import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.data.Accession;
import org.forester.phylogeny.data.BranchColor;
-import org.forester.phylogeny.data.Distribution;
-import org.forester.phylogeny.data.Sequence;
import org.forester.phylogeny.data.Taxonomy;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
Arrays.sort( AVAILABLE_FONT_FAMILIES_SORTED );
}
+ public static MaskFormatter createMaskFormatter( final String s ) {
+ MaskFormatter formatter = null;
+ try {
+ formatter = new MaskFormatter( s );
+ }
+ catch ( final ParseException e ) {
+ throw new IllegalArgumentException( e );
+ }
+ return formatter;
+ }
+
+ final static public boolean isHasAtLeastNodeWithEvent( final Phylogeny phy ) {
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ while ( it.hasNext() ) {
+ if ( it.next().getNodeData().isHasEvent() ) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Returns true if at least one branch has a length larger than zero.
+ *
+ *
+ * @param phy
+ */
+ final static public boolean isHasAtLeastOneBranchLengthLargerThanZero( final Phylogeny phy ) {
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ while ( it.hasNext() ) {
+ if ( it.next().getDistanceToParent() > 0.0 ) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ final static public boolean isHasAtLeastOneBranchWithSupportValues( final Phylogeny phy ) {
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ while ( it.hasNext() ) {
+ if ( it.next().getBranchData().isHasConfidences() ) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ final public static void launchWebBrowser( final URI uri,
+ final boolean is_applet,
+ final JApplet applet,
+ final String frame_name ) throws IOException {
+ if ( is_applet ) {
+ applet.getAppletContext().showDocument( uri.toURL(), frame_name );
+ }
+ else {
+ // This requires Java 1.6:
+ // =======================
+ // boolean no_desktop = false;
+ // try {
+ // if ( Desktop.isDesktopSupported() ) {
+ // System.out.println( "desktop supported" );
+ // final Desktop dt = Desktop.getDesktop();
+ // dt.browse( uri );
+ // }
+ // else {
+ // no_desktop = true;
+ // }
+ // }
+ // catch ( final Exception ex ) {
+ // ex.printStackTrace();
+ // no_desktop = true;
+ // }
+ // catch ( final Error er ) {
+ // er.printStackTrace();
+ // no_desktop = true;
+ // }
+ // if ( no_desktop ) {
+ // System.out.println( "desktop not supported" );
+ try {
+ openUrlInWebBrowser( uri.toString() );
+ }
+ catch ( final Exception e ) {
+ throw new IOException( e );
+ }
+ // }
+ }
+ }
+
+ public final static Accession obtainSequenceAccessionFromName( final String sequence_name ) {
+ final String n = sequence_name.trim();
+ final Matcher matcher1 = seq_identifier_pattern_1.matcher( n );
+ String group1 = "";
+ String group2 = "";
+ if ( matcher1.matches() ) {
+ group1 = matcher1.group( 1 );
+ group2 = matcher1.group( 2 );
+ }
+ else {
+ final Matcher matcher2 = seq_identifier_pattern_2.matcher( n );
+ if ( matcher2.matches() ) {
+ group1 = matcher2.group( 1 );
+ group2 = matcher2.group( 2 );
+ }
+ }
+ if ( ForesterUtil.isEmpty( group1 ) || ForesterUtil.isEmpty( group2 ) ) {
+ return null;
+ }
+ return new Accession( group2, group1 );
+ }
+
+ public final static void printWarningMessage( final String name, final String message ) {
+ System.out.println( "[" + name + "] > " + message );
+ }
+
+ final public static void showErrorMessage( final Component parent, final String error_msg ) {
+ printAppletMessage( Constants.PRG_NAME, error_msg );
+ JOptionPane.showMessageDialog( parent, error_msg, "[" + Constants.PRG_NAME + " " + Constants.VERSION
+ + "] Error", JOptionPane.ERROR_MESSAGE );
+ }
+
+ public final static void showExtDescNodeDataUserSelectedHelper( final ControlPanel cp,
+ final PhylogenyNode node,
+ final List<String> data ) {
+ final StringBuilder sb = new StringBuilder();
+ if ( cp.isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) {
+ showExtDescNodeDataUserSelectedHelperHelper( node.getName(), sb );
+ }
+ if ( cp.isShowGeneNames() && node.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) {
+ showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getName(), sb );
+ }
+ if ( cp.isShowGeneSymbols() && node.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) {
+ showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getSymbol(), sb );
+ }
+ if ( cp.isShowSequenceAcc() && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getAccession() != null )
+ && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().toString() ) ) {
+ showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getAccession().toString(), sb );
+ }
+ if ( cp.isShowTaxonomyCode() && node.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+ showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getTaxonomyCode(), sb );
+ }
+ if ( cp.isShowTaxonomyScientificNames() && node.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) {
+ showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getScientificName(), sb );
+ }
+ if ( ( cp.isShowGeneNames() || cp.isShowGeneSymbols() || cp.isShowSequenceAcc() )
+ && node.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
+ showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getMolecularSequence(), sb );
+ }
+ final String s = sb.toString().trim();
+ if ( !ForesterUtil.isEmpty( s ) ) {
+ data.add( s );
+ }
+ }
+
+ public final static void showExtDescNodeDataUserSelectedHelperHelper( final String s, final StringBuilder sb ) {
+ if ( sb.length() > 0 ) {
+ sb.append( "\t" );
+ }
+ sb.append( s );
+ }
+
+ final public static void showInformationMessage( final Component parent, final String title, final String msg ) {
+ JOptionPane.showMessageDialog( parent, msg, title, JOptionPane.INFORMATION_MESSAGE );
+ }
+
+ public static void writePhylogenyToGraphicsFile( final File intree,
+ final File outfile,
+ final int width,
+ final int height,
+ final GraphicsExportType type,
+ final Configuration config ) throws IOException {
+ final PhylogenyParser parser = ParserUtils.createParserDependingOnFileType( intree, true );
+ Phylogeny[] phys = null;
+ phys = PhylogenyMethods.readPhylogenies( parser, intree );
+ writePhylogenyToGraphicsFile( phys[ 0 ], outfile, width, height, type, config );
+ }
+
+ public static void writePhylogenyToGraphicsFile( final Phylogeny phy,
+ final File outfile,
+ final int width,
+ final int height,
+ final GraphicsExportType type,
+ final Configuration config ) throws IOException {
+ final Phylogeny[] phys = new Phylogeny[ 1 ];
+ phys[ 0 ] = phy;
+ final MainFrameApplication mf = MainFrameApplication.createInstance( phys, config );
+ AptxUtil.writePhylogenyToGraphicsFileNonInteractive( outfile, width, height, mf.getMainPanel()
+ .getCurrentTreePanel(), mf.getMainPanel().getControlPanel(), type, mf.getOptions() );
+ mf.end();
+ }
+
+ public final static void writePhylogenyToGraphicsFileNonInteractive( final File outfile,
+ final int width,
+ final int height,
+ final TreePanel tree_panel,
+ final ControlPanel ac,
+ final GraphicsExportType type,
+ final Options options ) throws IOException {
+ tree_panel.setParametersForPainting( width, height, true );
+ tree_panel.resetPreferredSize();
+ tree_panel.repaint();
+ final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
+ RenderingHints.VALUE_RENDER_QUALITY );
+ rendering_hints.put( RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_QUALITY );
+ if ( options.isAntialiasPrint() ) {
+ rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
+ rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
+ }
+ else {
+ rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
+ rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
+ }
+ final Phylogeny phylogeny = tree_panel.getPhylogeny();
+ if ( ( phylogeny == null ) || phylogeny.isEmpty() ) {
+ return;
+ }
+ if ( outfile.isDirectory() ) {
+ throw new IOException( "\"" + outfile + "\" is a directory" );
+ }
+ final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB );
+ final Graphics2D g2d = buffered_img.createGraphics();
+ g2d.setRenderingHints( rendering_hints );
+ tree_panel.paintPhylogeny( g2d, false, true, width, height, 0, 0 );
+ if ( type == GraphicsExportType.TIFF ) {
+ writeToTiff( outfile, buffered_img );
+ }
+ else {
+ ImageIO.write( buffered_img, type.toString(), outfile );
+ }
+ g2d.dispose();
+ }
+
final static void addPhylogeniesToTabs( final Phylogeny[] phys,
final String default_name,
final String full_path,
return iter.hasNext();
}
- final public static void collapseSpeciesSpecificSubtrees( final Phylogeny phy ) {
+ final static void collapseSpeciesSpecificSubtrees( final Phylogeny phy ) {
boolean inferred = false;
for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
final PhylogenyNode n = it.next();
}
}
- private static void colorizeSubtree( final PhylogenyNode node, final BranchColor c ) {
- node.getBranchData().setBranchColor( c );
- final List<PhylogenyNode> descs = PhylogenyMethods.getAllDescendants( node );
- for( final PhylogenyNode desc : descs ) {
- desc.getBranchData().setBranchColor( c );
- }
- }
-
final static void colorPhylogenyAccordingToConfidenceValues( final Phylogeny tree, final TreePanel tree_panel ) {
double max_conf = 0.0;
for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) {
return desc.toString();
}
- public static MaskFormatter createMaskFormatter( final String s ) {
- MaskFormatter formatter = null;
- try {
- formatter = new MaskFormatter( s );
- }
- catch ( final ParseException e ) {
- throw new IllegalArgumentException( e );
- }
- return formatter;
- }
-
/**
* Exits with -1.
*
System.exit( -1 );
}
- final public static void ensurePresenceOfDate( final PhylogenyNode node ) {
- if ( !node.getNodeData().isHasDate() ) {
- node.getNodeData().setDate( new org.forester.phylogeny.data.Date() );
- }
- }
-
- final public static void ensurePresenceOfDistribution( final PhylogenyNode node ) {
- if ( !node.getNodeData().isHasDistribution() ) {
- node.getNodeData().setDistribution( new Distribution( "" ) );
- }
- }
-
- public static void ensurePresenceOfSequence( final PhylogenyNode node ) {
- if ( !node.getNodeData().isHasSequence() ) {
- node.getNodeData().setSequence( new Sequence() );
- }
- }
-
- public static void ensurePresenceOfTaxonomy( final PhylogenyNode node ) {
- if ( !node.getNodeData().isHasTaxonomy() ) {
- node.getNodeData().setTaxonomy( new Taxonomy() );
- }
- }
-
- public static String[] getAllPossibleRanks() {
+ final static String[] getAllPossibleRanks() {
final String[] str_array = new String[ PhyloXmlUtil.TAXONOMY_RANKS_LIST.size() - 2 ];
int i = 0;
for( final String e : PhyloXmlUtil.TAXONOMY_RANKS_LIST ) {
return true;
}
- final static public boolean isHasAtLeastNodeWithEvent( final Phylogeny phy ) {
- final PhylogenyNodeIterator it = phy.iteratorPostorder();
- while ( it.hasNext() ) {
- if ( it.next().getNodeData().isHasEvent() ) {
- return true;
- }
- }
- return false;
- }
-
- /**
- * Returns true if at least one branch has a length larger than zero.
- *
- *
- * @param phy
- */
- final static public boolean isHasAtLeastOneBranchLengthLargerThanZero( final Phylogeny phy ) {
- final PhylogenyNodeIterator it = phy.iteratorPostorder();
- while ( it.hasNext() ) {
- if ( it.next().getDistanceToParent() > 0.0 ) {
- return true;
- }
- }
- return false;
- }
-
- final static public boolean isHasAtLeastOneBranchWithSupportValues( final Phylogeny phy ) {
- final PhylogenyNodeIterator it = phy.iteratorPostorder();
- while ( it.hasNext() ) {
- if ( it.next().getBranchData().isHasConfidences() ) {
- return true;
- }
- }
- return false;
- }
-
final static boolean isJava15() {
try {
final String s = ForesterUtil.JAVA_VERSION;
}
}
- final public static void launchWebBrowser( final URI uri,
- final boolean is_applet,
- final JApplet applet,
- final String frame_name ) throws IOException {
- if ( is_applet ) {
- applet.getAppletContext().showDocument( uri.toURL(), frame_name );
- }
- else {
- // This requires Java 1.6:
- // =======================
- // boolean no_desktop = false;
- // try {
- // if ( Desktop.isDesktopSupported() ) {
- // System.out.println( "desktop supported" );
- // final Desktop dt = Desktop.getDesktop();
- // dt.browse( uri );
- // }
- // else {
- // no_desktop = true;
- // }
- // }
- // catch ( final Exception ex ) {
- // ex.printStackTrace();
- // no_desktop = true;
- // }
- // catch ( final Error er ) {
- // er.printStackTrace();
- // no_desktop = true;
- // }
- // if ( no_desktop ) {
- // System.out.println( "desktop not supported" );
- try {
- openUrlInWebBrowser( uri.toString() );
- }
- catch ( final Exception e ) {
- throw new IOException( e );
- }
- // }
- }
- }
-
final static void lookAtSomeTreePropertiesForAptxControlSettings( final Phylogeny t,
final ControlPanel atv_control,
final Configuration configuration ) {
}
}
- final private static char normalizeCharForRGB( char c ) {
- c -= 65;
- c *= 10.2;
- c = c > 255 ? 255 : c;
- c = c < 0 ? 0 : c;
- return c;
- }
-
- public final static Accession obtainSequenceAccessionFromName( final String sequence_name ) {
- final String n = sequence_name.trim();
- final Matcher matcher1 = seq_identifier_pattern_1.matcher( n );
- String group1 = "";
- String group2 = "";
- if ( matcher1.matches() ) {
- group1 = matcher1.group( 1 );
- group2 = matcher1.group( 2 );
- }
- else {
- final Matcher matcher2 = seq_identifier_pattern_2.matcher( n );
- if ( matcher2.matches() ) {
- group1 = matcher2.group( 1 );
- group2 = matcher2.group( 2 );
- }
- }
- if ( ForesterUtil.isEmpty( group1 ) || ForesterUtil.isEmpty( group2 ) ) {
- return null;
- }
- return new Accession( group2, group1 );
- }
-
- final private static void openUrlInWebBrowser( final String url ) throws IOException, ClassNotFoundException,
- SecurityException, NoSuchMethodException, IllegalArgumentException, IllegalAccessException,
- InvocationTargetException, InterruptedException {
- final String os = System.getProperty( "os.name" );
- final Runtime runtime = Runtime.getRuntime();
- if ( os.toLowerCase().startsWith( "win" ) ) {
- Runtime.getRuntime().exec( "rundll32 url.dll,FileProtocolHandler " + url );
- }
- else if ( isMac() ) {
- final Class<?> file_mgr = Class.forName( "com.apple.eio.FileManager" );
- final Method open_url = file_mgr.getDeclaredMethod( "openURL", new Class[] { String.class } );
- open_url.invoke( null, new Object[] { url } );
- }
- else {
- final String[] browsers = { "firefox", "opera", "konqueror", "mozilla", "netscape", "epiphany" };
- String browser = null;
- for( int i = 0; ( i < browsers.length ) && ( browser == null ); ++i ) {
- if ( runtime.exec( new String[] { "which", browsers[ i ] } ).waitFor() == 0 ) {
- browser = browsers[ i ];
- }
- }
- if ( browser == null ) {
- throw new IOException( "could not find a web browser to open [" + url + "] in" );
- }
- else {
- runtime.exec( new String[] { browser, url } );
- }
- }
- }
-
final static void openWebsite( final String url, final boolean is_applet, final JApplet applet ) throws IOException {
try {
AptxUtil.launchWebBrowser( new URI( url ), is_applet, applet, Constants.PRG_NAME );
System.out.println( "[" + applet_name + "] > " + message );
}
- public final static void printWarningMessage( final String name, final String message ) {
- System.out.println( "[" + name + "] > " + message );
- }
-
final static Phylogeny[] readPhylogeniesFromUrl( final URL url, final boolean phyloxml_validate_against_xsd )
throws FileNotFoundException, IOException {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
}
}
- final public static void showErrorMessage( final Component parent, final String error_msg ) {
- printAppletMessage( Constants.PRG_NAME, error_msg );
- JOptionPane.showMessageDialog( parent, error_msg, "[" + Constants.PRG_NAME + " " + Constants.VERSION
- + "] Error", JOptionPane.ERROR_MESSAGE );
- }
-
- public final static void showExtDescNodeDataUserSelectedHelper( final ControlPanel cp,
- final PhylogenyNode node,
- final List<String> data ) {
- final StringBuilder sb = new StringBuilder();
- if ( cp.isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) {
- showExtDescNodeDataUserSelectedHelperHelper( node.getName(), sb );
- }
- if ( cp.isShowGeneNames() && node.getNodeData().isHasSequence()
- && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) {
- showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getName(), sb );
- }
- if ( cp.isShowGeneSymbols() && node.getNodeData().isHasSequence()
- && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) {
- showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getSymbol(), sb );
- }
- if ( cp.isShowSequenceAcc() && node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getAccession() != null )
- && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().toString() ) ) {
- showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getAccession().toString(), sb );
- }
- if ( cp.isShowTaxonomyCode() && node.getNodeData().isHasTaxonomy()
- && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
- showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getTaxonomyCode(), sb );
- }
- if ( cp.isShowTaxonomyScientificNames() && node.getNodeData().isHasTaxonomy()
- && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) {
- showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getScientificName(), sb );
- }
- if ( ( cp.isShowGeneNames() || cp.isShowGeneSymbols() || cp.isShowSequenceAcc() )
- && node.getNodeData().isHasSequence()
- && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
- showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getMolecularSequence(), sb );
- }
- final String s = sb.toString().trim();
- if ( !ForesterUtil.isEmpty( s ) ) {
- data.add( s );
- }
- }
-
- public final static void showExtDescNodeDataUserSelectedHelperHelper( final String s, final StringBuilder sb ) {
- if ( sb.length() > 0 ) {
- sb.append( "\t" );
- }
- sb.append( s );
- }
-
- final public static void showInformationMessage( final Component parent, final String title, final String msg ) {
- JOptionPane.showMessageDialog( parent, msg, title, JOptionPane.INFORMATION_MESSAGE );
- }
-
final static void unexpectedError( final Error err ) {
err.printStackTrace();
final StringBuffer sb = new StringBuffer();
return msg;
}
- public static void writePhylogenyToGraphicsFile( final File intree,
- final File outfile,
- final int width,
- final int height,
- final GraphicsExportType type,
- final Configuration config ) throws IOException {
- final PhylogenyParser parser = ParserUtils.createParserDependingOnFileType( intree, true );
- Phylogeny[] phys = null;
- phys = PhylogenyMethods.readPhylogenies( parser, intree );
- writePhylogenyToGraphicsFile( phys[ 0 ], outfile, width, height, type, config );
- }
-
- public static void writePhylogenyToGraphicsFile( final Phylogeny phy,
- final File outfile,
- final int width,
- final int height,
- final GraphicsExportType type,
- final Configuration config ) throws IOException {
- final Phylogeny[] phys = new Phylogeny[ 1 ];
- phys[ 0 ] = phy;
- final MainFrameApplication mf = MainFrameApplication.createInstance( phys, config );
- AptxUtil.writePhylogenyToGraphicsFileNonInteractive( outfile, width, height, mf.getMainPanel()
- .getCurrentTreePanel(), mf.getMainPanel().getControlPanel(), type, mf.getOptions() );
- mf.end();
- }
-
final static String writePhylogenyToGraphicsFile( final String file_name,
int width,
int height,
return msg;
}
- public final static void writePhylogenyToGraphicsFileNonInteractive( final File outfile,
- final int width,
- final int height,
- final TreePanel tree_panel,
- final ControlPanel ac,
- final GraphicsExportType type,
- final Options options ) throws IOException {
- tree_panel.setParametersForPainting( width, height, true );
- tree_panel.resetPreferredSize();
- tree_panel.repaint();
- final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
- RenderingHints.VALUE_RENDER_QUALITY );
- rendering_hints.put( RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_QUALITY );
- if ( options.isAntialiasPrint() ) {
- rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
- rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
- }
- else {
- rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
- rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
- }
- final Phylogeny phylogeny = tree_panel.getPhylogeny();
- if ( ( phylogeny == null ) || phylogeny.isEmpty() ) {
- return;
- }
- if ( outfile.isDirectory() ) {
- throw new IOException( "\"" + outfile + "\" is a directory" );
- }
- final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB );
- final Graphics2D g2d = buffered_img.createGraphics();
- g2d.setRenderingHints( rendering_hints );
- tree_panel.paintPhylogeny( g2d, false, true, width, height, 0, 0 );
- if ( type == GraphicsExportType.TIFF ) {
- writeToTiff( outfile, buffered_img );
- }
- else {
- ImageIO.write( buffered_img, type.toString(), outfile );
- }
- g2d.dispose();
- }
-
final static void writeToTiff( final File file, final BufferedImage image ) throws IOException {
// See: http://log.robmeek.com/2005/08/write-tiff-in-java.html
ImageWriter writer = null;
writer.write( null, iio_image, image_write_param );
}
+ private static void colorizeSubtree( final PhylogenyNode node, final BranchColor c ) {
+ node.getBranchData().setBranchColor( c );
+ final List<PhylogenyNode> descs = PhylogenyMethods.getAllDescendants( node );
+ for( final PhylogenyNode desc : descs ) {
+ desc.getBranchData().setBranchColor( c );
+ }
+ }
+
+ final private static char normalizeCharForRGB( char c ) {
+ c -= 65;
+ c *= 10.2;
+ c = c > 255 ? 255 : c;
+ c = c < 0 ? 0 : c;
+ return c;
+ }
+
+ final private static void openUrlInWebBrowser( final String url ) throws IOException, ClassNotFoundException,
+ SecurityException, NoSuchMethodException, IllegalArgumentException, IllegalAccessException,
+ InvocationTargetException, InterruptedException {
+ final String os = System.getProperty( "os.name" );
+ final Runtime runtime = Runtime.getRuntime();
+ if ( os.toLowerCase().startsWith( "win" ) ) {
+ Runtime.getRuntime().exec( "rundll32 url.dll,FileProtocolHandler " + url );
+ }
+ else if ( isMac() ) {
+ final Class<?> file_mgr = Class.forName( "com.apple.eio.FileManager" );
+ final Method open_url = file_mgr.getDeclaredMethod( "openURL", new Class[] { String.class } );
+ open_url.invoke( null, new Object[] { url } );
+ }
+ else {
+ final String[] browsers = { "firefox", "opera", "konqueror", "mozilla", "netscape", "epiphany" };
+ String browser = null;
+ for( int i = 0; ( i < browsers.length ) && ( browser == null ); ++i ) {
+ if ( runtime.exec( new String[] { "which", browsers[ i ] } ).waitFor() == 0 ) {
+ browser = browsers[ i ];
+ }
+ }
+ if ( browser == null ) {
+ throw new IOException( "could not find a web browser to open [" + url + "] in" );
+ }
+ else {
+ runtime.exec( new String[] { browser, url } );
+ }
+ }
+ }
+
// See: http://www.xml.nig.ac.jp/tutorial/rest/index.html#2.2
// static void openDDBJRest() throws IOException {
// //set URL
}
displayedPhylogenyMightHaveChanged( true );
}
- else if ( e.getSource() == _color_according_to_annotation ) {
- if ( ( _show_annotation != null ) && _color_according_to_annotation.isSelected() ) {
- _show_annotation.setSelected( true );
- }
- displayedPhylogenyMightHaveChanged( false );
- }
- else if ( e.getSource() == _show_annotation ) {
- if ( ( _color_according_to_annotation != null ) && !_show_annotation.isSelected() ) {
- _color_according_to_annotation.setSelected( false );
- }
- displayedPhylogenyMightHaveChanged( false );
- }
else if ( e.getSource() == _show_domain_architectures ) {
search();
displayedPhylogenyMightHaveChanged( false );
}
}
+ public JCheckBox getColorAccSpeciesCb() {
+ return _color_acc_species;
+ }
+
+ public JCheckBox getColorBranchesCb() {
+ return _color_branches_cb;
+ }
+
+ public JCheckBox getDisplayAsPhylogramCb() {
+ return _display_as_phylogram_cb;
+ }
+
+ public JCheckBox getDynamicallyHideData() {
+ return _dynamically_hide_data;
+ }
+
+ public JCheckBox getNodeDescPopupCb() {
+ return _node_desc_popup_cb;
+ }
+
+ public Sequence getSelectedQuerySequence() {
+ return _selected_query_seq;
+ }
+
+ public JComboBox getSequenceRelationBox() {
+ if ( _show_sequence_relations == null ) {
+ _show_sequence_relations = new JComboBox();
+ _show_sequence_relations.setFocusable( false );
+ _show_sequence_relations.setMaximumRowCount( 20 );
+ _show_sequence_relations.setFont( ControlPanel.js_font );
+ if ( !_configuration.isUseNativeUI() ) {
+ _show_sequence_relations.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
+ _show_sequence_relations.setForeground( getConfiguration().getGuiButtonTextColor() );
+ }
+ _show_sequence_relations.addItem( "-----" );
+ _show_sequence_relations.setToolTipText( "To display orthology information for selected query" );
+ }
+ return _show_sequence_relations;
+ }
+
+ /* GUILHEM_BEG */
+ public JComboBox getSequenceRelationTypeBox() {
+ if ( _sequence_relation_type_box == null ) {
+ _sequence_relation_type_box = new JComboBox();
+ for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : SequenceRelation.SEQUENCE_RELATION_TYPE.values() ) {
+ _sequence_relation_type_box.addItem( type );
+ }
+ _sequence_relation_type_box.addActionListener( new ActionListener() {
+
+ @Override
+ public void actionPerformed( final ActionEvent e ) {
+ if ( _mainpanel.getCurrentPhylogeny() != null ) {
+ setSequenceRelationQueries( getMainPanel().getCurrentPhylogeny().getSequenceRelationQueries() );
+ }
+ }
+ } );
+ }
+ return _sequence_relation_type_box;
+ }
+
+ public JCheckBox getShowEventsCb() {
+ return _show_events;
+ }
+
+ public JCheckBox getWriteConfidenceCb() {
+ return _write_confidence;
+ }
+
+ public boolean isShowProperties() {
+ return ( ( _show_properties_cb != null ) && _show_properties_cb.isSelected() );
+ }
+
+ public boolean isShowTaxonomyImages() {
+ return ( ( _show_taxo_images_cb != null ) && _show_taxo_images_cb.isSelected() );
+ }
+
+ public boolean isShowVectorData() {
+ return ( ( _show_vector_data_cb != null ) && _show_vector_data_cb.isSelected() );
+ }
+
+ public void setSequenceRelationQueries( final Collection<Sequence> sequenceRelationQueries ) {
+ final JComboBox box = getSequenceRelationBox();
+ while ( box.getItemCount() > 1 ) {
+ box.removeItemAt( 1 );
+ }
+ final HashMap<String, Sequence> sequencesByName = new HashMap<String, Sequence>();
+ final SequenceRelation.SEQUENCE_RELATION_TYPE relationType = ( SequenceRelation.SEQUENCE_RELATION_TYPE ) _sequence_relation_type_box
+ .getSelectedItem();
+ if ( relationType == null ) {
+ return;
+ }
+ final ArrayList<String> sequenceNamesToAdd = new ArrayList<String>();
+ for( final Sequence seq : sequenceRelationQueries ) {
+ if ( seq.hasSequenceRelations() ) {
+ boolean fFoundForCurrentType = false;
+ for( final SequenceRelation sq : seq.getSequenceRelations() ) {
+ if ( sq.getType().equals( relationType ) ) {
+ fFoundForCurrentType = true;
+ break;
+ }
+ }
+ if ( fFoundForCurrentType ) {
+ sequenceNamesToAdd.add( seq.getName() );
+ sequencesByName.put( seq.getName(), seq );
+ }
+ }
+ }
+ // sort sequences by name before adding them to the combo
+ final String[] sequenceNameArray = sequenceNamesToAdd.toArray( new String[ sequenceNamesToAdd.size() ] );
+ Arrays.sort( sequenceNameArray, String.CASE_INSENSITIVE_ORDER );
+ for( final String seqName : sequenceNameArray ) {
+ box.addItem( seqName );
+ }
+ for( final ItemListener oldItemListener : box.getItemListeners() ) {
+ box.removeItemListener( oldItemListener );
+ }
+ box.addItemListener( new ItemListener() {
+
+ @Override
+ public void itemStateChanged( final ItemEvent e ) {
+ _selected_query_seq = sequencesByName.get( e.getItem() );
+ _mainpanel.getCurrentTreePanel().repaint();
+ }
+ } );
+ }
+
void activateButtonToReturnToSuperTree( int index ) {
--index;
if ( index > 0 ) {
}
}// addCheckbox
- private void addClickToOption( final int which, final String title ) {
- _click_to_combobox.addItem( title );
- _click_to_names.add( title );
- _all_click_to_names.put( new Integer( which ), title );
- if ( !_configuration.isUseNativeUI() ) {
- _click_to_combobox.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
- _click_to_combobox.setForeground( getConfiguration().getGuiButtonTextColor() );
- }
- }
-
void addJButton( final JButton jb, final JPanel p ) {
jb.setFocusPainted( false );
jb.setFont( ControlPanel.jcb_font );
tf.addActionListener( this );
}
- /* GUILHEM_BEG */
- private void addSequenceRelationBlock() {
- final JLabel spacer = new JLabel( "" );
- spacer.setSize( 1, 1 );
- add( spacer );
- final JLabel mainLabel = new JLabel( "Sequence relations to display" );
- final JLabel typeLabel = customizeLabel( new JLabel( "(type) " ), getConfiguration() );
- typeLabel.setFont( ControlPanel.js_font.deriveFont( 7 ) );
- getSequenceRelationTypeBox().setFocusable( false );
- _sequence_relation_type_box.setFont( ControlPanel.js_font );
- if ( !_configuration.isUseNativeUI() ) {
- _sequence_relation_type_box.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
- _sequence_relation_type_box.setForeground( getConfiguration().getGuiButtonTextColor() );
- }
- _sequence_relation_type_box.setRenderer( new ListCellRenderer() {
-
- @Override
- public Component getListCellRendererComponent( final JList list,
- final Object value,
- final int index,
- final boolean isSelected,
- final boolean cellHasFocus ) {
- final Component component = new DefaultListCellRenderer().getListCellRendererComponent( list,
- value,
- index,
- isSelected,
- cellHasFocus );
- if ( ( value != null ) && ( value instanceof SequenceRelation.SEQUENCE_RELATION_TYPE ) ) {
- ( ( DefaultListCellRenderer ) component ).setText( SequenceRelation
- .getPrintableNameByType( ( SequenceRelation.SEQUENCE_RELATION_TYPE ) value ) );
- }
- return component;
- }
- } );
- final GridBagLayout gbl = new GridBagLayout();
- _sequence_relation_type_box.setMinimumSize( new Dimension( 115, 17 ) );
- _sequence_relation_type_box.setPreferredSize( new Dimension( 115, 20 ) );
- final JPanel horizGrid = new JPanel( gbl );
- horizGrid.setBackground( getBackground() );
- horizGrid.add( typeLabel );
- horizGrid.add( _sequence_relation_type_box );
- add( customizeLabel( mainLabel, getConfiguration() ) );
- add( horizGrid );
- add( getSequenceRelationBox() );
- if ( _configuration.doDisplayOption( Configuration.show_relation_confidence ) ) {
- addCheckbox( Configuration.show_relation_confidence,
- _configuration.getDisplayTitle( Configuration.show_relation_confidence ) );
- setCheckbox( Configuration.show_relation_confidence,
- _configuration.doCheckOption( Configuration.show_relation_confidence ) );
- }
- }// addSequenceRelationBlock
-
void deactivateButtonToReturnToSuperTree() {
_return_to_super_tree.setText( RETURN_TO_SUPER_TREE_TEXT );
_return_to_super_tree.setForeground( getConfiguration().getGuiButtonTextColor() );
return _annotation_colors;
}
- public JCheckBox getColorBranchesCb() {
- return _color_branches_cb;
- }
-
- public JCheckBox getColorAccSpeciesCb() {
- return _color_acc_species;
- }
-
Configuration getConfiguration() {
return _configuration;
}
return getMainPanel().getCurrentTreePanel();
}
- public JCheckBox getDisplayAsPhylogramCb() {
- return _display_as_phylogram_cb;
+ MainPanel getMainPanel() {
+ return _mainpanel;
}
- public JCheckBox getDynamicallyHideData() {
- return _dynamically_hide_data;
+ Options getOptions() {
+ return getMainPanel().getOptions();
}
- /* GUILHEM_END */
- private List<Boolean> getIsDrawPhylogramList() {
- return _draw_phylogram;
+ JTextField getSearchTextField() {
+ return _search_tf;
}
- MainPanel getMainPanel() {
- return _mainpanel;
+ List<String> getSingleClickToNames() {
+ return _click_to_names;
}
- public JCheckBox getNodeDescPopupCb() {
- return _node_desc_popup_cb;
+ Map<String, Color> getSpeciesColors() {
+ return _species_colors;
}
- Options getOptions() {
- return getMainPanel().getOptions();
+ boolean isAntialiasScreenText() {
+ return true;
}
- private JLabel getSearchFoundCountsLabel() {
- return _search_found_label;
+ boolean isColorAccordingToAnnotation() {
+ return ( ( _color_according_to_annotation != null ) && _color_according_to_annotation.isSelected() );
}
- private JButton getSearchResetButton() {
- return _search_reset_button;
+ boolean isColorAccordingToTaxonomy() {
+ return ( ( _color_acc_species != null ) && _color_acc_species.isSelected() );
}
- JTextField getSearchTextField() {
- return _search_tf;
+ boolean isColorBranches() {
+ return ( ( ( getColorBranchesCb() != null ) && getColorBranchesCb().isSelected() ) || ( ( getColorBranchesCb() == null ) && _color_branches ) );
}
- public Sequence getSelectedQuerySequence() {
- return _selected_query_seq;
- }
-
- public JComboBox getSequenceRelationBox() {
- if ( _show_sequence_relations == null ) {
- _show_sequence_relations = new JComboBox();
- _show_sequence_relations.setFocusable( false );
- _show_sequence_relations.setMaximumRowCount( 20 );
- _show_sequence_relations.setFont( ControlPanel.js_font );
- if ( !_configuration.isUseNativeUI() ) {
- _show_sequence_relations.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
- _show_sequence_relations.setForeground( getConfiguration().getGuiButtonTextColor() );
- }
- _show_sequence_relations.addItem( "-----" );
- _show_sequence_relations.setToolTipText( "To display orthology information for selected query" );
- }
- return _show_sequence_relations;
- }
-
- /* GUILHEM_BEG */
- public JComboBox getSequenceRelationTypeBox() {
- if ( _sequence_relation_type_box == null ) {
- _sequence_relation_type_box = new JComboBox();
- for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : SequenceRelation.SEQUENCE_RELATION_TYPE.values() ) {
- _sequence_relation_type_box.addItem( type );
- }
- _sequence_relation_type_box.addActionListener( new ActionListener() {
-
- @Override
- public void actionPerformed( final ActionEvent e ) {
- if ( _mainpanel.getCurrentPhylogeny() != null ) {
- setSequenceRelationQueries( getMainPanel().getCurrentPhylogeny().getSequenceRelationQueries() );
- }
- }
- } );
- }
- return _sequence_relation_type_box;
- }
-
- public JCheckBox getShowEventsCb() {
- return _show_events;
- }
-
- List<String> getSingleClickToNames() {
- return _click_to_names;
- }
-
- Map<String, Color> getSpeciesColors() {
- return _species_colors;
- }
-
- public JCheckBox getWriteConfidenceCb() {
- return _write_confidence;
- }
-
- private void init() {
- _draw_phylogram = new ArrayList<Boolean>();
- setSpeciesColors( new HashMap<String, Color>() );
- setAnnotationColors( new HashMap<String, Color>() );
- }
-
- boolean isAntialiasScreenText() {
- return true;
- }
-
- boolean isColorAccordingToAnnotation() {
- return ( ( _color_according_to_annotation != null ) && _color_according_to_annotation.isSelected() );
- }
-
- boolean isColorAccordingToTaxonomy() {
- return ( ( _color_acc_species != null ) && _color_acc_species.isSelected() );
- }
-
- boolean isColorBranches() {
- return ( ( ( getColorBranchesCb() != null ) && getColorBranchesCb().isSelected() ) || ( ( getColorBranchesCb() == null ) && _color_branches ) );
- }
-
- boolean isDrawPhylogram() {
- return isDrawPhylogram( getMainPanel().getCurrentTabIndex() );
- }
-
- private boolean isDrawPhylogram( final int index ) {
- return getIsDrawPhylogramList().get( index );
+ boolean isDrawPhylogram() {
+ return isDrawPhylogram( getMainPanel().getCurrentTabIndex() );
}
boolean isDynamicallyHideData() {
return ( ( _show_gene_names != null ) && _show_gene_names.isSelected() );
}
- public boolean isShowVectorData() {
- return ( ( _show_vector_data_cb != null ) && _show_vector_data_cb.isSelected() );
- }
-
- public boolean isShowProperties() {
- return ( ( _show_properties_cb != null ) && _show_properties_cb.isSelected() );
- }
-
boolean isShowGeneSymbols() {
return ( ( _show_gene_symbols != null ) && _show_gene_symbols.isSelected() );
}
return ( ( _show_taxo_code != null ) && _show_taxo_code.isSelected() );
}
- public boolean isShowTaxonomyImages() {
- return ( ( _show_taxo_images_cb != null ) && _show_taxo_images_cb.isSelected() );
- }
-
boolean isShowTaxonomyCommonNames() {
return ( ( _show_taxo_common_names != null ) && _show_taxo_common_names.isSelected() );
}
}
}
- private void search( final MainPanel main_panel, final Phylogeny tree, final String query_str ) {
- getSearchFoundCountsLabel().setVisible( true );
- getSearchResetButton().setEnabled( true );
- getSearchResetButton().setVisible( true );
- String[] queries = null;
- List<PhylogenyNode> nodes = null;
- if ( query_str.indexOf( ',' ) >= 0 ) {
- queries = query_str.split( ",+" );
- }
- else {
- queries = new String[ 1 ];
- queries[ 0 ] = query_str.trim();
- }
- if ( ( queries != null ) && ( queries.length > 0 ) ) {
- nodes = new ArrayList<PhylogenyNode>();
- for( String query : queries ) {
- if ( ForesterUtil.isEmpty( query ) ) {
- continue;
- }
- query = query.trim();
- if ( query.indexOf( '+' ) >= 0 ) {
- nodes.addAll( PhylogenyMethods.searchDataLogicalAnd( query.split( "\\++" ),
- tree,
- getOptions().isSearchCaseSensitive(),
- !getOptions().isMatchWholeTermsOnly(),
- isShowDomainArchitectures() ) );
- }
- else {
- nodes.addAll( PhylogenyMethods.searchData( query,
- tree,
- getOptions().isSearchCaseSensitive(),
- !getOptions().isMatchWholeTermsOnly(),
- isShowDomainArchitectures() ) );
- }
- }
- if ( getOptions().isInverseSearchResult() ) {
- final List<PhylogenyNode> all = PhylogenyMethods.obtainAllNodesAsList( tree );
- all.removeAll( nodes );
- nodes = all;
- }
- }
- if ( ( nodes != null ) && ( nodes.size() > 0 ) ) {
- main_panel.getCurrentTreePanel().setFoundNodes( new HashSet<Integer>() );
- for( final PhylogenyNode node : nodes ) {
- main_panel.getCurrentTreePanel().getFoundNodes().add( node.getId() );
- }
- setSearchFoundCountsOnLabel( nodes.size() );
- }
- else {
- setSearchFoundCountsOnLabel( 0 );
- searchReset();
- }
- }
-
- private void searchReset() {
- if ( getMainPanel().getCurrentTreePanel() != null ) {
- getMainPanel().getCurrentTreePanel().setFoundNodes( null );
- }
- }
-
void setActionWhenNodeClicked( final NodeClickAction action ) {
_action_when_node_clicked = action;
}
setDrawPhylogram( getMainPanel().getCurrentTabIndex(), b );
}
- private void setDrawPhylogram( final int index, final boolean b ) {
- getIsDrawPhylogramList().set( index, b );
- }
-
void setDrawPhylogramEnabled( final boolean b ) {
getDisplayAsPhylogramCb().setEnabled( b );
}
// }
}
- private void setSearchFoundCountsOnLabel( final int counts ) {
- getSearchFoundCountsLabel().setText( "Found: " + counts );
- }
-
- public void setSequenceRelationQueries( final Collection<Sequence> sequenceRelationQueries ) {
- final JComboBox box = getSequenceRelationBox();
- while ( box.getItemCount() > 1 ) {
- box.removeItemAt( 1 );
- }
- final HashMap<String, Sequence> sequencesByName = new HashMap<String, Sequence>();
- final SequenceRelation.SEQUENCE_RELATION_TYPE relationType = ( SequenceRelation.SEQUENCE_RELATION_TYPE ) _sequence_relation_type_box
- .getSelectedItem();
- if ( relationType == null ) {
- return;
- }
- final ArrayList<String> sequenceNamesToAdd = new ArrayList<String>();
- for( final Sequence seq : sequenceRelationQueries ) {
- if ( seq.hasSequenceRelations() ) {
- boolean fFoundForCurrentType = false;
- for( final SequenceRelation sq : seq.getSequenceRelations() ) {
- if ( sq.getType().equals( relationType ) ) {
- fFoundForCurrentType = true;
- break;
- }
- }
- if ( fFoundForCurrentType ) {
- sequenceNamesToAdd.add( seq.getName() );
- sequencesByName.put( seq.getName(), seq );
- }
- }
- }
- // sort sequences by name before adding them to the combo
- final String[] sequenceNameArray = sequenceNamesToAdd.toArray( new String[ sequenceNamesToAdd.size() ] );
- Arrays.sort( sequenceNameArray, String.CASE_INSENSITIVE_ORDER );
- for( final String seqName : sequenceNameArray ) {
- box.addItem( seqName );
- }
- for( final ItemListener oldItemListener : box.getItemListeners() ) {
- box.removeItemListener( oldItemListener );
- }
- box.addItemListener( new ItemListener() {
-
- @Override
- public void itemStateChanged( final ItemEvent e ) {
- _selected_query_seq = sequencesByName.get( e.getItem() );
- _mainpanel.getCurrentTreePanel().repaint();
- }
- } );
- }
-
void setShowEvents( final boolean show_events ) {
if ( getShowEventsCb() == null ) {
_show_events = new JCheckBox( "" );
_species_colors = species_colors;
}
- private void setupClickToOptions() {
- final int default_option = _configuration.getDefaultDisplayClicktoOption();
- int selected_index = 0;
- int cb_index = 0;
- if ( _configuration.doDisplayClickToOption( Configuration.display_node_data ) ) {
- _show_data_item = cb_index;
- addClickToOption( Configuration.display_node_data,
- _configuration.getClickToTitle( Configuration.display_node_data ) );
- if ( default_option == Configuration.display_node_data ) {
- selected_index = cb_index;
- }
- cb_index++;
+ /* GUILHEM_END */
+ /*
+ * Set up the controls from the config settings. 11/26/05
+ */
+ void setupControls() {
+ // The tree display options:
+ setupDisplayCheckboxes();
+ /* GUILHEM_BEG */
+ // The sequence relation query selection combo-box
+ if ( _configuration.displaySequenceRelations() ) {
+ addSequenceRelationBlock();
}
- if ( _configuration.doDisplayClickToOption( Configuration.collapse_uncollapse ) ) {
- _collapse_cb_item = cb_index;
- addClickToOption( Configuration.collapse_uncollapse,
- _configuration.getClickToTitle( Configuration.collapse_uncollapse ) );
- if ( default_option == Configuration.collapse_uncollapse ) {
- selected_index = cb_index;
- }
- cb_index++;
+ /* GUILHEM_END */
+ // Click-to options
+ startClickToOptions();
+ setupClickToOptions();
+ endClickToOptions();
+ // Zoom and quick edit buttons
+ addButtons();
+ setupSearchTools();
+ }
+
+ void setUpControlsForDomainStrucures() {
+ _domain_display_label = new JLabel( "Domain Display:" );
+ add( customizeLabel( _domain_display_label, getConfiguration() ) );
+ add( _domain_display_label );
+ _zoom_in_domain_structure = new JButton( "d+" );
+ _zoom_out_domain_structure = new JButton( "d-" );
+ _decr_domain_structure_evalue_thr = new JButton( "-" );
+ _incr_domain_structure_evalue_thr = new JButton( "+" );
+ _zoom_in_domain_structure.setPreferredSize( new Dimension( 10, 10 ) );
+ _zoom_out_domain_structure.setPreferredSize( new Dimension( 10, 10 ) );
+ _decr_domain_structure_evalue_thr.setPreferredSize( new Dimension( 10, 10 ) );
+ _incr_domain_structure_evalue_thr.setPreferredSize( new Dimension( 10, 10 ) );
+ _incr_domain_structure_evalue_thr.setToolTipText( "Increase the E-value threshold by a factor of 10" );
+ _decr_domain_structure_evalue_thr.setToolTipText( "Decrease the E-value threshold by a factor of 10" );
+ _domain_structure_evalue_thr_tf = new JTextField( 3 );
+ _domain_structure_evalue_thr_tf.setEditable( false );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ _domain_structure_evalue_thr_tf.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
+ _domain_structure_evalue_thr_tf.setBackground( getConfiguration().getGuiCheckboxTextColor() );
+ _domain_structure_evalue_thr_tf.setBorder( null );
}
- if ( _configuration.doDisplayClickToOption( Configuration.reroot ) ) {
- _reroot_cb_item = cb_index;
- addClickToOption( Configuration.reroot, _configuration.getClickToTitle( Configuration.reroot ) );
- if ( default_option == Configuration.reroot ) {
+ final JPanel d1_panel = new JPanel( new GridLayout( 1, 2, 0, 0 ) );
+ final JPanel d2_panel = new JPanel( new GridLayout( 1, 3, 0, 0 ) );
+ if ( !_configuration.isUseNativeUI() ) {
+ d1_panel.setBackground( getBackground() );
+ d2_panel.setBackground( getBackground() );
+ }
+ add( d1_panel );
+ add( d2_panel );
+ addJButton( _zoom_out_domain_structure, d1_panel );
+ addJButton( _zoom_in_domain_structure, d1_panel );
+ addJButton( _decr_domain_structure_evalue_thr, d2_panel );
+ addJTextField( _domain_structure_evalue_thr_tf, d2_panel );
+ addJButton( _incr_domain_structure_evalue_thr, d2_panel );
+ }
+
+ void setupSearchTools() {
+ final String tip = "Enter text to search for. Use ',' for multiple searches (logical OR) and '+' for logical AND.";
+ final JLabel search_label = new JLabel( "Search:" );
+ search_label.setFont( ControlPanel.jcb_bold_font );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ search_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
+ }
+ add( search_label );
+ search_label.setToolTipText( tip );
+ _search_found_label = new JLabel();
+ getSearchFoundCountsLabel().setVisible( false );
+ _search_found_label.setFont( ControlPanel.jcb_bold_font );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ _search_found_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
+ }
+ _search_tf = new JTextField( 3 );
+ _search_tf.setToolTipText( tip );
+ _search_tf.setEditable( true );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ _search_tf.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
+ _search_tf.setBackground( getConfiguration().getGuiCheckboxTextColor() );
+ _search_tf.setBorder( null );
+ }
+ _search_reset_button = new JButton();
+ getSearchResetButton().setText( "Reset" );
+ getSearchResetButton().setEnabled( false );
+ getSearchResetButton().setVisible( false );
+ final JPanel s_panel_1 = new JPanel( new BorderLayout() );
+ final JPanel s_panel_2 = new JPanel( new GridLayout( 1, 2, 0, 0 ) );
+ s_panel_1.setBackground( getBackground() );
+ add( s_panel_1 );
+ s_panel_2.setBackground( getBackground() );
+ add( s_panel_2 );
+ final KeyAdapter key_adapter = new KeyAdapter() {
+
+ @Override
+ public void keyReleased( final KeyEvent key_event ) {
+ search();
+ displayedPhylogenyMightHaveChanged( true );
+ }
+ };
+ final ActionListener action_listener = new ActionListener() {
+
+ @Override
+ public void actionPerformed( final ActionEvent e ) {
+ searchReset();
+ setSearchFoundCountsOnLabel( 0 );
+ getSearchFoundCountsLabel().setVisible( false );
+ getSearchTextField().setText( "" );
+ getSearchResetButton().setEnabled( false );
+ getSearchResetButton().setVisible( false );
+ displayedPhylogenyMightHaveChanged( true );
+ }
+ };
+ _search_reset_button.addActionListener( action_listener );
+ _search_tf.addKeyListener( key_adapter );
+ addJTextField( _search_tf, s_panel_1 );
+ s_panel_2.add( _search_found_label );
+ addJButton( _search_reset_button, s_panel_2 );
+ }
+
+ /**
+ * Fit entire tree into window.
+ */
+ void showWhole() {
+ if ( ( _mainpanel.getCurrentScrollPane() == null ) || _mainpanel.getCurrentTreePanel().getPhylogeny().isEmpty() ) {
+ return;
+ }
+ getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
+ displayedPhylogenyMightHaveChanged( true );
+ _mainpanel.getCurrentTreePanel().updateOvSettings();
+ _mainpanel.getCurrentTreePanel().validate();
+ _mainpanel.validate();
+ _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getSizeOfViewport().width,
+ _mainpanel.getSizeOfViewport().height,
+ true );
+ _mainpanel.getCurrentTreePanel().resetPreferredSize();
+ _mainpanel.adjustJScrollPane();
+ _mainpanel.getCurrentTreePanel().repaint();
+ _mainpanel.getCurrentTreePanel().validate();
+ _mainpanel.validate();
+ _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getSizeOfViewport().width,
+ _mainpanel.getSizeOfViewport().height,
+ true );
+ _mainpanel.getCurrentTreePanel().resetPreferredSize();
+ _mainpanel.adjustJScrollPane();
+ _mainpanel.getCurrentTreePanel().repaint();
+ _mainpanel.getCurrentTreePanel().updateOvSizes();
+ }
+
+ void showWholeAll() {
+ for( final TreePanel tree_panel : _mainpanel.getTreePanels() ) {
+ if ( tree_panel != null ) {
+ tree_panel.validate();
+ tree_panel.setParametersForPainting( _mainpanel.getSizeOfViewport().width,
+ _mainpanel.getSizeOfViewport().height,
+ true );
+ tree_panel.resetPreferredSize();
+ tree_panel.repaint();
+ }
+ }
+ }
+
+ // Create header for click-to combo box.
+ void startClickToOptions() {
+ final JLabel spacer = new JLabel( "" );
+ spacer.setFont( ControlPanel.jcb_font );
+ add( spacer );
+ _click_to_label = new JLabel( "Click on Node to:" );
+ add( customizeLabel( _click_to_label, getConfiguration() ) );
+ _click_to_combobox = new JComboBox();
+ _click_to_combobox.setFocusable( false );
+ _click_to_combobox.setMaximumRowCount( 14 );
+ _click_to_combobox.setFont( ControlPanel.js_font );
+ if ( !_configuration.isUseNativeUI() ) {
+ _click_to_combobox.setBackground( getConfiguration().getGuiBackgroundColor() );
+ }
+ // don't add listener until all items are set (or each one will trigger
+ // an event)
+ // click_to_list.addActionListener(this);
+ add( _click_to_combobox );
+ // Correlates option names to titles
+ _all_click_to_names = new HashMap<Integer, String>();
+ _click_to_names = new ArrayList<String>();
+ }
+
+ void tabChanged() {
+ if ( getMainPanel().getTabbedPane().getTabCount() > 0 ) {
+ if ( getCurrentTreePanel().isPhyHasBranchLengths()
+ && ( getCurrentTreePanel().getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
+ setDrawPhylogramEnabled( true );
+ setDrawPhylogram( isDrawPhylogram() );
+ }
+ else {
+ setDrawPhylogramEnabled( false );
+ setDrawPhylogram( false );
+ }
+ if ( getMainPanel().getMainFrame() == null ) {
+ // Must be "E" applet version.
+ final ArchaeopteryxE e = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
+ e.setSelectedTypeInTypeMenu( e.getCurrentTreePanel().getPhylogenyGraphicsType() );
+ }
+ else {
+ getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getMainPanel().getCurrentTreePanel()
+ .getPhylogenyGraphicsType() );
+ }
+ getMainPanel().getCurrentTreePanel().updateSubSuperTreeButton();
+ getMainPanel().getControlPanel().search();
+ getSequenceRelationTypeBox().removeAllItems();
+ for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
+ .getRelevantSequenceRelationTypes() ) {
+ _sequence_relation_type_box.addItem( type );
+ }
+ //setSequenceRelationQueries( getMainPanel().getCurrentPhylogeny().getSequenceRelationQueries() );
+ // according to GUILHEM the line above can be removed.
+ }
+ }
+
+ /**
+ * Uncollapse all nodes.
+ */
+ void uncollapseAll( final TreePanel tp ) {
+ final Phylogeny t = tp.getPhylogeny();
+ if ( ( t != null ) && !t.isEmpty() ) {
+ for( final PhylogenyNodeIterator iter = t.iteratorPreorder(); iter.hasNext(); ) {
+ final PhylogenyNode node = iter.next();
+ node.setCollapse( false );
+ }
+ tp.resetNodeIdToDistToLeafMap();
+ tp.updateSetOfCollapsedExternalNodes();
+ t.recalculateNumberOfExternalDescendants( false );
+ tp.setNodeInPreorderToNull();
+ t.clearHashIdToNodeMap();
+ showWhole();
+ }
+ }
+
+ void updateDomainStructureEvaluethresholdDisplay() {
+ if ( _domain_structure_evalue_thr_tf != null ) {
+ _domain_structure_evalue_thr_tf.setText( "10^"
+ + getMainPanel().getCurrentTreePanel().getDomainStructureEvalueThreshold() );
+ }
+ }
+
+ void zoomInX( final float factor, final float x_correction_factor ) {
+ final JScrollBar sb = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar();
+ final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
+ treepanel.multiplyUrtFactor( 1f );
+ if ( ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
+ || ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
+ || isDrawPhylogram( getMainPanel().getCurrentTabIndex() )
+ || ( getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP ) ) {
+ final double x = ( sb.getMaximum() - sb.getMinimum() ) / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
+ treepanel.setXdistance( ( treepanel.getXdistance() * factor ) );
+ treepanel.setXcorrectionFactor( ( treepanel.getXcorrectionFactor() * x_correction_factor ) );
+ getMainPanel().adjustJScrollPane();
+ treepanel.resetPreferredSize();
+ getMainPanel().getCurrentScrollPane().getViewport().validate();
+ sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
+ - ( sb.getVisibleAmount() / 2.0 ) ) );
+ }
+ else {
+ final int x = sb.getMaximum() - sb.getMinimum() - sb.getVisibleAmount() - sb.getValue();
+ treepanel.setXdistance( ( treepanel.getXdistance() * factor ) );
+ treepanel.setXcorrectionFactor( ( treepanel.getXcorrectionFactor() * x_correction_factor ) );
+ getMainPanel().adjustJScrollPane();
+ treepanel.resetPreferredSize();
+ getMainPanel().getCurrentScrollPane().getViewport().validate();
+ sb.setValue( sb.getMaximum() - sb.getMinimum() - x - sb.getVisibleAmount() );
+ }
+ treepanel.resetPreferredSize();
+ treepanel.updateOvSizes();
+ }
+
+ void zoomInY( final float factor ) {
+ final JScrollBar sb = getMainPanel().getCurrentScrollPane().getVerticalScrollBar();
+ final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
+ treepanel.multiplyUrtFactor( 1.1f );
+ final double x = ( sb.getMaximum() - sb.getMinimum() ) / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
+ treepanel.setYdistance( ( treepanel.getYdistance() * factor ) );
+ getMainPanel().adjustJScrollPane();
+ treepanel.resetPreferredSize();
+ getMainPanel().getCurrentScrollPane().getViewport().validate();
+ sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
+ - ( sb.getVisibleAmount() / 2.0 ) ) );
+ treepanel.resetPreferredSize();
+ treepanel.updateOvSizes();
+ }
+
+ void zoomOutX( final float factor, final float x_correction_factor ) {
+ final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
+ treepanel.multiplyUrtFactor( 1f );
+ if ( ( treepanel.getXdistance() * factor ) > 0.0 ) {
+ final JScrollBar sb = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar();
+ if ( ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
+ || ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
+ || isDrawPhylogram( getMainPanel().getCurrentTabIndex() )
+ || ( getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP ) ) {
+ getMainPanel().adjustJScrollPane();
+ treepanel.resetPreferredSize();
+ getMainPanel().getCurrentScrollPane().getViewport().validate();
+ final double x = ( sb.getMaximum() - sb.getMinimum() )
+ / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
+ treepanel.setXdistance( ( treepanel.getXdistance() * factor ) );
+ treepanel.setXcorrectionFactor( ( treepanel.getXcorrectionFactor() * x_correction_factor ) );
+ getMainPanel().adjustJScrollPane();
+ treepanel.resetPreferredSize();
+ getMainPanel().getCurrentScrollPane().getViewport().validate();
+ sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
+ - ( sb.getVisibleAmount() / 2.0 ) ) );
+ }
+ else {
+ final int x = sb.getMaximum() - sb.getMinimum() - sb.getVisibleAmount() - sb.getValue();
+ treepanel.setXdistance( treepanel.getXdistance() * factor );
+ treepanel.setXcorrectionFactor( treepanel.getXcorrectionFactor() * x_correction_factor );
+ if ( x > 0 ) {
+ getMainPanel().adjustJScrollPane();
+ treepanel.resetPreferredSize();
+ getMainPanel().getCurrentScrollPane().getViewport().validate();
+ sb.setValue( sb.getMaximum() - sb.getMinimum() - x - sb.getVisibleAmount() );
+ }
+ }
+ treepanel.resetPreferredSize();
+ treepanel.updateOvSizes();
+ }
+ }
+
+ void zoomOutY( final float factor ) {
+ final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
+ treepanel.multiplyUrtFactor( 0.9f );
+ if ( ( treepanel.getYdistance() * factor ) > 0.0 ) {
+ final JScrollBar sb = getMainPanel().getCurrentScrollPane().getVerticalScrollBar();
+ final double x = ( sb.getMaximum() - sb.getMinimum() ) / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
+ treepanel.setYdistance( ( treepanel.getYdistance() * factor ) );
+ getMainPanel().adjustJScrollPane();
+ treepanel.resetPreferredSize();
+ getMainPanel().getCurrentScrollPane().getViewport().validate();
+ sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
+ - ( sb.getVisibleAmount() / 2.0 ) ) );
+ treepanel.resetPreferredSize();
+ treepanel.updateOvSizes();
+ }
+ }
+
+ private void addClickToOption( final int which, final String title ) {
+ _click_to_combobox.addItem( title );
+ _click_to_names.add( title );
+ _all_click_to_names.put( new Integer( which ), title );
+ if ( !_configuration.isUseNativeUI() ) {
+ _click_to_combobox.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
+ _click_to_combobox.setForeground( getConfiguration().getGuiButtonTextColor() );
+ }
+ }
+
+ /* GUILHEM_BEG */
+ private void addSequenceRelationBlock() {
+ final JLabel spacer = new JLabel( "" );
+ spacer.setSize( 1, 1 );
+ add( spacer );
+ final JLabel mainLabel = new JLabel( "Sequence relations to display" );
+ final JLabel typeLabel = customizeLabel( new JLabel( "(type) " ), getConfiguration() );
+ typeLabel.setFont( ControlPanel.js_font.deriveFont( 7 ) );
+ getSequenceRelationTypeBox().setFocusable( false );
+ _sequence_relation_type_box.setFont( ControlPanel.js_font );
+ if ( !_configuration.isUseNativeUI() ) {
+ _sequence_relation_type_box.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
+ _sequence_relation_type_box.setForeground( getConfiguration().getGuiButtonTextColor() );
+ }
+ _sequence_relation_type_box.setRenderer( new ListCellRenderer() {
+
+ @Override
+ public Component getListCellRendererComponent( final JList list,
+ final Object value,
+ final int index,
+ final boolean isSelected,
+ final boolean cellHasFocus ) {
+ final Component component = new DefaultListCellRenderer().getListCellRendererComponent( list,
+ value,
+ index,
+ isSelected,
+ cellHasFocus );
+ if ( ( value != null ) && ( value instanceof SequenceRelation.SEQUENCE_RELATION_TYPE ) ) {
+ ( ( DefaultListCellRenderer ) component ).setText( SequenceRelation
+ .getPrintableNameByType( ( SequenceRelation.SEQUENCE_RELATION_TYPE ) value ) );
+ }
+ return component;
+ }
+ } );
+ final GridBagLayout gbl = new GridBagLayout();
+ _sequence_relation_type_box.setMinimumSize( new Dimension( 115, 17 ) );
+ _sequence_relation_type_box.setPreferredSize( new Dimension( 115, 20 ) );
+ final JPanel horizGrid = new JPanel( gbl );
+ horizGrid.setBackground( getBackground() );
+ horizGrid.add( typeLabel );
+ horizGrid.add( _sequence_relation_type_box );
+ add( customizeLabel( mainLabel, getConfiguration() ) );
+ add( horizGrid );
+ add( getSequenceRelationBox() );
+ if ( _configuration.doDisplayOption( Configuration.show_relation_confidence ) ) {
+ addCheckbox( Configuration.show_relation_confidence,
+ _configuration.getDisplayTitle( Configuration.show_relation_confidence ) );
+ setCheckbox( Configuration.show_relation_confidence,
+ _configuration.doCheckOption( Configuration.show_relation_confidence ) );
+ }
+ }// addSequenceRelationBlock
+
+ /* GUILHEM_END */
+ private List<Boolean> getIsDrawPhylogramList() {
+ return _draw_phylogram;
+ }
+
+ JLabel getSearchFoundCountsLabel() {
+ return _search_found_label;
+ }
+
+ JButton getSearchResetButton() {
+ return _search_reset_button;
+ }
+
+ private void init() {
+ _draw_phylogram = new ArrayList<Boolean>();
+ setSpeciesColors( new HashMap<String, Color>() );
+ setAnnotationColors( new HashMap<String, Color>() );
+ }
+
+ private boolean isDrawPhylogram( final int index ) {
+ return getIsDrawPhylogramList().get( index );
+ }
+
+ private void search( final MainPanel main_panel, final Phylogeny tree, final String query_str ) {
+ getSearchFoundCountsLabel().setVisible( true );
+ getSearchResetButton().setEnabled( true );
+ getSearchResetButton().setVisible( true );
+ String[] queries = null;
+ List<PhylogenyNode> nodes = null;
+ if ( query_str.indexOf( ',' ) >= 0 ) {
+ queries = query_str.split( ",+" );
+ }
+ else {
+ queries = new String[ 1 ];
+ queries[ 0 ] = query_str.trim();
+ }
+ if ( ( queries != null ) && ( queries.length > 0 ) ) {
+ nodes = new ArrayList<PhylogenyNode>();
+ for( String query : queries ) {
+ if ( ForesterUtil.isEmpty( query ) ) {
+ continue;
+ }
+ query = query.trim();
+ if ( query.indexOf( '+' ) >= 0 ) {
+ nodes.addAll( PhylogenyMethods.searchDataLogicalAnd( query.split( "\\++" ),
+ tree,
+ getOptions().isSearchCaseSensitive(),
+ !getOptions().isMatchWholeTermsOnly(),
+ isShowDomainArchitectures() ) );
+ }
+ else {
+ nodes.addAll( PhylogenyMethods.searchData( query,
+ tree,
+ getOptions().isSearchCaseSensitive(),
+ !getOptions().isMatchWholeTermsOnly(),
+ isShowDomainArchitectures() ) );
+ }
+ }
+ if ( getOptions().isInverseSearchResult() ) {
+ final List<PhylogenyNode> all = PhylogenyMethods.obtainAllNodesAsList( tree );
+ all.removeAll( nodes );
+ nodes = all;
+ }
+ }
+ if ( ( nodes != null ) && ( nodes.size() > 0 ) ) {
+ main_panel.getCurrentTreePanel().setFoundNodes( new HashSet<Integer>() );
+ for( final PhylogenyNode node : nodes ) {
+ main_panel.getCurrentTreePanel().getFoundNodes().add( node.getId() );
+ }
+ setSearchFoundCountsOnLabel( nodes.size() );
+ }
+ else {
+ setSearchFoundCountsOnLabel( 0 );
+ searchReset();
+ }
+ }
+
+ void searchReset() {
+ if ( getMainPanel().getCurrentTreePanel() != null ) {
+ getMainPanel().getCurrentTreePanel().setFoundNodes( null );
+ }
+ }
+
+ private void setDrawPhylogram( final int index, final boolean b ) {
+ getIsDrawPhylogramList().set( index, b );
+ }
+
+ void setSearchFoundCountsOnLabel( final int counts ) {
+ getSearchFoundCountsLabel().setText( "Found: " + counts );
+ }
+
+ private void setupClickToOptions() {
+ final int default_option = _configuration.getDefaultDisplayClicktoOption();
+ int selected_index = 0;
+ int cb_index = 0;
+ if ( _configuration.doDisplayClickToOption( Configuration.display_node_data ) ) {
+ _show_data_item = cb_index;
+ addClickToOption( Configuration.display_node_data,
+ _configuration.getClickToTitle( Configuration.display_node_data ) );
+ if ( default_option == Configuration.display_node_data ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.collapse_uncollapse ) ) {
+ _collapse_cb_item = cb_index;
+ addClickToOption( Configuration.collapse_uncollapse,
+ _configuration.getClickToTitle( Configuration.collapse_uncollapse ) );
+ if ( default_option == Configuration.collapse_uncollapse ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.reroot ) ) {
+ _reroot_cb_item = cb_index;
+ addClickToOption( Configuration.reroot, _configuration.getClickToTitle( Configuration.reroot ) );
+ if ( default_option == Configuration.reroot ) {
selected_index = cb_index;
}
cb_index++;
setClickToAction( selected_index );
}
- /* GUILHEM_END */
- /*
- * Set up the controls from the config settings. 11/26/05
- */
- void setupControls() {
- // The tree display options:
- setupDisplayCheckboxes();
- /* GUILHEM_BEG */
- // The sequence relation query selection combo-box
- if ( _configuration.displaySequenceRelations() ) {
- addSequenceRelationBlock();
- }
- /* GUILHEM_END */
- // Click-to options
- startClickToOptions();
- setupClickToOptions();
- endClickToOptions();
- // Zoom and quick edit buttons
- addButtons();
- setupSearchTools();
- }
-
- void setUpControlsForDomainStrucures() {
- _domain_display_label = new JLabel( "Domain Display:" );
- add( customizeLabel( _domain_display_label, getConfiguration() ) );
- add( _domain_display_label );
- _zoom_in_domain_structure = new JButton( "d+" );
- _zoom_out_domain_structure = new JButton( "d-" );
- _decr_domain_structure_evalue_thr = new JButton( "-" );
- _incr_domain_structure_evalue_thr = new JButton( "+" );
- _zoom_in_domain_structure.setPreferredSize( new Dimension( 10, 10 ) );
- _zoom_out_domain_structure.setPreferredSize( new Dimension( 10, 10 ) );
- _decr_domain_structure_evalue_thr.setPreferredSize( new Dimension( 10, 10 ) );
- _incr_domain_structure_evalue_thr.setPreferredSize( new Dimension( 10, 10 ) );
- _incr_domain_structure_evalue_thr.setToolTipText( "Increase the E-value threshold by a factor of 10" );
- _decr_domain_structure_evalue_thr.setToolTipText( "Decrease the E-value threshold by a factor of 10" );
- _domain_structure_evalue_thr_tf = new JTextField( 3 );
- _domain_structure_evalue_thr_tf.setEditable( false );
- if ( !getConfiguration().isUseNativeUI() ) {
- _domain_structure_evalue_thr_tf.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
- _domain_structure_evalue_thr_tf.setBackground( getConfiguration().getGuiCheckboxTextColor() );
- _domain_structure_evalue_thr_tf.setBorder( null );
- }
- final JPanel d1_panel = new JPanel( new GridLayout( 1, 2, 0, 0 ) );
- final JPanel d2_panel = new JPanel( new GridLayout( 1, 3, 0, 0 ) );
- if ( !_configuration.isUseNativeUI() ) {
- d1_panel.setBackground( getBackground() );
- d2_panel.setBackground( getBackground() );
- }
- add( d1_panel );
- add( d2_panel );
- addJButton( _zoom_out_domain_structure, d1_panel );
- addJButton( _zoom_in_domain_structure, d1_panel );
- addJButton( _decr_domain_structure_evalue_thr, d2_panel );
- addJTextField( _domain_structure_evalue_thr_tf, d2_panel );
- addJButton( _incr_domain_structure_evalue_thr, d2_panel );
- }
-
private void setupDisplayCheckboxes() {
if ( _configuration.doDisplayOption( Configuration.display_as_phylogram ) ) {
addCheckbox( Configuration.display_as_phylogram,
addCheckbox( Configuration.show_binary_characters,
_configuration.getDisplayTitle( Configuration.show_binary_characters ) );
setCheckbox( Configuration.show_binary_characters,
- _configuration.doCheckOption( Configuration.show_binary_characters ) );
- }
- if ( _configuration.doDisplayOption( Configuration.show_binary_character_counts ) ) {
- addCheckbox( Configuration.show_binary_character_counts,
- _configuration.getDisplayTitle( Configuration.show_binary_character_counts ) );
- setCheckbox( Configuration.show_binary_character_counts,
- _configuration.doCheckOption( Configuration.show_binary_character_counts ) );
- }
- if ( _configuration.doDisplayOption( Configuration.show_domain_architectures ) ) {
- addCheckbox( Configuration.show_domain_architectures,
- _configuration.getDisplayTitle( Configuration.show_domain_architectures ) );
- setCheckbox( Configuration.show_domain_architectures,
- _configuration.doCheckOption( Configuration.show_domain_architectures ) );
- }
- if ( _configuration.doDisplayOption( Configuration.write_confidence_values ) ) {
- addCheckbox( Configuration.write_confidence_values,
- _configuration.getDisplayTitle( Configuration.write_confidence_values ) );
- setCheckbox( Configuration.write_confidence_values,
- _configuration.doCheckOption( Configuration.write_confidence_values ) );
- }
- if ( _configuration.doDisplayOption( Configuration.write_events ) ) {
- addCheckbox( Configuration.write_events, _configuration.getDisplayTitle( Configuration.write_events ) );
- setCheckbox( Configuration.write_events, _configuration.doCheckOption( Configuration.write_events ) );
- }
- if ( _configuration.doDisplayOption( Configuration.show_vector_data ) ) {
- addCheckbox( Configuration.show_vector_data,
- _configuration.getDisplayTitle( Configuration.show_vector_data ) );
- setCheckbox( Configuration.show_vector_data, _configuration.doCheckOption( Configuration.show_vector_data ) );
- }
- if ( _configuration.doDisplayOption( Configuration.show_properties ) ) {
- addCheckbox( Configuration.show_properties, _configuration.getDisplayTitle( Configuration.show_properties ) );
- setCheckbox( Configuration.show_properties, _configuration.doCheckOption( Configuration.show_properties ) );
- }
- }
-
- void setupSearchTools() {
- final String tip = "Enter text to search for. Use ',' for multiple searches (logical OR) and '+' for logical AND.";
- final JLabel search_label = new JLabel( "Search:" );
- search_label.setFont( ControlPanel.jcb_bold_font );
- if ( !getConfiguration().isUseNativeUI() ) {
- search_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
- }
- add( search_label );
- search_label.setToolTipText( tip );
- _search_found_label = new JLabel();
- getSearchFoundCountsLabel().setVisible( false );
- _search_found_label.setFont( ControlPanel.jcb_bold_font );
- if ( !getConfiguration().isUseNativeUI() ) {
- _search_found_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
- }
- _search_tf = new JTextField( 3 );
- _search_tf.setToolTipText( tip );
- _search_tf.setEditable( true );
- if ( !getConfiguration().isUseNativeUI() ) {
- _search_tf.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
- _search_tf.setBackground( getConfiguration().getGuiCheckboxTextColor() );
- _search_tf.setBorder( null );
- }
- _search_reset_button = new JButton();
- getSearchResetButton().setText( "Reset" );
- getSearchResetButton().setEnabled( false );
- getSearchResetButton().setVisible( false );
- final JPanel s_panel_1 = new JPanel( new BorderLayout() );
- final JPanel s_panel_2 = new JPanel( new GridLayout( 1, 2, 0, 0 ) );
- s_panel_1.setBackground( getBackground() );
- add( s_panel_1 );
- s_panel_2.setBackground( getBackground() );
- add( s_panel_2 );
- final KeyAdapter key_adapter = new KeyAdapter() {
-
- @Override
- public void keyReleased( final KeyEvent key_event ) {
- search();
- displayedPhylogenyMightHaveChanged( true );
- }
- };
- final ActionListener action_listener = new ActionListener() {
-
- @Override
- public void actionPerformed( final ActionEvent e ) {
- searchReset();
- setSearchFoundCountsOnLabel( 0 );
- getSearchFoundCountsLabel().setVisible( false );
- getSearchTextField().setText( "" );
- getSearchResetButton().setEnabled( false );
- getSearchResetButton().setVisible( false );
- displayedPhylogenyMightHaveChanged( true );
- }
- };
- _search_reset_button.addActionListener( action_listener );
- _search_tf.addKeyListener( key_adapter );
- addJTextField( _search_tf, s_panel_1 );
- s_panel_2.add( _search_found_label );
- addJButton( _search_reset_button, s_panel_2 );
+ _configuration.doCheckOption( Configuration.show_binary_characters ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_binary_character_counts ) ) {
+ addCheckbox( Configuration.show_binary_character_counts,
+ _configuration.getDisplayTitle( Configuration.show_binary_character_counts ) );
+ setCheckbox( Configuration.show_binary_character_counts,
+ _configuration.doCheckOption( Configuration.show_binary_character_counts ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_domain_architectures ) ) {
+ addCheckbox( Configuration.show_domain_architectures,
+ _configuration.getDisplayTitle( Configuration.show_domain_architectures ) );
+ setCheckbox( Configuration.show_domain_architectures,
+ _configuration.doCheckOption( Configuration.show_domain_architectures ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.write_confidence_values ) ) {
+ addCheckbox( Configuration.write_confidence_values,
+ _configuration.getDisplayTitle( Configuration.write_confidence_values ) );
+ setCheckbox( Configuration.write_confidence_values,
+ _configuration.doCheckOption( Configuration.write_confidence_values ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.write_events ) ) {
+ addCheckbox( Configuration.write_events, _configuration.getDisplayTitle( Configuration.write_events ) );
+ setCheckbox( Configuration.write_events, _configuration.doCheckOption( Configuration.write_events ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_vector_data ) ) {
+ addCheckbox( Configuration.show_vector_data,
+ _configuration.getDisplayTitle( Configuration.show_vector_data ) );
+ setCheckbox( Configuration.show_vector_data, _configuration.doCheckOption( Configuration.show_vector_data ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_properties ) ) {
+ addCheckbox( Configuration.show_properties, _configuration.getDisplayTitle( Configuration.show_properties ) );
+ setCheckbox( Configuration.show_properties, _configuration.doCheckOption( Configuration.show_properties ) );
+ }
}
private void setVisibilityOfDomainStrucureControls() {
}
}
- /**
- * Fit entire tree into window.
- */
- void showWhole() {
- if ( ( _mainpanel.getCurrentScrollPane() == null ) || _mainpanel.getCurrentTreePanel().getPhylogeny().isEmpty() ) {
- return;
- }
- getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
- displayedPhylogenyMightHaveChanged( true );
- _mainpanel.getCurrentTreePanel().updateOvSettings();
- _mainpanel.getCurrentTreePanel().validate();
- _mainpanel.validate();
- _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getSizeOfViewport().width,
- _mainpanel.getSizeOfViewport().height,
- true );
- _mainpanel.getCurrentTreePanel().resetPreferredSize();
- _mainpanel.adjustJScrollPane();
- _mainpanel.getCurrentTreePanel().repaint();
- _mainpanel.getCurrentTreePanel().validate();
- _mainpanel.validate();
- _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getSizeOfViewport().width,
- _mainpanel.getSizeOfViewport().height,
- true );
- _mainpanel.getCurrentTreePanel().resetPreferredSize();
- _mainpanel.adjustJScrollPane();
- _mainpanel.getCurrentTreePanel().repaint();
- _mainpanel.getCurrentTreePanel().updateOvSizes();
- }
-
- void showWholeAll() {
- for( final TreePanel tree_panel : _mainpanel.getTreePanels() ) {
- if ( tree_panel != null ) {
- tree_panel.validate();
- tree_panel.setParametersForPainting( _mainpanel.getSizeOfViewport().width,
- _mainpanel.getSizeOfViewport().height,
- true );
- tree_panel.resetPreferredSize();
- tree_panel.repaint();
- }
- }
- }
-
- // Create header for click-to combo box.
- void startClickToOptions() {
- final JLabel spacer = new JLabel( "" );
- spacer.setFont( ControlPanel.jcb_font );
- add( spacer );
- _click_to_label = new JLabel( "Click on Node to:" );
- add( customizeLabel( _click_to_label, getConfiguration() ) );
- _click_to_combobox = new JComboBox();
- _click_to_combobox.setFocusable( false );
- _click_to_combobox.setMaximumRowCount( 14 );
- _click_to_combobox.setFont( ControlPanel.js_font );
- if ( !_configuration.isUseNativeUI() ) {
- _click_to_combobox.setBackground( getConfiguration().getGuiBackgroundColor() );
- }
- // don't add listener until all items are set (or each one will trigger
- // an event)
- // click_to_list.addActionListener(this);
- add( _click_to_combobox );
- // Correlates option names to titles
- _all_click_to_names = new HashMap<Integer, String>();
- _click_to_names = new ArrayList<String>();
- }
-
- void tabChanged() {
- if ( getMainPanel().getTabbedPane().getTabCount() > 0 ) {
- if ( getCurrentTreePanel().isPhyHasBranchLengths()
- && ( getCurrentTreePanel().getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
- setDrawPhylogramEnabled( true );
- setDrawPhylogram( isDrawPhylogram() );
- }
- else {
- setDrawPhylogramEnabled( false );
- setDrawPhylogram( false );
- }
- if ( getMainPanel().getMainFrame() == null ) {
- // Must be "E" applet version.
- final ArchaeopteryxE e = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
- e.setSelectedTypeInTypeMenu( e.getCurrentTreePanel().getPhylogenyGraphicsType() );
- }
- else {
- getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getMainPanel().getCurrentTreePanel()
- .getPhylogenyGraphicsType() );
- }
- getMainPanel().getCurrentTreePanel().updateSubSuperTreeButton();
- getMainPanel().getControlPanel().search();
- getSequenceRelationTypeBox().removeAllItems();
- for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
- .getRelevantSequenceRelationTypes() ) {
- _sequence_relation_type_box.addItem( type );
- }
- //setSequenceRelationQueries( getMainPanel().getCurrentPhylogeny().getSequenceRelationQueries() );
- // according to GUILHEM the line above can be removed.
- }
- }
-
- /**
- * Uncollapse all nodes.
- */
- void uncollapseAll( final TreePanel tp ) {
- final Phylogeny t = tp.getPhylogeny();
- if ( ( t != null ) && !t.isEmpty() ) {
- for( final PhylogenyNodeIterator iter = t.iteratorPreorder(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- node.setCollapse( false );
- }
- tp.resetNodeIdToDistToLeafMap();
- tp.updateSetOfCollapsedExternalNodes();
- t.recalculateNumberOfExternalDescendants( false );
- tp.setNodeInPreorderToNull();
- t.clearHashIdToNodeMap();
- showWhole();
- }
- }
-
- void updateDomainStructureEvaluethresholdDisplay() {
- if ( _domain_structure_evalue_thr_tf != null ) {
- _domain_structure_evalue_thr_tf.setText( "10^"
- + getMainPanel().getCurrentTreePanel().getDomainStructureEvalueThreshold() );
- }
- }
-
- void zoomInX( final float factor, final float x_correction_factor ) {
- final JScrollBar sb = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar();
- final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
- treepanel.multiplyUrtFactor( 1f );
- if ( ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
- || ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
- || isDrawPhylogram( getMainPanel().getCurrentTabIndex() )
- || ( getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP ) ) {
- final double x = ( sb.getMaximum() - sb.getMinimum() ) / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
- treepanel.setXdistance( ( treepanel.getXdistance() * factor ) );
- treepanel.setXcorrectionFactor( ( treepanel.getXcorrectionFactor() * x_correction_factor ) );
- getMainPanel().adjustJScrollPane();
- treepanel.resetPreferredSize();
- getMainPanel().getCurrentScrollPane().getViewport().validate();
- sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
- - ( sb.getVisibleAmount() / 2.0 ) ) );
- }
- else {
- final int x = sb.getMaximum() - sb.getMinimum() - sb.getVisibleAmount() - sb.getValue();
- treepanel.setXdistance( ( treepanel.getXdistance() * factor ) );
- treepanel.setXcorrectionFactor( ( treepanel.getXcorrectionFactor() * x_correction_factor ) );
- getMainPanel().adjustJScrollPane();
- treepanel.resetPreferredSize();
- getMainPanel().getCurrentScrollPane().getViewport().validate();
- sb.setValue( sb.getMaximum() - sb.getMinimum() - x - sb.getVisibleAmount() );
- }
- treepanel.resetPreferredSize();
- treepanel.updateOvSizes();
- }
-
- void zoomInY( final float factor ) {
- final JScrollBar sb = getMainPanel().getCurrentScrollPane().getVerticalScrollBar();
- final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
- treepanel.multiplyUrtFactor( 1.1f );
- final double x = ( sb.getMaximum() - sb.getMinimum() ) / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
- treepanel.setYdistance( ( treepanel.getYdistance() * factor ) );
- getMainPanel().adjustJScrollPane();
- treepanel.resetPreferredSize();
- getMainPanel().getCurrentScrollPane().getViewport().validate();
- sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
- - ( sb.getVisibleAmount() / 2.0 ) ) );
- treepanel.resetPreferredSize();
- treepanel.updateOvSizes();
- }
-
- void zoomOutX( final float factor, final float x_correction_factor ) {
- final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
- treepanel.multiplyUrtFactor( 1f );
- if ( ( treepanel.getXdistance() * factor ) > 0.0 ) {
- final JScrollBar sb = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar();
- if ( ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
- || ( treepanel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
- || isDrawPhylogram( getMainPanel().getCurrentTabIndex() )
- || ( getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP ) ) {
- getMainPanel().adjustJScrollPane();
- treepanel.resetPreferredSize();
- getMainPanel().getCurrentScrollPane().getViewport().validate();
- final double x = ( sb.getMaximum() - sb.getMinimum() )
- / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
- treepanel.setXdistance( ( treepanel.getXdistance() * factor ) );
- treepanel.setXcorrectionFactor( ( treepanel.getXcorrectionFactor() * x_correction_factor ) );
- getMainPanel().adjustJScrollPane();
- treepanel.resetPreferredSize();
- getMainPanel().getCurrentScrollPane().getViewport().validate();
- sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
- - ( sb.getVisibleAmount() / 2.0 ) ) );
- }
- else {
- final int x = sb.getMaximum() - sb.getMinimum() - sb.getVisibleAmount() - sb.getValue();
- treepanel.setXdistance( treepanel.getXdistance() * factor );
- treepanel.setXcorrectionFactor( treepanel.getXcorrectionFactor() * x_correction_factor );
- if ( x > 0 ) {
- getMainPanel().adjustJScrollPane();
- treepanel.resetPreferredSize();
- getMainPanel().getCurrentScrollPane().getViewport().validate();
- sb.setValue( sb.getMaximum() - sb.getMinimum() - x - sb.getVisibleAmount() );
- }
- }
- treepanel.resetPreferredSize();
- treepanel.updateOvSizes();
- }
- }
-
- void zoomOutY( final float factor ) {
- final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
- treepanel.multiplyUrtFactor( 0.9f );
- if ( ( treepanel.getYdistance() * factor ) > 0.0 ) {
- final JScrollBar sb = getMainPanel().getCurrentScrollPane().getVerticalScrollBar();
- final double x = ( sb.getMaximum() - sb.getMinimum() ) / ( sb.getValue() + ( sb.getVisibleAmount() / 2.0 ) );
- treepanel.setYdistance( ( treepanel.getYdistance() * factor ) );
- getMainPanel().adjustJScrollPane();
- treepanel.resetPreferredSize();
- getMainPanel().getCurrentScrollPane().getViewport().validate();
- sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x )
- - ( sb.getVisibleAmount() / 2.0 ) ) );
- treepanel.resetPreferredSize();
- treepanel.updateOvSizes();
- }
- }
-
static JLabel customizeLabel( final JLabel label, final Configuration configuration ) {
label.setFont( ControlPanel.jcb_bold_font );
if ( !configuration.isUseNativeUI() ) {
import java.util.Locale;
import java.util.Map;
import java.util.NoSuchElementException;
+import java.util.Set;
+import javax.swing.Box;
import javax.swing.JApplet;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JFrame;
+import javax.swing.JLabel;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
+import javax.swing.JPanel;
import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JTextField;
import javax.swing.SwingUtilities;
import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
import org.forester.archaeopteryx.tools.ProcessPool;
import org.forester.archaeopteryx.tools.ProcessRunning;
import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
+import org.forester.phylogeny.data.Annotation;
import org.forester.phylogeny.data.NodeVisualization.NodeFill;
import org.forester.phylogeny.data.NodeVisualization.NodeShape;
import org.forester.util.ForesterConstants;
JMenuItem _move_node_names_to_tax_sn_jmi;
JMenuItem _move_node_names_to_seq_names_jmi;
JMenuItem _extract_tax_code_from_node_names_jmi;
+ JMenuItem _annotate_item;
// font size menu:
JMenuItem _super_tiny_fonts_item;
JMenuItem _tiny_fonts_item;
Options _options;
InferenceManager _inference_manager;
final ProcessPool _process_pool;
+ private String _previous_node_annotation_ref;
MainFrame() {
_process_pool = ProcessPool.createInstance();
}
- public ProcessPool getProcessPool() {
- return _process_pool;
- }
-
/**
* Action performed.
*/
}
midpointRoot();
}
+ else if ( o == _annotate_item ) {
+ annotateSequences();
+ }
else if ( o == _switch_colors_mi ) {
switchColors();
}
_contentpane.repaint();
}
- boolean isSubtreeDisplayed() {
- if ( getCurrentTreePanel() != null ) {
- if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
- JOptionPane
- .showMessageDialog( this,
- "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
- "Operation can not be exectuted on a sub-tree",
- JOptionPane.WARNING_MESSAGE );
- return true;
+ public Configuration getConfiguration() {
+ return _configuration;
+ }
+
+ public InferenceManager getInferenceManager() {
+ return _inference_manager;
+ }
+
+ public MainPanel getMainPanel() {
+ return _mainpanel;
+ }
+
+ public Options getOptions() {
+ return _options;
+ }
+
+ public ProcessPool getProcessPool() {
+ return _process_pool;
+ }
+
+ public void showTextFrame( final String s, final String title ) {
+ checkTextFrames();
+ _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
+ }
+
+ public void showWhole() {
+ _mainpanel.getControlPanel().showWhole();
+ }
+
+ public void updateProcessMenu() {
+ // In general Swing is not thread safe.
+ // See "Swing's Threading Policy".
+ SwingUtilities.invokeLater( new Runnable() {
+
+ @Override
+ public void run() {
+ doUpdateProcessMenu();
}
- }
- return false;
+ } );
}
void activateSaveAllIfNeeded() {
_jmenubar.add( _help_jmenu );
}
- public void updateProcessMenu() {
- // In general Swing is not thread safe.
- // See "Swing's Threading Policy".
- SwingUtilities.invokeLater( new Runnable() {
-
- @Override
- public void run() {
- doUpdateProcessMenu();
- }
- } );
- }
-
- private void doUpdateProcessMenu() {
- if ( _process_pool.size() > 0 ) {
- if ( _process_menu == null ) {
- _process_menu = createMenu( "", getConfiguration() );
- _process_menu.setForeground( Color.RED );
- }
- _process_menu.removeAll();
- final String text = "processes running: " + _process_pool.size();
- _process_menu.setText( text );
- _jmenubar.add( _process_menu );
- for( int i = 0; i < _process_pool.size(); ++i ) {
- final ProcessRunning p = _process_pool.getProcessByIndex( i );
- _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );
- }
- }
- else {
- if ( _process_menu != null ) {
- _process_menu.removeAll();
- _jmenubar.remove( _process_menu );
- }
- }
- _jmenubar.validate();
- _jmenubar.repaint();
- repaint();
- }
-
void buildTypeMenu() {
_type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );
_type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );
_jmenubar.add( _view_jmenu );
}
- private void chooseFont() {
- final FontChooser fc = new FontChooser();
- fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
- fc.showDialog( this, "Select the Base Font" );
- getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
- }
-
- private void chooseMinimalConfidence() {
- final String s = ( String ) JOptionPane
- .showInputDialog( this,
- "Please enter the minimum for confidence values to be displayed.\n"
- + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
- "Minimal Confidence Value",
- JOptionPane.QUESTION_MESSAGE,
- null,
- null,
- getOptions().getMinConfidenceValue() );
- if ( !ForesterUtil.isEmpty( s ) ) {
- boolean success = true;
- double m = 0.0;
- final String m_str = s.trim();
- if ( !ForesterUtil.isEmpty( m_str ) ) {
- try {
- m = Double.parseDouble( m_str );
- }
- catch ( final Exception ex ) {
- success = false;
- }
- }
- else {
- success = false;
- }
- if ( success && ( m >= 0.0 ) ) {
- getOptions().setMinConfidenceValue( m );
- }
- }
- }
-
- static void chooseNodeSize( final Options options, final Component parent ) {
- final String s = ( String ) JOptionPane.showInputDialog( parent,
- "Please enter the default size for node shapes.\n"
- + "[current value: "
- + options.getDefaultNodeShapeSize() + "]\n",
- "Node Shape Size",
- JOptionPane.QUESTION_MESSAGE,
- null,
- null,
- options.getDefaultNodeShapeSize() );
- if ( !ForesterUtil.isEmpty( s ) ) {
- boolean success = true;
- double m = 0.0;
- final String m_str = s.trim();
- if ( !ForesterUtil.isEmpty( m_str ) ) {
- try {
- m = Double.parseDouble( m_str );
+ void checkTextFrames() {
+ if ( _textframes.size() > 5 ) {
+ try {
+ if ( _textframes.getFirst() != null ) {
+ _textframes.getFirst().removeMe();
}
- catch ( final Exception ex ) {
- success = false;
+ else {
+ _textframes.removeFirst();
}
}
- else {
- success = false;
- }
- if ( success && ( m >= 0.0 ) ) {
- final short size = ForesterUtil.roundToShort( m );
- if ( size >= 0.0 ) {
- options.setDefaultNodeShapeSize( size );
- }
+ catch ( final NoSuchElementException e ) {
+ // Ignore.
}
}
}
dispose();
}
- void confColor() {
- if ( _mainpanel.getCurrentTreePanel() != null ) {
- _mainpanel.getCurrentTreePanel().confColor();
- }
- }
-
void colorRank() {
if ( _mainpanel.getCurrentTreePanel() != null ) {
final String[] ranks = AptxUtil.getAllPossibleRanks();
}
}
+ void confColor() {
+ if ( _mainpanel.getCurrentTreePanel() != null ) {
+ _mainpanel.getCurrentTreePanel().confColor();
+ }
+ }
+
void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {
if ( item != null ) {
item.setFont( MainFrame.menu_font );
}
}
+ void displayBasicInformation() {
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
+ String title = "Basic Information";
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
+ title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
+ }
+ showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny() ), title );
+ }
+ }
+
void exceptionOccuredDuringOpenFile( final Exception e ) {
try {
_mainpanel.getCurrentTreePanel().setArrowCursor();
}
}
- public Configuration getConfiguration() {
- return _configuration;
- }
-
TreePanel getCurrentTreePanel() {
return getMainPanel().getCurrentTreePanel();
}
return _label_direction_cbmi;
}
- public MainPanel getMainPanel() {
- return _mainpanel;
- }
-
JMenuBar getMenuBarOfMainFrame() {
return _jmenubar;
}
- public Options getOptions() {
- return _options;
- }
-
- void initializeTypeMenu( final Options options ) {
- setTypeMenuToAllUnselected();
- switch ( options.getPhylogenyGraphicsType() ) {
- case CONVEX:
- _convex_type_cbmi.setSelected( true );
- break;
- case CURVED:
- _curved_type_cbmi.setSelected( true );
- break;
- case EURO_STYLE:
- _euro_type_cbmi.setSelected( true );
- break;
- case ROUNDED:
- _rounded_type_cbmi.setSelected( true );
- break;
- case TRIANGULAR:
- _triangular_type_cbmi.setSelected( true );
- break;
- case UNROOTED:
- _unrooted_type_cbmi.setSelected( true );
- break;
- case CIRCULAR:
- _circular_type_cbmi.setSelected( true );
- break;
- default:
- _rectangular_type_cbmi.setSelected( true );
- break;
- }
- }
-
- void midpointRoot() {
- if ( _mainpanel.getCurrentTreePanel() != null ) {
- _mainpanel.getCurrentTreePanel().midpointRoot();
- }
- }
-
- abstract void readPhylogeniesFromURL();
-
- void readPhylogeniesFromWebservice( final int i ) {
- final UrlTreeReader reader = new UrlTreeReader( this, i );
- new Thread( reader ).start();
- }
-
- private void removeBranchColors() {
- if ( getMainPanel().getCurrentPhylogeny() != null ) {
- AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
- }
- }
-
- void checkTextFrames() {
- if ( _textframes.size() > 5 ) {
- try {
- if ( _textframes.getFirst() != null ) {
- _textframes.getFirst().removeMe();
- }
- else {
- _textframes.removeFirst();
- }
+ void help( final Map<String, WebLink> weblinks ) {
+ final StringBuilder sb = new StringBuilder();
+ sb.append( "Display options\n" );
+ sb.append( "-------------------\n" );
+ sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
+ sb.append( "Clickable tree nodes\n" );
+ sb.append( "--------------------\n" );
+ sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
+ sb.append( "or by right clicking:\n" );
+ sb.append( "o Display Node Data -- display information for a node\n" );
+ sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
+ sb.append( "o Root/Reroot -- change tree root to clicked node\n" );
+ sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
+ sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" );
+ sb.append( "o Colorize Subtree -- color a subtree\n" );
+ sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" );
+ sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
+ sb.append( "- there may be additional choices depending on this particular setup\n\n" );
+ sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
+ sb.append( "Zooming\n" );
+ sb.append( "---------\n" );
+ sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
+ sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
+ sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
+ sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
+ sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
+ sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
+ sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
+ sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
+ sb.append( "Quick tree manipulation:\n" );
+ sb.append( "------------------------\n" );
+ sb.append( "Order Subtrees -- order the tree by branch length\n" );
+ sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
+ sb.append( "Memory problems (Java heap space error)\n" );
+ sb.append( "---------------------------------------\n" );
+ sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
+ sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
+ sb.append( "the '-Xmx' Java command line option. For example:\n" );
+ sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
+ if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
+ sb.append( "Active web links\n" );
+ sb.append( "--------------------\n" );
+ for( final String key : weblinks.keySet() ) {
+ sb.append( " " + weblinks.get( key ).toString() + "\n" );
}
- catch ( final NoSuchElementException e ) {
- // Ignore.
+ }
+ // + "General remarks\n"
+ // + "---------------\n"
+ // +
+ // "o The application version permits copying to the clipboard \n"
+ // +
+ // " in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"
+ // +
+ // "o Changes made to a subtree affect this subtree and its subtrees,\n"
+ // + " but not any of its parent tree(s).\n"
+ // +
+ // "o Archaeopteryx tries to detect whether the numerical values in a NH tree\n"
+ // +
+ // " are likely to be bootstrap values instead of branch length values.\n\n"
+ // +
+ // " Remarks regarding SDI (Speciation Duplication Inference):\n"
+ // +
+ // "o Each external node of the gene tree (in display) needs to be associated with\n"
+ // +
+ // " a species: either directly through the \"Species\" field, or the species\n"
+ // +
+ // " is part of the sequence name in the form \"XXXX_SPECIES\"\n"
+ // +
+ // " (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"
+ // +
+ // "o A species tree for each species of the gene tree needs to be loaded with\n"
+ // +
+ // " \"SDI\"|\"Load species tree\" prior the SDI execution.\n"
+ // +
+ // "o !External nodes of the gene tree associated with species not present in\n"
+ // +
+ // " the species tree are REMOVED prior to SDI execution!\n"
+ // +
+ // "o Both the gene tree and the species tree must be completely binary.\n"
+ // +
+ // "o Duplications and speciations are a function of the position of the root.\n"
+ // +
+ // " Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"
+ // + " incorrect and need to be inferred again\n"
+ // +
+ // " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"
+ sb.append( "\n" );
+ sb.append( "phyloXML\n" );
+ sb.append( "-------------------\n" );
+ sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
+ sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
+ sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
+ sb.append( "\n" );
+ sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
+ sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
+ TextFrame.instantiate( sb.toString(), "Help", _textframes );
+ }
+
+ void initializeTypeMenu( final Options options ) {
+ setTypeMenuToAllUnselected();
+ switch ( options.getPhylogenyGraphicsType() ) {
+ case CONVEX:
+ _convex_type_cbmi.setSelected( true );
+ break;
+ case CURVED:
+ _curved_type_cbmi.setSelected( true );
+ break;
+ case EURO_STYLE:
+ _euro_type_cbmi.setSelected( true );
+ break;
+ case ROUNDED:
+ _rounded_type_cbmi.setSelected( true );
+ break;
+ case TRIANGULAR:
+ _triangular_type_cbmi.setSelected( true );
+ break;
+ case UNROOTED:
+ _unrooted_type_cbmi.setSelected( true );
+ break;
+ case CIRCULAR:
+ _circular_type_cbmi.setSelected( true );
+ break;
+ default:
+ _rectangular_type_cbmi.setSelected( true );
+ break;
+ }
+ }
+
+ boolean isSubtreeDisplayed() {
+ if ( getCurrentTreePanel() != null ) {
+ if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
+ JOptionPane
+ .showMessageDialog( this,
+ "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
+ "Operation can not be exectuted on a sub-tree",
+ JOptionPane.WARNING_MESSAGE );
+ return true;
}
}
+ return false;
+ }
+
+ void midpointRoot() {
+ if ( _mainpanel.getCurrentTreePanel() != null ) {
+ _mainpanel.getCurrentTreePanel().midpointRoot();
+ }
+ }
+
+ abstract void readPhylogeniesFromURL();
+
+ void readPhylogeniesFromWebservice( final int i ) {
+ final UrlTreeReader reader = new UrlTreeReader( this, i );
+ new Thread( reader ).start();
}
void removeAllTextFrames() {
_configuration = configuration;
}
- void setOptions( final Options options ) {
- _options = options;
- }
-
void setInferenceManager( final InferenceManager i ) {
_inference_manager = i;
}
- public InferenceManager getInferenceManager() {
- return _inference_manager;
+ void setOptions( final Options options ) {
+ _options = options;
}
void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {
_circular_type_cbmi.setSelected( false );
}
- public void showWhole() {
- _mainpanel.getControlPanel().showWhole();
- }
-
void switchColors() {
final TreeColorSet colorset = _mainpanel.getTreeColorSet();
final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
( ( JCheckBoxMenuItem ) o ).setSelected( true );
}
- void displayBasicInformation() {
- if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
- String title = "Basic Information";
- if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
- title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
- }
- showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny() ), title );
- }
- }
-
void viewAsNexus() {
if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
String title = "Nexus";
}
}
- public void showTextFrame( final String s, final String title ) {
- checkTextFrames();
- _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );
+ private void annotateSequences() {
+ if ( getCurrentTreePanel() != null ) {
+ final Set<Integer> nodes = getCurrentTreePanel().getFoundNodes();
+ if ( ( nodes == null ) || nodes.isEmpty() ) {
+ JOptionPane
+ .showMessageDialog( this,
+ "Need to select nodes, either via direct selection or via the \"Search\" function",
+ "No nodes selected for annotation",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
+ if ( ( phy != null ) && !phy.isEmpty() ) {
+ final JTextField xField = new JTextField( 10 );
+ final JTextField yField = new JTextField( 20 );
+ xField.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""
+ : getPreviousNodeAnnotationReference() );
+ final JPanel myPanel = new JPanel();
+ myPanel.add( new JLabel( "Reference " ) );
+ myPanel.add( xField );
+ myPanel.add( Box.createHorizontalStrut( 15 ) );
+ myPanel.add( new JLabel( "Description " ) );
+ myPanel.add( yField );
+ final int result = JOptionPane.showConfirmDialog( null,
+ myPanel,
+ "Enter the sequence annotation(s) for the "
+ + nodes.size() + " selected nodes",
+ JOptionPane.OK_CANCEL_OPTION );
+ if ( result == JOptionPane.OK_OPTION ) {
+ String ref = xField.getText();
+ String desc = yField.getText();
+ if ( ref != null ) {
+ ref = ref.trim();
+ ref = ref.replaceAll( "\\s+", " " );
+ }
+ if ( desc != null ) {
+ desc = desc.trim();
+ desc = desc.replaceAll( "\\s+", " " );
+ }
+ if ( ref != null ) {
+ setPreviousNodeAnnotationReference( ref );
+ }
+ if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {
+ for( final Integer id : nodes ) {
+ final PhylogenyNode n = phy.getNode( id );
+ ForesterUtil.ensurePresenceOfSequence( n );
+ final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()
+ : new Annotation( ref );
+ if ( !ForesterUtil.isEmpty( desc ) ) {
+ ann.setDesc( desc );
+ }
+ n.getNodeData().getSequence().addAnnotation( ann );
+ }
+ }
+ }
+ }
+ }
+ }
+
+ private String getPreviousNodeAnnotationReference() {
+ return _previous_node_annotation_ref;
+ }
+
+ private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {
+ _previous_node_annotation_ref = previous_node_annotation_ref;
+ }
+
+ private void chooseFont() {
+ final FontChooser fc = new FontChooser();
+ fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
+ fc.showDialog( this, "Select the Base Font" );
+ getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
+ }
+
+ private void chooseMinimalConfidence() {
+ final String s = ( String ) JOptionPane
+ .showInputDialog( this,
+ "Please enter the minimum for confidence values to be displayed.\n"
+ + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",
+ "Minimal Confidence Value",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ null,
+ getOptions().getMinConfidenceValue() );
+ if ( !ForesterUtil.isEmpty( s ) ) {
+ boolean success = true;
+ double m = 0.0;
+ final String m_str = s.trim();
+ if ( !ForesterUtil.isEmpty( m_str ) ) {
+ try {
+ m = Double.parseDouble( m_str );
+ }
+ catch ( final Exception ex ) {
+ success = false;
+ }
+ }
+ else {
+ success = false;
+ }
+ if ( success && ( m >= 0.0 ) ) {
+ getOptions().setMinConfidenceValue( m );
+ }
+ }
+ }
+
+ private void doUpdateProcessMenu() {
+ if ( _process_pool.size() > 0 ) {
+ if ( _process_menu == null ) {
+ _process_menu = createMenu( "", getConfiguration() );
+ _process_menu.setForeground( Color.RED );
+ }
+ _process_menu.removeAll();
+ final String text = "processes running: " + _process_pool.size();
+ _process_menu.setText( text );
+ _jmenubar.add( _process_menu );
+ for( int i = 0; i < _process_pool.size(); ++i ) {
+ final ProcessRunning p = _process_pool.getProcessByIndex( i );
+ _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );
+ }
+ }
+ else {
+ if ( _process_menu != null ) {
+ _process_menu.removeAll();
+ _jmenubar.remove( _process_menu );
+ }
+ }
+ _jmenubar.validate();
+ _jmenubar.repaint();
+ repaint();
+ }
+
+ private void removeBranchColors() {
+ if ( getMainPanel().getCurrentPhylogeny() != null ) {
+ AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
+ }
}
/**
JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
}
+ static void chooseNodeSize( final Options options, final Component parent ) {
+ final String s = ( String ) JOptionPane.showInputDialog( parent,
+ "Please enter the default size for node shapes.\n"
+ + "[current value: "
+ + options.getDefaultNodeShapeSize() + "]\n",
+ "Node Shape Size",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ null,
+ options.getDefaultNodeShapeSize() );
+ if ( !ForesterUtil.isEmpty( s ) ) {
+ boolean success = true;
+ double m = 0.0;
+ final String m_str = s.trim();
+ if ( !ForesterUtil.isEmpty( m_str ) ) {
+ try {
+ m = Double.parseDouble( m_str );
+ }
+ catch ( final Exception ex ) {
+ success = false;
+ }
+ }
+ else {
+ success = false;
+ }
+ if ( success && ( m >= 0.0 ) ) {
+ final short size = ForesterUtil.roundToShort( m );
+ if ( size >= 0.0 ) {
+ options.setDefaultNodeShapeSize( size );
+ }
+ }
+ }
+ }
+
static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {
return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();
}
return label;
}
- static void cycleOverview( final Options op, final TreePanel tree_panel ) {
- switch ( op.getOvPlacement() ) {
- case LOWER_LEFT:
- op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
- break;
- case LOWER_RIGHT:
- op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
- break;
- case UPPER_LEFT:
- op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
- break;
- case UPPER_RIGHT:
- op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
- break;
- default:
- throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
- }
- if ( tree_panel != null ) {
- tree_panel.updateOvSettings();
- }
- }
-
static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {
switch ( op.getDefaultNodeFill() ) {
case GRADIENT:
}
}
- void help( final Map<String, WebLink> weblinks ) {
- final StringBuilder sb = new StringBuilder();
- sb.append( "Display options\n" );
- sb.append( "-------------------\n" );
- sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
- sb.append( "Clickable tree nodes\n" );
- sb.append( "--------------------\n" );
- sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
- sb.append( "or by right clicking:\n" );
- sb.append( "o Display Node Data -- display information for a node\n" );
- sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
- sb.append( "o Root/Reroot -- change tree root to clicked node\n" );
- sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
- sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" );
- sb.append( "o Colorize Subtree -- color a subtree\n" );
- sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" );
- sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
- sb.append( "- there may be additional choices depending on this particular setup\n\n" );
- sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
- sb.append( "Zooming\n" );
- sb.append( "---------\n" );
- sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
- sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
- sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
- sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
- sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
- sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
- sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
- sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
- sb.append( "Quick tree manipulation:\n" );
- sb.append( "------------------------\n" );
- sb.append( "Order Subtrees -- order the tree by branch length\n" );
- sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
- sb.append( "Memory problems (Java heap space error)\n" );
- sb.append( "---------------------------------------\n" );
- sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
- sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
- sb.append( "the '-Xmx' Java command line option. For example:\n" );
- sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
- if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
- sb.append( "Active web links\n" );
- sb.append( "--------------------\n" );
- for( final String key : weblinks.keySet() ) {
- sb.append( " " + weblinks.get( key ).toString() + "\n" );
- }
- }
- // + "General remarks\n"
- // + "---------------\n"
- // +
- // "o The application version permits copying to the clipboard \n"
- // +
- // " in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"
- // +
- // "o Changes made to a subtree affect this subtree and its subtrees,\n"
- // + " but not any of its parent tree(s).\n"
- // +
- // "o Archaeopteryx tries to detect whether the numerical values in a NH tree\n"
- // +
- // " are likely to be bootstrap values instead of branch length values.\n\n"
- // +
- // " Remarks regarding SDI (Speciation Duplication Inference):\n"
- // +
- // "o Each external node of the gene tree (in display) needs to be associated with\n"
- // +
- // " a species: either directly through the \"Species\" field, or the species\n"
- // +
- // " is part of the sequence name in the form \"XXXX_SPECIES\"\n"
- // +
- // " (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"
- // +
- // "o A species tree for each species of the gene tree needs to be loaded with\n"
- // +
- // " \"SDI\"|\"Load species tree\" prior the SDI execution.\n"
- // +
- // "o !External nodes of the gene tree associated with species not present in\n"
- // +
- // " the species tree are REMOVED prior to SDI execution!\n"
- // +
- // "o Both the gene tree and the species tree must be completely binary.\n"
- // +
- // "o Duplications and speciations are a function of the position of the root.\n"
- // +
- // " Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"
- // + " incorrect and need to be inferred again\n"
- // +
- // " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"
- sb.append( "\n" );
- sb.append( "phyloXML\n" );
- sb.append( "-------------------\n" );
- sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
- sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
- sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
- sb.append( "\n" );
- sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
- sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
- TextFrame.instantiate( sb.toString(), "Help", _textframes );
- }
-
- static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
- if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
- mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
+ static void cycleOverview( final Options op, final TreePanel tree_panel ) {
+ switch ( op.getOvPlacement() ) {
+ case LOWER_LEFT:
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
+ break;
+ case LOWER_RIGHT:
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );
+ break;
+ case UPPER_LEFT:
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );
+ break;
+ case UPPER_RIGHT:
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );
+ break;
+ default:
+ throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );
}
- else {
- mi.setText( "Cycle Overview Placement..." );
+ if ( tree_panel != null ) {
+ tree_panel.updateOvSettings();
}
}
}
}
+ static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {
+ if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {
+ mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );
+ }
+ else {
+ mi.setText( "Cycle Overview Placement..." );
+ }
+ }
+
static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
mi.setText( "Select Colors... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName() + ")" );
_remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny" );
customizeJMenuItem( _remove_branch_color_item );
_tools_menu.addSeparator();
+ _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );
+ customizeJMenuItem( _annotate_item );
+ _tools_menu.addSeparator();
_tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
customizeJMenuItem( _midpoint_root_item );
_tools_menu.addSeparator();
}
private List<Point> obtainPoints() {
- AptxUtil.ensurePresenceOfDistribution( getMyNode() );
+ ForesterUtil.ensurePresenceOfDistribution( getMyNode() );
Distribution d = getMyNode().getNodeData().getDistribution();
if ( d.getPoints() == null ) {
d = new Distribution( d.getDesc(), new ArrayList<Point>(), d.getPolygons() );
}
break;
case TAXONOMY_CODE:
- AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
+ ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
try {
getMyNode().getNodeData().getTaxonomy().setTaxonomyCode( value );
}
}
break;
case TAXONOMY_SCIENTIFIC_NAME:
- AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
+ ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
getMyNode().getNodeData().getTaxonomy().setScientificName( value );
break;
case TAXONOMY_COMMON_NAME:
- AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
+ ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
getMyNode().getNodeData().getTaxonomy().setCommonName( value );
break;
case TAXONOMY_RANK:
- AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
+ ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
try {
getMyNode().getNodeData().getTaxonomy().setRank( value.toLowerCase() );
}
}
break;
case TAXONOMY_AUTHORITY:
- AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
+ ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
getMyNode().getNodeData().getTaxonomy().setAuthority( value );
break;
case TAXONOMY_URI: {
}
}
if ( uri != null ) {
- AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
+ ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
}
addUri( mtn, uri, number, getMyNode().getNodeData().getTaxonomy() );
break;
}
else if ( getMyNode().getNodeData().getTaxonomy().getSynonyms().size() == number ) {
if ( !ForesterUtil.isEmpty( value ) ) {
- AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
+ ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
getMyNode().getNodeData().getTaxonomy().getSynonyms().add( value );
}
}
}
break;
case TAXONOMY_ID_VALUE:
- AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
+ ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
if ( getMyNode().getNodeData().getTaxonomy().getIdentifier() == null ) {
getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( value ) );
}
}
break;
case TAXONOMY_ID_PROVIDER:
- AptxUtil.ensurePresenceOfTaxonomy( getMyNode() );
+ ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
if ( getMyNode().getNodeData().getTaxonomy().getIdentifier() == null ) {
getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( "", value ) );
}
}
break;
case SEQ_LOCATION:
- AptxUtil.ensurePresenceOfSequence( getMyNode() );
+ ForesterUtil.ensurePresenceOfSequence( getMyNode() );
getMyNode().getNodeData().getSequence().setLocation( value );
break;
case SEQ_MOL_SEQ:
- AptxUtil.ensurePresenceOfSequence( getMyNode() );
+ ForesterUtil.ensurePresenceOfSequence( getMyNode() );
getMyNode().getNodeData().getSequence().setMolecularSequence( value.replaceAll( "[^a-zA-Z-]", "" ) );
break;
case SEQ_NAME:
- AptxUtil.ensurePresenceOfSequence( getMyNode() );
+ ForesterUtil.ensurePresenceOfSequence( getMyNode() );
getMyNode().getNodeData().getSequence().setName( value );
break;
case SEQ_SYMBOL:
- AptxUtil.ensurePresenceOfSequence( getMyNode() );
+ ForesterUtil.ensurePresenceOfSequence( getMyNode() );
try {
getMyNode().getNodeData().getSequence().setSymbol( value );
}
}
break;
case SEQ_TYPE:
- AptxUtil.ensurePresenceOfSequence( getMyNode() );
+ ForesterUtil.ensurePresenceOfSequence( getMyNode() );
try {
getMyNode().getNodeData().getSequence().setType( value.toLowerCase() );
}
}
break;
case SEQ_ACC_SOURCE:
- AptxUtil.ensurePresenceOfSequence( getMyNode() );
+ ForesterUtil.ensurePresenceOfSequence( getMyNode() );
if ( getMyNode().getNodeData().getSequence().getAccession() == null ) {
getMyNode().getNodeData().getSequence().setAccession( new Accession( "", value ) );
}
}
break;
case SEQ_ACC_VALUE:
- AptxUtil.ensurePresenceOfSequence( getMyNode() );
+ ForesterUtil.ensurePresenceOfSequence( getMyNode() );
if ( getMyNode().getNodeData().getSequence().getAccession() == null ) {
getMyNode().getNodeData().getSequence().setAccession( new Accession( value, "" ) );
}
}
}
if ( uri != null ) {
- AptxUtil.ensurePresenceOfSequence( getMyNode() );
+ ForesterUtil.ensurePresenceOfSequence( getMyNode() );
}
addUri( mtn, uri, number, getMyNode().getNodeData().getSequence() );
break;
getMyNode().getNodeData().getEvent().setGeneLosses( parsePositiveInt( mtn, value ) );
break;
case DATE_DESCRIPTION:
- AptxUtil.ensurePresenceOfDate( getMyNode() );
+ ForesterUtil.ensurePresenceOfDate( getMyNode() );
getMyNode().getNodeData().getDate().setDesc( value );
break;
case DATE_MAX:
- AptxUtil.ensurePresenceOfDate( getMyNode() );
+ ForesterUtil.ensurePresenceOfDate( getMyNode() );
getMyNode().getNodeData().getDate().setMax( parseBigDecimal( mtn, value ) );
break;
case DATE_MIN:
- AptxUtil.ensurePresenceOfDate( getMyNode() );
+ ForesterUtil.ensurePresenceOfDate( getMyNode() );
getMyNode().getNodeData().getDate().setMin( parseBigDecimal( mtn, value ) );
break;
case DATE_UNIT:
- AptxUtil.ensurePresenceOfDate( getMyNode() );
+ ForesterUtil.ensurePresenceOfDate( getMyNode() );
getMyNode().getNodeData().getDate().setUnit( value );
break;
case DATE_VALUE:
- AptxUtil.ensurePresenceOfDate( getMyNode() );
+ ForesterUtil.ensurePresenceOfDate( getMyNode() );
getMyNode().getNodeData().getDate().setValue( parseBigDecimal( mtn, value ) );
break;
case DIST_ALT: {
break;
}
case DIST_DESC: {
- AptxUtil.ensurePresenceOfDistribution( getMyNode() );
+ ForesterUtil.ensurePresenceOfDistribution( getMyNode() );
final Distribution d = getMyNode().getNodeData().getDistribution();
getMyNode().getNodeData().setDistribution( new Distribution( value, d.getPoints(), d.getPolygons() ) );
break;
import org.forester.phylogeny.data.NodeVisualization;
import org.forester.phylogeny.data.NodeVisualization.NodeFill;
import org.forester.phylogeny.data.NodeVisualization.NodeShape;
-import org.forester.phylogeny.data.PhylogenyData;
import org.forester.phylogeny.data.PhylogenyDataUtil;
import org.forester.phylogeny.data.PropertiesMap;
import org.forester.phylogeny.data.Property;
private boolean _edited = false;
private Popup _node_desc_popup;
private JTextArea _rollover_popup;
- // private final int _box_size;
- // private final int _half_box_size;
- //private final short _skip_counter = 0;
private final StringBuffer _popup_buffer = new StringBuffer();
final private static Font POPUP_FONT = new Font( Configuration.getDefaultFontFamilyName(),
Font.PLAIN,
final void selectNode( final PhylogenyNode node ) {
if ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) ) {
getFoundNodes().remove( node.getId() );
+ getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().size() );
+ if ( getFoundNodes().size() < 1 ) {
+ getControlPanel().searchReset();
+ }
}
else {
+ getControlPanel().getSearchFoundCountsLabel().setVisible( true );
+ getControlPanel().getSearchResetButton().setEnabled( true );
+ getControlPanel().getSearchResetButton().setVisible( true );
if ( getFoundNodes() == null ) {
setFoundNodes( new HashSet<Integer>() );
}
getFoundNodes().add( node.getId() );
+ getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().size() );
}
}
}
}
- final private Color calculateColorForAnnotation( final PhylogenyData ann ) {
+ final private Color calculateColorForAnnotation( final Annotation ann ) {
Color c = getTreeColorSet().getAnnotationColor();
if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) {
- c = getControlPanel().getAnnotationColors().get( ann.asSimpleText().toString() );
- if ( c == null ) {
- c = getTreeColorSet().getAnnotationColor();
+ final String ann_str = !ForesterUtil.isEmpty( ann.getRef() ) ? ann.getRef() : ann.getDesc();
+ if ( !ForesterUtil.isEmpty( ann_str ) ) {
+ c = getControlPanel().getAnnotationColors().get( ann_str );
+ if ( c == null ) {
+ c = AptxUtil.calculateColorFromString( ann_str );
+ getControlPanel().getAnnotationColors().put( ann_str, c );
+ }
+ if ( c == null ) {
+ c = getTreeColorSet().getAnnotationColor();
+ }
}
}
return c;
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
g.setColor( getTaxonomyBasedColor( node ) );
}
+ else if ( getControlPanel().isColorAccordingToAnnotation()
+ && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
+ .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
+ g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotation( 0 ) ) );
+ }
else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
&& ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
g.setColor( Color.BLACK );
}
- else {
+ else if ( getControlPanel().isColorAccordingToAnnotation() ) {
g.setColor( calculateColorForAnnotation( ann ) );
}
final String ann_str = ann.asSimpleText().toString();
import javax.swing.JOptionPane;
-import org.forester.archaeopteryx.AptxUtil;
import org.forester.archaeopteryx.MainFrameApplication;
import org.forester.evoinference.distance.NeighborJoining;
import org.forester.evoinference.distance.PairwiseDistanceCalculator;
final String seq_name = name_m.group( 3 );
final String tax_sn = name_m.group( 4 );
if ( !ForesterUtil.isEmpty( acc_source ) && !ForesterUtil.isEmpty( acc ) ) {
- AptxUtil.ensurePresenceOfSequence( node );
+ ForesterUtil.ensurePresenceOfSequence( node );
node.getNodeData().getSequence( 0 ).setAccession( new Accession( acc, acc_source ) );
}
if ( !ForesterUtil.isEmpty( seq_name ) ) {
- AptxUtil.ensurePresenceOfSequence( node );
+ ForesterUtil.ensurePresenceOfSequence( node );
node.getNodeData().getSequence( 0 ).setName( seq_name );
}
if ( !ForesterUtil.isEmpty( tax_sn ) ) {
- AptxUtil.ensurePresenceOfTaxonomy( node );
+ ForesterUtil.ensurePresenceOfTaxonomy( node );
node.getNodeData().getTaxonomy( 0 ).setScientificName( tax_sn );
}
}
public Annotation( final String ref ) {
if ( ForesterUtil.isEmpty( ref ) ) {
- throw new IllegalArgumentException( "illegal attempt to create Annotation with null or empty reference" );
+ throw new IllegalArgumentException( "annotation reference is empty or null" );
}
if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.length() < 3 ) ) {
- throw new IllegalArgumentException( "illegal format for Annotation reference: [" + ref + "]" );
+ throw new IllegalArgumentException( "illegal format for annotation reference: [" + ref + "]" );
}
_ref = ref;
init();
}
+ public Annotation() {
+ _ref = "";
+ init();
+ }
+
@Override
public StringBuffer asSimpleText() {
- return new StringBuffer( getDesc() );
+ return new StringBuffer( !ForesterUtil.isEmpty( getRef() ) ? getRef() : getDesc() );
}
@Override
public StringBuffer asText() {
- return new StringBuffer( getDesc() );
+ return asSimpleText();
}
@Override
import java.util.Map;
import java.util.regex.Pattern;
-import org.forester.archaeopteryx.AptxUtil;
import org.forester.io.parsers.nhx.NHXFormatException;
import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
import org.forester.phylogeny.Phylogeny;
}
if ( new_values != null ) {
if ( new_values.containsKey( TP_TAXONOMY_CODE ) ) {
- AptxUtil.ensurePresenceOfTaxonomy( node );
+ ForesterUtil.ensurePresenceOfTaxonomy( node );
node.getNodeData().getTaxonomy().setTaxonomyCode( new_values.get( TP_TAXONOMY_CODE ) );
}
if ( new_values.containsKey( TP_TAXONOMY_ID )
&& new_values.containsKey( TP_TAXONOMY_ID_PROVIDER ) ) {
- AptxUtil.ensurePresenceOfTaxonomy( node );
+ ForesterUtil.ensurePresenceOfTaxonomy( node );
node.getNodeData()
.getTaxonomy()
.setIdentifier( new Identifier( new_values.get( TP_TAXONOMY_ID ),
new_values.get( TP_TAXONOMY_ID_PROVIDER ) ) );
}
else if ( new_values.containsKey( TP_TAXONOMY_ID ) ) {
- AptxUtil.ensurePresenceOfTaxonomy( node );
+ ForesterUtil.ensurePresenceOfTaxonomy( node );
node.getNodeData().getTaxonomy()
.setIdentifier( new Identifier( new_values.get( TP_TAXONOMY_ID ) ) );
}
if ( new_values.containsKey( TP_TAXONOMY_SN ) ) {
- AptxUtil.ensurePresenceOfTaxonomy( node );
+ ForesterUtil.ensurePresenceOfTaxonomy( node );
node.getNodeData().getTaxonomy().setScientificName( new_values.get( TP_TAXONOMY_SN ) );
}
if ( new_values.containsKey( TP_TAXONOMY_CN ) ) {
- AptxUtil.ensurePresenceOfTaxonomy( node );
+ ForesterUtil.ensurePresenceOfTaxonomy( node );
node.getNodeData().getTaxonomy().setCommonName( new_values.get( TP_TAXONOMY_CN ) );
}
if ( new_values.containsKey( TP_TAXONOMY_SYN ) ) {
- AptxUtil.ensurePresenceOfTaxonomy( node );
+ ForesterUtil.ensurePresenceOfTaxonomy( node );
node.getNodeData().getTaxonomy().getSynonyms().add( new_values.get( TP_TAXONOMY_SYN ) );
}
if ( new_values.containsKey( TP_SEQ_ACCESSION )
&& new_values.containsKey( TP_SEQ_ACCESSION_SOURCE ) ) {
- AptxUtil.ensurePresenceOfSequence( node );
+ ForesterUtil.ensurePresenceOfSequence( node );
node.getNodeData()
.getSequence()
.setAccession( new Accession( new_values.get( TP_SEQ_ACCESSION ),
new_values.get( TP_SEQ_ACCESSION_SOURCE ) ) );
}
if ( new_values.containsKey( TP_SEQ_ANNOTATION_DESC ) ) {
- AptxUtil.ensurePresenceOfSequence( node );
- final Annotation ann = new Annotation( "?" );
+ ForesterUtil.ensurePresenceOfSequence( node );
+ final Annotation ann = new Annotation();
ann.setDesc( new_values.get( TP_SEQ_ANNOTATION_DESC ) );
node.getNodeData().getSequence().addAnnotation( ann );
}
if ( new_values.containsKey( TP_SEQ_ANNOTATION_REF ) ) {
- AptxUtil.ensurePresenceOfSequence( node );
+ ForesterUtil.ensurePresenceOfSequence( node );
final Annotation ann = new Annotation( new_values.get( TP_SEQ_ANNOTATION_REF ) );
node.getNodeData().getSequence().addAnnotation( ann );
}
if ( new_values.containsKey( TP_SEQ_SYMBOL ) ) {
- AptxUtil.ensurePresenceOfSequence( node );
+ ForesterUtil.ensurePresenceOfSequence( node );
node.getNodeData().getSequence().setSymbol( new_values.get( TP_SEQ_SYMBOL ) );
}
if ( new_values.containsKey( TP_SEQ_NAME ) ) {
- AptxUtil.ensurePresenceOfSequence( node );
+ ForesterUtil.ensurePresenceOfSequence( node );
node.getNodeData().getSequence().setName( new_values.get( TP_SEQ_NAME ) );
}
if ( new_values.containsKey( TP_SEQ_MOL_SEQ ) ) {
- AptxUtil.ensurePresenceOfSequence( node );
+ ForesterUtil.ensurePresenceOfSequence( node );
node.getNodeData().getSequence().setMolecularSequence( new_values.get( TP_SEQ_MOL_SEQ ) );
}
if ( new_values.containsKey( TP_NODE_NAME ) ) {
if ( PhylogenyDecorator.VERBOSE ) {
System.out.println( name + ": " + new_value );
}
- AptxUtil.ensurePresenceOfTaxonomy( node );
+ ForesterUtil.ensurePresenceOfTaxonomy( node );
node.getNodeData().getTaxonomy().setTaxonomyCode( new_value );
break;
case TAXONOMY_SCIENTIFIC_NAME:
if ( PhylogenyDecorator.VERBOSE ) {
System.out.println( name + ": " + new_value );
}
- AptxUtil.ensurePresenceOfTaxonomy( node );
+ ForesterUtil.ensurePresenceOfTaxonomy( node );
node.getNodeData().getTaxonomy().setScientificName( new_value );
break;
case SEQUENCE_NAME:
private static String extractBracketedScientificNames( final PhylogenyNode node, final String new_value ) {
final int i = new_value.lastIndexOf( "[" );
final String scientific_name = new_value.substring( i + 1, new_value.length() - 1 );
- AptxUtil.ensurePresenceOfTaxonomy( node );
+ ForesterUtil.ensurePresenceOfTaxonomy( node );
node.getNodeData().getTaxonomy().setScientificName( scientific_name );
return new_value.substring( 0, i - 1 ).trim();
}
private static String extractBracketedTaxCodes( final PhylogenyNode node, final String new_value ) {
final int i = new_value.lastIndexOf( "[" );
final String tc = new_value.substring( i + 1, new_value.length() - 1 );
- AptxUtil.ensurePresenceOfTaxonomy( node );
+ ForesterUtil.ensurePresenceOfTaxonomy( node );
try {
node.getNodeData().getTaxonomy().setTaxonomyCode( tc );
}
import java.util.TreeSet;
import java.util.regex.Pattern;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.Distribution;
+import org.forester.phylogeny.data.Sequence;
+import org.forester.phylogeny.data.Taxonomy;
+
public final class ForesterUtil {
public final static String FILE_SEPARATOR = System.getProperty( "file.separator" );
private ForesterUtil() {
}
+ public static void ensurePresenceOfTaxonomy( final PhylogenyNode node ) {
+ if ( !node.getNodeData().isHasTaxonomy() ) {
+ node.getNodeData().setTaxonomy( new Taxonomy() );
+ }
+ }
+
+ public static void ensurePresenceOfSequence( final PhylogenyNode node ) {
+ if ( !node.getNodeData().isHasSequence() ) {
+ node.getNodeData().setSequence( new Sequence() );
+ }
+ }
+
+ final public static void ensurePresenceOfDistribution( final PhylogenyNode node ) {
+ if ( !node.getNodeData().isHasDistribution() ) {
+ node.getNodeData().setDistribution( new Distribution( "" ) );
+ }
+ }
+
+ final public static void ensurePresenceOfDate( final PhylogenyNode node ) {
+ if ( !node.getNodeData().isHasDate() ) {
+ node.getNodeData().setDate( new org.forester.phylogeny.data.Date() );
+ }
+ }
+
final public static void appendSeparatorIfNotEmpty( final StringBuffer sb, final char separator ) {
if ( sb.length() > 0 ) {
sb.append( separator );
git://source.jalview.org / jalview.git / commitdiff