import java.util.Set;
import java.util.SortedSet;
+import javax.net.ssl.HttpsURLConnection;
+import javax.net.ssl.SSLContext;
+
import org.forester.application.support_transfer;
import org.forester.archaeopteryx.AptxUtil;
import org.forester.archaeopteryx.TreePanelUtil;
import org.forester.ws.seqdb.SequenceDatabaseEntry;
import org.forester.ws.seqdb.SequenceDbWsTools;
import org.forester.ws.seqdb.UniProtTaxonomy;
-import org.forester.ws.wabi.TxSearch;
-import org.forester.ws.wabi.TxSearch.RANKS;
-import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
-import org.forester.ws.wabi.TxSearch.TAX_RANK;
+
@SuppressWarnings( "unused")
public final class Test {
private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
private final static double ZERO_DIFF = 1.0E-9;
- public static boolean isEqual( final double a, final double b ) {
+ private static boolean isEqual( final double a, final double b ) {
return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
}
System.exit( -1 );
}
final long start_time = new Date().getTime();
+
System.out.print( "Basic node methods: " );
if ( Test.testBasicNodeMethods() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
+ System.out.print( "Node construction and parsing of NHX (node level): " );
+ if ( Test.testNHXNodeParsing2() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
System.out.print( "NHX parsing iterating: " );
if ( Test.testNHParsingIter() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
+ System.out.print( "NH parsing - special chars: " );
+ if ( Test.testNHParsingSpecialChars() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
System.out.print( "Conversion to NHX (node level): " );
if ( Test.testNHXconversion() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
+ System.out.print( "UTF-8 parsing from file: " );
+ if ( Test.testUTF8ParsingFromFile() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
System.out.print( "Copying of node data: " );
if ( Test.testCopyOfNodeData() ) {
System.out.println( "OK." );
}
}
if ( PERFORM_WEB_TREE_ACCESS ) {
- System.out.print( "NHX parsing from URL: " );
- if ( Test.testNHXparsingFromURL() ) {
+ System.out.print( "TreeBase acccess: " );
+ if ( Test.testTreeBaseReading() ) {
System.out.println( "OK." );
succeeded++;
}
System.out.println( "failed." );
failed++;
}
- System.out.print( "NHX parsing from URL 2: " );
- if ( Test.testNHXparsingFromURL2() ) {
+ System.out.print( "ToL access: " );
+ if ( Test.testToLReading() ) {
System.out.println( "OK." );
succeeded++;
}
System.out.println( "failed." );
failed++;
}
- System.out.print( "phyloXML parsing from URL: " );
- if ( Test.testPhyloXMLparsingFromURL() ) {
+ System.out.print( "NHX parsing from URL: " );
+ if ( Test.testNHXparsingFromURL() ) {
System.out.println( "OK." );
succeeded++;
}
System.out.println( "failed." );
failed++;
}
- System.out.print( "TreeBase acccess: " );
- if ( Test.testTreeBaseReading() ) {
+ System.out.print( "NHX parsing from URL 2: " );
+ if ( Test.testNHXparsingFromURL2() ) {
System.out.println( "OK." );
succeeded++;
}
System.out.println( "failed." );
failed++;
}
- //
- System.out.print( "ToL access: " );
- if ( Test.testToLReading() ) {
+ System.out.print( "phyloXML parsing from URL: " );
+ if ( Test.testPhyloXMLparsingFromURL() ) {
System.out.println( "OK." );
succeeded++;
}
System.out.println( "failed." );
failed++;
}
- //
System.out.print( "TreeFam access: " );
if ( Test.testTreeFamReading() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
- //
- //
System.out.print( "Pfam tree access: " );
if ( Test.testPfamTreeReading() ) {
System.out.println( "OK." );
}
}
- public static boolean testEngulfingOverlapRemoval() {
+ private static boolean testEngulfingOverlapRemoval() {
try {
final Domain d0 = new BasicDomain( "d0", 0, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
final Domain d1 = new BasicDomain( "d1", 0, 1, ( short ) 1, ( short ) 1, 0.1, 1 );
return true;
}
- public static final boolean testNHXparsingFromURL2() {
+ private static final boolean testNHXparsingFromURL2() {
try {
final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh";
final Phylogeny phys[] = AptxUtil.readPhylogeniesFromUrl( new URL( s ),
return true;
}
- public static final boolean testNHXparsingFromURL() {
+ private static final boolean testNHXparsingFromURL() {
try {
final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh";
final URL u = new URL( s );
return true;
}
- public static boolean testOverlapRemoval() {
+ private static boolean testOverlapRemoval() {
try {
final Domain d0 = new BasicDomain( "d0", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 0.1, 1 );
final Domain d1 = new BasicDomain( "d1", ( short ) 7, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
return true;
}
- public static final boolean testPfamTreeReading() {
+ private static final boolean testPfamTreeReading() {
try {
final URL u = new URL( WebserviceUtil.PFAM_SERVER + "/family/PF" + "01849" + "/tree/download" );
final NHXParser parser = new NHXParser();
parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
parser.setReplaceUnderscores( false );
parser.setGuessRootedness( true );
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final Phylogeny[] phys = factory.create( u.openStream(), parser );
+ final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, parser);
if ( ( phys == null ) || ( phys.length != 1 ) ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace();
+ return false;
}
return true;
}
- public static final boolean testPhyloXMLparsingFromURL() {
+ private static final boolean testPhyloXMLparsingFromURL() {
try {
final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/archaeopteryx_a/apaf_bcl2.xml";
final URL u = new URL( s );
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final Phylogeny[] phys = factory.create( u.openStream(), PhyloXmlParser.createPhyloXmlParser() );
+ final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, PhyloXmlParser.createPhyloXmlParser() );
+
if ( ( phys == null ) || ( phys.length != 2 ) ) {
return false;
}
+ final Phylogeny[] phys2 = ForesterUtil.readPhylogeniesFromUrl( u, PhyloXmlParser.createPhyloXmlParser() );
+
+ if ( ( phys2 == null ) || ( phys2.length != 2 ) ) {
+ return false;
+ }
}
catch ( final Exception e ) {
e.printStackTrace();
+ return false;
}
return true;
}
- public static final boolean testToLReading() {
+ private static final boolean testToLReading() {
try {
final URL u = new URL( WebserviceUtil.TOL_URL_BASE + "15079" );
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final Phylogeny[] phys = factory.create( u.openStream(), new TolParser() );
+ final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, new TolParser() );
if ( ( phys == null ) || ( phys.length != 1 ) ) {
return false;
}
if ( phys[ 0 ].getNumberOfExternalNodes() < 5 ) {
return false;
}
+ //
+ final URL u2 = new URL( WebserviceUtil.TOL_URL_BASE + "17706" );
+ final Phylogeny[] phys2 = ForesterUtil.readPhylogeniesFromUrl( u2, new TolParser() );
+ if ( ( phys2 == null ) || ( phys2.length != 1 ) ) {
+ return false;
+ }
+ if ( !phys2[ 0 ].getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "17706" ) ) {
+ return false;
+ }
+ if ( phys2[ 0 ].getNumberOfExternalNodes() < 5 ) {
+ return false;
+ }
}
catch ( final Exception e ) {
e.printStackTrace();
+ return false;
}
return true;
}
- public static final boolean testTreeBaseReading() {
+ private static final boolean testTreeBaseReading() {
try {
- final URL u = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "825?format=nexus" );
+ final URL u = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "72557?format=nexus" );
final NexusPhylogeniesParser parser = new NexusPhylogeniesParser();
parser.setReplaceUnderscores( true );
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final Phylogeny[] phys = factory.create( u.openStream(), parser );
+ final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, parser );
if ( ( phys == null ) || ( phys.length != 1 ) ) {
return false;
}
+ final URL u_1 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "2406?format=nexus" );
+ final NexusPhylogeniesParser parser_1 = new NexusPhylogeniesParser();
+ final Phylogeny[] phys_1 = ForesterUtil.readPhylogeniesFromUrl( u_1, parser_1 );
+ if ( ( phys_1 == null ) || ( phys_1.length != 1 ) ) {
+ return false;
+ }
+ final URL u_2 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "422?format=nexus" );
+ final NexusPhylogeniesParser parser_2 = new NexusPhylogeniesParser();
+ final Phylogeny[] phys_2 = ForesterUtil.readPhylogeniesFromUrl( u_2, parser_2 );
+ if ( ( phys_2 == null ) || ( phys_2.length != 1 ) ) {
+ return false;
+ }
+ final URL u_3 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "2654?format=nexus" );
+ final NexusPhylogeniesParser parser_3 = new NexusPhylogeniesParser();
+ final Phylogeny[] phys_3 = ForesterUtil.readPhylogeniesFromUrl( u_3, parser_3 );
+ if ( ( phys_3 == null ) || ( phys_3.length != 1 ) ) {
+ return false;
+ }
+ final URL u_4 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "825?format=nexus" );
+ final NexusPhylogeniesParser parser_4 = new NexusPhylogeniesParser();
+ final Phylogeny[] phys_4 = ForesterUtil.readPhylogeniesFromUrl( u_4, parser_4 );
+ if ( ( phys_4 == null ) || ( phys_4.length != 1 ) ) {
+ return false;
+ }
final URL u2 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "15613?format=nexus" );
final NexusPhylogeniesParser parser2 = new NexusPhylogeniesParser();
parser2.setReplaceUnderscores( true );
- final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
- final Phylogeny[] phys2 = factory2.create( u2.openStream(), parser2 );
+ final Phylogeny[] phys2 = ForesterUtil.readPhylogeniesFromUrl( u2, parser2 );
if ( ( phys2 == null ) || ( phys2.length != 9 ) ) {
return false;
}
+ final URL u3 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "14909?format=nexus" );
+ final NexusPhylogeniesParser parser3 = new NexusPhylogeniesParser();
+ final Phylogeny[] phys3 = ForesterUtil.readPhylogeniesFromUrl( u3, parser3 );
+ if ( ( phys3 == null ) || ( phys3.length != 2 ) ) {
+ return false;
+ }
+ final Phylogeny[] phys4 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "14525?format=nexus" ),
+ new NexusPhylogeniesParser() );
+ if ( ( phys4 == null ) || ( phys4.length != 1 ) ) {
+ return false;
+ }
+ final Phylogeny[] phys5 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "15632?format=nexus" ) ,
+ new NexusPhylogeniesParser() );
+ if ( ( phys5 == null ) || ( phys5.length != 1 ) ) {
+ return false;
+ }
+ final Phylogeny[] phys6 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "10190?format=nexus" ) ,
+ new NexusPhylogeniesParser() );
+ if ( ( phys6 == null ) || ( phys6.length != 1 ) ) {
+ return false;
+ }
+ final Phylogeny[] phys7 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "13246?format=nexus" ) ,
+ new NexusPhylogeniesParser() );
+ if ( ( phys7 == null ) || ( phys7.length != 2 ) ) {
+ return false;
+ }
+ final Phylogeny[] phys8 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "11662?format=nexus" ) ,
+ new NexusPhylogeniesParser() );
+ if ( ( phys8 == null ) || ( phys8.length != 2 ) ) {
+ return false;
+ }
+ final Phylogeny[] phys9 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "562?format=nexus" ) ,
+ new NexusPhylogeniesParser() );
+ if ( ( phys9 == null ) || ( phys9.length != 4 ) ) {
+ return false;
+ }
+ final Phylogeny[] phys16424 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "16424?format=nexus" ) ,
+ new NexusPhylogeniesParser() );
+ if ( ( phys16424 == null ) || ( phys16424.length != 1 ) ) {
+ return false;
+ }
+ final Phylogeny[] phys17878 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "17878?format=nexus" ) ,
+ new NexusPhylogeniesParser() );
+ if ( ( phys17878 == null ) || ( phys17878.length != 17 ) ) {
+ return false;
+ }
+ final Phylogeny[] phys18804 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "18804?format=nexus" ) ,
+ new NexusPhylogeniesParser() );
+ if ( ( phys18804 == null ) || ( phys18804.length != 2 ) ) {
+ return false;
+ }
+ final Phylogeny[] phys346 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "346?format=nexus" ) ,
+ new NexusPhylogeniesParser() );
+ if ( ( phys346 == null ) || ( phys346.length != 1 ) ) {
+ return false;
+ }
}
catch ( final Exception e ) {
e.printStackTrace();
+ return false;
}
return true;
}
- public static final boolean testTreeFamReading() {
+ private static final boolean testTreeFamReading() {
try {
final URL u = new URL( WebserviceUtil.TREE_FAM_URL_BASE + "101004" + "/tree/newick" );
final NHXParser parser = new NHXParser();
parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
parser.setReplaceUnderscores( false );
parser.setGuessRootedness( true );
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final Phylogeny[] phys = factory.create( u.openStream(), parser );
+ final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, parser );
if ( ( phys == null ) || ( phys.length != 1 ) ) {
return false;
}
}
catch ( final Exception e ) {
e.printStackTrace();
+ return false;
}
return true;
}
}
return true;
}
+
+ private static boolean testUTF8ParsingFromFile() {
+ try {
+ final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
+ final Phylogeny[] phylogenies_xml = ParserBasedPhylogenyFactory.getInstance().create( new File( Test.PATH_TO_TEST_DATA + "chars.xml" ),
+ xml_parser );
+ if ( xml_parser.getErrorCount() > 0 ) {
+ System.out.println( xml_parser.getErrorMessages().toString() );
+ return false;
+ }
+ if ( phylogenies_xml.length != 1 ) {
+ return false;
+ }
+
+ final Phylogeny[] phylogenies_xml2 = ParserBasedPhylogenyFactory.getInstance().create( new StringBuffer( phylogenies_xml[0].toPhyloXML( 0 )),
+ xml_parser );
+
+ final Phylogeny[] phylogenies_nh = ParserBasedPhylogenyFactory.getInstance().create( new File( Test.PATH_TO_TEST_DATA + "chars.nh" ), new NHXParser() );
+ if ( phylogenies_nh.length != 1 ) {
+ return false;
+ }
+
+ final Phylogeny[] phylogenies_nex = ParserBasedPhylogenyFactory.getInstance().create( new File( Test.PATH_TO_TEST_DATA + "chars.nex" ), new NexusPhylogeniesParser() );
+ if ( phylogenies_nex.length != 1 ) {
+ return false;
+ }
+
+ final String[] xml_n = phylogenies_xml[0].getAllExternalNodeNames();
+ final String[] xml_n2 = phylogenies_xml2[0].getAllExternalNodeNames();
+ final String[] nh_n = phylogenies_nh[0].getAllExternalNodeNames();
+ final String[] nex_n = phylogenies_nex[0].getAllExternalNodeNames();
+ final String n0 = "AQ~!@#$%^&*()_+-=\\{}|;:\"<>?,./";
+ final String n1 = "€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“”•–—˜˜˜™š›œžŸ¡¢£¤¥¦§¨©ª«¬®¯°±¹²³´µ¶·¸º»¼¿À÷þÿ";
+ final String n2 = "漢字ひらがなカタカナ";
+ final String n3 = "อักษรไทย";
+ final String n4 = "繁體字";
+ final String n5 = "한글";
+ final String n6 = "देवनागरी";
+
+ final String n7 = "chữ Quốc ngữ";
+ final String n8 = "ру́сский язы́к";
+ final String n9 = "អក្សរខ្មែរ";
+
+ if ( !xml_n[0].equals( n0 ) ) {
+ System.out.println( xml_n[0] );
+ System.out.println( n0 );
+ return false;
+ }
+ if ( !xml_n2[0].equals( n0 ) ) {
+ System.out.println( xml_n2[0] );
+ System.out.println( n0 );
+ return false;
+ }
+ if ( !nh_n[0].equals( n0 ) ) {
+ System.out.println( nh_n[0] );
+ System.out.println( n0 );
+ return false;
+ }
+ if ( !nex_n[0].equals( n0 ) ) {
+ System.out.println( nex_n[0] );
+ System.out.println( n0 );
+ return false;
+ }
+
+ if ( !xml_n[1].equals( n1 ) ) {
+ System.out.println( xml_n[1] );
+ System.out.println( n1 );
+ return false;
+ }
+ if ( !xml_n2[1].equals( n1 ) ) {
+ System.out.println( xml_n2[1] );
+ System.out.println( n1 );
+ return false;
+ }
+ if ( !nh_n[1].equals( n1 ) ) {
+ System.out.println( nh_n[1] );
+ System.out.println( n1 );
+ return false;
+ }
+ if ( !nex_n[1].equals( n1 ) ) {
+ System.out.println( nex_n[1] );
+ System.out.println( n1 );
+ return false;
+ }
+
+ if ( !xml_n[2].equals( n2 ) ) {
+ System.out.println( xml_n[2] );
+ System.out.println( n2 );
+ return false;
+ }
+ if ( !xml_n2[2].equals( n2 ) ) {
+ System.out.println( xml_n2[2] );
+ System.out.println( n2 );
+ return false;
+ }
+ if ( !nh_n[2].equals( n2 ) ) {
+ System.out.println( nh_n[2] );
+ System.out.println( n2 );
+ return false;
+ }
+ if ( !nex_n[2].equals( n2 ) ) {
+ System.out.println( nex_n[2] );
+ System.out.println( n2 );
+ return false;
+ }
+ //
+ if ( !xml_n[3].equals( n3 ) ) {
+ System.out.println( xml_n[3] );
+ System.out.println( n3 );
+ return false;
+ }
+ if ( !xml_n2[3].equals( n3 ) ) {
+ System.out.println( xml_n2[3] );
+ System.out.println( n3 );
+ return false;
+ }
+ if ( !nh_n[3].equals( n3 ) ) {
+ System.out.println( nh_n[3] );
+ System.out.println( n3 );
+ return false;
+ }
+ if ( !nex_n[3].equals( n3 ) ) {
+ System.out.println( nex_n[3] );
+ System.out.println( n3 );
+ return false;
+ }
+ //
+ if ( !xml_n[4].equals( n4 ) ) {
+ System.out.println( xml_n[4] );
+ System.out.println( n4 );
+ return false;
+ }
+ if ( !nh_n[4].equals( n4 ) ) {
+ System.out.println( nh_n[4] );
+ System.out.println( n4 );
+ return false;
+ }
+ if ( !nex_n[4].equals( n4 ) ) {
+ System.out.println( nex_n[4] );
+ System.out.println( n4 );
+ return false;
+ }
+ //
+ if ( !xml_n[5].equals( n5 ) ) {
+ System.out.println( xml_n[5] );
+ System.out.println( n5 );
+ return false;
+ }
+ if ( !nh_n[5].equals( n5 ) ) {
+ System.out.println( nh_n[5] );
+ System.out.println( n5 );
+ return false;
+ }
+ if ( !nex_n[5].equals( n5 ) ) {
+ System.out.println( nex_n[5] );
+ System.out.println( n5 );
+ return false;
+ }
+ //
+ if ( !xml_n[6].equals( n6 ) ) {
+ System.out.println( xml_n[6] );
+ System.out.println( n6 );
+ return false;
+ }
+ if ( !nh_n[6].equals( n6 ) ) {
+ System.out.println( nh_n[6] );
+ System.out.println( n6 );
+ return false;
+ }
+ if ( !nex_n[6].equals( n6 ) ) {
+ System.out.println( nex_n[6] );
+ System.out.println( n6 );
+ return false;
+ }
+ //
+ if ( !xml_n[7].equals( n7 ) ) {
+ System.out.println( xml_n[7] );
+ System.out.println( n7 );
+ return false;
+ }
+ if ( !nh_n[7].equals( n7 ) ) {
+ System.out.println( nh_n[7] );
+ System.out.println( n7 );
+ return false;
+ }
+ if ( !nex_n[7].equals( n7 ) ) {
+ System.out.println( nex_n[7] );
+ System.out.println( n7 );
+ return false;
+ }
+ if ( !xml_n[8].equals( n8 ) ) {
+ System.out.println( xml_n[8] );
+ System.out.println( n8 );
+ return false;
+ }
+ if ( !nh_n[8].equals( n8 ) ) {
+ System.out.println( nh_n[8] );
+ System.out.println( n8 );
+ return false;
+ }
+ if ( !nex_n[8].equals( n8 ) ) {
+ System.out.println( nex_n[8] );
+ System.out.println( n8 );
+ return false;
+ }
+ if ( !xml_n[9].equals( n9 ) ) {
+ System.out.println( xml_n[9] );
+ System.out.println( n9 );
+ return false;
+ }
+ if ( !xml_n2[9].equals( n9 ) ) {
+ System.out.println( xml_n2[9] );
+ System.out.println( n9 );
+ return false;
+ }
+ if ( !nh_n[9].equals( n9 ) ) {
+ System.out.println( nh_n[9] );
+ System.out.println( n9 );
+ return false;
+ }
+ if ( !nex_n[9].equals( n9 ) ) {
+ System.out.println( nex_n[9] );
+ System.out.println( n9 );
+ return false;
+ }
+ if (!phylogenies_xml[0].toNewHampshire().equals(
+ phylogenies_nh[0].toNewHampshire() ) ) {
+ System.out.println( phylogenies_xml[0].toNewHampshire() );
+ System.out.println( phylogenies_nh[0].toNewHampshire() );
+ return false;
+ }
+ if (!phylogenies_xml[0].toNewHampshire().equals(
+ phylogenies_nex[0].toNewHampshire() ) ) {
+ System.out.println( phylogenies_xml[0].toNewHampshire() );
+ System.out.println( phylogenies_nex[0].toNewHampshire() );
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+
private static boolean testBasicPhyloXMLparsing() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
- final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
+ final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml" ),
xml_parser );
if ( xml_parser.getErrorCount() > 0 ) {
System.out.println( xml_parser.getErrorMessages().toString() );
else {
xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
}
- final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
+ final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml" ),
xml_parser );
if ( xml_parser.getErrorCount() > 0 ) {
System.out.println( xml_parser.getErrorMessages().toString() );
}
if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
.equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489–493." ) ) ) {
+ System.out.println( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription() );
return false;
}
if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
}
}
- final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
+ final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml" ),
xml_parser );
if ( xml_parser.getErrorCount() > 0 ) {
System.out.println( xml_parser.getErrorMessages().toString() );
return false;
}
final String x2 = Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml";
- final Phylogeny[] phylogenies_1 = factory.create( x2, xml_parser );
+ final Phylogeny[] phylogenies_1 = factory.create( new File( x2 ), xml_parser );
if ( xml_parser.getErrorCount() > 0 ) {
System.out.println( "errors:" );
System.out.println( xml_parser.getErrorMessages().toString() );
if ( phylogenies_1.length != 4 ) {
return false;
}
- final Phylogeny[] phylogenies_2 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml",
+ final Phylogeny[] phylogenies_2 = factory.create( new File(Test.PATH_TO_TEST_DATA + "phyloxml_test_t3.xml" ),
xml_parser );
if ( xml_parser.getErrorCount() > 0 ) {
System.out.println( "errors:" );
if ( phylogenies_2[ 0 ].getNumberOfExternalNodes() != 2 ) {
return false;
}
- final Phylogeny[] phylogenies_3 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml",
+ final Phylogeny[] phylogenies_3 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_test_t4.xml" ),
xml_parser );
if ( xml_parser.getErrorCount() > 0 ) {
System.out.println( xml_parser.getErrorMessages().toString() );
if ( !a.getNode( "node b1" ).getNodeData().getTaxonomy().getCommonName().equals( "b1 species" ) ) {
return false;
}
- final Phylogeny[] phylogenies_4 = factory.create( Test.PATH_TO_TEST_DATA + "special_characters.xml",
+ final Phylogeny[] phylogenies_4 = factory.create( new File( Test.PATH_TO_TEST_DATA + "special_characters.xml") ,
xml_parser );
if ( xml_parser.getErrorCount() > 0 ) {
System.out.println( xml_parser.getErrorMessages().toString() );
return false;
}
final StringBuffer sb5 = new StringBuffer( "(((A11:2)A1:2,(A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:3,D:8)" );
- final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
+ final Phylogeny t5 = factory.create( sb5.toString(), new NHXParser() )[ 0 ];
if ( t5.getNumberOfExternalNodes() != 8 ) {
return false;
}
return false;
}
final StringBuffer sb6 = new StringBuffer( "(X,Y,Z,(((A111)A11:2)A1:2,(X,Y,Z,A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:3,D:8)" );
- final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
+ final Phylogeny t6 = factory.create( sb6.toString(), new NHXParser() )[ 0 ];
if ( t6.getHeight() != 15 ) {
return false;
}
final StringBuffer sb7 = new StringBuffer( "(((A11:2)A1:2,(A21:1,A22:2,A23)A2:11,A3:2)A:2,B:10,C:15,D:8)" );
- final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
+ final Phylogeny t7 = factory.create( sb7.toString(), new NHXParser() )[ 0 ];
if ( t7.getHeight() != 15 ) {
return false;
}
final StringBuffer sb8 = new StringBuffer( "(((A11:11)A1:2,(A21:2,A22:2,A23,A24,AA:)A2:11,A3:2)A:2,B:15,C:15,D:15)" );
- final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
+ final Phylogeny t8 = factory.create( sb8.toString(), new NHXParser() )[ 0 ];
if ( t8.getNumberOfExternalNodes() != 10 ) {
return false;
}
System.out.println( entry.getAnnotations().first().getRefSource() );
return false;
}
- if ( entry.getCrossReferences().size() != 5 ) {
+ if ( entry.getCrossReferences().size() < 1 ) {
return false;
}
final SequenceDatabaseEntry entry1 = SequenceDbWsTools.obtainEntry( "ABJ16409" );
System.out.println( entry1.getGeneName() );
return false;
}
- if ( entry1.getCrossReferences().size() != 6 ) {
+ if ( entry1.getCrossReferences().size() < 1 ) {
return false;
}
final SequenceDatabaseEntry entry2 = SequenceDbWsTools.obtainEntry( "NM_184234" );
System.out.println( entry2.getGeneName() );
return false;
}
- if ( entry2.getCrossReferences().size() != 3 ) {
+ if ( entry2.getCrossReferences().size() < 1 ) {
+ return false;
+ }
+ if ( !entry2.getChromosome().equals( "20" ) ) {
+ return false;
+ }
+ if ( !entry2.getMap().equals( "20q11.22" ) ) {
return false;
}
- //
final SequenceDatabaseEntry entry3 = SequenceDbWsTools.obtainEntry( "HM043801" );
if ( !entry3.getAccession().equals( "HM043801" ) ) {
return false;
if ( !ForesterUtil.isEmpty( entry3.getGeneName() ) ) {
return false;
}
- if ( entry3.getCrossReferences().size() < 7 ) {
+ if ( entry3.getCrossReferences().size() < 1 ) {
return false;
}
final SequenceDatabaseEntry entry4 = SequenceDbWsTools.obtainEntry( "AAA36557.1" );
System.out.println( entry4.getGeneName() );
return false;
}
- // if ( !entry4.getChromosome().equals( "ras" ) ) {
- // System.out.println( entry4.getChromosome() );
- // return false;
- // }
- // if ( !entry4.getMap().equals( "ras" ) ) {
- // System.out.println( entry4.getMap() );
- // return false;
- // }
- //TODO FIXME gi...
- //
- //TODO fails:
- // final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "M30539" );
- // if ( !entry5.getAccession().equals( "HM043801" ) ) {
- // return false;
- // }
final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "AAZ45343.1" );
if ( !entry5.getAccession().equals( "AAZ45343" ) ) {
return false;
System.out.println( entry5.getTaxonomyIdentifier() );
return false;
}
+ final SequenceDatabaseEntry entry6 = SequenceDbWsTools.obtainEntry( "M30539" );
+ if ( !entry6.getAccession().equals( "M30539" ) ) {
+ return false;
+ }
+ if ( !entry6.getGeneName().equals( "ras" ) ) {
+ return false;
+ }
+ if ( !entry6.getSequenceName().equals( "Human SK2 c-Ha-ras-1 oncogene-encoded protein gene, exon 1" ) ) {
+ return false;
+ }
+ if ( !entry6.getTaxonomyIdentifier().equals( "9606" ) ) {
+ return false;
+ }
+ if ( !entry6.getTaxonomyScientificName().equals( "Homo sapiens" ) ) {
+ return false;
+ }
+ if ( entry6.getCrossReferences().size() < 1 ) {
+ return false;
+ }
}
catch ( final IOException e ) {
System.out.println();
private static boolean testFastaParser() {
try {
- if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) {
+ FileInputStream fis1 = new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" );
+ if ( !FastaParser.isLikelyFasta( fis1 ) ) {
+ fis1.close();
return false;
}
- if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) {
+ else {
+ fis1.close();
+ }
+ FileInputStream fis2 = new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" );
+ if ( FastaParser.isLikelyFasta( fis2 ) ) {
+ fis2.close();
return false;
}
+ else {
+ fis2.close();
+ }
final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) );
if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) {
return false;
PhylogenyNode n;
List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
- final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
+ final Phylogeny t0 = factory.create( sb0.toString(), new NHXParser() )[ 0 ];
t0.getNode( "cd" ).setCollapse( true );
t0.getNode( "cde" ).setCollapse( true );
n = t0.getFirstExternalNode();
}
ext.clear();
final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
- final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
+ final Phylogeny t1 = factory.create( sb1.toString(), new NHXParser() )[ 0 ];
t1.getNode( "ab" ).setCollapse( true );
t1.getNode( "cd" ).setCollapse( true );
t1.getNode( "cde" ).setCollapse( true );
}
ext.clear();
final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
- final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
+ final Phylogeny t2 = factory.create( sb2.toString(), new NHXParser() )[ 0 ];
t2.getNode( "ab" ).setCollapse( true );
t2.getNode( "cd" ).setCollapse( true );
t2.getNode( "cde" ).setCollapse( true );
}
ext.clear();
final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
- final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
+ final Phylogeny t3 = factory.create( sb3.toString(), new NHXParser() )[ 0 ];
t3.getNode( "ab" ).setCollapse( true );
t3.getNode( "cd" ).setCollapse( true );
t3.getNode( "cde" ).setCollapse( true );
}
ext.clear();
final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
- final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
+ final Phylogeny t4 = factory.create( sb4.toString(), new NHXParser() )[ 0 ];
t4.getNode( "ab" ).setCollapse( true );
t4.getNode( "cd" ).setCollapse( true );
t4.getNode( "cde" ).setCollapse( true );
return false;
}
final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
- final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
+ final Phylogeny t5 = factory.create( sb5.toString(), new NHXParser() )[ 0 ];
ext.clear();
n = t5.getFirstExternalNode();
while ( n != null ) {
return false;
}
final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
- final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
+ final Phylogeny t6 = factory.create( sb6.toString(), new NHXParser() )[ 0 ];
ext.clear();
t6.getNode( "ab" ).setCollapse( true );
n = t6.getNode( "ab" );
return false;
}
final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
- final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
+ final Phylogeny t7 = factory.create( sb7.toString(), new NHXParser() )[ 0 ];
ext.clear();
t7.getNode( "cd" ).setCollapse( true );
n = t7.getNode( "a" );
return false;
}
final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
- final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
+ final Phylogeny t8 = factory.create( sb8.toString(), new NHXParser() )[ 0 ];
ext.clear();
t8.getNode( "cd" ).setCollapse( true );
t8.getNode( "c" ).setCollapse( true );
return false;
}
final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
- final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
+ final Phylogeny t9 = factory.create( sb9.toString(), new NHXParser() )[ 0 ];
ext.clear();
t9.getNode( "gh" ).setCollapse( true );
n = t9.getNode( "a" );
return false;
}
final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
- final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
+ final Phylogeny t10 = factory.create( sb10.toString(), new NHXParser() )[ 0 ];
ext.clear();
t10.getNode( "gh" ).setCollapse( true );
t10.getNode( "g" ).setCollapse( true );
return false;
}
final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
- final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
+ final Phylogeny t11 = factory.create( sb11.toString(), new NHXParser() )[ 0 ];
ext.clear();
t11.getNode( "gh" ).setCollapse( true );
t11.getNode( "fgh" ).setCollapse( true );
return false;
}
final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
- final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
+ final Phylogeny t12 = factory.create( sb12.toString(), new NHXParser() )[ 0 ];
ext.clear();
t12.getNode( "gh" ).setCollapse( true );
t12.getNode( "fgh" ).setCollapse( true );
return false;
}
final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
- final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
+ final Phylogeny t13 = factory.create( sb13.toString(), new NHXParser() )[ 0 ];
ext.clear();
t13.getNode( "ab" ).setCollapse( true );
t13.getNode( "b" ).setCollapse( true );
return false;
}
final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
- final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
+ final Phylogeny t14 = factory.create( sb14.toString(), new NHXParser() )[ 0 ];
ext.clear();
t14.getNode( "ab" ).setCollapse( true );
t14.getNode( "a" ).setCollapse( true );
return false;
}
final StringBuffer sb15 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
- final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
+ final Phylogeny t15 = factory.create( sb15.toString(), new NHXParser() )[ 0 ];
ext.clear();
t15.getNode( "ab" ).setCollapse( true );
t15.getNode( "a" ).setCollapse( true );
//
//
final StringBuffer sb16 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
- final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
+ final Phylogeny t16 = factory.create( sb16.toString(), new NHXParser() )[ 0 ];
ext.clear();
t16.getNode( "ab" ).setCollapse( true );
t16.getNode( "a" ).setCollapse( true );
if ( !p1b.toNewHampshire().equals( "(';A;',';B;1;');" ) ) {
return false;
}
- final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ), new NHXParser() )[ 0 ];
+ final Phylogeny p2 = factory.create( new StringBuffer( "(A,B2)" ).toString(), 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 p5 = factory.create( new StringBuffer( "(A,B5);" ).toString(), 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() );
if ( p46.length != 0 ) {
return false;
}
- final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ), new NHXParser() )[ 0 ];
+ final Phylogeny p47 = factory.create( new StringBuffer( "((A,B)ab:2[0.44],C)" ).toString(), new NHXParser() )[ 0 ];
if ( !isEqual( 0.44, p47.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
return false;
}
- final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
+ final Phylogeny p48 = factory.create( new StringBuffer( "((A,B)ab:2[88],C)" ).toString(), new NHXParser() )[ 0 ];
if ( !isEqual( 88, p48.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
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)" ),
+ .create( new StringBuffer( "((A,B)a[comment:a,b;(a)]b:2[0.44][comment(a,b,b);],C)" ).toString(),
new NHXParser() )[ 0 ];
if ( !isEqual( 0.44, p49.getNode( "ab" ).getBranchData().getConfidence( 0 ).getValue() ) ) {
return false;
}
- final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
+ final Phylogeny p50 = factory.create( new StringBuffer( "((\"A\",B)ab:2[88],C)" ).toString(), new NHXParser() )[ 0 ];
if ( p50.getNode( "A" ) == null ) {
return false;
}
.equals( "((A,B)88:2.0,C);" ) ) {
return false;
}
- final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
+ final Phylogeny p51 = factory.create( new StringBuffer( "((\"A(A\",B)ab:2[88],C)" ).toString(), new NHXParser() )[ 0 ];
if ( p51.getNode( "A(A" ) == null ) {
return false;
}
- final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ), new NHXParser() )[ 0 ];
+ final Phylogeny p52 = factory.create( new StringBuffer( "(('A(A',B)ab:2[88],C)" ).toString(), new NHXParser() )[ 0 ];
if ( p52.getNode( "A(A" ) == null ) {
return false;
}
final Phylogeny p53 = factory
- .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ),
+ .create( new StringBuffer( "(('A(A',\"B (x (a' ,b) f(x);\"[com])[ment]ab:2[88],C)" ).toString(),
new NHXParser() )[ 0 ];
if ( p53.getNode( "B (x (a' ,b) f(x);" ) == null ) {
return false;
}
- final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ), new NHXParser() )[ 0 ];
+ final Phylogeny p54 = factory.create( new StringBuffer( "((A,B):[88],C)" ).toString(), new NHXParser() )[ 0 ];
if ( p54.getNode( "A" ) == null ) {
return false;
}
return false;
}
final Phylogeny p55 = factory
- .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1x\":0.0798012);" ),
+ .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1x\":0.0798012);" ).toString(),
new NHXParser() )[ 0 ];
if ( !p55
.toNewHampshire()
return false;
}
final Phylogeny p56 = factory
- .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ),
+ .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ).toString(),
new NHXParser() )[ 0 ];
if ( !p56
.toNewHampshire()
return false;
}
final Phylogeny p57 = factory
- .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ),
+ .create( new StringBuffer( "((\"lcl|HPV32_L1.:1 s\":0.195593,\"lcl|HPV30_L1.1|;a\":0.114\n237):0.0359322,\"lcl|HPV56_L1.1|,d\":0.0727412,\"lcl|HPV66_L1.1:x\":0.0798012);" ).toString(),
new NHXParser() )[ 0 ];
if ( !p57
.toNewHampshire()
return false;
}
final String s58 = "('Homo \"man\" sapiens:1',\"Homo 'man' sapiens;\")';root \"1_ )';";
- final Phylogeny p58 = factory.create( new StringBuffer( s58 ), new NHXParser() )[ 0 ];
+ final Phylogeny p58 = factory.create( s58, new NHXParser() )[ 0 ];
if ( !p58.toNewHampshire().equals( s58 ) ) {
System.out.println( p58.toNewHampshire() );
return false;
}
final String s59 = "('Homo \"man sapiens:1',\"Homo 'man sapiens\")\"root; '1_ )\";";
- final Phylogeny p59 = factory.create( new StringBuffer( s59 ), new NHXParser() )[ 0 ];
+ final Phylogeny p59 = factory.create( s59 , new NHXParser() )[ 0 ];
if ( !p59.toNewHampshire().equals( s59 ) ) {
System.out.println( p59.toNewHampshire() );
return false;
}
final String s60 = "('\" ;,:\":\"',\"'abc def' g's_\",'=:0.45+,.:%~`!@#$%^&*()_-+={} | ;,');";
- final Phylogeny p60 = factory.create( new StringBuffer( s60 ), new NHXParser() )[ 0 ];
+ final Phylogeny p60 = factory.create( s60, new NHXParser() )[ 0 ];
if ( !p60.toNewHampshire().equals( s60 ) ) {
System.out.println( p60.toNewHampshire() );
return false;
}
final String s61 = "('H[omo] \"man\" sapiens:1',\"H[omo] 'man' sapiens;\",H[omo] sapiens)';root \"1_ )';";
- final Phylogeny p61 = factory.create( new StringBuffer( s61 ), new NHXParser() )[ 0 ];
+ final Phylogeny p61 = factory.create( s61, new NHXParser() )[ 0 ];
if ( !p61.toNewHampshire()
.equals( "('H{omo} \"man\" sapiens:1',\"H{omo} 'man' sapiens;\",Hsapiens)';root \"1_ )';" ) ) {
System.out.println( p61.toNewHampshire() );
}
return true;
}
-
+
+ private static boolean testNHParsingSpecialChars() {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final String i0 = "(A!+=~QWERTY!@#$%^&*-,€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“”•–—˜˜˜™š›œžŸ¡¢£¤¥¦§¨©ª«¬®¯°±¹²³´µ¶·¸º»¼¿À÷þÿ)";
+ final Phylogeny p0 = factory.create( i0, new NHXParser() )[ 0 ];
+ if ( !p0.toNewHampshireX().equals( i0 ) ) {
+ System.out.println();
+ System.out.println( p0.toNewHampshireX() );
+ System.out.println( i0 );
+ return false;
+ }
+ final String i1 = "(हिंदी,한글,ไทย,'Tiếng Việt',ひらがなカタカナ漢字,繁體字,русский)";
+ final Phylogeny p1 = factory.create( i1, new NHXParser() )[ 0 ];
+ if ( !p1.toNewHampshireX().equals( i1 ) ) {
+ System.out.println();
+ System.out.println( p1.toNewHampshireX() );
+ System.out.println( i1 );
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+
+
private static boolean testNHParsingIter() {
try {
final String p0_str = "(A,B);";
return true;
}
+
+ private static boolean testNHXNodeParsing2() {
+ try {
+
+ final PhylogenyNode n0_0 = PhylogenyNode
+ .createInstanceFromNhxString( "n0:[ignore me 123]:1E-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+ if ( !n0_0.getName().equals( "n0" ) ) {
+ return false;
+ }
+ if ( !isEqual( n0_0.getDistanceToParent(), 0.001 ) ) {
+ return false;
+ }
+ final PhylogenyNode n0_1 = PhylogenyNode
+ .createInstanceFromNhxString( "n0[ignore me 123]:1E-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+ if ( !n0_1.getName().equals( "n0" ) ) {
+ return false;
+ }
+ if ( !isEqual( n0_1.getDistanceToParent(), 0.001 ) ) {
+ return false;
+ }
+ final PhylogenyNode n0_2 = PhylogenyNode
+ .createInstanceFromNhxString( "n0:1E-3[ignore me 123]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+ if ( !n0_2.getName().equals( "n0" ) ) {
+ return false;
+ }
+ if ( !isEqual( n0_2.getDistanceToParent(), 0.001 ) ) {
+ return false;
+ }
+ final PhylogenyNode n0_3 = PhylogenyNode
+ .createInstanceFromNhxString( "n0:1E-3:[ignore me 123]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+ if ( !n0_3.getName().equals( "n0" ) ) {
+ return false;
+ }
+ if ( !isEqual( n0_3.getDistanceToParent(), 0.001 ) ) {
+ return false;
+ }
+ final PhylogenyNode n0_4 = PhylogenyNode
+ .createInstanceFromNhxString( "n0:0.001:[ignore me 123]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+ if ( !n0_4.getName().equals( "n0" ) ) {
+ return false;
+ }
+ if ( !isEqual( n0_4.getDistanceToParent(), 0.001 ) ) {
+ return false;
+ }
+ final PhylogenyNode n1_0 = PhylogenyNode
+ .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&!color=#FFFFFF]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+ if ( !n1_0.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+ return false;
+ }
+ if ( n1_0.getBranchData().getBranchColor().getValue().getGreen()!=255 ) {
+ return false;
+ }
+ final PhylogenyNode n1_1 = PhylogenyNode
+ .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&!color=#FFFFFF]:0.001", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+ if ( !n1_1.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+ return false;
+ }
+ if ( n1_1.getBranchData().getBranchColor().getValue().getGreen()!=255 ) {
+ return false;
+ }
+ if ( !isEqual( n1_1.getDistanceToParent(), 0.001 ) ) {
+ return false;
+ }
+ final PhylogenyNode n1_2 = PhylogenyNode
+ .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada:0.001[&!color=#FFFFFF]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+ if ( !n1_2.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+ return false;
+ }
+ if ( n1_2.getBranchData().getBranchColor().getValue().getGreen()!=255 ) {
+ return false;
+ }
+ if ( !isEqual( n1_2.getDistanceToParent(), 0.001 ) ) {
+ return false;
+ }
+ final PhylogenyNode n1_3 = PhylogenyNode
+ .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada:1e-3[&boostrap=69,&!color=#FFFFFF]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+ if ( !n1_3.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+ return false;
+ }
+ if ( n1_3.getBranchData().getBranchColor().getValue().getGreen()!=255 ) {
+ return false;
+ }
+ if ( !isEqual( n1_3.getDistanceToParent(), 0.001 ) ) {
+ return false;
+ }
+ if ( !isEqual( n1_3.getBranchData().getConfidence( 0 ).getValue(), 69 ) ) {
+ return false;
+ }
+ if ( !n1_3.getBranchData().getConfidence( 0 ).getType().equals( "bootstrap" ) ) {
+ return false;
+ }
+ final PhylogenyNode n1_4 = PhylogenyNode
+ .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&bootstrap=69,&!colour=#FFFFFF]:1e-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+ if ( !n1_4.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+ return false;
+ }
+ if ( n1_4.getBranchData().getBranchColor().getValue().getGreen()!=255 ) {
+ return false;
+ }
+ if ( !isEqual( n1_4.getDistanceToParent(), 0.001 ) ) {
+ return false;
+ }
+ if ( !isEqual( n1_4.getBranchData().getConfidence( 0 ).getValue(), 69 ) ) {
+ return false;
+ }
+ if ( !n1_4.getBranchData().getConfidence( 0 ).getType().equals( "bootstrap" ) ) {
+ return false;
+ }
+ final PhylogenyNode n1_5 = PhylogenyNode
+ .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada:1e-3[69.0]", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+ if ( !n1_5.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+ return false;
+ }
+ if ( !isEqual( n1_5.getDistanceToParent(), 0.001 ) ) {
+ return false;
+ }
+ if ( !isEqual( n1_5.getBranchData().getConfidence( 0 ).getValue(), 69 ) ) {
+ return false;
+ }
+ final PhylogenyNode n1_6 = PhylogenyNode
+ .createInstanceFromNhxString( "xyz|A/American_duck/NH/00321/|Duck|Canada[&prob=0.9500000000000000e+00,prob_stddev=0.1100000000000000e+00]:1e-3", NHXParser.TAXONOMY_EXTRACTION.NO, true, true );
+ if ( !n1_6.getName().equals( "xyz|A/American duck/NH/00321/|Duck|Canada" ) ) {
+ return false;
+ }
+
+ if ( !isEqual( n1_6.getDistanceToParent(), 0.001 ) ) {
+ return false;
+ }
+ if ( !isEqual( n1_6.getBranchData().getConfidence( 0 ).getStandardDeviation(), 0.11 ) ) {
+ return false;
+ }
+ if ( !isEqual( n1_6.getBranchData().getConfidence( 0 ).getValue(), 0.95 ) ) {
+ return false;
+ }
+ if ( !n1_6.getBranchData().getConfidence( 0 ).getType().equals( "posterior probability" ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
private static boolean testNHXParsing() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
}
}
- final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml",
+ final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_distribution.xml" ),
xml_parser );
if ( xml_parser.getErrorCount() > 0 ) {
System.out.println( xml_parser.getErrorMessages().toString() );
}
return true;
}
-
- private static boolean testWabiTxSearch() {
- try {
- String result = "";
- result = TxSearch.searchSimple( "nematostella" );
- result = TxSearch.getTxId( "nematostella" );
- if ( !result.equals( "45350" ) ) {
- return false;
- }
- result = TxSearch.getTxName( "45350" );
- if ( !result.equals( "Nematostella" ) ) {
- return false;
- }
- result = TxSearch.getTxId( "nematostella vectensis" );
- if ( !result.equals( "45351" ) ) {
- return false;
- }
- result = TxSearch.getTxName( "45351" );
- if ( !result.equals( "Nematostella vectensis" ) ) {
- return false;
- }
- result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" );
- if ( !result.equals( "536089" ) ) {
- return false;
- }
- result = TxSearch.getTxName( "536089" );
- if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) {
- return false;
- }
- final List<String> queries = new ArrayList<String>();
- queries.add( "Campylobacter coli" );
- queries.add( "Escherichia coli" );
- queries.add( "Arabidopsis" );
- queries.add( "Trichoplax" );
- queries.add( "Samanea saman" );
- queries.add( "Kluyveromyces marxianus" );
- queries.add( "Bacillus subtilis subsp. subtilis str. N170" );
- queries.add( "Bornavirus parrot/PDD/2008" );
- final List<RANKS> ranks = new ArrayList<RANKS>();
- ranks.add( RANKS.SUPERKINGDOM );
- ranks.add( RANKS.KINGDOM );
- ranks.add( RANKS.FAMILY );
- ranks.add( RANKS.GENUS );
- ranks.add( RANKS.TRIBE );
- result = TxSearch.searchLineage( queries, ranks );
- result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true );
- result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true );
- }
- catch ( final Exception e ) {
- System.out.println();
- System.out.println( "the following might be due to absence internet connection:" );
- e.printStackTrace( System.out );
- return false;
- }
- return true;
- }
+
+
}
git://source.jalview.org / jalview.git / blobdiff