- void readPhylogeniesFromURL() {\r
- URL url = null;\r
- Phylogeny[] phys = null;\r
- final String message = "Please enter a complete URL, for example \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\"";\r
- final String url_string = JOptionPane.showInputDialog( this,\r
- message,\r
- "Use URL/webservice to obtain a phylogeny",\r
- JOptionPane.QUESTION_MESSAGE );\r
- boolean nhx_or_nexus = false;\r
- if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {\r
- try {\r
- url = new URL( url_string );\r
- PhylogenyParser parser = null;\r
- if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {\r
- parser = new TolParser();\r
- }\r
- else {\r
- parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()\r
- .isValidatePhyloXmlAgainstSchema() );\r
- }\r
- if ( parser instanceof NexusPhylogeniesParser ) {\r
- nhx_or_nexus = true;\r
- }\r
- else if ( parser instanceof NHXParser ) {\r
- nhx_or_nexus = true;\r
- }\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().setWaitCursor();\r
- }\r
- else {\r
- _mainpanel.setWaitCursor();\r
- }\r
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();\r
- phys = factory.create( url.openStream(), parser );\r
- }\r
- catch ( final MalformedURLException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),\r
- "Malformed URL",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
- catch ( final IOException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Could not read from " + url + "\n"\r
- + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
- "Failed to read URL",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( this,\r
- ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
- "Unexpected Exception",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
- finally {\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().setArrowCursor();\r
- }\r
- else {\r
- _mainpanel.setArrowCursor();\r
- }\r
- }\r
- if ( ( phys != null ) && ( phys.length > 0 ) ) {\r
- if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {\r
- for( final Phylogeny phy : phys ) {\r
- PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );\r
- }\r
- }\r
- AptxUtil.addPhylogeniesToTabs( phys,\r
- new File( url.getFile() ).getName(),\r
- new File( url.getFile() ).toString(),\r
- getConfiguration(),\r
- getMainPanel() );\r
- _mainpanel.getControlPanel().showWhole();\r
- }\r
- }\r
- activateSaveAllIfNeeded();\r
- System.gc();\r
- }\r
-\r
- void setMsa( final Msa msa ) {\r
- _msa = msa;\r
- }\r
-\r
- void setMsaFile( final File msa_file ) {\r
- _msa_file = msa_file;\r
- }\r
-\r
- void setSeqs( final List<MolecularSequence> seqs ) {\r
- _seqs = seqs;\r
- }\r
-\r
- void setSeqsFile( final File seqs_file ) {\r
- _seqs_file = seqs_file;\r
- }\r
-\r
- void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {\r
- _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),\r
- _mainpanel.getCurrentTreePanel().getHeight(),\r
- true );\r
- String file_written_to = "";\r
- boolean error = false;\r
- try {\r
- file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,\r
- _mainpanel.getCurrentTreePanel().getWidth(),\r
- _mainpanel.getCurrentTreePanel().getHeight(),\r
- _mainpanel.getCurrentTreePanel(),\r
- _mainpanel.getControlPanel(),\r
- type,\r
- getOptions() );\r
- }\r
- catch ( final IOException e ) {\r
- error = true;\r
- JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
- }\r
- if ( !error ) {\r
- if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Wrote image to: " + file_written_to,\r
- "Graphics Export",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "There was an unknown problem when attempting to write to an image file: \""\r
- + file_name + "\"",\r
- "Error",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
- }\r
- _contentpane.repaint();\r
- }\r
-\r
- private void addExpressionValuesFromFile() {\r
- if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Need to load evolutionary tree first",\r
- "Can Not Read Expression Values",\r
- JOptionPane.WARNING_MESSAGE );\r
- return;\r
- }\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _values_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _values_filechooser.showOpenDialog( _contentpane );\r
- final File file = _values_filechooser.getSelectedFile();\r
- if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- BasicTable<String> t = null;\r
- try {\r
- t = BasicTableParser.parse( file, '\t' );\r
- if ( t.getNumberOfColumns() < 2 ) {\r
- t = BasicTableParser.parse( file, ',' );\r
- }\r
- if ( t.getNumberOfColumns() < 2 ) {\r
- t = BasicTableParser.parse( file, ' ' );\r
- }\r
- }\r
- catch ( final IOException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- e.getMessage(),\r
- "Could Not Read Expression Value Table",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( t.getNumberOfColumns() < 2 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Table contains " + t.getNumberOfColumns() + " column(s)",\r
- "Problem with Expression Value Table",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( t.getNumberOfRows() < 1 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Table contains zero rows",\r
- "Problem with Expression Value Table",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Table contains " + t.getNumberOfRows() + " rows, but tree contains "\r
- + phy.getNumberOfExternalNodes() + " external nodes",\r
- "Warning",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- final DescriptiveStatistics stats = new BasicDescriptiveStatistics();\r
- int not_found = 0;\r
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {\r
- final PhylogenyNode node = iter.next();\r
- final String node_name = node.getName();\r
- if ( !ForesterUtil.isEmpty( node_name ) ) {\r
- int row = -1;\r
- try {\r
- row = t.findRow( node_name );\r
- }\r
- catch ( final IllegalArgumentException e ) {\r
- JOptionPane\r
- .showMessageDialog( this,\r
- e.getMessage(),\r
- "Error Mapping Node Identifiers to Expression Value Identifiers",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( row < 0 ) {\r
- if ( node.isExternal() ) {\r
- not_found++;\r
- }\r
- continue;\r
- }\r
- final List<Double> l = new ArrayList<Double>();\r
- for( int col = 1; col < t.getNumberOfColumns(); ++col ) {\r
- double d = -100;\r
- try {\r
- d = Double.parseDouble( t.getValueAsString( col, row ) );\r
- }\r
- catch ( final NumberFormatException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Could not parse \"" + t.getValueAsString( col, row )\r
- + "\" into a decimal value",\r
- "Issue with Expression Value Table",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- stats.addValue( d );\r
- l.add( d );\r
- }\r
- if ( !l.isEmpty() ) {\r
- if ( node.getNodeData().getProperties() != null ) {\r
- node.getNodeData().getProperties()\r
- .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );\r
- }\r
- node.getNodeData().setVector( l );\r
- }\r
- }\r
- }\r
- if ( not_found > 0 ) {\r
- JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found\r
- + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );\r
- }\r
- getCurrentTreePanel().setStatisticsForExpressionValues( stats );\r
- }\r
- }\r
-\r
- private void addSequencesFromFile() {\r
- if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Need to load evolutionary tree first",\r
- "Can Not Read Sequences",\r
- JOptionPane.WARNING_MESSAGE );\r
- return;\r
- }\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _sequences_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _sequences_filechooser.showOpenDialog( _contentpane );\r
- final File file = _sequences_filechooser.getSelectedFile();\r
- List<MolecularSequence> seqs = null;\r
- if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- try {\r
- if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {\r
- seqs = FastaParser.parse( new FileInputStream( file ) );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "Format does not appear to be Fasta",\r
- "Multiple sequence file format error",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- }\r
- catch ( final MsaFormatException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Multiple sequence file format error",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final IOException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Failed to read multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final Exception e ) {\r
- setArrowCursor();\r
- e.printStackTrace();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Unexpected error during reading of multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Multiple sequence file is empty",\r
- "Empty multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- setArrowCursor();\r
- return;\r
- }\r
- }\r
- if ( seqs != null ) {\r
- for( final MolecularSequence seq : seqs ) {\r
- System.out.println( seq.getIdentifier() );\r
- }\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- int total_counter = 0;\r
- int attached_counter = 0;\r
- for( final MolecularSequence seq : seqs ) {\r
- ++total_counter;\r
- final String seq_name = seq.getIdentifier();\r
- if ( !ForesterUtil.isEmpty( seq_name ) ) {\r
- List<PhylogenyNode> nodes = phy.getNodesViaSequenceName( seq_name );\r
- if ( nodes.isEmpty() ) {\r
- nodes = phy.getNodesViaSequenceSymbol( seq_name );\r
- }\r
- if ( nodes.isEmpty() ) {\r
- nodes = phy.getNodesViaGeneName( seq_name );\r
- }\r
- if ( nodes.isEmpty() ) {\r
- nodes = phy.getNodes( seq_name );\r
- }\r
- if ( nodes.size() > 1 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Sequence name \"" + seq_name + "\" is not unique",\r
- "Sequence name not unique",\r
- JOptionPane.ERROR_MESSAGE );\r
- setArrowCursor();\r
- return;\r
- }\r
- final String[] a = seq_name.split( "\\s" );\r
- if ( nodes.isEmpty() && ( a.length > 1 ) ) {\r
- final String seq_name_split = a[ 0 ];\r
- nodes = phy.getNodesViaSequenceName( seq_name_split );\r
- if ( nodes.isEmpty() ) {\r
- nodes = phy.getNodesViaSequenceSymbol( seq_name_split );\r
- }\r
- if ( nodes.isEmpty() ) {\r
- nodes = phy.getNodes( seq_name_split );\r
- }\r
- if ( nodes.size() > 1 ) {\r
- JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split\r
- + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );\r
- setArrowCursor();\r
- return;\r
- }\r
- }\r
- if ( nodes.size() == 1 ) {\r
- ++attached_counter;\r
- final PhylogenyNode n = nodes.get( 0 );\r
- if ( !n.getNodeData().isHasSequence() ) {\r
- n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() );\r
- }\r
- n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() );\r
- if ( ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {\r
- n.getNodeData().getSequence().setName( seq_name );\r
- }\r
- }\r
- }\r
- }\r
- if ( attached_counter > 0 ) {\r
- int ext_nodes = 0;\r
- int ext_nodes_with_seq = 0;\r
- for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {\r
- ++ext_nodes;\r
- final PhylogenyNode n = iter.next();\r
- if ( n.getNodeData().isHasSequence()\r
- && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {\r
- ++ext_nodes_with_seq;\r
- }\r
- }\r
- final String s;\r
- if ( ext_nodes == ext_nodes_with_seq ) {\r
- s = "All " + ext_nodes_with_seq + " external nodes now have a molecular sequence attached to them.";\r
- }\r
- else {\r
- s = ext_nodes_with_seq + " out of " + ext_nodes\r
- + " external nodes now have a molecular sequence attached to them.";\r
- }\r
- if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Attached all " + total_counter + " sequences to tree nodes.\n" + s,\r
- "All sequences attached",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this, "Attached " + attached_counter\r
- + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter\r
- + " sequences attached", JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter\r
- + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );\r
- }\r
- }\r
- }\r
-\r
- private void choosePdfWidth() {\r
- final String s = ( String ) JOptionPane.showInputDialog( this,\r
- "Please enter the default line width for PDF export.\n"\r
- + "[current value: "\r
- + getOptions().getPrintLineWidth() + "]\n",\r
- "Line Width for PDF Export",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getPrintLineWidth() );\r
- if ( !ForesterUtil.isEmpty( s ) ) {\r
- boolean success = true;\r
- float f = 0.0f;\r
- final String m_str = s.trim();\r
- if ( !ForesterUtil.isEmpty( m_str ) ) {\r
- try {\r
- f = Float.parseFloat( m_str );\r
- }\r
- catch ( final Exception ex ) {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
- }\r
- if ( success && ( f > 0.0 ) ) {\r
- getOptions().setPrintLineWidth( f );\r
- }\r
- }\r
- }\r
-\r
- private void choosePrintSize() {\r
- final String s = ( String ) JOptionPane.showInputDialog( this,\r
- "Please enter values for width and height,\nseparated by a comma.\n"\r
- + "[current values: "\r
- + getOptions().getPrintSizeX() + ", "\r
- + getOptions().getPrintSizeY() + "]\n"\r
- + "[A4: " + Constants.A4_SIZE_X + ", "\r
- + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "\r
- + Constants.US_LETTER_SIZE_X + ", "\r
- + Constants.US_LETTER_SIZE_Y + "]",\r
- "Default Size for Graphics Export",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getPrintSizeX() + ", "\r
- + getOptions().getPrintSizeY() );\r
- if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {\r
- boolean success = true;\r
- int x = 0;\r
- int y = 0;\r
- final String[] str_ary = s.split( "," );\r
- if ( str_ary.length == 2 ) {\r
- final String x_str = str_ary[ 0 ].trim();\r
- final String y_str = str_ary[ 1 ].trim();\r
- if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {\r
- try {\r
- x = Integer.parseInt( x_str );\r
- y = Integer.parseInt( y_str );\r
- }\r
- catch ( final Exception ex ) {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
- }\r
- if ( success && ( x > 1 ) && ( y > 1 ) ) {\r
- getOptions().setPrintSizeX( x );\r
- getOptions().setPrintSizeY( y );\r
- }\r
- }\r
- }\r
-\r
- private void closeCurrentPane() {\r
- if ( getMainPanel().getCurrentTreePanel() != null ) {\r
- if ( getMainPanel().getCurrentTreePanel().isEdited() ) {\r
- final int r = JOptionPane.showConfirmDialog( this,\r
- "Close tab despite potentially unsaved changes?",\r
- "Close Tab?",\r
- JOptionPane.YES_NO_OPTION );\r
- if ( r != JOptionPane.YES_OPTION ) {\r
- return;\r
- }\r
- }\r
- getMainPanel().closeCurrentPane();\r
- activateSaveAllIfNeeded();\r
- }\r
- }\r
-\r
- private void collapse( final Phylogeny phy, final double m ) {\r