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;
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." );
}
}
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;
}
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;
}
return true;
}
+
+
}
git://source.jalview.org / jalview.git / blobdiff