From 10297bd8b8a4b4ab198a17a42fc6ff24ae2ed49b Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Tue, 18 Nov 2014 22:49:47 +0000 Subject: [PATCH] --- .../analysis/AncestralTaxonomyInference.java | 14 +- .../org/forester/analysis/TaxonomyDataManager.java | 18 +- .../src/org/forester/application/annotator.java | 6 +- .../java/src/org/forester/application/confadd.java | 16 +- .../org/forester/application/count_support.java | 14 +- .../src/org/forester/application/decorator.java | 22 +- .../java/src/org/forester/application/dom_dup.java | 4 +- .../forester/application/gene_tree_preprocess.java | 4 +- .../java/src/org/forester/application/goac.java | 4 +- .../java/src/org/forester/application/gsdi.java | 22 +- .../org/forester/application/meta_ontologizer.java | 4 +- .../org/forester/application/msa_compactor.java | 26 +- forester/java/src/org/forester/application/nj.java | 2 +- .../src/org/forester/application/obo_tool.java | 2 +- .../java/src/org/forester/application/pccx.java | 6 +- .../forester/application/pfam2go_extractor.java | 2 +- .../java/src/org/forester/application/pfam_go.java | 2 +- .../src/org/forester/application/pfamacc2go.java | 2 +- .../src/org/forester/application/phylostrip.java | 2 +- .../forester/application/phyloxml_converter.java | 34 +- .../java/src/org/forester/application/rio.java | 30 +- .../forester/application/support_statistics.java | 2 +- .../org/forester/application/support_transfer.java | 8 +- .../src/org/forester/application/surfacing.java | 364 +++++++-------- .../src/org/forester/archaeopteryx/AptxUtil.java | 14 +- .../org/forester/archaeopteryx/ArchaeopteryxA.java | 4 +- .../org/forester/archaeopteryx/ArchaeopteryxE.java | 18 +- .../org/forester/archaeopteryx/Configuration.java | 6 +- .../org/forester/archaeopteryx/ControlPanel.java | 13 +- .../src/org/forester/archaeopteryx/MainFrame.java | 12 +- .../forester/archaeopteryx/MainFrameApplet.java | 3 +- .../archaeopteryx/MainFrameApplication.java | 14 +- .../src/org/forester/archaeopteryx/Options.java | 4 - .../src/org/forester/archaeopteryx/Printer.java | 4 +- .../src/org/forester/archaeopteryx/TextFrame.java | 2 +- .../org/forester/archaeopteryx/TreeColorSet.java | 70 +-- .../src/org/forester/archaeopteryx/TreePanel.java | 306 ++++++------- .../org/forester/archaeopteryx/TreePanelUtil.java | 2 +- .../data/RenderableDomainArchitecture.java | 8 +- .../phylogeny/data/RenderablePhylogenyData.java | 2 +- .../org/forester/archaeopteryx/tools/Blast.java | 8 +- .../forester/archaeopteryx/tools/ImageLoader.java | 8 +- .../archaeopteryx/tools/InferenceManager.java | 2 +- .../archaeopteryx/tools/PhyloInferenceDialog.java | 8 +- .../archaeopteryx/tools/PhylogeneticInferrer.java | 26 +- .../archaeopteryx/tools/RunnableProcess.java | 2 +- .../archaeopteryx/tools/SequenceDataRetriver.java | 2 +- .../webservices/PhylogeniesWebserviceClient.java | 30 +- .../archaeopteryx/webservices/WebserviceUtil.java | 38 +- .../src/org/forester/datastructures/Queue.java | 12 +- .../org/forester/development/AbstractRenderer.java | 2 +- .../org/forester/development/DevelopmentTools.java | 8 +- .../org/forester/development/ResidueRenderer.java | 2 +- .../java/src/org/forester/development/Test.java | 4 +- .../java/src/org/forester/development/neTest.java | 484 ++++++++++---------- .../evoinference/TestPhylogenyReconstruction.java | 20 +- .../evoinference/distance/NeighborJoining.java | 6 +- .../evoinference/distance/NeighborJoiningF.java | 6 +- .../evoinference/distance/NeighborJoiningR.java | 8 +- .../distance/PairwiseDistanceCalculator.java | 10 +- .../org/forester/evoinference/distance/Sarray.java | 2 +- .../org/forester/evoinference/distance/Sset.java | 6 +- .../character/BasicCharacterStateMatrix.java | 8 +- .../evoinference/parsimony/DolloParsimony.java | 22 +- .../evoinference/parsimony/FitchParsimony.java | 50 +- .../evoinference/parsimony/SankoffParsimony.java | 56 +-- .../src/org/forester/go/BasicGoRelationship.java | 4 +- .../java/src/org/forester/go/BasicGoSubset.java | 2 +- forester/java/src/org/forester/go/BasicGoTerm.java | 12 +- forester/java/src/org/forester/go/BasicGoXRef.java | 4 +- forester/java/src/org/forester/go/GoUtils.java | 10 +- .../java/src/org/forester/go/PfamToGoMapping.java | 4 +- forester/java/src/org/forester/go/TestGo.java | 32 +- .../src/org/forester/go/etc/MetaOntologizer.java | 38 +- .../src/org/forester/go/etc/OntologizerResult.java | 2 +- .../src/org/forester/io/parsers/FastaParser.java | 2 +- .../org/forester/io/parsers/GeneralMsaParser.java | 4 +- .../forester/io/parsers/HmmPfamOutputParser.java | 24 +- .../io/parsers/HmmscanPerDomainTableParser.java | 16 +- .../org/forester/io/parsers/PhylogenyParser.java | 2 +- .../parsers/SymmetricalDistanceMatrixParser.java | 20 +- .../src/org/forester/io/parsers/nhx/NHXParser.java | 68 +-- .../io/parsers/phyloxml/PhyloXmlHandler.java | 8 +- .../io/parsers/phyloxml/PhyloXmlParser.java | 4 +- .../forester/io/parsers/phyloxml/PhyloXmlUtil.java | 4 +- .../forester/io/parsers/phyloxml/XmlElement.java | 2 +- .../io/parsers/phyloxml/data/AnnotationParser.java | 2 +- .../phyloxml/data/BinaryCharactersParser.java | 4 +- .../io/parsers/phyloxml/data/ConfidenceParser.java | 2 +- .../phyloxml/data/DomainArchitectureParser.java | 4 +- .../parsers/phyloxml/data/ProteinDomainParser.java | 2 +- .../io/parsers/phyloxml/data/SequenceParser.java | 6 +- .../phyloxml/data/SequenceRelationParser.java | 2 +- .../src/org/forester/io/parsers/tol/TolParser.java | 6 +- .../org/forester/io/parsers/tol/TolXmlHandler.java | 2 +- .../org/forester/io/parsers/util/ParserUtils.java | 52 +-- .../io/parsers/util/PhylogenyParserException.java | 4 +- .../forester/io/writers/PhyloXmlNodeWriter.java | 2 +- .../org/forester/io/writers/PhylogenyWriter.java | 26 +- forester/java/src/org/forester/msa/BasicMsa.java | 2 +- .../java/src/org/forester/msa/ClustalOmega.java | 6 +- forester/java/src/org/forester/msa/Mafft.java | 4 +- .../java/src/org/forester/msa/MsaInferrer.java | 2 +- forester/java/src/org/forester/msa/MsaMethods.java | 8 +- .../java/src/org/forester/msa/ResampleableMsa.java | 2 +- .../org/forester/msa_compactor/MsaCompactor.java | 20 +- .../BasicExternalNodeBasedCoverageExtender.java | 2 +- .../pccx/BranchCountingBasedScoringMethod.java | 2 +- .../pccx/BranchLengthBasedScoringMethod.java | 2 +- .../pccx/ExternalNodeBasedCoverageMethod.java | 14 +- .../ExternalNodeBasedCoverageMethodOptions.java | 2 +- .../pccx/LogBranchLengthBasedScoringMethod.java | 2 +- .../pccx/ScoringMethodForExternalNode.java | 16 +- .../java/src/org/forester/phylogeny/Phylogeny.java | 58 +-- .../org/forester/phylogeny/PhylogenyMethods.java | 52 +-- .../src/org/forester/phylogeny/PhylogenyNode.java | 60 +-- .../forester/phylogeny/data/BinaryCharacters.java | 18 +- .../org/forester/phylogeny/data/BranchColor.java | 2 +- .../org/forester/phylogeny/data/BranchData.java | 2 +- .../org/forester/phylogeny/data/Confidence.java | 32 +- .../java/src/org/forester/phylogeny/data/Date.java | 6 +- .../phylogeny/data/DomainArchitecture.java | 4 +- .../src/org/forester/phylogeny/data/Event.java | 8 +- .../src/org/forester/phylogeny/data/NodeData.java | 28 +- .../forester/phylogeny/data/NodeVisualData.java | 20 +- .../org/forester/phylogeny/data/PhylogenyData.java | 10 +- .../forester/phylogeny/data/PhylogenyDataUtil.java | 2 +- .../src/org/forester/phylogeny/data/Point.java | 10 +- .../src/org/forester/phylogeny/data/Property.java | 6 +- .../src/org/forester/phylogeny/data/Sequence.java | 2 +- .../src/org/forester/phylogeny/data/Taxonomy.java | 8 +- .../phylogeny/factories/PhylogenyFactory.java | 4 +- .../iterators/ExternalForwardIterator.java | 8 +- .../iterators/LevelOrderTreeIterator.java | 20 +- .../phylogeny/iterators/PhylogenyNodeIterator.java | 2 +- .../phylogeny/iterators/PostOrderStackObject.java | 2 +- .../phylogeny/iterators/PreorderTreeIterator.java | 4 +- .../java/src/org/forester/protein/BasicDomain.java | 4 +- .../src/org/forester/protein/BasicProtein.java | 24 +- .../java/src/org/forester/protein/Protein.java | 4 +- .../java/src/org/forester/protein/ProteinId.java | 2 +- forester/java/src/org/forester/rio/RIO.java | 44 +- .../java/src/org/forester/rio/RIOException.java | 2 +- forester/java/src/org/forester/rio/TestRIO.java | 2 +- forester/java/src/org/forester/sdi/GSDI.java | 18 +- forester/java/src/org/forester/sdi/GSDIR.java | 6 +- forester/java/src/org/forester/sdi/SDI.java | 36 +- .../java/src/org/forester/sdi/SDIException.java | 2 +- forester/java/src/org/forester/sdi/SDIR.java | 22 +- forester/java/src/org/forester/sdi/SDIutil.java | 8 +- forester/java/src/org/forester/sdi/TestGSDI.java | 14 +- .../src/org/forester/sequence/BasicSequence.java | 10 +- .../BasicGenomeWideCombinableDomains.java | 132 +++--- .../org/forester/surfacing/CombinableDomains.java | 18 +- .../CountsBasedPairwiseDomainSimilarity.java | 6 +- ...rchitectureBasedGenomeSimilarityCalculator.java | 22 +- .../surfacing/DomainCountsDifferenceUtil.java | 32 +- .../src/org/forester/surfacing/DomainLengths.java | 10 +- .../org/forester/surfacing/DomainLengthsTable.java | 2 +- .../surfacing/DomainParsimonyCalculator.java | 28 +- .../org/forester/surfacing/DomainSimilarity.java | 18 +- .../surfacing/DomainSimilarityCalculator.java | 12 +- .../surfacing/GenomeWideCombinableDomains.java | 8 +- .../surfacing/PairwiseDomainSimilarity.java | 2 +- .../surfacing/PairwiseGenomeComparator.java | 18 +- .../surfacing/PrintableSpeciesSpecificDcData.java | 2 +- .../forester/surfacing/SpeciesSpecificDcData.java | 2 +- .../src/org/forester/surfacing/SurfacingUtil.java | 374 +++++++-------- .../src/org/forester/surfacing/TestSurfacing.java | 70 +-- forester/java/src/org/forester/test/Test.java | 147 +++--- .../src/org/forester/tools/ConfidenceAssessor.java | 8 +- .../src/org/forester/tools/PhylogenyDecorator.java | 32 +- .../java/src/org/forester/tools/SupportCount.java | 14 +- .../src/org/forester/tools/TreeSplitMatrix.java | 4 +- .../forester/util/BasicDescriptiveStatistics.java | 2 +- .../src/org/forester/util/BasicTableParser.java | 4 +- .../org/forester/util/CommandLineArguments.java | 4 +- .../org/forester/util/CommandProcessBuilder.java | 2 +- .../org/forester/util/DescriptiveStatistics.java | 4 +- .../util/FailedConditionCheckException.java | 2 +- .../java/src/org/forester/util/ForesterUtil.java | 46 +- .../forester/util/IllegalFormatUseException.java | 2 +- .../org/forester/util/SequenceAccessionTools.java | 24 +- .../org/forester/util/SystemCommandExecutor.java | 20 +- .../org/forester/util/ThreadedStreamHandler.java | 28 +- .../java/src/org/forester/util/WindowsUtils.java | 4 +- .../java/src/org/forester/ws/seqdb/EbiDbEntry.java | 32 +- .../org/forester/ws/seqdb/SequenceDbWsTools.java | 20 +- .../src/org/forester/ws/seqdb/UniProtEntry.java | 2 +- .../src/org/forester/ws/seqdb/UniProtTaxonomy.java | 12 +- .../java/src/org/forester/ws/wabi/RestUtil.java | 2 +- .../java/src/org/forester/ws/wabi/TxSearch.java | 6 +- 192 files changed, 2051 insertions(+), 2074 deletions(-) diff --git a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java index 25021bc..94453ff 100644 --- a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java +++ b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java @@ -40,7 +40,7 @@ import org.forester.ws.seqdb.UniProtTaxonomy; public final class AncestralTaxonomyInference { public static void inferTaxonomyFromDescendents( final Phylogeny phy ) throws IOException, - AncestralTaxonomyInferenceException { + AncestralTaxonomyInferenceException { TaxonomyDataManager.clearCachesIfTooLarge(); for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) { final PhylogenyNode node = iter.next(); @@ -51,7 +51,7 @@ public final class AncestralTaxonomyInference { } private static void inferTaxonomyFromDescendents( final PhylogenyNode n ) throws IOException, - AncestralTaxonomyInferenceException { + AncestralTaxonomyInferenceException { if ( n.isExternal() ) { throw new IllegalArgumentException( "attempt to infer taxonomy from descendants of external node" ); } @@ -65,9 +65,9 @@ public final class AncestralTaxonomyInference { || !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getScientificName() ) || !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getLineage() ) || !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getTaxonomyCode() ) || !ForesterUtil - .isEmpty( desc.getNodeData().getTaxonomy().getCommonName() ) ) ) { + .isEmpty( desc.getNodeData().getTaxonomy().getCommonName() ) ) ) { final UniProtTaxonomy up_tax = TaxonomyDataManager.obtainUniProtTaxonomy( desc.getNodeData() - .getTaxonomy(), null, null ); + .getTaxonomy(), null, null ); if ( ( up_tax == null ) && ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getLineage() ) ) { String desc_str = ""; if ( !ForesterUtil.isEmpty( desc.getName() ) ) { @@ -78,9 +78,9 @@ public final class AncestralTaxonomyInference { } System.out.println( desc.getNodeData().getTaxonomy().toString() ); System.out.println( ForesterUtil.stringListToString( desc.getNodeData().getTaxonomy().getLineage(), - " > " ) ); + " > " ) ); throw new AncestralTaxonomyInferenceException( "a taxonomy for node " + desc_str - + " could not be established from the database" ); + + " could not be established from the database" ); } String[] lineage = ForesterUtil.stringListToArray( desc.getNodeData().getTaxonomy().getLineage() ); if ( ( lineage == null ) || ( lineage.length < 1 ) ) { @@ -104,7 +104,7 @@ public final class AncestralTaxonomyInference { node = "[" + desc.getId() + "]"; } throw new AncestralTaxonomyInferenceException( "node " + node - + " has no or inappropriate taxonomic information" ); + + " has no or inappropriate taxonomic information" ); } } final List last_common_lineage = new ArrayList(); diff --git a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java index d78720c..4cc61cd 100644 --- a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java +++ b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java @@ -133,7 +133,7 @@ public final class TaxonomyDataManager extends RunnableProcess { private final static UniProtTaxonomy obtainTaxonomy( final HashMap cache, final Object query, final QUERY_TYPE qt ) throws IOException, - AncestralTaxonomyInferenceException { + AncestralTaxonomyInferenceException { if ( cache.containsKey( query ) ) { return cache.get( query ).copy(); } @@ -202,7 +202,7 @@ public final class TaxonomyDataManager extends RunnableProcess { //FIXME fix "SPHAR" issue if ( ( ( query.indexOf( "XX" ) == 3 ) && TaxonomyUtil.isHasTaxIdFromFakeTaxCode( query ) ) || query.equals( "SPHAR" ) /* TODO remove me, is same as Sphingomonas aromaticivorans */ - ) { + ) { final int id = TaxonomyUtil.getTaxIdFromFakeTaxCode( query ); return SequenceDbWsTools.getTaxonomiesFromId( String.valueOf( id ), MAX_TAXONOMIES_TO_RETURN ); } @@ -219,7 +219,7 @@ public final class TaxonomyDataManager extends RunnableProcess { synchronized final private static SortedSet obtainDetailedTaxonomicInformation( final Phylogeny phy, final boolean delete, final boolean allow_to_use_basic_node_names ) - throws IOException, AncestralTaxonomyInferenceException { + throws IOException, AncestralTaxonomyInferenceException { clearCachesIfTooLarge(); final SortedSet not_found = new TreeSet(); List not_found_external_nodes = null; @@ -254,7 +254,7 @@ public final class TaxonomyDataManager extends RunnableProcess { if ( ( ( tax != null ) && ( isHasAppropriateId( tax ) || !ForesterUtil.isEmpty( tax.getScientificName() ) || !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) || !ForesterUtil - .isEmpty( tax.getCommonName() ) ) ) ) { + .isEmpty( tax.getCommonName() ) ) ) ) { uniprot_tax = obtainUniProtTaxonomy( tax, null, qt ); } else { @@ -376,7 +376,7 @@ public final class TaxonomyDataManager extends RunnableProcess { else { final List matching_taxonomies = new ArrayList(); final List up_taxonomies = getTaxonomiesFromScientificName( lineage - .get( lineage.size() - 1 ) ); + .get( lineage.size() - 1 ) ); if ( ( up_taxonomies != null ) && ( up_taxonomies.size() > 0 ) ) { for( final UniProtTaxonomy up_taxonomy : up_taxonomies ) { boolean match = true; @@ -425,7 +425,7 @@ public final class TaxonomyDataManager extends RunnableProcess { } else { throw new AncestralTaxonomyInferenceException( "taxonomy \"" + ( lineage.get( lineage.size() - 1 ) ) - + "\" not found" ); + + "\" not found" ); } } } @@ -434,7 +434,7 @@ public final class TaxonomyDataManager extends RunnableProcess { final PhylogenyNode node, final Taxonomy tax, final UniProtTaxonomy up_tax ) - throws PhyloXmlDataFormatException { + throws PhyloXmlDataFormatException { if ( ( qt != QUERY_TYPE.SN ) && !ForesterUtil.isEmpty( up_tax.getScientificName() ) && ForesterUtil.isEmpty( tax.getScientificName() ) ) { tax.setScientificName( up_tax.getScientificName() ); @@ -512,7 +512,7 @@ public final class TaxonomyDataManager extends RunnableProcess { JOptionPane.WARNING_MESSAGE ); } catch ( final Exception e ) { - // Not important if this fails, do nothing. + // Not important if this fails, do nothing. } return; } @@ -564,7 +564,7 @@ public final class TaxonomyDataManager extends RunnableProcess { JOptionPane.WARNING_MESSAGE ); } catch ( final Exception e ) { - // Not important if this fails, do nothing. + // Not important if this fails, do nothing. } } else { diff --git a/forester/java/src/org/forester/application/annotator.java b/forester/java/src/org/forester/application/annotator.java index 358b7cf..4374f53 100644 --- a/forester/java/src/org/forester/application/annotator.java +++ b/forester/java/src/org/forester/application/annotator.java @@ -94,8 +94,8 @@ public final class annotator { } catch ( final Exception e ) { ForesterUtil - .fatalError( PRG_NAME, "failed to read phylgenies from [" + infile + "] [" + e.getMessage() - + "]" ); + .fatalError( PRG_NAME, "failed to read phylgenies from [" + infile + "] [" + e.getMessage() + + "]" ); } try { obtainSeqInformation( phy ); @@ -129,7 +129,7 @@ public final class annotator { } private static void inferTaxonomyFromDescendents( final Phylogeny phy ) throws IOException, - AncestralTaxonomyInferenceException { + AncestralTaxonomyInferenceException { AncestralTaxonomyInference.inferTaxonomyFromDescendents( phy ); } diff --git a/forester/java/src/org/forester/application/confadd.java b/forester/java/src/org/forester/application/confadd.java index b48cde9..7684899 100644 --- a/forester/java/src/org/forester/application/confadd.java +++ b/forester/java/src/org/forester/application/confadd.java @@ -142,8 +142,8 @@ public class confadd { } if ( ( first < 0 ) || ( last < 0 ) ) { ForesterUtil - .fatalError( PRG_NAME, - "attempt to set first or last evaluator topology to use to a number less than zero" ); + .fatalError( PRG_NAME, + "attempt to set first or last evaluator topology to use to a number less than zero" ); } if ( norm < 0 ) { ForesterUtil.fatalError( PRG_NAME, "illegal value for normalizer [" + norm + "]" ); @@ -200,7 +200,7 @@ public class confadd { } if ( ( last >= evaluators.length ) || ( last <= first ) ) { ForesterUtil.fatalError( PRG_NAME, "illegal value for first or last evaluator topology to use [" + first - + ", " + last + "]" ); + + ", " + last + "]" ); } double value = 1; if ( norm > 0 ) { @@ -244,17 +244,17 @@ public class confadd { System.out.println( "Usage:" ); System.out.println(); System.out.println( PRG_NAME - + " [options] " ); + + " [options] " ); System.out.println(); System.out.println( "options:" ); System.out.println(); System.out.println( " -" + STRICT_OPTION - + " : strict [default: non-strict]: all nodes between 'target' and 'evaluators' must match" ); + + " : strict [default: non-strict]: all nodes between 'target' and 'evaluators' must match" ); System.out.println( " -" + NORMALIZE_OPTION - + "=: normalize to this value (e.g. 100 for most bootstrap analyses) [default: no normalization]" ); + + "=: normalize to this value (e.g. 100 for most bootstrap analyses) [default: no normalization]" ); System.out.println( " -" + FIRST_OPTION + "=: first evaluator topology to use (0-based) [default: 0]" ); System.out.println( " -" + LAST_OPTION - + "=: last evaluator topology to use (0-based) [default: use all until final topology]" ); + + "=: last evaluator topology to use (0-based) [default: use all until final topology]" ); System.out.println(); } @@ -265,7 +265,7 @@ public class confadd { final PhylogenyNode node = it.next(); if ( ext_nodes.contains( node ) ) { throw new IllegalArgumentException( "external node [" + node.toString() + "] of " + msg - + " is not unique" ); + + " is not unique" ); } ext_nodes.add( node ); } diff --git a/forester/java/src/org/forester/application/count_support.java b/forester/java/src/org/forester/application/count_support.java index 9be5f89..8e85263 100644 --- a/forester/java/src/org/forester/application/count_support.java +++ b/forester/java/src/org/forester/application/count_support.java @@ -67,10 +67,10 @@ public class count_support { System.out.println( count_support.PRG_NAME + ": wrong number of arguments" ); System.out.println(); System.out - .println( "Usage: \"count_support [options] [outfile for evaluator phylogenies, " - + "always unstripped if -t= option is used, otherwise strippedness is dependent on -s option]\"\n" ); + .println( "Usage: \"count_support [options] [outfile for evaluator phylogenies, " + + "always unstripped if -t= option is used, otherwise strippedness is dependent on -s option]\"\n" ); System.out - .println( " Options: -s strip external nodes from evaluator phylogenies not found in phylogeny to be evaluated" ); + .println( " Options: -s strip external nodes from evaluator phylogenies not found in phylogeny to be evaluated" ); System.out.println( " : -t= threshold for similarity (0.0 to 1.0)" ); System.out.println( " : -n no branch lengths in outfile for evaluator phylogenies" ); System.out.println(); @@ -105,7 +105,7 @@ public class count_support { else { if ( !branch_lengths_in_ev_out ) { ForesterUtil.fatalError( count_support.PRG_NAME, - "Cannot use -n option if no outfile for evaluators specified" ); + "Cannot use -n option if no outfile for evaluators specified" ); } } Phylogeny p = null; @@ -142,7 +142,7 @@ public class count_support { } if ( ( threshhold < 0 ) || ( threshhold > 1.0 ) ) { ForesterUtil.fatalError( count_support.PRG_NAME, - "support threshold has to be between 0.0 and 1.0 (inclusive)" ); + "support threshold has to be between 0.0 and 1.0 (inclusive)" ); } } List evaluator_phylogenies_above_threshold = null; @@ -163,7 +163,7 @@ public class count_support { if ( threshhold >= 0 ) { count_support.normalizeSupport( p, 100, evaluator_phylogenies_above_threshold.size() ); System.out.println( evaluator_phylogenies_above_threshold.size() + " out of " + ev.length - + " evaluator phylogenies are above threshold of " + threshhold ); + + " evaluator phylogenies are above threshold of " + threshhold ); } try { final PhylogenyWriter w = new PhylogenyWriter(); @@ -179,7 +179,7 @@ public class count_support { final PhylogenyWriter w = new PhylogenyWriter(); if ( evaluator_phylogenies_above_threshold != null ) { System.out.println( "Writing " + evaluator_phylogenies_above_threshold.size() - + " evaluator phylogenies above threshold of " + threshhold + " to: " + evaluators_outfile ); + + " evaluator phylogenies above threshold of " + threshhold + " to: " + evaluators_outfile ); if ( count_support.WRITE_EVALUATORS_AS_NHX ) { w.toNewHampshireX( evaluator_phylogenies_above_threshold, evaluators_outfile, ";" + ForesterUtil.getLineSeparator() ); diff --git a/forester/java/src/org/forester/application/decorator.java b/forester/java/src/org/forester/application/decorator.java index 7f4c304..a7dd6ee 100644 --- a/forester/java/src/org/forester/application/decorator.java +++ b/forester/java/src/org/forester/application/decorator.java @@ -249,7 +249,7 @@ public final class decorator { } else { ForesterUtil.fatalError( decorator.PRG_NAME, "unknown value for \"" + decorator.FIELD_OPTION - + "\" option: \"" + field_str + "\"" ); + + "\" option: \"" + field_str + "\"" ); } } } @@ -271,7 +271,7 @@ public final class decorator { } catch ( final Exception e ) { ForesterUtil.fatalError( decorator.PRG_NAME, "failed to read phylgenies from [" + phylogenies_infile - + "] [" + e.getMessage() + "]" ); + + "] [" + e.getMessage() + "]" ); } Map map = null; if ( !advanced_table ) { @@ -326,7 +326,7 @@ public final class decorator { if ( ( phylogenies.length > 1 ) && ( !ForesterUtil.isEmpty( tree_name ) || !ForesterUtil.isEmpty( tree_id ) ) ) { ForesterUtil.fatalError( decorator.PRG_NAME, - "attempt to set same name or id on more than one phylogeny" ); + "attempt to set same name or id on more than one phylogeny" ); } if ( !ForesterUtil.isEmpty( tree_name ) ) { phylogenies[ 0 ].setName( tree_name ); @@ -409,17 +409,17 @@ public final class decorator { } if ( ForesterUtil.isEmpty( seqs ) ) { ForesterUtil.fatalError( decorator.PRG_NAME, "fasta-file [" + mapping_infile - + "] is devoid of fasta-formatted sequences" ); + + "] is devoid of fasta-formatted sequences" ); } final Map map = new HashMap(); for( final MolecularSequence seq : seqs ) { if ( ForesterUtil.isEmpty( seq.getIdentifier() ) ) { ForesterUtil.fatalError( decorator.PRG_NAME, "fasta-file [" + mapping_infile - + "] contains sequence with empty identifier" ); + + "] contains sequence with empty identifier" ); } if ( map.containsKey( seq.getIdentifier() ) ) { ForesterUtil.fatalError( decorator.PRG_NAME, "sequence identifier [" + seq.getIdentifier() - + "] is not unique" ); + + "] is not unique" ); } if ( seq.getLength() < 1 ) { ForesterUtil.fatalError( decorator.PRG_NAME, "sequence [" + seq.getIdentifier() + "] is empty" ); @@ -450,11 +450,11 @@ public final class decorator { System.out.println(); System.out.println( " -f= : field to be replaced: " + NODE_NAME_FIELD + " : node name" ); System.out.println( " " + SEQUENCE_ANNOTATION_DESC - + " : sequence annotation description" ); + + " : sequence annotation description" ); System.out.println( " " + DS_FILED + " : domain structure" ); System.out.println( " " + TAXONOMY_CODE_FIELD + " : taxonomy code" ); System.out.println( " " + TAXONOMY_SCIENTIFIC_NAME_FIELD - + ": taxonomy scientific name" ); + + ": taxonomy scientific name" ); System.out.println( " " + SEQUENCE_NAME_FIELD + " : sequence name" ); System.out.println( " " + MOL_SEQ + " : molecular sequence" ); System.out.println( " -k= : key column in mapping table (0 based)," ); @@ -462,13 +462,13 @@ public final class decorator { System.out.println( " -v= : value column in mapping table (0 based)," ); System.out.println( " data which with to decorate - default is 1" ); System.out.println( " -" + EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION - + " : to extract bracketed scientific names, e.g. [Nematostella vectensis]" ); + + " : to extract bracketed scientific names, e.g. [Nematostella vectensis]" ); System.out.println( " -" + EXTRACT_BRACKETED_TAXONOMIC_CODE_OPTION - + " : to extract bracketed taxonomic codes, e.g. [NEMVE]" ); + + " : to extract bracketed taxonomic codes, e.g. [NEMVE]" ); System.out.println( " -s= : column separator in mapping file, default is tab" ); System.out.println( " -c : cut name after first space (only for -f=n)" ); System.out.println( " -" + decorator.TRIM_AFTER_TILDE_OPTION - + " : trim node name to be replaced after tilde" ); + + " : trim node name to be replaced after tilde" ); System.out.println( " -" + decorator.MIDPOINT_ROOT_OPTION + " : to midpoint-root the tree" ); System.out.println( " -" + decorator.ORDER_TREE_OPTION + " : to order tree branches" ); System.out.println( " -" + decorator.VERBOSE_OPTION + " : verbose" ); diff --git a/forester/java/src/org/forester/application/dom_dup.java b/forester/java/src/org/forester/application/dom_dup.java index e9cdba0..7981966 100644 --- a/forester/java/src/org/forester/application/dom_dup.java +++ b/forester/java/src/org/forester/application/dom_dup.java @@ -30,7 +30,7 @@ import org.forester.util.ForesterUtil; public class dom_dup { // HUMAN MOUSE - // ARATH SOYBN VOLCA CYAME PARTE THAPS EMIHU NAEGR + // ARATH SOYBN VOLCA CYAME PARTE THAPS EMIHU NAEGR final static private String HELP_OPTION_1 = "help"; final static private String HELP_OPTION_2 = "h"; final static private String PRG_NAME = "dom_dup"; @@ -192,7 +192,7 @@ public class dom_dup { System.out.println( " example: " ); System.out.println(); System.out - .println( "dom_dup \"HUMAN~[12]-2\" groups.txt RRMa_ALL_plus_RRMa_ee3_50_hmmalign_05_40_fme_gsdi.phylo.xml" ); + .println( "dom_dup \"HUMAN~[12]-2\" groups.txt RRMa_ALL_plus_RRMa_ee3_50_hmmalign_05_40_fme_gsdi.phylo.xml" ); System.out.println(); System.out.println(); } diff --git a/forester/java/src/org/forester/application/gene_tree_preprocess.java b/forester/java/src/org/forester/application/gene_tree_preprocess.java index 06f2803..581381c 100644 --- a/forester/java/src/org/forester/application/gene_tree_preprocess.java +++ b/forester/java/src/org/forester/application/gene_tree_preprocess.java @@ -73,7 +73,7 @@ public class gene_tree_preprocess { "failed to read phylogeny from [" + in + "]: " + e.getLocalizedMessage() ); } final File outtree = new File( ForesterUtil.removeSuffix( in.toString() ) - + "_preprocessed_gene_tree.phylo.xml" ); + + "_preprocessed_gene_tree.phylo.xml" ); final File removed_nodes = new File( ForesterUtil.removeSuffix( in.toString() ) + "_removed_nodes.txt" ); final File present_species = new File( ForesterUtil.removeSuffix( in.toString() ) + "_species_present.txt" ); checkForOutputFileWriteability( outtree ); @@ -81,7 +81,7 @@ public class gene_tree_preprocess { checkForOutputFileWriteability( present_species ); if ( phy.getNumberOfExternalNodes() < 2 ) { ForesterUtil.fatalError( PRG_NAME, "phylogeny has " + phy.getNumberOfExternalNodes() - + " external node(s), aborting" ); + + " external node(s), aborting" ); } final SortedSet not_found = SequenceDbWsTools.obtainSeqInformation( phy, true, diff --git a/forester/java/src/org/forester/application/goac.java b/forester/java/src/org/forester/application/goac.java index 37b9d12..7fbb22e 100644 --- a/forester/java/src/org/forester/application/goac.java +++ b/forester/java/src/org/forester/application/goac.java @@ -200,8 +200,8 @@ public class goac { System.out.println( "Usage:" ); System.out.println(); System.out - .println( PRG_NAME - + " " ); + .println( PRG_NAME + + " " ); System.out.println(); System.out.println(); } diff --git a/forester/java/src/org/forester/application/gsdi.java b/forester/java/src/org/forester/application/gsdi.java index 7e2d514..a77ac2d 100644 --- a/forester/java/src/org/forester/application/gsdi.java +++ b/forester/java/src/org/forester/application/gsdi.java @@ -283,9 +283,9 @@ public final class gsdi { fatalError( "unexpected error", e.toString(), log_writer ); } System.out.println( "Running time (excluding I/O) : " + ( new Date().getTime() - start_time ) - + "ms" ); + + "ms" ); log_writer.println( "Running time (excluding I/O) : " + ( new Date().getTime() - start_time ) - + "ms" ); + + "ms" ); System.out.println( "Mapping based on : " + gsdii.getTaxCompBase() ); log_writer.println( "Mapping based on : " + gsdii.getTaxCompBase() ); try { @@ -304,14 +304,14 @@ public final class gsdi { System.out.println( "Wrote resulting gene tree to : " + out_file.getCanonicalPath() ); log_writer.println( "Wrote resulting gene tree to : " + out_file.getCanonicalPath() ); final File species_tree_used_file = new File( ForesterUtil.removeSuffix( out_file.toString() ) - + SUFFIX_FOR_SPECIES_TREE_USED ); + + SUFFIX_FOR_SPECIES_TREE_USED ); try { final PhylogenyWriter writer = new PhylogenyWriter(); writer.toPhyloXML( species_tree_used_file, species_tree, 0 ); } catch ( final IOException e ) { ForesterUtil.fatalError( PRG_NAME, "Failed to write to [" + species_tree_used_file.getCanonicalPath() - + "]: " + e.getMessage() ); + + "]: " + e.getMessage() ); } System.out.println( "Wrote (stripped) species tree to : " + species_tree_used_file.getCanonicalPath() ); log_writer.println( "Wrote (stripped) species tree to : " + species_tree_used_file.getCanonicalPath() ); @@ -380,21 +380,21 @@ public final class gsdi { private static void print_help() { System.out.println( "Usage: " + gsdi.PRG_NAME - + " [-options] " ); + + " [-options] " ); System.out.println(); System.out.println( "Options:" ); System.out.println( " -" + gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION - + ": to allow stripping of gene tree nodes without a matching species" ); + + ": to allow stripping of gene tree nodes without a matching species" ); System.out.println( " -" + gsdi.MOST_PARSIMONIOUS_OPTION - + ": use most parimonious duplication model for GSDI: " ); + + ": use most parimonious duplication model for GSDI: " ); System.out.println( " assign nodes as speciations which would otherwise be assiged" ); System.out.println( " as potential duplications due to polytomies in the species tree" ); System.out.println( " -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE - + ": to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)" ); + + ": to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)" ); System.out.println( " -" + gsdi.GSDIR_OPTION - + ": to use GSDIR algorithm instead of GSDI algorithm (re-rooting)" ); + + ": to use GSDIR algorithm instead of GSDI algorithm (re-rooting)" ); System.out.println( " -" + TRANSFER_TAXONOMY_OPTION - + ": to transfer taxonomic data from species tree to gene tree\n" ); + + ": to transfer taxonomic data from species tree to gene tree\n" ); System.out.println(); System.out.println( "Gene tree:" ); System.out.println( " in phyloXM format, with taxonomy and sequence data in appropriate fields" ); @@ -403,7 +403,7 @@ public final class gsdi { System.out.println( " in phyloXML format (unless option -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE + " is used)" ); System.out.println(); System.out.println( "Example: gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION - + " gene_tree.xml tree_of_life.xml out.xml" ); + + " gene_tree.xml tree_of_life.xml out.xml" ); System.out.println(); } diff --git a/forester/java/src/org/forester/application/meta_ontologizer.java b/forester/java/src/org/forester/application/meta_ontologizer.java index b1125f6..3d1cf58 100644 --- a/forester/java/src/org/forester/application/meta_ontologizer.java +++ b/forester/java/src/org/forester/application/meta_ontologizer.java @@ -134,8 +134,8 @@ public class meta_ontologizer { System.out.println( "Usage:" ); System.out.println(); System.out - .println( PRG_NAME - + " -p= [domain gain loss file] " ); + .println( PRG_NAME + + " -p= [domain gain loss file] " ); System.out.println(); } } diff --git a/forester/java/src/org/forester/application/msa_compactor.java b/forester/java/src/org/forester/application/msa_compactor.java index 329af42..d48df05 100644 --- a/forester/java/src/org/forester/application/msa_compactor.java +++ b/forester/java/src/org/forester/application/msa_compactor.java @@ -70,7 +70,7 @@ public class msa_compactor { final static private String OUTPUT_REMOVED_SEQS_OPTION = "ro"; final static private String MAFFT_OPTIONS = "mo"; final static private String PERFORM_PHYLOGENETIC_INFERENCE = "t"; - // + // final static private String PATH_TO_MAFFT_OPTION = "mafft"; final static private String DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION = "nn"; final static private String PRG_NAME = "msa_compactor"; @@ -169,7 +169,7 @@ public class msa_compactor { if ( length >= msa.getLength() ) { ForesterUtil.fatalError( PRG_NAME, "target length is out of range [longer than MSA (" + msa.getLength() - + ")]: " + length ); + + ")]: " + length ); } else if ( length < initial_msa_stats.getMin() ) { ForesterUtil.fatalError( PRG_NAME, @@ -269,8 +269,8 @@ public class msa_compactor { if ( chart_only ) { if ( ( out != null ) || ( removed_seqs_out_base != null ) ) { ForesterUtil - .fatalError( PRG_NAME, - "chart only, no outfile(s) produced, thus no need to indicate output file(s)" ); + .fatalError( PRG_NAME, + "chart only, no outfile(s) produced, thus no need to indicate output file(s)" ); } if ( !realign && cla.isOptionSet( STEP_OPTION ) ) { ForesterUtil.fatalError( PRG_NAME, @@ -281,7 +281,7 @@ public class msa_compactor { if ( perform_phylogenetic_inference ) { if ( step_for_diagnostics != 1 ) { ForesterUtil.fatalError( PRG_NAME, - "step for diagnostics reports needs to be set to 1 for tree calculation" ); + "step for diagnostics reports needs to be set to 1 for tree calculation" ); } } ForesterUtil.printProgramInformation( PRG_NAME, @@ -422,7 +422,7 @@ public class msa_compactor { else { if ( ForesterUtil.isEmpty( path_to_mafft ) ) { ForesterUtil.fatalError( PRG_NAME, "no MAFFT executable found, use -\"" + PATH_TO_MAFFT_OPTION - + "=\" option" ); + + "=\" option" ); } else { ForesterUtil.fatalError( PRG_NAME, "no MAFFT executable at \"" + path_to_mafft + "\"" ); @@ -453,25 +453,25 @@ public class msa_compactor { System.out.println( " options: " ); System.out.println(); System.out.println( " -" + REMOVE_WORST_OFFENDERS_OPTION - + "= number of worst offender sequences to remove" ); + + "= number of worst offender sequences to remove" ); System.out.println( " -" + LENGTH_OPTION + "= target MSA length" ); System.out.println( " -" + AV_GAPINESS_OPTION + "= target gap-ratio (0.0-1.0)" ); System.out.println( " -" + REALIGN_OPTION + " to realign using MAFFT" + mafft_comment ); System.out.println( " -" + MAFFT_OPTIONS + "= options for MAFFT (default: --auto)" ); System.out.println( " -" + STEP_OPTION + "= step for output and re-aligning (default: 1)" ); System.out.println( " -" + STEP_FOR_DIAGNOSTICS_OPTION - + "= step for diagnostics reports (default: 1)" ); + + "= step for diagnostics reports (default: 1)" ); System.out.println( " -" + REPORT_ENTROPY - + " to calculate normalized Shannon Entropy (not recommended for very large alignments)" ); + + " to calculate normalized Shannon Entropy (not recommended for very large alignments)" ); System.out.println( " -" + OUTPUT_FORMAT_OPTION - + "= format for output alignments: f for fasta (default), p for phylip, or n for nexus" ); + + "= format for output alignments: f for fasta (default), p for phylip, or n for nexus" ); System.out.println( " -" + OUTPUT_REMOVED_SEQS_OPTION + "= to output the removed sequences" ); System.out.println( " -" + MIN_LENGTH_OPTION - + "= minimal effecive sequence length (for deleting of shorter sequences)" ); + + "= minimal effecive sequence length (for deleting of shorter sequences)" ); System.out.println( " -" + GAP_RATIO_LENGTH_OPTION - + "= maximal allowed gap ratio per column (for deleting of columms) (0.0-1.0)" ); + + "= maximal allowed gap ratio per column (for deleting of columms) (0.0-1.0)" ); System.out.println( " -" + PERFORM_PHYLOGENETIC_INFERENCE - + " to calculate a simple phylogenetic tree (Kimura distances, NJ)" ); + + " to calculate a simple phylogenetic tree (Kimura distances, NJ)" ); System.out.println(); System.out.println(); System.out.println(); diff --git a/forester/java/src/org/forester/application/nj.java b/forester/java/src/org/forester/application/nj.java index ad38946..dca5d08 100644 --- a/forester/java/src/org/forester/application/nj.java +++ b/forester/java/src/org/forester/application/nj.java @@ -142,7 +142,7 @@ public class nj { System.out.println( "Usage:" ); System.out.println(); System.out.println( "% java -cp forester.jar org.forester.applications." + PRG_NAME - + " [options] " ); + + " [options] " ); System.out.println(); System.out.println( " Options: " ); System.out.println( VERBOSE_OPTION + ": verbose on" ); diff --git a/forester/java/src/org/forester/application/obo_tool.java b/forester/java/src/org/forester/application/obo_tool.java index abd1cba..0afbabe 100644 --- a/forester/java/src/org/forester/application/obo_tool.java +++ b/forester/java/src/org/forester/application/obo_tool.java @@ -98,7 +98,7 @@ public class obo_tool { ForesterUtil.fatalError( PRG_NAME, e.toString() ); } ForesterUtil.programMessage( PRG_NAME, "successfully read in " + go_terms.size() + " GO terms from [" + infile - + "]" ); + + "]" ); if ( output_ids_to_names ) { final File outfile_ids_to_names = new File( outfile + IDS_TO_NAMES_SUFFIX ); final String error = ForesterUtil.isWritableFile( outfile_ids_to_names ); diff --git a/forester/java/src/org/forester/application/pccx.java b/forester/java/src/org/forester/application/pccx.java index 369d514..e3c8167 100644 --- a/forester/java/src/org/forester/application/pccx.java +++ b/forester/java/src/org/forester/application/pccx.java @@ -263,7 +263,7 @@ public class pccx { } catch ( final IOException e ) { ForesterUtil.fatalError( pccx.PRG_NAME, "Failed to write to \"" + annotated_phylogenies_outfile - + "\" [" + e.getMessage() + "]" ); + + "\" [" + e.getMessage() + "]" ); } } } @@ -283,7 +283,7 @@ public class pccx { System.out.println( "Usage:" ); System.out.println(); System.out.println( pccx.PRG_NAME - + " [options] [external node name 1] [name 2] ... [name n]" ); + + " [options] [external node name 1] [name 2] ... [name n]" ); System.out.println(); System.out.println( " Options: " ); System.out.println(); @@ -294,7 +294,7 @@ public class pccx { System.out.println( " -o= : write output to " ); System.out.println( " -i= : read (new-line separated) external node names from " ); System.out.println( " -" + pccx.OUTPUT_ANNOTATED_PHYLOGENIES_OPTION - + "= : write output as annotated phylogeny to (only first" ); + + "= : write output as annotated phylogeny to (only first" ); System.out.println( " phylogeny in phylogenies infile is used)" ); System.out.println(); } diff --git a/forester/java/src/org/forester/application/pfam2go_extractor.java b/forester/java/src/org/forester/application/pfam2go_extractor.java index 6852d05..f086af3 100644 --- a/forester/java/src/org/forester/application/pfam2go_extractor.java +++ b/forester/java/src/org/forester/application/pfam2go_extractor.java @@ -96,7 +96,7 @@ public class pfam2go_extractor { private static void printHelp() { System.out.println(); System.out.println( PRG_NAME - + " [more GO ids]" ); + + " [more GO ids]" ); System.out.println(); } } diff --git a/forester/java/src/org/forester/application/pfam_go.java b/forester/java/src/org/forester/application/pfam_go.java index 0da8a2d..df679e1 100644 --- a/forester/java/src/org/forester/application/pfam_go.java +++ b/forester/java/src/org/forester/application/pfam_go.java @@ -150,7 +150,7 @@ public class pfam_go { System.out.println( "Usage:" ); System.out.println(); System.out.println( PRG_NAME + " [-" + ALLOW_DUPLICATES_OPTION - + " to allow duplicates] " ); + + " to allow duplicates] " ); System.out.println(); System.out.println(); } diff --git a/forester/java/src/org/forester/application/pfamacc2go.java b/forester/java/src/org/forester/application/pfamacc2go.java index 82ff0b8..9f69cdd 100644 --- a/forester/java/src/org/forester/application/pfamacc2go.java +++ b/forester/java/src/org/forester/application/pfamacc2go.java @@ -105,7 +105,7 @@ public class pfamacc2go { private static void printHelp() { System.out.println(); System.out.println( PRG_NAME - + " " ); + + " " ); System.out.println(); } } diff --git a/forester/java/src/org/forester/application/phylostrip.java b/forester/java/src/org/forester/application/phylostrip.java index 2981cd9..6145e12 100644 --- a/forester/java/src/org/forester/application/phylostrip.java +++ b/forester/java/src/org/forester/application/phylostrip.java @@ -46,7 +46,7 @@ public class phylostrip { if ( args.length < 4 ) { System.out.println( "\nstrip: Wrong number of arguments.\n" ); System.out - .println( "Usage: \"phylostrip [name1] [name2] ... OR [ref-tree]\"\n" ); + .println( "Usage: \"phylostrip [name1] [name2] ... OR [ref-tree]\"\n" ); System.out.println( " Options: -knn to keep listed nodes" ); System.out.println( " -rnn to remove listed nodes" ); System.out.println( " -knnp to keep nodes found in [ref-tree]" ); diff --git a/forester/java/src/org/forester/application/phyloxml_converter.java b/forester/java/src/org/forester/application/phyloxml_converter.java index d258bfc..0dac775 100644 --- a/forester/java/src/org/forester/application/phyloxml_converter.java +++ b/forester/java/src/org/forester/application/phyloxml_converter.java @@ -210,12 +210,12 @@ public class phyloxml_converter { && ( field != PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME ) ) { if ( extr_taxonomy_pf_only ) { ( ( NHXParser ) parser ) - .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); replace_underscores = false; } else if ( extr_taxonomy ) { ( ( NHXParser ) parser ) - .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); + .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); replace_underscores = false; } } @@ -360,10 +360,10 @@ public class phyloxml_converter { System.out.println( "Usage:" ); System.out.println(); System.out - .println( PRG_NAME - + " -" - + FIELD_OPTION - + "= [options] " ); + .println( PRG_NAME + + " -" + + FIELD_OPTION + + "= [options] " ); System.out.println(); System.out.println( " field options: " ); System.out.println(); @@ -375,28 +375,28 @@ public class phyloxml_converter { System.out.println( " " + FIELD_SEQUENCE_SYMBOL + ": transfer name to sequence symbol" ); System.out.println( " " + FIELD_DUMMY + ": to convert NHX formatted trees to phyloXML" ); System.out.println( " " + FIELD_UNIPROT_TAXONOMY_ID_SPLIT_1 - + ": transfer/split name to taxonomy uniprot identifier" ); + + ": transfer/split name to taxonomy uniprot identifier" ); System.out.println( " (split at underscore if \"id_name\" pattern, e.g. \"817_SusD\")" ); System.out.println( " " + FIELD_UNIPROT_TAXONOMY_ID_SPLIT_2 - + ": transfer/split name to taxonomy uniprot identifier" ); + + ": transfer/split name to taxonomy uniprot identifier" ); System.out.println( " (split at underscore if \"name_id\" pattern, e.g. \"SusD_817\")" ); System.out.println(); System.out.println( " options: " ); System.out.println( " -" + INTERNAL_NAMES_ARE_BOOT_SUPPPORT - + " : internal names in NH or NHX tree are bootstrap support values" ); + + " : internal names in NH or NHX tree are bootstrap support values" ); System.out.println( " -" + REPLACE_UNDER_SCORES + " : replace all underscores with spaces" ); System.out.println( " -" + MIDPOINT_REROOT + " : midpoint reroot" ); System.out.println( " -" + ORDER_SUBTREES + " : order subtrees" ); System.out - .println( " -" - + EXTRACT_TAXONOMY - + " : extract taxonomy to taxonomy code from \"seqname_TAXON\"-style names (cannot be used with the following field options: " - + FIELD_TAXONOMY_CODE + ", " + FIELD_TAXONOMY_COMM_NAME + ", " + FIELD_TAXONOMY_SCI_NAME + ")" ); + .println( " -" + + EXTRACT_TAXONOMY + + " : extract taxonomy to taxonomy code from \"seqname_TAXON\"-style names (cannot be used with the following field options: " + + FIELD_TAXONOMY_CODE + ", " + FIELD_TAXONOMY_COMM_NAME + ", " + FIELD_TAXONOMY_SCI_NAME + ")" ); System.out - .println( " -" - + EXTRACT_TAXONOMY_PF - + " : extract taxonomy to taxonomy code from Pfam (\"seqname_TAXON/x-y\") style names only (cannot be used with the following field options: " - + FIELD_TAXONOMY_CODE + ", " + FIELD_TAXONOMY_COMM_NAME + ", " + FIELD_TAXONOMY_SCI_NAME + ")" ); + .println( " -" + + EXTRACT_TAXONOMY_PF + + " : extract taxonomy to taxonomy code from Pfam (\"seqname_TAXON/x-y\") style names only (cannot be used with the following field options: " + + FIELD_TAXONOMY_CODE + ", " + FIELD_TAXONOMY_COMM_NAME + ", " + FIELD_TAXONOMY_SCI_NAME + ")" ); System.out.println( " -" + NO_TREE_LEVEL_INDENDATION + " : no tree level indendation in phyloXML output" ); System.out.println( " -" + IGNORE_QUOTES + ": ignore quotes and whitespace (e.g. \"a b\" becomes ab)" ); System.out.println(); diff --git a/forester/java/src/org/forester/application/rio.java b/forester/java/src/org/forester/application/rio.java index 27c4ee0..fd0127e 100644 --- a/forester/java/src/org/forester/application/rio.java +++ b/forester/java/src/org/forester/application/rio.java @@ -161,7 +161,7 @@ public class rio { } else { ForesterUtil - .fatalError( "values for re-rooting are: 'none', 'midpoint', or 'outgroup' (minizming duplications is default)" ); + .fatalError( "values for re-rooting are: 'none', 'midpoint', or 'outgroup' (minizming duplications is default)" ); } } if ( ForesterUtil.isEmpty( outgroup ) && ( rerooting == REROOTING.OUTGROUP ) ) { @@ -422,37 +422,37 @@ public class rio { System.out.println( "Usage" ); System.out.println(); System.out - .println( PRG_NAME - + " [options] [logfile]" ); + .println( PRG_NAME + + " [options] [logfile]" ); System.out.println(); System.out.println( " Options" ); System.out.println( " -" + GT_FIRST + "= : first gene tree to analyze (0-based index)" ); System.out.println( " -" + GT_LAST + "= : last gene tree to analyze (0-based index)" ); System.out.println( " -" + REROOTING_OPT - + "=: re-rooting method for gene trees, possible values or 'none', 'midpoint'," ); + + "=: re-rooting method for gene trees, possible values or 'none', 'midpoint'," ); System.out.println( " or 'outgroup' (default: by minizming duplications)" ); System.out.println( " -" + OUTGROUP - + "= : for rooting by outgroup, name of outgroup (external gene tree node)" ); + + "= : for rooting by outgroup, name of outgroup (external gene tree node)" ); System.out - .println( " -" + RETURN_SPECIES_TREE + "= : to write the (stripped) species tree to file" ); + .println( " -" + RETURN_SPECIES_TREE + "= : to write the (stripped) species tree to file" ); System.out.println( " -" + RETURN_BEST_GENE_TREE - + "= : to write (one) minimal duplication gene tree to file" ); + + "= : to write (one) minimal duplication gene tree to file" ); System.out - .println( " -" - + TRANSFER_TAXONOMY_OPTION - + " : to transfer taxonomic data from species tree to returned minimal duplication gene tree\n" - + " (if -" + RETURN_BEST_GENE_TREE + " option is used)" ); + .println( " -" + + TRANSFER_TAXONOMY_OPTION + + " : to transfer taxonomic data from species tree to returned minimal duplication gene tree\n" + + " (if -" + RETURN_BEST_GENE_TREE + " option is used)" ); System.out.println( " -" + USE_SDIR - + " : to use SDIR instead of GSDIR (faster, but non-binary species trees are" ); + + " : to use SDIR instead of GSDIR (faster, but non-binary species trees are" ); System.out.println( " disallowed, as are most options)" ); System.out.println(); System.out.println( " Formats" ); System.out - .println( " The gene trees, as well as the species tree, ideally are in phyloXML (www.phyloxml.org) format," ); + .println( " The gene trees, as well as the species tree, ideally are in phyloXML (www.phyloxml.org) format," ); System.out - .println( " but can also be in New Hamphshire (Newick) or Nexus format as long as species information can be" ); + .println( " but can also be in New Hamphshire (Newick) or Nexus format as long as species information can be" ); System.out - .println( " extracted from the gene names (e.g. \"HUMAN\" from \"BCL2_HUMAN\") and matched to a single species" ); + .println( " extracted from the gene names (e.g. \"HUMAN\" from \"BCL2_HUMAN\") and matched to a single species" ); System.out.println( " in the species tree." ); System.out.println(); System.out.println( " Examples" ); diff --git a/forester/java/src/org/forester/application/support_statistics.java b/forester/java/src/org/forester/application/support_statistics.java index ae8083a..938f5e0 100644 --- a/forester/java/src/org/forester/application/support_statistics.java +++ b/forester/java/src/org/forester/application/support_statistics.java @@ -118,7 +118,7 @@ public final class support_statistics { if ( dss_comp != null ) { sb.append( ForesterUtil.getLineSeparator() ); sb.append( "\t" + ForesterUtil.normalizeString( "values for support means:", max_length, true, ' ' ) - + "\t\t" ); + + "\t\t" ); sb.append( ForesterUtil.round( dss_comp.arithmeticMean(), support_statistics.PLACES ) + "\t" ); sb.append( ForesterUtil.round( dss_comp.sampleStandardDeviation(), support_statistics.PLACES ) + "\t" ); sb.append( ForesterUtil.round( dss_comp.getMin(), support_statistics.PLACES ) + "\t" ); diff --git a/forester/java/src/org/forester/application/support_transfer.java b/forester/java/src/org/forester/application/support_transfer.java index a96b834..340bcf4 100644 --- a/forester/java/src/org/forester/application/support_transfer.java +++ b/forester/java/src/org/forester/application/support_transfer.java @@ -48,7 +48,7 @@ public final class support_transfer { * Transfers branch length values from one Phylogeny to another. It is * mainly a "main method" for method "copyBranchLengthValuesFrom( Phylogeny )" * of org.forester.phylogeny.Phylogeny, to be used in other (Perl) programs. - * + * * @param args[0] * Filename (String) for Phylogeny which has correct branch * length values @@ -60,8 +60,8 @@ public final class support_transfer { * @param args[2] * String Filename (String) for outputfile * @param args[3] - * String [number of tree with correct bl to use in case treefile contains more than one, default 0] - + * String [number of tree with correct bl to use in case treefile contains more than one, default 0] + */ public static void main( final String args[] ) { Phylogeny phylogeny_w_bl = null; // Has correct branch lengths @@ -147,7 +147,7 @@ public final class support_transfer { * Important (but obvious): The topology of both trees needs to be the same. * The method is not robust, and might produce wrong results if the internal * topology differs or if the external node names are not unique. - * + * * @param from * the Phylogeny to copy the support values from * @param to diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java index 141db17..2b5c7c4 100644 --- a/forester/java/src/org/forester/application/surfacing.java +++ b/forester/java/src/org/forester/application/surfacing.java @@ -119,13 +119,13 @@ public class surfacing { // --- public final static String PRG_NAME = "surfacing"; public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_d_dollo" - + ForesterConstants.PHYLO_XML_SUFFIX; + + ForesterConstants.PHYLO_XML_SUFFIX; public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH = "_d_fitch" - + ForesterConstants.PHYLO_XML_SUFFIX; + + ForesterConstants.PHYLO_XML_SUFFIX; public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_dc_dollo" - + ForesterConstants.PHYLO_XML_SUFFIX; + + ForesterConstants.PHYLO_XML_SUFFIX; public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH = "_dc_fitch" - + ForesterConstants.PHYLO_XML_SUFFIX; + + ForesterConstants.PHYLO_XML_SUFFIX; public static final String NEXUS_EXTERNAL_DOMAINS = "_dom.nex"; public static final String NEXUS_EXTERNAL_DOMAIN_COMBINATIONS = "_dc.nex"; public static final String NEXUS_SECONDARY_FEATURES = "_secondary_features.nex"; @@ -135,7 +135,7 @@ public class surfacing { public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES = "_dollo_losses_secondary_features"; public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES = "_dollo_present_secondary_features"; public static final String SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_secondary_features_dollo" - + ForesterConstants.PHYLO_XML_SUFFIX; + + ForesterConstants.PHYLO_XML_SUFFIX; public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES = "_dollo_goid_d"; public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES = "_fitch_goid_dc"; final static private String HELP_OPTION_1 = "help"; @@ -204,11 +204,11 @@ public class surfacing { final static private String MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX = "_domains.pwd"; final static private String MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX = "_bin_combinations.pwd"; final static private String NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX = "_mean_score_NJ" - + ForesterConstants.PHYLO_XML_SUFFIX; + + ForesterConstants.PHYLO_XML_SUFFIX; final static private String NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX = "_domains_NJ" - + ForesterConstants.PHYLO_XML_SUFFIX; + + ForesterConstants.PHYLO_XML_SUFFIX; final static private String NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX = "_bin_combinations_NJ" - + ForesterConstants.PHYLO_XML_SUFFIX; + + ForesterConstants.PHYLO_XML_SUFFIX; final static private String FILTER_POSITIVE_OPTION = "pos_filter"; final static private String FILTER_NEGATIVE_OPTION = "neg_filter"; final static private String FILTER_NEGATIVE_DOMAINS_OPTION = "neg_dom_filter"; @@ -264,7 +264,7 @@ public class surfacing { public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_unique.txt"; public static final String LIMIT_SPEC_FOR_PROT_EX = null; // e.g. "HUMAN"; set to null for not using this feature (default). public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED = "_dc_MAPPED_secondary_features_fitch" - + ForesterConstants.PHYLO_XML_SUFFIX; + + ForesterConstants.PHYLO_XML_SUFFIX; public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_counts_MAPPED.txt"; public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists_MAPPED.txt"; public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_MAPPED.txt"; @@ -505,8 +505,8 @@ public class surfacing { && ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) || cla .isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) ) { ForesterUtil - .fatalError( surfacing.PRG_NAME, - "attempt to use both negative or positive protein filter together wirh a negative domains filter" ); + .fatalError( surfacing.PRG_NAME, + "attempt to use both negative or positive protein filter together wirh a negative domains filter" ); } if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.FILTER_NEGATIVE_OPTION ) ) { @@ -541,7 +541,7 @@ public class surfacing { final String msg = ForesterUtil.isReadableFile( negative_domains_filter_file ); if ( !ForesterUtil.isEmpty( msg ) ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + negative_domains_filter_file - + "\": " + msg ); + + "\": " + msg ); } } final List plus_minus_analysis_high_copy_base_species = new ArrayList(); @@ -563,7 +563,7 @@ public class surfacing { final String msg = ForesterUtil.isReadableFile( input_genomes_file ); if ( !ForesterUtil.isEmpty( msg ) ) { ForesterUtil - .fatalError( surfacing.PRG_NAME, "can not read from \"" + input_genomes_file + "\": " + msg ); + .fatalError( surfacing.PRG_NAME, "can not read from \"" + input_genomes_file + "\": " + msg ); } } else { @@ -592,9 +592,9 @@ public class surfacing { } else { ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + scoring_str - + "\" for scoring method for domain combinations similarity calculation: \"-" - + surfacing.SCORING_OPTION + "=<" + surfacing.SCORING_DOMAIN_COUNT_BASED + "|" - + surfacing.SCORING_PROTEIN_COUNT_BASED + "|" + surfacing.SCORING_COMBINATION_BASED + ">\"" ); + + "\" for scoring method for domain combinations similarity calculation: \"-" + + surfacing.SCORING_OPTION + "=<" + surfacing.SCORING_DOMAIN_COUNT_BASED + "|" + + surfacing.SCORING_PROTEIN_COUNT_BASED + "|" + surfacing.SCORING_COMBINATION_BASED + ">\"" ); } } boolean sort_by_species_count_first = false; @@ -660,10 +660,10 @@ public class surfacing { if ( cla.isOptionSet( surfacing.SEQ_EXTRACT_OPTION ) ) { if ( !cla.isOptionValueSet( surfacing.SEQ_EXTRACT_OPTION ) ) { ForesterUtil - .fatalError( surfacing.PRG_NAME, - "no domain ids given for sequences with given domains to be extracted : -" - + surfacing.SEQ_EXTRACT_OPTION - + "=" ); + .fatalError( surfacing.PRG_NAME, + "no domain ids given for sequences with given domains to be extracted : -" + + surfacing.SEQ_EXTRACT_OPTION + + "=" ); } query_domain_ids = cla.getOptionValue( surfacing.SEQ_EXTRACT_OPTION ); } @@ -719,14 +719,14 @@ public class surfacing { } else { ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort_str - + "\" for domain combinations similarities sorting: \"-" - + surfacing.DOMAIN_SIMILARITY_SORT_OPTION + "=<" + surfacing.DOMAIN_SIMILARITY_SORT_ALPHA + "|" - + surfacing.DOMAIN_SIMILARITY_SORT_MAX + "|" + surfacing.DOMAIN_SIMILARITY_SORT_MIN + "|" - + surfacing.DOMAIN_SIMILARITY_SORT_MEAN + "|" + surfacing.DOMAIN_SIMILARITY_SORT_DIFF + "|" - + surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|" - + surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|" + "|" - + surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|" + surfacing.DOMAIN_SIMILARITY_SORT_SD - + ">\"" ); + + "\" for domain combinations similarities sorting: \"-" + + surfacing.DOMAIN_SIMILARITY_SORT_OPTION + "=<" + surfacing.DOMAIN_SIMILARITY_SORT_ALPHA + "|" + + surfacing.DOMAIN_SIMILARITY_SORT_MAX + "|" + surfacing.DOMAIN_SIMILARITY_SORT_MIN + "|" + + surfacing.DOMAIN_SIMILARITY_SORT_MEAN + "|" + surfacing.DOMAIN_SIMILARITY_SORT_DIFF + "|" + + surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|" + + surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|" + "|" + + surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|" + surfacing.DOMAIN_SIMILARITY_SORT_SD + + ">\"" ); } } DomainSimilarity.PRINT_OPTION domain_similarity_print_option = DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT; @@ -778,10 +778,10 @@ public class surfacing { } else { ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort - + "\" for sorting of domain counts: \"-" + surfacing.DOMAIN_COUNT_SORT_OPTION + "=<" - + surfacing.DOMAIN_COUNT_SORT_ALPHA + "|" + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|" - + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|" - + surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" ); + + "\" for sorting of domain counts: \"-" + surfacing.DOMAIN_COUNT_SORT_OPTION + "=<" + + surfacing.DOMAIN_COUNT_SORT_ALPHA + "|" + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|" + + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|" + + surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" ); } } final String[][] input_file_properties = SurfacingUtil.processInputGenomesFile( input_genomes_file ); @@ -826,7 +826,7 @@ public class surfacing { domain_id_to_go_ids_map = SurfacingUtil.createDomainIdToGoIdMap( pfam_to_go_mappings ); if ( parser.getMappingCount() < domain_id_to_go_ids_map.size() ) { ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, - "parser.getMappingCount() < domain_id_to_go_ids_map.size()" ); + "parser.getMappingCount() < domain_id_to_go_ids_map.size()" ); } domain_id_to_go_ids_count = parser.getMappingCount(); } @@ -889,10 +889,10 @@ public class surfacing { } else { ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + go_namespace_limit_str - + "\" for GO namespace limit: \"-" + surfacing.GO_NAMESPACE_LIMIT_OPTION + "=<" - + surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|" - + surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|" - + surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" ); + + "\" for GO namespace limit: \"-" + surfacing.GO_NAMESPACE_LIMIT_OPTION + "=<" + + surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|" + + surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|" + + surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" ); } } if ( ( domain_similarity_sort_field == DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE ) @@ -961,7 +961,7 @@ public class surfacing { Map>[] domain_id_to_secondary_features_maps = null; File[] secondary_features_map_files = null; final File domain_lengths_analysis_outfile = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file - + DOMAIN_LENGTHS_ANALYSIS_SUFFIX ); + + DOMAIN_LENGTHS_ANALYSIS_SUFFIX ); if ( domain_length_analysis ) { SurfacingUtil.checkForOutputFileWriteability( domain_lengths_analysis_outfile ); } @@ -1020,21 +1020,21 @@ public class surfacing { if ( positive_filter_file != null ) { final int filter_size = filter.size(); System.out.println( "Positive protein filter : " + positive_filter_file + " [" + filter_size - + " domain ids]" ); + + " domain ids]" ); html_desc.append( "Positive protein filter:" + positive_filter_file + " [" + filter_size - + " domain ids]" + nl ); + + " domain ids]" + nl ); } if ( negative_filter_file != null ) { final int filter_size = filter.size(); System.out.println( "Negative protein filter : " + negative_filter_file + " [" + filter_size - + " domain ids]" ); + + " domain ids]" ); html_desc.append( "Negative protein filter:" + negative_filter_file + " [" + filter_size - + " domain ids]" + nl ); + + " domain ids]" + nl ); } if ( negative_domains_filter_file != null ) { final int filter_size = filter.size(); System.out.println( "Negative domain filter : " + negative_domains_filter_file + " [" + filter_size - + " domain ids]" ); + + " domain ids]" ); html_desc.append( "Negative domain filter:" + negative_domains_filter_file + " [" + filter_size + " domain ids]" + nl ); } @@ -1053,7 +1053,7 @@ public class surfacing { } System.out.println( "Plus-minus analysis : " + plus1 + "&& " + plus0 + "&& " + minus ); html_desc.append( "Plus-minus analysis:" + plus1 + "&& " + plus0 + "&& " + minus - + "" + nl ); + + "" + nl ); } if ( cutoff_scores_file != null ) { System.out.println( "Cutoff scores file : " + cutoff_scores_file ); @@ -1086,16 +1086,16 @@ public class surfacing { if ( no_engulfing_overlaps ) { System.out.println( "Ignore engulfed domains : " + no_engulfing_overlaps ); html_desc.append( "Ignore (lower confidence) engulfed domains:" + no_engulfing_overlaps - + "" + nl ); + + "" + nl ); } System.out.println( "Ignore singlet domains : " + ignore_domains_without_combs_in_all_spec ); html_desc - .append( "Ignore singlet domains for domain combination similarity analyses (not for parsimony analyses):" - + ignore_domains_without_combs_in_all_spec + "" + nl ); + .append( "Ignore singlet domains for domain combination similarity analyses (not for parsimony analyses):" + + ignore_domains_without_combs_in_all_spec + "" + nl ); System.out.println( "Ignore species specific doms: " + ignore_species_specific_domains ); html_desc - .append( "Ignore species specific domains for domain combination similarity analyses (not for parsimony analyses):" - + ignore_species_specific_domains + "" + nl ); + .append( "Ignore species specific domains for domain combination similarity analyses (not for parsimony analyses):" + + ignore_species_specific_domains + "" + nl ); System.out.println( "Ignore combination with self: " + ignore_combination_with_same ); html_desc.append( "Ignore combination with self for domain combination similarity analyses:" + ignore_combination_with_same + "" + nl ); @@ -1115,14 +1115,14 @@ public class surfacing { if ( perform_dc_fich ) { System.out.println( "Use last in Fitch parsimony : " + use_last_in_fitch_parsimony ); html_desc.append( "Use last in Fitch parsimony:" + use_last_in_fitch_parsimony - + "" + nl ); + + "" + nl ); } System.out.println( "Write to Nexus files : " + write_to_nexus ); html_desc.append( "Write to Nexus files:" + write_to_nexus + "" + nl ); if ( perform_dc_fich ) { System.out.println( "DC regain prot stats : " + perform_dc_regain_proteins_stats ); html_desc.append( "DC regain prot stats:" + perform_dc_regain_proteins_stats - + "" + nl ); + + "" + nl ); } System.out.println( "DA analysis : " + da_analysis ); html_desc.append( "DA analysis :" + da_analysis + "" + nl ); @@ -1150,7 +1150,7 @@ public class surfacing { } if ( domain_id_to_go_ids_map != null ) { System.out.println( "Pfam to GO mappings from : " + pfam_to_go_file + " [" + domain_id_to_go_ids_count - + " mappings]" ); + + " mappings]" ); html_desc.append( "Pfam to GO mappings from:" + pfam_to_go_file + " [" + domain_id_to_go_ids_count + " mappings]" + "" + nl ); } @@ -1166,7 +1166,7 @@ public class surfacing { if ( perform_pwc ) { System.out.println( "Suffix for PWC files : " + automated_pairwise_comparison_suffix ); html_desc.append( "Suffix for PWC files" + automated_pairwise_comparison_suffix - + "" + nl ); + + "" + nl ); } if ( out_dir != null ) { System.out.println( "Output directory : " + out_dir ); @@ -1303,14 +1303,14 @@ public class surfacing { break; default: ForesterUtil - .unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for similarities" ); + .unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for similarities" ); } System.out.println(); html_desc.append( "" + nl ); if ( ( intrees != null ) && ( intrees.length > 0 ) ) { for( final File intree_file : intree_files ) { html_desc.append( "Intree for gain/loss parsimony analysis:" + intree_file - + "" + nl ); + + "" + nl ); System.out.println( " Intree for gain/loss pars.: " + intree_file ); } } @@ -1343,7 +1343,7 @@ public class surfacing { } // if ( perform_pwc ) { System.out.println(); html_desc.append( "Command line:" + nl + nl + cla.getCommandLineArgsAsString() + nl + nl - + "" + nl ); + + "" + nl ); System.out.println( "Command line : " + cla.getCommandLineArgsAsString() ); BufferedWriter[] query_domains_writer_ary = null; List[] query_domain_ids_array = null; @@ -1391,7 +1391,7 @@ public class surfacing { all_bin_domain_combinations_lost_fitch = new ArrayList(); } final File per_genome_domain_promiscuity_statistics_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR - + output_file + D_PROMISCUITY_FILE_SUFFIX ); + + output_file + D_PROMISCUITY_FILE_SUFFIX ); BufferedWriter per_genome_domain_promiscuity_statistics_writer = null; try { per_genome_domain_promiscuity_statistics_writer = new BufferedWriter( new FileWriter( per_genome_domain_promiscuity_statistics_file ) ); @@ -1434,7 +1434,7 @@ public class surfacing { BufferedWriter domains_per_potein_stats_writer = null; try { domains_per_potein_stats_writer = new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR - + output_file + "_domains_per_potein_stats.txt" ) ); + + output_file + "_domains_per_potein_stats.txt" ) ); domains_per_potein_stats_writer.write( "Genome" ); domains_per_potein_stats_writer.write( "\t" ); domains_per_potein_stats_writer.write( "Mean" ); @@ -1555,8 +1555,8 @@ public class surfacing { System.out.println( "Coverage : " + ForesterUtil.roundToInt( 100.0 * coverage ) + "%" ); SurfacingUtil.log( "Coverage : " - + ForesterUtil.roundToInt( 100.0 * coverage ) + "%", - log_writer ); + + ForesterUtil.roundToInt( 100.0 * coverage ) + "%", + log_writer ); System.out.println( "Domains encountered : " + parser.getDomainsEncountered() ); SurfacingUtil.log( "Domains encountered : " + parser.getDomainsEncountered(), log_writer ); @@ -1570,53 +1570,53 @@ public class surfacing { System.out.println( "Domains ignored due to individual score cutoffs: " + parser.getDomainsIgnoredDueToIndividualScoreCutoff() ); SurfacingUtil.log( "Domains ignored due to individual score cutoffs: " - + parser.getDomainsIgnoredDueToIndividualScoreCutoff(), - log_writer ); + + parser.getDomainsIgnoredDueToIndividualScoreCutoff(), + log_writer ); System.out.println( "Domains ignored due to FS E-value : " + parser.getDomainsIgnoredDueToFsEval() ); SurfacingUtil.log( "Domains ignored due to FS E-value : " - + parser.getDomainsIgnoredDueToFsEval(), - log_writer ); + + parser.getDomainsIgnoredDueToFsEval(), + log_writer ); System.out.println( "Domains ignored due to iE-value : " + parser.getDomainsIgnoredDueToIEval() ); SurfacingUtil.log( "Domains ignored due to iE-value : " - + parser.getDomainsIgnoredDueToIEval(), - log_writer ); + + parser.getDomainsIgnoredDueToIEval(), + log_writer ); System.out.println( "Domains ignored due to DUF designation : " + parser.getDomainsIgnoredDueToDuf() ); SurfacingUtil - .log( "Domains ignored due to DUF designation : " + parser.getDomainsIgnoredDueToDuf(), - log_writer ); + .log( "Domains ignored due to DUF designation : " + parser.getDomainsIgnoredDueToDuf(), + log_writer ); if ( ignore_virus_like_ids ) { System.out.println( "Domains ignored due virus like ids : " + parser.getDomainsIgnoredDueToVirusLikeIds() ); SurfacingUtil.log( "Domains ignored due virus like ids : " - + parser.getDomainsIgnoredDueToVirusLikeIds(), - log_writer ); + + parser.getDomainsIgnoredDueToVirusLikeIds(), + log_writer ); } System.out.println( "Domains ignored due negative domain filter : " + parser.getDomainsIgnoredDueToNegativeDomainFilter() ); SurfacingUtil.log( "Domains ignored due negative domain filter : " - + parser.getDomainsIgnoredDueToNegativeDomainFilter(), - log_writer ); + + parser.getDomainsIgnoredDueToNegativeDomainFilter(), + log_writer ); System.out.println( "Domains ignored due to overlap : " + parser.getDomainsIgnoredDueToOverlap() ); SurfacingUtil.log( "Domains ignored due to overlap : " - + parser.getDomainsIgnoredDueToOverlap(), - log_writer ); + + parser.getDomainsIgnoredDueToOverlap(), + log_writer ); if ( negative_filter_file != null ) { System.out.println( "Proteins ignored due to negative filter : " + parser.getProteinsIgnoredDueToFilter() ); SurfacingUtil.log( "Proteins ignored due to negative filter : " - + parser.getProteinsIgnoredDueToFilter(), - log_writer ); + + parser.getProteinsIgnoredDueToFilter(), + log_writer ); } if ( positive_filter_file != null ) { System.out.println( "Proteins ignored due to positive filter : " + parser.getProteinsIgnoredDueToFilter() ); SurfacingUtil.log( "Proteins ignored due to positive filter : " - + parser.getProteinsIgnoredDueToFilter(), - log_writer ); + + parser.getProteinsIgnoredDueToFilter(), + log_writer ); } if ( da_analysis ) { System.out.println( "Distinct domain architectures stored : " + distinct_das ); @@ -1628,7 +1628,7 @@ public class surfacing { int count = 0; for( final Protein protein : protein_list ) { dc_data_writer.write( SurfacingUtil.proteinToDomainCombinations( protein, count + "", "\t" ) - .toString() ); + .toString() ); ++count; for( final Domain d : protein.getProteinDomains() ) { final String d_str = d.getDomainId().toString(); @@ -1655,22 +1655,22 @@ public class surfacing { } if ( !da_analysis ) { gwcd_list.add( BasicGenomeWideCombinableDomains - .createInstance( protein_list, - ignore_combination_with_same, - new BasicSpecies( input_file_properties[ i ][ 1 ] ), - domain_id_to_go_ids_map, - dc_type, - protein_length_stats_by_dc, - domain_number_stats_by_dc ) ); + .createInstance( protein_list, + ignore_combination_with_same, + new BasicSpecies( input_file_properties[ i ][ 1 ] ), + domain_id_to_go_ids_map, + dc_type, + protein_length_stats_by_dc, + domain_number_stats_by_dc ) ); if ( gwcd_list.get( i ).getSize() > 0 ) { if ( output_binary_domain_combinationsfor_counts ) { SurfacingUtil - .writeDomainCombinationsCountsFile( input_file_properties, - out_dir, - per_genome_domain_promiscuity_statistics_writer, - gwcd_list.get( i ), - i, - dc_sort_order ); + .writeDomainCombinationsCountsFile( input_file_properties, + out_dir, + per_genome_domain_promiscuity_statistics_writer, + gwcd_list.get( i ), + i, + dc_sort_order ); } if ( output_binary_domain_combinationsfor_graph_analysis ) { SurfacingUtil.writeBinaryDomainCombinationsFileForGraphAnalysis( input_file_properties, @@ -1718,9 +1718,9 @@ public class surfacing { distinct_domain_architecuture_counts, 10, new File( out_dir.toString() + "/" + output_file - + "_DA_counts.txt" ), - new File( out_dir.toString() + "/" + output_file - + "_unique_DAs.txt" ) ); + + "_DA_counts.txt" ), + new File( out_dir.toString() + "/" + output_file + + "_unique_DAs.txt" ) ); distinct_domain_architecutures_per_genome.clear(); distinct_domain_architecuture_counts.clear(); System.gc(); @@ -1746,13 +1746,13 @@ public class surfacing { all_genomes_domains_per_potein_stats = null; SurfacingUtil.printOutPercentageOfMultidomainProteins( all_genomes_domains_per_potein_histo, log_writer ); ForesterUtil.map2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file - + "_all_genomes_domains_per_potein_histo.txt" ), all_genomes_domains_per_potein_histo, "\t", "\n" ); + + "_all_genomes_domains_per_potein_histo.txt" ), all_genomes_domains_per_potein_histo, "\t", "\n" ); ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file - + "_domains_always_single_.txt" ), domains_which_are_always_single, "\n" ); + + "_domains_always_single_.txt" ), domains_which_are_always_single, "\n" ); ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file - + "_domains_single_or_combined.txt" ), domains_which_are_sometimes_single_sometimes_not, "\n" ); + + "_domains_single_or_combined.txt" ), domains_which_are_sometimes_single_sometimes_not, "\n" ); ForesterUtil.collection2file( new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file - + "_domains_always_combined.txt" ), domains_which_never_single, "\n" ); + + "_domains_always_combined.txt" ), domains_which_never_single, "\n" ); ForesterUtil.programMessage( PRG_NAME, "Average of proteins with a least one domain assigned: " + ( 100 * protein_coverage_stats.arithmeticMean() ) + "% (+/-" @@ -1761,13 +1761,13 @@ public class surfacing { + ( 100 * protein_coverage_stats.getMin() ) + "%-" + ( 100 * protein_coverage_stats.getMax() ) + "%" ); SurfacingUtil.log( "Average of prot with a least one dom assigned : " - + ( 100 * protein_coverage_stats.arithmeticMean() ) + "% (+/-" - + ( 100 * protein_coverage_stats.sampleStandardDeviation() ) + "%)", - log_writer ); + + ( 100 * protein_coverage_stats.arithmeticMean() ) + "% (+/-" + + ( 100 * protein_coverage_stats.sampleStandardDeviation() ) + "%)", + log_writer ); SurfacingUtil.log( "Range of prot with a least one dom assigned : " - + ( 100 * protein_coverage_stats.getMin() ) + "%-" - + ( 100 * protein_coverage_stats.getMax() ) + "%", - log_writer ); + + ( 100 * protein_coverage_stats.getMin() ) + "%-" + + ( 100 * protein_coverage_stats.getMax() ) + "%", + log_writer ); protein_coverage_stats = null; } catch ( final IOException e2 ) { @@ -1862,13 +1862,13 @@ public class surfacing { html_desc.append( "Sum of all distinct binary combinations:" + all_bin_domain_combinations_encountered.size() + "" + nl ); html_desc.append( "Sum of all distinct domains:" + all_domains_encountered.size() - + "" + nl ); + + "" + nl ); html_desc.append( "Analysis date/time:" + new java.text.SimpleDateFormat( "yyyy.MM.dd HH:mm:ss" ).format( new java.util.Date() ) + "" + nl ); html_desc.append( "" + nl ); final Writer simple_tab_writer = new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR - + my_outfile + ".tsv" ) ); + + my_outfile + ".tsv" ) ); SurfacingUtil.writeDomainSimilaritiesToFile( html_desc, new StringBuilder( number_of_genomes + " genomes" ), simple_tab_writer, @@ -1932,23 +1932,23 @@ public class surfacing { output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file ); } SurfacingUtil.writeMatrixToFile( new File( matrix_output_file - + surfacing.MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc.getDomainDistanceScoresMeans() ); + + surfacing.MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc.getDomainDistanceScoresMeans() ); SurfacingUtil - .writeMatrixToFile( new File( matrix_output_file - + surfacing.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), - pwgc.getSharedBinaryCombinationsBasedDistances() ); + .writeMatrixToFile( new File( matrix_output_file + + surfacing.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), + pwgc.getSharedBinaryCombinationsBasedDistances() ); SurfacingUtil.writeMatrixToFile( new File( matrix_output_file - + surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), - pwgc.getSharedDomainsBasedDistances() ); + + surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), + pwgc.getSharedDomainsBasedDistances() ); final Phylogeny nj_gd = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file - + surfacing.NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc.getDomainDistanceScoresMeans() - .get( 0 ) ); + + surfacing.NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc.getDomainDistanceScoresMeans() + .get( 0 ) ); final Phylogeny nj_bc = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file - + surfacing.NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc - .getSharedBinaryCombinationsBasedDistances().get( 0 ) ); + + surfacing.NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc + .getSharedBinaryCombinationsBasedDistances().get( 0 ) ); final Phylogeny nj_d = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file - + surfacing.NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc - .getSharedDomainsBasedDistances().get( 0 ) ); + + surfacing.NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc + .getSharedDomainsBasedDistances().get( 0 ) ); inferred_trees = new ArrayList(); inferred_trees.add( nj_gd ); inferred_trees.add( nj_bc ); @@ -1989,18 +1989,18 @@ public class surfacing { parameters_sb.toString(), domain_id_to_secondary_features_maps, positive_filter_file == null ? null : filter, - output_binary_domain_combinationsfor_graph_analysis, - all_bin_domain_combinations_gained_fitch, - all_bin_domain_combinations_lost_fitch, - dc_type, - protein_length_stats_by_dc, - domain_number_stats_by_dc, - domain_length_stats_by_domain, - tax_code_to_id_map, - write_to_nexus, - use_last_in_fitch_parsimony, - perform_dc_fich ); - // Listing of all domain combinations gained is only done if only one input tree is used. + output_binary_domain_combinationsfor_graph_analysis, + all_bin_domain_combinations_gained_fitch, + all_bin_domain_combinations_lost_fitch, + dc_type, + protein_length_stats_by_dc, + domain_number_stats_by_dc, + domain_length_stats_by_domain, + tax_code_to_id_map, + write_to_nexus, + use_last_in_fitch_parsimony, + perform_dc_fich ); + // Listing of all domain combinations gained is only done if only one input tree is used. if ( ( domain_id_to_secondary_features_maps != null ) && ( domain_id_to_secondary_features_maps.length > 0 ) ) { int j = 0; @@ -2009,14 +2009,14 @@ public class surfacing { final DomainParsimonyCalculator secondary_features_parsimony = DomainParsimonyCalculator .createInstance( intree, gwcd_list, domain_id_to_secondary_features_map ); SurfacingUtil - .executeParsimonyAnalysisForSecondaryFeatures( outfile_name - + "_" - + secondary_features_map_files[ j++ ], - secondary_features_parsimony, - intree, - parameters_sb.toString(), - mapping_results_map, - use_last_in_fitch_parsimony ); + .executeParsimonyAnalysisForSecondaryFeatures( outfile_name + + "_" + + secondary_features_map_files[ j++ ], + secondary_features_parsimony, + intree, + parameters_sb.toString(), + mapping_results_map, + use_last_in_fitch_parsimony ); if ( i == 0 ) { System.out.println(); System.out.println( "Mapping to secondary features:" ); @@ -2063,12 +2063,12 @@ public class surfacing { if ( all_bin_domain_combinations_gained_fitch != null ) { try { SurfacingUtil - .executeFitchGainsAnalysis( new File( output_file - + surfacing.OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX ), - all_bin_domain_combinations_gained_fitch, - all_domains_encountered.size(), - all_bin_domain_combinations_encountered, - true ); + .executeFitchGainsAnalysis( new File( output_file + + surfacing.OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX ), + all_bin_domain_combinations_gained_fitch, + all_domains_encountered.size(), + all_bin_domain_combinations_encountered, + true ); } catch ( final IOException e ) { ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); @@ -2077,12 +2077,12 @@ public class surfacing { if ( all_bin_domain_combinations_lost_fitch != null ) { try { SurfacingUtil - .executeFitchGainsAnalysis( new File( output_file - + surfacing.OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX ), - all_bin_domain_combinations_lost_fitch, - all_domains_encountered.size(), - all_bin_domain_combinations_encountered, - false ); + .executeFitchGainsAnalysis( new File( output_file + + surfacing.OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX ), + all_bin_domain_combinations_lost_fitch, + all_domains_encountered.size(), + all_bin_domain_combinations_encountered, + false ); } catch ( final IOException e ) { ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); @@ -2092,7 +2092,7 @@ public class surfacing { final long free_memory = rt.freeMemory() / 1000000; final long total_memory = rt.totalMemory() / 1000000; ForesterUtil.programMessage( PRG_NAME, "Time for analysis : " + ( new Date().getTime() - analysis_start_time ) - + "ms" ); + + "ms" ); ForesterUtil.programMessage( PRG_NAME, "Total running time: " + ( new Date().getTime() - start_time ) + "ms " ); ForesterUtil.programMessage( PRG_NAME, "Free memory : " + free_memory + "MB, total memory: " + total_memory + "MB" ); @@ -2107,28 +2107,28 @@ public class surfacing { System.out.println( "Usage:" ); System.out.println(); System.out.println( "% java -Xms256m -Xmx512m -cp forester.jar org.forester.applications." + surfacing.PRG_NAME - + " [options] [external node name 1] [name 2] ... [name n]" ); + + " [options] [external node name 1] [name 2] ... [name n]" ); System.out.println(); System.out.println( " Note: This software might need a significant amount of memory (heap space);" ); System.out - .println( " hence use \"-Xms128m -Xmx512m\" (or more) to prevent a \"java.lang.OutOfMemoryError\"." ); + .println( " hence use \"-Xms128m -Xmx512m\" (or more) to prevent a \"java.lang.OutOfMemoryError\"." ); System.out.println(); System.out.println( " Options: " ); System.out.println( surfacing.DETAILEDNESS_OPTION + ": level of detail for similarities output file (default:" + DETAILEDNESS_DEFAULT + ")" ); System.out.println( surfacing.IGNORE_COMBINATION_WITH_SAME_OPTION - + ": to ignore combinations with self (default: not to ignore)" ); + + ": to ignore combinations with self (default: not to ignore)" ); System.out - .println( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION - + ": to ignore domains without combinations in any species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" ); + .println( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION + + ": to ignore domains without combinations in any species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" ); System.out - .println( surfacing.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION - + ": to ignore domains specific to one species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" ); + .println( surfacing.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION + + ": to ignore domains specific to one species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" ); System.out.println( surfacing.NOT_IGNORE_DUFS_OPTION - + ": to _not_ ignore DUFs (domains with unknown function) (default: ignore DUFs)" ); + + ": to _not_ ignore DUFs (domains with unknown function) (default: ignore DUFs)" ); System.out - .println( surfacing.IGNORE_VIRAL_IDS - + ": to ignore domains with ids containing 'vir', 'retro', 'transpos', 'phage', or starting with 'rv' or 'gag_'" ); + .println( surfacing.IGNORE_VIRAL_IDS + + ": to ignore domains with ids containing 'vir', 'retro', 'transpos', 'phage', or starting with 'rv' or 'gag_'" ); System.out.println( surfacing.DOMAIN_SIMILARITY_SORT_OPTION + ": sorting for similarities (default: " + DOMAIN_SORT_FILD_DEFAULT + ")" ); System.out.println( surfacing.OUTPUT_FILE_OPTION + ": name for (main) output file (mandatory)" ); @@ -2144,45 +2144,45 @@ public class surfacing { + DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT + ")" ); System.out.println( surfacing.CUTOFF_SCORE_FILE_OPTION + ": cutoff score file" ); System.out.println( surfacing.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION - + ": sort by species count first" ); + + ": sort by species count first" ); System.out.println( surfacing.OUTPUT_DIR_OPTION + ": output directory" ); System.out.println( surfacing.PFAM_TO_GO_FILE_USE_OPTION + ": Pfam to GO mapping file" ); System.out.println( surfacing.GO_OBO_FILE_USE_OPTION + ": GO terms file (OBO format)" ); System.out.println( surfacing.GO_NAMESPACE_LIMIT_OPTION + ": limit GO term to one GO namespace" ); System.out.println( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION - + "[=]: to perform pairwise comparison based analyses" ); + + "[=]: to perform pairwise comparison based analyses" ); System.out.println( surfacing.INPUT_SPECIES_TREE_OPTION - + ": species tree, to perform (Dollo, Fitch) parismony analyses" ); + + ": species tree, to perform (Dollo, Fitch) parismony analyses" ); System.out - .println( surfacing.INPUT_SPECIES_TREE_OPTION - + "=: to infer domain/binary domain combination gains/losses on given species trees" ); + .println( surfacing.INPUT_SPECIES_TREE_OPTION + + "=: to infer domain/binary domain combination gains/losses on given species trees" ); System.out.println( surfacing.FILTER_POSITIVE_OPTION - + "=: to filter out proteins not containing at least one domain listed in " ); + + "=: to filter out proteins not containing at least one domain listed in " ); System.out.println( surfacing.FILTER_NEGATIVE_OPTION - + "=: to filter out proteins containing at least one domain listed in " ); + + "=: to filter out proteins containing at least one domain listed in " ); System.out.println( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION - + "=: to filter out (ignore) domains listed in " ); + + "=: to filter out (ignore) domains listed in " ); System.out.println( surfacing.INPUT_GENOMES_FILE_OPTION + "=: to read input files from " ); System.out - .println( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION - + "=: seed for random number generator for Fitch Parsimony analysis (type: long, default: no randomization - given a choice, prefer absence" ); + .println( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION + + "=: seed for random number generator for Fitch Parsimony analysis (type: long, default: no randomization - given a choice, prefer absence" ); System.out.println( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS - + ": to consider directedness in binary combinations: e.g. A-B != B-A" ); + + ": to consider directedness in binary combinations: e.g. A-B != B-A" ); System.out.println( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY - + ": to consider directedness and adjacency in binary combinations" ); + + ": to consider directedness and adjacency in binary combinations" ); System.out - .println( surfacing.SEQ_EXTRACT_OPTION - + "=: to extract sequence names of sequences containing matching domains and/or domain-sequences (order N to C) (domain separator: '~', domain sequences speparator: '#', e.g. 'NACHT#BIR~CARD')" ); + .println( surfacing.SEQ_EXTRACT_OPTION + + "=: to extract sequence names of sequences containing matching domains and/or domain-sequences (order N to C) (domain separator: '~', domain sequences speparator: '#', e.g. 'NACHT#BIR~CARD')" ); System.out.println( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE - + "=: to perfom parsimony analysis on secondary features" ); + + "=: to perfom parsimony analysis on secondary features" ); System.out.println( surfacing.PLUS_MINUS_ANALYSIS_OPTION + "=: to presence/absence genome analysis" ); System.out.println( surfacing.DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION - + ": to output binary domain counts (as individual files)" ); + + ": to output binary domain counts (as individual files)" ); System.out.println( surfacing.DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS - + ": to output binary domain combinations for (downstream) graph analysis" ); + + ": to output binary domain combinations for (downstream) graph analysis" ); System.out.println( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS + ": to output all proteins per domain" ); System.out.println( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION - + ": e value max per domain for output of all proteins per domain" ); + + ": e value max per domain for output of all proteins per domain" ); System.out.println( surfacing.USE_LAST_IN_FITCH_OPTION + ": to use last in Fitch parsimony" ); System.out.println( surfacing.WRITE_TO_NEXUS_OPTION + ": to output in Nexus format" ); System.out.println( PERFORM_DC_FITCH + ": to perform DC Fitch parsimony" ); @@ -2192,10 +2192,10 @@ public class surfacing { System.out.println(); System.out.println(); System.out - .println( "Example 1: surfacing -p2g=pfam2go.txt -obo=go.obo -species_tree=tol_156.xml -no_eo -ie=0.01 -dufs -genomes=genomes_all.txt -pos_filter=tf_1.txt -out_dir=_tf1 -o=tf1" ); + .println( "Example 1: surfacing -p2g=pfam2go.txt -obo=go.obo -species_tree=tol_156.xml -no_eo -ie=0.01 -dufs -genomes=genomes_all.txt -pos_filter=tf_1.txt -out_dir=_tf1 -o=tf1" ); System.out.println(); System.out - .println( "Example 2: surfacing -p2g=pfam2go.txt -obo=go.obo -species_tree=tol_156.xml -last -ignore_viral_ids -no_eo -ie=0.1 -dufs -genomes=genomes_all.txt -pos_filter=tf_1.txt -all_prot -all_prot_e=0.1 -out_dir=_tf1_e01_ape01 -o=tf1_e01_ape01" ); + .println( "Example 2: surfacing -p2g=pfam2go.txt -obo=go.obo -species_tree=tol_156.xml -last -ignore_viral_ids -no_eo -ie=0.1 -dufs -genomes=genomes_all.txt -pos_filter=tf_1.txt -all_prot -all_prot_e=0.1 -out_dir=_tf1_e01_ape01 -o=tf1_e01_ape01" ); System.out.println(); } } diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java index b2c3dd8..3ac6c56 100644 --- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java +++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java @@ -112,8 +112,8 @@ public final class AptxUtil { /** * Returns true if at least one branch has a length larger than zero. - * - * + * + * * @param phy */ final static public boolean isHasAtLeastOneBranchLengthLargerThanZero( final Phylogeny phy ) { @@ -271,7 +271,7 @@ public final class AptxUtil { final ControlPanel ac, final GraphicsExportType type, final Options options ) throws IOException { - tree_panel.calcParametersForPainting( width, height, true ); + tree_panel.calcParametersForPainting( width, height ); tree_panel.resetPreferredSize(); tree_panel.repaint(); final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING, @@ -572,8 +572,8 @@ public final class AptxUtil { /** * Exits with -1. - * - * + * + * * @param message * to message to be printed */ @@ -801,7 +801,7 @@ public final class AptxUtil { if ( options.isGraphicsExportVisibleOnly() ) { throw new IllegalArgumentException( "cannot export visible rectangle only without exporting in actual size" ); } - tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true ); + tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY() ); tree_panel.resetPreferredSize(); tree_panel.repaint(); } @@ -866,7 +866,7 @@ public final class AptxUtil { if ( options.isGraphicsExportVisibleOnly() ) { throw new IllegalArgumentException( "cannot export visible rectangle only without exporting in actual size" ); } - tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true ); + tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY() ); tree_panel.resetPreferredSize(); tree_panel.repaint(); } diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxA.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxA.java index 1ec5d96..c78bde4 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxA.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxA.java @@ -66,7 +66,7 @@ public class ArchaeopteryxA extends JApplet { * has been selected by the user by clicking the "Return ..." * menu item. This method is expected to be called from Javascript or * something like it. - * + * * @return current external node data as String */ public String getCurrentExternalNodesDataBuffer() { @@ -195,7 +195,7 @@ public class ArchaeopteryxA extends JApplet { /** * Prints message when initialization is finished. Called automatically. - * + * * @param g * Graphics */ diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index 3738cf4..68671ef 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java @@ -392,7 +392,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { * has been selected by the user by clicking the "Return ..." * menu item. This method is expected to be called from Javascript or * something like it. - * + * * @return current external node data as String */ public String getCurrentExternalNodesDataBuffer() { @@ -409,7 +409,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { /** * This method returns the current phylogeny as a string in the chosen format - * + * * @param format must be NH, NHX, NEXUS or PHYLOXML * @return the phylogeny string * @author Herve Menager @@ -436,10 +436,10 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } /** - * This method returns a view of the current phylogeny in a chosen + * This method returns a view of the current phylogeny in a chosen * graphics format, base64-encoded in a string so that in can be used * from javascript. - * + * * @param format must be GraphicsExportType (gif, jpg, pdf, png, tif, bmp) * @return the phylogeny string * @author Herve Menager @@ -609,10 +609,12 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { @Override public void componentResized( final ComponentEvent e ) { if ( getMainPanel().getCurrentTreePanel() != null ) { - getMainPanel().getCurrentTreePanel() - .calcParametersForPainting( getMainPanel().getCurrentTreePanel().getWidth(), - getMainPanel().getCurrentTreePanel().getHeight(), - getOptions().isAllowFontSizeChange() ); + getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel() + .getCurrentTreePanel() + .getWidth(), + getMainPanel() + .getCurrentTreePanel() + .getHeight() ); } } } ); diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index 7d6aff2..2d09a77 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -355,7 +355,7 @@ public final class Configuration { /** * Will attempt to use the phylogeny to determine whether to check * this or not (e.g. phylogram) - * + * */ boolean doGuessCheckOption( final int which ) { return display_options[ which ][ 2 ].equals( "?" ); @@ -701,7 +701,7 @@ public final class Configuration { /** * Convenience method. - * + * * @return true if value in configuration file was 'yes' */ boolean isDrawAsPhylogram() { @@ -868,7 +868,7 @@ public final class Configuration { /** * read each line of config file, process non-comment lines - * @throws IOException + * @throws IOException */ private void readConfig( final BufferedReader conf_in ) throws IOException { String line; diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java index 29e4578..26d5c6b 100644 --- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java +++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java @@ -126,7 +126,7 @@ final class ControlPanel extends JPanel implements ActionListener { private int _paste_subtree_item; private int _reroot_cb_item; private JButton _return_to_super_tree; - // Search + // Search private JLabel _search_found_label_0; private JLabel _search_found_label_1; private JButton _search_reset_button_0; @@ -766,7 +766,7 @@ final class ControlPanel extends JPanel implements ActionListener { /** * Indicates what action should be execute when a node is clicked - * + * * @return the click-on action */ NodeClickAction getActionWhenNodeClicked() { @@ -1510,16 +1510,14 @@ final class ControlPanel extends JPanel implements ActionListener { _mainpanel.getCurrentTreePanel().validate(); _mainpanel.validate(); _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getSizeOfViewport().width, - _mainpanel.getSizeOfViewport().height, - true ); + _mainpanel.getSizeOfViewport().height ); _mainpanel.getCurrentTreePanel().resetPreferredSize(); _mainpanel.adjustJScrollPane(); _mainpanel.getCurrentTreePanel().repaint(); _mainpanel.getCurrentTreePanel().validate(); _mainpanel.validate(); _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getSizeOfViewport().width, - _mainpanel.getSizeOfViewport().height, - true ); + _mainpanel.getSizeOfViewport().height ); _mainpanel.getCurrentTreePanel().resetPreferredSize(); _mainpanel.adjustJScrollPane(); _mainpanel.getCurrentTreePanel().repaint(); @@ -1531,8 +1529,7 @@ final class ControlPanel extends JPanel implements ActionListener { if ( tree_panel != null ) { tree_panel.validate(); tree_panel.calcParametersForPainting( _mainpanel.getSizeOfViewport().width, - _mainpanel.getSizeOfViewport().height, - true ); + _mainpanel.getSizeOfViewport().height ); tree_panel.resetPreferredSize(); tree_panel.repaint(); } diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index 6d2ebfc..c0881be 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -77,7 +77,7 @@ import org.forester.util.ForesterUtil; public abstract class MainFrame extends JFrame implements ActionListener { static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]"; - static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME + static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE; private static final long serialVersionUID = 3655000897845508358L; final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(), @@ -90,8 +90,8 @@ public abstract class MainFrame extends JFrame implements ActionListener { static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular"; static final String CONVEX_TYPE_CBMI_LABEL = "Convex"; static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded"; - static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO - static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO + static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO + static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO static final String OPTIONS_HEADER = "Options"; static final String SEARCH_SUBHEADER = "Search:"; static final String DISPLAY_SUBHEADER = "Display:"; @@ -186,7 +186,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { JRadioButtonMenuItem _uniform_cladograms_rbmi; JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi; JCheckBoxMenuItem _color_by_taxonomic_group_cbmi; - JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me + JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me JCheckBoxMenuItem _show_overview_cbmi; JCheckBoxMenuItem _show_domain_labels; JCheckBoxMenuItem _show_annotation_ref_source; @@ -253,7 +253,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { // Handy pointers to child components: MainPanel _mainpanel; Container _contentpane; - final LinkedList _textframes = new LinkedList(); ; + final LinkedList _textframes = new LinkedList(); ; Configuration _configuration; Options _options; private Phylogeny _species_tree; @@ -675,7 +675,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { * has been selected by the user by clicking the "Return ..." * menu item. This method is expected to be called from Javascript or * something like it. - * + * * @return current external node data as String */ public String getCurrentExternalNodesDataBuffer() { diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java index c2196ac..74588a2 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java @@ -114,8 +114,7 @@ public final class MainFrameApplet extends MainFrame { _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel() .getWidth(), _mainpanel.getCurrentTreePanel() - .getHeight(), - getOptions().isAllowFontSizeChange() ); + .getHeight() ); } } } ); diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index e6d6092..57c2cb4 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -389,8 +389,7 @@ public final class MainFrameApplication extends MainFrame { _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel() .getWidth(), _mainpanel.getCurrentTreePanel() - .getHeight(), - getOptions().isAllowFontSizeChange() ); + .getHeight() ); } } } ); @@ -1293,8 +1292,7 @@ public final class MainFrameApplication extends MainFrame { void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) { _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(), - _mainpanel.getCurrentTreePanel().getHeight(), - true ); + _mainpanel.getCurrentTreePanel().getHeight() ); String file_written_to = ""; boolean error = false; try { @@ -2145,8 +2143,7 @@ public final class MainFrameApplication extends MainFrame { } if ( !getOptions().isPrintUsingActualSize() ) { getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX() - 80, - getOptions().getPrintSizeY() - 140, - true ); + getOptions().getPrintSizeY() - 140 ); getCurrentTreePanel().resetPreferredSize(); getCurrentTreePanel().repaint(); } @@ -2174,9 +2171,8 @@ public final class MainFrameApplication extends MainFrame { private void printPhylogenyToPdf( final String file_name ) { if ( !getOptions().isPrintUsingActualSize() ) { - getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX(), - getOptions().getPrintSizeY(), - true ); + getCurrentTreePanel() + .calcParametersForPainting( getOptions().getPrintSizeX(), getOptions().getPrintSizeY() ); getCurrentTreePanel().resetPreferredSize(); getCurrentTreePanel().repaint(); } diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java index 8167a92..ec72006 100644 --- a/forester/java/src/org/forester/archaeopteryx/Options.java +++ b/forester/java/src/org/forester/archaeopteryx/Options.java @@ -101,10 +101,6 @@ final public class Options { return _allow_errors_in_distance_to_parent; } - public boolean isAllowFontSizeChange() { - return true; - } - public final boolean isShowAnnotationRefSource() { return _show_annotation_ref_source; } diff --git a/forester/java/src/org/forester/archaeopteryx/Printer.java b/forester/java/src/org/forester/archaeopteryx/Printer.java index ff00be5..43fed3c 100644 --- a/forester/java/src/org/forester/archaeopteryx/Printer.java +++ b/forester/java/src/org/forester/archaeopteryx/Printer.java @@ -38,9 +38,9 @@ final class Printer { /** * Returns null if printing has been aborted by the user, - * a String otherwise -- if a printer name was obtained this String is + * a String otherwise -- if a printer name was obtained this String is * the printer name, an empty String otherwise. - * + * * @param tree_panel * @param job_name * @return diff --git a/forester/java/src/org/forester/archaeopteryx/TextFrame.java b/forester/java/src/org/forester/archaeopteryx/TextFrame.java index 11954fa..6d52a26 100644 --- a/forester/java/src/org/forester/archaeopteryx/TextFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/TextFrame.java @@ -52,7 +52,7 @@ import javax.swing.JTextArea; final class TextFrame extends JFrame implements ActionListener, ClipboardOwner { /** - * + * */ private static final long serialVersionUID = -5012834229705518363L; private static Color ta_text_color = new Color( 0, 0, 0 ), diff --git a/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java b/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java index 2906ae7..4dcf9f1 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java +++ b/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java @@ -64,7 +64,7 @@ public final class TreeColorSet { new Color( 0, 100, 100 ), // background_color_gradient_bottom new Color( 230, 230, 230 ), // sequence __ Default (same as Black) new Color( 180, 180, 180 ), // taxonomy - new Color( 180, 180, 180 ), // support + new Color( 180, 180, 180 ), // support new Color( 140, 140, 140 ), // branch_length_color new Color( 255, 255, 255 ), // branch_color new Color( 255, 255, 255 ), // box_color @@ -75,16 +75,16 @@ public final class TreeColorSet { new Color( 255, 0, 0 ), // duplication_box_color new Color( 0, 255, 0 ), // speciation_box_color new Color( 255, 255, 0 ), // duplication_speciation_color - new Color( 230, 230, 230 ), // domain_label - new Color( 100, 100, 100 ), // domains_base - new Color( 65, 105, 255 ), // binary_domain_combinations_color + new Color( 230, 230, 230 ), // domain_label + new Color( 100, 100, 100 ), // domains_base + new Color( 65, 105, 255 ), // binary_domain_combinations_color new Color( 173, 255, 47 ) // annotation , new Color( 130, 130, 130 ) // overview }, { new Color( 0, 0, 0 ), // background_color - new Color( 0, 255, 255 ), // background_color_gradient_bottom + new Color( 0, 255, 255 ), // background_color_gradient_bottom new Color( 230, 230, 230 ), // sequence __ Black new Color( 180, 180, 180 ), // taxonomy - new Color( 180, 180, 180 ), // support + new Color( 180, 180, 180 ), // support new Color( 140, 140, 140 ), // branch_length_color new Color( 255, 255, 255 ), // branch_color new Color( 255, 255, 255 ), // box_color @@ -95,8 +95,8 @@ public final class TreeColorSet { new Color( 255, 0, 0 ), // duplication_box_color new Color( 0, 255, 0 ), // speciation_box_color new Color( 255, 255, 0 ), // duplication_speciation_color - new Color( 230, 230, 230 ), // domain_label - new Color( 100, 100, 100 ), // domains_base + new Color( 230, 230, 230 ), // domain_label + new Color( 100, 100, 100 ), // domains_base new Color( 65, 105, 255 ), // binary_domain_combinations_color new Color( 173, 255, 47 ) // annotation , new Color( 130, 130, 130 ) // ov @@ -104,7 +104,7 @@ public final class TreeColorSet { new Color( 0, 255, 255 ), // background_color_gradient_bottom new Color( 0, 0, 0 ), // sequence __ Black & White new Color( 0, 0, 0 ), // taxonomy - new Color( 0, 0, 0 ), // support + new Color( 0, 0, 0 ), // support new Color( 0, 0, 0 ), // branch_length_color new Color( 0, 0, 0 ), // branch_color new Color( 0, 0, 0 ), // box_color @@ -115,8 +115,8 @@ public final class TreeColorSet { new Color( 255, 0, 0 ), // duplication_box_color new Color( 0, 255, 0 ), // speciation_box_color new Color( 255, 255, 0 ), // duplication_speciation_color - new Color( 0, 0, 0 ), // domain_label - new Color( 100, 100, 100 ), // domains_base + new Color( 0, 0, 0 ), // domain_label + new Color( 100, 100, 100 ), // domains_base new Color( 0, 0, 0 ), // binary_domain_combinations_color new Color( 0, 0, 0 ) // annotation , new Color( 220, 220, 220 ) // ov @@ -124,7 +124,7 @@ public final class TreeColorSet { new Color( 0, 255, 255 ), // background_color_gradient_bottom new Color( 220, 220, 220 ), // sequence __ Silver new Color( 180, 180, 180 ), // taxonomy - new Color( 140, 140, 140 ), // support + new Color( 140, 140, 140 ), // support new Color( 140, 140, 140 ), // branch_length_color new Color( 240, 240, 240 ), // branch_color new Color( 140, 140, 140 ), // box_color @@ -135,8 +135,8 @@ public final class TreeColorSet { new Color( 255, 0, 0 ), // duplication_box_color new Color( 0, 255, 0 ), // speciation_box_color new Color( 255, 255, 0 ), // duplication_speciation_color - new Color( 230, 230, 230 ), // domain_label - new Color( 100, 100, 100 ), // domains_base + new Color( 230, 230, 230 ), // domain_label + new Color( 100, 100, 100 ), // domains_base new Color( 180, 180, 180 ), // binary_domain_combinations_color new Color( 140, 140, 140 ) // annotation , new Color( 40, 40, 40 ) // ov @@ -144,7 +144,7 @@ public final class TreeColorSet { new Color( 0, 255, 255 ), // background_color_gradient_bottom new Color( 0, 255, 0 ), // sequence __ the Matrix new Color( 30, 200, 30 ), // taxonomy - new Color( 0, 155, 0 ), // support + new Color( 0, 155, 0 ), // support new Color( 0, 100, 0 ), // branch_length_color new Color( 0, 155, 0 ), // branch_color new Color( 0, 255, 0 ), // box_color @@ -155,8 +155,8 @@ public final class TreeColorSet { new Color( 255, 0, 0 ), // duplication_box_color new Color( 0, 255, 0 ), // speciation_box_color new Color( 255, 255, 0 ), // duplication_speciation_color - new Color( 230, 230, 230 ), // domain_label - new Color( 100, 100, 100 ), // domains_base + new Color( 230, 230, 230 ), // domain_label + new Color( 100, 100, 100 ), // domains_base new Color( 0, 235, 0 ), // binary_domain_combinations_color new Color( 0, 235, 0 ) // annotation , new Color( 40, 40, 40 ) // ov @@ -164,7 +164,7 @@ public final class TreeColorSet { new Color( 0, 255, 255 ), // background_color_gradient_bottom new Color( 0, 0, 0 ), //sequence __ White & Blue new Color( 40, 40, 40 ), // taxonomy - new Color( 0, 125, 0 ), // support + new Color( 0, 125, 0 ), // support new Color( 70, 70, 0 ), // branch_length_color new Color( 0, 20, 200 ), // branch_color new Color( 0, 20, 200 ), // box_color @@ -175,8 +175,8 @@ public final class TreeColorSet { new Color( 255, 0, 0 ), // duplication_box_color new Color( 0, 255, 0 ), // speciation_box_color new Color( 255, 255, 0 ), // duplication_speciation_color - new Color( 0, 0, 0 ), // domain_label - new Color( 50, 50, 50 ), // domains_base + new Color( 0, 0, 0 ), // domain_label + new Color( 50, 50, 50 ), // domains_base new Color( 65, 105, 225 ), // binary_domain_combinations_color new Color( 173, 255, 47 ) // annotation , new Color( 220, 220, 220 ) // ov @@ -184,7 +184,7 @@ public final class TreeColorSet { new Color( 0, 255, 255 ), // background_color_gradient_bottom new Color( 255, 255, 255 ), // sequence __ Cyan new Color( 200, 200, 200 ), // taxonomy - new Color( 255, 255, 255 ), // support + new Color( 255, 255, 255 ), // support new Color( 200, 200, 200 ), // branch_length_color new Color( 0, 255, 255 ), // branch_color new Color( 0, 255, 255 ), // box_color @@ -195,8 +195,8 @@ public final class TreeColorSet { new Color( 255, 0, 0 ), // duplication_box_color new Color( 0, 255, 0 ), // speciation_box_color new Color( 255, 255, 0 ), // duplication_speciation_color - new Color( 230, 230, 230 ), // domain_label - new Color( 100, 100, 100 ), // domains_base + new Color( 230, 230, 230 ), // domain_label + new Color( 100, 100, 100 ), // domains_base new Color( 65, 105, 225 ), // binary_domain_combinations_color new Color( 173, 255, 47 ) // annotation , new Color( 0, 120, 120 ) // ov @@ -204,7 +204,7 @@ public final class TreeColorSet { new Color( 0, 255, 255 ), // background_color_gradient_bottom new Color( 255, 200, 0 ), // sequence __ Clockwork new Color( 255, 200, 0 ), // taxonomy - new Color( 255, 200, 0 ), // support + new Color( 255, 200, 0 ), // support new Color( 255, 200, 0 ), // branch_length_color new Color( 255, 200, 0 ), // branch_color new Color( 255, 200, 0 ), // box_color @@ -215,8 +215,8 @@ public final class TreeColorSet { new Color( 255, 0, 0 ), // duplication_box_color new Color( 0, 255, 0 ), // speciation_box_color new Color( 255, 255, 0 ), // duplication_speciation_color - new Color( 255, 200, 0 ), // domain_label - new Color( 255, 200, 0 ), // domains_base + new Color( 255, 200, 0 ), // domain_label + new Color( 255, 200, 0 ), // domains_base new Color( 150, 150, 150 ), // binary_domain_combinations_color new Color( 150, 150, 150 ) // annotation , new Color( 150, 150, 150 ) // ov @@ -224,7 +224,7 @@ public final class TreeColorSet { new Color( 0, 255, 255 ), // background_color_gradient_bottom new Color( 255, 255, 255 ), // sequence __ Blue new Color( 255, 255, 255 ), // taxonomy - new Color( 255, 0, 0 ), // support + new Color( 255, 0, 0 ), // support new Color( 255, 0, 0 ), // branch_length_color new Color( 255, 0, 0 ), // branch_color new Color( 255, 0, 0 ), // box_color @@ -235,8 +235,8 @@ public final class TreeColorSet { new Color( 255, 0, 0 ), // duplication_box_color new Color( 0, 255, 0 ), // speciation_box_color new Color( 255, 255, 0 ), // duplication_speciation_color - new Color( 255, 255, 255 ), // domain_label - new Color( 100, 100, 100 ), // domains_base + new Color( 255, 255, 255 ), // domain_label + new Color( 100, 100, 100 ), // domains_base new Color( 255, 255, 255 ), // binary_domain_combinations_color new Color( 255, 255, 255 ) // annotation , new Color( 77, 77, 255 ) // ov @@ -244,7 +244,7 @@ public final class TreeColorSet { new Color( 0, 255, 255 ), // background_color_gradient_bottom new Color( 255, 255, 255 ), // sequence __ blue & white new Color( 255, 255, 255 ), // taxonomy - new Color( 255, 255, 255 ), // support + new Color( 255, 255, 255 ), // support new Color( 0, 191, 255 ), // branch_length_color new Color( 0, 191, 255 ), // branch_color new Color( 0, 191, 255 ), // box_color @@ -255,8 +255,8 @@ public final class TreeColorSet { new Color( 255, 0, 0 ), // duplication_box_color new Color( 0, 255, 0 ), // speciation_box_color new Color( 255, 255, 0 ), // duplication_speciation_color - new Color( 255, 255, 255 ), // domain_label - new Color( 150, 150, 150 ), // domains_base + new Color( 255, 255, 255 ), // domain_label + new Color( 150, 150, 150 ), // domains_base new Color( 255, 255, 255 ), // binary_domain_combinations_color new Color( 255, 255, 255 ) // annotation , new Color( 170, 187, 204 ) // ov @@ -264,7 +264,7 @@ public final class TreeColorSet { new Color( 255, 255, 0 ), // background_color_gradient_bottom new Color( 127, 255, 0 ), // sequence __ Neon new Color( 255, 110, 199 ), // taxonomy - new Color( 234, 173, 234 ), // support + new Color( 234, 173, 234 ), // support new Color( 77, 77, 255 ), // branch_length_color new Color( 234, 173, 234 ), // branch_color new Color( 77, 77, 255 ), // box_color @@ -275,8 +275,8 @@ public final class TreeColorSet { new Color( 255, 0, 0 ), // duplication_box_color new Color( 0, 255, 0 ), // speciation_box_color new Color( 255, 255, 0 ), // duplication_speciation_color - new Color( 127, 255, 0 ), // domain_label - new Color( 234, 173, 234 ), // domains_base + new Color( 127, 255, 0 ), // domain_label + new Color( 234, 173, 234 ), // domains_base new Color( 27, 255, 0 ), // binary_domain_combinations_color new Color( 27, 255, 0 ) // annotation , new Color( 77, 77, 255 ) // ov diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index 9e88db2..107a557 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -305,7 +305,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee calculateScaleDistance(); FORMATTER_CONFIDENCE.setMaximumFractionDigits( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() ); FORMATTER_BRANCH_LENGTH.setMaximumFractionDigits( configuration - .getNumberOfDigitsAfterCommaForBranchLengthValues() ); + .getNumberOfDigitsAfterCommaForBranchLengthValues() ); } @Override @@ -337,8 +337,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } /** - * Get a pointer to the phylogeny - * + * Get a pointer to the phylogeny + * * @return a pointer to the phylogeny */ public final Phylogeny getPhylogeny() { @@ -471,7 +471,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee /** * Set a phylogeny tree. - * + * * @param t * an instance of a Phylogeny */ @@ -498,35 +498,29 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee /** * Set parameters for printing the displayed tree - * + * */ - final void calcParametersForPainting( final int x, final int y, final boolean recalc_longest_ext_node_info ) { + final void calcParametersForPainting( final int x, final int y ) { // updateStyle(); not needed? if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) { initNodeData(); - if ( recalc_longest_ext_node_info ) { - calculateLongestExtNodeInfo(); - if ( getOptions().isAllowFontSizeChange() ) { - if ( ( getLongestExtNodeInfo() > ( x * 0.6 ) ) - && ( getTreeFontSet().getLargeFont().getSize() > ( 2 + TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) ) { - while ( ( getLongestExtNodeInfo() > ( x * 0.7 ) ) - && ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) { - getMainPanel().getTreeFontSet().decreaseFontSize( getConfiguration().getMinBaseFontSize(), - true ); - calculateLongestExtNodeInfo(); - } - } - else { - while ( ( getLongestExtNodeInfo() < ( x * 0.6 ) ) - && ( getTreeFontSet().getLargeFont().getSize() <= ( getTreeFontSet() - .getLargeFontMemory().getSize() - TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) ) { - getMainPanel().getTreeFontSet().increaseFontSize(); - calculateLongestExtNodeInfo(); - } - } + calculateLongestExtNodeInfo(); + if ( ( getLongestExtNodeInfo() > ( x * 0.6 ) ) + && ( getTreeFontSet().getLargeFont().getSize() > ( 2 + TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) ) { + while ( ( getLongestExtNodeInfo() > ( x * 0.7 ) ) && ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) { + getMainPanel().getTreeFontSet().decreaseFontSize( getConfiguration().getMinBaseFontSize(), true ); + calculateLongestExtNodeInfo(); + } + } + else { + while ( ( getLongestExtNodeInfo() < ( x * 0.6 ) ) + && ( getTreeFontSet().getLargeFont().getSize() <= ( getTreeFontSet().getLargeFontMemory() + .getSize() - TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) ) { + getMainPanel().getTreeFontSet().increaseFontSize(); + calculateLongestExtNodeInfo(); } - _length_of_longest_text = calcLengthOfLongestText(); } + _length_of_longest_text = calcLengthOfLongestText(); int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes(); final int max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny ); if ( ext_nodes == 1 ) { @@ -573,24 +567,22 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _circ_max_depth = max_depth; setUpUrtFactor(); // - if ( getOptions().isAllowFontSizeChange() ) { - if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) - && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { - // int dynamic_hiding_factor = calcDynamicHidingFactor(); - // if ( dynamic_hiding_factor > 1 ) { - // while ( dynamic_hiding_factor > 1 - // && getTreeFontSet()._fm_large.getHeight() > TreeFontSet.SMALL_FONTS_BASE ) { - // getTreeFontSet().decreaseFontSize( 1, true ); - // dynamic_hiding_factor = calcDynamicHidingFactor(); - // } - // } - // else if ( getTreeFontSet().isDecreasedSizeBySystem() ) { - // while ( dynamic_hiding_factor < 1 && getTreeFontSet()._fm_large.getHeight() < 12 ) { - // getTreeFontSet().increaseFontSize(); - // dynamic_hiding_factor = calcDynamicHidingFactor(); - // } - // } - } + if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) + && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { + // int dynamic_hiding_factor = calcDynamicHidingFactor(); + // if ( dynamic_hiding_factor > 1 ) { + // while ( dynamic_hiding_factor > 1 + // && getTreeFontSet()._fm_large.getHeight() > TreeFontSet.SMALL_FONTS_BASE ) { + // getTreeFontSet().decreaseFontSize( 1, true ); + // dynamic_hiding_factor = calcDynamicHidingFactor(); + // } + // } + // else if ( getTreeFontSet().isDecreasedSizeBySystem() ) { + // while ( dynamic_hiding_factor < 1 && getTreeFontSet()._fm_large.getHeight() < 12 ) { + // getTreeFontSet().increaseFontSize(); + // dynamic_hiding_factor = calcDynamicHidingFactor(); + // } + // } } // } @@ -601,7 +593,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return; } int max_length = ForesterUtil.roundToInt( ( getSize().getWidth() - MOVE ) - * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO ); + * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO ); if ( max_length < 40 ) { max_length = 40; } @@ -637,7 +629,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) { sum += getFontMetricsForLargeDefaultFont().stringWidth( node.getNodeData().getBinaryCharacters() - .getGainedCharactersAsStringBuffer().toString() ); + .getGainedCharactersAsStringBuffer().toString() ); } if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null ) && ( node.getNodeData().getVector().size() > 0 ) ) { @@ -650,7 +642,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) { - // FIXME + // FIXME // TODO this might need some clean up final DomainArchitecture d = node.getNodeData().getSequence().getDomainArchitecture(); sum += ( ( _domain_structure_width / ( ( RenderableDomainArchitecture ) d ).getOriginalSize() @@ -662,7 +654,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() ) && ( node.getNodeData().getSequence().isMolecularSequenceAligned() ) && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) { - // FIXME + // FIXME sum += RenderableMsaSequence.DEFAULT_WIDTH + 30; } if ( sum >= max_length ) { @@ -793,7 +785,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } catch ( final NumberFormatException e ) { JOptionPane.showMessageDialog( this, "Could not parse \"" + value_str - + "\" into a decimal value", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE ); + + "\" into a decimal value", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE ); return; } int i = -1; @@ -803,7 +795,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee catch ( final NumberFormatException e ) { JOptionPane.showMessageDialog( this, "Could not parse \"" + index_str - + "\" into index for vector data", + + "\" into index for vector data", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE ); return; @@ -838,7 +830,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee /** * Collapse the tree from the given node - * + * * @param node * a PhylogenyNode */ @@ -955,7 +947,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee /** * Find the node, if any, at the given location - * + * * @param x * @param y * @return pointer to the node at x,y, null if not found @@ -1100,11 +1092,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( !( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) { if ( SPECIAL_DOMAIN_COLORING ) { rds = new RenderableDomainArchitecture( node.getNodeData().getSequence() - .getDomainArchitecture(), node.getName() ); + .getDomainArchitecture(), node.getName() ); } else { rds = new RenderableDomainArchitecture( node.getNodeData().getSequence() - .getDomainArchitecture() ); + .getDomainArchitecture() ); } node.getNodeData().getSequence().setDomainArchitecture( rds ); } @@ -1137,14 +1129,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return ( ( e.getX() > ( getVisibleRect().x + getOvXPosition() + 1 ) ) && ( e.getX() < ( ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() ) - 1 ) ) && ( e.getY() > ( getVisibleRect().y + getOvYPosition() + 1 ) ) && ( e.getY() < ( ( getVisibleRect().y - + getOvYPosition() + getOvMaxHeight() ) - 1 ) ) ); + + getOvYPosition() + getOvMaxHeight() ) - 1 ) ) ); } final boolean inOvRectangle( final MouseEvent e ) { return ( ( e.getX() >= ( getOvRectangle().getX() - 1 ) ) && ( e.getX() <= ( getOvRectangle().getX() + getOvRectangle().getWidth() + 1 ) ) && ( e.getY() >= ( getOvRectangle().getY() - 1 ) ) && ( e.getY() <= ( getOvRectangle().getY() - + getOvRectangle().getHeight() + 1 ) ) ); + + getOvRectangle().getHeight() + 1 ) ) ); } final boolean isApplet() { @@ -1249,7 +1241,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee y = max_y; } getMainPanel().getCurrentScrollPane().getViewport() - .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) ); + .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) ); setInOvRect( true ); repaint(); } @@ -1497,7 +1489,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( isInFoundNodes( c ) || isInCurrentExternalNodes( c ) ) { g.setColor( getColorForFoundNode( c ) ); drawRectFilled( c.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, c.getYSecondary() - - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g ); + - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g ); } } @@ -1587,7 +1579,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else { if ( !to_graphics_file ) { g.setPaint( new GradientPaint( r.x, r.y, getTreeColorSet().getBackgroundColor(), r.x, r.y - + r.height, getTreeColorSet().getBackgroundColorGradientBottom() ) ); + + r.height, getTreeColorSet().getBackgroundColorGradientBottom() ) ); g.fill( r ); } else { @@ -1621,7 +1613,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } // Position starting Y of tree _phylogeny.getRoot().setYcoord( ( getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes() ) - + ( TreePanel.MOVE / 2.0f ) ); + + ( TreePanel.MOVE / 2.0f ) ); final int dynamic_hiding_factor = calcDynamicHidingFactor(); if ( getControlPanel().isDynamicallyHideData() ) { if ( dynamic_hiding_factor > 1 ) { @@ -1757,7 +1749,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee y_pos + radius_ov, ( int ) ( radius_ov - ( getLongestExtNodeInfo() / ( getVisibleRect().width / getOvRectangle() .getWidth() ) ) ), - g ); + g ); g.setTransform( _at ); paintOvRectangle( g ); } @@ -1839,20 +1831,20 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee x = TreePanel.MOVE + getLongestExtNodeInfo() + ForesterUtil - .roundToInt( ( getXcorrectionFactor() * getPhylogeny().getHeight() ) + getXdistance() ); + .roundToInt( ( getXcorrectionFactor() * getPhylogeny().getHeight() ) + getXdistance() ); } else { if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) { x = TreePanel.MOVE + getLongestExtNodeInfo() + ForesterUtil.roundToInt( getXdistance() - * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) ); + * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) ); } else { x = TreePanel.MOVE + getLongestExtNodeInfo() + ForesterUtil.roundToInt( getXdistance() - * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) ); + * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) ); } } setPreferredSize( new Dimension( x, y ) ); @@ -2375,7 +2367,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee /** * Calculate the length of the distance between the given node and its * parent. - * + * * @param node * @param ext_node_x * @factor @@ -3113,7 +3105,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return ( ( x >= ( getOvVirtualRectangle().x - 1 ) ) && ( x <= ( getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 ) ) && ( y >= ( getOvVirtualRectangle().y - 1 ) ) && ( y <= ( getOvVirtualRectangle().y - + getOvVirtualRectangle().height + 1 ) ) ); + + getOvVirtualRectangle().height + 1 ) ) ); } final private boolean inOvVirtualRectangle( final MouseEvent e ) { @@ -3140,8 +3132,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee && ( ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node - .getNodeData().getTaxonomy().getIdentifier() != null ) && !ForesterUtil.isEmpty( node - .getNodeData().getTaxonomy().getIdentifier().getValue() ) ) ) ) { + .getNodeData().getTaxonomy().getIdentifier() != null ) && !ForesterUtil.isEmpty( node + .getNodeData().getTaxonomy().getIdentifier().getValue() ) ) ) ) { return true; } else { @@ -3176,14 +3168,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - y_dist ) ) || ( node.getYcoord() > ( getVisibleRect().getMaxY() + y_dist ) ) || ( ( node.getParent() != null ) && ( node - .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) ); + .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) ); } final private boolean isNodeDataInvisibleUnrootedCirc( final PhylogenyNode node ) { return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - 20 ) ) || ( node.getYcoord() > ( getVisibleRect().getMaxY() + 20 ) ) || ( node.getXcoord() < ( getVisibleRect().getMinX() - 20 ) ) || ( node.getXcoord() > ( getVisibleRect() - .getMaxX() + 20 ) ) ); + .getMaxX() + 20 ) ) ); } final private boolean isNonLinedUpCladogram() { @@ -3623,7 +3615,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), isApplet() ? obtainApplet() : null, - "_aptx_seq" ); + "_aptx_seq" ); } catch ( final IOException e ) { AptxUtil.showErrorMessage( this, e.toString() ); @@ -3651,7 +3643,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), isApplet() ? obtainApplet() : null, - "_aptx_seq" ); + "_aptx_seq" ); } catch ( final IOException e ) { AptxUtil.showErrorMessage( this, e.toString() ); @@ -3734,7 +3726,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), isApplet() ? obtainApplet() : null, - "_aptx_tax" ); + "_aptx_tax" ); } catch ( final IOException e ) { AptxUtil.showErrorMessage( this, e.toString() ); @@ -3764,20 +3756,20 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( !node.isRoot() ) { if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) { TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent() - .getXcoord() + EURO_D, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g ); + .getXcoord() + EURO_D, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g ); } else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) { TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent() - .getXcoord() + ROUNDED_D, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g ); + .getXcoord() + ROUNDED_D, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g ); } else { TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent() - .getXcoord() + 3, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g ); + .getXcoord() + 3, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g ); } } else { TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), 3, node.getYcoord() - - getTreeFontSet().getSmallMaxDescent(), g ); + - getTreeFontSet().getSmallMaxDescent(), g ); } } @@ -3799,7 +3791,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final float dx = x2 - x1; final float dy = y2 - y1; _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1 - + ( dy * 0.8f ), x2, y2 ); + + ( dy * 0.8f ), x2, y2 ); ( g ).draw( _cubic_curve ); } else { @@ -3816,7 +3808,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee /** * Paint a branch which consists of a vertical and a horizontal bar - * @param is_ind_found_nodes + * @param is_ind_found_nodes */ final private void paintBranchRectangular( final Graphics2D g, final float x1, @@ -3838,7 +3830,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final float dx = x2 - x1; final float dy = y2 - y1; _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1 - + ( dy * 0.8f ), x2, y2 ); + + ( dy * 0.8f ), x2, y2 ); g.draw( _cubic_curve ); } else { @@ -4101,13 +4093,13 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee not_first = true; } sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions() - .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); + .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); if ( getOptions().isShowConfidenceStddev() ) { if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) { sb.append( "(" ); sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence - .getStandardDeviation(), getOptions() - .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); + .getStandardDeviation(), getOptions() + .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); sb.append( ")" ); } } @@ -4133,10 +4125,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final String conf_str = sb.toString(); TreePanel.drawString( conf_str, parent_x - + ( ( x - parent_x - getTreeFontSet().getFontMetricsSmall() - .stringWidth( conf_str ) ) / 2 ), - ( node.getYcoord() + getTreeFontSet().getSmallMaxAscent() ) - 1, - g ); + + ( ( x - parent_x - getTreeFontSet().getFontMetricsSmall() + .stringWidth( conf_str ) ) / 2 ), + ( node.getYcoord() + getTreeFontSet().getSmallMaxAscent() ) - 1, + g ); } } @@ -4153,24 +4145,24 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee g.setColor( Color.BLUE ); } TreePanel - .drawString( gained, - parent_x - + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( gained ) ) / 2 ), - ( node.getYcoord() - getFontMetricsForLargeDefaultFont().getMaxDescent() ), - g ); + .drawString( gained, + parent_x + + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( gained ) ) / 2 ), + ( node.getYcoord() - getFontMetricsForLargeDefaultFont().getMaxDescent() ), + g ); g.setColor( getTreeColorSet().getLostCharactersColor() ); TreePanel - .drawString( lost, - parent_x - + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( lost ) ) / 2 ), - ( node.getYcoord() + getFontMetricsForLargeDefaultFont().getMaxAscent() ), - g ); + .drawString( lost, + parent_x + + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( lost ) ) / 2 ), + ( node.getYcoord() + getFontMetricsForLargeDefaultFont().getMaxAscent() ), + g ); } } /** * Draw a box at the indicated node. - * + * * @param x * @param y * @param node @@ -4197,16 +4189,16 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee || ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() ) || ( getOptions().isShowDefaultNodeShapesForMarkedNodes() && ( node.getNodeData().getNodeVisualData() != null ) && ( !node.getNodeData() - .getNodeVisualData().isEmpty() ) ) - || ( getControlPanel().isUseVisualStyles() && ( ( node.getNodeData().getNodeVisualData() != null ) && ( ( node - .getNodeData().getNodeVisualData().getNodeColor() != null ) - || ( node.getNodeData().getNodeVisualData().getSize() != NodeVisualData.DEFAULT_SIZE ) - || ( node.getNodeData().getNodeVisualData().getFillType() != NodeFill.DEFAULT ) || ( node - .getNodeData().getNodeVisualData().getShape() != NodeShape.DEFAULT ) ) ) ) - || ( getControlPanel().isEvents() && node.isHasAssignedEvent() && ( node.getNodeData().getEvent() - .isDuplication() - || node.getNodeData().getEvent().isSpeciation() || node.getNodeData().getEvent() - .isSpeciationOrDuplication() ) ) ) { + .getNodeVisualData().isEmpty() ) ) + || ( getControlPanel().isUseVisualStyles() && ( ( node.getNodeData().getNodeVisualData() != null ) && ( ( node + .getNodeData().getNodeVisualData().getNodeColor() != null ) + || ( node.getNodeData().getNodeVisualData().getSize() != NodeVisualData.DEFAULT_SIZE ) + || ( node.getNodeData().getNodeVisualData().getFillType() != NodeFill.DEFAULT ) || ( node + .getNodeData().getNodeVisualData().getShape() != NodeShape.DEFAULT ) ) ) ) + || ( getControlPanel().isEvents() && node.isHasAssignedEvent() && ( node.getNodeData().getEvent() + .isDuplication() + || node.getNodeData().getEvent().isSpeciation() || node.getNodeData().getEvent() + .isSpeciationOrDuplication() ) ) ) { NodeVisualData vis = null; if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null ) && ( !node.getNodeData().getNodeVisualData().isEmpty() ) ) { @@ -4366,7 +4358,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( getControlPanel().isWriteBranchLengthValues() && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) ) - && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) { + && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) { paintBranchLength( g, node, to_pdf, to_graphics_file ); } if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) { @@ -4434,21 +4426,21 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence ) || seqRelation .getRef1().isEqual( _query_sequence ) ) && seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox() - .getSelectedItem() ); + .getSelectedItem() ); if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query final double linePosX = node.getXcoord() + 2 + half_box_size; final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation .getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue() - + ")"; + + ")"; if ( sConfidence != null ) { float confidenceX = pos_x; if ( sb_str.length() > 0 ) { confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth() + CONFIDENCE_LEFT_MARGIN; } - if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code + if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc ) - .getBounds().getWidth(); + .getBounds().getWidth(); TreePanel.drawString( sConfidence, confidenceX, pos_y, g ); x += CONFIDENCE_LEFT_MARGIN + confidenceWidth; } @@ -4462,7 +4454,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee nodeTextBoundsWidth += 2; } g.drawLine( ( int ) linePosX + 1, 3 + ( int ) pos_y, ( int ) linePosX + x - + nodeTextBoundsWidth, 3 + ( int ) pos_y ); + + nodeTextBoundsWidth, 3 + ( int ) pos_y ); break; } } @@ -4493,7 +4485,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } final String ann_str = TreePanelUtil.createAnnotationString( ann, getOptions().isShowAnnotationRefSource() ); TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord() - + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ), g ); + + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ), g ); _sb.setLength( 0 ); _sb.append( ann_str ); if ( _sb.length() > 0 ) { @@ -4518,22 +4510,22 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } if ( getControlPanel().isShowBinaryCharacters() ) { TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer() - .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord() - + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ), g ); + .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord() + + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ), g ); paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters() - .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters() - .getLostCharactersAsStringBuffer().toString() ); + .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters() + .getLostCharactersAsStringBuffer().toString() ); } else { TreePanel - .drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(), - node.getXcoord() + x + 4 + half_box_size, - node.getYcoord() - + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ), - g ); + .drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(), + node.getXcoord() + x + 4 + half_box_size, + node.getYcoord() + + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ), + g ); paintGainedAndLostCharacters( g, node, "+" + node.getNodeData().getBinaryCharacters().getGainedCount(), "-" - + node.getNodeData().getBinaryCharacters().getLostCount() ); + + node.getNodeData().getBinaryCharacters().getLostCount() ); } } } @@ -4690,7 +4682,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) { g.setColor( getColorForFoundNode( node ) ); drawRectFilled( node.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, node.getYSecondary() - - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g ); + - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g ); } float new_x = 0; if ( !node.isExternal() && !node.isCollapse() ) { @@ -4752,7 +4744,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee && !node.isRoot() && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) ) - && node.getBranchData().isHasConfidences() ) { + && node.getBranchData().isHasConfidences() ) { paintConfidenceValues( g, node, to_pdf, to_graphics_file ); } // Draw a line to root: @@ -4822,7 +4814,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee && !is_in_found_nodes && ( ( node.isExternal() && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) ) || ( !node .isExternal() && ( ( new_x_min < 20 ) || ( ( _y_distance * node.getNumberOfExternalNodes() ) < getFontMetricsForLargeDefaultFont() - .getHeight() ) ) ) ) ) { + .getHeight() ) ) ) ) ) { return; } final int x = paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes ); @@ -4863,7 +4855,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( getOptions().isRightLineUpDomains() ) { rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + _length_of_longest_text + ( ( _longest_domain - rds.getTotalLength() ) * rds - .getRenderingFactorWidth() ) ), node.getYcoord() - ( h / 2.0f ), g, this, to_pdf ); + .getRenderingFactorWidth() ) ), node.getYcoord() - ( h / 2.0f ), g, this, to_pdf ); } else { rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + _length_of_longest_text ), @@ -4880,12 +4872,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else { if ( getOptions().isRightLineUpDomains() ) { rds.render( ( ( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text ) - 20 ) - + ( ( _longest_domain - rds.getTotalLength() ) * rds - .getRenderingFactorWidth() ), - node.getYcoord() - ( h / 2.0f ), - g, - this, - to_pdf ); + + ( ( _longest_domain - rds.getTotalLength() ) * rds + .getRenderingFactorWidth() ), + node.getYcoord() - ( h / 2.0f ), + g, + this, + to_pdf ); } else { rds.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text, @@ -4924,7 +4916,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee && ( node.getNodeData().getSequence().isMolecularSequenceAligned() ) && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) { final RenderableMsaSequence rs = RenderableMsaSequence.createInstance( node.getNodeData().getSequence() - .getMolecularSequence(), node.getNodeData().getSequence().getType(), getConfiguration() ); + .getMolecularSequence(), node.getNodeData().getSequence().getType(), getConfiguration() ); if ( rs != null ) { final int default_height = 7; float y = getYdistance(); @@ -4999,9 +4991,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final private void paintPhylogenyLite( final Graphics2D g ) { _phylogeny - .getRoot() - .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle() - .getWidth() ) ) ) ); + .getRoot() + .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle() + .getWidth() ) ) ) ); _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) ); final Stroke s = g.getStroke(); g.setStroke( STROKE_05 ); @@ -5015,8 +5007,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee /** * Paint the root branch. (Differs from others because it will always be a * single horizontal line). - * @param to_graphics_file - * + * @param to_graphics_file + * * @return new x1 value */ final private void paintRootBranch( final Graphics2D g, @@ -5101,7 +5093,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final Rectangle2D nodeTextBounds = new TextLayout( label, g.getFont(), new FontRenderContext( null, false, false ) ) - .getBounds(); + .getBounds(); g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 ); g.setColor( getTreeColorSet().getBackgroundColor() ); } @@ -5586,7 +5578,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee ann_str = ann.toString(); } sb.append( SequenceWriter.toFasta( ann_str, n.getNodeData().getSequence() - .getMolecularSequence(), 60 ) ); + .getMolecularSequence(), 60 ) ); data.add( sb.toString() ); } break; @@ -5639,7 +5631,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) { if ( sb.length() < 1 ) { TreePanelUtil.showInformationMessage( this, "No Appropriate Data (" + obtainTitleForExtDescNodeData() - + ")", "Descendants of selected node do not contain selected data" ); + + ")", "Descendants of selected node do not contain selected data" ); clearCurrentExternalNodesDataBuffer(); } else { @@ -5681,10 +5673,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee try { if ( ( node.getName().length() > 0 ) || ( node.getNodeData().isHasTaxonomy() && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData() - .getTaxonomy() ) ) - || ( node.getNodeData().isHasSequence() && !TreePanelUtil.isSequenceEmpty( node.getNodeData() - .getSequence() ) ) || ( node.getNodeData().isHasDate() ) - || ( node.getNodeData().isHasDistribution() ) || node.getBranchData().isHasConfidences() ) { + .getTaxonomy() ) ) + || ( node.getNodeData().isHasSequence() && !TreePanelUtil.isSequenceEmpty( node.getNodeData() + .getSequence() ) ) || ( node.getNodeData().isHasDate() ) + || ( node.getNodeData().isHasDistribution() ) || node.getBranchData().isHasConfidences() ) { _popup_buffer.setLength( 0 ); short lines = 0; if ( node.getName().length() > 0 ) { @@ -5848,14 +5840,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _popup_buffer.append( "] " ); } _popup_buffer - .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(), - getOptions() - .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); + .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(), + getOptions() + .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) { _popup_buffer.append( " (sd=" ); _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence - .getStandardDeviation(), getOptions() - .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); + .getStandardDeviation(), getOptions() + .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); _popup_buffer.append( ")" ); } } @@ -5876,7 +5868,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( _popup_buffer.length() > 0 ) { if ( !getConfiguration().isUseNativeUI() ) { _rollover_popup - .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) ); + .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) ); _rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() ); if ( isInFoundNodes0( node ) && !isInFoundNodes1( node ) ) { _rollover_popup.setForeground( getTreeColorSet().getFoundColor0() ); @@ -5899,7 +5891,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _rollover_popup, e.getLocationOnScreen().x + 10, e.getLocationOnScreen().y - - ( lines * 20 ) ); + - ( lines * 20 ) ); _node_desc_popup.show(); } } @@ -5985,7 +5977,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( getMainPanel().getMainFrame() == null ) { // Must be "E" applet version. ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() ) - .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() ); + .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() ); } else { getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() ); diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java b/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java index 6f6999d..5d7d2fa 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java @@ -120,7 +120,7 @@ public class TreePanelUtil { * all external nodes of node. * If at least one the external nodes has no taxonomy, * null is returned. - * + * */ public static Set obtainDistinctTaxonomies( final PhylogenyNode node ) { final List descs = node.getAllExternalDescendants(); diff --git a/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java b/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java index 5b66db8..70b7a1c 100644 --- a/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java +++ b/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java @@ -104,7 +104,7 @@ public final class RenderableDomainArchitecture extends DomainArchitecture imple } for( double i = 0; i < heigth; i += step ) { g.setColor( org.forester.util.ForesterUtil - .calcColor( i >= h2 ? heigth - i : i, 0, h2, color_one, color_two ) ); + .calcColor( i >= h2 ? heigth - i : i, 0, h2, color_one, color_two ) ); _rectangle.setFrame( x, i + y, width, step ); g.fill( _rectangle ); } @@ -126,7 +126,7 @@ public final class RenderableDomainArchitecture extends DomainArchitecture imple } for( double i = 0; i < heigth; i += step ) { g.setColor( org.forester.util.ForesterUtil - .calcColor( i >= h2 ? heigth - i : i, 0, h2, color_one, color_two ) ); + .calcColor( i >= h2 ? heigth - i : i, 0, h2, color_one, color_two ) ); _rectangle.setFrame( x, i + y, width, step ); g.fill( _rectangle ); } @@ -236,8 +236,8 @@ public final class RenderableDomainArchitecture extends DomainArchitecture imple g.setColor( Constants.DOMAIN_LABEL_COLOR_FOR_PDF ); } g.drawString( d.getName(), xa, y1 - + tree_panel.getMainPanel().getTreeFontSet().getFontMetricsSmall().getAscent() - + _rendering_height ); + + tree_panel.getMainPanel().getTreeFontSet().getFontMetricsSmall().getAscent() + + _rendering_height ); } if ( TreePanel.SPECIAL_DOMAIN_COLORING && ( _node_name.indexOf( "~" ) > 1 ) && ( d.getName().equals( SPECIAL_DOMAIN ) ) diff --git a/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderablePhylogenyData.java b/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderablePhylogenyData.java index d610fd1..860130d 100644 --- a/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderablePhylogenyData.java +++ b/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderablePhylogenyData.java @@ -43,7 +43,7 @@ public interface RenderablePhylogenyData extends PhylogenyData { * This can be used to render phylogeny data as graphics (for example, * display of the domain structure). In most Renderable implementations this * will do nothing (i.e. just return). - * + * * @param g * the Graphics to render to */ diff --git a/forester/java/src/org/forester/archaeopteryx/tools/Blast.java b/forester/java/src/org/forester/archaeopteryx/tools/Blast.java index cddfba3..cf34f4e 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/Blast.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/Blast.java @@ -82,21 +82,21 @@ public final class Blast { if ( ForesterUtil.isEmpty( query ) && ( node.getNodeData().getSequence().getAccession() != null ) && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() ) ) { final Accession id = SequenceAccessionTools.parseAccessorFromString( node.getNodeData().getSequence() - .getAccession().getValue() ); + .getAccession().getValue() ); if ( id != null ) { query = id.getValue(); } } if ( ForesterUtil.isEmpty( query ) && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) { final Accession id = SequenceAccessionTools.parseAccessorFromString( node.getNodeData().getSequence() - .getName() ); + .getName() ); if ( id != null ) { query = id.getValue(); } } if ( ForesterUtil.isEmpty( query ) && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) { final Accession id = SequenceAccessionTools.parseAccessorFromString( node.getNodeData().getSequence() - .getSymbol() ); + .getSymbol() ); if ( id != null ) { query = id.getValue(); } @@ -104,7 +104,7 @@ public final class Blast { if ( ForesterUtil.isEmpty( query ) && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getGeneName() ) ) { final Accession id = SequenceAccessionTools.parseAccessorFromString( node.getNodeData().getSequence() - .getGeneName() ); + .getGeneName() ); if ( id != null ) { query = id.getValue(); } diff --git a/forester/java/src/org/forester/archaeopteryx/tools/ImageLoader.java b/forester/java/src/org/forester/archaeopteryx/tools/ImageLoader.java index 6e6b4e0..b431697 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/ImageLoader.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/ImageLoader.java @@ -98,18 +98,18 @@ public class ImageLoader implements Runnable { catch ( final MalformedURLException e ) { AptxUtil.printWarningMessage( Constants.PRG_NAME, "could not load image from \"" + uri.getValue() - + "\": Malformed URL Exception: " - + e.getLocalizedMessage() ); + + "\": Malformed URL Exception: " + + e.getLocalizedMessage() ); } catch ( final IOException e ) { AptxUtil.printWarningMessage( Constants.PRG_NAME, "could not load image from \"" + uri.getValue() - + "\": IO Exception: " + e.getLocalizedMessage() ); + + "\": IO Exception: " + e.getLocalizedMessage() ); } catch ( final CMMException e ) { AptxUtil.printWarningMessage( Constants.PRG_NAME, "could not load image from \"" + uri.getValue() - + "\": CMMException: " + e.getLocalizedMessage() ); + + "\": CMMException: " + e.getLocalizedMessage() ); } if ( bi != null ) { image_map.put( uri_str, bi ); diff --git a/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java b/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java index d7fe243..f38940b 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/InferenceManager.java @@ -8,7 +8,7 @@ import org.forester.archaeopteryx.Configuration; public final class InferenceManager { private final static String DEFAULT_PATHS[] = { "C:\\Program Files\\", "C:\\Program Files (x86)\\", "/bin/", - "/usr/local/bin/", "/usr/bin/" }; + "/usr/local/bin/", "/usr/bin/" }; private final File _path_to_local_mafft; private final File _path_to_local_fastme; private final File _path_to_local_raxml; diff --git a/forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java b/forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java index 8850d2b..b1cd8b6 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java @@ -203,7 +203,7 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener { distance_calc_pnl_1.add( _distance_calc_kimura_rb = new JRadioButton( "Kimura correction" ) ); distance_calc_pnl_1.add( _distance_calc_poisson_rb = new JRadioButton( "Poisson" ) ); distance_calc_pnl_1 - .add( _distance_calc_fract_dissimilarity_rb = new JRadioButton( "Fractional dissimilarity" ) ); + .add( _distance_calc_fract_dissimilarity_rb = new JRadioButton( "Fractional dissimilarity" ) ); final ButtonGroup distance_calc_group_1 = new ButtonGroup(); distance_calc_group_1.add( _distance_calc_kimura_rb ); distance_calc_group_1.add( _distance_calc_poisson_rb ); @@ -333,7 +333,7 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener { private void processMsaProcessing() { getPhylogeneticInferenceOptions().setExecuteMsaProcessing( _execute_msa_processing_cb.isSelected() ); getPhylogeneticInferenceOptions() - .setMsaProcessingRemoveAllGapColumns( _msa_processing_remove_all_gap_columns_cb.isSelected() ); + .setMsaProcessingRemoveAllGapColumns( _msa_processing_remove_all_gap_columns_cb.isSelected() ); int min_length = -1; try { min_length = Integer.parseInt( _msa_processing_min_allowed_length_tf.getText().trim() ); @@ -347,7 +347,7 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener { double msa_processing_max_allowed_gap_ratio = -1.0; try { msa_processing_max_allowed_gap_ratio = Double.parseDouble( _msa_processing_max_allowed_gap_ratio_tf - .getText().trim() ); + .getText().trim() ); } catch ( final NumberFormatException e ) { msa_processing_max_allowed_gap_ratio = -1.0; @@ -409,7 +409,7 @@ public class PhyloInferenceDialog extends JDialog implements ActionListener { private void updateMsaProcessingItem() { _execute_msa_processing_cb.setSelected( getPhylogeneticInferenceOptions().isExecuteMsaProcessing() ); _msa_processing_remove_all_gap_columns_cb.setSelected( getPhylogeneticInferenceOptions() - .isMsaProcessingRemoveAllGapColumns() ); + .isMsaProcessingRemoveAllGapColumns() ); if ( _opts.getMsaProcessingMaxAllowedGapRatio() > 0 ) { _msa_processing_max_allowed_gap_ratio_tf.setText( _opts.getMsaProcessingMaxAllowedGapRatio() + "" ); } diff --git a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java index 0f29e93..1e8f3fc 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java @@ -167,8 +167,8 @@ public class PhylogeneticInferrer extends RunnableProcess { + _options.getMsaPrg() + "\" and the following parameters:\n\"" + _options.getMsaPrgParameters() + "\"\nError: " + e.getLocalizedMessage(), - "Failed to Calculate MSA", - JOptionPane.ERROR_MESSAGE ); + "Failed to Calculate MSA", + JOptionPane.ERROR_MESSAGE ); if ( DEBUG ) { e.printStackTrace(); } @@ -181,8 +181,8 @@ public class PhylogeneticInferrer extends RunnableProcess { + _options.getMsaPrg() + "\" and the following parameters:\n\"" + _options.getMsaPrgParameters() + "\"\nError: " + e.getLocalizedMessage(), - "Unexpected Exception During MSA Calculation", - JOptionPane.ERROR_MESSAGE ); + "Unexpected Exception During MSA Calculation", + JOptionPane.ERROR_MESSAGE ); if ( DEBUG ) { e.printStackTrace(); } @@ -194,8 +194,8 @@ public class PhylogeneticInferrer extends RunnableProcess { "Could not create multiple sequence alignment with " + _options.getMsaPrg() + "\nand the following parameters:\n\"" + _options.getMsaPrgParameters() + "\"", - "Failed to Calculate MSA", - JOptionPane.ERROR_MESSAGE ); + "Failed to Calculate MSA", + JOptionPane.ERROR_MESSAGE ); return; } if ( DEBUG ) { @@ -213,8 +213,8 @@ public class PhylogeneticInferrer extends RunnableProcess { "Less than two sequences longer than " + _options.getMsaProcessingMinAllowedLength() + " residues left after MSA processing", - "MSA Processing Settings Too Stringent", - JOptionPane.ERROR_MESSAGE ); + "MSA Processing Settings Too Stringent", + JOptionPane.ERROR_MESSAGE ); return; } } @@ -231,7 +231,7 @@ public class PhylogeneticInferrer extends RunnableProcess { if ( _options.isPerformBootstrapResampling() && ( n > 0 ) ) { final ResampleableMsa resampleable_msa = new ResampleableMsa( ( BasicMsa ) _msa ); final int[][] resampled_column_positions = BootstrapResampler.createResampledColumnPositions( _msa - .getLength(), n, seed ); + .getLength(), n, seed ); final Phylogeny[] eval_phys = new Phylogeny[ n ]; for( int i = 0; i < n; ++i ) { resampleable_msa.resample( resampled_column_positions[ i ] ); @@ -261,10 +261,10 @@ public class PhylogeneticInferrer extends RunnableProcess { } private Msa runMAFFT( final List seqs, final List opts ) throws IOException, - InterruptedException { + InterruptedException { Msa msa = null; final MsaInferrer mafft = Mafft.createInstance( _mf.getInferenceManager().getPathToLocalMafft() - .getCanonicalPath() ); + .getCanonicalPath() ); try { msa = mafft.infer( seqs, opts ); } @@ -278,11 +278,11 @@ public class PhylogeneticInferrer extends RunnableProcess { if ( !ForesterUtil.isEmpty( _options.getIntermediateFilesBase() ) ) { try { final BufferedWriter msa_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase() - + MSA_FILE_SUFFIX ) ); + + MSA_FILE_SUFFIX ) ); _msa.write( msa_writer, MSA_FORMAT.PHYLIP ); msa_writer.close(); final BufferedWriter pwd_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase() - + PWD_FILE_SUFFIX ) ); + + PWD_FILE_SUFFIX ) ); m.write( pwd_writer ); pwd_writer.close(); } diff --git a/forester/java/src/org/forester/archaeopteryx/tools/RunnableProcess.java b/forester/java/src/org/forester/archaeopteryx/tools/RunnableProcess.java index 9fe35fa..60ff4d4 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/RunnableProcess.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/RunnableProcess.java @@ -26,7 +26,7 @@ public abstract class RunnableProcess implements Runnable { final boolean removed = mf.getProcessPool().removeProcess( getProcessId() ); if ( !removed ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not remove process " + getProcessId() - + " from process pool" ); + + " from process pool" ); } mf.updateProcessMenu(); } diff --git a/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java b/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java index fcb71fc..1cd6b54 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java @@ -117,7 +117,7 @@ public final class SequenceDataRetriver extends RunnableProcess { JOptionPane.WARNING_MESSAGE ); } catch ( final Exception e ) { - // Not important if this fails, do nothing. + // Not important if this fails, do nothing. } } else { diff --git a/forester/java/src/org/forester/archaeopteryx/webservices/PhylogeniesWebserviceClient.java b/forester/java/src/org/forester/archaeopteryx/webservices/PhylogeniesWebserviceClient.java index 232a215..011decf 100644 --- a/forester/java/src/org/forester/archaeopteryx/webservices/PhylogeniesWebserviceClient.java +++ b/forester/java/src/org/forester/archaeopteryx/webservices/PhylogeniesWebserviceClient.java @@ -36,75 +36,75 @@ public interface PhylogeniesWebserviceClient { /** * A short description of the webservice (~20 characters). - * + * * @return a short description of the webservice (~20 characters) */ public String getDescription(); /** * Instructions (and examples) on how to use the webservice. - * + * * @return instructions (and examples) on how to use the webservice */ public String getInstructions(); /** * A name/description which can appear on a menu. - * + * * @return A name/description which can appear on a menu */ public String getMenuName(); /** * The name of the webservice. - * - * + * + * * @return the name of the webservice */ public String getName(); /** * The node data field in which to place node names from simple unannotated formats - * (such as Newick). Null means avoiding any such postprocessing. - * + * (such as Newick). Null means avoiding any such postprocessing. + * * @return the field code */ public PhylogenyMethods.PhylogenyNodeField getNodeField(); /** * This is used to indicate any kind of special processing. - * - * + * + * * @return a reference */ public Object getProcessingInstructions(); /** * To get a type of reference for the webservice (an URL or citation, for example). - * - * + * + * * @return a reference */ public String getReference(); /** * The expected format of the response. - * + * * @return the expected format of the response */ public WsPhylogenyFormat getReturnFormat(); /** * Use QUERY_PLACEHOLDER to indicate position of query variable. - * + * * @return the URL */ public String getUrl(); /** * Is the query a number? - * - * + * + * * @return */ public boolean isQueryInteger(); diff --git a/forester/java/src/org/forester/archaeopteryx/webservices/WebserviceUtil.java b/forester/java/src/org/forester/archaeopteryx/webservices/WebserviceUtil.java index 0dad04a..201be29 100644 --- a/forester/java/src/org/forester/archaeopteryx/webservices/WebserviceUtil.java +++ b/forester/java/src/org/forester/archaeopteryx/webservices/WebserviceUtil.java @@ -49,7 +49,7 @@ public final class WebserviceUtil { public static final String TOL_NAME = "Tree of Life (ToL)"; public static final String TOL_URL_BASE = "http://tolweb.org/onlinecontributors/app?service=external&page=xml/TreeStructureService&node_id="; public static final String TOL_WEBSERVER = TOL_URL_BASE - + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER; + + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER; public static final String TREE_BASE_DESC = "This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment."; public static final String TREE_BASE_INST = "treebase"; public static final String TREE_BASE_NAME = "TreeBASE"; @@ -68,8 +68,8 @@ public final class WebserviceUtil { WsPhylogenyFormat.TREEBASE_STUDY, null, TREEBASE_PHYLOWS_STUDY_URL_BASE - + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER - + "?format=nexus", + + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER + + "?format=nexus", true, "http://www.treebase.org", TREE_BASE_INST ) ); @@ -80,8 +80,8 @@ public final class WebserviceUtil { WsPhylogenyFormat.TREEBASE_TREE, null, TREEBASE_PHYLOWS_TREE_URL_BASE - + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER - + "?format=nexus", + + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER + + "?format=nexus", true, "http://www.treebase.org", TREE_BASE_INST ) ); @@ -94,9 +94,9 @@ public final class WebserviceUtil { PFAM_SERVER + "/family/PF" + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER + "/tree/download", - false, - PFAM_SERVER, - PFAM_INST ) ); + false, + PFAM_SERVER, + PFAM_INST ) ); clients.add( new BasicPhylogeniesWebserviceClient( TREE_FAM_NAME, "Read Gene Tree from TreeFam...", "Use TreeFam to obtain a gene tree", @@ -104,8 +104,8 @@ public final class WebserviceUtil { WsPhylogenyFormat.NHX, null, TREE_FAM_URL_BASE - + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER - + "/tree/newick", + + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER + + "/tree/newick", true, "http://www.treefam.org", TREE_FAM_INST ) ); @@ -114,12 +114,12 @@ public final class WebserviceUtil { "Use ToL webservice to obtain a evolutionary tree", "Please enter a Tree of Life node identifier\n(Examples: " + "14923 for ray-finned fishes, 19386 for Cephalopoda, 2461 for Cnidaria)", - WsPhylogenyFormat.TOL_XML_RESPONSE, - PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME, - WebserviceUtil.TOL_WEBSERVER, - true, - "http://tolweb.org", - null ) ); + WsPhylogenyFormat.TOL_XML_RESPONSE, + PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME, + WebserviceUtil.TOL_WEBSERVER, + true, + "http://tolweb.org", + null ) ); return clients; } @@ -217,9 +217,9 @@ public final class WebserviceUtil { } if ( n.getNodeData().isHasTaxonomy() && ( n.getNodeData().getTaxonomy().getIdentifier() != null ) ) { n.getNodeData() - .getTaxonomy() - .setIdentifier( new Identifier( n.getNodeData().getTaxonomy().getIdentifier().getValue(), - "ncbi" ) ); + .getTaxonomy() + .setIdentifier( new Identifier( n.getNodeData().getTaxonomy().getIdentifier().getValue(), + "ncbi" ) ); } } } diff --git a/forester/java/src/org/forester/datastructures/Queue.java b/forester/java/src/org/forester/datastructures/Queue.java index 03e0f94..fa77834 100644 --- a/forester/java/src/org/forester/datastructures/Queue.java +++ b/forester/java/src/org/forester/datastructures/Queue.java @@ -31,9 +31,9 @@ import java.util.NoSuchElementException; /* * A simple Queue data structure. Created: 10/23/2005 by Christian M. Zmasek. * Last modified: 10/23/2005 by Christian M. Zmasek. - * + * * @author Christian M. Zmasek - * + * * @version 1.000 */ public class Queue { @@ -60,7 +60,7 @@ public class Queue { /** * Dequeues one element from this queue. - * + * * @return the dequeued object * @throws NoSuchElementException * if this queue is empty @@ -76,7 +76,7 @@ public class Queue { // -------------- /** * Adds Object element to thisqueue. - * + * * @param element * the Object to be enqueued */ @@ -88,7 +88,7 @@ public class Queue { // --------------- /** * Returns the LinkedList upon which this queue is based. - * + * * @return the LinkedList upon which this queue is based */ private LinkedList getData() { @@ -97,7 +97,7 @@ public class Queue { /** * Returns whether or not this queue is empty. - * + * * @return true if this queue is empty, false otherwise */ public boolean isEmpty() { diff --git a/forester/java/src/org/forester/development/AbstractRenderer.java b/forester/java/src/org/forester/development/AbstractRenderer.java index d3fe715..8d4f944 100644 --- a/forester/java/src/org/forester/development/AbstractRenderer.java +++ b/forester/java/src/org/forester/development/AbstractRenderer.java @@ -33,7 +33,7 @@ import javax.swing.JComponent; public abstract class AbstractRenderer extends JComponent { /** - * + * */ private static final long serialVersionUID = 7236434322552764776L; static final Color DEFAULT_COLOR = new Color( 0, 0, 0 ); diff --git a/forester/java/src/org/forester/development/DevelopmentTools.java b/forester/java/src/org/forester/development/DevelopmentTools.java index 3cbc385..9c26d2c 100644 --- a/forester/java/src/org/forester/development/DevelopmentTools.java +++ b/forester/java/src/org/forester/development/DevelopmentTools.java @@ -36,7 +36,7 @@ public final class DevelopmentTools { /** * Creates a completely unbalanced Phylogeny with i external nodes. - * + * * @return a newly created unbalanced Phylogeny */ // public static Phylogeny createUnbalancedTree( int i ) { @@ -46,7 +46,7 @@ public final class DevelopmentTools { // try { // PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); // t1 = factory.create( ":S=", new SimpleNHXParser() ); - // + // // t1.setRooted( true ); // // for ( int j = 1; j < i; ++j ) { @@ -71,7 +71,7 @@ public final class DevelopmentTools { /** * Creates a completely balanced rooted phylogeny with a given number of levels and * children per node. - * + * * @param levels * @param children_per_node * @return a completely balanced rooted phylogeny @@ -165,7 +165,7 @@ public final class DevelopmentTools { /** * Sets the species names of the external Nodes of Phylogeny t to a random * positive integer number between (and including) min and max. - * + * * @param t * whose external species names are to be randomized * @param min diff --git a/forester/java/src/org/forester/development/ResidueRenderer.java b/forester/java/src/org/forester/development/ResidueRenderer.java index 90f4dae..fe07389 100644 --- a/forester/java/src/org/forester/development/ResidueRenderer.java +++ b/forester/java/src/org/forester/development/ResidueRenderer.java @@ -39,7 +39,7 @@ public class ResidueRenderer extends AbstractRenderer { static final int DISTANCE_OVAL_BORDER = 1; static final int SIZE_LIMIT = 7; /** - * + * */ private static final long serialVersionUID = -2331160296913478874L; private final char _value; diff --git a/forester/java/src/org/forester/development/Test.java b/forester/java/src/org/forester/development/Test.java index d929aa3..1dd9e63 100644 --- a/forester/java/src/org/forester/development/Test.java +++ b/forester/java/src/org/forester/development/Test.java @@ -37,12 +37,12 @@ import org.forester.util.ForesterUtil; public class Test { private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator() - + "test_data" + ForesterUtil.getFileSeparator(); + + "test_data" + ForesterUtil.getFileSeparator(); public static void main( final String[] args ) { System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" ); System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION - + "]" ); + + "]" ); Locale.setDefault( Locale.US ); System.out.println( "[Locale: " + Locale.getDefault() + "]" ); final int failed = 0; diff --git a/forester/java/src/org/forester/development/neTest.java b/forester/java/src/org/forester/development/neTest.java index 9b02188..58309c5 100644 --- a/forester/java/src/org/forester/development/neTest.java +++ b/forester/java/src/org/forester/development/neTest.java @@ -62,7 +62,7 @@ public class neTest { // } // } // } /* tridiag */ - // Givens tridiagonalization + // Givens tridiagonalization void tridiag( final double a[][], final int n, final double accuracy ) { int i, j; double s, c; @@ -109,7 +109,7 @@ public class neTest { // } // } /* shiftqr */ // - // QR eigenvalue-finder + // QR eigenvalue-finder void shiftqr( final double a[][], final int n, final double accuracy ) { int i, j; double approx; @@ -169,7 +169,7 @@ public class neTest { //} //} /* givens */ // - // Givens transform at i,j for 1..n with angle theta + // Givens transform at i,j for 1..n with angle theta void givens( final double a[][], final int i, final int j, @@ -192,260 +192,260 @@ public class neTest { } } } - // this jtt matrix decomposition due to Elisabeth Tillier + // this jtt matrix decomposition due to Elisabeth Tillier final private static double jtteigs[] = { +0.00000000000000, -1.81721720738768, -1.87965834528616, - -1.61403121885431, -1.53896608443751, -1.40486966367848, -1.30995061286931, -1.24668414819041, - -1.17179756521289, -0.31033320987464, -0.34602837857034, -1.06031718484613, -0.99900602987105, - -0.45576774888948, -0.86014403434677, -0.54569432735296, -0.76866956571861, -0.60593589295327, - -0.65119724379348, -0.70249806480753 }; + -1.61403121885431, -1.53896608443751, -1.40486966367848, -1.30995061286931, -1.24668414819041, + -1.17179756521289, -0.31033320987464, -0.34602837857034, -1.06031718484613, -0.99900602987105, + -0.45576774888948, -0.86014403434677, -0.54569432735296, -0.76866956571861, -0.60593589295327, + -0.65119724379348, -0.70249806480753 }; final private static double jttprobs[][] = { - { +0.07686196156903, +0.05105697447152, +0.04254597872702, +0.05126897436552, +0.02027898986051, + { +0.07686196156903, +0.05105697447152, +0.04254597872702, +0.05126897436552, +0.02027898986051, +0.04106097946952, +0.06181996909002, +0.07471396264303, +0.02298298850851, +0.05256897371552, +0.09111095444453, +0.05949797025102, +0.02341398829301, +0.04052997973502, +0.05053197473402, +0.06822496588753, +0.05851797074102, +0.01433599283201, +0.03230298384851, +0.06637396681302 }, { -0.04445795120462, -0.01557336502860, -0.09314817363516, +0.04411372100382, -0.00511178725134, - +0.00188472427522, -0.02176250428454, -0.01330231089224, +0.01004072641973, +0.02707838224285, - -0.00785039050721, +0.02238829876349, +0.00257470703483, -0.00510311699563, -0.01727154263346, - +0.20074235330882, -0.07236268502973, -0.00012690116016, -0.00215974664431, -0.01059243778174 }, - { +0.09480046389131, +0.00082658405814, +0.01530023104155, -0.00639909042723, +0.00160605602061, - +0.00035896642912, +0.00199161318384, -0.00220482855717, -0.00112601328033, +0.14840201765438, - -0.00344295714983, -0.00123976286718, -0.00439399942758, +0.00032478785709, -0.00104270266394, - -0.02596605592109, -0.05645800566901, +0.00022319903170, -0.00022792271829, -0.16133258048606 }, - { -0.06924141195400, -0.01816245289173, -0.08104005811201, +0.08985697111009, +0.00279659017898, - +0.01083740322821, -0.06449599336038, +0.01794514261221, +0.01036809141699, +0.04283504450449, - +0.00634472273784, +0.02339134834111, -0.01748667848380, +0.00161859106290, +0.00622486432503, - -0.05854130195643, +0.15083728660504, +0.00030733757661, -0.00143739522173, -0.05295810171941 }, - { -0.14637948915627, +0.02029296323583, +0.02615316895036, -0.10311538564943, -0.00183412744544, - -0.02589124656591, +0.11073673851935, +0.00848581728407, +0.00106057791901, +0.05530240732939, - -0.00031533506946, -0.03124002869407, -0.01533984125301, -0.00288717337278, +0.00272787410643, - +0.06300929916280, +0.07920438311152, -0.00041335282410, -0.00011648873397, -0.03944076085434 }, - { -0.05558229086909, +0.08935293782491, +0.04869509588770, +0.04856877988810, -0.00253836047720, - +0.07651693957635, -0.06342453535092, -0.00777376246014, -0.08570270266807, +0.01943016473512, - -0.00599516526932, -0.09157595008575, -0.00397735155663, -0.00440093863690, -0.00232998056918, - +0.02979967701162, -0.00477299485901, -0.00144011795333, +0.01795114942404, -0.00080059359232 }, - { +0.05807741644682, +0.14654292420341, -0.06724975334073, +0.02159062346633, -0.00339085518294, - -0.06829036785575, +0.03520631903157, -0.02766062718318, +0.03485632707432, -0.02436836692465, - -0.00397566003573, -0.10095488644404, +0.02456887654357, +0.00381764117077, -0.00906261340247, - -0.01043058066362, +0.01651199513994, -0.00210417220821, -0.00872508520963, -0.01495915462580 }, - { +0.02564617106907, +0.02960554611436, -0.00052356748770, +0.00989267817318, -0.00044034172141, - -0.02279910634723, -0.00363768356471, -0.01086345665971, +0.01229721799572, +0.02633650142592, - +0.06282966783922, -0.00734486499924, -0.13863936313277, -0.00993891943390, -0.00655309682350, - -0.00245191788287, -0.02431633805559, -0.00068554031525, -0.00121383858869, +0.06280025239509 }, - { +0.11362428251792, -0.02080375718488, -0.08802750967213, -0.06531316372189, -0.00166626058292, - +0.06846081717224, +0.07007301248407, -0.01713112936632, -0.05900588794853, -0.04497159138485, - +0.04222484636983, +0.00129043178508, -0.01550337251561, -0.01553102163852, -0.04363429852047, - +0.01600063777880, +0.05787328925647, -0.00008265841118, +0.02870014572813, -0.02657681214523 }, - { +0.01840541226842, +0.00610159018805, +0.01368080422265, +0.02383751807012, -0.00923516894192, - +0.01209943150832, +0.02906782189141, +0.01992384905334, +0.00197323568330, +0.00017531415423, - -0.01796698381949, +0.01887083962858, -0.00063335886734, -0.02365277334702, +0.01209445088200, - +0.01308086447947, +0.01286727242301, -0.11420358975688, -0.01886991700613, +0.00238338728588 }, - { -0.01100105031759, -0.04250695864938, -0.02554356700969, -0.05473632078607, +0.00725906469946, - -0.03003724918191, -0.07051526125013, -0.06939439879112, -0.00285883056088, +0.05334304124753, - +0.12839241846919, -0.05883473754222, +0.02424304967487, +0.09134510778469, -0.00226003347193, - -0.01280041778462, -0.00207988305627, -0.02957493909199, +0.05290385686789, +0.05465710875015 }, - { -0.01421274522011, +0.02074863337778, -0.01006411985628, +0.03319995456446, -0.00005371699269, - -0.12266046460835, +0.02419847062899, -0.00441168706583, -0.08299118738167, -0.00323230913482, - +0.02954035119881, +0.09212856795583, +0.00718635627257, -0.02706936115539, +0.04473173279913, - -0.01274357634785, -0.01395862740618, -0.00071538848681, +0.04767640012830, -0.00729728326990 }, - { -0.03797680968123, +0.01280286509478, -0.08614616553187, -0.01781049963160, +0.00674319990083, - +0.04208667754694, +0.05991325707583, +0.03581015660092, -0.01529816709967, +0.06885987924922, - -0.11719120476535, -0.00014333663810, +0.00074336784254, +0.02893416406249, +0.07466151360134, - -0.08182016471377, -0.06581536577662, -0.00018195976501, +0.00167443595008, +0.09015415667825 }, - { +0.03577726799591, -0.02139253448219, -0.01137813538175, -0.01954939202830, -0.04028242801611, - -0.01777500032351, -0.02106862264440, +0.00465199658293, -0.02824805812709, +0.06618860061778, - +0.08437791757537, -0.02533125946051, +0.02806344654855, -0.06970805797879, +0.02328376968627, - +0.00692992333282, +0.02751392122018, +0.01148722812804, -0.11130404325078, +0.07776346000559 }, - { -0.06014297925310, -0.00711674355952, -0.02424493472566, +0.00032464353156, +0.00321221847573, - +0.03257969053884, +0.01072805771161, +0.06892027923996, +0.03326534127710, -0.01558838623875, - +0.13794237677194, -0.04292623056646, +0.01375763233229, -0.11125153774789, +0.03510076081639, - -0.04531670712549, -0.06170413486351, -0.00182023682123, +0.05979891871679, -0.02551802851059 }, - { -0.03515069991501, +0.02310847227710, +0.00474493548551, +0.02787717003457, -0.12038329679812, - +0.03178473522077, +0.04445111601130, -0.05334957493090, +0.01290386678474, -0.00376064171612, - +0.03996642737967, +0.04777677295520, +0.00233689200639, +0.03917715404594, -0.01755598277531, - -0.03389088626433, -0.02180780263389, +0.00473402043911, +0.01964539477020, -0.01260807237680 }, - { -0.04120428254254, +0.00062717164978, -0.01688703578637, +0.01685776910152, +0.02102702093943, - +0.01295781834163, +0.03541815979495, +0.03968150445315, -0.02073122710938, -0.06932247350110, - +0.11696314241296, -0.00322523765776, -0.01280515661402, +0.08717664266126, +0.06297225078802, - -0.01290501780488, -0.04693925076877, -0.00177653675449, -0.08407812137852, -0.08380714022487 }, - { +0.03138655228534, -0.09052573757196, +0.00874202219428, +0.06060593729292, -0.03426076652151, - -0.04832468257386, +0.04735628794421, +0.14504653737383, -0.01709111334001, -0.00278794215381, - -0.03513813820550, -0.11690294831883, -0.00836264902624, +0.03270980973180, -0.02587764129811, - +0.01638786059073, +0.00485499822497, +0.00305477087025, +0.02295754527195, +0.00616929722958 }, - { -0.04898722042023, -0.01460879656586, +0.00508708857036, +0.07730497806331, +0.04252420017435, - +0.00484232580349, +0.09861807969412, -0.05169447907187, -0.00917820907880, +0.03679081047330, - +0.04998537112655, +0.00769330211980, +0.01805447683564, -0.00498723245027, -0.14148416183376, - -0.05170281760262, -0.03230723310784, -0.00032890672639, -0.02363523071957, +0.03801365471627 }, - { -0.02047562162108, +0.06933781779590, -0.02101117884731, -0.06841945874842, -0.00860967572716, - -0.00886650271590, -0.07185241332269, +0.16703684361030, -0.00635847581692, +0.00811478913823, - +0.01847205842216, +0.06700967948643, +0.00596607376199, +0.02318239240593, -0.10552958537847, - -0.01980199747773, -0.02003785382406, -0.00593392430159, -0.00965391033612, +0.00743094349652 } }; - // PMB matrix decomposition courtesy of Elisabeth Tillier + +0.00188472427522, -0.02176250428454, -0.01330231089224, +0.01004072641973, +0.02707838224285, + -0.00785039050721, +0.02238829876349, +0.00257470703483, -0.00510311699563, -0.01727154263346, + +0.20074235330882, -0.07236268502973, -0.00012690116016, -0.00215974664431, -0.01059243778174 }, + { +0.09480046389131, +0.00082658405814, +0.01530023104155, -0.00639909042723, +0.00160605602061, + +0.00035896642912, +0.00199161318384, -0.00220482855717, -0.00112601328033, +0.14840201765438, + -0.00344295714983, -0.00123976286718, -0.00439399942758, +0.00032478785709, -0.00104270266394, + -0.02596605592109, -0.05645800566901, +0.00022319903170, -0.00022792271829, -0.16133258048606 }, + { -0.06924141195400, -0.01816245289173, -0.08104005811201, +0.08985697111009, +0.00279659017898, + +0.01083740322821, -0.06449599336038, +0.01794514261221, +0.01036809141699, +0.04283504450449, + +0.00634472273784, +0.02339134834111, -0.01748667848380, +0.00161859106290, +0.00622486432503, + -0.05854130195643, +0.15083728660504, +0.00030733757661, -0.00143739522173, -0.05295810171941 }, + { -0.14637948915627, +0.02029296323583, +0.02615316895036, -0.10311538564943, -0.00183412744544, + -0.02589124656591, +0.11073673851935, +0.00848581728407, +0.00106057791901, +0.05530240732939, + -0.00031533506946, -0.03124002869407, -0.01533984125301, -0.00288717337278, +0.00272787410643, + +0.06300929916280, +0.07920438311152, -0.00041335282410, -0.00011648873397, -0.03944076085434 }, + { -0.05558229086909, +0.08935293782491, +0.04869509588770, +0.04856877988810, -0.00253836047720, + +0.07651693957635, -0.06342453535092, -0.00777376246014, -0.08570270266807, +0.01943016473512, + -0.00599516526932, -0.09157595008575, -0.00397735155663, -0.00440093863690, -0.00232998056918, + +0.02979967701162, -0.00477299485901, -0.00144011795333, +0.01795114942404, -0.00080059359232 }, + { +0.05807741644682, +0.14654292420341, -0.06724975334073, +0.02159062346633, -0.00339085518294, + -0.06829036785575, +0.03520631903157, -0.02766062718318, +0.03485632707432, -0.02436836692465, + -0.00397566003573, -0.10095488644404, +0.02456887654357, +0.00381764117077, -0.00906261340247, + -0.01043058066362, +0.01651199513994, -0.00210417220821, -0.00872508520963, -0.01495915462580 }, + { +0.02564617106907, +0.02960554611436, -0.00052356748770, +0.00989267817318, -0.00044034172141, + -0.02279910634723, -0.00363768356471, -0.01086345665971, +0.01229721799572, +0.02633650142592, + +0.06282966783922, -0.00734486499924, -0.13863936313277, -0.00993891943390, -0.00655309682350, + -0.00245191788287, -0.02431633805559, -0.00068554031525, -0.00121383858869, +0.06280025239509 }, + { +0.11362428251792, -0.02080375718488, -0.08802750967213, -0.06531316372189, -0.00166626058292, + +0.06846081717224, +0.07007301248407, -0.01713112936632, -0.05900588794853, -0.04497159138485, + +0.04222484636983, +0.00129043178508, -0.01550337251561, -0.01553102163852, -0.04363429852047, + +0.01600063777880, +0.05787328925647, -0.00008265841118, +0.02870014572813, -0.02657681214523 }, + { +0.01840541226842, +0.00610159018805, +0.01368080422265, +0.02383751807012, -0.00923516894192, + +0.01209943150832, +0.02906782189141, +0.01992384905334, +0.00197323568330, +0.00017531415423, + -0.01796698381949, +0.01887083962858, -0.00063335886734, -0.02365277334702, +0.01209445088200, + +0.01308086447947, +0.01286727242301, -0.11420358975688, -0.01886991700613, +0.00238338728588 }, + { -0.01100105031759, -0.04250695864938, -0.02554356700969, -0.05473632078607, +0.00725906469946, + -0.03003724918191, -0.07051526125013, -0.06939439879112, -0.00285883056088, +0.05334304124753, + +0.12839241846919, -0.05883473754222, +0.02424304967487, +0.09134510778469, -0.00226003347193, + -0.01280041778462, -0.00207988305627, -0.02957493909199, +0.05290385686789, +0.05465710875015 }, + { -0.01421274522011, +0.02074863337778, -0.01006411985628, +0.03319995456446, -0.00005371699269, + -0.12266046460835, +0.02419847062899, -0.00441168706583, -0.08299118738167, -0.00323230913482, + +0.02954035119881, +0.09212856795583, +0.00718635627257, -0.02706936115539, +0.04473173279913, + -0.01274357634785, -0.01395862740618, -0.00071538848681, +0.04767640012830, -0.00729728326990 }, + { -0.03797680968123, +0.01280286509478, -0.08614616553187, -0.01781049963160, +0.00674319990083, + +0.04208667754694, +0.05991325707583, +0.03581015660092, -0.01529816709967, +0.06885987924922, + -0.11719120476535, -0.00014333663810, +0.00074336784254, +0.02893416406249, +0.07466151360134, + -0.08182016471377, -0.06581536577662, -0.00018195976501, +0.00167443595008, +0.09015415667825 }, + { +0.03577726799591, -0.02139253448219, -0.01137813538175, -0.01954939202830, -0.04028242801611, + -0.01777500032351, -0.02106862264440, +0.00465199658293, -0.02824805812709, +0.06618860061778, + +0.08437791757537, -0.02533125946051, +0.02806344654855, -0.06970805797879, +0.02328376968627, + +0.00692992333282, +0.02751392122018, +0.01148722812804, -0.11130404325078, +0.07776346000559 }, + { -0.06014297925310, -0.00711674355952, -0.02424493472566, +0.00032464353156, +0.00321221847573, + +0.03257969053884, +0.01072805771161, +0.06892027923996, +0.03326534127710, -0.01558838623875, + +0.13794237677194, -0.04292623056646, +0.01375763233229, -0.11125153774789, +0.03510076081639, + -0.04531670712549, -0.06170413486351, -0.00182023682123, +0.05979891871679, -0.02551802851059 }, + { -0.03515069991501, +0.02310847227710, +0.00474493548551, +0.02787717003457, -0.12038329679812, + +0.03178473522077, +0.04445111601130, -0.05334957493090, +0.01290386678474, -0.00376064171612, + +0.03996642737967, +0.04777677295520, +0.00233689200639, +0.03917715404594, -0.01755598277531, + -0.03389088626433, -0.02180780263389, +0.00473402043911, +0.01964539477020, -0.01260807237680 }, + { -0.04120428254254, +0.00062717164978, -0.01688703578637, +0.01685776910152, +0.02102702093943, + +0.01295781834163, +0.03541815979495, +0.03968150445315, -0.02073122710938, -0.06932247350110, + +0.11696314241296, -0.00322523765776, -0.01280515661402, +0.08717664266126, +0.06297225078802, + -0.01290501780488, -0.04693925076877, -0.00177653675449, -0.08407812137852, -0.08380714022487 }, + { +0.03138655228534, -0.09052573757196, +0.00874202219428, +0.06060593729292, -0.03426076652151, + -0.04832468257386, +0.04735628794421, +0.14504653737383, -0.01709111334001, -0.00278794215381, + -0.03513813820550, -0.11690294831883, -0.00836264902624, +0.03270980973180, -0.02587764129811, + +0.01638786059073, +0.00485499822497, +0.00305477087025, +0.02295754527195, +0.00616929722958 }, + { -0.04898722042023, -0.01460879656586, +0.00508708857036, +0.07730497806331, +0.04252420017435, + +0.00484232580349, +0.09861807969412, -0.05169447907187, -0.00917820907880, +0.03679081047330, + +0.04998537112655, +0.00769330211980, +0.01805447683564, -0.00498723245027, -0.14148416183376, + -0.05170281760262, -0.03230723310784, -0.00032890672639, -0.02363523071957, +0.03801365471627 }, + { -0.02047562162108, +0.06933781779590, -0.02101117884731, -0.06841945874842, -0.00860967572716, + -0.00886650271590, -0.07185241332269, +0.16703684361030, -0.00635847581692, +0.00811478913823, + +0.01847205842216, +0.06700967948643, +0.00596607376199, +0.02318239240593, -0.10552958537847, + -0.01980199747773, -0.02003785382406, -0.00593392430159, -0.00965391033612, +0.00743094349652 } }; + // PMB matrix decomposition courtesy of Elisabeth Tillier final private static double pmbeigs[] = { 0.0000001586972220, -1.8416770496147100, -1.6025046986139100, - -1.5801012515121300, -1.4987794099715900, -1.3520794233801900, -1.3003469390479700, -1.2439503327631300, - -1.1962574080244200, -1.1383730501367500, -1.1153278910708000, -0.4934843510654760, -0.5419014550215590, - -0.9657997830826700, -0.6276075673757390, -0.6675927795018510, -0.6932641383465870, -0.8897872681859630, - -0.8382698977371710, -0.8074694642446040 }; + -1.5801012515121300, -1.4987794099715900, -1.3520794233801900, -1.3003469390479700, -1.2439503327631300, + -1.1962574080244200, -1.1383730501367500, -1.1153278910708000, -0.4934843510654760, -0.5419014550215590, + -0.9657997830826700, -0.6276075673757390, -0.6675927795018510, -0.6932641383465870, -0.8897872681859630, + -0.8382698977371710, -0.8074694642446040 }; final private static double pmbprobs[][] = { - { 0.0771762457248147, 0.0531913844998640, 0.0393445076407294, 0.0466756566755510, 0.0286348361997465, + { 0.0771762457248147, 0.0531913844998640, 0.0393445076407294, 0.0466756566755510, 0.0286348361997465, 0.0312327748383639, 0.0505410248721427, 0.0767106611472993, 0.0258916271688597, 0.0673140562194124, 0.0965705469252199, 0.0515979465932174, 0.0250628079438675, 0.0503492018628350, 0.0399908189418273, 0.0641898881894471, 0.0517539616710987, 0.0143507440546115, 0.0357994592438322, 0.0736218495862984 }, { 0.0368263046116572, -0.0006728917107827, 0.0008590805287740, -0.0002764255356960, 0.0020152937187455, - 0.0055743720652960, 0.0003213317669367, 0.0000449190281568, -0.0004226254397134, 0.1805040629634510, - -0.0272246813586204, 0.0005904606533477, -0.0183743200073889, -0.0009194625608688, 0.0008173657533167, - -0.0262629806302238, 0.0265738757209787, 0.0002176606241904, 0.0021315644838566, -0.1823229927207580 }, - { -0.0194800075560895, 0.0012068088610652, -0.0008803318319596, -0.0016044273960017, -0.0002938633803197, - -0.0535796754602196, 0.0155163896648621, -0.0015006360762140, 0.0021601372013703, 0.0268513218744797, - -0.1085292493742730, 0.0149753083138452, 0.1346457366717310, -0.0009371698759829, 0.0013501708044116, - 0.0346352293103622, -0.0276963770242276, 0.0003643142783940, 0.0002074817333067, -0.0174108903914110 }, - { 0.0557839400850153, 0.0023271577185437, 0.0183481103396687, 0.0023339480096311, 0.0002013267015151, - -0.0227406863569852, 0.0098644845475047, 0.0064721276774396, 0.0001389408104210, -0.0473713878768274, - -0.0086984445005797, 0.0026913674934634, 0.0283724052562196, 0.0001063665179457, 0.0027442574779383, - -0.1875312134708470, 0.1279864877057640, 0.0005103347834563, 0.0003155113168637, 0.0081451082759554 }, - { 0.0037510125027265, 0.0107095920636885, 0.0147305410328404, -0.0112351252180332, -0.0001500408626446, - -0.1523450933729730, 0.0611532413339872, -0.0005496748939503, 0.0048714378736644, -0.0003826320053999, - 0.0552010244407311, 0.0482555671001955, -0.0461664995115847, -0.0021165008617978, -0.0004574454232187, - 0.0233755883688949, -0.0035484915422384, 0.0009090698422851, 0.0013840637687758, -0.0073895139302231 }, - { -0.0111512564930024, 0.1025460064723080, 0.0396772456883791, -0.0298408501361294, -0.0001656742634733, - -0.0079876311843289, 0.0712644184507945, -0.0010780604625230, -0.0035880882043592, 0.0021070399334252, - 0.0016716329894279, -0.1810123023850110, 0.0015141703608724, -0.0032700852781804, 0.0035503782441679, - 0.0118634302028026, 0.0044561606458028, -0.0001576678495964, 0.0023470722225751, -0.0027457045397157 }, - { 0.1474525743949170, -0.0054432538500293, 0.0853848892349828, -0.0137787746207348, -0.0008274830358513, - 0.0042248844582553, 0.0019556229305563, -0.0164191435175148, -0.0024501858854849, 0.0120908948084233, - -0.0381456105972653, 0.0101271614855119, -0.0061945941321859, 0.0178841099895867, -0.0014577779202600, - -0.0752120602555032, -0.1426985695849920, 0.0002862275078983, -0.0081191734261838, 0.0313401149422531 }, - { 0.0542034611735289, -0.0078763926211829, 0.0060433542506096, 0.0033396210615510, 0.0013965072374079, - 0.0067798903832256, -0.0135291136622509, -0.0089982442731848, -0.0056744537593887, -0.0766524225176246, - 0.1881210263933930, -0.0065875518675173, 0.0416627569300375, -0.0953804133524747, -0.0012559228448735, - 0.0101622644292547, -0.0304742453119050, 0.0011702318499737, 0.0454733434783982, -0.1119239362388150 }, - { 0.1069409037912470, 0.0805064400880297, -0.1127352030714600, 0.1001181253523260, -0.0021480427488769, - -0.0332884841459003, -0.0679837575848452, -0.0043812841356657, 0.0153418716846395, -0.0079441315103188, - -0.0121766182046363, -0.0381127991037620, -0.0036338726532673, 0.0195324059593791, -0.0020165963699984, - -0.0061222685010268, -0.0253761448771437, -0.0005246410999057, -0.0112205170502433, 0.0052248485517237 }, - { -0.0325247648326262, 0.0238753651653669, 0.0203684886605797, 0.0295666232678825, -0.0003946714764213, - -0.0157242718469554, -0.0511737848084862, 0.0084725632040180, -0.0167068828528921, 0.0686962159427527, - -0.0659702890616198, -0.0014289912494271, -0.0167000964093416, -0.1276689083678200, 0.0036575057830967, - -0.0205958145531018, 0.0000368919612829, 0.0014413626622426, 0.1064360941926030, 0.0863372661517408 }, - { -0.0463777468104402, 0.0394712148670596, 0.1118686750747160, 0.0440711686389031, -0.0026076286506751, - -0.0268454015202516, -0.1464943067133240, -0.0137514051835380, -0.0094395514284145, -0.0144124844774228, - 0.0249103379323744, -0.0071832157138676, 0.0035592787728526, 0.0415627419826693, 0.0027040097365669, - 0.0337523666612066, 0.0316121324137152, -0.0011350177559026, -0.0349998884574440, -0.0302651879823361 }, - { 0.0142360925194728, 0.0413145623127025, 0.0324976427846929, 0.0580930922002398, -0.0586974207121084, - 0.0202001168873069, 0.0492204086749069, 0.1126593173463060, 0.0116620013776662, -0.0780333711712066, - -0.1109786767320410, 0.0407775100936731, -0.0205013161312652, -0.0653458585025237, 0.0347351829703865, - 0.0304448983224773, 0.0068813748197884, -0.0189002309261882, -0.0334507528405279, -0.0668143558699485 }, - { -0.0131548829657936, 0.0044244322828034, -0.0050639951827271, -0.0038668197633889, -0.1536822386530220, - 0.0026336969165336, 0.0021585651200470, -0.0459233839062969, 0.0046854727140565, 0.0393815434593599, - 0.0619554007991097, 0.0027456299925622, 0.0117574347936383, 0.0373018612990383, 0.0024818527553328, - -0.0133956606027299, -0.0020457128424105, 0.0154178819990401, 0.0246524142683911, 0.0275363065682921 }, - { -0.1542307272455030, 0.0364861558267547, -0.0090880407008181, 0.0531673937889863, 0.0157585615170580, - 0.0029986538457297, 0.0180194047699875, 0.0652152443589317, 0.0266842840376180, 0.0388457366405908, - 0.0856237634510719, 0.0126955778952183, 0.0099593861698250, -0.0013941794862563, 0.0294065511237513, - -0.1151906949298290, -0.0852991447389655, 0.0028699120202636, -0.0332087026659522, 0.0006811857297899 }, - { 0.0281300736924501, -0.0584072081898638, -0.0178386569847853, -0.0536470338171487, -0.0186881656029960, - -0.0240008730656106, -0.0541064820498883, 0.2217137098936020, -0.0260500001542033, 0.0234505236798375, - 0.0311127151218573, -0.0494139126682672, 0.0057093465049849, 0.0124937286655911, -0.0298322975915689, - 0.0006520211333102, -0.0061018680727128, -0.0007081999479528, -0.0060523759094034, 0.0215845995364623 }, - { 0.0295321046399105, -0.0088296411830544, -0.0065057049917325, -0.0053478115612781, -0.0100646496794634, - -0.0015473619084872, 0.0008539960632865, -0.0376381933046211, -0.0328135588935604, 0.0672161874239480, - 0.0667626853916552, -0.0026511651464901, 0.0140451514222062, -0.0544836996133137, 0.0427485157912094, - 0.0097455780205802, 0.0177309072915667, -0.0828759701187452, -0.0729504795471370, 0.0670731961252313 }, - { 0.0082646581043963, -0.0319918630534466, -0.0188454445200422, -0.0374976353856606, 0.0037131290686848, - -0.0132507796987883, -0.0306958830735725, -0.0044119395527308, -0.0140786756619672, -0.0180512599925078, - -0.0208243802903953, -0.0232202769398931, -0.0063135878270273, 0.0110442171178168, 0.1824538048228460, - -0.0006644614422758, -0.0069909097436659, 0.0255407650654681, 0.0099119399501151, -0.0140911517070698 }, - { 0.0261344441524861, -0.0714454044548650, 0.0159436926233439, 0.0028462736216688, -0.0044572637889080, - -0.0089474834434532, -0.0177570282144517, -0.0153693244094452, 0.1160919467206400, 0.0304911481385036, - 0.0047047513411774, -0.0456535116423972, 0.0004491494948617, -0.0767108879444462, -0.0012688533741441, - 0.0192445965934123, 0.0202321954782039, 0.0281039933233607, -0.0590403018490048, 0.0364080426546883 }, - { 0.0115826306265004, 0.1340228176509380, -0.0236200652949049, -0.1284484655137340, -0.0004742338006503, - 0.0127617346949511, -0.0428560878860394, 0.0060030732454125, 0.0089182609926781, 0.0085353834972860, - 0.0048464809638033, 0.0709740071429510, 0.0029940462557054, -0.0483434904493132, -0.0071713680727884, - -0.0036840391887209, 0.0031454003250096, 0.0246243550241551, -0.0449551277644180, 0.0111449232769393 }, - { 0.0140356721886765, -0.0196518236826680, 0.0030517022326582, 0.0582672093364850, -0.0000973895685457, - 0.0021704767224292, 0.0341806268602705, -0.0152035987563018, -0.0903198657739177, 0.0259623214586925, - 0.0155832497882743, -0.0040543568451651, 0.0036477631918247, -0.0532892744763217, -0.0142569373662724, - 0.0104500681408622, 0.0103483945857315, 0.0679534422398752, -0.0768068882938636, 0.0280289727046158 } }; - // dcmut version of PAM model from http://www.ebi.ac.uk/goldman-srv/dayhoff/ + 0.0055743720652960, 0.0003213317669367, 0.0000449190281568, -0.0004226254397134, 0.1805040629634510, + -0.0272246813586204, 0.0005904606533477, -0.0183743200073889, -0.0009194625608688, 0.0008173657533167, + -0.0262629806302238, 0.0265738757209787, 0.0002176606241904, 0.0021315644838566, -0.1823229927207580 }, + { -0.0194800075560895, 0.0012068088610652, -0.0008803318319596, -0.0016044273960017, -0.0002938633803197, + -0.0535796754602196, 0.0155163896648621, -0.0015006360762140, 0.0021601372013703, 0.0268513218744797, + -0.1085292493742730, 0.0149753083138452, 0.1346457366717310, -0.0009371698759829, 0.0013501708044116, + 0.0346352293103622, -0.0276963770242276, 0.0003643142783940, 0.0002074817333067, -0.0174108903914110 }, + { 0.0557839400850153, 0.0023271577185437, 0.0183481103396687, 0.0023339480096311, 0.0002013267015151, + -0.0227406863569852, 0.0098644845475047, 0.0064721276774396, 0.0001389408104210, -0.0473713878768274, + -0.0086984445005797, 0.0026913674934634, 0.0283724052562196, 0.0001063665179457, 0.0027442574779383, + -0.1875312134708470, 0.1279864877057640, 0.0005103347834563, 0.0003155113168637, 0.0081451082759554 }, + { 0.0037510125027265, 0.0107095920636885, 0.0147305410328404, -0.0112351252180332, -0.0001500408626446, + -0.1523450933729730, 0.0611532413339872, -0.0005496748939503, 0.0048714378736644, -0.0003826320053999, + 0.0552010244407311, 0.0482555671001955, -0.0461664995115847, -0.0021165008617978, -0.0004574454232187, + 0.0233755883688949, -0.0035484915422384, 0.0009090698422851, 0.0013840637687758, -0.0073895139302231 }, + { -0.0111512564930024, 0.1025460064723080, 0.0396772456883791, -0.0298408501361294, -0.0001656742634733, + -0.0079876311843289, 0.0712644184507945, -0.0010780604625230, -0.0035880882043592, 0.0021070399334252, + 0.0016716329894279, -0.1810123023850110, 0.0015141703608724, -0.0032700852781804, 0.0035503782441679, + 0.0118634302028026, 0.0044561606458028, -0.0001576678495964, 0.0023470722225751, -0.0027457045397157 }, + { 0.1474525743949170, -0.0054432538500293, 0.0853848892349828, -0.0137787746207348, -0.0008274830358513, + 0.0042248844582553, 0.0019556229305563, -0.0164191435175148, -0.0024501858854849, 0.0120908948084233, + -0.0381456105972653, 0.0101271614855119, -0.0061945941321859, 0.0178841099895867, -0.0014577779202600, + -0.0752120602555032, -0.1426985695849920, 0.0002862275078983, -0.0081191734261838, 0.0313401149422531 }, + { 0.0542034611735289, -0.0078763926211829, 0.0060433542506096, 0.0033396210615510, 0.0013965072374079, + 0.0067798903832256, -0.0135291136622509, -0.0089982442731848, -0.0056744537593887, -0.0766524225176246, + 0.1881210263933930, -0.0065875518675173, 0.0416627569300375, -0.0953804133524747, -0.0012559228448735, + 0.0101622644292547, -0.0304742453119050, 0.0011702318499737, 0.0454733434783982, -0.1119239362388150 }, + { 0.1069409037912470, 0.0805064400880297, -0.1127352030714600, 0.1001181253523260, -0.0021480427488769, + -0.0332884841459003, -0.0679837575848452, -0.0043812841356657, 0.0153418716846395, -0.0079441315103188, + -0.0121766182046363, -0.0381127991037620, -0.0036338726532673, 0.0195324059593791, -0.0020165963699984, + -0.0061222685010268, -0.0253761448771437, -0.0005246410999057, -0.0112205170502433, 0.0052248485517237 }, + { -0.0325247648326262, 0.0238753651653669, 0.0203684886605797, 0.0295666232678825, -0.0003946714764213, + -0.0157242718469554, -0.0511737848084862, 0.0084725632040180, -0.0167068828528921, 0.0686962159427527, + -0.0659702890616198, -0.0014289912494271, -0.0167000964093416, -0.1276689083678200, 0.0036575057830967, + -0.0205958145531018, 0.0000368919612829, 0.0014413626622426, 0.1064360941926030, 0.0863372661517408 }, + { -0.0463777468104402, 0.0394712148670596, 0.1118686750747160, 0.0440711686389031, -0.0026076286506751, + -0.0268454015202516, -0.1464943067133240, -0.0137514051835380, -0.0094395514284145, -0.0144124844774228, + 0.0249103379323744, -0.0071832157138676, 0.0035592787728526, 0.0415627419826693, 0.0027040097365669, + 0.0337523666612066, 0.0316121324137152, -0.0011350177559026, -0.0349998884574440, -0.0302651879823361 }, + { 0.0142360925194728, 0.0413145623127025, 0.0324976427846929, 0.0580930922002398, -0.0586974207121084, + 0.0202001168873069, 0.0492204086749069, 0.1126593173463060, 0.0116620013776662, -0.0780333711712066, + -0.1109786767320410, 0.0407775100936731, -0.0205013161312652, -0.0653458585025237, 0.0347351829703865, + 0.0304448983224773, 0.0068813748197884, -0.0189002309261882, -0.0334507528405279, -0.0668143558699485 }, + { -0.0131548829657936, 0.0044244322828034, -0.0050639951827271, -0.0038668197633889, -0.1536822386530220, + 0.0026336969165336, 0.0021585651200470, -0.0459233839062969, 0.0046854727140565, 0.0393815434593599, + 0.0619554007991097, 0.0027456299925622, 0.0117574347936383, 0.0373018612990383, 0.0024818527553328, + -0.0133956606027299, -0.0020457128424105, 0.0154178819990401, 0.0246524142683911, 0.0275363065682921 }, + { -0.1542307272455030, 0.0364861558267547, -0.0090880407008181, 0.0531673937889863, 0.0157585615170580, + 0.0029986538457297, 0.0180194047699875, 0.0652152443589317, 0.0266842840376180, 0.0388457366405908, + 0.0856237634510719, 0.0126955778952183, 0.0099593861698250, -0.0013941794862563, 0.0294065511237513, + -0.1151906949298290, -0.0852991447389655, 0.0028699120202636, -0.0332087026659522, 0.0006811857297899 }, + { 0.0281300736924501, -0.0584072081898638, -0.0178386569847853, -0.0536470338171487, -0.0186881656029960, + -0.0240008730656106, -0.0541064820498883, 0.2217137098936020, -0.0260500001542033, 0.0234505236798375, + 0.0311127151218573, -0.0494139126682672, 0.0057093465049849, 0.0124937286655911, -0.0298322975915689, + 0.0006520211333102, -0.0061018680727128, -0.0007081999479528, -0.0060523759094034, 0.0215845995364623 }, + { 0.0295321046399105, -0.0088296411830544, -0.0065057049917325, -0.0053478115612781, -0.0100646496794634, + -0.0015473619084872, 0.0008539960632865, -0.0376381933046211, -0.0328135588935604, 0.0672161874239480, + 0.0667626853916552, -0.0026511651464901, 0.0140451514222062, -0.0544836996133137, 0.0427485157912094, + 0.0097455780205802, 0.0177309072915667, -0.0828759701187452, -0.0729504795471370, 0.0670731961252313 }, + { 0.0082646581043963, -0.0319918630534466, -0.0188454445200422, -0.0374976353856606, 0.0037131290686848, + -0.0132507796987883, -0.0306958830735725, -0.0044119395527308, -0.0140786756619672, -0.0180512599925078, + -0.0208243802903953, -0.0232202769398931, -0.0063135878270273, 0.0110442171178168, 0.1824538048228460, + -0.0006644614422758, -0.0069909097436659, 0.0255407650654681, 0.0099119399501151, -0.0140911517070698 }, + { 0.0261344441524861, -0.0714454044548650, 0.0159436926233439, 0.0028462736216688, -0.0044572637889080, + -0.0089474834434532, -0.0177570282144517, -0.0153693244094452, 0.1160919467206400, 0.0304911481385036, + 0.0047047513411774, -0.0456535116423972, 0.0004491494948617, -0.0767108879444462, -0.0012688533741441, + 0.0192445965934123, 0.0202321954782039, 0.0281039933233607, -0.0590403018490048, 0.0364080426546883 }, + { 0.0115826306265004, 0.1340228176509380, -0.0236200652949049, -0.1284484655137340, -0.0004742338006503, + 0.0127617346949511, -0.0428560878860394, 0.0060030732454125, 0.0089182609926781, 0.0085353834972860, + 0.0048464809638033, 0.0709740071429510, 0.0029940462557054, -0.0483434904493132, -0.0071713680727884, + -0.0036840391887209, 0.0031454003250096, 0.0246243550241551, -0.0449551277644180, 0.0111449232769393 }, + { 0.0140356721886765, -0.0196518236826680, 0.0030517022326582, 0.0582672093364850, -0.0000973895685457, + 0.0021704767224292, 0.0341806268602705, -0.0152035987563018, -0.0903198657739177, 0.0259623214586925, + 0.0155832497882743, -0.0040543568451651, 0.0036477631918247, -0.0532892744763217, -0.0142569373662724, + 0.0104500681408622, 0.0103483945857315, 0.0679534422398752, -0.0768068882938636, 0.0280289727046158 } }; + // dcmut version of PAM model from http://www.ebi.ac.uk/goldman-srv/dayhoff/ final private static double pameigs[] = { 0, -1.93321786301018, -2.20904642493621, -1.74835983874903, - -1.64854548332072, -1.54505559488222, -1.33859384676989, -1.29786201193594, -0.235548517495575, - -0.266951066089808, -0.28965813670665, -1.10505826965282, -1.04323310568532, -0.430423720979904, - -0.541719761016713, -0.879636093986914, -0.711249353378695, -0.725050487280602, -0.776855937389452, - -0.808735559461343 }; + -1.64854548332072, -1.54505559488222, -1.33859384676989, -1.29786201193594, -0.235548517495575, + -0.266951066089808, -0.28965813670665, -1.10505826965282, -1.04323310568532, -0.430423720979904, + -0.541719761016713, -0.879636093986914, -0.711249353378695, -0.725050487280602, -0.776855937389452, + -0.808735559461343 }; final private static double pamprobs[][] = { - { 0.08712695644, 0.04090397955, 0.04043197978, 0.04687197656, 0.03347398326, 0.03825498087, 0.04952997524, + { 0.08712695644, 0.04090397955, 0.04043197978, 0.04687197656, 0.03347398326, 0.03825498087, 0.04952997524, 0.08861195569, 0.03361898319, 0.03688598156, 0.08535695732, 0.08048095976, 0.01475299262, 0.03977198011, 0.05067997466, 0.06957696521, 0.05854197073, 0.01049399475, 0.02991598504, 0.06471796764 }, { 0.07991048383, 0.006888314018, 0.03857806206, 0.07947073194, 0.004895492884, 0.03815829405, - -0.1087562465, 0.008691167141, -0.0140554828, 0.001306404001, -0.001888411299, -0.006921303342, - 0.0007655604228, 0.001583298443, 0.006879590446, -0.171806883, 0.04890917949, 0.0006700432804, - 0.0002276237277, -0.01350591875 }, - { -0.01641514483, -0.007233933239, -0.1377830621, 0.1163201333, -0.002305138017, 0.01557250366, - -0.07455879489, -0.003225343503, 0.0140630487, 0.005112274204, 0.001405731862, 0.01975833782, - -0.001348402973, -0.001085733262, -0.003880514478, 0.0851493313, -0.01163526615, -0.0001197903399, - 0.002056153393, 0.0001536095643 }, - { 0.009669278686, -0.006905863869, 0.101083544, 0.01179903104, -0.003780967591, 0.05845105878, - -0.09138357299, -0.02850503638, -0.03233951408, 0.008708065876, -0.004700705411, -0.02053221579, - 0.001165851398, -0.001366585849, -0.01317695074, 0.1199985703, -0.1146346193, -0.0005953021314, - -0.0004297615194, 0.007475695618 }, - { 0.1722243502, -0.003737582995, -0.02964873222, -0.02050116381, -0.0004530478465, -0.02460043205, - 0.02280768412, -0.02127364909, 0.01570095258, 0.1027744285, -0.005330539586, 0.0179697651, -0.002904077286, - -0.007068126663, -0.0142869583, -0.01444241844, -0.08218861544, 0.0002069181629, 0.001099671379, - -0.1063484263 }, - { -0.1553433627, -0.001169168032, 0.02134785337, 0.0007602305436, 0.0001395330122, 0.03194992019, - -0.01290252206, 0.03281720789, -0.01311103735, 0.1177254769, -0.008008783885, -0.02375317548, - -0.002817809762, -0.008196682776, 0.01731267617, 0.01853526375, 0.08249908546, -2.788771776e-05, - 0.001266182191, -0.09902299976 }, - { -0.03671080341, 0.0274168035, 0.04625877597, 0.07520706414, -0.0001833803619, -0.1207833161, - -0.006415807779, -0.005465629648, 0.02778273972, 0.007589688485, -0.02945266034, -0.03797542064, - 0.07044042052, -0.002018573865, 0.01845277071, 0.006901513991, -0.02430934639, -0.0005919635873, - -0.001266962331, -0.01487591261 }, - { -0.03060317816, 0.01182361623, 0.04200270053, 0.05406235279, -0.0003920498815, -0.09159709348, - -0.009602690652, -0.00382944418, 0.01761361993, 0.01605684317, 0.05198878008, 0.02198696949, - -0.09308930025, -0.00102622863, 0.01477637127, 0.0009314065393, -0.01860959472, -0.0005964703968, - -0.002694284083, 0.02079767439 }, - { 0.0195976494, -0.005104484936, 0.007406728707, 0.01236244954, 0.0201446796, 0.007039564785, - 0.01276942134, 0.02641595685, 0.002764624354, 0.001273314658, -0.01335316035, 0.01105658671, - 2.148773499e-05, -0.02692205639, 0.0118684991, 0.01212624708, 0.01127770094, -0.09842754796, - -0.01942336432, 0.007105703151 }, - { -0.01819461888, -0.01509348507, -0.01297636935, -0.01996453439, 0.1715705905, -0.01601550692, - -0.02122706144, -0.02854628494, -0.009351082371, -0.001527995472, -0.010198224, -0.03609537551, - -0.003153182095, 0.02395980501, -0.01378664626, -0.005992611421, -0.01176810875, 0.003132361603, - 0.03018439539, -0.004956065656 }, - { -0.02733614784, -0.02258066705, -0.0153112506, -0.02475728664, -0.04480525045, -0.01526640341, - -0.02438517425, -0.04836914601, -0.00635964824, 0.02263169831, 0.09794101931, -0.04004304158, - 0.008464393478, 0.1185443142, -0.02239294163, -0.0281550321, -0.01453581604, -0.0246742804, 0.0879619849, - 0.02342867605 }, - { 0.06483718238, 0.1260012082, -0.006496013283, 0.009914915531, -0.004181603532, 0.0003493226286, - 0.01408035752, -0.04881663016, -0.03431167356, -0.01768005602, 0.02362447761, -0.1482364784, - -0.01289035619, -0.001778893279, -0.05240099752, 0.05536174567, 0.06782165352, -0.003548568717, - 0.001125301173, -0.03277489363 }, - { 0.06520296909, -0.0754802543, 0.03139281903, -0.03266449554, -0.004485188002, -0.03389072036, - -0.06163274338, -0.06484769882, 0.05722658289, -0.02824079619, 0.01544837349, 0.03909752708, - 0.002029218884, 0.003151939572, -0.05471208363, 0.07962008342, 0.125916047, 0.0008696184937, - -0.01086027514, -0.05314092355 }, - { 0.004543119081, 0.01935177735, 0.01905511007, 0.02682993409, -0.01199617967, 0.01426278655, - 0.02472521255, 0.03864795501, 0.02166224804, -0.04754243479, -0.1921545477, 0.03621321546, -0.02120627881, - 0.04928097895, 0.009396088815, 0.01748042052, -6.173742851e-05, -0.003168033098, 0.07723565812, - -0.08255529309 }, - { 0.06710378668, -0.09441410284, -0.004801776989, 0.008830272165, -0.01021645042, -0.02764365608, - 0.004250361851, 0.1648777542, -0.037446109, 0.004541057635, -0.0296980702, -0.1532325189, -0.008940580901, - 0.006998050812, 0.02338809379, 0.03175059182, 0.02033965512, 0.006388075608, 0.001762762044, 0.02616280361 }, - { 0.01915943021, -0.05432967274, 0.01249342683, 0.06836622457, 0.002054462161, -0.01233535859, - 0.07087282652, -0.08948637051, -0.1245896013, -0.02204522882, 0.03791481736, 0.06557467874, 0.005529294156, - -0.006296644235, 0.02144530752, 0.01664230081, 0.02647078439, 0.001737725271, 0.01414149877, -0.05331990116 }, - { 0.0266659303, 0.0564142853, -0.0263767738, -0.08029726006, -0.006059357163, -0.06317558457, - -0.0911894019, 0.05401487057, -0.08178072458, 0.01580699778, -0.05370550396, 0.09798653264, 0.003934944022, - 0.01977291947, 0.0441198541, 0.02788220393, 0.03201877081, -0.00206161759, -0.005101423308, 0.03113033802 }, - { 0.02980360751, -0.009513246268, -0.009543527165, -0.02190644172, -0.006146440672, 0.01207009085, - -0.0126989156, -0.1378266418, 0.0275235217, 0.00551720592, -0.03104791544, -0.07111701247, -0.006081754489, - -0.01337494521, 0.1783961085, 0.01453225059, 0.01938736048, 0.0004488631071, 0.0110844398, 0.02049339243 }, - { -0.01433508581, 0.01258858175, -0.004294252236, -0.007146532854, 0.009541628809, 0.008040155729, - -0.006857781832, 0.05584120066, 0.007749418365, -0.05867835844, 0.08008131283, -0.004877854222, - -0.0007128540743, 0.09489058424, 0.06421121962, 0.00271493526, -0.03229944773, -0.001732026038, - -0.08053448316, -0.1241903609 }, - { -0.009854113227, 0.01294129929, -0.00593064392, -0.03016833115, -0.002018439732, -0.00792418722, - -0.03372768732, 0.07828561288, 0.007722254639, -0.05067377561, 0.1191848621, 0.005059475202, - 0.004762387166, -0.1029870175, 0.03537190114, 0.001089956203, -0.02139157573, -0.001015245062, - 0.08400521847, -0.08273195059 } }; + -0.1087562465, 0.008691167141, -0.0140554828, 0.001306404001, -0.001888411299, -0.006921303342, + 0.0007655604228, 0.001583298443, 0.006879590446, -0.171806883, 0.04890917949, 0.0006700432804, + 0.0002276237277, -0.01350591875 }, + { -0.01641514483, -0.007233933239, -0.1377830621, 0.1163201333, -0.002305138017, 0.01557250366, + -0.07455879489, -0.003225343503, 0.0140630487, 0.005112274204, 0.001405731862, 0.01975833782, + -0.001348402973, -0.001085733262, -0.003880514478, 0.0851493313, -0.01163526615, -0.0001197903399, + 0.002056153393, 0.0001536095643 }, + { 0.009669278686, -0.006905863869, 0.101083544, 0.01179903104, -0.003780967591, 0.05845105878, + -0.09138357299, -0.02850503638, -0.03233951408, 0.008708065876, -0.004700705411, -0.02053221579, + 0.001165851398, -0.001366585849, -0.01317695074, 0.1199985703, -0.1146346193, -0.0005953021314, + -0.0004297615194, 0.007475695618 }, + { 0.1722243502, -0.003737582995, -0.02964873222, -0.02050116381, -0.0004530478465, -0.02460043205, + 0.02280768412, -0.02127364909, 0.01570095258, 0.1027744285, -0.005330539586, 0.0179697651, -0.002904077286, + -0.007068126663, -0.0142869583, -0.01444241844, -0.08218861544, 0.0002069181629, 0.001099671379, + -0.1063484263 }, + { -0.1553433627, -0.001169168032, 0.02134785337, 0.0007602305436, 0.0001395330122, 0.03194992019, + -0.01290252206, 0.03281720789, -0.01311103735, 0.1177254769, -0.008008783885, -0.02375317548, + -0.002817809762, -0.008196682776, 0.01731267617, 0.01853526375, 0.08249908546, -2.788771776e-05, + 0.001266182191, -0.09902299976 }, + { -0.03671080341, 0.0274168035, 0.04625877597, 0.07520706414, -0.0001833803619, -0.1207833161, + -0.006415807779, -0.005465629648, 0.02778273972, 0.007589688485, -0.02945266034, -0.03797542064, + 0.07044042052, -0.002018573865, 0.01845277071, 0.006901513991, -0.02430934639, -0.0005919635873, + -0.001266962331, -0.01487591261 }, + { -0.03060317816, 0.01182361623, 0.04200270053, 0.05406235279, -0.0003920498815, -0.09159709348, + -0.009602690652, -0.00382944418, 0.01761361993, 0.01605684317, 0.05198878008, 0.02198696949, + -0.09308930025, -0.00102622863, 0.01477637127, 0.0009314065393, -0.01860959472, -0.0005964703968, + -0.002694284083, 0.02079767439 }, + { 0.0195976494, -0.005104484936, 0.007406728707, 0.01236244954, 0.0201446796, 0.007039564785, + 0.01276942134, 0.02641595685, 0.002764624354, 0.001273314658, -0.01335316035, 0.01105658671, + 2.148773499e-05, -0.02692205639, 0.0118684991, 0.01212624708, 0.01127770094, -0.09842754796, + -0.01942336432, 0.007105703151 }, + { -0.01819461888, -0.01509348507, -0.01297636935, -0.01996453439, 0.1715705905, -0.01601550692, + -0.02122706144, -0.02854628494, -0.009351082371, -0.001527995472, -0.010198224, -0.03609537551, + -0.003153182095, 0.02395980501, -0.01378664626, -0.005992611421, -0.01176810875, 0.003132361603, + 0.03018439539, -0.004956065656 }, + { -0.02733614784, -0.02258066705, -0.0153112506, -0.02475728664, -0.04480525045, -0.01526640341, + -0.02438517425, -0.04836914601, -0.00635964824, 0.02263169831, 0.09794101931, -0.04004304158, + 0.008464393478, 0.1185443142, -0.02239294163, -0.0281550321, -0.01453581604, -0.0246742804, 0.0879619849, + 0.02342867605 }, + { 0.06483718238, 0.1260012082, -0.006496013283, 0.009914915531, -0.004181603532, 0.0003493226286, + 0.01408035752, -0.04881663016, -0.03431167356, -0.01768005602, 0.02362447761, -0.1482364784, + -0.01289035619, -0.001778893279, -0.05240099752, 0.05536174567, 0.06782165352, -0.003548568717, + 0.001125301173, -0.03277489363 }, + { 0.06520296909, -0.0754802543, 0.03139281903, -0.03266449554, -0.004485188002, -0.03389072036, + -0.06163274338, -0.06484769882, 0.05722658289, -0.02824079619, 0.01544837349, 0.03909752708, + 0.002029218884, 0.003151939572, -0.05471208363, 0.07962008342, 0.125916047, 0.0008696184937, + -0.01086027514, -0.05314092355 }, + { 0.004543119081, 0.01935177735, 0.01905511007, 0.02682993409, -0.01199617967, 0.01426278655, + 0.02472521255, 0.03864795501, 0.02166224804, -0.04754243479, -0.1921545477, 0.03621321546, -0.02120627881, + 0.04928097895, 0.009396088815, 0.01748042052, -6.173742851e-05, -0.003168033098, 0.07723565812, + -0.08255529309 }, + { 0.06710378668, -0.09441410284, -0.004801776989, 0.008830272165, -0.01021645042, -0.02764365608, + 0.004250361851, 0.1648777542, -0.037446109, 0.004541057635, -0.0296980702, -0.1532325189, -0.008940580901, + 0.006998050812, 0.02338809379, 0.03175059182, 0.02033965512, 0.006388075608, 0.001762762044, 0.02616280361 }, + { 0.01915943021, -0.05432967274, 0.01249342683, 0.06836622457, 0.002054462161, -0.01233535859, + 0.07087282652, -0.08948637051, -0.1245896013, -0.02204522882, 0.03791481736, 0.06557467874, 0.005529294156, + -0.006296644235, 0.02144530752, 0.01664230081, 0.02647078439, 0.001737725271, 0.01414149877, -0.05331990116 }, + { 0.0266659303, 0.0564142853, -0.0263767738, -0.08029726006, -0.006059357163, -0.06317558457, + -0.0911894019, 0.05401487057, -0.08178072458, 0.01580699778, -0.05370550396, 0.09798653264, 0.003934944022, + 0.01977291947, 0.0441198541, 0.02788220393, 0.03201877081, -0.00206161759, -0.005101423308, 0.03113033802 }, + { 0.02980360751, -0.009513246268, -0.009543527165, -0.02190644172, -0.006146440672, 0.01207009085, + -0.0126989156, -0.1378266418, 0.0275235217, 0.00551720592, -0.03104791544, -0.07111701247, -0.006081754489, + -0.01337494521, 0.1783961085, 0.01453225059, 0.01938736048, 0.0004488631071, 0.0110844398, 0.02049339243 }, + { -0.01433508581, 0.01258858175, -0.004294252236, -0.007146532854, 0.009541628809, 0.008040155729, + -0.006857781832, 0.05584120066, 0.007749418365, -0.05867835844, 0.08008131283, -0.004877854222, + -0.0007128540743, 0.09489058424, 0.06421121962, 0.00271493526, -0.03229944773, -0.001732026038, + -0.08053448316, -0.1241903609 }, + { -0.009854113227, 0.01294129929, -0.00593064392, -0.03016833115, -0.002018439732, -0.00792418722, + -0.03372768732, 0.07828561288, 0.007722254639, -0.05067377561, 0.1191848621, 0.005059475202, + 0.004762387166, -0.1029870175, 0.03537190114, 0.001089956203, -0.02139157573, -0.001015245062, + 0.08400521847, -0.08273195059 } }; } diff --git a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java index 52d97d3..0e554f8 100644 --- a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java +++ b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java @@ -437,7 +437,7 @@ public class TestPhylogenyReconstruction { private static boolean testDistanceCalculationMethods( final File test_dir ) { try { final Msa msa0 = GeneralMsaParser.parse( new FileInputStream( test_dir + ForesterUtil.FILE_SEPARATOR - + "bcl.aln" ) ); + + "bcl.aln" ) ); final BasicSymmetricalDistanceMatrix pwd0 = PairwiseDistanceCalculator.calcKimuraDistances( msa0 ); if ( pwd0.getSize() != 120 ) { return false; @@ -465,7 +465,7 @@ public class TestPhylogenyReconstruction { final String p1_str = "((((((a,b)ab,c)ac,d)ad,(e,f)ef)af,(g,h)gh)ah,i)r"; final Phylogeny p1 = factory1.create( p1_str, new NHXParser() )[ 0 ]; CharacterStateMatrix m1 = new BasicCharacterStateMatrix( 9, - 1 ); + 1 ); m1.setIdentifier( 0, "a" ); m1.setIdentifier( 1, "b" ); m1.setIdentifier( 2, "c" ); @@ -538,7 +538,7 @@ public class TestPhylogenyReconstruction { final String p2_str = "((((((a,b)ab,c)ac,d)ad,(e,f)ef)af,(g,h,i)gi)ai,((j,k,l)jl,(m,n,o)mo,(p,q,r)pr)jr)root"; final Phylogeny p2 = factory2.create( p2_str, new NHXParser() )[ 0 ]; final CharacterStateMatrix m2 = new BasicCharacterStateMatrix( 18, - 4 ); + 4 ); m2.setIdentifier( 0, "a" ); m2.setIdentifier( 1, "b" ); m2.setIdentifier( 2, "c" ); @@ -847,7 +847,7 @@ public class TestPhylogenyReconstruction { final String p10_str = "((((((a,b)ab,c)ac,d)ad,(e,f)ef)af,(g,h)gh)ah,i)r"; final Phylogeny p10 = factory10.create( p10_str, new NHXParser() )[ 0 ]; final CharacterStateMatrix m10 = new BasicCharacterStateMatrix( 9, - 1 ); + 1 ); m10.setIdentifier( 0, "a" ); m10.setIdentifier( 1, "b" ); m10.setIdentifier( 2, "c" ); @@ -890,7 +890,7 @@ public class TestPhylogenyReconstruction { final String p1_str = "((((((a,b,y)aby,c)ac,d)ad,(e,f)ef)af,(g,h)gh)ah,i)r"; final Phylogeny p1 = factory1.create( p1_str, new NHXParser() )[ 0 ]; final CharacterStateMatrix m1 = new BasicCharacterStateMatrix( 10, - 1 ); + 1 ); m1.setIdentifier( 0, "a" ); m1.setIdentifier( 1, "b" ); m1.setIdentifier( 2, "y" ); @@ -961,7 +961,7 @@ public class TestPhylogenyReconstruction { final String p2_str = "((((((a,b,y)aby,c,d)cad,e,f)af,(g,h)gh)ah,i))r"; final Phylogeny p2 = factory2.create( p2_str, new NHXParser() )[ 0 ]; final CharacterStateMatrix m2 = new BasicCharacterStateMatrix( 10, - 1 ); + 1 ); m2.setIdentifier( 0, "a" ); m2.setIdentifier( 1, "b" ); m2.setIdentifier( 2, "y" ); @@ -2121,7 +2121,7 @@ public class TestPhylogenyReconstruction { return false; } if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getParent() - .getDistanceToParent(), 0.458845 ) ) { + .getDistanceToParent(), 0.458845 ) ) { return false; } m = new BasicSymmetricalDistanceMatrix( 4 ); @@ -2236,11 +2236,11 @@ public class TestPhylogenyReconstruction { return false; } if ( isUnequal( p2f.getNode( "Chimp" ).getParent().getParent().getParent().getParent() - .getDistanceToParent(), 0.42027 ) ) { + .getDistanceToParent(), 0.42027 ) ) { return false; } if ( isUnequal( p2f.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getParent() - .getDistanceToParent(), 0.458845 ) ) { + .getDistanceToParent(), 0.458845 ) ) { return false; } } @@ -2669,7 +2669,7 @@ public class TestPhylogenyReconstruction { return false; } if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getParent() - .getDistanceToParent(), 0.458845 ) ) { + .getDistanceToParent(), 0.458845 ) ) { return false; } // diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java index 1f06010..f63af04 100644 --- a/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java +++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java @@ -214,9 +214,9 @@ public final class NeighborJoining { + " (" + ( ForesterUtil.isEmpty( n.getChildNode1().getName() ) ? n.getChildNode1().getId() : n.getChildNode1() .getName() ) - + "+" - + ( ForesterUtil.isEmpty( n.getChildNode2().getName() ) ? n.getChildNode2().getId() : n.getChildNode2() - .getName() ) + ")"; + + "+" + + ( ForesterUtil.isEmpty( n.getChildNode2().getName() ) ? n.getChildNode2().getId() : n.getChildNode2() + .getName() ) + ")"; } // only the values in the lower triangle are used. diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningF.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningF.java index ff35f4a..217cdba 100644 --- a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningF.java +++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningF.java @@ -207,9 +207,9 @@ public final class NeighborJoiningF { + " (" + ( ForesterUtil.isEmpty( n.getChildNode1().getName() ) ? n.getChildNode1().getId() : n.getChildNode1() .getName() ) - + "+" - + ( ForesterUtil.isEmpty( n.getChildNode2().getName() ) ? n.getChildNode2().getId() : n.getChildNode2() - .getName() ) + ")"; + + "+" + + ( ForesterUtil.isEmpty( n.getChildNode2().getName() ) ? n.getChildNode2().getId() : n.getChildNode2() + .getName() ) + ")"; } // only the values in the lower triangle are used. diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java index 081be11..209b93f 100644 --- a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java +++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java @@ -120,7 +120,7 @@ public final class NeighborJoiningR { if ( _verbose ) { System.out.println( "" ); System.out - .println( "----------------------------------------------------------------------------------" ); + .println( "----------------------------------------------------------------------------------" ); System.out.println( "" ); } } @@ -259,9 +259,9 @@ public final class NeighborJoiningR { + " (" + ( ForesterUtil.isEmpty( n.getChildNode1().getName() ) ? n.getChildNode1().getId() : n.getChildNode1() .getName() ) - + "+" - + ( ForesterUtil.isEmpty( n.getChildNode2().getName() ) ? n.getChildNode2().getId() : n.getChildNode2() - .getName() ) + ")"; + + "+" + + ( ForesterUtil.isEmpty( n.getChildNode2().getName() ) ? n.getChildNode2().getId() : n.getChildNode2() + .getName() ) + ")"; } // only the values in the lower triangle are used. diff --git a/forester/java/src/org/forester/evoinference/distance/PairwiseDistanceCalculator.java b/forester/java/src/org/forester/evoinference/distance/PairwiseDistanceCalculator.java index 67d4b53..39a446f 100644 --- a/forester/java/src/org/forester/evoinference/distance/PairwiseDistanceCalculator.java +++ b/forester/java/src/org/forester/evoinference/distance/PairwiseDistanceCalculator.java @@ -53,7 +53,7 @@ public final class PairwiseDistanceCalculator { /** * "Kimura Distance" * Kimura, 1983 - * + * * @param row_1 * @param row_2 * @return @@ -143,23 +143,23 @@ public final class PairwiseDistanceCalculator { public static BasicSymmetricalDistanceMatrix calcFractionalDissimilarities( final Msa msa ) { return new PairwiseDistanceCalculator( msa, DEFAULT_VALUE_FOR_TOO_LARGE_DISTANCE_FOR_KIMURA_FORMULA ) - .calcFractionalDissimilarities(); + .calcFractionalDissimilarities(); } public static BasicSymmetricalDistanceMatrix calcPoissonDistances( final Msa msa ) { return new PairwiseDistanceCalculator( msa, DEFAULT_VALUE_FOR_TOO_LARGE_DISTANCE_FOR_KIMURA_FORMULA ) - .calcPoissonDistances(); + .calcPoissonDistances(); } public static BasicSymmetricalDistanceMatrix calcKimuraDistances( final Msa msa ) { return new PairwiseDistanceCalculator( msa, DEFAULT_VALUE_FOR_TOO_LARGE_DISTANCE_FOR_KIMURA_FORMULA ) - .calcKimuraDistances(); + .calcKimuraDistances(); } public static BasicSymmetricalDistanceMatrix calcKimuraDistances( final Msa msa, final double value_for_too_large_distance_for_kimura_formula ) { return new PairwiseDistanceCalculator( msa, value_for_too_large_distance_for_kimura_formula ) - .calcKimuraDistances(); + .calcKimuraDistances(); } public enum PWD_DISTANCE_METHOD { diff --git a/forester/java/src/org/forester/evoinference/distance/Sarray.java b/forester/java/src/org/forester/evoinference/distance/Sarray.java index 6e30f5c..2e961b8 100644 --- a/forester/java/src/org/forester/evoinference/distance/Sarray.java +++ b/forester/java/src/org/forester/evoinference/distance/Sarray.java @@ -65,7 +65,7 @@ public final class Sarray { if ( x == null ) { System.out.println(); System.out - .println( "________________________________________________________________________________________" ); + .println( "________________________________________________________________________________________" ); System.out.println( toString() ); throw new IllegalArgumentException( "key " + key + " (->" + value + ") does not exist for row " + j ); } diff --git a/forester/java/src/org/forester/evoinference/distance/Sset.java b/forester/java/src/org/forester/evoinference/distance/Sset.java index 6ad7df3..c8f912f 100644 --- a/forester/java/src/org/forester/evoinference/distance/Sset.java +++ b/forester/java/src/org/forester/evoinference/distance/Sset.java @@ -67,7 +67,7 @@ public final class Sset { if ( x == null ) { System.out.println(); System.out - .println( "________________________________________________________________________________________" ); + .println( "________________________________________________________________________________________" ); System.out.println( toString() ); throw new IllegalArgumentException( "key " + key + " (->" + value + ") does not exist for row " + j ); } @@ -77,7 +77,7 @@ public final class Sset { if ( !x.contains( value ) ) { System.out.println(); System.out - .println( "________________________________________________________________________________________" ); + .println( "________________________________________________________________________________________" ); System.out.println( toString() ); throw new IllegalArgumentException( "pairing " + key + "->" + value + " does not exist for row " + j ); @@ -89,7 +89,7 @@ public final class Sset { if ( DEBUG ) { if ( !x.remove( value ) ) { throw new IllegalArgumentException( "pairing " + key + "->" + value - + " does not exist (could not be removed) for row " + j ); + + " does not exist (could not be removed) for row " + j ); } } else { diff --git a/forester/java/src/org/forester/evoinference/matrix/character/BasicCharacterStateMatrix.java b/forester/java/src/org/forester/evoinference/matrix/character/BasicCharacterStateMatrix.java index 4bf6a26..7b1055f 100644 --- a/forester/java/src/org/forester/evoinference/matrix/character/BasicCharacterStateMatrix.java +++ b/forester/java/src/org/forester/evoinference/matrix/character/BasicCharacterStateMatrix.java @@ -102,7 +102,7 @@ public class BasicCharacterStateMatrix implements CharacterStateMatrix { @Override public CharacterStateMatrix copy() { final CharacterStateMatrix new_matrix = new BasicCharacterStateMatrix( getNumberOfIdentifiers(), - getNumberOfCharacters() ); + getNumberOfCharacters() ); for( int character = 0; character < getNumberOfCharacters(); ++character ) { if ( getCharacter( character ) != null ) { new_matrix.setCharacter( character, getCharacter( character ) ); @@ -129,7 +129,7 @@ public class BasicCharacterStateMatrix implements CharacterStateMatrix { } else if ( o.getClass() != this.getClass() ) { throw new IllegalArgumentException( "attempt to check character state matrix to " + o + " [" + o.getClass() - + "]" ); + + "]" ); } else { final CharacterStateMatrix other = ( CharacterStateMatrix ) o; @@ -247,7 +247,7 @@ public class BasicCharacterStateMatrix implements CharacterStateMatrix { @Override public CharacterStateMatrix pivot() { final CharacterStateMatrix new_matrix = new BasicCharacterStateMatrix( getNumberOfCharacters(), - getNumberOfIdentifiers() ); + getNumberOfIdentifiers() ); for( int character = 0; character < getNumberOfCharacters(); ++character ) { if ( getCharacter( character ) != null ) { new_matrix.setIdentifier( character, getCharacter( character ) ); @@ -424,7 +424,7 @@ public class BasicCharacterStateMatrix implements CharacterStateMatrix { public void writeNexusBinaryChractersBlock( final Writer w ) throws IOException { //BEGIN CHARACTERS; // DIMENSIONS NCHAR=x; - //BEGIN CHARSTATELABELS + //BEGIN CHARSTATELABELS // 1 bcl, // 2 tir, //END; diff --git a/forester/java/src/org/forester/evoinference/parsimony/DolloParsimony.java b/forester/java/src/org/forester/evoinference/parsimony/DolloParsimony.java index 57df9c7..0946218 100644 --- a/forester/java/src/org/forester/evoinference/parsimony/DolloParsimony.java +++ b/forester/java/src/org/forester/evoinference/parsimony/DolloParsimony.java @@ -135,7 +135,7 @@ public class DolloParsimony { final BinaryStates state = matrix.getState( indentifier_index, character_index ); if ( state == null ) { throw new IllegalArgumentException( "value at [" + indentifier_index + ", " + character_index - + "] is null" ); + + "] is null" ); } states.put( p.getNode( matrix.getIdentifier( indentifier_index ) ), state ); } @@ -176,8 +176,8 @@ public class DolloParsimony { nodes.add( postorder.next() ); } setGainLossMatrix( new BasicCharacterStateMatrix( nodes.size(), - external_node_states_matrix - .getNumberOfCharacters() ) ); + external_node_states_matrix + .getNumberOfCharacters() ) ); int identifier_index = 0; for( final PhylogenyNode node : nodes ) { getGainLossMatrix().setIdentifier( identifier_index++, @@ -200,8 +200,8 @@ public class DolloParsimony { } } setInternalStatesMatrix( new BasicCharacterStateMatrix( internal_nodes.size(), - external_node_states_matrix - .getNumberOfCharacters() ) ); + external_node_states_matrix + .getNumberOfCharacters() ) ); int identifier_index = 0; for( final PhylogenyNode node : internal_nodes ) { getInternalStatesMatrix().setIdentifier( identifier_index++, @@ -314,17 +314,17 @@ public class DolloParsimony { final PhylogenyNode node, final GainLossStates state ) { getGainLossMatrix().setState( ForesterUtil.isEmpty( node.getName() ) ? node.getId() + "" : node.getName(), - character_state_column, - state ); + character_state_column, + state ); } private void setInternalNodeState( final Map states, final int character_state_column, final PhylogenyNode node ) { getInternalStatesMatrix() - .setState( ForesterUtil.isEmpty( node.getName() ) ? node.getId() + "" : node.getName(), - character_state_column, - states.get( node ) ); + .setState( ForesterUtil.isEmpty( node.getName() ) ? node.getId() + "" : node.getName(), + character_state_column, + states.get( node ) ); } private void setInternalStatesMatrix( final CharacterStateMatrix internal_states_matrix ) { @@ -368,7 +368,7 @@ public class DolloParsimony { final PhylogenyNode node_child = node.getChildNode( i ); if ( !states.containsKey( node_child ) ) { throw new RuntimeException( "this should not have happened: node [" + node_child.getName() - + "] not found in node state map" ); + + "] not found in node state map" ); } if ( ( states.get( node_child ) == BinaryStates.PRESENT ) || ( states.get( node_child ) == BinaryStates.UNKNOWN ) ) { diff --git a/forester/java/src/org/forester/evoinference/parsimony/FitchParsimony.java b/forester/java/src/org/forester/evoinference/parsimony/FitchParsimony.java index df22cbc..7c7c9f2 100644 --- a/forester/java/src/org/forester/evoinference/parsimony/FitchParsimony.java +++ b/forester/java/src/org/forester/evoinference/parsimony/FitchParsimony.java @@ -148,7 +148,7 @@ public class FitchParsimony { /** * Returns a view of the internal states prior to trace-back. - * + * * @return */ public CharacterStateMatrix> getInternalStatesMatrixPriorToTraceback() { @@ -200,13 +200,13 @@ public class FitchParsimony { * This sets whether to use the first or last state in the sorted * states at the undecided internal nodes. * For randomized choices set randomize to true (and this to false). - * + * * Note. It might be advisable to set this to false * for BinaryStates if absence at the root is preferred - * (given the enum BinaryStates sorts in the following order: + * (given the enum BinaryStates sorts in the following order: * ABSENT, UNKNOWN, PRESENT). - * - * + * + * * @param use_last */ public void setUseLast( final boolean use_last ) { @@ -245,7 +245,7 @@ public class FitchParsimony { final PhylogenyNode node_child = node.getChildNode( i ); if ( !states.containsKey( node_child ) ) { throw new AssertionError( "this should not have happened: node [" + node_child.getName() - + "] not found in node state map" ); + + "] not found in node state map" ); } if ( i == 0 ) { states_in_child_nodes.addAll( states.get( node_child ) ); @@ -282,7 +282,7 @@ public class FitchParsimony { final STATE_TYPE state = matrix.getState( indentifier_index, character_index ); if ( state == null ) { throw new IllegalArgumentException( "value at [" + indentifier_index + ", " + character_index - + "] is null" ); + + "] is null" ); } final SortedSet l = new TreeSet(); l.add( state ); @@ -299,7 +299,7 @@ public class FitchParsimony { final STATE_TYPE state = matrix.getState( indentifier_index, character_index ); if ( state == null ) { throw new IllegalArgumentException( "value at [" + indentifier_index + ", " + character_index - + "] is null" ); + + "] is null" ); } states.put( p.getNode( matrix.getIdentifier( indentifier_index ) ), state ); } @@ -313,7 +313,7 @@ public class FitchParsimony { final PhylogenyNode node_child = node.getChildNode( i ); if ( !states.containsKey( node_child ) ) { throw new AssertionError( "this should not have happened: node [" + node_child.getName() - + "] not found in node state map" ); + + "] not found in node state map" ); } states_in_child_nodes.addAll( states.get( node_child ) ); } @@ -340,8 +340,8 @@ public class FitchParsimony { nodes.add( postorder.next() ); } setGainLossMatrix( new BasicCharacterStateMatrix( nodes.size(), - external_node_states_matrix - .getNumberOfCharacters() ) ); + external_node_states_matrix + .getNumberOfCharacters() ) ); int identifier_index = 0; for( final PhylogenyNode node : nodes ) { getGainLossMatrix().setIdentifier( identifier_index++, @@ -364,11 +364,11 @@ public class FitchParsimony { } } setInternalStatesMatrixPriorToTraceback( new BasicCharacterStateMatrix>( internal_nodes.size(), - external_node_states_matrix - .getNumberOfCharacters() ) ); + external_node_states_matrix + .getNumberOfCharacters() ) ); setInternalStatesMatrixTraceback( new BasicCharacterStateMatrix( internal_nodes.size(), - external_node_states_matrix - .getNumberOfCharacters() ) ); + external_node_states_matrix + .getNumberOfCharacters() ) ); int identifier_index = 0; for( final PhylogenyNode node : internal_nodes ) { getInternalStatesMatrix().setIdentifier( identifier_index, @@ -384,7 +384,7 @@ public class FitchParsimony { external_node_states_matrix.getCharacter( character_index ) ); getInternalStatesMatrixPriorToTraceback().setCharacter( character_index, external_node_states_matrix - .getCharacter( character_index ) ); + .getCharacter( character_index ) ); } } @@ -482,7 +482,7 @@ public class FitchParsimony { else if ( current_binary_state == ABSENT ) {//new setGainLossState( character_state_column, current_node, UNCHANGED_ABSENT );//new }//new - // setGainLossState( character_state_column, current_node, UNKNOWN_GAIN_LOSS ); + // setGainLossState( character_state_column, current_node, UNKNOWN_GAIN_LOSS ); } } } @@ -507,26 +507,26 @@ public class FitchParsimony { final PhylogenyNode node, final GainLossStates state ) { getGainLossMatrix().setState( ForesterUtil.isEmpty( node.getName() ) ? node.getId() + "" : node.getName(), - character_state_column, - state ); + character_state_column, + state ); } private void setInternalNodeState( final Map states, final int character_state_column, final PhylogenyNode node ) { getInternalStatesMatrix() - .setState( ForesterUtil.isEmpty( node.getName() ) ? node.getId() + "" : node.getName(), - character_state_column, - states.get( node ) ); + .setState( ForesterUtil.isEmpty( node.getName() ) ? node.getId() + "" : node.getName(), + character_state_column, + states.get( node ) ); } private void setInternalNodeStatePriorToTraceback( final Map> states, final int character_state_column, final PhylogenyNode node ) { getInternalStatesMatrixPriorToTraceback() - .setState( ForesterUtil.isEmpty( node.getName() ) ? String.valueOf( node.getId() ) : node.getName(), - character_state_column, - toListSorted( states.get( node ) ) ); + .setState( ForesterUtil.isEmpty( node.getName() ) ? String.valueOf( node.getId() ) : node.getName(), + character_state_column, + toListSorted( states.get( node ) ) ); } private void setInternalStatesMatrixPriorToTraceback( final CharacterStateMatrix> internal_states_matrix_prior_to_traceback ) { diff --git a/forester/java/src/org/forester/evoinference/parsimony/SankoffParsimony.java b/forester/java/src/org/forester/evoinference/parsimony/SankoffParsimony.java index ecad514..88a0619 100644 --- a/forester/java/src/org/forester/evoinference/parsimony/SankoffParsimony.java +++ b/forester/java/src/org/forester/evoinference/parsimony/SankoffParsimony.java @@ -45,11 +45,11 @@ import org.forester.phylogeny.iterators.PhylogenyNodeIterator; import org.forester.util.ForesterUtil; /** - * + * * IN PROGRESS! * DO NOT USE! - * - * + * + * * @param */ public class SankoffParsimony { @@ -154,7 +154,7 @@ public class SankoffParsimony { /** * Returns a view of the internal states prior to trace-back. - * + * * @return */ public CharacterStateMatrix> getInternalStatesMatrixPriorToTraceback() { @@ -171,7 +171,7 @@ public class SankoffParsimony { final PhylogenyNode node_child = node.getChildNode( i ); if ( !states.containsKey( node_child ) ) { throw new AssertionError( "this should not have happened: node [" + node_child.getName() - + "] not found in node state map" ); + + "] not found in node state map" ); } if ( i == 0 ) { states_in_child_nodes.addAll( states.get( node_child ) ); @@ -208,7 +208,7 @@ public class SankoffParsimony { final STATE_TYPE state = matrix.getState( indentifier_index, character_index ); if ( state == null ) { throw new IllegalArgumentException( "value at [" + indentifier_index + ", " + character_index - + "] is null" ); + + "] is null" ); } final SortedSet l = new TreeSet(); l.add( state ); @@ -225,7 +225,7 @@ public class SankoffParsimony { final STATE_TYPE state = matrix.getState( indentifier_index, character_index ); if ( state == null ) { throw new IllegalArgumentException( "value at [" + indentifier_index + ", " + character_index - + "] is null" ); + + "] is null" ); } states.put( p.getNode( matrix.getIdentifier( indentifier_index ) ), state ); } @@ -251,7 +251,7 @@ public class SankoffParsimony { final PhylogenyNode node_child = node.getChildNode( i ); if ( !states.containsKey( node_child ) ) { throw new AssertionError( "this should not have happened: node [" + node_child.getName() - + "] not found in node state map" ); + + "] not found in node state map" ); } states_in_child_nodes.addAll( states.get( node_child ) ); } @@ -278,8 +278,8 @@ public class SankoffParsimony { nodes.add( postorder.next() ); } setGainLossMatrix( new BasicCharacterStateMatrix( nodes.size(), - external_node_states_matrix - .getNumberOfCharacters() ) ); + external_node_states_matrix + .getNumberOfCharacters() ) ); int identifier_index = 0; for( final PhylogenyNode node : nodes ) { getGainLossMatrix().setIdentifier( identifier_index++, @@ -302,11 +302,11 @@ public class SankoffParsimony { } } setInternalStatesMatrixPriorToTraceback( new BasicCharacterStateMatrix>( internal_nodes.size(), - external_node_states_matrix - .getNumberOfCharacters() ) ); + external_node_states_matrix + .getNumberOfCharacters() ) ); setInternalStatesMatrixTraceback( new BasicCharacterStateMatrix( internal_nodes.size(), - external_node_states_matrix - .getNumberOfCharacters() ) ); + external_node_states_matrix + .getNumberOfCharacters() ) ); int identifier_index = 0; for( final PhylogenyNode node : internal_nodes ) { getInternalStatesMatrix().setIdentifier( identifier_index, @@ -322,7 +322,7 @@ public class SankoffParsimony { external_node_states_matrix.getCharacter( character_index ) ); getInternalStatesMatrixPriorToTraceback().setCharacter( character_index, external_node_states_matrix - .getCharacter( character_index ) ); + .getCharacter( character_index ) ); } } @@ -421,7 +421,7 @@ public class SankoffParsimony { else if ( current_binary_state == ABSENT ) {//new setGainLossState( character_state_column, current_node, UNCHANGED_ABSENT );//new }//new - // setGainLossState( character_state_column, current_node, UNKNOWN_GAIN_LOSS ); + // setGainLossState( character_state_column, current_node, UNKNOWN_GAIN_LOSS ); } } } @@ -446,26 +446,26 @@ public class SankoffParsimony { final PhylogenyNode node, final GainLossStates state ) { getGainLossMatrix().setState( ForesterUtil.isEmpty( node.getName() ) ? node.getId() + "" : node.getName(), - character_state_column, - state ); + character_state_column, + state ); } private void setInternalNodeState( final Map states, final int character_state_column, final PhylogenyNode node ) { getInternalStatesMatrix() - .setState( ForesterUtil.isEmpty( node.getName() ) ? node.getId() + "" : node.getName(), - character_state_column, - states.get( node ) ); + .setState( ForesterUtil.isEmpty( node.getName() ) ? node.getId() + "" : node.getName(), + character_state_column, + states.get( node ) ); } private void setInternalNodeStatePriorToTraceback( final Map> states, final int character_state_column, final PhylogenyNode node ) { getInternalStatesMatrixPriorToTraceback().setState( ForesterUtil.isEmpty( node.getName() ) ? node.getId() + "" - : node.getName(), - character_state_column, - toListSorted( states.get( node ) ) ); + : node.getName(), + character_state_column, + toListSorted( states.get( node ) ) ); } private void setInternalStatesMatrixPriorToTraceback( final CharacterStateMatrix> internal_states_matrix_prior_to_traceback ) { @@ -518,13 +518,13 @@ public class SankoffParsimony { * This sets whether to use the first or last state in the sorted * states at the undecided internal nodes. * For randomized choices set randomize to true (and this to false). - * + * * Note. It might be advisable to set this to false * for BinaryStates if absence at the root is preferred - * (given the enum BinaryStates sorts in the following order: + * (given the enum BinaryStates sorts in the following order: * ABSENT, UNKNOWN, PRESENT). - * - * + * + * * @param use_last */ public void setUseLast( final boolean use_last ) { diff --git a/forester/java/src/org/forester/go/BasicGoRelationship.java b/forester/java/src/org/forester/go/BasicGoRelationship.java index 270f31a..d539947 100644 --- a/forester/java/src/org/forester/go/BasicGoRelationship.java +++ b/forester/java/src/org/forester/go/BasicGoRelationship.java @@ -83,8 +83,8 @@ public class BasicGoRelationship implements GoRelationship { /** * Based on value and type. - * - * + * + * */ @Override public boolean equals( final Object o ) { diff --git a/forester/java/src/org/forester/go/BasicGoSubset.java b/forester/java/src/org/forester/go/BasicGoSubset.java index 420f01b..8dd8f64 100644 --- a/forester/java/src/org/forester/go/BasicGoSubset.java +++ b/forester/java/src/org/forester/go/BasicGoSubset.java @@ -82,7 +82,7 @@ public class BasicGoSubset implements GoSubset { } else if ( o.getClass() != this.getClass() ) { throw new IllegalArgumentException( "attempt to check go subset equality to " + o + " [" + o.getClass() - + "]" ); + + "]" ); } else { return ( getType() == ( ( GoSubset ) o ).getType() ); diff --git a/forester/java/src/org/forester/go/BasicGoTerm.java b/forester/java/src/org/forester/go/BasicGoTerm.java index f438d2f..ecf48f8 100644 --- a/forester/java/src/org/forester/go/BasicGoTerm.java +++ b/forester/java/src/org/forester/go/BasicGoTerm.java @@ -81,7 +81,7 @@ public class BasicGoTerm implements GoTerm { /** * Compares based on GO id. - * + * */ @Override public int compareTo( final GoTerm go_term ) { @@ -90,8 +90,8 @@ public class BasicGoTerm implements GoTerm { /** * Makes a shallow copy. - * - * + * + * */ @Override public PhylogenyData copy() { @@ -106,7 +106,7 @@ public class BasicGoTerm implements GoTerm { /** * Return true if both GO id and namespace are equal. - * + * */ @Override public boolean equals( final Object o ) { @@ -177,8 +177,8 @@ public class BasicGoTerm implements GoTerm { /** * Hashcode is based on hashcode of GO id. - * - * + * + * */ @Override public int hashCode() { diff --git a/forester/java/src/org/forester/go/BasicGoXRef.java b/forester/java/src/org/forester/go/BasicGoXRef.java index 548a7a6..9d48797 100644 --- a/forester/java/src/org/forester/go/BasicGoXRef.java +++ b/forester/java/src/org/forester/go/BasicGoXRef.java @@ -117,8 +117,8 @@ public class BasicGoXRef implements GoXRef { /** * Based on value and type. - * - * + * + * */ @Override public boolean equals( final Object o ) { diff --git a/forester/java/src/org/forester/go/GoUtils.java b/forester/java/src/org/forester/go/GoUtils.java index adec9fb..fa08ef2 100644 --- a/forester/java/src/org/forester/go/GoUtils.java +++ b/forester/java/src/org/forester/go/GoUtils.java @@ -50,9 +50,9 @@ public final class GoUtils { /** * This is for counting the how many times each GO term in 'categories' - * is a (direct or indirect) super term of the GO terms in 'experiment_set'. - * - * + * is a (direct or indirect) super term of the GO terms in 'experiment_set'. + * + * * @param categories the set of super terms to be counted * @param experiment_set the list of GO terms to be analyzed * @param all_go_terms all terms in the ontology @@ -160,7 +160,7 @@ public final class GoUtils { penultimate = my_go_term; if ( !map.containsKey( my_go_term.getSuperGoIds().get( 0 ) ) ) { throw new IllegalArgumentException( "GO-id [" + my_go_term.getSuperGoIds().get( 0 ) - + "] not found in map" ); + + "] not found in map" ); } my_go_term = map.get( my_go_term.getSuperGoIds().get( 0 ) ); } @@ -172,7 +172,7 @@ public final class GoUtils { while ( ( my_go_term.getSuperGoIds() != null ) && ( my_go_term.getSuperGoIds().size() > 0 ) ) { if ( !map.containsKey( my_go_term.getSuperGoIds().get( 0 ) ) ) { throw new IllegalArgumentException( "GO-id [" + my_go_term.getSuperGoIds().get( 0 ) - + "] not found in map" ); + + "] not found in map" ); } my_go_term = map.get( my_go_term.getSuperGoIds().get( 0 ) ); } diff --git a/forester/java/src/org/forester/go/PfamToGoMapping.java b/forester/java/src/org/forester/go/PfamToGoMapping.java index 33815ab..7d9056b 100644 --- a/forester/java/src/org/forester/go/PfamToGoMapping.java +++ b/forester/java/src/org/forester/go/PfamToGoMapping.java @@ -45,8 +45,8 @@ public class PfamToGoMapping implements Mapping { /** * Based on key and value. - * - * + * + * */ @Override public boolean equals( final Object o ) { diff --git a/forester/java/src/org/forester/go/TestGo.java b/forester/java/src/org/forester/go/TestGo.java index 9d5f0c7..593d06d 100644 --- a/forester/java/src/org/forester/go/TestGo.java +++ b/forester/java/src/org/forester/go/TestGo.java @@ -395,7 +395,7 @@ public class TestGo { private static boolean testPfamToGoParser( final File test_dir ) { try { final PfamToGoParser parser = new PfamToGoParser( new File( test_dir + ForesterUtil.getFileSeparator() - + "pfam_to_go_test" ) ); + + "pfam_to_go_test" ) ); final List mappings = parser.parse(); if ( parser.getMappingCount() != 426 ) { return false; @@ -476,7 +476,7 @@ public class TestGo { private static boolean testSuperTermCounting( final File test_dir ) { try { final OBOparser parser = new OBOparser( new File( test_dir + ForesterUtil.getFileSeparator() - + "gene_ontology_edit.obo" ), OBOparser.ReturnType.BASIC_GO_TERM ); + + "gene_ontology_edit.obo" ), OBOparser.ReturnType.BASIC_GO_TERM ); final List all_go_terms = parser.parse(); if ( parser.getGoTermCount() != 27748 ) { return false; @@ -485,23 +485,23 @@ public class TestGo { final List categories = new ArrayList(); final List experiment_set = new ArrayList(); experiment_set.add( new BasicGoTerm( new GoId( "GO:0005690" ), "snRNP U4atac", GoNameSpace - .createUnassigned(), false ) ); + .createUnassigned(), false ) ); experiment_set.add( new BasicGoTerm( new GoId( "GO:0009698" ), "phenylpropanoid metabolic process", GoNameSpace.createUnassigned(), false ) ); experiment_set.add( new BasicGoTerm( new GoId( "GO:0008150" ), "biological_process", GoNameSpace - .createUnassigned(), false ) ); + .createUnassigned(), false ) ); experiment_set.add( new BasicGoTerm( new GoId( "GO:0006915" ), "apoptosis", GoNameSpace.createUnassigned(), false ) ); experiment_set.add( new BasicGoTerm( new GoId( "GO:0001783" ), "B cell apoptosis", GoNameSpace - .createUnassigned(), false ) ); + .createUnassigned(), false ) ); experiment_set.add( new BasicGoTerm( new GoId( "GO:0010657" ), "muscle cell apoptosis", GoNameSpace - .createUnassigned(), false ) ); + .createUnassigned(), false ) ); experiment_set.add( new BasicGoTerm( new GoId( "GO:0010657" ), "muscle cell apoptosis", GoNameSpace - .createUnassigned(), false ) ); + .createUnassigned(), false ) ); experiment_set.add( new BasicGoTerm( new GoId( "GO:0010658" ), "striated muscle cell apoptosis", GoNameSpace.createUnassigned(), @@ -511,25 +511,25 @@ public class TestGo { GoNameSpace.createUnassigned(), false ) ); categories - .add( new BasicGoTerm( new GoId( "GO:0016265" ), "death", GoNameSpace.createUnassigned(), false ) ); + .add( new BasicGoTerm( new GoId( "GO:0016265" ), "death", GoNameSpace.createUnassigned(), false ) ); categories.add( new BasicGoTerm( new GoId( "GO:0006915" ), "apoptosis", GoNameSpace.createUnassigned(), false ) ); categories.add( new BasicGoTerm( new GoId( "GO:0008150" ), "biological_process", GoNameSpace - .createUnassigned(), false ) ); + .createUnassigned(), false ) ); categories.add( new BasicGoTerm( new GoId( "GO:0010657" ), "muscle cell apoptosis", GoNameSpace - .createUnassigned(), false ) ); + .createUnassigned(), false ) ); categories.add( new BasicGoTerm( new GoId( "GO:0010658" ), "striated muscle cell apoptosis", GoNameSpace - .createUnassigned(), false ) ); + .createUnassigned(), false ) ); categories.add( new BasicGoTerm( new GoId( "GO:0046242" ), "o-xylene biosynthetic process", GoNameSpace - .createUnassigned(), false ) ); + .createUnassigned(), false ) ); categories.add( new BasicGoTerm( new GoId( "GO:0016326" ), "kinesin motor activity", GoNameSpace - .createUnassigned(), false ) ); + .createUnassigned(), false ) ); categories.add( new BasicGoTerm( new GoId( "GO:0005575" ), "cellular_component", GoNameSpace - .createUnassigned(), false ) ); + .createUnassigned(), false ) ); categories.add( new BasicGoTerm( new GoId( "GO:0032502" ), "developmental process", GoNameSpace - .createUnassigned(), false ) ); + .createUnassigned(), false ) ); categories.add( new BasicGoTerm( new GoId( "GO:0051094" ), "positive regulation of developmental process", GoNameSpace.createUnassigned(), @@ -647,7 +647,7 @@ public class TestGo { private static boolean testSuperTermGetting( final File test_dir ) { try { final OBOparser parser = new OBOparser( new File( test_dir + ForesterUtil.getFileSeparator() - + "gene_ontology_edit.obo" ), OBOparser.ReturnType.BASIC_GO_TERM ); + + "gene_ontology_edit.obo" ), OBOparser.ReturnType.BASIC_GO_TERM ); final List go_terms = parser.parse(); if ( parser.getGoTermCount() != 27748 ) { return false; diff --git a/forester/java/src/org/forester/go/etc/MetaOntologizer.java b/forester/java/src/org/forester/go/etc/MetaOntologizer.java index 98bf943..36b2801 100644 --- a/forester/java/src/org/forester/go/etc/MetaOntologizer.java +++ b/forester/java/src/org/forester/go/etc/MetaOntologizer.java @@ -117,7 +117,7 @@ public class MetaOntologizer { species = matcher.group( 1 ); if ( VERBOSE ) { ForesterUtil - .programMessage( PRG_NAME, "species for [" + ontologizer_outfile + "] is [" + species + "]" ); + .programMessage( PRG_NAME, "species for [" + ontologizer_outfile + "] is [" + species + "]" ); } } else { @@ -226,7 +226,7 @@ public class MetaOntologizer { } if ( ( p_adjusted_upper_limit < 0.0 ) || ( p_adjusted_upper_limit > 1.0 ) ) { throw new IllegalArgumentException( "adjusted P values limit [" + p_adjusted_upper_limit - + "] is out of range" ); + + "] is out of range" ); } SortedMap> speciesto_to_domain_id = null; if ( domain_gain_loss_file != null ) { @@ -236,7 +236,7 @@ public class MetaOntologizer { speciesto_to_domain_id = parseDomainGainLossFile( domain_gain_loss_file ); if ( VERBOSE ) { ForesterUtil.programMessage( PRG_NAME, "parsed gain/loss domains for " + speciesto_to_domain_id.size() - + " species from [" + domain_gain_loss_file + "]" ); + + " species from [" + domain_gain_loss_file + "]" ); } } final String[] children = ontologizer_outdir.list(); @@ -253,7 +253,7 @@ public class MetaOntologizer { } if ( VERBOSE ) { ForesterUtil.programMessage( PRG_NAME, "need to analyze " + ontologizer_outfiles.size() - + " Ontologizer outfiles from [" + ontologizer_outdir + "]" ); + + " Ontologizer outfiles from [" + ontologizer_outdir + "]" ); } final OBOparser parser = new OBOparser( obo_file, OBOparser.ReturnType.BASIC_GO_TERM ); final List go_terms = parser.parse(); @@ -281,7 +281,7 @@ public class MetaOntologizer { for( final File ontologizer_outfile : ontologizer_outfiles ) { final String species = obtainSpecies( ontologizer_outfile ); final List ontologizer_results = OntologizerResult.parse( new File( ontologizer_outdir - + ForesterUtil.FILE_SEPARATOR + ontologizer_outfile ) ); + + ForesterUtil.FILE_SEPARATOR + ontologizer_outfile ) ); final SortedSet filtered_ontologizer_results = new TreeSet(); for( final OntologizerResult ontologizer_result : ontologizer_results ) { if ( ontologizer_result.getPAdjusted() <= p_adjusted_upper_limit ) { @@ -300,18 +300,18 @@ public class MetaOntologizer { writeHtmlHeader( b_html_writer, GoNameSpace.GoNamespaceType.BIOLOGICAL_PROCESS.toString() + " | Pmax = " + p_adjusted_upper_limit + " | " + comment, - ontologizer_outdir.getAbsolutePath(), - domain_gain_loss_file_full_path_str ); + ontologizer_outdir.getAbsolutePath(), + domain_gain_loss_file_full_path_str ); writeHtmlHeader( c_html_writer, GoNameSpace.GoNamespaceType.CELLULAR_COMPONENT.toString() + " | Pmax = " + p_adjusted_upper_limit + " | " + comment, - ontologizer_outdir.getAbsolutePath(), - domain_gain_loss_file_full_path_str ); + ontologizer_outdir.getAbsolutePath(), + domain_gain_loss_file_full_path_str ); writeHtmlHeader( m_html_writer, GoNameSpace.GoNamespaceType.MOLECULAR_FUNCTION.toString() + " | Pmax = " + p_adjusted_upper_limit + " | " + comment, - ontologizer_outdir.getAbsolutePath(), - domain_gain_loss_file_full_path_str ); + ontologizer_outdir.getAbsolutePath(), + domain_gain_loss_file_full_path_str ); for( final String species : species_to_results_map.keySet() ) { if ( hasResultsForSpecies( go_id_to_terms, species_to_results_map, @@ -381,17 +381,17 @@ public class MetaOntologizer { m_tab_writer.close(); if ( VERBOSE ) { ForesterUtil.programMessage( PRG_NAME, "successfully wrote biological process summary to [" + b_file_html - + "]" ); + + "]" ); ForesterUtil.programMessage( PRG_NAME, "successfully wrote biological process summary to [" + b_file_txt - + "]" ); + + "]" ); ForesterUtil.programMessage( PRG_NAME, "successfully wrote molecular function summary to [" + m_file_html - + "]" ); + + "]" ); ForesterUtil.programMessage( PRG_NAME, "successfully wrote molecular function summary to [" + m_file_txt - + "]" ); + + "]" ); ForesterUtil.programMessage( PRG_NAME, "successfully wrote cellular component summary to [" + c_file_html - + "]" ); + + "]" ); ForesterUtil.programMessage( PRG_NAME, "successfully wrote cellular component summary to [" + c_file_txt - + "]" ); + + "]" ); } } @@ -404,7 +404,7 @@ public class MetaOntologizer { for( final String domain : domains ) { if ( !domain_ids_with_go_annot.contains( domain ) ) { writer.write( "[" + domain + "] " ); + + "\">" + domain + "] " ); } } } @@ -573,7 +573,7 @@ public class MetaOntologizer { writer.write( "" ); writer.write( "" ); writer.write( "" + ontologizer_result.getGoId().getId() + "" ); + + "\" target=\"amigo_window\">" + ontologizer_result.getGoId().getId() + "" ); writer.write( "" ); writer.write( "" ); writer.write( FORMATER.format( ontologizer_result.getPAdjusted() ) ); diff --git a/forester/java/src/org/forester/go/etc/OntologizerResult.java b/forester/java/src/org/forester/go/etc/OntologizerResult.java index 47751e8..24cda30 100644 --- a/forester/java/src/org/forester/go/etc/OntologizerResult.java +++ b/forester/java/src/org/forester/go/etc/OntologizerResult.java @@ -36,7 +36,7 @@ import org.forester.go.GoId; import org.forester.util.ForesterUtil; /* - * + * * Note: this class has a natural ordering that is inconsistent with equals. */ public class OntologizerResult implements Comparable { diff --git a/forester/java/src/org/forester/io/parsers/FastaParser.java b/forester/java/src/org/forester/io/parsers/FastaParser.java index 0b863e0..dc4fc46 100644 --- a/forester/java/src/org/forester/io/parsers/FastaParser.java +++ b/forester/java/src/org/forester/io/parsers/FastaParser.java @@ -51,7 +51,7 @@ public class FastaParser { private static final Pattern ANYTHING_REGEX = Pattern.compile( "[\\d\\s]+" ); //>gi|71834668|ref|NP_001025424.1| Bcl2 [Danio rerio] public static final Pattern FASTA_DESC_LINE = Pattern - .compile( ">?\\s*([^|]+)\\|([^|]+)\\S*\\s+(.+)\\s+\\[(.+)\\]" ); + .compile( ">?\\s*([^|]+)\\|([^|]+)\\S*\\s+(.+)\\s+\\[(.+)\\]" ); public static void main( final String[] args ) { final String a = ">gi|71834668|ref|NP_001025424.1| Bcl2 [Danio rerio]"; diff --git a/forester/java/src/org/forester/io/parsers/GeneralMsaParser.java b/forester/java/src/org/forester/io/parsers/GeneralMsaParser.java index 4b6ddf5..f4db6cb 100644 --- a/forester/java/src/org/forester/io/parsers/GeneralMsaParser.java +++ b/forester/java/src/org/forester/io/parsers/GeneralMsaParser.java @@ -161,7 +161,7 @@ public final class GeneralMsaParser { } else { throw new MsaFormatException( "illegal msa format (line: " + line_counter + "):\n\"" + trim( line ) - + "\"" ); + + "\"" ); } if ( is_first ) { is_first = false; @@ -171,7 +171,7 @@ public final class GeneralMsaParser { final List seqs = new ArrayList(); for( int i = 0; i < names_in_order.size(); ++i ) { seqs.add( BasicSequence.createAaSequence( names_in_order.get( i ), temp_msa.get( names_in_order.get( i ) ) - .toString() ) ); + .toString() ) ); } final Msa msa = BasicMsa.createInstance( seqs ); return msa; diff --git a/forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java b/forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java index 534eadc..96729a4 100644 --- a/forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java +++ b/forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java @@ -333,8 +333,8 @@ public final class HmmPfamOutputParser { } else if ( isVerbose() ) { ForesterUtil.printWarningMessage( getClass().getName(), "query \"" + query - + "\" is not unique [line " + line_number + "] in [" - + getInputFile().getCanonicalPath() + "]" ); + + "\" is not unique [line " + line_number + "] in [" + + getInputFile().getCanonicalPath() + "]" ); } } else { @@ -433,28 +433,28 @@ public final class HmmPfamOutputParser { } catch ( final NumberFormatException e ) { throw new IOException( "could not parse seq-f from \"" + line + "\" [line " + line_number - + "] in [" + getInputFile().getCanonicalPath() + "]" ); + + "] in [" + getInputFile().getCanonicalPath() + "]" ); } try { to = Integer.valueOf( to_str ).intValue(); } catch ( final NumberFormatException e ) { throw new IOException( "could not parse seq-t from \"" + line + "\" [line " + line_number - + "] in [" + getInputFile().getCanonicalPath() + "]" ); + + "] in [" + getInputFile().getCanonicalPath() + "]" ); } try { score = Double.valueOf( score_str ).doubleValue(); } catch ( final NumberFormatException e ) { throw new IOException( "could not parse score from \"" + line + "\" [line " + line_number - + "] in [" + getInputFile().getCanonicalPath() + "]" ); + + "] in [" + getInputFile().getCanonicalPath() + "]" ); } try { e_value = Double.valueOf( e_value_str ).doubleValue(); } catch ( final NumberFormatException e ) { throw new IOException( "could not parse E-value from \"" + line + "\" [line " + line_number - + "] in [" + getInputFile().getCanonicalPath() + "]" ); + + "] in [" + getInputFile().getCanonicalPath() + "]" ); } if ( hmm_match_str.equals( "[]" ) ) { //is_complete_hmm_match = true; @@ -486,14 +486,14 @@ public final class HmmPfamOutputParser { } catch ( final NumberFormatException e ) { throw new IOException( "could not parse domain number from \"" + line + "\" [line " + line_number - + "] in [" + getInputFile().getCanonicalPath() + "]" ); + + "] in [" + getInputFile().getCanonicalPath() + "]" ); } try { total = Integer.valueOf( ( total_str ) ).intValue(); } catch ( final NumberFormatException e ) { throw new IOException( "could not parse domain count from \"" + line + "\" [line " + line_number - + "] in [" + getInputFile().getCanonicalPath() + "]" ); + + "] in [" + getInputFile().getCanonicalPath() + "]" ); } ++_domains_encountered; boolean failed_cutoff = false; @@ -506,7 +506,7 @@ public final class HmmPfamOutputParser { } else { throw new IOException( "could not find a score cutoff value for domain id \"" + id - + "\" [line " + line_number + "] in [" + getInputFile().getCanonicalPath() + "]" ); + + "\" [line " + line_number + "] in [" + getInputFile().getCanonicalPath() + "]" ); } } final String uc_id = id.toUpperCase(); @@ -613,8 +613,8 @@ public final class HmmPfamOutputParser { /** * To ignore domains which are completely engulfed by domains (individual * ones or stretches of overlapping ones) with better support values. - * - * + * + * * @param ignored_engulfed_domains */ public void setIgnoreEngulfedDomains( final boolean ignore_engulfed_domains ) { @@ -628,7 +628,7 @@ public final class HmmPfamOutputParser { /** * Sets the individual domain score cutoff values (for example, gathering * thresholds from Pfam). Domain ids are the keys, cutoffs the values. - * + * * @param individual_domain_score_cutoffs */ public void setIndividualDomainScoreCutoffs( final Map individual_domain_score_cutoffs ) { diff --git a/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java b/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java index f063866..5e0ba9c 100644 --- a/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java +++ b/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java @@ -372,7 +372,7 @@ public final class HmmscanPerDomainTableParser { if ( ForesterUtil.isEmpty( line ) || line.startsWith( "#" ) ) { continue; } - // 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 + // 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 // # --- full sequence --- -------------- this domain ------------- hmm coord ali coord env coord // # target name accession tlen query name accession qlen E-value score bias # of c-Evalue i-Evalue score bias from to from to from to acc description of target // #------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- --------------------- @@ -406,7 +406,7 @@ public final class HmmscanPerDomainTableParser { if ( !isAllowProteinsWithSameName() ) { if ( query.equals( prev_query ) ) { throw new IOException( "more than one protein named [" + query + "]" + " lengths: " + qlen - + ", " + prev_qlen ); + + ", " + prev_qlen ); } if ( prev_queries.contains( query ) ) { throw new IOException( "more than one protein named [" + query + "]" ); @@ -442,7 +442,7 @@ public final class HmmscanPerDomainTableParser { } else { throw new IOException( "could not find a score cutoff value for domain id \"" + target_id - + "\" [line " + line_number + "] in [" + getInputFile().getCanonicalPath() + "]" ); + + "\" [line " + line_number + "] in [" + getInputFile().getCanonicalPath() + "]" ); } } final String uc_id = target_id.toUpperCase(); @@ -513,7 +513,7 @@ public final class HmmscanPerDomainTableParser { } catch ( final NumberFormatException e ) { throw new IOException( "could not parse \" +label + \" from \"" + double_str + "\" [line " + line_number - + "] in [" + getInputFile().getCanonicalPath() + "]" ); + + "] in [" + getInputFile().getCanonicalPath() + "]" ); } return d; } @@ -525,7 +525,7 @@ public final class HmmscanPerDomainTableParser { } catch ( final NumberFormatException e ) { throw new IOException( "could not parse \"" + label + "\" from \"" + double_str + "\" [line " + line_number - + "] in [" + getInputFile().getCanonicalPath() + "]" ); + + "] in [" + getInputFile().getCanonicalPath() + "]" ); } return i; } @@ -599,8 +599,8 @@ public final class HmmscanPerDomainTableParser { /** * To ignore domains which are completely engulfed by domains (individual * ones or stretches of overlapping ones) with better support values. - * - * + * + * * @param ignored_engulfed_domains */ public void setIgnoreEngulfedDomains( final boolean ignore_engulfed_domains ) { @@ -614,7 +614,7 @@ public final class HmmscanPerDomainTableParser { /** * Sets the individual score cutoff values (for example, gathering * thresholds from Pfam). Domain ids are the keys, cutoffs the values. - * + * * @param individual_score_cutoffs */ public void setIndividualScoreCutoffs( final Map individual_score_cutoffs ) { diff --git a/forester/java/src/org/forester/io/parsers/PhylogenyParser.java b/forester/java/src/org/forester/io/parsers/PhylogenyParser.java index df27bc9..71d801a 100644 --- a/forester/java/src/org/forester/io/parsers/PhylogenyParser.java +++ b/forester/java/src/org/forester/io/parsers/PhylogenyParser.java @@ -32,7 +32,7 @@ import org.forester.phylogeny.Phylogeny; /* * @author Christian Zmasek - * + * * TODO To change the template for this generated type comment go to Window - * Preferences - Java - Code Style - Code Templates */ diff --git a/forester/java/src/org/forester/io/parsers/SymmetricalDistanceMatrixParser.java b/forester/java/src/org/forester/io/parsers/SymmetricalDistanceMatrixParser.java index 0bdafe1..c527140 100644 --- a/forester/java/src/org/forester/io/parsers/SymmetricalDistanceMatrixParser.java +++ b/forester/java/src/org/forester/io/parsers/SymmetricalDistanceMatrixParser.java @@ -39,16 +39,16 @@ import org.forester.util.ForesterUtil; * This can read full, lower triangular, and upper triangular distance matrices. * In the case of a full matrix, the lower triangular values are used. Format * (by example): id1 0 id2 0.3 0 id3 0.4 0.4 0 - * + * * OR - * + * * id1 id2 0.3 id3 0.4 0.4 - * + * * Numbers before are after the data are ignored. - * - * - * - * + * + * + * + * * @author Christian M Zmasek */ public class SymmetricalDistanceMatrixParser { @@ -75,11 +75,11 @@ public class SymmetricalDistanceMatrixParser { } catch ( final NumberFormatException e ) { throw new IOException( "illegal format for distance [" + table_value + "] at [" + ( i - 1 ) + ", " + row - + "]" ); + + "]" ); } if ( !ForesterUtil.isEqual( 0.0, d ) ) { throw new IOException( "attempt to use non-zero diagonal value [" + table_value + "] at [" + ( i - 1 ) - + ", " + row + "]" ); + + ", " + row + "]" ); } } @@ -140,7 +140,7 @@ public class SymmetricalDistanceMatrixParser { } catch ( final NumberFormatException e ) { throw new IOException( "illegal format for distance [" + table_value + "] at [" + ( col - 1 ) + ", " + row - + "]" ); + + "]" ); } distance_matrix.setValue( ( col - 1 ) + col_offset, row, d ); } diff --git a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java index 7a30ce9..6989602 100644 --- a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java +++ b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java @@ -130,7 +130,7 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse //int c = 0; while ( hasNext() ) { l.add( next() ); - // c++; + // c++; } final Phylogeny[] p = new Phylogeny[ l.size() ]; for( int i = 0; i < l.size(); ++i ) { @@ -244,12 +244,12 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse _input_type = NHXParser.BUFFERED_READER; _source_length = 0; if ( _my_source_br != null ) { - // I am REALLY not sure if it a "good" NOT to close the stream... -// try { -// _my_source_br.close(); -// } -// catch ( final IOException e ) { -// } + //I am REALLY not sure if it is a "good" idea NOT to close the stream... + // try { + // _my_source_br.close(); + // } + // catch ( final IOException e ) { + // } } final File f = ( File ) nhx_source; final String error = ForesterUtil.isReadableFile( f ); @@ -262,12 +262,12 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse _input_type = NHXParser.BUFFERED_READER; _source_length = 0; if ( _my_source_br != null ) { -// I am REALLY not sure if it a "good" NOT to close the stream... -// try { -// _my_source_br.close(); -// } -// catch ( final IOException e ) { -// } + //I am REALLY not sure if it is a "good" idea NOT to close the stream... + // try { + // _my_source_br.close(); + // } + // catch ( final IOException e ) { + // } } final InputStreamReader isr = new InputStreamReader( ( ( URL ) nhx_source ).openStream() ); _nhx_source = new BufferedReader( isr ); @@ -276,12 +276,12 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse _input_type = NHXParser.BUFFERED_READER; _source_length = 0; if ( _my_source_br != null ) { - // I am REALLY not sure if it a "good" NOT to close the stream... -// try { -// _my_source_br.close(); -// } -// catch ( final IOException e ) { -// } + //I am REALLY not sure if it is a "good" idea NOT to close the stream... + // try { + // _my_source_br.close(); + // } + // catch ( final IOException e ) { + // } } final InputStreamReader isr = new InputStreamReader( ( InputStream ) nhx_source ); _nhx_source = new BufferedReader( isr ); @@ -294,14 +294,14 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse } private final Phylogeny finishPhylogeny() throws PhylogenyParserException, NHXFormatException, - PhyloXmlDataFormatException { + PhyloXmlDataFormatException { if ( _current_phylogeny != null ) { parseNHX( _current_anotation != null ? _current_anotation.toString() : "", - _current_phylogeny.getRoot(), - getTaxonomyExtraction(), - isReplaceUnderscores(), - isAllowErrorsInDistanceToParent(), - true ); + _current_phylogeny.getRoot(), + getTaxonomyExtraction(), + isReplaceUnderscores(), + isAllowErrorsInDistanceToParent(), + true ); if ( GUESS_IF_SUPPORT_VALUES ) { if ( isBranchLengthsLikeBootstrapValues( _current_phylogeny ) ) { moveBranchLengthsToConfidenceValues( _current_phylogeny ); @@ -320,7 +320,7 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse } private final Phylogeny finishSingleNodePhylogeny() throws PhylogenyParserException, NHXFormatException, - PhyloXmlDataFormatException { + PhyloXmlDataFormatException { final PhylogenyNode new_node = new PhylogenyNode(); parseNHX( _current_anotation.toString(), new_node, @@ -479,7 +479,7 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse _current_anotation.append( c ); } ++_i; - } // while ( true ) + } // while ( true ) if ( _clade_level != 0 ) { throw new PhylogenyParserException( "error in NH (Newick) formatted data: most likely cause: number of open parens does not equal number of close parens" ); } @@ -511,7 +511,7 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse } private final void processCloseParen() throws PhylogenyParserException, NHXFormatException, - PhyloXmlDataFormatException { + PhyloXmlDataFormatException { if ( _clade_level < 0 ) { throw new PhylogenyParserException( "error in NH (Newick)/NHX formatted data: most likely cause: number of close parens is larger than number of open parens" ); } @@ -569,7 +569,7 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse } private final Phylogeny processOpenParen() throws PhylogenyParserException, NHXFormatException, - PhyloXmlDataFormatException { + PhyloXmlDataFormatException { Phylogeny phy = null; final PhylogenyNode new_node = new PhylogenyNode(); if ( _clade_level == 0 ) { @@ -606,7 +606,7 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse final boolean replace_underscores, final boolean allow_errors_in_distance_to_parent, final boolean replace_bell ) throws NHXFormatException, - PhyloXmlDataFormatException { + PhyloXmlDataFormatException { if ( ( taxonomy_extraction != TAXONOMY_EXTRACTION.NO ) && replace_underscores ) { throw new IllegalArgumentException( "cannot extract taxonomies and replace under scores at the same time" ); } @@ -703,7 +703,7 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse node_to_annotate.getNodeData().setSequence( new Sequence() ); } node_to_annotate.getNodeData().getSequence() - .setAccession( new Accession( s.substring( 3 ), "?" ) ); + .setAccession( new Accession( s.substring( 3 ), "?" ) ); } else if ( s.startsWith( NHXtags.GENE_NAME ) ) { if ( !node_to_annotate.getNodeData().isHasSequence() ) { @@ -711,7 +711,7 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse } node_to_annotate.getNodeData().getSequence().setName( s.substring( 3 ) ); } - } // while ( t.hasMoreTokens() ) + } // while ( t.hasMoreTokens() ) } } } @@ -778,7 +778,7 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse if ( prob >= 0.0 ) { if ( sd >= 0.0 ) { node_to_annotate.getBranchData() - .addConfidence( new Confidence( prob, "posterior probability", sd ) ); + .addConfidence( new Confidence( prob, "posterior probability", sd ) ); } else { node_to_annotate.getBranchData().addConfidence( new Confidence( prob, "posterior probability" ) ); @@ -793,7 +793,7 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse } catch ( final NumberFormatException e ) { throw new NHXFormatException( "failed to parse median branch length (Mr Bayes output) from \"" + s - + "\"" ); + + "\"" ); } if ( bl >= 0.0 ) { node_to_annotate.setDistanceToParent( bl ); diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java index 2c347a1..3e2f6a7 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java @@ -309,7 +309,7 @@ public final class PhyloXmlHandler extends DefaultHandler { } else if ( qualified_name.equals( PhyloXmlMapping.BINARY_CHARACTERS ) ) { node.getNodeData().setBinaryCharacters( ( BinaryCharacters ) BinaryCharactersParser.getInstance() - .parse( element ) ); + .parse( element ) ); } else if ( qualified_name.equals( PhyloXmlMapping.COLOR ) ) { node.getBranchData().setBranchColor( ( BranchColor ) ColorParser.getInstance().parse( element ) ); @@ -406,15 +406,15 @@ public final class PhyloXmlHandler extends DefaultHandler { final XmlElement element = new XmlElement( namespace_uri, local_name, local_name, attributes ); if ( element.isHasAttribute( PhyloXmlMapping.PHYLOGENY_IS_REROOTABLE_ATTR ) ) { getCurrentPhylogeny().setRerootable( Boolean.parseBoolean( element - .getAttribute( PhyloXmlMapping.PHYLOGENY_IS_REROOTABLE_ATTR ) ) ); + .getAttribute( PhyloXmlMapping.PHYLOGENY_IS_REROOTABLE_ATTR ) ) ); } if ( element.isHasAttribute( PhyloXmlMapping.PHYLOGENY_BRANCHLENGTH_UNIT_ATTR ) ) { getCurrentPhylogeny() - .setDistanceUnit( element.getAttribute( PhyloXmlMapping.PHYLOGENY_BRANCHLENGTH_UNIT_ATTR ) ); + .setDistanceUnit( element.getAttribute( PhyloXmlMapping.PHYLOGENY_BRANCHLENGTH_UNIT_ATTR ) ); } if ( element.isHasAttribute( PhyloXmlMapping.PHYLOGENY_IS_ROOTED_ATTR ) ) { getCurrentPhylogeny().setRooted( Boolean.parseBoolean( element - .getAttribute( PhyloXmlMapping.PHYLOGENY_IS_ROOTED_ATTR ) ) ); + .getAttribute( PhyloXmlMapping.PHYLOGENY_IS_ROOTED_ATTR ) ) ); } if ( element.isHasAttribute( PhyloXmlMapping.PHYLOGENY_TYPE_ATTR ) ) { getCurrentPhylogeny().setType( ( element.getAttribute( PhyloXmlMapping.PHYLOGENY_TYPE_ATTR ) ) ); diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlParser.java index 735de4b..4779189 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlParser.java @@ -182,7 +182,7 @@ public class PhyloXmlParser implements PhylogenyParser { final Reader reader = getReaderFromZipFile(); if ( reader == null ) { throw new PhylogenyParserException( "zip file \"" + getSource() - + "\" appears not to contain any entries" ); + + "\" appears not to contain any entries" ); } xml_reader.parse( new InputSource( reader ) ); } @@ -224,7 +224,7 @@ public class PhyloXmlParser implements PhylogenyParser { } catch ( final ParserConfigurationException parser_config_exception ) { throw new PhylogenyParserException( "failed to parse [" + getSource() - + "]. Problem with XML parser configuration: " + parser_config_exception.getLocalizedMessage() ); + + "]. Problem with XML parser configuration: " + parser_config_exception.getLocalizedMessage() ); } catch ( final IOException e ) { throw new PhylogenyParserException( "problem with input source: " + e.getLocalizedMessage() ); diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlUtil.java b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlUtil.java index e585cb3..ba80282 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlUtil.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlUtil.java @@ -39,9 +39,9 @@ public final class PhyloXmlUtil { public static final String UNKNOWN = "unknown"; public final static Pattern SEQUENCE_SYMBOL_PATTERN = Pattern.compile( "\\S{1,20}" ); public final static Pattern TAXOMONY_CODE_PATTERN = Pattern - .compile( ParserUtils.TAX_CODE ); + .compile( ParserUtils.TAX_CODE ); public final static Pattern LIT_REF_DOI_PATTERN = Pattern - .compile( "[a-zA-Z0-9_\\.]+\\S+" ); + .compile( "[a-zA-Z0-9_\\.]+\\S+" ); public final static Set SEQUENCE_TYPES = new HashSet(); public final static List TAXONOMY_RANKS_LIST = new ArrayList(); public final static Set TAXONOMY_RANKS_SET = new HashSet(); diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/XmlElement.java b/forester/java/src/org/forester/io/parsers/phyloxml/XmlElement.java index e0cc08c..ac46584 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/XmlElement.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/XmlElement.java @@ -181,7 +181,7 @@ public class XmlElement { /** * [Careful, this does not call "new String(...)"] - * + * * @param value */ public void setValue( final String value ) { diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/AnnotationParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/AnnotationParser.java index cab3bef..66023d4 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/data/AnnotationParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/AnnotationParser.java @@ -84,7 +84,7 @@ public class AnnotationParser implements PhylogenyDataPhyloXmlParser { annotation.setProperties( new PropertiesMap() ); } annotation.getProperties() - .addProperty( ( Property ) PropertyParser.getInstance().parse( child_element ) ); + .addProperty( ( Property ) PropertyParser.getInstance().parse( child_element ) ); } } return annotation; diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/BinaryCharactersParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/BinaryCharactersParser.java index d8692f0..1fb5ee0 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/data/BinaryCharactersParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/BinaryCharactersParser.java @@ -64,11 +64,11 @@ public class BinaryCharactersParser implements PhylogenyDataPhyloXmlParser { try { if ( element.isHasAttribute( PhyloXmlMapping.BINARY_CHARACTERS_PRESENT_COUNT_ATTR ) ) { present_count = Integer.parseInt( element - .getAttribute( PhyloXmlMapping.BINARY_CHARACTERS_PRESENT_COUNT_ATTR ) ); + .getAttribute( PhyloXmlMapping.BINARY_CHARACTERS_PRESENT_COUNT_ATTR ) ); } if ( element.isHasAttribute( PhyloXmlMapping.BINARY_CHARACTERS_GAINED_COUNT_ATTR ) ) { gained_count = Integer.parseInt( element - .getAttribute( PhyloXmlMapping.BINARY_CHARACTERS_GAINED_COUNT_ATTR ) ); + .getAttribute( PhyloXmlMapping.BINARY_CHARACTERS_GAINED_COUNT_ATTR ) ); } if ( element.isHasAttribute( PhyloXmlMapping.BINARY_CHARACTERS_LOST_COUNT_ATTR ) ) { lost_count = Integer diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/ConfidenceParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/ConfidenceParser.java index 917efe9..bbe207e 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/data/ConfidenceParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/ConfidenceParser.java @@ -56,7 +56,7 @@ public class ConfidenceParser implements PhylogenyDataPhyloXmlParser { if ( element.isHasAttribute( PhyloXmlMapping.CONFIDENCE_SD_ATTR ) ) { try { confidence.setStandardDeviation( Double.parseDouble( element - .getAttribute( PhyloXmlMapping.CONFIDENCE_SD_ATTR ) ) ); + .getAttribute( PhyloXmlMapping.CONFIDENCE_SD_ATTR ) ) ); } catch ( final NumberFormatException ex ) { throw new PhyloXmlDataFormatException( "attempt to parse [" diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/DomainArchitectureParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/DomainArchitectureParser.java index 4010912..c1b6a71 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/data/DomainArchitectureParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/DomainArchitectureParser.java @@ -51,7 +51,7 @@ public class DomainArchitectureParser implements PhylogenyDataPhyloXmlParser { final DomainArchitecture architecure = new DomainArchitecture(); if ( !element.isHasAttribute( PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_LENGTH ) ) { throw new PhyloXmlDataFormatException( PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_LENGTH - + " attribute is required for domain architecture" ); + + " attribute is required for domain architecture" ); } final String lenght_str = element.getAttribute( PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_LENGTH ); try { @@ -59,7 +59,7 @@ public class DomainArchitectureParser implements PhylogenyDataPhyloXmlParser { } catch ( final NumberFormatException e ) { throw new PhyloXmlDataFormatException( "could not extract domain architecture length from [" + lenght_str - + "]: " + e.getMessage() ); + + "]: " + e.getMessage() ); } for( int i = 0; i < element.getNumberOfChildElements(); ++i ) { final XmlElement child_element = element.getChildElement( i ); diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/ProteinDomainParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/ProteinDomainParser.java index e6a15df..1985f77 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/data/ProteinDomainParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/ProteinDomainParser.java @@ -57,7 +57,7 @@ public class ProteinDomainParser implements PhylogenyDataPhyloXmlParser { .parseInt( element.getAttribute( PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_FROM ) ); t = Integer.parseInt( element.getAttribute( PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_TO ) ); conf = Double.parseDouble( element - .getAttribute( PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_CONFIDENCE ) ); + .getAttribute( PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_CONFIDENCE ) ); if ( element.isHasAttribute( PhyloXmlMapping.IDENTIFIER ) ) { id = element.getAttribute( PhyloXmlMapping.IDENTIFIER ); } diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/SequenceParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/SequenceParser.java index 56a7ea1..1a9cea9 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/data/SequenceParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/SequenceParser.java @@ -72,7 +72,7 @@ public class SequenceParser implements PhylogenyDataPhyloXmlParser { else if ( child_element.getQualifiedName().equals( PhyloXmlMapping.SEQUENCE_MOL_SEQ ) ) { if ( child_element.isHasAttribute( PhyloXmlMapping.SEQUENCE_MOL_SEQ_ALIGNED_ATTR ) ) { sequence.setMolecularSequenceAligned( Boolean.parseBoolean( child_element - .getAttribute( PhyloXmlMapping.SEQUENCE_MOL_SEQ_ALIGNED_ATTR ) ) ); + .getAttribute( PhyloXmlMapping.SEQUENCE_MOL_SEQ_ALIGNED_ATTR ) ) ); } sequence.setMolecularSequence( child_element.getValueAsString() ); } @@ -87,7 +87,7 @@ public class SequenceParser implements PhylogenyDataPhyloXmlParser { } else if ( child_element.getQualifiedName().equals( PhyloXmlMapping.SEQUENCE_DOMAIN_ARCHITECURE ) ) { sequence.setDomainArchitecture( ( DomainArchitecture ) DomainArchitectureParser.getInstance() - .parse( child_element ) ); + .parse( child_element ) ); } else if ( child_element.getQualifiedName().equals( PhyloXmlMapping.URI ) ) { sequence.addUri( ( Uri ) UriParser.getInstance().parse( child_element ) ); @@ -96,7 +96,7 @@ public class SequenceParser implements PhylogenyDataPhyloXmlParser { for( int j = 0; j < child_element.getNumberOfChildElements(); ++j ) { // final XmlElement c = child_element.getChildElement( j ); sequence.addCrossReference( ( Accession ) AccessionParser.getInstance().parse( child_element - .getChildElement( j ) ) ); + .getChildElement( j ) ) ); } //sequence.addUri( ( Uri ) UriParser.getInstance().parse( child_element ) ); } diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/SequenceRelationParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/SequenceRelationParser.java index 468adc9..23df0da 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/data/SequenceRelationParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/SequenceRelationParser.java @@ -68,7 +68,7 @@ public class SequenceRelationParser implements PhylogenyDataPhyloXmlParser { } if ( element.isHasAttribute( PhyloXmlMapping.SEQUENCE_RELATION_DISTANCE ) ) { seqRelation - .setDistance( Double.valueOf( element.getAttribute( PhyloXmlMapping.SEQUENCE_RELATION_DISTANCE ) ) ); + .setDistance( Double.valueOf( element.getAttribute( PhyloXmlMapping.SEQUENCE_RELATION_DISTANCE ) ) ); } for( int i = 0; i < element.getNumberOfChildElements(); ++i ) { final XmlElement child_element = element.getChildElement( i ); diff --git a/forester/java/src/org/forester/io/parsers/tol/TolParser.java b/forester/java/src/org/forester/io/parsers/tol/TolParser.java index 8299b78..6248f4a 100644 --- a/forester/java/src/org/forester/io/parsers/tol/TolParser.java +++ b/forester/java/src/org/forester/io/parsers/tol/TolParser.java @@ -174,7 +174,7 @@ public class TolParser implements PhylogenyParser { final Reader reader = getReaderFromZipFile(); if ( reader == null ) { throw new PhylogenyParserException( "Zip file \"" + getSource() - + "\" appears not to contain any entries" ); + + "\" appears not to contain any entries" ); } xml_reader.parse( new InputSource( reader ) ); } @@ -194,7 +194,7 @@ public class TolParser implements PhylogenyParser { final Reader reader = new InputStreamReader( zip_is ); if ( reader == null ) { throw new PhylogenyParserException( "Zip input stream \"" + getSource() - + "\" appears not to contain any data" ); + + "\" appears not to contain any data" ); } xml_reader.parse( new InputSource( reader ) ); } @@ -218,7 +218,7 @@ public class TolParser implements PhylogenyParser { } catch ( final ParserConfigurationException parser_config_exception ) { throw new PhylogenyParserException( "Failed to parse [" + getSource() - + "] Problem with xml parser _configuration: " + parser_config_exception.getMessage() ); + + "] Problem with xml parser _configuration: " + parser_config_exception.getMessage() ); } catch ( final IOException e ) { throw new PhylogenyParserException( "Problem with input source [" + getSource() + "]: \n" + e.getMessage() ); diff --git a/forester/java/src/org/forester/io/parsers/tol/TolXmlHandler.java b/forester/java/src/org/forester/io/parsers/tol/TolXmlHandler.java index 3575986..afd515f 100644 --- a/forester/java/src/org/forester/io/parsers/tol/TolXmlHandler.java +++ b/forester/java/src/org/forester/io/parsers/tol/TolXmlHandler.java @@ -244,7 +244,7 @@ public final class TolXmlHandler extends DefaultHandler { node.getNodeData().setTaxonomy( new Taxonomy() ); } node.getNodeData().getTaxonomy() - .setIdentifier( new Identifier( id, TolXmlMapping.TOL_TAXONOMY_ID_TYPE ) ); + .setIdentifier( new Identifier( id, TolXmlMapping.TOL_TAXONOMY_ID_TYPE ) ); } } final boolean put_into_scientific_name = true; // Allways put into scientific name. diff --git a/forester/java/src/org/forester/io/parsers/util/ParserUtils.java b/forester/java/src/org/forester/io/parsers/util/ParserUtils.java index 6b70303..e86ed49 100644 --- a/forester/java/src/org/forester/io/parsers/util/ParserUtils.java +++ b/forester/java/src/org/forester/io/parsers/util/ParserUtils.java @@ -59,44 +59,44 @@ public final class ParserUtils { final public static String TAX_CODE = "(?:[A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA"; final public static String TAX_CODE_LO = "(?:[A-Z]{5})|RAT|PIG|PEA"; final public static Pattern TAXOMONY_CODE_PATTERN_A = Pattern.compile( "(?:\\b|_)(" + TAX_CODE - + ")(?:\\b|_)" ); + + ")(?:\\b|_)" ); final public static Pattern TAXOMONY_CODE_PATTERN_A_LO = Pattern.compile( "_(" + TAX_CODE_LO - + ")(?:\\b|_)" ); + + ")(?:\\b|_)" ); final public static Pattern TAXOMONY_CODE_PATTERN_BRACKETED = Pattern.compile( "\\[(" + TAX_CODE + ")\\]" ); final public static Pattern TAXOMONY_CODE_PATTERN_PFR = Pattern.compile( "(?:\\b|_)[a-zA-Z0-9]{3,}_(" - + TAX_CODE + ")\\b" ); + + TAX_CODE + ")\\b" ); final public static Pattern TAXOMONY_SN_PATTERN_GENUS = Pattern.compile( "([A-Z][a-z]{2,30})" ); final public static Pattern TAXOMONY_SN_PATTERN_SN = Pattern.compile( "(?:\\b|_)(" + SN_BN - + ")(?:(\\s*$)|([_ ][a-z]*[A-Z0-9]))" ); + + ")(?:(\\s*$)|([_ ][a-z]*[A-Z0-9]))" ); final public static Pattern TAXOMONY_SN_PATTERN_SNS = Pattern.compile( "(?:\\b|_)(" + SN_BN - + "[_ ][a-z]{3,30}" - + ")[_ ][a-z]*[A-Z0-9]" ); + + "[_ ][a-z]{3,30}" + + ")[_ ][a-z]*[A-Z0-9]" ); final public static Pattern TAXOMONY_SN_PATTERN_SNS2 = Pattern.compile( "[A-Z0-9][a-z]*[_ ](" + SN_BN - + "[_ ][a-z]{3,30}" + ")\\s*$" ); + + "[_ ][a-z]{3,30}" + ")\\s*$" ); final public static Pattern TAXOMONY_SN_PATTERN_SP = Pattern - .compile( "(?:\\b|_)([A-Z][a-z]{2,30}[_ ]sp\\.?)(?:\\b|_)?" ); + .compile( "(?:\\b|_)([A-Z][a-z]{2,30}[_ ]sp\\.?)(?:\\b|_)?" ); final public static Pattern TAXOMONY_SN_PATTERN_STRAIN_1 = Pattern - .compile( "(?:\\b|_)(" - + SN_BN - + "[_ ](?:str|subsp|ssp|var)[a-z]{0,5}\\.?[_ ]\\S{1,60})(?:\\b|_)" ); + .compile( "(?:\\b|_)(" + + SN_BN + + "[_ ](?:str|subsp|ssp|var)[a-z]{0,5}\\.?[_ ]\\S{1,60})(?:\\b|_)" ); final public static Pattern TAXOMONY_SN_PATTERN_STRAIN_2 = Pattern - .compile( "(?:\\b|_)(" - + SN_BN - + "[_ ]\\((?:str|subsp|ssp|var)[a-z]{0,5}\\.?[_ ]\\S{1,60}\\))" ); + .compile( "(?:\\b|_)(" + + SN_BN + + "[_ ]\\((?:str|subsp|ssp|var)[a-z]{0,5}\\.?[_ ]\\S{1,60}\\))" ); final public static Pattern TAXOMONY_SN_PATTERN_STRAIN_SUBSTRAIN = Pattern - .compile( "(?:\\b|_)(" - + SN_BN - + "[_ ]str[a-z]{0,3}\\.?[_ ]\\S{1,60}[_ ]substr[a-z]{0,3}\\.?[_ ]\\S{1,60})(?:\\b|_)" ); + .compile( "(?:\\b|_)(" + + SN_BN + + "[_ ]str[a-z]{0,3}\\.?[_ ]\\S{1,60}[_ ]substr[a-z]{0,3}\\.?[_ ]\\S{1,60})(?:\\b|_)" ); final private static Pattern TAXOMONY_CODE_PATTERN_PFS = Pattern.compile( "(?:\\b|_)[A-Z0-9]{4,}_(" - + TAX_CODE + ")/\\d+-\\d+\\b" ); + + TAX_CODE + ")/\\d+-\\d+\\b" ); final private static Pattern TAXOMONY_UNIPROT_ID_PATTERN_PFR = Pattern - .compile( "(?:\\b|_)[A-Z0-9]{1,}_(\\d{1,7})\\b" ); + .compile( "(?:\\b|_)[A-Z0-9]{1,}_(\\d{1,7})\\b" ); final private static Pattern TAXOMONY_UNIPROT_ID_PATTERN_PFS = Pattern - .compile( "(?:\\b|_)[A-Z0-9]{4,}_(\\d{1,7})/\\d+-\\d+\\b" ); + .compile( "(?:\\b|_)[A-Z0-9]{4,}_(\\d{1,7})/\\d+-\\d+\\b" ); final public static PhylogenyParser createParserDependingFileContents( final File file, final boolean phyloxml_validate_against_xsd ) - throws FileNotFoundException, IOException { + throws FileNotFoundException, IOException { PhylogenyParser parser = null; final String first_line = ForesterUtil.getFirstLine( file ).trim().toLowerCase(); if ( first_line.startsWith( "<" ) ) { @@ -127,7 +127,7 @@ public final class ParserUtils { final public static PhylogenyParser createParserDependingOnFileType( final File file, final boolean phyloxml_validate_against_xsd ) - throws FileNotFoundException, IOException { + throws FileNotFoundException, IOException { PhylogenyParser parser = null; parser = ParserUtils.createParserDependingOnSuffix( file.getName(), phyloxml_validate_against_xsd ); if ( parser == null ) { @@ -146,7 +146,7 @@ public final class ParserUtils { final public static PhylogenyParser createParserDependingOnUrlContents( final URL url, final boolean phyloxml_validate_against_xsd ) - throws FileNotFoundException, IOException { + throws FileNotFoundException, IOException { final String lc_filename = url.getFile().toString().toLowerCase(); PhylogenyParser parser = createParserDependingOnSuffix( lc_filename, phyloxml_validate_against_xsd ); if ( parser == null ) { @@ -213,7 +213,7 @@ public final class ParserUtils { } else { throw new IllegalArgumentException( "attempt to parse object of type [" + source.getClass() - + "] (can only parse objects of type File/String, InputStream, StringBuffer, or StringBuilder)" ); + + "] (can only parse objects of type File/String, InputStream, StringBuffer, or StringBuilder)" ); } return reader; } @@ -317,7 +317,7 @@ public final class ParserUtils { public final static String extractTaxonomyDataFromNodeName( final PhylogenyNode node, final NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction ) - throws PhyloXmlDataFormatException { + throws PhyloXmlDataFormatException { if ( taxonomy_extraction == TAXONOMY_EXTRACTION.NO ) { throw new IllegalArgumentException(); } @@ -384,7 +384,7 @@ public final class ParserUtils { /** * Return null if it can not guess the parser to use based on name suffix. - * + * * @param filename * @return */ diff --git a/forester/java/src/org/forester/io/parsers/util/PhylogenyParserException.java b/forester/java/src/org/forester/io/parsers/util/PhylogenyParserException.java index d4dc9b7..4522021 100644 --- a/forester/java/src/org/forester/io/parsers/util/PhylogenyParserException.java +++ b/forester/java/src/org/forester/io/parsers/util/PhylogenyParserException.java @@ -33,12 +33,12 @@ import java.io.IOException; public class PhylogenyParserException extends IOException { /** - * + * */ private static final long serialVersionUID = -4810333295377881086L; /** - * + * */ public PhylogenyParserException() { super(); diff --git a/forester/java/src/org/forester/io/writers/PhyloXmlNodeWriter.java b/forester/java/src/org/forester/io/writers/PhyloXmlNodeWriter.java index f072c58..c92e1d7 100644 --- a/forester/java/src/org/forester/io/writers/PhyloXmlNodeWriter.java +++ b/forester/java/src/org/forester/io/writers/PhyloXmlNodeWriter.java @@ -47,7 +47,7 @@ public class PhyloXmlNodeWriter { } if ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) { PhylogenyDataUtil.appendElement( w, PhyloXmlMapping.BRANCH_LENGTH, String.valueOf( ForesterUtil.round( node - .getDistanceToParent(), PhyloXmlUtil.ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT ) ), indentation ); + .getDistanceToParent(), PhyloXmlUtil.ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT ) ), indentation ); } if ( node.getBranchData() != null ) { node.getBranchData().toPhyloXML( w, level, ind ); diff --git a/forester/java/src/org/forester/io/writers/PhylogenyWriter.java b/forester/java/src/org/forester/io/writers/PhylogenyWriter.java index 6aee097..8c40eae 100644 --- a/forester/java/src/org/forester/io/writers/PhylogenyWriter.java +++ b/forester/java/src/org/forester/io/writers/PhylogenyWriter.java @@ -54,17 +54,17 @@ public final class PhylogenyWriter { public final static String PHYLO_XML_INTENDATION_BASE = " "; public final static String PHYLO_XML_VERSION_ENCODING_LINE = ""; public final static String PHYLO_XML_NAMESPACE_LINE = ""; + + ForesterConstants.XML_SCHEMA_INSTANCE + + "\" xsi:schemaLocation=\"" + + ForesterConstants.PHYLO_XML_LOCATION + + " " + + ForesterConstants.PHYLO_XML_LOCATION + + "/" + + ForesterConstants.PHYLO_XML_VERSION + + "/" + ForesterConstants.PHYLO_XML_XSD + + "\" " + "xmlns=\"" + + ForesterConstants.PHYLO_XML_LOCATION + + "\">"; public final static String PHYLO_XML_END = ""; private boolean _saw_comma; private StringBuffer _buffer; @@ -112,7 +112,7 @@ public final class PhylogenyWriter { if ( tree.getConfidence() != null ) { if ( ForesterUtil.isEmpty( tree.getConfidence().getType() ) ) { PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.CONFIDENCE, tree.getConfidence().getValue() - + "", indentation ); + + "", indentation ); } PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.CONFIDENCE, @@ -583,7 +583,7 @@ public final class PhylogenyWriter { PhylogenyDataUtil.appendOpen( getWriter(), PhyloXmlMapping.CLADE, PhyloXmlMapping.NODE_COLLAPSE, - "true" ); + "true" ); } else { PhylogenyDataUtil.appendOpen( getWriter(), PhyloXmlMapping.CLADE ); diff --git a/forester/java/src/org/forester/msa/BasicMsa.java b/forester/java/src/org/forester/msa/BasicMsa.java index 25f0db7..02da257 100644 --- a/forester/java/src/org/forester/msa/BasicMsa.java +++ b/forester/java/src/org/forester/msa/BasicMsa.java @@ -143,7 +143,7 @@ public class BasicMsa implements Msa { } if ( _identifiers_set.contains( id ) ) { throw new IllegalArgumentException( "illegal attempt to create msa with non-unique identifiers [" + id - + "]" ); + + "]" ); } _identifiers_set.add( id ); _identifiers[ row ] = id; diff --git a/forester/java/src/org/forester/msa/ClustalOmega.java b/forester/java/src/org/forester/msa/ClustalOmega.java index de57797..2b7a066 100644 --- a/forester/java/src/org/forester/msa/ClustalOmega.java +++ b/forester/java/src/org/forester/msa/ClustalOmega.java @@ -73,7 +73,7 @@ public final class ClustalOmega extends MsaInferrer { @Override public Msa infer( final List seqs, final List opts ) throws IOException, - InterruptedException { + InterruptedException { final File file = File.createTempFile( "__clustalo_input_", ".fasta" ); file.deleteOnExit(); final BufferedWriter writer = new BufferedWriter( new FileWriter( file ) ); @@ -99,12 +99,12 @@ public final class ClustalOmega extends MsaInferrer { _error = stderr.toString(); if ( _exit_code != 0 ) { throw new IOException( "Clustal Omega program failed, exit code: " + _exit_code + "\nCommand:\n" + my_opts - + "\nError:\n" + stderr ); + + "\nError:\n" + stderr ); } final StringBuilder stdout = command_executor.getStandardOutputFromCommand(); if ( ( stdout == null ) || ( stdout.length() < 2 ) ) { throw new IOException( "Clustal Omega program did not produce any output\nCommand:\n" + my_opts - + "\nError:\n" + stderr ); + + "\nError:\n" + stderr ); } final Msa msa = FastaParser.parseMsa( stdout.toString() ); return msa; diff --git a/forester/java/src/org/forester/msa/Mafft.java b/forester/java/src/org/forester/msa/Mafft.java index b1daad5..5a96bc3 100644 --- a/forester/java/src/org/forester/msa/Mafft.java +++ b/forester/java/src/org/forester/msa/Mafft.java @@ -73,7 +73,7 @@ public final class Mafft extends MsaInferrer { @Override public Msa infer( final List seqs, final List opts ) throws IOException, - InterruptedException { + InterruptedException { final File file = File.createTempFile( "__mafft_input_", ".fasta" ); file.deleteOnExit(); final BufferedWriter writer = new BufferedWriter( new FileWriter( file ) ); @@ -99,7 +99,7 @@ public final class Mafft extends MsaInferrer { _error = stderr.toString(); if ( _exit_code != 0 ) { throw new IOException( "MAFFT program failed, exit code: " + _exit_code + "\nCommand:\n" + my_opts - + "\nError:\n" + stderr ); + + "\nError:\n" + stderr ); } final StringBuilder stdout = command_executor.getStandardOutputFromCommand(); if ( ( stdout == null ) || ( stdout.length() < 2 ) ) { diff --git a/forester/java/src/org/forester/msa/MsaInferrer.java b/forester/java/src/org/forester/msa/MsaInferrer.java index f26b329..45fec85 100644 --- a/forester/java/src/org/forester/msa/MsaInferrer.java +++ b/forester/java/src/org/forester/msa/MsaInferrer.java @@ -50,5 +50,5 @@ public abstract class MsaInferrer { public abstract Msa infer( File path_to_input_seqs, List opts ) throws IOException, InterruptedException; public abstract Msa infer( final List seqs, final List opts ) throws IOException, - InterruptedException; + InterruptedException; } diff --git a/forester/java/src/org/forester/msa/MsaMethods.java b/forester/java/src/org/forester/msa/MsaMethods.java index edca9b7..ee5188e 100644 --- a/forester/java/src/org/forester/msa/MsaMethods.java +++ b/forester/java/src/org/forester/msa/MsaMethods.java @@ -324,8 +324,8 @@ public final class MsaMethods { final private static HashMap calcResidueDistribution6( final Msa msa, final int col ) { // Residues are classified into one of tex2html_wrap199 types: - // aliphatic [AVLIMC], aromatic [FWYH], polar [STNQ], positive [KR], negative [DE], - // special conformations [GP] and gaps. This convention follows that + // aliphatic [AVLIMC], aromatic [FWYH], polar [STNQ], positive [KR], negative [DE], + // special conformations [GP] and gaps. This convention follows that // of Mirny & Shakhnovich (1999, J Mol Biol 291:177-196). final HashMap counts = new HashMap(); for( int row = 0; row < msa.getNumberOfSequences(); ++row ) { @@ -370,8 +370,8 @@ public final class MsaMethods { final private static HashMap calcResidueDistribution7( final Msa msa, final int col ) { // Residues are classified into one of tex2html_wrap199 types: - // aliphatic [AVLIMC], aromatic [FWYH], polar [STNQ], positive [KR], negative [DE], - // special conformations [GP] and gaps. This convention follows that + // aliphatic [AVLIMC], aromatic [FWYH], polar [STNQ], positive [KR], negative [DE], + // special conformations [GP] and gaps. This convention follows that // of Mirny & Shakhnovich (1999, J Mol Biol 291:177-196). final HashMap counts = new HashMap(); for( int row = 0; row < msa.getNumberOfSequences(); ++row ) { diff --git a/forester/java/src/org/forester/msa/ResampleableMsa.java b/forester/java/src/org/forester/msa/ResampleableMsa.java index 1ab7ac7..a44c5d1 100644 --- a/forester/java/src/org/forester/msa/ResampleableMsa.java +++ b/forester/java/src/org/forester/msa/ResampleableMsa.java @@ -47,7 +47,7 @@ public final class ResampleableMsa extends BasicMsa { final public void resample( final int[] resampled_column_positions ) { if ( resampled_column_positions.length != getLength() ) { throw new IllegalArgumentException( "illegal attempt to use " + resampled_column_positions.length - + " resampled column positions on msa of length " + getLength() ); + + " resampled column positions on msa of length " + getLength() ); } _resampled_column_positions = resampled_column_positions; } diff --git a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java index cea2460..494b771 100644 --- a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java +++ b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java @@ -225,14 +225,14 @@ public class MsaCompactor { } else { n.getNodeData() - .getNodeVisualData() - .setNodeColor( ForesterUtil.calcColor( msa_prop.getLength(), - min, - max, - mean, - min_color, - max_color, - mean_color ) ); + .getNodeVisualData() + .setNodeColor( ForesterUtil.calcColor( msa_prop.getLength(), + min, + max, + mean, + min_color, + max_color, + mean_color ) ); } } } @@ -282,7 +282,7 @@ public class MsaCompactor { } public final List removeViaGapAverage( final double mean_gapiness ) throws IOException, - InterruptedException { + InterruptedException { final GapContribution stats[] = calcGapContribtionsStats( _norm ); final List to_remove_ids = new ArrayList(); final List msa_props = new ArrayList(); @@ -383,7 +383,7 @@ public class MsaCompactor { } public final List removeWorstOffenders( final int to_remove ) throws IOException, - InterruptedException { + InterruptedException { final GapContribution stats[] = calcGapContribtionsStats( _norm ); final List to_remove_ids = new ArrayList(); final List msa_props = new ArrayList(); diff --git a/forester/java/src/org/forester/pccx/BasicExternalNodeBasedCoverageExtender.java b/forester/java/src/org/forester/pccx/BasicExternalNodeBasedCoverageExtender.java index 83fcda5..6e00da6 100644 --- a/forester/java/src/org/forester/pccx/BasicExternalNodeBasedCoverageExtender.java +++ b/forester/java/src/org/forester/pccx/BasicExternalNodeBasedCoverageExtender.java @@ -86,7 +86,7 @@ public class BasicExternalNodeBasedCoverageExtender implements CoverageExtender /* * (non-Javadoc) - * + * * @see org.forester.tools.modeling.CoverageExtender#find(java.util.List, * java.util.List, int, * org.forester.tools.modeling.CoverageCalculationMethod, diff --git a/forester/java/src/org/forester/pccx/BranchCountingBasedScoringMethod.java b/forester/java/src/org/forester/pccx/BranchCountingBasedScoringMethod.java index 00b4d48..fdb9b17 100644 --- a/forester/java/src/org/forester/pccx/BranchCountingBasedScoringMethod.java +++ b/forester/java/src/org/forester/pccx/BranchCountingBasedScoringMethod.java @@ -33,7 +33,7 @@ import org.forester.phylogeny.PhylogenyNode; /* * Scoring method according to an idea by Adam Godzik, PhD. - * + * * @author Christian M. Zmasek */ public class BranchCountingBasedScoringMethod implements ScoringMethodForExternalNode { diff --git a/forester/java/src/org/forester/pccx/BranchLengthBasedScoringMethod.java b/forester/java/src/org/forester/pccx/BranchLengthBasedScoringMethod.java index 5086f7d..2424e0e 100644 --- a/forester/java/src/org/forester/pccx/BranchLengthBasedScoringMethod.java +++ b/forester/java/src/org/forester/pccx/BranchLengthBasedScoringMethod.java @@ -31,7 +31,7 @@ import org.forester.phylogeny.PhylogenyNode; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; /* - * + * * @author Christian M. Zmasek */ public class BranchLengthBasedScoringMethod extends BranchCountingBasedScoringMethod { diff --git a/forester/java/src/org/forester/pccx/ExternalNodeBasedCoverageMethod.java b/forester/java/src/org/forester/pccx/ExternalNodeBasedCoverageMethod.java index 5e73593..76b3134 100644 --- a/forester/java/src/org/forester/pccx/ExternalNodeBasedCoverageMethod.java +++ b/forester/java/src/org/forester/pccx/ExternalNodeBasedCoverageMethod.java @@ -120,13 +120,13 @@ public class ExternalNodeBasedCoverageMethod implements CoverageCalculationMetho final PhylogenyNode node = ( PhylogenyNode ) element.getKey(); final double normalized_value = ( Double ) element.getValue() * normalization_factor; PhylogenyMethods.setBranchColorValue( node, ForesterUtil - .calcColor( normalized_value, - min, - max, - median, - ExternalNodeBasedCoverageMethod.MINIMAL_COV_COLOR, - ExternalNodeBasedCoverageMethod.MAXIMAL_COV_COLOR, - ExternalNodeBasedCoverageMethod.MEAN_COVERAGE_COLOR ) ); + .calcColor( normalized_value, + min, + max, + median, + ExternalNodeBasedCoverageMethod.MINIMAL_COV_COLOR, + ExternalNodeBasedCoverageMethod.MAXIMAL_COV_COLOR, + ExternalNodeBasedCoverageMethod.MEAN_COVERAGE_COLOR ) ); } PhylogenyMethods.postorderBranchColorAveragingExternalNodeBased( phylogeny ); } diff --git a/forester/java/src/org/forester/pccx/ExternalNodeBasedCoverageMethodOptions.java b/forester/java/src/org/forester/pccx/ExternalNodeBasedCoverageMethodOptions.java index bd5da8b..5e57218 100644 --- a/forester/java/src/org/forester/pccx/ExternalNodeBasedCoverageMethodOptions.java +++ b/forester/java/src/org/forester/pccx/ExternalNodeBasedCoverageMethodOptions.java @@ -33,7 +33,7 @@ public class ExternalNodeBasedCoverageMethodOptions implements CoverageCalculati /** * This constructor sets the class name for the scoring method e.g. * "org.forester.tools.modeling.BranchCountingBasedScoringMethod" - * + * * @param scoring_method * class name for the scoring method */ diff --git a/forester/java/src/org/forester/pccx/LogBranchLengthBasedScoringMethod.java b/forester/java/src/org/forester/pccx/LogBranchLengthBasedScoringMethod.java index 7ba40cb..8867ffb 100644 --- a/forester/java/src/org/forester/pccx/LogBranchLengthBasedScoringMethod.java +++ b/forester/java/src/org/forester/pccx/LogBranchLengthBasedScoringMethod.java @@ -31,7 +31,7 @@ import org.forester.phylogeny.PhylogenyNode; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; /* - * + * * @author Christian M. Zmasek */ public class LogBranchLengthBasedScoringMethod extends BranchCountingBasedScoringMethod { diff --git a/forester/java/src/org/forester/pccx/ScoringMethodForExternalNode.java b/forester/java/src/org/forester/pccx/ScoringMethodForExternalNode.java index d34fa09..78a816e 100644 --- a/forester/java/src/org/forester/pccx/ScoringMethodForExternalNode.java +++ b/forester/java/src/org/forester/pccx/ScoringMethodForExternalNode.java @@ -34,15 +34,15 @@ import org.forester.phylogeny.PhylogenyNode; /* * Interface providing implementations of scoring methods used by * ExternalNodeBasedCoverageMethod. - * + * * @author Christian M. Zmasek */ public interface ScoringMethodForExternalNode { /** * This calculates the coverage score for one external node. - * - * + * + * * @param external_node_scores * SortedMap in which the external node * scores are stored (node->score) @@ -52,8 +52,8 @@ public interface ScoringMethodForExternalNode { * PhylogenyNod for which to calculate the score * @param options * CoverageCalculationOptions - * @param annotate_phylogeny - * + * @param annotate_phylogeny + * */ public void calculateScoreForExternalNode( final SortedMap external_node_scores, final Phylogeny phylogeny, @@ -62,7 +62,7 @@ public interface ScoringMethodForExternalNode { /** * This returns a short description of this scoring method - * + * * @return short description of this scoring method */ public String getDesciption(); @@ -70,8 +70,8 @@ public interface ScoringMethodForExternalNode { /** * This calculates a normalization factor, so that a normalized score of 1.0 * means complete coverage. - * - * + * + * * @param phylogeny * Phylogeny containing the external nodes to score * @return normalization factor diff --git a/forester/java/src/org/forester/phylogeny/Phylogeny.java b/forester/java/src/org/forester/phylogeny/Phylogeny.java index 115e885..3d94dd7 100644 --- a/forester/java/src/org/forester/phylogeny/Phylogeny.java +++ b/forester/java/src/org/forester/phylogeny/Phylogeny.java @@ -86,7 +86,7 @@ public class Phylogeny { /** * Adds this Phylogeny to the list of child nodes of PhylogenyNode parent * and sets the parent of this to parent. - * + * * @param n * the PhylogenyNode to add */ @@ -126,7 +126,7 @@ public class Phylogeny { /** * This calculates the height of the subtree emanating at n for rooted, * tree-shaped phylogenies - * + * * @param n * the root-node of a subtree * @return the height of the subtree emanating at n @@ -222,9 +222,9 @@ public class Phylogeny { /** * Need to call clearHashIdToNodeMap() afterwards (not done automatically * to allow client multiple deletions in linear time). - * Need to call 'recalculateNumberOfExternalDescendants(boolean)' after this + * Need to call 'recalculateNumberOfExternalDescendants(boolean)' after this * if tree is to be displayed. - * + * * @param remove_us the parent node of the subtree to be deleted */ public void deleteSubtree( final PhylogenyNode remove_us, final boolean collapse_resulting_node_with_one_desc ) { @@ -261,12 +261,12 @@ public class Phylogeny { final int pi = p.getChildNodeIndex(); if ( removed_node.isFirstChildNode() ) { p.getChildNode( 1 ).setDistanceToParent( PhylogenyMethods.addPhylogenyDistances( p - .getDistanceToParent(), p.getChildNode( 1 ).getDistanceToParent() ) ); + .getDistanceToParent(), p.getChildNode( 1 ).getDistanceToParent() ) ); pp.setChildNode( pi, p.getChildNode( 1 ) ); } else { p.getChildNode( 0 ).setDistanceToParent( PhylogenyMethods.addPhylogenyDistances( p - .getDistanceToParent(), p.getChildNode( 0 ).getDistanceToParent() ) ); + .getDistanceToParent(), p.getChildNode( 0 ).getDistanceToParent() ) ); pp.setChildNode( pi, p.getChildNode( 0 ) ); } } @@ -313,10 +313,10 @@ public class Phylogeny { } /** - * + * * Warning. The order of the returned nodes is random * -- and hence cannot be relied on. - * + * * @return Unordered set of PhylogenyNode */ public List getExternalNodes() { @@ -342,7 +342,7 @@ public class Phylogeny { /** * Sets the number of duplications of this Phylogeny (int). A value of -1 * indicates that the number of duplications is unknown. - * + * * @param clean_nh * set to true for clean NH format */ @@ -373,7 +373,7 @@ public class Phylogeny { * height is the longest distance from the root to an external node. Please * note. Child nodes of collapsed nodes are ignored -- which is useful for * display purposes but might be misleading for other applications. - * + * * @return the height for rooted, tree-shaped phylogenies */ public double getHeight() { @@ -411,7 +411,7 @@ public class Phylogeny { /** * Returns a PhylogenyNode of this Phylogeny which has a matching name. * Throws an Exception if seqname is not present in this or not unique. - * + * * @param name * name (String) of PhylogenyNode to find * @return PhylogenyNode with matchin name @@ -432,7 +432,7 @@ public class Phylogeny { /** * This is time-inefficient since it runs a iterator each time it is called. - * + * */ public int getNodeCount() { if ( isEmpty() ) { @@ -448,7 +448,7 @@ public class Phylogeny { /** * Returns a List with references to all Nodes of this Phylogeny which have * a matching name. - * + * * @param name * name (String) of Nodes to find * @return Vector of references to Nodes of this Phylogeny with matching @@ -529,7 +529,7 @@ public class Phylogeny { /** * Returns a Vector with references to all Nodes of this Phylogeny which * have a matching species name. - * + * * @param specname * species name (String) of Nodes to find * @return Vector of references to Nodes of this Phylogeny with matching @@ -629,7 +629,7 @@ public class Phylogeny { *

* (Last modified: 11/22/00) Olivier CHABROL : * olivier.chabrol@univ-provence.fr - * + * * @param n * external PhylogenyNode whose orthologs are to be returned * @return Vector of references to all orthologous Nodes of PhylogenyNode n @@ -658,11 +658,11 @@ public class Phylogeny { if ( node.isDuplication() && isContains( taxIdList, taxonomyCodeRangeList ) ) { if ( node.getChildNode1() == prev ) { v.addAll( getNodeByTaxonomyID( searchNodeSpeciesId, node.getChildNode2() - .getAllExternalDescendants() ) ); + .getAllExternalDescendants() ) ); } else { v.addAll( getNodeByTaxonomyID( searchNodeSpeciesId, node.getChildNode1() - .getAllExternalDescendants() ) ); + .getAllExternalDescendants() ) ); } } } @@ -711,7 +711,7 @@ public class Phylogeny { /** * Returns whether this is a completely binary tree (i.e. all internal nodes * are bifurcations). - * + * */ public boolean isCompletelyBinary() { if ( isEmpty() ) { @@ -728,7 +728,7 @@ public class Phylogeny { /** * Checks whether a Phylogeny object is deleted (or empty). - * + * * @return true if the tree is deleted (or empty), false otherwise */ public boolean isEmpty() { @@ -770,7 +770,7 @@ public class Phylogeny { * Resets the ID numbers of the nodes of this Phylogeny in level order, * starting with start_label (for the root).
* WARNING. After this method has been called, node IDs are no longer - * unique. + * unique. */ public void levelOrderReID() { if ( isEmpty() ) { @@ -810,7 +810,7 @@ public class Phylogeny { * (Re)counts the number of children for each PhylogenyNode of this * Phylogeny. As an example, this method needs to be called after a * Phylogeny has been reRooted and it is to be displayed. - * + * * @param consider_collapsed_nodes * set to true to take into account collapsed nodes (collapsed * nodes have 1 child). @@ -843,7 +843,7 @@ public class Phylogeny { *

*

  • recalculateNumberOfExternalDescendants(boolean) *
  • recalculateAndReset() - * + * * @param id * ID (int) of PhylogenyNode of this Phylogeny */ @@ -863,7 +863,7 @@ public class Phylogeny { * *

    * (Last modified: 10/01/01) - * + * * @param n * PhylogenyNode of this Phylogeny\ */ @@ -995,7 +995,7 @@ public class Phylogeny { } else { node.setDistanceToParent( ( c.getDistanceToParent() >= 0.0 ? c.getDistanceToParent() : 0.0 ) - + ( node.getDistanceToParent() >= 0.0 ? node.getDistanceToParent() : 0.0 ) ); + + ( node.getDistanceToParent() >= 0.0 ? node.getDistanceToParent() : 0.0 ) ); } if ( c.getBranchDataDirectly() != null ) { node.setBranchData( ( BranchData ) c.getBranchDataDirectly().copy() ); @@ -1146,7 +1146,7 @@ public class Phylogeny { // --------------------------------------------------------- /** * Converts this Phylogeny to a New Hampshire X (String) representation. - * + * * @return New Hampshire X (String) representation of this * @see #toNewHampshireX() */ @@ -1180,7 +1180,7 @@ public class Phylogeny { /** * Return Node by TaxonomyId Olivier CHABROL : * olivier.chabrol@univ-provence.fr - * + * * @param taxonomyID * search taxonomy identifier * @param nodes @@ -1200,7 +1200,7 @@ public class Phylogeny { /** * List all species contains in all leaf under a node Olivier CHABROL : * olivier.chabrol@univ-provence.fr - * + * * @param node * PhylogenyNode whose sub node species are returned * @return species contains in all leaf under the param node @@ -1223,7 +1223,7 @@ public class Phylogeny { * Create a map [], the list contains the * species contains in all leaf under phylogeny node Olivier CHABROL : * olivier.chabrol@univ-provence.fr - * + * * @param node * the tree root node * @param map @@ -1246,7 +1246,7 @@ public class Phylogeny { /** * Util method to check if all element of a list is contains in the * rangeList. Olivier CHABROL : olivier.chabrol@univ-provence.fr - * + * * @param list * list to be check * @param rangeList diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java index 5bb29e1..459138b 100644 --- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java +++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java @@ -133,7 +133,7 @@ public class PhylogenyMethods { if ( !ForesterUtil.isEmpty( stats.get( i ).getDescription() ) ) { if ( !stats.get( i ).getDescription().equalsIgnoreCase( c.getType() ) ) { throw new IllegalArgumentException( "support values in node [" + n.toString() - + "] appear inconsistently ordered" ); + + "] appear inconsistently ordered" ); } } stats.get( i ).setDescription( c.getType() ); @@ -148,8 +148,8 @@ public class PhylogenyMethods { /** * Calculates the distance between PhylogenyNodes node1 and node2. - * - * + * + * * @param node1 * @param node2 * @return distance between node1 and node2 @@ -163,8 +163,8 @@ public class PhylogenyMethods { /** * Returns the LCA of PhylogenyNodes node1 and node2. - * - * + * + * * @param node1 * @param node2 * @return LCA of node1 and node2 @@ -209,8 +209,8 @@ public class PhylogenyMethods { /** * Returns the LCA of PhylogenyNodes node1 and node2. * Precondition: ids are in pre-order (or level-order). - * - * + * + * * @param node1 * @param node2 * @return LCA of node1 and node2 @@ -500,9 +500,9 @@ public class PhylogenyMethods { } /** - * + * * Convenience method - * + * * @param node * @return */ @@ -553,9 +553,9 @@ public class PhylogenyMethods { } /** - * Returns taxonomy t if all external descendants have + * Returns taxonomy t if all external descendants have * the same taxonomy t, null otherwise. - * + * */ public static Taxonomy getExternalDescendantsTaxonomy( final PhylogenyNode node ) { final List descs = node.getAllExternalDescendants(); @@ -683,7 +683,7 @@ public class PhylogenyMethods { /* * This is case insensitive. - * + * */ public synchronized static boolean isTaxonomyHasIdentifierOfGivenProvider( final Taxonomy tax, final String[] providers ) { @@ -777,7 +777,7 @@ public class PhylogenyMethods { * all external nodes of node. * If at least one of the external nodes has no taxonomy, * null is returned. - * + * */ public static Map obtainDistinctTaxonomyCounts( final PhylogenyNode node ) { final List descs = node.getAllExternalDescendants(); @@ -801,10 +801,10 @@ public class PhylogenyMethods { * Arranges the order of childern for each node of this Phylogeny in such a * way that either the branch with more children is on top (right) or on * bottom (left), dependent on the value of boolean order. - * + * * @param order * decides in which direction to order - * @param pri + * @param pri */ public static void orderAppearance( final PhylogenyNode n, final boolean order, @@ -1239,7 +1239,7 @@ public class PhylogenyMethods { /** * Convenience method. - * Sets value for the first confidence value (created if not present, values overwritten otherwise). + * Sets value for the first confidence value (created if not present, values overwritten otherwise). */ public static void setBootstrapConfidence( final PhylogenyNode node, final double bootstrap_confidence_value ) { setConfidence( node, bootstrap_confidence_value, "bootstrap" ); @@ -1261,7 +1261,7 @@ public class PhylogenyMethods { /** * Convenience method. - * Sets value for the first confidence value (created if not present, values overwritten otherwise). + * Sets value for the first confidence value (created if not present, values overwritten otherwise). */ public static void setConfidence( final PhylogenyNode node, final double confidence_value ) { setConfidence( node, confidence_value, "" ); @@ -1269,7 +1269,7 @@ public class PhylogenyMethods { /** * Convenience method. - * Sets value for the first confidence value (created if not present, values overwritten otherwise). + * Sets value for the first confidence value (created if not present, values overwritten otherwise). */ public static void setConfidence( final PhylogenyNode node, final double confidence_value, final String type ) { Confidence c = null; @@ -1293,11 +1293,11 @@ public class PhylogenyMethods { /** * Convenience method to set the taxonomy code of a phylogeny node. - * - * + * + * * @param node * @param taxonomy_code - * @throws PhyloXmlDataFormatException + * @throws PhyloXmlDataFormatException */ public static void setTaxonomyCode( final PhylogenyNode node, final String taxonomy_code ) throws PhyloXmlDataFormatException { @@ -1330,7 +1330,7 @@ public class PhylogenyMethods { /** * Removes from Phylogeny to_be_stripped all external Nodes which are * associated with a species NOT found in Phylogeny reference. - * + * * @param reference * a reference Phylogeny * @param to_be_stripped @@ -1365,7 +1365,7 @@ public class PhylogenyMethods { else if ( !( ref_ext_taxo.contains( n.getNodeData().getTaxonomy().getScientificName() ) ) && !( ref_ext_taxo.contains( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) && !( ( n.getNodeData().getTaxonomy().getIdentifier() != null ) && ref_ext_taxo.contains( n - .getNodeData().getTaxonomy().getIdentifier().getValuePlusProvider() ) ) ) { + .getNodeData().getTaxonomy().getIdentifier().getValuePlusProvider() ) ) ) { nodes_to_delete.add( n ); } } @@ -1502,7 +1502,7 @@ public class PhylogenyMethods { n.setName( "" ); } n.getNodeData().getTaxonomy() - .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) ); + .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) ); break; } case TAXONOMY_ID_UNIPROT_2: { @@ -1518,7 +1518,7 @@ public class PhylogenyMethods { n.setName( "" ); } n.getNodeData().getTaxonomy() - .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) ); + .setIdentifier( new Identifier( id, PhyloXmlUtil.UNIPROT_TAX_PROVIDER ) ); break; } case TAXONOMY_ID: { @@ -1617,7 +1617,7 @@ public class PhylogenyMethods { /** * Calculates the distance between PhylogenyNodes n1 and n2. * PRECONDITION: n1 is a descendant of n2. - * + * * @param n1 * a descendant of n2 * @param n2 diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java index e7ef81b..899c0cc 100644 --- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java +++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java @@ -42,7 +42,7 @@ import org.forester.phylogeny.iterators.PreorderTreeIterator; import org.forester.util.ForesterUtil; /** - * Warning. Implementation of method 'compareTo' only looks at + * Warning. Implementation of method 'compareTo' only looks at * node name. Thus, use of this class in SortedSets might lead * to unexpected behavior. * @@ -95,7 +95,7 @@ public final class PhylogenyNode implements Comparable { /** * Adds PhylogenyNode n to the list of child nodes and sets the _parent of n * to this. - * + * * @param n * the PhylogenyNode to add */ @@ -141,8 +141,8 @@ public final class PhylogenyNode implements Comparable { * Returns a new PhylogenyNode which has its data copied from this * PhylogenyNode. Links to the other Nodes in the same Phylogeny are NOT * copied (e.g. _link to _parent). Field "_link" IS copied. - * - * @see #getLink() + * + * @see #getLink() */ final public PhylogenyNode copyNodeData() { final PhylogenyNode node = new PhylogenyNode(); @@ -168,8 +168,8 @@ public final class PhylogenyNode implements Comparable { * Returns a new PhylogenyNode which has the same data as this * PhylogenyNode. Links to the other Nodes in the same Phylogeny are NOT * copied (e.g. _link to _parent). Field "_link" IS copied. - * - * @see #getLink() + * + * @see #getLink() */ final public PhylogenyNode copyNodeDataShallow() { final PhylogenyNode node = new PhylogenyNode(); @@ -190,8 +190,8 @@ public final class PhylogenyNode implements Comparable { @Override /** * Based on node name, sequence, and taxonomy. - * - * + * + * */ final public boolean equals( final Object o ) { if ( this == o ) { @@ -239,7 +239,7 @@ public final class PhylogenyNode implements Comparable { /** * Returns a List containing references to all external children of this * PhylogenyNode. - * + * * @return List of references to external Nodes */ final public List getAllExternalDescendants() { @@ -267,7 +267,7 @@ public final class PhylogenyNode implements Comparable { /** * Returns a List containing references to all names of the external * children of this PhylogenyNode. - * + * * @return List of references to names of external Nodes */ final public List getAllExternalDescendantsNames() { @@ -288,7 +288,7 @@ public final class PhylogenyNode implements Comparable { /** * This return child node n of this node. - * + * * @param n * the index of the child to get * @return the child node with index n @@ -327,7 +327,7 @@ public final class PhylogenyNode implements Comparable { /** * This gets the child node index of this node. *

    - * + * * @return the child node index of this node * @throws UnsupportedOperationException * if this node is a root node @@ -341,7 +341,7 @@ public final class PhylogenyNode implements Comparable { * parent *

    * [last modified Aug 14, 2006 by CMZ] - * + * * @return the child node index of this node * @throws UnsupportedOperationException * if this node is a root node @@ -377,7 +377,7 @@ public final class PhylogenyNode implements Comparable { * Convenience method. Returns the first child node of this node. *

    * [last modified May 18, 2005 by CMZ] - * + * * @return the first child node of this node */ public final PhylogenyNode getFirstChildNode() { @@ -402,7 +402,7 @@ public final class PhylogenyNode implements Comparable { * Convenience method. Returns the last child node of this node. *

    * [last modified May 18, 2005 by CMZ] - * + * * @return the last child node of this node */ public final PhylogenyNode getLastChildNode() { @@ -616,7 +616,7 @@ public final class PhylogenyNode implements Comparable { /** * Checks whether this PhylogenyNode is external (tip). - * + * * @return true if this PhylogenyNode is external, false otherwise */ final public boolean isExternal() { @@ -663,7 +663,7 @@ public final class PhylogenyNode implements Comparable { /** * Checks whether this PhylogenyNode is internal (tip). - * + * * @return true if this PhylogenyNode is external, false otherwise */ final public boolean isInternal() { @@ -674,7 +674,7 @@ public final class PhylogenyNode implements Comparable { * Returns true if this node is the last child node of its _parent. *

    * [last modified June 01, 2005 by CMZ] - * + * * @return true if this node is the last child node of its _parent, false * otherwise */ @@ -701,7 +701,7 @@ public final class PhylogenyNode implements Comparable { /** * Checks whether this PhylogenyNode is a root. - * + * * @return true if this PhylogenyNode is the root, false otherwise */ final public boolean isRoot() { @@ -772,7 +772,7 @@ public final class PhylogenyNode implements Comparable { * child nodes. This does not allow null slots in the list of child nodes: * If i is larger than the number of child nodes, n is just added to the * list, not place at index i. - * + * * @param i * the index of position where to add the child * @param n @@ -876,7 +876,7 @@ public final class PhylogenyNode implements Comparable { } if ( getNumberOfDescendants() != 2 ) { throw new RuntimeException( "attempt to swap descendants of node with " + getNumberOfDescendants() - + " descendants" ); + + " descendants" ); } final PhylogenyNode a = getChildNode( 0 ); final PhylogenyNode b = getChildNode( 1 ); @@ -894,8 +894,8 @@ public final class PhylogenyNode implements Comparable { if ( getBranchData().isHasConfidences() && ( getBranchData().getConfidence( 0 ).getValue() != Confidence.CONFIDENCE_DEFAULT_VALUE ) ) { data = Confidence.FORMATTER.format( ForesterUtil - .round( getBranchData().getConfidence( 0 ).getValue(), - PhyloXmlUtil.ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT ) ); + .round( getBranchData().getConfidence( 0 ).getValue(), + PhyloXmlUtil.ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT ) ); } } else if ( !ForesterUtil.isEmpty( getName() ) ) { @@ -933,8 +933,8 @@ public final class PhylogenyNode implements Comparable { && ( getBranchData().getConfidence( 0 ).getValue() != Confidence.CONFIDENCE_DEFAULT_VALUE ) ) { sb.append( "[" ); sb.append( Confidence.FORMATTER.format( ForesterUtil - .round( getBranchData().getConfidence( 0 ).getValue(), - PhyloXmlUtil.ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT ) ) ); + .round( getBranchData().getConfidence( 0 ).getValue(), + PhyloXmlUtil.ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT ) ) ); sb.append( "]" ); } return sb.toString(); @@ -1056,7 +1056,7 @@ public final class PhylogenyNode implements Comparable { /** * Adds PhylogenyNode n to the list of child nodes. But does NOT set the * _parent of n to this. - * + * * @see addAsChild( PhylogenyNode n ) * @param n * the PhylogenyNode to add @@ -1066,26 +1066,26 @@ public final class PhylogenyNode implements Comparable { } public static PhylogenyNode createInstanceFromNhxString( final String nhx ) throws NHXFormatException, - PhyloXmlDataFormatException { + PhyloXmlDataFormatException { return new PhylogenyNode( nhx, NHXParser.TAXONOMY_EXTRACTION.NO, false ); } public static PhylogenyNode createInstanceFromNhxString( final String nhx, final NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction ) - throws NHXFormatException, PhyloXmlDataFormatException { + throws NHXFormatException, PhyloXmlDataFormatException { return new PhylogenyNode( nhx, taxonomy_extraction, false ); } public static PhylogenyNode createInstanceFromNhxString( final String nhx, final NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction, final boolean replace_underscores ) - throws NHXFormatException, PhyloXmlDataFormatException { + throws NHXFormatException, PhyloXmlDataFormatException { return new PhylogenyNode( nhx, taxonomy_extraction, replace_underscores ); } /** * Returns the total number of all Nodes created so far. - * + * * @return total number of Nodes (long) */ synchronized final public static long getNodeCount() { diff --git a/forester/java/src/org/forester/phylogeny/data/BinaryCharacters.java b/forester/java/src/org/forester/phylogeny/data/BinaryCharacters.java index cea856f..0ee99bf 100644 --- a/forester/java/src/org/forester/phylogeny/data/BinaryCharacters.java +++ b/forester/java/src/org/forester/phylogeny/data/BinaryCharacters.java @@ -94,7 +94,7 @@ public class BinaryCharacters implements PhylogenyData { public void addGainedCharacter( final String binary_character ) { if ( getLostCharacters().contains( binary_character ) ) { throw new IllegalArgumentException( "attempt to add binary character [" + binary_character - + "] to gained characters but is already listed as lost" ); + + "] to gained characters but is already listed as lost" ); } getGainedCharacters().add( binary_character ); } @@ -102,11 +102,11 @@ public class BinaryCharacters implements PhylogenyData { public void addLostCharacter( final String binary_character ) { if ( getPresentCharacters().contains( binary_character ) ) { throw new IllegalArgumentException( "attempt to add binary character [" + binary_character - + "] to lost characters but is already listed as present" ); + + "] to lost characters but is already listed as present" ); } if ( getGainedCharacters().contains( binary_character ) ) { throw new IllegalArgumentException( "attempt to add binary character [" + binary_character - + "] to lost characters but is already listed as gained" ); + + "] to lost characters but is already listed as gained" ); } getLostCharacters().add( binary_character ); } @@ -114,7 +114,7 @@ public class BinaryCharacters implements PhylogenyData { public void addPresentCharacter( final String binary_character ) { if ( getLostCharacters().contains( binary_character ) ) { throw new IllegalArgumentException( "attempt to add binary character [" + binary_character - + "] to present characters but is already listed as lost" ); + + "] to present characters but is already listed as lost" ); } getPresentCharacters().add( binary_character ); } @@ -148,7 +148,7 @@ public class BinaryCharacters implements PhylogenyData { @Override /** * Not a deep copy. - * + * */ public PhylogenyData copy() { validate(); @@ -238,10 +238,10 @@ public class BinaryCharacters implements PhylogenyData { getType(), PhyloXmlMapping.BINARY_CHARACTERS_GAINED_COUNT_ATTR, getGainedCount() != COUNT_DEFAULT ? String.valueOf( getGainedCount() ) : "", - PhyloXmlMapping.BINARY_CHARACTERS_LOST_COUNT_ATTR, - getLostCount() != COUNT_DEFAULT ? String.valueOf( getLostCount() ) : "", - PhyloXmlMapping.BINARY_CHARACTERS_PRESENT_COUNT_ATTR, - getPresentCount() != COUNT_DEFAULT ? String.valueOf( getPresentCount() ) : "" ); + PhyloXmlMapping.BINARY_CHARACTERS_LOST_COUNT_ATTR, + getLostCount() != COUNT_DEFAULT ? String.valueOf( getLostCount() ) : "", + PhyloXmlMapping.BINARY_CHARACTERS_PRESENT_COUNT_ATTR, + getPresentCount() != COUNT_DEFAULT ? String.valueOf( getPresentCount() ) : "" ); final String my_ind = indentation + PhylogenyWriter.PHYLO_XML_INTENDATION_BASE; if ( getGainedCharacters().size() > 0 ) { writer.write( ForesterUtil.LINE_SEPARATOR ); diff --git a/forester/java/src/org/forester/phylogeny/data/BranchColor.java b/forester/java/src/org/forester/phylogeny/data/BranchColor.java index e3ceaf0..7d47e24 100644 --- a/forester/java/src/org/forester/phylogeny/data/BranchColor.java +++ b/forester/java/src/org/forester/phylogeny/data/BranchColor.java @@ -57,7 +57,7 @@ public class BranchColor implements PhylogenyData { @Override /** * Not a deep copy. - * + * */ public PhylogenyData copy() { final BranchColor bc = new BranchColor(); diff --git a/forester/java/src/org/forester/phylogeny/data/BranchData.java b/forester/java/src/org/forester/phylogeny/data/BranchData.java index 51d895d..6e8ded3 100644 --- a/forester/java/src/org/forester/phylogeny/data/BranchData.java +++ b/forester/java/src/org/forester/phylogeny/data/BranchData.java @@ -39,7 +39,7 @@ public class BranchData implements PhylogenyData { private BranchWidth _branch_width; public BranchData() { - // Doing nothing. + // Doing nothing. } public void addConfidence( final Confidence confidence ) { diff --git a/forester/java/src/org/forester/phylogeny/data/Confidence.java b/forester/java/src/org/forester/phylogeny/data/Confidence.java index 4ea14ef..8b12491 100644 --- a/forester/java/src/org/forester/phylogeny/data/Confidence.java +++ b/forester/java/src/org/forester/phylogeny/data/Confidence.java @@ -167,25 +167,25 @@ public class Confidence implements PhylogenyData, Comparable { writer.write( indentation ); if ( getStandardDeviation() != CONFIDENCE_DEFAULT_VALUE ) { PhylogenyDataUtil - .appendElement( writer, - PhyloXmlMapping.CONFIDENCE, - FORMATTER.format( ForesterUtil - .round( getValue(), PhyloXmlUtil.ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT ) ), - PhyloXmlMapping.CONFIDENCE_TYPE_ATTR, - ForesterUtil.isEmpty( getType() ) ? "unknown" : getType(), - PhyloXmlMapping.CONFIDENCE_SD_ATTR, - String.valueOf( ForesterUtil - .round( getStandardDeviation(), - PhyloXmlUtil.ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT ) ) ); + .appendElement( writer, + PhyloXmlMapping.CONFIDENCE, + FORMATTER.format( ForesterUtil + .round( getValue(), PhyloXmlUtil.ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT ) ), + PhyloXmlMapping.CONFIDENCE_TYPE_ATTR, + ForesterUtil.isEmpty( getType() ) ? "unknown" : getType(), + PhyloXmlMapping.CONFIDENCE_SD_ATTR, + String.valueOf( ForesterUtil + .round( getStandardDeviation(), + PhyloXmlUtil.ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT ) ) ); } else { PhylogenyDataUtil - .appendElement( writer, - PhyloXmlMapping.CONFIDENCE, - FORMATTER.format( ForesterUtil - .round( getValue(), PhyloXmlUtil.ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT ) ), - PhyloXmlMapping.CONFIDENCE_TYPE_ATTR, - ForesterUtil.isEmpty( getType() ) ? "unknown" : getType() ); + .appendElement( writer, + PhyloXmlMapping.CONFIDENCE, + FORMATTER.format( ForesterUtil + .round( getValue(), PhyloXmlUtil.ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT ) ), + PhyloXmlMapping.CONFIDENCE_TYPE_ATTR, + ForesterUtil.isEmpty( getType() ) ? "unknown" : getType() ); } } diff --git a/forester/java/src/org/forester/phylogeny/data/Date.java b/forester/java/src/org/forester/phylogeny/data/Date.java index 5cd1039..113d7b4 100644 --- a/forester/java/src/org/forester/phylogeny/data/Date.java +++ b/forester/java/src/org/forester/phylogeny/data/Date.java @@ -95,9 +95,9 @@ public class Date implements PhylogenyData { public PhylogenyData copy() { return new Date( getDesc(), getValue() == null ? null : new BigDecimal( getValue().toPlainString() ), - getMin() == null ? null : new BigDecimal( getMin().toPlainString() ), - getMax() == null ? null : new BigDecimal( getMax().toPlainString() ), - getUnit() ); + getMin() == null ? null : new BigDecimal( getMin().toPlainString() ), + getMax() == null ? null : new BigDecimal( getMax().toPlainString() ), + getUnit() ); } public String getDesc() { diff --git a/forester/java/src/org/forester/phylogeny/data/DomainArchitecture.java b/forester/java/src/org/forester/phylogeny/data/DomainArchitecture.java index 0f09c55..8510259 100644 --- a/forester/java/src/org/forester/phylogeny/data/DomainArchitecture.java +++ b/forester/java/src/org/forester/phylogeny/data/DomainArchitecture.java @@ -154,8 +154,8 @@ public class DomainArchitecture implements PhylogenyData { /** * Returns true if the names and the order of the domains match (domain and * linker lengths are ignored). - * - * + * + * */ @Override public boolean isEqual( final PhylogenyData domain_architecture ) { diff --git a/forester/java/src/org/forester/phylogeny/data/Event.java b/forester/java/src/org/forester/phylogeny/data/Event.java index afd714c..afccbcd 100644 --- a/forester/java/src/org/forester/phylogeny/data/Event.java +++ b/forester/java/src/org/forester/phylogeny/data/Event.java @@ -216,7 +216,7 @@ public class Event implements PhylogenyData { /** * Returns true if this event contains one or more duplications events only - * + * * @return true if this event contains one or more duplications events only */ public boolean isDuplication() { @@ -250,7 +250,7 @@ public class Event implements PhylogenyData { /** * Returns true if this event contains one or more gene loss events only - * + * * @return true if this event contains one or more gene loss events only */ public boolean isGeneLoss() { @@ -267,7 +267,7 @@ public class Event implements PhylogenyData { /** * Returns true if this event contains one or more speciation events only - * + * * @return true if this event contains one or more speciation events only */ public boolean isSpeciation() { @@ -331,7 +331,7 @@ public class Event implements PhylogenyData { PhylogenyDataUtil.appendOpen( writer, PhyloXmlMapping.EVENTS ); if ( ( getEventType() != EventType.unassigned ) && ( getEventType() != EventType.mixed ) ) { PhylogenyDataUtil - .appendElement( writer, PhyloXmlMapping.EVENT_TYPE, getEventType().toString(), indentation ); + .appendElement( writer, PhyloXmlMapping.EVENT_TYPE, getEventType().toString(), indentation ); } if ( getNumberOfDuplications() > 0 ) { PhylogenyDataUtil.appendElement( writer, diff --git a/forester/java/src/org/forester/phylogeny/data/NodeData.java b/forester/java/src/org/forester/phylogeny/data/NodeData.java index ab6f055..28bedb9 100644 --- a/forester/java/src/org/forester/phylogeny/data/NodeData.java +++ b/forester/java/src/org/forester/phylogeny/data/NodeData.java @@ -184,7 +184,7 @@ public class NodeData implements PhylogenyData { /** * Convenience method -- always returns the first Distribution. - * + * * @return Distribution */ public Distribution getDistribution() { @@ -209,9 +209,9 @@ public class NodeData implements PhylogenyData { /** * Convenience method -- always returns the first Reference. - * + * * @return Reference - * + * */ public Reference getReference() { return getReference( 0 ); @@ -227,7 +227,7 @@ public class NodeData implements PhylogenyData { /** * Convenience method -- always returns the first Sequence. - * + * * @return Sequence */ public Sequence getSequence() { @@ -248,9 +248,9 @@ public class NodeData implements PhylogenyData { /** * Convenience method -- always returns the first Taxonomy. - * + * * @return Taxonomy - * + * */ public Taxonomy getTaxonomy() { return getTaxonomy( 0 ); @@ -272,21 +272,21 @@ public class NodeData implements PhylogenyData { public boolean isEmpty() { return ( ForesterUtil.isEmpty( _node_name ) && !isHasSequence() && !isHasTaxonomy() && !isHasBinaryCharacters() && !isHasDate() && !isHasDistribution() && !isHasEvent() && !isHasProperties() && !isHasReference() && ( ( _vector == null ) || _vector - .isEmpty() ) ); + .isEmpty() ) ); } public boolean isHasDate() { return ( getDate() != null ) && ( !ForesterUtil.isEmpty( getDate().getDesc() ) || !ForesterUtil.isNull( getDate().getMax() ) || !ForesterUtil.isNull( getDate().getMin() ) || !ForesterUtil.isNull( getDate().getValue() ) || !ForesterUtil - .isEmpty( getDate().getUnit() ) ); + .isEmpty( getDate().getUnit() ) ); } public boolean isHasDistribution() { return ( ( ( getDistributions() != null ) && ( getDistributions().size() > 0 ) ) && ( ( !ForesterUtil .isEmpty( getDistribution().getDesc() ) ) || ( ( getDistribution().getPoints() != null ) && ( getDistribution().getPoints().size() > 0 ) ) || ( ( getDistribution() - .getPolygons() != null ) && ( getDistribution().getPolygons().size() > 0 ) ) ) ); + .getPolygons() != null ) && ( getDistribution().getPolygons().size() > 0 ) ) ) ); } public boolean isHasEvent() { @@ -300,7 +300,7 @@ public class NodeData implements PhylogenyData { public boolean isHasReference() { return ( ( getReferences() != null ) && ( getReferences().size() > 0 ) ) && ( !ForesterUtil.isEmpty( getReference().getDoi() ) || !ForesterUtil.isEmpty( getReference() - .getDescription() ) ); + .getDescription() ) ); } public boolean isHasSequence() { @@ -321,7 +321,7 @@ public class NodeData implements PhylogenyData { /** * Convenience method -- always sets the first Distribution. - * + * */ public void setDistribution( final Distribution distribution ) { if ( _distributions == null ) { @@ -363,7 +363,7 @@ public class NodeData implements PhylogenyData { /** * Convenience method -- always sets the first Reference. - * + * */ public void setReference( final Reference reference ) { if ( _references == null ) { @@ -390,7 +390,7 @@ public class NodeData implements PhylogenyData { /** * Convenience method -- always sets the first Sequence. - * + * */ public void setSequence( final Sequence sequence ) { if ( _sequences == null ) { @@ -421,7 +421,7 @@ public class NodeData implements PhylogenyData { /** * Convenience method -- always sets the first Taxonomy. - * + * */ public void setTaxonomy( final Taxonomy taxonomy ) { if ( _taxonomies == null ) { diff --git a/forester/java/src/org/forester/phylogeny/data/NodeVisualData.java b/forester/java/src/org/forester/phylogeny/data/NodeVisualData.java index b3f4b5c..691f024 100644 --- a/forester/java/src/org/forester/phylogeny/data/NodeVisualData.java +++ b/forester/java/src/org/forester/phylogeny/data/NodeVisualData.java @@ -93,16 +93,16 @@ public final class NodeVisualData implements PhylogenyData { @Override public final PhylogenyData copy() { return new NodeVisualData( !ForesterUtil.isEmpty( getFontName() ) ? new String( getFontName() ) : null, - getFontStyle(), - getFontSize(), - getFontColor() != null ? new Color( getFontColor().getRed(), getFontColor() - .getGreen(), getFontColor().getBlue() ) : null, - getShape(), - getFillType(), - getNodeColor() != null ? new Color( getNodeColor().getRed(), getNodeColor() - .getGreen(), getNodeColor().getBlue() ) : null, - getSize(), - getTransparency() ); + getFontStyle(), + getFontSize(), + getFontColor() != null ? new Color( getFontColor().getRed(), getFontColor() + .getGreen(), getFontColor().getBlue() ) : null, + getShape(), + getFillType(), + getNodeColor() != null ? new Color( getNodeColor().getRed(), getNodeColor() + .getGreen(), getNodeColor().getBlue() ) : null, + getSize(), + getTransparency() ); } public final NodeFill getFillType() { diff --git a/forester/java/src/org/forester/phylogeny/data/PhylogenyData.java b/forester/java/src/org/forester/phylogeny/data/PhylogenyData.java index 2db9364..f94a2b9 100644 --- a/forester/java/src/org/forester/phylogeny/data/PhylogenyData.java +++ b/forester/java/src/org/forester/phylogeny/data/PhylogenyData.java @@ -41,8 +41,8 @@ public interface PhylogenyData { * Creates a new PhylogenyData object with identical values as this * PhylogenyData. * This ~should~ return a deep copy, but not there yet. - * - * + * + * * @return a ~deep~ copy of this PhylogenyData */ public PhylogenyData copy(); @@ -50,7 +50,7 @@ public interface PhylogenyData { /** * Compares this PhylogenyData to PhylogenyData data. In general, this * should return true if and only if all fiels are exactly identical. - * + * * @param PhylogenyData * the PhylogenyData to compare to * @return in general, true if and only if all fiels are exactly identical, @@ -62,11 +62,11 @@ public interface PhylogenyData { /** * Writes a phyloXML representation of this phylogeny data. - * + * * @param writer * @param level * @param indentation - * @throws IOException + * @throws IOException */ public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException; } \ No newline at end of file diff --git a/forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.java b/forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.java index 76d60b7..48da0e0 100644 --- a/forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.java +++ b/forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.java @@ -351,7 +351,7 @@ public final class PhylogenyDataUtil { /** * Creates a deep copy of ArrayList of PhylogenyData objects. - * + * * @param list * an ArrayList of PhylogenyData objects * @return a deep copy of ArrayList list diff --git a/forester/java/src/org/forester/phylogeny/data/Point.java b/forester/java/src/org/forester/phylogeny/data/Point.java index 7684f16..f36494b 100644 --- a/forester/java/src/org/forester/phylogeny/data/Point.java +++ b/forester/java/src/org/forester/phylogeny/data/Point.java @@ -57,7 +57,7 @@ public class Point implements PhylogenyData { } else { return new StringBuffer( "[" + getLatitude().toPlainString() + ", " + getLongitude() + ", " + getAltitude() - + getAltiudeUnit() + "]" ); + + getAltiudeUnit() + "]" ); } } @@ -70,9 +70,9 @@ public class Point implements PhylogenyData { public PhylogenyData copy() { return new Point( getGeodeticDatum(), getLatitude() == null ? null : new BigDecimal( getLatitude().toPlainString() ), - getLongitude() == null ? null : new BigDecimal( getLongitude().toPlainString() ), - getAltitude() == null ? null : new BigDecimal( getAltitude().toPlainString() ), - getAltiudeUnit() ); + getLongitude() == null ? null : new BigDecimal( getLongitude().toPlainString() ), + getAltitude() == null ? null : new BigDecimal( getAltitude().toPlainString() ), + getAltiudeUnit() ); } public BigDecimal getAltitude() { @@ -156,6 +156,6 @@ public class Point implements PhylogenyData { && ( ( p.getLatitude() == null ) || ( p.getLatitude().compareTo( BigDecimal.ZERO ) <= 0 ) ) && ( ForesterUtil.isEmpty( p.getGeodeticDatum() ) || p.getGeodeticDatum() .equalsIgnoreCase( UNKNOWN_GEODETIC_DATUM ) ) && ( ForesterUtil.isEmpty( p.getAltiudeUnit() ) || p - .getAltiudeUnit().equalsIgnoreCase( "?" ) ) ); + .getAltiudeUnit().equalsIgnoreCase( "?" ) ) ); } } diff --git a/forester/java/src/org/forester/phylogeny/data/Property.java b/forester/java/src/org/forester/phylogeny/data/Property.java index a1fba96..14a3341 100644 --- a/forester/java/src/org/forester/phylogeny/data/Property.java +++ b/forester/java/src/org/forester/phylogeny/data/Property.java @@ -74,15 +74,15 @@ public class Property implements PhylogenyData { final String id_ref ) { if ( !ForesterUtil.isEmpty( ref ) && ( ref.indexOf( ":" ) < 1 ) ) { throw new IllegalArgumentException( "property reference [" + ref - + "] is not in the expected format (missing a \":\")" ); + + "] is not in the expected format (missing a \":\")" ); } if ( !ForesterUtil.isEmpty( unit ) && ( unit.indexOf( ":" ) < 1 ) ) { throw new IllegalArgumentException( "property unit [" + unit - + "] is not in the expected format (missing a \":\")" ); + + "] is not in the expected format (missing a \":\")" ); } if ( !ForesterUtil.isEmpty( datatype ) && ( datatype.indexOf( ":" ) < 1 ) ) { throw new IllegalArgumentException( "property datatype [" + unit - + "] is not in the expected format (missing a \":\")" ); + + "] is not in the expected format (missing a \":\")" ); } _ref = ref; _unit = unit; diff --git a/forester/java/src/org/forester/phylogeny/data/Sequence.java b/forester/java/src/org/forester/phylogeny/data/Sequence.java index bedb112..fd366c6 100644 --- a/forester/java/src/org/forester/phylogeny/data/Sequence.java +++ b/forester/java/src/org/forester/phylogeny/data/Sequence.java @@ -158,7 +158,7 @@ public class Sequence implements PhylogenyData, MultipleUris, Comparable _protein_domains; public static Comparator DomainMidPositionComparator = new Comparator() { - @Override - public int compare( final Domain d1, - final Domain d2 ) { - final int m1 = ( d1.getTo() + d1.getFrom() ); - final int m2 = ( d2.getTo() + d2.getFrom() ); - return m1 < m2 ? -1 : m1 > m2 ? 1 : d1 - .getDomainId() - .compareTo( d2.getDomainId() ); - } - }; + @Override + public int compare( final Domain d1, + final Domain d2 ) { + final int m1 = ( d1.getTo() + d1.getFrom() ); + final int m2 = ( d2.getTo() + d2.getFrom() ); + return m1 < m2 ? -1 : m1 > m2 ? 1 : d1 + .getDomainId() + .compareTo( d2.getDomainId() ); + } + }; public BasicProtein( final String id_str, final String species_str, final int length ) { if ( length < 0 ) { @@ -88,10 +88,10 @@ public class BasicProtein implements Protein { * If in_nc_order is set to true, this returns true only and only if * the order in List 'domains' and this protein (as determined by the start positions * of the domains of this proteins, _not_ by their index) are the same - * (interspersing, 'other', domains in this are ignored). + * (interspersing, 'other', domains in this are ignored). * If in_nc_order is set to false, this returns true only and only if * this contains all domains listed in 'domains' (order and count do not matter). - * + * * @param domains a list of domain ids in a certain order. * @param in_nc_order to consider order * @return diff --git a/forester/java/src/org/forester/protein/Protein.java b/forester/java/src/org/forester/protein/Protein.java index 4b81f46..eccc7d7 100644 --- a/forester/java/src/org/forester/protein/Protein.java +++ b/forester/java/src/org/forester/protein/Protein.java @@ -38,10 +38,10 @@ public interface Protein { * If in_nc_order is set to true, this should return true only and only if * the order in List 'domains' and this protein (as determined by the start positions * of the domains of this proteins, _not_ by their index) are the same - * (interspersing, 'other', domains in this are ignored). + * (interspersing, 'other', domains in this are ignored). * If in_nc_order is set to false, this should return true only and only if * this contains all domains listed in 'domains' (order and count do not matter). - * + * * @param domains a list of domain ids in a certain order. * @param in_nc_order to consider order * @return diff --git a/forester/java/src/org/forester/protein/ProteinId.java b/forester/java/src/org/forester/protein/ProteinId.java index bb13c6b..28bd0a6 100644 --- a/forester/java/src/org/forester/protein/ProteinId.java +++ b/forester/java/src/org/forester/protein/ProteinId.java @@ -57,7 +57,7 @@ public class ProteinId implements Comparable { } else if ( o.getClass() != this.getClass() ) { throw new IllegalArgumentException( "attempt to check protein id equality to " + o + " [" + o.getClass() - + "]" ); + + "]" ); } else { return getId().equals( ( ( ProteinId ) o ).getId() ); diff --git a/forester/java/src/org/forester/rio/RIO.java b/forester/java/src/org/forester/rio/RIO.java index 1f4f3e6..4552ba4 100644 --- a/forester/java/src/org/forester/rio/RIO.java +++ b/forester/java/src/org/forester/rio/RIO.java @@ -158,7 +158,7 @@ public final class RIO { /** * Returns the numbers of number of ext nodes in gene trees analyzed (after * stripping). - * + * * @return number of ext nodes in gene trees analyzed (after stripping) */ public final int getExtNodesOfAnalyzedGeneTrees() { @@ -172,7 +172,7 @@ public final class RIO { /** * Returns the numbers of number of int nodes in gene trees analyzed (after * stripping). - * + * * @return number of int nodes in gene trees analyzed (after stripping) */ public final int getIntNodesOfAnalyzedGeneTrees() { @@ -206,7 +206,7 @@ public final class RIO { int first, final int last, final boolean transfer_taxonomy ) throws SDIException, RIOException, - FileNotFoundException, IOException { + FileNotFoundException, IOException { if ( !parser.hasNext() ) { throw new RIOException( "no gene trees to analyze" ); } @@ -288,7 +288,7 @@ public final class RIO { final int first, final int last, final boolean transfer_taxonomy ) throws SDIException, RIOException, - FileNotFoundException, IOException { + FileNotFoundException, IOException { if ( algorithm == ALGORITHM.SDIR ) { // Removes from species_tree all species not found in gene_tree. PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( gene_trees[ 0 ], species_tree ); @@ -398,7 +398,7 @@ public final class RIO { final String outgroup, final int i, final boolean transfer_taxonomy ) throws SDIException, - RIOException { + RIOException { final Phylogeny assigned_tree; switch ( algorithm ) { case SDIR: { @@ -430,7 +430,7 @@ public final class RIO { final String outgroup, final int i, final boolean transfer_taxonomy ) throws SDIException, - RIOException { + RIOException { final Phylogeny assigned_tree; final int dups; if ( _rerooting == REROOTING.BY_ALGORITHM ) { @@ -463,7 +463,7 @@ public final class RIO { for( final PhylogenyNode r : _removed_gene_tree_nodes ) { if ( !r.getNodeData().isHasTaxonomy() ) { throw new RIOException( "node with no (appropriate) taxonomic information found in gene tree #" + i - + ": " + r.toString() ); + + ": " + r.toString() ); } } assigned_tree = gene_tree; @@ -500,13 +500,13 @@ public final class RIO { } log( "Gene trees analyzed : " + _duplications_stats.getN() ); log( "Mean number of duplications : " + df.format( _duplications_stats.arithmeticMean() ) - + " (sd: " + df.format( _duplications_stats.sampleStandardDeviation() ) + ")" + " (" - + df.format( ( 100.0 * _duplications_stats.arithmeticMean() ) / getIntNodesOfAnalyzedGeneTrees() ) - + "%)" ); + + " (sd: " + df.format( _duplications_stats.sampleStandardDeviation() ) + ")" + " (" + + df.format( ( 100.0 * _duplications_stats.arithmeticMean() ) / getIntNodesOfAnalyzedGeneTrees() ) + + "%)" ); if ( _duplications_stats.getN() > 3 ) { log( "Median number of duplications : " + df.format( _duplications_stats.median() ) - + " (" + df.format( ( 100.0 * _duplications_stats.median() ) / getIntNodesOfAnalyzedGeneTrees() ) - + "%)" ); + + " (" + df.format( ( 100.0 * _duplications_stats.median() ) / getIntNodesOfAnalyzedGeneTrees() ) + + "%)" ); } log( "Minimum duplications : " + ( int ) _duplications_stats.getMin() + " (" + df.format( ( 100.0 * _duplications_stats.getMin() ) / getIntNodesOfAnalyzedGeneTrees() ) + "%)" ); @@ -580,7 +580,7 @@ public final class RIO { final boolean produce_log, final boolean verbose, final boolean transfer_taxonomy ) throws IOException, SDIException, - RIOException { + RIOException { final Phylogeny[] gene_trees = parseGeneTrees( gene_trees_file ); if ( gene_trees.length < 1 ) { throw new RIOException( "\"" + gene_trees_file + "\" is devoid of appropriate gene trees" ); @@ -610,7 +610,7 @@ public final class RIO { final boolean produce_log, final boolean verbose, final boolean transfer_taxonomy ) throws IOException, SDIException, - RIOException { + RIOException { return new RIO( parseGeneTrees( gene_trees_file ), species_tree, algorithm, @@ -633,7 +633,7 @@ public final class RIO { final boolean produce_log, final boolean verbose, final boolean transfer_taxonomy ) throws IOException, SDIException, - RIOException { + RIOException { return new RIO( parseGeneTrees( gene_trees_file ), species_tree, algorithm, @@ -656,7 +656,7 @@ public final class RIO { final boolean produce_log, final boolean verbose, final boolean transfer_taxonomy ) throws IOException, SDIException, - RIOException { + RIOException { final Phylogeny g0 = p.next(); if ( ( g0 == null ) || g0.isEmpty() || ( g0.getNumberOfExternalNodes() < 2 ) ) { throw new RIOException( "input file does not seem to contain any gene trees" ); @@ -687,7 +687,7 @@ public final class RIO { final boolean produce_log, final boolean verbose, final boolean transfer_taxonomy ) throws IOException, SDIException, - RIOException { + RIOException { return new RIO( p, species_tree, algorithm, @@ -710,7 +710,7 @@ public final class RIO { final boolean produce_log, final boolean verbose, final boolean transfer_taxonomy ) throws IOException, SDIException, - RIOException { + RIOException { return new RIO( p, species_tree, algorithm, @@ -745,7 +745,7 @@ public final class RIO { final boolean produce_log, final boolean verbose, final boolean transfer_taxonomy ) throws IOException, SDIException, - RIOException { + RIOException { return new RIO( gene_trees, species_tree, algorithm, @@ -768,7 +768,7 @@ public final class RIO { final boolean produce_log, final boolean verbose, final boolean transfer_taxonomy ) throws IOException, SDIException, - RIOException { + RIOException { return new RIO( gene_trees, species_tree, algorithm, @@ -898,7 +898,7 @@ public final class RIO { } private final static Phylogeny[] parseGeneTrees( final File gene_trees_file ) throws FileNotFoundException, - IOException { + IOException { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( gene_trees_file, true ); if ( p instanceof NHXParser ) { @@ -921,7 +921,7 @@ public final class RIO { if ( o > 0 ) { if ( verbose ) { System.out.println( "warning: species tree has " + o - + " internal nodes with only one descendent which are therefore going to be removed" ); + + " internal nodes with only one descendent which are therefore going to be removed" ); } PhylogenyMethods.deleteInternalNodesWithOnlyOneDescendent( species_tree ); } diff --git a/forester/java/src/org/forester/rio/RIOException.java b/forester/java/src/org/forester/rio/RIOException.java index 44114c2..358d996 100644 --- a/forester/java/src/org/forester/rio/RIOException.java +++ b/forester/java/src/org/forester/rio/RIOException.java @@ -4,7 +4,7 @@ package org.forester.rio; public class RIOException extends Exception { /** - * + * */ private static final long serialVersionUID = 4691098852783522097L; diff --git a/forester/java/src/org/forester/rio/TestRIO.java b/forester/java/src/org/forester/rio/TestRIO.java index 2fdfc09..fa704b7 100644 --- a/forester/java/src/org/forester/rio/TestRIO.java +++ b/forester/java/src/org/forester/rio/TestRIO.java @@ -18,7 +18,7 @@ import org.forester.util.ForesterUtil; public final class TestRIO { private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator() - + "test_data" + ForesterUtil.getFileSeparator(); + + "test_data" + ForesterUtil.getFileSeparator(); public static void main( final String[] args ) { if ( !testRIO_GSDIR() ) { diff --git a/forester/java/src/org/forester/sdi/GSDI.java b/forester/java/src/org/forester/sdi/GSDI.java index fa7a52c..4ab6395 100644 --- a/forester/java/src/org/forester/sdi/GSDI.java +++ b/forester/java/src/org/forester/sdi/GSDI.java @@ -152,10 +152,10 @@ public final class GSDI implements GSDII { * Preconditions: Mapping M for external nodes must have been calculated and * the species tree must be labeled in preorder. *

    - * @param transfer_taxonomy - * @return - * @throws SDIException - * + * @param transfer_taxonomy + * @return + * @throws SDIException + * */ final static GSDIsummaryResult geneTreePostOrderTraversal( final Phylogeny gene_tree, final boolean most_parsimonious_duplication_model, @@ -166,7 +166,7 @@ public final class GSDI implements GSDII { if ( g.isInternal() ) { if ( g.getNumberOfDescendants() != 2 ) { throw new SDIException( "gene tree contains internal node with " + g.getNumberOfDescendants() - + " descendents" ); + + " descendents" ); } PhylogenyNode s1 = g.getChildNode1().getLink(); PhylogenyNode s2 = g.getChildNode2().getLink(); @@ -197,7 +197,7 @@ public final class GSDI implements GSDII { if ( g.isInternal() ) { if ( g.getNumberOfDescendants() != 2 ) { throw new SDIException( "gene tree contains internal node with " + g.getNumberOfDescendants() - + " descendents" ); + + " descendents" ); } PhylogenyNode s1 = g.getChildNode1().getLink(); PhylogenyNode s2 = g.getChildNode2().getLink(); @@ -234,8 +234,8 @@ public final class GSDI implements GSDII { * This allows for linking of internal nodes of the species tree (as opposed * to just external nodes, as in the method it overrides. * If TaxonomyComparisonBase is null, it will try to determine it. - * @throws SDIException - * + * @throws SDIException + * */ final static NodesLinkingResult linkNodesOfG( final Phylogeny gene_tree, final Phylogeny species_tree, @@ -299,7 +299,7 @@ public final class GSDI implements GSDII { } else { throw new SDIException( "taxonomy \"" + g.getNodeData().getTaxonomy() - + "\" not present in species tree" ); + + "\" not present in species tree" ); } } else { diff --git a/forester/java/src/org/forester/sdi/GSDIR.java b/forester/java/src/org/forester/sdi/GSDIR.java index 52620a2..651383d 100644 --- a/forester/java/src/org/forester/sdi/GSDIR.java +++ b/forester/java/src/org/forester/sdi/GSDIR.java @@ -73,7 +73,7 @@ public class GSDIR implements GSDII { } if ( gene_tree.getRoot().getNumberOfDescendants() == 2 ) { gene_tree_branches_post_order.add( new PhylogenyBranch( gene_tree.getRoot().getChildNode1(), gene_tree - .getRoot().getChildNode2() ) ); + .getRoot().getChildNode2() ) ); } int min_duplications_sum = Integer.MAX_VALUE; int speciations_sum = 0; @@ -188,7 +188,7 @@ public class GSDIR implements GSDII { /** * Places the root of this Phylogeny on Branch b. The new root is always * placed on the middle of the branch b. - * + * */ static final void reRoot( final PhylogenyBranch b, final Phylogeny phy ) { final PhylogenyNode n1 = b.getFirstNode(); @@ -208,7 +208,7 @@ public class GSDIR implements GSDII { // else if ( ( n1.getParent() != null ) && n1.getParent().isRoot() // && ( ( n1.getParent().getChildNode1() == n2 ) || ( n1.getParent().getChildNode2() == n2 ) ) ) { // phy.reRoot( n1 ); - // + // // } else { throw new IllegalArgumentException( "reRoot( Branch b ): b is not a branch." ); diff --git a/forester/java/src/org/forester/sdi/SDI.java b/forester/java/src/org/forester/sdi/SDI.java index 2c59efa..535d99e 100644 --- a/forester/java/src/org/forester/sdi/SDI.java +++ b/forester/java/src/org/forester/sdi/SDI.java @@ -51,18 +51,18 @@ import org.forester.util.ForesterUtil; * "stripTree(Phylogeny,Phylogeny)" of class Phylogeny

    The recursion * part is accomplished by this class' method * "geneTreePostOrderTraversal(PhylogenyNode)".

    Requires JDK 1.2 or greater. - * + * * @see SDI#linkNodesOfG() - * + * * @see Phylogeny#preorderReID(int) - * + * * @see * PhylogenyMethods#taxonomyBasedDeletionOfExternalNodes(Phylogeny,Phylogeny) - * + * * @see #geneTreePostOrderTraversal(PhylogenyNode) - * + * * @author Christian M. Zmasek - * + * * @version 1.102 -- last modified: 10/02/01 */ public class SDI { @@ -81,7 +81,7 @@ public class SDI { * "computeMappingCost()". *

    * (Last modified: 01/11/01) - * + * * @see #infer(boolean) * @see SDI#computeMappingCostL() * @param gene_tree @@ -92,7 +92,7 @@ public class SDI { * reference to a rooted binary species Phylogeny which might get * stripped in the process, must have species names in the * species name fields for all external nodes - * @throws SDIException + * @throws SDIException */ public SDI( final Phylogeny gene_tree, final Phylogeny species_tree ) throws SDIException { if ( species_tree.isEmpty() || gene_tree.isEmpty() ) { @@ -118,7 +118,7 @@ public class SDI { * Reference. Zhang, L. (1997) On a Mirkin-Muchnik-Smith Conjecture for * Comparing Molecular Phylogenies. Journal of Computational Biology 4 * 177-187. - * + * * @return the mapping cost "L" */ public int computeMappingCostL() { @@ -130,7 +130,7 @@ public class SDI { /** * Returns the number of duplications. - * + * * @return number of duplications */ public int getDuplicationsSum() { @@ -139,7 +139,7 @@ public class SDI { /** * Returns the gene tree. - * + * * @return gene tree */ public Phylogeny getGeneTree() { @@ -148,7 +148,7 @@ public class SDI { /** * Returns the species tree. - * + * * @return species tree */ public Phylogeny getSpeciesTree() { @@ -175,7 +175,7 @@ public class SDI { * the species tree must be labelled in preorder. *

    * (Last modified: 01/11/01) - * + * * @param g * starting node of a gene tree - normally the root */ @@ -213,7 +213,7 @@ public class SDI { * links (sets the field "link" of PhylogenyNode) each external * PhylogenyNode of gene_tree to the external PhylogenyNode of species_tree * which has the same species name. - * @throws SDIException + * @throws SDIException */ final void linkNodesOfG() throws SDIException { final Map speciestree_ext_nodes = new HashMap(); @@ -225,7 +225,7 @@ public class SDI { final String tax_str = SDIutil.taxonomyToString( s, tax_comp_base ); if ( speciestree_ext_nodes.containsKey( tax_str ) ) { throw new IllegalArgumentException( "taxonomy [" + s.getNodeData().getTaxonomy() - + "] is not unique in species phylogeny" ); + + "] is not unique in species phylogeny" ); } speciestree_ext_nodes.put( tax_str, s ); } @@ -236,7 +236,7 @@ public class SDI { final PhylogenyNode s = speciestree_ext_nodes.get( tax_str ); if ( s == null ) { throw new IllegalArgumentException( "taxonomy [" + g.getNodeData().getTaxonomy() - + "] not present in species tree" ); + + "] not present in species tree" ); } g.setLink( s ); } @@ -250,7 +250,7 @@ public class SDI { * To be used ONLY by method "SDIunrooted.fastInfer(Phylogeny,Phylogeny)". *

    * (Last modfied: 10/02/01) - * + * * @param prev_root_was_dup * true if the previous root was a duplication, false otherwise * @param prev_root_c1 @@ -403,7 +403,7 @@ public class SDI { final HashMap speciestree_ext_nodes = new HashMap(); if ( _species_tree.getFirstExternalNode().isRoot() ) { speciestree_ext_nodes.put( _species_tree.getFirstExternalNode().getNodeData().getTaxonomy().getIdentifier() - .getValue(), _species_tree.getFirstExternalNode() ); + .getValue(), _species_tree.getFirstExternalNode() ); } else { for( final PhylogenyNodeIterator iter = _species_tree.iteratorExternalForward(); iter.hasNext(); ) { diff --git a/forester/java/src/org/forester/sdi/SDIException.java b/forester/java/src/org/forester/sdi/SDIException.java index a5b38f8..28a463e 100644 --- a/forester/java/src/org/forester/sdi/SDIException.java +++ b/forester/java/src/org/forester/sdi/SDIException.java @@ -4,7 +4,7 @@ package org.forester.sdi; public class SDIException extends Exception { /** - * + * */ private static final long serialVersionUID = 5154733429066500435L; diff --git a/forester/java/src/org/forester/sdi/SDIR.java b/forester/java/src/org/forester/sdi/SDIR.java index dbab226..a21fd6b 100644 --- a/forester/java/src/org/forester/sdi/SDIR.java +++ b/forester/java/src/org/forester/sdi/SDIR.java @@ -45,11 +45,11 @@ import org.forester.phylogeny.iterators.PhylogenyNodeIterator; *

  • Mapping cost L
  • Phylogeny height - which is the largest distance from * root to external node (minimizing of which is the same as "midpoint rooting") * - * + * * @see SDIse - * + * * @see SDI - * + * * @author Christian M. Zmasek */ public class SDIR { @@ -76,7 +76,7 @@ public class SDIR { /** * Returns the number of differently rooted trees which minimize the * (rooting) "criterion" - as determined by method "infer". - * + * * @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean) * @return number of differently rooted trees which minimized the criterion */ @@ -97,7 +97,7 @@ public class SDIR { * not necessarily zero. *

    * (Last modified: 01/22/00) - * + * * @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean) * @return the minimal difference in tree heights -- IF calculated by * "infer" @@ -113,7 +113,7 @@ public class SDIR { * IMPORTANT : If the tree is not rooted by minimizing the sum of * duplications or the mapping cost L, then this number is NOT NECESSARILY * the MINIMAL number of duplications. - * + * * @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean) * @return (minimal) number of duplications */ @@ -126,7 +126,7 @@ public class SDIR { * minimize_mapping_cost is set to true. *

    * (Last modified: 11/07/00) - * + * * @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean) * @return the minimal mapping cost "L" -- IF calculated by "infer" */ @@ -142,7 +142,7 @@ public class SDIR { * first criterion. *

    * (Last modified: 01/12/00) - * + * * @see #infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean) * @return the minimal tree height -- IF calculated by "infer" */ @@ -153,7 +153,7 @@ public class SDIR { /** * Returns the sum of times (in ms) needed to run method infer of class SDI. * Final variable TIME needs to be set to true. - * + * * @return sum of times (in ms) needed to run method infer of class SDI */ public long getTimeSumSDI() { @@ -188,7 +188,7 @@ public class SDIR { * *

    * (Last modified: 10/01/01) - * + * * @param gene_tree * a binary (except deepest node) gene Phylogeny * @param species_tree @@ -212,7 +212,7 @@ public class SDIR { * Array) must be no lower than 1 * @return array of rooted Trees with duplication vs. speciation assigned if * return_trees is set to true, null otherwise - * @throws SDIException + * @throws SDIException */ public Phylogeny[] infer( final Phylogeny gene_tree, final Phylogeny species_tree, diff --git a/forester/java/src/org/forester/sdi/SDIutil.java b/forester/java/src/org/forester/sdi/SDIutil.java index 077f818..4e12ae6 100644 --- a/forester/java/src/org/forester/sdi/SDIutil.java +++ b/forester/java/src/org/forester/sdi/SDIutil.java @@ -73,7 +73,7 @@ public class SDIutil { final boolean replace_undescores_in_nhx_trees, final boolean ignore_quotes_in_nhx_trees, final TAXONOMY_EXTRACTION taxonomy_extraction_in_nhx_trees ) - throws FileNotFoundException, PhyloXmlDataFormatException, IOException, SDIException { + throws FileNotFoundException, PhyloXmlDataFormatException, IOException, SDIException { Phylogeny species_tree; final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( species_tree_file, true ); @@ -99,9 +99,9 @@ public class SDIutil { switch ( comp_base ) { case SCIENTIFIC_NAME: PhylogenyMethods - .transferNodeNameToField( species_tree, - PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME, - true ); + .transferNodeNameToField( species_tree, + PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME, + true ); break; case CODE: PhylogenyMethods.transferNodeNameToField( species_tree, diff --git a/forester/java/src/org/forester/sdi/TestGSDI.java b/forester/java/src/org/forester/sdi/TestGSDI.java index 027e09b..7b4b17e 100644 --- a/forester/java/src/org/forester/sdi/TestGSDI.java +++ b/forester/java/src/org/forester/sdi/TestGSDI.java @@ -41,7 +41,7 @@ import org.forester.util.ForesterUtil; public final class TestGSDI { private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator() - + "test_data" + ForesterUtil.getFileSeparator(); + + "test_data" + ForesterUtil.getFileSeparator(); public static void main( final String[] args ) { if ( !TestGSDI.testGSDI_against_binary_gene_tree() ) { @@ -1283,7 +1283,7 @@ public final class TestGSDI { //-- final Phylogeny tol_143_ = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA + "tol_143.xml" )[ 0 ]; final Phylogeny gene_tree_tax_code_4_ = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA - + "gene_tree_tax_code_4.xml" )[ 0 ]; + + "gene_tree_tax_code_4.xml" )[ 0 ]; final GSDI gsdi_143_4_1 = new GSDI( gene_tree_tax_code_4_.copy(), tol_143_.copy(), false, true, true ); if ( gsdi_143_4_1.getDuplicationsSum() != 21 ) { return false; @@ -1296,7 +1296,7 @@ public final class TestGSDI { } //-- final Phylogeny gsdi_test_gene_tree_sn_wnt = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA - + "gsdi_test_gene_tree_sn_wnt.xml" )[ 0 ]; + + "gsdi_test_gene_tree_sn_wnt.xml" )[ 0 ]; gsdi_test_gene_tree_sn_wnt.setRooted( true ); final GSDI a = new GSDI( gsdi_test_gene_tree_sn_wnt.copy(), tol_143_.copy(), false, true, true ); if ( a.getDuplicationsSum() != 33 ) { @@ -1319,7 +1319,7 @@ public final class TestGSDI { } //-- final Phylogeny gsdi_test_species_tree_sn_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA - + "gsdi_test_species_tree_sn.xml" )[ 0 ]; + + "gsdi_test_species_tree_sn.xml" )[ 0 ]; final GSDI b = new GSDI( gsdi_test_gene_tree_sn_wnt.copy(), gsdi_test_species_tree_sn_xml.copy(), false, @@ -1386,9 +1386,9 @@ public final class TestGSDI { } //-- final Phylogeny gsdi_test_gene_tree_codes_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA - + "gsdi_test_gene_tree_codes.xml" )[ 0 ]; + + "gsdi_test_gene_tree_codes.xml" )[ 0 ]; final Phylogeny gsdi_test_species_tree_codes_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA - + "gsdi_test_species_tree_codes.xml" )[ 0 ]; + + "gsdi_test_species_tree_codes.xml" )[ 0 ]; final GSDI d = new GSDI( gsdi_test_gene_tree_codes_xml.copy(), gsdi_test_species_tree_codes_xml.copy(), false, @@ -1420,7 +1420,7 @@ public final class TestGSDI { } //-- final Phylogeny gsdi_test_gene_tree_sn_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA - + "gsdi_test_gene_tree_sn.xml" )[ 0 ]; + + "gsdi_test_gene_tree_sn.xml" )[ 0 ]; final GSDI e = new GSDI( gsdi_test_gene_tree_sn_xml.copy(), gsdi_test_species_tree_sn_xml.copy(), false, diff --git a/forester/java/src/org/forester/sequence/BasicSequence.java b/forester/java/src/org/forester/sequence/BasicSequence.java index f7a8917..42861fb 100644 --- a/forester/java/src/org/forester/sequence/BasicSequence.java +++ b/forester/java/src/org/forester/sequence/BasicSequence.java @@ -36,7 +36,7 @@ public class BasicSequence implements MolecularSequence { /** * Only use if you know what you are doing! - * + * */ public BasicSequence( final String identifier, final String mol_sequence, final TYPE type ) { if ( ForesterUtil.isEmpty( identifier ) ) { @@ -52,7 +52,7 @@ public class BasicSequence implements MolecularSequence { /** * Only use if you know what you are doing! - * + * */ public BasicSequence( final String identifier, final char[] mol_sequence, final TYPE type ) { if ( ForesterUtil.isEmpty( identifier ) ) { @@ -145,17 +145,17 @@ public class BasicSequence implements MolecularSequence { public static MolecularSequence createAaSequence( final String identifier, final String mol_sequence ) { return new BasicSequence( identifier, mol_sequence.toUpperCase().replaceAll( "\\.", GAP_STR ) - .replaceAll( AA_REGEXP, Character.toString( UNSPECIFIED_AA ) ), TYPE.AA ); + .replaceAll( AA_REGEXP, Character.toString( UNSPECIFIED_AA ) ), TYPE.AA ); } public static MolecularSequence createDnaSequence( final String identifier, final String mol_sequence ) { return new BasicSequence( identifier, mol_sequence.toUpperCase().replaceAll( "\\.", GAP_STR ) - .replaceAll( DNA_REGEXP, Character.toString( UNSPECIFIED_NUC ) ), TYPE.DNA ); + .replaceAll( DNA_REGEXP, Character.toString( UNSPECIFIED_NUC ) ), TYPE.DNA ); } public static MolecularSequence createRnaSequence( final String identifier, final String mol_sequence ) { return new BasicSequence( identifier, mol_sequence.toUpperCase().replaceAll( "\\.", GAP_STR ) - .replaceAll( RNA_REGEXP, Character.toString( UNSPECIFIED_NUC ) ), TYPE.RNA ); + .replaceAll( RNA_REGEXP, Character.toString( UNSPECIFIED_NUC ) ), TYPE.RNA ); } @Override diff --git a/forester/java/src/org/forester/surfacing/BasicGenomeWideCombinableDomains.java b/forester/java/src/org/forester/surfacing/BasicGenomeWideCombinableDomains.java index 1d115b2..2813185 100644 --- a/forester/java/src/org/forester/surfacing/BasicGenomeWideCombinableDomains.java +++ b/forester/java/src/org/forester/surfacing/BasicGenomeWideCombinableDomains.java @@ -28,70 +28,70 @@ public class BasicGenomeWideCombinableDomains implements GenomeWideCombinableDom private static final Comparator DESCENDING_COMBINATIONS_COUNT_ORDER = new Comparator() { - @Override - public int compare( final CombinableDomains d1, - final CombinableDomains d2 ) { - if ( d1.getNumberOfCombinableDomains() < d2 - .getNumberOfCombinableDomains() ) { - return 1; - } - else if ( d1 - .getNumberOfCombinableDomains() > d2 - .getNumberOfCombinableDomains() ) { - return -1; - } - else { - return d1 - .getKeyDomain() - .compareTo( d2 - .getKeyDomain() ); - } - } - }; + @Override + public int compare( final CombinableDomains d1, + final CombinableDomains d2 ) { + if ( d1.getNumberOfCombinableDomains() < d2 + .getNumberOfCombinableDomains() ) { + return 1; + } + else if ( d1 + .getNumberOfCombinableDomains() > d2 + .getNumberOfCombinableDomains() ) { + return -1; + } + else { + return d1 + .getKeyDomain() + .compareTo( d2 + .getKeyDomain() ); + } + } + }; private static final Comparator DESCENDING_KEY_DOMAIN_COUNT_ORDER = new Comparator() { - @Override - public int compare( final CombinableDomains d1, - final CombinableDomains d2 ) { - if ( d1.getKeyDomainCount() < d2 - .getKeyDomainCount() ) { - return 1; - } - else if ( d1 - .getKeyDomainCount() > d2 - .getKeyDomainCount() ) { - return -1; - } - else { - return d1 - .getKeyDomain() - .compareTo( d2 - .getKeyDomain() ); - } - } - }; + @Override + public int compare( final CombinableDomains d1, + final CombinableDomains d2 ) { + if ( d1.getKeyDomainCount() < d2 + .getKeyDomainCount() ) { + return 1; + } + else if ( d1 + .getKeyDomainCount() > d2 + .getKeyDomainCount() ) { + return -1; + } + else { + return d1 + .getKeyDomain() + .compareTo( d2 + .getKeyDomain() ); + } + } + }; private static final Comparator DESCENDING_KEY_DOMAIN_PROTEINS_COUNT_ORDER = new Comparator() { - @Override - public int compare( final CombinableDomains d1, - final CombinableDomains d2 ) { - if ( d1.getKeyDomainProteinsCount() < d2 - .getKeyDomainProteinsCount() ) { - return 1; - } - else if ( d1 - .getKeyDomainProteinsCount() > d2 - .getKeyDomainProteinsCount() ) { - return -1; - } - else { - return d1 - .getKeyDomain() - .compareTo( d2 - .getKeyDomain() ); - } - } - }; + @Override + public int compare( final CombinableDomains d1, + final CombinableDomains d2 ) { + if ( d1.getKeyDomainProteinsCount() < d2 + .getKeyDomainProteinsCount() ) { + return 1; + } + else if ( d1 + .getKeyDomainProteinsCount() > d2 + .getKeyDomainProteinsCount() ) { + return -1; + } + else { + return d1 + .getKeyDomain() + .compareTo( d2 + .getKeyDomain() ); + } + } + }; final private SortedMap _combinable_domains_map; final private DomainCombinationType _dc_type; final private Species _species; @@ -185,10 +185,10 @@ public class BasicGenomeWideCombinableDomains implements GenomeWideCombinableDom return toStringBuilder( GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID ).toString(); } - // Produces something like: - // 2-oxoacid_dh 5 5 2 Biotin_lipoyl [4], E3_binding [3] - @Override - public StringBuilder toStringBuilder( final GenomeWideCombinableDomainsSortOrder sort_order ) { + // Produces something like: + // 2-oxoacid_dh 5 5 2 Biotin_lipoyl [4], E3_binding [3] + @Override + public StringBuilder toStringBuilder( final GenomeWideCombinableDomainsSortOrder sort_order ) { final StringBuilder sb = new StringBuilder(); final List combinable_domains = new ArrayList(); for( final String key : getAllCombinableDomainsIds().keySet() ) { @@ -251,7 +251,7 @@ public class BasicGenomeWideCombinableDomains implements GenomeWideCombinableDom for( final Protein protein : protein_list ) { if ( !protein.getSpecies().equals( species ) ) { throw new IllegalArgumentException( "species (" + protein.getSpecies() - + ") does not match species of combinable domains collection (" + species + ")" ); + + ") does not match species of combinable domains collection (" + species + ")" ); } final Set saw_i = new HashSet(); final Set saw_c = new HashSet(); @@ -297,7 +297,7 @@ public class BasicGenomeWideCombinableDomains implements GenomeWideCombinableDom saw_j.add( id ); if ( dc_type != DomainCombinationType.DIRECTED_ADJACTANT ) { domain_combination - .addCombinableDomain( protein.getProteinDomain( j ).getDomainId() ); + .addCombinableDomain( protein.getProteinDomain( j ).getDomainId() ); } else { if ( closest == null ) { diff --git a/forester/java/src/org/forester/surfacing/CombinableDomains.java b/forester/java/src/org/forester/surfacing/CombinableDomains.java index 28fa0e2..307da8e 100644 --- a/forester/java/src/org/forester/surfacing/CombinableDomains.java +++ b/forester/java/src/org/forester/surfacing/CombinableDomains.java @@ -37,7 +37,7 @@ public interface CombinableDomains { /** * To add a new combinable domain. - * + * * @param protein_domain */ public void addCombinableDomain( final String protein_domain ); @@ -46,7 +46,7 @@ public interface CombinableDomains { * Returns the combinable domain identifiers sorted in alphabetical manner: - * keys are the combinable domain identifiers - values are the counts of * proteins exhibiting a particular combination - * + * * @return combining domain identifiers sorted in alphabetical manner */ public SortedMap getCombinableDomainsIds(); @@ -56,7 +56,7 @@ public interface CombinableDomains { /** * Returns the domain whose combinable domains are in stored in this * combinable domains. - * + * * @return the domain identifier */ public String getKeyDomain(); @@ -64,7 +64,7 @@ public interface CombinableDomains { /** * Returns how many times the key domain is present in a given species * genome. - * + * * @return key domain count in species */ public int getKeyDomainCount(); @@ -74,7 +74,7 @@ public interface CombinableDomains { /** * Returns how many proteins with the key domain are present in a given * species genome. - * + * * @return key domain proteins count in species */ public int getKeyDomainProteinsCount(); @@ -85,7 +85,7 @@ public interface CombinableDomains { /** * Returns the species of this combinable domains. - * + * * @return the species */ public Species getSpecies(); @@ -97,10 +97,10 @@ public interface CombinableDomains { void addKeyDomainProtein( String protein ); /** - * + * * This must return all domains in this set of combinable domains (i.e. * the key domain and all domains which can combine with the key domain). - * + * * @return all domains */ List getAllDomains(); @@ -109,7 +109,7 @@ public interface CombinableDomains { /** * Sets how many times the key domain is present in a given species genome. - * + * * @param key_domain_count * key domain count in species */ diff --git a/forester/java/src/org/forester/surfacing/CountsBasedPairwiseDomainSimilarity.java b/forester/java/src/org/forester/surfacing/CountsBasedPairwiseDomainSimilarity.java index 8439f4c..f4bfd16 100644 --- a/forester/java/src/org/forester/surfacing/CountsBasedPairwiseDomainSimilarity.java +++ b/forester/java/src/org/forester/surfacing/CountsBasedPairwiseDomainSimilarity.java @@ -34,8 +34,8 @@ public class CountsBasedPairwiseDomainSimilarity implements PairwiseDomainSimila /** * counts_difference: (counts for domain 1) minus (counts for domain 2). - * - * + * + * * @param counts_difference value of domain_1 minus value of domain_2 * @param counts_sum */ @@ -52,7 +52,7 @@ public class CountsBasedPairwiseDomainSimilarity implements PairwiseDomainSimila /** * Returns (counts for domain 1) minus (counts for domain 2). - * + * */ @Override public int getDifferenceInCounts() { diff --git a/forester/java/src/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java b/forester/java/src/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java index a61ba30..a17df67 100644 --- a/forester/java/src/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java +++ b/forester/java/src/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java @@ -69,16 +69,16 @@ public class DomainArchitectureBasedGenomeSimilarityCalculator { } /** - * This returns a score between 0.0 (no binary domain combination in common) + * This returns a score between 0.0 (no binary domain combination in common) * and 1.0 (all binary domain combinations in common) measuring the similarity between two * genomes based on the number of shared binary domain combinations: - * + * * t: sum of (distinct) binary domain combinations * s: sum of shared (distinct) binary domain combinations * * 1 - ( ( t - s ) / t ) - * - * @return shared binary domain combinations based similarity score + * + * @return shared binary domain combinations based similarity score */ public double calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore() { final double t = getAllBinaryDomainCombinations().size(); @@ -90,16 +90,16 @@ public class DomainArchitectureBasedGenomeSimilarityCalculator { } /** - * This returns a score between 0.0 (no domains in common) + * This returns a score between 0.0 (no domains in common) * and 1.0 (all domains in common) measuring the similarity between two * genomes based on the number of shared domains: - * + * * t: sum of (distinct) domains * s: sum of shared (distinct) domains * * 1 - ( ( t - s ) / t ) - * - * @return shared domains based similarity score + * + * @return shared domains based similarity score */ public double calculateSharedDomainsBasedGenomeSimilarityScore() { final double t = getAllDomains().size(); @@ -118,7 +118,7 @@ public class DomainArchitectureBasedGenomeSimilarityCalculator { /** * Does not return binary combinations which contain one or two domains * to be ignored -- if ignoring is allowed. - * + * * @return SortedSet */ public Set getAllBinaryDomainCombinations() { @@ -139,8 +139,8 @@ public class DomainArchitectureBasedGenomeSimilarityCalculator { /** * Does not return domains which are to be * ignored -- if ignoring is allowed. - * - * + * + * * @return */ public Set getAllDomains() { diff --git a/forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java b/forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java index 8f9a249..a9643a8 100644 --- a/forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java +++ b/forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java @@ -87,7 +87,7 @@ public final class DomainCountsDifferenceUtil { if ( high_copy_base_species.contains( high_copy_target_species ) || low_copy_species.contains( high_copy_target_species ) ) { throw new IllegalArgumentException( "species [" + high_copy_target_species - + "] appears in other list as well" ); + + "] appears in other list as well" ); } if ( min_diff < 0 ) { throw new IllegalArgumentException( "attempt to use negative addition [" + min_diff + "]" ); @@ -235,7 +235,7 @@ public final class DomainCountsDifferenceUtil { writeGoIdsToFile( passing_gos_writer, go_ids_of_passing_domains ); } - //FIXME really needs to be tested! + //FIXME really needs to be tested! private static void addCounts( final SortedMap> copy_counts, final BinaryDomainCombination dc, final GenomeWideCombinableDomains genome, @@ -293,7 +293,7 @@ public final class DomainCountsDifferenceUtil { private static void appendGoTerm( final StringBuilder sb, final GoTerm go_term ) { final GoId go_id = go_term.getGoId(); sb.append( "" + go_id - + "" ); + + "" ); sb.append( ":" ); sb.append( go_term.getName() ); sb.append( " [" ); @@ -538,7 +538,7 @@ public final class DomainCountsDifferenceUtil { final SortedMap low_copy_values, final SortedSet all_bdcs, final Map> bdcs_per_genome ) - throws IOException { + throws IOException { int counter = 0; int total_absense_counter = 0; int not_total_absense_counter = 0; @@ -556,8 +556,8 @@ public final class DomainCountsDifferenceUtil { } ++counter; html_writer.write( "" + bdc.getId0() + " = " + bdc.getId1() + "" ); + + "\">" + bdc.getId0() + " = " + bdc.getId1() + "" ); html_writer.write( "" ); html_writer.write( "" ); for( final GenomeWideCombinableDomains genome : genomes ) { @@ -570,7 +570,7 @@ public final class DomainCountsDifferenceUtil { bdcs_per_genome, species, html_writer, - "#0000FF" ); + "#0000FF" ); html_writer.write( "" ); } else if ( low_copy_species.contains( species ) ) { @@ -581,7 +581,7 @@ public final class DomainCountsDifferenceUtil { bdcs_per_genome, species, html_writer, - "#A0A0A0" ); + "#A0A0A0" ); html_writer.write( "" ); } else if ( high_copy_base_species.contains( species ) ) { @@ -592,7 +592,7 @@ public final class DomainCountsDifferenceUtil { bdcs_per_genome, species, html_writer, - "#404040" ); + "#404040" ); html_writer.write( "" ); } } @@ -662,7 +662,7 @@ public final class DomainCountsDifferenceUtil { final SortedSet all_domains, final SortedSet go_ids_of_passing_domains, final SortedMap> protein_lists_per_species ) - throws IOException { + throws IOException { int counter = 0; int total_absense_counter = 0; int not_total_absense_counter = 0; @@ -687,9 +687,9 @@ public final class DomainCountsDifferenceUtil { plain_writer.write( domain_id ); plain_writer.write( SurfacingConstants.NL ); html_writer.write( "
    " + domain_id + "" ); + + "\">" + domain_id + "" ); html_writer.write( addGoInformation( domain_id, domain_id_to_go_ids_map, go_id_to_term_map ) - .toString() ); + .toString() ); html_writer.write( "" ); html_writer.write( "" ); for( final GenomeWideCombinableDomains genome : genomes ) { @@ -702,7 +702,7 @@ public final class DomainCountsDifferenceUtil { species, plain_writer, html_writer, - "#0000FF" ); + "#0000FF" ); html_writer.write( "" ); } else if ( low_copy_species.contains( species ) ) { @@ -713,7 +713,7 @@ public final class DomainCountsDifferenceUtil { species, plain_writer, html_writer, - "#A0A0A0" ); + "#A0A0A0" ); html_writer.write( "" ); } else if ( high_copy_base_species.contains( species ) ) { @@ -724,7 +724,7 @@ public final class DomainCountsDifferenceUtil { species, plain_writer, html_writer, - "#404040" ); + "#404040" ); html_writer.write( "" ); } } @@ -813,7 +813,7 @@ public final class DomainCountsDifferenceUtil { final SortedMap> protein_lists_per_species, final String domain_id ) throws IOException { final File my_proteins_file = new File( proteins_file_base.getParentFile() + ForesterUtil.FILE_SEPARATOR - + domain_id + PLUS_MINUS_PROTEINS_FILE_DOM_SUFFIX ); + + domain_id + PLUS_MINUS_PROTEINS_FILE_DOM_SUFFIX ); SurfacingUtil.checkForOutputFileWriteability( my_proteins_file ); final Writer proteins_file_writer = new BufferedWriter( new FileWriter( my_proteins_file ) ); SurfacingUtil.extractProteinNames( protein_lists_per_species, diff --git a/forester/java/src/org/forester/surfacing/DomainLengths.java b/forester/java/src/org/forester/surfacing/DomainLengths.java index 5bb71cf..6d39b61 100644 --- a/forester/java/src/org/forester/surfacing/DomainLengths.java +++ b/forester/java/src/org/forester/surfacing/DomainLengths.java @@ -54,9 +54,9 @@ public class DomainLengths { /** * Returns descriptive statistics based on the arithmetic means - * for each species. - * - * + * for each species. + * + * * @return */ public DescriptiveStatistics calculateMeanBasedStatistics() { @@ -68,10 +68,10 @@ public class DomainLengths { } /** - * + * * Note. This is not technically a Z-score since the distribution * of means is unknown (and not normal). - * + * * @param species * @return */ diff --git a/forester/java/src/org/forester/surfacing/DomainLengthsTable.java b/forester/java/src/org/forester/surfacing/DomainLengthsTable.java index 9ef11cc..2b291eb 100644 --- a/forester/java/src/org/forester/surfacing/DomainLengthsTable.java +++ b/forester/java/src/org/forester/surfacing/DomainLengthsTable.java @@ -150,7 +150,7 @@ public class DomainLengthsTable { private void addDomainLengths( final DomainLengths domain_lengths ) { if ( getDomainLengths().containsKey( domain_lengths.getDomainId() ) ) { throw new IllegalArgumentException( "domain lengths for [" + domain_lengths.getDomainId() - + "] already added" ); + + "] already added" ); } getDomainLengths().put( domain_lengths.getDomainId(), domain_lengths ); } diff --git a/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java b/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java index bffe413..4b5f1bb 100644 --- a/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java +++ b/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java @@ -149,9 +149,9 @@ public final class DomainParsimonyCalculator { throw new IllegalArgumentException( "binary states matrix number of identifiers is not equal to the number of tree nodes provided" ); } final CharacterStateMatrix gl_matrix = new BasicCharacterStateMatrix( binary_states_matrix - .getNumberOfIdentifiers(), - binary_states_matrix - .getNumberOfCharacters() ); + .getNumberOfIdentifiers(), + binary_states_matrix + .getNumberOfCharacters() ); int total_gains = 0; int total_losses = 0; int total_unchanged = 0; @@ -166,7 +166,7 @@ public final class DomainParsimonyCalculator { final PhylogenyNode node = it.next(); final String name = node.getName(); final BinaryStates bin_state = binary_states_matrix.getState( binary_states_matrix - .getIdentifierIndex( name ), c ); + .getIdentifierIndex( name ), c ); final PhylogenyNode parent_node = getPhylogeny().getNode( name ).getParent(); GainLossStates gl_state = null; if ( node.isRoot() ) { @@ -180,7 +180,7 @@ public final class DomainParsimonyCalculator { } else { final BinaryStates parent_bin_state = binary_states_matrix.getState( binary_states_matrix - .getIdentifierIndex( parent_node.getName() ), c ); + .getIdentifierIndex( parent_node.getName() ), c ); if ( bin_state == BinaryStates.ABSENT ) { if ( parent_bin_state == BinaryStates.ABSENT ) { ++total_unchanged; @@ -530,7 +530,7 @@ public final class DomainParsimonyCalculator { final List gwcd_list ) { if ( phylogeny.getNumberOfExternalNodes() != gwcd_list.size() ) { throw new IllegalArgumentException( "number of external nodes [" + phylogeny.getNumberOfExternalNodes() - + "] does not equal size of genome wide combinable domains list [" + gwcd_list.size() + "]" ); + + "] does not equal size of genome wide combinable domains list [" + gwcd_list.size() + "]" ); } return new DomainParsimonyCalculator( phylogeny, gwcd_list ); } @@ -562,7 +562,7 @@ public final class DomainParsimonyCalculator { } final int number_of_characters = all_binary_combinations.size(); final CharacterStateMatrix matrix = new BasicCharacterStateMatrix( number_of_identifiers, - number_of_characters ); + number_of_characters ); int character_index = 0; for( final BinaryDomainCombination bc : all_binary_combinations ) { matrix.setCharacter( character_index++, bc.toString() ); @@ -616,7 +616,7 @@ public final class DomainParsimonyCalculator { } int number_of_characters = all_domain_ids.size(); if ( positive_filter != null ) { - //number_of_characters = positive_filter.size(); -- bad if doms in filter but not in genomes + //number_of_characters = positive_filter.size(); -- bad if doms in filter but not in genomes number_of_characters = 0; for( final String id : all_domain_ids ) { if ( positive_filter.contains( id ) ) { @@ -625,7 +625,7 @@ public final class DomainParsimonyCalculator { } } final CharacterStateMatrix matrix = new BasicCharacterStateMatrix( number_of_identifiers, - number_of_characters ); + number_of_characters ); int character_index = 0; for( final String id : all_domain_ids ) { if ( positive_filter == null ) { @@ -689,14 +689,14 @@ public final class DomainParsimonyCalculator { } if ( !no_mappings.isEmpty() ) { ForesterUtil.programMessage( surfacing.PRG_NAME, "No mappings for the following (" + no_mappings.size() - + "):" ); + + "):" ); for( final String id : no_mappings ) { ForesterUtil.programMessage( surfacing.PRG_NAME, id ); } } final int number_of_characters = all_binary_combinations_mapped.size(); final CharacterStateMatrix matrix = new BasicCharacterStateMatrix( number_of_identifiers, - number_of_characters ); + number_of_characters ); int character_index = 0; for( final BinaryDomainCombination bc : all_binary_combinations_mapped ) { matrix.setCharacter( character_index++, bc.toString() ); @@ -739,8 +739,8 @@ public final class DomainParsimonyCalculator { /** * For folds instead of Pfam-domains, for example - * - * + * + * * @param gwcd_list * @return */ @@ -777,7 +777,7 @@ public final class DomainParsimonyCalculator { } final int number_of_characters = all_secondary_features.size(); final CharacterStateMatrix matrix = new BasicCharacterStateMatrix( number_of_identifiers, - number_of_characters ); + number_of_characters ); int character_index = 0; for( final String second_id : all_secondary_features ) { matrix.setCharacter( character_index++, second_id ); diff --git a/forester/java/src/org/forester/surfacing/DomainSimilarity.java b/forester/java/src/org/forester/surfacing/DomainSimilarity.java index 144e3b8..db25dd5 100644 --- a/forester/java/src/org/forester/surfacing/DomainSimilarity.java +++ b/forester/java/src/org/forester/surfacing/DomainSimilarity.java @@ -110,7 +110,7 @@ public class DomainSimilarity implements Comparable { final int s = species_data.size(); if ( ( ( s * s ) - s ) != ( getN() * 2 ) ) { throw new IllegalArgumentException( "illegal species count and n: species count:" + s + ", n:" + _n - + " for domain " + combinable_domains.getKeyDomain() ); + + " for domain " + combinable_domains.getKeyDomain() ); } if ( s > 2 ) { if ( getMaximalDifferenceInCounts() < 0 ) { @@ -192,10 +192,10 @@ public class DomainSimilarity implements Comparable { /** * For pairwise similarities, this should return the "difference"; for example the difference in counts * for copy number based features (the same as getMaximalDifferenceInCounts(), or the number - * of actually different domain combinations. + * of actually different domain combinations. * For pairwise similarities, this should return the difference, * while for comparisons of more than two domains, this should return the maximal difference - * + * */ public int getMaximalDifference() { return _max_difference; @@ -205,8 +205,8 @@ public class DomainSimilarity implements Comparable { * For pairwise similarities, this should return the difference in counts, * while for comparisons of more than two domains, this should return the maximal difference * in counts - * - * + * + * * @return the (maximal) difference in counts */ public int getMaximalDifferenceInCounts() { @@ -228,7 +228,7 @@ public class DomainSimilarity implements Comparable { /** * This should return the number of pairwise distances used to calculate * this similarity score - * + * * @return the number of pairwise distances */ public int getN() { @@ -250,8 +250,8 @@ public class DomainSimilarity implements Comparable { /** * This should return a map, which maps species names to * SpeciesSpecificDomainSimilariyData - * - * + * + * * @return SortedMap */ public SortedMap getSpeciesData() { @@ -538,7 +538,7 @@ public class DomainSimilarity implements Comparable { sb.append( "" ); sb.append( "" ); if ( getMaximalSimilarityScore() > 0 ) { sb.append( "" ); + + "\">" + similarity.getDomainId() + + "" ); } else { single_writer.write( "" ); + + "\">" + similarity.getDomainId() + + "" ); } else { local_writer.write( "" ); writeDomainIdsToHtml( out, domain_0, domain_1, prefix_for_html, domain_id_to_secondary_features_maps ); @@ -3281,7 +3281,7 @@ public final class SurfacingUtil { final String domain_1, final String prefix_for_detailed_html, final Map>[] domain_id_to_secondary_features_maps ) - throws IOException { + throws IOException { out.write( "
    " ); sb.append( "gs" ); + + "\" target=\"gs_window\">gs" ); sb.append( "" ); diff --git a/forester/java/src/org/forester/surfacing/DomainSimilarityCalculator.java b/forester/java/src/org/forester/surfacing/DomainSimilarityCalculator.java index a1c944a..3983dd6 100644 --- a/forester/java/src/org/forester/surfacing/DomainSimilarityCalculator.java +++ b/forester/java/src/org/forester/surfacing/DomainSimilarityCalculator.java @@ -37,11 +37,11 @@ public interface DomainSimilarityCalculator { final boolean ignore_domains_without_combinations_in_any_genome, final boolean ignore_domains_specific_to_one_genome );; - public static enum Detailedness { - BASIC, LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES, PUNCTILIOUS - } + public static enum Detailedness { + BASIC, LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES, PUNCTILIOUS + } - public static enum GoAnnotationOutput { - ALL, NONE - } + public static enum GoAnnotationOutput { + ALL, NONE + } } diff --git a/forester/java/src/org/forester/surfacing/GenomeWideCombinableDomains.java b/forester/java/src/org/forester/surfacing/GenomeWideCombinableDomains.java index 810e409..81fd861 100644 --- a/forester/java/src/org/forester/surfacing/GenomeWideCombinableDomains.java +++ b/forester/java/src/org/forester/surfacing/GenomeWideCombinableDomains.java @@ -45,7 +45,7 @@ public interface GenomeWideCombinableDomains { /** * This should return all domains ids present in the genome. - * + * * @return a sorted set of domains ids */ public SortedSet getAllDomainIds(); @@ -53,9 +53,9 @@ public interface GenomeWideCombinableDomains { public DomainCombinationType getDomainCombinationType(); /** - * This should return a statistic for per domain + * This should return a statistic for per domain * promiscuity in a genome. - * + * * @return descriptive statistics for per domain promiscuity in a genome */ public DescriptiveStatistics getPerGenomeDomainPromiscuityStatistics(); @@ -66,7 +66,7 @@ public interface GenomeWideCombinableDomains { /** * This should return all binary domain combinations present in the genome. - * + * * @return a sorted set of binary domain combinations */ public SortedSet toBinaryDomainCombinations(); diff --git a/forester/java/src/org/forester/surfacing/PairwiseDomainSimilarity.java b/forester/java/src/org/forester/surfacing/PairwiseDomainSimilarity.java index 2fa6f4e..a781898 100644 --- a/forester/java/src/org/forester/surfacing/PairwiseDomainSimilarity.java +++ b/forester/java/src/org/forester/surfacing/PairwiseDomainSimilarity.java @@ -32,7 +32,7 @@ public interface PairwiseDomainSimilarity { * This should return the -- not normalized, not absolute -- difference in * counts (for example domain counts) for the two domains. * It is important that it is: (counts for domain 1) minus (counts for domain 2). - * + * * @return the difference in counts */ public int getDifferenceInCounts(); diff --git a/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java b/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java index d0d2590..b23f82b 100644 --- a/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java +++ b/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java @@ -122,11 +122,11 @@ public class PairwiseGenomeComparator { if ( ( list_of_genome_wide_combinable_domains.get( i ).getSize() < 1 ) || ( list_of_genome_wide_combinable_domains.get( j ).getSize() < 1 ) ) { domain_distance_scores_means - .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE ); + .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE ); shared_domains_based_distances - .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE ); + .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE ); shared_binary_combinations_based_distances - .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE ); + .setValue( i, j, DomainArchitectureBasedGenomeSimilarityCalculator.MAX_SIMILARITY_SCORE ); continue; } final List genome_pair = new ArrayList( 2 ); @@ -151,9 +151,9 @@ public class PairwiseGenomeComparator { .calculateDescriptiveStatisticsForMeanValues( similarities ); final String species_j = species[ j ].getSpeciesId(); final DomainArchitectureBasedGenomeSimilarityCalculator genome_similarity_calculator = new DomainArchitectureBasedGenomeSimilarityCalculator( list_of_genome_wide_combinable_domains - .get( i ), + .get( i ), list_of_genome_wide_combinable_domains - .get( j ) ); + .get( j ) ); genome_similarity_calculator.setAllowDomainsToBeIgnored( false ); double dissimilarity_score_mean; if ( stats.getN() < 1 ) { @@ -275,15 +275,15 @@ public class PairwiseGenomeComparator { genome_pair.add( list_of_genome_wide_combinable_domains.get( i ) ); genome_pair.add( list_of_genome_wide_combinable_domains.get( j ) ); final DomainArchitectureBasedGenomeSimilarityCalculator genome_simiarity_calculator = new DomainArchitectureBasedGenomeSimilarityCalculator( list_of_genome_wide_combinable_domains - .get( i ), + .get( i ), list_of_genome_wide_combinable_domains - .get( j ) ); + .get( j ) ); genome_simiarity_calculator.setAllowDomainsToBeIgnored( true ); genome_simiarity_calculator.setDomainIdsToIgnore( domain_ids_to_ignore ); shared_domains_based_distances.setValue( i, j, 1.0 - genome_simiarity_calculator - .calculateSharedDomainsBasedGenomeSimilarityScore() ); + .calculateSharedDomainsBasedGenomeSimilarityScore() ); shared_binary_combinations_based_distances.setValue( i, j, 1.0 - genome_simiarity_calculator - .calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore() ); + .calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore() ); } } getSharedDomainsBasedDistances().add( shared_domains_based_distances ); diff --git a/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDcData.java b/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDcData.java index be2fcc7..56d0239 100644 --- a/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDcData.java +++ b/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDcData.java @@ -129,7 +129,7 @@ class PrintableSpeciesSpecificDcData implements SpeciesSpecificDcData { sb.append( " " ); if ( html ) { sb.append( "" + domain_id - + "" ); + + "" ); } else { sb.append( domain_id ); diff --git a/forester/java/src/org/forester/surfacing/SpeciesSpecificDcData.java b/forester/java/src/org/forester/surfacing/SpeciesSpecificDcData.java index be08c39..fffe217 100644 --- a/forester/java/src/org/forester/surfacing/SpeciesSpecificDcData.java +++ b/forester/java/src/org/forester/surfacing/SpeciesSpecificDcData.java @@ -40,7 +40,7 @@ interface SpeciesSpecificDcData { /** * This should return a sorted map mapping domain ids to their corresponding * counts - * + * * @return a sorted map mapping domain ids to their corresponding counts */ public SortedMap getCombinableDomainIdToCountsMap(); diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java index e646ba4..ea51d19 100644 --- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java +++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java @@ -104,22 +104,22 @@ public final class SurfacingUtil { private final static Map _TAXCODE_TAXGROUP_MAP = new HashMap(); private static final Comparator ASCENDING_CONFIDENCE_VALUE_ORDER = new Comparator() { - @Override - public int compare( final Domain d1, - final Domain d2 ) { - if ( d1.getPerDomainEvalue() < d2 - .getPerDomainEvalue() ) { - return -1; - } - else if ( d1.getPerDomainEvalue() > d2 - .getPerDomainEvalue() ) { - return 1; - } - else { - return d1.compareTo( d2 ); - } - } - }; + @Override + public int compare( final Domain d1, + final Domain d2 ) { + if ( d1.getPerDomainEvalue() < d2 + .getPerDomainEvalue() ) { + return -1; + } + else if ( d1.getPerDomainEvalue() > d2 + .getPerDomainEvalue() ) { + return 1; + } + else { + return d1.compareTo( d2 ); + } + } + }; private final static NumberFormat FORMATTER_3 = new DecimalFormat( "0.000" ); private SurfacingUtil() { @@ -198,15 +198,15 @@ public final class SurfacingUtil { || ( !get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.LOSS ) ) ) { if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) { all_binary_domains_combination_gained.add( AdjactantDirectedBinaryDomainCombination - .obtainInstance( matrix.getCharacter( c ) ) ); + .obtainInstance( matrix.getCharacter( c ) ) ); } else if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED ) { all_binary_domains_combination_gained.add( DirectedBinaryDomainCombination - .obtainInstance( matrix.getCharacter( c ) ) ); + .obtainInstance( matrix.getCharacter( c ) ) ); } else { all_binary_domains_combination_gained.add( BasicBinaryDomainCombination.obtainInstance( matrix - .getCharacter( c ) ) ); + .getCharacter( c ) ) ); } } } @@ -289,59 +289,59 @@ public final class SurfacingUtil { final String my_outfile, final Map split_writers ) throws IOException { split_writers.put( 'a', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_A.html" ) ) ); + + "_domains_A.html" ) ) ); split_writers.put( 'b', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_B.html" ) ) ); + + "_domains_B.html" ) ) ); split_writers.put( 'c', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_C.html" ) ) ); + + "_domains_C.html" ) ) ); split_writers.put( 'd', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_D.html" ) ) ); + + "_domains_D.html" ) ) ); split_writers.put( 'e', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_E.html" ) ) ); + + "_domains_E.html" ) ) ); split_writers.put( 'f', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_F.html" ) ) ); + + "_domains_F.html" ) ) ); split_writers.put( 'g', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_G.html" ) ) ); + + "_domains_G.html" ) ) ); split_writers.put( 'h', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_H.html" ) ) ); + + "_domains_H.html" ) ) ); split_writers.put( 'i', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_I.html" ) ) ); + + "_domains_I.html" ) ) ); split_writers.put( 'j', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_J.html" ) ) ); + + "_domains_J.html" ) ) ); split_writers.put( 'k', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_K.html" ) ) ); + + "_domains_K.html" ) ) ); split_writers.put( 'l', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_L.html" ) ) ); + + "_domains_L.html" ) ) ); split_writers.put( 'm', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_M.html" ) ) ); + + "_domains_M.html" ) ) ); split_writers.put( 'n', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_N.html" ) ) ); + + "_domains_N.html" ) ) ); split_writers.put( 'o', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_O.html" ) ) ); + + "_domains_O.html" ) ) ); split_writers.put( 'p', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_P.html" ) ) ); + + "_domains_P.html" ) ) ); split_writers.put( 'q', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_Q.html" ) ) ); + + "_domains_Q.html" ) ) ); split_writers.put( 'r', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_R.html" ) ) ); + + "_domains_R.html" ) ) ); split_writers.put( 's', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_S.html" ) ) ); + + "_domains_S.html" ) ) ); split_writers.put( 't', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_T.html" ) ) ); + + "_domains_T.html" ) ) ); split_writers.put( 'u', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_U.html" ) ) ); + + "_domains_U.html" ) ) ); split_writers.put( 'v', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_V.html" ) ) ); + + "_domains_V.html" ) ) ); split_writers.put( 'w', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_W.html" ) ) ); + + "_domains_W.html" ) ) ); split_writers.put( 'x', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_X.html" ) ) ); + + "_domains_X.html" ) ) ); split_writers.put( 'y', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_Y.html" ) ) ); + + "_domains_Y.html" ) ) ); split_writers.put( 'z', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_Z.html" ) ) ); + + "_domains_Z.html" ) ) ); split_writers.put( '0', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile - + "_domains_0.html" ) ) ); + + "_domains_0.html" ) ) ); } public static Map createTaxCodeToIdMap( final Phylogeny phy ) { @@ -582,14 +582,14 @@ public final class SurfacingUtil { /** * Warning: This side-effects 'all_bin_domain_combinations_encountered'! - * - * + * + * * @param output_file * @param all_bin_domain_combinations_changed * @param sum_of_all_domains_encountered * @param all_bin_domain_combinations_encountered * @param is_gains_analysis - * @param protein_length_stats_by_dc + * @param protein_length_stats_by_dc * @throws IOException */ public static void executeFitchGainsAnalysis( final File output_file, @@ -634,9 +634,9 @@ public final class SurfacingUtil { } if ( is_gains_analysis ) { out.write( "Sum of all distinct domain combinations appearing once : " + one - + ForesterUtil.LINE_SEPARATOR ); + + ForesterUtil.LINE_SEPARATOR ); out.write( "Sum of all distinct domain combinations appearing more than once : " + above_one - + ForesterUtil.LINE_SEPARATOR ); + + ForesterUtil.LINE_SEPARATOR ); out.write( "Sum of all distinct domains in combinations apppearing only once : " + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR ); out.write( "Sum of all distinct domains in combinations apppearing more than once: " @@ -644,32 +644,32 @@ public final class SurfacingUtil { } else { out.write( "Sum of all distinct domain combinations never lost : " + never_lost - + ForesterUtil.LINE_SEPARATOR ); + + ForesterUtil.LINE_SEPARATOR ); out.write( "Sum of all distinct domain combinations lost once : " + one - + ForesterUtil.LINE_SEPARATOR ); + + ForesterUtil.LINE_SEPARATOR ); out.write( "Sum of all distinct domain combinations lost more than once : " + above_one - + ForesterUtil.LINE_SEPARATOR ); + + ForesterUtil.LINE_SEPARATOR ); out.write( "Sum of all distinct domains in combinations lost only once : " + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR ); out.write( "Sum of all distinct domains in combinations lost more than once: " + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR ); } out.write( "All binary combinations : " + all - + ForesterUtil.LINE_SEPARATOR ); + + ForesterUtil.LINE_SEPARATOR ); out.write( "All domains : " + sum_of_all_domains_encountered ); out.close(); ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote fitch domain combination dynamics counts analysis to \"" + output_file - + "\"" ); + + "\"" ); } /** - * - * @param all_binary_domains_combination_lost_fitch - * @param use_last_in_fitch_parsimony - * @param perform_dc_fich - * @param consider_directedness_and_adjacency_for_bin_combinations + * + * @param all_binary_domains_combination_lost_fitch + * @param use_last_in_fitch_parsimony + * @param perform_dc_fich + * @param consider_directedness_and_adjacency_for_bin_combinations * @param all_binary_domains_combination_gained if null ignored, otherwise this is to list all binary domain combinations * which were gained under unweighted (Fitch) parsimony. */ @@ -715,9 +715,9 @@ public final class SurfacingUtil { domain_parsimony.executeDolloParsimonyOnDomainPresence(); } SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name - + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS, Format.FORESTER ); + + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS, Format.FORESTER ); SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name - + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS, Format.FORESTER ); + + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS, Format.FORESTER ); SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), CharacterStateMatrix.GainLossStates.GAIN, outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_D, @@ -731,7 +731,7 @@ public final class SurfacingUtil { ForesterUtil.LINE_SEPARATOR, null ); SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name - + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_D, sep, ForesterUtil.LINE_SEPARATOR, null ); + + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_D, sep, ForesterUtil.LINE_SEPARATOR, null ); //HTML: writeBinaryStatesMatrixToList( domain_id_to_go_ids_map, go_id_to_term_map, @@ -788,7 +788,7 @@ public final class SurfacingUtil { "dollo_on_domains_" + outfile_name, parameters_str ); SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name - + surfacing.DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO ); + + surfacing.DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO ); try { writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, true, outfile_name, "_dollo_all_gains_d" ); writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, false, outfile_name, "_dollo_all_losses_d" ); @@ -810,25 +810,25 @@ public final class SurfacingUtil { domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( use_last_in_fitch_parsimony ); } SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name - + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER ); + + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER ); SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name - + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER ); + + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER ); SurfacingUtil - .writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), - CharacterStateMatrix.GainLossStates.GAIN, - outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_BC, - sep, - ForesterUtil.LINE_SEPARATOR, - null ); + .writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), + CharacterStateMatrix.GainLossStates.GAIN, + outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_BC, + sep, + ForesterUtil.LINE_SEPARATOR, + null ); SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), CharacterStateMatrix.GainLossStates.LOSS, outfile_name - + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_BC, + + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_BC, sep, ForesterUtil.LINE_SEPARATOR, null ); SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name - + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC, sep, ForesterUtil.LINE_SEPARATOR, null ); + + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC, sep, ForesterUtil.LINE_SEPARATOR, null ); if ( all_binary_domains_combination_gained_fitch != null ) { collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), dc_type, @@ -843,14 +843,14 @@ public final class SurfacingUtil { } if ( output_binary_domain_combinations_for_graphs ) { SurfacingUtil - .writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( domain_parsimony - .getGainLossMatrix(), - null, - outfile_name - + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS, - sep, - ForesterUtil.LINE_SEPARATOR, - BinaryDomainCombination.OutputFormat.DOT ); + .writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( domain_parsimony + .getGainLossMatrix(), + null, + outfile_name + + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS, + sep, + ForesterUtil.LINE_SEPARATOR, + BinaryDomainCombination.OutputFormat.DOT ); } // HTML: writeBinaryStatesMatrixToList( domain_id_to_go_ids_map, @@ -915,19 +915,19 @@ public final class SurfacingUtil { date_time, "Fitch parsimony on binary domain combination presence/absence randomization: " + randomization, - "fitch_on_binary_domain_combinations_" + outfile_name, - parameters_str ); + "fitch_on_binary_domain_combinations_" + outfile_name, + parameters_str ); SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name - + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH ); + + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH ); calculateIndependentDomainCombinationGains( local_phylogeny_l, outfile_name - + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX, + + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX, outfile_name - + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX, + + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX, outfile_name - + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX, + + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX, outfile_name - + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX, + + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX, outfile_name + "_indep_dc_gains_fitch_lca_ranks.txt", outfile_name + "_indep_dc_gains_fitch_lca_taxonomies.txt", outfile_name + "_indep_dc_gains_fitch_protein_statistics.txt", @@ -952,33 +952,33 @@ public final class SurfacingUtil { Phylogeny local_phylogeny_copy = phylogeny.copy(); secondary_features_parsimony.executeDolloParsimonyOnSecondaryFeatures( mapping_results_map ); SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossMatrix(), outfile_name - + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER ); + + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER ); SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossCountsMatrix(), outfile_name - + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER ); + + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER ); SurfacingUtil - .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(), - CharacterStateMatrix.GainLossStates.GAIN, - outfile_name - + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES, - sep, - ForesterUtil.LINE_SEPARATOR, - null ); + .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(), + CharacterStateMatrix.GainLossStates.GAIN, + outfile_name + + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES, + sep, + ForesterUtil.LINE_SEPARATOR, + null ); SurfacingUtil - .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(), - CharacterStateMatrix.GainLossStates.LOSS, - outfile_name - + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES, - sep, - ForesterUtil.LINE_SEPARATOR, - null ); + .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(), + CharacterStateMatrix.GainLossStates.LOSS, + outfile_name + + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES, + sep, + ForesterUtil.LINE_SEPARATOR, + null ); SurfacingUtil - .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(), - null, - outfile_name - + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES, - sep, - ForesterUtil.LINE_SEPARATOR, - null ); + .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(), + null, + outfile_name + + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES, + sep, + ForesterUtil.LINE_SEPARATOR, + null ); preparePhylogeny( local_phylogeny_copy, secondary_features_parsimony, date_time, @@ -986,29 +986,29 @@ public final class SurfacingUtil { "dollo_on_secondary_features_" + outfile_name, parameters_str ); SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name - + surfacing.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO ); + + surfacing.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO ); // FITCH DOMAIN COMBINATIONS // ------------------------- local_phylogeny_copy = phylogeny.copy(); final String randomization = "no"; secondary_features_parsimony - .executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( use_last_in_fitch_parsimony ); + .executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( use_last_in_fitch_parsimony ); preparePhylogeny( local_phylogeny_copy, secondary_features_parsimony, date_time, "Fitch parsimony on secondary binary domain combination presence/absence randomization: " + randomization, - "fitch_on_binary_domain_combinations_" + outfile_name, - parameters_str ); + "fitch_on_binary_domain_combinations_" + outfile_name, + parameters_str ); SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name - + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED ); + + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED ); calculateIndependentDomainCombinationGains( local_phylogeny_copy, outfile_name - + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX, outfile_name - + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX, outfile_name - + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX, outfile_name - + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX, outfile_name - + "_MAPPED_indep_dc_gains_fitch_lca_ranks.txt", outfile_name - + "_MAPPED_indep_dc_gains_fitch_lca_taxonomies.txt", null, null, null, null ); + + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX, outfile_name + + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX, outfile_name + + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX, outfile_name + + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX, outfile_name + + "_MAPPED_indep_dc_gains_fitch_lca_ranks.txt", outfile_name + + "_MAPPED_indep_dc_gains_fitch_lca_taxonomies.txt", null, null, null, null ); } public static void executePlusMinusAnalysis( final File output_file, @@ -1029,7 +1029,7 @@ public final class SurfacingUtil { final File html_out_dc = new File( output_file + surfacing.PLUS_MINUS_DC_SUFFIX_HTML ); final File all_domains_go_ids_out_dom = new File( output_file + surfacing.PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX ); final File passing_domains_go_ids_out_dom = new File( output_file - + surfacing.PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX ); + + surfacing.PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX ); final File proteins_file_base = new File( output_file + "" ); final int min_diff = ( ( Integer ) plus_minus_analysis_numbers.get( 0 ) ).intValue(); final double factor = ( ( Double ) plus_minus_analysis_numbers.get( 1 ) ).doubleValue(); @@ -1058,7 +1058,7 @@ public final class SurfacingUtil { ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \"" + plain_out_dom + "\"" ); ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \"" + html_out_dc - + "\"" ); + + "\"" ); ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis based passing GO ids to \"" + passing_domains_go_ids_out_dom + "\"" ); ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis based all GO ids to \"" @@ -1225,9 +1225,9 @@ public final class SurfacingUtil { final PhylogenyNode n = it.next(); if ( ForesterUtil.isEmpty( n.getName() ) && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy() - .getScientificName() ) ) - && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy() - .getCommonName() ) ) ) { + .getScientificName() ) ) + && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy() + .getCommonName() ) ) ) { if ( n.getParent() != null ) { names.append( " " ); names.append( n.getParent().getName() ); @@ -1269,17 +1269,17 @@ public final class SurfacingUtil { .create( intree_file, ParserUtils.createParserDependingOnFileType( intree_file, true ) ); if ( p_array.length < 1 ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file - + "] does not contain any phylogeny in phyloXML format" ); + + "] does not contain any phylogeny in phyloXML format" ); } else if ( p_array.length > 1 ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file - + "] contains more than one phylogeny in phyloXML format" ); + + "] contains more than one phylogeny in phyloXML format" ); } intree = p_array[ 0 ]; } catch ( final Exception e ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to read input tree from file [" + intree_file - + "]: " + error ); + + "]: " + error ); } if ( ( intree == null ) || intree.isEmpty() ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is empty" ); @@ -1290,9 +1290,9 @@ public final class SurfacingUtil { if ( intree.getNumberOfExternalNodes() < number_of_genomes ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "number of external nodes [" + intree.getNumberOfExternalNodes() - + "] of input tree [" + intree_file - + "] is smaller than the number of genomes the be analyzed [" - + number_of_genomes + "]" ); + + "] of input tree [" + intree_file + + "] is smaller than the number of genomes the be analyzed [" + + number_of_genomes + "]" ); } final StringBuilder parent_names = new StringBuilder(); final int nodes_lacking_name = getNumberOfNodesLackingName( intree, parent_names ); @@ -1303,7 +1303,7 @@ public final class SurfacingUtil { preparePhylogenyForParsimonyAnalyses( intree, input_file_properties ); if ( !intree.isCompletelyBinary() ) { ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "input tree [" + intree_file - + "] is not completely binary" ); + + "] is not completely binary" ); } intrees[ i++ ] = intree; } @@ -1321,11 +1321,11 @@ public final class SurfacingUtil { .create( intree_file, ParserUtils.createParserDependingOnFileType( intree_file, true ) ); if ( phys.length < 1 ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file - + "] does not contain any phylogeny in phyloXML format" ); + + "] does not contain any phylogeny in phyloXML format" ); } else if ( phys.length > 1 ) { ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file - + "] contains more than one phylogeny in phyloXML format" ); + + "] contains more than one phylogeny in phyloXML format" ); } intree = phys[ 0 ]; } @@ -1373,14 +1373,14 @@ public final class SurfacingUtil { final Color c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( group ); if ( c == null ) { throw new IllegalArgumentException( "no color found for taxonomy group \"" + group - + "\" for code \"" + tax_code + "\"" ); + + "\" for code \"" + tax_code + "\"" ); } final String hex = String.format( "#%02x%02x%02x", c.getRed(), c.getGreen(), c.getBlue() ); _TAXCODE_HEXCOLORSTRING_MAP.put( tax_code, hex ); } else { throw new IllegalArgumentException( "unable to obtain color for code " + tax_code - + " (tree is null or empty and code is not in map)" ); + + " (tree is null or empty and code is not in map)" ); } } return _TAXCODE_HEXCOLORSTRING_MAP.get( tax_code ); @@ -1403,7 +1403,7 @@ public final class SurfacingUtil { if ( n.getNodeData().isHasTaxonomy() && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) { group = ForesterUtil.obtainNormalizedTaxonomyGroup( n.getNodeData().getTaxonomy() - .getScientificName() ); + .getScientificName() ); } if ( ForesterUtil.isEmpty( group ) && !ForesterUtil.isEmpty( n.getName() ) ) { group = ForesterUtil.obtainNormalizedTaxonomyGroup( n.getName() ); @@ -1420,7 +1420,7 @@ public final class SurfacingUtil { } else { throw new IllegalArgumentException( "unable to obtain group for code " + tax_code - + " (tree is null or empty and code is not in map)" ); + + " (tree is null or empty and code is not in map)" ); } } return _TAXCODE_TAXGROUP_MAP.get( tax_code ); @@ -1523,8 +1523,8 @@ public final class SurfacingUtil { } else { ForesterUtil - .fatalError( surfacing.PRG_NAME, - "node with no name, scientific name, common name, or taxonomy code present" ); + .fatalError( surfacing.PRG_NAME, + "node with no name, scientific name, common name, or taxonomy code present" ); } } } @@ -1700,9 +1700,9 @@ public final class SurfacingUtil { } else { ForesterUtil - .fatalError( surfacing.PRG_NAME, - "species/genome names in 'plus minus' file must begin with '*' (high copy target genome), '+' (high copy base genomes), '-' (low copy genomes), '$D=' minimal Difference (default is 1), '$F=' factor (default is 1.0), double), or '#' (ignore) suffix, encountered: \"" - + species + "\"" ); + .fatalError( surfacing.PRG_NAME, + "species/genome names in 'plus minus' file must begin with '*' (high copy target genome), '+' (high copy base genomes), '-' (low copy genomes), '$D=' minimal Difference (default is 1), '$F=' factor (default is 1.0), double), or '#' (ignore) suffix, encountered: \"" + + species + "\"" ); } numbers.add( new Integer( min_diff + "" ) ); numbers.add( new Double( factor + "" ) ); @@ -1715,8 +1715,8 @@ public final class SurfacingUtil { /* * species | protein id | n-terminal domain | c-terminal domain | n-terminal domain per domain E-value | c-terminal domain per domain E-value - * - * + * + * */ static public StringBuffer proteinToDomainCombinations( final Protein protein, final String protein_id, @@ -1851,7 +1851,7 @@ public final class SurfacingUtil { final SortedSet domains = collectAllDomainsChangedOnSubtree( node, get_gains ); if ( domains.size() > 0 ) { final Writer writer = ForesterUtil.createBufferedWriter( base_dir + ForesterUtil.FILE_SEPARATOR - + node.getName() + suffix_for_filename ); + + node.getName() + suffix_for_filename ); for( final String domain : domains ) { writer.write( domain ); writer.write( ForesterUtil.LINE_SEPARATOR ); @@ -1878,7 +1878,7 @@ public final class SurfacingUtil { final BufferedWriter out_dot = new BufferedWriter( new FileWriter( dc_outfile_dot ) ); for( final BinaryDomainCombination bdc : binary_combinations ) { out_dot.write( bdc.toGraphDescribingLanguage( BinaryDomainCombination.OutputFormat.DOT, null, null ) - .toString() ); + .toString() ); out_dot.write( SurfacingConstants.NL ); } out_dot.close(); @@ -2084,7 +2084,7 @@ public final class SurfacingUtil { per_node_counter = 0; if ( matrix.getNumberOfCharacters() > 0 ) { per_node_go_mapped_domain_gain_loss_outfile = new File( per_node_go_mapped_domain_gain_loss_files_base_dir - + ForesterUtil.FILE_SEPARATOR + id + suffix_for_per_node_events_file ); + + ForesterUtil.FILE_SEPARATOR + id + suffix_for_per_node_events_file ); SurfacingUtil.checkForOutputFileWriteability( per_node_go_mapped_domain_gain_loss_outfile ); per_node_go_mapped_domain_gain_loss_outfile_writer = ForesterUtil .createBufferedWriter( per_node_go_mapped_domain_gain_loss_outfile ); @@ -2153,7 +2153,7 @@ public final class SurfacingUtil { out.write( SurfacingConstants.NL ); out.write( "
    " ); out.write( SurfacingConstants.NL ); - } // for( final String id : sorted_ids ) { + } // for( final String id : sorted_ids ) { out.write( "" ); out.write( SurfacingConstants.NL ); out.write( "" ); @@ -2196,7 +2196,7 @@ public final class SurfacingUtil { } else { per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats - .sampleStandardDeviation() ) + "\t" ); + .sampleStandardDeviation() ) + "\t" ); } per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.median() ) + "\t" ); per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMin() + "\t" ); @@ -2279,8 +2279,8 @@ public final class SurfacingUtil { if ( single_writer != null ) { if ( !ForesterUtil.isEmpty( pos_filter_doms ) && pos_filter_doms.contains( similarity.getDomainId() ) ) { single_writer.write( "
    " + similarity.getDomainId() - + "
    " @@ -2290,14 +2290,14 @@ public final class SurfacingUtil { } else { Writer local_writer = split_writers.get( ( similarity.getDomainId().charAt( 0 ) + "" ).toLowerCase() - .charAt( 0 ) ); + .charAt( 0 ) ); if ( local_writer == null ) { local_writer = split_writers.get( '0' ); } if ( !ForesterUtil.isEmpty( pos_filter_doms ) && pos_filter_doms.contains( similarity.getDomainId() ) ) { local_writer.write( "
    " + similarity.getDomainId() - + "
    " @@ -2372,7 +2372,7 @@ public final class SurfacingUtil { } else { Writer local_writer = split_writers.get( ( similarity.getDomainId().charAt( 0 ) + "" ).toLowerCase() - .charAt( 0 ) ); + .charAt( 0 ) ); if ( local_writer == null ) { local_writer = split_writers.get( '0' ); } @@ -2504,8 +2504,8 @@ public final class SurfacingUtil { writeMatrixToFile( DomainParsimonyCalculator.createMatrixOfDomainPresenceOrAbsence( gwcd_list, positive_filter_file == null ? null : filter ), - output_file + surfacing.DOMAINS_PRESENT_NEXUS, - Format.NEXUS_BINARY ); + output_file + surfacing.DOMAINS_PRESENT_NEXUS, + Format.NEXUS_BINARY ); writeMatrixToFile( DomainParsimonyCalculator.createMatrixOfBinaryDomainCombinationPresenceOrAbsence( gwcd_list ), output_file + surfacing.BDC_PRESENT_NEXUS, Format.NEXUS_BINARY ); @@ -2554,17 +2554,17 @@ public final class SurfacingUtil { writer.write( " [" ); if ( ( tax_code_to_id_map != null ) && tax_code_to_id_map.containsKey( species ) ) { writer.write( "uniprot" ); + + tax_code_to_id_map.get( species ) + "\" target=\"taxonomy_window\">uniprot" ); } else { writer.write( "eol" ); + + "\" target=\"taxonomy_window\">eol" ); writer.write( "|" ); writer.write( "scholar" ); + + "\" target=\"taxonomy_window\">scholar" ); writer.write( "|" ); writer.write( "google" ); + + "\" target=\"taxonomy_window\">google" ); } writer.write( "]" ); } @@ -2672,14 +2672,14 @@ public final class SurfacingUtil { dc_reapp_counts_to_protein_length_stats.put( count, new BasicDescriptiveStatistics() ); } dc_reapp_counts_to_protein_length_stats.get( count ).addValue( protein_length_stats_by_dc.get( dc ) - .arithmeticMean() ); + .arithmeticMean() ); } if ( domain_number_stats_by_dc != null ) { if ( !dc_reapp_counts_to_domain_number_stats.containsKey( count ) ) { dc_reapp_counts_to_domain_number_stats.put( count, new BasicDescriptiveStatistics() ); } dc_reapp_counts_to_domain_number_stats.get( count ).addValue( domain_number_stats_by_dc.get( dc ) - .arithmeticMean() ); + .arithmeticMean() ); } if ( domain_length_stats_by_domain != null ) { if ( !dc_reapp_counts_to_domain_lengths_stats.containsKey( count ) ) { @@ -2687,9 +2687,9 @@ public final class SurfacingUtil { } final String[] ds = dc.split( "=" ); dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain - .get( ds[ 0 ] ).arithmeticMean() ); + .get( ds[ 0 ] ).arithmeticMean() ); dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain - .get( ds[ 1 ] ).arithmeticMean() ); + .get( ds[ 1 ] ).arithmeticMean() ); } if ( count > 1 ) { more_than_once.add( dc ); @@ -2934,32 +2934,32 @@ public final class SurfacingUtil { final CharacterStateMatrix.GainLossStates state, final String outfile ) { File per_node_go_mapped_domain_gain_loss_files_base_dir = new File( new File( outfile ).getParent() - + ForesterUtil.FILE_SEPARATOR + base_dir ); + + ForesterUtil.FILE_SEPARATOR + base_dir ); if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) { per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir(); } if ( domain_combinations ) { per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir - + ForesterUtil.FILE_SEPARATOR + "DC" ); + + ForesterUtil.FILE_SEPARATOR + "DC" ); } else { per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir - + ForesterUtil.FILE_SEPARATOR + "DOMAINS" ); + + ForesterUtil.FILE_SEPARATOR + "DOMAINS" ); } if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) { per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir(); } if ( state == GainLossStates.GAIN ) { per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir - + ForesterUtil.FILE_SEPARATOR + "GAINS" ); + + ForesterUtil.FILE_SEPARATOR + "GAINS" ); } else if ( state == GainLossStates.LOSS ) { per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir - + ForesterUtil.FILE_SEPARATOR + "LOSSES" ); + + ForesterUtil.FILE_SEPARATOR + "LOSSES" ); } else { per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir - + ForesterUtil.FILE_SEPARATOR + "PRESENT" ); + + ForesterUtil.FILE_SEPARATOR + "PRESENT" ); } if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) { per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir(); @@ -3032,7 +3032,7 @@ public final class SurfacingUtil { final SortedSet all_pfams_encountered ) { final File all_pfams_encountered_file = new File( outfile_name + surfacing.ALL_PFAMS_ENCOUNTERED_SUFFIX ); final File all_pfams_encountered_with_go_annotation_file = new File( outfile_name - + surfacing.ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX ); + + surfacing.ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX ); final File encountered_pfams_summary_file = new File( outfile_name + surfacing.ENCOUNTERED_PFAMS_SUMMARY_SUFFIX ); int biological_process_counter = 0; int cellular_component_counter = 0; @@ -3101,10 +3101,10 @@ public final class SurfacingUtil { all_pfams_encountered_writer.close(); all_pfams_encountered_with_go_annotation_writer.close(); ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + all_pfams_encountered.size() - + "] encountered Pfams to: \"" + all_pfams_encountered_file + "\"" ); + + "] encountered Pfams to: \"" + all_pfams_encountered_file + "\"" ); ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + pfams_with_mappings_counter - + "] encountered Pfams with GO mappings to: \"" + all_pfams_encountered_with_go_annotation_file - + "\"" ); + + "] encountered Pfams with GO mappings to: \"" + all_pfams_encountered_with_go_annotation_file + + "\"" ); ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote summary (including all [" + pfams_without_mappings_counter + "] encountered Pfams without GO mappings) to: \"" + encountered_pfams_summary_file + "\"" ); @@ -3135,7 +3135,7 @@ public final class SurfacingUtil { summary_writer.write( "# Sum of Pfams encountered : " + all_pfams_encountered.size() ); summary_writer.write( ForesterUtil.LINE_SEPARATOR ); summary_writer.write( "# Pfams without a mapping : " + pfams_without_mappings_counter - + " [" + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" ); + + " [" + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" ); summary_writer.write( ForesterUtil.LINE_SEPARATOR ); summary_writer.write( "# Pfams without mapping to proc. or func. : " + pfams_without_mappings_to_bp_or_mf_counter + " [" @@ -3189,7 +3189,7 @@ public final class SurfacingUtil { if ( ForesterUtil.isEmpty( domain_1 ) ) { domain_count = 1; } - // The following has a difficult to understand logic. + // The following has a difficult to understand logic. for( int d = 0; d < domain_count; ++d ) { List go_ids = null; boolean go_annotation_present = false; @@ -3234,7 +3234,7 @@ public final class SurfacingUtil { final String go_id_str = go_id.getId(); out.write( "" ); out.write( "" + go_id_str + "" ); + + "\" target=\"amigo_window\">" + go_id_str + "" ); out.write( "" ); out.write( go_term.getName() ); if ( domain_count == 2 ) { @@ -3262,7 +3262,7 @@ public final class SurfacingUtil { out.write( SurfacingConstants.NL ); } } - } // for( int d = 0; d < domain_count; ++d ) + } // for( int d = 0; d < domain_count; ++d ) if ( !any_go_annotation_present ) { out.write( "
    " ); if ( !ForesterUtil.isEmpty( prefix_for_detailed_html ) ) { out.write( prefix_for_detailed_html ); @@ -3311,7 +3311,7 @@ public final class SurfacingUtil { } writer.close(); ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote " + pfams.size() + " pfams to [" + outfile_name - + "]" ); + + "]" ); } catch ( final IOException e ) { ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e ); @@ -3323,7 +3323,7 @@ public final class SurfacingUtil { final Phylogeny phylogeny ) { if ( !( matrix instanceof BasicCharacterStateMatrix ) ) { throw new IllegalArgumentException( "can only write matrices of type [" + BasicCharacterStateMatrix.class - + "] to nexus" ); + + "] to nexus" ); } final BasicCharacterStateMatrix my_matrix = ( org.forester.evoinference.matrix.character.BasicCharacterStateMatrix ) matrix; final List phylogenies = new ArrayList( 1 ); diff --git a/forester/java/src/org/forester/surfacing/TestSurfacing.java b/forester/java/src/org/forester/surfacing/TestSurfacing.java index 1ccaf70..6e1e6dc 100644 --- a/forester/java/src/org/forester/surfacing/TestSurfacing.java +++ b/forester/java/src/org/forester/surfacing/TestSurfacing.java @@ -1315,7 +1315,7 @@ public class TestSurfacing { final BinaryStates O = BinaryStates.ABSENT; try { final CharacterStateMatrix binary_states_matrix_0 = new BasicCharacterStateMatrix( 7, - 6 ); + 6 ); binary_states_matrix_0.setIdentifier( 0, "A" ); binary_states_matrix_0.setIdentifier( 1, "B" ); binary_states_matrix_0.setIdentifier( 2, "C" ); @@ -1821,7 +1821,7 @@ public class TestSurfacing { final GenomeWideCombinableDomains gwcd_1 = BasicGenomeWideCombinableDomains .createInstance( list_1, false, new BasicSpecies( "1" ), DomainCombinationType.DIRECTED ); if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "A", - "B" ) ) ) { + "B" ) ) ) { return false; } if ( gwcd_1.toBinaryDomainCombinations() @@ -1833,7 +1833,7 @@ public class TestSurfacing { return false; } if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "A", - "C" ) ) ) { + "C" ) ) ) { return false; } if ( gwcd_1.toBinaryDomainCombinations() @@ -1841,27 +1841,27 @@ public class TestSurfacing { return false; } if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "B", - "C" ) ) ) { + "C" ) ) ) { return false; } if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "C", - "X" ) ) ) { + "X" ) ) ) { return false; } if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "C", - "Y" ) ) ) { + "Y" ) ) ) { return false; } if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "A", - "X" ) ) ) { + "X" ) ) ) { return false; } if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "A", - "Y" ) ) ) { + "Y" ) ) ) { return false; } if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "Y", - "A" ) ) ) { + "A" ) ) ) { return false; } if ( gwcd_1.toBinaryDomainCombinations() @@ -1873,19 +1873,19 @@ public class TestSurfacing { return false; } if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "X", - "Y" ) ) ) { + "Y" ) ) ) { return false; } if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "Y", - "X" ) ) ) { + "X" ) ) ) { return false; } if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "A", - "Y" ) ) ) { + "Y" ) ) ) { return false; } if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "A", - "X" ) ) ) { + "X" ) ) ) { return false; } if ( gwcd_1.toBinaryDomainCombinations() @@ -1893,19 +1893,19 @@ public class TestSurfacing { return false; } if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "M", - "N" ) ) ) { + "N" ) ) ) { return false; } if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "N", - "M" ) ) ) { + "M" ) ) ) { return false; } if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "N", - "P" ) ) ) { + "P" ) ) ) { return false; } if ( !gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "M", - "P" ) ) ) { + "P" ) ) ) { return false; } if ( gwcd_1.toBinaryDomainCombinations() @@ -1917,11 +1917,11 @@ public class TestSurfacing { return false; } if ( gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "XX", - "YY" ) ) ) { + "YY" ) ) ) { return false; } if ( gwcd_1.toBinaryDomainCombinations().contains( DirectedBinaryDomainCombination.obtainInstance( "YY", - "XX" ) ) ) { + "XX" ) ) ) { return false; } if ( gwcd_1.toBinaryDomainCombinations() @@ -1941,7 +1941,7 @@ public class TestSurfacing { // if ( matrix_bc.getState( 0, 0 ) != X ) { // return false; // } - // + // // // final BasicCharacterStateMatrix dm = new BasicCharacterStateMatrix( new BinaryStates[][] { // { X, X, X, X, X, X }, { X, X, X, X, X, X } } ); @@ -3226,23 +3226,23 @@ public class TestSurfacing { return false; } if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "v", - "u" ) ) ) { + "u" ) ) ) { return false; } if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "w", - "v" ) ) ) { + "v" ) ) ) { return false; } if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "w", - "x" ) ) ) { + "x" ) ) ) { return false; } if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "w", - "u" ) ) ) { + "u" ) ) ) { return false; } if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "z", - "y" ) ) ) { + "y" ) ) ) { return false; } calc_u.setAllowDomainsToBeIgnored( true ); @@ -3333,23 +3333,23 @@ public class TestSurfacing { return false; } if ( calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "v", - "u" ) ) ) { + "u" ) ) ) { return false; } if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "w", - "v" ) ) ) { + "v" ) ) ) { return false; } if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "w", - "x" ) ) ) { + "x" ) ) ) { return false; } if ( calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "w", - "u" ) ) ) { + "u" ) ) ) { return false; } if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "z", - "y" ) ) ) { + "y" ) ) ) { return false; } calc_u.setAllowDomainsToBeIgnored( false ); @@ -3431,7 +3431,7 @@ public class TestSurfacing { return false; } if ( !calc_u.getAllBinaryDomainCombinations().contains( BasicBinaryDomainCombination.obtainInstance( "z", - "y" ) ) ) { + "y" ) ) ) { return false; } if ( !isEqual( calc_u.calculateSharedBinaryDomainCombinationBasedGenomeSimilarityScore(), @@ -3476,7 +3476,7 @@ public class TestSurfacing { private static boolean testDomainCombinationCounting( final File test_dir ) { try { final HmmPfamOutputParser parser = new HmmPfamOutputParser( new File( test_dir - + ForesterUtil.getFileSeparator() + "hmmpfam_output2" ), "human", "ls" ); + + ForesterUtil.getFileSeparator() + "hmmpfam_output2" ), "human", "ls" ); parser.setEValueMaximum( 0.2 ); parser.setIgnoreDufs( true ); parser.setReturnType( HmmPfamOutputParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN ); @@ -4549,7 +4549,7 @@ public class TestSurfacing { private static boolean testHmmPfamOutputParser( final File test_dir ) { try { final HmmPfamOutputParser parser = new HmmPfamOutputParser( new File( test_dir - + ForesterUtil.getFileSeparator() + "hmmpfam_output" ), "human", "ls" ); + + ForesterUtil.getFileSeparator() + "hmmpfam_output" ), "human", "ls" ); parser.setEValueMaximum( 0.2 ); parser.setIgnoreDufs( true ); parser.setReturnType( HmmPfamOutputParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN ); @@ -4627,7 +4627,7 @@ public class TestSurfacing { return false; } final HmmPfamOutputParser parser2 = new HmmPfamOutputParser( new File( test_dir - + ForesterUtil.getFileSeparator() + "hmmpfam_output_short" ), "human", "ls" ); + + ForesterUtil.getFileSeparator() + "hmmpfam_output_short" ), "human", "ls" ); parser2.setEValueMaximum( 0.2 ); parser2.setIgnoreDufs( true ); parser2.setReturnType( HmmPfamOutputParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN ); @@ -4718,7 +4718,7 @@ public class TestSurfacing { private static boolean testHmmPfamOutputParserWithFilter( final File test_dir ) { try { HmmPfamOutputParser parser = new HmmPfamOutputParser( new File( test_dir + ForesterUtil.getFileSeparator() - + "hmmpfam_output3" ), "human", "ls" ); + + "hmmpfam_output3" ), "human", "ls" ); parser.setEValueMaximum( 0.2 ); parser.setIgnoreDufs( true ); parser.setReturnType( HmmPfamOutputParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN ); diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java index 14c18ef..d6e508a 100644 --- a/forester/java/src/org/forester/test/Test.java +++ b/forester/java/src/org/forester/test/Test.java @@ -134,19 +134,19 @@ import org.forester.ws.wabi.TxSearch.TAX_RANK; public final class Test { private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" ) - + ForesterUtil.getFileSeparator() + "resources" - + ForesterUtil.getFileSeparator(); + + ForesterUtil.getFileSeparator() + "resources" + + ForesterUtil.getFileSeparator(); private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" ) - + ForesterUtil.getFileSeparator() + "test_data" - + ForesterUtil.getFileSeparator(); + + ForesterUtil.getFileSeparator() + "test_data" + + ForesterUtil.getFileSeparator(); private final static boolean PERFORM_DB_TESTS = false; private static final boolean PERFORM_WEB_TREE_ACCESS = true; private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/" - + ForesterConstants.PHYLO_XML_VERSION + "/" - + ForesterConstants.PHYLO_XML_XSD; + + ForesterConstants.PHYLO_XML_VERSION + "/" + + ForesterConstants.PHYLO_XML_XSD; private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/" - + ForesterConstants.PHYLO_XML_VERSION + "/" - + ForesterConstants.PHYLO_XML_XSD; + + ForesterConstants.PHYLO_XML_VERSION + "/" + + ForesterConstants.PHYLO_XML_XSD; private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true; private final static double ZERO_DIFF = 1.0E-9; @@ -157,7 +157,7 @@ public final class Test { public static void main( final String[] args ) { System.out.println( "[Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" ); System.out.println( "[OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " " + ForesterUtil.OS_VERSION - + "]" ); + + "]" ); Locale.setDefault( Locale.US ); System.out.println( "[Locale: " + Locale.getDefault() + "]" ); int failed = 0; @@ -181,9 +181,6 @@ public final class Test { System.exit( -1 ); } final long start_time = new Date().getTime(); - - - System.out.print( "MSA entropy: " ); if ( Test.testMsaEntropy() ) { System.out.println( "OK." ); @@ -1243,9 +1240,7 @@ public final class Test { System.out.println( phys[ 1 ].toNewHampshire() ); return false; } - final URL u2 = new URL( s ); - final Phylogeny[] phys2 = factory.create( u2.openStream(), new NHXParser() ); if ( ( phys2 == null ) || ( phys2.length != 5 ) ) { return false; @@ -1289,7 +1284,7 @@ public final class Test { } } catch ( final Exception e ) { - System.out.println( e.toString()); + System.out.println( e.toString() ); e.printStackTrace(); return false; } @@ -4630,17 +4625,17 @@ public final class Test { } if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) - .equals( "MOUSE" ) ) { + .equals( "MOUSE" ) ) { return false; } if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE+function = 23445", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) - .equals( "MOUSE" ) ) { + .equals( "MOUSE" ) ) { return false; } if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) - .equals( "MOUSE" ) ) { + .equals( "MOUSE" ) ) { return false; } if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445", @@ -5811,10 +5806,10 @@ public final class Test { final String test_dir = Test.PATH_TO_TEST_DATA; try { final HmmscanPerDomainTableParser parser1 = new HmmscanPerDomainTableParser( new File( test_dir - + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE ); + + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_1" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE ); parser1.parse(); final HmmscanPerDomainTableParser parser2 = new HmmscanPerDomainTableParser( new File( test_dir - + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE ); + + ForesterUtil.getFileSeparator() + "hmmscan30b3_output_2" ), "MONBR", INDIVIDUAL_SCORE_CUTOFF.NONE ); final List proteins = parser2.parse(); if ( parser2.getProteinsEncountered() != 4 ) { return false; @@ -7300,11 +7295,11 @@ public final class Test { return false; } if ( !isEqual( 0.48039661496919533, phylogenies[ 0 ].getNode( "Diadocidia_spinosula" ) - .getDistanceToParent() ) ) { + .getDistanceToParent() ) ) { return false; } if ( !isEqual( 0.3959796191512233, phylogenies[ 0 ].getNode( "Diadocidia_stanfordensis" ) - .getDistanceToParent() ) ) { + .getDistanceToParent() ) ) { return false; } if ( !phylogenies[ 0 ].getName().equals( "Family Diadocidiidae MLT (Imported_tree_0)" ) ) { @@ -8165,9 +8160,9 @@ public final class Test { final Phylogeny[] p11 = factory.create( "(A,B11);(C,D11) (E,F11)\t(G,H11)", new NHXParser() ); final Phylogeny[] p12 = factory.create( "(A,B12) (C,D12) (E,F12) (G,H12)", new NHXParser() ); final Phylogeny[] p13 = factory.create( " ; (;A; , ; B ; 1 3 ; \n)\t ( \n ;" - + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; " - + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;", - new NHXParser() ); + + " C ; ,; D;13;);;;;;;(;E;,;F;13 ;) ; " + + "; ; ( \t\n\r\b; G ;, ;H ;1 3; ) ; ; ;", + new NHXParser() ); if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) { return false; } @@ -9010,7 +9005,7 @@ public final class Test { if ( !n7.toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) .equals( "'gks:dr-m4 \" ` `@:[]sadq04'" ) ) { System.out.println( n7 - .toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) ); + .toNewHampshire( true, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ) ); return false; } } @@ -9493,15 +9488,15 @@ public final class Test { } final Phylogeny p2 = factory .create( "(1[something_else(?)s,prob=0.9500000000000000e+00{}(((,p)rob_stddev=0.110000000000e+00," - + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\"," - + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02," - + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02," - + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00," - + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\"," - + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02," - + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02," - + "7.369400000000000e-02}])", - new NHXParser() )[ 0 ]; + + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\"," + + "prob+-sd=\"100+-0\"]:4.129000000000000e-02[&length_mean=4.153987461671767e-02," + + "length_median=4.129000000000000e-02,length_95%HPD={3.217800000000000e-02," + + "5.026800000000000e-02}],2[&prob=0.810000000000000e+00,prob_stddev=0.000000000000000e+00," + + "prob_range={1.000000000000000e+00,1.000000000000000e+00},prob(percent)=\"100\"," + + "prob+-sd=\"100+-0\"]:6.375699999999999e-02[&length_mean=6.395210411945065e-02," + + "length_median=6.375699999999999e-02,length_95%HPD={5.388600000000000e-02," + + "7.369400000000000e-02}])", + new NHXParser() )[ 0 ]; if ( p2.getNode( "1" ) == null ) { return false; } @@ -10632,13 +10627,13 @@ public final class Test { // J. of Comput Bio. Vol. 4, No 2, pp.177-187 final Phylogeny species6 = factory .create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2," - + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)", - new NHXParser() )[ 0 ]; + + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)", + new NHXParser() )[ 0 ]; final Phylogeny gene6 = factory .create( "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1,3:0.1[&&NHX:S=3])1-2-3:0.1," - + "((4:0.1[&&NHX:S=4],(5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.1)4-5-6:0.1," - + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],9:0.1[&&NHX:S=9])8-9:0.1)7-8-9:0.1)4-5-6-7-8-9:0.1)r;", - new NHXParser() )[ 0 ]; + + "((4:0.1[&&NHX:S=4],(5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.1)4-5-6:0.1," + + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8],9:0.1[&&NHX:S=9])8-9:0.1)7-8-9:0.1)4-5-6-7-8-9:0.1)r;", + new NHXParser() )[ 0 ]; species6.setRooted( true ); gene6.setRooted( true ); final SDI sdi6 = new SDI( gene6, species6 ); @@ -10972,15 +10967,15 @@ public final class Test { } final Phylogeny species6 = factory .create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2," - + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)", - new NHXParser() )[ 0 ]; + + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)", + new NHXParser() )[ 0 ]; final Phylogeny gene6 = factory .create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4]," - + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2]," - + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8]," - + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])" - + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])", - new NHXParser() )[ 0 ]; + + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2]," + + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8]," + + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])" + + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])", + new NHXParser() )[ 0 ]; species6.setRooted( true ); gene6.setRooted( true ); Phylogeny[] p6 = sdi_unrooted.infer( gene6, species6, false, true, true, true, 10 ); @@ -11026,15 +11021,15 @@ public final class Test { p6 = null; final Phylogeny species7 = factory .create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2," - + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)", - new NHXParser() )[ 0 ]; + + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)", + new NHXParser() )[ 0 ]; final Phylogeny gene7 = factory .create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4]," - + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2]," - + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8]," - + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])" - + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])", - new NHXParser() )[ 0 ]; + + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2]," + + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8]," + + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])" + + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])", + new NHXParser() )[ 0 ]; species7.setRooted( true ); gene7.setRooted( true ); Phylogeny[] p7 = sdi_unrooted.infer( gene7, species7, true, true, true, true, 10 ); @@ -11080,15 +11075,15 @@ public final class Test { p7 = null; final Phylogeny species8 = factory .create( "(((1:[&&NHX:S=1],5:[&&NHX:S=5])1-5,((4:[&&NHX:S=4],6:[&&NHX:S=6])4-6,2:[&&NHX:S=2])4-6-2)1-5-4-6-2," - + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)", - new NHXParser() )[ 0 ]; + + "((9:[&&NHX:S=9],3:[&&NHX:S=3])9-3,(8:[&&NHX:S=8],7:[&&NHX:S=7])8-7)9-3-8-7)", + new NHXParser() )[ 0 ]; final Phylogeny gene8 = factory .create( "((5:0.1[&&NHX:S=5],6:0.1[&&NHX:S=6])5-6:0.05[&&NHX:S=6],(4:0.1[&&NHX:S=4]," - + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2]," - + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8]," - + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])" - + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])", - new NHXParser() )[ 0 ]; + + "(((1:0.1[&&NHX:S=1],2:0.1[&&NHX:S=2])1-2:0.1[&&NHX:S=2],3:0.25[&&NHX:S=3])1-2-3:0.2[&&NHX:S=2]," + + "(7:0.1[&&NHX:S=7],(8:0.1[&&NHX:S=8]," + + "9:0.1[&&NHX:S=9])8-9:0.1[&&NHX:S=9])7-8-9:0.1[&&NHX:S=8])" + + "4-5-6-7-8-9:0.1[&&NHX:S=5])4-5-6:0.05[&&NHX:S=5])", + new NHXParser() )[ 0 ]; species8.setRooted( true ); gene8.setRooted( true ); Phylogeny[] p8 = sdi_unrooted.infer( gene8, species8, false, false, true, true, 10 ); @@ -12231,24 +12226,24 @@ public final class Test { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); final Phylogeny t0_1 = factory.create( "(((A,B),C),(D,E))", new NHXParser() )[ 0 ]; final Phylogeny[] phylogenies_1 = factory.create( "(((A,B),C),(D,E)) " + "(((C,B),A),(D,E))" - + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))" - + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))" - + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))" - + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))", - new NHXParser() ); + + "(((A,B),C),(D,E)) " + "(((A,B),C),(D,E))" + + "(((A,B),C),(D,E))" + "(((C,B),A),(D,E))" + + "(((E,B),D),(C,A))" + "(((C,B),A),(D,E))" + + "(((A,B),C),(D,E))" + "(((A,B),C),(D,E))", + new NHXParser() ); SupportCount.count( t0_1, phylogenies_1, true, false ); final Phylogeny t0_2 = factory.create( "(((((A,B),C),D),E),(F,G))", new NHXParser() )[ 0 ]; final Phylogeny[] phylogenies_2 = factory.create( "(((((A,B),C),D),E),(F,G))" - + "(((((A,B),C),D),E),((F,G),X))" - + "(((((A,Y),B),C),D),((F,G),E))" - + "(((((A,B),C),D),E),(F,G))" - + "(((((A,B),C),D),E),(F,G))" - + "(((((A,B),C),D),E),(F,G))" - + "(((((A,B),C),D),E),(F,G),Z)" - + "(((((A,B),C),D),E),(F,G))" - + "((((((A,B),C),D),E),F),G)" - + "(((((X,Y),F,G),E),((A,B),C)),D)", - new NHXParser() ); + + "(((((A,B),C),D),E),((F,G),X))" + + "(((((A,Y),B),C),D),((F,G),E))" + + "(((((A,B),C),D),E),(F,G))" + + "(((((A,B),C),D),E),(F,G))" + + "(((((A,B),C),D),E),(F,G))" + + "(((((A,B),C),D),E),(F,G),Z)" + + "(((((A,B),C),D),E),(F,G))" + + "((((((A,B),C),D),E),F),G)" + + "(((((X,Y),F,G),E),((A,B),C)),D)", + new NHXParser() ); SupportCount.count( t0_2, phylogenies_2, true, false ); final PhylogenyNodeIterator it = t0_2.iteratorPostorder(); while ( it.hasNext() ) { diff --git a/forester/java/src/org/forester/tools/ConfidenceAssessor.java b/forester/java/src/org/forester/tools/ConfidenceAssessor.java index 2dc710c..18c9307 100644 --- a/forester/java/src/org/forester/tools/ConfidenceAssessor.java +++ b/forester/java/src/org/forester/tools/ConfidenceAssessor.java @@ -90,7 +90,7 @@ public final class ConfidenceAssessor { for( final Confidence confidence : confidences ) { if ( confidence.getType().equals( confidence_type ) ) { throw new IllegalArgumentException( "confidence [" + confidence_type - + "] is already present in target" ); + + "] is already present in target" ); } } } @@ -128,9 +128,9 @@ public final class ConfidenceAssessor { if ( strict ) { if ( evaluator.getNumberOfExternalNodes() != target.getNumberOfExternalNodes() ) { throw new IllegalArgumentException( "evaluator #" + counter - + " does not have the same number of external nodes [" - + evaluator.getNumberOfExternalNodes() + "] than the corresponding target [" - + target.getNumberOfExternalNodes() + "]" ); + + " does not have the same number of external nodes [" + + evaluator.getNumberOfExternalNodes() + "] than the corresponding target [" + + target.getNumberOfExternalNodes() + "]" ); } } final TreeSplitMatrix s = new TreeSplitMatrix( evaluator, strict, target ); diff --git a/forester/java/src/org/forester/tools/PhylogenyDecorator.java b/forester/java/src/org/forester/tools/PhylogenyDecorator.java index a44115c..8aa59d8 100644 --- a/forester/java/src/org/forester/tools/PhylogenyDecorator.java +++ b/forester/java/src/org/forester/tools/PhylogenyDecorator.java @@ -87,14 +87,14 @@ public final class PhylogenyDecorator { && new_values.containsKey( TP_TAXONOMY_ID_PROVIDER ) ) { ForesterUtil.ensurePresenceOfTaxonomy( node ); node.getNodeData() - .getTaxonomy() - .setIdentifier( new Identifier( new_values.get( TP_TAXONOMY_ID ), - new_values.get( TP_TAXONOMY_ID_PROVIDER ) ) ); + .getTaxonomy() + .setIdentifier( new Identifier( new_values.get( TP_TAXONOMY_ID ), + new_values.get( TP_TAXONOMY_ID_PROVIDER ) ) ); } else if ( new_values.containsKey( TP_TAXONOMY_ID ) ) { ForesterUtil.ensurePresenceOfTaxonomy( node ); node.getNodeData().getTaxonomy() - .setIdentifier( new Identifier( new_values.get( TP_TAXONOMY_ID ) ) ); + .setIdentifier( new Identifier( new_values.get( TP_TAXONOMY_ID ) ) ); } if ( new_values.containsKey( TP_TAXONOMY_SN ) ) { ForesterUtil.ensurePresenceOfTaxonomy( node ); @@ -112,9 +112,9 @@ public final class PhylogenyDecorator { && new_values.containsKey( TP_SEQ_ACCESSION_SOURCE ) ) { ForesterUtil.ensurePresenceOfSequence( node ); node.getNodeData() - .getSequence() - .setAccession( new Accession( new_values.get( TP_SEQ_ACCESSION ), - new_values.get( TP_SEQ_ACCESSION_SOURCE ) ) ); + .getSequence() + .setAccession( new Accession( new_values.get( TP_SEQ_ACCESSION ), + new_values.get( TP_SEQ_ACCESSION_SOURCE ) ) ); } if ( new_values.containsKey( TP_SEQ_ANNOTATION_DESC ) ) { ForesterUtil.ensurePresenceOfSequence( node ); @@ -142,7 +142,7 @@ public final class PhylogenyDecorator { if ( new_values.containsKey( TP_NODE_NAME ) ) { node.setName( new_values.get( TP_NODE_NAME ) ); } - } // if ( new_values != null ) + } // if ( new_values != null ) } // if ( map.containsKey( name ) || ( numbers_of_chars_allowed_to_remove_if_not_found_in_map > 0 ) ) else if ( picky ) { throw new IllegalArgumentException( "\"" + name + "\" not found in name map" ); @@ -160,7 +160,7 @@ public final class PhylogenyDecorator { final boolean cut_name_after_space, final boolean trim_after_tilde, final boolean verbose ) throws IllegalArgumentException, NHXFormatException, - PhyloXmlDataFormatException { + PhyloXmlDataFormatException { return PhylogenyDecorator.decorate( phylogeny, map, field, @@ -174,9 +174,9 @@ public final class PhylogenyDecorator { } /** - * - * - * + * + * + * * @param phylogeny * @param map * maps names (in phylogeny) to new values if intermediate_map is @@ -186,7 +186,7 @@ public final class PhylogenyDecorator { * @param intermediate_map * maps name (in phylogeny) to a intermediate value * @throws IllegalArgumentException - * @throws PhyloXmlDataFormatException + * @throws PhyloXmlDataFormatException */ public static String decorate( final Phylogeny phylogeny, final Map map, @@ -255,7 +255,7 @@ public final class PhylogenyDecorator { } else if ( picky ) { throw new IllegalArgumentException( " could not get taxonomy from \"" + new_value - + "\"" ); + + "\"" ); } } switch ( field ) { @@ -299,7 +299,7 @@ public final class PhylogenyDecorator { node.getNodeData().setSequence( new Sequence() ); } node.getNodeData().getSequence() - .setDomainArchitecture( new DomainArchitecture( new_value ) ); + .setDomainArchitecture( new DomainArchitecture( new_value ) ); break; case TAXONOMY_CODE: if ( verbose ) { @@ -359,7 +359,7 @@ public final class PhylogenyDecorator { } } return "updated " + ext_nodes_updated + "/" + ext_nodes + " external nodes, updated " + int_nodes_updated + "/" - + int_nodes + " internal nodes"; + + int_nodes + " internal nodes"; } public static Map> parseMappingTable( final File mapping_table_file ) diff --git a/forester/java/src/org/forester/tools/SupportCount.java b/forester/java/src/org/forester/tools/SupportCount.java index 283668c..d68a516 100644 --- a/forester/java/src/org/forester/tools/SupportCount.java +++ b/forester/java/src/org/forester/tools/SupportCount.java @@ -40,8 +40,8 @@ import org.forester.phylogeny.iterators.PhylogenyNodeIterator; /* * A simple class containing a static method to evaluate the topology of a given * phylogeny with a list of resampled phylogenies. - * - * + * + * * @author Christian M Zmasek */ public final class SupportCount { @@ -74,18 +74,18 @@ public final class SupportCount { } /** - * + * * Precondition: phylogeny and evaluator_phylogeny have to be rooted in the * same manner. - * + * * Returns a measure of the similarity ("average bootstrap similarity") * between the topologies of phylogeny and evaluator_phylogeny: (sum of * branches which divide phylogeny in a manner consitent with * evaluator_phylogeny)/sum of branches in phylogeny. Therefore, this * measure is 1.0 for indentical topologies and 0.0 for completely * incompatible topologies. - * - * + * + * * @param phylogeny * @param evaluator_phylogeny * @param external_names_per_node @@ -160,7 +160,7 @@ public final class SupportCount { * phylogenies. If phylogenies contains topogies with names not present in * phylogeny, strip_phylogenies must be set to true. phylogeny must not * contain names not found in all phylogenies. - * + * * @param phylogeny * the topology to be evaluated * @param evaluator_phylogenies diff --git a/forester/java/src/org/forester/tools/TreeSplitMatrix.java b/forester/java/src/org/forester/tools/TreeSplitMatrix.java index 58d6eb6..7b00eb2 100644 --- a/forester/java/src/org/forester/tools/TreeSplitMatrix.java +++ b/forester/java/src/org/forester/tools/TreeSplitMatrix.java @@ -68,8 +68,8 @@ public class TreeSplitMatrix { /** * If strict is true, target nodes (all external nodes of the phylogeny for * which support values are to be calculated) is not used for anything during construction. - * - * + * + * * @param target * @param evaluator * @param strict diff --git a/forester/java/src/org/forester/util/BasicDescriptiveStatistics.java b/forester/java/src/org/forester/util/BasicDescriptiveStatistics.java index 057b388..f3dfb80 100644 --- a/forester/java/src/org/forester/util/BasicDescriptiveStatistics.java +++ b/forester/java/src/org/forester/util/BasicDescriptiveStatistics.java @@ -306,7 +306,7 @@ public class BasicDescriptiveStatistics implements DescriptiveStatistics { * Computes the sample standard unit (z-score). Used to compute 'value' in * terms of standard units. Note that 'value', 'mean' and 'sd' must be all * from the same sample data. - * + * * @param value * a double in the sample for which * @param mean diff --git a/forester/java/src/org/forester/util/BasicTableParser.java b/forester/java/src/org/forester/util/BasicTableParser.java index 4e5f4b3..8d7f887 100644 --- a/forester/java/src/org/forester/util/BasicTableParser.java +++ b/forester/java/src/org/forester/util/BasicTableParser.java @@ -61,7 +61,7 @@ public class BasicTableParser { final boolean use_last_separator_only, final String start_of_comment_line, final boolean tables_separated_by_single_string_line ) - throws IOException { + throws IOException { if ( use_first_separator_only && use_last_separator_only ) { throw new IllegalArgumentException(); } @@ -77,7 +77,7 @@ public class BasicTableParser { if ( !ForesterUtil.isEmpty( line ) && ( ( ( line.charAt( 0 ) == '"' ) && ( line.charAt( line.length() - 1 ) == '"' ) && ( ForesterUtil .countChars( line, '"' ) == 2 ) ) || ( ( line.charAt( 0 ) == '\'' ) - && ( line.charAt( line.length() - 1 ) == '\'' ) && ( ForesterUtil.countChars( line, '\'' ) == 2 ) ) ) ) { + && ( line.charAt( line.length() - 1 ) == '\'' ) && ( ForesterUtil.countChars( line, '\'' ) == 2 ) ) ) ) { line = line.substring( 1, line.length() - 1 ).trim(); } if ( saw_first_table diff --git a/forester/java/src/org/forester/util/CommandLineArguments.java b/forester/java/src/org/forester/util/CommandLineArguments.java index efbce62..f75eb69 100644 --- a/forester/java/src/org/forester/util/CommandLineArguments.java +++ b/forester/java/src/org/forester/util/CommandLineArguments.java @@ -106,7 +106,7 @@ public final class CommandLineArguments { /** * Removes quotes - * + * */ public String getOptionValueAsCleanString( final String option_name ) throws IllegalArgumentException { return getOptionValue( option_name ).replaceAll( "\"", "" ).replaceAll( "\'", "" ); @@ -224,7 +224,7 @@ public final class CommandLineArguments { // } if ( getAllOptions().containsKey( key ) ) { throw new IllegalArgumentException( "attempt to set option \"" + key + "\" mutiple times [" + option - + "]" ); + + "]" ); } options_map.put( key, value ); } diff --git a/forester/java/src/org/forester/util/CommandProcessBuilder.java b/forester/java/src/org/forester/util/CommandProcessBuilder.java index b5887a8..3236838 100644 --- a/forester/java/src/org/forester/util/CommandProcessBuilder.java +++ b/forester/java/src/org/forester/util/CommandProcessBuilder.java @@ -36,7 +36,7 @@ import java.util.List; public class CommandProcessBuilder { public static Process execute( final List command, final File working_dir ) throws InterruptedException, - IOException { + IOException { final ProcessBuilder builder = new ProcessBuilder( command ); if ( working_dir != null ) { if ( !working_dir.exists() ) { diff --git a/forester/java/src/org/forester/util/DescriptiveStatistics.java b/forester/java/src/org/forester/util/DescriptiveStatistics.java index beeade9..2788b47 100644 --- a/forester/java/src/org/forester/util/DescriptiveStatistics.java +++ b/forester/java/src/org/forester/util/DescriptiveStatistics.java @@ -40,7 +40,7 @@ public interface DescriptiveStatistics { /** * Computes the coefficient of variation. Used to express standard deviation * independent of units of measure. - * + * * @return */ public abstract double coefficientOfVariation(); @@ -68,7 +68,7 @@ public interface DescriptiveStatistics { /** * Determines relationship between the mean and the median. This reflects * how the data differs from the normal bell shaped distribution. - * + * * @return */ public abstract double pearsonianSkewness(); diff --git a/forester/java/src/org/forester/util/FailedConditionCheckException.java b/forester/java/src/org/forester/util/FailedConditionCheckException.java index 82c65c1..23eef6d 100644 --- a/forester/java/src/org/forester/util/FailedConditionCheckException.java +++ b/forester/java/src/org/forester/util/FailedConditionCheckException.java @@ -29,7 +29,7 @@ package org.forester.util; public class FailedConditionCheckException extends RuntimeException { /** - * + * */ private static final long serialVersionUID = -860013990231493438L; diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java index 8d36a6e..b3eb0f2 100644 --- a/forester/java/src/org/forester/util/ForesterUtil.java +++ b/forester/java/src/org/forester/util/ForesterUtil.java @@ -115,13 +115,13 @@ public final class ForesterUtil { * This calculates a color. If value is equal to min the returned color is * minColor, if value is equal to max the returned color is maxColor, * otherwise a color 'proportional' to value is returned. - * + * * @param value - * the value + * the value * @param min - * the smallest value + * the smallest value * @param max - * the largest value + * the largest value * @param minColor * the color for min * @param maxColor @@ -152,15 +152,15 @@ public final class ForesterUtil { * value is equal to mean the returned color is meanColor, otherwise a color * 'proportional' to value is returned -- either between min-mean or * mean-max - * + * * @param value * the value * @param min * the smallest value * @param max - * the largest value + * the largest value * @param mean - * the mean/median value + * the mean/median value * @param minColor * the color for min * @param maxColor @@ -203,7 +203,7 @@ public final class ForesterUtil { /** * Helper method for calcColor methods. - * + * * @param smallercolor_component_x * color component the smaller color * @param largercolor_component_x @@ -220,8 +220,8 @@ public final class ForesterUtil { /** * Helper method for calcColor methods. - * - * + * + * * @param value * the value * @param larger @@ -583,7 +583,7 @@ public final class ForesterUtil { /** * Returns true is Domain domain falls in an uninterrupted stretch of * covered positions. - * + * * @param domain * @param covered_positions * @return @@ -609,7 +609,7 @@ public final class ForesterUtil { * This determines whether String[] a and String[] b have at least one * String in common (intersect). Returns false if at least one String[] is * null or empty. - * + * * @param a * a String[] b a String[] * @return true if both a and b or not empty or null and contain at least @@ -969,7 +969,7 @@ public final class ForesterUtil { } else { throw new IllegalArgumentException( "attempt to parse object of type [" + source.getClass() - + "] (can only parse objects of type File, InputStream, String, or StringBuffer)" ); + + "] (can only parse objects of type File, InputStream, String, or StringBuffer)" ); } return reader; } @@ -1113,16 +1113,16 @@ public final class ForesterUtil { } /** - * + * * Example regarding engulfment: ------------0.1 ----------0.2 --0.3 => * domain with 0.3 is ignored - * + * * -----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored - * - * + * + * * ------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_ * ignored - * + * * @param max_allowed_overlap * maximal allowed overlap (inclusive) to be still considered not * overlapping (zero or negative value to allow any overlap) @@ -1136,7 +1136,7 @@ public final class ForesterUtil { final boolean remove_engulfed_domains, final Protein protein ) { final Protein pruned_protein = new BasicProtein( protein.getProteinId().getId(), protein.getSpecies() - .getSpeciesId(), protein.getLength() ); + .getSpeciesId(), protein.getLength() ); final List sorted = SurfacingUtil.sortDomainsWithAscendingConfidenceValues( protein ); final List covered_positions = new ArrayList(); for( final Domain domain : sorted ) { @@ -1171,7 +1171,7 @@ public final class ForesterUtil { /** * Removes all white space from String s. - * + * * @return String s with white space removed */ final public static String removeWhiteSpace( String s ) { @@ -1342,7 +1342,7 @@ public final class ForesterUtil { final public static void unexpectedFatalError( final String prg_name, final Exception e ) { System.err.println(); System.err.println( "[" + prg_name - + "] > unexpected error; should not have occured! Please contact program author(s)." ); + + "] > unexpected error; should not have occured! Please contact program author(s)." ); e.printStackTrace( System.err ); System.err.println(); System.exit( -1 ); @@ -1351,7 +1351,7 @@ public final class ForesterUtil { final public static void unexpectedFatalError( final String prg_name, final String message ) { System.err.println(); System.err.println( "[" + prg_name - + "] > unexpected error: should not have occured! Please contact program author(s)." ); + + "] > unexpected error: should not have occured! Please contact program author(s)." ); System.err.println( message ); System.err.println(); System.exit( -1 ); @@ -1360,7 +1360,7 @@ public final class ForesterUtil { final public static void unexpectedFatalError( final String prg_name, final String message, final Exception e ) { System.err.println(); System.err.println( "[" + prg_name - + "] > unexpected error: should not have occured! Please contact program author(s)." ); + + "] > unexpected error: should not have occured! Please contact program author(s)." ); System.err.println( message ); e.printStackTrace( System.err ); System.err.println(); diff --git a/forester/java/src/org/forester/util/IllegalFormatUseException.java b/forester/java/src/org/forester/util/IllegalFormatUseException.java index 6580cf9..6b47e68 100644 --- a/forester/java/src/org/forester/util/IllegalFormatUseException.java +++ b/forester/java/src/org/forester/util/IllegalFormatUseException.java @@ -28,7 +28,7 @@ package org.forester.util; public class IllegalFormatUseException extends IllegalArgumentException { /** - * + * */ private static final long serialVersionUID = -1126329548396073983L; diff --git a/forester/java/src/org/forester/util/SequenceAccessionTools.java b/forester/java/src/org/forester/util/SequenceAccessionTools.java index 3efcb2b..82bcae9 100644 --- a/forester/java/src/org/forester/util/SequenceAccessionTools.java +++ b/forester/java/src/org/forester/util/SequenceAccessionTools.java @@ -43,28 +43,28 @@ public final class SequenceAccessionTools { //Protein: 3 letters + 5 numerals //http://www.ncbi.nlm.nih.gov/Sequin/acc.html public final static Pattern GENBANK_NUC_PATTERN_1 = Pattern - .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" ); + .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" ); public final static Pattern GENBANK_NUC_PATTERN_2 = Pattern - .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}\\d{6}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" ); + .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}\\d{6}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" ); public final static Pattern GENBANK_PROT_PATTERN = Pattern - .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{3}\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" ); + .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{3}\\d{5}(?:\\.\\d+)?)(?:[^a-zA-Z0-9]|\\Z)" ); public final static Pattern GI_PATTERN = Pattern - .compile( "(?:\\b|_)(?:GI|gi)[|_=:](\\d+)(?:\\b|_)" ); + .compile( "(?:\\b|_)(?:GI|gi)[|_=:](\\d+)(?:\\b|_)" ); public final static String UNIPROT_KB_BASE_PATTERN_STR = "((?:[OPQ][0-9][A-Z0-9]{3}[0-9])|(?:[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}))"; public final static Pattern UNIPROT_KB_PATTERN_0 = Pattern.compile( "(?:\\b|_)" - + UNIPROT_KB_BASE_PATTERN_STR + "(?:\\b|_)" ); + + UNIPROT_KB_BASE_PATTERN_STR + "(?:\\b|_)" ); public final static Pattern UNIPROT_KB_PATTERN_1 = Pattern.compile( "(?:\\b|_)(?:sp|tr)[\\.|\\-_=/\\\\]" - + UNIPROT_KB_BASE_PATTERN_STR + "(?:\\b|_)" ); + + UNIPROT_KB_BASE_PATTERN_STR + "(?:\\b|_)" ); public final static Pattern UNIPROT_KB_PATTERN_2 = Pattern - .compile( "(?:\\b|_)(?:[A-Z0-9]{2,5}|" - + UNIPROT_KB_BASE_PATTERN_STR - + ")_(([A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA)(?:\\b|_)" ); + .compile( "(?:\\b|_)(?:[A-Z0-9]{2,5}|" + + UNIPROT_KB_BASE_PATTERN_STR + + ")_(([A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA)(?:\\b|_)" ); public final static Pattern ENSEMBL_PATTERN = Pattern.compile( "(?:\\b|_)(ENS[A-Z]*[0-9]+)(?:\\b|_)" ); - // RefSeq accession numbers can be distinguished from GenBank accessions + // RefSeq accession numbers can be distinguished from GenBank accessions // by their distinct prefix format of 2 characters followed by an - // underscore character ('_'). For example, a RefSeq protein accession is NP_015325. + // underscore character ('_'). For example, a RefSeq protein accession is NP_015325. private final static Pattern REFSEQ_PATTERN = Pattern - .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}_\\d{6,})(?:[^a-zA-Z0-9]|\\Z)" ); + .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}_\\d{6,})(?:[^a-zA-Z0-9]|\\Z)" ); private SequenceAccessionTools() { // Hiding the constructor. diff --git a/forester/java/src/org/forester/util/SystemCommandExecutor.java b/forester/java/src/org/forester/util/SystemCommandExecutor.java index 6160382..a4cdec5 100644 --- a/forester/java/src/org/forester/util/SystemCommandExecutor.java +++ b/forester/java/src/org/forester/util/SystemCommandExecutor.java @@ -3,28 +3,28 @@ * This class can be used to execute a system command from a Java application. * See the documentation for the public methods of this class for more * information. - * + * * Documentation for this class is available at this URL: - * + * * http://devdaily.com/java/java-processbuilder-process-system-exec - * + * * Copyright 2010 alvin j. alexander, devdaily.com. - * + * * This program is free software: you can redistribute it and/or modify it under * the terms of the GNU Lesser Public License as published by the Free Software * Foundation, either version 3 of the License, or (at your option) any later * version. - * + * * This program is distributed in the hope that it will be useful, but WITHOUT * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS * FOR A PARTICULAR PURPOSE. See the GNU Lesser Public License for more details. - * + * * You should have received a copy of the GNU Lesser Public License along with * this program. If not, see . - * + * * Please see the following page for the LGPL license: * http://www.gnu.org/licenses/lgpl.txt - * + * */ package org.forester.util; @@ -44,7 +44,7 @@ public class SystemCommandExecutor { /** * Pass in the system command you want to run as a List of Strings, as shown here: - * + * * List commands = new ArrayList(); * commands.add("/sbin/ping"); * commands.add("-c"); @@ -52,7 +52,7 @@ public class SystemCommandExecutor { * commands.add("www.google.com"); * SystemCommandExecutor commandExecutor = new SystemCommandExecutor(commands); * commandExecutor.executeCommand(); - * + * * Note: I've removed the other constructor that was here to support executing * the sudo command. I'll add that back in when I get the sudo command * working to the point where it won't hang when the given password is diff --git a/forester/java/src/org/forester/util/ThreadedStreamHandler.java b/forester/java/src/org/forester/util/ThreadedStreamHandler.java index a8a91e8..b5253eb 100644 --- a/forester/java/src/org/forester/util/ThreadedStreamHandler.java +++ b/forester/java/src/org/forester/util/ThreadedStreamHandler.java @@ -2,34 +2,34 @@ /** * This class is intended to be used with the SystemCommandExecutor class to let * users execute system commands from Java applications. - * + * * This class is based on work that was shared in a JavaWorld article named * "When System.exec() won't". That article is available at this url: - * + * * http://www.javaworld.com/javaworld/jw-12-2000/jw-1229-traps.html - * + * * Documentation for this class is available at this URL: - * + * * http://devdaily.com/java/java-processbuilder-process-system-exec - * - * + * + * * Copyright 2010 alvin j. alexander, devdaily.com. - * + * * This program is free software: you can redistribute it and/or modify it under * the terms of the GNU Lesser Public License as published by the Free Software * Foundation, either version 3 of the License, or (at your option) any later * version. - * + * * This program is distributed in the hope that it will be useful, but WITHOUT * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS * FOR A PARTICULAR PURPOSE. See the GNU Lesser Public License for more details. - * + * * You should have received a copy of the GNU Lesser Public License along with * this program. If not, see . - * + * * Please ee the following page for the LGPL license: * http://www.gnu.org/licenses/lgpl.txt - * + * */ package org.forester.util; @@ -54,7 +54,7 @@ class ThreadedStreamHandler extends Thread { * A simple constructor for when the sudo command is not necessary. * This constructor will just run the command you provide, without * running sudo before the command, and without expecting a password. - * + * * @param inputStream * @param streamType */ @@ -65,9 +65,9 @@ class ThreadedStreamHandler extends Thread { /** * Use this constructor when you want to invoke the 'sudo' command. * The outputStream must not be null. If it is, you'll regret it. :) - * + * * TODO this currently hangs if the admin password given for the sudo command is wrong. - * + * * @param inputStream * @param streamType * @param outputStream diff --git a/forester/java/src/org/forester/util/WindowsUtils.java b/forester/java/src/org/forester/util/WindowsUtils.java index b65d9fe..67dafa1 100644 --- a/forester/java/src/org/forester/util/WindowsUtils.java +++ b/forester/java/src/org/forester/util/WindowsUtils.java @@ -32,8 +32,8 @@ public class WindowsUtils { private static final String REGQUERY_UTIL = "reg query "; private static final String REGSTR_TOKEN = "REG_SZ"; private static final String DESKTOP_FOLDER_CMD = REGQUERY_UTIL - + "\"HKCU\\Software\\Microsoft\\Windows\\CurrentVersion\\" - + "Explorer\\Shell Folders\" /v DESKTOP"; + + "\"HKCU\\Software\\Microsoft\\Windows\\CurrentVersion\\" + + "Explorer\\Shell Folders\" /v DESKTOP"; private WindowsUtils() { } diff --git a/forester/java/src/org/forester/ws/seqdb/EbiDbEntry.java b/forester/java/src/org/forester/ws/seqdb/EbiDbEntry.java index df739ed..8c2ce9a 100644 --- a/forester/java/src/org/forester/ws/seqdb/EbiDbEntry.java +++ b/forester/java/src/org/forester/ws/seqdb/EbiDbEntry.java @@ -54,12 +54,12 @@ public final class EbiDbEntry implements SequenceDatabaseEntry { private String _tax_id; // TODO PUBMED 15798186 - //TODO (FEATURES) + //TODO (FEATURES) // source /db_xref="taxon:9606" - // gene 1..2881 - // /gene="RBM39" + // gene 1..2881 + // /gene="RBM39" // - // /db_xref="MIM:604739" + // /db_xref="MIM:604739" // CDS // /gene="RBM39" // /db_xref="MIM:604739" @@ -164,7 +164,7 @@ public final class EbiDbEntry implements SequenceDatabaseEntry { reference sequence was derived from DC346351.1, BC141835.1 and C75555.1. On Jun 16, 2011 this sequence version replaced gi:35493810. - + Summary: This gene encodes a member of the U2AF65 family of proteins. The encoded protein is found in the nucleus, where it co-localizes with core spliceosomal proteins. It has been shown to @@ -173,14 +173,14 @@ public final class EbiDbEntry implements SequenceDatabaseEntry { coregulator of the viral oncoprotein v-Rel. Multiple transcript variants have been observed for this gene. A related pseudogene has been identified on chromosome X. [provided by RefSeq, Aug 2011]. - + Transcript Variant: This variant (1) encodes the longest isoform (a, also called CC1.4). - + Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. - + ##Evidence-Data-START## Transcript exon combination :: BC141835.1, L10911.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support @@ -262,12 +262,12 @@ public final class EbiDbEntry implements SequenceDatabaseEntry { recorded" /note="N-acetylalanine; propagated from UniProtKB/Swiss-Prot (Q14498.2); acetylation site" - + exon 461..510 /gene="RBM39" /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2" /inference="alignment:Splign:1.39.8" - + exon 1902..2874 /gene="RBM39" /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2" @@ -287,23 +287,23 @@ public final class EbiDbEntry implements SequenceDatabaseEntry { /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2" /standard_name="REN58785" /db_xref="UniSTS:383585" - + polyA_signal 2851..2856 /gene="RBM39" /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2" polyA_site 2874 /gene="RBM39" /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2" - ORIGIN + ORIGIN 1 atttggagct tggggcagct tctcgcgaga gcccgtgctg agggctctgt gaggccccgt 61 gtgtttgtgt gtgtgtatgt gtgctggtga atgtgagtac agggaagcag cggccgccat 121 ttcagggagc ttgtcgacgc tgtcgcaggg gtggatcctg agctgccgaa gccgccgtcc 181 tgctctcccg cgtgggcttc tctaattcca ttgttttttt tagattctct cgggcctagc 241 cgtccttgga acccgatatt cgggctgggc ggttccgcgg cctgggccta ggggcttaac - - - - */ + + + + */ private EbiDbEntry() { } diff --git a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java index 606d35a..9106c38 100644 --- a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java +++ b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java @@ -69,7 +69,7 @@ public final class SequenceDbWsTools { public static List getTaxonomiesFromCommonNameStrict( final String cn, final int max_taxonomies_return ) - throws IOException { + throws IOException { final List taxonomies = getTaxonomiesFromCommonName( cn, max_taxonomies_return ); if ( ( taxonomies != null ) && ( taxonomies.size() > 0 ) ) { final List filtered_taxonomies = new ArrayList(); @@ -96,11 +96,11 @@ public final class SequenceDbWsTools { * Does not return "sub-types". * For example, for "Mus musculus" only returns "Mus musculus" * and not "Mus musculus", "Mus musculus bactrianus", ... - * + * */ public static List getTaxonomiesFromScientificNameStrict( final String sn, final int max_taxonomies_return ) - throws IOException { + throws IOException { final List taxonomies = getTaxonomiesFromScientificName( sn, max_taxonomies_return ); if ( ( taxonomies != null ) && ( taxonomies.size() > 0 ) ) { final List filtered_taxonomies = new ArrayList(); @@ -116,7 +116,7 @@ public final class SequenceDbWsTools { public static List getTaxonomiesFromTaxonomyCode( final String code, final int max_taxonomies_return ) - throws IOException { + throws IOException { final String my_code = new String( code ); final List result = getTaxonomyStringFromTaxonomyCode( my_code, max_taxonomies_return ); if ( result.size() > 0 ) { @@ -142,7 +142,7 @@ public final class SequenceDbWsTools { final Accession acc = SequenceAccessionTools.parseAccessorFromString( acc_str ); if ( acc == null ) { throw new IllegalArgumentException( "could not extract acceptable sequence db accessor from \"" + acc_str - + "\"" ); + + "\"" ); } if ( acc.getSource().equals( Source.REFSEQ.toString() ) || acc.getSource().equals( Source.EMBL.toString() ) || acc.getSource().equals( Source.NCBI.toString() ) ) { @@ -153,7 +153,7 @@ public final class SequenceDbWsTools { } else { throw new IllegalArgumentException( "don't know how to handle request for source \"" + acc.getSource() - + "\"" ); + + "\"" ); } } @@ -251,7 +251,7 @@ public final class SequenceDbWsTools { } in.close(); try { - // To prevent accessing online dbs in too quick succession. + // To prevent accessing online dbs in too quick succession. Thread.sleep( SLEEP ); } catch ( final InterruptedException e ) { @@ -301,7 +301,7 @@ public final class SequenceDbWsTools { final int i_b = target.indexOf( b ); if ( ( i_a < 0 ) || ( i_b < i_a ) ) { throw new IllegalArgumentException( "attempt to extract from \"" + target + "\" between \"" + a - + "\" and \"" + b + "\"" ); + + "\" and \"" + b + "\"" ); } return target.substring( i_a + a.length(), i_b ).trim(); } @@ -455,7 +455,7 @@ public final class SequenceDbWsTools { private static List getTaxonomiesFromScientificName( final String sn, final int max_taxonomies_return ) - throws IOException { + throws IOException { final List result = getTaxonomyStringFromScientificName( sn, max_taxonomies_return ); if ( result.size() > 0 ) { return parseUniProtTaxonomy( result ); @@ -487,7 +487,7 @@ public final class SequenceDbWsTools { return ( !( ( acc == null ) || ForesterUtil.isEmpty( acc.getSource() ) || ForesterUtil.isEmpty( acc.getValue() ) || ( ( acc .getSource().equals( Source.UNIPROT.toString() ) ) && ( acc.getSource().toString().equals( Source.EMBL.toString() ) ) && ( acc.getSource().toString() - .equals( Source.REFSEQ.toString() ) ) ) ) ); + .equals( Source.REFSEQ.toString() ) ) ) ) ); } private static List parseUniProtTaxonomy( final List result ) throws IOException { diff --git a/forester/java/src/org/forester/ws/seqdb/UniProtEntry.java b/forester/java/src/org/forester/ws/seqdb/UniProtEntry.java index 77ebe4e..a3ea1e3 100644 --- a/forester/java/src/org/forester/ws/seqdb/UniProtEntry.java +++ b/forester/java/src/org/forester/ws/seqdb/UniProtEntry.java @@ -123,7 +123,7 @@ public final class UniProtEntry implements SequenceDatabaseEntry { && ForesterUtil.isEmpty( getTaxonomyScientificName() ) && ForesterUtil.isEmpty( getSequenceSymbol() ) && ForesterUtil.isEmpty( getGeneName() ) && ForesterUtil.isEmpty( getTaxonomyIdentifier() ) && ForesterUtil.isEmpty( getSequenceSymbol() ) && ( ( getGoTerms() == null ) || getGoTerms().isEmpty() ) && ( ( getCrossReferences() == null ) || getCrossReferences() - .isEmpty() ) ); + .isEmpty() ) ); } private void addCrossReference( final Accession accession ) { diff --git a/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java b/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java index c379607..09f869f 100644 --- a/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java +++ b/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java @@ -117,17 +117,17 @@ public final class UniProtTaxonomy { /** * Creates deep copy for all fields, except lineage. - * + * * @return */ public UniProtTaxonomy copy() { return new UniProtTaxonomy( getLineage(), getCode() != null ? new String( getCode() ) : null, - getCommonName() != null ? new String( getCommonName() ) : null, - getScientificName() != null ? new String( getScientificName() ) : null, - getSynonym() != null ? new String( getSynonym() ) : null, - getRank() != null ? new String( getRank() ) : null, - getId() != null ? new String( getId() ) : null ); + getCommonName() != null ? new String( getCommonName() ) : null, + getScientificName() != null ? new String( getScientificName() ) : null, + getSynonym() != null ? new String( getSynonym() ) : null, + getRank() != null ? new String( getRank() ) : null, + getId() != null ? new String( getId() ) : null ); } public String getCode() { diff --git a/forester/java/src/org/forester/ws/wabi/RestUtil.java b/forester/java/src/org/forester/ws/wabi/RestUtil.java index cce2569..2050c0e 100644 --- a/forester/java/src/org/forester/ws/wabi/RestUtil.java +++ b/forester/java/src/org/forester/ws/wabi/RestUtil.java @@ -36,7 +36,7 @@ import java.net.URLEncoder; import java.util.List; /** - * + * * This is to access the Web API for Biology (WABI) at DDBJ. * See: http://xml.nig.ac.jp/ * diff --git a/forester/java/src/org/forester/ws/wabi/TxSearch.java b/forester/java/src/org/forester/ws/wabi/TxSearch.java index 78ac76c..e96e592 100644 --- a/forester/java/src/org/forester/ws/wabi/TxSearch.java +++ b/forester/java/src/org/forester/ws/wabi/TxSearch.java @@ -31,12 +31,12 @@ import java.util.ArrayList; import java.util.List; /** - * + * * This is to access the Web API for Biology (WABI) at DDBJ. * See: http://xml.nig.ac.jp/ - * + * * Service Description: - * TXSearch is a retrieval system for a Taxonomy Database which + * TXSearch is a retrieval system for a Taxonomy Database which * was unified by DDBJ, GenBank and EMBL, which is developed by DDBJ. * See: http://xml.nig.ac.jp/wabi/Method?serviceName=TxSearch&mode=methodList * -- 1.7.10.2