sa_sc_range_ann.xml -eukaryotic_transcriptional_cd_sa_cutl_ann.xml -eukaryotic_transcriptional_cd_sa_gl_ann.xml -eukaryotic_transcriptional_cd_sa_range_ann.xml -eukaryotic_transcriptional_unit.xml -eukaryotic_transcriptional_unit_enumerated.xml -eukaryotic_transcriptional_unit_sampled.xml -gfp_reporter_act_ann.xml -gfp_reporter_activity_combDeri.xml -gfp_reporter_comDeri_ann.xml -gfp_reporter_combDeri.xml -gfp_reporter_combDeri_ann.xml -gfp_reporter_combDeri_ann2.xml -gfp_reporter_combDeri_varComp.xml -gfp_reporter_combDeri_varComp_ann.xml -gfp_reporter_template.xml -gfp_reporter_template_enumerated.xml -gfp_reporter_template_sampled.xml -god_example.xml -implementation_ann.xml -model.xml -model_ann.xml -plan_ann.xml -singleComponentDefinition_component.xml diff --git a/SBOL2_nc/manifest b/SBOL2_nc/manifest deleted file mode 100644 index fa68b99..0000000 --- a/SBOL2_nc/manifest +++ /dev/null @@ -1,31 +0,0 @@ -BBa_I0462_orig.xml -BBa_T9002_orig.xml -SBOL1and2Test.xml -igem1.xml -igem2.xml -igem3.xml -labhost_All_orig.xml -labhost_Aspergillus_nidulans_orig.xml -labhost_Bacillus_subtilis_orig.xml -labhost_Drosophila_melanogaster_orig.xml -labhost_Escherichia_Coli_orig.xml -labhost_Gram-negative_bacteria_orig.xml -labhost_Insect_Cells_orig.xml -labhost_Kluyveromyces_lactis_orig.xml -labhost_Mammalian_Cells_orig.xml -labhost_Pichia_pastoris_orig.xml -labhost_Plant_Cells_orig.xml -labhost_Saccharomyces_cerevisiae_orig.xml -labhost_Schizosaccharomyces_pombe_orig.xml -labhost_Unspecified_orig.xml -pIKE_pTAK_cassettes 2_orig.xml -pIKE_pTAK_cassettes_2_orig.xml -pIKE_pTAK_cassettes_orig.xml -pIKE_pTAK_left_right_cassettes_orig.xml -pIKE_pTAK_toggle_switches_orig.xml -partial_pIKE_left_cassette_orig.xml -partial_pIKE_right_casette_orig.xml -partial_pIKE_right_cassette_orig.xml -partial_pTAK_left_cassette_orig.xml -partial_pTAK_right_cassette_orig.xml -was-generated-bys-derived-froms.xml diff --git a/manifest.sh b/manifest.sh index 8a2178c..cb9ab63 100755 --- a/manifest.sh +++ b/manifest.sh @@ -6,3 +6,5 @@ do find * -not -name "manifest" -type f -print > manifest cd .. done + +echo "Manifests generated!" diff --git a/pom.xml b/pom.xml index bf684c2..1247c46 100644 --- a/pom.xml +++ b/pom.xml @@ -40,6 +40,22 @@ 1.8 + + exec-maven-plugin + org.codehaus.mojo + + + Generate Manifests + generate-sources + + exec + + + + + ${basedir}/manifest.sh + + - \ No newline at end of file + diff --git a/site_resources/manifest b/site_resources/manifest deleted file mode 100644 index 61c85f7..0000000 --- a/site_resources/manifest +++ /dev/null @@ -1,2 +0,0 @@ -graph-1.png -graph.pdf diff --git a/src/manifest b/src/manifest deleted file mode 100644 index 2d02709..0000000 --- a/src/manifest +++ /dev/null @@ -1,560 +0,0 @@ -main/resources/SBOLTestSuite/SBOL2/multipleGenericTopLevel.xml -main/resources/SBOLTestSuite/SBOL2/test_Model_remove.xml -main/resources/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl_cd_sa_comp.xml -main/resources/SBOLTestSuite/SBOL2/partial_pTAK_left_cassette.xml -main/resources/SBOLTestSuite/SBOL2/AnnotationOutput.xml -main/resources/SBOLTestSuite/SBOL2/singleGenericTopLevel.xml -main/resources/SBOLTestSuite/SBOL2/labhost_Escherichia_Coli.xml -main/resources/SBOLTestSuite/SBOL2/partial_pIKE_right_casette.xml -main/resources/SBOLTestSuite/SBOL2/SequenceConstraintOutput.xml -main/resources/SBOLTestSuite/SBOL2/labhost_Mammalian_Cells.xml -main/resources/SBOLTestSuite/SBOL2/simple_attachment_plan_ann.xml -main/resources/SBOLTestSuite/SBOL2/CD_SA_Range_Example.xml -main/resources/SBOLTestSuite/SBOL2/CreateAndRemoveModel.xml -main/resources/SBOLTestSuite/SBOL2/multipleSequences.xml -main/resources/SBOLTestSuite/SBOL2/Provenance_CodonOptimization.xml -main/resources/SBOLTestSuite/SBOL2/memberAnnotations.xml -main/resources/SBOLTestSuite/SBOL2/SequenceOutput.xml -main/resources/SBOLTestSuite/SBOL2/memberAnnotations_int_md.xml -main/resources/SBOLTestSuite/SBOL2/Provenance_SpecifyCutOperation_Ag.xml -main/resources/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl_noRange.xml -main/resources/SBOLTestSuite/SBOL2/labhost_Kluyveromyces_lactis.xml -main/resources/SBOLTestSuite/SBOL2/ModelOutput.xml -main/resources/SBOLTestSuite/SBOL2/memberAnnotations_md_ann.xml -main/resources/SBOLTestSuite/SBOL2/test_ModuleDefinition_remove.xml -main/resources/SBOLTestSuite/SBOL2/CreateAndRemoveGenericTopLevel.xml -main/resources/SBOLTestSuite/SBOL2/Provenance_SpecifyCutOperation_ag_ann.xml -main/resources/SBOLTestSuite/SBOL2/singleModel.xml -main/resources/SBOLTestSuite/SBOL2/SBOLDocumentOutput.xml -main/resources/SBOLTestSuite/SBOL2/partial_pIKE_left_cassette.xml -main/resources/SBOLTestSuite/SBOL2/GenericTopLevelOutput.xml -main/resources/SBOLTestSuite/SBOL2/labhost_Gram-negative_bacteria.xml -main/resources/SBOLTestSuite/SBOL2/labhost_Bacillus_subtilis.xml -main/resources/SBOLTestSuite/SBOL2/ModuleDefinitionOutput_int_md_ann.xml -main/resources/SBOLTestSuite/SBOL2/partial_pIKE_right_cassette.xml -main/resources/SBOLTestSuite/SBOL2/singleModuleDefinition.xml -main/resources/SBOLTestSuite/SBOL2/ComponentDefinitionOutput.xml -main/resources/SBOLTestSuite/SBOL2/singleCollection.xml -main/resources/SBOLTestSuite/SBOL2/BBa_I0462.xml -main/resources/SBOLTestSuite/SBOL2/Provenance_StrainDerivation.xml -main/resources/SBOLTestSuite/SBOL2/labhost_Plant_Cells.xml -main/resources/SBOLTestSuite/SBOL2/attachment_ann.xml -main/resources/SBOLTestSuite/SBOL2/CreateAndRemoveModuleDefinition.xml -main/resources/SBOLTestSuite/SBOL2/CreateAndRemoveComponentDefinition.xml -main/resources/SBOLTestSuite/SBOL2/simple_attachment_ref.xml -main/resources/SBOLTestSuite/SBOL2/singleCompDef_withSeq.xml -main/resources/SBOLTestSuite/SBOL2/design_usa_act_ann.xml -main/resources/SBOLTestSuite/SBOL2/pIKE_pTAK_left_right_cassettes.xml -main/resources/SBOLTestSuite/SBOL2/pIKE_pTAK_cassettes_2.xml -main/resources/SBOLTestSuite/SBOL2/singleFunctionalComponent.xml -main/resources/SBOLTestSuite/SBOL2/Provenance_CodonOptimization_Agent_Act_CD.xml -main/resources/SBOLTestSuite/SBOL2/CD_SA_Cut_Example.xml -main/resources/SBOLTestSuite/SBOL2/act_example.xml -main/resources/SBOLTestSuite/SBOL2/eukaryotic_transcriptional_cd_sa_gl.xml -main/resources/SBOLTestSuite/SBOL2/pIKE_pTAK_toggle_switches.xml -main/resources/SBOLTestSuite/SBOL2/Provenance_SpecifyCutOperation_Ag_Act.xml -main/resources/SBOLTestSuite/SBOL2/labhost_All.xml -main/resources/SBOLTestSuite/SBOL2/labhost_Unspecified.xml -main/resources/SBOLTestSuite/SBOL2/ModuleDefinitionOutput.xml -main/resources/SBOLTestSuite/SBOL2/labhost_Schizosaccharomyces_pombe.xml -main/resources/SBOLTestSuite/SBOL2/sequence_ann.xml -main/resources/SBOLTestSuite/SBOL2/multipleCollections_no_Members.xml -main/resources/SBOLTestSuite/SBOL2/RepressionModel.xml -main/resources/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl.xml -main/resources/SBOLTestSuite/SBOL2/Collection.xml -main/resources/SBOLTestSuite/SBOL2/labhost_Pichia_pastoris.xml -main/resources/SBOLTestSuite/SBOL2/labhost_Insect_Cells.xml -main/resources/SBOLTestSuite/SBOL2/GenericTopLevelOutput_ann.xml -main/resources/SBOLTestSuite/SBOL2/memberAnnotations_interaction.xml -main/resources/SBOLTestSuite/SBOL2/sequence4.xml -main/resources/SBOLTestSuite/SBOL2/memberAnnotations_md_mod_ann.xml -main/resources/SBOLTestSuite/SBOL2/implementation_example.xml -main/resources/SBOLTestSuite/SBOL2/CreateAndRemoveCollections.xml -main/resources/SBOLTestSuite/SBOL2/attachment.xml -main/resources/SBOLTestSuite/SBOL2/test_ComponentDefinition_remove.xml -main/resources/SBOLTestSuite/SBOL2/EF587312.xml -main/resources/SBOLTestSuite/SBOL2/sequence1.xml -main/resources/SBOLTestSuite/SBOL2/Provenance_SpecifyJoinOperation_act_us.xml -main/resources/SBOLTestSuite/SBOL2/pIKE_pTAK_cassettes.xml -main/resources/SBOLTestSuite/SBOL2/test_Collection_remove.xml -main/resources/SBOLTestSuite/SBOL2/partial_pTAK_right_cassette.xml -main/resources/SBOLTestSuite/SBOL2/labhost_Saccharomyces_cerevisiae.xml -main/resources/SBOLTestSuite/SBOL2/test_GenericTopLevel_remove.xml -main/resources/SBOLTestSuite/SBOL2/sequence2.xml -main/resources/SBOLTestSuite/SBOL2/pIKE_pTAK_cassettes 2.xml -main/resources/SBOLTestSuite/SBOL2/labhost_Drosophila_melanogaster.xml -main/resources/SBOLTestSuite/SBOL2/labhost_Aspergillus_nidulans.xml -main/resources/SBOLTestSuite/SBOL2/test_Sequence_remove.xml -main/resources/SBOLTestSuite/SBOL2/singleComponentDefinition.xml -main/resources/SBOLTestSuite/SBOL2/toggle.xml -main/resources/SBOLTestSuite/SBOL2/singleSequence.xml -main/resources/SBOLTestSuite/SBOL2/sequence3.xml -main/java/org/sboltestcharacterization/cluster_analysis.java -main/java/org/sboltestcharacterization/cluster_coverage.java -main/java/org/sboltestcharacterization/count_classes.java -main/java/org/sboltestcharacterization/cluster.java -test/resources/.gitignore -test/resources/SBOLTestSuite/SBOL2_ic/ModuleDefinitionOutput_maps_md_mod.xml -test/resources/SBOLTestSuite/SBOL2_ic/eukaryotic_transcriptional_cd_com_sa_sc_range_ann.xml -test/resources/SBOLTestSuite/SBOL2_ic/eukaryotic_transcriptional_unit_enumerated.xml -test/resources/SBOLTestSuite/SBOL2_ic/ModuleDefinitionOutput_maps_md_fc.xml -test/resources/SBOLTestSuite/SBOL2_ic/eukaryotic_transcriptional_cd_sa_cutl_ann.xml -test/resources/SBOLTestSuite/SBOL2_ic/SimpleModuleDefinition.xml -test/resources/SBOLTestSuite/SBOL2_ic/eukaryotic_transcriptional_cd_sa_range_ann.xml -test/resources/SBOLTestSuite/SBOL2_ic/ModuleDefinitionOutput_md_fc_ann.xml -test/resources/SBOLTestSuite/SBOL2_ic/ModuleDefinitionOutput_mod_md.xml -test/resources/SBOLTestSuite/SBOL2_ic/design-build-test-learn6.xml -test/resources/SBOLTestSuite/SBOL2_ic/ModuleDefinitionOutput_int_md_mod.xml -test/resources/SBOLTestSuite/SBOL2_ic/singleComponentDefinition_component.xml -test/resources/SBOLTestSuite/SBOL2_ic/design-build-test-learn7.xml -test/resources/SBOLTestSuite/SBOL2_ic/god_example.xml -test/resources/SBOLTestSuite/SBOL2_ic/gfp_reporter_activity_combDeri.xml -test/resources/SBOLTestSuite/SBOL2_ic/design-build-test-learn_imp.xml -test/resources/SBOLTestSuite/SBOL2_ic/design-build-test-learn5.xml -test/resources/SBOLTestSuite/SBOL2_ic/ModuleDefinitionOutput_mod_fc_md.xml -test/resources/SBOLTestSuite/SBOL2_ic/design-build-test-learn4.xml -test/resources/SBOLTestSuite/SBOL2_ic/ModuleDefinitionOutput_md_mod_int.xml -test/resources/SBOLTestSuite/SBOL2_ic/ModuleDefinitionOutput_int_fc_md_ann.xml -test/resources/SBOLTestSuite/SBOL2_ic/ModuleDefinitionOutput_int_md_mod_fc.xml -test/resources/SBOLTestSuite/SBOL2_ic/model.xml -test/resources/SBOLTestSuite/SBOL2_ic/eukaryotic_transcriptional_cd_com_sa_sc_cut.xml -test/resources/SBOLTestSuite/SBOL2_ic/design-build-test-learn3.xml -test/resources/SBOLTestSuite/SBOL2_ic/plan_ann.xml -test/resources/SBOLTestSuite/SBOL2_ic/ModuleDefinitionOutput_pa_int_fc_md.xml -test/resources/SBOLTestSuite/SBOL2_ic/gfp_reporter_template.xml -test/resources/SBOLTestSuite/SBOL2_ic/design_assoc_act_ann.xml -test/resources/SBOLTestSuite/SBOL2_ic/design-build-test-learn2.xml -test/resources/SBOLTestSuite/SBOL2_ic/gfp_reporter_combDeri_varComp_ann.xml -test/resources/SBOLTestSuite/SBOL2_ic/ModuleDefinitionOutput_int_md_mod_fc_ann.xml -test/resources/SBOLTestSuite/SBOL2_ic/gfp_reporter_template_enumerated.xml -test/resources/SBOLTestSuite/SBOL2_ic/eukaryotic_transcriptional_cd_sa_gl_ann.xml -test/resources/SBOLTestSuite/SBOL2_ic/ModuleDefinitionOutput_pa_maps_mod_int_md2.xml -test/resources/SBOLTestSuite/SBOL2_ic/gfp_reporter_template_sampled.xml -test/resources/SBOLTestSuite/SBOL2_ic/design_usa_assoc_act.xml -test/resources/SBOLTestSuite/SBOL2_ic/design-build-test-learn_plan.xml -test/resources/SBOLTestSuite/SBOL2_ic/eukaryotic_transcriptional_cd_com_sa_sc_ran_ann.xml -test/resources/SBOLTestSuite/SBOL2_ic/gfp_reporter_combDeri_varComp.xml -test/resources/SBOLTestSuite/SBOL2_ic/CollectionOutput.xml -test/resources/SBOLTestSuite/SBOL2_ic/eukaryotic_transcriptional_cd_com_sa_sc_gl_ann.xml -test/resources/SBOLTestSuite/SBOL2_ic/eukaryotic_promoters_sampled.xml -test/resources/SBOLTestSuite/SBOL2_ic/eukaryotic_transcriptional_cd_com_sa_sc_gl.xml -test/resources/SBOLTestSuite/SBOL2_ic/eukaryotic_transcriptional_cd_com_sa_range.xml -test/resources/SBOLTestSuite/SBOL2_ic/design_usa_assoc_act_ann.xml -test/resources/SBOLTestSuite/SBOL2_ic/eukaryotic_transcriptional_cd_com_sa_sc_cut_ann.xml -test/resources/SBOLTestSuite/SBOL2_ic/eukaryotic_promoters_enumerated.xml -test/resources/SBOLTestSuite/SBOL2_ic/ModuleDefinitionOutput_mod_fc_model_md.xml -test/resources/SBOLTestSuite/SBOL2_ic/eukaryotic_transcriptional_unit.xml -test/resources/SBOLTestSuite/SBOL2_ic/SimpleModuleDefinition_fc_md.xml -test/resources/SBOLTestSuite/SBOL2_ic/act_agent_assoc_example.xml -test/resources/SBOLTestSuite/SBOL2_ic/implementation_ann.xml -test/resources/SBOLTestSuite/SBOL2_ic/eukaryotic_promoters.xml -test/resources/SBOLTestSuite/SBOL2_ic/gfp_reporter_combDeri_ann.xml -test/resources/SBOLTestSuite/SBOL2_ic/gfp_reporter_combDeri_ann2.xml -test/resources/SBOLTestSuite/SBOL2_ic/ModuleDefinitionOutput_md_mod_fc_ann.xml -test/resources/SBOLTestSuite/SBOL2_ic/gfp_reporter_comDeri_ann.xml -test/resources/SBOLTestSuite/SBOL2_ic/ModuleDefinitionOutput_pa_int_md_mod_fc_ann.xml -test/resources/SBOLTestSuite/SBOL2_ic/eukaryotic_transcriptional_unit_sampled.xml -test/resources/SBOLTestSuite/SBOL2_ic/act_assoc_example.xml -test/resources/SBOLTestSuite/SBOL2_ic/gfp_reporter_act_ann.xml -test/resources/SBOLTestSuite/SBOL2_ic/gfp_reporter_combDeri.xml -test/resources/SBOLTestSuite/SBOL2_ic/ModuleDefinitionOutput_pa_maps_mod_int_md.xml -test/resources/SBOLTestSuite/SBOL2_ic/eukaryotic_transcriptional_cd_com_sa_cut.xml -test/resources/SBOLTestSuite/SBOL2_ic/eukaryotic_transcriptional_cd_com_sa_sc_range.xml -test/resources/SBOLTestSuite/SBOL2_ic/ModuleDefinitionOutput_pa_int_md_mod_fc.xml -test/resources/SBOLTestSuite/SBOL2_ic/model_ann.xml -test/resources/SBOLTestSuite/SBOL2_ic/attachment_pointers.xml -test/resources/SBOLTestSuite/SBOL2_ic/ModuleDefinitionOutput_pa_int_fc_md_ann.xml -test/resources/SBOLTestSuite/SBOL2_ic/eukaryotic_transcriptional_cd_com_sa.xml -test/resources/SBOLTestSuite/SBOL2/multipleGenericTopLevel.xml -test/resources/SBOLTestSuite/SBOL2/test_Model_remove.xml -test/resources/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl_cd_sa_comp.xml -test/resources/SBOLTestSuite/SBOL2/partial_pTAK_left_cassette.xml -test/resources/SBOLTestSuite/SBOL2/AnnotationOutput.xml -test/resources/SBOLTestSuite/SBOL2/singleGenericTopLevel.xml -test/resources/SBOLTestSuite/SBOL2/labhost_Escherichia_Coli.xml -test/resources/SBOLTestSuite/SBOL2/partial_pIKE_right_casette.xml -test/resources/SBOLTestSuite/SBOL2/SequenceConstraintOutput.xml -test/resources/SBOLTestSuite/SBOL2/labhost_Mammalian_Cells.xml -test/resources/SBOLTestSuite/SBOL2/simple_attachment_plan_ann.xml -test/resources/SBOLTestSuite/SBOL2/CD_SA_Range_Example.xml -test/resources/SBOLTestSuite/SBOL2/CreateAndRemoveModel.xml -test/resources/SBOLTestSuite/SBOL2/multipleSequences.xml -test/resources/SBOLTestSuite/SBOL2/Provenance_CodonOptimization.xml -test/resources/SBOLTestSuite/SBOL2/memberAnnotations.xml -test/resources/SBOLTestSuite/SBOL2/SequenceOutput.xml -test/resources/SBOLTestSuite/SBOL2/memberAnnotations_int_md.xml -test/resources/SBOLTestSuite/SBOL2/Provenance_SpecifyCutOperation_Ag.xml -test/resources/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl_noRange.xml -test/resources/SBOLTestSuite/SBOL2/labhost_Kluyveromyces_lactis.xml -test/resources/SBOLTestSuite/SBOL2/ModelOutput.xml -test/resources/SBOLTestSuite/SBOL2/memberAnnotations_md_ann.xml -test/resources/SBOLTestSuite/SBOL2/test_ModuleDefinition_remove.xml -test/resources/SBOLTestSuite/SBOL2/CreateAndRemoveGenericTopLevel.xml -test/resources/SBOLTestSuite/SBOL2/Provenance_SpecifyCutOperation_ag_ann.xml -test/resources/SBOLTestSuite/SBOL2/singleModel.xml -test/resources/SBOLTestSuite/SBOL2/SBOLDocumentOutput.xml -test/resources/SBOLTestSuite/SBOL2/partial_pIKE_left_cassette.xml -test/resources/SBOLTestSuite/SBOL2/GenericTopLevelOutput.xml -test/resources/SBOLTestSuite/SBOL2/labhost_Gram-negative_bacteria.xml -test/resources/SBOLTestSuite/SBOL2/labhost_Bacillus_subtilis.xml -test/resources/SBOLTestSuite/SBOL2/ModuleDefinitionOutput_int_md_ann.xml -test/resources/SBOLTestSuite/SBOL2/partial_pIKE_right_cassette.xml -test/resources/SBOLTestSuite/SBOL2/singleModuleDefinition.xml -test/resources/SBOLTestSuite/SBOL2/ComponentDefinitionOutput.xml -test/resources/SBOLTestSuite/SBOL2/singleCollection.xml -test/resources/SBOLTestSuite/SBOL2/BBa_I0462.xml -test/resources/SBOLTestSuite/SBOL2/Provenance_StrainDerivation.xml -test/resources/SBOLTestSuite/SBOL2/labhost_Plant_Cells.xml -test/resources/SBOLTestSuite/SBOL2/attachment_ann.xml -test/resources/SBOLTestSuite/SBOL2/CreateAndRemoveModuleDefinition.xml -test/resources/SBOLTestSuite/SBOL2/CreateAndRemoveComponentDefinition.xml -test/resources/SBOLTestSuite/SBOL2/simple_attachment_ref.xml -test/resources/SBOLTestSuite/SBOL2/singleCompDef_withSeq.xml -test/resources/SBOLTestSuite/SBOL2/design_usa_act_ann.xml -test/resources/SBOLTestSuite/SBOL2/pIKE_pTAK_left_right_cassettes.xml -test/resources/SBOLTestSuite/SBOL2/pIKE_pTAK_cassettes_2.xml -test/resources/SBOLTestSuite/SBOL2/singleFunctionalComponent.xml -test/resources/SBOLTestSuite/SBOL2/Provenance_CodonOptimization_Agent_Act_CD.xml -test/resources/SBOLTestSuite/SBOL2/CD_SA_Cut_Example.xml -test/resources/SBOLTestSuite/SBOL2/act_example.xml -test/resources/SBOLTestSuite/SBOL2/eukaryotic_transcriptional_cd_sa_gl.xml -test/resources/SBOLTestSuite/SBOL2/pIKE_pTAK_toggle_switches.xml -test/resources/SBOLTestSuite/SBOL2/Provenance_SpecifyCutOperation_Ag_Act.xml -test/resources/SBOLTestSuite/SBOL2/labhost_All.xml -test/resources/SBOLTestSuite/SBOL2/labhost_Unspecified.xml -test/resources/SBOLTestSuite/SBOL2/ModuleDefinitionOutput.xml -test/resources/SBOLTestSuite/SBOL2/labhost_Schizosaccharomyces_pombe.xml -test/resources/SBOLTestSuite/SBOL2/sequence_ann.xml -test/resources/SBOLTestSuite/SBOL2/multipleCollections_no_Members.xml -test/resources/SBOLTestSuite/SBOL2/RepressionModel.xml -test/resources/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl.xml -test/resources/SBOLTestSuite/SBOL2/Collection.xml -test/resources/SBOLTestSuite/SBOL2/labhost_Pichia_pastoris.xml -test/resources/SBOLTestSuite/SBOL2/labhost_Insect_Cells.xml -test/resources/SBOLTestSuite/SBOL2/GenericTopLevelOutput_ann.xml -test/resources/SBOLTestSuite/SBOL2/memberAnnotations_interaction.xml -test/resources/SBOLTestSuite/SBOL2/sequence4.xml -test/resources/SBOLTestSuite/SBOL2/memberAnnotations_md_mod_ann.xml -test/resources/SBOLTestSuite/SBOL2/implementation_example.xml -test/resources/SBOLTestSuite/SBOL2/CreateAndRemoveCollections.xml -test/resources/SBOLTestSuite/SBOL2/attachment.xml -test/resources/SBOLTestSuite/SBOL2/test_ComponentDefinition_remove.xml -test/resources/SBOLTestSuite/SBOL2/EF587312.xml -test/resources/SBOLTestSuite/SBOL2/sequence1.xml -test/resources/SBOLTestSuite/SBOL2/Provenance_SpecifyJoinOperation_act_us.xml -test/resources/SBOLTestSuite/SBOL2/pIKE_pTAK_cassettes.xml -test/resources/SBOLTestSuite/SBOL2/test_Collection_remove.xml -test/resources/SBOLTestSuite/SBOL2/partial_pTAK_right_cassette.xml -test/resources/SBOLTestSuite/SBOL2/labhost_Saccharomyces_cerevisiae.xml -test/resources/SBOLTestSuite/SBOL2/test_GenericTopLevel_remove.xml -test/resources/SBOLTestSuite/SBOL2/sequence2.xml -test/resources/SBOLTestSuite/SBOL2/pIKE_pTAK_cassettes 2.xml -test/resources/SBOLTestSuite/SBOL2/labhost_Drosophila_melanogaster.xml -test/resources/SBOLTestSuite/SBOL2/labhost_Aspergillus_nidulans.xml -test/resources/SBOLTestSuite/SBOL2/test_Sequence_remove.xml -test/resources/SBOLTestSuite/SBOL2/singleComponentDefinition.xml -test/resources/SBOLTestSuite/SBOL2/toggle.xml -test/resources/SBOLTestSuite/SBOL2/singleSequence.xml -test/resources/SBOLTestSuite/SBOL2/sequence3.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11406.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11412.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10903.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10526.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13013.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11604.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13007.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11002.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12906.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12912.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12913.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12907.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11201.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13006.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11605.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13012.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10527.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10902.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11413.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13204.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11407.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13206.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11411.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11405.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10525.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13004.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13010.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10519.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11607.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12911.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12905.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12904.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12910.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11202.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11606.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10518.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13011.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13005.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10524.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10901.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11404.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11410.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13207.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11414.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10905.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13001.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13015.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11602.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10520.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12914.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12901.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10521.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13014.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10904.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11401.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13202.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11403.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10709.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10906.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13016.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11601.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13002.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10523.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12903.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12902.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10522.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13003.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13017.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10708.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13201.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11402.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10223.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12408.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11101.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11511.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10801.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11504.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11706.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12409.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10222.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10220.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10208.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11102.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11704.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10803.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10802.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11507.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11705.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11103.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10221.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11301.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10219.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10225.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11701.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13102.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10807.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11502.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13103.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10224.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10218.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11104.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10226.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13101.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11702.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10811.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10805.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10804.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10810.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11501.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11703.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10227.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12801.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12603.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10202.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10216.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12401.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11901.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10606.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10809.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10808.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10607.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12004.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10405.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10217.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10203.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12602.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10215.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12402.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10201.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10407.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11902.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10605.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12007.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10604.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12403.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12601.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12605.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12407.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10204.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10402.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11907.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12003.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12002.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11906.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10403.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12406.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12604.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12606.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12410.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10213.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12404.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10401.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10603.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10602.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11508.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12001.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11905.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12405.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10212.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10206.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12411.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10507.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10513.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11802.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12502.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12701.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12503.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10512.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10706.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10909.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13019.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11801.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10302.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12501.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10101.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10303.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13018.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10511.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10707.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11409.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13020.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10529.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12302.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13008.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10501.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10307.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12504.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10105.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12909.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12908.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12505.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10306.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13009.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12303.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10528.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13021.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10702.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12101.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12103.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10502.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10516.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11608.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12301.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12507.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10304.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10106.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12506.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-11609.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10503.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13022.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-12102.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-13208.xml -test/resources/SBOLTestSuite/InvalidFiles/sbol-10701.xml -test/resources/SBOLTestSuite/SBOL2_nc/labhost_Kluyveromyces_lactis_orig.xml -test/resources/SBOLTestSuite/SBOL2_nc/labhost_Mammalian_Cells_orig.xml -test/resources/SBOLTestSuite/SBOL2_nc/SBOL1and2Test.xml -test/resources/SBOLTestSuite/SBOL2_nc/partial_pTAK_right_cassette_orig.xml -test/resources/SBOLTestSuite/SBOL2_nc/labhost_Insect_Cells_orig.xml -test/resources/SBOLTestSuite/SBOL2_nc/partial_pIKE_right_casette_orig.xml -test/resources/SBOLTestSuite/SBOL2_nc/BBa_T9002_orig.xml -test/resources/SBOLTestSuite/SBOL2_nc/was-generated-bys-derived-froms.xml -test/resources/SBOLTestSuite/SBOL2_nc/labhost_Saccharomyces_cerevisiae_orig.xml -test/resources/SBOLTestSuite/SBOL2_nc/labhost_Schizosaccharomyces_pombe_orig.xml -test/resources/SBOLTestSuite/SBOL2_nc/partial_pIKE_left_cassette_orig.xml -test/resources/SBOLTestSuite/SBOL2_nc/labhost_Aspergillus_nidulans_orig.xml -test/resources/SBOLTestSuite/SBOL2_nc/labhost_Escherichia_Coli_orig.xml -test/resources/SBOLTestSuite/SBOL2_nc/labhost_Plant_Cells_orig.xml -test/resources/SBOLTestSuite/SBOL2_nc/labhost_All_orig.xml -test/resources/SBOLTestSuite/SBOL2_nc/labhost_Unspecified_orig.xml -test/resources/SBOLTestSuite/SBOL2_nc/BBa_I0462_orig.xml -test/resources/SBOLTestSuite/SBOL2_nc/labhost_Bacillus_subtilis_orig.xml -test/resources/SBOLTestSuite/SBOL2_nc/pIKE_pTAK_cassettes_2_orig.xml -test/resources/SBOLTestSuite/SBOL2_nc/pIKE_pTAK_cassettes 2_orig.xml -test/resources/SBOLTestSuite/SBOL2_nc/pIKE_pTAK_cassettes_orig.xml -test/resources/SBOLTestSuite/SBOL2_nc/partial_pTAK_left_cassette_orig.xml -test/resources/SBOLTestSuite/SBOL2_nc/pIKE_pTAK_left_right_cassettes_orig.xml -test/resources/SBOLTestSuite/SBOL2_nc/pIKE_pTAK_toggle_switches_orig.xml -test/resources/SBOLTestSuite/SBOL2_nc/partial_pIKE_right_cassette_orig.xml -test/resources/SBOLTestSuite/SBOL2_nc/labhost_Drosophila_melanogaster_orig.xml -test/resources/SBOLTestSuite/SBOL2_nc/igem1.xml -test/resources/SBOLTestSuite/SBOL2_nc/igem3.xml -test/resources/SBOLTestSuite/SBOL2_nc/labhost_Gram-negative_bacteria_orig.xml -test/resources/SBOLTestSuite/SBOL2_nc/igem2.xml -test/resources/SBOLTestSuite/SBOL2_nc/labhost_Pichia_pastoris_orig.xml -test/resources/SBOLTestSuite/SBOL1/partial_pTAK_left_cassette.xml -test/resources/SBOLTestSuite/SBOL1/labhost_Escherichia_Coli.xml -test/resources/SBOLTestSuite/SBOL1/partial_pIKE_right_casette.xml -test/resources/SBOLTestSuite/SBOL1/labhost_Mammalian_Cells.xml -test/resources/SBOLTestSuite/SBOL1/labhost_Kluyveromyces_lactis.xml -test/resources/SBOLTestSuite/SBOL1/partial_pIKE_left_cassette.xml -test/resources/SBOLTestSuite/SBOL1/pACPc_invF.xml -test/resources/SBOLTestSuite/SBOL1/labhost_Gram-negative_bacteria.xml -test/resources/SBOLTestSuite/SBOL1/labhost_Bacillus_subtilis.xml -test/resources/SBOLTestSuite/SBOL1/partial_pIKE_right_cassette.xml -test/resources/SBOLTestSuite/SBOL1/BBa_I0462.xml -test/resources/SBOLTestSuite/SBOL1/labhost_Plant_Cells.xml -test/resources/SBOLTestSuite/SBOL1/pIKE_pTAK_left_right_cassettes.xml -test/resources/SBOLTestSuite/SBOL1/pIKE_pTAK_toggle_switches.xml -test/resources/SBOLTestSuite/SBOL1/precedesTest.xml -test/resources/SBOLTestSuite/SBOL1/labhost_All.xml -test/resources/SBOLTestSuite/SBOL1/labhost_Unspecified.xml -test/resources/SBOLTestSuite/SBOL1/labhost_Schizosaccharomyces_pombe.xml -test/resources/SBOLTestSuite/SBOL1/labhost_Pichia_pastoris.xml -test/resources/SBOLTestSuite/SBOL1/labhost_Insect_Cells.xml -test/resources/SBOLTestSuite/SBOL1/BBa_T9002.xml -test/resources/SBOLTestSuite/SBOL1/pIKE_pTAK_cassettes.xml -test/resources/SBOLTestSuite/SBOL1/partial_pTAK_right_cassette.xml -test/resources/SBOLTestSuite/SBOL1/labhost_Saccharomyces_cerevisiae.xml -test/resources/SBOLTestSuite/SBOL1/pIKE_pTAK_cassettes 2.xml -test/resources/SBOLTestSuite/SBOL1/labhost_Drosophila_melanogaster.xml -test/resources/SBOLTestSuite/SBOL1/labhost_Aspergillus_nidulans.xml -test/resources/SBOLTestSuite/GenBank/sequence1.gb -test/resources/SBOLTestSuite/GenBank/sequence4.gb -test/resources/SBOLTestSuite/GenBank/genomes/NW_003020110.gbk -test/resources/SBOLTestSuite/GenBank/genomes/M.mycoides-JCVI-Syn1.0-CP001621.gb -test/resources/SBOLTestSuite/GenBank/genomes/SCU49845.gbk -test/resources/SBOLTestSuite/GenBank/genomes/18500.gbk -test/resources/SBOLTestSuite/GenBank/genomes/M.mycoides-JCVI-Syn1.0-CP001668.gb -test/resources/SBOLTestSuite/GenBank/genomes/cms_psb1c3.gb -test/resources/SBOLTestSuite/GenBank/genomes/5535.gbk -test/resources/SBOLTestSuite/GenBank/genomes/18625.gbk -test/resources/SBOLTestSuite/GenBank/genomes/20027.gbk -test/resources/SBOLTestSuite/GenBank/EF587312.gb -test/resources/SBOLTestSuite/GenBank/sequence3.gb -test/resources/SBOLTestSuite/GenBank/sequence2.gb -test/resources/SBOLTestSuite/SBOL2_bp/Provenance_SpecifyCutOperation2.xml -test/resources/SBOLTestSuite/SBOL2_bp/Provenance_SpecifyAmplifyOperation.xml -test/resources/SBOLTestSuite/SBOL2_bp/Provenance_SpecifyJoinOperation.xml -test/resources/SBOLTestSuite/SBOL2_bp/Provenance_SpecifyCutOperation_redone.xml -test/resources/SBOLTestSuite/SBOL2_bp/Provenance_SpecifyCutOperation.xml -test/resources/SBOLTestSuite/SBOL2_bp/design-build-test-learn.xml -test/resources/SBOLTestSuite/SBOL2_bp/BBa_T9002.xml -test/resources/SBOLTestSuite/SBOL2_bp/CutExample.xml -test/resources/SBOLTestSuite/SBOL2_bp/SimpleComponentDefinitionExample.xml -test/resources/SBOLTestSuite/SBOL2_bp/Provenance_SpecifyCutOperation_Ag_Act_CD.xml -test/resources/SBOLTestSuite/RDF/igem1.xml -test/resources/SBOLTestSuite/RDF/igem3.xml -test/resources/SBOLTestSuite/RDF/igem2.xml -test/resources/SBOLTestSuite/RDF/toggle.xml -test/java/org/ValidationTesting/SBOL2ValidationTest.java -test/java/org/ValidationTesting/SBOL1ValidationTest.java -test/java/org/ValidationTesting/InvalidValidationTest.java diff --git a/target/maven-status/maven-compiler-plugin/compile/default-compile/.gitignore b/target/maven-status/maven-compiler-plugin/compile/default-compile/.gitignore deleted file mode 100644 index 8908822..0000000 --- a/target/maven-status/maven-compiler-plugin/compile/default-compile/.gitignore +++ /dev/null @@ -1,2 +0,0 @@ -/createdFiles.lst -/inputFiles.lst diff --git a/target/maven-status/maven-compiler-plugin/testCompile/default-testCompile/.gitignore b/target/maven-status/maven-compiler-plugin/testCompile/default-testCompile/.gitignore deleted file mode 100644 index 8908822..0000000 --- a/target/maven-status/maven-compiler-plugin/testCompile/default-testCompile/.gitignore +++ /dev/null @@ -1,2 +0,0 @@ -/createdFiles.lst -/inputFiles.lst diff --git a/target/surefire-reports/.gitignore b/target/surefire-reports/.gitignore deleted file mode 100644 index 262aa14..0000000 --- a/target/surefire-reports/.gitignore +++ /dev/null @@ -1,6 +0,0 @@ -/org.ValidationTesting.InvalidValidationTest.txt -/org.ValidationTesting.SBOL1ValidationTest.txt -/org.ValidationTesting.SBOL2ValidationTest.txt -/TEST-org.ValidationTesting.InvalidValidationTest.xml -/TEST-org.ValidationTesting.SBOL1ValidationTest.xml -/TEST-org.ValidationTesting.SBOL2ValidationTest.xml