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;
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." );
if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "XM_002122186" ) ) {
return false;
}
- n.setName( "AAA34956" );
+ n.setName( "dgh_AAA34956_gdg" );
if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
return false;
}
- n.setName( "Q06891.1" );
- if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "Q06891" ) ) {
+ 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;
}
}
private static boolean testExtractTaxonomyCodeFromNodeName() {
try {
- if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
- .equals( "MOUSE" ) ) {
+ if ( ParserUtils.extractTaxonomyCodeFromNodeName( "MOUSE", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
return false;
}
- if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "RAT", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
- .equals( "RAT" ) ) {
+ 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( "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",
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_MOUSE+function = 23445",
TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
.equals( "MOUSE" ) ) {
return false;
TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
return false;
}
- if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT_function = 23445",
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "BCL2_RAT function = 23445",
TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ).equals( "RAT" ) ) {
return false;
}
.equals( "MOUSE" ) ) {
return false;
}
- if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE_", TAXONOMY_EXTRACTION.AGRESSIVE )
- .equals( "MOUSE" ) ) {
- return false;
- }
- if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE_", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
- .equals( "MOUSE" ) ) {
- return false;
- }
- if ( ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE_", TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ) != null ) {
- return false;
- }
- if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "x_MOUSE_x", TAXONOMY_EXTRACTION.AGRESSIVE )
- .equals( "MOUSE" ) ) {
+ if ( ParserUtils.extractTaxonomyCodeFromNodeName( "_MOUSE ", TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ) != null ) {
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:",
System.out.println( n1.toString() );
return false;
}
- final PhylogenyNode n2 = PhylogenyNode
- .createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.AGRESSIVE );
- if ( !n2.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
- System.out.println( n2.toString() );
- return false;
- }
final PhylogenyNode n2x = PhylogenyNode
.createInstanceFromNhxString( "12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( n2x.getNodeData().isHasTaxonomy() ) {
return false;
}
final PhylogenyNode n9 = PhylogenyNode
- .createInstanceFromNhxString( "blag_12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ .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;
return false;
}
final PhylogenyNode n11 = PhylogenyNode
- .createInstanceFromNhxString( "blag_Mus_musculus", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ .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.PFAM_STYLE_RELAXED );
+ .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.PFAM_STYLE_RELAXED );
+ .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.PFAM_STYLE_RELAXED );
- if ( n14.getNodeData().isHasTaxonomy() ) {
- System.out.println( n14.toString() );
- return false;
- }
- final PhylogenyNode n15 = PhylogenyNode
- .createInstanceFromNhxString( "blag_Mus_musculus_v11",
- NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
- 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.PFAM_STYLE_RELAXED );
- if ( n16.getNodeData().isHasTaxonomy() ) {
- System.out.println( n16.toString() );
- return false;
- }
- final PhylogenyNode n17 = PhylogenyNode
- .createInstanceFromNhxString( "blag_Mus_musculus_v",
- NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
- 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_STRICT );
- 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",
+ .createInstanceFromNhxString( "ABCD_ECOLI/1-12:0.01",
NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
- if ( !n9.getName().equals( "n9_ECOLI/12=12" ) ) {
+ 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
return false;
}
final PhylogenyNode n20 = PhylogenyNode
- .createInstanceFromNhxString( "n20_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
- 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.PFAM_STYLE_RELAXED );
- if ( !n20x.getName().equals( "n20_ECOL1/1-2" ) ) {
+ .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_STRICT );
- 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 n21 = PhylogenyNode
- .createInstanceFromNhxString( "n21_PIG", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
- if ( !n21.getName().equals( "n21_PIG" ) ) {
+ .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 a = PhylogenyNode
- .createInstanceFromNhxString( "n10_ECOLI/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
- 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_STRICT );
- 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_STRICT );
- 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_STRICT );
- 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",
+ .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( c2 ).equals( "" ) ) {
- return false;
- }
- final PhylogenyNode d = PhylogenyNode
- .createInstanceFromNhxString( "n10_RAT1/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
- if ( !d.getName().equals( "n10_RAT1/1-2" ) ) {
- return false;
- }
- if ( PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) {
+ if ( !c2.getName().equals( "N10_Bovin_1/1000-2000" ) ) {
return false;
}
- final PhylogenyNode e = PhylogenyNode
- .createInstanceFromNhxString( "n10_RAT1", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
- 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.PFAM_STYLE_RELAXED );
- if ( !e2.getName().equals( "n10_RAT1" ) ) {
- return false;
- }
- if ( PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) {
+ if ( PhylogenyMethods.getSpecies( c2 ).length() > 0 ) {
return false;
}
final PhylogenyNode e3 = PhylogenyNode
return false;
}
final PhylogenyNode n11 = PhylogenyNode
- .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4",
+ .createInstanceFromNhxString( "N111111_ECOLI/1-2:0.4",
NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
- if ( !n11.getName().equals( "n111111_ECOLI/jdj" ) ) {
+ 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",
+ .createInstanceFromNhxString( "N111111-ECOLI---/jdj:0.4",
NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
- if ( !n12.getName().equals( "n111111-ECOLI---/jdj" ) ) {
+ 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.PFAM_STYLE_RELAXED );
- 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.PFAM_STYLE_RELAXED );
- if ( !o.getName().equals( "n10_MOUSE_" ) ) {
+ .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.AGRESSIVE );
+ .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_9QX45/1-2", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
- if ( !n14.getName().equals( "blah_9QX45/1-2" ) ) {
+ .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( "9QX45" ) ) {
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 );
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