import org.forester.archaeopteryx.TreePanel;
import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
import org.forester.archaeopteryx.tools.RunnableProcess;
+import org.forester.io.parsers.nhx.NHXParser;
import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
+import org.forester.io.parsers.util.ParserUtils;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.data.Identifier;
if ( ( ( tax != null ) && ( isHasAppropriateId( tax ) || !ForesterUtil.isEmpty( tax.getScientificName() )
|| !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) || !ForesterUtil.isEmpty( tax.getCommonName() ) ) )
|| ( allow_to_use_basic_node_names && !ForesterUtil.isEmpty( node.getName() ) ) ) {
- if ( tax != null ) {
+ if ( ( ( tax != null ) && ( isHasAppropriateId( tax )
+ || !ForesterUtil.isEmpty( tax.getScientificName() )
+ || !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) || !ForesterUtil
+ .isEmpty( tax.getCommonName() ) ) ) ) {
uniprot_tax = obtainUniProtTaxonomy( tax, null, qt );
}
else {
if ( tax == null ) {
tax = new Taxonomy();
node.getNodeData().addTaxonomy( tax );
- node.setName( "" );
}
updateTaxonomy( qt, node, tax, uniprot_tax );
}
if ( ForesterUtil.isEmpty( simple_name ) ) {
throw new IllegalArgumentException( "illegal attempt to use empty simple name" );
}
- qt = QUERY_TYPE.SN;
- UniProtTaxonomy ut = obtainTaxonomy( TaxonomyDataManager.getSnTaxCacheMap(), simple_name, qt );
- if ( ut == null ) {
+ UniProtTaxonomy ut = null;
+ final String code = ParserUtils.extractTaxonomyCodeFromNodeName( simple_name,
+ NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !ForesterUtil.isEmpty( code ) ) {
qt = QUERY_TYPE.CODE;
- ut = obtainTaxonomy( TaxonomyDataManager.getCodeTaxCacheMap(), simple_name, qt );
+ ut = obtainTaxonomy( TaxonomyDataManager.getCodeTaxCacheMap(), code, qt );
}
if ( ut == null ) {
- qt = QUERY_TYPE.CN;
- ut = obtainTaxonomy( TaxonomyDataManager.getCnTaxCacheMap(), simple_name, qt );
+ final String sn = ParserUtils.extractScientificNameFromNodeName( simple_name );
+ if ( !ForesterUtil.isEmpty( sn ) ) {
+ qt = QUERY_TYPE.SN;
+ ut = obtainTaxonomy( TaxonomyDataManager.getSnTaxCacheMap(), sn, qt );
+ }
+ }
+ if ( ut == null ) {
+ final String id = ParserUtils
+ .extractUniprotTaxonomyIdFromNodeName( simple_name,
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !ForesterUtil.isEmpty( id ) ) {
+ qt = QUERY_TYPE.ID;
+ ut = obtainTaxonomy( TaxonomyDataManager.getIdTaxCacheMap(), id, qt );
+ }
}
+ //
+ // qt = QUERY_TYPE.SN;
+ // UniProtTaxonomy ut = obtainTaxonomy( TaxonomyDataManager.getSnTaxCacheMap(), simple_name, qt );
+ // if ( ut == null ) {
+ // qt = QUERY_TYPE.CODE;
+ // ut = obtainTaxonomy( TaxonomyDataManager.getCodeTaxCacheMap(), simple_name, qt );
+ // }
+ // if ( ut == null ) {
+ // qt = QUERY_TYPE.CN;
+ // ut = obtainTaxonomy( TaxonomyDataManager.getCnTaxCacheMap(), simple_name, qt );
+ // }
return ut;
}
public final static boolean __SYNTH_LF = false; // TODO remove me
public final static boolean ALLOW_DDBJ_BLAST = false;
public final static String PRG_NAME = "Archaeopteryx";
- final static String VERSION = "0.987 J";
- final static String PRG_DATE = "140319";
+ final static String VERSION = "0.988 SR";
+ final static String PRG_DATE = "140418";
final static String DEFAULT_CONFIGURATION_FILE_NAME = "_aptx_configuration_file";
final static String[] DEFAULT_FONT_CHOICES = { "Arial", "Helvetica",
"Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" };
JMenuItem _lineage_inference;
// file menu:
JMenuItem _open_item;
- JMenuItem _open_url_item;
JMenuItem _save_item;
JMenuItem _save_all_item;
JMenuItem _close_item;
applet = getCurrentTreePanel().obtainApplet();
}
}
- if ( o == _open_url_item ) {
- readPhylogeniesFromURL();
- }
- else if ( o == _exit_item ) {
+ if ( o == _exit_item ) {
close();
}
else if ( o == _gsdi_item ) {
void buildFileMenu() {
_file_jmenu = createMenu( "File", getConfiguration() );
- _file_jmenu.add( _open_url_item = new JMenuItem( "Read tree from URL/webservice..." ) );
- _file_jmenu.addSeparator();
_file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
- customizeJMenuItem( _open_url_item );
customizeJMenuItem( _exit_item );
_jmenubar.add( _file_jmenu );
}
}
}
- abstract void readPhylogeniesFromURL();
-
void readPhylogeniesFromWebservice( final int i ) {
final UrlTreeReader reader = new UrlTreeReader( this, i );
new Thread( reader ).start();
JApplet getApplet() {
return _applet;
}
-
- @Override
- void readPhylogeniesFromURL() {
- throw new NoSuchMethodError( "not implemented" );
- }
}
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
-import java.net.MalformedURLException;
-import java.net.URL;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.data.Taxonomy;
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
-import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.sequence.Sequence;
import org.forester.util.BasicDescriptiveStatistics;
_file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
_file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );
_file_jmenu.addSeparator();
- _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );
- _file_jmenu.addSeparator();
final WebservicesManager webservices_manager = WebservicesManager.getInstance();
_load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager
.getAvailablePhylogeniesWebserviceClients().size() ];
customizeJMenuItem( _open_item );
_open_item
.setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );
- customizeJMenuItem( _open_url_item );
for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );
}
System.exit( 0 );
}
- @Override
- void readPhylogeniesFromURL() {
- URL url = null;
- Phylogeny[] phys = null;
- final String message = "Please enter a complete URL, for example \"http://www.phyloxml.org/examples/apaf.xml\"";
- final String url_string = JOptionPane.showInputDialog( this,
- message,
- "Use URL/webservice to obtain a phylogeny",
- JOptionPane.QUESTION_MESSAGE );
- boolean nhx_or_nexus = false;
- if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
- try {
- url = new URL( url_string );
- PhylogenyParser parser = null;
- if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
- parser = new TolParser();
- }
- else {
- parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()
- .isValidatePhyloXmlAgainstSchema() );
- }
- if ( parser instanceof NexusPhylogeniesParser ) {
- nhx_or_nexus = true;
- }
- else if ( parser instanceof NHXParser ) {
- nhx_or_nexus = true;
- }
- if ( _mainpanel.getCurrentTreePanel() != null ) {
- _mainpanel.getCurrentTreePanel().setWaitCursor();
- }
- else {
- _mainpanel.setWaitCursor();
- }
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- phys = factory.create( url.openStream(), parser );
- }
- catch ( final MalformedURLException e ) {
- JOptionPane.showMessageDialog( this,
- "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
- "Malformed URL",
- JOptionPane.ERROR_MESSAGE );
- }
- catch ( final IOException e ) {
- JOptionPane.showMessageDialog( this,
- "Could not read from " + url + "\n"
- + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
- "Failed to read URL",
- JOptionPane.ERROR_MESSAGE );
- }
- catch ( final Exception e ) {
- JOptionPane.showMessageDialog( this,
- ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
- "Unexpected Exception",
- JOptionPane.ERROR_MESSAGE );
- }
- finally {
- if ( _mainpanel.getCurrentTreePanel() != null ) {
- _mainpanel.getCurrentTreePanel().setArrowCursor();
- }
- else {
- _mainpanel.setArrowCursor();
- }
- }
- if ( ( phys != null ) && ( phys.length > 0 ) ) {
- if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
- for( final Phylogeny phy : phys ) {
- PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
- }
- }
- AptxUtil.addPhylogeniesToTabs( phys,
- new File( url.getFile() ).getName(),
- new File( url.getFile() ).toString(),
- getConfiguration(),
- getMainPanel() );
- _mainpanel.getControlPanel().showWhole();
- }
- }
- activateSaveAllIfNeeded();
- System.gc();
- }
-
void setMsa( final Msa msa ) {
_msa = msa;
}
final private static String tree = NexusConstants.TREE.toLowerCase();
final private static Pattern TREE_NAME_PATTERN = Pattern.compile( "\\s*.?Tree\\s+(.+?)\\s*=.+",
Pattern.CASE_INSENSITIVE );
+ final private static Pattern TRANSLATE_PATTERN = Pattern.compile( "([0-9A-Za-z]+)\\s+(.+)" );
final private static String utree = NexusConstants.UTREE.toLowerCase();
private BufferedReader _br;
private boolean _ignore_quotes_in_nh_data = Constants.NH_PARSING_IGNORE_QUOTES_DEFAULT;
if ( s.endsWith( ";" ) ) {
s = s.substring( 0, s.length() - 1 ).trim();
}
- for( final String pair : s.split( "," ) ) {
- final String[] kv = pair.trim().split( "\\s+" );
- if ( ( kv.length < 2 ) || ( kv.length > 3 ) ) {
- throw new IOException( "ill-formatted translate values: " + pair );
- }
- if ( ( kv.length == 3 ) && !kv[ 0 ].toLowerCase().trim().equals( translate ) ) {
- throw new IOException( "ill-formatted translate values: " + pair );
- }
+ for( String pair : s.split( "," ) ) {
String key = "";
String value = "";
- if ( kv.length == 3 ) {
- key = kv[ 1 ];
- value = kv[ 2 ];
+ final int ti = pair.toLowerCase().indexOf( "translate" );
+ if ( ti > -1 ) {
+ pair = pair.substring( ti + 9 );
+ }
+ final Matcher m = TRANSLATE_PATTERN.matcher( pair );
+ if ( m.find() ) {
+ key = m.group( 1 );
+ value = m.group( 2 ).replaceAll( "\'", "" ).replaceAll( "\"", "" ).trim();
}
else {
- key = kv[ 0 ];
- value = kv[ 1 ];
+ throw new IOException( "ill-formatted translate values: " + pair );
}
if ( value.endsWith( ";" ) ) {
value = value.substring( 0, value.length() - 1 );
final public static Pattern TAXOMONY_SN_PATTERN = Pattern
.compile( "(?:\\b|_)[a-zA-Z0-9]{3,}_([A-Z][a-z]+_[a-z]{2,}(?:_[a-z][a-z0-9_]+)?)\\b" );
final public static Pattern TAXOMONY_SN_PATTERN_SN = Pattern
- .compile( "\\b([A-Z][a-z]+_[a-z]{2,}(?:_[a-z][a-z0-9_]+)?)(?:\\b|_)" );
+ .compile( "\\b([A-Z][a-z]+[_ ][a-z]{2,}(?:[_ ][a-z]+)?)(?:\\b|_)" );
final private static Pattern TAXOMONY_CODE_PATTERN_PFS = Pattern.compile( "(?:\\b|_)[A-Z0-9]{4,}_("
+ TAX_CODE + ")/\\d+-\\d+\\b" );
final private static Pattern TAXOMONY_UNIPROT_ID_PATTERN_PFR = Pattern
.equals( "Aranaeus" ) ) {
return false;
}
+ phylogenies = factory.create( Test.PATH_TO_TEST_DATA + "S14117.nex", parser );
+ if ( phylogenies.length != 3 ) {
+ return false;
+ }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
System.out.println( n13.toString() );
return false;
}
+ final PhylogenyNode n14 = PhylogenyNode
+ .createInstanceFromNhxString( "Mus_musculus_392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n14.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
+ System.out.println( n14.toString() );
+ return false;
+ }
+ final PhylogenyNode n15 = PhylogenyNode
+ .createInstanceFromNhxString( "Mus_musculus_K392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n15.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
+ System.out.println( n15.toString() );
+ return false;
+ }
+ final PhylogenyNode n16 = PhylogenyNode
+ .createInstanceFromNhxString( "Mus musculus 392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n16.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
+ System.out.println( n16.toString() );
+ return false;
+ }
+ final PhylogenyNode n17 = PhylogenyNode
+ .createInstanceFromNhxString( "Mus musculus K392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n17.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
+ System.out.println( n17.toString() );
+ return false;
+ }
+ //
+ final PhylogenyNode n18 = PhylogenyNode
+ .createInstanceFromNhxString( "Mus_musculus_musculus_392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n18.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
+ System.out.println( n18.toString() );
+ return false;
+ }
+ final PhylogenyNode n19 = PhylogenyNode
+ .createInstanceFromNhxString( "Mus_musculus_musculus_K392",
+ NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n19.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
+ System.out.println( n19.toString() );
+ return false;
+ }
+ final PhylogenyNode n20 = PhylogenyNode
+ .createInstanceFromNhxString( "Mus musculus musculus 392", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n20.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
+ System.out.println( n20.toString() );
+ return false;
+ }
+ final PhylogenyNode n21 = PhylogenyNode
+ .createInstanceFromNhxString( "Mus musculus musculus K392",
+ NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n21.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
+ System.out.println( n21.toString() );
+ return false;
+ }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
git://source.jalview.org / jalview.git / commitdiff