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.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( "Nexus tree parsing iterating: " );
+ if ( Test.testNexusTreeParsingIterating() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
System.out.print( "Nexus tree parsing: " );
if ( Test.testNexusTreeParsing() ) {
System.out.println( "OK." );
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( "RAT1", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
+ 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( "qwerty SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ .equals( "SOYBN" ) ) {
return false;
}
- if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.YES ).equals( "RAT" ) ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "qwerty_SOYBN", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ .equals( "SOYBN" ) ) {
return false;
}
- if ( ParserUtils.extractTaxonomyCodeFromNodeName( "RAT1", TAXONOMY_EXTRACTION.YES ) != null ) {
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "ABCD_SOYBN ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
+ .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( ",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:",
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 ( !phylogenies[ 0 ].getFirstExternalNode().getName().equals( "Scarabaeus" ) ) {
+ if ( p.hasNext() ) {
return false;
}
- if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getName().equals( "Drosophila" ) ) {
+ phy = p.next();
+ if ( phy != null ) {
return false;
}
- if ( !phylogenies[ 0 ].getFirstExternalNode().getNextExternalNode().getNextExternalNode().getName()
+ ////
+ 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;
}
return false;
}
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 );
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( "" ) ) {
+ .createInstanceFromNhxString( "N10_Bovin_1/1000-2000",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ if ( !c2.getName().equals( "N10_Bovin_1/1000-2000" ) ) {
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" ) ) {
+ if ( PhylogenyMethods.getSpecies( c2 ).length() > 0 ) {
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" ) ) {
- return false;
- }
- if ( PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) {
- 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 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