import java.util.Set;
import org.forester.application.support_transfer;
+import org.forester.archaeopteryx.AptxUtil;
import org.forester.development.DevelopmentTools;
import org.forester.evoinference.TestPhylogenyReconstruction;
import org.forester.evoinference.matrix.character.CharacterStateMatrix;
import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
import org.forester.io.parsers.nhx.NHXParser;
import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
-import org.forester.io.parsers.nhx.NHXParser2;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
import org.forester.io.parsers.tol.TolParser;
import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.writers.PhylogenyWriter;
+import org.forester.io.writers.SequenceWriter;
import org.forester.msa.BasicMsa;
import org.forester.msa.Mafft;
import org.forester.msa.Msa;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
+import org.forester.phylogeny.data.Accession;
import org.forester.phylogeny.data.BinaryCharacters;
import org.forester.phylogeny.data.BranchWidth;
import org.forester.phylogeny.data.Confidence;
System.exit( -1 );
}
final long start_time = new Date().getTime();
+ System.out.print( "Sequence writer: " );
+ if ( testSequenceWriter() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
System.out.print( "Sequence id parsing: " );
if ( testSequenceIdParsing() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
+ System.out.print( "SN extraction: " );
+ if ( Test.testExtractSNFromNodeName() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
System.out.print( "Taxonomy extraction (general): " );
if ( Test.testTaxonomyExtraction() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
+ System.out.print( "UniProtKB id extraction: " );
+ if ( Test.testExtractUniProtKbProteinSeqIdentifier() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ System.out.print( "Uri for Aptx web sequence accession: " );
+ if ( Test.testCreateUriForSeqWeb() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
System.out.print( "Basic node construction and parsing of NHX (node level): " );
if ( Test.testNHXNodeParsing() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
+ System.out.print( "NHX parsing iterating: " );
+ if ( Test.testNHParsingIter() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
System.out.print( "NH parsing: " );
if ( Test.testNHParsing() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
- System.out.print( "NHX parsing iterating: " );
- if ( Test.testNHParsingIter() ) {
+ System.out.print( "Nexus characters parsing: " );
+ if ( Test.testNexusCharactersParsing() ) {
System.out.println( "OK." );
succeeded++;
}
System.out.println( "failed." );
failed++;
}
- System.exit( 0 );
- System.out.print( "Nexus characters parsing: " );
- if ( Test.testNexusCharactersParsing() ) {
+ System.out.print( "Nexus tree parsing iterating: " );
+ if ( Test.testNexusTreeParsingIterating() ) {
System.out.println( "OK." );
succeeded++;
}
System.out.println( "failed." );
failed++;
}
+ System.out.print( "Tree methods: " );
+ if ( Test.testTreeMethods() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
System.out.print( "Postorder Iterator: " );
if ( Test.testPostOrderIterator() ) {
System.out.println( "OK." );
}
}
+ private static boolean testExtractUniProtKbProteinSeqIdentifier() {
+ try {
+ PhylogenyNode n = new PhylogenyNode();
+ n.setName( "tr|B3RJ64" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ return false;
+ }
+ n.setName( "tr.B3RJ64" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ return false;
+ }
+ n.setName( "tr=B3RJ64" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ return false;
+ }
+ n.setName( "tr-B3RJ64" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ return false;
+ }
+ n.setName( "tr/B3RJ64" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ return false;
+ }
+ n.setName( "tr\\B3RJ64" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ return false;
+ }
+ n.setName( "tr_B3RJ64" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ return false;
+ }
+ n.setName( " tr|B3RJ64 " );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ return false;
+ }
+ n.setName( "-tr|B3RJ64-" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ return false;
+ }
+ n.setName( "-tr=B3RJ64-" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ return false;
+ }
+ n.setName( "_tr=B3RJ64_" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ return false;
+ }
+ n.setName( " tr_tr|B3RJ64_sp|123 " );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ return false;
+ }
+ n.setName( "sp|B3RJ64" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ return false;
+ }
+ n.setName( "ssp|B3RJ64" );
+ if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+ return false;
+ }
+ n.setName( "sp|B3RJ64C" );
+ if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+ return false;
+ }
+ n.setName( "sp B3RJ64" );
+ if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+ return false;
+ }
+ n.setName( "sp|B3RJ6X" );
+ if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+ return false;
+ }
+ n.setName( "sp|B3RJ6" );
+ if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+ return false;
+ }
+ n.setName( "K1PYK7_CRAGI" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_CRAGI" ) ) {
+ return false;
+ }
+ n.setName( "K1PYK7_PEA" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_PEA" ) ) {
+ return false;
+ }
+ n.setName( "K1PYK7_RAT" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_RAT" ) ) {
+ return false;
+ }
+ n.setName( "K1PYK7_PIG" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_PIG" ) ) {
+ return false;
+ }
+ n.setName( "~K1PYK7_PIG~" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_PIG" ) ) {
+ return false;
+ }
+ n.setName( "123456_ECOLI-K1PYK7_CRAGI-sp" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_CRAGI" ) ) {
+ return false;
+ }
+ n.setName( "K1PYKX_CRAGI" );
+ if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+ return false;
+ }
+ n.setName( "XXXXX_CRAGI" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "XXXXX_CRAGI" ) ) {
+ return false;
+ }
+ n.setName( "tr|H3IB65|H3IB65_STRPU~2-2" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "H3IB65" ) ) {
+ return false;
+ }
+ n.setName( "jgi|Lacbi2|181470|Lacbi1.estExt_GeneWisePlus_human.C_10729~2-3" );
+ if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+ return false;
+ }
+ n.setName( "sp|Q86U06|RBM23_HUMAN~2-2" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "Q86U06" ) ) {
+ return false;
+ }
+ n = new PhylogenyNode();
+ org.forester.phylogeny.data.Sequence seq = new org.forester.phylogeny.data.Sequence();
+ seq.setSymbol( "K1PYK7_CRAGI" );
+ n.getNodeData().addSequence( seq );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_CRAGI" ) ) {
+ return false;
+ }
+ seq.setSymbol( "tr|B3RJ64" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ return false;
+ }
+ n = new PhylogenyNode();
+ seq = new org.forester.phylogeny.data.Sequence();
+ seq.setName( "K1PYK7_CRAGI" );
+ n.getNodeData().addSequence( seq );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_CRAGI" ) ) {
+ return false;
+ }
+ seq.setName( "tr|B3RJ64" );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ return false;
+ }
+ n = new PhylogenyNode();
+ seq = new org.forester.phylogeny.data.Sequence();
+ seq.setAccession( new Accession( "K1PYK8_CRAGI", "?" ) );
+ n.getNodeData().addSequence( seq );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK8_CRAGI" ) ) {
+ return false;
+ }
+ n = new PhylogenyNode();
+ seq = new org.forester.phylogeny.data.Sequence();
+ seq.setAccession( new Accession( "tr|B3RJ64", "?" ) );
+ n.getNodeData().addSequence( seq );
+ if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ return false;
+ }
+ //
+ n = new PhylogenyNode();
+ n.setName( "ACP19736" );
+ if ( !ForesterUtil.extractGenbankAccessor( n ).equals( "ACP19736" ) ) {
+ return false;
+ }
+ n = new PhylogenyNode();
+ n.setName( "_ACP19736_" );
+ if ( !ForesterUtil.extractGenbankAccessor( n ).equals( "ACP19736" ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testCreateUriForSeqWeb() {
+ try {
+ final PhylogenyNode n = new PhylogenyNode();
+ n.setName( "tr|B3RJ64" );
+ if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B3RJ64" ) ) {
+ return false;
+ }
+ n.setName( "B0LM41_HUMAN" );
+ if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B0LM41_HUMAN" ) ) {
+ return false;
+ }
+ n.setName( "NP_001025424" );
+ if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "NP_001025424" ) ) {
+ return false;
+ }
+ n.setName( "_NM_001030253-" );
+ if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "NM_001030253" ) ) {
+ return false;
+ }
+ n.setName( "XM_002122186" );
+ if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "XM_002122186" ) ) {
+ return false;
+ }
+ n.setName( "dgh_AAA34956_gdg" );
+ if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
+ return false;
+ }
+ n.setName( "j40f4_Q06891.1_fndn2 fnr3" );
+ if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "Q06891.1" ) ) {
+ return false;
+ }
+ n.setName( "GI:394892" );
+ if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
+ System.out.println( AptxUtil.createUriForSeqWeb( n, null, null ) );
+ return false;
+ }
+ n.setName( "gi_394892" );
+ if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
+ System.out.println( AptxUtil.createUriForSeqWeb( n, null, null ) );
+ return false;
+ }
+ n.setName( "gi6335_gi_394892_56635_Gi_43" );
+ if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
+ System.out.println( AptxUtil.createUriForSeqWeb( n, null, null ) );
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testExtractSNFromNodeName() {
+ try {
+ if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus" ).equals( "Mus musculus" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus_musculus" )
+ .equals( "Mus musculus musculus" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "BCDO2_Mus_musculus_musculus-12" )
+ .equals( "Mus musculus musculus" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( " -XS12_Mus_musculus-12" ).equals( "Mus musculus" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( " -1234_Mus_musculus-12 affrre e" )
+ .equals( "Mus musculus" ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
private static boolean testExtractTaxonomyCodeFromNodeName() {
try {
- if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.YES ).equals( "MOUSE" ) ) {
+ if ( ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
+ return false;
+ }
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ .equals( "SOYBN" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ .equals( "ARATH" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " ARATH ", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ .equals( "ARATH" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.AGGRESSIVE ).equals( "RAT" ) ) {
return false;
}
- if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
+ if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
return false;
}
- if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.YES ) != null ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( " _SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ .equals( "SOYBN" ) ) {
return false;
}
- if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445", TAXONOMY_EXTRACTION.YES )
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ .equals( "SOYBN" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ .equals( "SOYBN" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty_SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ .equals( "SOYBN" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "ABCD_SOYBN ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
+ .equals( "SOYBN" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ .equals( "SOYBN" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( ",SOYBN,", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ .equals( "SOYBN" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "xxx,SOYBN,xxx", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ .equals( "SOYBN" ) ) {
+ return false;
+ }
+ if ( ParserUtils.extractTaxonomyCodeFromNodeName( "xxxSOYBNxxx", TAXONOMY_EXTRACTION.AGGRESSIVE ) != null ) {
+ return false;
+ }
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "-SOYBN~", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ .equals( "SOYBN" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "NNN8_ECOLI/1-2:0.01",
+ TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ).equals( "ECOLI" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "blag_9YX45-blag", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ .equals( "9YX45" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE function = 23445",
+ TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
.equals( "MOUSE" ) ) {
return false;
}
- if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE_function = 23445", TAXONOMY_EXTRACTION.YES )
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE+function = 23445",
+ TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
.equals( "MOUSE" ) ) {
return false;
}
- if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445", TAXONOMY_EXTRACTION.YES )
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE|function = 23445",
+ TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
.equals( "MOUSE" ) ) {
return false;
}
- if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
+ if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEfunction = 23445",
+ TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
return false;
}
- if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
+ if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSEFunction = 23445",
+ TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
return false;
}
- if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445", TAXONOMY_EXTRACTION.YES )
- .equals( "RAT" ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445",
+ TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
return false;
}
- if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT_function = 23445", TAXONOMY_EXTRACTION.YES )
- .equals( "RAT" ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445",
+ TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
return false;
}
- if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445", TAXONOMY_EXTRACTION.YES )
- .equals( "RAT" ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT|function = 23445",
+ TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
return false;
}
- if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
+ if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATfunction = 23445",
+ TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
return false;
}
- if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445", TAXONOMY_EXTRACTION.YES ) != null ) {
+ if ( ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RATFunction = 23445",
+ TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
return false;
}
- if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
+ .equals( "RAT" ) ) {
return false;
}
- if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY )
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_PIG/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT )
.equals( "PIG" ) ) {
return false;
}
- if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.YES )
+ if ( !ParserUtils
+ .extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
.equals( "MOUSE" ) ) {
return false;
}
- if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY )
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE/1-3", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT )
.equals( "MOUSE" ) ) {
return false;
}
+ if ( ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
+ return false;
+ }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
}
final PhylogenyNode n1 = new PhylogenyNode();
final PhylogenyNode n2 = PhylogenyNode
- .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ .createInstanceFromNhxString( "", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
final PhylogenyNode n3 = PhylogenyNode
- .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ .createInstanceFromNhxString( "n3", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
final PhylogenyNode n4 = PhylogenyNode
- .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ .createInstanceFromNhxString( "n4:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
if ( n1.isHasAssignedEvent() ) {
return false;
}
source.append( "40 41 42 43" + l );
source.append( " # 1 1 1 1 1 " + l );
source.append( "50 51 52 53 54" + l );
- final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), " " );
+ final BasicTable<String> t1 = BasicTableParser.parse( source.toString(), ' ' );
if ( t1.getNumberOfColumns() != 5 ) {
return false;
}
source1.append( "40;41;42;43" + l );
source1.append( " # 1 1 1 1 1 " + l );
source1.append( ";;;50 ; ;52; 53;;54 " + l );
- final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ";" );
+ final BasicTable<String> t2 = BasicTableParser.parse( source1.toString(), ';' );
if ( t2.getNumberOfColumns() != 5 ) {
return false;
}
source2.append( " comment: 1 1 1 1 1 " + l );
source2.append( ";;;50 ; 52; 53;;54 " + l );
final List<BasicTable<String>> tl = BasicTableParser.parse( source2.toString(),
- ";",
+ ';',
false,
false,
"comment:",
if ( t8.getHeight() != 15 ) {
return false;
}
- final char[] a9 = new char[] {};
+ final char[] a9 = new char[] { 'a' };
final Phylogeny t9 = factory.create( a9, new NHXParser() )[ 0 ];
if ( t9.getHeight() != 0 ) {
return false;
return true;
}
+ private static boolean testTreeMethods() {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)", new NHXParser() )[ 0 ];
+ PhylogenyMethods.collapseSubtreeStructure( t0.getNode( "abcd" ) );
+ if ( !t0.toNewHampshireX().equals( "((A,B,C,D)abcd,E)" ) ) {
+ System.out.println( t0.toNewHampshireX() );
+ return false;
+ }
+ final Phylogeny t1 = factory.create( "((((A:0.1,B)ab:0.2,C)abc:0.3,D)abcd:0.4,E)", new NHXParser() )[ 0 ];
+ PhylogenyMethods.collapseSubtreeStructure( t1.getNode( "abcd" ) );
+ if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 0.6 ) ) {
+ return false;
+ }
+ if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 0.5 ) ) {
+ return false;
+ }
+ if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 0.3 ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
private static boolean testConfidenceAssessor() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
return true;
}
- private static boolean testNexusTreeParsingTranslating() {
+ private static boolean testNexusTreeParsingIterating() {
try {
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
- Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
- if ( phylogenies.length != 1 ) {
+ final NexusPhylogeniesParser p = new NexusPhylogeniesParser();
+ p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_1.nex" );
+ if ( !p.hasNext() ) {
return false;
}
- if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
+ Phylogeny phy = p.next();
+ if ( phy == null ) {
return false;
}
- if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
+ if ( phy.getNumberOfExternalNodes() != 25 ) {
return false;
}
- if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
+ if ( !phy.getName().equals( "" ) ) {
return false;
}
- if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ if ( p.hasNext() ) {
return false;
}
- if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
- .equals( "Aranaeus" ) ) {
+ phy = p.next();
+ if ( phy != null ) {
return false;
}
- phylogenies = null;
- phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
- if ( phylogenies.length != 3 ) {
+ //
+ p.reset();
+ if ( !p.hasNext() ) {
return false;
}
- if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
+ phy = p.next();
+ if ( phy == null ) {
return false;
}
- if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
+ if ( phy.getNumberOfExternalNodes() != 25 ) {
return false;
}
- if ( phylogenies[ 0 ].isRooted() ) {
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy != null ) {
+ return false;
+ }
+ ////
+ p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_2.nex" );
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "name" ) ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy != null ) {
+ return false;
+ }
+ //
+ p.reset();
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "name" ) ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy != null ) {
+ return false;
+ }
+ ////
+ p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_3.nex" );
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( phy.isRooted() ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy != null ) {
+ return false;
+ }
+ //
+ p.reset();
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy != null ) {
+ return false;
+ }
+ ////
+ p.setSource( Test.PATH_TO_TEST_DATA + "nexus_test_4_1.nex" );
+ // if ( phylogenies.length != 18 ) {
+ // return false;
+ // }
+ //0
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 0" ) ) {
+ return false;
+ }
+ //1
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 1" ) ) {
+ return false;
+ }
+ //2
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( phy.isRooted() ) {
+ return false;
+ }
+ //3
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 4 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //4
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 5 ) {
+ System.out.println( phy.getNumberOfExternalNodes() );
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //5
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( phy.isRooted() ) {
+ return false;
+ }
+ //6
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 2 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //7
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //8
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.toNewHampshire().equals( "((AA,BB),CC);" ) ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 8" ) ) {
+ return false;
+ }
+ //9
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.toNewHampshire().equals( "((a,b),cc);" ) ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 9" ) ) {
+ return false;
+ }
+ //10
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 10" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //11
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.toNewHampshire().equals( "((1,2),3);" ) ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 11" ) ) {
+ return false;
+ }
+ if ( phy.isRooted() ) {
+ return false;
+ }
+ //12
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.toNewHampshire().equals( "((aa,bb),cc);" ) ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 12" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //13
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.toNewHampshire().equals( "((a,b),c);" ) ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 13" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //14
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ System.out.println( phy.getNumberOfExternalNodes() );
+ return false;
+ }
+ if ( !phy
+ .toNewHampshire()
+ .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
+ System.out.println( phy.toNewHampshire() );
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 14" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //15
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ System.out.println( phy.getNumberOfExternalNodes() );
+ return false;
+ }
+ if ( !phy
+ .toNewHampshire()
+ .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
+ System.out.println( phy.toNewHampshire() );
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 15" ) ) {
+ return false;
+ }
+ if ( phy.isRooted() ) {
+ return false;
+ }
+ //16
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ System.out.println( phy.getNumberOfExternalNodes() );
+ return false;
+ }
+ if ( !phy
+ .toNewHampshire()
+ .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
+ System.out.println( phy.toNewHampshire() );
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 16" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //17
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ System.out.println( phy.getNumberOfExternalNodes() );
+ return false;
+ }
+ if ( !phy
+ .toNewHampshire()
+ .equals( "(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.32368):0.103875):0.41354):0.254687):0.095341):0.079254):0.0;" ) ) {
+ System.out.println( phy.toNewHampshire() );
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 17" ) ) {
+ return false;
+ }
+ if ( phy.isRooted() ) {
+ return false;
+ }
+ //
+ if ( p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy != null ) {
+ return false;
+ }
+ p.reset();
+ //0
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 0" ) ) {
+ return false;
+ }
+ //1
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 10 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "tree 1" ) ) {
+ return false;
+ }
+ //2
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( phy.isRooted() ) {
+ return false;
+ }
+ //3
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 4 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //4
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 5 ) {
+ System.out.println( phy.getNumberOfExternalNodes() );
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( !phy.isRooted() ) {
+ return false;
+ }
+ //5
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ phy = p.next();
+ if ( phy == null ) {
+ return false;
+ }
+ if ( phy.getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phy.getName().equals( "" ) ) {
+ return false;
+ }
+ if ( phy.isRooted() ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testNexusTreeParsingTranslating() {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
+ Phylogeny[] phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_5.nex", parser );
+ if ( phylogenies.length != 1 ) {
+ return false;
+ }
+ if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
+ .equals( "Aranaeus" ) ) {
+ return false;
+ }
+ phylogenies = null;
+ phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_6.nex", parser );
+ if ( phylogenies.length != 3 ) {
+ return false;
+ }
+ if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
+ return false;
+ }
+ if ( phylogenies[ 0 ].isRooted() ) {
+ return false;
+ }
+ if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
+ .equals( "Aranaeus" ) ) {
+ return false;
+ }
+ if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
+ return false;
+ }
+ if ( phylogenies[ 1 ].isRooted() ) {
+ return false;
+ }
+ if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
+ .equals( "Aranaeus" ) ) {
+ return false;
+ }
+ if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 2 ].isRooted() ) {
+ return false;
+ }
+ if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
+ .equals( "Aranaeus" ) ) {
+ return false;
+ }
+ phylogenies = null;
+ phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
+ if ( phylogenies.length != 3 ) {
+ return false;
+ }
+ if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
+ return false;
+ }
+ if ( phylogenies[ 0 ].isRooted() ) {
return false;
}
if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
return false;
}
- if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
+ .equals( "Aranaeus" ) ) {
+ return false;
+ }
+ if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
+ return false;
+ }
+ if ( phylogenies[ 1 ].isRooted() ) {
+ return false;
+ }
+ if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
+ .equals( "Aranaeus" ) ) {
+ return false;
+ }
+ if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
+ return false;
+ }
+ if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 2 ].isRooted() ) {
+ return false;
+ }
+ if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ return false;
+ }
+ if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
+ .equals( "Aranaeus" ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testNHParsing() {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
+ if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
+ return false;
+ }
+ final NHXParser nhxp = new NHXParser();
+ nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
+ nhxp.setReplaceUnderscores( true );
+ final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
+ if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
+ return false;
+ }
+ if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
+ return false;
+ }
+ final Phylogeny p1b = factory
+ .create( " \n \t \b \r \f ; ( \n \t \b \r \f; A ; \n \t \b \r \f, \n \t \b \r \f; B ; \n \t \b \r \f 1 \n \t \b \r \f ; \n \t \b \r \f );;;;; \n \t \b \r \f;;; \n \t \b \r \f ",
+ new NHXParser() )[ 0 ];
+ if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
+ return false;
+ }
+ if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
+ return false;
+ }
+ final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
+ final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
+ final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
+ final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
+ final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
+ final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
+ final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
+ final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
+ 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() );
+ if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
+ return false;
+ }
+ if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
+ return false;
+ }
+ if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
+ return false;
+ }
+ if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
+ return false;
+ }
+ final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
+ final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
+ final String p16_S = "((A,B),C)";
+ final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
+ if ( p16.length != 1 ) {
+ return false;
+ }
+ if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
+ return false;
+ }
+ final String p17_S = "(C,(A,B))";
+ final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
+ if ( p17.length != 1 ) {
+ return false;
+ }
+ if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
+ return false;
+ }
+ final String p18_S = "((A,B),(C,D))";
+ final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
+ if ( p18.length != 1 ) {
+ return false;
+ }
+ if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
+ return false;
+ }
+ final String p19_S = "(((A,B),C),D)";
+ final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
+ if ( p19.length != 1 ) {
+ return false;
+ }
+ if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
+ return false;
+ }
+ final String p20_S = "(A,(B,(C,D)))";
+ final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
+ if ( p20.length != 1 ) {
+ return false;
+ }
+ if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
+ return false;
+ }
+ final String p21_S = "(A,(B,(C,(D,E))))";
+ final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
+ if ( p21.length != 1 ) {
+ return false;
+ }
+ if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
+ return false;
+ }
+ final String p22_S = "((((A,B),C),D),E)";
+ final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
+ if ( p22.length != 1 ) {
+ return false;
+ }
+ if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
+ return false;
+ }
+ final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
+ final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
+ if ( p23.length != 1 ) {
+ System.out.println( "xl=" + p23.length );
+ System.exit( -1 );
+ return false;
+ }
+ if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
+ return false;
+ }
+ final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
+ final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
+ if ( p24.length != 1 ) {
+ return false;
+ }
+ if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
+ return false;
+ }
+ final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
+ final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
+ final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
+ if ( p241.length != 2 ) {
+ return false;
+ }
+ if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
+ return false;
+ }
+ if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
+ return false;
+ }
+ final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
+ + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
+ + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
+ + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
+ + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
+ + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
+ + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
+ + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
+ final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
+ if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
+ return false;
+ }
+ final String p26_S = "(A,B)ab";
+ final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
+ if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
+ return false;
+ }
+ final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
+ final Phylogeny[] p27s = factory.create( p27_S, new NHXParser() );
+ if ( p27s.length != 1 ) {
+ System.out.println( "xxl=" + p27s.length );
+ System.exit( -1 );
+ return false;
+ }
+ if ( !p27s[ 0 ].toNewHampshireX().equals( p27_S ) ) {
+ System.out.println( p27s[ 0 ].toNewHampshireX() );
+ System.exit( -1 );
+ return false;
+ }
+ final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
+ new NHXParser() );
+ if ( p27.length != 1 ) {
+ System.out.println( "yl=" + p27.length );
+ System.exit( -1 );
+ return false;
+ }
+ if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
+ System.out.println( p27[ 0 ].toNewHampshireX() );
+ System.exit( -1 );
+ return false;
+ }
+ final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
+ final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
+ final String p28_S3 = "(A,B)ab";
+ final String p28_S4 = "((((A,B),C),D),;E;)";
+ final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
+ new NHXParser() );
+ if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
+ return false;
+ }
+ if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
+ return false;
+ }
+ if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
+ return false;
+ }
+ if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
+ return false;
+ }
+ if ( p28.length != 4 ) {
+ return false;
+ }
+ final String p29_S = "((((A:0.01,B:0.684)ab:0.345,C:0.3451)abc:0.3451,D:1.5)abcd:0.134,E:0.32)abcde:0.1345";
+ final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
+ if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
+ return false;
+ }
+ final String p30_S = "((((A:0.01,B:0.02):0.93,C:0.04):0.05,D:1.4):0.06,E):0.72";
+ final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
+ if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
+ return false;
+ }
+ final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
+ final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
+ if ( ( p32.length != 0 ) ) {
+ return false;
+ }
+ final String p33_S = "A";
+ final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
+ if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
+ return false;
+ }
+ final String p34_S = "B;";
+ final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
+ if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
+ return false;
+ }
+ final String p35_S = "B:0.2";
+ final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
+ if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
+ return false;
+ }
+ final String p36_S = "(A)";
+ final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
+ if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
+ return false;
+ }
+ final String p37_S = "((A))";
+ final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
+ if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
+ return false;
+ }
+ final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
+ final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
+ if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
+ return false;
+ }
+ final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
+ final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
+ if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
+ return false;
+ }
+ final String p40_S = "(A,B,C)";
+ final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
+ if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
+ return false;
+ }
+ final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
+ final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
+ if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
+ return false;
+ }
+ final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
+ final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
+ if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
return false;
}
- if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
- .equals( "Aranaeus" ) ) {
+ final String p43_S = "(A,B,C,(AA,BB,CC,(CCC,DDD,EEE,(FFFF,GGGG)x)y,DD,EE,FF,GG,HH),D,E,(EE,FF),F,G,H,(((((5)4)3)2)1),I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,(XX,(YY)),Y,Z)";
+ final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
+ if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
return false;
}
- if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
+ final String p44_S = "(((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)))";
+ final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
+ if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
return false;
}
- if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
+ final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
+ final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
+ if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
return false;
}
- if ( phylogenies[ 1 ].isRooted() ) {
+ final String p46_S = "";
+ final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
+ if ( p46.length != 0 ) {
return false;
}
- if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
+ final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
+ if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
return false;
}
- if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
+ if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
return false;
}
- if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
- .equals( "Aranaeus" ) ) {
+ final Phylogeny p49 = factory
+ .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
+ new NHXParser() )[ 0 ];
+ if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
return false;
}
- if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
+ final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
+ if ( p50.getNode( "A" ) == null ) {
return false;
}
- if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
+ if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
+ .equals( "((A,B)ab:2.0[88],C);" ) ) {
return false;
}
- if ( !phylogenies[ 2 ].isRooted() ) {
+ if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
return false;
}
- if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
+ if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
+ .equals( "((A,B)88:2.0,C);" ) ) {
return false;
}
- if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
+ if ( p51.getNode( "A(A" ) == null ) {
return false;
}
- if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
- .equals( "Aranaeus" ) ) {
+ final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
+ if ( p52.getNode( "A(A" ) == null ) {
return false;
}
- phylogenies = null;
- phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "nexus_test_7.nex", parser );
- if ( phylogenies.length != 3 ) {
+ final Phylogeny p53 = factory
+ .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
+ new NHXParser() )[ 0 ];
+ if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
return false;
}
- if ( phylogenies[ 0 ].getNumberOfExternalNodes() != 3 ) {
+ //
+ final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
+ if ( p54.getNode( "A" ) == null ) {
return false;
}
- if ( !phylogenies[ 0 ].getName().equals( "Tree0" ) ) {
+ if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
+ .equals( "((A,B)[88],C);" ) ) {
return false;
}
- if ( phylogenies[ 0 ].isRooted() ) {
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testNHParsingIter() {
+ try {
+ final String p0_str = "(A,B);";
+ final NHXParser p = new NHXParser();
+ p.setSource( p0_str );
+ if ( !p.hasNext() ) {
return false;
}
- if ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
+ final Phylogeny p0 = p.next();
+ if ( !p0.toNewHampshire().equals( p0_str ) ) {
+ System.out.println( p0.toNewHampshire() );
return false;
}
- if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ if ( p.hasNext() ) {
return false;
}
- if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
- .equals( "Aranaeus" ) ) {
+ if ( p.next() != null ) {
return false;
}
- if ( phylogenies[ 1 ].getNumberOfExternalNodes() != 3 ) {
+ //
+ final String p00_str = "(A,B)root;";
+ p.setSource( p00_str );
+ final Phylogeny p00 = p.next();
+ if ( !p00.toNewHampshire().equals( p00_str ) ) {
+ System.out.println( p00.toNewHampshire() );
return false;
}
- if ( !phylogenies[ 1 ].getName().equals( "Tree1" ) ) {
+ //
+ final String p000_str = "A;";
+ p.setSource( p000_str );
+ final Phylogeny p000 = p.next();
+ if ( !p000.toNewHampshire().equals( p000_str ) ) {
+ System.out.println( p000.toNewHampshire() );
return false;
}
- if ( phylogenies[ 1 ].isRooted() ) {
+ //
+ final String p0000_str = "A";
+ p.setSource( p0000_str );
+ final Phylogeny p0000 = p.next();
+ if ( !p0000.toNewHampshire().equals( "A;" ) ) {
+ System.out.println( p0000.toNewHampshire() );
return false;
}
- if ( !phylogenies[ 1 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
+ //
+ p.setSource( "(A)" );
+ final Phylogeny p00000 = p.next();
+ if ( !p00000.toNewHampshire().equals( "(A);" ) ) {
+ System.out.println( p00000.toNewHampshire() );
return false;
}
- if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ //
+ final String p1_str = "(A,B)(C,D)(E,F)(G,H)";
+ p.setSource( p1_str );
+ if ( !p.hasNext() ) {
return false;
}
- if ( !phylogenies[ 1 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
- .equals( "Aranaeus" ) ) {
+ final Phylogeny p1_0 = p.next();
+ if ( !p1_0.toNewHampshire().equals( "(A,B);" ) ) {
+ System.out.println( p1_0.toNewHampshire() );
return false;
}
- if ( phylogenies[ 2 ].getNumberOfExternalNodes() != 3 ) {
+ if ( !p.hasNext() ) {
return false;
}
- if ( !phylogenies[ 2 ].getName().equals( "Tree2" ) ) {
+ final Phylogeny p1_1 = p.next();
+ if ( !p1_1.toNewHampshire().equals( "(C,D);" ) ) {
+ System.out.println( "(C,D) != " + p1_1.toNewHampshire() );
return false;
}
- if ( !phylogenies[ 2 ].isRooted() ) {
+ if ( !p.hasNext() ) {
return false;
}
- if ( !phylogenies[ 2 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
+ final Phylogeny p1_2 = p.next();
+ if ( !p1_2.toNewHampshire().equals( "(E,F);" ) ) {
+ System.out.println( "(E,F) != " + p1_2.toNewHampshire() );
return false;
}
- if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ if ( !p.hasNext() ) {
return false;
}
- if ( !phylogenies[ 2 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
- .equals( "Aranaeus" ) ) {
+ final Phylogeny p1_3 = p.next();
+ if ( !p1_3.toNewHampshire().equals( "(G,H);" ) ) {
+ System.out.println( "(G,H) != " + p1_3.toNewHampshire() );
return false;
}
- }
- catch ( final Exception e ) {
- e.printStackTrace( System.out );
- return false;
- }
- return true;
- }
-
- private static boolean testNHParsing() {
- try {
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final Phylogeny p1 = factory.create( "(A,B1)", new NHXParser() )[ 0 ];
- if ( !p1.toNewHampshireX().equals( "(A,B1)" ) ) {
+ if ( p.hasNext() ) {
return false;
}
- final NHXParser nhxp = new NHXParser();
- nhxp.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
- nhxp.setReplaceUnderscores( true );
- final Phylogeny uc0 = factory.create( "(A__A_,_B_B)", nhxp )[ 0 ];
- if ( !uc0.getRoot().getChildNode( 0 ).getName().equals( "A A " ) ) {
+ if ( p.next() != null ) {
return false;
}
- if ( !uc0.getRoot().getChildNode( 1 ).getName().equals( " B B" ) ) {
+ //
+ final String p2_str = "((1,2,3),B);(C,D) (E,F)root;(G,H); ;(X)";
+ p.setSource( p2_str );
+ if ( !p.hasNext() ) {
return false;
}
- final Phylogeny p1b = factory
- .create( " \n \t \b \r \f ; ( \n \t \b \r \f; A ; \n \t \b \r \f, \n \t \b \r \f; B ; \n \t \b \r \f 1 \n \t \b \r \f ; \n \t \b \r \f );;;;; \n \t \b \r \f;;; \n \t \b \r \f ",
- new NHXParser() )[ 0 ];
- if ( !p1b.toNewHampshireX().equals( "(';A;',';B;1;')" ) ) {
+ Phylogeny p2_0 = p.next();
+ if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
+ System.out.println( p2_0.toNewHampshire() );
return false;
}
- if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
+ if ( !p.hasNext() ) {
return false;
}
- final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
- final Phylogeny p3 = factory.create( new char[] { '(', 'A', ',', 'B', '3', ')' }, new NHXParser() )[ 0 ];
- final Phylogeny p4 = factory.create( "(A,B4);", new NHXParser() )[ 0 ];
- final Phylogeny p5 = factory.create( new StringBuffer( "(A,B5);" ), new NHXParser() )[ 0 ];
- final Phylogeny[] p7 = factory.create( "(A,B7);(C,D7)", new NHXParser() );
- final Phylogeny[] p8 = factory.create( "(A,B8) (C,D8)", new NHXParser() );
- final Phylogeny[] p9 = factory.create( "(A,B9)\n(C,D9)", new NHXParser() );
- final Phylogeny[] p10 = factory.create( "(A,B10);(C,D10);", new NHXParser() );
- 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() );
- if ( !p13[ 0 ].toNewHampshireX().equals( "(';A;',';B;13;')" ) ) {
+ Phylogeny p2_1 = p.next();
+ if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
+ System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
return false;
}
- if ( !p13[ 1 ].toNewHampshireX().equals( "(';C;',';D;13;')" ) ) {
+ if ( !p.hasNext() ) {
return false;
}
- if ( !p13[ 2 ].toNewHampshireX().equals( "(';E;',';F;13;')" ) ) {
+ Phylogeny p2_2 = p.next();
+ if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
+ System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
return false;
}
- if ( !p13[ 3 ].toNewHampshireX().equals( "(';G;',';H;13;')" ) ) {
+ if ( !p.hasNext() ) {
return false;
}
- final Phylogeny[] p14 = factory.create( "(A,B14)ab", new NHXParser() );
- final Phylogeny[] p15 = factory.create( "(A,B15)ab;", new NHXParser() );
- final String p16_S = "((A,B),C)";
- final Phylogeny[] p16 = factory.create( p16_S, new NHXParser() );
- if ( !p16[ 0 ].toNewHampshireX().equals( p16_S ) ) {
+ Phylogeny p2_3 = p.next();
+ if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
+ System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
return false;
}
- final String p17_S = "(C,(A,B))";
- final Phylogeny[] p17 = factory.create( p17_S, new NHXParser() );
- if ( !p17[ 0 ].toNewHampshireX().equals( p17_S ) ) {
+ if ( !p.hasNext() ) {
return false;
}
- final String p18_S = "((A,B),(C,D))";
- final Phylogeny[] p18 = factory.create( p18_S, new NHXParser() );
- if ( !p18[ 0 ].toNewHampshireX().equals( p18_S ) ) {
+ Phylogeny p2_4 = p.next();
+ if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
+ System.out.println( "(X) != " + p2_4.toNewHampshire() );
return false;
}
- final String p19_S = "(((A,B),C),D)";
- final Phylogeny[] p19 = factory.create( p19_S, new NHXParser() );
- if ( !p19[ 0 ].toNewHampshireX().equals( p19_S ) ) {
+ if ( p.hasNext() ) {
return false;
}
- final String p20_S = "(A,(B,(C,D)))";
- final Phylogeny[] p20 = factory.create( p20_S, new NHXParser() );
- if ( !p20[ 0 ].toNewHampshireX().equals( p20_S ) ) {
+ if ( p.next() != null ) {
return false;
}
- final String p21_S = "(A,(B,(C,(D,E))))";
- final Phylogeny[] p21 = factory.create( p21_S, new NHXParser() );
- if ( !p21[ 0 ].toNewHampshireX().equals( p21_S ) ) {
+ ////
+ p.reset();
+ if ( !p.hasNext() ) {
return false;
}
- final String p22_S = "((((A,B),C),D),E)";
- final Phylogeny[] p22 = factory.create( p22_S, new NHXParser() );
- if ( !p22[ 0 ].toNewHampshireX().equals( p22_S ) ) {
+ p2_0 = p.next();
+ if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
+ System.out.println( p2_0.toNewHampshire() );
return false;
}
- final String p23_S = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
- final Phylogeny[] p23 = factory.create( p23_S, new NHXParser() );
- if ( !p23[ 0 ].toNewHampshireX().equals( p23_S ) ) {
+ if ( !p.hasNext() ) {
return false;
}
- final String p24_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
- final Phylogeny[] p24 = factory.create( p24_S, new NHXParser() );
- if ( !p24[ 0 ].toNewHampshireX().equals( p24_S ) ) {
+ p2_1 = p.next();
+ if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
+ System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
return false;
}
- final String p241_S1 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
- final String p241_S2 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
- final Phylogeny[] p241 = factory.create( p241_S1 + p241_S2, new NHXParser() );
- if ( !p241[ 0 ].toNewHampshireX().equals( p241_S1 ) ) {
+ if ( !p.hasNext() ) {
return false;
}
- if ( !p241[ 1 ].toNewHampshireX().equals( p241_S2 ) ) {
+ p2_2 = p.next();
+ if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
+ System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
return false;
}
- final String p25_S = "((((((((((((((A,B)ab,C)abc,D)abcd,E)"
- + "abcde,(B,(C,(D,E)de)cde)bcde)abcde,(B,((A,(B,(C,(D,"
- + "E)de)cde)bcde)abcde,(D,E)de)cde)bcde)abcde,B)ab,C)"
- + "abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde,"
- + "((((A,((((((((A,B)ab,C)abc,((((A,B)ab,C)abc,D)abcd,"
- + "E)abcde)abcd,E)abcde,((((A,B)ab,C)abc,D)abcd,E)abcde)"
- + "ab,C)abc,((((A,B)ab,C)abc,D)abcd,E)abcde)abcd,E)abcde"
- + ")ab,C)abc,D)abcd,E)abcde)ab,C)abc,((((A,B)ab,C)abc,D)" + "abcd,E)abcde)abcd,E)abcde";
- final Phylogeny[] p25 = factory.create( p25_S, new NHXParser() );
- if ( !p25[ 0 ].toNewHampshireX().equals( p25_S ) ) {
+ if ( !p.hasNext() ) {
return false;
}
- final String p26_S = "(A,B)ab";
- final Phylogeny[] p26 = factory.create( p26_S, new NHXParser() );
- if ( !p26[ 0 ].toNewHampshireX().equals( p26_S ) ) {
+ p2_3 = p.next();
+ if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
+ System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
return false;
}
- final String p27_S = "((((A,B)ab,C)abc,D)abcd,E)abcde";
- final Phylogeny[] p27 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ),
- new NHXParser() );
- if ( !p27[ 0 ].toNewHampshireX().equals( p27_S ) ) {
+ if ( !p.hasNext() ) {
return false;
}
- final String p28_S1 = "((((A,B)ab,C)abc,D)abcd,E)abcde";
- final String p28_S2 = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
- final String p28_S3 = "(A,B)ab";
- final String p28_S4 = "((((A,B),C),D),;E;)";
- final Phylogeny[] p28 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phylogeny28.nhx" ),
- new NHXParser() );
- if ( !p28[ 0 ].toNewHampshireX().equals( p28_S1 ) ) {
+ p2_4 = p.next();
+ if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
+ System.out.println( "(X) != " + p2_4.toNewHampshire() );
+ return false;
+ }
+ if ( p.hasNext() ) {
+ return false;
+ }
+ if ( p.next() != null ) {
+ return false;
+ }
+ //
+ final String p3_str = "((A,B),C)abc";
+ p.setSource( p3_str );
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ final Phylogeny p3_0 = p.next();
+ if ( !p3_0.toNewHampshire().equals( "((A,B),C)abc;" ) ) {
return false;
}
- if ( !p28[ 1 ].toNewHampshireX().equals( p28_S2 ) ) {
+ if ( p.hasNext() ) {
return false;
}
- if ( !p28[ 2 ].toNewHampshireX().equals( p28_S3 ) ) {
+ if ( p.next() != null ) {
return false;
}
- if ( !p28[ 3 ].toNewHampshireX().equals( "((((A,B),C),D),';E;')" ) ) {
+ //
+ final String p4_str = "((A,B)ab,C)abc";
+ p.setSource( p4_str );
+ if ( !p.hasNext() ) {
return false;
}
- final String p29_S = "((((A:0.01,B:0.684)ab:0.345,C:0.3451)abc:0.3451,D:1.5)abcd:0.134,E:0.32)abcde:0.1345";
- final Phylogeny[] p29 = factory.create( p29_S, new NHXParser() );
- if ( !p29[ 0 ].toNewHampshireX().equals( p29_S ) ) {
+ final Phylogeny p4_0 = p.next();
+ if ( !p4_0.toNewHampshire().equals( "((A,B)ab,C)abc;" ) ) {
return false;
}
- final String p30_S = "((((A:0.01,B:0.02):0.93,C:0.04):0.05,D:1.4):0.06,E):0.72";
- final Phylogeny[] p30 = factory.create( p30_S, new NHXParser() );
- if ( !p30[ 0 ].toNewHampshireX().equals( p30_S ) ) {
+ if ( p.hasNext() ) {
return false;
}
- final String p32_S = " ; ; \n \t \b \f \r ;;;;;; ";
- final Phylogeny[] p32 = factory.create( p32_S, new NHXParser() );
- if ( ( p32.length != 1 ) || !p32[ 0 ].isEmpty() ) {
+ if ( p.next() != null ) {
return false;
}
- final String p33_S = "A";
- final Phylogeny[] p33 = factory.create( p33_S, new NHXParser() );
- if ( !p33[ 0 ].toNewHampshireX().equals( p33_S ) ) {
+ //
+ final String p5_str = "(((A,B)ab,C)abc,D)abcd";
+ p.setSource( p5_str );
+ if ( !p.hasNext() ) {
return false;
}
- final String p34_S = "B;";
- final Phylogeny[] p34 = factory.create( p34_S, new NHXParser() );
- if ( !p34[ 0 ].toNewHampshireX().equals( "B" ) ) {
+ final Phylogeny p5_0 = p.next();
+ if ( !p5_0.toNewHampshire().equals( "(((A,B)ab,C)abc,D)abcd;" ) ) {
return false;
}
- final String p35_S = "B:0.2";
- final Phylogeny[] p35 = factory.create( p35_S, new NHXParser() );
- if ( !p35[ 0 ].toNewHampshireX().equals( p35_S ) ) {
+ if ( p.hasNext() ) {
return false;
}
- final String p36_S = "(A)";
- final Phylogeny[] p36 = factory.create( p36_S, new NHXParser() );
- if ( !p36[ 0 ].toNewHampshireX().equals( p36_S ) ) {
+ if ( p.next() != null ) {
return false;
}
- final String p37_S = "((A))";
- final Phylogeny[] p37 = factory.create( p37_S, new NHXParser() );
- if ( !p37[ 0 ].toNewHampshireX().equals( p37_S ) ) {
+ //
+ final String p6_str = "(A,(B,(C,(D,E)de)cde)bcde)abcde";
+ p.setSource( p6_str );
+ if ( !p.hasNext() ) {
return false;
}
- final String p38_S = "(((((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
- final Phylogeny[] p38 = factory.create( p38_S, new NHXParser() );
- if ( !p38[ 0 ].toNewHampshireX().equals( p38_S ) ) {
+ Phylogeny p6_0 = p.next();
+ if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
return false;
}
- final String p39_S = "(((B,((((A:0.2):0.2):0.3):0.4):0.5):0.6):0.7):0.8";
- final Phylogeny[] p39 = factory.create( p39_S, new NHXParser() );
- if ( !p39[ 0 ].toNewHampshireX().equals( p39_S ) ) {
+ if ( p.hasNext() ) {
return false;
}
- final String p40_S = "(A,B,C)";
- final Phylogeny[] p40 = factory.create( p40_S, new NHXParser() );
- if ( !p40[ 0 ].toNewHampshireX().equals( p40_S ) ) {
+ if ( p.next() != null ) {
return false;
}
- final String p41_S = "(A,B,C,D,E,F,G,H,I,J,K)";
- final Phylogeny[] p41 = factory.create( p41_S, new NHXParser() );
- if ( !p41[ 0 ].toNewHampshireX().equals( p41_S ) ) {
+ p.reset();
+ if ( !p.hasNext() ) {
return false;
}
- final String p42_S = "(A,B,(X,Y,Z),D,E,F,G,H,I,J,K)";
- final Phylogeny[] p42 = factory.create( p42_S, new NHXParser() );
- if ( !p42[ 0 ].toNewHampshireX().equals( p42_S ) ) {
+ p6_0 = p.next();
+ if ( !p6_0.toNewHampshire().equals( "(A,(B,(C,(D,E)de)cde)bcde)abcde;" ) ) {
return false;
}
- final String p43_S = "(A,B,C,(AA,BB,CC,(CCC,DDD,EEE,(FFFF,GGGG)x)y,DD,EE,FF,GG,HH),D,E,(EE,FF),F,G,H,(((((5)4)3)2)1),I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,(XX,(YY)),Y,Z)";
- final Phylogeny[] p43 = factory.create( p43_S, new NHXParser() );
- if ( !p43[ 0 ].toNewHampshireX().equals( p43_S ) ) {
+ if ( p.hasNext() ) {
return false;
}
- final String p44_S = "(((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)),((A,B,C,D),(A,B,C,D),(A,B,C,D),(A,B,C,D)))";
- final Phylogeny[] p44 = factory.create( p44_S, new NHXParser() );
- if ( !p44[ 0 ].toNewHampshireX().equals( p44_S ) ) {
+ if ( p.next() != null ) {
return false;
}
- final String p45_S = "((((((((((A))))))))),(((((((((B))))))))),(((((((((C))))))))))";
- final Phylogeny[] p45 = factory.create( p45_S, new NHXParser() );
- if ( !p45[ 0 ].toNewHampshireX().equals( p45_S ) ) {
+ //
+ final String p7_str = "((((A,B)ab,C)abc,D)abcd,E)abcde";
+ p.setSource( p7_str );
+ if ( !p.hasNext() ) {
return false;
}
- final String p46_S = "";
- final Phylogeny[] p46 = factory.create( p46_S, new NHXParser() );
- if ( ( p46.length != 1 ) || !p46[ 0 ].isEmpty() ) {
+ Phylogeny p7_0 = p.next();
+ if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
return false;
}
- final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
- if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
+ if ( p.hasNext() ) {
return false;
}
- final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
- if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
+ if ( p.next() != null ) {
return false;
}
- final Phylogeny p49 = factory
- .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ),
- new NHXParser() )[ 0 ];
- if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
+ p.reset();
+ if ( !p.hasNext() ) {
return false;
}
- final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
- if ( p50.getNode( "A" ) == null ) {
+ p7_0 = p.next();
+ if ( !p7_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
return false;
}
- if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
- .equals( "((A,B)ab:2.0[88],C);" ) ) {
+ if ( p.hasNext() ) {
return false;
}
- if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ).equals( "((A,B)ab:2.0,C);" ) ) {
+ if ( p.next() != null ) {
return false;
}
- if ( !p50.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES )
- .equals( "((A,B)88:2.0,C);" ) ) {
+ //
+ final String p8_str = "((((A,B)ab,C)abc,D)abcd,E)abcde ((((a,b)ab,c)abc,d)abcd,e)abcde";
+ p.setSource( p8_str );
+ if ( !p.hasNext() ) {
return false;
}
- final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
- if ( p51.getNode( "A(A" ) == null ) {
+ Phylogeny p8_0 = p.next();
+ if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
return false;
}
- final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
- if ( p52.getNode( "A(A" ) == null ) {
+ if ( !p.hasNext() ) {
return false;
}
- final Phylogeny p53 = factory
- .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
- new NHXParser() )[ 0 ];
- if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
+ if ( !p.hasNext() ) {
return false;
}
- //
- final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
- if ( p54.getNode( "A" ) == null ) {
+ Phylogeny p8_1 = p.next();
+ if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
return false;
}
- if ( !p54.toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS )
- .equals( "((A,B)[88],C);" ) ) {
+ if ( p.hasNext() ) {
return false;
}
- }
- catch ( final Exception e ) {
- e.printStackTrace( System.out );
- return false;
- }
- return true;
- }
-
- private static boolean testNHParsingIter() {
- try {
- String p0_str = "(A,B);";
- NHXParser2 p = new NHXParser2();
- p.setSource( p0_str );
- Phylogeny p0 = p.getNext();
- if ( !p0.toNewHampshire().equals( p0_str ) ) {
- System.out.println( p0.toNewHampshire() );
+ if ( p.next() != null ) {
return false;
}
- //if ( p.getNext() != null ) {
- // return false;
- //}
- //
- String p00_str = "(A,B)root;";
- //p = new NHXParser2();
- p.setSource( p00_str );
- Phylogeny p00 = p.getNext();
- if ( !p00.toNewHampshire().equals( p00_str ) ) {
- System.out.println( p00.toNewHampshire() );
+ p.reset();
+ if ( !p.hasNext() ) {
return false;
}
- //
- String p000_str = "A;";
- p.setSource( p000_str );
- Phylogeny p000 = p.getNext();
- if ( !p000.toNewHampshire().equals( p000_str ) ) {
- System.out.println( p000.toNewHampshire() );
+ p8_0 = p.next();
+ if ( !p8_0.toNewHampshire().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde;" ) ) {
return false;
}
- //
- String p0000_str = "A";
- p.setSource( p0000_str );
- Phylogeny p0000 = p.getNext();
- if ( !p0000.toNewHampshire().equals( "A;" ) ) {
- System.out.println( p0000.toNewHampshire() );
+ if ( !p.hasNext() ) {
return false;
}
- //
- p.setSource( "(A)" );
- Phylogeny p00000 = p.getNext();
- if ( !p00000.toNewHampshire().equals( "(A);" ) ) {
- System.out.println( p00000.toNewHampshire() );
+ p8_1 = p.next();
+ if ( !p8_1.toNewHampshire().equals( "((((a,b)ab,c)abc,d)abcd,e)abcde;" ) ) {
return false;
}
+ if ( p.hasNext() ) {
+ return false;
+ }
+ if ( p.next() != null ) {
+ return false;
+ }
+ p.reset();
//
- // p.setSource( " " );
- // Phylogeny p000000 = p.getNext();
- // if ( !p000000.toNewHampshire().equals( "(A);" ) ) {
- // System.out.println( p000000.toNewHampshire() );
- // return false;
- // }
- //
- String p1_str = "(A,B)(C,D)(E,F)(G,H)";
- p.setSource( p1_str );
- Phylogeny p1_0 = p.getNext();
- if ( !p1_0.toNewHampshire().equals( "(A,B);" ) ) {
- System.out.println( p1_0.toNewHampshire() );
+ p.setSource( "" );
+ if ( p.hasNext() ) {
return false;
}
- Phylogeny p1_1 = p.getNext();
- if ( !p1_1.toNewHampshire().equals( "(C,D);" ) ) {
- System.out.println( "(C,D) != " + p1_1.toNewHampshire() );
+ //
+ p.setSource( new File( Test.PATH_TO_TEST_DATA + "phylogeny27.nhx" ) );
+ if ( !p.hasNext() ) {
return false;
}
- Phylogeny p1_2 = p.getNext();
- if ( !p1_2.toNewHampshire().equals( "(E,F);" ) ) {
- System.out.println( "(E,F) != " + p1_2.toNewHampshire() );
+ Phylogeny p_27 = p.next();
+ if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
+ System.out.println( p_27.toNewHampshireX() );
+ System.exit( -1 );
return false;
}
- Phylogeny p1_3 = p.getNext();
- if ( !p1_3.toNewHampshire().equals( "(G,H);" ) ) {
- System.out.println( "(G,H) != " + p1_3.toNewHampshire() );
+ if ( p.hasNext() ) {
return false;
}
- //
- String p2_str = "((1,2,3),B);(C,D) (E,F)root;(G,H); ;(X)";
- p.setSource( p2_str );
- Phylogeny p2_0 = p.getNext();
- if ( !p2_0.toNewHampshire().equals( "((1,2,3),B);" ) ) {
- System.out.println( p2_0.toNewHampshire() );
+ if ( p.next() != null ) {
return false;
}
- Phylogeny p2_1 = p.getNext();
- if ( !p2_1.toNewHampshire().equals( "(C,D);" ) ) {
- System.out.println( "(C,D) != " + p2_1.toNewHampshire() );
+ p.reset();
+ if ( !p.hasNext() ) {
return false;
}
- Phylogeny p2_2 = p.getNext();
- if ( !p2_2.toNewHampshire().equals( "(E,F)root;" ) ) {
- System.out.println( "(E,F)root != " + p2_2.toNewHampshire() );
+ p_27 = p.next();
+ if ( !p_27.toNewHampshireX().equals( "((((A,B)ab,C)abc,D)abcd,E)abcde" ) ) {
+ System.out.println( p_27.toNewHampshireX() );
+ System.exit( -1 );
return false;
}
- Phylogeny p2_3 = p.getNext();
- if ( !p2_3.toNewHampshire().equals( "(G,H);" ) ) {
- System.out.println( "(G,H) != " + p2_3.toNewHampshire() );
+ if ( p.hasNext() ) {
return false;
}
- Phylogeny p2_4 = p.getNext();
- if ( !p2_4.toNewHampshire().equals( "(X);" ) ) {
- System.out.println( "(X) != " + p2_4.toNewHampshire() );
+ if ( p.next() != null ) {
return false;
}
}
final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "n3" );
final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "n4:0.01" );
final PhylogenyNode n5 = PhylogenyNode
- .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1:W=2:C=10.20.30:XN=S=tag1=value1=unit1]" );
+ .createInstanceFromNhxString( "n5:0.1[&&NHX:S=Ecoli:E=1.1.1.1:D=Y:Co=Y:B=56:T=1]" );
final PhylogenyNode n6 = PhylogenyNode
- .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1:W=2:C=0.0.0:XN=B=bool_tag=T]" );
+ .createInstanceFromNhxString( "n6:0.000001[&&NHX:S=Ecoli:E=1.1.1.1:D=N:Co=N:B=100:T=1]" );
if ( !n1.toNewHampshireX().equals( "" ) ) {
return false;
}
if ( !n4.toNewHampshireX().equals( "n4:0.01" ) ) {
return false;
}
- if ( !n5.toNewHampshireX()
- .equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:XN=S=tag1=value1=unit1:B=56:W=2.0:C=10.20.30]" ) ) {
+ if ( !n5.toNewHampshireX().equals( "n5:0.1[&&NHX:T=1:S=Ecoli:D=Y:B=56]" ) ) {
return false;
}
- if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:XN=B=bool_tag=T:B=100:W=2.0:C=0.0.0]" ) ) {
+ if ( !n6.toNewHampshireX().equals( "n6:1.0E-6[&&NHX:T=1:S=Ecoli:D=N:B=100]" ) ) {
+ System.out.println( n6.toNewHampshireX() );
return false;
}
}
private static boolean testTaxonomyExtraction() {
try {
- final PhylogenyNode n0 = PhylogenyNode.createInstanceFromNhxString( "sd_12345678",
- NHXParser.TAXONOMY_EXTRACTION.YES );
+ final PhylogenyNode n0 = PhylogenyNode
+ .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( n0.getNodeData().isHasTaxonomy() ) {
return false;
}
- final PhylogenyNode n1 = PhylogenyNode.createInstanceFromNhxString( "sd_12345x",
- NHXParser.TAXONOMY_EXTRACTION.YES );
+ final PhylogenyNode n1 = PhylogenyNode
+ .createInstanceFromNhxString( "sd_12345x", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( n1.getNodeData().isHasTaxonomy() ) {
System.out.println( n1.toString() );
return false;
}
- final PhylogenyNode n2 = PhylogenyNode.createInstanceFromNhxString( "12345",
- NHXParser.TAXONOMY_EXTRACTION.YES );
- if ( !n2.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
- System.out.println( n2.toString() );
+ final PhylogenyNode n2x = PhylogenyNode
+ .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( n2x.getNodeData().isHasTaxonomy() ) {
return false;
}
- final PhylogenyNode n3 = PhylogenyNode.createInstanceFromNhxString( "blag_12345",
- NHXParser.TAXONOMY_EXTRACTION.YES );
+ final PhylogenyNode n3 = PhylogenyNode
+ .createInstanceFromNhxString( "blag_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
System.out.println( n3.toString() );
return false;
}
- final PhylogenyNode n4 = PhylogenyNode.createInstanceFromNhxString( "blag-12345",
- NHXParser.TAXONOMY_EXTRACTION.YES );
+ final PhylogenyNode n4 = PhylogenyNode
+ .createInstanceFromNhxString( "blag-12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( n4.getNodeData().isHasTaxonomy() ) {
System.out.println( n4.toString() );
return false;
}
- final PhylogenyNode n5 = PhylogenyNode.createInstanceFromNhxString( "12345-blag",
- NHXParser.TAXONOMY_EXTRACTION.YES );
+ final PhylogenyNode n5 = PhylogenyNode
+ .createInstanceFromNhxString( "12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( n5.getNodeData().isHasTaxonomy() ) {
System.out.println( n5.toString() );
return false;
}
- final PhylogenyNode n6 = PhylogenyNode.createInstanceFromNhxString( "blag-12345-blag",
- NHXParser.TAXONOMY_EXTRACTION.YES );
+ final PhylogenyNode n6 = PhylogenyNode
+ .createInstanceFromNhxString( "blag-12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( n6.getNodeData().isHasTaxonomy() ) {
System.out.println( n6.toString() );
return false;
}
- final PhylogenyNode n7 = PhylogenyNode.createInstanceFromNhxString( "blag-12345_blag",
- NHXParser.TAXONOMY_EXTRACTION.YES );
+ final PhylogenyNode n7 = PhylogenyNode
+ .createInstanceFromNhxString( "blag-12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( n7.getNodeData().isHasTaxonomy() ) {
System.out.println( n7.toString() );
return false;
}
- final PhylogenyNode n8 = PhylogenyNode.createInstanceFromNhxString( "blag_12345-blag",
- NHXParser.TAXONOMY_EXTRACTION.YES );
+ final PhylogenyNode n8 = PhylogenyNode
+ .createInstanceFromNhxString( "blag_12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
System.out.println( n8.toString() );
return false;
}
- final PhylogenyNode n9 = PhylogenyNode.createInstanceFromNhxString( "blag_12345_blag",
- NHXParser.TAXONOMY_EXTRACTION.YES );
+ final PhylogenyNode n9 = PhylogenyNode
+ .createInstanceFromNhxString( "blag_12345/blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
System.out.println( n9.toString() );
return false;
}
- final PhylogenyNode n10 = PhylogenyNode.createInstanceFromNhxString( "blag_12X45-blag",
- NHXParser.TAXONOMY_EXTRACTION.YES );
- if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "12X45" ) ) {
+ final PhylogenyNode n10x = PhylogenyNode
+ .createInstanceFromNhxString( "blag_12X45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( n10x.getNodeData().isHasTaxonomy() ) {
+ System.out.println( n10x.toString() );
+ return false;
+ }
+ final PhylogenyNode n10xx = PhylogenyNode
+ .createInstanceFromNhxString( "blag_1YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( n10xx.getNodeData().isHasTaxonomy() ) {
+ System.out.println( n10xx.toString() );
+ return false;
+ }
+ final PhylogenyNode n10 = PhylogenyNode
+ .createInstanceFromNhxString( "blag_9YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9YX45" ) ) {
System.out.println( n10.toString() );
return false;
}
- final PhylogenyNode n11 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus",
- NHXParser.TAXONOMY_EXTRACTION.YES );
+ final PhylogenyNode n11 = PhylogenyNode
+ .createInstanceFromNhxString( "BLAG_Mus_musculus", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
System.out.println( n11.toString() );
return false;
}
- final PhylogenyNode n12 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_musculus",
- NHXParser.TAXONOMY_EXTRACTION.YES );
+ final PhylogenyNode n12 = PhylogenyNode
+ .createInstanceFromNhxString( "BLAG_Mus_musculus_musculus",
+ NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
if ( !n12.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
System.out.println( n12.toString() );
return false;
}
- final PhylogenyNode n13 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus1",
- NHXParser.TAXONOMY_EXTRACTION.YES );
+ final PhylogenyNode n13 = PhylogenyNode
+ .createInstanceFromNhxString( "BLAG_Mus_musculus1", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
if ( n13.getNodeData().isHasTaxonomy() ) {
System.out.println( n13.toString() );
return false;
}
- final PhylogenyNode n14 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_11",
- NHXParser.TAXONOMY_EXTRACTION.YES );
- if ( n14.getNodeData().isHasTaxonomy() ) {
- System.out.println( n14.toString() );
- return false;
- }
- final PhylogenyNode n15 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_v11",
- NHXParser.TAXONOMY_EXTRACTION.YES );
- if ( !n15.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus v11" ) ) {
- System.out.println( n15.toString() );
- return false;
- }
- final PhylogenyNode n16 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_/11",
- NHXParser.TAXONOMY_EXTRACTION.YES );
- if ( n16.getNodeData().isHasTaxonomy() ) {
- System.out.println( n16.toString() );
- return false;
- }
- final PhylogenyNode n17 = PhylogenyNode.createInstanceFromNhxString( "blag_Mus_musculus_v",
- NHXParser.TAXONOMY_EXTRACTION.YES );
- if ( n17.getNodeData().isHasTaxonomy() ) {
- System.out.println( n17.toString() );
- return false;
- }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
if ( !n5.isHasAssignedEvent() ) {
return false;
}
- if ( PhylogenyMethods.getBranchWidthValue( n5 ) != 2 ) {
- return false;
- }
final PhylogenyNode n8 = PhylogenyNode
- .createInstanceFromNhxString( "n8_ECOLI/12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !n8.getName().equals( "n8_ECOLI/12" ) ) {
+ .createInstanceFromNhxString( "ABCD_ECOLI/1-2:0.01",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n8.getName().equals( "ABCD_ECOLI/1-2" ) ) {
return false;
}
- if ( PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
+ if ( !PhylogenyMethods.getSpecies( n8 ).equals( "ECOLI" ) ) {
return false;
}
final PhylogenyNode n9 = PhylogenyNode
- .createInstanceFromNhxString( "n9_ECOLI/12=12:0.01", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
+ .createInstanceFromNhxString( "ABCD_ECOLI/1-12:0.01",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n9.getName().equals( "ABCD_ECOLI/1-12" ) ) {
return false;
}
- if ( PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
+ if ( !PhylogenyMethods.getSpecies( n9 ).equals( "ECOLI" ) ) {
return false;
}
final PhylogenyNode n10 = PhylogenyNode
- .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ .createInstanceFromNhxString( "n10.ECOLI", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
if ( !n10.getName().equals( "n10.ECOLI" ) ) {
return false;
}
final PhylogenyNode n20 = PhylogenyNode
- .createInstanceFromNhxString( "n20_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !n20.getName().equals( "n20_ECOLI/1-2" ) ) {
+ .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n20.getName().equals( "ABCD_ECOLI/1-2" ) ) {
return false;
}
if ( !PhylogenyMethods.getSpecies( n20 ).equals( "ECOLI" ) ) {
return false;
}
- final PhylogenyNode n20x = PhylogenyNode.createInstanceFromNhxString( "n20_ECOL1/1-2",
- NHXParser.TAXONOMY_EXTRACTION.YES );
- if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
+ final PhylogenyNode n20x = PhylogenyNode
+ .createInstanceFromNhxString( "N20_ECOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !n20x.getName().equals( "N20_ECOL1/1-2" ) ) {
return false;
}
if ( !PhylogenyMethods.getSpecies( n20x ).equals( "ECOL1" ) ) {
return false;
}
final PhylogenyNode n20xx = PhylogenyNode
- .createInstanceFromNhxString( "n20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !n20xx.getName().equals( "n20_eCOL1/1-2" ) ) {
+ .createInstanceFromNhxString( "N20_eCOL1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n20xx.getName().equals( "N20_eCOL1/1-2" ) ) {
return false;
}
if ( PhylogenyMethods.getSpecies( n20xx ).length() > 0 ) {
return false;
}
final PhylogenyNode n20xxx = PhylogenyNode
- .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ .createInstanceFromNhxString( "n20_ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
if ( !n20xxx.getName().equals( "n20_ecoli/1-2" ) ) {
return false;
}
return false;
}
final PhylogenyNode n20xxxx = PhylogenyNode
- .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ .createInstanceFromNhxString( "n20_Ecoli/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
if ( !n20xxxx.getName().equals( "n20_Ecoli/1-2" ) ) {
return false;
}
if ( PhylogenyMethods.getSpecies( n20xxxx ).length() > 0 ) {
return false;
}
- final PhylogenyNode n21 = PhylogenyNode.createInstanceFromNhxString( "n21_PIG",
- NHXParser.TAXONOMY_EXTRACTION.YES );
- if ( !n21.getName().equals( "n21_PIG" ) ) {
+ final PhylogenyNode n21 = PhylogenyNode
+ .createInstanceFromNhxString( "N21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !n21.getName().equals( "N21_PIG" ) ) {
return false;
}
if ( !PhylogenyMethods.getSpecies( n21 ).equals( "PIG" ) ) {
return false;
}
final PhylogenyNode n21x = PhylogenyNode
- .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
if ( !n21x.getName().equals( "n21_PIG" ) ) {
return false;
}
return false;
}
final PhylogenyNode n22 = PhylogenyNode
- .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ .createInstanceFromNhxString( "n22/PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
if ( !n22.getName().equals( "n22/PIG" ) ) {
return false;
}
return false;
}
final PhylogenyNode n23 = PhylogenyNode
- .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ .createInstanceFromNhxString( "n23/PIG_1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
if ( !n23.getName().equals( "n23/PIG_1" ) ) {
return false;
}
return false;
}
final PhylogenyNode a = PhylogenyNode
- .createInstanceFromNhxString( "n10_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) {
+ .createInstanceFromNhxString( "ABCD_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !a.getName().equals( "ABCD_ECOLI/1-2" ) ) {
return false;
}
if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) {
return false;
}
- final PhylogenyNode b = PhylogenyNode
- .createInstanceFromNhxString( "n10_ECOLI1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) {
- return false;
- }
- if ( PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) {
- return false;
- }
- final PhylogenyNode c = PhylogenyNode
- .createInstanceFromNhxString( "n10_RATAF12/1000-2000",
- NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) {
- return false;
- }
- if ( PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) {
- return false;
- }
final PhylogenyNode c1 = PhylogenyNode
- .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000",
- NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) {
+ .createInstanceFromNhxString( "n10_BOVIN/1000-2000",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !c1.getName().equals( "n10_BOVIN/1000-2000" ) ) {
return false;
}
- if ( PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
+ if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) {
return false;
}
final PhylogenyNode c2 = PhylogenyNode
- .createInstanceFromNhxString( "n10_Bovin_1/1000-2000",
- NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) {
- return false;
- }
- if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) {
- return false;
- }
- final PhylogenyNode d = PhylogenyNode
- .createInstanceFromNhxString( "n10_RAT1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
- return false;
- }
- if ( PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
- return false;
- }
- final PhylogenyNode e = PhylogenyNode
- .createInstanceFromNhxString( "n10_RAT1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !e.getName().equals( "n10_RAT1" ) ) {
- return false;
- }
- if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) {
- return false;
- }
- final PhylogenyNode e2 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT1",
- NHXParser.TAXONOMY_EXTRACTION.YES );
- if ( !e2.getName().equals( "n10_RAT1" ) ) {
+ .createInstanceFromNhxString( "N10_Bovin_1/1000-2000",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !c2.getName().equals( "N10_Bovin_1/1000-2000" ) ) {
return false;
}
- if ( PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) {
+ if ( PhylogenyMethods.getSpecies( c2 ).length() > 0 ) {
return false;
}
- final PhylogenyNode e3 = PhylogenyNode.createInstanceFromNhxString( "n10_RAT~",
- NHXParser.TAXONOMY_EXTRACTION.YES );
+ final PhylogenyNode e3 = PhylogenyNode
+ .createInstanceFromNhxString( "n10_RAT~", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( !e3.getName().equals( "n10_RAT~" ) ) {
return false;
}
return false;
}
final PhylogenyNode n11 = PhylogenyNode
- .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
- NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
+ .createInstanceFromNhxString( "N111111_ECOLI/1-2:0.4",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n11.getName().equals( "N111111_ECOLI/1-2" ) ) {
return false;
}
if ( n11.getDistanceToParent() != 0.4 ) {
return false;
}
- if ( PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
+ if ( !PhylogenyMethods.getSpecies( n11 ).equals( "ECOLI" ) ) {
return false;
}
final PhylogenyNode n12 = PhylogenyNode
- .createInstanceFromNhxString( "n111111-ECOLI---/jdj:0.4",
- NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
+ .createInstanceFromNhxString( "N111111-ECOLI---/jdj:0.4",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n12.getName().equals( "N111111-ECOLI---/jdj" ) ) {
return false;
}
if ( n12.getDistanceToParent() != 0.4 ) {
if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) {
return false;
}
- final PhylogenyNode m = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSEa",
- NHXParser.TAXONOMY_EXTRACTION.YES );
- if ( !m.getName().equals( "n10_MOUSEa" ) ) {
- return false;
- }
- if ( PhylogenyMethods.getSpecies( m ).equals( "MOUSE" ) ) {
- return false;
- }
- final PhylogenyNode o = PhylogenyNode.createInstanceFromNhxString( "n10_MOUSE_",
- NHXParser.TAXONOMY_EXTRACTION.YES );
- if ( !o.getName().equals( "n10_MOUSE_" ) ) {
+ final PhylogenyNode o = PhylogenyNode
+ .createInstanceFromNhxString( "ABCD_MOUSE", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !o.getName().equals( "ABCD_MOUSE" ) ) {
return false;
}
if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) {
return false;
}
final PhylogenyNode n00 = PhylogenyNode
- .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:ID=node_identifier:S=Ecoli:D=N:Co=N:B=100:T=1:On=100:SOn=100:SNn=100:W=2:C=0.0.0:XN=U=url_tag=www.yahoo.com]" );
+ .createInstanceFromNhxString( "n7:0.000001[&&NHX:GN=gene_name:AC=accession123:S=Ecoli:D=N:Co=N:B=100:T=1]" );
if ( !n00.getNodeData().getSequence().getName().equals( "gene_name" ) ) {
return false;
}
return false;
}
final PhylogenyNode n13 = PhylogenyNode
- .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ .createInstanceFromNhxString( "blah_12345/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( !n13.getName().equals( "blah_12345/1-2" ) ) {
return false;
}
return false;
}
final PhylogenyNode n14 = PhylogenyNode
- .createInstanceFromNhxString( "blah_12X45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
- if ( !n14.getName().equals( "blah_12X45/1-2" ) ) {
+ .createInstanceFromNhxString( "BLA1_9QX45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !n14.getName().equals( "BLA1_9QX45/1-2" ) ) {
return false;
}
- if ( !PhylogenyMethods.getSpecies( n14 ).equals( "12X45" ) ) {
+ if ( !PhylogenyMethods.getSpecies( n14 ).equals( "9QX45" ) ) {
return false;
}
final PhylogenyNode n15 = PhylogenyNode
.createInstanceFromNhxString( "something_wicked[123]",
- NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
if ( !n15.getName().equals( "something_wicked" ) ) {
return false;
}
return false;
}
final PhylogenyNode n16 = PhylogenyNode
- .createInstanceFromNhxString( "something_wicked2[9]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ .createInstanceFromNhxString( "something_wicked2[9]",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
if ( !n16.getName().equals( "something_wicked2" ) ) {
return false;
}
return false;
}
final PhylogenyNode n17 = PhylogenyNode
- .createInstanceFromNhxString( "something_wicked3[a]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ .createInstanceFromNhxString( "something_wicked3[a]",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
if ( !n17.getName().equals( "something_wicked3" ) ) {
return false;
}
return false;
}
final PhylogenyNode n18 = PhylogenyNode
- .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ .createInstanceFromNhxString( ":0.5[91]", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
if ( !isEqual( n18.getDistanceToParent(), 0.5 ) ) {
return false;
}
if ( !isEqual( n18.getBranchData().getConfidence( 0 ).getValue(), 91 ) ) {
return false;
}
- final PhylogenyNode n19 = PhylogenyNode.createInstanceFromNhxString( "blah_1-roejojoej",
- NHXParser.TAXONOMY_EXTRACTION.YES );
+ final PhylogenyNode n19 = PhylogenyNode
+ .createInstanceFromNhxString( "blah_1-roejojoej", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( !n19.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1" ) ) {
return false;
}
if ( !n19.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
return false;
}
- final PhylogenyNode n30 = PhylogenyNode.createInstanceFromNhxString( "blah_1234567-roejojoej",
- NHXParser.TAXONOMY_EXTRACTION.YES );
+ final PhylogenyNode n30 = PhylogenyNode
+ .createInstanceFromNhxString( "blah_1234567-roejojoej",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( !n30.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "1234567" ) ) {
return false;
}
if ( !n30.getNodeData().getTaxonomy().getIdentifier().getProvider().equals( "uniprot" ) ) {
return false;
}
- final PhylogenyNode n31 = PhylogenyNode.createInstanceFromNhxString( "blah_12345678-roejojoej",
- NHXParser.TAXONOMY_EXTRACTION.YES );
+ final PhylogenyNode n31 = PhylogenyNode
+ .createInstanceFromNhxString( "blah_12345678-roejojoej",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( n31.getNodeData().isHasTaxonomy() ) {
return false;
}
- final PhylogenyNode n32 = PhylogenyNode.createInstanceFromNhxString( "sd_12345678",
- NHXParser.TAXONOMY_EXTRACTION.YES );
+ final PhylogenyNode n32 = PhylogenyNode
+ .createInstanceFromNhxString( "sd_12345678", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( n32.getNodeData().isHasTaxonomy() ) {
return false;
}
+ final PhylogenyNode n40 = PhylogenyNode
+ .createInstanceFromNhxString( "bcl2_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !n40.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
+ return false;
+ }
+ final PhylogenyNode n41 = PhylogenyNode
+ .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( n41.getNodeData().isHasTaxonomy() ) {
+ return false;
+ }
+ final PhylogenyNode n42 = PhylogenyNode
+ .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( n42.getNodeData().isHasTaxonomy() ) {
+ return false;
+ }
+ final PhylogenyNode n43 = PhylogenyNode.createInstanceFromNhxString( "12345",
+ NHXParser.TAXONOMY_EXTRACTION.NO );
+ if ( n43.getNodeData().isHasTaxonomy() ) {
+ return false;
+ }
+ final PhylogenyNode n44 = PhylogenyNode
+ .createInstanceFromNhxString( "12345~1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( n44.getNodeData().isHasTaxonomy() ) {
+ return false;
+ }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final Phylogeny p = factory.create( "((1,2)A,(((X,Y,Z)a,b)3)B,(4,5,6)C)r", new NHXParser() )[ 0 ];
- final int count = PhylogenyNode.getNodeCount();
+ final long count = PhylogenyNode.getNodeCount();
p.levelOrderReID();
if ( p.getNode( "r" ).getId() != count ) {
return false;
if ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
return false;
}
- if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) {
+ if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861.2" ).equals( "AY423861.2" ) ) {
+ return false;
+ }
+ if ( !SequenceIdParser.parseGenbankAccessor( "345_.AY423861.24_345" ).equals( "AY423861.24" ) ) {
return false;
}
if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) {
}
private static boolean testUniprotEntryRetrieval() {
- if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
- return false;
- }
- if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
- return false;
- }
- if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
- return false;
- }
- if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
- return false;
- }
- if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) {
- return false;
- }
- if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
- return false;
- }
- if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
- return false;
- }
- if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
- return false;
- }
- if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
- return false;
- }
- if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
- return false;
- }
- if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
- return false;
- }
- if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
- return false;
- }
- if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
- return false;
- }
try {
final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
if ( !entry.getAccession().equals( "P12345" ) ) {
if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
return false;
}
- if ( !entry.getSequenceSymbol().equals( "GOT2" ) ) {
- return false;
- }
if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
return false;
}
return true;
}
+ private static boolean testSequenceWriter() {
+ try {
+ final String n = ForesterUtil.LINE_SEPARATOR;
+ if ( !SequenceWriter.toFasta( "name", "awes", 5 ).toString().equals( ">name" + n + "awes" ) ) {
+ return false;
+ }
+ if ( !SequenceWriter.toFasta( "name", "awes", 4 ).toString().equals( ">name" + n + "awes" ) ) {
+ return false;
+ }
+ if ( !SequenceWriter.toFasta( "name", "awes", 3 ).toString().equals( ">name" + n + "awe" + n + "s" ) ) {
+ return false;
+ }
+ if ( !SequenceWriter.toFasta( "name", "awes", 2 ).toString().equals( ">name" + n + "aw" + n + "es" ) ) {
+ return false;
+ }
+ if ( !SequenceWriter.toFasta( "name", "awes", 1 ).toString()
+ .equals( ">name" + n + "a" + n + "w" + n + "e" + n + "s" ) ) {
+ return false;
+ }
+ if ( !SequenceWriter.toFasta( "name", "abcdefghij", 3 ).toString()
+ .equals( ">name" + n + "abc" + n + "def" + n + "ghi" + n + "j" ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ return false;
+ }
+ return true;
+ }
+
private static boolean testCreateBalancedPhylogeny() {
try {
final Phylogeny p0 = DevelopmentTools.createBalancedPhylogeny( 6, 5 );
git://source.jalview.org / jalview.git / blobdiff