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( "MSA entropy: " );
- if ( Test.testMsaEntropy() ) {
- System.out.println( "OK." );
- succeeded++;
- }
- else {
- System.out.println( "failed." );
- failed++;
- }
+
System.out.print( "Basic node methods: " );
if ( Test.testBasicNodeMethods() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
+ System.out.print( "MSA entropy: " );
+ if ( Test.testMsaEntropy() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
if ( PERFORM_DB_TESTS ) {
System.out.print( "Uniprot Entry Retrieval: " );
if ( Test.testUniprotEntryRetrieval() ) {
}
}
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;
}
if ( phys[ 0 ].getNumberOfExternalNodes() < 10 ) {
return false;
}
+ final Phylogeny[] phys2 = ForesterUtil.readPhylogeniesFromUrl( u, parser);
+ if ( ( phys2 == null ) || ( phys2.length != 1 ) ) {
+ return false;
+ }
+ if ( phys2[ 0 ].getNumberOfExternalNodes() != phys[ 0 ].getNumberOfExternalNodes() ) {
+ 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;
}
if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) {
return false;
}
+ if ( !t3.getNode( "root node" ).isDuplication() ) {
+ return false;
+ }
+ if ( !t3.getNode( "node a" ).isDuplication() ) {
+ return false;
+ }
+ if ( t3.getNode( "node a" ).isSpeciation() ) {
+ return false;
+ }
+ if ( t3.getNode( "node bc" ).isDuplication() ) {
+ return false;
+ }
+ if ( !t3.getNode( "node bc" ).isSpeciation() ) {
+ return false;
+ }
if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) {
return false;
}
return false;
}
if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 )
- .getConfidence() != 2144 ) {
+ .getConfidence() != 0 ) {
return false;
}
if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId()
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;
l.add( s2 );
l.add( s3 );
final Msa msa = BasicMsa.createInstance( l );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 0 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 1 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 2 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 3 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 4 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 5 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 6 ) );
- System.out.println();
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 0 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 1 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 2 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 3 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 4 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 5 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 6 ) );
+ //TODO need to DO the tests!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+ //FIXME
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 0 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 1 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 2 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 3 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 4 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 5 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 6 ) );
+ // System.out.println();
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 0 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 1 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 2 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 3 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 4 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 5 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 6 ) );
final List<MolecularSequence> l2 = new ArrayList<MolecularSequence>();
l2.add( BasicSequence.createAaSequence( "1", "AAAAAAA" ) );
l2.add( BasicSequence.createAaSequence( "2", "AAAIACC" ) );
l2.add( BasicSequence.createAaSequence( "21", "AAIIIIF" ) );
l2.add( BasicSequence.createAaSequence( "22", "AIIIVVW" ) );
final Msa msa2 = BasicMsa.createInstance( l2 );
- System.out.println();
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 0 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 1 ) );
- System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 2 ) );
+ // System.out.println();
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 0 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 1 ) );
+ // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 2 ) );
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
if ( !p11.toNewHampshireX().equals( "(('A: \"':0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
return false;
}
- final Phylogeny p12 = factory
- .create( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]",
- new NHXParser() )[ 0 ];
+ final Phylogeny p12 = factory.create( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]",
+ new NHXParser() )[ 0 ];
if ( !p12.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) {
return false;
}
-
-
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
private static boolean testUniprotEntryRetrieval() {
try {
- final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
+ final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 5000 );
if ( !entry.getAccession().equals( "P12345" ) ) {
return false;
}
if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
return false;
}
+ if ( entry.getMolecularSequence() == null ) {
+ return false;
+ }
if ( !entry
.getMolecularSequence()
.getMolecularSequenceAsString()
.startsWith( "MALLHSARVLSGVASAFHPGLAAAASARASSWWAHVEMGPPDPILGVTEAYKRDTNSKKMNLGVGAYRDDNGKPYVLPSVRKAEAQIAAKGLDKEYLPIGGLAEFCRASAELALGENSEV" )
|| !entry.getMolecularSequence().getMolecularSequenceAsString().endsWith( "LAHAIHQVTK" ) ) {
- System.out.println( entry.getMolecularSequence().getMolecularSequenceAsString() );
+ System.out.println( "got: " + entry.getMolecularSequence().getMolecularSequenceAsString() );
+ System.out.println( "expected something else." );
return false;
}
}
e.printStackTrace( System.out );
return true;
}
+ catch ( final NullPointerException f ) {
+ f.printStackTrace( System.out );
+ return false;
+ }
catch ( final Exception e ) {
return false;
}
}
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