public final class AptxUtil {
+ public static enum GraphicsExportType {
+ BMP( "bmp" ), GIF( "gif" ), JPG( "jpg" ), PDF( "pdf" ), PNG( "png" ), TIFF( "tif" );
+
+ private final String _suffix;
+
+ private GraphicsExportType( final String suffix ) {
+ _suffix = suffix;
+ }
+
+ @Override
+ public String toString() {
+ return _suffix;
+ }
+ }
private final static String[] AVAILABLE_FONT_FAMILIES_SORTED = GraphicsEnvironment.getLocalGraphicsEnvironment()
- .getAvailableFontFamilyNames();
+ .getAvailableFontFamilyNames();
static {
Arrays.sort( AVAILABLE_FONT_FAMILIES_SORTED );
}
+ final public static Color calculateColorFromString( final String str, final boolean is_taxonomy ) {
+ final String my_str = str.toUpperCase();
+ char first = my_str.charAt( 0 );
+ char second = ' ';
+ char third = ' ';
+ if ( my_str.length() > 1 ) {
+ if ( is_taxonomy ) {
+ second = my_str.charAt( 1 );
+ }
+ else {
+ second = my_str.charAt( my_str.length() - 1 );
+ }
+ if ( is_taxonomy ) {
+ if ( my_str.length() > 2 ) {
+ if ( my_str.indexOf( " " ) > 0 ) {
+ third = my_str.charAt( my_str.indexOf( " " ) + 1 );
+ }
+ else {
+ third = my_str.charAt( 2 );
+ }
+ }
+ }
+ else if ( my_str.length() > 2 ) {
+ third = my_str.charAt( ( my_str.length() - 1 ) / 2 );
+ }
+ }
+ first = normalizeCharForRGB( first );
+ second = normalizeCharForRGB( second );
+ third = normalizeCharForRGB( third );
+ if ( ( first > 235 ) && ( second > 235 ) && ( third > 235 ) ) {
+ first = 0;
+ }
+ else if ( ( first < 60 ) && ( second < 60 ) && ( third < 60 ) ) {
+ second = 255;
+ }
+ return new Color( first, second, third );
+ }
+
public static MaskFormatter createMaskFormatter( final String s ) {
MaskFormatter formatter = null;
try {
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 public boolean isHasAtLeastOneBranchWithSupportSD( final Phylogeny phy ) {
final PhylogenyNodeIterator it = phy.iteratorPostorder();
while ( it.hasNext() ) {
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 public boolean isHasAtLeastOneNodeWithScientificName( final Phylogeny phy ) {
final PhylogenyNodeIterator it = phy.iteratorPostorder();
while ( it.hasNext() ) {
System.out.println( "[" + name + "] > " + message );
}
+ final public static Phylogeny[] readPhylogeniesFromUrl( final URL url,
+ final boolean phyloxml_validate_against_xsd,
+ final boolean replace_underscores,
+ final boolean internal_numbers_are_confidences,
+ final TAXONOMY_EXTRACTION taxonomy_extraction,
+ final boolean midpoint_reroot )
+ throws FileNotFoundException, IOException {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final PhylogenyParser parser;
+ boolean nhx_or_nexus = false;
+ if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
+ parser = new TolParser();
+ }
+ else {
+ parser = ParserUtils.createParserDependingOnUrlContents( url, phyloxml_validate_against_xsd );
+ if ( parser instanceof NHXParser ) {
+ nhx_or_nexus = true;
+ final NHXParser nhx = ( NHXParser ) parser;
+ nhx.setReplaceUnderscores( replace_underscores );
+ nhx.setIgnoreQuotes( false );
+ nhx.setTaxonomyExtraction( taxonomy_extraction );
+ }
+ else if ( parser instanceof NexusPhylogeniesParser ) {
+ nhx_or_nexus = true;
+ final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
+ nex.setReplaceUnderscores( replace_underscores );
+ nex.setIgnoreQuotes( false );
+ }
+ }
+ AptxUtil.printAppletMessage( "Archaeopteryx", "parser is " + parser.getName() );
+ final URLConnection url_connection = url.openConnection();
+ url_connection.setDefaultUseCaches( false );
+ final InputStream i = url_connection.getInputStream();
+ final Phylogeny[] phys = factory.create( i, parser );
+ i.close();
+ if ( phys != null ) {
+ if ( nhx_or_nexus && internal_numbers_are_confidences ) {
+ for( final Phylogeny phy : phys ) {
+ PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
+ }
+ }
+ if ( midpoint_reroot ) {
+ for( final Phylogeny phy : phys ) {
+ PhylogenyMethods.midpointRoot( phy );
+ PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
+ }
+ }
+ }
+ return phys;
+ }
+
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 );
+ + "] Error", JOptionPane.ERROR_MESSAGE );
}
public static void writePhylogenyToGraphicsFile( final File intree,
phys[ 0 ] = phy;
final MainFrameApplication mf = MainFrameApplication.createInstance( phys, config );
AptxUtil.writePhylogenyToGraphicsFileNonInteractive( outfile, width, height, mf.getMainPanel()
- .getCurrentTreePanel(), mf.getMainPanel().getControlPanel(), type, mf.getOptions() );
+ .getCurrentTreePanel(), mf.getMainPanel().getControlPanel(), type, mf.getOptions() );
mf.end();
}
g2d.dispose();
}
+ 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 ( ForesterUtil.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 addPhylogeniesToTabs( final Phylogeny[] phys,
final String default_name,
final String full_path,
final MainPanel main_panel ) {
if ( phys.length > Constants.MAX_TREES_TO_LOAD ) {
JOptionPane.showMessageDialog( main_panel, "Attempt to load " + phys.length
- + " phylogenies,\ngoing to load only the first " + Constants.MAX_TREES_TO_LOAD, Constants.PRG_NAME
- + " more than " + Constants.MAX_TREES_TO_LOAD + " phylogenies", JOptionPane.WARNING_MESSAGE );
+ + " phylogenies,\ngoing to load only the first " + Constants.MAX_TREES_TO_LOAD, Constants.PRG_NAME
+ + " more than " + Constants.MAX_TREES_TO_LOAD + " phylogenies", JOptionPane.WARNING_MESSAGE );
}
int i = 1;
for( final Phylogeny phy : phys ) {
JOptionPane.showMessageDialog( null,
"Java memory allocation might be too small, try \"-Xmx2048m\" java command line option"
+ "\n\nError: " + e.getLocalizedMessage(),
- "Out of Memory Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]",
- JOptionPane.ERROR_MESSAGE );
+ "Out of Memory Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]",
+ JOptionPane.ERROR_MESSAGE );
System.exit( -1 );
}
System.out.println( "[" + applet_name + "] > " + message );
}
- final public static Phylogeny[] readPhylogeniesFromUrl( final URL url,
- final boolean phyloxml_validate_against_xsd,
- final boolean replace_underscores,
- final boolean internal_numbers_are_confidences,
- final TAXONOMY_EXTRACTION taxonomy_extraction,
- final boolean midpoint_reroot )
- throws FileNotFoundException, IOException {
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final PhylogenyParser parser;
- boolean nhx_or_nexus = false;
- if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
- parser = new TolParser();
- }
- else {
- parser = ParserUtils.createParserDependingOnUrlContents( url, phyloxml_validate_against_xsd );
- if ( parser instanceof NHXParser ) {
- nhx_or_nexus = true;
- final NHXParser nhx = ( NHXParser ) parser;
- nhx.setReplaceUnderscores( replace_underscores );
- nhx.setIgnoreQuotes( false );
- nhx.setTaxonomyExtraction( taxonomy_extraction );
- }
- else if ( parser instanceof NexusPhylogeniesParser ) {
- nhx_or_nexus = true;
- final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
- nex.setReplaceUnderscores( replace_underscores );
- nex.setIgnoreQuotes( false );
- }
- }
- AptxUtil.printAppletMessage( "Archaeopteryx", "parser is " + parser.getName() );
- final URLConnection url_connection = url.openConnection();
- url_connection.setDefaultUseCaches( false );
- final InputStream i = url_connection.getInputStream();
- final Phylogeny[] phys = factory.create( i, parser );
- i.close();
- if ( phys != null ) {
- if ( nhx_or_nexus && internal_numbers_are_confidences ) {
- for( final Phylogeny phy : phys ) {
- PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
- }
- }
- if ( midpoint_reroot ) {
- for( final Phylogeny phy : phys ) {
- PhylogenyMethods.midpointRoot( phy );
- PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
- }
- }
- }
- return phys;
- }
-
final static void removeBranchColors( final Phylogeny phy ) {
for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
it.next().getBranchData().setBranchColor( null );
sb.append( s + "\n" );
}
JOptionPane
- .showMessageDialog( null,
- "An unexpected (possibly severe) error has occured - terminating. \nPlease contact: "
- + Constants.AUTHOR_EMAIL + " \nError: " + e.getLocalizedMessage() + "\n"
- + sb,
+ .showMessageDialog( null,
+ "An unexpected (possibly severe) error has occured - terminating. \nPlease contact: "
+ + Constants.AUTHOR_EMAIL + " \nError: " + e.getLocalizedMessage() + "\n"
+ + sb,
"Unexpected Severe Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]",
JOptionPane.ERROR_MESSAGE );
System.exit( -1 );
"An unexpected exception has occured. \nPlease contact: "
+ Constants.AUTHOR_EMAIL + " \nException: " + e.getLocalizedMessage()
+ "\n" + sb,
- "Unexpected Exception [" + Constants.PRG_NAME + Constants.VERSION + "]",
- JOptionPane.ERROR_MESSAGE );
+ "Unexpected Exception [" + Constants.PRG_NAME + Constants.VERSION + "]",
+ JOptionPane.ERROR_MESSAGE );
}
final static String writePhylogenyToGraphicsByteArrayOutputStream( final ByteArrayOutputStream baos,
final IIOImage iio_image = new IIOImage( image, null, null );
writer.write( null, iio_image, image_write_param );
}
-
- 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 ( ForesterUtil.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 } );
- }
- }
- }
-
- public static enum GraphicsExportType {
- BMP( "bmp" ), GIF( "gif" ), JPG( "jpg" ), PDF( "pdf" ), PNG( "png" ), TIFF( "tif" );
-
- private final String _suffix;
-
- private GraphicsExportType( final String suffix ) {
- _suffix = suffix;
- }
-
- @Override
- public String toString() {
- return _suffix;
- }
- }
-
- final public static Color calculateColorFromString( final String str, final boolean is_taxonomy ) {
- final String my_str = str.toUpperCase();
- char first = my_str.charAt( 0 );
- char second = ' ';
- char third = ' ';
- if ( my_str.length() > 1 ) {
- if ( is_taxonomy ) {
- second = my_str.charAt( 1 );
- }
- else {
- second = my_str.charAt( my_str.length() - 1 );
- }
- if ( is_taxonomy ) {
- if ( my_str.length() > 2 ) {
- if ( my_str.indexOf( " " ) > 0 ) {
- third = my_str.charAt( my_str.indexOf( " " ) + 1 );
- }
- else {
- third = my_str.charAt( 2 );
- }
- }
- }
- else if ( my_str.length() > 2 ) {
- third = my_str.charAt( ( my_str.length() - 1 ) / 2 );
- }
- }
- first = normalizeCharForRGB( first );
- second = normalizeCharForRGB( second );
- third = normalizeCharForRGB( third );
- if ( ( first > 235 ) && ( second > 235 ) && ( third > 235 ) ) {
- first = 0;
- }
- else if ( ( first < 60 ) && ( second < 60 ) && ( third < 60 ) ) {
- second = 255;
- }
- return new Color( first, second, third );
- }
-
- final private static char normalizeCharForRGB( char c ) {
- c -= 65;
- c *= 10.2;
- c = c > 255 ? 255 : c;
- c = c < 0 ? 0 : c;
- return c;
- }
}
return createApplication( phylogenies, "", "" );
}
+ public static MainFrame createApplication( final Phylogeny phylogeny, final Configuration config, final String title ) {
+ final Phylogeny[] phylogenies = new Phylogeny[ 1 ];
+ phylogenies[ 0 ] = phylogeny;
+ return MainFrameApplication.createInstance( phylogenies, config, title );
+ }
+
public static MainFrame createApplication( final Phylogeny[] phylogenies ) {
return createApplication( phylogenies, "", "" );
}
return MainFrameApplication.createInstance( phylogenies, config_file_name, title );
}
- public static MainFrame createApplication( final Phylogeny phylogeny, final Configuration config, final String title ) {
- final Phylogeny[] phylogenies = new Phylogeny[ 1 ];
- phylogenies[ 0 ] = phylogeny;
- return MainFrameApplication.createInstance( phylogenies, config, title );
- }
-
public static void main( final String args[] ) {
Phylogeny[] phylogenies = null;
String config_filename = null;
}
boolean nhx_or_nexus = false;
final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( f, conf
- .isValidatePhyloXmlAgainstSchema() );
+ .isValidatePhyloXmlAgainstSchema() );
if ( p instanceof NHXParser ) {
nhx_or_nexus = true;
final NHXParser nhx = ( NHXParser ) p;
getMainFrameApplet().close();
}
}
-
-
/**
* This method returns the current external node data which
_mainframe_applet = new MainFrameApplet( this, configuration, getSpeciesTreeUrlStr() );
final URL tree_url = new URL( getTreeUrlStr() );
final Phylogeny[] phys = AptxUtil.readPhylogeniesFromUrl( tree_url, configuration
- .isValidatePhyloXmlAgainstSchema(), configuration.isReplaceUnderscoresInNhParsing(), configuration
- .isInternalNumberAreConfidenceForNhParsing(), configuration.getTaxonomyExtraction(), configuration
- .isMidpointReroot() );
+ .isValidatePhyloXmlAgainstSchema(), configuration.isReplaceUnderscoresInNhParsing(), configuration
+ .isInternalNumberAreConfidenceForNhParsing(), configuration.getTaxonomyExtraction(), configuration
+ .isMidpointReroot() );
if ( phys == null ) {
ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + tree_url + "] are null" );
}
final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
if ( default_relation != null ) {
getMainFrameApplet().getMainPanel().getControlPanel().getSequenceRelationTypeBox()
- .setSelectedItem( default_relation );
+ .setSelectedItem( default_relation );
}
final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
if ( default_sequence != null ) {
getMainFrameApplet().getMainPanel().getControlPanel().getSequenceRelationBox()
- .setSelectedItem( default_sequence );
+ .setSelectedItem( default_sequence );
}
/* GUILHEM_END */
}
private JCheckBoxMenuItem _right_line_up_domains_cbmi;
private JCheckBoxMenuItem _line_up_renderable_data_cbmi;
// file menu:
- private JMenuItem _open_item;
- private JMenuItem _open_url_item;
private JMenuItem _save_item;
- private JMenuItem _save_all_item;
- private JMenuItem _close_item;
- private JMenuItem _exit_item;
- private JMenuItem _new_item;
private JMenuItem _print_item;
private JMenuItem _write_to_pdf_item;
private JMenuItem _write_to_jpg_item;
private JFileChooser _save_filechooser;
private JFileChooser _writetographics_filechooser;
- void setCurrentDir( final File current_dir ) {
- _current_dir = current_dir;
- }
-
- File getCurrentDir() {
- if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
- if ( ForesterUtil.isWindows() ) {
- try {
- _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
- }
- catch ( final Exception e ) {
- _current_dir = null;
- }
- }
- }
- if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
- if ( System.getProperty( "user.home" ) != null ) {
- _current_dir = new File( System.getProperty( "user.home" ) );
- }
- else if ( System.getProperty( "user.dir" ) != null ) {
- _current_dir = new File( System.getProperty( "user.dir" ) );
- }
- }
- return _current_dir;
- }
-
- void buildFileMenu() {
- _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
- _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
- _file_jmenu.addSeparator();
- _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
- if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
- _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
- }
- _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
- _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
- if ( AptxUtil.canWriteFormat( "gif" ) ) {
- _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
- }
- if ( AptxUtil.canWriteFormat( "bmp" ) ) {
- _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
- }
- _file_jmenu.addSeparator();
- _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
- _file_jmenu.addSeparator();
- _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
- customizeJMenuItem( _save_item );
- customizeJMenuItem( _write_to_pdf_item );
- customizeJMenuItem( _write_to_png_item );
- customizeJMenuItem( _write_to_jpg_item );
- customizeJMenuItem( _write_to_gif_item );
- customizeJMenuItem( _write_to_tif_item );
- customizeJMenuItem( _write_to_bmp_item );
- customizeJMenuItem( _print_item );
- customizeJMenuItem( _exit_item );
- _jmenubar.add( _file_jmenu );
- }
-
@Override
public void actionPerformed( final ActionEvent e ) {
final Object o = e.getSource();
MainFrame.print( getCurrentTreePanel(), getOptions(), this );
}
else if ( o == _save_item ) {
-
- final File new_dir = MainFrame.writeToFile( _mainpanel.getCurrentPhylogeny() ,
- getMainPanel(), _save_filechooser, _current_dir, getContentPane(), this );
-
- if ( new_dir != null ) {
- setCurrentDir( new_dir );
- }
-
-
+ final File new_dir = MainFrame.writeToFile( _mainpanel.getCurrentPhylogeny(),
+ getMainPanel(),
+ _save_filechooser,
+ _current_dir,
+ getContentPane(),
+ this );
+ if ( new_dir != null ) {
+ setCurrentDir( new_dir );
+ }
} // TODO
- // TODO
- // TODO
- // TODO
- // TODO
-
-
+ // TODO
+ // TODO
+ // TODO
+ // TODO
// else if ( o == _graphics_export_visible_only_cbmi ) {
// updateOptions( getOptions() );
// }
@Override
public void init() {
+ _writetographics_filechooser = new JFileChooser();
_writetopdf_filechooser = new JFileChooser();
+ _save_filechooser = new JFileChooser();
+ _save_filechooser.setMultiSelectionEnabled( false );
+ _save_filechooser.setFileFilter( MainFrame.xmlfilter );
+ _save_filechooser.addChoosableFileFilter( MainFrame.nhfilter );
+ _save_filechooser.addChoosableFileFilter( MainFrame.nexusfilter );
+ _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );
_writetographics_filechooser = new JFileChooser();
+ _writetographics_filechooser.addChoosableFileFilter( MainFrame.graphicsfilefilter );
+ try {
+ final String home_dir = System.getProperty( "user.home" );
+ _save_filechooser.setCurrentDirectory( new File( home_dir ) );
+ _writetopdf_filechooser.setCurrentDirectory( new File( home_dir ) );
+ _writetographics_filechooser.setCurrentDirectory( new File( home_dir ) );
+ }
+ catch ( final Exception e ) {
+ // Do nothing. Not important.
+ }
final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
final Configuration configuration = new Configuration( config_filename, true, true, true );
ForesterUtil.printErrorMessage( NAME, "error: " + e );
e.printStackTrace();
JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
- + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
+ + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
}
if ( phys_url == null ) {
ForesterUtil.printErrorMessage( NAME, "failed to get tree URL from "
}
catch ( final IOException e ) {
ForesterUtil.printErrorMessage( NAME, "could not read species tree from [" + species_tree_url_str
- + "]" );
+ + "]" );
JOptionPane.showMessageDialog( this, NAME + ": could not read species tree from ["
+ species_tree_url_str + "]", "Failed to read species tree", JOptionPane.ERROR_MESSAGE );
}
public void componentResized( final ComponentEvent e ) {
if ( getMainPanel().getCurrentTreePanel() != null ) {
getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel()
- .getCurrentTreePanel()
- .getWidth(),
+ .getCurrentTreePanel()
+ .getWidth(),
getMainPanel()
- .getCurrentTreePanel()
- .getHeight() );
+ .getCurrentTreePanel()
+ .getHeight() );
}
}
} );
AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
if ( getSpeciesTree() != null ) {
AptxUtil.printAppletMessage( NAME,
- "Warning: gsdi (gene duplication inference) only available tabbed display" );
+ "Warning: gsdi (gene duplication inference) only available tabbed display" );
}
AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
}
AptxUtil.printAppletMessage( NAME, "started" );
}
+ 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 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 customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
+ if ( item != null ) {
+ item.setFont( MainFrame.menu_font );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
+ item.setForeground( getConfiguration().getGuiMenuTextColor() );
+ }
+ item.setSelected( is_selected );
+ item.addActionListener( this );
+ }
+ }
+
+ private Phylogeny getSpeciesTree() {
+ return _species_tree;
+ }
+
+ private boolean isScreenAntialias() {
+ return true;
+ }
+
+ private void removeBranchColors() {
+ if ( getMainPanel().getCurrentPhylogeny() != null ) {
+ AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
+ }
+ }
+
+ private void removeVisualStyles() {
+ if ( getMainPanel().getCurrentPhylogeny() != null ) {
+ AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
+ }
+ }
+
+ private void setMainPanel( final MainPanelApplets main_panel ) {
+ _mainpanel = main_panel;
+ }
+
+ private void setSpeciesTree( final Phylogeny species_tree ) {
+ _species_tree = species_tree;
+ }
+
+ private void setupUI() {
+ try {
+ if ( getConfiguration().isUseNativeUI() ) {
+ UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
+ }
+ else {
+ UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
+ }
+ }
+ catch ( final UnsupportedLookAndFeelException e ) {
+ AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
+ }
+ catch ( final ClassNotFoundException e ) {
+ AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
+ }
+ catch ( final InstantiationException e ) {
+ AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
+ }
+ catch ( final IllegalAccessException e ) {
+ AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
+ }
+ catch ( final Exception e ) {
+ AptxUtil.dieWithSystemError( e.toString() );
+ }
+ }
+
void buildAnalysisMenu() {
_analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
_analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
_jmenubar.add( _analysis_menu );
}
+ void buildFileMenu() {
+ _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
+ _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
+ _file_jmenu.addSeparator();
+ _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
+ if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
+ _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
+ }
+ _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
+ _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
+ if ( AptxUtil.canWriteFormat( "gif" ) ) {
+ _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
+ }
+ if ( AptxUtil.canWriteFormat( "bmp" ) ) {
+ _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
+ }
+ _file_jmenu.addSeparator();
+ _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
+ customizeJMenuItem( _save_item );
+ customizeJMenuItem( _write_to_pdf_item );
+ customizeJMenuItem( _write_to_png_item );
+ customizeJMenuItem( _write_to_jpg_item );
+ customizeJMenuItem( _write_to_gif_item );
+ customizeJMenuItem( _write_to_tif_item );
+ customizeJMenuItem( _write_to_bmp_item );
+ customizeJMenuItem( _print_item );
+ _jmenubar.add( _file_jmenu );
+ }
+
void buildFontSizeMenu() {
_font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
_font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
MainFrame
- .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
+ .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
- .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
+ .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
_options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
getConfiguration() ) );
_options_jmenu
- .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
+ .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
_options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
_options_jmenu
- .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
+ .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) );
_radio_group_1 = new ButtonGroup();
_radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
_radio_group_1.add( _uniform_cladograms_rbmi );
_options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
_options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
_options_jmenu
- .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
+ .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
_options_jmenu
- .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
+ .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
_options_jmenu
- .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
+ .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
_options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
_options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
_options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
_options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
_options_jmenu
- .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
+ .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
_options_jmenu
- .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
+ .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
_color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
_options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
_options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
_options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
getConfiguration() ) );
_options_jmenu
- .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
+ .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
_options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
_options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );
_search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );
_options_jmenu
- .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
+ .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) );
customizeJMenuItem( _choose_font_mi );
customizeJMenuItem( _choose_minimal_confidence_mi );
customizeJMenuItem( _switch_colors_mi );
customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
- .isShowDefaultNodeShapesExternal() );
+ .isShowDefaultNodeShapesExternal() );
customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
- .isShowDefaultNodeShapesInternal() );
+ .isShowDefaultNodeShapesInternal() );
customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()
- .isShowDefaultNodeShapesForMarkedNodes() );
+ .isShowDefaultNodeShapesForMarkedNodes() );
customizeJMenuItem( _cycle_node_shape_mi );
customizeJMenuItem( _cycle_node_fill_mi );
customizeJMenuItem( _choose_node_size_mi );
_tools_menu.addSeparator();
_tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
_remove_visual_styles_item
- .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
+ .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
customizeJMenuItem( _remove_visual_styles_item );
_tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
_remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." );
void buildViewMenu() {
_view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
_view_jmenu
- .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
+ .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
_view_jmenu.addSeparator();
_view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
_view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
+ gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
+ "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
+ "Number of polytomies in species tree used: " + poly + "\n",
- "GSDI successfully completed",
- JOptionPane.WARNING_MESSAGE );
+ "GSDI successfully completed",
+ JOptionPane.WARNING_MESSAGE );
}
else {
JOptionPane.showMessageDialog( this,
+ gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
+ "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
+ "Number of polytomies in species tree used: " + poly + "\n",
- "GSDI successfully completed",
- JOptionPane.INFORMATION_MESSAGE );
+ "GSDI successfully completed",
+ JOptionPane.INFORMATION_MESSAGE );
}
}
+ gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
+ "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
+ "Number of polytomies in species tree used: " + poly + "\n",
- "GSDIR successfully completed",
- JOptionPane.WARNING_MESSAGE );
+ "GSDIR successfully completed",
+ JOptionPane.WARNING_MESSAGE );
}
else {
JOptionPane.showMessageDialog( this,
+ gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
+ "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
+ "Number of polytomies in species tree used: " + poly + "\n",
- "GSDIR successfully completed",
- JOptionPane.INFORMATION_MESSAGE );
+ "GSDIR successfully completed",
+ JOptionPane.INFORMATION_MESSAGE );
}
}
return _configuration;
}
+ File getCurrentDir() {
+ if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
+ if ( ForesterUtil.isWindows() ) {
+ try {
+ _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
+ }
+ catch ( final Exception e ) {
+ _current_dir = null;
+ }
+ }
+ }
+ if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
+ if ( System.getProperty( "user.home" ) != null ) {
+ _current_dir = new File( System.getProperty( "user.home" ) );
+ }
+ else if ( System.getProperty( "user.dir" ) != null ) {
+ _current_dir = new File( System.getProperty( "user.dir" ) );
+ }
+ }
+ return _current_dir;
+ }
+
TreePanel getCurrentTreePanel() {
return getMainPanel().getCurrentTreePanel();
}
return _label_direction_cbmi;
}
+ MainPanel getMainPanel() {
+ return _mainpanel;
+ }
+
Options getOtions() {
return _options;
}
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 );
+ .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;
}
}
_configuration = configuration;
}
+ void setCurrentDir( final File current_dir ) {
+ _current_dir = current_dir;
+ }
+
void setOptions( final Options options ) {
_options = options;
}
void updateOptions( final Options options ) {
options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );
options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
- && _background_gradient_cbmi.isSelected() );
+ && _background_gradient_cbmi.isSelected() );
options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
- && _show_annotation_ref_source.isSelected() );
+ && _show_annotation_ref_source.isSelected() );
options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
- && _abbreviate_scientific_names.isSelected() );
+ && _abbreviate_scientific_names.isSelected() );
options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
- && _color_labels_same_as_parent_branch.isSelected() );
+ && _color_labels_same_as_parent_branch.isSelected() );
options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
- && _show_default_node_shapes_internal_cbmi.isSelected() );
+ && _show_default_node_shapes_internal_cbmi.isSelected() );
options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
- && _show_default_node_shapes_external_cbmi.isSelected() );
+ && _show_default_node_shapes_external_cbmi.isSelected() );
options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )
- && _show_default_node_shapes_for_marked_cbmi.isSelected() );
+ && _show_default_node_shapes_for_marked_cbmi.isSelected() );
if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
}
options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
}
options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
- && _search_case_senstive_cbmi.isSelected() );
+ && _search_case_senstive_cbmi.isSelected() );
if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {
options.setShowScale( _show_scale_cbmi.isSelected() );
}
}
options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
- && _show_confidence_stddev_cbmi.isSelected() );
+ && _show_confidence_stddev_cbmi.isSelected() );
options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
- && _search_whole_words_only_cbmi.isSelected() );
+ && _search_whole_words_only_cbmi.isSelected() );
options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );
options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
- && _inverse_search_result_cbmi.isSelected() );
+ && _inverse_search_result_cbmi.isSelected() );
if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
}
title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
}
showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions()
- .getNhConversionSupportValueStyle() ),
- title );
+ .getNhConversionSupportValueStyle() ),
+ title );
}
}
title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
}
showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshire( getOptions()
- .getNhConversionSupportValueStyle() ),
- title );
+ .getNhConversionSupportValueStyle() ),
+ title );
}
}
}
}
- 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 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 customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {
- if ( item != null ) {
- item.setFont( MainFrame.menu_font );
- if ( !getConfiguration().isUseNativeUI() ) {
- item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
- item.setForeground( getConfiguration().getGuiMenuTextColor() );
- }
- item.setSelected( is_selected );
- item.addActionListener( this );
- }
- }
-
- MainPanel getMainPanel() {
- return _mainpanel;
- }
-
- private Phylogeny getSpeciesTree() {
- return _species_tree;
- }
-
- private boolean isScreenAntialias() {
- return true;
- }
-
- private void removeBranchColors() {
- if ( getMainPanel().getCurrentPhylogeny() != null ) {
- AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
- }
- }
-
- private void removeVisualStyles() {
- if ( getMainPanel().getCurrentPhylogeny() != null ) {
- AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
- }
- }
-
- private void setMainPanel( final MainPanelApplets main_panel ) {
- _mainpanel = main_panel;
- }
-
- private void setSpeciesTree( final Phylogeny species_tree ) {
- _species_tree = species_tree;
- }
-
- private void setupUI() {
- try {
- if ( getConfiguration().isUseNativeUI() ) {
- UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
- }
- else {
- UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
- }
- }
- catch ( final UnsupportedLookAndFeelException e ) {
- AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
- }
- catch ( final ClassNotFoundException e ) {
- AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
- }
- catch ( final InstantiationException e ) {
- AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() );
- }
- catch ( final IllegalAccessException e ) {
- AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() );
- }
- catch ( final Exception e ) {
- AptxUtil.dieWithSystemError( e.toString() );
- }
- }
-
static void setupScreenTextAntialias( final List<TreePanel> treepanels, final boolean antialias ) {
for( final TreePanel tree_panel : treepanels ) {
tree_panel.setTextAntialias();
final class ColorSchemeChooser extends JDialog implements ActionListener {
- private static final long serialVersionUID = 6150960100859081126L;
- private final TreeColorSet _colorset;
- private final JComboBox<String> _selector;
- private final JPanel _color_panel;
- private final JPanel _color_labels[];
- private final JButton _ok_btn;
- private final JButton _cancel_btn;
- private final MainPanel _main_panel;
- private final int _prev_selected_scheme;
- private int _selected_scheme;
+ private static final long serialVersionUID = 6150960100859081126L;
+ private final TreeColorSet _colorset;
+ private final JComboBox<String> _selector;
+ private final JPanel _color_panel;
+ private final JPanel _color_labels[];
+ private final JButton _ok_btn;
+ private final JButton _cancel_btn;
+ private final MainPanel _main_panel;
+ private final int _prev_selected_scheme;
+ private int _selected_scheme;
ColorSchemeChooser( final MainPanel parent, final TreeColorSet colorset ) {
setName( "Color Scheme Chooser" );
BUFFER_ONLY, CONSOLE, WINODW;
}
- static enum TRIPLET {
- FALSE, TRUE, UNKNOWN
- }
-
public enum UI {
CROSSPLATFORM, NATIVE, NIMBUS, UNKNOWN
}
+
+ static enum TRIPLET {
+ FALSE, TRUE, UNKNOWN
+ }
final static String clickto_options[][] = {
- { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
- { "Go to Sub-/Super-Tree", "display" }, { "Swap Descendants", "display" },
- { "Colorize Node(s)", "display" }, { "Change Node Font(s)", "display" },
- { "Colorize Subtree(s)", "display" }, { "Open Sequence DB", "display" }, { "Open PDB", "display" },
- { "Open Taxonomy DB", "display" }, { "Launch BLAST", "display" }, { "Cut Subtree", "display" },
- { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" },
- { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Sort Descendants", "display" },
- { "List Node Data", "display" }, { "Select Node(s)", "display" } };
+ { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
+ { "Go to Sub-/Super-Tree", "display" }, { "Swap Descendants", "display" },
+ { "Colorize Node(s)", "display" }, { "Change Node Font(s)", "display" },
+ { "Colorize Subtree(s)", "display" }, { "Open Sequence DB", "display" }, { "Open PDB", "display" },
+ { "Open Taxonomy DB", "display" }, { "Launch BLAST", "display" }, { "Cut Subtree", "display" },
+ { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" },
+ { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Sort Descendants", "display" },
+ { "List Node Data", "display" }, { "Select Node(s)", "display" } };
private final static String DEFAULT_SPECIES_COLORS[][] = {
- { "BRAFL", "0x00FFFF" }, { "SPHGR", "0x9620F0" }, { "STRPU", "0x9620F0" }, { "CIOIN", "0xFF1CAE" },
- { "CIOSA", "0xFF2CAE" }, { "BOVIN", "0x5C3317" }, { "CANFA", "0x8B2323" }, { "HUMAN", "0xFF2400" },
- { "PANTR", "0xCC2400" }, { "MOUSE", "0xFF7F00" }, { "RAT", "0xFFEF00" }, { "MONDO", "0xEE9A49" },
- { "ORNAN", "0xCD853F" }, { "XENLA", "0x6BAA23" }, { "XENTR", "0x6BAA23" }, { "CHICK", "0xFFC125" },
- { "FUGRU", "0x0000FF" }, { "BRARE", "0x0000DD" }, { "DANRE", "0x0000BB" }, { "TETNG", "0x0000AA" },
- { "ORYLA", "0x000088" }, { "GASAC", "0x000066" }, { "CAEEL", "0x666699" }, { "CAEBR", "0xB0B0B0" },
- { "DROME", "0x663366" }, { "DROPS", "0x996699" }, { "APIME", "0x7A7700" }, { "AEDAE", "0x8C5900" },
- { "TRICA", "0x918E00" }, { "NEMVE", "0x0066CC" }, { "HYDVU", "0x3399FF" }, { "LUBBA", "0xF7B5CB" },
- { "GEOCY", "0xF5A0BD" }, { "AMPQE", "0x009966" }, { "SUBDO", "0xC790B9" }, { "MONBE", "0xFC0FC0" },
- { "DICPU", "0xFFCC33" }, { "DICDI", "0xFFCC00" }, { "ENTHI", "0x5959AB" }, { "ARATH", "0x00FF00" },
- { "POPTR", "0x006400" }, { "VITVI", "0x00CD00" }, { "GLYMA", "0x00FF7F" }, { "ORYSA", "0x008B00" },
- { "ORYSJ", "0x008C00" }, { "SORBI", "0x00EE76" }, { "SELMO", "0x238E23" }, { "PHYPA", "0x09F911" },
- { "OSTLU", "0x7FFF00" }, { "OSTTA", "0x7FFF00" }, { "OSTRC", "0x7FFF00" }, { "MICPU", "0x66CD00" },
- { "MIC99", "0x66CD00" }, { "CHLRE", "0xB3EE3A" }, { "VOLCA", "0xC0FF3E" }, { "CHLSP", "0x6B8E23" },
- { "CYAME", "0xD02090" }, { "YEAST", "0xAAAAAA" }, { "BACFR", "0xFF0000" }, { "BACTN", "0xFFFF00" },
- { "MYXXD", "0x0000FF" }, { "STIAU", "0x00FFFF" }, { "BACOV", "0x8C5900" }, { "BACUN", "0x66CD00" },
- { "PORGI", "0x918E00" } };
+ { "BRAFL", "0x00FFFF" }, { "SPHGR", "0x9620F0" }, { "STRPU", "0x9620F0" }, { "CIOIN", "0xFF1CAE" },
+ { "CIOSA", "0xFF2CAE" }, { "BOVIN", "0x5C3317" }, { "CANFA", "0x8B2323" }, { "HUMAN", "0xFF2400" },
+ { "PANTR", "0xCC2400" }, { "MOUSE", "0xFF7F00" }, { "RAT", "0xFFEF00" }, { "MONDO", "0xEE9A49" },
+ { "ORNAN", "0xCD853F" }, { "XENLA", "0x6BAA23" }, { "XENTR", "0x6BAA23" }, { "CHICK", "0xFFC125" },
+ { "FUGRU", "0x0000FF" }, { "BRARE", "0x0000DD" }, { "DANRE", "0x0000BB" }, { "TETNG", "0x0000AA" },
+ { "ORYLA", "0x000088" }, { "GASAC", "0x000066" }, { "CAEEL", "0x666699" }, { "CAEBR", "0xB0B0B0" },
+ { "DROME", "0x663366" }, { "DROPS", "0x996699" }, { "APIME", "0x7A7700" }, { "AEDAE", "0x8C5900" },
+ { "TRICA", "0x918E00" }, { "NEMVE", "0x0066CC" }, { "HYDVU", "0x3399FF" }, { "LUBBA", "0xF7B5CB" },
+ { "GEOCY", "0xF5A0BD" }, { "AMPQE", "0x009966" }, { "SUBDO", "0xC790B9" }, { "MONBE", "0xFC0FC0" },
+ { "DICPU", "0xFFCC33" }, { "DICDI", "0xFFCC00" }, { "ENTHI", "0x5959AB" }, { "ARATH", "0x00FF00" },
+ { "POPTR", "0x006400" }, { "VITVI", "0x00CD00" }, { "GLYMA", "0x00FF7F" }, { "ORYSA", "0x008B00" },
+ { "ORYSJ", "0x008C00" }, { "SORBI", "0x00EE76" }, { "SELMO", "0x238E23" }, { "PHYPA", "0x09F911" },
+ { "OSTLU", "0x7FFF00" }, { "OSTTA", "0x7FFF00" }, { "OSTRC", "0x7FFF00" }, { "MICPU", "0x66CD00" },
+ { "MIC99", "0x66CD00" }, { "CHLRE", "0xB3EE3A" }, { "VOLCA", "0xC0FF3E" }, { "CHLSP", "0x6B8E23" },
+ { "CYAME", "0xD02090" }, { "YEAST", "0xAAAAAA" }, { "BACFR", "0xFF0000" }, { "BACTN", "0xFFFF00" },
+ { "MYXXD", "0x0000FF" }, { "STIAU", "0x00FFFF" }, { "BACOV", "0x8C5900" }, { "BACUN", "0x66CD00" },
+ { "PORGI", "0x918E00" } };
final static int display_node_data = 0;
final static int collapse_uncollapse = 1;
final static int reroot = 2;
// Click-to options
// ------------------
final static String display_options[][] = {
- { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
- { "Seq Annotations", "display", "no" }, { "Confidence Values", "display", "?" },
- { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" },
- { "Colorize by Sequence", "display", "no" }, { "Visual Styles/Branch Colors", "display", "no" },
- { "Branch Widths", "display", "no" }, { "Domain Architectures", "display", "no" },
- { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
- { "Seq Name", "display", "yes" }, { "Seq Accession", "display", "no" },
- { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },
- { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" },
- { "Colorize by Annotation", "display", "no" }, { "Seq Symbol", "display", "yes" },
- { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" },
- { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
- { "Properties", "display", "no" }, { "Gene Name", "display", "yes" },
- { "Multiple Seq Alignment", "display", "no" }, { "Branch Length Values", "display", "no" } };
+ { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
+ { "Seq Annotations", "display", "no" }, { "Confidence Values", "display", "?" },
+ { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" },
+ { "Colorize by Sequence", "display", "no" }, { "Visual Styles/Branch Colors", "display", "no" },
+ { "Branch Widths", "display", "no" }, { "Domain Architectures", "display", "no" },
+ { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
+ { "Seq Name", "display", "yes" }, { "Seq Accession", "display", "no" },
+ { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },
+ { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" },
+ { "Colorize by Annotation", "display", "no" }, { "Seq Symbol", "display", "yes" },
+ { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" },
+ { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
+ { "Properties", "display", "no" }, { "Gene Name", "display", "yes" },
+ { "Multiple Seq Alignment", "display", "no" }, { "Branch Length Values", "display", "no" } };
final static int display_as_phylogram = 0;
final static int show_node_names = 1;
final static int show_tax_code = 2;
}
}
- static String getDefaultFontFamilyName() {
- return DEFAULT_FONT_FAMILY;
- }
-
public Configuration() {
this( null, false, false, false );
}
}
}
- boolean displaySequenceRelations() {
- return _display_sequence_relations;
- }
-
- boolean doCheckOption( final int which ) {
- return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
- || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
- }
-
- boolean doDisplayClickToOption( final int which ) {
- return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
- }
-
- boolean doDisplayOption( final int which ) {
- return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
- }
-
- /**
- * Will attempt to use the phylogeny to determine whether to check
- * this or not (e.g. phylogram)
- *
- */
- boolean doGuessCheckOption( final int which ) {
- return display_options[ which ][ 2 ].equals( "?" );
- }
-
- Map<String, Color> getAnnotationColors() {
- if ( _annotation_colors == null ) {
- _annotation_colors = new Hashtable<String, Color>();
- }
- return _annotation_colors;
- }
-
public String getBaseFontFamilyName() {
return _base_font_family_name;
}
- int getBaseFontSize() {
- return _base_font_size;
- }
-
- CLADOGRAM_TYPE getCladogramType() {
- return _cladogram_type;
- }
-
- private int getClickToIndex( final String name ) {
- int index = -1;
- if ( name.equals( "edit_info" ) ) {
- index = Configuration.display_node_data;
- ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "configuration key [edit_info] is deprecated, use [display node data] instead" );
- }
- else if ( name.equals( "display_node_data" ) ) {
- index = Configuration.display_node_data;
- }
- else if ( name.equals( "collapse_uncollapse" ) ) {
- index = Configuration.collapse_uncollapse;
- }
- else if ( name.equals( "reroot" ) ) {
- index = Configuration.reroot;
- }
- else if ( name.equals( "subtree" ) ) {
- index = Configuration.subtree;
- }
- else if ( name.equals( "swap" ) ) {
- index = Configuration.swap;
- }
- else if ( name.equals( "sort_descendants" ) ) {
- index = Configuration.sort_descendents;
- }
- else if ( name.equals( "get_ext_descendents_data" ) ) {
- index = Configuration.get_ext_desc_data;
- }
- else if ( name.equals( "display_sequences" ) ) {
- ForesterUtil
- .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
- return DEPRECATED;
- }
- else if ( name.equals( "open_seq_web" ) ) {
- index = Configuration.open_seq_web;
- }
- else if ( name.equals( "open_pdb_web" ) ) {
- index = Configuration.open_pdb_web;
- }
- else if ( name.equals( "open_tax_web" ) ) {
- index = Configuration.open_tax_web;
- }
- else if ( name.equals( "blast" ) ) {
- index = Configuration.blast;
- }
- else if ( name.equals( "cut_subtree" ) ) {
- index = Configuration.cut_subtree;
- }
- else if ( name.equals( "copy_subtree" ) ) {
- index = Configuration.copy_subtree;
- }
- else if ( name.equals( "paste_subtree" ) ) {
- index = Configuration.paste_subtree;
- }
- else if ( name.equals( "delete" ) ) {
- index = Configuration.delete_subtree_or_node;
- }
- else if ( name.equals( "add_new_node" ) ) {
- index = Configuration.add_new_node;
- }
- else if ( name.equals( "edit_node_data" ) ) {
- index = Configuration.edit_node_data;
- }
- else if ( name.equals( "select_nodes" ) ) {
- index = Configuration.select_nodes;
- }
- else if ( name.equals( "display_node_popup" ) ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME,
- "configuration key [display_node_popup] is deprecated" );
- return DEPRECATED;
- }
- else if ( name.equals( "custom_option" ) ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
- return DEPRECATED;
- }
- else if ( name.equals( "color_subtree" ) ) {
- index = Configuration.color_subtree;
- }
- else if ( name.equals( "change_node_font" ) ) {
- index = Configuration.change_node_font;
- }
- else if ( name.equals( "color_node_font" ) ) {
- index = Configuration.color_node_font;
- }
- else if ( name.equals( "color_subtree" ) ) {
- index = Configuration.color_subtree;
- }
- return index;
- }
-
- int getClickToOptionsCount() {
- return clickto_options.length;
- }
-
- String getClickToTitle( final int which ) {
- return clickto_options[ which ][ 0 ];
- }
-
public int getDefaultBootstrapSamples() {
return _default_bootstrap_samples;
}
- int getDefaultDisplayClicktoOption() {
- return default_clickto;
- }
-
public NodeFill getDefaultNodeFill() {
return _default_node_fill;
}
return _default_node_shape_size;
}
- SortedMap<String, Color> getDisplayColors() {
- return _display_colors;
- }
-
- String getDisplayTitle( final int which ) {
- return display_options[ which ][ 0 ];
- }
-
- Map<String, Color> getDomainColors() {
- if ( _domain_colors == null ) {
- _domain_colors = new Hashtable<String, Color>();
- }
- return _domain_colors;
- }
-
public NodeDataField getExtDescNodeDataToReturn() {
return _ext_desc_data_to_return;
}
return _frame_y_size;
}
- int getGraphicsExportX() {
- return _graphics_export_x;
+ public String getLabelForGetExtDescendentsData() {
+ return _label_for_get_ext_descendents_data;
}
- int getGraphicsExportY() {
- return _graphics_export_y;
+ public File getPathToLocalFastme() {
+ return _path_to_local_fastme;
}
- Color getGuiBackgroundColor() {
- return _gui_background_color;
+ public File getPathToLocalMafft() {
+ return _path_to_local_mafft;
}
- Color getGuiButtonBackgroundColor() {
- return _gui_button_background_color;
+ public File getPathToLocalRaxml() {
+ return _path_to_local_raxml;
}
- Color getGuiButtonBorderColor() {
- return _gui_button_border_color;
+ public double getVectorDataHeight() {
+ return _vector_data_height;
}
- Color getGuiButtonTextColor() {
- return _gui_button_text_color;
+ public Color getVectorDataMaxColor() {
+ return _vector_data_max_color;
}
- Color getGuiCheckboxAndButtonActiveColor() {
- return _gui_checkbox_and_button_active_color;
+ public Color getVectorDataMeanColor() {
+ return _vector_data_mean_color;
}
- Color getGuiCheckboxTextColor() {
- return _gui_checkbox_text_color;
+ public Color getVectorDataMinColor() {
+ return _vector_data_min_color;
}
- Color getGuiMenuBackgroundColor() {
- return _gui_menu_background_color;
+ public int getVectorDataWidth() {
+ return _vector_data_width;
}
- Color getGuiMenuTextColor() {
- return _gui_menu_text_color;
+ public boolean isAbbreviateScientificTaxonNames() {
+ return _abbreviate_scientific_names;
}
- public String getLabelForGetExtDescendentsData() {
- return _label_for_get_ext_descendents_data;
+ public boolean isAllowThickStrokes() {
+ return _allow_thick_strokes;
}
- int getMaxBaseFontSize() {
- return _max_base_font_size;
+ public boolean isBackgroundColorGradient() {
+ return _background_color_gradient;
}
- int getMinBaseFontSize() {
- return _min_base_font_size;
+ public boolean isColorByTaxonomicGroup() {
+ return false;
}
- double getMinConfidenceValue() {
- return _min_confidence_value;
+ public boolean isColorLabelsSameAsParentBranch() {
+ return _color_labels_same_as_parent_branch;
}
- NODE_LABEL_DIRECTION getNodeLabelDirection() {
- return _node_label_direction;
+ final public boolean isLineUpRendarableNodeData() {
+ return _line_up_renderable_node_data;
}
- short getNumberOfDigitsAfterCommaForBranchLengthValues() {
- return _number_of_digits_after_comma_for_branch_length_values;
+ public boolean isMidpointReroot() {
+ return _midpoint_root;
}
- short getNumberOfDigitsAfterCommaForConfidenceValues() {
- return _number_of_digits_after_comma_for_confidence_values;
+ final public boolean isRightLineUpDomains() {
+ return _right_align_domains;
}
- short getOvMaxHeight() {
- return _ov_max_height;
+ public boolean isShowAnnotationRefSource() {
+ return _show_annotation_ref_source;
}
- short getOvMaxWidth() {
- return _ov_max_width;
+ public boolean isShowDefaultNodeShapesExternal() {
+ return _show_default_node_shapes_external;
}
- OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
- return _ov_placement;
+ public boolean isShowDefaultNodeShapesForMarkedNodes() {
+ return _show_default_node_shapes_for_marked_nodes;
}
- public File getPathToLocalFastme() {
- return _path_to_local_fastme;
+ public boolean isShowDefaultNodeShapesInternal() {
+ return _show_default_node_shapes_internal;
}
- public File getPathToLocalMafft() {
- return _path_to_local_mafft;
+ public boolean isShowDomainLabels() {
+ return _show_domain_labels;
}
- public File getPathToLocalRaxml() {
- return _path_to_local_raxml;
+ public void putDisplayColors( final String key, final Color color ) {
+ getDisplayColors().put( key, color );
}
- PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
- return _phylogeny_graphics_type;
+ public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
+ _abbreviate_scientific_names = abbreviate_scientific_names;
}
- float getPrintLineWidth() {
- return _print_line_width;
+ public void setAddTaxonomyImagesCB( final boolean b ) {
+ display_options[ show_taxonomy_images ][ 1 ] = b ? "yes" : "no";
}
- Hashtable<String, Color> getSequenceColors() {
- if ( _sequence_colors == null ) {
- _sequence_colors = new Hashtable<String, Color>();
- }
- return _sequence_colors;
+ public void setBackgroundColorGradient( final boolean background_color_gradient ) {
+ _background_color_gradient = background_color_gradient;
}
- Hashtable<String, Color> getSpeciesColors() {
- if ( _species_colors == null ) {
- initSpeciesColors();
- }
- return _species_colors;
+ public void setBaseFontFamilyName( final String base_font_family_name ) {
+ _base_font_family_name = base_font_family_name;
}
- final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
- return _taxonomy_extraction;
+ public void setBaseFontSize( final int base_font_size ) {
+ _base_font_size = base_font_size;
}
- public double getVectorDataHeight() {
- return _vector_data_height;
+ public void setColorizeBranches( final boolean b ) {
+ display_options[ use_style ][ 2 ] = b ? "yes" : "no";
}
- public Color getVectorDataMaxColor() {
- return _vector_data_max_color;
+ public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
+ _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
}
- public Color getVectorDataMeanColor() {
- return _vector_data_mean_color;
+ public void setDefaultNodeFill( final NodeFill default_node_fill ) {
+ _default_node_fill = default_node_fill;
}
- public Color getVectorDataMinColor() {
- return _vector_data_min_color;
+ public void setDefaultNodeShape( final NodeShape default_node_shape ) {
+ _default_node_shape = default_node_shape;
}
- public int getVectorDataWidth() {
- return _vector_data_width;
+ public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
+ _default_node_shape_size = default_node_shape_size;
}
- private final void initSpeciesColors() {
- _species_colors = new Hashtable<String, Color>();
- for( final String[] s : DEFAULT_SPECIES_COLORS ) {
- _species_colors.put( s[ 0 ], Color.decode( s[ 1 ] ) );
- }
+ public void setDisplayAsPhylogram( final boolean b ) {
+ display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
}
- public boolean isAbbreviateScientificTaxonNames() {
- return _abbreviate_scientific_names;
+ public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
+ _display_colors = display_colors;
}
- boolean isAntialiasScreen() {
- return _antialias_screen;
+ public void setDisplayConfidenceValues( final boolean b ) {
+ display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
}
- public boolean isBackgroundColorGradient() {
- return _background_color_gradient;
+ public void setDisplayGeneNames( final boolean b ) {
+ display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
}
- public boolean isColorByTaxonomicGroup() {
- return false;
+ public void setDisplayInternalData( final boolean b ) {
+ display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
}
- public boolean isColorLabelsSameAsParentBranch() {
- return _color_labels_same_as_parent_branch;
+ public void setDisplayMultipleSequenceAlignment( final boolean b ) {
+ display_options[ show_mol_seqs ][ 2 ] = b ? "yes" : "no";
}
- /**
- * Convenience method.
- *
- * @return true if value in configuration file was 'yes'
- */
- boolean isDrawAsPhylogram() {
- return doCheckOption( display_as_phylogram );
+ public void setDisplayNodeNames( final boolean b ) {
+ display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
}
- boolean isEditable() {
- return _editable;
+ public void setDisplaySequenceAcc( final boolean b ) {
+ display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
}
- /**
- * Only used by ArchaeoptryxE.
- *
- */
- boolean isHideControlPanelAndMenubar() {
- return _hide_controls_and_menus;
+ public void setDisplaySequenceNames( final boolean b ) {
+ display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no";
}
- boolean isInternalNumberAreConfidenceForNhParsing() {
- return _internal_number_are_confidence_for_nh_parsing;
+ public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
+ _display_sequence_relations = display_sequence_relations;
}
- final public boolean isLineUpRendarableNodeData() {
- return _line_up_renderable_node_data;
+ public void setDisplaySequenceSymbols( final boolean b ) {
+ display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no";
}
- public boolean isMidpointReroot() {
- return _midpoint_root;
+ public void setDisplayTaxonomyCode( final boolean b ) {
+ display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
}
- boolean isReplaceUnderscoresInNhParsing() {
- return _nh_parsing_replace_underscores;
+ public void setDisplayTaxonomyCommonNames( final boolean b ) {
+ display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
}
- final public boolean isRightLineUpDomains() {
- return _right_align_domains;
+ public void setDisplayTaxonomyImages( final boolean b ) {
+ display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
}
- public boolean isShowAnnotationRefSource() {
- return _show_annotation_ref_source;
+ public void setDisplayTaxonomyScientificNames( final boolean b ) {
+ display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
}
- public boolean isShowDefaultNodeShapesExternal() {
- return _show_default_node_shapes_external;
+ public void setDynamicallyHideData( final boolean b ) {
+ display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
}
- public boolean isShowDefaultNodeShapesForMarkedNodes() {
- return _show_default_node_shapes_for_marked_nodes;
+ public void setExtDescNodeDataToReturn( final NodeDataField ext_desc_data_to_return ) {
+ _ext_desc_data_to_return = ext_desc_data_to_return;
}
- public boolean isShowDefaultNodeShapesInternal() {
- return _show_default_node_shapes_internal;
+ public void setFrameXSize( final int frame_x_size ) {
+ _frame_x_size = frame_x_size;
}
- public boolean isShowDomainLabels() {
- return _show_domain_labels;
+ public void setFrameYSize( final int frame_y_size ) {
+ _frame_y_size = frame_y_size;
}
- boolean isShowOverview() {
- return _show_overview;
+ final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) {
+ _line_up_renderable_node_data = line_up_renderable_node_data;
}
- boolean isShowScale() {
- return _show_scale;
+ public void setMidpointReroot( final boolean midpoint_root ) {
+ _midpoint_root = midpoint_root;
}
- final boolean isUseNativeUI() {
- if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) {
- _ui = UI.NATIVE;
- }
- return _ui == UI.NATIVE;
+ public void setMinConfidenceValue( final double min_confidence_value ) {
+ _min_confidence_value = min_confidence_value;
}
- /**
- * Only used by ArchaeoptryxE.
- *
- */
- boolean isUseTabbedDisplay() {
- return _use_tabbed_display;
+ public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
+ _node_label_direction = node_label_direction;
}
- boolean isValidatePhyloXmlAgainstSchema() {
- return _validate_against_phyloxml_xsd_schema;
+ public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
+ _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
}
- private boolean parseBoolean( final String str ) {
- final String my_str = str.trim().toLowerCase();
- if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
- return true;
- }
- else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
- return false;
- }
- else {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
- return false;
- }
+ public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
+ _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
}
- private double parseDouble( final String str ) {
- double d = 0.0;
- try {
- d = Double.parseDouble( str.trim() );
- }
- catch ( final Exception e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
- d = 0.0;
- }
- return d;
+ public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
+ _phylogeny_graphics_type = phylogeny_graphics_type;
}
- private float parseFloat( final String str ) {
- float f = 0.0f;
- try {
- f = Float.parseFloat( str.trim() );
- }
- catch ( final Exception e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
- f = 0.0f;
- }
- return f;
+ public void setPrintLineWidth( final float print_line_width ) {
+ _print_line_width = print_line_width;
}
- private int parseInt( final String str ) {
- int i = -1;
- try {
- i = Integer.parseInt( str.trim() );
- }
- catch ( final Exception e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
- i = -1;
- }
- return i;
+ public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
+ _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
}
- private short parseShort( final String str ) {
- short i = -1;
- try {
- i = Short.parseShort( str.trim() );
- }
- catch ( final Exception e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
- i = -1;
- }
- return i;
+ final public void setRightLineUpDomains( final boolean right_align_domains ) {
+ _right_align_domains = right_align_domains;
}
- private void processFontFamily( final StringTokenizer st ) {
- setBaseFontFamilyName( "" );
- final String font_str = ( ( String ) st.nextElement() ).trim();
- final String[] fonts = font_str.split( ",+" );
- for( String font : fonts ) {
- font = font.replace( '_', ' ' ).trim();
- if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
- setBaseFontFamilyName( font );
- break;
- }
- }
+ public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
+ _show_default_node_shapes_external = show_default_node_shapes_external;
}
- public void putDisplayColors( final String key, final Color color ) {
- getDisplayColors().put( key, color );
+ public void setShowDefaultNodeShapesForMarkedNodes( final boolean show_default_node_shapes_for_marked_nodes ) {
+ _show_default_node_shapes_for_marked_nodes = show_default_node_shapes_for_marked_nodes;
}
- /**
- * read each line of config file, process non-comment lines
- * @throws IOException
- */
- private void readConfig( final BufferedReader conf_in ) throws IOException {
- String line;
- do {
- line = conf_in.readLine();
- if ( line != null ) {
- line = line.trim();
- // skip comments and blank lines
- if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
- // convert runs of spaces to tabs
- line = line.replaceAll( "\\s+", "\t" );
- final StringTokenizer st = new StringTokenizer( line, "\t" );
- setKeyValue( st );
- }
- }
- } while ( line != null );
- }
-
- public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
- _abbreviate_scientific_names = abbreviate_scientific_names;
- }
-
- public void setAddTaxonomyImagesCB( final boolean b ) {
- display_options[ show_taxonomy_images ][ 1 ] = b ? "yes" : "no";
- }
-
- private void setAntialiasScreen( final boolean antialias_screen ) {
- _antialias_screen = antialias_screen;
- }
-
- public void setBackgroundColorGradient( final boolean background_color_gradient ) {
- _background_color_gradient = background_color_gradient;
- }
-
- public void setBaseFontFamilyName( final String base_font_family_name ) {
- _base_font_family_name = base_font_family_name;
+ public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
+ _show_default_node_shapes_internal = show_default_node_shapes_internal;
}
- public void setBaseFontSize( final int base_font_size ) {
- _base_font_size = base_font_size;
+ public void setShowDomainLabels( final boolean show_domain_labels ) {
+ _show_domain_labels = show_domain_labels;
}
- private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
- _cladogram_type = cladogram_type;
+ public void setShowScale( final boolean show_scale ) {
+ _show_scale = show_scale;
}
- public void setColorizeBranches( final boolean b ) {
+ public void setUseStyle( final boolean b ) {
display_options[ use_style ][ 2 ] = b ? "yes" : "no";
}
- public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
- _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
- }
-
- private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
- _default_bootstrap_samples = default_bootstrap_samples;
- }
-
- public void setDefaultNodeFill( final NodeFill default_node_fill ) {
- _default_node_fill = default_node_fill;
- }
-
- public void setDefaultNodeShape( final NodeShape default_node_shape ) {
- _default_node_shape = default_node_shape;
- }
-
- public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
- _default_node_shape_size = default_node_shape_size;
- }
-
- public void setDisplayAsPhylogram( final boolean b ) {
- display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
- _display_colors = display_colors;
- }
-
- public void setDisplayConfidenceValues( final boolean b ) {
- display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setDisplayGeneNames( final boolean b ) {
- display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
+ private int getClickToIndex( final String name ) {
+ int index = -1;
+ if ( name.equals( "edit_info" ) ) {
+ index = Configuration.display_node_data;
+ ForesterUtil
+ .printWarningMessage( Constants.PRG_NAME,
+ "configuration key [edit_info] is deprecated, use [display node data] instead" );
+ }
+ else if ( name.equals( "display_node_data" ) ) {
+ index = Configuration.display_node_data;
+ }
+ else if ( name.equals( "collapse_uncollapse" ) ) {
+ index = Configuration.collapse_uncollapse;
+ }
+ else if ( name.equals( "reroot" ) ) {
+ index = Configuration.reroot;
+ }
+ else if ( name.equals( "subtree" ) ) {
+ index = Configuration.subtree;
+ }
+ else if ( name.equals( "swap" ) ) {
+ index = Configuration.swap;
+ }
+ else if ( name.equals( "sort_descendants" ) ) {
+ index = Configuration.sort_descendents;
+ }
+ else if ( name.equals( "get_ext_descendents_data" ) ) {
+ index = Configuration.get_ext_desc_data;
+ }
+ else if ( name.equals( "display_sequences" ) ) {
+ ForesterUtil
+ .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
+ return DEPRECATED;
+ }
+ else if ( name.equals( "open_seq_web" ) ) {
+ index = Configuration.open_seq_web;
+ }
+ else if ( name.equals( "open_pdb_web" ) ) {
+ index = Configuration.open_pdb_web;
+ }
+ else if ( name.equals( "open_tax_web" ) ) {
+ index = Configuration.open_tax_web;
+ }
+ else if ( name.equals( "blast" ) ) {
+ index = Configuration.blast;
+ }
+ else if ( name.equals( "cut_subtree" ) ) {
+ index = Configuration.cut_subtree;
+ }
+ else if ( name.equals( "copy_subtree" ) ) {
+ index = Configuration.copy_subtree;
+ }
+ else if ( name.equals( "paste_subtree" ) ) {
+ index = Configuration.paste_subtree;
+ }
+ else if ( name.equals( "delete" ) ) {
+ index = Configuration.delete_subtree_or_node;
+ }
+ else if ( name.equals( "add_new_node" ) ) {
+ index = Configuration.add_new_node;
+ }
+ else if ( name.equals( "edit_node_data" ) ) {
+ index = Configuration.edit_node_data;
+ }
+ else if ( name.equals( "select_nodes" ) ) {
+ index = Configuration.select_nodes;
+ }
+ else if ( name.equals( "display_node_popup" ) ) {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME,
+ "configuration key [display_node_popup] is deprecated" );
+ return DEPRECATED;
+ }
+ else if ( name.equals( "custom_option" ) ) {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
+ return DEPRECATED;
+ }
+ else if ( name.equals( "color_subtree" ) ) {
+ index = Configuration.color_subtree;
+ }
+ else if ( name.equals( "change_node_font" ) ) {
+ index = Configuration.change_node_font;
+ }
+ else if ( name.equals( "color_node_font" ) ) {
+ index = Configuration.color_node_font;
+ }
+ else if ( name.equals( "color_subtree" ) ) {
+ index = Configuration.color_subtree;
+ }
+ return index;
}
- public void setDisplayInternalData( final boolean b ) {
- display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
+ private final void initSpeciesColors() {
+ _species_colors = new Hashtable<String, Color>();
+ for( final String[] s : DEFAULT_SPECIES_COLORS ) {
+ _species_colors.put( s[ 0 ], Color.decode( s[ 1 ] ) );
+ }
}
- public void setDisplayNodeNames( final boolean b ) {
- display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
+ private boolean parseBoolean( final String str ) {
+ final String my_str = str.trim().toLowerCase();
+ if ( my_str.equals( "yes" ) || my_str.equals( "true" ) ) {
+ return true;
+ }
+ else if ( my_str.equals( "no" ) || my_str.equals( "false" ) ) {
+ return false;
+ }
+ else {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" );
+ return false;
+ }
}
- public void setDisplaySequenceAcc( final boolean b ) {
- display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
+ private double parseDouble( final String str ) {
+ double d = 0.0;
+ try {
+ d = Double.parseDouble( str.trim() );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
+ d = 0.0;
+ }
+ return d;
}
- public void setDisplaySequenceNames( final boolean b ) {
- display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no";
+ private float parseFloat( final String str ) {
+ float f = 0.0f;
+ try {
+ f = Float.parseFloat( str.trim() );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
+ f = 0.0f;
+ }
+ return f;
}
- public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
- _display_sequence_relations = display_sequence_relations;
+ private int parseInt( final String str ) {
+ int i = -1;
+ try {
+ i = Integer.parseInt( str.trim() );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
+ i = -1;
+ }
+ return i;
}
- public void setDisplaySequenceSymbols( final boolean b ) {
- display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no";
+ private short parseShort( final String str ) {
+ short i = -1;
+ try {
+ i = Short.parseShort( str.trim() );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
+ i = -1;
+ }
+ return i;
}
- public void setDisplayTaxonomyCode( final boolean b ) {
- display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
+ private void processFontFamily( final StringTokenizer st ) {
+ setBaseFontFamilyName( "" );
+ final String font_str = ( ( String ) st.nextElement() ).trim();
+ final String[] fonts = font_str.split( ",+" );
+ for( String font : fonts ) {
+ font = font.replace( '_', ' ' ).trim();
+ if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) {
+ setBaseFontFamilyName( font );
+ break;
+ }
+ }
}
- public void setDisplayTaxonomyCommonNames( final boolean b ) {
- display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
+ /**
+ * read each line of config file, process non-comment lines
+ * @throws IOException
+ */
+ private void readConfig( final BufferedReader conf_in ) throws IOException {
+ String line;
+ do {
+ line = conf_in.readLine();
+ if ( line != null ) {
+ line = line.trim();
+ // skip comments and blank lines
+ if ( !line.startsWith( "#" ) && ( !ForesterUtil.isEmpty( line ) ) ) {
+ // convert runs of spaces to tabs
+ line = line.replaceAll( "\\s+", "\t" );
+ final StringTokenizer st = new StringTokenizer( line, "\t" );
+ setKeyValue( st );
+ }
+ }
+ } while ( line != null );
}
- public void setDisplayTaxonomyImages( final boolean b ) {
- display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
+ private void setAntialiasScreen( final boolean antialias_screen ) {
+ _antialias_screen = antialias_screen;
}
- public void setDisplayTaxonomyScientificNames( final boolean b ) {
- display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
+ private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
+ _cladogram_type = cladogram_type;
}
- public void setDynamicallyHideData( final boolean b ) {
- display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setDisplayMultipleSequenceAlignment( final boolean b ) {
- display_options[ show_mol_seqs ][ 2 ] = b ? "yes" : "no";
+ private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
+ _default_bootstrap_samples = default_bootstrap_samples;
}
private void setEditable( final boolean editable ) {
_editable = editable;
}
- public void setExtDescNodeDataToReturn( final NodeDataField ext_desc_data_to_return ) {
- _ext_desc_data_to_return = ext_desc_data_to_return;
- }
-
private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
_ext_node_data_return_on = ext_node_data_return_on;
}
- public void setFrameXSize( final int frame_x_size ) {
- _frame_x_size = frame_x_size;
- }
-
- public void setFrameYSize( final int frame_y_size ) {
- _frame_y_size = frame_y_size;
- }
-
private void setGraphicsExportX( final int graphics_export_x ) {
_graphics_export_x = graphics_export_x;
}
default_clickto = getClickToIndex( clickto_name );
if ( default_clickto == -1 ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
- + "] for [default_click_to]" );
+ + "] for [default_click_to]" );
default_clickto = 0;
}
else if ( default_clickto == DEPRECATED ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
- + "]" );
+ + "]" );
_ui = UI.UNKNOWN;
}
}
else {
setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
- + "] for [phylogeny_graphics_type]" );
+ + "] for [phylogeny_graphics_type]" );
}
}
else if ( key.equals( "min_confidence_value" ) ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME,
- "value for [pdf_export_line_width] cannot be zero or negative" );
+ "value for [pdf_export_line_width] cannot be zero or negative" );
}
}
else if ( key.equals( "window_initial_size_x" ) ) {
}
else {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "value for [default_number_of_bootstrap_resamples] cannot be negative" );
+ .printWarningMessage( Constants.PRG_NAME,
+ "value for [default_number_of_bootstrap_resamples] cannot be negative" );
}
}
else if ( key.equals( "mafft_local" ) ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
- + "] for [cladogram_type]" );
+ + "] for [cladogram_type]" );
}
}
else if ( key.equals( "non_lined_up_cladogram" ) ) {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
+ .printWarningMessage( Constants.PRG_NAME,
+ "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
}
else if ( key.equals( "hide_controls_and_menus" ) ) {
_hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
else {
setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
- + "] for [overview_placement_type]" );
+ + "] for [overview_placement_type]" );
}
}
else if ( key.equals( "node_label_direction" ) ) {
else {
setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
- + "] for [node_label_direction]" );
+ + "] for [node_label_direction]" );
}
}
else if ( key.equals( "branch_length_value_digits" ) ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
- + "] for [branch_length_value_digits]" );
+ + "] for [branch_length_value_digits]" );
}
}
else if ( key.equals( "confidence_value_digits" ) ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
- + "] for [confidence_value_digits]" );
+ + "] for [confidence_value_digits]" );
}
}
else if ( key.equals( "allow_editing" ) ) {
final boolean r = parseBoolean( ( String ) st.nextElement() );
if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "attempt to extract taxonomies and replace underscores at the same time" );
+ .printWarningMessage( Constants.PRG_NAME,
+ "attempt to extract taxonomies and replace underscores at the same time" );
}
else {
setReplaceUnderscoresInNhParsing( r );
}
else {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "unknown value for \"taxonomy_extraction_in_nh_parsing\": "
- + s
- + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" );
+ .printWarningMessage( Constants.PRG_NAME,
+ "unknown value for \"taxonomy_extraction_in_nh_parsing\": "
+ + s
+ + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" );
}
if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "attempt to extract taxonomies and replace underscores at the same time" );
+ .printWarningMessage( Constants.PRG_NAME,
+ "attempt to extract taxonomies and replace underscores at the same time" );
}
}
else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
- + "] for [default_node_fill]" );
+ + "] for [default_node_fill]" );
}
}
else if ( key.equals( "default_node_shape" ) ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
- + "] for [default_node_shape]" );
+ + "] for [default_node_shape]" );
}
}
else if ( key.equals( "midpoint_reroot" ) ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
- + "] for [ext_descendents_data_to_return]" );
+ + "] for [ext_descendents_data_to_return]" );
}
}
else if ( key.equals( "list_node_data_custom_label" ) || key.equals( "label_for_get_ext_descendents_data" ) ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
- + "] for [ext_descendents_data_to_return_on]" );
+ + "] for [ext_descendents_data_to_return_on]" );
}
}
else if ( key.equals( "vector_data_min_color" ) ) {
else if ( key.equals( "color_branches" ) ) {
key_index = Configuration.use_style;
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" );
+ .printWarningMessage( Constants.PRG_NAME,
+ "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" );
}
else if ( key.equals( "width_branches" ) ) {
key_index = Configuration.width_branches;
}
else if ( key.equals( "annotation_color" ) ) {
getAnnotationColors()
- .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
+ .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
}
else if ( key.equals( "function_color" ) ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME,
- "configuration key [function_color] is deprecated" );
+ "configuration key [function_color] is deprecated" );
}
else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
- + "] in: " + config_filename );
+ + "] in: " + config_filename );
}
}
}
- else {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
- + config_filename );
+ else {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: "
+ + config_filename );
+ }
+ }
+
+ private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) {
+ _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
+ }
+
+ private void setMaxBaseFontSize( final int max_base_font_size ) {
+ _max_base_font_size = max_base_font_size;
+ }
+
+ private void setMinBaseFontSize( final int min_base_font_size ) {
+ _min_base_font_size = min_base_font_size;
+ }
+
+ private void setOvMaxHeight( final short ov_max_height ) {
+ _ov_max_height = ov_max_height;
+ }
+
+ private void setOvMaxWidth( final short ov_max_width ) {
+ _ov_max_width = ov_max_width;
+ }
+
+ private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
+ _ov_placement = ov_placement;
+ }
+
+ private void setPathToLocalFastme( final File path_to_local_fastme ) {
+ _path_to_local_fastme = path_to_local_fastme;
+ }
+
+ private void setPathToLocalMafft( final File path_to_local_mafft ) {
+ _path_to_local_mafft = path_to_local_mafft;
+ }
+
+ private void setPathToLocalRaxml( final File path_to_local_raxml ) {
+ _path_to_local_raxml = path_to_local_raxml;
+ }
+
+ private void setShowAnnotationRefSource( final boolean b ) {
+ _show_annotation_ref_source = b;
+ }
+
+ private void setShowOverview( final boolean show_overview ) {
+ _show_overview = show_overview;
+ }
+
+ private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
+ _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
+ }
+
+ boolean displaySequenceRelations() {
+ return _display_sequence_relations;
+ }
+
+ boolean doCheckOption( final int which ) {
+ return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
+ || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
+ }
+
+ boolean doDisplayClickToOption( final int which ) {
+ return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
+ }
+
+ boolean doDisplayOption( final int which ) {
+ return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
+ }
+
+ /**
+ * Will attempt to use the phylogeny to determine whether to check
+ * this or not (e.g. phylogram)
+ *
+ */
+ boolean doGuessCheckOption( final int which ) {
+ return display_options[ which ][ 2 ].equals( "?" );
+ }
+
+ Map<String, Color> getAnnotationColors() {
+ if ( _annotation_colors == null ) {
+ _annotation_colors = new Hashtable<String, Color>();
+ }
+ return _annotation_colors;
+ }
+
+ int getBaseFontSize() {
+ return _base_font_size;
+ }
+
+ CLADOGRAM_TYPE getCladogramType() {
+ return _cladogram_type;
+ }
+
+ int getClickToOptionsCount() {
+ return clickto_options.length;
+ }
+
+ String getClickToTitle( final int which ) {
+ return clickto_options[ which ][ 0 ];
+ }
+
+ int getDefaultDisplayClicktoOption() {
+ return default_clickto;
+ }
+
+ SortedMap<String, Color> getDisplayColors() {
+ return _display_colors;
+ }
+
+ String getDisplayTitle( final int which ) {
+ return display_options[ which ][ 0 ];
+ }
+
+ Map<String, Color> getDomainColors() {
+ if ( _domain_colors == null ) {
+ _domain_colors = new Hashtable<String, Color>();
}
+ return _domain_colors;
}
- private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) {
- _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
+ int getGraphicsExportX() {
+ return _graphics_export_x;
}
- final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) {
- _line_up_renderable_node_data = line_up_renderable_node_data;
+ int getGraphicsExportY() {
+ return _graphics_export_y;
}
- private void setMaxBaseFontSize( final int max_base_font_size ) {
- _max_base_font_size = max_base_font_size;
+ Color getGuiBackgroundColor() {
+ return _gui_background_color;
}
- public void setMidpointReroot( final boolean midpoint_root ) {
- _midpoint_root = midpoint_root;
+ Color getGuiButtonBackgroundColor() {
+ return _gui_button_background_color;
}
- private void setMinBaseFontSize( final int min_base_font_size ) {
- _min_base_font_size = min_base_font_size;
+ Color getGuiButtonBorderColor() {
+ return _gui_button_border_color;
}
- public void setMinConfidenceValue( final double min_confidence_value ) {
- _min_confidence_value = min_confidence_value;
+ Color getGuiButtonTextColor() {
+ return _gui_button_text_color;
}
- public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
- _node_label_direction = node_label_direction;
+ Color getGuiCheckboxAndButtonActiveColor() {
+ return _gui_checkbox_and_button_active_color;
}
- public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
- _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
+ Color getGuiCheckboxTextColor() {
+ return _gui_checkbox_text_color;
}
- public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
- _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
+ Color getGuiMenuBackgroundColor() {
+ return _gui_menu_background_color;
}
- private void setOvMaxHeight( final short ov_max_height ) {
- _ov_max_height = ov_max_height;
+ Color getGuiMenuTextColor() {
+ return _gui_menu_text_color;
}
- private void setOvMaxWidth( final short ov_max_width ) {
- _ov_max_width = ov_max_width;
+ int getMaxBaseFontSize() {
+ return _max_base_font_size;
}
- private void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) {
- _ov_placement = ov_placement;
+ int getMinBaseFontSize() {
+ return _min_base_font_size;
}
- private void setPathToLocalFastme( final File path_to_local_fastme ) {
- _path_to_local_fastme = path_to_local_fastme;
+ double getMinConfidenceValue() {
+ return _min_confidence_value;
}
- private void setPathToLocalMafft( final File path_to_local_mafft ) {
- _path_to_local_mafft = path_to_local_mafft;
+ NODE_LABEL_DIRECTION getNodeLabelDirection() {
+ return _node_label_direction;
}
- private void setPathToLocalRaxml( final File path_to_local_raxml ) {
- _path_to_local_raxml = path_to_local_raxml;
+ short getNumberOfDigitsAfterCommaForBranchLengthValues() {
+ return _number_of_digits_after_comma_for_branch_length_values;
}
- public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
- _phylogeny_graphics_type = phylogeny_graphics_type;
+ short getNumberOfDigitsAfterCommaForConfidenceValues() {
+ return _number_of_digits_after_comma_for_confidence_values;
}
- public void setPrintLineWidth( final float print_line_width ) {
- _print_line_width = print_line_width;
+ short getOvMaxHeight() {
+ return _ov_max_height;
}
- public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
- _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
+ short getOvMaxWidth() {
+ return _ov_max_width;
}
- final public void setRightLineUpDomains( final boolean right_align_domains ) {
- _right_align_domains = right_align_domains;
+ OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
+ return _ov_placement;
}
- private void setShowAnnotationRefSource( final boolean b ) {
- _show_annotation_ref_source = b;
+ PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
+ return _phylogeny_graphics_type;
}
- public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
- _show_default_node_shapes_external = show_default_node_shapes_external;
+ float getPrintLineWidth() {
+ return _print_line_width;
}
- public void setShowDefaultNodeShapesForMarkedNodes( final boolean show_default_node_shapes_for_marked_nodes ) {
- _show_default_node_shapes_for_marked_nodes = show_default_node_shapes_for_marked_nodes;
+ Hashtable<String, Color> getSequenceColors() {
+ if ( _sequence_colors == null ) {
+ _sequence_colors = new Hashtable<String, Color>();
+ }
+ return _sequence_colors;
}
- public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
- _show_default_node_shapes_internal = show_default_node_shapes_internal;
+ Hashtable<String, Color> getSpeciesColors() {
+ if ( _species_colors == null ) {
+ initSpeciesColors();
+ }
+ return _species_colors;
}
- public void setShowDomainLabels( final boolean show_domain_labels ) {
- _show_domain_labels = show_domain_labels;
+ final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
+ return _taxonomy_extraction;
}
- private void setShowOverview( final boolean show_overview ) {
- _show_overview = show_overview;
+ boolean isAntialiasScreen() {
+ return _antialias_screen;
}
- public void setShowScale( final boolean show_scale ) {
- _show_scale = show_scale;
+ /**
+ * Convenience method.
+ *
+ * @return true if value in configuration file was 'yes'
+ */
+ boolean isDrawAsPhylogram() {
+ return doCheckOption( display_as_phylogram );
}
- final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
- _taxonomy_extraction = taxonomy_extraction;
+ boolean isEditable() {
+ return _editable;
}
- public void setUseStyle( final boolean b ) {
- display_options[ use_style ][ 2 ] = b ? "yes" : "no";
+ /**
+ * Only used by ArchaeoptryxE.
+ *
+ */
+ boolean isHideControlPanelAndMenubar() {
+ return _hide_controls_and_menus;
}
- private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
- _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
+ boolean isInternalNumberAreConfidenceForNhParsing() {
+ return _internal_number_are_confidence_for_nh_parsing;
}
- public boolean isAllowThickStrokes() {
- return _allow_thick_strokes;
+ boolean isReplaceUnderscoresInNhParsing() {
+ return _nh_parsing_replace_underscores;
+ }
+
+ boolean isShowOverview() {
+ return _show_overview;
+ }
+
+ boolean isShowScale() {
+ return _show_scale;
+ }
+
+ final boolean isUseNativeUI() {
+ if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) {
+ _ui = UI.NATIVE;
+ }
+ return _ui == UI.NATIVE;
+ }
+
+ /**
+ * Only used by ArchaeoptryxE.
+ *
+ */
+ boolean isUseTabbedDisplay() {
+ return _use_tabbed_display;
+ }
+
+ boolean isValidatePhyloXmlAgainstSchema() {
+ return _validate_against_phyloxml_xsd_schema;
+ }
+
+ final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
+ _taxonomy_extraction = taxonomy_extraction;
+ }
+
+ static String getDefaultFontFamilyName() {
+ return DEFAULT_FONT_FAMILY;
}
}
final static String PRG_DATE = "150306";
final static String DEFAULT_CONFIGURATION_FILE_NAME = "_aptx_configuration_file";
final static String[] DEFAULT_FONT_CHOICES = { "Arial", "Helvetica",
- "Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" };
+ "Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" };
final static boolean VERBOSE_DEFAULT = false;
final static int DOMAIN_STRUCTURE_DEFAULT_WIDTH = 100;
final static String AUTHOR_EMAIL = "phyloxml@gmail.com";
final class ControlPanel extends JPanel implements ActionListener {
+ enum NodeClickAction {
+ ADD_NEW_NODE,
+ BLAST,
+ COLLAPSE,
+ COLOR_SUBTREE,
+ COPY_SUBTREE,
+ CUT_SUBTREE,
+ DELETE_NODE_OR_SUBTREE,
+ EDIT_NODE_DATA,
+ GET_EXT_DESC_DATA,
+ OPEN_PDB_WEB,
+ OPEN_SEQ_WEB,
+ OPEN_TAX_WEB,
+ PASTE_SUBTREE,
+ REROOT,
+ SELECT_NODES,
+ SHOW_DATA,
+ SORT_DESCENDENTS,
+ SUBTREE,
+ SWAP,
+ CHANGE_NODE_FONT,
+ COLOR_NODE_FONT;
+ }
final static Font jcb_bold_font = new Font( Configuration.getDefaultFontFamilyName(),
Font.BOLD,
9 );
}
}
- public JCheckBox getColorAccSpeciesCb() {
- return _color_acc_species;
- }
-
public JCheckBox getColorAccSequenceCb() {
return _color_acc_sequence;
}
- public JCheckBox getUseVisualStylesCb() {
- return _use_visual_styles_cb;
+ public JCheckBox getColorAccSpeciesCb() {
+ return _color_acc_species;
}
public JCheckBox getDisplayAsPhylogramCb() {
return _show_events;
}
+ public JCheckBox getUseVisualStylesCb() {
+ return _use_visual_styles_cb;
+ }
+
public JCheckBox getWriteConfidenceCb() {
return _write_confidence;
}
+ public boolean isShowMolSequences() {
+ return ( ( _show_mol_seqs != null ) && _show_mol_seqs.isSelected() );
+ }
+
public boolean isShowProperties() {
return ( ( _show_properties_cb != null ) && _show_properties_cb.isSelected() );
}
} );
}
- void activateButtonToReturnToSuperTree( int index ) {
- --index;
- if ( index > 0 ) {
- _return_to_super_tree.setText( RETURN_TO_SUPER_TREE_TEXT + " " + index );
- }
- else {
- _return_to_super_tree.setText( RETURN_TO_SUPER_TREE_TEXT );
+ 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() );
}
- _return_to_super_tree.setForeground( getConfiguration().getGuiCheckboxAndButtonActiveColor() );
- _return_to_super_tree.setEnabled( true );
}
- /**
- * Add zoom and quick edit buttons. (Last modified 8/9/04)
- */
- void addButtons() {
+ /* GUILHEM_BEG */
+ private void addSequenceRelationBlock() {
final JLabel spacer = new JLabel( "" );
- spacer.setOpaque( false );
+ spacer.setSize( 1, 1 );
add( spacer );
- final JPanel x_panel = new JPanel( new GridLayout( 1, 1, 0, 0 ) );
- final JPanel y_panel = new JPanel( new GridLayout( 1, 3, 0, 0 ) );
- final JPanel z_panel = new JPanel( new GridLayout( 1, 1, 0, 0 ) );
- if ( !getConfiguration().isUseNativeUI() ) {
- x_panel.setBackground( getBackground() );
- y_panel.setBackground( getBackground() );
- z_panel.setBackground( getBackground() );
+ 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() );
}
- add( _zoom_label = new JLabel( "Zoom:" ) );
- customizeLabel( _zoom_label, getConfiguration() );
- add( x_panel );
- add( y_panel );
- add( z_panel );
- if ( getConfiguration().isUseNativeUI() ) {
- _zoom_in_x = new JButton( "+" );
- _zoom_out_x = new JButton( "-" );
+ _sequence_relation_type_box.setRenderer( new ListCellRenderer<Object>() {
+
+ @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 ) );
}
- else {
- _zoom_in_x = new JButton( "X+" );
- _zoom_out_x = new JButton( "X-" );
+ }// addSequenceRelationBlock
+
+ /* GUILHEM_END */
+ private List<Boolean> getIsDrawPhylogramList() {
+ return _draw_phylogram;
+ }
+
+ // This takes care of ArchaeopteryxE-issue.
+ // Can, and will, return null prior to ArchaeopteryxE initialization completion.
+ final private MainFrame getMainFrame() {
+ MainFrame mf = getMainPanel().getMainFrame();
+ if ( mf == null ) {
+ // Must be "E" applet version.
+ final ArchaeopteryxE e = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
+ if ( e.getMainPanel() == null ) {
+ return null;
+ }
+ mf = e.getMainPanel().getMainFrame();
}
- _zoom_in_y = new JButton( "Y+" );
- _zoom_out_y = new JButton( "Y-" );
- _show_whole = new JButton( "F" );
- _show_whole.setToolTipText( "To fit the complete phylogeny to the current display size [F or Home]" );
- _zoom_in_x.setToolTipText( "To zoom in horizontally [Shift+cursor-right]" );
- _zoom_in_y.setToolTipText( "To zoom in vertically [Shift+cursor-up]" );
- _zoom_out_x.setToolTipText( "To zoom out horizontally [Shift+cursor-left]" );
- _zoom_out_y.setToolTipText( "To zoom out vertically [Shift+cursor-down]" );
- if ( getConfiguration().isUseNativeUI() && ForesterUtil.isMac() ) {
- _zoom_out_x.setPreferredSize( new Dimension( 55, 10 ) );
- _zoom_in_x.setPreferredSize( new Dimension( 55, 10 ) );
+ return mf;
+ }
+
+ private void init() {
+ _draw_phylogram = new ArrayList<Boolean>();
+ setSpeciesColors( new HashMap<String, Color>() );
+ setSequenceColors( new HashMap<String, Color>() );
+ setAnnotationColors( new HashMap<String, Color>() );
+ }
+
+ private boolean isDrawPhylogram( final int index ) {
+ return getIsDrawPhylogramList().get( index );
+ }
+
+ private void search0( final MainPanel main_panel, final Phylogeny tree, final String query_str ) {
+ getSearchFoundCountsLabel0().setVisible( true );
+ getSearchResetButton0().setEnabled( true );
+ getSearchResetButton0().setVisible( true );
+ String[] queries = null;
+ Set<PhylogenyNode> nodes = null;
+ if ( ( query_str.indexOf( ',' ) >= 0 ) && !getOptions().isSearchWithRegex() ) {
+ queries = query_str.split( ",+" );
}
else {
- _zoom_out_x.setPreferredSize( new Dimension( 10, 10 ) );
- _zoom_in_x.setPreferredSize( new Dimension( 10, 10 ) );
+ queries = new String[ 1 ];
+ queries[ 0 ] = query_str.trim();
}
- _zoom_out_y.setPreferredSize( new Dimension( 10, 10 ) );
- _zoom_in_y.setPreferredSize( new Dimension( 10, 10 ) );
- _show_whole.setPreferredSize( new Dimension( 10, 10 ) );
- _return_to_super_tree = new JButton( RETURN_TO_SUPER_TREE_TEXT );
- _return_to_super_tree.setEnabled( false );
- _order = new JButton( "Order Subtrees" );
- _uncollapse_all = new JButton( "Uncollapse All" );
- addJButton( _zoom_in_y, x_panel );
- addJButton( _zoom_out_x, y_panel );
- addJButton( _show_whole, y_panel );
- addJButton( _zoom_in_x, y_panel );
- addJButton( _zoom_out_y, z_panel );
- if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
- setUpControlsForDomainStrucures();
+ if ( ( queries != null ) && ( queries.length > 0 ) ) {
+ nodes = new HashSet<PhylogenyNode>();
+ for( String query : queries ) {
+ if ( ForesterUtil.isEmpty( query ) ) {
+ continue;
+ }
+ query = query.trim();
+ final TreePanel tp = getMainPanel().getCurrentTreePanel();
+ if ( ( query.indexOf( '+' ) > 0 ) && !getOptions().isSearchWithRegex() ) {
+ nodes.addAll( PhylogenyMethods.searchDataLogicalAnd( query.split( "\\++" ),
+ tree,
+ getOptions().isSearchCaseSensitive(),
+ !getOptions().isMatchWholeTermsOnly(),
+ isShowDomainArchitectures(),
+ tp != null ? Math.pow( 10,
+ tp.getDomainStructureEvalueThresholdExp() )
+ : 0 ) );
+ }
+ else {
+ nodes.addAll( PhylogenyMethods.searchData( query,
+ tree,
+ getOptions().isSearchCaseSensitive(),
+ !getOptions().isMatchWholeTermsOnly(),
+ getOptions().isSearchWithRegex(),
+ isShowDomainArchitectures(),
+ tp != null ? Math.pow( 10, tp
+ .getDomainStructureEvalueThresholdExp() ) : 0 ) );
+ }
+ }
+ if ( getOptions().isInverseSearchResult() ) {
+ final List<PhylogenyNode> all = PhylogenyMethods.obtainAllNodesAsList( tree );
+ all.removeAll( nodes );
+ nodes = new HashSet<PhylogenyNode>();
+ nodes.addAll( all );
+ }
+ }
+ if ( ( nodes != null ) && ( nodes.size() > 0 ) ) {
+ main_panel.getCurrentTreePanel().setFoundNodes0( new HashSet<Long>() );
+ for( final PhylogenyNode node : nodes ) {
+ main_panel.getCurrentTreePanel().getFoundNodes0().add( node.getId() );
+ }
+ setSearchFoundCountsOnLabel0( nodes.size() );
+ }
+ else {
+ setSearchFoundCountsOnLabel0( 0 );
+ searchReset0();
}
- final JLabel spacer2 = new JLabel( "" );
- add( spacer2 );
- addJButton( _return_to_super_tree, this );
- addJButton( _order, this );
- addJButton( _uncollapse_all, this );
- final JLabel spacer3 = new JLabel( "" );
- add( spacer3 );
- setVisibilityOfDomainStrucureControls();
}
- void addCheckbox( final int which, final String title ) {
- final JPanel ch_panel = new JPanel( new BorderLayout( 0, 0 ) );
- switch ( which ) {
- case Configuration.display_as_phylogram:
- _display_as_phylogram_cb = new JCheckBox( title );
- getDisplayAsPhylogramCb().setToolTipText( "To switch between phylogram and cladogram display" );
- addJCheckBox( getDisplayAsPhylogramCb(), ch_panel );
- add( ch_panel );
- break;
- case Configuration.display_internal_data:
- _display_internal_data = new JCheckBox( title );
- _display_internal_data.setToolTipText( "To allow or disallow display of internal labels" );
- addJCheckBox( _display_internal_data, ch_panel );
- add( ch_panel );
- break;
- case Configuration.color_according_to_species:
- _color_acc_species = new JCheckBox( title );
- _color_acc_species.setToolTipText( "To colorize node labels as a function of taxonomy" );
- addJCheckBox( _color_acc_species, ch_panel );
- add( ch_panel );
- break;
- case Configuration.color_according_to_sequence:
- _color_acc_sequence = new JCheckBox( title );
- _color_acc_sequence.setToolTipText( "To colorize node labels as a function of sequence name" );
- addJCheckBox( _color_acc_sequence, ch_panel );
- add( ch_panel );
- break;
- case Configuration.color_according_to_annotation:
- _color_according_to_annotation = new JCheckBox( title );
- _color_according_to_annotation
- .setToolTipText( "To colorize sequence annotation labels as a function of sequence annotation" );
- addJCheckBox( _color_according_to_annotation, ch_panel );
- add( ch_panel );
- break;
- case Configuration.show_node_names:
- _show_node_names = new JCheckBox( title );
- addJCheckBox( _show_node_names, ch_panel );
- add( ch_panel );
- break;
- case Configuration.show_taxonomy_scientific_names:
- _show_taxo_scientific_names = new JCheckBox( title );
- addJCheckBox( _show_taxo_scientific_names, ch_panel );
- add( ch_panel );
- break;
- case Configuration.show_taxonomy_common_names:
- _show_taxo_common_names = new JCheckBox( title );
- addJCheckBox( _show_taxo_common_names, ch_panel );
- add( ch_panel );
- break;
- case Configuration.show_tax_code:
- _show_taxo_code = new JCheckBox( title );
- addJCheckBox( _show_taxo_code, ch_panel );
- add( ch_panel );
- break;
- case Configuration.show_taxonomy_images:
- _show_taxo_images_cb = new JCheckBox( title );
- addJCheckBox( _show_taxo_images_cb, ch_panel );
- add( ch_panel );
- break;
- case Configuration.show_binary_characters:
- _show_binary_characters = new JCheckBox( title );
- addJCheckBox( _show_binary_characters, ch_panel );
- add( ch_panel );
- break;
- case Configuration.show_annotation:
- _show_annotation = new JCheckBox( title );
- addJCheckBox( _show_annotation, ch_panel );
- add( ch_panel );
- break;
- case Configuration.show_binary_character_counts:
- _show_binary_character_counts = new JCheckBox( title );
- addJCheckBox( _show_binary_character_counts, ch_panel );
- add( ch_panel );
- break;
- case Configuration.write_confidence_values:
- _write_confidence = new JCheckBox( title );
- addJCheckBox( getWriteConfidenceCb(), ch_panel );
- add( ch_panel );
- break;
- case Configuration.write_events:
- _show_events = new JCheckBox( title );
- addJCheckBox( getShowEventsCb(), ch_panel );
- add( ch_panel );
- break;
- case Configuration.use_style:
- _use_visual_styles_cb = new JCheckBox( title );
- getUseVisualStylesCb()
- .setToolTipText( "To use visual styles (node colors, fonts) and branch colors, if present" );
- addJCheckBox( getUseVisualStylesCb(), ch_panel );
- add( ch_panel );
- break;
- case Configuration.width_branches:
- _width_branches = new JCheckBox( title );
- _width_branches.setToolTipText( "To use branch width values, if present" );
- addJCheckBox( _width_branches, ch_panel );
- add( ch_panel );
- break;
- case Configuration.write_branch_length_values:
- _write_branch_length_values = new JCheckBox( title );
- addJCheckBox( _write_branch_length_values, ch_panel );
- add( ch_panel );
- break;
- case Configuration.show_domain_architectures:
- _show_domain_architectures = new JCheckBox( title );
- addJCheckBox( _show_domain_architectures, ch_panel );
- add( ch_panel );
- break;
- case Configuration.show_mol_seqs:
- _show_mol_seqs = new JCheckBox( title );
- addJCheckBox( _show_mol_seqs, ch_panel );
- add( ch_panel );
- break;
- case Configuration.show_seq_names:
- _show_seq_names = new JCheckBox( title );
- addJCheckBox( _show_seq_names, ch_panel );
- add( ch_panel );
- break;
- case Configuration.show_gene_names:
- _show_gene_names = new JCheckBox( title );
- addJCheckBox( _show_gene_names, ch_panel );
- add( ch_panel );
- break;
- case Configuration.show_seq_symbols:
- _show_seq_symbols = new JCheckBox( title );
- addJCheckBox( _show_seq_symbols, ch_panel );
- add( ch_panel );
- break;
- case Configuration.show_sequence_acc:
- _show_sequence_acc = new JCheckBox( title );
- addJCheckBox( _show_sequence_acc, ch_panel );
- add( ch_panel );
- break;
- case Configuration.dynamically_hide_data:
- _dynamically_hide_data = new JCheckBox( title );
- getDynamicallyHideData().setToolTipText( "To hide labels depending on expected visibility" );
- addJCheckBox( getDynamicallyHideData(), ch_panel );
- add( ch_panel );
- break;
- case Configuration.node_data_popup:
- _node_desc_popup_cb = new JCheckBox( title );
- getNodeDescPopupCb().setToolTipText( "To enable mouse rollover display of basic node data" );
- addJCheckBox( getNodeDescPopupCb(), ch_panel );
- add( ch_panel );
- break;
- case Configuration.show_relation_confidence:
- _seq_relation_confidence_switch = new JCheckBox( title );
- addJCheckBox( _seq_relation_confidence_switch, ch_panel );
- add( ch_panel );
- break;
- case Configuration.show_vector_data:
- _show_vector_data_cb = new JCheckBox( title );
- addJCheckBox( _show_vector_data_cb, ch_panel );
- add( ch_panel );
- break;
- case Configuration.show_properties:
- _show_properties_cb = new JCheckBox( title );
- addJCheckBox( _show_properties_cb, ch_panel );
- add( ch_panel );
- break;
- default:
- throw new RuntimeException( "unknown checkbox: " + which );
+ private void search1( final MainPanel main_panel, final Phylogeny tree, final String query_str ) {
+ getSearchFoundCountsLabel1().setVisible( true );
+ getSearchResetButton1().setEnabled( true );
+ getSearchResetButton1().setVisible( true );
+ String[] queries = null;
+ Set<PhylogenyNode> nodes = null;
+ if ( ( query_str.indexOf( ',' ) >= 0 ) && !getOptions().isSearchWithRegex() ) {
+ queries = query_str.split( ",+" );
}
- }// addCheckbox
-
- void addJButton( final JButton jb, final JPanel p ) {
- jb.setFocusPainted( false );
- jb.setFont( ControlPanel.jcb_font );
- if ( !_configuration.isUseNativeUI() ) {
- jb.setBorder( BorderFactory.createLineBorder( getConfiguration().getGuiButtonBorderColor() ) );
- jb.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
- jb.setForeground( getConfiguration().getGuiButtonTextColor() );
+ else {
+ queries = new String[ 1 ];
+ queries[ 0 ] = query_str.trim();
}
- p.add( jb );
- jb.addActionListener( this );
- }
-
- void addJCheckBox( final JCheckBox jcb, final JPanel p ) {
- jcb.setFocusPainted( false );
- jcb.setFont( ControlPanel.jcb_font );
- if ( !_configuration.isUseNativeUI() ) {
- jcb.setBackground( getConfiguration().getGuiBackgroundColor() );
- jcb.setForeground( getConfiguration().getGuiCheckboxTextColor() );
+ if ( ( queries != null ) && ( queries.length > 0 ) ) {
+ nodes = new HashSet<PhylogenyNode>();
+ for( String query : queries ) {
+ if ( ForesterUtil.isEmpty( query ) ) {
+ continue;
+ }
+ query = query.trim();
+ final TreePanel tp = getMainPanel().getCurrentTreePanel();
+ if ( ( query.indexOf( '+' ) > 0 ) && !getOptions().isSearchWithRegex() ) {
+ nodes.addAll( PhylogenyMethods.searchDataLogicalAnd( query.split( "\\++" ),
+ tree,
+ getOptions().isSearchCaseSensitive(),
+ !getOptions().isMatchWholeTermsOnly(),
+ isShowDomainArchitectures(),
+ tp != null ? Math.pow( 10,
+ tp.getDomainStructureEvalueThresholdExp() )
+ : 0 ) );
+ }
+ else {
+ nodes.addAll( PhylogenyMethods.searchData( query,
+ tree,
+ getOptions().isSearchCaseSensitive(),
+ !getOptions().isMatchWholeTermsOnly(),
+ getOptions().isSearchWithRegex(),
+ isShowDomainArchitectures(),
+ tp != null ? Math.pow( 10, tp
+ .getDomainStructureEvalueThresholdExp() ) : 0 ) );
+ }
+ }
+ if ( getOptions().isInverseSearchResult() ) {
+ final List<PhylogenyNode> all = PhylogenyMethods.obtainAllNodesAsList( tree );
+ all.removeAll( nodes );
+ nodes = new HashSet<PhylogenyNode>();
+ nodes.addAll( all );
+ }
}
- p.add( jcb, "Center" );
- jcb.addActionListener( this );
- }
-
- void addJTextField( final JTextField tf, final JPanel p ) {
- if ( !_configuration.isUseNativeUI() ) {
- tf.setForeground( getConfiguration().getGuiBackgroundColor() );
- tf.setFont( ControlPanel.jcb_font );
+ if ( ( nodes != null ) && ( nodes.size() > 0 ) ) {
+ main_panel.getCurrentTreePanel().setFoundNodes1( new HashSet<Long>() );
+ for( final PhylogenyNode node : nodes ) {
+ main_panel.getCurrentTreePanel().getFoundNodes1().add( node.getId() );
+ }
+ setSearchFoundCountsOnLabel1( nodes.size() );
+ }
+ else {
+ setSearchFoundCountsOnLabel1( 0 );
+ searchReset1();
}
- p.add( tf );
- tf.addActionListener( this );
}
- void deactivateButtonToReturnToSuperTree() {
- _return_to_super_tree.setText( RETURN_TO_SUPER_TREE_TEXT );
- _return_to_super_tree.setForeground( getConfiguration().getGuiButtonTextColor() );
- _return_to_super_tree.setEnabled( false );
+ private void setDrawPhylogram( final int index, final boolean b ) {
+ getIsDrawPhylogramList().set( index, b );
}
- void displayedPhylogenyMightHaveChanged( final boolean recalc_longest_ext_node_info ) {
- if ( ( _mainpanel != null )
- && ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
- if ( getOptions().isShowOverview() ) {
- _mainpanel.getCurrentTreePanel().updateOvSizes();
+ 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;
}
- _mainpanel.getCurrentTreePanel().recalculateMaxDistanceToRoot();
- setVisibilityOfDomainStrucureControls();
- updateDomainStructureEvaluethresholdDisplay();
- _mainpanel.getCurrentTreePanel().calculateScaleDistance();
- _mainpanel.getCurrentTreePanel().calcMaxDepth();
- _mainpanel.adjustJScrollPane();
- if ( recalc_longest_ext_node_info ) {
- _mainpanel.getCurrentTreePanel().initNodeData();
- _mainpanel.getCurrentTreePanel().calculateLongestExtNodeInfo();
+ 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;
}
- _mainpanel.getCurrentTreePanel().repaint();
- // _mainpanel.getCurrentTreePanel().setUpUrtFactors();
+ 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++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.subtree ) ) {
+ _subtree_cb_item = cb_index;
+ addClickToOption( Configuration.subtree, _configuration.getClickToTitle( Configuration.subtree ) );
+ if ( default_option == Configuration.subtree ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.swap ) ) {
+ _swap_cb_item = cb_index;
+ addClickToOption( Configuration.swap, _configuration.getClickToTitle( Configuration.swap ) );
+ if ( default_option == Configuration.swap ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.sort_descendents ) ) {
+ _sort_descendents_item = cb_index;
+ addClickToOption( Configuration.sort_descendents,
+ _configuration.getClickToTitle( Configuration.sort_descendents ) );
+ if ( default_option == Configuration.sort_descendents ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.color_node_font ) ) {
+ _color_node_font_item = cb_index;
+ addClickToOption( Configuration.color_node_font,
+ _configuration.getClickToTitle( Configuration.color_node_font ) );
+ if ( default_option == Configuration.color_node_font ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.change_node_font ) ) {
+ _change_node_font_item = cb_index;
+ addClickToOption( Configuration.change_node_font,
+ _configuration.getClickToTitle( Configuration.change_node_font ) );
+ if ( default_option == Configuration.change_node_font ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.color_subtree ) ) {
+ _color_subtree_cb_item = cb_index;
+ addClickToOption( Configuration.color_subtree, _configuration.getClickToTitle( Configuration.color_subtree ) );
+ if ( default_option == Configuration.color_subtree ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.open_seq_web ) ) {
+ _open_seq_web_item = cb_index;
+ addClickToOption( Configuration.open_seq_web, _configuration.getClickToTitle( Configuration.open_seq_web ) );
+ if ( default_option == Configuration.open_seq_web ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.open_pdb_web ) ) {
+ _open_pdb_item = cb_index;
+ addClickToOption( Configuration.open_pdb_web, _configuration.getClickToTitle( Configuration.open_pdb_web ) );
+ if ( default_option == Configuration.open_pdb_web ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.open_tax_web ) ) {
+ _open_tax_web_item = cb_index;
+ addClickToOption( Configuration.open_tax_web, _configuration.getClickToTitle( Configuration.open_tax_web ) );
+ if ( default_option == Configuration.open_tax_web ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.blast ) ) {
+ _blast_item = cb_index;
+ addClickToOption( Configuration.blast, _configuration.getClickToTitle( Configuration.blast ) );
+ if ( default_option == Configuration.blast ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.select_nodes ) ) {
+ _select_nodes_item = cb_index;
+ addClickToOption( Configuration.select_nodes, _configuration.getClickToTitle( Configuration.select_nodes ) );
+ if ( default_option == Configuration.select_nodes ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.get_ext_desc_data ) ) {
+ _get_ext_desc_data = cb_index;
+ if ( !ForesterUtil.isEmpty( getConfiguration().getLabelForGetExtDescendentsData() ) ) {
+ addClickToOption( Configuration.get_ext_desc_data, getConfiguration()
+ .getLabelForGetExtDescendentsData() );
+ }
+ else {
+ addClickToOption( Configuration.get_ext_desc_data,
+ getConfiguration().getClickToTitle( Configuration.get_ext_desc_data ) );
+ }
+ if ( default_option == Configuration.get_ext_desc_data ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( getOptions().isEditable() ) {
+ if ( _configuration.doDisplayClickToOption( Configuration.cut_subtree ) ) {
+ _cut_subtree_item = cb_index;
+ addClickToOption( Configuration.cut_subtree, _configuration.getClickToTitle( Configuration.cut_subtree ) );
+ if ( default_option == Configuration.cut_subtree ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.copy_subtree ) ) {
+ _copy_subtree_item = cb_index;
+ addClickToOption( Configuration.copy_subtree,
+ _configuration.getClickToTitle( Configuration.copy_subtree ) );
+ if ( default_option == Configuration.copy_subtree ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.paste_subtree ) ) {
+ _paste_subtree_item = cb_index;
+ addClickToOption( Configuration.paste_subtree,
+ _configuration.getClickToTitle( Configuration.paste_subtree ) );
+ if ( default_option == Configuration.paste_subtree ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.delete_subtree_or_node ) ) {
+ _delete_node_or_subtree_item = cb_index;
+ addClickToOption( Configuration.delete_subtree_or_node,
+ _configuration.getClickToTitle( Configuration.delete_subtree_or_node ) );
+ if ( default_option == Configuration.delete_subtree_or_node ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.add_new_node ) ) {
+ _add_new_node_item = cb_index;
+ addClickToOption( Configuration.add_new_node,
+ _configuration.getClickToTitle( Configuration.add_new_node ) );
+ if ( default_option == Configuration.add_new_node ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ if ( _configuration.doDisplayClickToOption( Configuration.edit_node_data ) ) {
+ _edit_node_data_item = cb_index;
+ addClickToOption( Configuration.edit_node_data,
+ _configuration.getClickToTitle( Configuration.edit_node_data ) );
+ if ( default_option == Configuration.edit_node_data ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+ }
+ }
+ // Set default selection and its action
+ _click_to_combobox.setSelectedIndex( selected_index );
+ setClickToAction( selected_index );
}
- void endClickToOptions() {
- _click_to_combobox.addActionListener( this );
- }
-
- /**
- * Indicates what action should be execute when a node is clicked
- *
- * @return the click-on action
- */
- NodeClickAction getActionWhenNodeClicked() {
- return _action_when_node_clicked;
- }
-
- Map<Integer, String> getAllClickToItems() {
- return _all_click_to_names;
- }
-
- Map<String, Color> getAnnotationColors() {
- return _annotation_colors;
- }
-
- Configuration getConfiguration() {
- return _configuration;
- }
-
- TreePanel getCurrentTreePanel() {
- return getMainPanel().getCurrentTreePanel();
- }
-
- MainPanel getMainPanel() {
- return _mainpanel;
- }
-
- Options getOptions() {
- return getMainPanel().getOptions();
- }
-
- JLabel getSearchFoundCountsLabel0() {
- return _search_found_label_0;
- }
-
- JLabel getSearchFoundCountsLabel1() {
- return _search_found_label_1;
- }
-
- JButton getSearchResetButton0() {
- return _search_reset_button_0;
- }
-
- JButton getSearchResetButton1() {
- return _search_reset_button_1;
- }
-
- JTextField getSearchTextField0() {
- return _search_tf_0;
- }
-
- JTextField getSearchTextField1() {
- return _search_tf_1;
- }
-
- List<String> getSingleClickToNames() {
- return _click_to_names;
- }
-
- Map<String, Color> getSpeciesColors() {
- return _species_colors;
- }
-
- Map<String, Color> getSequenceColors() {
- return _sequence_colors;
- }
-
- 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 isColorAccordingToSequence() {
- return ( ( _color_acc_sequence != null ) && _color_acc_sequence.isSelected() );
- }
-
- boolean isUseVisualStyles() {
- return ( ( ( getUseVisualStylesCb() != null ) && getUseVisualStylesCb().isSelected() ) || ( ( getUseVisualStylesCb() == null ) && _color_branches ) );
- }
-
- boolean isDrawPhylogram() {
- return isDrawPhylogram( getMainPanel().getCurrentTabIndex() );
- }
-
- boolean isDynamicallyHideData() {
- return ( ( getDynamicallyHideData() != null ) && getDynamicallyHideData().isSelected() );
- }
-
- boolean isEvents() {
- return ( ( getShowEventsCb() != null ) && getShowEventsCb().isSelected() );
- }
-
- boolean isNodeDescPopup() {
- return ( ( getNodeDescPopupCb() != null ) && getNodeDescPopupCb().isSelected() );
- }
-
- boolean isShowAnnotation() {
- return ( ( _show_annotation != null ) && _show_annotation.isSelected() );
- }
-
- boolean isShowBinaryCharacterCounts() {
- return ( ( _show_binary_character_counts != null ) && _show_binary_character_counts.isSelected() );
- }
-
- boolean isShowBinaryCharacters() {
- return ( ( _show_binary_characters != null ) && _show_binary_characters.isSelected() );
- }
-
- boolean isShowConfidenceValues() {
- return ( ( getWriteConfidenceCb() != null ) && getWriteConfidenceCb().isSelected() );
- }
-
- boolean isWriteBranchLengthValues() {
- return ( ( _write_branch_length_values != null ) && _write_branch_length_values.isSelected() );
- }
-
- boolean isShowDomainArchitectures() {
- return ( ( _show_domain_architectures != null ) && _show_domain_architectures.isSelected() );
- }
-
- public boolean isShowMolSequences() {
- return ( ( _show_mol_seqs != null ) && _show_mol_seqs.isSelected() );
- }
-
- boolean isShowGeneNames() {
- return ( ( _show_gene_names != null ) && _show_gene_names.isSelected() );
- }
-
- boolean isShowInternalData() {
- return ( ( _display_internal_data == null ) || _display_internal_data.isSelected() );
- }
-
- boolean isShowNodeNames() {
- return ( ( _show_node_names != null ) && _show_node_names.isSelected() );
- }
-
- boolean isShowSeqNames() {
- return ( ( _show_seq_names != null ) && _show_seq_names.isSelected() );
- }
-
- boolean isShowSeqSymbols() {
- return ( ( _show_seq_symbols != null ) && _show_seq_symbols.isSelected() );
- }
-
- boolean isShowSequenceAcc() {
- return ( ( _show_sequence_acc != null ) && _show_sequence_acc.isSelected() );
- }
-
- boolean isShowSequenceRelationConfidence() {
- return ( ( _seq_relation_confidence_switch != null ) && ( _seq_relation_confidence_switch.isSelected() ) );
- }
-
- boolean isShowSequenceRelations() {
- return ( ( _show_sequence_relations != null ) && ( _show_sequence_relations.getSelectedIndex() > 0 ) );
- }
-
- boolean isShowTaxonomyCode() {
- return ( ( _show_taxo_code != null ) && _show_taxo_code.isSelected() );
- }
-
- boolean isShowTaxonomyCommonNames() {
- return ( ( _show_taxo_common_names != null ) && _show_taxo_common_names.isSelected() );
- }
-
- boolean isShowTaxonomyScientificNames() {
- return ( ( _show_taxo_scientific_names != null ) && _show_taxo_scientific_names.isSelected() );
- }
-
- boolean isWidthBranches() {
- return ( ( _width_branches != null ) && _width_branches.isSelected() );
- }
-
- void phylogenyAdded( final Configuration configuration ) {
- getIsDrawPhylogramList().add( configuration.isDrawAsPhylogram() );
+ private void setupDisplayCheckboxes() {
+ if ( _configuration.doDisplayOption( Configuration.display_as_phylogram ) ) {
+ addCheckbox( Configuration.display_as_phylogram,
+ _configuration.getDisplayTitle( Configuration.display_as_phylogram ) );
+ setCheckbox( Configuration.display_as_phylogram,
+ _configuration.doCheckOption( Configuration.display_as_phylogram ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.dynamically_hide_data ) ) {
+ addCheckbox( Configuration.dynamically_hide_data,
+ _configuration.getDisplayTitle( Configuration.dynamically_hide_data ) );
+ setCheckbox( Configuration.dynamically_hide_data,
+ _configuration.doCheckOption( Configuration.dynamically_hide_data ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.node_data_popup ) ) {
+ addCheckbox( Configuration.node_data_popup, _configuration.getDisplayTitle( Configuration.node_data_popup ) );
+ setCheckbox( Configuration.node_data_popup, _configuration.doCheckOption( Configuration.node_data_popup ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.display_internal_data ) ) {
+ addCheckbox( Configuration.display_internal_data,
+ _configuration.getDisplayTitle( Configuration.display_internal_data ) );
+ setCheckbox( Configuration.display_internal_data,
+ _configuration.doCheckOption( Configuration.display_internal_data ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.color_according_to_sequence ) ) {
+ addCheckbox( Configuration.color_according_to_sequence,
+ _configuration.getDisplayTitle( Configuration.color_according_to_sequence ) );
+ setCheckbox( Configuration.color_according_to_sequence,
+ _configuration.doCheckOption( Configuration.color_according_to_sequence ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.color_according_to_species ) ) {
+ addCheckbox( Configuration.color_according_to_species,
+ _configuration.getDisplayTitle( Configuration.color_according_to_species ) );
+ setCheckbox( Configuration.color_according_to_species,
+ _configuration.doCheckOption( Configuration.color_according_to_species ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.color_according_to_annotation ) ) {
+ addCheckbox( Configuration.color_according_to_annotation,
+ _configuration.getDisplayTitle( Configuration.color_according_to_annotation ) );
+ setCheckbox( Configuration.color_according_to_annotation,
+ _configuration.doCheckOption( Configuration.color_according_to_annotation ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.use_style ) ) {
+ addCheckbox( Configuration.use_style, _configuration.getDisplayTitle( Configuration.use_style ) );
+ setCheckbox( Configuration.use_style, _configuration.doCheckOption( Configuration.use_style ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.width_branches ) ) {
+ addCheckbox( Configuration.width_branches, _configuration.getDisplayTitle( Configuration.width_branches ) );
+ setCheckbox( Configuration.width_branches, _configuration.doCheckOption( Configuration.width_branches ) );
+ }
+ final JLabel label = new JLabel( "Display Data:" );
+ label.setFont( ControlPanel.jcb_bold_font );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
+ }
+ add( label );
+ if ( _configuration.doDisplayOption( Configuration.show_node_names ) ) {
+ addCheckbox( Configuration.show_node_names, _configuration.getDisplayTitle( Configuration.show_node_names ) );
+ setCheckbox( Configuration.show_node_names, _configuration.doCheckOption( Configuration.show_node_names ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_tax_code ) ) {
+ addCheckbox( Configuration.show_tax_code, _configuration.getDisplayTitle( Configuration.show_tax_code ) );
+ setCheckbox( Configuration.show_tax_code, _configuration.doCheckOption( Configuration.show_tax_code ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_taxonomy_scientific_names ) ) {
+ addCheckbox( Configuration.show_taxonomy_scientific_names,
+ _configuration.getDisplayTitle( Configuration.show_taxonomy_scientific_names ) );
+ setCheckbox( Configuration.show_taxonomy_scientific_names,
+ _configuration.doCheckOption( Configuration.show_taxonomy_scientific_names ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_taxonomy_common_names ) ) {
+ addCheckbox( Configuration.show_taxonomy_common_names,
+ _configuration.getDisplayTitle( Configuration.show_taxonomy_common_names ) );
+ setCheckbox( Configuration.show_taxonomy_common_names,
+ _configuration.doCheckOption( Configuration.show_taxonomy_common_names ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_seq_names ) ) {
+ addCheckbox( Configuration.show_seq_names, _configuration.getDisplayTitle( Configuration.show_seq_names ) );
+ setCheckbox( Configuration.show_seq_names, _configuration.doCheckOption( Configuration.show_seq_names ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_gene_names ) ) {
+ addCheckbox( Configuration.show_gene_names, _configuration.getDisplayTitle( Configuration.show_gene_names ) );
+ setCheckbox( Configuration.show_gene_names, _configuration.doCheckOption( Configuration.show_gene_names ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_seq_symbols ) ) {
+ addCheckbox( Configuration.show_seq_symbols,
+ _configuration.getDisplayTitle( Configuration.show_seq_symbols ) );
+ setCheckbox( Configuration.show_seq_symbols, _configuration.doCheckOption( Configuration.show_seq_symbols ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_sequence_acc ) ) {
+ addCheckbox( Configuration.show_sequence_acc,
+ _configuration.getDisplayTitle( Configuration.show_sequence_acc ) );
+ setCheckbox( Configuration.show_sequence_acc,
+ _configuration.doCheckOption( Configuration.show_sequence_acc ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_annotation ) ) {
+ addCheckbox( Configuration.show_annotation, _configuration.getDisplayTitle( Configuration.show_annotation ) );
+ setCheckbox( Configuration.show_annotation, _configuration.doCheckOption( Configuration.show_annotation ) );
+ }
+ 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_branch_length_values ) ) {
+ addCheckbox( Configuration.write_branch_length_values,
+ _configuration.getDisplayTitle( Configuration.write_branch_length_values ) );
+ setCheckbox( Configuration.write_branch_length_values,
+ _configuration.doCheckOption( Configuration.write_branch_length_values ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_binary_characters ) ) {
+ 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.show_mol_seqs ) ) {
+ addCheckbox( Configuration.show_mol_seqs, _configuration.getDisplayTitle( Configuration.show_mol_seqs ) );
+ setCheckbox( Configuration.show_mol_seqs, _configuration.doCheckOption( Configuration.show_mol_seqs ) );
+ }
+ 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 ) );
+ }
+ if ( _configuration.doDisplayOption( Configuration.show_taxonomy_images ) ) {
+ addCheckbox( Configuration.show_taxonomy_images,
+ _configuration.getDisplayTitle( Configuration.show_taxonomy_images ) );
+ setCheckbox( Configuration.show_taxonomy_images,
+ _configuration.doCheckOption( Configuration.show_taxonomy_images ) );
+ }
}
- void phylogenyRemoved( final int index ) {
- getIsDrawPhylogramList().remove( index );
+ private void setVisibilityOfDomainStrucureControls() {
+ if ( _zoom_in_domain_structure != null ) {
+ final MainFrame mf = getMainFrame();
+ if ( mf != null ) {
+ if ( isShowDomainArchitectures() ) {
+ _domain_display_label.setVisible( true );
+ _zoom_in_domain_structure.setVisible( true );
+ _zoom_out_domain_structure.setVisible( true );
+ _decr_domain_structure_evalue_thr.setVisible( true );
+ _incr_domain_structure_evalue_thr.setVisible( true );
+ _domain_structure_evalue_thr_tf.setVisible( true );
+ if ( mf._right_line_up_domains_cbmi != null ) {
+ mf._right_line_up_domains_cbmi.setVisible( true );
+ }
+ if ( mf._show_domain_labels != null ) {
+ mf._show_domain_labels.setVisible( true );
+ }
+ }
+ else {
+ _domain_display_label.setVisible( false );
+ _zoom_in_domain_structure.setVisible( false );
+ _zoom_out_domain_structure.setVisible( false );
+ _decr_domain_structure_evalue_thr.setVisible( false );
+ _incr_domain_structure_evalue_thr.setVisible( false );
+ _domain_structure_evalue_thr_tf.setVisible( false );
+ if ( mf._right_line_up_domains_cbmi != null ) {
+ mf._right_line_up_domains_cbmi.setVisible( false );
+ }
+ if ( mf._show_domain_labels != null ) {
+ mf._show_domain_labels.setVisible( false );
+ }
+ }
+ }
+ }
}
- void search0() {
- final MainPanel main_panel = getMainPanel();
- final Phylogeny tree = main_panel.getCurrentPhylogeny();
- if ( ( tree == null ) || tree.isEmpty() ) {
- return;
- }
- String query = getSearchTextField0().getText();
- if ( query != null ) {
- query = query.trim();
- }
- if ( !ForesterUtil.isEmpty( query ) ) {
- search0( main_panel, tree, query );
+ void activateButtonToReturnToSuperTree( int index ) {
+ --index;
+ if ( index > 0 ) {
+ _return_to_super_tree.setText( RETURN_TO_SUPER_TREE_TEXT + " " + index );
}
else {
- getSearchFoundCountsLabel0().setVisible( false );
- getSearchResetButton0().setEnabled( false );
- getSearchResetButton0().setVisible( false );
- searchReset0();
+ _return_to_super_tree.setText( RETURN_TO_SUPER_TREE_TEXT );
}
+ _return_to_super_tree.setForeground( getConfiguration().getGuiCheckboxAndButtonActiveColor() );
+ _return_to_super_tree.setEnabled( true );
}
- void search1() {
- final MainPanel main_panel = getMainPanel();
- final Phylogeny tree = main_panel.getCurrentPhylogeny();
- if ( ( tree == null ) || tree.isEmpty() ) {
- return;
- }
- String query = getSearchTextField1().getText();
- if ( query != null ) {
- query = query.trim();
+ /**
+ * Add zoom and quick edit buttons. (Last modified 8/9/04)
+ */
+ void addButtons() {
+ final JLabel spacer = new JLabel( "" );
+ spacer.setOpaque( false );
+ add( spacer );
+ final JPanel x_panel = new JPanel( new GridLayout( 1, 1, 0, 0 ) );
+ final JPanel y_panel = new JPanel( new GridLayout( 1, 3, 0, 0 ) );
+ final JPanel z_panel = new JPanel( new GridLayout( 1, 1, 0, 0 ) );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ x_panel.setBackground( getBackground() );
+ y_panel.setBackground( getBackground() );
+ z_panel.setBackground( getBackground() );
}
- if ( !ForesterUtil.isEmpty( query ) ) {
- search1( main_panel, tree, query );
+ add( _zoom_label = new JLabel( "Zoom:" ) );
+ customizeLabel( _zoom_label, getConfiguration() );
+ add( x_panel );
+ add( y_panel );
+ add( z_panel );
+ if ( getConfiguration().isUseNativeUI() ) {
+ _zoom_in_x = new JButton( "+" );
+ _zoom_out_x = new JButton( "-" );
}
else {
- getSearchFoundCountsLabel1().setVisible( false );
- getSearchResetButton1().setEnabled( false );
- getSearchResetButton1().setVisible( false );
- searchReset1();
+ _zoom_in_x = new JButton( "X+" );
+ _zoom_out_x = new JButton( "X-" );
}
- }
-
- void searchReset0() {
- if ( getMainPanel().getCurrentTreePanel() != null ) {
- getMainPanel().getCurrentTreePanel().setFoundNodes0( null );
+ _zoom_in_y = new JButton( "Y+" );
+ _zoom_out_y = new JButton( "Y-" );
+ _show_whole = new JButton( "F" );
+ _show_whole.setToolTipText( "To fit the complete phylogeny to the current display size [F or Home]" );
+ _zoom_in_x.setToolTipText( "To zoom in horizontally [Shift+cursor-right]" );
+ _zoom_in_y.setToolTipText( "To zoom in vertically [Shift+cursor-up]" );
+ _zoom_out_x.setToolTipText( "To zoom out horizontally [Shift+cursor-left]" );
+ _zoom_out_y.setToolTipText( "To zoom out vertically [Shift+cursor-down]" );
+ if ( getConfiguration().isUseNativeUI() && ForesterUtil.isMac() ) {
+ _zoom_out_x.setPreferredSize( new Dimension( 55, 10 ) );
+ _zoom_in_x.setPreferredSize( new Dimension( 55, 10 ) );
}
- }
-
- void searchReset1() {
- if ( getMainPanel().getCurrentTreePanel() != null ) {
- getMainPanel().getCurrentTreePanel().setFoundNodes1( null );
+ else {
+ _zoom_out_x.setPreferredSize( new Dimension( 10, 10 ) );
+ _zoom_in_x.setPreferredSize( new Dimension( 10, 10 ) );
}
+ _zoom_out_y.setPreferredSize( new Dimension( 10, 10 ) );
+ _zoom_in_y.setPreferredSize( new Dimension( 10, 10 ) );
+ _show_whole.setPreferredSize( new Dimension( 10, 10 ) );
+ _return_to_super_tree = new JButton( RETURN_TO_SUPER_TREE_TEXT );
+ _return_to_super_tree.setEnabled( false );
+ _order = new JButton( "Order Subtrees" );
+ _uncollapse_all = new JButton( "Uncollapse All" );
+ addJButton( _zoom_in_y, x_panel );
+ addJButton( _zoom_out_x, y_panel );
+ addJButton( _show_whole, y_panel );
+ addJButton( _zoom_in_x, y_panel );
+ addJButton( _zoom_out_y, z_panel );
+ if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
+ setUpControlsForDomainStrucures();
+ }
+ final JLabel spacer2 = new JLabel( "" );
+ add( spacer2 );
+ addJButton( _return_to_super_tree, this );
+ addJButton( _order, this );
+ addJButton( _uncollapse_all, this );
+ final JLabel spacer3 = new JLabel( "" );
+ add( spacer3 );
+ setVisibilityOfDomainStrucureControls();
}
- void setActionWhenNodeClicked( final NodeClickAction action ) {
- _action_when_node_clicked = action;
- }
-
- void setAnnotationColors( final Map<String, Color> annotation_colors ) {
- _annotation_colors = annotation_colors;
- }
-
- void setCheckbox( final int which, final boolean state ) {
+ void addCheckbox( final int which, final String title ) {
+ final JPanel ch_panel = new JPanel( new BorderLayout( 0, 0 ) );
switch ( which ) {
case Configuration.display_as_phylogram:
- if ( getDisplayAsPhylogramCb() != null ) {
- getDisplayAsPhylogramCb().setSelected( state );
- }
+ _display_as_phylogram_cb = new JCheckBox( title );
+ getDisplayAsPhylogramCb().setToolTipText( "To switch between phylogram and cladogram display" );
+ addJCheckBox( getDisplayAsPhylogramCb(), ch_panel );
+ add( ch_panel );
break;
case Configuration.display_internal_data:
- if ( _display_internal_data != null ) {
- _display_internal_data.setSelected( state );
- }
+ _display_internal_data = new JCheckBox( title );
+ _display_internal_data.setToolTipText( "To allow or disallow display of internal labels" );
+ addJCheckBox( _display_internal_data, ch_panel );
+ add( ch_panel );
break;
case Configuration.color_according_to_species:
- if ( _color_acc_species != null ) {
- _color_acc_species.setSelected( state );
- }
+ _color_acc_species = new JCheckBox( title );
+ _color_acc_species.setToolTipText( "To colorize node labels as a function of taxonomy" );
+ addJCheckBox( _color_acc_species, ch_panel );
+ add( ch_panel );
break;
case Configuration.color_according_to_sequence:
- if ( _color_acc_sequence != null ) {
- _color_acc_sequence.setSelected( state );
- }
+ _color_acc_sequence = new JCheckBox( title );
+ _color_acc_sequence.setToolTipText( "To colorize node labels as a function of sequence name" );
+ addJCheckBox( _color_acc_sequence, ch_panel );
+ add( ch_panel );
break;
case Configuration.color_according_to_annotation:
- if ( _color_according_to_annotation != null ) {
- _color_according_to_annotation.setSelected( state );
- }
+ _color_according_to_annotation = new JCheckBox( title );
+ _color_according_to_annotation
+ .setToolTipText( "To colorize sequence annotation labels as a function of sequence annotation" );
+ addJCheckBox( _color_according_to_annotation, ch_panel );
+ add( ch_panel );
break;
case Configuration.show_node_names:
- if ( _show_node_names != null ) {
- _show_node_names.setSelected( state );
- }
+ _show_node_names = new JCheckBox( title );
+ addJCheckBox( _show_node_names, ch_panel );
+ add( ch_panel );
break;
case Configuration.show_taxonomy_scientific_names:
- if ( _show_taxo_scientific_names != null ) {
- _show_taxo_scientific_names.setSelected( state );
- }
+ _show_taxo_scientific_names = new JCheckBox( title );
+ addJCheckBox( _show_taxo_scientific_names, ch_panel );
+ add( ch_panel );
break;
case Configuration.show_taxonomy_common_names:
- if ( _show_taxo_common_names != null ) {
- _show_taxo_common_names.setSelected( state );
- }
+ _show_taxo_common_names = new JCheckBox( title );
+ addJCheckBox( _show_taxo_common_names, ch_panel );
+ add( ch_panel );
break;
case Configuration.show_tax_code:
- if ( _show_taxo_code != null ) {
- _show_taxo_code.setSelected( state );
- }
+ _show_taxo_code = new JCheckBox( title );
+ addJCheckBox( _show_taxo_code, ch_panel );
+ add( ch_panel );
break;
case Configuration.show_taxonomy_images:
- if ( _show_taxo_images_cb != null ) {
- _show_taxo_images_cb.setSelected( state );
- }
- break;
- case Configuration.show_annotation:
- if ( _show_annotation != null ) {
- _show_annotation.setSelected( state );
- }
+ _show_taxo_images_cb = new JCheckBox( title );
+ addJCheckBox( _show_taxo_images_cb, ch_panel );
+ add( ch_panel );
break;
case Configuration.show_binary_characters:
- if ( _show_binary_characters != null ) {
- _show_binary_characters.setSelected( state );
- }
+ _show_binary_characters = new JCheckBox( title );
+ addJCheckBox( _show_binary_characters, ch_panel );
+ add( ch_panel );
+ break;
+ case Configuration.show_annotation:
+ _show_annotation = new JCheckBox( title );
+ addJCheckBox( _show_annotation, ch_panel );
+ add( ch_panel );
break;
case Configuration.show_binary_character_counts:
- if ( _show_binary_character_counts != null ) {
- _show_binary_character_counts.setSelected( state );
- }
+ _show_binary_character_counts = new JCheckBox( title );
+ addJCheckBox( _show_binary_character_counts, ch_panel );
+ add( ch_panel );
break;
case Configuration.write_confidence_values:
- if ( getWriteConfidenceCb() != null ) {
- getWriteConfidenceCb().setSelected( state );
- }
+ _write_confidence = new JCheckBox( title );
+ addJCheckBox( getWriteConfidenceCb(), ch_panel );
+ add( ch_panel );
break;
case Configuration.write_events:
- if ( getShowEventsCb() != null ) {
- getShowEventsCb().setSelected( state );
- }
+ _show_events = new JCheckBox( title );
+ addJCheckBox( getShowEventsCb(), ch_panel );
+ add( ch_panel );
break;
case Configuration.use_style:
- if ( getUseVisualStylesCb() != null ) {
- getUseVisualStylesCb().setSelected( state );
- }
+ _use_visual_styles_cb = new JCheckBox( title );
+ getUseVisualStylesCb()
+ .setToolTipText( "To use visual styles (node colors, fonts) and branch colors, if present" );
+ addJCheckBox( getUseVisualStylesCb(), ch_panel );
+ add( ch_panel );
break;
case Configuration.width_branches:
- if ( _width_branches != null ) {
- _width_branches.setSelected( state );
- }
- break;
- case Configuration.show_domain_architectures:
- if ( _show_domain_architectures != null ) {
- _show_domain_architectures.setSelected( state );
- }
+ _width_branches = new JCheckBox( title );
+ _width_branches.setToolTipText( "To use branch width values, if present" );
+ addJCheckBox( _width_branches, ch_panel );
+ add( ch_panel );
break;
case Configuration.write_branch_length_values:
- if ( _write_branch_length_values != null ) {
- _write_branch_length_values.setSelected( state );
- }
+ _write_branch_length_values = new JCheckBox( title );
+ addJCheckBox( _write_branch_length_values, ch_panel );
+ add( ch_panel );
+ break;
+ case Configuration.show_domain_architectures:
+ _show_domain_architectures = new JCheckBox( title );
+ addJCheckBox( _show_domain_architectures, ch_panel );
+ add( ch_panel );
break;
case Configuration.show_mol_seqs:
- if ( _show_mol_seqs != null ) {
- _show_mol_seqs.setSelected( state );
- }
+ _show_mol_seqs = new JCheckBox( title );
+ addJCheckBox( _show_mol_seqs, ch_panel );
+ add( ch_panel );
break;
case Configuration.show_seq_names:
- if ( _show_seq_names != null ) {
- _show_seq_names.setSelected( state );
- }
+ _show_seq_names = new JCheckBox( title );
+ addJCheckBox( _show_seq_names, ch_panel );
+ add( ch_panel );
break;
case Configuration.show_gene_names:
- if ( _show_gene_names != null ) {
- _show_gene_names.setSelected( state );
- }
+ _show_gene_names = new JCheckBox( title );
+ addJCheckBox( _show_gene_names, ch_panel );
+ add( ch_panel );
break;
case Configuration.show_seq_symbols:
- if ( _show_seq_symbols != null ) {
- _show_seq_symbols.setSelected( state );
- }
- break;
- case Configuration.show_vector_data:
- if ( _show_vector_data_cb != null ) {
- _show_vector_data_cb.setSelected( state );
- }
- break;
- case Configuration.show_properties:
- if ( _show_properties_cb != null ) {
- _show_properties_cb.setSelected( state );
- }
+ _show_seq_symbols = new JCheckBox( title );
+ addJCheckBox( _show_seq_symbols, ch_panel );
+ add( ch_panel );
break;
case Configuration.show_sequence_acc:
- if ( _show_sequence_acc != null ) {
- _show_sequence_acc.setSelected( state );
- }
+ _show_sequence_acc = new JCheckBox( title );
+ addJCheckBox( _show_sequence_acc, ch_panel );
+ add( ch_panel );
break;
case Configuration.dynamically_hide_data:
- if ( getDynamicallyHideData() != null ) {
- getDynamicallyHideData().setSelected( state );
- }
+ _dynamically_hide_data = new JCheckBox( title );
+ getDynamicallyHideData().setToolTipText( "To hide labels depending on expected visibility" );
+ addJCheckBox( getDynamicallyHideData(), ch_panel );
+ add( ch_panel );
break;
case Configuration.node_data_popup:
- if ( getNodeDescPopupCb() != null ) {
- getNodeDescPopupCb().setSelected( state );
- }
+ _node_desc_popup_cb = new JCheckBox( title );
+ getNodeDescPopupCb().setToolTipText( "To enable mouse rollover display of basic node data" );
+ addJCheckBox( getNodeDescPopupCb(), ch_panel );
+ add( ch_panel );
+ break;
+ case Configuration.show_relation_confidence:
+ _seq_relation_confidence_switch = new JCheckBox( title );
+ addJCheckBox( _seq_relation_confidence_switch, ch_panel );
+ add( ch_panel );
+ break;
+ case Configuration.show_vector_data:
+ _show_vector_data_cb = new JCheckBox( title );
+ addJCheckBox( _show_vector_data_cb, ch_panel );
+ add( ch_panel );
break;
- /* GUILHEM_BEG */
- case Configuration.show_relation_confidence:
- if ( _seq_relation_confidence_switch != null ) {
- _seq_relation_confidence_switch.setSelected( state );
- }
+ case Configuration.show_properties:
+ _show_properties_cb = new JCheckBox( title );
+ addJCheckBox( _show_properties_cb, ch_panel );
+ add( ch_panel );
break;
- /* GUILHEM_END */
default:
- throw new AssertionError( "unknown checkbox: " + which );
+ throw new RuntimeException( "unknown checkbox: " + which );
}
- }
+ }// addCheckbox
- /**
- * Set this checkbox state. Not all checkboxes have been instantiated
- * depending on the config.
- */
- void setCheckbox( final JCheckBox cb, final boolean state ) {
- if ( cb != null ) {
- cb.setSelected( state );
+ void addJButton( final JButton jb, final JPanel p ) {
+ jb.setFocusPainted( false );
+ jb.setFont( ControlPanel.jcb_font );
+ if ( !_configuration.isUseNativeUI() ) {
+ jb.setBorder( BorderFactory.createLineBorder( getConfiguration().getGuiButtonBorderColor() ) );
+ jb.setBackground( getConfiguration().getGuiButtonBackgroundColor() );
+ jb.setForeground( getConfiguration().getGuiButtonTextColor() );
}
+ p.add( jb );
+ jb.addActionListener( this );
}
- void setClickToAction( final int action ) {
- // Set click-to action
- if ( action == _show_data_item ) {
- setActionWhenNodeClicked( NodeClickAction.SHOW_DATA );
- }
- else if ( action == _collapse_cb_item ) {
- setActionWhenNodeClicked( NodeClickAction.COLLAPSE );
- }
- else if ( action == _reroot_cb_item ) {
- setActionWhenNodeClicked( NodeClickAction.REROOT );
- }
- else if ( action == _subtree_cb_item ) {
- setActionWhenNodeClicked( NodeClickAction.SUBTREE );
- }
- else if ( action == _swap_cb_item ) {
- setActionWhenNodeClicked( NodeClickAction.SWAP );
- }
- else if ( action == _color_subtree_cb_item ) {
- setActionWhenNodeClicked( NodeClickAction.COLOR_SUBTREE );
- }
- else if ( action == _open_seq_web_item ) {
- setActionWhenNodeClicked( NodeClickAction.OPEN_SEQ_WEB );
- }
- else if ( action == _sort_descendents_item ) {
- setActionWhenNodeClicked( NodeClickAction.SORT_DESCENDENTS );
- }
- else if ( action == _blast_item ) {
- setActionWhenNodeClicked( NodeClickAction.BLAST );
- }
- else if ( action == _open_tax_web_item ) {
- setActionWhenNodeClicked( NodeClickAction.OPEN_TAX_WEB );
- }
- else if ( action == _cut_subtree_item ) {
- setActionWhenNodeClicked( NodeClickAction.CUT_SUBTREE );
- }
- else if ( action == _copy_subtree_item ) {
- setActionWhenNodeClicked( NodeClickAction.COPY_SUBTREE );
- }
- else if ( action == _delete_node_or_subtree_item ) {
- setActionWhenNodeClicked( NodeClickAction.DELETE_NODE_OR_SUBTREE );
- }
- else if ( action == _paste_subtree_item ) {
- setActionWhenNodeClicked( NodeClickAction.PASTE_SUBTREE );
- }
- else if ( action == _add_new_node_item ) {
- setActionWhenNodeClicked( NodeClickAction.ADD_NEW_NODE );
- }
- else if ( action == _edit_node_data_item ) {
- setActionWhenNodeClicked( NodeClickAction.EDIT_NODE_DATA );
- }
- else if ( action == _select_nodes_item ) {
- setActionWhenNodeClicked( NodeClickAction.SELECT_NODES );
- }
- else if ( action == _get_ext_desc_data ) {
- setActionWhenNodeClicked( NodeClickAction.GET_EXT_DESC_DATA );
- }
- else if ( action == _open_pdb_item ) {
- setActionWhenNodeClicked( NodeClickAction.OPEN_PDB_WEB );
- }
- else if ( action == _color_node_font_item ) {
- setActionWhenNodeClicked( NodeClickAction.COLOR_NODE_FONT );
+ void addJCheckBox( final JCheckBox jcb, final JPanel p ) {
+ jcb.setFocusPainted( false );
+ jcb.setFont( ControlPanel.jcb_font );
+ if ( !_configuration.isUseNativeUI() ) {
+ jcb.setBackground( getConfiguration().getGuiBackgroundColor() );
+ jcb.setForeground( getConfiguration().getGuiCheckboxTextColor() );
}
- else if ( action == _change_node_font_item ) {
- setActionWhenNodeClicked( NodeClickAction.CHANGE_NODE_FONT );
+ p.add( jcb, "Center" );
+ jcb.addActionListener( this );
+ }
+
+ void addJTextField( final JTextField tf, final JPanel p ) {
+ if ( !_configuration.isUseNativeUI() ) {
+ tf.setForeground( getConfiguration().getGuiBackgroundColor() );
+ tf.setFont( ControlPanel.jcb_font );
}
- else {
- throw new RuntimeException( "unknown action: " + action );
+ p.add( tf );
+ tf.addActionListener( this );
+ }
+
+ void deactivateButtonToReturnToSuperTree() {
+ _return_to_super_tree.setText( RETURN_TO_SUPER_TREE_TEXT );
+ _return_to_super_tree.setForeground( getConfiguration().getGuiButtonTextColor() );
+ _return_to_super_tree.setEnabled( false );
+ }
+
+ void displayedPhylogenyMightHaveChanged( final boolean recalc_longest_ext_node_info ) {
+ if ( ( _mainpanel != null )
+ && ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
+ if ( getOptions().isShowOverview() ) {
+ _mainpanel.getCurrentTreePanel().updateOvSizes();
+ }
+ _mainpanel.getCurrentTreePanel().recalculateMaxDistanceToRoot();
+ setVisibilityOfDomainStrucureControls();
+ updateDomainStructureEvaluethresholdDisplay();
+ _mainpanel.getCurrentTreePanel().calculateScaleDistance();
+ _mainpanel.getCurrentTreePanel().calcMaxDepth();
+ _mainpanel.adjustJScrollPane();
+ if ( recalc_longest_ext_node_info ) {
+ _mainpanel.getCurrentTreePanel().initNodeData();
+ _mainpanel.getCurrentTreePanel().calculateLongestExtNodeInfo();
+ }
+ _mainpanel.getCurrentTreePanel().repaint();
+ // _mainpanel.getCurrentTreePanel().setUpUrtFactors();
}
- // make sure drop down is displaying the correct action
- // in case this was called from outside the class
- _click_to_combobox.setSelectedIndex( action );
}
- void setColorBranches( final boolean color_branches ) {
- _color_branches = color_branches;
+ void endClickToOptions() {
+ _click_to_combobox.addActionListener( this );
}
- void setDrawPhylogram( final boolean b ) {
- getDisplayAsPhylogramCb().setSelected( b );
- setDrawPhylogram( getMainPanel().getCurrentTabIndex(), b );
+ /**
+ * Indicates what action should be execute when a node is clicked
+ *
+ * @return the click-on action
+ */
+ NodeClickAction getActionWhenNodeClicked() {
+ return _action_when_node_clicked;
}
- void setDrawPhylogramEnabled( final boolean b ) {
- getDisplayAsPhylogramCb().setEnabled( b );
+ Map<Integer, String> getAllClickToItems() {
+ return _all_click_to_names;
}
- void setDynamicHidingIsOn( final boolean is_on ) {
- if ( is_on ) {
- getDynamicallyHideData().setForeground( getConfiguration().getGuiCheckboxAndButtonActiveColor() );
- }
- else {
- if ( !_configuration.isUseNativeUI() ) {
- getDynamicallyHideData().setForeground( getConfiguration().getGuiButtonTextColor() );
- }
- else {
- getDynamicallyHideData().setForeground( Color.BLACK );
- }
- }
+ Map<String, Color> getAnnotationColors() {
+ return _annotation_colors;
}
- void setSearchFoundCountsOnLabel0( final int counts ) {
- getSearchFoundCountsLabel0().setText( "Found: " + counts );
+ Configuration getConfiguration() {
+ return _configuration;
}
- void setSearchFoundCountsOnLabel1( final int counts ) {
- getSearchFoundCountsLabel1().setText( "Found: " + counts );
+ TreePanel getCurrentTreePanel() {
+ return getMainPanel().getCurrentTreePanel();
}
- void setShowEvents( final boolean show_events ) {
- if ( getShowEventsCb() == null ) {
- _show_events = new JCheckBox( "" );
- }
- getShowEventsCb().setSelected( show_events );
+ MainPanel getMainPanel() {
+ return _mainpanel;
}
- void setSpeciesColors( final Map<String, Color> species_colors ) {
- _species_colors = species_colors;
+ Options getOptions() {
+ return getMainPanel().getOptions();
}
- void setSequenceColors( final Map<String, Color> sequence_colors ) {
- _sequence_colors = sequence_colors;
+ JLabel getSearchFoundCountsLabel0() {
+ return _search_found_label_0;
}
- 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();
- setupSearchTools0();
- setupSearchTools1();
+ JLabel getSearchFoundCountsLabel1() {
+ return _search_found_label_1;
}
- void setUpControlsForDomainStrucures() {
- _domain_display_label = new JLabel( "Domain Architectures:" );
- 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 );
+ JButton getSearchResetButton0() {
+ return _search_reset_button_0;
+ }
+
+ JButton getSearchResetButton1() {
+ return _search_reset_button_1;
}
- void setupSearchTools0() {
- final JLabel search_label = new JLabel( "Search (A):" );
- search_label.setFont( ControlPanel.jcb_bold_font );
- if ( !getConfiguration().isUseNativeUI() ) {
- search_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
- }
- add( search_label );
- search_label.setToolTipText( SEARCH_TIP_TEXT );
- _search_found_label_0 = new JLabel();
- getSearchFoundCountsLabel0().setVisible( false );
- _search_found_label_0.setFont( ControlPanel.jcb_bold_font );
- if ( !getConfiguration().isUseNativeUI() ) {
- _search_found_label_0.setForeground( getConfiguration().getGuiCheckboxTextColor() );
- }
- _search_tf_0 = new JTextField( 3 );
- _search_tf_0.setToolTipText( SEARCH_TIP_TEXT );
- _search_tf_0.setEditable( true );
- if ( !getConfiguration().isUseNativeUI() ) {
- _search_tf_0.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
- _search_tf_0.setBackground( getConfiguration().getGuiCheckboxTextColor() );
- _search_tf_0.setBorder( null );
- }
- _search_reset_button_0 = new JButton();
- getSearchResetButton0().setText( "Reset" );
- getSearchResetButton0().setEnabled( false );
- getSearchResetButton0().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() {
+ JTextField getSearchTextField0() {
+ return _search_tf_0;
+ }
- @Override
- public void keyReleased( final KeyEvent key_event ) {
- search0();
- displayedPhylogenyMightHaveChanged( true );
- }
- };
- final ActionListener action_listener = new ActionListener() {
+ JTextField getSearchTextField1() {
+ return _search_tf_1;
+ }
- @Override
- public void actionPerformed( final ActionEvent e ) {
- searchReset0();
- setSearchFoundCountsOnLabel0( 0 );
- getSearchFoundCountsLabel0().setVisible( false );
- getSearchTextField0().setText( "" );
- getSearchResetButton0().setEnabled( false );
- getSearchResetButton0().setVisible( false );
- displayedPhylogenyMightHaveChanged( true );
- }
- };
- _search_reset_button_0.addActionListener( action_listener );
- _search_tf_0.addKeyListener( key_adapter );
- addJTextField( _search_tf_0, s_panel_1 );
- s_panel_2.add( _search_found_label_0 );
- addJButton( _search_reset_button_0, s_panel_2 );
+ Map<String, Color> getSequenceColors() {
+ return _sequence_colors;
}
- void setupSearchTools1() {
- final JLabel search_label = new JLabel( "Search (B):" );
- search_label.setFont( ControlPanel.jcb_bold_font );
- if ( !getConfiguration().isUseNativeUI() ) {
- search_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
- }
- add( search_label );
- search_label.setToolTipText( SEARCH_TIP_TEXT );
- _search_found_label_1 = new JLabel();
- getSearchFoundCountsLabel1().setVisible( false );
- _search_found_label_1.setFont( ControlPanel.jcb_bold_font );
- if ( !getConfiguration().isUseNativeUI() ) {
- _search_found_label_1.setForeground( getConfiguration().getGuiCheckboxTextColor() );
- }
- _search_tf_1 = new JTextField( 3 );
- _search_tf_1.setToolTipText( SEARCH_TIP_TEXT );
- _search_tf_1.setEditable( true );
- if ( !getConfiguration().isUseNativeUI() ) {
- _search_tf_1.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
- _search_tf_1.setBackground( getConfiguration().getGuiCheckboxTextColor() );
- _search_tf_1.setBorder( null );
- }
- _search_reset_button_1 = new JButton();
- getSearchResetButton1().setText( "Reset" );
- getSearchResetButton1().setEnabled( false );
- getSearchResetButton1().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() {
+ List<String> getSingleClickToNames() {
+ return _click_to_names;
+ }
- @Override
- public void keyReleased( final KeyEvent key_event ) {
- search1();
- displayedPhylogenyMightHaveChanged( true );
- }
- };
- final ActionListener action_listener = new ActionListener() {
+ Map<String, Color> getSpeciesColors() {
+ return _species_colors;
+ }
- @Override
- public void actionPerformed( final ActionEvent e ) {
- searchReset1();
- setSearchFoundCountsOnLabel1( 0 );
- getSearchFoundCountsLabel1().setVisible( false );
- getSearchTextField1().setText( "" );
- getSearchResetButton1().setEnabled( false );
- getSearchResetButton1().setVisible( false );
- displayedPhylogenyMightHaveChanged( true );
- }
- };
- _search_reset_button_1.addActionListener( action_listener );
- _search_tf_1.addKeyListener( key_adapter );
- addJTextField( _search_tf_1, s_panel_1 );
- s_panel_2.add( _search_found_label_1 );
- addJButton( _search_reset_button_1, s_panel_2 );
+ boolean isAntialiasScreenText() {
+ return true;
}
- void showAnnotations() {
- if ( _show_annotation != null ) {
- _show_annotation.setSelected( true );
- }
- if ( _color_according_to_annotation != null ) {
- _color_according_to_annotation.setSelected( true );
- }
- if ( _color_acc_species != null ) {
- _color_acc_species.setSelected( false );
- }
- if ( _color_acc_sequence != null ) {
- _color_acc_sequence.setSelected( false );
- }
- _mainpanel.getCurrentTreePanel().repaint();
+ boolean isColorAccordingToAnnotation() {
+ return ( ( _color_according_to_annotation != null ) && _color_according_to_annotation.isSelected() );
}
- /**
- * 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().calcParametersForPainting( _mainpanel.getSizeOfViewport().width,
- _mainpanel.getSizeOfViewport().height );
- _mainpanel.getCurrentTreePanel().resetPreferredSize();
- _mainpanel.adjustJScrollPane();
- _mainpanel.getCurrentTreePanel().repaint();
- _mainpanel.getCurrentTreePanel().validate();
- _mainpanel.validate();
- _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getSizeOfViewport().width,
- _mainpanel.getSizeOfViewport().height );
- _mainpanel.getCurrentTreePanel().resetPreferredSize();
- _mainpanel.adjustJScrollPane();
- _mainpanel.getCurrentTreePanel().repaint();
- _mainpanel.getCurrentTreePanel().updateOvSizes();
+ boolean isColorAccordingToSequence() {
+ return ( ( _color_acc_sequence != null ) && _color_acc_sequence.isSelected() );
}
- void showWholeAll() {
- for( final TreePanel tree_panel : _mainpanel.getTreePanels() ) {
- if ( tree_panel != null ) {
- tree_panel.validate();
- tree_panel.calcParametersForPainting( _mainpanel.getSizeOfViewport().width,
- _mainpanel.getSizeOfViewport().height );
- tree_panel.resetPreferredSize();
- tree_panel.repaint();
- }
- }
+ boolean isColorAccordingToTaxonomy() {
+ return ( ( _color_acc_species != null ) && _color_acc_species.isSelected() );
}
- // 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<String>();
- _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>();
+ boolean isDrawPhylogram() {
+ return isDrawPhylogram( getMainPanel().getCurrentTabIndex() );
}
- 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().search0();
- getMainPanel().getControlPanel().search1();
- getMainPanel().getControlPanel().updateDomainStructureEvaluethresholdDisplay();
- getSequenceRelationTypeBox().removeAllItems();
- for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
- .getRelevantSequenceRelationTypes() ) {
- _sequence_relation_type_box.addItem( type );
- }
- getMainPanel().getCurrentTreePanel().repaint();
- //setSequenceRelationQueries( getMainPanel().getCurrentPhylogeny().getSequenceRelationQueries() );
- // according to GUILHEM the line above can be removed.
- }
+ boolean isDynamicallyHideData() {
+ return ( ( getDynamicallyHideData() != null ) && getDynamicallyHideData().isSelected() );
+ }
+
+ boolean isEvents() {
+ return ( ( getShowEventsCb() != null ) && getShowEventsCb().isSelected() );
+ }
+
+ boolean isNodeDescPopup() {
+ return ( ( getNodeDescPopupCb() != null ) && getNodeDescPopupCb().isSelected() );
+ }
+
+ boolean isShowAnnotation() {
+ return ( ( _show_annotation != null ) && _show_annotation.isSelected() );
+ }
+
+ boolean isShowBinaryCharacterCounts() {
+ return ( ( _show_binary_character_counts != null ) && _show_binary_character_counts.isSelected() );
}
- /**
- * 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();
- }
+ boolean isShowBinaryCharacters() {
+ return ( ( _show_binary_characters != null ) && _show_binary_characters.isSelected() );
}
- void updateDomainStructureEvaluethresholdDisplay() {
- if ( _domain_structure_evalue_thr_tf != null ) {
- _domain_structure_evalue_thr_tf.setText( "10^"
- + getMainPanel().getCurrentTreePanel().getDomainStructureEvalueThresholdExp() );
- }
+ boolean isShowConfidenceValues() {
+ return ( ( getWriteConfidenceCb() != null ) && getWriteConfidenceCb().isSelected() );
}
- 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();
+ boolean isShowDomainArchitectures() {
+ return ( ( _show_domain_architectures != null ) && _show_domain_architectures.isSelected() );
}
- 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();
+ boolean isShowGeneNames() {
+ return ( ( _show_gene_names != null ) && _show_gene_names.isSelected() );
}
- 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();
- }
+ boolean isShowInternalData() {
+ return ( ( _display_internal_data == null ) || _display_internal_data.isSelected() );
}
- 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();
- }
+ boolean isShowNodeNames() {
+ return ( ( _show_node_names != null ) && _show_node_names.isSelected() );
}
- 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() );
- }
+ boolean isShowSeqNames() {
+ return ( ( _show_seq_names != null ) && _show_seq_names.isSelected() );
}
- /* 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<Object>() {
+ boolean isShowSeqSymbols() {
+ return ( ( _show_seq_symbols != null ) && _show_seq_symbols.isSelected() );
+ }
- @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
+ boolean isShowSequenceAcc() {
+ return ( ( _show_sequence_acc != null ) && _show_sequence_acc.isSelected() );
+ }
- /* GUILHEM_END */
- private List<Boolean> getIsDrawPhylogramList() {
- return _draw_phylogram;
+ boolean isShowSequenceRelationConfidence() {
+ return ( ( _seq_relation_confidence_switch != null ) && ( _seq_relation_confidence_switch.isSelected() ) );
}
- private void init() {
- _draw_phylogram = new ArrayList<Boolean>();
- setSpeciesColors( new HashMap<String, Color>() );
- setSequenceColors( new HashMap<String, Color>() );
- setAnnotationColors( new HashMap<String, Color>() );
+ boolean isShowSequenceRelations() {
+ return ( ( _show_sequence_relations != null ) && ( _show_sequence_relations.getSelectedIndex() > 0 ) );
}
- private boolean isDrawPhylogram( final int index ) {
- return getIsDrawPhylogramList().get( index );
+ boolean isShowTaxonomyCode() {
+ return ( ( _show_taxo_code != null ) && _show_taxo_code.isSelected() );
}
- private void search0( final MainPanel main_panel, final Phylogeny tree, final String query_str ) {
- getSearchFoundCountsLabel0().setVisible( true );
- getSearchResetButton0().setEnabled( true );
- getSearchResetButton0().setVisible( true );
- String[] queries = null;
- Set<PhylogenyNode> nodes = null;
- if ( ( query_str.indexOf( ',' ) >= 0 ) && !getOptions().isSearchWithRegex() ) {
- queries = query_str.split( ",+" );
- }
- else {
- queries = new String[ 1 ];
- queries[ 0 ] = query_str.trim();
- }
- if ( ( queries != null ) && ( queries.length > 0 ) ) {
- nodes = new HashSet<PhylogenyNode>();
- for( String query : queries ) {
- if ( ForesterUtil.isEmpty( query ) ) {
- continue;
- }
- query = query.trim();
- final TreePanel tp = getMainPanel().getCurrentTreePanel();
- if ( ( query.indexOf( '+' ) > 0 ) && !getOptions().isSearchWithRegex() ) {
- nodes.addAll( PhylogenyMethods.searchDataLogicalAnd( query.split( "\\++" ),
- tree,
- getOptions().isSearchCaseSensitive(),
- !getOptions().isMatchWholeTermsOnly(),
- isShowDomainArchitectures(),
- tp != null ? Math.pow( 10,
- tp.getDomainStructureEvalueThresholdExp() )
- : 0 ) );
- }
- else {
- nodes.addAll( PhylogenyMethods.searchData( query,
- tree,
- getOptions().isSearchCaseSensitive(),
- !getOptions().isMatchWholeTermsOnly(),
- getOptions().isSearchWithRegex(),
- isShowDomainArchitectures(),
- tp != null ? Math.pow( 10, tp
- .getDomainStructureEvalueThresholdExp() ) : 0 ) );
- }
- }
- if ( getOptions().isInverseSearchResult() ) {
- final List<PhylogenyNode> all = PhylogenyMethods.obtainAllNodesAsList( tree );
- all.removeAll( nodes );
- nodes = new HashSet<PhylogenyNode>();
- nodes.addAll( all );
- }
+ boolean isShowTaxonomyCommonNames() {
+ return ( ( _show_taxo_common_names != null ) && _show_taxo_common_names.isSelected() );
+ }
+
+ boolean isShowTaxonomyScientificNames() {
+ return ( ( _show_taxo_scientific_names != null ) && _show_taxo_scientific_names.isSelected() );
+ }
+
+ boolean isUseVisualStyles() {
+ return ( ( ( getUseVisualStylesCb() != null ) && getUseVisualStylesCb().isSelected() ) || ( ( getUseVisualStylesCb() == null ) && _color_branches ) );
+ }
+
+ boolean isWidthBranches() {
+ return ( ( _width_branches != null ) && _width_branches.isSelected() );
+ }
+
+ boolean isWriteBranchLengthValues() {
+ return ( ( _write_branch_length_values != null ) && _write_branch_length_values.isSelected() );
+ }
+
+ void phylogenyAdded( final Configuration configuration ) {
+ getIsDrawPhylogramList().add( configuration.isDrawAsPhylogram() );
+ }
+
+ void phylogenyRemoved( final int index ) {
+ getIsDrawPhylogramList().remove( index );
+ }
+
+ void search0() {
+ final MainPanel main_panel = getMainPanel();
+ final Phylogeny tree = main_panel.getCurrentPhylogeny();
+ if ( ( tree == null ) || tree.isEmpty() ) {
+ return;
}
- if ( ( nodes != null ) && ( nodes.size() > 0 ) ) {
- main_panel.getCurrentTreePanel().setFoundNodes0( new HashSet<Long>() );
- for( final PhylogenyNode node : nodes ) {
- main_panel.getCurrentTreePanel().getFoundNodes0().add( node.getId() );
- }
- setSearchFoundCountsOnLabel0( nodes.size() );
+ String query = getSearchTextField0().getText();
+ if ( query != null ) {
+ query = query.trim();
+ }
+ if ( !ForesterUtil.isEmpty( query ) ) {
+ search0( main_panel, tree, query );
}
else {
- setSearchFoundCountsOnLabel0( 0 );
+ getSearchFoundCountsLabel0().setVisible( false );
+ getSearchResetButton0().setEnabled( false );
+ getSearchResetButton0().setVisible( false );
searchReset0();
}
}
- private void search1( final MainPanel main_panel, final Phylogeny tree, final String query_str ) {
- getSearchFoundCountsLabel1().setVisible( true );
- getSearchResetButton1().setEnabled( true );
- getSearchResetButton1().setVisible( true );
- String[] queries = null;
- Set<PhylogenyNode> nodes = null;
- if ( ( query_str.indexOf( ',' ) >= 0 ) && !getOptions().isSearchWithRegex() ) {
- queries = query_str.split( ",+" );
- }
- else {
- queries = new String[ 1 ];
- queries[ 0 ] = query_str.trim();
+ void search1() {
+ final MainPanel main_panel = getMainPanel();
+ final Phylogeny tree = main_panel.getCurrentPhylogeny();
+ if ( ( tree == null ) || tree.isEmpty() ) {
+ return;
}
- if ( ( queries != null ) && ( queries.length > 0 ) ) {
- nodes = new HashSet<PhylogenyNode>();
- for( String query : queries ) {
- if ( ForesterUtil.isEmpty( query ) ) {
- continue;
- }
- query = query.trim();
- final TreePanel tp = getMainPanel().getCurrentTreePanel();
- if ( ( query.indexOf( '+' ) > 0 ) && !getOptions().isSearchWithRegex() ) {
- nodes.addAll( PhylogenyMethods.searchDataLogicalAnd( query.split( "\\++" ),
- tree,
- getOptions().isSearchCaseSensitive(),
- !getOptions().isMatchWholeTermsOnly(),
- isShowDomainArchitectures(),
- tp != null ? Math.pow( 10,
- tp.getDomainStructureEvalueThresholdExp() )
- : 0 ) );
- }
- else {
- nodes.addAll( PhylogenyMethods.searchData( query,
- tree,
- getOptions().isSearchCaseSensitive(),
- !getOptions().isMatchWholeTermsOnly(),
- getOptions().isSearchWithRegex(),
- isShowDomainArchitectures(),
- tp != null ? Math.pow( 10, tp
- .getDomainStructureEvalueThresholdExp() ) : 0 ) );
- }
- }
- if ( getOptions().isInverseSearchResult() ) {
- final List<PhylogenyNode> all = PhylogenyMethods.obtainAllNodesAsList( tree );
- all.removeAll( nodes );
- nodes = new HashSet<PhylogenyNode>();
- nodes.addAll( all );
- }
+ String query = getSearchTextField1().getText();
+ if ( query != null ) {
+ query = query.trim();
}
- if ( ( nodes != null ) && ( nodes.size() > 0 ) ) {
- main_panel.getCurrentTreePanel().setFoundNodes1( new HashSet<Long>() );
- for( final PhylogenyNode node : nodes ) {
- main_panel.getCurrentTreePanel().getFoundNodes1().add( node.getId() );
- }
- setSearchFoundCountsOnLabel1( nodes.size() );
+ if ( !ForesterUtil.isEmpty( query ) ) {
+ search1( main_panel, tree, query );
}
else {
- setSearchFoundCountsOnLabel1( 0 );
+ getSearchFoundCountsLabel1().setVisible( false );
+ getSearchResetButton1().setEnabled( false );
+ getSearchResetButton1().setVisible( false );
searchReset1();
}
}
- private void setDrawPhylogram( final int index, final boolean b ) {
- getIsDrawPhylogramList().set( index, b );
+ void searchReset0() {
+ if ( getMainPanel().getCurrentTreePanel() != null ) {
+ getMainPanel().getCurrentTreePanel().setFoundNodes0( null );
+ }
}
- 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++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.subtree ) ) {
- _subtree_cb_item = cb_index;
- addClickToOption( Configuration.subtree, _configuration.getClickToTitle( Configuration.subtree ) );
- if ( default_option == Configuration.subtree ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.swap ) ) {
- _swap_cb_item = cb_index;
- addClickToOption( Configuration.swap, _configuration.getClickToTitle( Configuration.swap ) );
- if ( default_option == Configuration.swap ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.sort_descendents ) ) {
- _sort_descendents_item = cb_index;
- addClickToOption( Configuration.sort_descendents,
- _configuration.getClickToTitle( Configuration.sort_descendents ) );
- if ( default_option == Configuration.sort_descendents ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.color_node_font ) ) {
- _color_node_font_item = cb_index;
- addClickToOption( Configuration.color_node_font,
- _configuration.getClickToTitle( Configuration.color_node_font ) );
- if ( default_option == Configuration.color_node_font ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.change_node_font ) ) {
- _change_node_font_item = cb_index;
- addClickToOption( Configuration.change_node_font,
- _configuration.getClickToTitle( Configuration.change_node_font ) );
- if ( default_option == Configuration.change_node_font ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.color_subtree ) ) {
- _color_subtree_cb_item = cb_index;
- addClickToOption( Configuration.color_subtree, _configuration.getClickToTitle( Configuration.color_subtree ) );
- if ( default_option == Configuration.color_subtree ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.open_seq_web ) ) {
- _open_seq_web_item = cb_index;
- addClickToOption( Configuration.open_seq_web, _configuration.getClickToTitle( Configuration.open_seq_web ) );
- if ( default_option == Configuration.open_seq_web ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.open_pdb_web ) ) {
- _open_pdb_item = cb_index;
- addClickToOption( Configuration.open_pdb_web, _configuration.getClickToTitle( Configuration.open_pdb_web ) );
- if ( default_option == Configuration.open_pdb_web ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.open_tax_web ) ) {
- _open_tax_web_item = cb_index;
- addClickToOption( Configuration.open_tax_web, _configuration.getClickToTitle( Configuration.open_tax_web ) );
- if ( default_option == Configuration.open_tax_web ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.blast ) ) {
- _blast_item = cb_index;
- addClickToOption( Configuration.blast, _configuration.getClickToTitle( Configuration.blast ) );
- if ( default_option == Configuration.blast ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.select_nodes ) ) {
- _select_nodes_item = cb_index;
- addClickToOption( Configuration.select_nodes, _configuration.getClickToTitle( Configuration.select_nodes ) );
- if ( default_option == Configuration.select_nodes ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.get_ext_desc_data ) ) {
- _get_ext_desc_data = cb_index;
- if ( !ForesterUtil.isEmpty( getConfiguration().getLabelForGetExtDescendentsData() ) ) {
- addClickToOption( Configuration.get_ext_desc_data, getConfiguration()
- .getLabelForGetExtDescendentsData() );
- }
- else {
- addClickToOption( Configuration.get_ext_desc_data,
- getConfiguration().getClickToTitle( Configuration.get_ext_desc_data ) );
- }
- if ( default_option == Configuration.get_ext_desc_data ) {
- selected_index = cb_index;
- }
- cb_index++;
- }
- if ( getOptions().isEditable() ) {
- if ( _configuration.doDisplayClickToOption( Configuration.cut_subtree ) ) {
- _cut_subtree_item = cb_index;
- addClickToOption( Configuration.cut_subtree, _configuration.getClickToTitle( Configuration.cut_subtree ) );
- if ( default_option == Configuration.cut_subtree ) {
- selected_index = cb_index;
+ void searchReset1() {
+ if ( getMainPanel().getCurrentTreePanel() != null ) {
+ getMainPanel().getCurrentTreePanel().setFoundNodes1( null );
+ }
+ }
+
+ void setActionWhenNodeClicked( final NodeClickAction action ) {
+ _action_when_node_clicked = action;
+ }
+
+ void setAnnotationColors( final Map<String, Color> annotation_colors ) {
+ _annotation_colors = annotation_colors;
+ }
+
+ void setCheckbox( final int which, final boolean state ) {
+ switch ( which ) {
+ case Configuration.display_as_phylogram:
+ if ( getDisplayAsPhylogramCb() != null ) {
+ getDisplayAsPhylogramCb().setSelected( state );
}
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.copy_subtree ) ) {
- _copy_subtree_item = cb_index;
- addClickToOption( Configuration.copy_subtree,
- _configuration.getClickToTitle( Configuration.copy_subtree ) );
- if ( default_option == Configuration.copy_subtree ) {
- selected_index = cb_index;
+ break;
+ case Configuration.display_internal_data:
+ if ( _display_internal_data != null ) {
+ _display_internal_data.setSelected( state );
}
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.paste_subtree ) ) {
- _paste_subtree_item = cb_index;
- addClickToOption( Configuration.paste_subtree,
- _configuration.getClickToTitle( Configuration.paste_subtree ) );
- if ( default_option == Configuration.paste_subtree ) {
- selected_index = cb_index;
+ break;
+ case Configuration.color_according_to_species:
+ if ( _color_acc_species != null ) {
+ _color_acc_species.setSelected( state );
}
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.delete_subtree_or_node ) ) {
- _delete_node_or_subtree_item = cb_index;
- addClickToOption( Configuration.delete_subtree_or_node,
- _configuration.getClickToTitle( Configuration.delete_subtree_or_node ) );
- if ( default_option == Configuration.delete_subtree_or_node ) {
- selected_index = cb_index;
+ break;
+ case Configuration.color_according_to_sequence:
+ if ( _color_acc_sequence != null ) {
+ _color_acc_sequence.setSelected( state );
}
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.add_new_node ) ) {
- _add_new_node_item = cb_index;
- addClickToOption( Configuration.add_new_node,
- _configuration.getClickToTitle( Configuration.add_new_node ) );
- if ( default_option == Configuration.add_new_node ) {
- selected_index = cb_index;
+ break;
+ case Configuration.color_according_to_annotation:
+ if ( _color_according_to_annotation != null ) {
+ _color_according_to_annotation.setSelected( state );
}
- cb_index++;
- }
- if ( _configuration.doDisplayClickToOption( Configuration.edit_node_data ) ) {
- _edit_node_data_item = cb_index;
- addClickToOption( Configuration.edit_node_data,
- _configuration.getClickToTitle( Configuration.edit_node_data ) );
- if ( default_option == Configuration.edit_node_data ) {
- selected_index = cb_index;
+ break;
+ case Configuration.show_node_names:
+ if ( _show_node_names != null ) {
+ _show_node_names.setSelected( state );
}
- cb_index++;
- }
+ break;
+ case Configuration.show_taxonomy_scientific_names:
+ if ( _show_taxo_scientific_names != null ) {
+ _show_taxo_scientific_names.setSelected( state );
+ }
+ break;
+ case Configuration.show_taxonomy_common_names:
+ if ( _show_taxo_common_names != null ) {
+ _show_taxo_common_names.setSelected( state );
+ }
+ break;
+ case Configuration.show_tax_code:
+ if ( _show_taxo_code != null ) {
+ _show_taxo_code.setSelected( state );
+ }
+ break;
+ case Configuration.show_taxonomy_images:
+ if ( _show_taxo_images_cb != null ) {
+ _show_taxo_images_cb.setSelected( state );
+ }
+ break;
+ case Configuration.show_annotation:
+ if ( _show_annotation != null ) {
+ _show_annotation.setSelected( state );
+ }
+ break;
+ case Configuration.show_binary_characters:
+ if ( _show_binary_characters != null ) {
+ _show_binary_characters.setSelected( state );
+ }
+ break;
+ case Configuration.show_binary_character_counts:
+ if ( _show_binary_character_counts != null ) {
+ _show_binary_character_counts.setSelected( state );
+ }
+ break;
+ case Configuration.write_confidence_values:
+ if ( getWriteConfidenceCb() != null ) {
+ getWriteConfidenceCb().setSelected( state );
+ }
+ break;
+ case Configuration.write_events:
+ if ( getShowEventsCb() != null ) {
+ getShowEventsCb().setSelected( state );
+ }
+ break;
+ case Configuration.use_style:
+ if ( getUseVisualStylesCb() != null ) {
+ getUseVisualStylesCb().setSelected( state );
+ }
+ break;
+ case Configuration.width_branches:
+ if ( _width_branches != null ) {
+ _width_branches.setSelected( state );
+ }
+ break;
+ case Configuration.show_domain_architectures:
+ if ( _show_domain_architectures != null ) {
+ _show_domain_architectures.setSelected( state );
+ }
+ break;
+ case Configuration.write_branch_length_values:
+ if ( _write_branch_length_values != null ) {
+ _write_branch_length_values.setSelected( state );
+ }
+ break;
+ case Configuration.show_mol_seqs:
+ if ( _show_mol_seqs != null ) {
+ _show_mol_seqs.setSelected( state );
+ }
+ break;
+ case Configuration.show_seq_names:
+ if ( _show_seq_names != null ) {
+ _show_seq_names.setSelected( state );
+ }
+ break;
+ case Configuration.show_gene_names:
+ if ( _show_gene_names != null ) {
+ _show_gene_names.setSelected( state );
+ }
+ break;
+ case Configuration.show_seq_symbols:
+ if ( _show_seq_symbols != null ) {
+ _show_seq_symbols.setSelected( state );
+ }
+ break;
+ case Configuration.show_vector_data:
+ if ( _show_vector_data_cb != null ) {
+ _show_vector_data_cb.setSelected( state );
+ }
+ break;
+ case Configuration.show_properties:
+ if ( _show_properties_cb != null ) {
+ _show_properties_cb.setSelected( state );
+ }
+ break;
+ case Configuration.show_sequence_acc:
+ if ( _show_sequence_acc != null ) {
+ _show_sequence_acc.setSelected( state );
+ }
+ break;
+ case Configuration.dynamically_hide_data:
+ if ( getDynamicallyHideData() != null ) {
+ getDynamicallyHideData().setSelected( state );
+ }
+ break;
+ case Configuration.node_data_popup:
+ if ( getNodeDescPopupCb() != null ) {
+ getNodeDescPopupCb().setSelected( state );
+ }
+ break;
+ /* GUILHEM_BEG */
+ case Configuration.show_relation_confidence:
+ if ( _seq_relation_confidence_switch != null ) {
+ _seq_relation_confidence_switch.setSelected( state );
+ }
+ break;
+ /* GUILHEM_END */
+ default:
+ throw new AssertionError( "unknown checkbox: " + which );
}
- // Set default selection and its action
- _click_to_combobox.setSelectedIndex( selected_index );
- setClickToAction( selected_index );
}
- private void setupDisplayCheckboxes() {
- if ( _configuration.doDisplayOption( Configuration.display_as_phylogram ) ) {
- addCheckbox( Configuration.display_as_phylogram,
- _configuration.getDisplayTitle( Configuration.display_as_phylogram ) );
- setCheckbox( Configuration.display_as_phylogram,
- _configuration.doCheckOption( Configuration.display_as_phylogram ) );
+ /**
+ * Set this checkbox state. Not all checkboxes have been instantiated
+ * depending on the config.
+ */
+ void setCheckbox( final JCheckBox cb, final boolean state ) {
+ if ( cb != null ) {
+ cb.setSelected( state );
}
- if ( _configuration.doDisplayOption( Configuration.dynamically_hide_data ) ) {
- addCheckbox( Configuration.dynamically_hide_data,
- _configuration.getDisplayTitle( Configuration.dynamically_hide_data ) );
- setCheckbox( Configuration.dynamically_hide_data,
- _configuration.doCheckOption( Configuration.dynamically_hide_data ) );
+ }
+
+ void setClickToAction( final int action ) {
+ // Set click-to action
+ if ( action == _show_data_item ) {
+ setActionWhenNodeClicked( NodeClickAction.SHOW_DATA );
}
- if ( _configuration.doDisplayOption( Configuration.node_data_popup ) ) {
- addCheckbox( Configuration.node_data_popup, _configuration.getDisplayTitle( Configuration.node_data_popup ) );
- setCheckbox( Configuration.node_data_popup, _configuration.doCheckOption( Configuration.node_data_popup ) );
+ else if ( action == _collapse_cb_item ) {
+ setActionWhenNodeClicked( NodeClickAction.COLLAPSE );
}
- if ( _configuration.doDisplayOption( Configuration.display_internal_data ) ) {
- addCheckbox( Configuration.display_internal_data,
- _configuration.getDisplayTitle( Configuration.display_internal_data ) );
- setCheckbox( Configuration.display_internal_data,
- _configuration.doCheckOption( Configuration.display_internal_data ) );
+ else if ( action == _reroot_cb_item ) {
+ setActionWhenNodeClicked( NodeClickAction.REROOT );
}
- if ( _configuration.doDisplayOption( Configuration.color_according_to_sequence ) ) {
- addCheckbox( Configuration.color_according_to_sequence,
- _configuration.getDisplayTitle( Configuration.color_according_to_sequence ) );
- setCheckbox( Configuration.color_according_to_sequence,
- _configuration.doCheckOption( Configuration.color_according_to_sequence ) );
+ else if ( action == _subtree_cb_item ) {
+ setActionWhenNodeClicked( NodeClickAction.SUBTREE );
+ }
+ else if ( action == _swap_cb_item ) {
+ setActionWhenNodeClicked( NodeClickAction.SWAP );
+ }
+ else if ( action == _color_subtree_cb_item ) {
+ setActionWhenNodeClicked( NodeClickAction.COLOR_SUBTREE );
+ }
+ else if ( action == _open_seq_web_item ) {
+ setActionWhenNodeClicked( NodeClickAction.OPEN_SEQ_WEB );
+ }
+ else if ( action == _sort_descendents_item ) {
+ setActionWhenNodeClicked( NodeClickAction.SORT_DESCENDENTS );
+ }
+ else if ( action == _blast_item ) {
+ setActionWhenNodeClicked( NodeClickAction.BLAST );
}
- if ( _configuration.doDisplayOption( Configuration.color_according_to_species ) ) {
- addCheckbox( Configuration.color_according_to_species,
- _configuration.getDisplayTitle( Configuration.color_according_to_species ) );
- setCheckbox( Configuration.color_according_to_species,
- _configuration.doCheckOption( Configuration.color_according_to_species ) );
+ else if ( action == _open_tax_web_item ) {
+ setActionWhenNodeClicked( NodeClickAction.OPEN_TAX_WEB );
}
- if ( _configuration.doDisplayOption( Configuration.color_according_to_annotation ) ) {
- addCheckbox( Configuration.color_according_to_annotation,
- _configuration.getDisplayTitle( Configuration.color_according_to_annotation ) );
- setCheckbox( Configuration.color_according_to_annotation,
- _configuration.doCheckOption( Configuration.color_according_to_annotation ) );
+ else if ( action == _cut_subtree_item ) {
+ setActionWhenNodeClicked( NodeClickAction.CUT_SUBTREE );
}
- if ( _configuration.doDisplayOption( Configuration.use_style ) ) {
- addCheckbox( Configuration.use_style, _configuration.getDisplayTitle( Configuration.use_style ) );
- setCheckbox( Configuration.use_style, _configuration.doCheckOption( Configuration.use_style ) );
+ else if ( action == _copy_subtree_item ) {
+ setActionWhenNodeClicked( NodeClickAction.COPY_SUBTREE );
}
- if ( _configuration.doDisplayOption( Configuration.width_branches ) ) {
- addCheckbox( Configuration.width_branches, _configuration.getDisplayTitle( Configuration.width_branches ) );
- setCheckbox( Configuration.width_branches, _configuration.doCheckOption( Configuration.width_branches ) );
+ else if ( action == _delete_node_or_subtree_item ) {
+ setActionWhenNodeClicked( NodeClickAction.DELETE_NODE_OR_SUBTREE );
}
- final JLabel label = new JLabel( "Display Data:" );
- label.setFont( ControlPanel.jcb_bold_font );
- if ( !getConfiguration().isUseNativeUI() ) {
- label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
+ else if ( action == _paste_subtree_item ) {
+ setActionWhenNodeClicked( NodeClickAction.PASTE_SUBTREE );
}
- add( label );
- if ( _configuration.doDisplayOption( Configuration.show_node_names ) ) {
- addCheckbox( Configuration.show_node_names, _configuration.getDisplayTitle( Configuration.show_node_names ) );
- setCheckbox( Configuration.show_node_names, _configuration.doCheckOption( Configuration.show_node_names ) );
+ else if ( action == _add_new_node_item ) {
+ setActionWhenNodeClicked( NodeClickAction.ADD_NEW_NODE );
}
- if ( _configuration.doDisplayOption( Configuration.show_tax_code ) ) {
- addCheckbox( Configuration.show_tax_code, _configuration.getDisplayTitle( Configuration.show_tax_code ) );
- setCheckbox( Configuration.show_tax_code, _configuration.doCheckOption( Configuration.show_tax_code ) );
+ else if ( action == _edit_node_data_item ) {
+ setActionWhenNodeClicked( NodeClickAction.EDIT_NODE_DATA );
}
- if ( _configuration.doDisplayOption( Configuration.show_taxonomy_scientific_names ) ) {
- addCheckbox( Configuration.show_taxonomy_scientific_names,
- _configuration.getDisplayTitle( Configuration.show_taxonomy_scientific_names ) );
- setCheckbox( Configuration.show_taxonomy_scientific_names,
- _configuration.doCheckOption( Configuration.show_taxonomy_scientific_names ) );
+ else if ( action == _select_nodes_item ) {
+ setActionWhenNodeClicked( NodeClickAction.SELECT_NODES );
}
- if ( _configuration.doDisplayOption( Configuration.show_taxonomy_common_names ) ) {
- addCheckbox( Configuration.show_taxonomy_common_names,
- _configuration.getDisplayTitle( Configuration.show_taxonomy_common_names ) );
- setCheckbox( Configuration.show_taxonomy_common_names,
- _configuration.doCheckOption( Configuration.show_taxonomy_common_names ) );
+ else if ( action == _get_ext_desc_data ) {
+ setActionWhenNodeClicked( NodeClickAction.GET_EXT_DESC_DATA );
}
- if ( _configuration.doDisplayOption( Configuration.show_seq_names ) ) {
- addCheckbox( Configuration.show_seq_names, _configuration.getDisplayTitle( Configuration.show_seq_names ) );
- setCheckbox( Configuration.show_seq_names, _configuration.doCheckOption( Configuration.show_seq_names ) );
+ else if ( action == _open_pdb_item ) {
+ setActionWhenNodeClicked( NodeClickAction.OPEN_PDB_WEB );
}
- if ( _configuration.doDisplayOption( Configuration.show_gene_names ) ) {
- addCheckbox( Configuration.show_gene_names, _configuration.getDisplayTitle( Configuration.show_gene_names ) );
- setCheckbox( Configuration.show_gene_names, _configuration.doCheckOption( Configuration.show_gene_names ) );
+ else if ( action == _color_node_font_item ) {
+ setActionWhenNodeClicked( NodeClickAction.COLOR_NODE_FONT );
}
- if ( _configuration.doDisplayOption( Configuration.show_seq_symbols ) ) {
- addCheckbox( Configuration.show_seq_symbols,
- _configuration.getDisplayTitle( Configuration.show_seq_symbols ) );
- setCheckbox( Configuration.show_seq_symbols, _configuration.doCheckOption( Configuration.show_seq_symbols ) );
+ else if ( action == _change_node_font_item ) {
+ setActionWhenNodeClicked( NodeClickAction.CHANGE_NODE_FONT );
}
- if ( _configuration.doDisplayOption( Configuration.show_sequence_acc ) ) {
- addCheckbox( Configuration.show_sequence_acc,
- _configuration.getDisplayTitle( Configuration.show_sequence_acc ) );
- setCheckbox( Configuration.show_sequence_acc,
- _configuration.doCheckOption( Configuration.show_sequence_acc ) );
+ else {
+ throw new RuntimeException( "unknown action: " + action );
}
- if ( _configuration.doDisplayOption( Configuration.show_annotation ) ) {
- addCheckbox( Configuration.show_annotation, _configuration.getDisplayTitle( Configuration.show_annotation ) );
- setCheckbox( Configuration.show_annotation, _configuration.doCheckOption( Configuration.show_annotation ) );
+ // make sure drop down is displaying the correct action
+ // in case this was called from outside the class
+ _click_to_combobox.setSelectedIndex( action );
+ }
+
+ void setColorBranches( final boolean color_branches ) {
+ _color_branches = color_branches;
+ }
+
+ void setDrawPhylogram( final boolean b ) {
+ getDisplayAsPhylogramCb().setSelected( b );
+ setDrawPhylogram( getMainPanel().getCurrentTabIndex(), b );
+ }
+
+ void setDrawPhylogramEnabled( final boolean b ) {
+ getDisplayAsPhylogramCb().setEnabled( b );
+ }
+
+ void setDynamicHidingIsOn( final boolean is_on ) {
+ if ( is_on ) {
+ getDynamicallyHideData().setForeground( getConfiguration().getGuiCheckboxAndButtonActiveColor() );
}
- 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 ) );
+ else {
+ if ( !_configuration.isUseNativeUI() ) {
+ getDynamicallyHideData().setForeground( getConfiguration().getGuiButtonTextColor() );
+ }
+ else {
+ getDynamicallyHideData().setForeground( Color.BLACK );
+ }
}
- if ( _configuration.doDisplayOption( Configuration.write_branch_length_values ) ) {
- addCheckbox( Configuration.write_branch_length_values,
- _configuration.getDisplayTitle( Configuration.write_branch_length_values ) );
- setCheckbox( Configuration.write_branch_length_values,
- _configuration.doCheckOption( Configuration.write_branch_length_values ) );
+ }
+
+ void setSearchFoundCountsOnLabel0( final int counts ) {
+ getSearchFoundCountsLabel0().setText( "Found: " + counts );
+ }
+
+ void setSearchFoundCountsOnLabel1( final int counts ) {
+ getSearchFoundCountsLabel1().setText( "Found: " + counts );
+ }
+
+ void setSequenceColors( final Map<String, Color> sequence_colors ) {
+ _sequence_colors = sequence_colors;
+ }
+
+ void setShowEvents( final boolean show_events ) {
+ if ( getShowEventsCb() == null ) {
+ _show_events = new JCheckBox( "" );
}
- if ( _configuration.doDisplayOption( Configuration.show_binary_characters ) ) {
- addCheckbox( Configuration.show_binary_characters,
- _configuration.getDisplayTitle( Configuration.show_binary_characters ) );
- setCheckbox( Configuration.show_binary_characters,
- _configuration.doCheckOption( Configuration.show_binary_characters ) );
+ getShowEventsCb().setSelected( show_events );
+ }
+
+ void setSpeciesColors( final Map<String, Color> species_colors ) {
+ _species_colors = species_colors;
+ }
+
+ void setupControls() {
+ // The tree display options:
+ setupDisplayCheckboxes();
+ /* GUILHEM_BEG */
+ // The sequence relation query selection combo-box
+ if ( _configuration.displaySequenceRelations() ) {
+ addSequenceRelationBlock();
}
- 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 ) );
+ /* GUILHEM_END */
+ // Click-to options
+ startClickToOptions();
+ setupClickToOptions();
+ endClickToOptions();
+ // Zoom and quick edit buttons
+ addButtons();
+ setupSearchTools0();
+ setupSearchTools1();
+ }
+
+ void setUpControlsForDomainStrucures() {
+ _domain_display_label = new JLabel( "Domain Architectures:" );
+ 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.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 ) );
+ 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() );
}
- if ( _configuration.doDisplayOption( Configuration.show_mol_seqs ) ) {
- addCheckbox( Configuration.show_mol_seqs, _configuration.getDisplayTitle( Configuration.show_mol_seqs ) );
- setCheckbox( Configuration.show_mol_seqs, _configuration.doCheckOption( Configuration.show_mol_seqs ) );
+ 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 setupSearchTools0() {
+ final JLabel search_label = new JLabel( "Search (A):" );
+ search_label.setFont( ControlPanel.jcb_bold_font );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ search_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
}
- if ( _configuration.doDisplayOption( Configuration.write_events ) ) {
- addCheckbox( Configuration.write_events, _configuration.getDisplayTitle( Configuration.write_events ) );
- setCheckbox( Configuration.write_events, _configuration.doCheckOption( Configuration.write_events ) );
+ add( search_label );
+ search_label.setToolTipText( SEARCH_TIP_TEXT );
+ _search_found_label_0 = new JLabel();
+ getSearchFoundCountsLabel0().setVisible( false );
+ _search_found_label_0.setFont( ControlPanel.jcb_bold_font );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ _search_found_label_0.setForeground( getConfiguration().getGuiCheckboxTextColor() );
}
- 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 ) );
+ _search_tf_0 = new JTextField( 3 );
+ _search_tf_0.setToolTipText( SEARCH_TIP_TEXT );
+ _search_tf_0.setEditable( true );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ _search_tf_0.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
+ _search_tf_0.setBackground( getConfiguration().getGuiCheckboxTextColor() );
+ _search_tf_0.setBorder( null );
+ }
+ _search_reset_button_0 = new JButton();
+ getSearchResetButton0().setText( "Reset" );
+ getSearchResetButton0().setEnabled( false );
+ getSearchResetButton0().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 ) {
+ search0();
+ displayedPhylogenyMightHaveChanged( true );
+ }
+ };
+ final ActionListener action_listener = new ActionListener() {
+
+ @Override
+ public void actionPerformed( final ActionEvent e ) {
+ searchReset0();
+ setSearchFoundCountsOnLabel0( 0 );
+ getSearchFoundCountsLabel0().setVisible( false );
+ getSearchTextField0().setText( "" );
+ getSearchResetButton0().setEnabled( false );
+ getSearchResetButton0().setVisible( false );
+ displayedPhylogenyMightHaveChanged( true );
+ }
+ };
+ _search_reset_button_0.addActionListener( action_listener );
+ _search_tf_0.addKeyListener( key_adapter );
+ addJTextField( _search_tf_0, s_panel_1 );
+ s_panel_2.add( _search_found_label_0 );
+ addJButton( _search_reset_button_0, s_panel_2 );
+ }
+
+ void setupSearchTools1() {
+ final JLabel search_label = new JLabel( "Search (B):" );
+ search_label.setFont( ControlPanel.jcb_bold_font );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ search_label.setForeground( getConfiguration().getGuiCheckboxTextColor() );
}
- if ( _configuration.doDisplayOption( Configuration.show_properties ) ) {
- addCheckbox( Configuration.show_properties, _configuration.getDisplayTitle( Configuration.show_properties ) );
- setCheckbox( Configuration.show_properties, _configuration.doCheckOption( Configuration.show_properties ) );
+ add( search_label );
+ search_label.setToolTipText( SEARCH_TIP_TEXT );
+ _search_found_label_1 = new JLabel();
+ getSearchFoundCountsLabel1().setVisible( false );
+ _search_found_label_1.setFont( ControlPanel.jcb_bold_font );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ _search_found_label_1.setForeground( getConfiguration().getGuiCheckboxTextColor() );
}
- if ( _configuration.doDisplayOption( Configuration.show_taxonomy_images ) ) {
- addCheckbox( Configuration.show_taxonomy_images,
- _configuration.getDisplayTitle( Configuration.show_taxonomy_images ) );
- setCheckbox( Configuration.show_taxonomy_images,
- _configuration.doCheckOption( Configuration.show_taxonomy_images ) );
+ _search_tf_1 = new JTextField( 3 );
+ _search_tf_1.setToolTipText( SEARCH_TIP_TEXT );
+ _search_tf_1.setEditable( true );
+ if ( !getConfiguration().isUseNativeUI() ) {
+ _search_tf_1.setForeground( getConfiguration().getGuiMenuBackgroundColor() );
+ _search_tf_1.setBackground( getConfiguration().getGuiCheckboxTextColor() );
+ _search_tf_1.setBorder( null );
}
+ _search_reset_button_1 = new JButton();
+ getSearchResetButton1().setText( "Reset" );
+ getSearchResetButton1().setEnabled( false );
+ getSearchResetButton1().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 ) {
+ search1();
+ displayedPhylogenyMightHaveChanged( true );
+ }
+ };
+ final ActionListener action_listener = new ActionListener() {
+
+ @Override
+ public void actionPerformed( final ActionEvent e ) {
+ searchReset1();
+ setSearchFoundCountsOnLabel1( 0 );
+ getSearchFoundCountsLabel1().setVisible( false );
+ getSearchTextField1().setText( "" );
+ getSearchResetButton1().setEnabled( false );
+ getSearchResetButton1().setVisible( false );
+ displayedPhylogenyMightHaveChanged( true );
+ }
+ };
+ _search_reset_button_1.addActionListener( action_listener );
+ _search_tf_1.addKeyListener( key_adapter );
+ addJTextField( _search_tf_1, s_panel_1 );
+ s_panel_2.add( _search_found_label_1 );
+ addJButton( _search_reset_button_1, s_panel_2 );
}
- private void setVisibilityOfDomainStrucureControls() {
- if ( _zoom_in_domain_structure != null ) {
- final MainFrame mf = getMainFrame();
- if ( mf != null ) {
- if ( isShowDomainArchitectures() ) {
- _domain_display_label.setVisible( true );
- _zoom_in_domain_structure.setVisible( true );
- _zoom_out_domain_structure.setVisible( true );
- _decr_domain_structure_evalue_thr.setVisible( true );
- _incr_domain_structure_evalue_thr.setVisible( true );
- _domain_structure_evalue_thr_tf.setVisible( true );
- if ( mf._right_line_up_domains_cbmi != null ) {
- mf._right_line_up_domains_cbmi.setVisible( true );
- }
- if ( mf._show_domain_labels != null ) {
- mf._show_domain_labels.setVisible( true );
- }
+ void setVisibilityOfDomainStrucureCB() {
+ try {
+ if ( ( getCurrentTreePanel() != null )
+ && ( ( getCurrentTreePanel().getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( getCurrentTreePanel()
+ .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {
+ if ( getMainPanel().getMainFrame()._right_line_up_domains_cbmi != null ) {
+ getMainPanel().getMainFrame()._right_line_up_domains_cbmi.setVisible( false );
}
- else {
- _domain_display_label.setVisible( false );
- _zoom_in_domain_structure.setVisible( false );
- _zoom_out_domain_structure.setVisible( false );
- _decr_domain_structure_evalue_thr.setVisible( false );
- _incr_domain_structure_evalue_thr.setVisible( false );
- _domain_structure_evalue_thr_tf.setVisible( false );
- if ( mf._right_line_up_domains_cbmi != null ) {
- mf._right_line_up_domains_cbmi.setVisible( false );
- }
- if ( mf._show_domain_labels != null ) {
- mf._show_domain_labels.setVisible( false );
- }
+ if ( getMainPanel().getMainFrame()._show_domain_labels != null ) {
+ getMainPanel().getMainFrame()._show_domain_labels.setVisible( false );
}
}
- }
- }
-
- // This takes care of ArchaeopteryxE-issue.
- // Can, and will, return null prior to ArchaeopteryxE initialization completion.
- final private MainFrame getMainFrame() {
- MainFrame mf = getMainPanel().getMainFrame();
- if ( mf == null ) {
- // Must be "E" applet version.
- final ArchaeopteryxE e = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
- if ( e.getMainPanel() == null ) {
- return null;
+ else if ( isShowDomainArchitectures() ) {
+ if ( getMainPanel().getMainFrame()._right_line_up_domains_cbmi != null ) {
+ getMainPanel().getMainFrame()._right_line_up_domains_cbmi.setVisible( true );
+ }
+ if ( getMainPanel().getMainFrame()._show_domain_labels != null ) {
+ getMainPanel().getMainFrame()._show_domain_labels.setVisible( true );
+ }
+ }
+ else {
+ if ( getMainPanel().getMainFrame()._right_line_up_domains_cbmi != null ) {
+ getMainPanel().getMainFrame()._right_line_up_domains_cbmi.setVisible( false );
+ }
+ if ( getMainPanel().getMainFrame()._show_domain_labels != null ) {
+ getMainPanel().getMainFrame()._show_domain_labels.setVisible( false );
+ }
}
- mf = e.getMainPanel().getMainFrame();
}
- return mf;
+ catch ( final Exception ignore ) {
+ //not important...
+ }
}
void setVisibilityOfX() {
}
}
}
- if ( isDrawPhylogram()
- || ( ( getCurrentTreePanel() != null ) && ( ( getCurrentTreePanel().getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( getCurrentTreePanel()
- .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) ) {
- if ( mf._non_lined_up_cladograms_rbmi != null ) {
- mf._non_lined_up_cladograms_rbmi.setVisible( false );
- }
- if ( mf._uniform_cladograms_rbmi != null ) {
- mf._uniform_cladograms_rbmi.setVisible( false );
- }
- if ( mf._ext_node_dependent_cladogram_rbmi != null ) {
- mf._ext_node_dependent_cladogram_rbmi.setVisible( false );
- }
+ if ( isDrawPhylogram()
+ || ( ( getCurrentTreePanel() != null ) && ( ( getCurrentTreePanel().getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( getCurrentTreePanel()
+ .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) ) {
+ if ( mf._non_lined_up_cladograms_rbmi != null ) {
+ mf._non_lined_up_cladograms_rbmi.setVisible( false );
+ }
+ if ( mf._uniform_cladograms_rbmi != null ) {
+ mf._uniform_cladograms_rbmi.setVisible( false );
+ }
+ if ( mf._ext_node_dependent_cladogram_rbmi != null ) {
+ mf._ext_node_dependent_cladogram_rbmi.setVisible( false );
+ }
+ }
+ else {
+ if ( mf._non_lined_up_cladograms_rbmi != null ) {
+ mf._non_lined_up_cladograms_rbmi.setVisible( true );
+ }
+ if ( mf._uniform_cladograms_rbmi != null ) {
+ mf._uniform_cladograms_rbmi.setVisible( true );
+ }
+ if ( mf._ext_node_dependent_cladogram_rbmi != null ) {
+ mf._ext_node_dependent_cladogram_rbmi.setVisible( true );
+ }
+ }
+ if ( isDrawPhylogram() ) {
+ if ( mf._show_scale_cbmi != null ) {
+ mf._show_scale_cbmi.setVisible( true );
+ }
+ }
+ else {
+ if ( mf._show_scale_cbmi != null ) {
+ mf._show_scale_cbmi.setVisible( false );
+ }
+ }
+ if ( getCurrentTreePanel() != null ) {
+ if ( ( getCurrentTreePanel().getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
+ || ( getCurrentTreePanel().getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
+ if ( mf._label_direction_cbmi != null ) {
+ mf._label_direction_cbmi.setVisible( true );
+ }
+ }
+ else {
+ if ( mf._label_direction_cbmi != null ) {
+ mf._label_direction_cbmi.setVisible( false );
+ }
+ }
+ }
+ }
+ }
+
+ void showAnnotations() {
+ if ( _show_annotation != null ) {
+ _show_annotation.setSelected( true );
+ }
+ if ( _color_according_to_annotation != null ) {
+ _color_according_to_annotation.setSelected( true );
+ }
+ if ( _color_acc_species != null ) {
+ _color_acc_species.setSelected( false );
+ }
+ if ( _color_acc_sequence != null ) {
+ _color_acc_sequence.setSelected( false );
+ }
+ _mainpanel.getCurrentTreePanel().repaint();
+ }
+
+ /**
+ * 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().calcParametersForPainting( _mainpanel.getSizeOfViewport().width,
+ _mainpanel.getSizeOfViewport().height );
+ _mainpanel.getCurrentTreePanel().resetPreferredSize();
+ _mainpanel.adjustJScrollPane();
+ _mainpanel.getCurrentTreePanel().repaint();
+ _mainpanel.getCurrentTreePanel().validate();
+ _mainpanel.validate();
+ _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getSizeOfViewport().width,
+ _mainpanel.getSizeOfViewport().height );
+ _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.calcParametersForPainting( _mainpanel.getSizeOfViewport().width,
+ _mainpanel.getSizeOfViewport().height );
+ 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<String>();
+ _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 {
- if ( mf._non_lined_up_cladograms_rbmi != null ) {
- mf._non_lined_up_cladograms_rbmi.setVisible( true );
- }
- if ( mf._uniform_cladograms_rbmi != null ) {
- mf._uniform_cladograms_rbmi.setVisible( true );
- }
- if ( mf._ext_node_dependent_cladogram_rbmi != null ) {
- mf._ext_node_dependent_cladogram_rbmi.setVisible( true );
- }
+ setDrawPhylogramEnabled( false );
+ setDrawPhylogram( false );
}
- if ( isDrawPhylogram() ) {
- if ( mf._show_scale_cbmi != null ) {
- mf._show_scale_cbmi.setVisible( true );
- }
+ if ( getMainPanel().getMainFrame() == null ) {
+ // Must be "E" applet version.
+ final ArchaeopteryxE e = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
+ e.setSelectedTypeInTypeMenu( e.getCurrentTreePanel().getPhylogenyGraphicsType() );
}
else {
- if ( mf._show_scale_cbmi != null ) {
- mf._show_scale_cbmi.setVisible( false );
- }
+ getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getMainPanel().getCurrentTreePanel()
+ .getPhylogenyGraphicsType() );
}
- if ( getCurrentTreePanel() != null ) {
- if ( ( getCurrentTreePanel().getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
- || ( getCurrentTreePanel().getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
- if ( mf._label_direction_cbmi != null ) {
- mf._label_direction_cbmi.setVisible( true );
- }
- }
- else {
- if ( mf._label_direction_cbmi != null ) {
- mf._label_direction_cbmi.setVisible( false );
- }
- }
+ getMainPanel().getCurrentTreePanel().updateSubSuperTreeButton();
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
+ getMainPanel().getControlPanel().updateDomainStructureEvaluethresholdDisplay();
+ getSequenceRelationTypeBox().removeAllItems();
+ for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
+ .getRelevantSequenceRelationTypes() ) {
+ _sequence_relation_type_box.addItem( type );
}
+ getMainPanel().getCurrentTreePanel().repaint();
+ //setSequenceRelationQueries( getMainPanel().getCurrentPhylogeny().getSequenceRelationQueries() );
+ // according to GUILHEM the line above can be removed.
}
}
- void setVisibilityOfDomainStrucureCB() {
- try {
- if ( ( getCurrentTreePanel() != null )
- && ( ( getCurrentTreePanel().getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( getCurrentTreePanel()
- .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {
- if ( getMainPanel().getMainFrame()._right_line_up_domains_cbmi != null ) {
- getMainPanel().getMainFrame()._right_line_up_domains_cbmi.setVisible( false );
- }
- if ( getMainPanel().getMainFrame()._show_domain_labels != null ) {
- getMainPanel().getMainFrame()._show_domain_labels.setVisible( false );
- }
+ /**
+ * 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 );
}
- else if ( isShowDomainArchitectures() ) {
- if ( getMainPanel().getMainFrame()._right_line_up_domains_cbmi != null ) {
- getMainPanel().getMainFrame()._right_line_up_domains_cbmi.setVisible( true );
- }
- if ( getMainPanel().getMainFrame()._show_domain_labels != null ) {
- getMainPanel().getMainFrame()._show_domain_labels.setVisible( true );
- }
+ 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().getDomainStructureEvalueThresholdExp() );
+ }
+ }
+
+ 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 {
- if ( getMainPanel().getMainFrame()._right_line_up_domains_cbmi != null ) {
- getMainPanel().getMainFrame()._right_line_up_domains_cbmi.setVisible( false );
- }
- if ( getMainPanel().getMainFrame()._show_domain_labels != null ) {
- getMainPanel().getMainFrame()._show_domain_labels.setVisible( false );
+ 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();
}
- catch ( final Exception ignore ) {
- //not important...
+ }
+
+ 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();
}
}
}
return label;
}
-
- enum NodeClickAction {
- ADD_NEW_NODE,
- BLAST,
- COLLAPSE,
- COLOR_SUBTREE,
- COPY_SUBTREE,
- CUT_SUBTREE,
- DELETE_NODE_OR_SUBTREE,
- EDIT_NODE_DATA,
- GET_EXT_DESC_DATA,
- OPEN_PDB_WEB,
- OPEN_SEQ_WEB,
- OPEN_TAX_WEB,
- PASTE_SUBTREE,
- REROOT,
- SELECT_NODES,
- SHOW_DATA,
- SORT_DESCENDENTS,
- SUBTREE,
- SWAP,
- CHANGE_NODE_FONT,
- COLOR_NODE_FONT;
- }
}
public static final long serialVersionUID = 62256323L;
private static final String[] STYLE = { REGULAR, BOLD, ITALIC, BOLD_ITALIC };
private static final String[] SIZE = { "3", "4", "6", "8", "10", "12", "14", "16", "18", "20", "22",
- "24", "26", "28", "36", "72" };
+ "24", "26", "28", "36", "72" };
private static final int OK_OPTION = 1;
private static final int CANCEL_OPTION = 2;
private Font _font;
private String _type;
private int _style;
private int _size;
- private final JList<String> _font_list = new JList<String>( AptxUtil.getAvailableFontFamiliesSorted() );
- private final JList<String> _style_list = new JList<String>( STYLE );
- private final JList<String> _size_list = new JList<String>( SIZE );
+ private final JList<String> _font_list = new JList<String>( AptxUtil.getAvailableFontFamiliesSorted() );
+ private final JList<String> _style_list = new JList<String>( STYLE );
+ private final JList<String> _size_list = new JList<String>( SIZE );
private final JTextField _fonts_tf = new JTextField();
private final JTextField _style_tf = new JTextField();
private final JTextField _size_tf = new JTextField();
boolean found = false;
_type = _fonts_tf.getText();
for( int i = 0; i < _font_list.getModel().getSize(); i++ ) {
- if ( ( ( String ) _font_list.getModel().getElementAt( i ) ).startsWith( _fonts_tf.getText().trim() ) ) {
+ if ( _font_list.getModel().getElementAt( i ).startsWith( _fonts_tf.getText().trim() ) ) {
_font_list.setSelectedIndex( i );
setScrollPos( _font_jsp, _font_list, i );
found = true;
return _font.getStyle();
}
- private void parseSize() {
- try {
- _size = ( Integer.parseInt( _size_tf.getText().trim() ) );
- }
- catch ( final Exception ex ) {
- // Ignore.
- }
- if ( _size < 1 ) {
- _size = 1;
- }
- }
-
@Override
public void setFont( final Font font ) {
_font = font;
}
- private void setScrollPos( final JScrollPane sp, final JList<String> list, final int index ) {
- final int unit_size = sp.getVerticalScrollBar().getMaximum() / list.getModel().getSize();
- sp.getVerticalScrollBar().setValue( ( index - 2 ) * unit_size );
- }
-
public int showDialog( final Component parent, final String title ) {
boolean found = false;
_option = CANCEL_OPTION;
found = false;
for( int i = 0; i < _size_list.getModel().getSize(); i++ ) {
_size_list.setSelectedIndex( i );
- if ( _font.getSize() <= Integer.parseInt( ( String ) _size_list.getSelectedValue() ) ) {
+ if ( _font.getSize() <= Integer.parseInt( _size_list.getSelectedValue() ) ) {
found = true;
setScrollPos( _size_jsp, _size_list, i );
break;
public void valueChanged( final ListSelectionEvent e ) {
if ( e.getSource() == _font_list ) {
if ( _font_list.getSelectedValue() != null ) {
- _fonts_tf.setText( ( ( String ) ( _font_list.getSelectedValue() ) ) );
+ _fonts_tf.setText( ( ( _font_list.getSelectedValue() ) ) );
}
_type = _fonts_tf.getText();
_test_tf.setFont( new Font( _type, _style, _size ) );
}
else if ( e.getSource() == _style_list ) {
- _style_tf.setText( ( ( String ) ( _style_list.getSelectedValue() ) ) );
+ _style_tf.setText( ( ( _style_list.getSelectedValue() ) ) );
if ( _style_tf.getText().equals( REGULAR ) ) {
_style = 0;
}
}
else if ( e.getSource() == _size_list ) {
if ( _size_list.getSelectedValue() != null ) {
- _size_tf.setText( ( ( String ) ( _size_list.getSelectedValue() ) ) );
+ _size_tf.setText( ( ( _size_list.getSelectedValue() ) ) );
}
_size = ( Integer.parseInt( _size_tf.getText().trim() ) );
_test_tf.setFont( new Font( _type, _style, _size ) );
}
}
+
+ private void parseSize() {
+ try {
+ _size = ( Integer.parseInt( _size_tf.getText().trim() ) );
+ }
+ catch ( final Exception ex ) {
+ // Ignore.
+ }
+ if ( _size < 1 ) {
+ _size = 1;
+ }
+ }
+
+ private void setScrollPos( final JScrollPane sp, final JList<String> list, final int index ) {
+ final int unit_size = sp.getVerticalScrollBar().getMaximum() / list.getModel().getSize();
+ sp.getVerticalScrollBar().setValue( ( index - 2 ) * unit_size );
+ }
}
_save_filechooser = new JFileChooser();\r
_save_filechooser.setCurrentDirectory( new File( "." ) );\r
_save_filechooser.setMultiSelectionEnabled( false );\r
- _save_filechooser.setFileFilter( MainFrame.xmlfilter );\r
+ _save_filechooser.setFileFilter( xmlfilter );\r
_save_filechooser.addChoosableFileFilter( nhfilter );\r
_save_filechooser.addChoosableFileFilter( nexusfilter );\r
_save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );\r
if ( new_dir != null ) {\r
setCurrentDir( new_dir );\r
}\r
- \r
}\r
else if ( o == _write_to_tif_item ) {\r
final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),\r
if ( new_dir != null ) {\r
setCurrentDir( new_dir );\r
}\r
- \r
}\r
else if ( o == _write_to_bmp_item ) {\r
final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),\r
if ( new_dir != null ) {\r
setCurrentDir( new_dir );\r
}\r
- \r
}\r
else if ( o == _write_to_png_item ) {\r
final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),\r
print( getCurrentTreePanel(), getOptions(), this );\r
}\r
else if ( o == _save_item ) {\r
- \r
- final File new_dir = writeToFile( _mainpanel.getCurrentPhylogeny() ,\r
- getMainPanel(), _save_filechooser, _current_dir, getContentPane(), this );\r
- \r
+ final File new_dir = writeToFile( _mainpanel.getCurrentPhylogeny(),\r
+ getMainPanel(),\r
+ _save_filechooser,\r
+ _current_dir,\r
+ getContentPane(),\r
+ this );\r
if ( new_dir != null ) {\r
- setCurrentDir( new_dir ); \r
+ setCurrentDir( new_dir );\r
}\r
- \r
}\r
- \r
else if ( o == _graphics_export_visible_only_cbmi ) {\r
updateOptions( getOptions() );\r
}\r
} );\r
}\r
\r
- void activateSaveAllIfNeeded() {\r
- if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {\r
- _save_all_item.setEnabled( true );\r
- }\r
- else {\r
- _save_all_item.setEnabled( false );\r
- }\r
- }\r
-\r
- void buildFileMenu() {\r
- _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );\r
- _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );\r
- if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {\r
- _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );\r
- }\r
- _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );\r
- _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );\r
- if ( AptxUtil.canWriteFormat( "gif" ) ) {\r
- _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );\r
- }\r
- if ( AptxUtil.canWriteFormat( "bmp" ) ) {\r
- _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );\r
- }\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
- customizeJMenuItem( _save_item );\r
- customizeJMenuItem( _write_to_pdf_item );\r
- customizeJMenuItem( _write_to_png_item );\r
- customizeJMenuItem( _write_to_jpg_item );\r
- customizeJMenuItem( _write_to_gif_item );\r
- customizeJMenuItem( _write_to_tif_item );\r
- customizeJMenuItem( _write_to_bmp_item );\r
- customizeJMenuItem( _print_item );\r
- customizeJMenuItem( _exit_item );\r
- _jmenubar.add( _file_jmenu );\r
- }\r
-\r
- void buildFontSizeMenu() {\r
- _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );\r
- _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );\r
- _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );\r
- _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );\r
- _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );\r
- _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );\r
- customizeJMenuItem( _super_tiny_fonts_item );\r
- customizeJMenuItem( _tiny_fonts_item );\r
- customizeJMenuItem( _small_fonts_item );\r
- customizeJMenuItem( _medium_fonts_item );\r
- customizeJMenuItem( _large_fonts_item );\r
- _jmenubar.add( _font_size_menu );\r
- }\r
-\r
- void buildHelpMenu() {\r
- _help_jmenu = createMenu( "Help", getConfiguration() );\r
- _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );\r
- _help_jmenu.addSeparator();\r
- _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );\r
- _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...\r
- _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );\r
- _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );\r
- _help_jmenu.addSeparator();\r
- _help_jmenu.add( _about_item = new JMenuItem( "About" ) );\r
- customizeJMenuItem( _help_item );\r
- customizeJMenuItem( _website_item );\r
- customizeJMenuItem( _phyloxml_website_item );\r
- customizeJMenuItem( _aptx_ref_item );\r
- customizeJMenuItem( _phyloxml_ref_item );\r
- customizeJMenuItem( _about_item );\r
- _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );\r
- _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );\r
- _jmenubar.add( _help_jmenu );\r
- }\r
-\r
- void buildTypeMenu() {\r
- _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );\r
- _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );\r
- customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _triangular_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _euro_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _rounded_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _curved_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _convex_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _circular_type_cbmi, false );\r
- _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
- _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
- initializeTypeMenu( getOptions() );\r
- _jmenubar.add( _type_menu );\r
- }\r
-\r
- void buildViewMenu() {\r
- _view_jmenu = createMenu( "View", getConfiguration() );\r
- _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );\r
- _view_jmenu.addSeparator();\r
- _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );\r
- _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );\r
- _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );\r
- customizeJMenuItem( _display_basic_information_item );\r
- customizeJMenuItem( _view_as_NH_item );\r
- customizeJMenuItem( _view_as_XML_item );\r
- customizeJMenuItem( _view_as_nexus_item );\r
- _jmenubar.add( _view_jmenu );\r
- }\r
-\r
- void checkTextFrames() {\r
- if ( _textframes.size() > 5 ) {\r
- try {\r
- if ( _textframes.getFirst() != null ) {\r
- _textframes.getFirst().removeMe();\r
- }\r
- else {\r
- _textframes.removeFirst();\r
- }\r
+ private void annotateSequences() {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ List<PhylogenyNode> nodes = null;\r
+ if ( ( getCurrentTreePanel().getFoundNodes0() != null )\r
+ || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
+ nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
}\r
- catch ( final NoSuchElementException e ) {\r
- // Ignore.\r
+ if ( ( nodes == null ) || nodes.isEmpty() ) {\r
+ JOptionPane\r
+ .showMessageDialog( this,\r
+ "Need to select nodes, either via direct selection or via the \"Search\" function",\r
+ "No nodes selected for annotation",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
+ if ( ( phy != null ) && !phy.isEmpty() ) {\r
+ final JTextField ref_field = new JTextField( 10 );\r
+ final JTextField desc_filed = new JTextField( 20 );\r
+ ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""\r
+ : getPreviousNodeAnnotationReference() );\r
+ final JPanel my_panel = new JPanel();\r
+ my_panel.add( new JLabel( "Reference " ) );\r
+ my_panel.add( ref_field );\r
+ my_panel.add( Box.createHorizontalStrut( 15 ) );\r
+ my_panel.add( new JLabel( "Description " ) );\r
+ my_panel.add( desc_filed );\r
+ final int result = JOptionPane.showConfirmDialog( null,\r
+ my_panel,\r
+ "Enter the sequence annotation(s) for the "\r
+ + nodes.size() + " selected nodes",\r
+ JOptionPane.OK_CANCEL_OPTION );\r
+ if ( result == JOptionPane.OK_OPTION ) {\r
+ String ref = ref_field.getText();\r
+ String desc = desc_filed.getText();\r
+ if ( !ForesterUtil.isEmpty( ref ) ) {\r
+ ref = ref.trim();\r
+ ref = ref.replaceAll( "\\s+", " " );\r
+ if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )\r
+ || ( ref.length() < 3 ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Reference needs to be in the form of \"GO:1234567\"",\r
+ "Illegal Format for Annotation Reference",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ }\r
+ if ( ref != null ) {\r
+ setPreviousNodeAnnotationReference( ref );\r
+ }\r
+ if ( desc != null ) {\r
+ desc = desc.trim();\r
+ desc = desc.replaceAll( "\\s+", " " );\r
+ }\r
+ if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {\r
+ for( final PhylogenyNode n : nodes ) {\r
+ ForesterUtil.ensurePresenceOfSequence( n );\r
+ final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()\r
+ : new Annotation( ref );\r
+ if ( !ForesterUtil.isEmpty( desc ) ) {\r
+ ann.setDesc( desc );\r
+ }\r
+ n.getNodeData().getSequence().addAnnotation( ann );\r
+ }\r
+ }\r
+ getMainPanel().getControlPanel().showAnnotations();\r
+ }\r
}\r
}\r
}\r
\r
- void choosePdfWidth() {\r
- final String s = ( String ) JOptionPane.showInputDialog( this,\r
- "Please enter the default line width for PDF export.\n"\r
- + "[current value: "\r
- + getOptions().getPrintLineWidth() + "]\n",\r
- "Line Width for PDF Export",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getPrintLineWidth() );\r
+ private void chooseFont() {\r
+ final FontChooser fc = new FontChooser();\r
+ fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );\r
+ fc.showDialog( this, "Select the Base Font" );\r
+ getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );\r
+ }\r
+\r
+ private void chooseMinimalConfidence() {\r
+ final String s = ( String ) JOptionPane\r
+ .showInputDialog( this,\r
+ "Please enter the minimum for confidence values to be displayed.\n"\r
+ + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",\r
+ "Minimal Confidence Value",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getOptions().getMinConfidenceValue() );\r
if ( !ForesterUtil.isEmpty( s ) ) {\r
boolean success = true;\r
- float f = 0.0f;\r
+ double m = 0.0;\r
final String m_str = s.trim();\r
if ( !ForesterUtil.isEmpty( m_str ) ) {\r
try {\r
- f = Float.parseFloat( m_str );\r
+ m = Double.parseDouble( m_str );\r
}\r
catch ( final Exception ex ) {\r
success = false;\r
else {\r
success = false;\r
}\r
- if ( success && ( f > 0.0 ) ) {\r
- getOptions().setPrintLineWidth( f );\r
+ if ( success && ( m >= 0.0 ) ) {\r
+ getOptions().setMinConfidenceValue( m );\r
}\r
}\r
}\r
\r
- void choosePrintSize() {\r
- final String s = ( String ) JOptionPane.showInputDialog( this,\r
- "Please enter values for width and height,\nseparated by a comma.\n"\r
- + "[current values: "\r
- + getOptions().getPrintSizeX() + ", "\r
- + getOptions().getPrintSizeY() + "]\n"\r
- + "[A4: " + Constants.A4_SIZE_X + ", "\r
- + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "\r
- + Constants.US_LETTER_SIZE_X + ", "\r
- + Constants.US_LETTER_SIZE_Y + "]",\r
- "Default Size for Graphics Export",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getPrintSizeX() + ", "\r
- + getOptions().getPrintSizeY() );\r
- if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {\r
- boolean success = true;\r
- int x = 0;\r
- int y = 0;\r
- final String[] str_ary = s.split( "," );\r
- if ( str_ary.length == 2 ) {\r
- final String x_str = str_ary[ 0 ].trim();\r
- final String y_str = str_ary[ 1 ].trim();\r
- if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {\r
- try {\r
- x = Integer.parseInt( x_str );\r
- y = Integer.parseInt( y_str );\r
- }\r
- catch ( final Exception ex ) {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
+ private void deleteSelectedNodes( final boolean delete ) {\r
+ final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
+ if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {\r
+ return;\r
+ }\r
+ final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
+ if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
+ final List<PhylogenyNode> all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
+ for( final PhylogenyNode n : all_selected_nodes ) {\r
+ if ( n.isExternal() ) {\r
+ nodes.add( n );\r
}\r
}\r
- else {\r
- success = false;\r
+ }\r
+ String function = "Retain";\r
+ if ( delete ) {\r
+ function = "Delete";\r
+ }\r
+ if ( ( nodes == null ) || nodes.isEmpty() ) {\r
+ JOptionPane\r
+ .showMessageDialog( this,\r
+ "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
+ "No external nodes selected to " + function.toLowerCase(),\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final int todo = nodes.size();\r
+ final int ext = phy.getNumberOfExternalNodes();\r
+ int res = todo;\r
+ if ( delete ) {\r
+ res = ext - todo;\r
+ }\r
+ if ( res < 1 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Cannot delete all nodes",\r
+ "Attempt to delete all nodes ",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final int result = JOptionPane.showConfirmDialog( null, function + " " + todo\r
+ + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
+ + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
+ if ( result == JOptionPane.OK_OPTION ) {\r
+ if ( !delete ) {\r
+ final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
+ for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( !nodes.contains( n ) ) {\r
+ to_delete.add( n );\r
+ }\r
+ }\r
+ for( final PhylogenyNode n : to_delete ) {\r
+ phy.deleteSubtree( n, true );\r
+ }\r
}\r
- if ( success && ( x > 1 ) && ( y > 1 ) ) {\r
- getOptions().setPrintSizeX( x );\r
- getOptions().setPrintSizeY( y );\r
+ else {\r
+ for( final PhylogenyNode n : nodes ) {\r
+ phy.deleteSubtree( n, true );\r
+ }\r
}\r
+ resetSearch();\r
+ getCurrentTreePanel().setNodeInPreorderToNull();\r
+ phy.externalNodesHaveChanged();\r
+ phy.clearHashIdToNodeMap();\r
+ phy.recalculateNumberOfExternalDescendants( true );\r
+ getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
+ getCurrentTreePanel().setEdited( true );\r
+ repaint();\r
}\r
}\r
\r
- void close() {\r
- removeAllTextFrames();\r
- if ( _mainpanel != null ) {\r
- _mainpanel.terminate();\r
- }\r
- if ( _contentpane != null ) {\r
- _contentpane.removeAll();\r
+ private void doUpdateProcessMenu() {\r
+ if ( _process_pool.size() > 0 ) {\r
+ if ( _process_menu == null ) {\r
+ _process_menu = createMenu( "", getConfiguration() );\r
+ _process_menu.setForeground( Color.RED );\r
+ }\r
+ _process_menu.removeAll();\r
+ final String text = "processes running: " + _process_pool.size();\r
+ _process_menu.setText( text );\r
+ _jmenubar.add( _process_menu );\r
+ for( int i = 0; i < _process_pool.size(); ++i ) {\r
+ final ProcessRunning p = _process_pool.getProcessByIndex( i );\r
+ _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );\r
+ }\r
}\r
- setVisible( false );\r
- dispose();\r
- }\r
-\r
- void colorRank() {\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- final String[] ranks = AptxUtil.getAllPossibleRanks();\r
- final String rank = ( String ) JOptionPane\r
- .showInputDialog( this,\r
- "What rank should the colorization be based on",\r
- "Rank Selection",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- ranks,\r
- null );\r
- if ( !ForesterUtil.isEmpty( rank ) ) {\r
- _mainpanel.getCurrentTreePanel().colorRank( rank );\r
+ else {\r
+ if ( _process_menu != null ) {\r
+ _process_menu.removeAll();\r
+ _jmenubar.remove( _process_menu );\r
}\r
}\r
+ _jmenubar.validate();\r
+ _jmenubar.repaint();\r
+ repaint();\r
}\r
\r
- void confColor() {\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().confColor();\r
- }\r
+ private String getPreviousNodeAnnotationReference() {\r
+ return _previous_node_annotation_ref;\r
}\r
\r
- void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {\r
- if ( item != null ) {\r
- item.setFont( MainFrame.menu_font );\r
- if ( !getConfiguration().isUseNativeUI() ) {\r
- item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
- item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
- }\r
- item.setSelected( is_selected );\r
- item.addActionListener( this );\r
+ private void removeBranchColors() {\r
+ if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
+ AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );\r
}\r
}\r
\r
- JMenuItem customizeJMenuItem( final JMenuItem jmi ) {\r
- if ( jmi != null ) {\r
- jmi.setFont( MainFrame.menu_font );\r
- if ( !getConfiguration().isUseNativeUI() ) {\r
- jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
- jmi.setForeground( getConfiguration().getGuiMenuTextColor() );\r
- }\r
- jmi.addActionListener( this );\r
+ private void removeVisualStyles() {\r
+ if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
+ AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );\r
}\r
- return jmi;\r
}\r
\r
- void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {\r
- if ( item != null ) {\r
- item.setFont( MainFrame.menu_font );\r
- if ( !getConfiguration().isUseNativeUI() ) {\r
- item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
- item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
- }\r
- item.setSelected( is_selected );\r
- item.addActionListener( this );\r
- }\r
+ private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {\r
+ _previous_node_annotation_ref = previous_node_annotation_ref;\r
}\r
\r
- void displayBasicInformation( final File treefile ) {\r
- if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
- String title = "Basic Information";\r
- if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
- title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";\r
- }\r
- showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );\r
+ private void writeAllToFile() {\r
+ if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {\r
+ return;\r
}\r
- }\r
-\r
- void exceptionOccuredDuringOpenFile( final Exception e ) {\r
- try {\r
- _mainpanel.getCurrentTreePanel().setArrowCursor();\r
+ final File my_dir = getCurrentDir();\r
+ if ( my_dir != null ) {\r
+ _save_filechooser.setCurrentDirectory( my_dir );\r
}\r
- catch ( final Exception ex ) {\r
- // Do nothing.\r
+ _save_filechooser.setSelectedFile( new File( "" ) );\r
+ final int result = _save_filechooser.showSaveDialog( _contentpane );\r
+ final File file = _save_filechooser.getSelectedFile();\r
+ setCurrentDir( _save_filechooser.getCurrentDirectory() );\r
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ if ( file.exists() ) {\r
+ final int i = JOptionPane.showConfirmDialog( this,\r
+ file + " already exists. Overwrite?",\r
+ "Warning",\r
+ JOptionPane.OK_CANCEL_OPTION,\r
+ JOptionPane.WARNING_MESSAGE );\r
+ if ( i != JOptionPane.OK_OPTION ) {\r
+ return;\r
+ }\r
+ else {\r
+ try {\r
+ file.delete();\r
+ }\r
+ catch ( final Exception e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Failed to delete: " + file,\r
+ "Error",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ }\r
+ }\r
+ final int count = getMainPanel().getTabbedPane().getTabCount();\r
+ final List<Phylogeny> trees = new ArrayList<Phylogeny>();\r
+ for( int i = 0; i < count; ++i ) {\r
+ final Phylogeny phy = getMainPanel().getPhylogeny( i );\r
+ if ( ForesterUtil.isEmpty( phy.getName() )\r
+ && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) {\r
+ phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) );\r
+ }\r
+ trees.add( phy );\r
+ getMainPanel().getTreePanels().get( i ).setEdited( false );\r
+ }\r
+ final PhylogenyWriter writer = new PhylogenyWriter();\r
+ try {\r
+ writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );\r
+ }\r
+ catch ( final IOException e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Failed to write to: " + file,\r
+ "Error",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
}\r
- JOptionPane.showMessageDialog( this,\r
- ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
- "Error during File|Open",\r
- JOptionPane.ERROR_MESSAGE );\r
}\r
\r
- static void exceptionOccuredDuringSaveAs( final Exception e, \r
- final TreePanel tp,\r
- final Component comp ) {\r
- try {\r
- tp.setArrowCursor();\r
+ void activateSaveAllIfNeeded() {\r
+ if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {\r
+ _save_all_item.setEnabled( true );\r
}\r
- catch ( final Exception ex ) {\r
- // Do nothing.\r
+ else {\r
+ _save_all_item.setEnabled( false );\r
}\r
- JOptionPane.showMessageDialog( comp, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );\r
}\r
\r
- void executeGSDI() {\r
- if ( !isOKforSDI( false, true ) ) {\r
- return;\r
- }\r
- if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Gene tree is not rooted.",\r
- "Cannot execute GSDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
+ void buildFileMenu() {\r
+ _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );\r
+ _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );\r
+ if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {\r
+ _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );\r
}\r
- final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
- gene_tree.setAllNodesToNotCollapse();\r
- gene_tree.recalculateNumberOfExternalDescendants( false );\r
- GSDI gsdi = null;\r
- final Phylogeny species_tree = getSpeciesTree().copy();\r
- try {\r
- gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );\r
+ _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );\r
+ _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );\r
+ if ( AptxUtil.canWriteFormat( "gif" ) ) {\r
+ _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );\r
}\r
- catch ( final SDIException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Error during GSDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
+ if ( AptxUtil.canWriteFormat( "bmp" ) ) {\r
+ _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );\r
+ }\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
+ customizeJMenuItem( _save_item );\r
+ customizeJMenuItem( _write_to_pdf_item );\r
+ customizeJMenuItem( _write_to_png_item );\r
+ customizeJMenuItem( _write_to_jpg_item );\r
+ customizeJMenuItem( _write_to_gif_item );\r
+ customizeJMenuItem( _write_to_tif_item );\r
+ customizeJMenuItem( _write_to_bmp_item );\r
+ customizeJMenuItem( _print_item );\r
+ customizeJMenuItem( _exit_item );\r
+ _jmenubar.add( _file_jmenu );\r
+ }\r
+\r
+ void buildFontSizeMenu() {\r
+ _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );\r
+ _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );\r
+ _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );\r
+ _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );\r
+ _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );\r
+ _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );\r
+ customizeJMenuItem( _super_tiny_fonts_item );\r
+ customizeJMenuItem( _tiny_fonts_item );\r
+ customizeJMenuItem( _small_fonts_item );\r
+ customizeJMenuItem( _medium_fonts_item );\r
+ customizeJMenuItem( _large_fonts_item );\r
+ _jmenubar.add( _font_size_menu );\r
+ }\r
+\r
+ void buildHelpMenu() {\r
+ _help_jmenu = createMenu( "Help", getConfiguration() );\r
+ _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );\r
+ _help_jmenu.addSeparator();\r
+ _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );\r
+ _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...\r
+ _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );\r
+ _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );\r
+ _help_jmenu.addSeparator();\r
+ _help_jmenu.add( _about_item = new JMenuItem( "About" ) );\r
+ customizeJMenuItem( _help_item );\r
+ customizeJMenuItem( _website_item );\r
+ customizeJMenuItem( _phyloxml_website_item );\r
+ customizeJMenuItem( _aptx_ref_item );\r
+ customizeJMenuItem( _phyloxml_ref_item );\r
+ customizeJMenuItem( _about_item );\r
+ _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );\r
+ _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );\r
+ _jmenubar.add( _help_jmenu );\r
+ }\r
+\r
+ void buildTypeMenu() {\r
+ _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );\r
+ _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );\r
+ customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _triangular_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _euro_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _rounded_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _curved_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _convex_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _circular_type_cbmi, false );\r
+ _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
+ _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
+ initializeTypeMenu( getOptions() );\r
+ _jmenubar.add( _type_menu );\r
+ }\r
+\r
+ void buildViewMenu() {\r
+ _view_jmenu = createMenu( "View", getConfiguration() );\r
+ _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );\r
+ _view_jmenu.addSeparator();\r
+ _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );\r
+ _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );\r
+ _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );\r
+ customizeJMenuItem( _display_basic_information_item );\r
+ customizeJMenuItem( _view_as_NH_item );\r
+ customizeJMenuItem( _view_as_XML_item );\r
+ customizeJMenuItem( _view_as_nexus_item );\r
+ _jmenubar.add( _view_jmenu );\r
+ }\r
+\r
+ void checkTextFrames() {\r
+ if ( _textframes.size() > 5 ) {\r
+ try {\r
+ if ( _textframes.getFirst() != null ) {\r
+ _textframes.getFirst().removeMe();\r
+ }\r
+ else {\r
+ _textframes.removeFirst();\r
+ }\r
+ }\r
+ catch ( final NoSuchElementException e ) {\r
+ // Ignore.\r
+ }\r
+ }\r
+ }\r
+\r
+ void choosePdfWidth() {\r
+ final String s = ( String ) JOptionPane.showInputDialog( this,\r
+ "Please enter the default line width for PDF export.\n"\r
+ + "[current value: "\r
+ + getOptions().getPrintLineWidth() + "]\n",\r
+ "Line Width for PDF Export",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getOptions().getPrintLineWidth() );\r
+ if ( !ForesterUtil.isEmpty( s ) ) {\r
+ boolean success = true;\r
+ float f = 0.0f;\r
+ final String m_str = s.trim();\r
+ if ( !ForesterUtil.isEmpty( m_str ) ) {\r
+ try {\r
+ f = Float.parseFloat( m_str );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
+ }\r
+ }\r
+ else {\r
+ success = false;\r
+ }\r
+ if ( success && ( f > 0.0 ) ) {\r
+ getOptions().setPrintLineWidth( f );\r
+ }\r
+ }\r
+ }\r
+\r
+ void choosePrintSize() {\r
+ final String s = ( String ) JOptionPane.showInputDialog( this,\r
+ "Please enter values for width and height,\nseparated by a comma.\n"\r
+ + "[current values: "\r
+ + getOptions().getPrintSizeX() + ", "\r
+ + getOptions().getPrintSizeY() + "]\n"\r
+ + "[A4: " + Constants.A4_SIZE_X + ", "\r
+ + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "\r
+ + Constants.US_LETTER_SIZE_X + ", "\r
+ + Constants.US_LETTER_SIZE_Y + "]",\r
+ "Default Size for Graphics Export",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getOptions().getPrintSizeX() + ", "\r
+ + getOptions().getPrintSizeY() );\r
+ if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {\r
+ boolean success = true;\r
+ int x = 0;\r
+ int y = 0;\r
+ final String[] str_ary = s.split( "," );\r
+ if ( str_ary.length == 2 ) {\r
+ final String x_str = str_ary[ 0 ].trim();\r
+ final String y_str = str_ary[ 1 ].trim();\r
+ if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {\r
+ try {\r
+ x = Integer.parseInt( x_str );\r
+ y = Integer.parseInt( y_str );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
+ }\r
+ }\r
+ else {\r
+ success = false;\r
+ }\r
+ }\r
+ else {\r
+ success = false;\r
+ }\r
+ if ( success && ( x > 1 ) && ( y > 1 ) ) {\r
+ getOptions().setPrintSizeX( x );\r
+ getOptions().setPrintSizeY( y );\r
+ }\r
+ }\r
+ }\r
+\r
+ void close() {\r
+ removeAllTextFrames();\r
+ if ( _mainpanel != null ) {\r
+ _mainpanel.terminate();\r
+ }\r
+ if ( _contentpane != null ) {\r
+ _contentpane.removeAll();\r
+ }\r
+ setVisible( false );\r
+ dispose();\r
+ }\r
+\r
+ void colorRank() {\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ final String[] ranks = AptxUtil.getAllPossibleRanks();\r
+ final String rank = ( String ) JOptionPane\r
+ .showInputDialog( this,\r
+ "What rank should the colorization be based on",\r
+ "Rank Selection",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ ranks,\r
+ null );\r
+ if ( !ForesterUtil.isEmpty( rank ) ) {\r
+ _mainpanel.getCurrentTreePanel().colorRank( rank );\r
+ }\r
+ }\r
+ }\r
+\r
+ void confColor() {\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ _mainpanel.getCurrentTreePanel().confColor();\r
+ }\r
+ }\r
+\r
+ void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {\r
+ if ( item != null ) {\r
+ item.setFont( MainFrame.menu_font );\r
+ if ( !getConfiguration().isUseNativeUI() ) {\r
+ item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
+ item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
+ }\r
+ item.setSelected( is_selected );\r
+ item.addActionListener( this );\r
+ }\r
+ }\r
+\r
+ JMenuItem customizeJMenuItem( final JMenuItem jmi ) {\r
+ if ( jmi != null ) {\r
+ jmi.setFont( MainFrame.menu_font );\r
+ if ( !getConfiguration().isUseNativeUI() ) {\r
+ jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
+ jmi.setForeground( getConfiguration().getGuiMenuTextColor() );\r
+ }\r
+ jmi.addActionListener( this );\r
+ }\r
+ return jmi;\r
+ }\r
+\r
+ void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {\r
+ if ( item != null ) {\r
+ item.setFont( MainFrame.menu_font );\r
+ if ( !getConfiguration().isUseNativeUI() ) {\r
+ item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
+ item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
+ }\r
+ item.setSelected( is_selected );\r
+ item.addActionListener( this );\r
+ }\r
+ }\r
+\r
+ void displayBasicInformation( final File treefile ) {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+ String title = "Basic Information";\r
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
+ title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";\r
+ }\r
+ showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );\r
+ }\r
+ }\r
+\r
+ void exceptionOccuredDuringOpenFile( final Exception e ) {\r
+ try {\r
+ _mainpanel.getCurrentTreePanel().setArrowCursor();\r
+ }\r
+ catch ( final Exception ex ) {\r
+ // Do nothing.\r
+ }\r
+ JOptionPane.showMessageDialog( this,\r
+ ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
+ "Error during File|Open",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+\r
+ void executeGSDI() {\r
+ if ( !isOKforSDI( false, true ) ) {\r
+ return;\r
+ }\r
+ if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Gene tree is not rooted.",\r
+ "Cannot execute GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
+ gene_tree.setAllNodesToNotCollapse();\r
+ gene_tree.recalculateNumberOfExternalDescendants( false );\r
+ GSDI gsdi = null;\r
+ final Phylogeny species_tree = getSpeciesTree().copy();\r
+ try {\r
+ gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );\r
+ }\r
+ catch ( final SDIException e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Error during GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
}\r
catch ( final Exception e ) {\r
AptxUtil.unexpectedException( e );\r
+ gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
+ "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDI successfully completed",\r
- JOptionPane.WARNING_MESSAGE );\r
+ "GSDI successfully completed",\r
+ JOptionPane.WARNING_MESSAGE );\r
}\r
else {\r
JOptionPane.showMessageDialog( this,\r
+ gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
+ "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDI successfully completed",\r
- JOptionPane.INFORMATION_MESSAGE );\r
+ "GSDI successfully completed",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
}\r
}\r
\r
+ gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
+ "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDIR successfully completed",\r
- JOptionPane.WARNING_MESSAGE );\r
+ "GSDIR successfully completed",\r
+ JOptionPane.WARNING_MESSAGE );\r
}\r
else {\r
JOptionPane.showMessageDialog( this,\r
+ gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
+ "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDIR successfully completed",\r
- JOptionPane.INFORMATION_MESSAGE );\r
+ "GSDIR successfully completed",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
}\r
}\r
\r
}\r
}\r
\r
- ControlPanel getControlPanel() {\r
- return getMainPanel().getControlPanel();\r
- }\r
-\r
- File getCurrentDir() {\r
- if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
- if ( ForesterUtil.isWindows() ) {\r
- try {\r
- _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );\r
- }\r
- catch ( final Exception e ) {\r
- _current_dir = null;\r
- }\r
- }\r
- }\r
- if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
- if ( System.getProperty( "user.home" ) != null ) {\r
- _current_dir = new File( System.getProperty( "user.home" ) );\r
- }\r
- else if ( System.getProperty( "user.dir" ) != null ) {\r
- _current_dir = new File( System.getProperty( "user.dir" ) );\r
- }\r
- }\r
- return _current_dir;\r
- }\r
-\r
- TreePanel getCurrentTreePanel() {\r
- return getMainPanel().getCurrentTreePanel();\r
- }\r
-\r
- JMenu getHelpMenu() {\r
- return _help_jmenu;\r
- }\r
-\r
- JCheckBoxMenuItem getlabelDirectionCbmi() {\r
- return _label_direction_cbmi;\r
- }\r
-\r
- JMenuBar getMenuBarOfMainFrame() {\r
- return _jmenubar;\r
- }\r
-\r
- final Phylogeny getSpeciesTree() {\r
- return _species_tree;\r
- }\r
-\r
- void initializeTypeMenu( final Options options ) {\r
- setTypeMenuToAllUnselected();\r
- switch ( options.getPhylogenyGraphicsType() ) {\r
- case CONVEX:\r
- _convex_type_cbmi.setSelected( true );\r
- break;\r
- case CURVED:\r
- _curved_type_cbmi.setSelected( true );\r
- break;\r
- case EURO_STYLE:\r
- _euro_type_cbmi.setSelected( true );\r
- break;\r
- case ROUNDED:\r
- _rounded_type_cbmi.setSelected( true );\r
- break;\r
- case TRIANGULAR:\r
- _triangular_type_cbmi.setSelected( true );\r
- break;\r
- case UNROOTED:\r
- _unrooted_type_cbmi.setSelected( true );\r
- break;\r
- case CIRCULAR:\r
- _circular_type_cbmi.setSelected( true );\r
- break;\r
- default:\r
- _rectangular_type_cbmi.setSelected( true );\r
- break;\r
- }\r
- }\r
-\r
- boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {\r
- if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
- return false;\r
- }\r
- else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "No species tree loaded",\r
- "Cannot execute GSDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return false;\r
- }\r
- else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Species tree is not completely binary",\r
- "Cannot execute GSDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return false;\r
- }\r
- else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Gene tree is not completely binary",\r
- "Cannot execute GSDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return false;\r
- }\r
- else {\r
- return true;\r
- }\r
- }\r
-\r
- boolean isSubtreeDisplayed() {\r
- if ( getCurrentTreePanel() != null ) {\r
- if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {\r
- JOptionPane\r
- .showMessageDialog( this,\r
- "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
- "Operation can not be exectuted on a sub-tree",\r
- JOptionPane.WARNING_MESSAGE );\r
- return true;\r
- }\r
- }\r
- return false;\r
- }\r
-\r
- void midpointRoot() {\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().midpointRoot();\r
- }\r
- }\r
-\r
- static void printPhylogenyToPdf( final String file_name,\r
- final Options opts,\r
- final TreePanel tp,\r
- final Component comp ) {\r
- if ( !opts.isPrintUsingActualSize() ) {\r
- tp.calcParametersForPainting( opts.getPrintSizeX(), opts.getPrintSizeY() );\r
- tp.resetPreferredSize();\r
- tp.repaint();\r
- }\r
- String pdf_written_to = "";\r
- boolean error = false;\r
- try {\r
- if ( opts.isPrintUsingActualSize() ) {\r
- pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, tp, tp.getWidth(), tp.getHeight() );\r
- }\r
- else {\r
- pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,\r
- tp,\r
- opts.getPrintSizeX(),\r
- opts.getPrintSizeY() );\r
- }\r
- }\r
- catch ( final IOException e ) {\r
- error = true;\r
- JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
- }\r
- if ( !error ) {\r
- if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {\r
- JOptionPane.showMessageDialog( comp,\r
- "Wrote PDF to: " + pdf_written_to,\r
- "Information",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( comp,\r
- "There was an unknown problem when attempting to write to PDF file: \""\r
- + file_name + "\"",\r
- "Error",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
- }\r
- if ( !opts.isPrintUsingActualSize() ) {\r
- tp.getControlPanel().showWhole();\r
- }\r
- }\r
-\r
- void readPhylogeniesFromWebservice( final int i ) {\r
- final UrlTreeReader reader = new UrlTreeReader( this, i );\r
- new Thread( reader ).start();\r
+ ControlPanel getControlPanel() {\r
+ return getMainPanel().getControlPanel();\r
}\r
\r
- void removeAllTextFrames() {\r
- for( final TextFrame tf : _textframes ) {\r
- if ( tf != null ) {\r
- tf.close();\r
+ File getCurrentDir() {\r
+ if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
+ if ( ForesterUtil.isWindows() ) {\r
+ try {\r
+ _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );\r
+ }\r
+ catch ( final Exception e ) {\r
+ _current_dir = null;\r
+ }\r
}\r
}\r
- _textframes.clear();\r
+ if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
+ if ( System.getProperty( "user.home" ) != null ) {\r
+ _current_dir = new File( System.getProperty( "user.home" ) );\r
+ }\r
+ else if ( System.getProperty( "user.dir" ) != null ) {\r
+ _current_dir = new File( System.getProperty( "user.dir" ) );\r
+ }\r
+ }\r
+ return _current_dir;\r
}\r
\r
- void resetSearch() {\r
- getMainPanel().getCurrentTreePanel().setFoundNodes0( null );\r
- getMainPanel().getCurrentTreePanel().setFoundNodes1( null );\r
- getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );\r
- getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );\r
- getMainPanel().getControlPanel().getSearchTextField0().setText( "" );\r
- getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );\r
- getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );\r
- getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );\r
- getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );\r
- getMainPanel().getControlPanel().getSearchTextField1().setText( "" );\r
- getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );\r
- getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );\r
+ TreePanel getCurrentTreePanel() {\r
+ return getMainPanel().getCurrentTreePanel();\r
}\r
\r
- void setConfiguration( final Configuration configuration ) {\r
- _configuration = configuration;\r
+ JMenu getHelpMenu() {\r
+ return _help_jmenu;\r
}\r
\r
- void setCurrentDir( final File current_dir ) {\r
- _current_dir = current_dir;\r
+ JCheckBoxMenuItem getlabelDirectionCbmi() {\r
+ return _label_direction_cbmi;\r
}\r
\r
- void setInferenceManager( final InferenceManager i ) {\r
- _inference_manager = i;\r
+ JMenuBar getMenuBarOfMainFrame() {\r
+ return _jmenubar;\r
}\r
\r
- void setOptions( final Options options ) {\r
- _options = options;\r
+ final Phylogeny getSpeciesTree() {\r
+ return _species_tree;\r
}\r
\r
- void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {\r
+ void initializeTypeMenu( final Options options ) {\r
setTypeMenuToAllUnselected();\r
- switch ( type ) {\r
- case CIRCULAR:\r
- _circular_type_cbmi.setSelected( true );\r
- break;\r
+ switch ( options.getPhylogenyGraphicsType() ) {\r
case CONVEX:\r
_convex_type_cbmi.setSelected( true );\r
break;\r
case ROUNDED:\r
_rounded_type_cbmi.setSelected( true );\r
break;\r
- case RECTANGULAR:\r
- _rectangular_type_cbmi.setSelected( true );\r
- break;\r
case TRIANGULAR:\r
_triangular_type_cbmi.setSelected( true );\r
break;\r
case UNROOTED:\r
_unrooted_type_cbmi.setSelected( true );\r
break;\r
+ case CIRCULAR:\r
+ _circular_type_cbmi.setSelected( true );\r
+ break;\r
default:\r
- throw new IllegalArgumentException( "unknown type: " + type );\r
- }\r
- }\r
-\r
- final void setSpeciesTree( final Phylogeny species_tree ) {\r
- _species_tree = species_tree;\r
- }\r
-\r
- void setTypeMenuToAllUnselected() {\r
- _convex_type_cbmi.setSelected( false );\r
- _curved_type_cbmi.setSelected( false );\r
- _euro_type_cbmi.setSelected( false );\r
- _rounded_type_cbmi.setSelected( false );\r
- _triangular_type_cbmi.setSelected( false );\r
- _rectangular_type_cbmi.setSelected( false );\r
- _unrooted_type_cbmi.setSelected( false );\r
- _circular_type_cbmi.setSelected( false );\r
- }\r
-\r
- void switchColors() {\r
- final TreeColorSet colorset = _mainpanel.getTreeColorSet();\r
- final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );\r
- csc.setVisible( true );\r
- }\r
-\r
- void taxColor() {\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().taxColor();\r
- }\r
- }\r
-\r
- void typeChanged( final Object o ) {\r
- updateTypeCheckboxes( getOptions(), o );\r
- updateOptions( getOptions() );\r
- if ( getCurrentTreePanel() != null ) {\r
- final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();\r
- final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();\r
- if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
- || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )\r
- || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
- || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {\r
- getCurrentTreePanel().getControlPanel().showWhole();\r
- }\r
- if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
- getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );\r
- }\r
- else {\r
- getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );\r
- }\r
- getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );\r
- updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
- if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {\r
- if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {\r
- getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );\r
- }\r
- else {\r
- getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );\r
- }\r
- }\r
+ _rectangular_type_cbmi.setSelected( true );\r
+ break;\r
}\r
}\r
\r
- void updateOptions( final Options options ) {\r
- options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );\r
- options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )\r
- && _background_gradient_cbmi.isSelected() );\r
- options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );\r
- options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )\r
- && _show_annotation_ref_source.isSelected() );\r
- options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )\r
- && _abbreviate_scientific_names.isSelected() );\r
- options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )\r
- && _color_labels_same_as_parent_branch.isSelected() );\r
- options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )\r
- && _show_default_node_shapes_internal_cbmi.isSelected() );\r
- options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
- && _show_default_node_shapes_external_cbmi.isSelected() );\r
- options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )\r
- && _show_default_node_shapes_for_marked_cbmi.isSelected() );\r
- if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
- options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
- }\r
- else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {\r
- options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
- }\r
- else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {\r
- options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
- }\r
- options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )\r
- && _search_case_senstive_cbmi.isSelected() );\r
- if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {\r
- options.setShowScale( _show_scale_cbmi.isSelected() );\r
- }\r
- if ( _label_direction_cbmi != null ) {\r
- if ( _label_direction_cbmi.isSelected() ) {\r
- options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );\r
- }\r
- else {\r
- options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );\r
- }\r
- }\r
- options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );\r
- options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )\r
- && _show_confidence_stddev_cbmi.isSelected() );\r
- if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {\r
- options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );\r
- }\r
- options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )\r
- && ( _print_using_actual_size_cbmi.isSelected() ) );\r
- options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )\r
- && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
- options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );\r
- if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )\r
- && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
- options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
- }\r
- else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )\r
- && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
- options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
- }\r
- else {\r
- options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );\r
- }\r
- options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )\r
- && _print_black_and_white_cbmi.isSelected() );\r
- options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )\r
- && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
- if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {\r
- options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
- }\r
- else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {\r
- options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
- }\r
- else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {\r
- options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );\r
- }\r
- else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {\r
- options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );\r
- }\r
- options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )\r
- && _replace_underscores_cbmi.isSelected() );\r
- options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )\r
- && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
- options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )\r
- && _search_whole_words_only_cbmi.isSelected() );\r
- options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );\r
- options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )\r
- && _inverse_search_result_cbmi.isSelected() );\r
- if ( _graphics_export_visible_only_cbmi != null ) {\r
- options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );\r
- if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {\r
- _graphics_export_using_actual_size_cbmi.setSelected( true );\r
- _graphics_export_using_actual_size_cbmi.setEnabled( false );\r
- }\r
- else {\r
- _graphics_export_using_actual_size_cbmi.setEnabled( true );\r
- }\r
- }\r
- if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
- }\r
- else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );\r
- }\r
- else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );\r
- }\r
- else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );\r
- }\r
- else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );\r
- }\r
- else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );\r
+ boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+ return false;\r
}\r
- else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );\r
+ else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "No species tree loaded",\r
+ "Cannot execute GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return false;\r
}\r
- else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );\r
+ else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Species tree is not completely binary",\r
+ "Cannot execute GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return false;\r
}\r
- if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {\r
- options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );\r
+ else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Gene tree is not completely binary",\r
+ "Cannot execute GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return false;\r
}\r
- if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {\r
- options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );\r
+ else {\r
+ return true;\r
}\r
}\r
\r
- void updateTypeCheckboxes( final Options options, final Object o ) {\r
- setTypeMenuToAllUnselected();\r
- ( ( JCheckBoxMenuItem ) o ).setSelected( true );\r
- }\r
-\r
- void viewAsNexus() {\r
- if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
- String title = "Nexus";\r
- if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
- title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
+ boolean isSubtreeDisplayed() {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {\r
+ JOptionPane\r
+ .showMessageDialog( this,\r
+ "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
+ "Operation can not be exectuted on a sub-tree",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ return true;\r
}\r
- showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),\r
- title );\r
}\r
+ return false;\r
}\r
\r
- void viewAsNH() {\r
- if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
- String title = "New Hampshire";\r
- if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
- title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
- }\r
- showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()\r
- .getNhConversionSupportValueStyle() ),\r
- title );\r
+ void midpointRoot() {\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ _mainpanel.getCurrentTreePanel().midpointRoot();\r
}\r
}\r
\r
- void viewAsXML() {\r
- if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
- String title = "phyloXML";\r
- if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
- title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
+ void readPhylogeniesFromWebservice( final int i ) {\r
+ final UrlTreeReader reader = new UrlTreeReader( this, i );\r
+ new Thread( reader ).start();\r
+ }\r
+\r
+ void removeAllTextFrames() {\r
+ for( final TextFrame tf : _textframes ) {\r
+ if ( tf != null ) {\r
+ tf.close();\r
}\r
- showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );\r
}\r
+ _textframes.clear();\r
}\r
\r
- static boolean writeAsNewHampshire( final TreePanel tp,\r
- final Options op,\r
- boolean exception,\r
- final File file ) {\r
- try {\r
- final PhylogenyWriter writer = new PhylogenyWriter();\r
- writer.toNewHampshire( tp.getPhylogeny(), true, op.getNhConversionSupportValueStyle(), file );\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringSaveAs( e, tp, tp);\r
- }\r
- return exception;\r
+ void resetSearch() {\r
+ getMainPanel().getCurrentTreePanel().setFoundNodes0( null );\r
+ getMainPanel().getCurrentTreePanel().setFoundNodes1( null );\r
+ getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );\r
+ getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );\r
+ getMainPanel().getControlPanel().getSearchTextField0().setText( "" );\r
+ getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );\r
+ getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );\r
+ getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );\r
+ getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );\r
+ getMainPanel().getControlPanel().getSearchTextField1().setText( "" );\r
+ getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );\r
+ getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );\r
}\r
\r
- \r
- \r
- \r
- static boolean writeAsNexus( final TreePanel tp,\r
- final Options op,\r
- boolean exception,\r
- final File file ) {\r
- try {\r
- final PhylogenyWriter writer = new PhylogenyWriter();\r
- writer.toNexus(file , tp.getPhylogeny(), op.getNhConversionSupportValueStyle());\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringSaveAs( e, tp, tp);\r
- }\r
- return exception;\r
+ void setConfiguration( final Configuration configuration ) {\r
+ _configuration = configuration;\r
}\r
- \r
- \r
- \r
\r
- static boolean writeAsPhyloXml( final TreePanel tp,\r
- final Options op,\r
- boolean exception,\r
- final File file ) {\r
- try {\r
- final PhylogenyWriter writer = new PhylogenyWriter();\r
- writer.toPhyloXML( file, tp.getPhylogeny(), 0 );\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringSaveAs( e, tp, tp);\r
- }\r
- return exception;\r
+ void setCurrentDir( final File current_dir ) {\r
+ _current_dir = current_dir;\r
}\r
\r
- static void writePhylogenyToGraphicsFile( final String file_name,\r
- final GraphicsExportType type,\r
- final MainPanel mp,\r
- final Component comp,\r
- final Container contentpane ) {\r
- mp.getCurrentTreePanel().calcParametersForPainting( mp.getCurrentTreePanel().getWidth(),\r
- mp.getCurrentTreePanel().getHeight() );\r
- String file_written_to = "";\r
- boolean error = false;\r
- try {\r
- file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,\r
- mp.getCurrentTreePanel().getWidth(),\r
- mp.getCurrentTreePanel().getHeight(),\r
- mp.getCurrentTreePanel(),\r
- mp.getControlPanel(),\r
- type,\r
- mp.getOptions() );\r
- }\r
- catch ( final IOException e ) {\r
- error = true;\r
- JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
- }\r
- if ( !error ) {\r
- if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {\r
- JOptionPane.showMessageDialog( comp,\r
- "Wrote image to: " + file_written_to,\r
- "Graphics Export",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( comp,\r
- "There was an unknown problem when attempting to write to an image file: \""\r
- + file_name + "\"",\r
- "Error",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
- }\r
- contentpane.repaint();\r
+ void setInferenceManager( final InferenceManager i ) {\r
+ _inference_manager = i;\r
}\r
\r
- static File writeToFile( final Phylogeny t,\r
- final MainPanel mp,\r
- final JFileChooser save_filechooser,\r
- final File current_dir,\r
- Container contentpane,\r
- Component comp\r
- \r
- ) {\r
- File new_file = null;\r
- if ( t == null ) {\r
- return null;\r
- }\r
- String initial_filename = null;\r
- if ( mp.getCurrentTreePanel().getTreeFile() != null ) {\r
- try {\r
- initial_filename = mp.getCurrentTreePanel().getTreeFile().getCanonicalPath();\r
- }\r
- catch ( final IOException e ) {\r
- initial_filename = null;\r
- }\r
- }\r
- if ( !ForesterUtil.isEmpty( initial_filename ) ) {\r
- save_filechooser.setSelectedFile( new File( initial_filename ) );\r
- }\r
- else {\r
- save_filechooser.setSelectedFile( new File( "" ) );\r
- }\r
- final File my_dir = current_dir;\r
- if ( my_dir != null ) {\r
- save_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = save_filechooser.showSaveDialog( contentpane );\r
- final File file = save_filechooser.getSelectedFile();\r
- \r
- new_file = save_filechooser.getCurrentDirectory();\r
- boolean exception = false;\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( file.exists() ) {\r
- final int i = JOptionPane.showConfirmDialog( comp,\r
- file + " already exists.\nOverwrite?",\r
- "Overwrite?",\r
- JOptionPane.OK_CANCEL_OPTION,\r
- JOptionPane.QUESTION_MESSAGE );\r
- if ( i != JOptionPane.OK_OPTION ) {\r
- return null;\r
- }\r
- else {\r
- final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );\r
- try {\r
- ForesterUtil.copyFile( file, to );\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( comp,\r
- "Failed to create backup copy " + to,\r
- "Failed to Create Backup Copy",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- try {\r
- file.delete();\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( comp,\r
- "Failed to delete: " + file,\r
- "Failed to Delete",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- }\r
- if ( save_filechooser.getFileFilter() == MainFrame.nhfilter ) {\r
- \r
- \r
- exception = writeAsNewHampshire( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );\r
- }\r
- else if ( save_filechooser.getFileFilter() == MainFrame.xmlfilter ) {\r
- \r
- exception = writeAsPhyloXml( mp.getCurrentTreePanel(), mp.getOptions(),\r
- exception,\r
- file ) ;\r
- \r
- }\r
- else if ( save_filechooser.getFileFilter() == MainFrame.nexusfilter ) {\r
- \r
- exception = writeAsNexus( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );\r
- }\r
- // "*.*":\r
- else {\r
- final String file_name = file.getName().trim().toLowerCase();\r
- if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )\r
- || file_name.endsWith( ".tree" ) ) {\r
- exception = writeAsNewHampshire( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );\r
- \r
- }\r
- else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {\r
- exception = writeAsNexus( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );\r
- }\r
- // XML is default:\r
- else {\r
- exception = writeAsPhyloXml( mp.getCurrentTreePanel(), mp.getOptions(),\r
- exception,\r
- file ) ;\r
- }\r
- }\r
- if ( !exception ) {\r
- mp.setTitleOfSelectedTab( file.getName() );\r
- mp.getCurrentTreePanel().setTreeFile( file );\r
- mp.getCurrentTreePanel().setEdited( false );\r
- }\r
+ void setOptions( final Options options ) {\r
+ _options = options;\r
+ }\r
+\r
+ void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {\r
+ setTypeMenuToAllUnselected();\r
+ switch ( type ) {\r
+ case CIRCULAR:\r
+ _circular_type_cbmi.setSelected( true );\r
+ break;\r
+ case CONVEX:\r
+ _convex_type_cbmi.setSelected( true );\r
+ break;\r
+ case CURVED:\r
+ _curved_type_cbmi.setSelected( true );\r
+ break;\r
+ case EURO_STYLE:\r
+ _euro_type_cbmi.setSelected( true );\r
+ break;\r
+ case ROUNDED:\r
+ _rounded_type_cbmi.setSelected( true );\r
+ break;\r
+ case RECTANGULAR:\r
+ _rectangular_type_cbmi.setSelected( true );\r
+ break;\r
+ case TRIANGULAR:\r
+ _triangular_type_cbmi.setSelected( true );\r
+ break;\r
+ case UNROOTED:\r
+ _unrooted_type_cbmi.setSelected( true );\r
+ break;\r
+ default:\r
+ throw new IllegalArgumentException( "unknown type: " + type );\r
}\r
- return new_file;\r
}\r
\r
- static File writeToGraphicsFile( final Phylogeny t,\r
- final GraphicsExportType type,\r
- final MainPanel mp,\r
- final JFileChooser writetographics_filechooser,\r
- final Component component,\r
- final Container contentpane,\r
- final File current_dir ) {\r
- File new_dir = null;\r
- if ( ( t == null ) || t.isEmpty() ) {\r
- return null;\r
- }\r
- String initial_filename = "";\r
- if ( mp.getCurrentTreePanel().getTreeFile() != null ) {\r
- initial_filename = mp.getCurrentTreePanel().getTreeFile().toString();\r
- }\r
- if ( initial_filename.indexOf( '.' ) > 0 ) {\r
- initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
- }\r
- initial_filename = initial_filename + "." + type;\r
- writetographics_filechooser.setSelectedFile( new File( initial_filename ) );\r
- final File my_dir = current_dir;\r
- if ( my_dir != null ) {\r
- writetographics_filechooser.setCurrentDirectory( my_dir );\r
+ final void setSpeciesTree( final Phylogeny species_tree ) {\r
+ _species_tree = species_tree;\r
+ }\r
+\r
+ void setTypeMenuToAllUnselected() {\r
+ _convex_type_cbmi.setSelected( false );\r
+ _curved_type_cbmi.setSelected( false );\r
+ _euro_type_cbmi.setSelected( false );\r
+ _rounded_type_cbmi.setSelected( false );\r
+ _triangular_type_cbmi.setSelected( false );\r
+ _rectangular_type_cbmi.setSelected( false );\r
+ _unrooted_type_cbmi.setSelected( false );\r
+ _circular_type_cbmi.setSelected( false );\r
+ }\r
+\r
+ void switchColors() {\r
+ final TreeColorSet colorset = _mainpanel.getTreeColorSet();\r
+ final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );\r
+ csc.setVisible( true );\r
+ }\r
+\r
+ void taxColor() {\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ _mainpanel.getCurrentTreePanel().taxColor();\r
}\r
- final int result = writetographics_filechooser.showSaveDialog( contentpane );\r
- File file = writetographics_filechooser.getSelectedFile();\r
- //setCurrentDir( writetographics_filechooser.getCurrentDirectory() );\r
- new_dir = writetographics_filechooser.getCurrentDirectory();\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {\r
- file = new File( file.toString() + "." + type );\r
+ }\r
+\r
+ void typeChanged( final Object o ) {\r
+ updateTypeCheckboxes( getOptions(), o );\r
+ updateOptions( getOptions() );\r
+ if ( getCurrentTreePanel() != null ) {\r
+ final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();\r
+ final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();\r
+ if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
+ || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )\r
+ || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
+ || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {\r
+ getCurrentTreePanel().getControlPanel().showWhole();\r
}\r
- if ( file.exists() ) {\r
- final int i = JOptionPane.showConfirmDialog( component,\r
- file + " already exists. Overwrite?",\r
- "Warning",\r
- JOptionPane.OK_CANCEL_OPTION,\r
- JOptionPane.WARNING_MESSAGE );\r
- if ( i != JOptionPane.OK_OPTION ) {\r
- return null;\r
+ if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
+ getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );\r
+ }\r
+ else {\r
+ getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );\r
+ }\r
+ getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );\r
+ updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
+ if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {\r
+ if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {\r
+ getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );\r
}\r
else {\r
- try {\r
- file.delete();\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( component,\r
- "Failed to delete: " + file,\r
- "Error",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
+ getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );\r
}\r
}\r
- writePhylogenyToGraphicsFile( file.toString(), type, mp, component, contentpane );\r
}\r
- return new_dir;\r
}\r
\r
- static File writeToPdf( final Phylogeny t,\r
- final MainPanel mp,\r
- final JFileChooser writetopdf_filechooser,\r
- final File curr_dir,\r
- final Container contentpane,\r
- final Component component ) {\r
- if ( ( t == null ) || t.isEmpty() ) {\r
- return null;\r
+ void updateOptions( final Options options ) {\r
+ options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );\r
+ options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )\r
+ && _background_gradient_cbmi.isSelected() );\r
+ options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );\r
+ options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )\r
+ && _show_annotation_ref_source.isSelected() );\r
+ options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )\r
+ && _abbreviate_scientific_names.isSelected() );\r
+ options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )\r
+ && _color_labels_same_as_parent_branch.isSelected() );\r
+ options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )\r
+ && _show_default_node_shapes_internal_cbmi.isSelected() );\r
+ options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
+ && _show_default_node_shapes_external_cbmi.isSelected() );\r
+ options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )\r
+ && _show_default_node_shapes_for_marked_cbmi.isSelected() );\r
+ if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
+ options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
}\r
- String initial_filename = "";\r
- if ( mp.getCurrentTreePanel().getTreeFile() != null ) {\r
- initial_filename = mp.getCurrentTreePanel().getTreeFile().toString();\r
+ else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {\r
+ options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
}\r
- if ( initial_filename.indexOf( '.' ) > 0 ) {\r
- initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
+ else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {\r
+ options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
}\r
- initial_filename = initial_filename + ".pdf";\r
- writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );\r
- final File my_dir = curr_dir;\r
- if ( my_dir != null ) {\r
- writetopdf_filechooser.setCurrentDirectory( my_dir );\r
+ options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )\r
+ && _search_case_senstive_cbmi.isSelected() );\r
+ if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {\r
+ options.setShowScale( _show_scale_cbmi.isSelected() );\r
}\r
- final int result = writetopdf_filechooser.showSaveDialog( contentpane );\r
- File file = writetopdf_filechooser.getSelectedFile();\r
- // setCurrentDir( writetopdf_filechooser.getCurrentDirectory() );\r
- final File new_current_dir = writetopdf_filechooser.getCurrentDirectory();\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {\r
- file = new File( file.toString() + ".pdf" );\r
+ if ( _label_direction_cbmi != null ) {\r
+ if ( _label_direction_cbmi.isSelected() ) {\r
+ options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );\r
}\r
- if ( file.exists() ) {\r
- final int i = JOptionPane.showConfirmDialog( component,\r
- file + " already exists. Overwrite?",\r
- "WARNING",\r
- JOptionPane.OK_CANCEL_OPTION,\r
- JOptionPane.WARNING_MESSAGE );\r
- if ( i != JOptionPane.OK_OPTION ) {\r
- return null;\r
- }\r
+ else {\r
+ options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );\r
}\r
- printPhylogenyToPdf( file.toString(), mp.getOptions(), mp.getCurrentTreePanel(), component );\r
}\r
- return new_current_dir;\r
- }\r
-\r
- private void annotateSequences() {\r
- if ( getCurrentTreePanel() != null ) {\r
- List<PhylogenyNode> nodes = null;\r
- if ( ( getCurrentTreePanel().getFoundNodes0() != null )\r
- || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
- nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
- }\r
- if ( ( nodes == null ) || nodes.isEmpty() ) {\r
- JOptionPane\r
- .showMessageDialog( this,\r
- "Need to select nodes, either via direct selection or via the \"Search\" function",\r
- "No nodes selected for annotation",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- final JTextField ref_field = new JTextField( 10 );\r
- final JTextField desc_filed = new JTextField( 20 );\r
- ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""\r
- : getPreviousNodeAnnotationReference() );\r
- final JPanel my_panel = new JPanel();\r
- my_panel.add( new JLabel( "Reference " ) );\r
- my_panel.add( ref_field );\r
- my_panel.add( Box.createHorizontalStrut( 15 ) );\r
- my_panel.add( new JLabel( "Description " ) );\r
- my_panel.add( desc_filed );\r
- final int result = JOptionPane.showConfirmDialog( null,\r
- my_panel,\r
- "Enter the sequence annotation(s) for the "\r
- + nodes.size() + " selected nodes",\r
- JOptionPane.OK_CANCEL_OPTION );\r
- if ( result == JOptionPane.OK_OPTION ) {\r
- String ref = ref_field.getText();\r
- String desc = desc_filed.getText();\r
- if ( !ForesterUtil.isEmpty( ref ) ) {\r
- ref = ref.trim();\r
- ref = ref.replaceAll( "\\s+", " " );\r
- if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )\r
- || ( ref.length() < 3 ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Reference needs to be in the form of \"GO:1234567\"",\r
- "Illegal Format for Annotation Reference",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- }\r
- if ( ref != null ) {\r
- setPreviousNodeAnnotationReference( ref );\r
- }\r
- if ( desc != null ) {\r
- desc = desc.trim();\r
- desc = desc.replaceAll( "\\s+", " " );\r
- }\r
- if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {\r
- for( final PhylogenyNode n : nodes ) {\r
- ForesterUtil.ensurePresenceOfSequence( n );\r
- final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()\r
- : new Annotation( ref );\r
- if ( !ForesterUtil.isEmpty( desc ) ) {\r
- ann.setDesc( desc );\r
- }\r
- n.getNodeData().getSequence().addAnnotation( ann );\r
- }\r
- }\r
- getMainPanel().getControlPanel().showAnnotations();\r
- }\r
- }\r
+ options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );\r
+ options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )\r
+ && _show_confidence_stddev_cbmi.isSelected() );\r
+ if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {\r
+ options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );\r
}\r
- }\r
-\r
- private void chooseFont() {\r
- final FontChooser fc = new FontChooser();\r
- fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );\r
- fc.showDialog( this, "Select the Base Font" );\r
- getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );\r
- }\r
-\r
- private void chooseMinimalConfidence() {\r
- final String s = ( String ) JOptionPane\r
- .showInputDialog( this,\r
- "Please enter the minimum for confidence values to be displayed.\n"\r
- + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",\r
- "Minimal Confidence Value",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getMinConfidenceValue() );\r
- if ( !ForesterUtil.isEmpty( s ) ) {\r
- boolean success = true;\r
- double m = 0.0;\r
- final String m_str = s.trim();\r
- if ( !ForesterUtil.isEmpty( m_str ) ) {\r
- try {\r
- m = Double.parseDouble( m_str );\r
- }\r
- catch ( final Exception ex ) {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
- }\r
- if ( success && ( m >= 0.0 ) ) {\r
- getOptions().setMinConfidenceValue( m );\r
- }\r
+ options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )\r
+ && ( _print_using_actual_size_cbmi.isSelected() ) );\r
+ options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )\r
+ && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
+ options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );\r
+ if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )\r
+ && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
+ options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
}\r
- }\r
-\r
- private void deleteSelectedNodes( final boolean delete ) {\r
- final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
- if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {\r
- return;\r
+ else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )\r
+ && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
+ options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
}\r
- final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
- if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
- final List<PhylogenyNode> all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
- for( final PhylogenyNode n : all_selected_nodes ) {\r
- if ( n.isExternal() ) {\r
- nodes.add( n );\r
- }\r
- }\r
+ else {\r
+ options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );\r
}\r
- String function = "Retain";\r
- if ( delete ) {\r
- function = "Delete";\r
+ options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )\r
+ && _print_black_and_white_cbmi.isSelected() );\r
+ options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )\r
+ && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
+ if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {\r
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
}\r
- if ( ( nodes == null ) || nodes.isEmpty() ) {\r
- JOptionPane\r
- .showMessageDialog( this,\r
- "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
- "No external nodes selected to " + function.toLowerCase(),\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
+ else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {\r
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
}\r
- final int todo = nodes.size();\r
- final int ext = phy.getNumberOfExternalNodes();\r
- int res = todo;\r
- if ( delete ) {\r
- res = ext - todo;\r
+ else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {\r
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );\r
}\r
- if ( res < 1 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Cannot delete all nodes",\r
- "Attempt to delete all nodes ",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
+ else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {\r
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );\r
}\r
- final int result = JOptionPane.showConfirmDialog( null, function + " " + todo\r
- + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
- + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
- if ( result == JOptionPane.OK_OPTION ) {\r
- if ( !delete ) {\r
- final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
- for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
- final PhylogenyNode n = it.next();\r
- if ( !nodes.contains( n ) ) {\r
- to_delete.add( n );\r
- }\r
- }\r
- for( final PhylogenyNode n : to_delete ) {\r
- phy.deleteSubtree( n, true );\r
- }\r
+ options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )\r
+ && _replace_underscores_cbmi.isSelected() );\r
+ options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )\r
+ && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
+ options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )\r
+ && _search_whole_words_only_cbmi.isSelected() );\r
+ options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );\r
+ options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )\r
+ && _inverse_search_result_cbmi.isSelected() );\r
+ if ( _graphics_export_visible_only_cbmi != null ) {\r
+ options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );\r
+ if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {\r
+ _graphics_export_using_actual_size_cbmi.setSelected( true );\r
+ _graphics_export_using_actual_size_cbmi.setEnabled( false );\r
}\r
else {\r
- for( final PhylogenyNode n : nodes ) {\r
- phy.deleteSubtree( n, true );\r
- }\r
+ _graphics_export_using_actual_size_cbmi.setEnabled( true );\r
}\r
- resetSearch();\r
- getCurrentTreePanel().setNodeInPreorderToNull();\r
- phy.externalNodesHaveChanged();\r
- phy.clearHashIdToNodeMap();\r
- phy.recalculateNumberOfExternalDescendants( true );\r
- getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
- getCurrentTreePanel().setEdited( true );\r
- repaint();\r
}\r
- }\r
-\r
- private void doUpdateProcessMenu() {\r
- if ( _process_pool.size() > 0 ) {\r
- if ( _process_menu == null ) {\r
- _process_menu = createMenu( "", getConfiguration() );\r
- _process_menu.setForeground( Color.RED );\r
- }\r
- _process_menu.removeAll();\r
- final String text = "processes running: " + _process_pool.size();\r
- _process_menu.setText( text );\r
- _jmenubar.add( _process_menu );\r
- for( int i = 0; i < _process_pool.size(); ++i ) {\r
- final ProcessRunning p = _process_pool.getProcessByIndex( i );\r
- _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );\r
- }\r
+ if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
}\r
- else {\r
- if ( _process_menu != null ) {\r
- _process_menu.removeAll();\r
- _jmenubar.remove( _process_menu );\r
- }\r
+ else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );\r
}\r
- _jmenubar.validate();\r
- _jmenubar.repaint();\r
- repaint();\r
- }\r
-\r
- private String getPreviousNodeAnnotationReference() {\r
- return _previous_node_annotation_ref;\r
- }\r
-\r
- static void print( final TreePanel tp, final Options op, final Component c ) {\r
- if ( ( tp == null ) || ( tp.getPhylogeny() == null ) || tp.getPhylogeny().isEmpty() ) {\r
- return;\r
+ else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );\r
}\r
- if ( !op.isPrintUsingActualSize() ) {\r
- tp.calcParametersForPainting( op.getPrintSizeX() - 80, op.getPrintSizeY() - 140 );\r
- tp.resetPreferredSize();\r
- tp.repaint();\r
+ else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );\r
}\r
- final String job_name = Constants.PRG_NAME;\r
- boolean error = false;\r
- String printer_name = null;\r
- try {\r
- printer_name = Printer.print( tp, job_name );\r
+ else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );\r
}\r
- catch ( final Exception e ) {\r
- error = true;\r
- JOptionPane.showMessageDialog( c, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );\r
+ else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );\r
}\r
- if ( !error && ( printer_name != null ) ) {\r
- String msg = "Printing data sent to printer";\r
- if ( printer_name.length() > 1 ) {\r
- msg += " [" + printer_name + "]";\r
- }\r
- JOptionPane.showMessageDialog( c, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );\r
+ else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );\r
}\r
- if ( !op.isPrintUsingActualSize() ) {\r
- tp.getControlPanel().showWhole();\r
+ else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );\r
+ }\r
+ if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {\r
+ options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );\r
+ }\r
+ if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {\r
+ options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );\r
}\r
}\r
\r
- private void removeBranchColors() {\r
- if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
- AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );\r
- }\r
+ void updateTypeCheckboxes( final Options options, final Object o ) {\r
+ setTypeMenuToAllUnselected();\r
+ ( ( JCheckBoxMenuItem ) o ).setSelected( true );\r
}\r
\r
- private void removeVisualStyles() {\r
- if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
- AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );\r
+ void viewAsNexus() {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+ String title = "Nexus";\r
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
+ }\r
+ showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),\r
+ title );\r
}\r
}\r
\r
- private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {\r
- _previous_node_annotation_ref = previous_node_annotation_ref;\r
+ void viewAsNH() {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+ String title = "New Hampshire";\r
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
+ }\r
+ showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()\r
+ .getNhConversionSupportValueStyle() ),\r
+ title );\r
+ }\r
}\r
\r
- private void writeAllToFile() {\r
- if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {\r
- return;\r
- }\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _save_filechooser.setCurrentDirectory( my_dir );\r
+ void viewAsXML() {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+ String title = "phyloXML";\r
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
+ }\r
+ showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );\r
}\r
- _save_filechooser.setSelectedFile( new File( "" ) );\r
- final int result = _save_filechooser.showSaveDialog( _contentpane );\r
- final File file = _save_filechooser.getSelectedFile();\r
- setCurrentDir( _save_filechooser.getCurrentDirectory() );\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( file.exists() ) {\r
- final int i = JOptionPane.showConfirmDialog( this,\r
- file + " already exists. Overwrite?",\r
- "Warning",\r
- JOptionPane.OK_CANCEL_OPTION,\r
- JOptionPane.WARNING_MESSAGE );\r
- if ( i != JOptionPane.OK_OPTION ) {\r
- return;\r
+ }\r
+\r
+ private static void cycleNodeDataReturn( final Options op, final Configuration conf ) {\r
+ switch ( op.getExtDescNodeDataToReturn() ) {\r
+ case UNKNOWN:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );\r
+ break;\r
+ case DOMAINS_ALL:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );\r
+ break;\r
+ case DOMAINS_COLLAPSED_PER_PROTEIN:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );\r
+ break;\r
+ case SEQ_ANNOTATIONS:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );\r
+ break;\r
+ case GO_TERM_IDS:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );\r
+ break;\r
+ case SEQUENCE_MOL_SEQ_FASTA:\r
+ if ( ( conf != null ) && ( conf.getExtDescNodeDataToReturn() != null )\r
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL )\r
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN )\r
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS )\r
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS )\r
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA ) ) {\r
+ op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() );\r
}\r
else {\r
- try {\r
- file.delete();\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Failed to delete: " + file,\r
- "Error",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- }\r
- final int count = getMainPanel().getTabbedPane().getTabCount();\r
- final List<Phylogeny> trees = new ArrayList<Phylogeny>();\r
- for( int i = 0; i < count; ++i ) {\r
- final Phylogeny phy = getMainPanel().getPhylogeny( i );\r
- if ( ForesterUtil.isEmpty( phy.getName() )\r
- && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) {\r
- phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) );\r
+ op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
}\r
- trees.add( phy );\r
- getMainPanel().getTreePanels().get( i ).setEdited( false );\r
- }\r
- final PhylogenyWriter writer = new PhylogenyWriter();\r
- try {\r
- writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );\r
- }\r
- catch ( final IOException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Failed to write to: " + file,\r
- "Error",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
+ break;\r
+ default:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
}\r
}\r
\r
"Please enter the default size for node shapes.\n"\r
+ "[current value: "\r
+ options.getDefaultNodeShapeSize() + "]\n",\r
- "Node Shape Size",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- options.getDefaultNodeShapeSize() );\r
+ "Node Shape Size",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ options.getDefaultNodeShapeSize() );\r
if ( !ForesterUtil.isEmpty( s ) ) {\r
boolean success = true;\r
double m = 0.0;\r
}\r
}\r
\r
+ static void exceptionOccuredDuringSaveAs( final Exception e, final TreePanel tp, final Component comp ) {\r
+ try {\r
+ tp.setArrowCursor();\r
+ }\r
+ catch ( final Exception ex ) {\r
+ // Do nothing.\r
+ }\r
+ JOptionPane.showMessageDialog( comp, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );\r
+ }\r
+\r
+ static void print( final TreePanel tp, final Options op, final Component c ) {\r
+ if ( ( tp == null ) || ( tp.getPhylogeny() == null ) || tp.getPhylogeny().isEmpty() ) {\r
+ return;\r
+ }\r
+ if ( !op.isPrintUsingActualSize() ) {\r
+ tp.calcParametersForPainting( op.getPrintSizeX() - 80, op.getPrintSizeY() - 140 );\r
+ tp.resetPreferredSize();\r
+ tp.repaint();\r
+ }\r
+ final String job_name = Constants.PRG_NAME;\r
+ boolean error = false;\r
+ String printer_name = null;\r
+ try {\r
+ printer_name = Printer.print( tp, job_name );\r
+ }\r
+ catch ( final Exception e ) {\r
+ error = true;\r
+ JOptionPane.showMessageDialog( c, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ if ( !error && ( printer_name != null ) ) {\r
+ String msg = "Printing data sent to printer";\r
+ if ( printer_name.length() > 1 ) {\r
+ msg += " [" + printer_name + "]";\r
+ }\r
+ JOptionPane.showMessageDialog( c, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ if ( !op.isPrintUsingActualSize() ) {\r
+ tp.getControlPanel().showWhole();\r
+ }\r
+ }\r
+\r
+ static void printPhylogenyToPdf( final String file_name,\r
+ final Options opts,\r
+ final TreePanel tp,\r
+ final Component comp ) {\r
+ if ( !opts.isPrintUsingActualSize() ) {\r
+ tp.calcParametersForPainting( opts.getPrintSizeX(), opts.getPrintSizeY() );\r
+ tp.resetPreferredSize();\r
+ tp.repaint();\r
+ }\r
+ String pdf_written_to = "";\r
+ boolean error = false;\r
+ try {\r
+ if ( opts.isPrintUsingActualSize() ) {\r
+ pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, tp, tp.getWidth(), tp.getHeight() );\r
+ }\r
+ else {\r
+ pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,\r
+ tp,\r
+ opts.getPrintSizeX(),\r
+ opts.getPrintSizeY() );\r
+ }\r
+ }\r
+ catch ( final IOException e ) {\r
+ error = true;\r
+ JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ if ( !error ) {\r
+ if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {\r
+ JOptionPane.showMessageDialog( comp,\r
+ "Wrote PDF to: " + pdf_written_to,\r
+ "Information",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( comp,\r
+ "There was an unknown problem when attempting to write to PDF file: \""\r
+ + file_name + "\"",\r
+ "Error",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ }\r
+ if ( !opts.isPrintUsingActualSize() ) {\r
+ tp.getControlPanel().showWhole();\r
+ }\r
+ }\r
+\r
static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) {\r
if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) {\r
mi.setText( "Cycle Node Return Data... (current: " + options.getExtDescNodeDataToReturn().toString() + ")" );\r
}\r
- else {\r
- mi.setText( "Cycle Node Return Data..." );\r
+ else {\r
+ mi.setText( "Cycle Node Return Data..." );\r
+ }\r
+ }\r
+\r
+ static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {\r
+ if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {\r
+ mi.setText( "Cycle Node Shape Fill Type... (current: "\r
+ + options.getDefaultNodeFill().toString().toLowerCase() + ")" );\r
+ }\r
+ else {\r
+ mi.setText( "Cycle Node Shape Fill Type..." );\r
+ }\r
+ }\r
+\r
+ static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {\r
+ if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {\r
+ mi.setText( "Cycle Node Shape Fill Type... (current: "\r
+ + options.getDefaultNodeShape().toString().toLowerCase() + ")" );\r
+ }\r
+ else {\r
+ mi.setText( "Cycle Node Shape Fill Type..." );\r
+ }\r
+ }\r
+\r
+ static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {\r
+ if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {\r
+ mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );\r
+ }\r
+ else {\r
+ mi.setText( "Cycle Overview Placement..." );\r
+ }\r
+ }\r
+\r
+ static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
+ if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
+ mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
+ + ")" );\r
+ }\r
+ else {\r
+ mi.setText( "Select Color Scheme..." );\r
+ }\r
+ }\r
+\r
+ static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {\r
+ mi.setText( "Select Default Font... (current: " + font_desc + ")" );\r
+ }\r
+\r
+ static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {\r
+ mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "\r
+ + o.getPrintSizeY() + ")" );\r
+ }\r
+\r
+ static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {\r
+ mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );\r
+ }\r
+\r
+ static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {\r
+ if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {\r
+ mi.setEnabled( true );\r
+ }\r
+ else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {\r
+ mi.setEnabled( true );\r
+ }\r
+ else {\r
+ mi.setEnabled( false );\r
+ }\r
+ mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );\r
+ }\r
+\r
+ static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {\r
+ mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );\r
+ }\r
+\r
+ static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {\r
+ for( final TreePanel tree_panel : treepanels ) {\r
+ tree_panel.setTextAntialias();\r
+ }\r
+ }\r
+\r
+ static boolean writeAsNewHampshire( final TreePanel tp, final Options op, boolean exception, final File file ) {\r
+ try {\r
+ final PhylogenyWriter writer = new PhylogenyWriter();\r
+ writer.toNewHampshire( tp.getPhylogeny(), true, op.getNhConversionSupportValueStyle(), file );\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringSaveAs( e, tp, tp );\r
+ }\r
+ return exception;\r
+ }\r
+\r
+ static boolean writeAsNexus( final TreePanel tp, final Options op, boolean exception, final File file ) {\r
+ try {\r
+ final PhylogenyWriter writer = new PhylogenyWriter();\r
+ writer.toNexus( file, tp.getPhylogeny(), op.getNhConversionSupportValueStyle() );\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringSaveAs( e, tp, tp );\r
+ }\r
+ return exception;\r
+ }\r
+\r
+ static boolean writeAsPhyloXml( final TreePanel tp, final Options op, boolean exception, final File file ) {\r
+ try {\r
+ final PhylogenyWriter writer = new PhylogenyWriter();\r
+ writer.toPhyloXML( file, tp.getPhylogeny(), 0 );\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringSaveAs( e, tp, tp );\r
+ }\r
+ return exception;\r
+ }\r
+\r
+ static void writePhylogenyToGraphicsFile( final String file_name,\r
+ final GraphicsExportType type,\r
+ final MainPanel mp,\r
+ final Component comp,\r
+ final Container contentpane ) {\r
+ mp.getCurrentTreePanel().calcParametersForPainting( mp.getCurrentTreePanel().getWidth(),\r
+ mp.getCurrentTreePanel().getHeight() );\r
+ String file_written_to = "";\r
+ boolean error = false;\r
+ try {\r
+ file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,\r
+ mp.getCurrentTreePanel().getWidth(),\r
+ mp.getCurrentTreePanel().getHeight(),\r
+ mp.getCurrentTreePanel(),\r
+ mp.getControlPanel(),\r
+ type,\r
+ mp.getOptions() );\r
+ }\r
+ catch ( final IOException e ) {\r
+ error = true;\r
+ JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ if ( !error ) {\r
+ if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {\r
+ JOptionPane.showMessageDialog( comp,\r
+ "Wrote image to: " + file_written_to,\r
+ "Graphics Export",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( comp,\r
+ "There was an unknown problem when attempting to write to an image file: \""\r
+ + file_name + "\"",\r
+ "Error",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ }\r
+ contentpane.repaint();\r
+ }\r
+\r
+ static File writeToFile( final Phylogeny t,\r
+ final MainPanel mp,\r
+ final JFileChooser save_filechooser,\r
+ final File current_dir,\r
+ final Container contentpane,\r
+ final Component comp ) {\r
+ File new_file = null;\r
+ if ( t == null ) {\r
+ return null;\r
+ }\r
+ String initial_filename = null;\r
+ if ( mp.getCurrentTreePanel().getTreeFile() != null ) {\r
+ try {\r
+ initial_filename = mp.getCurrentTreePanel().getTreeFile().getCanonicalPath();\r
+ }\r
+ catch ( final IOException e ) {\r
+ initial_filename = null;\r
+ }\r
}\r
- }\r
-\r
- static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {\r
- if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {\r
- mi.setText( "Cycle Node Shape Fill Type... (current: "\r
- + options.getDefaultNodeFill().toString().toLowerCase() + ")" );\r
+ if ( !ForesterUtil.isEmpty( initial_filename ) ) {\r
+ save_filechooser.setSelectedFile( new File( initial_filename ) );\r
}\r
else {\r
- mi.setText( "Cycle Node Shape Fill Type..." );\r
+ save_filechooser.setSelectedFile( new File( "" ) );\r
}\r
- }\r
-\r
- static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {\r
- if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {\r
- mi.setText( "Cycle Node Shape Fill Type... (current: "\r
- + options.getDefaultNodeShape().toString().toLowerCase() + ")" );\r
+ final File my_dir = current_dir;\r
+ if ( my_dir != null ) {\r
+ save_filechooser.setCurrentDirectory( my_dir );\r
}\r
- else {\r
- mi.setText( "Cycle Node Shape Fill Type..." );\r
+ final int result = save_filechooser.showSaveDialog( contentpane );\r
+ final File file = save_filechooser.getSelectedFile();\r
+ new_file = save_filechooser.getCurrentDirectory();\r
+ boolean exception = false;\r
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ if ( file.exists() ) {\r
+ final int i = JOptionPane.showConfirmDialog( comp,\r
+ file + " already exists.\nOverwrite?",\r
+ "Overwrite?",\r
+ JOptionPane.OK_CANCEL_OPTION,\r
+ JOptionPane.QUESTION_MESSAGE );\r
+ if ( i != JOptionPane.OK_OPTION ) {\r
+ return null;\r
+ }\r
+ else {\r
+ final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );\r
+ try {\r
+ ForesterUtil.copyFile( file, to );\r
+ }\r
+ catch ( final Exception e ) {\r
+ JOptionPane.showMessageDialog( comp,\r
+ "Failed to create backup copy " + to,\r
+ "Failed to Create Backup Copy",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ try {\r
+ file.delete();\r
+ }\r
+ catch ( final Exception e ) {\r
+ JOptionPane.showMessageDialog( comp,\r
+ "Failed to delete: " + file,\r
+ "Failed to Delete",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ }\r
+ }\r
+ if ( save_filechooser.getFileFilter() == MainFrame.nhfilter ) {\r
+ exception = writeAsNewHampshire( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );\r
+ }\r
+ else if ( save_filechooser.getFileFilter() == MainFrame.xmlfilter ) {\r
+ exception = writeAsPhyloXml( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );\r
+ }\r
+ else if ( save_filechooser.getFileFilter() == MainFrame.nexusfilter ) {\r
+ exception = writeAsNexus( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );\r
+ }\r
+ // "*.*":\r
+ else {\r
+ final String file_name = file.getName().trim().toLowerCase();\r
+ if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )\r
+ || file_name.endsWith( ".tree" ) ) {\r
+ exception = writeAsNewHampshire( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );\r
+ }\r
+ else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {\r
+ exception = writeAsNexus( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );\r
+ }\r
+ // XML is default:\r
+ else {\r
+ exception = writeAsPhyloXml( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );\r
+ }\r
+ }\r
+ if ( !exception ) {\r
+ mp.setTitleOfSelectedTab( file.getName() );\r
+ mp.getCurrentTreePanel().setTreeFile( file );\r
+ mp.getCurrentTreePanel().setEdited( false );\r
+ }\r
}\r
+ return new_file;\r
}\r
\r
- static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {\r
- if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {\r
- mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );\r
+ static File writeToGraphicsFile( final Phylogeny t,\r
+ final GraphicsExportType type,\r
+ final MainPanel mp,\r
+ final JFileChooser writetographics_filechooser,\r
+ final Component component,\r
+ final Container contentpane,\r
+ final File current_dir ) {\r
+ File new_dir = null;\r
+ if ( ( t == null ) || t.isEmpty() ) {\r
+ return null;\r
}\r
- else {\r
- mi.setText( "Cycle Overview Placement..." );\r
+ String initial_filename = "";\r
+ if ( mp.getCurrentTreePanel().getTreeFile() != null ) {\r
+ initial_filename = mp.getCurrentTreePanel().getTreeFile().toString();\r
}\r
- }\r
-\r
- static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
- if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
- mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
- + ")" );\r
+ if ( initial_filename.indexOf( '.' ) > 0 ) {\r
+ initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
}\r
- else {\r
- mi.setText( "Select Color Scheme..." );\r
+ initial_filename = initial_filename + "." + type;\r
+ writetographics_filechooser.setSelectedFile( new File( initial_filename ) );\r
+ final File my_dir = current_dir;\r
+ if ( my_dir != null ) {\r
+ writetographics_filechooser.setCurrentDirectory( my_dir );\r
}\r
+ final int result = writetographics_filechooser.showSaveDialog( contentpane );\r
+ File file = writetographics_filechooser.getSelectedFile();\r
+ //setCurrentDir( writetographics_filechooser.getCurrentDirectory() );\r
+ new_dir = writetographics_filechooser.getCurrentDirectory();\r
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {\r
+ file = new File( file.toString() + "." + type );\r
+ }\r
+ if ( file.exists() ) {\r
+ final int i = JOptionPane.showConfirmDialog( component,\r
+ file + " already exists. Overwrite?",\r
+ "Warning",\r
+ JOptionPane.OK_CANCEL_OPTION,\r
+ JOptionPane.WARNING_MESSAGE );\r
+ if ( i != JOptionPane.OK_OPTION ) {\r
+ return null;\r
+ }\r
+ else {\r
+ try {\r
+ file.delete();\r
+ }\r
+ catch ( final Exception e ) {\r
+ JOptionPane.showMessageDialog( component,\r
+ "Failed to delete: " + file,\r
+ "Error",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ }\r
+ }\r
+ writePhylogenyToGraphicsFile( file.toString(), type, mp, component, contentpane );\r
+ }\r
+ return new_dir;\r
}\r
\r
- static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {\r
- mi.setText( "Select Default Font... (current: " + font_desc + ")" );\r
- }\r
-\r
- static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {\r
- mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "\r
- + o.getPrintSizeY() + ")" );\r
- }\r
-\r
- static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {\r
- mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );\r
- }\r
-\r
- static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {\r
- if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {\r
- mi.setEnabled( true );\r
+ static File writeToPdf( final Phylogeny t,\r
+ final MainPanel mp,\r
+ final JFileChooser writetopdf_filechooser,\r
+ final File curr_dir,\r
+ final Container contentpane,\r
+ final Component component ) {\r
+ if ( ( t == null ) || t.isEmpty() ) {\r
+ return null;\r
}\r
- else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {\r
- mi.setEnabled( true );\r
+ String initial_filename = "";\r
+ if ( mp.getCurrentTreePanel().getTreeFile() != null ) {\r
+ initial_filename = mp.getCurrentTreePanel().getTreeFile().toString();\r
}\r
- else {\r
- mi.setEnabled( false );\r
+ if ( initial_filename.indexOf( '.' ) > 0 ) {\r
+ initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
}\r
- mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );\r
- }\r
-\r
- static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {\r
- mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );\r
- }\r
-\r
- static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {\r
- for( final TreePanel tree_panel : treepanels ) {\r
- tree_panel.setTextAntialias();\r
+ initial_filename = initial_filename + ".pdf";\r
+ writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );\r
+ final File my_dir = curr_dir;\r
+ if ( my_dir != null ) {\r
+ writetopdf_filechooser.setCurrentDirectory( my_dir );\r
}\r
- }\r
-\r
- private static void cycleNodeDataReturn( final Options op, final Configuration conf ) {\r
- switch ( op.getExtDescNodeDataToReturn() ) {\r
- case UNKNOWN:\r
- op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );\r
- break;\r
- case DOMAINS_ALL:\r
- op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );\r
- break;\r
- case DOMAINS_COLLAPSED_PER_PROTEIN:\r
- op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );\r
- break;\r
- case SEQ_ANNOTATIONS:\r
- op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );\r
- break;\r
- case GO_TERM_IDS:\r
- op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );\r
- break;\r
- case SEQUENCE_MOL_SEQ_FASTA:\r
- if ( ( conf != null ) && ( conf.getExtDescNodeDataToReturn() != null )\r
- && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL )\r
- && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN )\r
- && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS )\r
- && ( conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS )\r
- && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA ) ) {\r
- op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() );\r
- }\r
- else {\r
- op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
+ final int result = writetopdf_filechooser.showSaveDialog( contentpane );\r
+ File file = writetopdf_filechooser.getSelectedFile();\r
+ // setCurrentDir( writetopdf_filechooser.getCurrentDirectory() );\r
+ final File new_current_dir = writetopdf_filechooser.getCurrentDirectory();\r
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {\r
+ file = new File( file.toString() + ".pdf" );\r
+ }\r
+ if ( file.exists() ) {\r
+ final int i = JOptionPane.showConfirmDialog( component,\r
+ file + " already exists. Overwrite?",\r
+ "WARNING",\r
+ JOptionPane.OK_CANCEL_OPTION,\r
+ JOptionPane.WARNING_MESSAGE );\r
+ if ( i != JOptionPane.OK_OPTION ) {\r
+ return null;\r
}\r
- break;\r
- default:\r
- op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
+ }\r
+ printPhylogenyToPdf( file.toString(), mp.getOptions(), mp.getCurrentTreePanel(), component );\r
}\r
+ return new_current_dir;\r
}\r
}\r
\r
_contentpane.setLayout( new BorderLayout() );
_contentpane.add( _mainpanel, BorderLayout.CENTER );
setSize( getConfiguration().getFrameXSize() > 40 ? getConfiguration().getFrameXSize() : DEFAULT_FRAME_X_SIZE,
- getConfiguration().getFrameYSize() > 40 ? getConfiguration().getFrameYSize() : DEFAULT_FRAME_Y_SIZE );
+ getConfiguration().getFrameYSize() > 40 ? getConfiguration().getFrameYSize() : DEFAULT_FRAME_Y_SIZE );
addWindowListener( new WindowAdapter() {
@Override
public void componentResized( final ComponentEvent e ) {
if ( _mainpanel.getCurrentTreePanel() != null ) {
_mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()
- .getWidth(),
+ .getWidth(),
_mainpanel.getCurrentTreePanel()
- .getHeight() );
+ .getHeight() );
}
}
} );
System.gc();
}
+ @Override
+ public MainPanel getMainPanel() {
+ return _mainpanel;
+ }
+
+ private void readSpeciesTree( final Configuration configuration, final String species_tree_url_str )
+ throws MalformedURLException, FileNotFoundException, IOException {
+ final URL species_tree_url = new URL( species_tree_url_str );
+ final Phylogeny[] species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url,
+ configuration
+ .isValidatePhyloXmlAgainstSchema(),
+ configuration
+ .isReplaceUnderscoresInNhParsing(),
+ false,
+ TAXONOMY_EXTRACTION.NO,
+ false );
+ if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
+ AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "successfully read species tree" );
+ if ( species_trees[ 0 ].isEmpty() ) {
+ ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "species tree is empty" );
+ }
+ else if ( !species_trees[ 0 ].isRooted() ) {
+ ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "species tree is not rooted" );
+ }
+ else {
+ setSpeciesTree( species_trees[ 0 ] );
+ AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "species tree OK" );
+ }
+ }
+ else {
+ ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "failed to read species tree from "
+ + species_tree_url_str );
+ }
+ }
+
void buildAnalysisMenu() {
_analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
_analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
MainFrame
- .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
+ .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, createCurrentFontDesc( getMainPanel()
- .getTreeFontSet() ) );
+ .getTreeFontSet() ) );
setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
_options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ),
getConfiguration() ) );
_options_jmenu
- .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
+ .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
_options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
_options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
_radio_group_1 = new ButtonGroup();
_options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
_options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
_options_jmenu
- .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
+ .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
_options_jmenu
- .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
+ .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
_options_jmenu
- .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
+ .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
_options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
_options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
_options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) );
_options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) );
_options_jmenu
- .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
+ .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
_options_jmenu
- .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
+ .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
_color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
_options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
_options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) );
_options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ),
getConfiguration() ) );
_options_jmenu
- .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
+ .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) );
_options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) );
_options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );
_search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );
_options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
_options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
_options_jmenu
- .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
+ .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
_options_jmenu
- .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
+ .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
_options_jmenu
- .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
+ .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
_options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
_options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
//
customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
- .isGraphicsExportUsingActualSize() );
+ .isGraphicsExportUsingActualSize() );
customizeJMenuItem( _print_size_mi );
customizeJMenuItem( _choose_pdf_width_mi );
//
customizeJMenuItem( _choose_minimal_confidence_mi );
customizeJMenuItem( _overview_placment_mi );
customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
- .isShowDefaultNodeShapesInternal() );
+ .isShowDefaultNodeShapesInternal() );
customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
- .isShowDefaultNodeShapesExternal() );
+ .isShowDefaultNodeShapesExternal() );
customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()
- .isShowDefaultNodeShapesForMarkedNodes() );
+ .isShowDefaultNodeShapesForMarkedNodes() );
customizeJMenuItem( _cycle_node_shape_mi );
customizeJMenuItem( _cycle_node_fill_mi );
customizeJMenuItem( _choose_node_size_mi );
_tools_menu.addSeparator();
_tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
_remove_visual_styles_item
- .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
+ .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
customizeJMenuItem( _remove_visual_styles_item );
_tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
_remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." );
JApplet getApplet() {
return _applet;
}
-
- @Override
- public MainPanel getMainPanel() {
- return _mainpanel;
- }
-
- private void readSpeciesTree( final Configuration configuration, final String species_tree_url_str )
- throws MalformedURLException, FileNotFoundException, IOException {
- final URL species_tree_url = new URL( species_tree_url_str );
- final Phylogeny[] species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url,
- configuration
- .isValidatePhyloXmlAgainstSchema(),
- configuration
- .isReplaceUnderscoresInNhParsing(),
- false,
- TAXONOMY_EXTRACTION.NO,
- false );
- if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
- AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "successfully read species tree" );
- if ( species_trees[ 0 ].isEmpty() ) {
- ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "species tree is empty" );
- }
- else if ( !species_trees[ 0 ].isRooted() ) {
- ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "species tree is not rooted" );
- }
- else {
- setSpeciesTree( species_trees[ 0 ] );
- AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "species tree OK" );
- }
- }
- else {
- ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "failed to read species tree from "
- + species_tree_url_str );
- }
- }
}
import javax.swing.plaf.synth.SynthLookAndFeel;\r
\r
import org.forester.analysis.TaxonomyDataManager;\r
-import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;\r
import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;\r
import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;\r
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;\r
import org.forester.io.parsers.phyloxml.PhyloXmlUtil;\r
import org.forester.io.parsers.tol.TolParser;\r
import org.forester.io.parsers.util.ParserUtils;\r
-import org.forester.io.writers.PhylogenyWriter;\r
import org.forester.io.writers.SequenceWriter;\r
import org.forester.msa.Msa;\r
import org.forester.msa.MsaFormatException;\r
\r
public final class MainFrameApplication extends MainFrame {\r
\r
- public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {\r
- return new MainFrameApplication( phys, config );\r
- }\r
-\r
- static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {\r
- return new MainFrameApplication( phys, config, title );\r
- }\r
-\r
- public static MainFrame createInstance( final Phylogeny[] phys,\r
- final Configuration config,\r
- final String title,\r
- final File current_dir ) {\r
- return new MainFrameApplication( phys, config, title, current_dir );\r
- }\r
-\r
- static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {\r
- return new MainFrameApplication( phys, config_file_name, title );\r
- }\r
-\r
- static void warnIfNotPhyloXmlValidation( final Configuration c ) {\r
- if ( !c.isValidatePhyloXmlAgainstSchema() ) {\r
- JOptionPane\r
- .showMessageDialog( null,\r
- ForesterUtil\r
- .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",\r
- 80 ),\r
- "Warning",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";\r
static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";\r
private final static int FRAME_X_SIZE = 800;\r
public void componentResized( final ComponentEvent e ) {\r
if ( _mainpanel.getCurrentTreePanel() != null ) {\r
_mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()\r
- .getWidth(),\r
+ .getWidth(),\r
_mainpanel.getCurrentTreePanel()\r
- .getHeight() );\r
+ .getHeight() );\r
}\r
}\r
} );\r
else if ( o == _new_item ) {\r
newTree();\r
}\r
- \r
else if ( o == _close_item ) {\r
closeCurrentPane();\r
}\r
- \r
else if ( o == _load_species_tree_item ) {\r
readSpeciesTreeFromFile();\r
}\r
}\r
}\r
\r
+ public void end() {\r
+ _mainpanel.terminate();\r
+ _contentpane.removeAll();\r
+ setVisible( false );\r
+ dispose();\r
+ }\r
+\r
+ @Override\r
+ public MainPanel getMainPanel() {\r
+ return _mainpanel;\r
+ }\r
+\r
+ public Msa getMsa() {\r
+ return _msa;\r
+ }\r
+\r
+ public File getMsaFile() {\r
+ return _msa_file;\r
+ }\r
+\r
+ public List<MolecularSequence> getSeqs() {\r
+ return _seqs;\r
+ }\r
+\r
+ public File getSeqsFile() {\r
+ return _seqs_file;\r
+ }\r
+\r
+ public void readMsaFromFile() {\r
+ // Set an initial directory if none set yet\r
+ final File my_dir = getCurrentDir();\r
+ _msa_filechooser.setMultiSelectionEnabled( false );\r
+ // Open file-open dialog and set current directory\r
+ if ( my_dir != null ) {\r
+ _msa_filechooser.setCurrentDirectory( my_dir );\r
+ }\r
+ final int result = _msa_filechooser.showOpenDialog( _contentpane );\r
+ // All done: get the msa\r
+ final File file = _msa_filechooser.getSelectedFile();\r
+ setCurrentDir( _msa_filechooser.getCurrentDirectory() );\r
+ if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ setMsaFile( null );\r
+ setMsa( null );\r
+ Msa msa = null;\r
+ try {\r
+ final InputStream is = new FileInputStream( file );\r
+ if ( FastaParser.isLikelyFasta( file ) ) {\r
+ msa = FastaParser.parseMsa( is );\r
+ }\r
+ else {\r
+ msa = GeneralMsaParser.parse( is );\r
+ }\r
+ }\r
+ catch ( final MsaFormatException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Multiple sequence alignment format error",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final IOException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Failed to read multiple sequence alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final IllegalArgumentException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Unexpected error during reading of multiple sequence alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final Exception e ) {\r
+ setArrowCursor();\r
+ e.printStackTrace();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Unexpected error during reading of multiple sequence alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Multiple sequence alignment is empty",\r
+ "Illegal Multiple Sequence Alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( msa.getNumberOfSequences() < 4 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Multiple sequence alignment needs to contain at least 3 sequences",\r
+ "Illegal multiple sequence alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( msa.getLength() < 2 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Multiple sequence alignment needs to contain at least 2 residues",\r
+ "Illegal multiple sequence alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ System.gc();\r
+ setMsaFile( _msa_filechooser.getSelectedFile() );\r
+ setMsa( msa );\r
+ }\r
+ }\r
+\r
+ public void readSeqsFromFileforPI() {\r
+ // Set an initial directory if none set yet\r
+ final File my_dir = getCurrentDir();\r
+ _seqs_pi_filechooser.setMultiSelectionEnabled( false );\r
+ // Open file-open dialog and set current directory\r
+ if ( my_dir != null ) {\r
+ _seqs_pi_filechooser.setCurrentDirectory( my_dir );\r
+ }\r
+ final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane );\r
+ // All done: get the seqs\r
+ final File file = _seqs_pi_filechooser.getSelectedFile();\r
+ setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() );\r
+ if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ setSeqsFile( null );\r
+ setSeqs( null );\r
+ List<MolecularSequence> seqs = null;\r
+ try {\r
+ if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {\r
+ seqs = FastaParser.parse( new FileInputStream( file ) );\r
+ for( final MolecularSequence seq : seqs ) {\r
+ System.out.println( SequenceWriter.toFasta( seq, 60 ) );\r
+ }\r
+ }\r
+ else {\r
+ //TODO error\r
+ }\r
+ }\r
+ catch ( final MsaFormatException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Multiple sequence file format error",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final IOException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Failed to read multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final IllegalArgumentException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Unexpected error during reading of multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final Exception e ) {\r
+ setArrowCursor();\r
+ e.printStackTrace();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Unexpected error during reading of multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Multiple sequence file is empty",\r
+ "Illegal multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( seqs.size() < 4 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Multiple sequence file needs to contain at least 3 sequences",\r
+ "Illegal multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ // if ( msa.getLength() < 2 ) {\r
+ // JOptionPane.showMessageDialog( this,\r
+ // "Multiple sequence alignment needs to contain at least 2 residues",\r
+ // "Illegal multiple sequence file",\r
+ // JOptionPane.ERROR_MESSAGE );\r
+ // return;\r
+ // }\r
+ System.gc();\r
+ setSeqsFile( _seqs_pi_filechooser.getSelectedFile() );\r
+ setSeqs( seqs );\r
+ }\r
+ }\r
+\r
private void addExpressionValuesFromFile() {\r
if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {\r
JOptionPane.showMessageDialog( this,\r
JOptionPane.showMessageDialog( this,\r
"Table contains " + t.getNumberOfRows() + " rows, but tree contains "\r
+ phy.getNumberOfExternalNodes() + " external nodes",\r
- "Warning",\r
- JOptionPane.WARNING_MESSAGE );\r
+ "Warning",\r
+ JOptionPane.WARNING_MESSAGE );\r
}\r
final DescriptiveStatistics stats = new BasicDescriptiveStatistics();\r
int not_found = 0;\r
}\r
catch ( final IllegalArgumentException e ) {\r
JOptionPane\r
- .showMessageDialog( this,\r
- e.getMessage(),\r
- "Error Mapping Node Identifiers to Expression Value Identifiers",\r
- JOptionPane.ERROR_MESSAGE );\r
+ .showMessageDialog( this,\r
+ e.getMessage(),\r
+ "Error Mapping Node Identifiers to Expression Value Identifiers",\r
+ JOptionPane.ERROR_MESSAGE );\r
return;\r
}\r
if ( row < 0 ) {\r
catch ( final NumberFormatException e ) {\r
JOptionPane.showMessageDialog( this,\r
"Could not parse \"" + t.getValueAsString( col, row )\r
- + "\" into a decimal value",\r
+ + "\" into a decimal value",\r
"Issue with Expression Value Table",\r
JOptionPane.ERROR_MESSAGE );\r
return;\r
if ( !l.isEmpty() ) {\r
if ( node.getNodeData().getProperties() != null ) {\r
node.getNodeData().getProperties()\r
- .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );\r
+ .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );\r
}\r
node.getNodeData().setVector( l );\r
}\r
}\r
if ( not_found > 0 ) {\r
JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found\r
- + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );\r
+ + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );\r
}\r
getCurrentTreePanel().setStatisticsForExpressionValues( stats );\r
}\r
}\r
if ( nodes.size() > 1 ) {\r
JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split\r
- + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );\r
+ + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );\r
setArrowCursor();\r
return;\r
}\r
}\r
else {\r
JOptionPane.showMessageDialog( this, "Attached " + attached_counter\r
- + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter\r
- + " sequences attached", JOptionPane.WARNING_MESSAGE );\r
+ + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter\r
+ + " sequences attached", JOptionPane.WARNING_MESSAGE );\r
}\r
}\r
else {\r
JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter\r
- + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );\r
+ + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );\r
}\r
}\r
}\r
\r
- void buildAnalysisMenu() {\r
- _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );\r
- _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );\r
- _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );\r
- _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );\r
- customizeJMenuItem( _gsdi_item );\r
- customizeJMenuItem( _gsdir_item );\r
- customizeJMenuItem( _load_species_tree_item );\r
- _analysis_menu.addSeparator();\r
- _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );\r
- customizeJMenuItem( _lineage_inference );\r
- _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );\r
- _jmenubar.add( _analysis_menu );\r
+ private void closeCurrentPane() {\r
+ if ( getMainPanel().getCurrentTreePanel() != null ) {\r
+ if ( getMainPanel().getCurrentTreePanel().isEdited() ) {\r
+ final int r = JOptionPane.showConfirmDialog( this,\r
+ "Close tab despite potentially unsaved changes?",\r
+ "Close Tab?",\r
+ JOptionPane.YES_NO_OPTION );\r
+ if ( r != JOptionPane.YES_OPTION ) {\r
+ return;\r
+ }\r
+ }\r
+ getMainPanel().closeCurrentPane();\r
+ activateSaveAllIfNeeded();\r
+ }\r
}\r
\r
- @Override\r
- void buildFileMenu() {\r
- _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );\r
- _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );\r
- _file_jmenu.addSeparator();\r
- final WebservicesManager webservices_manager = WebservicesManager.getInstance();\r
- _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager\r
- .getAvailablePhylogeniesWebserviceClients().size() ];\r
- for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {\r
- final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );\r
- _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );\r
- _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );\r
- }\r
- if ( getConfiguration().isEditable() ) {\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _new_item = new JMenuItem( "New" ) );\r
- _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );\r
- }\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );\r
- _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );\r
- _save_all_item.setToolTipText( "Write all phylogenies to one file." );\r
- _save_all_item.setEnabled( false );\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );\r
- if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {\r
- _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );\r
- }\r
- _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );\r
- _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );\r
- if ( AptxUtil.canWriteFormat( "gif" ) ) {\r
- _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );\r
- }\r
- if ( AptxUtil.canWriteFormat( "bmp" ) ) {\r
- _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );\r
+ private void collapse( final Phylogeny phy ) {\r
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();\r
+ final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();\r
+ double min_support = Double.MAX_VALUE;\r
+ boolean conf_present = false;\r
+ while ( it.hasNext() ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( !n.isExternal() && !n.isRoot() ) {\r
+ final List<Confidence> c = n.getBranchData().getConfidences();\r
+ if ( ( c != null ) && ( c.size() > 0 ) ) {\r
+ conf_present = true;\r
+ double max = 0;\r
+ for( final Confidence confidence : c ) {\r
+ if ( confidence.getValue() > max ) {\r
+ max = confidence.getValue();\r
+ }\r
+ }\r
+ if ( max < getMinNotCollapseConfidenceValue() ) {\r
+ to_be_removed.add( n );\r
+ }\r
+ if ( max < min_support ) {\r
+ min_support = max;\r
+ }\r
+ }\r
+ }\r
}\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );\r
- _close_item.setToolTipText( "To close the current pane." );\r
- _close_item.setEnabled( true );\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
- customizeJMenuItem( _open_item );\r
- _open_item\r
- .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );\r
- customizeJMenuItem( _open_url_item );\r
- for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {\r
- customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );\r
+ if ( conf_present ) {\r
+ for( final PhylogenyNode node : to_be_removed ) {\r
+ PhylogenyMethods.removeNode( node, phy );\r
+ }\r
+ if ( to_be_removed.size() > 0 ) {\r
+ phy.externalNodesHaveChanged();\r
+ phy.clearHashIdToNodeMap();\r
+ phy.recalculateNumberOfExternalDescendants( true );\r
+ getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
+ getCurrentTreePanel().updateSetOfCollapsedExternalNodes();\r
+ getCurrentTreePanel().calculateLongestExtNodeInfo();\r
+ getCurrentTreePanel().setNodeInPreorderToNull();\r
+ getCurrentTreePanel().recalculateMaxDistanceToRoot();\r
+ getCurrentTreePanel().resetPreferredSize();\r
+ getCurrentTreePanel().setEdited( true );\r
+ getCurrentTreePanel().repaint();\r
+ repaint();\r
+ }\r
+ if ( to_be_removed.size() > 0 ) {\r
+ JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()\r
+ + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "\r
+ + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "\r
+ + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
}\r
- customizeJMenuItem( _save_item );\r
- if ( getConfiguration().isEditable() ) {\r
- customizeJMenuItem( _new_item );\r
+ else {\r
+ JOptionPane.showMessageDialog( this,\r
+ "No branch collapsed because no confidence values present",\r
+ "No confidence values present",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
}\r
- customizeJMenuItem( _close_item );\r
- customizeJMenuItem( _save_all_item );\r
- customizeJMenuItem( _write_to_pdf_item );\r
- customizeJMenuItem( _write_to_png_item );\r
- customizeJMenuItem( _write_to_jpg_item );\r
- customizeJMenuItem( _write_to_gif_item );\r
- customizeJMenuItem( _write_to_tif_item );\r
- customizeJMenuItem( _write_to_bmp_item );\r
- customizeJMenuItem( _print_item );\r
- customizeJMenuItem( _exit_item );\r
- _jmenubar.add( _file_jmenu );\r
}\r
\r
- void buildOptionsMenu() {\r
- _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );\r
- _options_jmenu.addChangeListener( new ChangeListener() {\r
+ private void collapseBelowBranchLengthThreshold() {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
+ if ( ( phy != null ) && !phy.isEmpty() ) {\r
+ final String s = ( String ) JOptionPane\r
+ .showInputDialog( this,\r
+ "Please enter the minimum branch length value\n",\r
+ "Minimal Branch Length Value",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getMinNotCollapseBlValue() );\r
+ if ( !ForesterUtil.isEmpty( s ) ) {\r
+ boolean success = true;\r
+ double m = 0.0;\r
+ final String m_str = s.trim();\r
+ if ( !ForesterUtil.isEmpty( m_str ) ) {\r
+ try {\r
+ m = Double.parseDouble( m_str );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
+ }\r
+ }\r
+ else {\r
+ success = false;\r
+ }\r
+ if ( success && ( m >= 0.0 ) ) {\r
+ setMinNotCollapseBlValue( m );\r
+ collapseBl( phy );\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
\r
- @Override\r
- public void stateChanged( final ChangeEvent e ) {\r
- MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );\r
- MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );\r
- MainFrame\r
- .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );\r
- MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame\r
- .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );\r
- MainFrame.setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );\r
- MainFrame.setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );\r
- MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );\r
- MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );\r
- MainFrame.setCycleDataReturnMenuItem( _cycle_data_return, getOptions() );\r
- MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );\r
- try {\r
- getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();\r
- getMainPanel().getControlPanel().setVisibilityOfX();\r
+ private void collapseBelowThreshold() {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
+ if ( ( phy != null ) && !phy.isEmpty() ) {\r
+ final String s = ( String ) JOptionPane.showInputDialog( this,\r
+ "Please enter the minimum confidence value\n",\r
+ "Minimal Confidence Value",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getMinNotCollapseConfidenceValue() );\r
+ if ( !ForesterUtil.isEmpty( s ) ) {\r
+ boolean success = true;\r
+ double m = 0.0;\r
+ final String m_str = s.trim();\r
+ if ( !ForesterUtil.isEmpty( m_str ) ) {\r
+ try {\r
+ m = Double.parseDouble( m_str );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
+ }\r
+ }\r
+ else {\r
+ success = false;\r
+ }\r
+ if ( success && ( m >= 0.0 ) ) {\r
+ setMinNotCollapseConfidenceValue( m );\r
+ collapse( phy );\r
+ }\r
}\r
- catch ( final Exception ignore ) {\r
- // do nothing, not important.\r
+ }\r
+ }\r
+ }\r
+\r
+ private void collapseBl( final Phylogeny phy ) {\r
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();\r
+ final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();\r
+ double min_bl = Double.MAX_VALUE;\r
+ boolean bl_present = false;\r
+ while ( it.hasNext() ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( !n.isExternal() && !n.isRoot() ) {\r
+ final double bl = n.getDistanceToParent();\r
+ if ( bl != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {\r
+ bl_present = true;\r
+ if ( bl < getMinNotCollapseBlValue() ) {\r
+ to_be_removed.add( n );\r
+ }\r
+ if ( bl < min_bl ) {\r
+ min_bl = bl;\r
+ }\r
}\r
}\r
- } );\r
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );\r
- _options_jmenu\r
- .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );\r
- _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );\r
- _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );\r
- _radio_group_1 = new ButtonGroup();\r
- _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );\r
- _radio_group_1.add( _uniform_cladograms_rbmi );\r
- _radio_group_1.add( _non_lined_up_cladograms_rbmi );\r
- _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );\r
- _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );\r
- _options_jmenu\r
- .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );\r
- _options_jmenu\r
- .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );\r
- _options_jmenu\r
- .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );\r
- _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );\r
- if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {\r
- _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );\r
- _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );\r
}\r
- _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );\r
- _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );\r
- _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) );\r
- _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );\r
- _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );\r
- _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );\r
- _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );\r
- _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );\r
- _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );\r
- _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );\r
- _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );\r
- _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );\r
- _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );\r
- _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );\r
- _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );\r
- _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );\r
- _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );\r
- _options_jmenu.addSeparator();\r
- _options_jmenu.add( _cycle_data_return = new JMenuItem( "Cycle Data Return" ) );\r
- _options_jmenu.addSeparator();\r
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );\r
- _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );\r
- _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );\r
- _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );\r
- _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );\r
- _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );\r
- _options_jmenu.addSeparator();\r
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),\r
- getConfiguration() ) );\r
- _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );\r
- _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );\r
- _options_jmenu\r
- .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );\r
- _options_jmenu\r
- .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );\r
- _options_jmenu\r
- .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );\r
- _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );\r
- _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );\r
- _options_jmenu.addSeparator();\r
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );\r
- _options_jmenu\r
- .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );\r
- _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );\r
- _options_jmenu\r
- .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );\r
- _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );\r
- _options_jmenu\r
- .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );\r
- _options_jmenu\r
- .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) );\r
- _options_jmenu\r
- .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) );\r
- _extract_taxonomy_pfam_strict_rbmi\r
- .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" );\r
- _extract_taxonomy_pfam_relaxed_rbmi\r
- .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" );\r
- _extract_taxonomy_agressive_rbmi\r
- .setToolTipText( "To extract taxonomy codes/ids or scientific names from node names in the form of e.g. \"MOUSE\" or \"10090\" or \"xyz_Nematostella_vectensis\"" );\r
- _radio_group_2 = new ButtonGroup();\r
- _radio_group_2.add( _extract_taxonomy_no_rbmi );\r
- _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );\r
- _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );\r
- _radio_group_2.add( _extract_taxonomy_agressive_rbmi );\r
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );\r
- _options_jmenu\r
- .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );\r
- _use_brackets_for_conf_in_nh_export_cbmi\r
- .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );\r
- _options_jmenu\r
- .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );\r
- customizeJMenuItem( _choose_font_mi );\r
- customizeJMenuItem( _choose_minimal_confidence_mi );\r
- customizeJMenuItem( _switch_colors_mi );\r
- customizeJMenuItem( _print_size_mi );\r
- customizeJMenuItem( _choose_pdf_width_mi );\r
- customizeJMenuItem( _overview_placment_mi );\r
- customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()\r
- .isShowDefaultNodeShapesExternal() );\r
- customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()\r
- .isShowDefaultNodeShapesInternal() );\r
- customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()\r
- .isShowDefaultNodeShapesForMarkedNodes() );\r
- customizeJMenuItem( _cycle_node_shape_mi );\r
- customizeJMenuItem( _cycle_node_fill_mi );\r
- customizeJMenuItem( _choose_node_size_mi );\r
- customizeJMenuItem( _cycle_data_return );\r
- customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );\r
- customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );\r
- customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );\r
- customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );\r
- customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );\r
- customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );\r
- customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );\r
- customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );\r
- customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );\r
- customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,\r
- getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );\r
- customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,\r
- getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
- customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,\r
- getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
- customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );\r
- customizeCheckBoxMenuItem( _label_direction_cbmi,\r
- getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );\r
- customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );\r
- customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );\r
- customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()\r
- .isInternalNumberAreConfidenceForNhParsing() );\r
- customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,\r
- getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );\r
- customizeRadioButtonMenuItem( _extract_taxonomy_pfam_strict_rbmi,\r
- getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
- customizeRadioButtonMenuItem( _extract_taxonomy_pfam_relaxed_rbmi,\r
- getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
- customizeRadioButtonMenuItem( _extract_taxonomy_agressive_rbmi,\r
- getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE );\r
- customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );\r
- customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi, getOptions()\r
- .isReplaceUnderscoresInNhParsing() );\r
- customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );\r
- customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );\r
- customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );\r
- customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );\r
- customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );\r
- customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()\r
- .isGraphicsExportUsingActualSize() );\r
- customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );\r
- customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()\r
- .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
- customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()\r
- .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
- customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );\r
- customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );\r
- _jmenubar.add( _options_jmenu );\r
- }\r
-\r
- void buildPhylogeneticInferenceMenu() {\r
- final InferenceManager im = getInferenceManager();\r
- _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );\r
- _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );\r
- customizeJMenuItem( _inference_from_msa_item );\r
- _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );\r
- if ( im.canDoMsa() ) {\r
- _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );\r
- customizeJMenuItem( _inference_from_seqs_item );\r
- _inference_from_seqs_item\r
- .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );\r
- }\r
- else {\r
- _inference_menu\r
- .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );\r
- customizeJMenuItem( _inference_from_seqs_item );\r
- _inference_from_seqs_item.setEnabled( false );\r
- }\r
- _jmenubar.add( _inference_menu );\r
- }\r
-\r
- void buildToolsMenu() {\r
- _tools_menu = createMenu( "Tools", getConfiguration() );\r
- _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );\r
- customizeJMenuItem( _confcolor_item );\r
- _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );\r
- customizeJMenuItem( _color_rank_jmi );\r
- _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );\r
- _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );\r
- customizeJMenuItem( _taxcolor_item );\r
- _tools_menu.addSeparator();\r
- _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );\r
- _remove_visual_styles_item\r
- .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny" );\r
- customizeJMenuItem( _remove_visual_styles_item );\r
- _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );\r
- _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny" );\r
- customizeJMenuItem( _remove_branch_color_item );\r
- _tools_menu.addSeparator();\r
- _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );\r
- customizeJMenuItem( _annotate_item );\r
- _tools_menu.addSeparator();\r
- _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );\r
- customizeJMenuItem( _midpoint_root_item );\r
- _tools_menu.addSeparator();\r
- _tools_menu.add( _delete_selected_nodes_item = new JMenuItem( "Delete Selected Nodes" ) );\r
- _delete_selected_nodes_item.setToolTipText( "To delete all selected external nodes" );\r
- customizeJMenuItem( _delete_selected_nodes_item );\r
- _tools_menu.add( _delete_not_selected_nodes_item = new JMenuItem( "Retain Selected Nodes" ) );\r
- _delete_not_selected_nodes_item.setToolTipText( "To delete all not selected external nodes" );\r
- customizeJMenuItem( _delete_not_selected_nodes_item );\r
- _tools_menu.addSeparator();\r
- _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );\r
- customizeJMenuItem( _collapse_species_specific_subtrees );\r
- _collapse_species_specific_subtrees.setToolTipText( "To (reversibly) collapse species-specific subtrees" );\r
- _tools_menu\r
- .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );\r
- customizeJMenuItem( _collapse_below_threshold );\r
- _collapse_below_threshold\r
- .setToolTipText( "To (permanently) collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" );\r
- //\r
- _tools_menu\r
- .add( _collapse_below_branch_length = new JMenuItem( "Collapse Branches with Branch Lengths Below Threshold into Multifurcations" ) );\r
- customizeJMenuItem( _collapse_below_branch_length );\r
- _collapse_below_branch_length\r
- .setToolTipText( "To (permanently) collapse branches with branches with branch lengths below a threshold into multifurcations" );\r
- //\r
- _tools_menu.addSeparator();\r
- _tools_menu\r
- .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );\r
- customizeJMenuItem( _extract_tax_code_from_node_names_jmi );\r
- _extract_tax_code_from_node_names_jmi\r
- .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" );\r
- _tools_menu\r
- .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );\r
- customizeJMenuItem( _move_node_names_to_tax_sn_jmi );\r
- _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );\r
- _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );\r
- customizeJMenuItem( _move_node_names_to_seq_names_jmi );\r
- _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );\r
- _tools_menu.addSeparator();\r
- _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );\r
- customizeJMenuItem( _obtain_seq_information_jmi );\r
- _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );\r
- _tools_menu\r
- .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );\r
- customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );\r
- _obtain_detailed_taxonomic_information_jmi\r
- .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );\r
- _tools_menu\r
- .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );\r
- customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );\r
- _obtain_detailed_taxonomic_information_deleting_jmi\r
- .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );\r
- _tools_menu.addSeparator();\r
- _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) );\r
- customizeJMenuItem( _read_values_jmi );\r
- _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" );\r
- _jmenubar.add( _tools_menu );\r
- _tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) );\r
- customizeJMenuItem( _read_seqs_jmi );\r
- _read_seqs_jmi\r
- .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );\r
- _jmenubar.add( _tools_menu );\r
- }\r
-\r
- @Override\r
- void close() {\r
- if ( isUnsavedDataPresent() ) {\r
- final int r = JOptionPane.showConfirmDialog( this,\r
- "Exit despite potentially unsaved changes?",\r
- "Exit?",\r
- JOptionPane.YES_NO_OPTION );\r
- if ( r != JOptionPane.YES_OPTION ) {\r
- return;\r
- }\r
- }\r
- exit();\r
- }\r
-\r
- private void closeCurrentPane() {\r
- if ( getMainPanel().getCurrentTreePanel() != null ) {\r
- if ( getMainPanel().getCurrentTreePanel().isEdited() ) {\r
- final int r = JOptionPane.showConfirmDialog( this,\r
- "Close tab despite potentially unsaved changes?",\r
- "Close Tab?",\r
- JOptionPane.YES_NO_OPTION );\r
- if ( r != JOptionPane.YES_OPTION ) {\r
- return;\r
- }\r
- }\r
- getMainPanel().closeCurrentPane();\r
- activateSaveAllIfNeeded();\r
- }\r
- }\r
-\r
- private void collapse( final Phylogeny phy ) {\r
- final PhylogenyNodeIterator it = phy.iteratorPostorder();\r
- final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();\r
- double min_support = Double.MAX_VALUE;\r
- boolean conf_present = false;\r
- while ( it.hasNext() ) {\r
- final PhylogenyNode n = it.next();\r
- if ( !n.isExternal() && !n.isRoot() ) {\r
- final List<Confidence> c = n.getBranchData().getConfidences();\r
- if ( ( c != null ) && ( c.size() > 0 ) ) {\r
- conf_present = true;\r
- double max = 0;\r
- for( final Confidence confidence : c ) {\r
- if ( confidence.getValue() > max ) {\r
- max = confidence.getValue();\r
- }\r
- }\r
- if ( max < getMinNotCollapseConfidenceValue() ) {\r
- to_be_removed.add( n );\r
- }\r
- if ( max < min_support ) {\r
- min_support = max;\r
- }\r
- }\r
- }\r
- }\r
- if ( conf_present ) {\r
+ if ( bl_present ) {\r
for( final PhylogenyNode node : to_be_removed ) {\r
PhylogenyMethods.removeNode( node, phy );\r
}\r
}\r
if ( to_be_removed.size() > 0 ) {\r
JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()\r
- + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "\r
- + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );\r
+ + " branches with\nbranch length values below " + getMinNotCollapseBlValue(), "Collapsed "\r
+ + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );\r
}\r
else {\r
- JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "\r
- + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );\r
+ JOptionPane.showMessageDialog( this,\r
+ "No branch collapsed,\nminimum branch length is " + min_bl,\r
+ "No branch collapsed",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
}\r
}\r
else {\r
JOptionPane.showMessageDialog( this,\r
- "No branch collapsed because no confidence values present",\r
- "No confidence values present",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- }\r
-\r
- private void collapseBelowBranchLengthThreshold() {\r
- if ( getCurrentTreePanel() != null ) {\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- final String s = ( String ) JOptionPane\r
- .showInputDialog( this,\r
- "Please enter the minimum branch length value\n",\r
- "Minimal Branch Length Value",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getMinNotCollapseBlValue() );\r
- if ( !ForesterUtil.isEmpty( s ) ) {\r
- boolean success = true;\r
- double m = 0.0;\r
- final String m_str = s.trim();\r
- if ( !ForesterUtil.isEmpty( m_str ) ) {\r
- try {\r
- m = Double.parseDouble( m_str );\r
- }\r
- catch ( final Exception ex ) {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
- }\r
- if ( success && ( m >= 0.0 ) ) {\r
- setMinNotCollapseBlValue( m );\r
- collapseBl( phy );\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- private void collapseBelowThreshold() {\r
- if ( getCurrentTreePanel() != null ) {\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- final String s = ( String ) JOptionPane.showInputDialog( this,\r
- "Please enter the minimum confidence value\n",\r
- "Minimal Confidence Value",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getMinNotCollapseConfidenceValue() );\r
- if ( !ForesterUtil.isEmpty( s ) ) {\r
- boolean success = true;\r
- double m = 0.0;\r
- final String m_str = s.trim();\r
- if ( !ForesterUtil.isEmpty( m_str ) ) {\r
- try {\r
- m = Double.parseDouble( m_str );\r
- }\r
- catch ( final Exception ex ) {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
- }\r
- if ( success && ( m >= 0.0 ) ) {\r
- setMinNotCollapseConfidenceValue( m );\r
- collapse( phy );\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- private void collapseBl( final Phylogeny phy ) {\r
- final PhylogenyNodeIterator it = phy.iteratorPostorder();\r
- final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();\r
- double min_bl = Double.MAX_VALUE;\r
- boolean bl_present = false;\r
- while ( it.hasNext() ) {\r
- final PhylogenyNode n = it.next();\r
- if ( !n.isExternal() && !n.isRoot() ) {\r
- final double bl = n.getDistanceToParent();\r
- if ( bl != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {\r
- bl_present = true;\r
- if ( bl < getMinNotCollapseBlValue() ) {\r
- to_be_removed.add( n );\r
- }\r
- if ( bl < min_bl ) {\r
- min_bl = bl;\r
- }\r
- }\r
- }\r
- }\r
- if ( bl_present ) {\r
- for( final PhylogenyNode node : to_be_removed ) {\r
- PhylogenyMethods.removeNode( node, phy );\r
- }\r
- if ( to_be_removed.size() > 0 ) {\r
- phy.externalNodesHaveChanged();\r
- phy.clearHashIdToNodeMap();\r
- phy.recalculateNumberOfExternalDescendants( true );\r
- getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
- getCurrentTreePanel().updateSetOfCollapsedExternalNodes();\r
- getCurrentTreePanel().calculateLongestExtNodeInfo();\r
- getCurrentTreePanel().setNodeInPreorderToNull();\r
- getCurrentTreePanel().recalculateMaxDistanceToRoot();\r
- getCurrentTreePanel().resetPreferredSize();\r
- getCurrentTreePanel().setEdited( true );\r
- getCurrentTreePanel().repaint();\r
- repaint();\r
- }\r
- if ( to_be_removed.size() > 0 ) {\r
- JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()\r
- + " branches with\nbranch length values below " + getMinNotCollapseBlValue(), "Collapsed "\r
- + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "No branch collapsed,\nminimum branch length is " + min_bl,\r
- "No branch collapsed",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "No branch collapsed because no branch length values present",\r
- "No branch length values present",\r
+ "No branch collapsed because no branch length values present",\r
+ "No branch length values present",\r
JOptionPane.INFORMATION_MESSAGE );\r
}\r
}\r
return xml_parser;\r
}\r
\r
- public void end() {\r
- _mainpanel.terminate();\r
- _contentpane.removeAll();\r
- setVisible( false );\r
- dispose();\r
- }\r
-\r
- void executeLineageInference() {\r
- if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {\r
- return;\r
- }\r
- if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Phylogeny is not rooted.",\r
- "Cannot infer ancestral taxonomies",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,\r
- _mainpanel.getCurrentTreePanel(),\r
- _mainpanel.getCurrentPhylogeny()\r
- .copy() );\r
- new Thread( inferrer ).start();\r
- }\r
-\r
private void executePhyleneticInference( final boolean from_unaligned_seqs ) {\r
final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,\r
getPhylogeneticInferenceOptions(),\r
if ( getMsa() != null ) {\r
final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),\r
getPhylogeneticInferenceOptions()\r
- .copy(), this );\r
+ .copy(), this );\r
new Thread( inferrer ).start();\r
}\r
else {\r
if ( getSeqs() != null ) {\r
final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),\r
getPhylogeneticInferenceOptions()\r
- .copy(), this );\r
+ .copy(), this );\r
new Thread( inferrer ).start();\r
}\r
else {\r
}\r
}\r
\r
- void exit() {\r
- removeAllTextFrames();\r
- _mainpanel.terminate();\r
- _contentpane.removeAll();\r
- setVisible( false );\r
- dispose();\r
- // System.exit( 0 ); //TODO reconfirm that this is OK, then remove.\r
- }\r
-\r
private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException {\r
final StringBuilder sb = new StringBuilder();\r
final StringBuilder sb_failed = new StringBuilder();\r
}\r
JOptionPane.showMessageDialog( this,\r
"Extracted taxonomic data from " + all + counter\r
- + " named external nodes:\n" + sb.toString() + failed,\r
+ + " named external nodes:\n" + sb.toString() + failed,\r
"Taxonomic Data Extraction Completed",\r
counter_failed > 0 ? JOptionPane.WARNING_MESSAGE\r
: JOptionPane.INFORMATION_MESSAGE );\r
}\r
else {\r
JOptionPane\r
- .showMessageDialog( this,\r
- "Could not extract any taxonomic data.\nMaybe node names are empty\n"\r
- + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"\r
- + "or nodes already have taxonomic data?\n",\r
+ .showMessageDialog( this,\r
+ "Could not extract any taxonomic data.\nMaybe node names are empty\n"\r
+ + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"\r
+ + "or nodes already have taxonomic data?\n",\r
"No Taxonomic Data Extracted",\r
JOptionPane.ERROR_MESSAGE );\r
}\r
}\r
}\r
\r
- @Override\r
- public MainPanel getMainPanel() {\r
- return _mainpanel;\r
- }\r
-\r
private double getMinNotCollapseBlValue() {\r
return _min_not_collapse_bl;\r
}\r
return _min_not_collapse;\r
}\r
\r
- public Msa getMsa() {\r
- return _msa;\r
- }\r
-\r
- public File getMsaFile() {\r
- return _msa_file;\r
- }\r
-\r
private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {\r
if ( _phylogenetic_inference_options == null ) {\r
_phylogenetic_inference_options = new PhylogeneticInferenceOptions();\r
return _phylogenetic_inference_options;\r
}\r
\r
- public List<MolecularSequence> getSeqs() {\r
- return _seqs;\r
- }\r
-\r
- public File getSeqsFile() {\r
- return _seqs_file;\r
- }\r
-\r
private boolean isUnsavedDataPresent() {\r
final List<TreePanel> tps = getMainPanel().getTreePanels();\r
for( final TreePanel tp : tps ) {\r
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
if ( ( phy != null ) && !phy.isEmpty() ) {\r
PhylogenyMethods\r
- .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );\r
+ .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );\r
}\r
}\r
}\r
if ( getMainPanel().getMainFrame() == null ) {\r
// Must be "E" applet version.\r
( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )\r
- .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
+ .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
}\r
else {\r
getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
}\r
}\r
\r
- \r
-\r
- public void readMsaFromFile() {\r
+ private void readPhylogeniesFromFile() {\r
+ boolean exception = false;\r
+ Phylogeny[] phys = null;\r
// Set an initial directory if none set yet\r
final File my_dir = getCurrentDir();\r
- _msa_filechooser.setMultiSelectionEnabled( false );\r
+ _open_filechooser.setMultiSelectionEnabled( true );\r
// Open file-open dialog and set current directory\r
if ( my_dir != null ) {\r
- _msa_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _msa_filechooser.showOpenDialog( _contentpane );\r
- // All done: get the msa\r
- final File file = _msa_filechooser.getSelectedFile();\r
- setCurrentDir( _msa_filechooser.getCurrentDirectory() );\r
- if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- setMsaFile( null );\r
- setMsa( null );\r
- Msa msa = null;\r
- try {\r
- final InputStream is = new FileInputStream( file );\r
- if ( FastaParser.isLikelyFasta( file ) ) {\r
- msa = FastaParser.parseMsa( is );\r
- }\r
- else {\r
- msa = GeneralMsaParser.parse( is );\r
- }\r
- }\r
- catch ( final MsaFormatException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Multiple sequence alignment format error",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final IOException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Failed to read multiple sequence alignment",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final IllegalArgumentException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Unexpected error during reading of multiple sequence alignment",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final Exception e ) {\r
- setArrowCursor();\r
- e.printStackTrace();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Unexpected error during reading of multiple sequence alignment",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Multiple sequence alignment is empty",\r
- "Illegal Multiple Sequence Alignment",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( msa.getNumberOfSequences() < 4 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Multiple sequence alignment needs to contain at least 3 sequences",\r
- "Illegal multiple sequence alignment",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( msa.getLength() < 2 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Multiple sequence alignment needs to contain at least 2 residues",\r
- "Illegal multiple sequence alignment",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- System.gc();\r
- setMsaFile( _msa_filechooser.getSelectedFile() );\r
- setMsa( msa );\r
- }\r
- }\r
-\r
- private void readPhylogeniesFromFile() {\r
- boolean exception = false;\r
- Phylogeny[] phys = null;\r
- // Set an initial directory if none set yet\r
- final File my_dir = getCurrentDir();\r
- _open_filechooser.setMultiSelectionEnabled( true );\r
- // Open file-open dialog and set current directory\r
- if ( my_dir != null ) {\r
- _open_filechooser.setCurrentDirectory( my_dir );\r
+ _open_filechooser.setCurrentDirectory( my_dir );\r
}\r
final int result = _open_filechooser.showOpenDialog( _contentpane );\r
// All done: get the file\r
try {\r
final PhylogenyParser parser = ParserUtils\r
.createParserDependingOnFileType( file, getConfiguration()\r
- .isValidatePhyloXmlAgainstSchema() );\r
+ .isValidatePhyloXmlAgainstSchema() );\r
if ( parser instanceof NexusPhylogeniesParser ) {\r
final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;\r
setSpecialOptionsForNexParser( nex );\r
_mainpanel.getControlPanel().showWhole();\r
if ( nhx_or_nexus && one_desc ) {\r
JOptionPane\r
- .showMessageDialog( this,\r
- "One or more trees contain (a) node(s) with one descendant, "\r
- + ForesterUtil.LINE_SEPARATOR\r
- + "possibly indicating illegal parentheses within node names.",\r
+ .showMessageDialog( this,\r
+ "One or more trees contain (a) node(s) with one descendant, "\r
+ + ForesterUtil.LINE_SEPARATOR\r
+ + "possibly indicating illegal parentheses within node names.",\r
"Warning: Possible Error in New Hampshire Formatted Data",\r
JOptionPane.WARNING_MESSAGE );\r
}\r
}\r
}\r
}\r
- activateSaveAllIfNeeded();\r
- System.gc();\r
+ activateSaveAllIfNeeded();\r
+ System.gc();\r
+ }\r
+\r
+ private void readSpeciesTreeFromFile() {\r
+ Phylogeny t = null;\r
+ boolean exception = false;\r
+ final File my_dir = getCurrentDir();\r
+ _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );\r
+ if ( my_dir != null ) {\r
+ _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );\r
+ }\r
+ final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );\r
+ final File file = _open_filechooser_for_species_tree.getSelectedFile();\r
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.xmlfilter ) {\r
+ try {\r
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser\r
+ .createPhyloXmlParserXsdValidating(), file );\r
+ t = trees[ 0 ];\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringOpenFile( e );\r
+ }\r
+ }\r
+ else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.tolfilter ) {\r
+ try {\r
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );\r
+ t = trees[ 0 ];\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringOpenFile( e );\r
+ }\r
+ }\r
+ // "*.*":\r
+ else {\r
+ try {\r
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser\r
+ .createPhyloXmlParserXsdValidating(), file );\r
+ t = trees[ 0 ];\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringOpenFile( e );\r
+ }\r
+ }\r
+ if ( !exception && ( t != null ) && !t.isRooted() ) {\r
+ exception = true;\r
+ t = null;\r
+ JOptionPane.showMessageDialog( this,\r
+ "Species tree is not rooted",\r
+ "Species tree not loaded",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ if ( !exception && ( t != null ) ) {\r
+ final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();\r
+ for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {\r
+ final PhylogenyNode node = it.next();\r
+ if ( !node.getNodeData().isHasTaxonomy() ) {\r
+ exception = true;\r
+ t = null;\r
+ JOptionPane\r
+ .showMessageDialog( this,\r
+ "Species tree contains external node(s) without taxonomy information",\r
+ "Species tree not loaded",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ break;\r
+ }\r
+ else {\r
+ if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {\r
+ exception = true;\r
+ t = null;\r
+ JOptionPane.showMessageDialog( this,\r
+ "Taxonomy ["\r
+ + node.getNodeData().getTaxonomy().asSimpleText()\r
+ + "] is not unique in species tree",\r
+ "Species tree not loaded",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ break;\r
+ }\r
+ else {\r
+ tax_set.add( node.getNodeData().getTaxonomy() );\r
+ }\r
+ }\r
+ }\r
+ }\r
+ if ( !exception && ( t != null ) ) {\r
+ setSpeciesTree( t );\r
+ JOptionPane.showMessageDialog( this,\r
+ "Species tree successfully loaded",\r
+ "Species tree loaded",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ _contentpane.repaint();\r
+ System.gc();\r
+ }\r
+ }\r
+\r
+ private void setArrowCursor() {\r
+ try {\r
+ _mainpanel.getCurrentTreePanel().setArrowCursor();\r
+ }\r
+ catch ( final Exception ex ) {\r
+ // Do nothing.\r
+ }\r
+ }\r
+\r
+ private void setMinNotCollapseBlValue( final double min_not_collapse_bl ) {\r
+ _min_not_collapse_bl = min_not_collapse_bl;\r
+ }\r
+\r
+ private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {\r
+ _min_not_collapse = min_not_collapse;\r
+ }\r
+\r
+ private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {\r
+ _phylogenetic_inference_options = phylogenetic_inference_options;\r
+ }\r
+\r
+ private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {\r
+ nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );\r
+ nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );\r
+ }\r
+\r
+ private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {\r
+ nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );\r
+ nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );\r
+ nhx.setAllowErrorsInDistanceToParent( getOptions().isAllowErrorsInDistanceToParent() );\r
+ }\r
+\r
+ void buildAnalysisMenu() {\r
+ _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );\r
+ _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );\r
+ _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );\r
+ _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );\r
+ customizeJMenuItem( _gsdi_item );\r
+ customizeJMenuItem( _gsdir_item );\r
+ customizeJMenuItem( _load_species_tree_item );\r
+ _analysis_menu.addSeparator();\r
+ _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );\r
+ customizeJMenuItem( _lineage_inference );\r
+ _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );\r
+ _jmenubar.add( _analysis_menu );\r
+ }\r
+\r
+ @Override\r
+ void buildFileMenu() {\r
+ _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );\r
+ _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );\r
+ _file_jmenu.addSeparator();\r
+ final WebservicesManager webservices_manager = WebservicesManager.getInstance();\r
+ _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager\r
+ .getAvailablePhylogeniesWebserviceClients().size() ];\r
+ for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {\r
+ final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );\r
+ _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );\r
+ _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );\r
+ }\r
+ if ( getConfiguration().isEditable() ) {\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _new_item = new JMenuItem( "New" ) );\r
+ _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );\r
+ }\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );\r
+ _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );\r
+ _save_all_item.setToolTipText( "Write all phylogenies to one file." );\r
+ _save_all_item.setEnabled( false );\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );\r
+ if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {\r
+ _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );\r
+ }\r
+ _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );\r
+ _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );\r
+ if ( AptxUtil.canWriteFormat( "gif" ) ) {\r
+ _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );\r
+ }\r
+ if ( AptxUtil.canWriteFormat( "bmp" ) ) {\r
+ _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );\r
+ }\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );\r
+ _close_item.setToolTipText( "To close the current pane." );\r
+ _close_item.setEnabled( true );\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
+ customizeJMenuItem( _open_item );\r
+ _open_item\r
+ .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );\r
+ customizeJMenuItem( _open_url_item );\r
+ for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {\r
+ customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );\r
+ }\r
+ customizeJMenuItem( _save_item );\r
+ if ( getConfiguration().isEditable() ) {\r
+ customizeJMenuItem( _new_item );\r
+ }\r
+ customizeJMenuItem( _close_item );\r
+ customizeJMenuItem( _save_all_item );\r
+ customizeJMenuItem( _write_to_pdf_item );\r
+ customizeJMenuItem( _write_to_png_item );\r
+ customizeJMenuItem( _write_to_jpg_item );\r
+ customizeJMenuItem( _write_to_gif_item );\r
+ customizeJMenuItem( _write_to_tif_item );\r
+ customizeJMenuItem( _write_to_bmp_item );\r
+ customizeJMenuItem( _print_item );\r
+ customizeJMenuItem( _exit_item );\r
+ _jmenubar.add( _file_jmenu );\r
+ }\r
+\r
+ void buildOptionsMenu() {\r
+ _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );\r
+ _options_jmenu.addChangeListener( new ChangeListener() {\r
+\r
+ @Override\r
+ public void stateChanged( final ChangeEvent e ) {\r
+ MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );\r
+ MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );\r
+ MainFrame\r
+ .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );\r
+ MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame\r
+ .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );\r
+ MainFrame.setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );\r
+ MainFrame.setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );\r
+ MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );\r
+ MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );\r
+ MainFrame.setCycleDataReturnMenuItem( _cycle_data_return, getOptions() );\r
+ MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );\r
+ try {\r
+ getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();\r
+ getMainPanel().getControlPanel().setVisibilityOfX();\r
+ }\r
+ catch ( final Exception ignore ) {\r
+ // do nothing, not important.\r
+ }\r
+ }\r
+ } );\r
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );\r
+ _options_jmenu\r
+ .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );\r
+ _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );\r
+ _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );\r
+ _radio_group_1 = new ButtonGroup();\r
+ _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );\r
+ _radio_group_1.add( _uniform_cladograms_rbmi );\r
+ _radio_group_1.add( _non_lined_up_cladograms_rbmi );\r
+ _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );\r
+ _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );\r
+ _options_jmenu\r
+ .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );\r
+ _options_jmenu\r
+ .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );\r
+ _options_jmenu\r
+ .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );\r
+ _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );\r
+ if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {\r
+ _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );\r
+ _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );\r
+ }\r
+ _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );\r
+ _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );\r
+ _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) );\r
+ _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );\r
+ _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );\r
+ _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );\r
+ _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );\r
+ _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );\r
+ _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );\r
+ _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );\r
+ _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );\r
+ _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );\r
+ _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );\r
+ _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );\r
+ _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );\r
+ _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );\r
+ _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );\r
+ _options_jmenu.addSeparator();\r
+ _options_jmenu.add( _cycle_data_return = new JMenuItem( "Cycle Data Return" ) );\r
+ _options_jmenu.addSeparator();\r
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );\r
+ _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );\r
+ _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );\r
+ _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );\r
+ _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );\r
+ _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );\r
+ _options_jmenu.addSeparator();\r
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),\r
+ getConfiguration() ) );\r
+ _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );\r
+ _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );\r
+ _options_jmenu\r
+ .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );\r
+ _options_jmenu\r
+ .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );\r
+ _options_jmenu\r
+ .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );\r
+ _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );\r
+ _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );\r
+ _options_jmenu.addSeparator();\r
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );\r
+ _options_jmenu\r
+ .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );\r
+ _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );\r
+ _options_jmenu\r
+ .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );\r
+ _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );\r
+ _options_jmenu\r
+ .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );\r
+ _options_jmenu\r
+ .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) );\r
+ _options_jmenu\r
+ .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) );\r
+ _extract_taxonomy_pfam_strict_rbmi\r
+ .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" );\r
+ _extract_taxonomy_pfam_relaxed_rbmi\r
+ .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" );\r
+ _extract_taxonomy_agressive_rbmi\r
+ .setToolTipText( "To extract taxonomy codes/ids or scientific names from node names in the form of e.g. \"MOUSE\" or \"10090\" or \"xyz_Nematostella_vectensis\"" );\r
+ _radio_group_2 = new ButtonGroup();\r
+ _radio_group_2.add( _extract_taxonomy_no_rbmi );\r
+ _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );\r
+ _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );\r
+ _radio_group_2.add( _extract_taxonomy_agressive_rbmi );\r
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );\r
+ _options_jmenu\r
+ .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );\r
+ _use_brackets_for_conf_in_nh_export_cbmi\r
+ .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );\r
+ _options_jmenu\r
+ .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );\r
+ customizeJMenuItem( _choose_font_mi );\r
+ customizeJMenuItem( _choose_minimal_confidence_mi );\r
+ customizeJMenuItem( _switch_colors_mi );\r
+ customizeJMenuItem( _print_size_mi );\r
+ customizeJMenuItem( _choose_pdf_width_mi );\r
+ customizeJMenuItem( _overview_placment_mi );\r
+ customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()\r
+ .isShowDefaultNodeShapesExternal() );\r
+ customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()\r
+ .isShowDefaultNodeShapesInternal() );\r
+ customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()\r
+ .isShowDefaultNodeShapesForMarkedNodes() );\r
+ customizeJMenuItem( _cycle_node_shape_mi );\r
+ customizeJMenuItem( _cycle_node_fill_mi );\r
+ customizeJMenuItem( _choose_node_size_mi );\r
+ customizeJMenuItem( _cycle_data_return );\r
+ customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );\r
+ customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );\r
+ customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );\r
+ customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );\r
+ customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );\r
+ customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );\r
+ customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );\r
+ customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );\r
+ customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );\r
+ customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,\r
+ getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );\r
+ customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,\r
+ getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
+ customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,\r
+ getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
+ customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );\r
+ customizeCheckBoxMenuItem( _label_direction_cbmi,\r
+ getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );\r
+ customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );\r
+ customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );\r
+ customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()\r
+ .isInternalNumberAreConfidenceForNhParsing() );\r
+ customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,\r
+ getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );\r
+ customizeRadioButtonMenuItem( _extract_taxonomy_pfam_strict_rbmi,\r
+ getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
+ customizeRadioButtonMenuItem( _extract_taxonomy_pfam_relaxed_rbmi,\r
+ getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
+ customizeRadioButtonMenuItem( _extract_taxonomy_agressive_rbmi,\r
+ getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE );\r
+ customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );\r
+ customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi, getOptions()\r
+ .isReplaceUnderscoresInNhParsing() );\r
+ customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );\r
+ customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );\r
+ customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );\r
+ customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );\r
+ customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );\r
+ customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()\r
+ .isGraphicsExportUsingActualSize() );\r
+ customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );\r
+ customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()\r
+ .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
+ customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()\r
+ .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
+ customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );\r
+ customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );\r
+ _jmenubar.add( _options_jmenu );\r
+ }\r
+\r
+ void buildPhylogeneticInferenceMenu() {\r
+ final InferenceManager im = getInferenceManager();\r
+ _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );\r
+ _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );\r
+ customizeJMenuItem( _inference_from_msa_item );\r
+ _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );\r
+ if ( im.canDoMsa() ) {\r
+ _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );\r
+ customizeJMenuItem( _inference_from_seqs_item );\r
+ _inference_from_seqs_item\r
+ .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );\r
+ }\r
+ else {\r
+ _inference_menu\r
+ .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );\r
+ customizeJMenuItem( _inference_from_seqs_item );\r
+ _inference_from_seqs_item.setEnabled( false );\r
+ }\r
+ _jmenubar.add( _inference_menu );\r
+ }\r
+\r
+ void buildToolsMenu() {\r
+ _tools_menu = createMenu( "Tools", getConfiguration() );\r
+ _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );\r
+ customizeJMenuItem( _confcolor_item );\r
+ _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );\r
+ customizeJMenuItem( _color_rank_jmi );\r
+ _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );\r
+ _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );\r
+ customizeJMenuItem( _taxcolor_item );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );\r
+ _remove_visual_styles_item\r
+ .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny" );\r
+ customizeJMenuItem( _remove_visual_styles_item );\r
+ _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );\r
+ _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny" );\r
+ customizeJMenuItem( _remove_branch_color_item );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );\r
+ customizeJMenuItem( _annotate_item );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );\r
+ customizeJMenuItem( _midpoint_root_item );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _delete_selected_nodes_item = new JMenuItem( "Delete Selected Nodes" ) );\r
+ _delete_selected_nodes_item.setToolTipText( "To delete all selected external nodes" );\r
+ customizeJMenuItem( _delete_selected_nodes_item );\r
+ _tools_menu.add( _delete_not_selected_nodes_item = new JMenuItem( "Retain Selected Nodes" ) );\r
+ _delete_not_selected_nodes_item.setToolTipText( "To delete all not selected external nodes" );\r
+ customizeJMenuItem( _delete_not_selected_nodes_item );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );\r
+ customizeJMenuItem( _collapse_species_specific_subtrees );\r
+ _collapse_species_specific_subtrees.setToolTipText( "To (reversibly) collapse species-specific subtrees" );\r
+ _tools_menu\r
+ .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );\r
+ customizeJMenuItem( _collapse_below_threshold );\r
+ _collapse_below_threshold\r
+ .setToolTipText( "To (permanently) collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" );\r
+ //\r
+ _tools_menu\r
+ .add( _collapse_below_branch_length = new JMenuItem( "Collapse Branches with Branch Lengths Below Threshold into Multifurcations" ) );\r
+ customizeJMenuItem( _collapse_below_branch_length );\r
+ _collapse_below_branch_length\r
+ .setToolTipText( "To (permanently) collapse branches with branches with branch lengths below a threshold into multifurcations" );\r
+ //\r
+ _tools_menu.addSeparator();\r
+ _tools_menu\r
+ .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );\r
+ customizeJMenuItem( _extract_tax_code_from_node_names_jmi );\r
+ _extract_tax_code_from_node_names_jmi\r
+ .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" );\r
+ _tools_menu\r
+ .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );\r
+ customizeJMenuItem( _move_node_names_to_tax_sn_jmi );\r
+ _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );\r
+ _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );\r
+ customizeJMenuItem( _move_node_names_to_seq_names_jmi );\r
+ _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );\r
+ customizeJMenuItem( _obtain_seq_information_jmi );\r
+ _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );\r
+ _tools_menu\r
+ .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );\r
+ customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );\r
+ _obtain_detailed_taxonomic_information_jmi\r
+ .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );\r
+ _tools_menu\r
+ .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );\r
+ customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );\r
+ _obtain_detailed_taxonomic_information_deleting_jmi\r
+ .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) );\r
+ customizeJMenuItem( _read_values_jmi );\r
+ _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" );\r
+ _jmenubar.add( _tools_menu );\r
+ _tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) );\r
+ customizeJMenuItem( _read_seqs_jmi );\r
+ _read_seqs_jmi\r
+ .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );\r
+ _jmenubar.add( _tools_menu );\r
+ }\r
+\r
+ @Override\r
+ void close() {\r
+ if ( isUnsavedDataPresent() ) {\r
+ final int r = JOptionPane.showConfirmDialog( this,\r
+ "Exit despite potentially unsaved changes?",\r
+ "Exit?",\r
+ JOptionPane.YES_NO_OPTION );\r
+ if ( r != JOptionPane.YES_OPTION ) {\r
+ return;\r
+ }\r
+ }\r
+ exit();\r
+ }\r
+\r
+ void executeLineageInference() {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {\r
+ return;\r
+ }\r
+ if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Phylogeny is not rooted.",\r
+ "Cannot infer ancestral taxonomies",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,\r
+ _mainpanel.getCurrentTreePanel(),\r
+ _mainpanel.getCurrentPhylogeny()\r
+ .copy() );\r
+ new Thread( inferrer ).start();\r
+ }\r
+\r
+ void exit() {\r
+ removeAllTextFrames();\r
+ _mainpanel.terminate();\r
+ _contentpane.removeAll();\r
+ setVisible( false );\r
+ dispose();\r
+ // System.exit( 0 ); //TODO reconfirm that this is OK, then remove.\r
}\r
\r
void readPhylogeniesFromURL() {\r
}\r
else {\r
parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()\r
- .isValidatePhyloXmlAgainstSchema() );\r
+ .isValidatePhyloXmlAgainstSchema() );\r
}\r
if ( parser instanceof NexusPhylogeniesParser ) {\r
nhx_or_nexus = true;\r
JOptionPane.showMessageDialog( this,\r
"Could not read from " + url + "\n"\r
+ ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
- "Failed to read URL",\r
- JOptionPane.ERROR_MESSAGE );\r
+ "Failed to read URL",\r
+ JOptionPane.ERROR_MESSAGE );\r
}\r
catch ( final Exception e ) {\r
JOptionPane.showMessageDialog( this,\r
System.gc();\r
}\r
\r
- public void readSeqsFromFileforPI() {\r
- // Set an initial directory if none set yet\r
- final File my_dir = getCurrentDir();\r
- _seqs_pi_filechooser.setMultiSelectionEnabled( false );\r
- // Open file-open dialog and set current directory\r
- if ( my_dir != null ) {\r
- _seqs_pi_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane );\r
- // All done: get the seqs\r
- final File file = _seqs_pi_filechooser.getSelectedFile();\r
- setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() );\r
- if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- setSeqsFile( null );\r
- setSeqs( null );\r
- List<MolecularSequence> seqs = null;\r
- try {\r
- if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {\r
- seqs = FastaParser.parse( new FileInputStream( file ) );\r
- for( final MolecularSequence seq : seqs ) {\r
- System.out.println( SequenceWriter.toFasta( seq, 60 ) );\r
- }\r
- }\r
- else {\r
- //TODO error\r
- }\r
- }\r
- catch ( final MsaFormatException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Multiple sequence file format error",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final IOException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Failed to read multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final IllegalArgumentException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Unexpected error during reading of multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final Exception e ) {\r
- setArrowCursor();\r
- e.printStackTrace();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Unexpected error during reading of multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Multiple sequence file is empty",\r
- "Illegal multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( seqs.size() < 4 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Multiple sequence file needs to contain at least 3 sequences",\r
- "Illegal multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- // if ( msa.getLength() < 2 ) {\r
- // JOptionPane.showMessageDialog( this,\r
- // "Multiple sequence alignment needs to contain at least 2 residues",\r
- // "Illegal multiple sequence file",\r
- // JOptionPane.ERROR_MESSAGE );\r
- // return;\r
- // }\r
- System.gc();\r
- setSeqsFile( _seqs_pi_filechooser.getSelectedFile() );\r
- setSeqs( seqs );\r
- }\r
- }\r
-\r
- private void readSpeciesTreeFromFile() {\r
- Phylogeny t = null;\r
- boolean exception = false;\r
- final File my_dir = getCurrentDir();\r
- _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );\r
- if ( my_dir != null ) {\r
- _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );\r
- final File file = _open_filechooser_for_species_tree.getSelectedFile();\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.xmlfilter ) {\r
- try {\r
- final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser\r
- .createPhyloXmlParserXsdValidating(), file );\r
- t = trees[ 0 ];\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringOpenFile( e );\r
- }\r
- }\r
- else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.tolfilter ) {\r
- try {\r
- final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );\r
- t = trees[ 0 ];\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringOpenFile( e );\r
- }\r
- }\r
- // "*.*":\r
- else {\r
- try {\r
- final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser\r
- .createPhyloXmlParserXsdValidating(), file );\r
- t = trees[ 0 ];\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringOpenFile( e );\r
- }\r
- }\r
- if ( !exception && ( t != null ) && !t.isRooted() ) {\r
- exception = true;\r
- t = null;\r
- JOptionPane.showMessageDialog( this,\r
- "Species tree is not rooted",\r
- "Species tree not loaded",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
- if ( !exception && ( t != null ) ) {\r
- final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();\r
- for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {\r
- final PhylogenyNode node = it.next();\r
- if ( !node.getNodeData().isHasTaxonomy() ) {\r
- exception = true;\r
- t = null;\r
- JOptionPane\r
- .showMessageDialog( this,\r
- "Species tree contains external node(s) without taxonomy information",\r
- "Species tree not loaded",\r
- JOptionPane.ERROR_MESSAGE );\r
- break;\r
- }\r
- else {\r
- if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {\r
- exception = true;\r
- t = null;\r
- JOptionPane.showMessageDialog( this,\r
- "Taxonomy ["\r
- + node.getNodeData().getTaxonomy().asSimpleText()\r
- + "] is not unique in species tree",\r
- "Species tree not loaded",\r
- JOptionPane.ERROR_MESSAGE );\r
- break;\r
- }\r
- else {\r
- tax_set.add( node.getNodeData().getTaxonomy() );\r
- }\r
- }\r
- }\r
- }\r
- if ( !exception && ( t != null ) ) {\r
- setSpeciesTree( t );\r
- JOptionPane.showMessageDialog( this,\r
- "Species tree successfully loaded",\r
- "Species tree loaded",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- _contentpane.repaint();\r
- System.gc();\r
- }\r
- }\r
-\r
- private void setArrowCursor() {\r
- try {\r
- _mainpanel.getCurrentTreePanel().setArrowCursor();\r
- }\r
- catch ( final Exception ex ) {\r
- // Do nothing.\r
- }\r
- }\r
-\r
- private void setMinNotCollapseBlValue( final double min_not_collapse_bl ) {\r
- _min_not_collapse_bl = min_not_collapse_bl;\r
- }\r
-\r
- private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {\r
- _min_not_collapse = min_not_collapse;\r
- }\r
-\r
void setMsa( final Msa msa ) {\r
_msa = msa;\r
}\r
_msa_file = msa_file;\r
}\r
\r
- private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {\r
- _phylogenetic_inference_options = phylogenetic_inference_options;\r
- }\r
-\r
void setSeqs( final List<MolecularSequence> seqs ) {\r
_seqs = seqs;\r
}\r
_seqs_file = seqs_file;\r
}\r
\r
- private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {\r
- nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );\r
- nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );\r
+ public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {\r
+ return new MainFrameApplication( phys, config );\r
}\r
\r
- private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {\r
- nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );\r
- nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );\r
- nhx.setAllowErrorsInDistanceToParent( getOptions().isAllowErrorsInDistanceToParent() );\r
+ public static MainFrame createInstance( final Phylogeny[] phys,\r
+ final Configuration config,\r
+ final String title,\r
+ final File current_dir ) {\r
+ return new MainFrameApplication( phys, config, title, current_dir );\r
+ }\r
+\r
+ static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {\r
+ return new MainFrameApplication( phys, config, title );\r
+ }\r
+\r
+ static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {\r
+ return new MainFrameApplication( phys, config_file_name, title );\r
}\r
\r
- \r
+ static void warnIfNotPhyloXmlValidation( final Configuration c ) {\r
+ if ( !c.isValidatePhyloXmlAgainstSchema() ) {\r
+ JOptionPane\r
+ .showMessageDialog( null,\r
+ ForesterUtil\r
+ .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",\r
+ 80 ),\r
+ "Warning",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ }\r
} // MainFrameApplication.\r
private Hashtable<String, BufferedImage> _image_map;
private static Map<String, String> _lineage_to_rank_map;
- MainPanel() {
- }
-
public MainPanel( final Configuration configuration, final MainFrame parent ) {
if ( configuration == null ) {
throw new IllegalArgumentException( "configuration is null" );
getControlPanel().showWhole();
}
+ MainPanel() {
+ }
+
public void addPhylogenyInNewTab( final Phylogeny phy,
final Configuration config,
final String default_name,
getControlPanel().showWhole();
}
+ @Override
+ public void componentHidden( final ComponentEvent e ) {
+ // Do nothing.
+ }
+
+ @Override
+ public void componentMoved( final ComponentEvent e ) {
+ // Do nothing.
+ }
+
+ @Override
+ public void componentResized( final ComponentEvent e ) {
+ if ( getCurrentTreePanel() != null ) {
+ getCurrentTreePanel().updateOvSettings();
+ getCurrentTreePanel().updateOvSizes();
+ }
+ }
+
+ @Override
+ public void componentShown( final ComponentEvent e ) {
+ // Do nothing.
+ }
+
+ public ControlPanel getControlPanel() {
+ return _control_panel;
+ }
+
+ public Set<Long> getCopiedAndPastedNodes() {
+ return _copied_and_pasted_nodes;
+ }
+
+ public TreePanel getCurrentTreePanel() {
+ final int selected = getTabbedPane().getSelectedIndex();
+ if ( selected >= 0 ) {
+ return _treepanels.get( selected );
+ }
+ else {
+ if ( _treepanels.size() == 1 ) {
+ return _treepanels.get( 0 );
+ }
+ else {
+ return null;
+ }
+ }
+ }
+
+ public Options getOptions() {
+ return _mainframe.getOptions();
+ }
+
+ public JTabbedPane getTabbedPane() {
+ return _tabbed_pane;
+ }
+
+ public TreeFontSet getTreeFontSet() {
+ return _fontset;
+ }
+
+ public void setArrowCursor() {
+ setCursor( TreePanel.ARROW_CURSOR );
+ repaint();
+ }
+
+ public void setCopiedAndPastedNodes( final Set<Long> node_ids ) {
+ _copied_and_pasted_nodes = node_ids;
+ }
+
+ public void setWaitCursor() {
+ setCursor( TreePanel.WAIT_CURSOR );
+ repaint();
+ }
+
void addPhylogenyInPanel( final Phylogeny phy, final Configuration config ) {
final TreePanel treepanel = new TreePanel( phy, config, this );
getControlPanel().phylogenyAdded( config );
}
}
- @Override
- public void componentHidden( final ComponentEvent e ) {
- // Do nothing.
- }
-
- @Override
- public void componentMoved( final ComponentEvent e ) {
- // Do nothing.
- }
-
- @Override
- public void componentResized( final ComponentEvent e ) {
- if ( getCurrentTreePanel() != null ) {
- getCurrentTreePanel().updateOvSettings();
- getCurrentTreePanel().updateOvSizes();
- }
- }
-
- @Override
- public void componentShown( final ComponentEvent e ) {
- // Do nothing.
- }
-
Configuration getConfiguration() {
return _configuration;
}
- public ControlPanel getControlPanel() {
- return _control_panel;
- }
-
- public Set<Long> getCopiedAndPastedNodes() {
- return _copied_and_pasted_nodes;
- }
-
Phylogeny getCurrentPhylogeny() {
if ( getCurrentTreePanel() == null ) {
return null;
}
}
- void setTitleOfSelectedTab( final String title ) {
- final int selected = getTabbedPane().getSelectedIndex();
- if ( selected >= 0 ) {
- getTabbedPane().setTitleAt( selected, title );
- }
- }
-
- public TreePanel getCurrentTreePanel() {
- final int selected = getTabbedPane().getSelectedIndex();
- if ( selected >= 0 ) {
- return _treepanels.get( selected );
- }
- else {
- if ( _treepanels.size() == 1 ) {
- return _treepanels.get( 0 );
- }
- else {
- return null;
- }
- }
- }
-
Phylogeny getCutOrCopiedTree() {
return _cut_or_copied_tree;
}
- MainFrame getMainFrame() {
- return _mainframe;
+ synchronized Hashtable<String, BufferedImage> getImageMap() {
+ return _image_map;
}
- public Options getOptions() {
- return _mainframe.getOptions();
+ MainFrame getMainFrame() {
+ return _mainframe;
}
Phylogeny getPhylogeny( final int index ) {
return getCurrentScrollPane().getViewport().getExtentSize();
}
- public JTabbedPane getTabbedPane() {
- return _tabbed_pane;
- }
-
TreeColorSet getTreeColorSet() {
return _colorset;
}
- public TreeFontSet getTreeFontSet() {
- return _fontset;
- }
-
List<TreePanel> getTreePanels() {
return _treepanels;
}
add( _tabbed_pane, BorderLayout.CENTER );
}
- public void setArrowCursor() {
- setCursor( TreePanel.ARROW_CURSOR );
- repaint();
+ void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) {
+ _cut_or_copied_tree = cut_or_copied_tree;
}
- public void setCopiedAndPastedNodes( final Set<Long> node_ids ) {
- _copied_and_pasted_nodes = node_ids;
+ synchronized void setImageMap( final Hashtable<String, BufferedImage> image_map ) {
+ _image_map = image_map;
}
- void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) {
- _cut_or_copied_tree = cut_or_copied_tree;
+ void setTitleOfSelectedTab( final String title ) {
+ final int selected = getTabbedPane().getSelectedIndex();
+ if ( selected >= 0 ) {
+ getTabbedPane().setTitleAt( selected, title );
+ }
}
void setTreeColorSet( final TreeColorSet colorset ) {
RenderableDomainArchitecture.setColorMap( config_settings.getDomainColors() );
}
- public void setWaitCursor() {
- setCursor( TreePanel.WAIT_CURSOR );
- repaint();
- }
-
void terminate() {
for( final TreePanel atvtreepanel : _treepanels ) {
atvtreepanel.removeAllEditNodeJFrames();
}
}
- synchronized void setImageMap( final Hashtable<String, BufferedImage> image_map ) {
- _image_map = image_map;
- }
-
- synchronized Hashtable<String, BufferedImage> getImageMap() {
- return _image_map;
- }
-
public synchronized static Map<String, String> getLineageToRankMap() {
if ( _lineage_to_rank_map == null ) {
_lineage_to_rank_map = new HashMap<String, String>();
setupTreeGraphic( configuration, getControlPanel() );
}
- JApplet getApplet() {
- return _applet;
- }
-
- MainFrameApplet getAppletFrame() {
- return ( MainFrameApplet ) _mainframe;
- }
-
@Override
public Options getOptions() {
if ( _mainframe != null ) {
return ( ( ArchaeopteryxE ) _applet ).getOptions();
}
}
+
+ JApplet getApplet() {
+ return _applet;
+ }
+
+ MainFrameApplet getAppletFrame() {
+ return ( MainFrameApplet ) _mainframe;
+ }
}
\ No newline at end of file
class NodeEditPanel extends JPanel {
+ private enum PHYLOXML_TAG {
+ NODE_NAME,
+ NODE_BRANCH_LENGTH,
+ NODE_BRANCH_WIDTH,
+ TAXONOMY_CODE,
+ TAXONOMY_SCIENTIFIC_NAME,
+ TAXONOMY_AUTHORITY,
+ TAXONOMY_COMMON_NAME,
+ TAXONOMY_SYNONYM,
+ TAXONOMY_RANK,
+ TAXONOMY_URI,
+ SEQ_SYMBOL,
+ SEQ_NAME,
+ SEQ_GENE_NAME,
+ SEQ_LOCATION,
+ SEQ_TYPE,
+ SEQ_MOL_SEQ,
+ SEQ_URI,
+ DATE_DESCRIPTION,
+ DATE_VALUE,
+ DATE_MIN,
+ DATE_MAX,
+ DATE_UNIT,
+ TAXONOMY_ID_VALUE,
+ TAXONOMY_ID_PROVIDER,
+ SEQ_ACC_VALUE,
+ SEQ_ACC_SOURCE,
+ CONFIDENCE_VALUE,
+ CONFIDENCE_TYPE,
+ LIT_REFERENCE_DESC,
+ LIT_REFERENCE_DOI,
+ EVENTS_DUPLICATIONS,
+ EVENTS_SPECIATIONS,
+ EVENTS_GENE_LOSSES,
+ DIST_DESC,
+ DIST_GEODETIC,
+ DIST_LAT,
+ DIST_LONG,
+ DIST_ALT,
+ DIST_ALT_UNIT
+ }
+
+ private class TagNumber {
+
+ final private PHYLOXML_TAG _tag;
+ final private int _number;
+
+ TagNumber( final PHYLOXML_TAG tag, final int number ) {
+ _tag = tag;
+ _number = number;
+ }
+
+ @Override
+ public String toString() {
+ return getTag() + "_" + getNumber();
+ }
+
+ int getNumber() {
+ return _number;
+ }
+
+ PHYLOXML_TAG getTag() {
+ return _tag;
+ }
+ }
private static final long serialVersionUID = 5120159904388100771L;
private final JTree _tree;
private final JEditorPane _pane;
NodePanel.EVENTS_DUPLICATIONS,
String.valueOf( events.getNumberOfDuplications() >= 0 ? events.getNumberOfDuplications()
: 0 ),
- PHYLOXML_TAG.EVENTS_DUPLICATIONS );
+ PHYLOXML_TAG.EVENTS_DUPLICATIONS );
addSubelementEditable( category,
NodePanel.EVENTS_SPECIATIONS,
String.valueOf( events.getNumberOfSpeciations() >= 0 ? events.getNumberOfSpeciations()
: 0 ),
- PHYLOXML_TAG.EVENTS_SPECIATIONS );
+ PHYLOXML_TAG.EVENTS_SPECIATIONS );
addSubelementEditable( category,
NodePanel.EVENTS_GENE_LOSSES,
String.valueOf( events.getNumberOfGeneLosses() >= 0 ? events.getNumberOfGeneLosses() : 0 ),
for( final Uri uri : seq.getUris() ) {
if ( uri != null ) {
addSubelementEditable( category, NodePanel.SEQ_URI + " [" + uri_counter + "]", uri.getValue()
- .toString(), PHYLOXML_TAG.SEQ_URI, uri_counter++ );
+ .toString(), PHYLOXML_TAG.SEQ_URI, uri_counter++ );
}
}
}
for( final Uri uri : tax.getUris() ) {
if ( uri != null ) {
addSubelementEditable( category, NodePanel.TAXONOMY_URI + " [" + uri_counter + "]", uri.getValue()
- .toString(), PHYLOXML_TAG.TAXONOMY_URI, uri_counter++ );
+ .toString(), PHYLOXML_TAG.TAXONOMY_URI, uri_counter++ );
}
}
}
uri_counter );
}
+ private void addUri( final DefaultMutableTreeNode mtn, final Uri uri, final int number, final MultipleUris mu ) {
+ if ( uri != null ) {
+ if ( mu.getUris() == null ) {
+ mu.setUris( new ArrayList<Uri>() );
+ }
+ }
+ if ( ( uri != null ) && ( mu.getUris() == null ) ) {
+ mu.setUris( new ArrayList<Uri>() );
+ }
+ if ( ( uri != null ) && ( mu.getUris().size() == number ) ) {
+ mu.getUris().add( uri );
+ }
+ if ( ( mu.getUris() != null ) && ( mu.getUris().size() != number ) ) {
+ mu.getUris().set( number, uri );
+ }
+ final ImageLoader il = new ImageLoader( getTreePanel() );
+ new Thread( il ).start();
+ }
+
private void collapsePath( final String name ) {
final TreePath tp = getJTree().getNextMatch( name, 0, Position.Bias.Forward );
if ( tp != null ) {
return getMap().get( mtn );
}
- PhylogenyNode getMyNode() {
- return _my_node;
- }
-
private DefaultMutableTreeNode getSelectedTreeNode() {
final TreePath selectionPath = getJTree().getSelectionPath();
if ( selectionPath != null ) {
return i;
}
- void writeAll() {
- for( int i = 0; i < getJTree().getRowCount(); i++ ) {
- final TreePath p = getJTree().getPathForRow( i );
- writeBack( ( DefaultMutableTreeNode ) p.getLastPathComponent() );
- }
- }
-
private void writeBack( final DefaultMutableTreeNode mtn ) {
if ( !getMap().containsKey( mtn ) ) {
final DefaultMutableTreeNode parent = ( DefaultMutableTreeNode ) mtn.getParent();
getTreePanel().repaint();
}
- private void addUri( final DefaultMutableTreeNode mtn, final Uri uri, final int number, final MultipleUris mu ) {
- if ( uri != null ) {
- if ( mu.getUris() == null ) {
- mu.setUris( new ArrayList<Uri>() );
- }
- }
- if ( ( uri != null ) && ( mu.getUris() == null ) ) {
- mu.setUris( new ArrayList<Uri>() );
- }
- if ( ( uri != null ) && ( mu.getUris().size() == number ) ) {
- mu.getUris().add( uri );
- }
- if ( ( mu.getUris() != null ) && ( mu.getUris().size() != number ) ) {
- mu.getUris().set( number, uri );
- }
- final ImageLoader il = new ImageLoader( getTreePanel() );
- new Thread( il ).start();
- }
-
- private enum PHYLOXML_TAG {
- NODE_NAME,
- NODE_BRANCH_LENGTH,
- NODE_BRANCH_WIDTH,
- TAXONOMY_CODE,
- TAXONOMY_SCIENTIFIC_NAME,
- TAXONOMY_AUTHORITY,
- TAXONOMY_COMMON_NAME,
- TAXONOMY_SYNONYM,
- TAXONOMY_RANK,
- TAXONOMY_URI,
- SEQ_SYMBOL,
- SEQ_NAME,
- SEQ_GENE_NAME,
- SEQ_LOCATION,
- SEQ_TYPE,
- SEQ_MOL_SEQ,
- SEQ_URI,
- DATE_DESCRIPTION,
- DATE_VALUE,
- DATE_MIN,
- DATE_MAX,
- DATE_UNIT,
- TAXONOMY_ID_VALUE,
- TAXONOMY_ID_PROVIDER,
- SEQ_ACC_VALUE,
- SEQ_ACC_SOURCE,
- CONFIDENCE_VALUE,
- CONFIDENCE_TYPE,
- LIT_REFERENCE_DESC,
- LIT_REFERENCE_DOI,
- EVENTS_DUPLICATIONS,
- EVENTS_SPECIATIONS,
- EVENTS_GENE_LOSSES,
- DIST_DESC,
- DIST_GEODETIC,
- DIST_LAT,
- DIST_LONG,
- DIST_ALT,
- DIST_ALT_UNIT
+ PhylogenyNode getMyNode() {
+ return _my_node;
}
- private class TagNumber {
-
- final private PHYLOXML_TAG _tag;
- final private int _number;
-
- TagNumber( final PHYLOXML_TAG tag, final int number ) {
- _tag = tag;
- _number = number;
- }
-
- int getNumber() {
- return _number;
- }
-
- PHYLOXML_TAG getTag() {
- return _tag;
- }
-
- @Override
- public String toString() {
- return getTag() + "_" + getNumber();
+ void writeAll() {
+ for( int i = 0; i < getJTree().getRowCount(); i++ ) {
+ final TreePath p = getJTree().getPathForRow( i );
+ writeBack( ( DefaultMutableTreeNode ) p.getLastPathComponent() );
}
}
}
for( final String key : properties_map.keySet() ) {
final Property prop = properties_map.get( key );
category.add( new DefaultMutableTreeNode( prop.getRef() + "=" + prop.getValue() + " " + prop.getUnit()
- + " [" + prop.getAppliesTo().toString() + "]" ) );
+ + " [" + prop.getAppliesTo().toString() + "]" ) );
}
}
*/
final public class Options {
+ public static enum CLADOGRAM_TYPE {
+ EXT_NODE_SUM_DEP, NON_LINED_UP, TOTAL_NODE_SUM_DEP;
+ }
+
+ public static enum NODE_LABEL_DIRECTION {
+ HORIZONTAL, RADIAL;
+ }
+
+ public static enum PHYLOGENY_GRAPHICS_TYPE {
+ CIRCULAR, CONVEX, CURVED, EURO_STYLE, RECTANGULAR, ROUNDED, TRIANGULAR, UNROOTED;
+ }
+
+ static enum OVERVIEW_PLACEMENT_TYPE {
+ LOWER_LEFT( "lower left" ),
+ LOWER_RIGHT( "lower right" ),
+ UPPER_LEFT( "upper left" ),
+ UPPER_RIGHT( "upper right" );
+
+ private final String _name;
+
+ private OVERVIEW_PLACEMENT_TYPE( final String name ) {
+ _name = name;
+ }
+
+ @Override
+ public String toString() {
+ return _name;
+ }
+
+ public String toTag() {
+ return toString().replaceAll( " ", "_" );
+ }
+ }
static final double MIN_CONFIDENCE_DEFAULT = 0.0;
private boolean _abbreviate_scientific_names;
private boolean _allow_errors_in_distance_to_parent;
private NodeVisualData.NodeShape _default_node_shape;
private short _default_node_shape_size;
private boolean _editable;
- private NodeDataField _ext_desc_data_to_return;
+ private NodeDataField _ext_desc_data_to_return;
private boolean _graphics_export_using_actual_size;
private boolean _graphics_export_visible_only;
private boolean _internal_number_are_confidence_for_nh_parsing;
return _allow_errors_in_distance_to_parent;
}
+ final public boolean isLineUpRendarableNodeData() {
+ return _line_up_renderable_node_data;
+ }
+
+ final public boolean isRightLineUpDomains() {
+ return _right_align_domains;
+ }
+
public final boolean isShowAnnotationRefSource() {
return _show_annotation_ref_source;
}
_ext_desc_data_to_return = ext_desc_data_to_return;
}
+ final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) {
+ _line_up_renderable_node_data = line_up_renderable_node_data;
+ }
+
+ final public void setRightLineUpDomains( final boolean right_align_domains ) {
+ _right_align_domains = right_align_domains;
+ }
+
public final void setShowAnnotationRefSource( final boolean show_annotation_ref_source ) {
_show_annotation_ref_source = show_annotation_ref_source;
}
_show_domain_labels = show_domain_labels;
}
+ final private void init() {
+ _default_node_shape = NodeShape.CIRCLE;
+ _default_node_fill = NodeFill.GRADIENT;
+ _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
+ _internal_number_are_confidence_for_nh_parsing = false;
+ _show_scale = false;
+ _antialias_screen = true;
+ _antialias_print = true;
+ _graphics_export_visible_only = false;
+ _editable = true;
+ _background_color_gradient = false;
+ _show_default_node_shapes_internal = false;
+ _show_default_node_shapes_external = false;
+ _show_default_node_shapes_for_marked_nodes = false;
+ if ( AptxUtil.isUsOrCanada() ) {
+ _print_size_x = Constants.US_LETTER_SIZE_X;
+ _print_size_y = Constants.US_LETTER_SIZE_Y;
+ }
+ else {
+ _print_size_x = Constants.A4_SIZE_X;
+ _print_size_y = Constants.A4_SIZE_Y;
+ }
+ _min_confidence_value = MIN_CONFIDENCE_DEFAULT;
+ _print_black_and_white = false;
+ _print_using_actual_size = true;
+ _graphics_export_using_actual_size = true;
+ _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
+ _base_font = new Font( Configuration.getDefaultFontFamilyName(), Font.PLAIN, 10 );
+ _match_whole_terms_only = false;
+ _search_with_regex = false;
+ _search_case_sensitive = false;
+ _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
+ _show_overview = true;
+ _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
+ _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
+ _inverse_search_result = false;
+ _scale_bar_length = 0.0;
+ _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
+ _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
+ _nh_parsing_replace_underscores = false;
+ _taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
+ _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
+ _show_domain_labels = true;
+ _show_annotation_ref_source = true;
+ setAbbreviateScientificTaxonNames( false );
+ _color_labels_same_as_parent_branch = false;
+ _show_confidence_stddev = false;
+ _nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE;
+ _ext_desc_data_to_return = NodeDataField.UNKNOWN;
+ _line_up_renderable_node_data = true;
+ _right_align_domains = false;
+ }
+
+ final private void setNumberOfDigitsAfterCommaForBranchLength( final short number_of_digits_after_comma_for_branch_length_values ) {
+ _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
+ }
+
+ final private void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
+ _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
+ }
+
final Font getBaseFont() {
return _base_font;
}
return _match_whole_terms_only;
}
- final boolean isSearchWithRegex() {
- return _search_with_regex;
- }
-
final boolean isPrintBlackAndWhite() {
return _print_black_and_white;
}
return _search_case_sensitive;
}
+ final boolean isSearchWithRegex() {
+ return _search_with_regex;
+ }
+
boolean isShowConfidenceStddev() {
return _show_confidence_stddev;
}
_match_whole_terms_only = search_whole_words_only;
}
- final void setSearchWithRegex( final boolean search_with_regex ) {
- _search_with_regex = search_with_regex;
- }
-
final void setMinConfidenceValue( final double min_confidence_value ) {
_min_confidence_value = min_confidence_value;
}
_search_case_sensitive = search_case_sensitive;
}
+ final void setSearchWithRegex( final boolean search_with_regex ) {
+ _search_with_regex = search_with_regex;
+ }
+
void setShowConfidenceStddev( final boolean show_confidence_stddev ) {
_show_confidence_stddev = show_confidence_stddev;
}
_show_default_node_shapes_external = show_default_node_shapes_external;
}
- void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
- _show_default_node_shapes_internal = show_default_node_shapes_internal;
- }
-
void setShowDefaultNodeShapesForMarkedNodes( final boolean show_default_node_shapes_for_marked_nodes ) {
_show_default_node_shapes_for_marked_nodes = show_default_node_shapes_for_marked_nodes;
}
+ void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
+ _show_default_node_shapes_internal = show_default_node_shapes_internal;
+ }
+
final void setShowOverview( final boolean show_overview ) {
_show_overview = show_overview;
}
_taxonomy_extraction = taxonomy_extraction;
}
- final private void init() {
- _default_node_shape = NodeShape.CIRCLE;
- _default_node_fill = NodeFill.GRADIENT;
- _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
- _internal_number_are_confidence_for_nh_parsing = false;
- _show_scale = false;
- _antialias_screen = true;
- _antialias_print = true;
- _graphics_export_visible_only = false;
- _editable = true;
- _background_color_gradient = false;
- _show_default_node_shapes_internal = false;
- _show_default_node_shapes_external = false;
- _show_default_node_shapes_for_marked_nodes = false;
- if ( AptxUtil.isUsOrCanada() ) {
- _print_size_x = Constants.US_LETTER_SIZE_X;
- _print_size_y = Constants.US_LETTER_SIZE_Y;
- }
- else {
- _print_size_x = Constants.A4_SIZE_X;
- _print_size_y = Constants.A4_SIZE_Y;
- }
- _min_confidence_value = MIN_CONFIDENCE_DEFAULT;
- _print_black_and_white = false;
- _print_using_actual_size = true;
- _graphics_export_using_actual_size = true;
- _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
- _base_font = new Font( Configuration.getDefaultFontFamilyName(), Font.PLAIN, 10 );
- _match_whole_terms_only = false;
- _search_with_regex = false;
- _search_case_sensitive = false;
- _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
- _show_overview = true;
- _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT;
- _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL;
- _inverse_search_result = false;
- _scale_bar_length = 0.0;
- _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT;
- _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT;
- _nh_parsing_replace_underscores = false;
- _taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
- _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
- _show_domain_labels = true;
- _show_annotation_ref_source = true;
- setAbbreviateScientificTaxonNames( false );
- _color_labels_same_as_parent_branch = false;
- _show_confidence_stddev = false;
- _nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE;
- _ext_desc_data_to_return = NodeDataField.UNKNOWN;
- _line_up_renderable_node_data = true;
- _right_align_domains = false;
- }
-
- final private void setNumberOfDigitsAfterCommaForBranchLength( final short number_of_digits_after_comma_for_branch_length_values ) {
- _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
- }
-
- final private void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
- _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
- }
-
public final static Options createInstance( final Configuration configuration ) {
final Options instance = createDefaultInstance();
if ( configuration != null ) {
instance.setBackgroundColorGradient( configuration.isBackgroundColorGradient() );
if ( configuration.getNumberOfDigitsAfterCommaForBranchLengthValues() >= 0 ) {
instance.setNumberOfDigitsAfterCommaForBranchLength( configuration
- .getNumberOfDigitsAfterCommaForBranchLengthValues() );
+ .getNumberOfDigitsAfterCommaForBranchLengthValues() );
}
if ( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() >= 0 ) {
instance.setNumberOfDigitsAfterCommaForConfidenceValues( configuration
- .getNumberOfDigitsAfterCommaForConfidenceValues() );
+ .getNumberOfDigitsAfterCommaForConfidenceValues() );
}
instance.setTaxonomyExtraction( configuration.getTaxonomyExtraction() );
instance.setReplaceUnderscoresInNhParsing( configuration.isReplaceUnderscoresInNhParsing() );
instance.setInternalNumberAreConfidenceForNhParsing( configuration
- .isInternalNumberAreConfidenceForNhParsing() );
+ .isInternalNumberAreConfidenceForNhParsing() );
instance.setEditable( configuration.isEditable() );
instance.setColorLabelsSameAsParentBranch( configuration.isColorLabelsSameAsParentBranch() );
instance.setShowDomainLabels( configuration.isShowDomainLabels() );
}
if ( !ForesterUtil.isEmpty( configuration.getBaseFontFamilyName() ) ) {
instance.setBaseFont( new Font( configuration.getBaseFontFamilyName(), Font.PLAIN, instance
- .getBaseFont().getSize() ) );
+ .getBaseFont().getSize() ) );
}
if ( configuration.getPhylogenyGraphicsType() != null ) {
instance.setPhylogenyGraphicsType( configuration.getPhylogenyGraphicsType() );
final static Options createDefaultInstance() {
return new Options();
}
-
- public static enum CLADOGRAM_TYPE {
- EXT_NODE_SUM_DEP, NON_LINED_UP, TOTAL_NODE_SUM_DEP;
- }
-
- public static enum NODE_LABEL_DIRECTION {
- HORIZONTAL, RADIAL;
- }
-
- public static enum PHYLOGENY_GRAPHICS_TYPE {
- CIRCULAR, CONVEX, CURVED, EURO_STYLE, RECTANGULAR, ROUNDED, TRIANGULAR, UNROOTED;
- }
-
- static enum OVERVIEW_PLACEMENT_TYPE {
- LOWER_LEFT( "lower left" ),
- LOWER_RIGHT( "lower right" ),
- UPPER_LEFT( "upper left" ),
- UPPER_RIGHT( "upper right" );
-
- private final String _name;
-
- private OVERVIEW_PLACEMENT_TYPE( final String name ) {
- _name = name;
- }
-
- @Override
- public String toString() {
- return _name;
- }
-
- public String toTag() {
- return toString().replaceAll( " ", "_" );
- }
- }
-
- final public boolean isLineUpRendarableNodeData() {
- return _line_up_renderable_node_data;
- }
-
- final public boolean isRightLineUpDomains() {
- return _right_align_domains;
- }
-
- final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) {
- _line_up_renderable_node_data = line_up_renderable_node_data;
- }
-
- final public void setRightLineUpDomains( final boolean right_align_domains ) {
- _right_align_domains = right_align_domains;
- }
}
import com.itextpdf.text.pdf.PdfWriter;
/*
- *
+ *
* This uses iText.
- *
+ *
* See: http://www.lowagie.com/iText/
- *
+ *
* Current version: iText-2.1.7
*/
final class PdfExporter {
import java.awt.event.ActionListener;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
-import java.security.acl.Permission;
import java.util.LinkedList;
import javax.swing.JButton;
}
}
- void close() {
- setVisible( false );
- dispose();
- }
-
- void removeMe() {
- final int i = _tframes.indexOf( this );
- if ( i >= 0 ) {
- _tframes.remove( i );
- }
- close();
+ @Override
+ public void lostOwnership( final Clipboard clipboard, final Transferable contents ) {
}
private void copy() {
sys_clipboard.setContents( contents, this );
}
- @Override
- public void lostOwnership( final Clipboard clipboard, final Transferable contents ) {
+ void close() {
+ setVisible( false );
+ dispose();
+ }
+
+ void removeMe() {
+ final int i = _tframes.indexOf( this );
+ if ( i >= 0 ) {
+ _tframes.remove( i );
+ }
+ close();
}
static TextFrame instantiate( final String s, final String title, final LinkedList<TextFrame> tframes ) {
public static final String SPECIATION = "Speciation";
public static final String TAXONOMY = "Taxonomy";
static final String[] COLOR_FIELDS = { BACKGROUND, BACKGROUND_GRADIENT_BOTTOM, SEQUENCE,
- TAXONOMY, CONFIDENCE, BRANCH_LENGTH, BRANCH, NODE_BOX, COLLAPSED, MATCHING_NODES_A, MATCHING_NODES_B,
- MATCHING_NODES_A_AND_B, DUPLICATION, SPECIATION, DUPLICATION_OR_SPECATION, DOMAIN_LABEL, DOMAIN_BASE,
- BINARY_DOMAIN_COMBINATIONS, ANNOTATION, OVERVIEW };
+ TAXONOMY, CONFIDENCE, BRANCH_LENGTH, BRANCH, NODE_BOX, COLLAPSED, MATCHING_NODES_A, MATCHING_NODES_B,
+ MATCHING_NODES_A_AND_B, DUPLICATION, SPECIATION, DUPLICATION_OR_SPECATION, DOMAIN_LABEL, DOMAIN_BASE,
+ BINARY_DOMAIN_COMBINATIONS, ANNOTATION, OVERVIEW };
static final String[] SCHEME_NAMES = { "Default", "Black", "Black & White", "Silver", "Green",
- "White & Blue", "Cyan", "Orange", "Blue", "Blue & White", "Neon" };
+ "White & Blue", "Cyan", "Orange", "Blue", "Blue & White", "Neon" };
private int _color_scheme;
private final Color[][] _color_schemes = { { new Color( 0, 0, 0 ), // background_color
- new Color( 0, 100, 100 ), // background_color_gradient_bottom
- new Color( 230, 230, 230 ), // sequence __ Default (same as Black)
- new Color( 180, 180, 180 ), // taxonomy
- new Color( 180, 180, 180 ), // support
- new Color( 140, 140, 140 ), // branch_length_color
- new Color( 255, 255, 255 ), // branch_color
- new Color( 255, 255, 255 ), // box_color
- new Color( 255, 255, 255 ), // collapesed_fill_color
- new Color( 0, 255, 0 ), // found_color 0
- new Color( 255, 0, 0 ), // found_color 1
- new Color( 255, 255, 0 ), // found_color 1 + 2
- new Color( 255, 0, 0 ), // duplication_box_color
- new Color( 0, 255, 0 ), // speciation_box_color
- new Color( 255, 255, 0 ), // duplication_speciation_color
- new Color( 230, 230, 230 ), // domain_label
- new Color( 100, 100, 100 ), // domains_base
- new Color( 65, 105, 255 ), // binary_domain_combinations_color
- new Color( 173, 255, 47 ) // annotation
- , new Color( 130, 130, 130 ) // overview
- }, { new Color( 0, 0, 0 ), // background_color
- new Color( 0, 255, 255 ), // background_color_gradient_bottom
- new Color( 230, 230, 230 ), // sequence __ Black
- new Color( 180, 180, 180 ), // taxonomy
- new Color( 180, 180, 180 ), // support
- new Color( 140, 140, 140 ), // branch_length_color
- new Color( 255, 255, 255 ), // branch_color
- new Color( 255, 255, 255 ), // box_color
- new Color( 255, 255, 255 ), // collapesed_fill_color
- new Color( 0, 255, 0 ), // found_color 0
- new Color( 255, 0, 0 ), // found_color 1
- new Color( 255, 255, 0 ), // found_color 1 + 2
- new Color( 255, 0, 0 ), // duplication_box_color
- new Color( 0, 255, 0 ), // speciation_box_color
- new Color( 255, 255, 0 ), // duplication_speciation_color
- new Color( 230, 230, 230 ), // domain_label
- new Color( 100, 100, 100 ), // domains_base
- new Color( 65, 105, 255 ), // binary_domain_combinations_color
- new Color( 173, 255, 47 ) // annotation
- , new Color( 130, 130, 130 ) // ov
- }, { new Color( 255, 255, 255 ), // background_color
- new Color( 0, 255, 255 ), // background_color_gradient_bottom
- new Color( 0, 0, 0 ), // sequence __ Black & White
- new Color( 0, 0, 0 ), // taxonomy
- new Color( 0, 0, 0 ), // support
- new Color( 0, 0, 0 ), // branch_length_color
- new Color( 0, 0, 0 ), // branch_color
- new Color( 0, 0, 0 ), // box_color
- new Color( 0, 0, 0 ), // collapesed_fill_color
- new Color( 255, 0, 0 ), // found_color 0
- new Color( 0, 255, 0 ), // found_color 1
- new Color( 0, 0, 255 ), // found_color 1 + 2
- new Color( 255, 0, 0 ), // duplication_box_color
- new Color( 0, 255, 0 ), // speciation_box_color
- new Color( 255, 255, 0 ), // duplication_speciation_color
- new Color( 0, 0, 0 ), // domain_label
- new Color( 100, 100, 100 ), // domains_base
- new Color( 0, 0, 0 ), // binary_domain_combinations_color
- new Color( 0, 0, 0 ) // annotation
- , new Color( 220, 220, 220 ) // ov
- }, { new Color( 0, 0, 0 ), // background_color
- new Color( 0, 255, 255 ), // background_color_gradient_bottom
- new Color( 220, 220, 220 ), // sequence __ Silver
- new Color( 180, 180, 180 ), // taxonomy
- new Color( 140, 140, 140 ), // support
- new Color( 140, 140, 140 ), // branch_length_color
- new Color( 240, 240, 240 ), // branch_color
- new Color( 140, 140, 140 ), // box_color
- new Color( 240, 240, 240 ), // collapesed_fill_color
- new Color( 255, 0, 0 ), // found_color 0
- new Color( 0, 255, 0 ), // found_color 1
- new Color( 255, 255, 0 ), // found_color 1 + 2
- new Color( 255, 0, 0 ), // duplication_box_color
- new Color( 0, 255, 0 ), // speciation_box_color
- new Color( 255, 255, 0 ), // duplication_speciation_color
- new Color( 230, 230, 230 ), // domain_label
- new Color( 100, 100, 100 ), // domains_base
- new Color( 180, 180, 180 ), // binary_domain_combinations_color
- new Color( 140, 140, 140 ) // annotation
- , new Color( 40, 40, 40 ) // ov
- }, { new Color( 0, 10, 0 ), // background_color
- new Color( 0, 255, 255 ), // background_color_gradient_bottom
- new Color( 0, 255, 0 ), // sequence __ the Matrix
- new Color( 30, 200, 30 ), // taxonomy
- new Color( 0, 155, 0 ), // support
- new Color( 0, 100, 0 ), // branch_length_color
- new Color( 0, 155, 0 ), // branch_color
- new Color( 0, 255, 0 ), // box_color
- new Color( 0, 155, 0 ), // collapesed_fill_color
- new Color( 255, 0, 0 ), // found_color 0
- new Color( 0, 255, 0 ), // found_color 1
- new Color( 255, 255, 0 ), // found_color 1 + 2
- new Color( 255, 0, 0 ), // duplication_box_color
- new Color( 0, 255, 0 ), // speciation_box_color
- new Color( 255, 255, 0 ), // duplication_speciation_color
- new Color( 230, 230, 230 ), // domain_label
- new Color( 100, 100, 100 ), // domains_base
- new Color( 0, 235, 0 ), // binary_domain_combinations_color
- new Color( 0, 235, 0 ) // annotation
- , new Color( 40, 40, 40 ) // ov
- }, { new Color( 255, 255, 255 ), // background_color
- new Color( 0, 255, 255 ), // background_color_gradient_bottom
- new Color( 0, 0, 0 ), //sequence __ White & Blue
- new Color( 40, 40, 40 ), // taxonomy
- new Color( 0, 125, 0 ), // support
- new Color( 70, 70, 0 ), // branch_length_color
- new Color( 0, 20, 200 ), // branch_color
- new Color( 0, 20, 200 ), // box_color
- new Color( 0, 20, 200 ), // collapesed_fill_color
- new Color( 0, 255, 0 ), // found_color 0
- new Color( 255, 0, 0 ), // found_color 1
- new Color( 0, 0, 255 ), // found_color 0 + 1
- new Color( 255, 0, 0 ), // duplication_box_color
- new Color( 0, 255, 0 ), // speciation_box_color
- new Color( 255, 255, 0 ), // duplication_speciation_color
- new Color( 0, 0, 0 ), // domain_label
- new Color( 50, 50, 50 ), // domains_base
- new Color( 65, 105, 225 ), // binary_domain_combinations_color
- new Color( 173, 255, 47 ) // annotation
- , new Color( 220, 220, 220 ) // ov
- }, { new Color( 0, 0, 0 ), // background_color
- new Color( 0, 255, 255 ), // background_color_gradient_bottom
- new Color( 255, 255, 255 ), // sequence __ Cyan
- new Color( 200, 200, 200 ), // taxonomy
- new Color( 255, 255, 255 ), // support
- new Color( 200, 200, 200 ), // branch_length_color
- new Color( 0, 255, 255 ), // branch_color
- new Color( 0, 255, 255 ), // box_color
- new Color( 0, 255, 255 ), // collapesed_fill_color
- new Color( 0, 255, 0 ), // found_color 0
- new Color( 0, 0, 255 ), // found_color 1
- new Color( 0, 255, 255 ), // found_color 0 + 1
- new Color( 255, 0, 0 ), // duplication_box_color
- new Color( 0, 255, 0 ), // speciation_box_color
- new Color( 255, 255, 0 ), // duplication_speciation_color
- new Color( 230, 230, 230 ), // domain_label
- new Color( 100, 100, 100 ), // domains_base
- new Color( 65, 105, 225 ), // binary_domain_combinations_color
- new Color( 173, 255, 47 ) // annotation
- , new Color( 0, 120, 120 ) // ov
- }, { new Color( 0, 0, 0 ), // background_color
- new Color( 0, 255, 255 ), // background_color_gradient_bottom
- new Color( 255, 200, 0 ), // sequence __ Clockwork
- new Color( 255, 200, 0 ), // taxonomy
- new Color( 255, 200, 0 ), // support
- new Color( 255, 200, 0 ), // branch_length_color
- new Color( 255, 200, 0 ), // branch_color
- new Color( 255, 200, 0 ), // box_color
- new Color( 255, 200, 0 ), // collapesed_fill_color
- new Color( 255, 255, 0 ), // found_color 0
- new Color( 0, 255, 255 ), // found_color 1
- new Color( 255, 255, 255 ), // found_color 0 + 1
- new Color( 255, 0, 0 ), // duplication_box_color
- new Color( 0, 255, 0 ), // speciation_box_color
- new Color( 255, 255, 0 ), // duplication_speciation_color
- new Color( 255, 200, 0 ), // domain_label
- new Color( 255, 200, 0 ), // domains_base
- new Color( 150, 150, 150 ), // binary_domain_combinations_color
- new Color( 150, 150, 150 ) // annotation
- , new Color( 150, 150, 150 ) // ov
- }, { new Color( 0, 0, 100 ), // background_color
- new Color( 0, 255, 255 ), // background_color_gradient_bottom
- new Color( 255, 255, 255 ), // sequence __ Blue
- new Color( 255, 255, 255 ), // taxonomy
- new Color( 255, 0, 0 ), // support
- new Color( 255, 0, 0 ), // branch_length_color
- new Color( 255, 0, 0 ), // branch_color
- new Color( 255, 0, 0 ), // box_color
- new Color( 255, 0, 0 ), // collapesed_fill_color
- new Color( 0, 255, 0 ), // found_color
- new Color( 255, 0, 0 ), // found_color 1
- new Color( 255, 255, 0 ), // found_color 1 + 2
- new Color( 255, 0, 0 ), // duplication_box_color
- new Color( 0, 255, 0 ), // speciation_box_color
- new Color( 255, 255, 0 ), // duplication_speciation_color
- new Color( 255, 255, 255 ), // domain_label
- new Color( 100, 100, 100 ), // domains_base
- new Color( 255, 255, 255 ), // binary_domain_combinations_color
- new Color( 255, 255, 255 ) // annotation
- , new Color( 77, 77, 255 ) // ov
- }, { new Color( 0, 0, 0 ), // background_color
- new Color( 0, 255, 255 ), // background_color_gradient_bottom
- new Color( 255, 255, 255 ), // sequence __ blue & white
- new Color( 255, 255, 255 ), // taxonomy
- new Color( 255, 255, 255 ), // support
- new Color( 0, 191, 255 ), // branch_length_color
- new Color( 0, 191, 255 ), // branch_color
- new Color( 0, 191, 255 ), // box_color
- new Color( 0, 191, 255 ), // collapesed_fill_color
- new Color( 255, 0, 0 ), // found_color 0
- new Color( 0, 255, 0 ), // found_color 1
- new Color( 255, 255, 0 ), // found_color 0 + 1
- new Color( 255, 0, 0 ), // duplication_box_color
- new Color( 0, 255, 0 ), // speciation_box_color
- new Color( 255, 255, 0 ), // duplication_speciation_color
- new Color( 255, 255, 255 ), // domain_label
- new Color( 150, 150, 150 ), // domains_base
- new Color( 255, 255, 255 ), // binary_domain_combinations_color
- new Color( 255, 255, 255 ) // annotation
- , new Color( 170, 187, 204 ) // ov
- }, { new Color( 0, 0, 0 ), // background_color
- new Color( 255, 255, 0 ), // background_color_gradient_bottom
- new Color( 127, 255, 0 ), // sequence __ Neon
- new Color( 255, 110, 199 ), // taxonomy
- new Color( 234, 173, 234 ), // support
- new Color( 77, 77, 255 ), // branch_length_color
- new Color( 234, 173, 234 ), // branch_color
- new Color( 77, 77, 255 ), // box_color
- new Color( 234, 173, 234 ), // collapsed_fill_color
- new Color( 243, 243, 21 ), // found_color 0
- new Color( 255, 20, 147 ), // found_color 1
- new Color( 255, 255, 255 ), // found_color 1 + 2
- new Color( 255, 0, 0 ), // duplication_box_color
- new Color( 0, 255, 0 ), // speciation_box_color
- new Color( 255, 255, 0 ), // duplication_speciation_color
- new Color( 127, 255, 0 ), // domain_label
- new Color( 234, 173, 234 ), // domains_base
- new Color( 27, 255, 0 ), // binary_domain_combinations_color
- new Color( 27, 255, 0 ) // annotation
- , new Color( 77, 77, 255 ) // ov
- } };
+ new Color( 0, 100, 100 ), // background_color_gradient_bottom
+ new Color( 230, 230, 230 ), // sequence __ Default (same as Black)
+ new Color( 180, 180, 180 ), // taxonomy
+ new Color( 180, 180, 180 ), // support
+ new Color( 140, 140, 140 ), // branch_length_color
+ new Color( 255, 255, 255 ), // branch_color
+ new Color( 255, 255, 255 ), // box_color
+ new Color( 255, 255, 255 ), // collapesed_fill_color
+ new Color( 0, 255, 0 ), // found_color 0
+ new Color( 255, 0, 0 ), // found_color 1
+ new Color( 255, 255, 0 ), // found_color 1 + 2
+ new Color( 255, 0, 0 ), // duplication_box_color
+ new Color( 0, 255, 0 ), // speciation_box_color
+ new Color( 255, 255, 0 ), // duplication_speciation_color
+ new Color( 230, 230, 230 ), // domain_label
+ new Color( 100, 100, 100 ), // domains_base
+ new Color( 65, 105, 255 ), // binary_domain_combinations_color
+ new Color( 173, 255, 47 ) // annotation
+ , new Color( 130, 130, 130 ) // overview
+ }, { new Color( 0, 0, 0 ), // background_color
+ new Color( 0, 255, 255 ), // background_color_gradient_bottom
+ new Color( 230, 230, 230 ), // sequence __ Black
+ new Color( 180, 180, 180 ), // taxonomy
+ new Color( 180, 180, 180 ), // support
+ new Color( 140, 140, 140 ), // branch_length_color
+ new Color( 255, 255, 255 ), // branch_color
+ new Color( 255, 255, 255 ), // box_color
+ new Color( 255, 255, 255 ), // collapesed_fill_color
+ new Color( 0, 255, 0 ), // found_color 0
+ new Color( 255, 0, 0 ), // found_color 1
+ new Color( 255, 255, 0 ), // found_color 1 + 2
+ new Color( 255, 0, 0 ), // duplication_box_color
+ new Color( 0, 255, 0 ), // speciation_box_color
+ new Color( 255, 255, 0 ), // duplication_speciation_color
+ new Color( 230, 230, 230 ), // domain_label
+ new Color( 100, 100, 100 ), // domains_base
+ new Color( 65, 105, 255 ), // binary_domain_combinations_color
+ new Color( 173, 255, 47 ) // annotation
+ , new Color( 130, 130, 130 ) // ov
+ }, { new Color( 255, 255, 255 ), // background_color
+ new Color( 0, 255, 255 ), // background_color_gradient_bottom
+ new Color( 0, 0, 0 ), // sequence __ Black & White
+ new Color( 0, 0, 0 ), // taxonomy
+ new Color( 0, 0, 0 ), // support
+ new Color( 0, 0, 0 ), // branch_length_color
+ new Color( 0, 0, 0 ), // branch_color
+ new Color( 0, 0, 0 ), // box_color
+ new Color( 0, 0, 0 ), // collapesed_fill_color
+ new Color( 255, 0, 0 ), // found_color 0
+ new Color( 0, 255, 0 ), // found_color 1
+ new Color( 0, 0, 255 ), // found_color 1 + 2
+ new Color( 255, 0, 0 ), // duplication_box_color
+ new Color( 0, 255, 0 ), // speciation_box_color
+ new Color( 255, 255, 0 ), // duplication_speciation_color
+ new Color( 0, 0, 0 ), // domain_label
+ new Color( 100, 100, 100 ), // domains_base
+ new Color( 0, 0, 0 ), // binary_domain_combinations_color
+ new Color( 0, 0, 0 ) // annotation
+ , new Color( 220, 220, 220 ) // ov
+ }, { new Color( 0, 0, 0 ), // background_color
+ new Color( 0, 255, 255 ), // background_color_gradient_bottom
+ new Color( 220, 220, 220 ), // sequence __ Silver
+ new Color( 180, 180, 180 ), // taxonomy
+ new Color( 140, 140, 140 ), // support
+ new Color( 140, 140, 140 ), // branch_length_color
+ new Color( 240, 240, 240 ), // branch_color
+ new Color( 140, 140, 140 ), // box_color
+ new Color( 240, 240, 240 ), // collapesed_fill_color
+ new Color( 255, 0, 0 ), // found_color 0
+ new Color( 0, 255, 0 ), // found_color 1
+ new Color( 255, 255, 0 ), // found_color 1 + 2
+ new Color( 255, 0, 0 ), // duplication_box_color
+ new Color( 0, 255, 0 ), // speciation_box_color
+ new Color( 255, 255, 0 ), // duplication_speciation_color
+ new Color( 230, 230, 230 ), // domain_label
+ new Color( 100, 100, 100 ), // domains_base
+ new Color( 180, 180, 180 ), // binary_domain_combinations_color
+ new Color( 140, 140, 140 ) // annotation
+ , new Color( 40, 40, 40 ) // ov
+ }, { new Color( 0, 10, 0 ), // background_color
+ new Color( 0, 255, 255 ), // background_color_gradient_bottom
+ new Color( 0, 255, 0 ), // sequence __ the Matrix
+ new Color( 30, 200, 30 ), // taxonomy
+ new Color( 0, 155, 0 ), // support
+ new Color( 0, 100, 0 ), // branch_length_color
+ new Color( 0, 155, 0 ), // branch_color
+ new Color( 0, 255, 0 ), // box_color
+ new Color( 0, 155, 0 ), // collapesed_fill_color
+ new Color( 255, 0, 0 ), // found_color 0
+ new Color( 0, 255, 0 ), // found_color 1
+ new Color( 255, 255, 0 ), // found_color 1 + 2
+ new Color( 255, 0, 0 ), // duplication_box_color
+ new Color( 0, 255, 0 ), // speciation_box_color
+ new Color( 255, 255, 0 ), // duplication_speciation_color
+ new Color( 230, 230, 230 ), // domain_label
+ new Color( 100, 100, 100 ), // domains_base
+ new Color( 0, 235, 0 ), // binary_domain_combinations_color
+ new Color( 0, 235, 0 ) // annotation
+ , new Color( 40, 40, 40 ) // ov
+ }, { new Color( 255, 255, 255 ), // background_color
+ new Color( 0, 255, 255 ), // background_color_gradient_bottom
+ new Color( 0, 0, 0 ), //sequence __ White & Blue
+ new Color( 40, 40, 40 ), // taxonomy
+ new Color( 0, 125, 0 ), // support
+ new Color( 70, 70, 0 ), // branch_length_color
+ new Color( 0, 20, 200 ), // branch_color
+ new Color( 0, 20, 200 ), // box_color
+ new Color( 0, 20, 200 ), // collapesed_fill_color
+ new Color( 0, 255, 0 ), // found_color 0
+ new Color( 255, 0, 0 ), // found_color 1
+ new Color( 0, 0, 255 ), // found_color 0 + 1
+ new Color( 255, 0, 0 ), // duplication_box_color
+ new Color( 0, 255, 0 ), // speciation_box_color
+ new Color( 255, 255, 0 ), // duplication_speciation_color
+ new Color( 0, 0, 0 ), // domain_label
+ new Color( 50, 50, 50 ), // domains_base
+ new Color( 65, 105, 225 ), // binary_domain_combinations_color
+ new Color( 173, 255, 47 ) // annotation
+ , new Color( 220, 220, 220 ) // ov
+ }, { new Color( 0, 0, 0 ), // background_color
+ new Color( 0, 255, 255 ), // background_color_gradient_bottom
+ new Color( 255, 255, 255 ), // sequence __ Cyan
+ new Color( 200, 200, 200 ), // taxonomy
+ new Color( 255, 255, 255 ), // support
+ new Color( 200, 200, 200 ), // branch_length_color
+ new Color( 0, 255, 255 ), // branch_color
+ new Color( 0, 255, 255 ), // box_color
+ new Color( 0, 255, 255 ), // collapesed_fill_color
+ new Color( 0, 255, 0 ), // found_color 0
+ new Color( 0, 0, 255 ), // found_color 1
+ new Color( 0, 255, 255 ), // found_color 0 + 1
+ new Color( 255, 0, 0 ), // duplication_box_color
+ new Color( 0, 255, 0 ), // speciation_box_color
+ new Color( 255, 255, 0 ), // duplication_speciation_color
+ new Color( 230, 230, 230 ), // domain_label
+ new Color( 100, 100, 100 ), // domains_base
+ new Color( 65, 105, 225 ), // binary_domain_combinations_color
+ new Color( 173, 255, 47 ) // annotation
+ , new Color( 0, 120, 120 ) // ov
+ }, { new Color( 0, 0, 0 ), // background_color
+ new Color( 0, 255, 255 ), // background_color_gradient_bottom
+ new Color( 255, 200, 0 ), // sequence __ Clockwork
+ new Color( 255, 200, 0 ), // taxonomy
+ new Color( 255, 200, 0 ), // support
+ new Color( 255, 200, 0 ), // branch_length_color
+ new Color( 255, 200, 0 ), // branch_color
+ new Color( 255, 200, 0 ), // box_color
+ new Color( 255, 200, 0 ), // collapesed_fill_color
+ new Color( 255, 255, 0 ), // found_color 0
+ new Color( 0, 255, 255 ), // found_color 1
+ new Color( 255, 255, 255 ), // found_color 0 + 1
+ new Color( 255, 0, 0 ), // duplication_box_color
+ new Color( 0, 255, 0 ), // speciation_box_color
+ new Color( 255, 255, 0 ), // duplication_speciation_color
+ new Color( 255, 200, 0 ), // domain_label
+ new Color( 255, 200, 0 ), // domains_base
+ new Color( 150, 150, 150 ), // binary_domain_combinations_color
+ new Color( 150, 150, 150 ) // annotation
+ , new Color( 150, 150, 150 ) // ov
+ }, { new Color( 0, 0, 100 ), // background_color
+ new Color( 0, 255, 255 ), // background_color_gradient_bottom
+ new Color( 255, 255, 255 ), // sequence __ Blue
+ new Color( 255, 255, 255 ), // taxonomy
+ new Color( 255, 0, 0 ), // support
+ new Color( 255, 0, 0 ), // branch_length_color
+ new Color( 255, 0, 0 ), // branch_color
+ new Color( 255, 0, 0 ), // box_color
+ new Color( 255, 0, 0 ), // collapesed_fill_color
+ new Color( 0, 255, 0 ), // found_color
+ new Color( 255, 0, 0 ), // found_color 1
+ new Color( 255, 255, 0 ), // found_color 1 + 2
+ new Color( 255, 0, 0 ), // duplication_box_color
+ new Color( 0, 255, 0 ), // speciation_box_color
+ new Color( 255, 255, 0 ), // duplication_speciation_color
+ new Color( 255, 255, 255 ), // domain_label
+ new Color( 100, 100, 100 ), // domains_base
+ new Color( 255, 255, 255 ), // binary_domain_combinations_color
+ new Color( 255, 255, 255 ) // annotation
+ , new Color( 77, 77, 255 ) // ov
+ }, { new Color( 0, 0, 0 ), // background_color
+ new Color( 0, 255, 255 ), // background_color_gradient_bottom
+ new Color( 255, 255, 255 ), // sequence __ blue & white
+ new Color( 255, 255, 255 ), // taxonomy
+ new Color( 255, 255, 255 ), // support
+ new Color( 0, 191, 255 ), // branch_length_color
+ new Color( 0, 191, 255 ), // branch_color
+ new Color( 0, 191, 255 ), // box_color
+ new Color( 0, 191, 255 ), // collapesed_fill_color
+ new Color( 255, 0, 0 ), // found_color 0
+ new Color( 0, 255, 0 ), // found_color 1
+ new Color( 255, 255, 0 ), // found_color 0 + 1
+ new Color( 255, 0, 0 ), // duplication_box_color
+ new Color( 0, 255, 0 ), // speciation_box_color
+ new Color( 255, 255, 0 ), // duplication_speciation_color
+ new Color( 255, 255, 255 ), // domain_label
+ new Color( 150, 150, 150 ), // domains_base
+ new Color( 255, 255, 255 ), // binary_domain_combinations_color
+ new Color( 255, 255, 255 ) // annotation
+ , new Color( 170, 187, 204 ) // ov
+ }, { new Color( 0, 0, 0 ), // background_color
+ new Color( 255, 255, 0 ), // background_color_gradient_bottom
+ new Color( 127, 255, 0 ), // sequence __ Neon
+ new Color( 255, 110, 199 ), // taxonomy
+ new Color( 234, 173, 234 ), // support
+ new Color( 77, 77, 255 ), // branch_length_color
+ new Color( 234, 173, 234 ), // branch_color
+ new Color( 77, 77, 255 ), // box_color
+ new Color( 234, 173, 234 ), // collapsed_fill_color
+ new Color( 243, 243, 21 ), // found_color 0
+ new Color( 255, 20, 147 ), // found_color 1
+ new Color( 255, 255, 255 ), // found_color 1 + 2
+ new Color( 255, 0, 0 ), // duplication_box_color
+ new Color( 0, 255, 0 ), // speciation_box_color
+ new Color( 255, 255, 0 ), // duplication_speciation_color
+ new Color( 127, 255, 0 ), // domain_label
+ new Color( 234, 173, 234 ), // domains_base
+ new Color( 27, 255, 0 ), // binary_domain_combinations_color
+ new Color( 27, 255, 0 ) // annotation
+ , new Color( 77, 77, 255 ) // ov
+ } };
private Color annotation_color;
private Color background_color;
private Color background_color_gradient_bottom;
// Hidden constructor.
}
+ public Color getDomainBaseColor() {
+ return domain_base_color;
+ }
+
+ public Color getDomainLabelColor() {
+ return domain_label_color;
+ }
+
+ private void setColorForDefault( final int i, final Color color ) {
+ _color_schemes[ 0 ][ i ] = color;
+ }
+
void cycleColorScheme() {
if ( getCurrentColorScheme() >= ( _color_schemes.length - 1 ) ) {
setColorSchema( 0 );
return SCHEME_NAMES[ getCurrentColorScheme() ];
}
- public Color getDomainBaseColor() {
- return domain_base_color;
- }
-
- public Color getDomainLabelColor() {
- return domain_label_color;
- }
-
Color getDuplicationBoxColor() {
return dup_box_color;
}
_color_scheme = color_scheme;
}
- private void setColorForDefault( final int i, final Color color ) {
- _color_schemes[ 0 ][ i ] = color;
- }
-
static TreeColorSet createInstance() {
final TreeColorSet tcs = new TreeColorSet();
tcs.setColorSchema( 0 );
return _small_max_descent;
}
+ private Font getLargeFontSystem() {
+ return _large_font_system;
+ }
+
+ private void intializeFonts() {
+ final int small_size = getBaseFont().getSize() - 2;
+ int italic = Font.ITALIC;
+ if ( getBaseFont().getStyle() == Font.BOLD ) {
+ italic = italic + Font.BOLD;
+ }
+ _small_font = new Font( getBaseFont().getFontName(), getBaseFont().getStyle(), small_size );
+ _large_font = new Font( getBaseFont().getFontName(), getBaseFont().getStyle(), getBaseFont().getSize() );
+ _small_font_system = new Font( getBaseFont().getFontName(), getBaseFont().getStyle(), small_size );
+ _large_font_system = new Font( getBaseFont().getFontName(), getBaseFont().getStyle(), getBaseFont().getSize() );
+ _small_font_memory = _small_font;
+ _large_font_memory = _large_font;
+ setupFontMetrics();
+ }
+
+ private void setDecreasedSizeBySystem( final boolean decreased_size_by_system ) {
+ _decreased_size_by_system = decreased_size_by_system;
+ }
+
+ private void setupFontMetrics() {
+ _fm_small = _owner.getFontMetrics( _small_font );
+ _fm_large = _owner.getFontMetrics( _large_font );
+ _small_max_descent = _fm_small.getMaxDescent();
+ _small_max_ascent = _fm_small.getMaxAscent() + 1;
+ }
+
void decreaseFontSize( final int min, final boolean decreased_size_by_system ) {
if ( decreased_size_by_system && !isDecreasedSizeBySystem() ) {
_small_font_memory = _small_font;
_large_font = _large_font.deriveFont( 6f );
setupFontMetrics();
}
-
- private Font getLargeFontSystem() {
- return _large_font_system;
- }
-
- private void intializeFonts() {
- final int small_size = getBaseFont().getSize() - 2;
- int italic = Font.ITALIC;
- if ( getBaseFont().getStyle() == Font.BOLD ) {
- italic = italic + Font.BOLD;
- }
- _small_font = new Font( getBaseFont().getFontName(), getBaseFont().getStyle(), small_size );
- _large_font = new Font( getBaseFont().getFontName(), getBaseFont().getStyle(), getBaseFont().getSize() );
- _small_font_system = new Font( getBaseFont().getFontName(), getBaseFont().getStyle(), small_size );
- _large_font_system = new Font( getBaseFont().getFontName(), getBaseFont().getStyle(), getBaseFont().getSize() );
- _small_font_memory = _small_font;
- _large_font_memory = _large_font;
- setupFontMetrics();
- }
-
- private void setDecreasedSizeBySystem( final boolean decreased_size_by_system ) {
- _decreased_size_by_system = decreased_size_by_system;
- }
-
- private void setupFontMetrics() {
- _fm_small = _owner.getFontMetrics( _small_font );
- _fm_large = _owner.getFontMetrics( _large_font );
- _small_max_descent = _fm_small.getMaxDescent();
- _small_max_ascent = _fm_small.getMaxAscent() + 1;
- }
}
public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable {
+ final private class NodeColorizationActionListener implements ActionListener {
+
+ List<PhylogenyNode> _additional_nodes = null;
+ JColorChooser _chooser = null;
+ PhylogenyNode _node = null;
+
+ NodeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
+ _chooser = chooser;
+ _node = node;
+ }
+
+ NodeColorizationActionListener( final JColorChooser chooser,
+ final PhylogenyNode node,
+ final List<PhylogenyNode> additional_nodes ) {
+ _chooser = chooser;
+ _node = node;
+ _additional_nodes = additional_nodes;
+ }
+
+ @Override
+ public void actionPerformed( final ActionEvent e ) {
+ final Color c = _chooser.getColor();
+ if ( c != null ) {
+ colorizeNodes( c, _node, _additional_nodes );
+ }
+ }
+ }
+
+ final private class SubtreeColorizationActionListener implements ActionListener {
+
+ List<PhylogenyNode> _additional_nodes = null;
+ JColorChooser _chooser = null;
+ PhylogenyNode _node = null;
+
+ SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
+ _chooser = chooser;
+ _node = node;
+ }
+
+ SubtreeColorizationActionListener( final JColorChooser chooser,
+ final PhylogenyNode node,
+ final List<PhylogenyNode> additional_nodes ) {
+ _chooser = chooser;
+ _node = node;
+ _additional_nodes = additional_nodes;
+ }
+
+ @Override
+ public void actionPerformed( final ActionEvent e ) {
+ final Color c = _chooser.getColor();
+ if ( c != null ) {
+ colorizeSubtree( c, _node, _additional_nodes );
+ }
+ }
+ }
public final static boolean SPECIAL_DOMAIN_COLORING = true;
final static Cursor ARROW_CURSOR = Cursor.getPredefinedCursor( Cursor.DEFAULT_CURSOR );
final static Cursor CUT_CURSOR = Cursor.getPredefinedCursor( Cursor.CROSSHAIR_CURSOR );
private static final BasicStroke STROKE_2 = new BasicStroke( 2f );
private static final double TWO_PI = 2 * Math.PI;
private final static int WIGGLE = 2;
- private static final String SHOW_ONLY_THIS_CONF_TYPE = null; //TODO remove me
+ private static final String SHOW_ONLY_THIS_CONF_TYPE = null; //TODO remove me
HashMap<Long, Short> _nodeid_dist_to_leaf = new HashMap<Long, Short>();
final private Arc2D _arc = new Arc2D.Double();
private AffineTransform _at;
calculateScaleDistance();
FORMATTER_CONFIDENCE.setMaximumFractionDigits( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() );
FORMATTER_BRANCH_LENGTH.setMaximumFractionDigits( configuration
- .getNumberOfDigitsAfterCommaForBranchLengthValues() );
+ .getNumberOfDigitsAfterCommaForBranchLengthValues() );
}
@Override
return _phylogeny;
}
+ public final TreeColorSet getTreeColorSet() {
+ return getMainPanel().getTreeColorSet();
+ }
+
@Override
final public void mouseWheelMoved( final MouseWheelEvent e ) {
final int notches = e.getWheelRotation();
paint( g );
}
- final void calcMaxDepth() {
- if ( _phylogeny != null ) {
- _circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
- }
- }
-
- /**
- * Set parameters for printing the displayed tree
- *
- */
- final void calcParametersForPainting( final int x, final int y ) {
- // updateStyle(); not needed?
- if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
- initNodeData();
- calculateLongestExtNodeInfo();
- if ( ( getLongestExtNodeInfo() > ( x * 0.6 ) )
- && ( getTreeFontSet().getLargeFont().getSize() > ( 2 + TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) ) {
- while ( ( getLongestExtNodeInfo() > ( x * 0.7 ) ) && ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) {
- getMainPanel().getTreeFontSet().decreaseFontSize( getConfiguration().getMinBaseFontSize(), true );
- calculateLongestExtNodeInfo();
- }
- }
- else {
- while ( ( getLongestExtNodeInfo() < ( x * 0.6 ) )
- && ( getTreeFontSet().getLargeFont().getSize() <= ( getTreeFontSet().getLargeFontMemory()
- .getSize() - TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) ) {
- getMainPanel().getTreeFontSet().increaseFontSize();
- calculateLongestExtNodeInfo();
- }
- }
- //_length_of_longest_text = calcLengthOfLongestText();
- int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
- final int max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
- if ( ext_nodes == 1 ) {
- ext_nodes = max_depth;
- if ( ext_nodes < 1 ) {
- ext_nodes = 1;
- }
- }
- updateOvSizes();
- float xdist = 0;
- float ov_xdist = 0;
- if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
- xdist = ( float ) ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( ext_nodes + 3.0 ) );
- ov_xdist = ( float ) ( getOvMaxWidth() / ( ext_nodes + 3.0 ) );
- }
- else {
- xdist = ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( max_depth + 1 ) );
- ov_xdist = ( getOvMaxWidth() / ( max_depth + 1 ) );
- }
- float ydist = ( float ) ( ( y - TreePanel.MOVE ) / ( ext_nodes * 2.0 ) );
- if ( xdist < 0.0 ) {
- xdist = 0.0f;
- }
- if ( ov_xdist < 0.0 ) {
- ov_xdist = 0.0f;
- }
- if ( ydist < 0.0 ) {
- ydist = 0.0f;
- }
- setXdistance( xdist );
- setYdistance( ydist );
- setOvXDistance( ov_xdist );
- final double height = _phylogeny.getHeight();
- if ( height > 0 ) {
- final float corr = ( float ) ( ( x - TreePanel.MOVE - getLongestExtNodeInfo() - getXdistance() ) / height );
- setXcorrectionFactor( corr > 0 ? corr : 0 );
- final float ov_corr = ( float ) ( ( getOvMaxWidth() - getOvXDistance() ) / height );
- setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
- }
- else {
- setXcorrectionFactor( 0 );
- setOvXcorrectionFactor( 0 );
- }
- _circ_max_depth = max_depth;
- setUpUrtFactor();
- //
- if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
- && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
- // int dynamic_hiding_factor = calcDynamicHidingFactor();
- // if ( dynamic_hiding_factor > 1 ) {
- // while ( dynamic_hiding_factor > 1
- // && getTreeFontSet()._fm_large.getHeight() > TreeFontSet.SMALL_FONTS_BASE ) {
- // getTreeFontSet().decreaseFontSize( 1, true );
- // dynamic_hiding_factor = calcDynamicHidingFactor();
- // }
- // }
- // else if ( getTreeFontSet().isDecreasedSizeBySystem() ) {
- // while ( dynamic_hiding_factor < 1 && getTreeFontSet()._fm_large.getHeight() < 12 ) {
- // getTreeFontSet().increaseFontSize();
- // dynamic_hiding_factor = calcDynamicHidingFactor();
- // }
- // }
+ private void abbreviateScientificName( final String sn, final StringBuilder sb ) {
+ final String[] a = sn.split( "\\s+" );
+ sb.append( a[ 0 ].substring( 0, 1 ) );
+ sb.append( a[ 1 ].substring( 0, 2 ) );
+ if ( a.length > 2 ) {
+ for( int i = 2; i < a.length; i++ ) {
+ sb.append( " " );
+ sb.append( a[ i ] );
}
- //
}
}
- final void calculateLongestExtNodeInfo() {
- if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
+ final private void addEmptyNode( final PhylogenyNode node ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ errorMessageNoCutCopyPasteInUnrootedDisplay();
return;
}
- int max_length = ForesterUtil.roundToInt( ( getSize().getWidth() - MOVE )
- * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO );
- if ( max_length < 40 ) {
- max_length = 40;
- }
- int longest = 30;
- int longest_txt = 0;
- _longest_domain = 0;
- PhylogenyNode longest_txt_node = _phylogeny.getFirstExternalNode();
- for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
- int sum = 0;
- if ( node.isCollapse() ) {
- continue;
- }
- final StringBuilder sb = new StringBuilder();
- nodeDataAsSB( node, sb );
- if ( node.getNodeData().isHasTaxonomy() ) {
- nodeTaxonomyDataAsSB( node.getNodeData().getTaxonomy(), sb );
- }
- final int txt = sb.length();
- if ( txt > longest_txt ) {
- longest_txt = txt;
- longest_txt_node = node;
- }
- boolean use_vis = false;
- final Graphics2D g = ( Graphics2D ) getGraphics();
- if ( getControlPanel().isUseVisualStyles() ) {
- use_vis = setFont( g, node, false );
- }
- if ( !use_vis ) {
- sum = getFontMetricsForLargeDefaultFont().stringWidth( sb.toString() );
- }
- else {
- sum = getFontMetrics( g.getFont() ).stringWidth( sb.toString() );
- }
- if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
- sum += getFontMetricsForLargeDefaultFont().stringWidth( node.getNodeData().getBinaryCharacters()
- .getGainedCharactersAsStringBuffer().toString() );
- }
- if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
- && ( node.getNodeData().getVector().size() > 0 ) ) {
- if ( getConfiguration() != null ) {
- sum += getConfiguration().getVectorDataWidth() + 10;
- }
- else {
- sum += RenderableVector.VECTOR_DEFAULT_WIDTH + 10;
- }
- }
- if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
- // FIXME
- // TODO this might need some clean up
- final DomainArchitecture d = node.getNodeData().getSequence().getDomainArchitecture();
- sum += ( ( _domain_structure_width / ( ( RenderableDomainArchitecture ) d ).getOriginalSize()
- .getWidth() ) * d.getTotalLength() ) + 10;
- if ( d.getTotalLength() > _longest_domain ) {
- _longest_domain = d.getTotalLength();
- }
- }
- if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() )
- && ( node.getNodeData().getSequence().isMolecularSequenceAligned() )
- && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) {
- // FIXME
- sum += RenderableMsaSequence.DEFAULT_WIDTH + 30;
- }
- if ( sum >= max_length ) {
- _longest_ext_node_info = max_length;
- // return; //FIXME why?
- }
- if ( sum > longest ) {
- longest = sum;
- }
- }
- _ext_node_with_longest_txt_info = longest_txt_node;
- if ( longest >= max_length ) {
- _longest_ext_node_info = max_length;
+ final String label = createASimpleTextRepresentationOfANode( node );
+ String msg = "";
+ if ( ForesterUtil.isEmpty( label ) ) {
+ msg = "How to add the new, empty node?";
}
else {
- _longest_ext_node_info = longest;
- }
- _length_of_longest_text = calcLengthOfLongestText();
- }
-
- final void calculateScaleDistance() {
- if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
- return;
+ msg = "How to add the new, empty node to node" + label + "?";
}
- final double height = getMaxDistanceToRoot();
- if ( height > 0 ) {
- if ( ( height <= 0.5 ) ) {
- setScaleDistance( 0.01 );
- }
- else if ( height <= 5.0 ) {
- setScaleDistance( 0.1 );
- }
- else if ( height <= 50.0 ) {
- setScaleDistance( 1 );
- }
- else if ( height <= 500.0 ) {
- setScaleDistance( 10 );
- }
- else {
- setScaleDistance( 100 );
+ final Object[] options = { "As sibling", "As descendant", "Cancel" };
+ final int r = JOptionPane.showOptionDialog( this,
+ msg,
+ "Addition of Empty New Node",
+ JOptionPane.CLOSED_OPTION,
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ options,
+ options[ 2 ] );
+ boolean add_as_sibling = true;
+ if ( r == 1 ) {
+ add_as_sibling = false;
+ }
+ else if ( r != 0 ) {
+ return;
+ }
+ final Phylogeny phy = new Phylogeny();
+ phy.setRoot( new PhylogenyNode() );
+ phy.setRooted( true );
+ if ( add_as_sibling ) {
+ if ( node.isRoot() ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot add sibling to root",
+ "Attempt to add sibling to root",
+ JOptionPane.ERROR_MESSAGE );
+ return;
}
+ phy.addAsSibling( node );
}
else {
- setScaleDistance( 0.0 );
- }
- String scale_label = String.valueOf( getScaleDistance() );
- if ( !ForesterUtil.isEmpty( _phylogeny.getDistanceUnit() ) ) {
- scale_label += " [" + _phylogeny.getDistanceUnit() + "]";
+ phy.addAsChild( node );
}
- setScaleLabel( scale_label );
+ setNodeInPreorderToNull();
+ _phylogeny.externalNodesHaveChanged();
+ _phylogeny.clearHashIdToNodeMap();
+ _phylogeny.recalculateNumberOfExternalDescendants( true );
+ resetNodeIdToDistToLeafMap();
+ setEdited( true );
+ repaint();
}
- final Color calculateTaxonomyBasedColor( final Taxonomy tax ) {
- if ( getOptions().isColorByTaxonomicGroup() ) {
- if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
- boolean ex = false;
- String group = null;
- try {
- group = TaxonomyUtil.getTaxGroupByTaxCode( tax.getTaxonomyCode() );
- }
- catch ( final Exception e ) {
- ex = true;
- }
- if ( !ex && !ForesterUtil.isEmpty( group ) ) {
- final Color c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( group );
- if ( c != null ) {
- return c;
- }
- }
- }
- return getTreeColorSet().getTaxonomyColor();
- }
- else {
- if ( ForesterUtil.isEmpty( tax.getTaxonomyCode() ) && ForesterUtil.isEmpty( tax.getScientificName() ) ) {
- return getTreeColorSet().getTaxonomyColor();
- }
- Color c = null;
- if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
- c = getControlPanel().getSpeciesColors().get( tax.getTaxonomyCode() );
- }
- if ( ( c == null ) && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
- c = getControlPanel().getSpeciesColors().get( tax.getScientificName() );
- }
- if ( c == null ) {
- if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
- c = AptxUtil.calculateColorFromString( tax.getTaxonomyCode(), true );
- getControlPanel().getSpeciesColors().put( tax.getTaxonomyCode(), c );
- }
- else {
- c = AptxUtil.calculateColorFromString( tax.getScientificName(), true );
- getControlPanel().getSpeciesColors().put( tax.getScientificName(), c );
- }
- }
- return c;
+ final private void addToCurrentExternalNodes( final long i ) {
+ if ( _current_external_nodes == null ) {
+ _current_external_nodes = new HashSet<Long>();
}
+ _current_external_nodes.add( i );
}
- final Color calculateSequenceBasedColor( final Sequence seq ) {
- if ( ForesterUtil.isEmpty( seq.getName() ) ) {
- return getTreeColorSet().getSequenceColor();
+ final private void assignGraphicsForBranchWithColorForParentBranch( final PhylogenyNode node,
+ final boolean is_vertical,
+ final Graphics g,
+ final boolean to_pdf,
+ final boolean to_graphics_file ) {
+ final NodeClickAction action = _control_panel.getActionWhenNodeClicked();
+ if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
+ g.setColor( Color.BLACK );
}
- Color c = null;
- final String seq_name = seq.getName();
- c = getControlPanel().getSequenceColors().get( seq_name );
- if ( c == null ) {
- c = AptxUtil.calculateColorFromString( seq_name, false );
- getControlPanel().getSequenceColors().put( seq_name, c );
+ else if ( ( ( action == NodeClickAction.COPY_SUBTREE ) || ( action == NodeClickAction.CUT_SUBTREE )
+ || ( action == NodeClickAction.DELETE_NODE_OR_SUBTREE ) || ( action == NodeClickAction.PASTE_SUBTREE ) || ( action == NodeClickAction.ADD_NEW_NODE ) )
+ && ( getCutOrCopiedTree() != null )
+ && ( getCopiedAndPastedNodes() != null )
+ && !to_pdf
+ && !to_graphics_file && getCopiedAndPastedNodes().contains( node.getId() ) ) {
+ g.setColor( getTreeColorSet().getFoundColor0() );
+ }
+ else if ( getControlPanel().isUseVisualStyles() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
+ g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
+ }
+ else if ( to_pdf ) {
+ g.setColor( getTreeColorSet().getBranchColorForPdf() );
+ }
+ else {
+ g.setColor( getTreeColorSet().getBranchColor() );
}
- return c;
}
- void checkForVectorProperties( final Phylogeny phy ) {
- final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- if ( node.getNodeData().getProperties() != null ) {
- final PropertiesMap pm = node.getNodeData().getProperties();
- final double[] vector = new double[ pm.getProperties().size() ];
- int counter = 0;
- for( final String ref : pm.getProperties().keySet() ) {
- if ( ref.startsWith( PhyloXmlUtil.VECTOR_PROPERTY_REF ) ) {
- final Property p = pm.getProperty( ref );
- final String value_str = p.getValue();
- final String index_str = ref
- .substring( PhyloXmlUtil.VECTOR_PROPERTY_REF.length(), ref.length() );
- double d = -100;
- try {
- d = Double.parseDouble( value_str );
- }
- catch ( final NumberFormatException e ) {
- JOptionPane.showMessageDialog( this, "Could not parse \"" + value_str
- + "\" into a decimal value", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE );
- return;
+ final private void blast( final PhylogenyNode node ) {
+ if ( !isCanBlast( node ) ) {
+ JOptionPane.showMessageDialog( this,
+ "Insufficient information present",
+ "Cannot Blast",
+ JOptionPane.INFORMATION_MESSAGE );
+ return;
+ }
+ else {
+ final String query = Blast.obtainQueryForBlast( node );
+ System.out.println( "query for BLAST is: " + query );
+ char type = '?';
+ if ( !ForesterUtil.isEmpty( query ) ) {
+ if ( node.getNodeData().isHasSequence() ) {
+ if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getType() ) ) {
+ if ( node.getNodeData().getSequence().getType().toLowerCase()
+ .equals( PhyloXmlUtil.SEQ_TYPE_PROTEIN ) ) {
+ type = 'p';
}
- int i = -1;
- try {
- i = Integer.parseInt( index_str );
+ else {
+ type = 'n';
}
- catch ( final NumberFormatException e ) {
- JOptionPane.showMessageDialog( this,
- "Could not parse \"" + index_str
- + "\" into index for vector data",
- "Problem with Vector Data",
- JOptionPane.ERROR_MESSAGE );
- return;
+ }
+ else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
+ if ( ForesterUtil.seqIsLikelyToBeAa( node.getNodeData().getSequence().getMolecularSequence() ) ) {
+ type = 'p';
}
- if ( i < 0 ) {
- JOptionPane.showMessageDialog( this,
- "Attempt to use negative index for vector data",
- "Problem with Vector Data",
- JOptionPane.ERROR_MESSAGE );
- return;
+ else {
+ type = 'n';
}
- vector[ i ] = d;
- ++counter;
- stats.addValue( d );
}
}
- final List<Double> vector_l = new ArrayList<Double>( counter );
- for( int i = 0; i < counter; ++i ) {
- vector_l.add( vector[ i ] );
+ if ( type == '?' ) {
+ if ( SequenceAccessionTools.isProteinDbQuery( query ) ) {
+ type = 'p';
+ }
+ else {
+ type = 'n';
+ }
+ }
+ JApplet applet = null;
+ if ( isApplet() ) {
+ applet = obtainApplet();
+ }
+ try {
+ Blast.openNcbiBlastWeb( query, type == 'n', applet, this );
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ }
+ if ( Constants.ALLOW_DDBJ_BLAST ) {
+ try {
+ System.out.println( "trying: " + query );
+ final Blast s = new Blast();
+ s.ddbjBlast( query );
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ }
}
- node.getNodeData().setVector( vector_l );
}
}
- if ( stats.getN() > 0 ) {
- _statistics_for_vector_data = stats;
- }
}
- void clearCurrentExternalNodesDataBuffer() {
- setCurrentExternalNodesDataBuffer( new StringBuilder() );
+ private final int calcDynamicHidingFactor() {
+ return ( int ) ( 0.5 + ( getFontMetricsForLargeDefaultFont().getHeight() / ( 1.5 * getYdistance() ) ) );
+ }
+
+ final private int calcLengthOfLongestText() {
+ final StringBuilder sb = new StringBuilder();
+ if ( _ext_node_with_longest_txt_info != null ) {
+ nodeDataAsSB( _ext_node_with_longest_txt_info, sb );
+ if ( _ext_node_with_longest_txt_info.getNodeData().isHasTaxonomy() ) {
+ nodeTaxonomyDataAsSB( _ext_node_with_longest_txt_info.getNodeData().getTaxonomy(), sb );
+ }
+ }
+ return getFontMetricsForLargeDefaultFont().stringWidth( sb.toString() );
}
/**
- * Collapse the tree from the given node
+ * Calculate the length of the distance between the given node and its
+ * parent.
*
* @param node
- * a PhylogenyNode
+ * @param ext_node_x
+ * @factor
+ * @return the distance value
*/
- final void collapse( final PhylogenyNode node ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- JOptionPane.showMessageDialog( this,
- "Cannot collapse in unrooted display type",
- "Attempt to collapse in unrooted display",
- JOptionPane.WARNING_MESSAGE );
- return;
+ final private float calculateBranchLengthToParent( final PhylogenyNode node, final float factor ) {
+ if ( getControlPanel().isDrawPhylogram() ) {
+ if ( node.getDistanceToParent() < 0.0 ) {
+ return 0.0f;
+ }
+ return ( float ) ( getXcorrectionFactor() * node.getDistanceToParent() );
}
- if ( !node.isExternal() && !node.isRoot() ) {
- final boolean collapse = !node.isCollapse();
- TreePanelUtil.collapseSubtree( node, collapse );
- updateSetOfCollapsedExternalNodes();
- _phylogeny.recalculateNumberOfExternalDescendants( true );
- resetNodeIdToDistToLeafMap();
- calculateLongestExtNodeInfo();
- setNodeInPreorderToNull();
- _control_panel.displayedPhylogenyMightHaveChanged( true );
- resetPreferredSize();
- updateOvSizes();
- _main_panel.adjustJScrollPane();
- repaint();
+ else {
+ if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
+ return getXdistance();
+ }
+ return getXdistance() * factor;
}
}
- final void collapseSpeciesSpecificSubtrees() {
- if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
- return;
+ final private Color calculateColorForAnnotation( final SortedSet<Annotation> ann ) {
+ Color c = getTreeColorSet().getAnnotationColor();
+ if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) {
+ final StringBuilder sb = new StringBuilder();
+ for( final Annotation a : ann ) {
+ sb.append( !ForesterUtil.isEmpty( a.getRefValue() ) ? a.getRefValue() : a.getDesc() );
+ }
+ final String ann_str = sb.toString();
+ if ( !ForesterUtil.isEmpty( ann_str ) ) {
+ c = getControlPanel().getAnnotationColors().get( ann_str );
+ if ( c == null ) {
+ c = AptxUtil.calculateColorFromString( ann_str, false );
+ getControlPanel().getAnnotationColors().put( ann_str, c );
+ }
+ if ( c == null ) {
+ c = getTreeColorSet().getAnnotationColor();
+ }
+ }
}
- setWaitCursor();
- TreePanelUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
- updateSetOfCollapsedExternalNodes();
- _phylogeny.recalculateNumberOfExternalDescendants( true );
- resetNodeIdToDistToLeafMap();
- calculateLongestExtNodeInfo();
- setNodeInPreorderToNull();
- resetPreferredSize();
- _main_panel.adjustJScrollPane();
- setArrowCursor();
- repaint();
+ return c;
}
- final void colorRank( final String rank ) {
- if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
- return;
- }
- setWaitCursor();
- AptxUtil.removeBranchColors( _phylogeny );
- final int colorizations = TreePanelUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
- if ( colorizations > 0 ) {
- _control_panel.setColorBranches( true );
- if ( _control_panel.getUseVisualStylesCb() != null ) {
- _control_panel.getUseVisualStylesCb().setSelected( true );
- }
- if ( _control_panel.getColorAccSpeciesCb() != null ) {
- _control_panel.getColorAccSpeciesCb().setSelected( false );
- }
- _options.setColorLabelsSameAsParentBranch( true );
- if ( getMainPanel().getMainFrame()._color_labels_same_as_parent_branch != null ) {
- getMainPanel().getMainFrame()._color_labels_same_as_parent_branch.setSelected( true );
+ final private float calculateOvBranchLengthToParent( final PhylogenyNode node, final int factor ) {
+ if ( getControlPanel().isDrawPhylogram() ) {
+ if ( node.getDistanceToParent() < 0.0 ) {
+ return 0.0f;
}
- _control_panel.repaint();
+ return ( float ) ( getOvXcorrectionFactor() * node.getDistanceToParent() );
}
- setArrowCursor();
- repaint();
- if ( colorizations > 0 ) {
- String msg = "Taxonomy colorization via " + rank + " completed:\n";
- if ( colorizations > 1 ) {
- msg += "colorized " + colorizations + " subtrees";
- }
- else {
- msg += "colorized one subtree";
+ else {
+ if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
+ return getOvXDistance();
}
- setEdited( true );
- JOptionPane.showMessageDialog( this,
- msg,
- "Taxonomy Colorization Completed (" + rank + ")",
- JOptionPane.INFORMATION_MESSAGE );
+ return getOvXDistance() * factor;
+ }
+ }
+
+ final private void cannotOpenBrowserWarningMessage( final String type_type ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot launch web browser for " + type_type + " data of this node",
+ "Cannot launch web browser",
+ JOptionPane.WARNING_MESSAGE );
+ }
+
+ private void changeNodeFont( final PhylogenyNode node ) {
+ final FontChooser fc = new FontChooser();
+ Font f = null;
+ if ( ( node.getNodeData().getNodeVisualData() != null ) && !node.getNodeData().getNodeVisualData().isEmpty() ) {
+ f = node.getNodeData().getNodeVisualData().getFont();
+ }
+ if ( f != null ) {
+ fc.setFont( f );
}
else {
- String msg = "Could not taxonomy colorize any subtree via " + rank + ".\n";
- msg += "Possible solutions (given that suitable taxonomic information is present):\n";
- msg += "select a different rank (e.g. phylum, genus, ...)\n";
- msg += " and/or\n";
- msg += "execute:\n";
- msg += "1. \"" + MainFrameApplication.OBTAIN_DETAILED_TAXONOMIC_INFORMATION + "\" (Tools)\n";
- msg += "2. \"" + MainFrameApplication.INFER_ANCESTOR_TAXONOMIES + "\" (Analysis)";
- JOptionPane.showMessageDialog( this, msg, "Taxonomy Colorization Failed", JOptionPane.WARNING_MESSAGE );
+ fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
+ }
+ List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
+ if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
+ nodes = getFoundNodesAsListOfPhylogenyNodes();
+ }
+ if ( !nodes.contains( node ) ) {
+ nodes.add( node );
+ }
+ final int count = nodes.size();
+ String title = "Change the font for ";
+ if ( count == 1 ) {
+ title += "one node";
+ }
+ else {
+ title += ( count + " nodes" );
+ }
+ fc.showDialog( this, title );
+ if ( ( fc.getFont() != null ) && !ForesterUtil.isEmpty( fc.getFont().getFamily().trim() ) ) {
+ for( final PhylogenyNode n : nodes ) {
+ if ( n.getNodeData().getNodeVisualData() == null ) {
+ n.getNodeData().setNodeVisualData( new NodeVisualData() );
+ }
+ final NodeVisualData vd = n.getNodeData().getNodeVisualData();
+ final Font ff = fc.getFont();
+ vd.setFontName( ff.getFamily().trim() );
+ int s = ff.getSize();
+ if ( s < 0 ) {
+ s = 0;
+ }
+ if ( s > Byte.MAX_VALUE ) {
+ s = Byte.MAX_VALUE;
+ }
+ vd.setFontSize( s );
+ vd.setFontStyle( ff.getStyle() );
+ }
+ if ( _control_panel.getUseVisualStylesCb() != null ) {
+ getControlPanel().getUseVisualStylesCb().setSelected( true );
+ }
}
+ setEdited( true );
+ repaint();
}
- final void confColor() {
- if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
- return;
- }
- setWaitCursor();
- AptxUtil.removeBranchColors( _phylogeny );
- TreePanelUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
+ final private void colorizeNodes( final Color c,
+ final PhylogenyNode node,
+ final List<PhylogenyNode> additional_nodes ) {
_control_panel.setColorBranches( true );
if ( _control_panel.getUseVisualStylesCb() != null ) {
_control_panel.getUseVisualStylesCb().setSelected( true );
}
- setArrowCursor();
+ if ( node != null ) {
+ colorizeNodesHelper( c, node );
+ }
+ if ( additional_nodes != null ) {
+ for( final PhylogenyNode n : additional_nodes ) {
+ colorizeNodesHelper( c, n );
+ }
+ }
repaint();
}
- final void decreaseDomainStructureEvalueThresholdExp() {
- if ( _domain_structure_e_value_thr_exp > -20 ) {
- _domain_structure_e_value_thr_exp -= 1;
+ final private void colorizeSubtree( final Color c,
+ final PhylogenyNode node,
+ final List<PhylogenyNode> additional_nodes ) {
+ _control_panel.setColorBranches( true );
+ if ( _control_panel.getUseVisualStylesCb() != null ) {
+ _control_panel.getUseVisualStylesCb().setSelected( true );
}
- }
-
- /**
- * Find the node, if any, at the given location
- *
- * @param x
- * @param y
- * @return pointer to the node at x,y, null if not found
- */
- final PhylogenyNode findNode( final int x, final int y ) {
- if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
- return null;
+ if ( node != null ) {
+ for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
+ it.next().getBranchData().setBranchColor( new BranchColor( c ) );
+ }
}
- final int half_box_size_plus_wiggle = ( getOptions().getDefaultNodeShapeSize() / 2 ) + WIGGLE;
- for( final PhylogenyNodeIterator iter = _phylogeny.iteratorPostorder(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- if ( ( _phylogeny.isRooted() || !node.isRoot() || ( node.getNumberOfDescendants() > 2 ) )
- && ( ( node.getXcoord() - half_box_size_plus_wiggle ) <= x )
- && ( ( node.getXcoord() + half_box_size_plus_wiggle ) >= x )
- && ( ( node.getYcoord() - half_box_size_plus_wiggle ) <= y )
- && ( ( node.getYcoord() + half_box_size_plus_wiggle ) >= y ) ) {
- return node;
+ if ( additional_nodes != null ) {
+ for( final PhylogenyNode an : additional_nodes ) {
+ for( final PreorderTreeIterator it = new PreorderTreeIterator( an ); it.hasNext(); ) {
+ it.next().getBranchData().setBranchColor( new BranchColor( c ) );
+ }
}
}
- return null;
- }
-
- final Configuration getConfiguration() {
- return _configuration;
- }
-
- final ControlPanel getControlPanel() {
- return _control_panel;
- }
-
- String getCurrentExternalNodesDataBufferAsString() {
- return _current_external_nodes_data_buffer.toString();
- }
-
- int getCurrentExternalNodesDataBufferChangeCounter() {
- return _current_external_nodes_data_buffer_change_counter;
- }
-
- final int getDomainStructureEvalueThresholdExp() {
- return _domain_structure_e_value_thr_exp;
- }
-
- final Set<Long> getFoundNodes0() {
- return _found_nodes_0;
+ repaint();
}
- final Set<Long> getFoundNodes1() {
- return _found_nodes_1;
+ private void colorNodeFont( final PhylogenyNode node ) {
+ _color_chooser.setPreviewPanel( new JPanel() );
+ NodeColorizationActionListener al;
+ int count = 1;
+ if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
+ final List<PhylogenyNode> additional_nodes = getFoundNodesAsListOfPhylogenyNodes();
+ al = new NodeColorizationActionListener( _color_chooser, node, additional_nodes );
+ count = additional_nodes.size();
+ if ( !additional_nodes.contains( node ) ) {
+ count++;
+ }
+ }
+ else {
+ al = new NodeColorizationActionListener( _color_chooser, node );
+ }
+ String title = "Change the (node and font) color for ";
+ if ( count == 1 ) {
+ title += "one node";
+ }
+ else {
+ title += ( count + " nodes" );
+ }
+ final JDialog dialog = JColorChooser.createDialog( this, title, true, _color_chooser, al, null );
+ setEdited( true );
+ dialog.setVisible( true );
}
- final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) {
- if ( getControlPanel().isUseVisualStyles() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
- return ( PhylogenyMethods.getBranchColorValue( node ) );
+ final private void colorSubtree( final PhylogenyNode node ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot colorize subtree in unrooted display type",
+ "Attempt to colorize subtree in unrooted display",
+ JOptionPane.WARNING_MESSAGE );
+ return;
+ }
+ _color_chooser.setPreviewPanel( new JPanel() );
+ SubtreeColorizationActionListener al;
+ if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
+ final List<PhylogenyNode> additional_nodes = getFoundNodesAsListOfPhylogenyNodes();
+ al = new SubtreeColorizationActionListener( _color_chooser, node, additional_nodes );
}
else {
- return ( getTreeColorSet().getBranchColor() );
+ al = new SubtreeColorizationActionListener( _color_chooser, node );
}
+ final JDialog dialog = JColorChooser
+ .createDialog( this, "Subtree colorization", true, _color_chooser, al, null );
+ setEdited( true );
+ dialog.setVisible( true );
}
- final int getLongestExtNodeInfo() {
- return _longest_ext_node_info;
+ final private void copySubtree( final PhylogenyNode node ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ errorMessageNoCutCopyPasteInUnrootedDisplay();
+ return;
+ }
+ setNodeInPreorderToNull();
+ setCutOrCopiedTree( _phylogeny.copy( node ) );
+ final List<PhylogenyNode> nodes = PhylogenyMethods.getAllDescendants( node );
+ final Set<Long> node_ids = new HashSet<Long>( nodes.size() );
+ for( final PhylogenyNode n : nodes ) {
+ node_ids.add( n.getId() );
+ }
+ node_ids.add( node.getId() );
+ setCopiedAndPastedNodes( node_ids );
+ repaint();
}
- final Options getOptions() {
- if ( _options == null ) {
- _options = getControlPanel().getOptions();
+ final private String createASimpleTextRepresentationOfANode( final PhylogenyNode node ) {
+ final String tax = PhylogenyMethods.getSpecies( node );
+ String label = node.getName();
+ if ( !ForesterUtil.isEmpty( label ) && !ForesterUtil.isEmpty( tax ) ) {
+ label = label + " " + tax;
}
- return _options;
+ else if ( !ForesterUtil.isEmpty( tax ) ) {
+ label = tax;
+ }
+ else {
+ label = "";
+ }
+ if ( !ForesterUtil.isEmpty( label ) ) {
+ label = " [" + label + "]";
+ }
+ return label;
}
- final Rectangle2D getOvRectangle() {
- return _ov_rectangle;
+ final private void cutSubtree( final PhylogenyNode node ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ errorMessageNoCutCopyPasteInUnrootedDisplay();
+ return;
+ }
+ if ( node.isRoot() ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot cut entire tree as subtree",
+ "Attempt to cut entire tree",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final String label = createASimpleTextRepresentationOfANode( node );
+ final int r = JOptionPane.showConfirmDialog( null,
+ "Cut subtree" + label + "?",
+ "Confirm Cutting of Subtree",
+ JOptionPane.YES_NO_OPTION );
+ if ( r != JOptionPane.OK_OPTION ) {
+ return;
+ }
+ setNodeInPreorderToNull();
+ setCopiedAndPastedNodes( null );
+ setCutOrCopiedTree( _phylogeny.copy( node ) );
+ _phylogeny.deleteSubtree( node, true );
+ _phylogeny.clearHashIdToNodeMap();
+ _phylogeny.recalculateNumberOfExternalDescendants( true );
+ resetNodeIdToDistToLeafMap();
+ setEdited( true );
+ repaint();
}
- final Rectangle getOvVirtualRectangle() {
- return _ov_virtual_rectangle;
+ final private void cycleColors() {
+ getMainPanel().getTreeColorSet().cycleColorScheme();
+ for( final TreePanel tree_panel : getMainPanel().getTreePanels() ) {
+ tree_panel.setBackground( getMainPanel().getTreeColorSet().getBackgroundColor() );
+ }
}
- final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
- return _graphics_type;
+ final private void decreaseOvSize() {
+ if ( ( getOvMaxWidth() > 20 ) && ( getOvMaxHeight() > 20 ) ) {
+ setOvMaxWidth( getOvMaxWidth() - 5 );
+ setOvMaxHeight( getOvMaxHeight() - 5 );
+ updateOvSettings();
+ getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ }
}
- final double getStartingAngle() {
- return _urt_starting_angle;
+ final private void deleteNodeOrSubtree( final PhylogenyNode node ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ errorMessageNoCutCopyPasteInUnrootedDisplay();
+ return;
+ }
+ if ( node.isRoot() && ( node.getNumberOfDescendants() != 1 ) ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot delete entire tree",
+ "Attempt to delete entire tree",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final String label = createASimpleTextRepresentationOfANode( node );
+ final Object[] options = { "Node only", "Entire subtree", "Cancel" };
+ final int r = JOptionPane.showOptionDialog( this,
+ "Delete" + label + "?",
+ "Delete Node/Subtree",
+ JOptionPane.CLOSED_OPTION,
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ options,
+ options[ 2 ] );
+ setNodeInPreorderToNull();
+ boolean node_only = true;
+ if ( r == 1 ) {
+ node_only = false;
+ }
+ else if ( r != 0 ) {
+ return;
+ }
+ if ( node_only ) {
+ PhylogenyMethods.removeNode( node, _phylogeny );
+ }
+ else {
+ _phylogeny.deleteSubtree( node, true );
+ }
+ _phylogeny.externalNodesHaveChanged();
+ _phylogeny.clearHashIdToNodeMap();
+ _phylogeny.recalculateNumberOfExternalDescendants( true );
+ resetNodeIdToDistToLeafMap();
+ setEdited( true );
+ repaint();
}
- DescriptiveStatistics getStatisticsForExpressionValues() {
- return _statistics_for_vector_data;
+ final private void displayNodePopupMenu( final PhylogenyNode node, final int x, final int y ) {
+ makePopupMenus( node );
+ _node_popup_menu.putClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY, node );
+ _node_popup_menu.show( this, x, y );
}
- final Color getTaxonomyBasedColor( final PhylogenyNode node ) {
- if ( node.isExternal() && node.getNodeData().isHasTaxonomy() ) {
- return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() );
- }
- // return non-colorized color
- return getTreeColorSet().getTaxonomyColor();
+ final private void drawArc( final double x,
+ final double y,
+ final double width,
+ final double heigth,
+ final double start_angle,
+ final double arc_angle,
+ final Graphics2D g ) {
+ _arc.setArc( x, y, width, heigth, _180_OVER_PI * start_angle, _180_OVER_PI * arc_angle, Arc2D.OPEN );
+ g.draw( _arc );
}
- final Color getSequenceBasedColor( final PhylogenyNode node ) {
- if ( node.getNodeData().isHasSequence() ) {
- return calculateSequenceBasedColor( node.getNodeData().getSequence() );
+ final private void drawLine( final double x1, final double y1, final double x2, final double y2, final Graphics2D g ) {
+ if ( ( x1 == x2 ) && ( y1 == y2 ) ) {
+ return;
}
- // return non-colorized color
- return getTreeColorSet().getSequenceColor();
+ _line.setLine( x1, y1, x2, y2 );
+ g.draw( _line );
}
- public final TreeColorSet getTreeColorSet() {
- return getMainPanel().getTreeColorSet();
+ final private void drawOval( final double x,
+ final double y,
+ final double width,
+ final double heigth,
+ final Graphics2D g ) {
+ _ellipse.setFrame( x, y, width, heigth );
+ g.draw( _ellipse );
}
- final File getTreeFile() {
- return _treefile;
+ final private void drawOvalFilled( final double x,
+ final double y,
+ final double width,
+ final double heigth,
+ final Graphics2D g ) {
+ _ellipse.setFrame( x, y, width, heigth );
+ g.fill( _ellipse );
}
- final float getXcorrectionFactor() {
- return _x_correction_factor;
+ final private void drawOvalGradient( final float x,
+ final float y,
+ final float width,
+ final float heigth,
+ final Graphics2D g,
+ final Color color_1,
+ final Color color_2,
+ final Color color_border ) {
+ _ellipse.setFrame( x, y, width, heigth );
+ g.setPaint( new GradientPaint( x, y, color_1, ( x + width ), ( y + heigth ), color_2, false ) );
+ g.fill( _ellipse );
+ if ( color_border != null ) {
+ g.setPaint( color_border );
+ g.draw( _ellipse );
+ }
}
- final float getXdistance() {
- return _x_distance;
+ final private void drawRect( final float x, final float y, final float width, final float heigth, final Graphics2D g ) {
+ _rectangle.setFrame( x, y, width, heigth );
+ g.draw( _rectangle );
}
- final float getYdistance() {
- return _y_distance;
+ final private void drawRectFilled( final double x,
+ final double y,
+ final double width,
+ final double heigth,
+ final Graphics2D g ) {
+ _rectangle.setFrame( x, y, width, heigth );
+ g.fill( _rectangle );
}
- final void increaseDomainStructureEvalueThresholdExp() {
- if ( _domain_structure_e_value_thr_exp < 3 ) {
- _domain_structure_e_value_thr_exp += 1;
+ final private void drawRectGradient( final float x,
+ final float y,
+ final float width,
+ final float heigth,
+ final Graphics2D g,
+ final Color color_1,
+ final Color color_2,
+ final Color color_border ) {
+ _rectangle.setFrame( x, y, width, heigth );
+ g.setPaint( new GradientPaint( x, y, color_1, ( x + width ), ( y + heigth ), color_2, false ) );
+ g.fill( _rectangle );
+ if ( color_border != null ) {
+ g.setPaint( color_border );
+ g.draw( _rectangle );
}
}
- final void initNodeData() {
- if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
- return;
- }
- double _max_original_domain_structure_width = 0.0;
- for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
- if ( node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
- RenderableDomainArchitecture rds = null;
- if ( !( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
- if ( SPECIAL_DOMAIN_COLORING ) {
- rds = new RenderableDomainArchitecture( node.getNodeData().getSequence()
- .getDomainArchitecture(), node.getName() );
- }
- else {
- rds = new RenderableDomainArchitecture( node.getNodeData().getSequence()
- .getDomainArchitecture() );
- }
- node.getNodeData().getSequence().setDomainArchitecture( rds );
- }
- else {
- rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
- }
- if ( getControlPanel().isShowDomainArchitectures() ) {
- final double dsw = rds.getOriginalSize().getWidth();
- if ( dsw > _max_original_domain_structure_width ) {
- _max_original_domain_structure_width = dsw;
- }
- }
+ private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) {
+ final List<Uri> us = new ArrayList<Uri>();
+ for( final Taxonomy t : node.getNodeData().getTaxonomies() ) {
+ for( final Uri uri : t.getUris() ) {
+ us.add( uri );
}
}
- if ( getControlPanel().isShowDomainArchitectures() ) {
- final float ds_factor_width = ( float ) ( _domain_structure_width / _max_original_domain_structure_width );
- for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
- if ( node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
- final RenderableDomainArchitecture rds = ( RenderableDomainArchitecture ) node.getNodeData()
- .getSequence().getDomainArchitecture();
- rds.setRenderingFactorWidth( ds_factor_width );
- rds.setParameter( _domain_structure_e_value_thr_exp );
+ double offset = 0;
+ for( final Uri uri : us ) {
+ if ( uri != null ) {
+ final String uri_str = uri.getValue().toString().toLowerCase();
+ if ( getImageMap().containsKey( uri_str ) ) {
+ final BufferedImage bi = getImageMap().get( uri_str );
+ if ( ( bi != null ) && ( bi.getHeight() > 5 ) && ( bi.getWidth() > 5 ) ) {
+ double scaling_factor = 1;
+ if ( getOptions().isAllowMagnificationOfTaxonomyImages()
+ || ( bi.getHeight() > ( 1.8 * getYdistance() ) ) ) {
+ scaling_factor = ( 1.8 * getYdistance() ) / bi.getHeight();
+ }
+ // y = y - ( 0.9 * getYdistance() );
+ final double hs = bi.getHeight() * scaling_factor;
+ double ws = ( bi.getWidth() * scaling_factor ) + offset;
+ final double my_y = y - ( 0.5 * hs );
+ final int x_w = ( int ) ( x + ws + 0.5 );
+ final int y_h = ( int ) ( my_y + hs + 0.5 );
+ if ( ( ( x_w - x ) > 7 ) && ( ( y_h - my_y ) > 7 ) ) {
+ g.drawImage( bi,
+ ( int ) ( x + 0.5 + offset ),
+ ( int ) ( my_y + 0.5 ),
+ x_w,
+ y_h,
+ 0,
+ 0,
+ bi.getWidth(),
+ bi.getHeight(),
+ null );
+ ws += 8;
+ }
+ else {
+ ws = 0.0;
+ }
+ offset = ws;
+ }
}
}
}
+ return offset;
}
- final boolean inOv( final MouseEvent e ) {
- return ( ( e.getX() > ( getVisibleRect().x + getOvXPosition() + 1 ) )
- && ( e.getX() < ( ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() ) - 1 ) )
- && ( e.getY() > ( getVisibleRect().y + getOvYPosition() + 1 ) ) && ( e.getY() < ( ( getVisibleRect().y
- + getOvYPosition() + getOvMaxHeight() ) - 1 ) ) );
+ final private void errorMessageNoCutCopyPasteInUnrootedDisplay() {
+ JOptionPane.showMessageDialog( this,
+ "Cannot cut, copy, paste, add, or delete subtrees/nodes in unrooted display",
+ "Attempt to cut/copy/paste/add/delete in unrooted display",
+ JOptionPane.ERROR_MESSAGE );
}
- final boolean inOvRectangle( final MouseEvent e ) {
- return ( ( e.getX() >= ( getOvRectangle().getX() - 1 ) )
- && ( e.getX() <= ( getOvRectangle().getX() + getOvRectangle().getWidth() + 1 ) )
- && ( e.getY() >= ( getOvRectangle().getY() - 1 ) ) && ( e.getY() <= ( getOvRectangle().getY()
- + getOvRectangle().getHeight() + 1 ) ) );
+ private final Color getColorForFoundNode( final PhylogenyNode n ) {
+ if ( isInCurrentExternalNodes( n ) ) {
+ return getTreeColorSet().getFoundColor0();
+ }
+ else if ( isInFoundNodes0( n ) && !isInFoundNodes1( n ) ) {
+ return getTreeColorSet().getFoundColor0();
+ }
+ else if ( !isInFoundNodes0( n ) && isInFoundNodes1( n ) ) {
+ return getTreeColorSet().getFoundColor1();
+ }
+ else {
+ return getTreeColorSet().getFoundColor0and1();
+ }
}
- final boolean isApplet() {
- return getMainPanel() instanceof MainPanelApplets;
+ final private Set<Long> getCopiedAndPastedNodes() {
+ return getMainPanel().getCopiedAndPastedNodes();
}
- final boolean isCanCollapse() {
- return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
+ final private Set<Long> getCurrentExternalNodes() {
+ return _current_external_nodes;
}
- final boolean isCanColorSubtree() {
- return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
+ final private Phylogeny getCutOrCopiedTree() {
+ return getMainPanel().getCutOrCopiedTree();
}
- final boolean isCanCopy() {
- return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
+ private FontMetrics getFontMetricsForLargeDefaultFont() {
+ return getTreeFontSet().getFontMetricsLarge();
}
- final boolean isCanCut( final PhylogenyNode node ) {
- return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() && !node
- .isRoot() );
+ final private float getLastDragPointX() {
+ return _last_drag_point_x;
}
- final boolean isCanDelete() {
- return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
+ final private float getLastDragPointY() {
+ return _last_drag_point_y;
}
- final boolean isCanPaste() {
- return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable()
- && ( getCutOrCopiedTree() != null ) && !getCutOrCopiedTree().isEmpty() );
+ final private short getMaxBranchesToLeaf( final PhylogenyNode node ) {
+ if ( !_nodeid_dist_to_leaf.containsKey( node.getId() ) ) {
+ final short m = PhylogenyMethods.calculateMaxBranchesToLeaf( node );
+ _nodeid_dist_to_leaf.put( node.getId(), m );
+ return m;
+ }
+ else {
+ return _nodeid_dist_to_leaf.get( node.getId() );
+ }
}
- final boolean isCanReroot() {
- return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( _subtree_index < 1 ) );
+ final private double getMaxDistanceToRoot() {
+ if ( _max_distance_to_root < 0 ) {
+ recalculateMaxDistanceToRoot();
+ }
+ return _max_distance_to_root;
}
- final boolean isCanSubtree( final PhylogenyNode node ) {
- return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && !node.isExternal() && ( !node
- .isRoot() || ( _subtree_index > 0 ) ) );
+ final private float getOvMaxHeight() {
+ return _ov_max_height;
}
- final boolean isCurrentTreeIsSubtree() {
- return ( _subtree_index > 0 );
+ final private float getOvMaxWidth() {
+ return _ov_max_width;
}
- final boolean isEdited() {
- return _edited;
+ final private float getOvXcorrectionFactor() {
+ return _ov_x_correction_factor;
}
- final boolean isInOvRect() {
- return _in_ov_rect;
+ final private float getOvXDistance() {
+ return _ov_x_distance;
}
- final boolean isOvOn() {
- return _ov_on;
+ final private int getOvXPosition() {
+ return _ov_x_position;
}
- final boolean isPhyHasBranchLengths() {
- return _phy_has_branch_lengths;
+ final private float getOvYDistance() {
+ return _ov_y_distance;
}
- final void midpointRoot() {
- if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
- return;
- }
- if ( !_phylogeny.isRerootable() ) {
- JOptionPane.showMessageDialog( this,
- "This is not rerootable",
- "Not rerootable",
- JOptionPane.WARNING_MESSAGE );
- return;
- }
- setNodeInPreorderToNull();
- setWaitCursor();
- PhylogenyMethods.midpointRoot( _phylogeny );
- resetNodeIdToDistToLeafMap();
- setArrowCursor();
- setEdited( true );
- repaint();
+ final private int getOvYPosition() {
+ return _ov_y_position;
}
- final void mouseClicked( final MouseEvent e ) {
- if ( getOptions().isShowOverview() && isOvOn() && isInOv() ) {
- final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
- final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
- double x = ( e.getX() - getVisibleRect().x - getOvXPosition() - ( getOvRectangle().getWidth() / 2.0 ) )
- * w_ratio;
- double y = ( e.getY() - getVisibleRect().y - getOvYPosition() - ( getOvRectangle().getHeight() / 2.0 ) )
- * h_ratio;
- if ( x < 0 ) {
- x = 0;
- }
- if ( y < 0 ) {
- y = 0;
- }
- final double max_x = getWidth() - getVisibleRect().width;
- final double max_y = getHeight() - getVisibleRect().height;
- if ( x > max_x ) {
- x = max_x;
- }
- if ( y > max_y ) {
- y = max_y;
+ final private int getOvYStart() {
+ return _ov_y_start;
+ }
+
+ final private List<Accession> getPdbAccs( final PhylogenyNode node ) {
+ final List<Accession> pdb_ids = new ArrayList<Accession>();
+ if ( node.getNodeData().isHasSequence() ) {
+ final Sequence seq = node.getNodeData().getSequence();
+ if ( !ForesterUtil.isEmpty( seq.getCrossReferences() ) ) {
+ final SortedSet<Accession> cross_refs = seq.getCrossReferences();
+ for( final Accession acc : cross_refs ) {
+ if ( acc.getSource().equalsIgnoreCase( "pdb" ) ) {
+ pdb_ids.add( acc );
+ }
+ }
}
- getMainPanel().getCurrentScrollPane().getViewport()
- .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) );
- setInOvRect( true );
- repaint();
}
- else {
- final PhylogenyNode node = findNode( e.getX(), e.getY() );
- if ( node != null ) {
- if ( !node.isRoot() && node.getParent().isCollapse() ) {
- return;
- }
- _highlight_node = node;
- // Check if shift key is down
- if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) {
- // Yes, so add to _found_nodes
- if ( getFoundNodes0() == null ) {
- setFoundNodes0( new HashSet<Long>() );
- }
- getFoundNodes0().add( node.getId() );
- // Check if control key is down
- }
- else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) {
- // Yes, so pop-up menu
- displayNodePopupMenu( node, e.getX(), e.getY() );
- // Handle unadorned click
- }
- else {
- // Check for right mouse button
- if ( e.getModifiers() == 4 ) {
- displayNodePopupMenu( node, e.getX(), e.getY() );
- }
- else {
- // if not in _found_nodes, clear _found_nodes
- handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
- }
- }
- }
- else {
- // no node was clicked
- _highlight_node = null;
- }
- }
- repaint();
+ return pdb_ids;
}
- final void mouseDragInBrowserPanel( final MouseEvent e ) {
- setCursor( MOVE_CURSOR );
- final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
- scroll_position.x -= ( e.getX() - getLastDragPointX() );
- scroll_position.y -= ( e.getY() - getLastDragPointY() );
- if ( scroll_position.x < 0 ) {
- scroll_position.x = 0;
- }
- else {
- final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
- - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
- if ( scroll_position.x > max_x ) {
- scroll_position.x = max_x;
- }
- }
- if ( scroll_position.y < 0 ) {
- scroll_position.y = 0;
- }
- else {
- final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
- - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
- if ( scroll_position.y > max_y ) {
- scroll_position.y = max_y;
- }
- }
- if ( isOvOn() || getOptions().isShowScale() ) {
- repaint();
- }
- getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
+ final private double getScaleDistance() {
+ return _scale_distance;
}
- final void mouseDragInOvRectangle( final MouseEvent e ) {
- setCursor( HAND_CURSOR );
- final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
- final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
- final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
- double dx = ( ( w_ratio * e.getX() ) - ( w_ratio * getLastDragPointX() ) );
- double dy = ( ( h_ratio * e.getY() ) - ( h_ratio * getLastDragPointY() ) );
- scroll_position.x = ForesterUtil.roundToInt( scroll_position.x + dx );
- scroll_position.y = ForesterUtil.roundToInt( scroll_position.y + dy );
- if ( scroll_position.x <= 0 ) {
- scroll_position.x = 0;
- dx = 0;
- }
- else {
- final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
- - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
- if ( scroll_position.x >= max_x ) {
- dx = 0;
- scroll_position.x = max_x;
- }
- }
- if ( scroll_position.y <= 0 ) {
- dy = 0;
- scroll_position.y = 0;
- }
- else {
- final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
- - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
- if ( scroll_position.y >= max_y ) {
- dy = 0;
- scroll_position.y = max_y;
- }
- }
- repaint();
- getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
- setLastMouseDragPointX( ( float ) ( e.getX() + dx ) );
- setLastMouseDragPointY( ( float ) ( e.getY() + dy ) );
+ final private String getScaleLabel() {
+ return _scale_label;
}
- final void mouseMoved( final MouseEvent e ) {
- requestFocusInWindow();
- if ( _current_external_nodes != null ) {
- _current_external_nodes = null;
- repaint();
- }
- if ( getControlPanel().isNodeDescPopup() ) {
- if ( _node_desc_popup != null ) {
- _node_desc_popup.hide();
- _node_desc_popup = null;
- }
- }
- if ( getOptions().isShowOverview() && isOvOn() ) {
- if ( inOvVirtualRectangle( e ) ) {
- if ( !isInOvRect() ) {
- setInOvRect( true );
- repaint();
- }
- }
- else {
- if ( isInOvRect() ) {
- setInOvRect( false );
- repaint();
- }
- }
- }
- if ( inOv( e ) && getOptions().isShowOverview() && isOvOn() ) {
- if ( !isInOv() ) {
- setInOv( true );
- }
- }
- else {
- if ( isInOv() ) {
- setInOv( false );
- }
- final PhylogenyNode node = findNode( e.getX(), e.getY() );
- if ( ( node != null ) && ( node.isRoot() || !node.getParent().isCollapse() ) ) {
- if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.GET_EXT_DESC_DATA ) ) {
- for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
- addToCurrentExternalNodes( n.getId() );
- }
- setCursor( HAND_CURSOR );
- repaint();
- }
- else if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.CUT_SUBTREE )
- || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.COPY_SUBTREE )
- || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.PASTE_SUBTREE )
- || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.DELETE_NODE_OR_SUBTREE )
- || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.REROOT )
- || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.ADD_NEW_NODE ) ) {
- setCursor( CUT_CURSOR );
- }
- else {
- setCursor( HAND_CURSOR );
- if ( getControlPanel().isNodeDescPopup() ) {
- showNodeDataPopup( e, node );
- }
- }
- }
- else {
- setCursor( ARROW_CURSOR );
- }
- }
+ final private TreeFontSet getTreeFontSet() {
+ return getMainPanel().getTreeFontSet();
}
- final void mouseReleasedInBrowserPanel( final MouseEvent e ) {
- setCursor( ARROW_CURSOR );
+ final private float getUrtFactor() {
+ return _urt_factor;
}
- final void multiplyUrtFactor( final float f ) {
- _urt_factor *= f;
+ final private float getUrtFactorOv() {
+ return _urt_factor_ov;
}
- final JApplet obtainApplet() {
- return ( ( MainPanelApplets ) getMainPanel() ).getApplet();
+ final private void handleClickToAction( final NodeClickAction action, final PhylogenyNode node ) {
+ switch ( action ) {
+ case SHOW_DATA:
+ showNodeFrame( node );
+ break;
+ case COLLAPSE:
+ collapse( node );
+ break;
+ case REROOT:
+ reRoot( node );
+ break;
+ case SUBTREE:
+ subTree( node );
+ break;
+ case SWAP:
+ swap( node );
+ break;
+ case COLOR_SUBTREE:
+ colorSubtree( node );
+ break;
+ case COLOR_NODE_FONT:
+ colorNodeFont( node );
+ break;
+ case CHANGE_NODE_FONT:
+ changeNodeFont( node );
+ break;
+ case OPEN_SEQ_WEB:
+ openSeqWeb( node );
+ break;
+ case BLAST:
+ blast( node );
+ break;
+ case OPEN_TAX_WEB:
+ openTaxWeb( node );
+ break;
+ case OPEN_PDB_WEB:
+ openPdbWeb( node );
+ break;
+ case CUT_SUBTREE:
+ cutSubtree( node );
+ break;
+ case COPY_SUBTREE:
+ copySubtree( node );
+ break;
+ case PASTE_SUBTREE:
+ pasteSubtree( node );
+ break;
+ case DELETE_NODE_OR_SUBTREE:
+ deleteNodeOrSubtree( node );
+ break;
+ case ADD_NEW_NODE:
+ addEmptyNode( node );
+ break;
+ case EDIT_NODE_DATA:
+ showNodeEditFrame( node );
+ break;
+ case SELECT_NODES:
+ selectNode( node );
+ break;
+ case SORT_DESCENDENTS:
+ sortDescendants( node );
+ break;
+ case GET_EXT_DESC_DATA:
+ showExtDescNodeData( node );
+ break;
+ default:
+ throw new IllegalArgumentException( "unknown action: " + action );
+ }
}
- final void paintBranchCircular( final PhylogenyNode p,
- final PhylogenyNode c,
- final Graphics2D g,
- final boolean radial_labels,
- final boolean to_pdf,
- final boolean to_graphics_file ) {
- final double angle = _urt_nodeid_angle_map.get( c.getId() );
- final double root_x = _root.getXcoord();
- final double root_y = _root.getYcoord();
- final double dx = root_x - p.getXcoord();
- final double dy = root_y - p.getYcoord();
- final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) );
- final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
- assignGraphicsForBranchWithColorForParentBranch( c, false, g, to_pdf, to_graphics_file );
- if ( ( c.isFirstChildNode() || c.isLastChildNode() )
- && ( ( Math.abs( parent_radius * arc ) > 1.5 ) || to_pdf || to_graphics_file ) ) {
- final double r2 = 2.0 * parent_radius;
- drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
- }
- drawLine( c.getXcoord(),
- c.getYcoord(),
- root_x + ( Math.cos( angle ) * parent_radius ),
- root_y + ( Math.sin( angle ) * parent_radius ),
- g );
- paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file );
- if ( c.isExternal() ) {
- final boolean is_in_found_nodes = isInFoundNodes0( c ) || isInFoundNodes1( c )
- || isInCurrentExternalNodes( c );
- if ( ( _dynamic_hiding_factor > 1 ) && !is_in_found_nodes
- && ( ( _urt_nodeid_index_map.get( c.getId() ) % _dynamic_hiding_factor ) != 1 ) ) {
- return;
- }
- paintNodeDataUnrootedCirc( g, c, to_pdf, to_graphics_file, radial_labels, 0, is_in_found_nodes );
- }
+ final private void increaseCurrentExternalNodesDataBufferChangeCounter() {
+ _current_external_nodes_data_buffer_change_counter++;
}
- final void paintBranchCircularLite( final PhylogenyNode p, final PhylogenyNode c, final Graphics2D g ) {
- final double angle = _urt_nodeid_angle_map.get( c.getId() );
- final double root_x = _root.getXSecondary();
- final double root_y = _root.getYSecondary();
- final double dx = root_x - p.getXSecondary();
- final double dy = root_y - p.getYSecondary();
- final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
- final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) );
- g.setColor( getTreeColorSet().getOvColor() );
- if ( ( c.isFirstChildNode() || c.isLastChildNode() ) && ( Math.abs( arc ) > 0.02 ) ) {
- final double r2 = 2.0 * parent_radius;
- drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
- }
- drawLine( c.getXSecondary(),
- c.getYSecondary(),
- root_x + ( Math.cos( angle ) * parent_radius ),
- root_y + ( Math.sin( angle ) * parent_radius ),
- g );
- if ( isInFoundNodes( c ) || isInCurrentExternalNodes( c ) ) {
- g.setColor( getColorForFoundNode( c ) );
- drawRectFilled( c.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, c.getYSecondary()
- - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g );
+ final private void increaseOvSize() {
+ if ( ( getOvMaxWidth() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth() / 2 ) )
+ && ( getOvMaxHeight() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect()
+ .getHeight() / 2 ) ) ) {
+ setOvMaxWidth( getOvMaxWidth() + 5 );
+ setOvMaxHeight( getOvMaxHeight() + 5 );
+ updateOvSettings();
+ getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
}
- final void paintCircular( final Phylogeny phy,
- final double starting_angle,
- final int center_x,
- final int center_y,
- final int radius,
- final Graphics2D g,
- final boolean to_pdf,
- final boolean to_graphics_file ) {
- final int circ_num_ext_nodes = phy.getNumberOfExternalNodes() - _collapsed_external_nodeid_set.size();
- System.out.println( "# collapsed external = " + _collapsed_external_nodeid_set.size() );
- _root = phy.getRoot();
- _root.setXcoord( center_x );
- _root.setYcoord( center_y );
- final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
- double current_angle = starting_angle;
- int i = 0;
- for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
- final PhylogenyNode n = it.next();
- if ( !n.isCollapse() ) {
- n.setXcoord( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
- n.setYcoord( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
- _urt_nodeid_angle_map.put( n.getId(), current_angle );
- _urt_nodeid_index_map.put( n.getId(), i++ );
- current_angle += ( TWO_PI / circ_num_ext_nodes );
- }
- else {
- //TODO remove me
- System.out.println( "is collapse" + n.getName() );
- }
+ final private void init() {
+ _color_chooser = new JColorChooser();
+ _rollover_popup = new JTextArea();
+ _rollover_popup.setFont( POPUP_FONT );
+ resetNodeIdToDistToLeafMap();
+ setTextAntialias();
+ setTreeFile( null );
+ setEdited( false );
+ initializeOvSettings();
+ setStartingAngle( ( TWO_PI * 3 ) / 4 );
+ final ImageLoader il = new ImageLoader( this );
+ new Thread( il ).start();
+ }
+
+ final private void initializeOvSettings() {
+ setOvMaxHeight( getConfiguration().getOvMaxHeight() );
+ setOvMaxWidth( getConfiguration().getOvMaxWidth() );
+ }
+
+ final private boolean inOvVirtualRectangle( final int x, final int y ) {
+ return ( ( x >= ( getOvVirtualRectangle().x - 1 ) )
+ && ( x <= ( getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 ) )
+ && ( y >= ( getOvVirtualRectangle().y - 1 ) ) && ( y <= ( getOvVirtualRectangle().y
+ + getOvVirtualRectangle().height + 1 ) ) );
+ }
+
+ final private boolean inOvVirtualRectangle( final MouseEvent e ) {
+ return ( inOvVirtualRectangle( e.getX(), e.getY() ) );
+ }
+
+ final private boolean isCanBlast( final PhylogenyNode node ) {
+ if ( !node.getNodeData().isHasSequence() && ForesterUtil.isEmpty( node.getName() ) ) {
+ return false;
}
- paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file );
- paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file );
+ return Blast.isContainsQueryForBlast( node );
}
- final void paintCircularLite( final Phylogeny phy,
- final double starting_angle,
- final int center_x,
- final int center_y,
- final int radius,
- final Graphics2D g ) {
- final int circ_num_ext_nodes = phy.getNumberOfExternalNodes();
- _root = phy.getRoot();
- _root.setXSecondary( center_x );
- _root.setYSecondary( center_y );
- double current_angle = starting_angle;
- for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
- final PhylogenyNode n = it.next();
- n.setXSecondary( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
- n.setYSecondary( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
- _urt_nodeid_angle_map.put( n.getId(), current_angle );
- current_angle += ( TWO_PI / circ_num_ext_nodes );
+ final private String isCanOpenSeqWeb( final PhylogenyNode node ) {
+ final Accession a = SequenceAccessionTools.obtainAccessorFromDataFields( node );
+ if ( a != null ) {
+ return a.getValue();
}
- paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g );
+ return null;
}
- final void paintPhylogeny( final Graphics2D g,
- final boolean to_pdf,
- final boolean to_graphics_file,
- final int graphics_file_width,
- final int graphics_file_height,
- final int graphics_file_x,
- final int graphics_file_y ) {
- if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
- return;
+ final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
+ if ( node.getNodeData().isHasTaxonomy()
+ && ( ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
+ || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) )
+ || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node
+ .getNodeData().getTaxonomy().getIdentifier() != null ) && !ForesterUtil.isEmpty( node
+ .getNodeData().getTaxonomy().getIdentifier().getValue() ) ) ) ) {
+ return true;
}
- if ( _control_panel.isShowSequenceRelations() ) {
- _query_sequence = _control_panel.getSelectedQuerySequence();
+ else {
+ return false;
}
- // Color the background
- if ( !to_pdf ) {
- final Rectangle r = getVisibleRect();
- if ( !getOptions().isBackgroundColorGradient() || getOptions().isPrintBlackAndWhite() ) {
- g.setColor( getTreeColorSet().getBackgroundColor() );
- if ( !to_graphics_file ) {
- g.fill( r );
- }
- else {
- if ( getOptions().isPrintBlackAndWhite() ) {
- g.setColor( Color.WHITE );
- }
- g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
+ }
+
+ final private boolean isInCurrentExternalNodes( final PhylogenyNode node ) {
+ return ( ( getCurrentExternalNodes() != null ) && getCurrentExternalNodes().contains( node.getId() ) );
+ }
+
+ private boolean isInFoundNodes( final PhylogenyNode n ) {
+ return isInFoundNodes0( n ) || isInFoundNodes1( n );
+ }
+
+ final private boolean isInFoundNodes0( final PhylogenyNode node ) {
+ return ( ( getFoundNodes0() != null ) && getFoundNodes0().contains( node.getId() ) );
+ }
+
+ final private boolean isInFoundNodes1( final PhylogenyNode node ) {
+ return ( ( getFoundNodes1() != null ) && getFoundNodes1().contains( node.getId() ) );
+ }
+
+ final private boolean isInOv() {
+ return _in_ov;
+ }
+
+ final private boolean isNodeDataInvisible( final PhylogenyNode node ) {
+ int y_dist = 40;
+ if ( getControlPanel().isShowTaxonomyImages() ) {
+ y_dist = 40 + ( int ) getYdistance();
+ }
+ return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - y_dist ) )
+ || ( node.getYcoord() > ( getVisibleRect().getMaxY() + y_dist ) ) || ( ( node.getParent() != null ) && ( node
+ .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) );
+ }
+
+ final private boolean isNodeDataInvisibleUnrootedCirc( final PhylogenyNode node ) {
+ return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - 20 ) )
+ || ( node.getYcoord() > ( getVisibleRect().getMaxY() + 20 ) )
+ || ( node.getXcoord() < ( getVisibleRect().getMinX() - 20 ) ) || ( node.getXcoord() > ( getVisibleRect()
+ .getMaxX() + 20 ) ) );
+ }
+
+ final private boolean isNonLinedUpCladogram() {
+ return getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP;
+ }
+
+ final private boolean isUniformBranchLengthsForCladogram() {
+ return getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP;
+ }
+
+ final private void keyPressedCalls( final KeyEvent e ) {
+ if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) {
+ if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) {
+ if ( !isInOvRect() ) {
+ setInOvRect( true );
}
}
- else {
- if ( !to_graphics_file ) {
- g.setPaint( new GradientPaint( r.x, r.y, getTreeColorSet().getBackgroundColor(), r.x, r.y
- + r.height, getTreeColorSet().getBackgroundColorGradientBottom() ) );
- g.fill( r );
- }
- else {
- g.setPaint( new GradientPaint( graphics_file_x,
- graphics_file_y,
- getTreeColorSet().getBackgroundColor(),
- graphics_file_x,
- graphics_file_y + graphics_file_height,
- getTreeColorSet().getBackgroundColorGradientBottom() ) );
- g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
- }
+ else if ( isInOvRect() ) {
+ setInOvRect( false );
}
- setupStroke( g );
}
- else {
- g.setStroke( new BasicStroke( getOptions().getPrintLineWidth() ) );
- }
- if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
- && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
- _external_node_index = 0;
- // Position starting X of tree
- if ( !_phylogeny.isRooted() /*|| ( _subtree_index > 0 )*/) {
- _phylogeny.getRoot().setXcoord( TreePanel.MOVE );
+ if ( e.getModifiersEx() == InputEvent.CTRL_DOWN_MASK ) {
+ if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
+ || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
+ getMainPanel().getTreeFontSet().mediumFonts();
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
}
- else if ( ( _phylogeny.getRoot().getDistanceToParent() > 0.0 ) && getControlPanel().isDrawPhylogram() ) {
- _phylogeny.getRoot().setXcoord( ( float ) ( TreePanel.MOVE + ( _phylogeny.getRoot()
- .getDistanceToParent() * getXcorrectionFactor() ) ) );
+ else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
+ getMainPanel().getTreeFontSet().decreaseFontSize( 1, false );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
}
- else {
- _phylogeny.getRoot().setXcoord( TreePanel.MOVE + getXdistance() );
+ else if ( plusPressed( e.getKeyCode() ) ) {
+ getMainPanel().getTreeFontSet().increaseFontSize();
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
}
- // Position starting Y of tree
- _phylogeny.getRoot().setYcoord( ( getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes() )
- + ( TreePanel.MOVE / 2.0f ) );
- final int dynamic_hiding_factor = calcDynamicHidingFactor();
- if ( getControlPanel().isDynamicallyHideData() ) {
- if ( dynamic_hiding_factor > 1 ) {
- getControlPanel().setDynamicHidingIsOn( true );
+ }
+ else {
+ if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
+ || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
+ getControlPanel().showWhole();
+ }
+ else if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN )
+ || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) {
+ if ( e.getModifiersEx() == InputEvent.SHIFT_DOWN_MASK ) {
+ if ( e.getKeyCode() == KeyEvent.VK_UP ) {
+ getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ }
+ else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
+ getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ }
+ else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
+ getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
+ Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ }
+ else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
+ getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
+ Constants.WHEEL_ZOOM_IN_FACTOR );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ }
}
else {
- getControlPanel().setDynamicHidingIsOn( false );
+ final int d = 80;
+ int dx = 0;
+ int dy = -d;
+ if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
+ dy = d;
+ }
+ else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
+ dx = -d;
+ dy = 0;
+ }
+ else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
+ dx = d;
+ dy = 0;
+ }
+ final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
+ scroll_position.x = scroll_position.x + dx;
+ scroll_position.y = scroll_position.y + dy;
+ if ( scroll_position.x <= 0 ) {
+ scroll_position.x = 0;
+ }
+ else {
+ final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
+ - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
+ if ( scroll_position.x >= max_x ) {
+ scroll_position.x = max_x;
+ }
+ }
+ if ( scroll_position.y <= 0 ) {
+ scroll_position.y = 0;
+ }
+ else {
+ final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
+ - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
+ if ( scroll_position.y >= max_y ) {
+ scroll_position.y = max_y;
+ }
+ }
+ repaint();
+ getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
}
}
- if ( _nodes_in_preorder == null ) {
- _nodes_in_preorder = new PhylogenyNode[ _phylogeny.getNodeCount() ];
- int i = 0;
- for( final PhylogenyNodeIterator it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
- _nodes_in_preorder[ i++ ] = it.next();
- }
+ else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
+ getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
+ getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
+ Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
- final boolean disallow_shortcutting = ( dynamic_hiding_factor < 40 )
- || getControlPanel().isUseVisualStyles() || getOptions().isShowDefaultNodeShapesForMarkedNodes()
- || ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() )
- || ( ( getFoundNodes1() != null ) && !getFoundNodes1().isEmpty() )
- || ( ( getCurrentExternalNodes() != null ) && !getCurrentExternalNodes().isEmpty() )
- || to_graphics_file || to_pdf;
- for( final PhylogenyNode element : _nodes_in_preorder ) {
- paintNodeRectangular( g,
- element,
- to_pdf,
- getControlPanel().isDynamicallyHideData() && ( dynamic_hiding_factor > 1 ),
- dynamic_hiding_factor,
- to_graphics_file,
- disallow_shortcutting );
+ else if ( plusPressed( e.getKeyCode() ) ) {
+ getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
+ Constants.WHEEL_ZOOM_IN_FACTOR );
+ getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
+ getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
- if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) {
- if ( !( to_graphics_file || to_pdf ) ) {
- paintScale( g,
- getVisibleRect().x,
- getVisibleRect().y + getVisibleRect().height,
- to_pdf,
- to_graphics_file );
- }
- else {
- paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
+ else if ( e.getKeyCode() == KeyEvent.VK_S ) {
+ if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
+ || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
+ setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
+ getControlPanel().displayedPhylogenyMightHaveChanged( false );
}
}
- if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
- paintPhylogenyLite( g );
- }
- }
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- if ( getControlPanel().getDynamicallyHideData() != null ) {
- getControlPanel().setDynamicHidingIsOn( false );
- }
- final double angle = getStartingAngle();
- final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
- _dynamic_hiding_factor = 0;
- if ( getControlPanel().isDynamicallyHideData() ) {
- _dynamic_hiding_factor = ( int ) ( ( getFontMetricsForLargeDefaultFont().getHeight() * 1.5 * getPhylogeny()
- .getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) );
+ else if ( e.getKeyCode() == KeyEvent.VK_A ) {
+ if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
+ || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
+ setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
+ if ( getStartingAngle() < 0 ) {
+ setStartingAngle( TWO_PI + getStartingAngle() );
+ }
+ getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ }
}
- if ( getControlPanel().getDynamicallyHideData() != null ) {
- if ( _dynamic_hiding_factor > 1 ) {
- getControlPanel().setDynamicHidingIsOn( true );
+ else if ( e.getKeyCode() == KeyEvent.VK_D ) {
+ boolean selected = false;
+ if ( getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.HORIZONTAL ) {
+ getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
+ selected = true;
}
else {
- getControlPanel().setDynamicHidingIsOn( false );
+ getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
}
- }
- paintUnrooted( _phylogeny.getRoot(),
- angle,
- ( float ) ( angle + ( 2 * Math.PI ) ),
- radial_labels,
- g,
- to_pdf,
- to_graphics_file );
- if ( getOptions().isShowScale() ) {
- if ( !( to_graphics_file || to_pdf ) ) {
- paintScale( g,
- getVisibleRect().x,
- getVisibleRect().y + getVisibleRect().height,
- to_pdf,
- to_graphics_file );
+ if ( getMainPanel().getMainFrame() == null ) {
+ // Must be "E" applet version.
+ final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
+ if ( ae.getlabelDirectionCbmi() != null ) {
+ ae.getlabelDirectionCbmi().setSelected( selected );
+ }
}
else {
- paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
+ getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected );
}
+ repaint();
}
- if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
- g.setColor( getTreeColorSet().getOvColor() );
- paintUnrootedLite( _phylogeny.getRoot(),
- angle,
- angle + ( 2 * Math.PI ),
- g,
- ( getUrtFactorOv() / ( getVisibleRect().width / getOvMaxWidth() ) ) );
- paintOvRectangle( g );
+ else if ( e.getKeyCode() == KeyEvent.VK_X ) {
+ switchDisplaygetPhylogenyGraphicsType();
+ repaint();
}
- }
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
- final int radius = ( int ) ( ( Math.min( getPreferredSize().getWidth(), getPreferredSize().getHeight() ) / 2 ) - ( MOVE + getLongestExtNodeInfo() ) );
- final int d = radius + MOVE + getLongestExtNodeInfo();
- _dynamic_hiding_factor = 0;
- if ( getControlPanel().isDynamicallyHideData() && ( radius > 0 ) ) {
- _dynamic_hiding_factor = ( int ) ( ( getFontMetricsForLargeDefaultFont().getHeight() * 1.5 * getPhylogeny()
- .getNumberOfExternalNodes() ) / ( TWO_PI * radius ) );
+ else if ( e.getKeyCode() == KeyEvent.VK_C ) {
+ cycleColors();
+ repaint();
}
- if ( getControlPanel().getDynamicallyHideData() != null ) {
- if ( _dynamic_hiding_factor > 1 ) {
- getControlPanel().setDynamicHidingIsOn( true );
- }
- else {
- getControlPanel().setDynamicHidingIsOn( false );
- }
+ else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_O ) ) {
+ MainFrame.cycleOverview( getOptions(), this );
+ repaint();
}
- paintCircular( _phylogeny, getStartingAngle(), d, d, radius > 0 ? radius : 0, g, to_pdf, to_graphics_file );
- if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
- final int radius_ov = ( int ) ( getOvMaxHeight() < getOvMaxWidth() ? getOvMaxHeight() / 2
- : getOvMaxWidth() / 2 );
- double x_scale = 1.0;
- double y_scale = 1.0;
- int x_pos = getVisibleRect().x + getOvXPosition();
- int y_pos = getVisibleRect().y + getOvYPosition();
- if ( getWidth() > getHeight() ) {
- x_scale = ( double ) getHeight() / getWidth();
- x_pos = ForesterUtil.roundToInt( x_pos / x_scale );
- }
- else {
- y_scale = ( double ) getWidth() / getHeight();
- y_pos = ForesterUtil.roundToInt( y_pos / y_scale );
- }
- _at = g.getTransform();
- g.scale( x_scale, y_scale );
- paintCircularLite( _phylogeny,
- getStartingAngle(),
- x_pos + radius_ov,
- y_pos + radius_ov,
- ( int ) ( radius_ov - ( getLongestExtNodeInfo() / ( getVisibleRect().width / getOvRectangle()
- .getWidth() ) ) ),
- g );
- g.setTransform( _at );
- paintOvRectangle( g );
+ else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_I ) ) {
+ increaseOvSize();
}
+ else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_U ) ) {
+ decreaseOvSize();
+ }
+ e.consume();
}
}
- final void recalculateMaxDistanceToRoot() {
- _max_distance_to_root = PhylogenyMethods.calculateMaxDistanceToRoot( getPhylogeny() );
- }
-
- /**
- * Remove all edit-node frames
- */
- final void removeAllEditNodeJFrames() {
- for( int i = 0; i <= ( TreePanel.MAX_NODE_FRAMES - 1 ); i++ ) {
- if ( _node_frames[ i ] != null ) {
- _node_frames[ i ].dispose();
- _node_frames[ i ] = null;
+ final private void makePopupMenus( final PhylogenyNode node ) {
+ _node_popup_menu = new JPopupMenu();
+ final List<String> clickto_names = _main_panel.getControlPanel().getSingleClickToNames();
+ _node_popup_menu_items = new JMenuItem[ clickto_names.size() ];
+ for( int i = 0; i < clickto_names.size(); i++ ) {
+ final String title = clickto_names.get( i );
+ _node_popup_menu_items[ i ] = new JMenuItem( title );
+ if ( title.equals( Configuration.clickto_options[ Configuration.open_seq_web ][ 0 ] ) ) {
+ final String id = isCanOpenSeqWeb( node );
+ if ( !ForesterUtil.isEmpty( id ) ) {
+ _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" + id + "]" );
+ _node_popup_menu_items[ i ].setEnabled( true );
+ }
+ else {
+ _node_popup_menu_items[ i ].setEnabled( false );
+ }
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.open_pdb_web ][ 0 ] ) ) {
+ final List<Accession> accs = getPdbAccs( node );
+ _node_popup_menu_items[ i ] = new JMenuItem( title );
+ if ( !ForesterUtil.isEmpty( accs ) ) {
+ if ( accs.size() == 1 ) {
+ _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
+ + TreePanelUtil.pdbAccToString( accs, 0 ) + "]" );
+ _node_popup_menu_items[ i ].setEnabled( true );
+ }
+ else if ( accs.size() == 2 ) {
+ _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
+ + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
+ + TreePanelUtil.pdbAccToString( accs, 1 ) + "]" );
+ _node_popup_menu_items[ i ].setEnabled( true );
+ }
+ else if ( accs.size() == 3 ) {
+ _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
+ + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
+ + TreePanelUtil.pdbAccToString( accs, 1 ) + ", "
+ + TreePanelUtil.pdbAccToString( accs, 2 ) + "]" );
+ _node_popup_menu_items[ i ].setEnabled( true );
+ }
+ else {
+ _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
+ + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
+ + TreePanelUtil.pdbAccToString( accs, 1 ) + ", "
+ + TreePanelUtil.pdbAccToString( accs, 2 ) + ", + " + ( accs.size() - 3 ) + " more]" );
+ _node_popup_menu_items[ i ].setEnabled( true );
+ }
+ }
+ else {
+ _node_popup_menu_items[ i ].setEnabled( false );
+ }
+ }
+ else if ( title.startsWith( Configuration.clickto_options[ Configuration.get_ext_desc_data ][ 0 ] ) ) {
+ _node_popup_menu_items[ i ]
+ .setText( Configuration.clickto_options[ Configuration.get_ext_desc_data ][ 0 ] + ": "
+ + getOptions().getExtDescNodeDataToReturn().toString() );
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
+ _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.blast ][ 0 ] ) ) {
+ _node_popup_menu_items[ i ].setEnabled( isCanBlast( node ) );
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.delete_subtree_or_node ][ 0 ] ) ) {
+ if ( !getOptions().isEditable() ) {
+ continue;
+ }
+ _node_popup_menu_items[ i ].setEnabled( isCanDelete() );
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.cut_subtree ][ 0 ] ) ) {
+ if ( !getOptions().isEditable() ) {
+ continue;
+ }
+ _node_popup_menu_items[ i ].setEnabled( isCanCut( node ) );
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.copy_subtree ][ 0 ] ) ) {
+ if ( !getOptions().isEditable() ) {
+ continue;
+ }
+ _node_popup_menu_items[ i ].setEnabled( isCanCopy() );
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.paste_subtree ][ 0 ] ) ) {
+ if ( !getOptions().isEditable() ) {
+ continue;
+ }
+ _node_popup_menu_items[ i ].setEnabled( isCanPaste() );
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.edit_node_data ][ 0 ] ) ) {
+ if ( !getOptions().isEditable() ) {
+ continue;
+ }
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.add_new_node ][ 0 ] ) ) {
+ if ( !getOptions().isEditable() ) {
+ continue;
+ }
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.reroot ][ 0 ] ) ) {
+ _node_popup_menu_items[ i ].setEnabled( isCanReroot() );
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.collapse_uncollapse ][ 0 ] ) ) {
+ _node_popup_menu_items[ i ].setEnabled( ( isCanCollapse() && !node.isExternal() ) );
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.color_subtree ][ 0 ] ) ) {
+ _node_popup_menu_items[ i ].setEnabled( isCanColorSubtree() );
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.subtree ][ 0 ] ) ) {
+ _node_popup_menu_items[ i ].setEnabled( isCanSubtree( node ) );
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.swap ][ 0 ] ) ) {
+ _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() == 2 );
+ }
+ else if ( title.equals( Configuration.clickto_options[ Configuration.sort_descendents ][ 0 ] ) ) {
+ _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() > 1 );
}
+ _node_popup_menu_items[ i ].addActionListener( this );
+ _node_popup_menu.add( _node_popup_menu_items[ i ] );
}
- _node_frame_index = 0;
}
- /**
- * Remove a node-edit frame.
- */
- final void removeEditNodeFrame( final int i ) {
- _node_frame_index--;
- _node_frames[ i ] = null;
- if ( i < _node_frame_index ) {
- for( int j = 0; j < ( _node_frame_index - 1 ); j++ ) {
- _node_frames[ j ] = _node_frames[ j + 1 ];
+ private final void nodeDataAsSB( final PhylogenyNode node, final StringBuilder sb ) {
+ if ( node != null ) {
+ if ( getControlPanel().isShowNodeNames() && ( !ForesterUtil.isEmpty( node.getName() ) ) ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ sb.append( node.getName() );
+ }
+ if ( node.getNodeData().isHasSequence() ) {
+ if ( getControlPanel().isShowSeqSymbols()
+ && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ sb.append( node.getNodeData().getSequence().getSymbol() );
+ }
+ if ( getControlPanel().isShowGeneNames()
+ && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ sb.append( node.getNodeData().getSequence().getGeneName() );
+ }
+ if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ sb.append( node.getNodeData().getSequence().getName() );
+ }
+ if ( getControlPanel().isShowSequenceAcc()
+ && ( node.getNodeData().getSequence().getAccession() != null ) ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
+ sb.append( node.getNodeData().getSequence().getAccession().getSource() );
+ sb.append( ":" );
+ }
+ sb.append( node.getNodeData().getSequence().getAccession().getValue() );
+ }
+ }
+ if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ sb.append( propertiesToString( node ) );
}
- _node_frames[ _node_frame_index ] = null;
}
}
- final void reRoot( final PhylogenyNode node ) {
- if ( !getPhylogeny().isRerootable() ) {
- JOptionPane.showMessageDialog( this,
- "This is not rerootable",
- "Not rerootable",
- JOptionPane.WARNING_MESSAGE );
- return;
+ private final void nodeTaxonomyDataAsSB( final Taxonomy taxonomy, final StringBuilder sb ) {
+ if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
+ sb.append( taxonomy.getTaxonomyCode() );
+ sb.append( " " );
}
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- JOptionPane.showMessageDialog( this,
- "Cannot reroot in unrooted display type",
- "Attempt to reroot tree in unrooted display",
- JOptionPane.WARNING_MESSAGE );
- return;
+ if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
+ if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
+ && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
+ if ( getOptions().isAbbreviateScientificTaxonNames()
+ && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
+ abbreviateScientificName( taxonomy.getScientificName(), sb );
+ }
+ else {
+ sb.append( taxonomy.getScientificName() );
+ }
+ sb.append( " (" );
+ sb.append( taxonomy.getCommonName() );
+ sb.append( ") " );
+ }
+ else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
+ if ( getOptions().isAbbreviateScientificTaxonNames()
+ && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
+ abbreviateScientificName( taxonomy.getScientificName(), sb );
+ }
+ else {
+ sb.append( taxonomy.getScientificName() );
+ }
+ sb.append( " " );
+ }
+ else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
+ sb.append( taxonomy.getCommonName() );
+ sb.append( " " );
+ }
}
- getPhylogeny().reRoot( node );
- getPhylogeny().recalculateNumberOfExternalDescendants( true );
- resetNodeIdToDistToLeafMap();
- setNodeInPreorderToNull();
- resetPreferredSize();
- getMainPanel().adjustJScrollPane();
- setEdited( true );
- repaint();
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
- getControlPanel().showWhole();
+ else if ( _control_panel.isShowTaxonomyScientificNames() ) {
+ if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
+ if ( getOptions().isAbbreviateScientificTaxonNames()
+ && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
+ abbreviateScientificName( taxonomy.getScientificName(), sb );
+ }
+ else {
+ sb.append( taxonomy.getScientificName() );
+ }
+ sb.append( " " );
+ }
+ }
+ else if ( _control_panel.isShowTaxonomyCommonNames() ) {
+ if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
+ sb.append( taxonomy.getCommonName() );
+ sb.append( " " );
+ }
}
}
- final void resetNodeIdToDistToLeafMap() {
- _nodeid_dist_to_leaf = new HashMap<Long, Short>();
+ private final String obtainTitleForExtDescNodeData() {
+ return getOptions().getExtDescNodeDataToReturn().toString();
}
- final void resetPreferredSize() {
- if ( ( getPhylogeny() == null ) || getPhylogeny().isEmpty() ) {
- return;
- }
- int x = 0;
- int y = 0;
- y = TreePanel.MOVE
- + ForesterUtil.roundToInt( getYdistance() * getPhylogeny().getRoot().getNumberOfExternalNodes() * 2 );
- if ( getControlPanel().isDrawPhylogram() ) {
- x = TreePanel.MOVE
- + getLongestExtNodeInfo()
- + ForesterUtil
- .roundToInt( ( getXcorrectionFactor() * getPhylogeny().getHeight() ) + getXdistance() );
- }
- else {
- if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
- x = TreePanel.MOVE
- + getLongestExtNodeInfo()
- + ForesterUtil.roundToInt( getXdistance()
- * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) );
- }
- else {
- x = TreePanel.MOVE
- + getLongestExtNodeInfo()
- + ForesterUtil.roundToInt( getXdistance()
- * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) );
- }
+ final private void openPdbWeb( final PhylogenyNode node ) {
+ final List<Accession> pdb_ids = getPdbAccs( node );
+ if ( ForesterUtil.isEmpty( pdb_ids ) ) {
+ cannotOpenBrowserWarningMessage( "PDB" );
+ return;
}
- setPreferredSize( new Dimension( x, y ) );
- }
-
- final void selectNode( final PhylogenyNode node ) {
- if ( ( getFoundNodes0() != null ) && getFoundNodes0().contains( node.getId() ) ) {
- getFoundNodes0().remove( node.getId() );
- getControlPanel().setSearchFoundCountsOnLabel0( getFoundNodes0().size() );
- if ( getFoundNodes0().size() < 1 ) {
- getControlPanel().searchReset0();
+ final List<String> uri_strs = TreePanelUtil.createUrisForPdbWeb( node, pdb_ids, getConfiguration(), this );
+ if ( !ForesterUtil.isEmpty( uri_strs ) ) {
+ for( final String uri_str : uri_strs ) {
+ try {
+ AptxUtil.launchWebBrowser( new URI( uri_str ),
+ isApplet(),
+ isApplet() ? obtainApplet() : null,
+ "_aptx_seq" );
+ }
+ catch ( final IOException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
+ }
+ catch ( final URISyntaxException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
+ }
}
}
else {
- getControlPanel().getSearchFoundCountsLabel0().setVisible( true );
- getControlPanel().getSearchResetButton0().setEnabled( true );
- getControlPanel().getSearchResetButton0().setVisible( true );
- if ( getFoundNodes0() == null ) {
- setFoundNodes0( new HashSet<Long>() );
- }
- getFoundNodes0().add( node.getId() );
- getControlPanel().setSearchFoundCountsOnLabel0( getFoundNodes0().size() );
+ cannotOpenBrowserWarningMessage( "PDB" );
}
}
- final void setArrowCursor() {
- setCursor( ARROW_CURSOR );
- repaint();
- }
-
- final void setControlPanel( final ControlPanel atv_control ) {
- _control_panel = atv_control;
- }
-
- void setCurrentExternalNodesDataBuffer( final StringBuilder sb ) {
- increaseCurrentExternalNodesDataBufferChangeCounter();
- _current_external_nodes_data_buffer = sb;
- }
-
- final void setFoundNodes0( final Set<Long> found_nodes ) {
- _found_nodes_0 = found_nodes;
- }
-
- final void setFoundNodes1( final Set<Long> found_nodes ) {
- _found_nodes_1 = found_nodes;
- }
-
- final void setInOvRect( final boolean in_ov_rect ) {
- _in_ov_rect = in_ov_rect;
- }
-
- final void setLargeFonts() {
- getTreeFontSet().largeFonts();
- }
-
- final void setLastMouseDragPointX( final float x ) {
- _last_drag_point_x = x;
- }
-
- final void setLastMouseDragPointY( final float y ) {
- _last_drag_point_y = y;
- }
-
- final void setMediumFonts() {
- getTreeFontSet().mediumFonts();
- }
-
- final void setNodeInPreorderToNull() {
- _nodes_in_preorder = null;
- }
-
- final void setOvOn( final boolean ov_on ) {
- _ov_on = ov_on;
- }
-
- final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE graphics_type ) {
- _graphics_type = graphics_type;
- setTextAntialias();
- }
-
- final void setSmallFonts() {
- getTreeFontSet().smallFonts();
- }
-
- final void setStartingAngle( final double starting_angle ) {
- _urt_starting_angle = starting_angle;
- }
-
- void setStatisticsForExpressionValues( final DescriptiveStatistics statistics_for_expression_values ) {
- _statistics_for_vector_data = statistics_for_expression_values;
- }
-
- final void setSuperTinyFonts() {
- getTreeFontSet().superTinyFonts();
- }
-
- final void setTextAntialias() {
- if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
- if ( _phylogeny.getNumberOfExternalNodes() <= LIMIT_FOR_HQ_RENDERING ) {
- _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY );
+ final private void openSeqWeb( final PhylogenyNode node ) {
+ if ( ForesterUtil.isEmpty( isCanOpenSeqWeb( node ) ) ) {
+ cannotOpenBrowserWarningMessage( "sequence" );
+ return;
+ }
+ final String uri_str = TreePanelUtil.createUriForSeqWeb( node, getConfiguration(), this );
+ if ( !ForesterUtil.isEmpty( uri_str ) ) {
+ try {
+ AptxUtil.launchWebBrowser( new URI( uri_str ),
+ isApplet(),
+ isApplet() ? obtainApplet() : null,
+ "_aptx_seq" );
}
- else {
- _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED );
+ catch ( final IOException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
+ }
+ catch ( final URISyntaxException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
}
- }
- if ( getMainPanel().getOptions().isAntialiasScreen() ) {
- _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
- // try {
- _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB );
- // }
- // catch ( final Throwable e ) {
- // _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_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 );
+ cannotOpenBrowserWarningMessage( "sequence" );
}
}
- final void setTinyFonts() {
- getTreeFontSet().tinyFonts();
- }
-
- final void setTreeFile( final File treefile ) {
- _treefile = treefile;
- }
-
- final void setXcorrectionFactor( final float f ) {
- _x_correction_factor = f;
- }
-
- final void setXdistance( final float x ) {
- _x_distance = x;
- }
-
- final void setYdistance( final float y ) {
- _y_distance = y;
- }
-
- final void sortDescendants( final PhylogenyNode node ) {
- if ( !node.isExternal() ) {
- DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
- if ( getControlPanel().isShowTaxonomyScientificNames() || getControlPanel().isShowTaxonomyCode() ) {
- pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
+ final private void openTaxWeb( final PhylogenyNode node ) {
+ if ( !isCanOpenTaxWeb( node ) ) {
+ cannotOpenBrowserWarningMessage( "taxonomic" );
+ return;
+ }
+ String uri_str = null;
+ final Taxonomy tax = node.getNodeData().getTaxonomy();
+ if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
+ && tax.getIdentifier().getValue().startsWith( "http://" ) ) {
+ try {
+ uri_str = new URI( tax.getIdentifier().getValue() ).toString();
}
- else if ( getControlPanel().isShowSeqNames() || getControlPanel().isShowSeqSymbols()
- || getControlPanel().isShowGeneNames() ) {
- pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
+ catch ( final URISyntaxException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ uri_str = null;
+ e.printStackTrace();
}
- PhylogenyMethods.sortNodeDescendents( node, pri );
- setNodeInPreorderToNull();
- _phylogeny.externalNodesHaveChanged();
- _phylogeny.clearHashIdToNodeMap();
- _phylogeny.recalculateNumberOfExternalDescendants( true );
- resetNodeIdToDistToLeafMap();
- setEdited( true );
}
- repaint();
- }
-
- final void subTree( final PhylogenyNode node ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- JOptionPane.showMessageDialog( this,
- "Cannot get a sub/super tree in unrooted display",
- "Attempt to get sub/super tree in unrooted display",
- JOptionPane.WARNING_MESSAGE );
- return;
+ else if ( ( tax.getIdentifier() != null )
+ && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
+ && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() )
+ && ( tax.getIdentifier().getProvider().equalsIgnoreCase( "ncbi" ) || tax.getIdentifier().getProvider()
+ .equalsIgnoreCase( "uniprot" ) ) ) {
+ try {
+ uri_str = "http://www.uniprot.org/taxonomy/"
+ + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
+ }
+ catch ( final UnsupportedEncodingException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
+ }
}
- if ( node.isExternal() ) {
- JOptionPane.showMessageDialog( this,
- "Cannot get a subtree of a external node",
- "Attempt to get subtree of external node",
- JOptionPane.WARNING_MESSAGE );
- return;
+ else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
+ try {
+ uri_str = "http://www.uniprot.org/taxonomy/?query="
+ + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
+ }
+ catch ( final UnsupportedEncodingException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
+ }
}
- if ( node.isRoot() && !isCurrentTreeIsSubtree() ) {
- JOptionPane.showMessageDialog( this,
- "Cannot get a subtree of the root node",
- "Attempt to get subtree of root node",
- JOptionPane.WARNING_MESSAGE );
- return;
- }
- setNodeInPreorderToNull();
- if ( !node.isExternal() && !node.isRoot() && ( _subtree_index <= ( TreePanel.MAX_SUBTREES - 1 ) ) ) {
- _sub_phylogenies[ _subtree_index ] = _phylogeny;
- _sub_phylogenies_temp_roots[ _subtree_index ] = node;
- ++_subtree_index;
- _phylogeny = TreePanelUtil.subTree( node, _phylogeny );
- updateSubSuperTreeButton();
- }
- else if ( node.isRoot() && isCurrentTreeIsSubtree() ) {
- superTree();
- }
- _main_panel.getControlPanel().showWhole();
- repaint();
- }
-
- final void superTree() {
- setNodeInPreorderToNull();
- final PhylogenyNode temp_root = _sub_phylogenies_temp_roots[ _subtree_index - 1 ];
- for( final PhylogenyNode n : temp_root.getDescendants() ) {
- n.setParent( temp_root );
+ else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
+ try {
+ uri_str = "http://www.uniprot.org/taxonomy/?query="
+ + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 );
+ }
+ catch ( final UnsupportedEncodingException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
+ }
}
- _sub_phylogenies[ _subtree_index ] = null;
- _sub_phylogenies_temp_roots[ _subtree_index ] = null;
- _phylogeny = _sub_phylogenies[ --_subtree_index ];
- updateSubSuperTreeButton();
- }
-
- final void swap( final PhylogenyNode node ) {
- if ( node.isExternal() || ( node.getNumberOfDescendants() < 2 ) ) {
- return;
+ else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
+ try {
+ uri_str = "http://www.uniprot.org/taxonomy/?query="
+ + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
+ }
+ catch ( final UnsupportedEncodingException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
+ }
}
- if ( node.getNumberOfDescendants() > 2 ) {
- JOptionPane.showMessageDialog( this,
- "Cannot swap descendants of nodes with more than 2 descendants",
- "Cannot swap descendants",
- JOptionPane.ERROR_MESSAGE );
- return;
+ if ( !ForesterUtil.isEmpty( uri_str ) ) {
+ try {
+ AptxUtil.launchWebBrowser( new URI( uri_str ),
+ isApplet(),
+ isApplet() ? obtainApplet() : null,
+ "_aptx_tax" );
+ }
+ catch ( final IOException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
+ }
+ catch ( final URISyntaxException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
+ }
}
- if ( !node.isExternal() ) {
- node.swapChildren();
- setNodeInPreorderToNull();
- _phylogeny.externalNodesHaveChanged();
- _phylogeny.clearHashIdToNodeMap();
- _phylogeny.recalculateNumberOfExternalDescendants( true );
- resetNodeIdToDistToLeafMap();
- setEdited( true );
+ else {
+ cannotOpenBrowserWarningMessage( "taxonomic" );
}
- repaint();
}
- final void taxColor() {
- if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
- return;
- }
- setWaitCursor();
- TreePanelUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
- _control_panel.setColorBranches( true );
- if ( _control_panel.getUseVisualStylesCb() != null ) {
- _control_panel.getUseVisualStylesCb().setSelected( true );
+ final private void paintBranchLength( final Graphics2D g,
+ final PhylogenyNode node,
+ final boolean to_pdf,
+ final boolean to_graphics_file ) {
+ g.setFont( getTreeFontSet().getSmallFont() );
+ if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
+ g.setColor( Color.BLACK );
}
- setEdited( true );
- setArrowCursor();
- repaint();
- }
-
- final void updateOvSettings() {
- switch ( getOptions().getOvPlacement() ) {
- case LOWER_LEFT:
- setOvXPosition( OV_BORDER );
- setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
- setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
- break;
- case LOWER_RIGHT:
- setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
- setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
- setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
- break;
- case UPPER_RIGHT:
- setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
- setOvYPosition( OV_BORDER );
- setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
- break;
- default:
- setOvXPosition( OV_BORDER );
- setOvYPosition( OV_BORDER );
- setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
- break;
+ else {
+ g.setColor( getTreeColorSet().getBranchLengthColor() );
}
- }
-
- final void updateOvSizes() {
- if ( ( getWidth() > ( 1.05 * getVisibleRect().width ) ) || ( getHeight() > ( 1.05 * getVisibleRect().height ) ) ) {
- setOvOn( true );
- float l = getLongestExtNodeInfo();
- final float w_ratio = getOvMaxWidth() / getWidth();
- l *= w_ratio;
- final int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
- setOvYDistance( getOvMaxHeight() / ( 2 * ext_nodes ) );
- float ov_xdist = 0;
- if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
- ov_xdist = ( ( getOvMaxWidth() - l ) / ( ext_nodes ) );
- }
- else {
- ov_xdist = ( ( getOvMaxWidth() - l ) / ( PhylogenyMethods.calculateMaxDepth( _phylogeny ) ) );
- }
- float ydist = ( float ) ( ( getOvMaxWidth() / ( ext_nodes * 2.0 ) ) );
- if ( ov_xdist < 0.0 ) {
- ov_xdist = 0.0f;
- }
- if ( ydist < 0.0 ) {
- ydist = 0.0f;
+ if ( !node.isRoot() ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
+ TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
+ .getXcoord() + EURO_D, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g );
}
- setOvXDistance( ov_xdist );
- final double height = _phylogeny.getHeight();
- if ( height > 0 ) {
- final float ov_corr = ( float ) ( ( ( getOvMaxWidth() - l ) - getOvXDistance() ) / height );
- setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
+ TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
+ .getXcoord() + ROUNDED_D, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g );
}
else {
- setOvXcorrectionFactor( 0 );
+ TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
+ .getXcoord() + 3, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g );
}
}
else {
- setOvOn( false );
+ TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), 3, node.getYcoord()
+ - getTreeFontSet().getSmallMaxDescent(), g );
}
}
- void updateSetOfCollapsedExternalNodes() {
- final Phylogeny phy = getPhylogeny();
- _collapsed_external_nodeid_set.clear();
- if ( phy != null ) {
- E: for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
- final PhylogenyNode ext_node = it.next();
- PhylogenyNode n = ext_node;
- while ( !n.isRoot() ) {
- if ( n.isCollapse() ) {
- _collapsed_external_nodeid_set.add( ext_node.getId() );
- ext_node.setCollapse( true );
- continue E;
- }
- n = n.getParent();
- }
- }
+ final private void paintBranchLite( final Graphics2D g,
+ final float x1,
+ final float x2,
+ final float y1,
+ final float y2,
+ final PhylogenyNode node ) {
+ g.setColor( getTreeColorSet().getOvColor() );
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
+ drawLine( x1, y1, x2, y2, g );
}
- }
-
- final void updateSubSuperTreeButton() {
- if ( _subtree_index < 1 ) {
- getControlPanel().deactivateButtonToReturnToSuperTree();
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
+ _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
+ ( g ).draw( _quad_curve );
+ }
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
+ final float dx = x2 - x1;
+ final float dy = y2 - y1;
+ _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
+ + ( dy * 0.8f ), x2, y2 );
+ ( g ).draw( _cubic_curve );
}
else {
- getControlPanel().activateButtonToReturnToSuperTree( _subtree_index );
+ final float x2a = x2;
+ final float x1a = x1;
+ // draw the vertical line
+ if ( node.isFirstChildNode() || node.isLastChildNode() ) {
+ drawLine( x1, y1, x1, y2, g );
+ }
+ // draw the horizontal line
+ drawLine( x1a, y2, x2a, y2, g );
}
}
- final void zoomInDomainStructure() {
- if ( _domain_structure_width < 2000 ) {
- _domain_structure_width *= 1.2;
+ /**
+ * Paint a branch which consists of a vertical and a horizontal bar
+ * @param is_ind_found_nodes
+ */
+ final private void paintBranchRectangular( final Graphics2D g,
+ final float x1,
+ final float x2,
+ final float y1,
+ final float y2,
+ final PhylogenyNode node,
+ final boolean to_pdf,
+ final boolean to_graphics_file ) {
+ assignGraphicsForBranchWithColorForParentBranch( node, false, g, to_pdf, to_graphics_file );
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
+ drawLine( x1, y1, x2, y2, g );
}
- }
-
- final void zoomOutDomainStructure() {
- if ( _domain_structure_width > 20 ) {
- _domain_structure_width *= 0.8;
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
+ _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
+ g.draw( _quad_curve );
}
- }
-
- private void abbreviateScientificName( final String sn, final StringBuilder sb ) {
- final String[] a = sn.split( "\\s+" );
- sb.append( a[ 0 ].substring( 0, 1 ) );
- sb.append( a[ 1 ].substring( 0, 2 ) );
- if ( a.length > 2 ) {
- for( int i = 2; i < a.length; i++ ) {
- sb.append( " " );
- sb.append( a[ i ] );
- }
- }
- }
-
- final private void addEmptyNode( final PhylogenyNode node ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- errorMessageNoCutCopyPasteInUnrootedDisplay();
- return;
- }
- final String label = createASimpleTextRepresentationOfANode( node );
- String msg = "";
- if ( ForesterUtil.isEmpty( label ) ) {
- msg = "How to add the new, empty node?";
- }
- else {
- msg = "How to add the new, empty node to node" + label + "?";
- }
- final Object[] options = { "As sibling", "As descendant", "Cancel" };
- final int r = JOptionPane.showOptionDialog( this,
- msg,
- "Addition of Empty New Node",
- JOptionPane.CLOSED_OPTION,
- JOptionPane.QUESTION_MESSAGE,
- null,
- options,
- options[ 2 ] );
- boolean add_as_sibling = true;
- if ( r == 1 ) {
- add_as_sibling = false;
- }
- else if ( r != 0 ) {
- return;
- }
- final Phylogeny phy = new Phylogeny();
- phy.setRoot( new PhylogenyNode() );
- phy.setRooted( true );
- if ( add_as_sibling ) {
- if ( node.isRoot() ) {
- JOptionPane.showMessageDialog( this,
- "Cannot add sibling to root",
- "Attempt to add sibling to root",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- phy.addAsSibling( node );
- }
- else {
- phy.addAsChild( node );
- }
- setNodeInPreorderToNull();
- _phylogeny.externalNodesHaveChanged();
- _phylogeny.clearHashIdToNodeMap();
- _phylogeny.recalculateNumberOfExternalDescendants( true );
- resetNodeIdToDistToLeafMap();
- setEdited( true );
- repaint();
- }
-
- final private void addToCurrentExternalNodes( final long i ) {
- if ( _current_external_nodes == null ) {
- _current_external_nodes = new HashSet<Long>();
- }
- _current_external_nodes.add( i );
- }
-
- final private void assignGraphicsForBranchWithColorForParentBranch( final PhylogenyNode node,
- final boolean is_vertical,
- final Graphics g,
- final boolean to_pdf,
- final boolean to_graphics_file ) {
- final NodeClickAction action = _control_panel.getActionWhenNodeClicked();
- if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- g.setColor( Color.BLACK );
- }
- else if ( ( ( action == NodeClickAction.COPY_SUBTREE ) || ( action == NodeClickAction.CUT_SUBTREE )
- || ( action == NodeClickAction.DELETE_NODE_OR_SUBTREE ) || ( action == NodeClickAction.PASTE_SUBTREE ) || ( action == NodeClickAction.ADD_NEW_NODE ) )
- && ( getCutOrCopiedTree() != null )
- && ( getCopiedAndPastedNodes() != null )
- && !to_pdf
- && !to_graphics_file && getCopiedAndPastedNodes().contains( node.getId() ) ) {
- g.setColor( getTreeColorSet().getFoundColor0() );
- }
- else if ( getControlPanel().isUseVisualStyles() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
- g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
- }
- else if ( to_pdf ) {
- g.setColor( getTreeColorSet().getBranchColorForPdf() );
- }
- else {
- g.setColor( getTreeColorSet().getBranchColor() );
- }
- }
-
- final private void blast( final PhylogenyNode node ) {
- if ( !isCanBlast( node ) ) {
- JOptionPane.showMessageDialog( this,
- "Insufficient information present",
- "Cannot Blast",
- JOptionPane.INFORMATION_MESSAGE );
- return;
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
+ final float dx = x2 - x1;
+ final float dy = y2 - y1;
+ _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
+ + ( dy * 0.8f ), x2, y2 );
+ g.draw( _cubic_curve );
}
else {
- final String query = Blast.obtainQueryForBlast( node );
- System.out.println( "query for BLAST is: " + query );
- char type = '?';
- if ( !ForesterUtil.isEmpty( query ) ) {
- if ( node.getNodeData().isHasSequence() ) {
- if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getType() ) ) {
- if ( node.getNodeData().getSequence().getType().toLowerCase()
- .equals( PhyloXmlUtil.SEQ_TYPE_PROTEIN ) ) {
- type = 'p';
- }
- else {
- type = 'n';
+ final float x2a = x2;
+ final float x1a = x1;
+ float y2_r = 0;
+ if ( node.isFirstChildNode() || node.isLastChildNode()
+ || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
+ || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
+ if ( !to_graphics_file
+ && !to_pdf
+ && ( ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) && ( y1 < ( getVisibleRect().getMinY() - 20 ) ) ) || ( ( y2 > ( getVisibleRect()
+ .getMaxY() + 20 ) ) && ( y1 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) ) {
+ // Do nothing.
+ }
+ else {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
+ float x2c = x1 + EURO_D;
+ if ( x2c > x2a ) {
+ x2c = x2a;
}
+ drawLine( x1, y1, x2c, y2, g );
}
- else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
- if ( ForesterUtil.seqIsLikelyToBeAa( node.getNodeData().getSequence().getMolecularSequence() ) ) {
- type = 'p';
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
+ if ( y2 > y1 ) {
+ y2_r = y2 - ROUNDED_D;
+ if ( y2_r < y1 ) {
+ y2_r = y1;
+ }
+ drawLine( x1, y1, x1, y2_r, g );
}
else {
- type = 'n';
+ y2_r = y2 + ROUNDED_D;
+ if ( y2_r > y1 ) {
+ y2_r = y1;
+ }
+ drawLine( x1, y1, x1, y2_r, g );
}
}
- }
- if ( type == '?' ) {
- if ( SequenceAccessionTools.isProteinDbQuery( query ) ) {
- type = 'p';
- }
else {
- type = 'n';
+ drawLine( x1, y1, x1, y2, g );
}
}
- JApplet applet = null;
- if ( isApplet() ) {
- applet = obtainApplet();
+ }
+ // draw the horizontal line
+ if ( !to_graphics_file && !to_pdf
+ && ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) || ( y2 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) {
+ return;
+ }
+ float x1_r = 0;
+ if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
+ x1_r = x1a + ROUNDED_D;
+ if ( x1_r < x2a ) {
+ drawLine( x1_r, y2, x2a, y2, g );
+ }
}
- try {
- Blast.openNcbiBlastWeb( query, type == 'n', applet, this );
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
+ final float x1c = x1a + EURO_D;
+ if ( x1c < x2a ) {
+ drawLine( x1c, y2, x2a, y2, g );
+ }
}
- catch ( final Exception e ) {
- e.printStackTrace();
+ else {
+ drawLine( x1a, y2, x2a, y2, g );
}
- if ( Constants.ALLOW_DDBJ_BLAST ) {
- try {
- System.out.println( "trying: " + query );
- final Blast s = new Blast();
- s.ddbjBlast( query );
+ }
+ else {
+ final double w = PhylogenyMethods.getBranchWidthValue( node );
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
+ x1_r = x1a + ROUNDED_D;
+ if ( x1_r < x2a ) {
+ drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );
}
- catch ( final Exception e ) {
- e.printStackTrace();
+ }
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
+ final float x1c = x1a + EURO_D;
+ if ( x1c < x2a ) {
+ drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );
}
}
+ else {
+ drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
+ }
+ }
+ if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
+ if ( x1_r > x2a ) {
+ x1_r = x2a;
+ }
+ if ( y2 > y2_r ) {
+ final double diff = y2 - y2_r;
+ _arc.setArc( x1, y2_r - diff, 2 * ( x1_r - x1 ), 2 * diff, 180, 90, Arc2D.OPEN );
+ }
+ else {
+ _arc.setArc( x1, y2, 2 * ( x1_r - x1 ), 2 * ( y2_r - y2 ), 90, 90, Arc2D.OPEN );
+ }
+ g.draw( _arc );
}
}
+ if ( node.isExternal() ) {
+ paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file );
+ }
}
- private final int calcDynamicHidingFactor() {
- return ( int ) ( 0.5 + ( getFontMetricsForLargeDefaultFont().getHeight() / ( 1.5 * getYdistance() ) ) );
- }
-
- /**
- * Calculate the length of the distance between the given node and its
- * parent.
- *
- * @param node
- * @param ext_node_x
- * @factor
- * @return the distance value
- */
- final private float calculateBranchLengthToParent( final PhylogenyNode node, final float factor ) {
- if ( getControlPanel().isDrawPhylogram() ) {
- if ( node.getDistanceToParent() < 0.0 ) {
- return 0.0f;
+ final private double paintCirculars( final PhylogenyNode n,
+ final Phylogeny phy,
+ final float center_x,
+ final float center_y,
+ final double radius,
+ final boolean radial_labels,
+ final Graphics2D g,
+ final boolean to_pdf,
+ final boolean to_graphics_file ) {
+ if ( n.isExternal() || n.isCollapse() ) { //~~circ collapse
+ if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) {
+ System.out.println( "no " + n + " =====>>>>>>> ERROR!" );//TODO
}
- return ( float ) ( getXcorrectionFactor() * node.getDistanceToParent() );
+ return _urt_nodeid_angle_map.get( n.getId() );
}
else {
- if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
- return getXdistance();
- }
- return getXdistance() * factor;
- }
- }
-
- final private Color calculateColorForAnnotation( final SortedSet<Annotation> ann ) {
- Color c = getTreeColorSet().getAnnotationColor();
- if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) {
- final StringBuilder sb = new StringBuilder();
- for( final Annotation a : ann ) {
- sb.append( !ForesterUtil.isEmpty( a.getRefValue() ) ? a.getRefValue() : a.getDesc() );
+ final List<PhylogenyNode> descs = n.getDescendants();
+ double sum = 0;
+ for( final PhylogenyNode desc : descs ) {
+ sum += paintCirculars( desc,
+ phy,
+ center_x,
+ center_y,
+ radius,
+ radial_labels,
+ g,
+ to_pdf,
+ to_graphics_file );
}
- final String ann_str = sb.toString();
- if ( !ForesterUtil.isEmpty( ann_str ) ) {
- c = getControlPanel().getAnnotationColors().get( ann_str );
- if ( c == null ) {
- c = AptxUtil.calculateColorFromString( ann_str, false );
- getControlPanel().getAnnotationColors().put( ann_str, c );
- }
- if ( c == null ) {
- c = getTreeColorSet().getAnnotationColor();
- }
+ double r = 0;
+ if ( !n.isRoot() ) {
+ r = 1 - ( ( ( double ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );
+ }
+ final double theta = sum / descs.size();
+ n.setXcoord( ( float ) ( center_x + ( r * radius * Math.cos( theta ) ) ) );
+ n.setYcoord( ( float ) ( center_y + ( r * radius * Math.sin( theta ) ) ) );
+ _urt_nodeid_angle_map.put( n.getId(), theta );
+ for( final PhylogenyNode desc : descs ) {
+ paintBranchCircular( n, desc, g, radial_labels, to_pdf, to_graphics_file );
}
+ return theta;
}
- return c;
}
- final private float calculateOvBranchLengthToParent( final PhylogenyNode node, final int factor ) {
- if ( getControlPanel().isDrawPhylogram() ) {
- if ( node.getDistanceToParent() < 0.0 ) {
- return 0.0f;
- }
- return ( float ) ( getOvXcorrectionFactor() * node.getDistanceToParent() );
+ final private void paintCircularsLite( final PhylogenyNode n,
+ final Phylogeny phy,
+ final int center_x,
+ final int center_y,
+ final int radius,
+ final Graphics2D g ) {
+ if ( n.isExternal() ) {
+ return;
}
else {
- if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
- return getOvXDistance();
+ final List<PhylogenyNode> descs = n.getDescendants();
+ for( final PhylogenyNode desc : descs ) {
+ paintCircularsLite( desc, phy, center_x, center_y, radius, g );
+ }
+ float r = 0;
+ if ( !n.isRoot() ) {
+ r = 1 - ( ( ( float ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );
+ }
+ final double theta = _urt_nodeid_angle_map.get( n.getId() );
+ n.setXSecondary( ( float ) ( center_x + ( radius * r * Math.cos( theta ) ) ) );
+ n.setYSecondary( ( float ) ( center_y + ( radius * r * Math.sin( theta ) ) ) );
+ for( final PhylogenyNode desc : descs ) {
+ paintBranchCircularLite( n, desc, g );
}
- return getOvXDistance() * factor;
}
}
- final private void cannotOpenBrowserWarningMessage( final String type_type ) {
- JOptionPane.showMessageDialog( this,
- "Cannot launch web browser for " + type_type + " data of this node",
- "Cannot launch web browser",
- JOptionPane.WARNING_MESSAGE );
- }
-
- private void changeNodeFont( final PhylogenyNode node ) {
- final FontChooser fc = new FontChooser();
- Font f = null;
- if ( ( node.getNodeData().getNodeVisualData() != null ) && !node.getNodeData().getNodeVisualData().isEmpty() ) {
- f = node.getNodeData().getNodeVisualData().getFont();
- }
- if ( f != null ) {
- fc.setFont( f );
+ final private void paintCollapsedNode( final Graphics2D g,
+ final PhylogenyNode node,
+ final boolean to_graphics_file,
+ final boolean to_pdf,
+ final boolean is_in_found_nodes ) {
+ Color c = null;
+ if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
+ c = Color.BLACK;
}
- else {
- fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
+ else if ( is_in_found_nodes ) {
+ c = getColorForFoundNode( node );
}
- List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
- if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
- nodes = getFoundNodesAsListOfPhylogenyNodes();
+ else if ( getControlPanel().isColorAccordingToSequence() ) {
+ c = getSequenceBasedColor( node );
}
- if ( !nodes.contains( node ) ) {
- nodes.add( node );
+ else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
+ c = getTaxonomyBasedColor( node );
}
- final int count = nodes.size();
- String title = "Change the font for ";
- if ( count == 1 ) {
- title += "one node";
+ else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isUseVisualStyles()
+ && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
+ c = PhylogenyMethods.getBranchColorValue( node );
}
else {
- title += ( count + " nodes" );
- }
- fc.showDialog( this, title );
- if ( ( fc.getFont() != null ) && !ForesterUtil.isEmpty( fc.getFont().getFamily().trim() ) ) {
- for( final PhylogenyNode n : nodes ) {
- if ( n.getNodeData().getNodeVisualData() == null ) {
- n.getNodeData().setNodeVisualData( new NodeVisualData() );
- }
- final NodeVisualData vd = n.getNodeData().getNodeVisualData();
- final Font ff = fc.getFont();
- vd.setFontName( ff.getFamily().trim() );
- int s = ff.getSize();
- if ( s < 0 ) {
- s = 0;
- }
- if ( s > Byte.MAX_VALUE ) {
- s = Byte.MAX_VALUE;
- }
- vd.setFontSize( s );
- vd.setFontStyle( ff.getStyle() );
- }
- if ( _control_panel.getUseVisualStylesCb() != null ) {
- getControlPanel().getUseVisualStylesCb().setSelected( true );
- }
+ c = getTreeColorSet().getCollapseFillColor();
}
- setEdited( true );
- repaint();
- }
-
- private void colorNodeFont( final PhylogenyNode node ) {
- _color_chooser.setPreviewPanel( new JPanel() );
- NodeColorizationActionListener al;
- int count = 1;
- if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
- final List<PhylogenyNode> additional_nodes = getFoundNodesAsListOfPhylogenyNodes();
- al = new NodeColorizationActionListener( _color_chooser, node, additional_nodes );
- count = additional_nodes.size();
- if ( !additional_nodes.contains( node ) ) {
- count++;
- }
+ double d = node.getAllExternalDescendants().size();
+ if ( d > 1000 ) {
+ d = ( 3 * _y_distance ) / 3;
}
else {
- al = new NodeColorizationActionListener( _color_chooser, node );
- }
- String title = "Change the (node and font) color for ";
- if ( count == 1 ) {
- title += "one node";
+ d = ( Math.log10( d ) * _y_distance ) / 2.5;
}
- else {
- title += ( count + " nodes" );
+ final int box_size = getOptions().getDefaultNodeShapeSize() + 1;
+ if ( d < box_size ) {
+ d = box_size;
}
- final JDialog dialog = JColorChooser.createDialog( this, title, true, _color_chooser, al, null );
- setEdited( true );
- dialog.setVisible( true );
- }
-
- final private void colorizeNodes( final Color c,
- final PhylogenyNode node,
- final List<PhylogenyNode> additional_nodes ) {
- _control_panel.setColorBranches( true );
- if ( _control_panel.getUseVisualStylesCb() != null ) {
- _control_panel.getUseVisualStylesCb().setSelected( true );
+ final float xx = node.getXcoord() - ( 2 * box_size );
+ final float xxx = xx > ( node.getParent().getXcoord() + 1 ) ? xx : node.getParent().getXcoord() + 1;
+ _polygon.reset();
+ _polygon.moveTo( xxx, node.getYcoord() );
+ _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() - d );
+ _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() + d );
+ _polygon.closePath();
+ if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.SOLID ) {
+ g.setColor( c );
+ g.fill( _polygon );
}
- if ( node != null ) {
- colorizeNodesHelper( c, node );
+ else if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.NONE ) {
+ g.setColor( getBackground() );
+ g.fill( _polygon );
+ g.setColor( c );
+ g.draw( _polygon );
}
- if ( additional_nodes != null ) {
- for( final PhylogenyNode n : additional_nodes ) {
- colorizeNodesHelper( c, n );
- }
+ else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
+ g.setPaint( new GradientPaint( xxx, node.getYcoord(), getBackground(), node.getXcoord(), ( float ) ( node
+ .getYcoord() - d ), c, false ) );
+ g.fill( _polygon );
+ g.setPaint( c );
+ g.draw( _polygon );
}
- repaint();
+ paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
}
- final private void colorizeSubtree( final Color c,
- final PhylogenyNode node,
- final List<PhylogenyNode> additional_nodes ) {
- _control_panel.setColorBranches( true );
- if ( _control_panel.getUseVisualStylesCb() != null ) {
- _control_panel.getUseVisualStylesCb().setSelected( true );
- }
- if ( node != null ) {
- for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
- it.next().getBranchData().setBranchColor( new BranchColor( c ) );
- }
- }
- if ( additional_nodes != null ) {
- for( final PhylogenyNode an : additional_nodes ) {
- for( final PreorderTreeIterator it = new PreorderTreeIterator( an ); it.hasNext(); ) {
- it.next().getBranchData().setBranchColor( new BranchColor( c ) );
+ final private void paintConfidenceValues( final Graphics2D g,
+ final PhylogenyNode node,
+ final boolean to_pdf,
+ final boolean to_graphics_file ) {
+ final List<Confidence> confidences = node.getBranchData().getConfidences();
+ boolean not_first = false;
+ Collections.sort( confidences );
+ final StringBuilder sb = new StringBuilder();
+ for( final Confidence confidence : confidences ) {
+ if ( ForesterUtil.isEmpty( SHOW_ONLY_THIS_CONF_TYPE )
+ || ( !ForesterUtil.isEmpty( confidence.getType() ) && confidence.getType()
+ .equalsIgnoreCase( SHOW_ONLY_THIS_CONF_TYPE ) ) ) {
+ final double value = confidence.getValue();
+ if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
+ if ( value < getOptions().getMinConfidenceValue() ) {
+ return;
+ }
+ if ( not_first ) {
+ sb.append( "/" );
+ }
+ else {
+ not_first = true;
+ }
+ sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
+ .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+ if ( getOptions().isShowConfidenceStddev() ) {
+ if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
+ sb.append( "(" );
+ sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence
+ .getStandardDeviation(), getOptions()
+ .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+ sb.append( ")" );
+ }
+ }
}
}
}
- repaint();
- }
-
- final private void colorSubtree( final PhylogenyNode node ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- JOptionPane.showMessageDialog( this,
- "Cannot colorize subtree in unrooted display type",
- "Attempt to colorize subtree in unrooted display",
- JOptionPane.WARNING_MESSAGE );
- return;
- }
- _color_chooser.setPreviewPanel( new JPanel() );
- SubtreeColorizationActionListener al;
- if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
- final List<PhylogenyNode> additional_nodes = getFoundNodesAsListOfPhylogenyNodes();
- al = new SubtreeColorizationActionListener( _color_chooser, node, additional_nodes );
- }
- else {
- al = new SubtreeColorizationActionListener( _color_chooser, node );
- }
- final JDialog dialog = JColorChooser
- .createDialog( this, "Subtree colorization", true, _color_chooser, al, null );
- setEdited( true );
- dialog.setVisible( true );
- }
-
- final private void copySubtree( final PhylogenyNode node ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- errorMessageNoCutCopyPasteInUnrootedDisplay();
- return;
- }
- setNodeInPreorderToNull();
- setCutOrCopiedTree( _phylogeny.copy( node ) );
- final List<PhylogenyNode> nodes = PhylogenyMethods.getAllDescendants( node );
- final Set<Long> node_ids = new HashSet<Long>( nodes.size() );
- for( final PhylogenyNode n : nodes ) {
- node_ids.add( n.getId() );
- }
- node_ids.add( node.getId() );
- setCopiedAndPastedNodes( node_ids );
- repaint();
- }
-
- final private String createASimpleTextRepresentationOfANode( final PhylogenyNode node ) {
- final String tax = PhylogenyMethods.getSpecies( node );
- String label = node.getName();
- if ( !ForesterUtil.isEmpty( label ) && !ForesterUtil.isEmpty( tax ) ) {
- label = label + " " + tax;
- }
- else if ( !ForesterUtil.isEmpty( tax ) ) {
- label = tax;
- }
- else {
- label = "";
- }
- if ( !ForesterUtil.isEmpty( label ) ) {
- label = " [" + label + "]";
- }
- return label;
- }
-
- final private void cutSubtree( final PhylogenyNode node ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- errorMessageNoCutCopyPasteInUnrootedDisplay();
- return;
- }
- if ( node.isRoot() ) {
- JOptionPane.showMessageDialog( this,
- "Cannot cut entire tree as subtree",
- "Attempt to cut entire tree",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- final String label = createASimpleTextRepresentationOfANode( node );
- final int r = JOptionPane.showConfirmDialog( null,
- "Cut subtree" + label + "?",
- "Confirm Cutting of Subtree",
- JOptionPane.YES_NO_OPTION );
- if ( r != JOptionPane.OK_OPTION ) {
- return;
+ if ( sb.length() > 0 ) {
+ final float parent_x = node.getParent().getXcoord();
+ float x = node.getXcoord();
+ g.setFont( getTreeFontSet().getSmallFont() );
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
+ x += EURO_D;
+ }
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
+ x += ROUNDED_D;
+ }
+ if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
+ g.setColor( Color.BLACK );
+ }
+ else {
+ g.setColor( getTreeColorSet().getConfidenceColor() );
+ }
+ final String conf_str = sb.toString();
+ TreePanel.drawString( conf_str,
+ parent_x
+ + ( ( x - parent_x - getTreeFontSet().getFontMetricsSmall()
+ .stringWidth( conf_str ) ) / 2 ),
+ ( node.getYcoord() + getTreeFontSet().getSmallMaxAscent() ) - 1,
+ g );
}
- setNodeInPreorderToNull();
- setCopiedAndPastedNodes( null );
- setCutOrCopiedTree( _phylogeny.copy( node ) );
- _phylogeny.deleteSubtree( node, true );
- _phylogeny.clearHashIdToNodeMap();
- _phylogeny.recalculateNumberOfExternalDescendants( true );
- resetNodeIdToDistToLeafMap();
- setEdited( true );
- repaint();
}
- final private void cycleColors() {
- getMainPanel().getTreeColorSet().cycleColorScheme();
- for( final TreePanel tree_panel : getMainPanel().getTreePanels() ) {
- tree_panel.setBackground( getMainPanel().getTreeColorSet().getBackgroundColor() );
+ final private void paintGainedAndLostCharacters( final Graphics2D g,
+ final PhylogenyNode node,
+ final String gained,
+ final String lost ) {
+ if ( node.getParent() != null ) {
+ final float parent_x = node.getParent().getXcoord();
+ final float x = node.getXcoord();
+ g.setFont( getTreeFontSet().getLargeFont() );
+ g.setColor( getTreeColorSet().getGainedCharactersColor() );
+ if ( Constants.SPECIAL_CUSTOM ) {
+ g.setColor( Color.BLUE );
+ }
+ TreePanel
+ .drawString( gained,
+ parent_x
+ + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( gained ) ) / 2 ),
+ ( node.getYcoord() - getFontMetricsForLargeDefaultFont().getMaxDescent() ),
+ g );
+ g.setColor( getTreeColorSet().getLostCharactersColor() );
+ TreePanel
+ .drawString( lost,
+ parent_x
+ + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( lost ) ) / 2 ),
+ ( node.getYcoord() + getFontMetricsForLargeDefaultFont().getMaxAscent() ),
+ g );
}
}
- final private void decreaseOvSize() {
- if ( ( getOvMaxWidth() > 20 ) && ( getOvMaxHeight() > 20 ) ) {
- setOvMaxWidth( getOvMaxWidth() - 5 );
- setOvMaxHeight( getOvMaxHeight() - 5 );
- updateOvSettings();
- getControlPanel().displayedPhylogenyMightHaveChanged( false );
+ private void paintMolecularSequences( final Graphics2D g, final PhylogenyNode node, final boolean to_pdf ) {
+ final RenderableMsaSequence rs = RenderableMsaSequence.createInstance( node.getNodeData().getSequence()
+ .getMolecularSequence(), node.getNodeData().getSequence().getType(), getConfiguration() );
+ if ( rs != null ) {
+ final int default_height = 8;
+ final float y = getYdistance();
+ final int h = ( y / 2 ) < default_height ? ForesterUtil.roundToInt( y * 2 ) : default_height;
+ rs.setRenderingHeight( h > 1 ? h : 1 );
+ if ( getControlPanel().isDrawPhylogram() ) {
+ rs.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + _length_of_longest_text ),
+ node.getYcoord() - ( h / 2.0f ),
+ g,
+ this,
+ to_pdf );
+ }
+ else {
+ rs.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text,
+ node.getYcoord() - ( h / 2.0f ),
+ g,
+ this,
+ to_pdf );
+ }
}
}
- final private void deleteNodeOrSubtree( final PhylogenyNode node ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- errorMessageNoCutCopyPasteInUnrootedDisplay();
- return;
- }
- if ( node.isRoot() && ( node.getNumberOfDescendants() != 1 ) ) {
- JOptionPane.showMessageDialog( this,
- "Cannot delete entire tree",
- "Attempt to delete entire tree",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- final String label = createASimpleTextRepresentationOfANode( node );
- final Object[] options = { "Node only", "Entire subtree", "Cancel" };
- final int r = JOptionPane.showOptionDialog( this,
- "Delete" + label + "?",
- "Delete Node/Subtree",
- JOptionPane.CLOSED_OPTION,
- JOptionPane.QUESTION_MESSAGE,
- null,
- options,
- options[ 2 ] );
- setNodeInPreorderToNull();
- boolean node_only = true;
- if ( r == 1 ) {
- node_only = false;
- }
- else if ( r != 0 ) {
+ /**
+ * Draw a box at the indicated node.
+ *
+ * @param x
+ * @param y
+ * @param node
+ * @param g
+ */
+ final private void paintNodeBox( final float x,
+ final float y,
+ final PhylogenyNode node,
+ final Graphics2D g,
+ final boolean to_pdf,
+ final boolean to_graphics_file ) {
+ if ( node.isCollapse() ) {
return;
}
- if ( node_only ) {
- PhylogenyMethods.removeNode( node, _phylogeny );
- }
- else {
- _phylogeny.deleteSubtree( node, true );
- }
- _phylogeny.externalNodesHaveChanged();
- _phylogeny.clearHashIdToNodeMap();
- _phylogeny.recalculateNumberOfExternalDescendants( true );
- resetNodeIdToDistToLeafMap();
- setEdited( true );
- repaint();
- }
-
- final private void displayNodePopupMenu( final PhylogenyNode node, final int x, final int y ) {
- makePopupMenus( node );
- _node_popup_menu.putClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY, node );
- _node_popup_menu.show( this, x, y );
- }
-
- final private void drawArc( final double x,
- final double y,
- final double width,
- final double heigth,
- final double start_angle,
- final double arc_angle,
- final Graphics2D g ) {
- _arc.setArc( x, y, width, heigth, _180_OVER_PI * start_angle, _180_OVER_PI * arc_angle, Arc2D.OPEN );
- g.draw( _arc );
- }
-
- final private void drawLine( final double x1, final double y1, final double x2, final double y2, final Graphics2D g ) {
- if ( ( x1 == x2 ) && ( y1 == y2 ) ) {
- return;
+ // if this node should be highlighted, do so
+ if ( ( _highlight_node == node ) && !to_pdf && !to_graphics_file ) {
+ g.setColor( getTreeColorSet().getFoundColor0() );
+ drawOval( x - 8, y - 8, 16, 16, g );
+ drawOval( x - 9, y - 8, 17, 17, g );
+ drawOval( x - 9, y - 9, 18, 18, g );
}
- _line.setLine( x1, y1, x2, y2 );
- g.draw( _line );
- }
-
- final private void drawOval( final double x,
- final double y,
- final double width,
- final double heigth,
- final Graphics2D g ) {
- _ellipse.setFrame( x, y, width, heigth );
- g.draw( _ellipse );
- }
-
- final private void drawOvalFilled( final double x,
- final double y,
- final double width,
- final double heigth,
- final Graphics2D g ) {
- _ellipse.setFrame( x, y, width, heigth );
- g.fill( _ellipse );
- }
-
- final private void drawOvalGradient( final float x,
- final float y,
- final float width,
- final float heigth,
- final Graphics2D g,
- final Color color_1,
- final Color color_2,
- final Color color_border ) {
- _ellipse.setFrame( x, y, width, heigth );
- g.setPaint( new GradientPaint( x, y, color_1, ( x + width ), ( y + heigth ), color_2, false ) );
- g.fill( _ellipse );
- if ( color_border != null ) {
- g.setPaint( color_border );
- g.draw( _ellipse );
- }
- }
-
- final private void drawRect( final float x, final float y, final float width, final float heigth, final Graphics2D g ) {
- _rectangle.setFrame( x, y, width, heigth );
- g.draw( _rectangle );
- }
-
- final private void drawRectFilled( final double x,
- final double y,
- final double width,
- final double heigth,
- final Graphics2D g ) {
- _rectangle.setFrame( x, y, width, heigth );
- g.fill( _rectangle );
- }
-
- final private void drawRectGradient( final float x,
- final float y,
- final float width,
- final float heigth,
- final Graphics2D g,
- final Color color_1,
- final Color color_2,
- final Color color_border ) {
- _rectangle.setFrame( x, y, width, heigth );
- g.setPaint( new GradientPaint( x, y, color_1, ( x + width ), ( y + heigth ), color_2, false ) );
- g.fill( _rectangle );
- if ( color_border != null ) {
- g.setPaint( color_border );
- g.draw( _rectangle );
- }
- }
-
- private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) {
- final List<Uri> us = new ArrayList<Uri>();
- for( final Taxonomy t : node.getNodeData().getTaxonomies() ) {
- for( final Uri uri : t.getUris() ) {
- us.add( uri );
+ if ( ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) )
+ || ( getOptions().isShowDefaultNodeShapesExternal() && node.isExternal() )
+ || ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() )
+ || ( getOptions().isShowDefaultNodeShapesForMarkedNodes()
+ && ( node.getNodeData().getNodeVisualData() != null ) && ( !node.getNodeData()
+ .getNodeVisualData().isEmpty() ) )
+ || ( getControlPanel().isUseVisualStyles() && ( ( node.getNodeData().getNodeVisualData() != null ) && ( ( node
+ .getNodeData().getNodeVisualData().getNodeColor() != null )
+ || ( node.getNodeData().getNodeVisualData().getSize() != NodeVisualData.DEFAULT_SIZE )
+ || ( node.getNodeData().getNodeVisualData().getFillType() != NodeFill.DEFAULT ) || ( node
+ .getNodeData().getNodeVisualData().getShape() != NodeShape.DEFAULT ) ) ) )
+ || ( getControlPanel().isEvents() && node.isHasAssignedEvent() && ( node.getNodeData().getEvent()
+ .isDuplication()
+ || node.getNodeData().getEvent().isSpeciation() || node.getNodeData().getEvent()
+ .isSpeciationOrDuplication() ) ) ) {
+ NodeVisualData vis = null;
+ if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null )
+ && ( !node.getNodeData().getNodeVisualData().isEmpty() ) ) {
+ vis = node.getNodeData().getNodeVisualData();
}
- }
- double offset = 0;
- for( final Uri uri : us ) {
- if ( uri != null ) {
- final String uri_str = uri.getValue().toString().toLowerCase();
- if ( getImageMap().containsKey( uri_str ) ) {
- final BufferedImage bi = getImageMap().get( uri_str );
- if ( ( bi != null ) && ( bi.getHeight() > 5 ) && ( bi.getWidth() > 5 ) ) {
- double scaling_factor = 1;
- if ( getOptions().isAllowMagnificationOfTaxonomyImages()
- || ( bi.getHeight() > ( 1.8 * getYdistance() ) ) ) {
- scaling_factor = ( 1.8 * getYdistance() ) / bi.getHeight();
- }
- // y = y - ( 0.9 * getYdistance() );
- final double hs = bi.getHeight() * scaling_factor;
- double ws = ( bi.getWidth() * scaling_factor ) + offset;
- final double my_y = y - ( 0.5 * hs );
- final int x_w = ( int ) ( x + ws + 0.5 );
- final int y_h = ( int ) ( my_y + hs + 0.5 );
- if ( ( ( x_w - x ) > 7 ) && ( ( y_h - my_y ) > 7 ) ) {
- g.drawImage( bi,
- ( int ) ( x + 0.5 + offset ),
- ( int ) ( my_y + 0.5 ),
- x_w,
- y_h,
- 0,
- 0,
- bi.getWidth(),
- bi.getHeight(),
- null );
- ws += 8;
- }
- else {
- ws = 0.0;
- }
- offset = ws;
+ float box_size = getOptions().getDefaultNodeShapeSize();
+ if ( ( vis != null ) && ( vis.getSize() != NodeVisualData.DEFAULT_SIZE ) ) {
+ box_size = vis.getSize();
+ }
+ final float half_box_size = box_size / 2.0f;
+ Color outline_color = null;
+ if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
+ outline_color = Color.BLACK;
+ }
+ else if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
+ outline_color = getColorForFoundNode( node );
+ }
+ else if ( vis != null ) {
+ if ( vis.getNodeColor() != null ) {
+ outline_color = vis.getNodeColor();
+ }
+ else if ( vis.getFontColor() != null ) {
+ outline_color = vis.getFontColor();
+ }
+ }
+ else if ( getControlPanel().isEvents() && TreePanelUtil.isHasAssignedEvent( node ) ) {
+ final Event event = node.getNodeData().getEvent();
+ if ( event.isDuplication() ) {
+ outline_color = getTreeColorSet().getDuplicationBoxColor();
+ }
+ else if ( event.isSpeciation() ) {
+ outline_color = getTreeColorSet().getSpecBoxColor();
+ }
+ else if ( event.isSpeciationOrDuplication() ) {
+ outline_color = getTreeColorSet().getDuplicationOrSpeciationColor();
+ }
+ }
+ if ( outline_color == null ) {
+ outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node );
+ if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) {
+ outline_color = getTreeColorSet().getBranchColorForPdf();
+ }
+ }
+ NodeShape shape = null;
+ if ( vis != null ) {
+ if ( vis.getShape() == NodeShape.CIRCLE ) {
+ shape = NodeShape.CIRCLE;
+ }
+ else if ( vis.getShape() == NodeShape.RECTANGLE ) {
+ shape = NodeShape.RECTANGLE;
+ }
+ }
+ if ( shape == null ) {
+ if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
+ shape = NodeShape.CIRCLE;
+ }
+ else if ( getOptions().getDefaultNodeShape() == NodeShape.RECTANGLE ) {
+ shape = NodeShape.RECTANGLE;
+ }
+ }
+ NodeFill fill = null;
+ if ( vis != null ) {
+ if ( vis.getFillType() == NodeFill.SOLID ) {
+ fill = NodeFill.SOLID;
+ }
+ else if ( vis.getFillType() == NodeFill.NONE ) {
+ fill = NodeFill.NONE;
+ }
+ else if ( vis.getFillType() == NodeFill.GRADIENT ) {
+ fill = NodeFill.GRADIENT;
+ }
+ }
+ if ( fill == null ) {
+ if ( getOptions().getDefaultNodeFill() == NodeFill.SOLID ) {
+ fill = NodeFill.SOLID;
+ }
+ else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
+ fill = NodeFill.NONE;
+ }
+ else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
+ fill = NodeFill.GRADIENT;
+ }
+ }
+ Color vis_fill_color = null;
+ if ( ( vis != null ) && ( vis.getNodeColor() != null ) ) {
+ vis_fill_color = vis.getNodeColor();
+ }
+ if ( shape == NodeShape.CIRCLE ) {
+ if ( fill == NodeFill.GRADIENT ) {
+ drawOvalGradient( x - half_box_size, y - half_box_size, box_size, box_size, g, to_pdf ? Color.WHITE
+ : outline_color, to_pdf ? outline_color : getBackground(), outline_color );
+ }
+ else if ( fill == NodeFill.NONE ) {
+ Color background = getBackground();
+ if ( to_pdf ) {
+ background = Color.WHITE;
+ }
+ drawOvalGradient( x - half_box_size,
+ y - half_box_size,
+ box_size,
+ box_size,
+ g,
+ background,
+ background,
+ outline_color );
+ }
+ else if ( fill == NodeVisualData.NodeFill.SOLID ) {
+ if ( vis_fill_color != null ) {
+ g.setColor( vis_fill_color );
+ }
+ else {
+ g.setColor( outline_color );
+ }
+ drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
+ }
+ }
+ else if ( shape == NodeVisualData.NodeShape.RECTANGLE ) {
+ if ( fill == NodeVisualData.NodeFill.GRADIENT ) {
+ drawRectGradient( x - half_box_size, y - half_box_size, box_size, box_size, g, to_pdf ? Color.WHITE
+ : outline_color, to_pdf ? outline_color : getBackground(), outline_color );
+ }
+ else if ( fill == NodeVisualData.NodeFill.NONE ) {
+ Color background = getBackground();
+ if ( to_pdf ) {
+ background = Color.WHITE;
+ }
+ drawRectGradient( x - half_box_size,
+ y - half_box_size,
+ box_size,
+ box_size,
+ g,
+ background,
+ background,
+ outline_color );
+ }
+ else if ( fill == NodeVisualData.NodeFill.SOLID ) {
+ if ( vis_fill_color != null ) {
+ g.setColor( vis_fill_color );
+ }
+ else {
+ g.setColor( outline_color );
}
+ drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
}
}
}
- return offset;
- }
-
- final private void errorMessageNoCutCopyPasteInUnrootedDisplay() {
- JOptionPane.showMessageDialog( this,
- "Cannot cut, copy, paste, add, or delete subtrees/nodes in unrooted display",
- "Attempt to cut/copy/paste/add/delete in unrooted display",
- JOptionPane.ERROR_MESSAGE );
}
- private final Color getColorForFoundNode( final PhylogenyNode n ) {
- if ( isInCurrentExternalNodes( n ) ) {
- return getTreeColorSet().getFoundColor0();
- }
- else if ( isInFoundNodes0( n ) && !isInFoundNodes1( n ) ) {
- return getTreeColorSet().getFoundColor0();
+ final private int paintNodeData( final Graphics2D g,
+ final PhylogenyNode node,
+ final boolean to_graphics_file,
+ final boolean to_pdf,
+ final boolean is_in_found_nodes ) {
+ if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) {
+ return 0;
}
- else if ( !isInFoundNodes0( n ) && isInFoundNodes1( n ) ) {
- return getTreeColorSet().getFoundColor1();
+ if ( getControlPanel().isWriteBranchLengthValues()
+ && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
+ || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
+ && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
+ paintBranchLength( g, node, to_pdf, to_graphics_file );
+ }
+ if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
+ return 0;
+ }
+ _sb.setLength( 0 );
+ int x = 0;
+ final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
+ if ( getControlPanel().isShowTaxonomyImages()
+ && ( getImageMap() != null )
+ && !getImageMap().isEmpty()
+ && node.getNodeData().isHasTaxonomy()
+ && ( ( node.getNodeData().getTaxonomy().getUris() != null ) && !node.getNodeData().getTaxonomy()
+ .getUris().isEmpty() ) ) {
+ x += drawTaxonomyImage( node.getXcoord() + 2 + half_box_size, node.getYcoord(), node, g );
+ }
+ if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
+ .isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) {
+ x += paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file, x );
+ }
+ setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getSequenceColor() );
+ if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
+ if ( _sb.length() > 0 ) {
+ _sb.setLength( 0 );
+ _sb.append( " (" );
+ _sb.append( node.getAllExternalDescendants().size() );
+ _sb.append( ")" );
+ }
}
else {
- return getTreeColorSet().getFoundColor0and1();
+ _sb.setLength( 0 );
}
- }
-
- final private Set<Long> getCopiedAndPastedNodes() {
- return getMainPanel().getCopiedAndPastedNodes();
- }
-
- final private Set<Long> getCurrentExternalNodes() {
- return _current_external_nodes;
- }
-
- final private Phylogeny getCutOrCopiedTree() {
- return getMainPanel().getCutOrCopiedTree();
- }
-
- private FontMetrics getFontMetricsForLargeDefaultFont() {
- return getTreeFontSet().getFontMetricsLarge();
- }
-
- List<PhylogenyNode> getFoundNodesAsListOfPhylogenyNodes() {
- final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
- if ( getFoundNodes0() != null ) {
- for( final Long id : getFoundNodes0() ) {
- final PhylogenyNode n = _phylogeny.getNode( id );
- if ( n != null ) {
- additional_nodes.add( n );
+ nodeDataAsSB( node, _sb );
+ final boolean using_visual_font = setFont( g, node, is_in_found_nodes );
+ float down_shift_factor = 3.0f;
+ if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
+ down_shift_factor = 1;
+ }
+ final float pos_x = node.getXcoord() + x + 2 + half_box_size;
+ float pos_y;
+ if ( !using_visual_font ) {
+ pos_y = ( node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ) );
+ }
+ else {
+ pos_y = ( node.getYcoord() + ( getFontMetrics( g.getFont() ).getAscent() / down_shift_factor ) );
+ }
+ final String sb_str = _sb.toString();
+ // GUILHEM_BEG ______________
+ if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence()
+ && ( _query_sequence != null ) ) {
+ int nodeTextBoundsWidth = 0;
+ if ( sb_str.length() > 0 ) {
+ final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how...
+ nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth();
+ }
+ if ( node.getNodeData().getSequence().equals( _query_sequence ) ) {
+ if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence
+ g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 );
+ g.setColor( getTreeColorSet().getBackgroundColor() );
}
}
- }
- if ( getFoundNodes1() != null ) {
- for( final Long id : getFoundNodes1() ) {
- if ( ( getFoundNodes0() == null ) || !getFoundNodes0().contains( id ) ) {
- final PhylogenyNode n = _phylogeny.getNode( id );
- if ( n != null ) {
- additional_nodes.add( n );
+ else {
+ final List<SequenceRelation> seqRelations = node.getNodeData().getSequence().getSequenceRelations();
+ for( final SequenceRelation seqRelation : seqRelations ) {
+ final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence ) || seqRelation
+ .getRef1().isEqual( _query_sequence ) )
+ && seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox()
+ .getSelectedItem() );
+ if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query
+ final double linePosX = node.getXcoord() + 2 + half_box_size;
+ final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation
+ .getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue()
+ + ")";
+ if ( sConfidence != null ) {
+ float confidenceX = pos_x;
+ if ( sb_str.length() > 0 ) {
+ confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth()
+ + CONFIDENCE_LEFT_MARGIN;
+ }
+ if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code
+ final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc )
+ .getBounds().getWidth();
+ TreePanel.drawString( sConfidence, confidenceX, pos_y, g );
+ x += CONFIDENCE_LEFT_MARGIN + confidenceWidth;
+ }
+ }
+ if ( ( x + nodeTextBoundsWidth ) > 0 ) /* we only underline if there is something displayed */
+ {
+ if ( nodeTextBoundsWidth == 0 ) {
+ nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */
+ }
+ else {
+ nodeTextBoundsWidth += 2;
+ }
+ g.drawLine( ( int ) linePosX + 1, 3 + ( int ) pos_y, ( int ) linePosX + x
+ + nodeTextBoundsWidth, 3 + ( int ) pos_y );
+ break;
+ }
}
}
}
}
- return additional_nodes;
- }
-
- final private float getLastDragPointX() {
- return _last_drag_point_x;
- }
-
- final private float getLastDragPointY() {
- return _last_drag_point_y;
- }
-
- final private short getMaxBranchesToLeaf( final PhylogenyNode node ) {
- if ( !_nodeid_dist_to_leaf.containsKey( node.getId() ) ) {
- final short m = PhylogenyMethods.calculateMaxBranchesToLeaf( node );
- _nodeid_dist_to_leaf.put( node.getId(), m );
- return m;
+ if ( sb_str.length() > 0 ) {
+ TreePanel.drawString( sb_str, pos_x, pos_y, g );
}
- else {
- return _nodeid_dist_to_leaf.get( node.getId() );
+ // GUILHEM_END _____________
+ if ( _sb.length() > 0 ) {
+ if ( !using_visual_font && !is_in_found_nodes ) {
+ x += getFontMetricsForLargeDefaultFont().stringWidth( _sb.toString() ) + 5;
+ }
+ else {
+ x += getFontMetrics( g.getFont() ).stringWidth( _sb.toString() ) + 5;
+ }
}
- }
-
- final private double getMaxDistanceToRoot() {
- if ( _max_distance_to_root < 0 ) {
- recalculateMaxDistanceToRoot();
+ if ( getControlPanel().isShowAnnotation() && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getAnnotations() != null )
+ && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
+ final SortedSet<Annotation> ann = node.getNodeData().getSequence().getAnnotations();
+ if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
+ g.setColor( Color.BLACK );
+ }
+ else if ( getControlPanel().isColorAccordingToAnnotation() ) {
+ g.setColor( calculateColorForAnnotation( ann ) );
+ }
+ final String ann_str = TreePanelUtil.createAnnotationString( ann, getOptions().isShowAnnotationRefSource() );
+ TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord()
+ + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ), g );
+ _sb.setLength( 0 );
+ _sb.append( ann_str );
+ if ( _sb.length() > 0 ) {
+ if ( !using_visual_font && !is_in_found_nodes ) {
+ x += getFontMetricsForLargeDefaultFont().stringWidth( _sb.toString() ) + 5;
+ }
+ else {
+ x += getFontMetrics( g.getFont() ).stringWidth( _sb.toString() ) + 5;
+ }
+ }
}
- return _max_distance_to_root;
- }
-
- final private float getOvMaxHeight() {
- return _ov_max_height;
- }
-
- final private float getOvMaxWidth() {
- return _ov_max_width;
- }
-
- final private float getOvXcorrectionFactor() {
- return _ov_x_correction_factor;
- }
-
- final private float getOvXDistance() {
- return _ov_x_distance;
- }
-
- final private int getOvXPosition() {
- return _ov_x_position;
- }
-
- final private float getOvYDistance() {
- return _ov_y_distance;
- }
-
- final private int getOvYPosition() {
- return _ov_y_position;
- }
-
- final private int getOvYStart() {
- return _ov_y_start;
- }
-
- final private List<Accession> getPdbAccs( final PhylogenyNode node ) {
- final List<Accession> pdb_ids = new ArrayList<Accession>();
- if ( node.getNodeData().isHasSequence() ) {
- final Sequence seq = node.getNodeData().getSequence();
- if ( !ForesterUtil.isEmpty( seq.getCrossReferences() ) ) {
- final SortedSet<Accession> cross_refs = seq.getCrossReferences();
- for( final Accession acc : cross_refs ) {
- if ( acc.getSource().equalsIgnoreCase( "pdb" ) ) {
- pdb_ids.add( acc );
- }
+ if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
+ || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
+ || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
+ if ( ( getControlPanel().isShowBinaryCharacters() || getControlPanel().isShowBinaryCharacterCounts() )
+ && node.getNodeData().isHasBinaryCharacters() ) {
+ if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
+ g.setColor( Color.BLACK );
+ }
+ else {
+ g.setColor( getTreeColorSet().getBinaryDomainCombinationsColor() );
+ }
+ if ( getControlPanel().isShowBinaryCharacters() ) {
+ TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()
+ .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord()
+ + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ), g );
+ paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters()
+ .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters()
+ .getLostCharactersAsStringBuffer().toString() );
+ }
+ else {
+ TreePanel
+ .drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
+ node.getXcoord() + x + 4 + half_box_size,
+ node.getYcoord()
+ + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ),
+ g );
+ paintGainedAndLostCharacters( g, node, "+"
+ + node.getNodeData().getBinaryCharacters().getGainedCount(), "-"
+ + node.getNodeData().getBinaryCharacters().getLostCount() );
}
}
}
- return pdb_ids;
- }
-
- final private double getScaleDistance() {
- return _scale_distance;
- }
-
- final private String getScaleLabel() {
- return _scale_label;
+ return x;
}
- final private TreeFontSet getTreeFontSet() {
- return getMainPanel().getTreeFontSet();
- }
-
- final private float getUrtFactor() {
- return _urt_factor;
- }
-
- final private float getUrtFactorOv() {
- return _urt_factor_ov;
- }
-
- final private void handleClickToAction( final NodeClickAction action, final PhylogenyNode node ) {
- switch ( action ) {
- case SHOW_DATA:
- showNodeFrame( node );
- break;
- case COLLAPSE:
- collapse( node );
- break;
- case REROOT:
- reRoot( node );
- break;
- case SUBTREE:
- subTree( node );
- break;
- case SWAP:
- swap( node );
- break;
- case COLOR_SUBTREE:
- colorSubtree( node );
- break;
- case COLOR_NODE_FONT:
- colorNodeFont( node );
- break;
- case CHANGE_NODE_FONT:
- changeNodeFont( node );
- break;
- case OPEN_SEQ_WEB:
- openSeqWeb( node );
- break;
- case BLAST:
- blast( node );
- break;
- case OPEN_TAX_WEB:
- openTaxWeb( node );
- break;
- case OPEN_PDB_WEB:
- openPdbWeb( node );
- break;
- case CUT_SUBTREE:
- cutSubtree( node );
- break;
- case COPY_SUBTREE:
- copySubtree( node );
- break;
- case PASTE_SUBTREE:
- pasteSubtree( node );
- break;
- case DELETE_NODE_OR_SUBTREE:
- deleteNodeOrSubtree( node );
- break;
- case ADD_NEW_NODE:
- addEmptyNode( node );
- break;
- case EDIT_NODE_DATA:
- showNodeEditFrame( node );
- break;
- case SELECT_NODES:
- selectNode( node );
- break;
- case SORT_DESCENDENTS:
- sortDescendants( node );
- break;
- case GET_EXT_DESC_DATA:
- showExtDescNodeData( node );
- break;
- default:
- throw new IllegalArgumentException( "unknown action: " + action );
- }
- }
-
- final private void increaseCurrentExternalNodesDataBufferChangeCounter() {
- _current_external_nodes_data_buffer_change_counter++;
- }
-
- final private void increaseOvSize() {
- if ( ( getOvMaxWidth() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth() / 2 ) )
- && ( getOvMaxHeight() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect()
- .getHeight() / 2 ) ) ) {
- setOvMaxWidth( getOvMaxWidth() + 5 );
- setOvMaxHeight( getOvMaxHeight() + 5 );
- updateOvSettings();
- getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
- }
-
- final private void init() {
- _color_chooser = new JColorChooser();
- _rollover_popup = new JTextArea();
- _rollover_popup.setFont( POPUP_FONT );
- resetNodeIdToDistToLeafMap();
- setTextAntialias();
- setTreeFile( null );
- setEdited( false );
- initializeOvSettings();
- setStartingAngle( ( TWO_PI * 3 ) / 4 );
- final ImageLoader il = new ImageLoader( this );
- new Thread( il ).start();
- }
-
- final private void initializeOvSettings() {
- setOvMaxHeight( getConfiguration().getOvMaxHeight() );
- setOvMaxWidth( getConfiguration().getOvMaxWidth() );
- }
-
- final private boolean inOvVirtualRectangle( final int x, final int y ) {
- return ( ( x >= ( getOvVirtualRectangle().x - 1 ) )
- && ( x <= ( getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 ) )
- && ( y >= ( getOvVirtualRectangle().y - 1 ) ) && ( y <= ( getOvVirtualRectangle().y
- + getOvVirtualRectangle().height + 1 ) ) );
- }
-
- final private boolean inOvVirtualRectangle( final MouseEvent e ) {
- return ( inOvVirtualRectangle( e.getX(), e.getY() ) );
- }
-
- final private boolean isCanBlast( final PhylogenyNode node ) {
- if ( !node.getNodeData().isHasSequence() && ForesterUtil.isEmpty( node.getName() ) ) {
- return false;
- }
- return Blast.isContainsQueryForBlast( node );
- }
-
- final private String isCanOpenSeqWeb( final PhylogenyNode node ) {
- final Accession a = SequenceAccessionTools.obtainAccessorFromDataFields( node );
- if ( a != null ) {
- return a.getValue();
+ final private void paintNodeDataUnrootedCirc( final Graphics2D g,
+ final PhylogenyNode node,
+ final boolean to_pdf,
+ final boolean to_graphics_file,
+ final boolean radial_labels,
+ final double ur_angle,
+ final boolean is_in_found_nodes ) {
+ if ( isNodeDataInvisibleUnrootedCirc( node ) && !to_graphics_file && !to_pdf ) {
+ return;
}
- return null;
- }
-
- final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
+ _sb.setLength( 0 );
+ _sb.append( " " );
if ( node.getNodeData().isHasTaxonomy()
- && ( ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
- || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) )
- || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node
- .getNodeData().getTaxonomy().getIdentifier() != null ) && !ForesterUtil.isEmpty( node
- .getNodeData().getTaxonomy().getIdentifier().getValue() ) ) ) ) {
- return true;
- }
- else {
- return false;
- }
- }
-
- final private boolean isInCurrentExternalNodes( final PhylogenyNode node ) {
- return ( ( getCurrentExternalNodes() != null ) && getCurrentExternalNodes().contains( node.getId() ) );
- }
-
- private boolean isInFoundNodes( final PhylogenyNode n ) {
- return isInFoundNodes0( n ) || isInFoundNodes1( n );
- }
-
- final private boolean isInFoundNodes0( final PhylogenyNode node ) {
- return ( ( getFoundNodes0() != null ) && getFoundNodes0().contains( node.getId() ) );
- }
-
- final private boolean isInFoundNodes1( final PhylogenyNode node ) {
- return ( ( getFoundNodes1() != null ) && getFoundNodes1().contains( node.getId() ) );
- }
-
- final private boolean isInOv() {
- return _in_ov;
- }
-
- final private boolean isNodeDataInvisible( final PhylogenyNode node ) {
- int y_dist = 40;
- if ( getControlPanel().isShowTaxonomyImages() ) {
- y_dist = 40 + ( int ) getYdistance();
- }
- return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - y_dist ) )
- || ( node.getYcoord() > ( getVisibleRect().getMaxY() + y_dist ) ) || ( ( node.getParent() != null ) && ( node
- .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) );
- }
-
- final private boolean isNodeDataInvisibleUnrootedCirc( final PhylogenyNode node ) {
- return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - 20 ) )
- || ( node.getYcoord() > ( getVisibleRect().getMaxY() + 20 ) )
- || ( node.getXcoord() < ( getVisibleRect().getMinX() - 20 ) ) || ( node.getXcoord() > ( getVisibleRect()
- .getMaxX() + 20 ) ) );
- }
-
- final private boolean isNonLinedUpCladogram() {
- return getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP;
- }
-
- final private boolean isUniformBranchLengthsForCladogram() {
- return getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP;
- }
-
- final private void keyPressedCalls( final KeyEvent e ) {
- if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) {
- if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) {
- if ( !isInOvRect() ) {
- setInOvRect( true );
- }
+ && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
+ .isShowTaxonomyCommonNames() ) ) {
+ final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
+ if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
+ _sb.append( taxonomy.getTaxonomyCode() );
+ _sb.append( " " );
}
- else if ( isInOvRect() ) {
- setInOvRect( false );
+ if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
+ if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
+ && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
+ _sb.append( taxonomy.getScientificName() );
+ _sb.append( " (" );
+ _sb.append( taxonomy.getCommonName() );
+ _sb.append( ") " );
+ }
+ else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
+ _sb.append( taxonomy.getScientificName() );
+ _sb.append( " " );
+ }
+ else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
+ _sb.append( taxonomy.getCommonName() );
+ _sb.append( " " );
+ }
}
- }
- if ( e.getModifiersEx() == InputEvent.CTRL_DOWN_MASK ) {
- if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
- || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
- getMainPanel().getTreeFontSet().mediumFonts();
- getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
+ else if ( _control_panel.isShowTaxonomyScientificNames() ) {
+ if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
+ _sb.append( taxonomy.getScientificName() );
+ _sb.append( " " );
+ }
}
- else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
- getMainPanel().getTreeFontSet().decreaseFontSize( 1, false );
- getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
+ else if ( _control_panel.isShowTaxonomyCommonNames() ) {
+ if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
+ _sb.append( taxonomy.getCommonName() );
+ _sb.append( " " );
+ }
}
- else if ( plusPressed( e.getKeyCode() ) ) {
- getMainPanel().getTreeFontSet().increaseFontSize();
- getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
+ }
+ if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
+ _sb.append( " [" );
+ _sb.append( node.getAllExternalDescendants().size() );
+ _sb.append( "]" );
+ }
+ if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
+ if ( _sb.length() > 0 ) {
+ _sb.append( " " );
}
+ _sb.append( node.getName() );
}
- else {
- if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
- || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
- getControlPanel().showWhole();
+ if ( node.getNodeData().isHasSequence() ) {
+ if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
+ if ( _sb.length() > 0 ) {
+ _sb.append( " " );
+ }
+ if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
+ _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
+ _sb.append( ":" );
+ }
+ _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
}
- else if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN )
- || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) {
- if ( e.getModifiersEx() == InputEvent.SHIFT_DOWN_MASK ) {
- if ( e.getKeyCode() == KeyEvent.VK_UP ) {
- getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
- getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
- else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
- getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
- getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
- else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
- getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
- Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
- getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
- else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
- getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
- Constants.WHEEL_ZOOM_IN_FACTOR );
- getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
+ if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
+ if ( _sb.length() > 0 ) {
+ _sb.append( " " );
}
- else {
- final int d = 80;
- int dx = 0;
- int dy = -d;
- if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
- dy = d;
- }
- else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
- dx = -d;
- dy = 0;
- }
- else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
- dx = d;
- dy = 0;
- }
- final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
- scroll_position.x = scroll_position.x + dx;
- scroll_position.y = scroll_position.y + dy;
- if ( scroll_position.x <= 0 ) {
- scroll_position.x = 0;
+ _sb.append( node.getNodeData().getSequence().getName() );
+ }
+ }
+ //g.setFont( getTreeFontSet().getLargeFont() );
+ //if ( is_in_found_nodes ) {
+ // g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
+ // }
+ if ( _sb.length() > 1 ) {
+ setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getSequenceColor() );
+ final boolean using_visual_font = setFont( g, node, is_in_found_nodes );
+ final String sb_str = _sb.toString();
+ double m = 0;
+ if ( _graphics_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
+ m = _urt_nodeid_angle_map.get( node.getId() ) % TWO_PI;
+ }
+ else {
+ m = ( float ) ( ur_angle % TWO_PI );
+ }
+ _at = g.getTransform();
+ boolean need_to_reset = false;
+ final float x_coord = node.getXcoord();
+ float y_coord;
+ if ( !using_visual_font ) {
+ y_coord = node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent() / 3.0f );
+ }
+ else {
+ y_coord = node.getYcoord() + ( getFontMetrics( g.getFont() ).getAscent() / 3.0f );
+ }
+ if ( radial_labels ) {
+ need_to_reset = true;
+ boolean left = false;
+ if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
+ m -= PI;
+ left = true;
+ }
+ g.rotate( m, x_coord, node.getYcoord() );
+ if ( left ) {
+ if ( !using_visual_font ) {
+ g.translate( -( getFontMetricsForLargeDefaultFont().getStringBounds( sb_str, g ).getWidth() ),
+ 0 );
}
else {
- final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
- - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
- if ( scroll_position.x >= max_x ) {
- scroll_position.x = max_x;
- }
+ g.translate( -( getFontMetrics( g.getFont() ).getStringBounds( sb_str, g ).getWidth() ), 0 );
}
- if ( scroll_position.y <= 0 ) {
- scroll_position.y = 0;
+ }
+ }
+ else {
+ if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
+ need_to_reset = true;
+ if ( !using_visual_font ) {
+ g.translate( -getFontMetricsForLargeDefaultFont().getStringBounds( sb_str, g ).getWidth(), 0 );
}
else {
- final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
- - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
- if ( scroll_position.y >= max_y ) {
- scroll_position.y = max_y;
- }
+ g.translate( -getFontMetrics( g.getFont() ).getStringBounds( sb_str, g ).getWidth(), 0 );
}
- repaint();
- getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
}
}
- else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
- getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
- getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
- Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
- getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
- else if ( plusPressed( e.getKeyCode() ) ) {
- getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
- Constants.WHEEL_ZOOM_IN_FACTOR );
- getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
- getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
- else if ( e.getKeyCode() == KeyEvent.VK_S ) {
- if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
- || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
- setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
- getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
+ TreePanel.drawString( sb_str, x_coord, y_coord, g );
+ if ( need_to_reset ) {
+ g.setTransform( _at );
}
- else if ( e.getKeyCode() == KeyEvent.VK_A ) {
- if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
- || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
- setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
- if ( getStartingAngle() < 0 ) {
- setStartingAngle( TWO_PI + getStartingAngle() );
- }
- getControlPanel().displayedPhylogenyMightHaveChanged( false );
- }
+ }
+ }
+
+ final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) {
+ if ( node.isCollapse() ) {
+ if ( !node.isRoot() && !node.getParent().isCollapse() ) {
+ paintCollapsedNode( g, node, false, false, false );
}
- else if ( e.getKeyCode() == KeyEvent.VK_D ) {
- boolean selected = false;
- if ( getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.HORIZONTAL ) {
- getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
- selected = true;
+ return;
+ }
+ if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
+ g.setColor( getColorForFoundNode( node ) );
+ drawRectFilled( node.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, node.getYSecondary()
+ - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g );
+ }
+ float new_x = 0;
+ if ( !node.isExternal() && !node.isCollapse() ) {
+ boolean first_child = true;
+ float y2 = 0.0f;
+ final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
+ for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
+ final PhylogenyNode child_node = node.getChildNode( i );
+ int factor_x;
+ if ( !isUniformBranchLengthsForCladogram() ) {
+ factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
}
else {
- getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
+ factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
}
- if ( getMainPanel().getMainFrame() == null ) {
- // Must be "E" applet version.
- final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
- if ( ae.getlabelDirectionCbmi() != null ) {
- ae.getlabelDirectionCbmi().setSelected( selected );
- }
+ if ( first_child ) {
+ first_child = false;
+ y2 = node.getYSecondary()
+ - ( getOvYDistance() * ( node.getNumberOfExternalNodes() - child_node
+ .getNumberOfExternalNodes() ) );
}
else {
- getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected );
+ y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
}
- repaint();
- }
- else if ( e.getKeyCode() == KeyEvent.VK_X ) {
- switchDisplaygetPhylogenyGraphicsType();
- repaint();
- }
- else if ( e.getKeyCode() == KeyEvent.VK_C ) {
- cycleColors();
- repaint();
- }
- else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_O ) ) {
- MainFrame.cycleOverview( getOptions(), this );
- repaint();
- }
- else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_I ) ) {
- increaseOvSize();
- }
- else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_U ) ) {
- decreaseOvSize();
+ final float x2 = calculateOvBranchLengthToParent( child_node, factor_x );
+ new_x = x2 + node.getXSecondary();
+ final float diff_y = node.getYSecondary() - y2;
+ final float diff_x = node.getXSecondary() - new_x;
+ if ( ( diff_y > 2 ) || ( diff_y < -2 ) || ( diff_x > 2 ) || ( diff_x < -2 ) ) {
+ paintBranchLite( g, node.getXSecondary(), new_x, node.getYSecondary(), y2, child_node );
+ }
+ child_node.setXSecondary( new_x );
+ child_node.setYSecondary( y2 );
+ y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
}
- e.consume();
}
}
- final private void makePopupMenus( final PhylogenyNode node ) {
- _node_popup_menu = new JPopupMenu();
- final List<String> clickto_names = _main_panel.getControlPanel().getSingleClickToNames();
- _node_popup_menu_items = new JMenuItem[ clickto_names.size() ];
- for( int i = 0; i < clickto_names.size(); i++ ) {
- final String title = clickto_names.get( i );
- _node_popup_menu_items[ i ] = new JMenuItem( title );
- if ( title.equals( Configuration.clickto_options[ Configuration.open_seq_web ][ 0 ] ) ) {
- final String id = isCanOpenSeqWeb( node );
- if ( !ForesterUtil.isEmpty( id ) ) {
- _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" + id + "]" );
- _node_popup_menu_items[ i ].setEnabled( true );
- }
- else {
- _node_popup_menu_items[ i ].setEnabled( false );
- }
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.open_pdb_web ][ 0 ] ) ) {
- final List<Accession> accs = getPdbAccs( node );
- _node_popup_menu_items[ i ] = new JMenuItem( title );
- if ( !ForesterUtil.isEmpty( accs ) ) {
- if ( accs.size() == 1 ) {
- _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
- + TreePanelUtil.pdbAccToString( accs, 0 ) + "]" );
- _node_popup_menu_items[ i ].setEnabled( true );
- }
- else if ( accs.size() == 2 ) {
- _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
- + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
- + TreePanelUtil.pdbAccToString( accs, 1 ) + "]" );
- _node_popup_menu_items[ i ].setEnabled( true );
- }
- else if ( accs.size() == 3 ) {
- _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
- + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
- + TreePanelUtil.pdbAccToString( accs, 1 ) + ", "
- + TreePanelUtil.pdbAccToString( accs, 2 ) + "]" );
- _node_popup_menu_items[ i ].setEnabled( true );
- }
- else {
- _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
- + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
- + TreePanelUtil.pdbAccToString( accs, 1 ) + ", "
- + TreePanelUtil.pdbAccToString( accs, 2 ) + ", + " + ( accs.size() - 3 ) + " more]" );
- _node_popup_menu_items[ i ].setEnabled( true );
- }
- }
- else {
- _node_popup_menu_items[ i ].setEnabled( false );
- }
+ final private void paintNodeRectangular( final Graphics2D g,
+ final PhylogenyNode node,
+ final boolean to_pdf,
+ final boolean dynamically_hide,
+ final int dynamic_hiding_factor,
+ final boolean to_graphics_file,
+ final boolean disallow_shortcutting ) {
+ final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node );
+ if ( node.isCollapse() ) {
+ if ( ( !node.isRoot() && !node.getParent().isCollapse() ) ) {
+ paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
}
- else if ( title.startsWith( Configuration.clickto_options[ Configuration.get_ext_desc_data ][ 0 ] ) ) {
- _node_popup_menu_items[ i ]
- .setText( Configuration.clickto_options[ Configuration.get_ext_desc_data ][ 0 ] + ": "
- + getOptions().getExtDescNodeDataToReturn().toString() );
+ return;
+ }
+ if ( node.isExternal() ) {
+ ++_external_node_index;
+ }
+ // Confidence values
+ if ( getControlPanel().isShowConfidenceValues()
+ && !node.isExternal()
+ && !node.isRoot()
+ && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
+ || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
+ && node.getBranchData().isHasConfidences() ) {
+ paintConfidenceValues( g, node, to_pdf, to_graphics_file );
+ }
+ // Draw a line to root:
+ if ( node.isRoot() && _phylogeny.isRooted() ) {
+ paintRootBranch( g, node.getXcoord(), node.getYcoord(), node, to_pdf, to_graphics_file );
+ }
+ float new_x = 0;
+ float new_x_min = Float.MAX_VALUE;
+ float min_dist = 1.5f;
+ if ( !disallow_shortcutting ) {
+ if ( dynamic_hiding_factor > 4000 ) {
+ min_dist = 4;
}
- else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
- _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
+ else if ( dynamic_hiding_factor > 1000 ) {
+ min_dist = 3;
}
- else if ( title.equals( Configuration.clickto_options[ Configuration.blast ][ 0 ] ) ) {
- _node_popup_menu_items[ i ].setEnabled( isCanBlast( node ) );
+ else if ( dynamic_hiding_factor > 100 ) {
+ min_dist = 2;
}
- else if ( title.equals( Configuration.clickto_options[ Configuration.delete_subtree_or_node ][ 0 ] ) ) {
- if ( !getOptions().isEditable() ) {
- continue;
+ }
+ if ( !node.isExternal() && !node.isCollapse() ) {
+ boolean first_child = true;
+ float y2 = 0.0f;
+ final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
+ for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
+ final PhylogenyNode child_node = node.getChildNode( i );
+ int factor_x;
+ if ( !isUniformBranchLengthsForCladogram() ) {
+ factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
}
- _node_popup_menu_items[ i ].setEnabled( isCanDelete() );
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.cut_subtree ][ 0 ] ) ) {
- if ( !getOptions().isEditable() ) {
- continue;
+ else {
+ factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
}
- _node_popup_menu_items[ i ].setEnabled( isCanCut( node ) );
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.copy_subtree ][ 0 ] ) ) {
- if ( !getOptions().isEditable() ) {
- continue;
+ if ( first_child ) {
+ first_child = false;
+ y2 = node.getYcoord()
+ - ( _y_distance * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) );
}
- _node_popup_menu_items[ i ].setEnabled( isCanCopy() );
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.paste_subtree ][ 0 ] ) ) {
- if ( !getOptions().isEditable() ) {
- continue;
+ else {
+ y2 += _y_distance * child_node.getNumberOfExternalNodes();
}
- _node_popup_menu_items[ i ].setEnabled( isCanPaste() );
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.edit_node_data ][ 0 ] ) ) {
- if ( !getOptions().isEditable() ) {
- continue;
+ final float x2 = calculateBranchLengthToParent( child_node, factor_x );
+ new_x = x2 + node.getXcoord();
+ if ( dynamically_hide && ( x2 < new_x_min ) ) {
+ new_x_min = x2;
}
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.add_new_node ][ 0 ] ) ) {
- if ( !getOptions().isEditable() ) {
- continue;
+ final float diff_y = node.getYcoord() - y2;
+ final float diff_x = node.getXcoord() - new_x;
+ if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist )
+ || ( diff_x < -min_dist ) ) {
+ paintBranchRectangular( g,
+ node.getXcoord(),
+ new_x,
+ node.getYcoord(),
+ y2,
+ child_node,
+ to_pdf,
+ to_graphics_file );
}
+ child_node.setXcoord( new_x );
+ child_node.setYcoord( y2 );
+ y2 += _y_distance * child_node.getNumberOfExternalNodes();
}
- else if ( title.equals( Configuration.clickto_options[ Configuration.reroot ][ 0 ] ) ) {
- _node_popup_menu_items[ i ].setEnabled( isCanReroot() );
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.collapse_uncollapse ][ 0 ] ) ) {
- _node_popup_menu_items[ i ].setEnabled( ( isCanCollapse() && !node.isExternal() ) );
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.color_subtree ][ 0 ] ) ) {
- _node_popup_menu_items[ i ].setEnabled( isCanColorSubtree() );
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.subtree ][ 0 ] ) ) {
- _node_popup_menu_items[ i ].setEnabled( isCanSubtree( node ) );
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.swap ][ 0 ] ) ) {
- _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() == 2 );
- }
- else if ( title.equals( Configuration.clickto_options[ Configuration.sort_descendents ][ 0 ] ) ) {
- _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() > 1 );
- }
- _node_popup_menu_items[ i ].addActionListener( this );
- _node_popup_menu.add( _node_popup_menu_items[ i ] );
+ paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file );
+ }
+ if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() )
+ && ( node.getNodeData().getSequence().isMolecularSequenceAligned() )
+ && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) {
+ paintMolecularSequences( g, node, to_pdf );
+ }
+ if ( dynamically_hide
+ && !is_in_found_nodes
+ && ( ( node.isExternal() && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) ) || ( !node
+ .isExternal() && ( ( new_x_min < 20 ) || ( ( _y_distance * node.getNumberOfExternalNodes() ) < getFontMetricsForLargeDefaultFont()
+ .getHeight() ) ) ) ) ) {
+ return;
}
+ final int x = paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
+ paintNodeWithRenderableData( x, g, node, to_graphics_file, to_pdf );
}
- private final void nodeDataAsSB( final PhylogenyNode node, final StringBuilder sb ) {
- if ( node != null ) {
- if ( getControlPanel().isShowNodeNames() && ( !ForesterUtil.isEmpty( node.getName() ) ) ) {
- if ( sb.length() > 0 ) {
- sb.append( " " );
- }
- sb.append( node.getName() );
+ final private void paintNodeWithRenderableData( final int x,
+ final Graphics2D g,
+ final PhylogenyNode node,
+ final boolean to_graphics_file,
+ final boolean to_pdf ) {
+ if ( isNodeDataInvisible( node ) && !( to_graphics_file || to_pdf ) ) {
+ return;
+ }
+ if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) {
+ return;
+ }
+ if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getDomainArchitecture() != null )
+ && ( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
+ RenderableDomainArchitecture rds = null;
+ try {
+ rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
}
- if ( node.getNodeData().isHasSequence() ) {
- if ( getControlPanel().isShowSeqSymbols()
- && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
- if ( sb.length() > 0 ) {
- sb.append( " " );
- }
- sb.append( node.getNodeData().getSequence().getSymbol() );
+ catch ( final ClassCastException cce ) {
+ cce.printStackTrace();
+ }
+ if ( rds != null ) {
+ final int default_height = 7;
+ float y = getYdistance();
+ if ( getControlPanel().isDynamicallyHideData() ) {
+ y = getTreeFontSet().getFontMetricsLarge().getHeight();
}
- if ( getControlPanel().isShowGeneNames()
- && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) {
- if ( sb.length() > 0 ) {
- sb.append( " " );
+ final int h = y < default_height ? ForesterUtil.roundToInt( y ) : default_height;
+ rds.setRenderingHeight( h > 1 ? h : 2 );
+ if ( getControlPanel().isDrawPhylogram() ) {
+ if ( getOptions().isLineUpRendarableNodeData() ) {
+ if ( getOptions().isRightLineUpDomains() ) {
+ rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() )
+ + _length_of_longest_text + ( ( _longest_domain - rds.getTotalLength() ) * rds
+ .getRenderingFactorWidth() ) ), node.getYcoord() - ( h / 2.0f ), g, this, to_pdf );
+ }
+ else {
+ rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + _length_of_longest_text ),
+ node.getYcoord() - ( h / 2.0f ),
+ g,
+ this,
+ to_pdf );
+ }
}
- sb.append( node.getNodeData().getSequence().getGeneName() );
- }
- if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
- if ( sb.length() > 0 ) {
- sb.append( " " );
+ else {
+ rds.render( node.getXcoord() + x, node.getYcoord() - ( h / 2.0f ), g, this, to_pdf );
}
- sb.append( node.getNodeData().getSequence().getName() );
}
- if ( getControlPanel().isShowSequenceAcc()
- && ( node.getNodeData().getSequence().getAccession() != null ) ) {
- if ( sb.length() > 0 ) {
- sb.append( " " );
- }
- if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
- sb.append( node.getNodeData().getSequence().getAccession().getSource() );
- sb.append( ":" );
+ else {
+ if ( getOptions().isRightLineUpDomains() ) {
+ rds.render( ( ( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text ) - 20 )
+ + ( ( _longest_domain - rds.getTotalLength() ) * rds
+ .getRenderingFactorWidth() ),
+ node.getYcoord() - ( h / 2.0f ),
+ g,
+ this,
+ to_pdf );
+ }
+ else {
+ rds.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text,
+ node.getYcoord() - ( h / 2.0f ),
+ g,
+ this,
+ to_pdf );
}
- sb.append( node.getNodeData().getSequence().getAccession().getValue() );
- }
- }
- if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
- if ( sb.length() > 0 ) {
- sb.append( " " );
}
- sb.append( propertiesToString( node ) );
}
}
- }
-
- private final void nodeTaxonomyDataAsSB( final Taxonomy taxonomy, final StringBuilder sb ) {
- if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
- sb.append( taxonomy.getTaxonomyCode() );
- sb.append( " " );
- }
- if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
- if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
- && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
- if ( getOptions().isAbbreviateScientificTaxonNames()
- && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
- abbreviateScientificName( taxonomy.getScientificName(), sb );
- }
- else {
- sb.append( taxonomy.getScientificName() );
+ if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
+ && ( node.getNodeData().getVector().size() > 0 ) && ( getStatisticsForExpressionValues() != null ) ) {
+ final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(),
+ getStatisticsForExpressionValues(),
+ getConfiguration() );
+ if ( rv != null ) {
+ double domain_add = 0;
+ if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
+ domain_add = _domain_structure_width + 10;
}
- sb.append( " (" );
- sb.append( taxonomy.getCommonName() );
- sb.append( ") " );
- }
- else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
- if ( getOptions().isAbbreviateScientificTaxonNames()
- && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
- abbreviateScientificName( taxonomy.getScientificName(), sb );
+ if ( getControlPanel().isDrawPhylogram() ) {
+ rv.render( ( float ) ( node.getXcoord() + x + domain_add ), node.getYcoord() - 3, g, this, to_pdf );
}
else {
- sb.append( taxonomy.getScientificName() );
+ rv.render( ( float ) ( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text + domain_add ),
+ node.getYcoord() - 3,
+ g,
+ this,
+ to_pdf );
}
- sb.append( " " );
- }
- else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
- sb.append( taxonomy.getCommonName() );
- sb.append( " " );
}
}
- else if ( _control_panel.isShowTaxonomyScientificNames() ) {
- if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
- if ( getOptions().isAbbreviateScientificTaxonNames()
- && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
- abbreviateScientificName( taxonomy.getScientificName(), sb );
- }
- else {
- sb.append( taxonomy.getScientificName() );
- }
- sb.append( " " );
- }
+ //if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() )
+ // && ( node.getNodeData().getSequence().isMolecularSequenceAligned() )
+ // && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) {
+ // paintMolecularSequences( g, node, to_pdf );
+ //}
+ }
+
+ final private void paintOvRectangle( final Graphics2D g ) {
+ final float w_ratio = ( ( float ) getWidth() ) / getVisibleRect().width;
+ final float h_ratio = ( ( float ) getHeight() ) / getVisibleRect().height;
+ final float x_ratio = ( ( float ) getWidth() ) / getVisibleRect().x;
+ final float y_ratio = ( ( float ) getHeight() ) / getVisibleRect().y;
+ final float width = getOvMaxWidth() / w_ratio;
+ final float height = getOvMaxHeight() / h_ratio;
+ final float x = getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / x_ratio );
+ final float y = getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / y_ratio );
+ g.setColor( getTreeColorSet().getFoundColor0() );
+ getOvRectangle().setRect( x, y, width, height );
+ final Stroke s = g.getStroke();
+ g.setStroke( STROKE_1 );
+ if ( ( width < 6 ) && ( height < 6 ) ) {
+ drawRectFilled( x, y, 6, 6, g );
+ getOvVirtualRectangle().setRect( x, y, 6, 6 );
}
- else if ( _control_panel.isShowTaxonomyCommonNames() ) {
- if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
- sb.append( taxonomy.getCommonName() );
- sb.append( " " );
+ else if ( width < 6 ) {
+ drawRectFilled( x, y, 6, height, g );
+ getOvVirtualRectangle().setRect( x, y, 6, height );
+ }
+ else if ( height < 6 ) {
+ drawRectFilled( x, y, width, 6, g );
+ getOvVirtualRectangle().setRect( x, y, width, 6 );
+ }
+ else {
+ drawRect( x, y, width, height, g );
+ if ( isInOvRect() ) {
+ drawRect( x + 1, y + 1, width - 2, height - 2, g );
}
+ getOvVirtualRectangle().setRect( x, y, width, height );
}
+ g.setStroke( s );
}
- private final String obtainTitleForExtDescNodeData() {
- return getOptions().getExtDescNodeDataToReturn().toString();
+ final private void paintPhylogenyLite( final Graphics2D g ) {
+ _phylogeny
+ .getRoot()
+ .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle()
+ .getWidth() ) ) ) );
+ _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
+ final Stroke s = g.getStroke();
+ g.setStroke( STROKE_05 );
+ for( final PhylogenyNode element : _nodes_in_preorder ) {
+ paintNodeLite( g, element );
+ }
+ g.setStroke( s );
+ paintOvRectangle( g );
}
- final private void openPdbWeb( final PhylogenyNode node ) {
- final List<Accession> pdb_ids = getPdbAccs( node );
- if ( ForesterUtil.isEmpty( pdb_ids ) ) {
- cannotOpenBrowserWarningMessage( "PDB" );
- return;
+ /**
+ * Paint the root branch. (Differs from others because it will always be a
+ * single horizontal line).
+ * @param to_graphics_file
+ *
+ * @return new x1 value
+ */
+ final private void paintRootBranch( final Graphics2D g,
+ final float x1,
+ final float y1,
+ final PhylogenyNode root,
+ final boolean to_pdf,
+ final boolean to_graphics_file ) {
+ assignGraphicsForBranchWithColorForParentBranch( root, false, g, to_pdf, to_graphics_file );
+ float d = getXdistance();
+ if ( getControlPanel().isDrawPhylogram() && ( root.getDistanceToParent() > 0.0 ) ) {
+ d = ( float ) ( getXcorrectionFactor() * root.getDistanceToParent() );
}
- final List<String> uri_strs = TreePanelUtil.createUrisForPdbWeb( node, pdb_ids, getConfiguration(), this );
- if ( !ForesterUtil.isEmpty( uri_strs ) ) {
- for( final String uri_str : uri_strs ) {
- try {
- AptxUtil.launchWebBrowser( new URI( uri_str ),
- isApplet(),
- isApplet() ? obtainApplet() : null,
- "_aptx_seq" );
- }
- catch ( final IOException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
- }
- catch ( final URISyntaxException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
- }
- }
+ if ( d < MIN_ROOT_LENGTH ) {
+ d = MIN_ROOT_LENGTH;
+ }
+ if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( root ) == 1 ) ) {
+ drawLine( x1 - d, root.getYcoord(), x1, root.getYcoord(), g );
}
else {
- cannotOpenBrowserWarningMessage( "PDB" );
+ final double w = PhylogenyMethods.getBranchWidthValue( root );
+ drawRectFilled( x1 - d, root.getYcoord() - ( w / 2 ), d, w, g );
}
+ paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file );
}
- final private void openSeqWeb( final PhylogenyNode node ) {
- if ( ForesterUtil.isEmpty( isCanOpenSeqWeb( node ) ) ) {
- cannotOpenBrowserWarningMessage( "sequence" );
- return;
- }
- final String uri_str = TreePanelUtil.createUriForSeqWeb( node, getConfiguration(), this );
- if ( !ForesterUtil.isEmpty( uri_str ) ) {
- try {
- AptxUtil.launchWebBrowser( new URI( uri_str ),
- isApplet(),
- isApplet() ? obtainApplet() : null,
- "_aptx_seq" );
- }
- catch ( final IOException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
- }
- catch ( final URISyntaxException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
- }
+ final private void paintScale( final Graphics2D g,
+ int x1,
+ int y1,
+ final boolean to_pdf,
+ final boolean to_graphics_file ) {
+ x1 += MOVE;
+ final double x2 = x1 + ( getScaleDistance() * getXcorrectionFactor() );
+ y1 -= 12;
+ final int y2 = y1 - 8;
+ final int y3 = y1 - 4;
+ g.setFont( getTreeFontSet().getSmallFont() );
+ if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
+ g.setColor( Color.BLACK );
}
else {
- cannotOpenBrowserWarningMessage( "sequence" );
+ g.setColor( getTreeColorSet().getBranchLengthColor() );
+ }
+ final Stroke s = g.getStroke();
+ g.setStroke( STROKE_1 );
+ drawLine( x1, y1, x1, y2, g );
+ drawLine( x2, y1, x2, y2, g );
+ drawLine( x1, y3, x2, y3, g );
+ if ( getScaleLabel() != null ) {
+ g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 );
}
+ g.setStroke( s );
}
- final private void openTaxWeb( final PhylogenyNode node ) {
- if ( !isCanOpenTaxWeb( node ) ) {
- cannotOpenBrowserWarningMessage( "taxonomic" );
- return;
+ final private int paintTaxonomy( final Graphics2D g,
+ final PhylogenyNode node,
+ final boolean is_in_found_nodes,
+ final boolean to_pdf,
+ final boolean to_graphics_file,
+ final float x_shift ) {
+ final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
+ final boolean using_visual_font = setFont( g, node, is_in_found_nodes );
+ setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getTaxonomyColor() );
+ final float start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift;
+ float start_y;
+ if ( !using_visual_font ) {
+ start_y = node.getYcoord()
+ + ( getFontMetricsForLargeDefaultFont().getAscent() / ( node.getNumberOfDescendants() == 1 ? 1
+ : 3.0f ) );
}
- String uri_str = null;
- final Taxonomy tax = node.getNodeData().getTaxonomy();
- if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
- && tax.getIdentifier().getValue().startsWith( "http://" ) ) {
- try {
- uri_str = new URI( tax.getIdentifier().getValue() ).toString();
- }
- catch ( final URISyntaxException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- uri_str = null;
- e.printStackTrace();
- }
+ else {
+ start_y = node.getYcoord()
+ + ( getFontMetrics( g.getFont() ).getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0f ) );
}
- else if ( ( tax.getIdentifier() != null )
- && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
- && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() )
- && ( tax.getIdentifier().getProvider().equalsIgnoreCase( "ncbi" ) || tax.getIdentifier().getProvider()
- .equalsIgnoreCase( "uniprot" ) ) ) {
- try {
- uri_str = "http://www.uniprot.org/taxonomy/"
- + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
- }
- catch ( final UnsupportedEncodingException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
- }
+ _sb.setLength( 0 );
+ nodeTaxonomyDataAsSB( taxonomy, _sb );
+ final String label = _sb.toString();
+ /* GUILHEM_BEG */
+ if ( _control_panel.isShowSequenceRelations() && ( label.length() > 0 )
+ && ( node.getNodeData().isHasSequence() ) && node.getNodeData().getSequence().equals( _query_sequence ) ) {
+ // invert font color and background color to show that this is the query sequence
+ final Rectangle2D nodeTextBounds = new TextLayout( label, g.getFont(), new FontRenderContext( null,
+ false,
+ false ) )
+ .getBounds();
+ g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 );
+ g.setColor( getTreeColorSet().getBackgroundColor() );
}
- else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
- try {
- uri_str = "http://www.uniprot.org/taxonomy/?query="
- + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
- }
- catch ( final UnsupportedEncodingException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
- }
+ /* GUILHEM_END */
+ TreePanel.drawString( label, start_x, start_y, g );
+ if ( !using_visual_font && !is_in_found_nodes ) {
+ return getFontMetricsForLargeDefaultFont().stringWidth( label );
}
- else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
- try {
- uri_str = "http://www.uniprot.org/taxonomy/?query="
- + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 );
- }
- catch ( final UnsupportedEncodingException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
- }
+ return getFontMetrics( g.getFont() ).stringWidth( label );
+ }
+
+ final private void paintUnrooted( final PhylogenyNode n,
+ final double low_angle,
+ final double high_angle,
+ final boolean radial_labels,
+ final Graphics2D g,
+ final boolean to_pdf,
+ final boolean to_graphics_file ) {
+ if ( n.isRoot() ) {
+ n.setXcoord( getWidth() / 2 );
+ n.setYcoord( getHeight() / 2 );
}
- else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
- try {
- uri_str = "http://www.uniprot.org/taxonomy/?query="
- + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
- }
- catch ( final UnsupportedEncodingException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
- }
+ if ( n.isExternal() ) {
+ paintNodeDataUnrootedCirc( g,
+ n,
+ to_pdf,
+ to_graphics_file,
+ radial_labels,
+ ( high_angle + low_angle ) / 2,
+ isInFoundNodes( n ) || isInCurrentExternalNodes( n ) );
+ return;
}
- if ( !ForesterUtil.isEmpty( uri_str ) ) {
- try {
- AptxUtil.launchWebBrowser( new URI( uri_str ),
- isApplet(),
- isApplet() ? obtainApplet() : null,
- "_aptx_tax" );
- }
- catch ( final IOException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
+ final float num_enclosed = n.getNumberOfExternalNodes();
+ final float x = n.getXcoord();
+ final float y = n.getYcoord();
+ double current_angle = low_angle;
+ // final boolean n_below = n.getYcoord() < getVisibleRect().getMinY() - 20;
+ // final boolean n_above = n.getYcoord() > getVisibleRect().getMaxY() + 20;
+ // final boolean n_left = n.getXcoord() < getVisibleRect().getMinX() - 20;
+ // final boolean n_right = n.getXcoord() > getVisibleRect().getMaxX() + 20;
+ for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
+ final PhylogenyNode desc = n.getChildNode( i );
+ /// if ( ( ( n_below ) & ( desc.getYcoord() < getVisibleRect().getMinY() - 20 ) )
+ // || ( ( n_above ) & ( desc.getYcoord() > getVisibleRect().getMaxY() + 20 ) )
+ // || ( ( n_left ) & ( desc.getXcoord() < getVisibleRect().getMinX() - 20 ) )
+ // || ( ( n_right ) & ( desc.getXcoord() > getVisibleRect().getMaxX() + 20 ) ) ) {
+ // continue;
+ // }
+ //if ( ( desc.getYcoord() > n.getYcoord() ) && ( n.getYcoord() > getVisibleRect().getMaxY() - 20 ) ) {
+ // continue;
+ //}
+ //if ( ( desc.getYcoord() < n.getYcoord() ) && ( n.getYcoord() < getVisibleRect().getMinY() + 20 ) ) {
+ // continue;
+ // }
+ final int desc_num_enclosed = desc.getNumberOfExternalNodes();
+ final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
+ float length;
+ if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
+ if ( desc.getDistanceToParent() < 0 ) {
+ length = 0;
+ }
+ else {
+ length = ( float ) ( desc.getDistanceToParent() * getUrtFactor() );
+ }
}
- catch ( final URISyntaxException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
+ else {
+ length = getUrtFactor();
}
+ final double mid_angle = current_angle + ( arc_size / 2 );
+ final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
+ final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );
+ desc.setXcoord( new_x );
+ desc.setYcoord( new_y );
+ paintUnrooted( desc, current_angle, current_angle + arc_size, radial_labels, g, to_pdf, to_graphics_file );
+ current_angle += arc_size;
+ assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file );
+ drawLine( x, y, new_x, new_y, g );
+ paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file );
}
- else {
- cannotOpenBrowserWarningMessage( "taxonomic" );
+ if ( n.isRoot() ) {
+ paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file );
}
}
- final private void paintBranchLength( final Graphics2D g,
- final PhylogenyNode node,
- final boolean to_pdf,
- final boolean to_graphics_file ) {
- g.setFont( getTreeFontSet().getSmallFont() );
- if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- g.setColor( Color.BLACK );
+ final private void paintUnrootedLite( final PhylogenyNode n,
+ final double low_angle,
+ final double high_angle,
+ final Graphics2D g,
+ final float urt_ov_factor ) {
+ if ( n.isRoot() ) {
+ final int x_pos = ( int ) ( getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / 2 ) );
+ final int y_pos = ( int ) ( getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / 2 ) );
+ n.setXSecondary( x_pos );
+ n.setYSecondary( y_pos );
}
- else {
- g.setColor( getTreeColorSet().getBranchLengthColor() );
+ if ( n.isExternal() ) {
+ return;
}
- if ( !node.isRoot() ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
- TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
- .getXcoord() + EURO_D, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g );
- }
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
- TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
- .getXcoord() + ROUNDED_D, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g );
+ final float num_enclosed = n.getNumberOfExternalNodes();
+ final float x = n.getXSecondary();
+ final float y = n.getYSecondary();
+ double current_angle = low_angle;
+ for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
+ final PhylogenyNode desc = n.getChildNode( i );
+ final int desc_num_enclosed = desc.getNumberOfExternalNodes();
+ final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
+ float length;
+ if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
+ if ( desc.getDistanceToParent() < 0 ) {
+ length = 0;
+ }
+ else {
+ length = ( float ) ( desc.getDistanceToParent() * urt_ov_factor );
+ }
}
else {
- TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
- .getXcoord() + 3, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g );
+ length = urt_ov_factor;
}
- }
- else {
- TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), 3, node.getYcoord()
- - getTreeFontSet().getSmallMaxDescent(), g );
+ final double mid_angle = current_angle + ( arc_size / 2 );
+ final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
+ final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );
+ desc.setXSecondary( new_x );
+ desc.setYSecondary( new_y );
+ if ( isInFoundNodes( desc ) || isInCurrentExternalNodes( desc ) ) {
+ g.setColor( getColorForFoundNode( desc ) );
+ drawRectFilled( desc.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF,
+ desc.getYSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF,
+ OVERVIEW_FOUND_NODE_BOX_SIZE,
+ OVERVIEW_FOUND_NODE_BOX_SIZE,
+ g );
+ g.setColor( getTreeColorSet().getOvColor() );
+ }
+ paintUnrootedLite( desc, current_angle, current_angle + arc_size, g, urt_ov_factor );
+ current_angle += arc_size;
+ drawLine( x, y, new_x, new_y, g );
}
}
- final private void paintBranchLite( final Graphics2D g,
- final float x1,
- final float x2,
- final float y1,
- final float y2,
- final PhylogenyNode node ) {
- g.setColor( getTreeColorSet().getOvColor() );
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
- drawLine( x1, y1, x2, y2, g );
+ final private void pasteSubtree( final PhylogenyNode node ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ errorMessageNoCutCopyPasteInUnrootedDisplay();
+ return;
}
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
- _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
- ( g ).draw( _quad_curve );
+ if ( ( getCutOrCopiedTree() == null ) || getCutOrCopiedTree().isEmpty() ) {
+ JOptionPane.showMessageDialog( this,
+ "No tree in buffer (need to copy or cut a subtree first)",
+ "Attempt to paste with empty buffer",
+ JOptionPane.ERROR_MESSAGE );
+ return;
}
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
- final float dx = x2 - x1;
- final float dy = y2 - y1;
- _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
- + ( dy * 0.8f ), x2, y2 );
- ( g ).draw( _cubic_curve );
+ final String label = createASimpleTextRepresentationOfANode( getCutOrCopiedTree().getRoot() );
+ final Object[] options = { "As sibling", "As descendant", "Cancel" };
+ final int r = JOptionPane.showOptionDialog( this,
+ "How to paste subtree" + label + "?",
+ "Paste Subtree",
+ JOptionPane.CLOSED_OPTION,
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ options,
+ options[ 2 ] );
+ boolean paste_as_sibling = true;
+ if ( r == 1 ) {
+ paste_as_sibling = false;
}
- else {
- final float x2a = x2;
- final float x1a = x1;
- // draw the vertical line
- if ( node.isFirstChildNode() || node.isLastChildNode() ) {
- drawLine( x1, y1, x1, y2, g );
- }
- // draw the horizontal line
- drawLine( x1a, y2, x2a, y2, g );
+ else if ( r != 0 ) {
+ return;
}
- }
-
- /**
- * Paint a branch which consists of a vertical and a horizontal bar
- * @param is_ind_found_nodes
- */
- final private void paintBranchRectangular( final Graphics2D g,
- final float x1,
- final float x2,
- final float y1,
- final float y2,
- final PhylogenyNode node,
- final boolean to_pdf,
- final boolean to_graphics_file ) {
- assignGraphicsForBranchWithColorForParentBranch( node, false, g, to_pdf, to_graphics_file );
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
- drawLine( x1, y1, x2, y2, g );
- }
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
- _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
- g.draw( _quad_curve );
- }
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
- final float dx = x2 - x1;
- final float dy = y2 - y1;
- _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
- + ( dy * 0.8f ), x2, y2 );
- g.draw( _cubic_curve );
- }
- else {
- final float x2a = x2;
- final float x1a = x1;
- float y2_r = 0;
- if ( node.isFirstChildNode() || node.isLastChildNode()
- || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
- || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
- if ( !to_graphics_file
- && !to_pdf
- && ( ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) && ( y1 < ( getVisibleRect().getMinY() - 20 ) ) ) || ( ( y2 > ( getVisibleRect()
- .getMaxY() + 20 ) ) && ( y1 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) ) {
- // Do nothing.
- }
- else {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
- float x2c = x1 + EURO_D;
- if ( x2c > x2a ) {
- x2c = x2a;
- }
- drawLine( x1, y1, x2c, y2, g );
- }
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
- if ( y2 > y1 ) {
- y2_r = y2 - ROUNDED_D;
- if ( y2_r < y1 ) {
- y2_r = y1;
- }
- drawLine( x1, y1, x1, y2_r, g );
- }
- else {
- y2_r = y2 + ROUNDED_D;
- if ( y2_r > y1 ) {
- y2_r = y1;
- }
- drawLine( x1, y1, x1, y2_r, g );
- }
- }
- else {
- drawLine( x1, y1, x1, y2, g );
- }
- }
- }
- // draw the horizontal line
- if ( !to_graphics_file && !to_pdf
- && ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) || ( y2 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) {
+ final Phylogeny buffer_phy = getCutOrCopiedTree().copy();
+ buffer_phy.setAllNodesToNotCollapse();
+ PhylogenyMethods.preOrderReId( buffer_phy );
+ buffer_phy.setRooted( true );
+ boolean need_to_show_whole = false;
+ if ( paste_as_sibling ) {
+ if ( node.isRoot() ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot paste sibling to root",
+ "Attempt to paste sibling to root",
+ JOptionPane.ERROR_MESSAGE );
return;
}
- float x1_r = 0;
- if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
- x1_r = x1a + ROUNDED_D;
- if ( x1_r < x2a ) {
- drawLine( x1_r, y2, x2a, y2, g );
- }
- }
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
- final float x1c = x1a + EURO_D;
- if ( x1c < x2a ) {
- drawLine( x1c, y2, x2a, y2, g );
- }
- }
- else {
- drawLine( x1a, y2, x2a, y2, g );
- }
+ buffer_phy.addAsSibling( node );
+ }
+ else {
+ if ( ( node.getNumberOfExternalNodes() == 1 ) && node.isRoot() ) {
+ need_to_show_whole = true;
+ _phylogeny = buffer_phy;
}
else {
- final double w = PhylogenyMethods.getBranchWidthValue( node );
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
- x1_r = x1a + ROUNDED_D;
- if ( x1_r < x2a ) {
- drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );
- }
- }
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
- final float x1c = x1a + EURO_D;
- if ( x1c < x2a ) {
- drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );
- }
- }
- else {
- drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
- }
- }
- if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
- if ( x1_r > x2a ) {
- x1_r = x2a;
- }
- if ( y2 > y2_r ) {
- final double diff = y2 - y2_r;
- _arc.setArc( x1, y2_r - diff, 2 * ( x1_r - x1 ), 2 * diff, 180, 90, Arc2D.OPEN );
- }
- else {
- _arc.setArc( x1, y2, 2 * ( x1_r - x1 ), 2 * ( y2_r - y2 ), 90, 90, Arc2D.OPEN );
- }
- g.draw( _arc );
+ buffer_phy.addAsChild( node );
}
}
- if ( node.isExternal() ) {
- paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file );
+ if ( getCopiedAndPastedNodes() == null ) {
+ setCopiedAndPastedNodes( new HashSet<Long>() );
}
- }
-
- final private double paintCirculars( final PhylogenyNode n,
- final Phylogeny phy,
- final float center_x,
- final float center_y,
- final double radius,
- final boolean radial_labels,
- final Graphics2D g,
- final boolean to_pdf,
- final boolean to_graphics_file ) {
- if ( n.isExternal() || n.isCollapse() ) { //~~circ collapse
- if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) {
- System.out.println( "no " + n + " =====>>>>>>> ERROR!" );//TODO
- }
- return _urt_nodeid_angle_map.get( n.getId() );
+ final List<PhylogenyNode> nodes = PhylogenyMethods.obtainAllNodesAsList( buffer_phy );
+ final Set<Long> node_ids = new HashSet<Long>( nodes.size() );
+ for( final PhylogenyNode n : nodes ) {
+ node_ids.add( n.getId() );
}
- else {
- final List<PhylogenyNode> descs = n.getDescendants();
- double sum = 0;
- for( final PhylogenyNode desc : descs ) {
- sum += paintCirculars( desc,
- phy,
- center_x,
- center_y,
- radius,
- radial_labels,
- g,
- to_pdf,
- to_graphics_file );
- }
- double r = 0;
- if ( !n.isRoot() ) {
- r = 1 - ( ( ( double ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );
- }
- final double theta = sum / descs.size();
- n.setXcoord( ( float ) ( center_x + ( r * radius * Math.cos( theta ) ) ) );
- n.setYcoord( ( float ) ( center_y + ( r * radius * Math.sin( theta ) ) ) );
- _urt_nodeid_angle_map.put( n.getId(), theta );
- for( final PhylogenyNode desc : descs ) {
- paintBranchCircular( n, desc, g, radial_labels, to_pdf, to_graphics_file );
- }
- return theta;
+ node_ids.add( node.getId() );
+ getCopiedAndPastedNodes().addAll( node_ids );
+ setNodeInPreorderToNull();
+ _phylogeny.externalNodesHaveChanged();
+ _phylogeny.clearHashIdToNodeMap();
+ _phylogeny.recalculateNumberOfExternalDescendants( true );
+ resetNodeIdToDistToLeafMap();
+ setEdited( true );
+ if ( need_to_show_whole ) {
+ getControlPanel().showWhole();
}
+ repaint();
}
- final private void paintCircularsLite( final PhylogenyNode n,
- final Phylogeny phy,
- final int center_x,
- final int center_y,
- final int radius,
- final Graphics2D g ) {
- if ( n.isExternal() ) {
- return;
- }
- else {
- final List<PhylogenyNode> descs = n.getDescendants();
- for( final PhylogenyNode desc : descs ) {
- paintCircularsLite( desc, phy, center_x, center_y, radius, g );
+ private final StringBuffer propertiesToString( final PhylogenyNode node ) {
+ final PropertiesMap properties = node.getNodeData().getProperties();
+ final StringBuffer sb = new StringBuffer();
+ boolean first = true;
+ for( final String ref : properties.getPropertyRefs() ) {
+ if ( first ) {
+ first = false;
}
- float r = 0;
- if ( !n.isRoot() ) {
- r = 1 - ( ( ( float ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );
+ else {
+ sb.append( " " );
}
- final double theta = _urt_nodeid_angle_map.get( n.getId() );
- n.setXSecondary( ( float ) ( center_x + ( radius * r * Math.cos( theta ) ) ) );
- n.setYSecondary( ( float ) ( center_y + ( radius * r * Math.sin( theta ) ) ) );
- for( final PhylogenyNode desc : descs ) {
- paintBranchCircularLite( n, desc, g );
+ final Property p = properties.getProperty( ref );
+ sb.append( TreePanelUtil.getPartAfterColon( p.getRef() ) );
+ sb.append( "=" );
+ sb.append( p.getValue() );
+ if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
+ sb.append( TreePanelUtil.getPartAfterColon( p.getUnit() ) );
}
}
+ return sb;
}
- final private void paintCollapsedNode( final Graphics2D g,
- final PhylogenyNode node,
- final boolean to_graphics_file,
- final boolean to_pdf,
- final boolean is_in_found_nodes ) {
- Color c = null;
+ private void setColor( final Graphics2D g,
+ final PhylogenyNode node,
+ final boolean to_graphics_file,
+ final boolean to_pdf,
+ final boolean is_in_found_nodes,
+ final Color default_color ) {
if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- c = Color.BLACK;
+ g.setColor( Color.BLACK );
}
else if ( is_in_found_nodes ) {
- c = getColorForFoundNode( node );
+ g.setColor( getColorForFoundNode( node ) );
+ }
+ else if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null )
+ && ( node.getNodeData().getNodeVisualData().getFontColor() != null ) ) {
+ g.setColor( node.getNodeData().getNodeVisualData().getFontColor() );
}
else if ( getControlPanel().isColorAccordingToSequence() ) {
- c = getSequenceBasedColor( node );
+ g.setColor( getSequenceBasedColor( node ) );
}
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
- c = getTaxonomyBasedColor( node );
+ 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().getAnnotations() ) );
}
else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isUseVisualStyles()
&& ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
- c = PhylogenyMethods.getBranchColorValue( node );
+ g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
+ }
+ else if ( to_pdf ) {
+ g.setColor( Color.BLACK );
}
else {
- c = getTreeColorSet().getCollapseFillColor();
+ g.setColor( default_color );
}
- double d = node.getAllExternalDescendants().size();
- if ( d > 1000 ) {
- d = ( 3 * _y_distance ) / 3;
+ }
+
+ final private void setCopiedAndPastedNodes( final Set<Long> nodeIds ) {
+ getMainPanel().setCopiedAndPastedNodes( nodeIds );
+ }
+
+ final private void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) {
+ getMainPanel().setCutOrCopiedTree( cut_or_copied_tree );
+ }
+
+ private boolean setFont( final Graphics2D g, final PhylogenyNode node, final boolean is_in_found_nodes ) {
+ Font visual_font = null;
+ if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null ) ) {
+ visual_font = node.getNodeData().getNodeVisualData().getFont();
+ g.setFont( visual_font != null ? visual_font : getTreeFontSet().getLargeFont() );
}
else {
- d = ( Math.log10( d ) * _y_distance ) / 2.5;
+ g.setFont( getTreeFontSet().getLargeFont() );
}
- final int box_size = getOptions().getDefaultNodeShapeSize() + 1;
- if ( d < box_size ) {
- d = box_size;
+ if ( is_in_found_nodes ) {
+ g.setFont( g.getFont().deriveFont( Font.BOLD ) );
}
- final float xx = node.getXcoord() - ( 2 * box_size );
- final float xxx = xx > ( node.getParent().getXcoord() + 1 ) ? xx : node.getParent().getXcoord() + 1;
- _polygon.reset();
- _polygon.moveTo( xxx, node.getYcoord() );
- _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() - d );
- _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() + d );
- _polygon.closePath();
- if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.SOLID ) {
- g.setColor( c );
- g.fill( _polygon );
+ return visual_font != null;
+ }
+
+ final private void setInOv( final boolean in_ov ) {
+ _in_ov = in_ov;
+ }
+
+ final private void setOvMaxHeight( final float ov_max_height ) {
+ _ov_max_height = ov_max_height;
+ }
+
+ final private void setOvMaxWidth( final float ov_max_width ) {
+ _ov_max_width = ov_max_width;
+ }
+
+ final private void setOvXcorrectionFactor( final float f ) {
+ _ov_x_correction_factor = f;
+ }
+
+ final private void setOvXDistance( final float ov_x_distance ) {
+ _ov_x_distance = ov_x_distance;
+ }
+
+ final private void setOvXPosition( final int ov_x_position ) {
+ _ov_x_position = ov_x_position;
+ }
+
+ final private void setOvYDistance( final float ov_y_distance ) {
+ _ov_y_distance = ov_y_distance;
+ }
+
+ final private void setOvYPosition( final int ov_y_position ) {
+ _ov_y_position = ov_y_position;
+ }
+
+ final private void setOvYStart( final int ov_y_start ) {
+ _ov_y_start = ov_y_start;
+ }
+
+ final private void setScaleDistance( final double scale_distance ) {
+ _scale_distance = scale_distance;
+ }
+
+ final private void setScaleLabel( final String scale_label ) {
+ _scale_label = scale_label;
+ }
+
+ private final void setupStroke( final Graphics2D g ) {
+ if ( getYdistance() < 0.0001 ) {
+ g.setStroke( STROKE_0025 );
}
- else if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.NONE ) {
- g.setColor( getBackground() );
- g.fill( _polygon );
- g.setColor( c );
- g.draw( _polygon );
+ if ( getYdistance() < 0.001 ) {
+ g.setStroke( STROKE_005 );
}
- else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
- g.setPaint( new GradientPaint( xxx, node.getYcoord(), getBackground(), node.getXcoord(), ( float ) ( node
- .getYcoord() - d ), c, false ) );
- g.fill( _polygon );
- g.setPaint( c );
- g.draw( _polygon );
+ else if ( getYdistance() < 0.01 ) {
+ g.setStroke( STROKE_01 );
+ }
+ else if ( getYdistance() < 0.5 ) {
+ g.setStroke( STROKE_025 );
+ }
+ else if ( getYdistance() < 1 ) {
+ g.setStroke( STROKE_05 );
+ }
+ else if ( getYdistance() < 2 ) {
+ g.setStroke( STROKE_075 );
+ }
+ else if ( ( getYdistance() < 20 ) || !getConfiguration().isAllowThickStrokes() ) {
+ g.setStroke( STROKE_1 );
+ }
+ else {
+ g.setStroke( STROKE_2 );
}
- paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
}
- final private void paintConfidenceValues( final Graphics2D g,
- final PhylogenyNode node,
- final boolean to_pdf,
- final boolean to_graphics_file ) {
- final List<Confidence> confidences = node.getBranchData().getConfidences();
- boolean not_first = false;
- Collections.sort( confidences );
- final StringBuilder sb = new StringBuilder();
- for( final Confidence confidence : confidences ) {
- if ( ForesterUtil.isEmpty( SHOW_ONLY_THIS_CONF_TYPE )
- || ( !ForesterUtil.isEmpty( confidence.getType() ) && confidence.getType()
- .equalsIgnoreCase( SHOW_ONLY_THIS_CONF_TYPE ) ) ) {
- final double value = confidence.getValue();
- if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
- if ( value < getOptions().getMinConfidenceValue() ) {
- return;
- }
- if ( not_first ) {
- sb.append( "/" );
- }
- else {
- not_first = true;
- }
- sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
- .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
- if ( getOptions().isShowConfidenceStddev() ) {
- if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
- sb.append( "(" );
- sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence
- .getStandardDeviation(), getOptions()
- .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
- sb.append( ")" );
- }
- }
- }
- }
+ final private void setUpUrtFactor() {
+ final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width
+ : getVisibleRect().height;
+ if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
+ setUrtFactor( ( float ) ( d / ( 2 * getMaxDistanceToRoot() ) ) );
}
- if ( sb.length() > 0 ) {
- final float parent_x = node.getParent().getXcoord();
- float x = node.getXcoord();
- g.setFont( getTreeFontSet().getSmallFont() );
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
- x += EURO_D;
- }
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
- x += ROUNDED_D;
- }
- if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- g.setColor( Color.BLACK );
+ else {
+ final int max_depth = _circ_max_depth;
+ if ( max_depth > 0 ) {
+ setUrtFactor( d / ( 2 * max_depth ) );
}
else {
- g.setColor( getTreeColorSet().getConfidenceColor() );
+ setUrtFactor( d / 2 );
}
- final String conf_str = sb.toString();
- TreePanel.drawString( conf_str,
- parent_x
- + ( ( x - parent_x - getTreeFontSet().getFontMetricsSmall()
- .stringWidth( conf_str ) ) / 2 ),
- ( node.getYcoord() + getTreeFontSet().getSmallMaxAscent() ) - 1,
- g );
}
+ setUrtFactorOv( getUrtFactor() );
}
- final private void paintGainedAndLostCharacters( final Graphics2D g,
- final PhylogenyNode node,
- final String gained,
- final String lost ) {
- if ( node.getParent() != null ) {
- final float parent_x = node.getParent().getXcoord();
- final float x = node.getXcoord();
- g.setFont( getTreeFontSet().getLargeFont() );
- g.setColor( getTreeColorSet().getGainedCharactersColor() );
- if ( Constants.SPECIAL_CUSTOM ) {
- g.setColor( Color.BLUE );
- }
- TreePanel
- .drawString( gained,
- parent_x
- + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( gained ) ) / 2 ),
- ( node.getYcoord() - getFontMetricsForLargeDefaultFont().getMaxDescent() ),
- g );
- g.setColor( getTreeColorSet().getLostCharactersColor() );
- TreePanel
- .drawString( lost,
- parent_x
- + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( lost ) ) / 2 ),
- ( node.getYcoord() + getFontMetricsForLargeDefaultFont().getMaxAscent() ),
- g );
- }
+ final private void setUrtFactor( final float urt_factor ) {
+ _urt_factor = urt_factor;
}
- /**
- * Draw a box at the indicated node.
- *
- * @param x
- * @param y
- * @param node
- * @param g
- */
- final private void paintNodeBox( final float x,
- final float y,
- final PhylogenyNode node,
- final Graphics2D g,
- final boolean to_pdf,
- final boolean to_graphics_file ) {
- if ( node.isCollapse() ) {
- return;
- }
- // if this node should be highlighted, do so
- if ( ( _highlight_node == node ) && !to_pdf && !to_graphics_file ) {
- g.setColor( getTreeColorSet().getFoundColor0() );
- drawOval( x - 8, y - 8, 16, 16, g );
- drawOval( x - 9, y - 8, 17, 17, g );
- drawOval( x - 9, y - 9, 18, 18, g );
- }
- if ( ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) )
- || ( getOptions().isShowDefaultNodeShapesExternal() && node.isExternal() )
- || ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() )
- || ( getOptions().isShowDefaultNodeShapesForMarkedNodes()
- && ( node.getNodeData().getNodeVisualData() != null ) && ( !node.getNodeData()
- .getNodeVisualData().isEmpty() ) )
- || ( getControlPanel().isUseVisualStyles() && ( ( node.getNodeData().getNodeVisualData() != null ) && ( ( node
- .getNodeData().getNodeVisualData().getNodeColor() != null )
- || ( node.getNodeData().getNodeVisualData().getSize() != NodeVisualData.DEFAULT_SIZE )
- || ( node.getNodeData().getNodeVisualData().getFillType() != NodeFill.DEFAULT ) || ( node
- .getNodeData().getNodeVisualData().getShape() != NodeShape.DEFAULT ) ) ) )
- || ( getControlPanel().isEvents() && node.isHasAssignedEvent() && ( node.getNodeData().getEvent()
- .isDuplication()
- || node.getNodeData().getEvent().isSpeciation() || node.getNodeData().getEvent()
- .isSpeciationOrDuplication() ) ) ) {
- NodeVisualData vis = null;
- if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null )
- && ( !node.getNodeData().getNodeVisualData().isEmpty() ) ) {
- vis = node.getNodeData().getNodeVisualData();
- }
- float box_size = getOptions().getDefaultNodeShapeSize();
- if ( ( vis != null ) && ( vis.getSize() != NodeVisualData.DEFAULT_SIZE ) ) {
- box_size = vis.getSize();
- }
- final float half_box_size = box_size / 2.0f;
- Color outline_color = null;
- if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- outline_color = Color.BLACK;
- }
- else if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
- outline_color = getColorForFoundNode( node );
+ final private void setUrtFactorOv( final float urt_factor_ov ) {
+ _urt_factor_ov = urt_factor_ov;
+ }
+
+ private void showExtDescNodeData( final PhylogenyNode node ) {
+ final List<String> data = new ArrayList<String>();
+ final List<PhylogenyNode> nodes = node.getAllExternalDescendants();
+ if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
+ for( final PhylogenyNode n : getFoundNodesAsListOfPhylogenyNodes() ) {
+ if ( !nodes.contains( n ) ) {
+ nodes.add( n );
+ }
}
- else if ( vis != null ) {
- if ( vis.getNodeColor() != null ) {
- outline_color = vis.getNodeColor();
- }
- else if ( vis.getFontColor() != null ) {
- outline_color = vis.getFontColor();
- }
+ }
+ for( final PhylogenyNode n : nodes ) {
+ switch ( getOptions().getExtDescNodeDataToReturn() ) {
+ case NODE_NAME:
+ if ( !ForesterUtil.isEmpty( n.getName() ) ) {
+ data.add( n.getName() );
+ }
+ break;
+ case SEQUENCE_NAME:
+ if ( n.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
+ data.add( n.getNodeData().getSequence().getName() );
+ }
+ break;
+ case GENE_NAME:
+ if ( n.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) {
+ data.add( n.getNodeData().getSequence().getGeneName() );
+ }
+ break;
+ case SEQUENCE_SYMBOL:
+ if ( n.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
+ data.add( n.getNodeData().getSequence().getSymbol() );
+ }
+ break;
+ case SEQUENCE_MOL_SEQ_FASTA:
+ final StringBuilder sb = new StringBuilder();
+ if ( n.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
+ final StringBuilder ann = new StringBuilder();
+ if ( !ForesterUtil.isEmpty( n.getName() ) ) {
+ ann.append( n.getName() );
+ ann.append( "|" );
+ }
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
+ ann.append( "SYM=" );
+ ann.append( n.getNodeData().getSequence().getSymbol() );
+ ann.append( "|" );
+ }
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
+ ann.append( "NAME=" );
+ ann.append( n.getNodeData().getSequence().getName() );
+ ann.append( "|" );
+ }
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) {
+ ann.append( "GN=" );
+ ann.append( n.getNodeData().getSequence().getGeneName() );
+ ann.append( "|" );
+ }
+ if ( n.getNodeData().getSequence().getAccession() != null ) {
+ ann.append( "ACC=" );
+ ann.append( n.getNodeData().getSequence().getAccession().asText() );
+ ann.append( "|" );
+ }
+ if ( n.getNodeData().isHasTaxonomy() ) {
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+ ann.append( "TAXID=" );
+ ann.append( n.getNodeData().getTaxonomy().getTaxonomyCode() );
+ ann.append( "|" );
+ }
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+ ann.append( "SN=" );
+ ann.append( n.getNodeData().getTaxonomy().getScientificName() );
+ ann.append( "|" );
+ }
+ }
+ String ann_str;
+ if ( ann.charAt( ann.length() - 1 ) == '|' ) {
+ ann_str = ann.substring( 0, ann.length() - 1 );
+ }
+ else {
+ ann_str = ann.toString();
+ }
+ sb.append( SequenceWriter.toFasta( ann_str, n.getNodeData().getSequence()
+ .getMolecularSequence(), 60 ) );
+ data.add( sb.toString() );
+ }
+ break;
+ case SEQUENCE_ACC:
+ if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null )
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().toString() ) ) {
+ data.add( n.getNodeData().getSequence().getAccession().toString() );
+ }
+ break;
+ case TAXONOMY_SCIENTIFIC_NAME:
+ if ( n.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+ data.add( n.getNodeData().getTaxonomy().getScientificName() );
+ }
+ break;
+ case TAXONOMY_CODE:
+ if ( n.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+ data.add( n.getNodeData().getTaxonomy().getTaxonomyCode() );
+ }
+ break;
+ case DOMAINS_ALL:
+ case DOMAINS_COLLAPSED_PER_PROTEIN:
+ if ( n.getNodeData().isHasSequence()
+ && ( n.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
+ final DomainArchitecture da = n.getNodeData().getSequence().getDomainArchitecture();
+ final Set<String> s = new HashSet<String>();
+ for( int i = 0; i < da.getDomains().size(); ++i ) {
+ final ProteinDomain d = da.getDomain( i );
+ if ( d.getConfidence() <= Math.pow( 10, getDomainStructureEvalueThresholdExp() ) ) {
+ final String name = d.getName();
+ if ( !( s.contains( name ) ) ) {
+ data.add( name );
+ if ( getOptions().getExtDescNodeDataToReturn() == NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN ) {
+ s.add( name );
+ }
+ }
+ }
+ }
+ }
+ break;
+ case SEQ_ANNOTATIONS:
+ if ( n.getNodeData().isHasSequence() ) {
+ if ( n.getNodeData().isHasSequence()
+ && ( n.getNodeData().getSequence().getAnnotations() != null ) ) {
+ final SortedSet<Annotation> a = n.getNodeData().getSequence().getAnnotations();
+ for( int i = 0; i < a.size(); ++i ) {
+ data.add( n.getNodeData().getSequence().getAnnotation( i ).toString() );
+ }
+ }
+ }
+ break;
+ case GO_TERM_IDS:
+ if ( n.getNodeData().isHasSequence() ) {
+ if ( n.getNodeData().isHasSequence()
+ && ( n.getNodeData().getSequence().getAnnotations() != null ) ) {
+ final SortedSet<Annotation> a = n.getNodeData().getSequence().getAnnotations();
+ for( int i = 0; i < a.size(); ++i ) {
+ final Annotation ann = n.getNodeData().getSequence().getAnnotation( i );
+ final String ref = ann.getRef();
+ if ( ref.toUpperCase().startsWith( "GO:" ) ) {
+ data.add( ref );
+ }
+ }
+ }
+ }
+ break;
+ case UNKNOWN:
+ TreePanelUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data );
+ break;
+ default:
+ throw new IllegalArgumentException( "unknown data element: "
+ + getOptions().getExtDescNodeDataToReturn() );
}
- else if ( getControlPanel().isEvents() && TreePanelUtil.isHasAssignedEvent( node ) ) {
- final Event event = node.getNodeData().getEvent();
- if ( event.isDuplication() ) {
- outline_color = getTreeColorSet().getDuplicationBoxColor();
- }
- else if ( event.isSpeciation() ) {
- outline_color = getTreeColorSet().getSpecBoxColor();
- }
- else if ( event.isSpeciationOrDuplication() ) {
- outline_color = getTreeColorSet().getDuplicationOrSpeciationColor();
- }
+ } // for loop
+ final StringBuilder sb = new StringBuilder();
+ final int size = TreePanelUtil.nodeDataIntoStringBuffer( data, getOptions(), sb );
+ if ( ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE )
+ || ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ) ) {
+ if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
+ System.out.println( sb );
}
- if ( outline_color == null ) {
- outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node );
- if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) {
- outline_color = getTreeColorSet().getBranchColorForPdf();
- }
+ if ( sb.length() < 1 ) {
+ clearCurrentExternalNodesDataBuffer();
}
- NodeShape shape = null;
- if ( vis != null ) {
- if ( vis.getShape() == NodeShape.CIRCLE ) {
- shape = NodeShape.CIRCLE;
- }
- else if ( vis.getShape() == NodeShape.RECTANGLE ) {
- shape = NodeShape.RECTANGLE;
- }
+ else {
+ setCurrentExternalNodesDataBuffer( sb );
}
- if ( shape == null ) {
- if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
- shape = NodeShape.CIRCLE;
- }
- else if ( getOptions().getDefaultNodeShape() == NodeShape.RECTANGLE ) {
- shape = NodeShape.RECTANGLE;
- }
+ }
+ else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) {
+ if ( sb.length() < 1 ) {
+ TreePanelUtil.showInformationMessage( this, "No Appropriate Data (" + obtainTitleForExtDescNodeData()
+ + ")", "Descendants of selected node do not contain selected data" );
+ clearCurrentExternalNodesDataBuffer();
}
- NodeFill fill = null;
- if ( vis != null ) {
- if ( vis.getFillType() == NodeFill.SOLID ) {
- fill = NodeFill.SOLID;
- }
- else if ( vis.getFillType() == NodeFill.NONE ) {
- fill = NodeFill.NONE;
- }
- else if ( vis.getFillType() == NodeFill.GRADIENT ) {
- fill = NodeFill.GRADIENT;
+ else {
+ setCurrentExternalNodesDataBuffer( sb );
+ String title;
+ if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) {
+ title = ( getOptions().getExtDescNodeDataToReturn() == NodeDataField.UNKNOWN ? "Data"
+ : obtainTitleForExtDescNodeData() )
+ + " for "
+ + data.size()
+ + " nodes, unique entries: "
+ + size;
}
- }
- if ( fill == null ) {
- if ( getOptions().getDefaultNodeFill() == NodeFill.SOLID ) {
- fill = NodeFill.SOLID;
+ else {
+ title = ( getOptions().getExtDescNodeDataToReturn() == NodeDataField.UNKNOWN ? "Data"
+ : obtainTitleForExtDescNodeData() )
+ + " for "
+ + data.size()
+ + "/"
+ + node.getNumberOfExternalNodes()
+ + " external descendats of node "
+ + node
+ + ", unique entries: " + size;
}
- else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
- fill = NodeFill.NONE;
+ final String s = sb.toString().trim();
+ if ( getMainPanel().getMainFrame() == null ) {
+ // Must be "E" applet version.
+ final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
+ ae.showTextFrame( s, title );
}
- else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
- fill = NodeFill.GRADIENT;
+ else {
+ getMainPanel().getMainFrame().showTextFrame( s, title );
}
}
- Color vis_fill_color = null;
- if ( ( vis != null ) && ( vis.getNodeColor() != null ) ) {
- vis_fill_color = vis.getNodeColor();
- }
- if ( shape == NodeShape.CIRCLE ) {
- if ( fill == NodeFill.GRADIENT ) {
- drawOvalGradient( x - half_box_size, y - half_box_size, box_size, box_size, g, to_pdf ? Color.WHITE
- : outline_color, to_pdf ? outline_color : getBackground(), outline_color );
- }
- else if ( fill == NodeFill.NONE ) {
- Color background = getBackground();
- if ( to_pdf ) {
- background = Color.WHITE;
+ }
+ }
+
+ final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) {
+ try {
+ if ( ( node.getName().length() > 0 )
+ || ( node.getNodeData().isHasTaxonomy() && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData()
+ .getTaxonomy() ) )
+ || ( node.getNodeData().isHasSequence() && !TreePanelUtil.isSequenceEmpty( node.getNodeData()
+ .getSequence() ) ) || ( node.getNodeData().isHasDate() )
+ || ( node.getNodeData().isHasDistribution() ) || node.getBranchData().isHasConfidences() ) {
+ _popup_buffer.setLength( 0 );
+ short lines = 0;
+ if ( node.getName().length() > 0 ) {
+ lines++;
+ _popup_buffer.append( node.getName() );
+ }
+ if ( node.getNodeData().isHasTaxonomy()
+ && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) {
+ lines++;
+ boolean enc_data = false;
+ final Taxonomy tax = node.getNodeData().getTaxonomy();
+ if ( _popup_buffer.length() > 0 ) {
+ _popup_buffer.append( "\n" );
+ }
+ if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
+ _popup_buffer.append( "[" );
+ _popup_buffer.append( tax.getTaxonomyCode() );
+ _popup_buffer.append( "]" );
+ enc_data = true;
+ }
+ if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
+ if ( enc_data ) {
+ _popup_buffer.append( " " );
+ }
+ _popup_buffer.append( tax.getScientificName() );
+ enc_data = true;
+ }
+ if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
+ if ( enc_data ) {
+ _popup_buffer.append( " (" );
+ }
+ else {
+ _popup_buffer.append( "(" );
+ }
+ _popup_buffer.append( tax.getCommonName() );
+ _popup_buffer.append( ")" );
+ enc_data = true;
+ }
+ if ( !ForesterUtil.isEmpty( tax.getAuthority() ) ) {
+ if ( enc_data ) {
+ _popup_buffer.append( " (" );
+ }
+ else {
+ _popup_buffer.append( "(" );
+ }
+ _popup_buffer.append( tax.getAuthority() );
+ _popup_buffer.append( ")" );
+ enc_data = true;
+ }
+ if ( !ForesterUtil.isEmpty( tax.getRank() ) ) {
+ if ( enc_data ) {
+ _popup_buffer.append( " [" );
+ }
+ else {
+ _popup_buffer.append( "[" );
+ }
+ _popup_buffer.append( tax.getRank() );
+ _popup_buffer.append( "]" );
+ enc_data = true;
+ }
+ if ( tax.getSynonyms().size() > 0 ) {
+ if ( enc_data ) {
+ _popup_buffer.append( " " );
+ }
+ _popup_buffer.append( "[" );
+ int counter = 1;
+ for( final String syn : tax.getSynonyms() ) {
+ if ( !ForesterUtil.isEmpty( syn ) ) {
+ enc_data = true;
+ _popup_buffer.append( syn );
+ if ( counter < tax.getSynonyms().size() ) {
+ _popup_buffer.append( ", " );
+ }
+ }
+ counter++;
+ }
+ _popup_buffer.append( "]" );
+ }
+ if ( !enc_data ) {
+ if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
+ if ( !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
+ _popup_buffer.append( "[" );
+ _popup_buffer.append( tax.getIdentifier().getProvider() );
+ _popup_buffer.append( "] " );
+ }
+ _popup_buffer.append( tax.getIdentifier().getValue() );
+ }
}
- drawOvalGradient( x - half_box_size,
- y - half_box_size,
- box_size,
- box_size,
- g,
- background,
- background,
- outline_color );
}
- else if ( fill == NodeVisualData.NodeFill.SOLID ) {
- if ( vis_fill_color != null ) {
- g.setColor( vis_fill_color );
+ if ( node.getNodeData().isHasSequence()
+ && !TreePanelUtil.isSequenceEmpty( node.getNodeData().getSequence() ) ) {
+ lines++;
+ boolean enc_data = false;
+ if ( _popup_buffer.length() > 0 ) {
+ _popup_buffer.append( "\n" );
}
- else {
- g.setColor( outline_color );
+ final Sequence seq = node.getNodeData().getSequence();
+ if ( seq.getAccession() != null ) {
+ _popup_buffer.append( "[" );
+ if ( !ForesterUtil.isEmpty( seq.getAccession().getSource() ) ) {
+ _popup_buffer.append( seq.getAccession().getSource() );
+ _popup_buffer.append( ":" );
+ }
+ _popup_buffer.append( seq.getAccession().getValue() );
+ _popup_buffer.append( "]" );
+ enc_data = true;
+ }
+ if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
+ if ( enc_data ) {
+ _popup_buffer.append( " [" );
+ }
+ else {
+ _popup_buffer.append( "[" );
+ }
+ _popup_buffer.append( seq.getSymbol() );
+ _popup_buffer.append( "]" );
+ enc_data = true;
+ }
+ if ( !ForesterUtil.isEmpty( seq.getGeneName() ) ) {
+ if ( enc_data ) {
+ _popup_buffer.append( " [" );
+ }
+ else {
+ _popup_buffer.append( "[" );
+ }
+ _popup_buffer.append( seq.getGeneName() );
+ _popup_buffer.append( "]" );
+ enc_data = true;
+ }
+ if ( !ForesterUtil.isEmpty( seq.getName() ) ) {
+ if ( enc_data ) {
+ _popup_buffer.append( " " );
+ }
+ _popup_buffer.append( seq.getName() );
}
- drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
}
- }
- else if ( shape == NodeVisualData.NodeShape.RECTANGLE ) {
- if ( fill == NodeVisualData.NodeFill.GRADIENT ) {
- drawRectGradient( x - half_box_size, y - half_box_size, box_size, box_size, g, to_pdf ? Color.WHITE
- : outline_color, to_pdf ? outline_color : getBackground(), outline_color );
+ if ( node.getNodeData().isHasDate() ) {
+ lines++;
+ if ( _popup_buffer.length() > 0 ) {
+ _popup_buffer.append( "\n" );
+ }
+ _popup_buffer.append( node.getNodeData().getDate().asSimpleText() );
}
- else if ( fill == NodeVisualData.NodeFill.NONE ) {
- Color background = getBackground();
- if ( to_pdf ) {
- background = Color.WHITE;
+ if ( node.getNodeData().isHasDistribution() ) {
+ lines++;
+ if ( _popup_buffer.length() > 0 ) {
+ _popup_buffer.append( "\n" );
}
- drawRectGradient( x - half_box_size,
- y - half_box_size,
- box_size,
- box_size,
- g,
- background,
- background,
- outline_color );
+ _popup_buffer.append( node.getNodeData().getDistribution().asSimpleText() );
}
- else if ( fill == NodeVisualData.NodeFill.SOLID ) {
- if ( vis_fill_color != null ) {
- g.setColor( vis_fill_color );
+ if ( node.getBranchData().isHasConfidences() ) {
+ final List<Confidence> confs = node.getBranchData().getConfidences();
+ for( final Confidence confidence : confs ) {
+ lines++;
+ if ( _popup_buffer.length() > 0 ) {
+ _popup_buffer.append( "\n" );
+ }
+ if ( !ForesterUtil.isEmpty( confidence.getType() ) ) {
+ _popup_buffer.append( "[" );
+ _popup_buffer.append( confidence.getType() );
+ _popup_buffer.append( "] " );
+ }
+ _popup_buffer
+ .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(),
+ getOptions()
+ .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+ if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
+ _popup_buffer.append( " (sd=" );
+ _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence
+ .getStandardDeviation(), getOptions()
+ .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+ _popup_buffer.append( ")" );
+ }
+ }
+ }
+ if ( node.getNodeData().isHasProperties() ) {
+ final PropertiesMap properties = node.getNodeData().getProperties();
+ for( final String ref : properties.getPropertyRefs() ) {
+ _popup_buffer.append( "\n" );
+ final Property p = properties.getProperty( ref );
+ _popup_buffer.append( TreePanelUtil.getPartAfterColon( p.getRef() ) );
+ _popup_buffer.append( "=" );
+ _popup_buffer.append( p.getValue() );
+ if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
+ _popup_buffer.append( TreePanelUtil.getPartAfterColon( p.getUnit() ) );
+ }
+ }
+ }
+ if ( _popup_buffer.length() > 0 ) {
+ if ( !getConfiguration().isUseNativeUI() ) {
+ _rollover_popup
+ .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
+ _rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() );
+ if ( isInFoundNodes0( node ) && !isInFoundNodes1( node ) ) {
+ _rollover_popup.setForeground( getTreeColorSet().getFoundColor0() );
+ }
+ else if ( !isInFoundNodes0( node ) && isInFoundNodes1( node ) ) {
+ _rollover_popup.setForeground( getTreeColorSet().getFoundColor1() );
+ }
+ else if ( isInFoundNodes0( node ) && isInFoundNodes1( node ) ) {
+ _rollover_popup.setForeground( getTreeColorSet().getFoundColor0and1() );
+ }
+ else {
+ _rollover_popup.setForeground( getTreeColorSet().getSequenceColor() );
+ }
}
else {
- g.setColor( outline_color );
+ _rollover_popup.setBorder( BorderFactory.createLineBorder( Color.BLACK ) );
}
- drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
+ _rollover_popup.setText( _popup_buffer.toString() );
+ _node_desc_popup = PopupFactory.getSharedInstance().getPopup( null,
+ _rollover_popup,
+ e.getLocationOnScreen().x + 10,
+ e.getLocationOnScreen().y
+ - ( lines * 20 ) );
+ _node_desc_popup.show();
}
}
}
+ catch ( final Exception ex ) {
+ // Do nothing.
+ }
}
- final private int paintNodeData( final Graphics2D g,
- final PhylogenyNode node,
- final boolean to_graphics_file,
- final boolean to_pdf,
- final boolean is_in_found_nodes ) {
- if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) {
- return 0;
- }
- if ( getControlPanel().isWriteBranchLengthValues()
- && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
- || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
- && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
- paintBranchLength( g, node, to_pdf, to_graphics_file );
+ final private void showNodeEditFrame( final PhylogenyNode n ) {
+ if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
+ // pop up edit box for single node
+ _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index, "" );
+ _node_frame_index++;
}
- if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
- return 0;
+ else {
+ JOptionPane.showMessageDialog( this, "too many node windows are open" );
}
- _sb.setLength( 0 );
- int x = 0;
- final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
- if ( getControlPanel().isShowTaxonomyImages()
- && ( getImageMap() != null )
- && !getImageMap().isEmpty()
- && node.getNodeData().isHasTaxonomy()
- && ( ( node.getNodeData().getTaxonomy().getUris() != null ) && !node.getNodeData().getTaxonomy()
- .getUris().isEmpty() ) ) {
- x += drawTaxonomyImage( node.getXcoord() + 2 + half_box_size, node.getYcoord(), node, g );
+ }
+
+ final private void showNodeFrame( final PhylogenyNode n ) {
+ if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
+ // pop up edit box for single node
+ _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index );
+ _node_frame_index++;
}
- if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
- .isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) {
- x += paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file, x );
+ else {
+ JOptionPane.showMessageDialog( this, "too many node windows are open" );
}
- setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getSequenceColor() );
- if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
- if ( _sb.length() > 0 ) {
- _sb.setLength( 0 );
- _sb.append( " (" );
- _sb.append( node.getAllExternalDescendants().size() );
- _sb.append( ")" );
+ }
+
+ final private void switchDisplaygetPhylogenyGraphicsType() {
+ switch ( getPhylogenyGraphicsType() ) {
+ case RECTANGULAR:
+ setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
+ getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
+ break;
+ case EURO_STYLE:
+ setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
+ getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
+ break;
+ case ROUNDED:
+ setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
+ getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
+ break;
+ case CURVED:
+ setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
+ getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
+ break;
+ case TRIANGULAR:
+ setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
+ getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
+ break;
+ case CONVEX:
+ setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
+ getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
+ break;
+ case UNROOTED:
+ setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
+ getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
+ break;
+ case CIRCULAR:
+ setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
+ getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
+ break;
+ default:
+ throw new RuntimeException( "unkwnown display type: " + getPhylogenyGraphicsType() );
+ }
+ if ( getControlPanel().getDynamicallyHideData() != null ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ getControlPanel().getDynamicallyHideData().setEnabled( false );
+ }
+ else {
+ getControlPanel().getDynamicallyHideData().setEnabled( true );
}
}
- else {
- _sb.setLength( 0 );
+ if ( isPhyHasBranchLengths() && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
+ getControlPanel().setDrawPhylogramEnabled( true );
}
- nodeDataAsSB( node, _sb );
- final boolean using_visual_font = setFont( g, node, is_in_found_nodes );
- float down_shift_factor = 3.0f;
- if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
- down_shift_factor = 1;
+ else {
+ getControlPanel().setDrawPhylogramEnabled( false );
}
- final float pos_x = node.getXcoord() + x + 2 + half_box_size;
- float pos_y;
- if ( !using_visual_font ) {
- pos_y = ( node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ) );
+ if ( getMainPanel().getMainFrame() == null ) {
+ // Must be "E" applet version.
+ ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
+ .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
}
else {
- pos_y = ( node.getYcoord() + ( getFontMetrics( g.getFont() ).getAscent() / down_shift_factor ) );
+ getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
}
- final String sb_str = _sb.toString();
- // GUILHEM_BEG ______________
- if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence()
- && ( _query_sequence != null ) ) {
- int nodeTextBoundsWidth = 0;
- if ( sb_str.length() > 0 ) {
- final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how...
- nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth();
- }
- if ( node.getNodeData().getSequence().equals( _query_sequence ) ) {
- if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence
- g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 );
- g.setColor( getTreeColorSet().getBackgroundColor() );
+ }
+
+ final void calcMaxDepth() {
+ if ( _phylogeny != null ) {
+ _circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
+ }
+ }
+
+ /**
+ * Set parameters for printing the displayed tree
+ *
+ */
+ final void calcParametersForPainting( final int x, final int y ) {
+ // updateStyle(); not needed?
+ if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
+ initNodeData();
+ calculateLongestExtNodeInfo();
+ if ( ( getLongestExtNodeInfo() > ( x * 0.6 ) )
+ && ( getTreeFontSet().getLargeFont().getSize() > ( 2 + TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) ) {
+ while ( ( getLongestExtNodeInfo() > ( x * 0.7 ) ) && ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) {
+ getMainPanel().getTreeFontSet().decreaseFontSize( getConfiguration().getMinBaseFontSize(), true );
+ calculateLongestExtNodeInfo();
}
}
else {
- final List<SequenceRelation> seqRelations = node.getNodeData().getSequence().getSequenceRelations();
- for( final SequenceRelation seqRelation : seqRelations ) {
- final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence ) || seqRelation
- .getRef1().isEqual( _query_sequence ) )
- && seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox()
- .getSelectedItem() );
- if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query
- final double linePosX = node.getXcoord() + 2 + half_box_size;
- final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation
- .getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue()
- + ")";
- if ( sConfidence != null ) {
- float confidenceX = pos_x;
- if ( sb_str.length() > 0 ) {
- confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth()
- + CONFIDENCE_LEFT_MARGIN;
- }
- if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code
- final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc )
- .getBounds().getWidth();
- TreePanel.drawString( sConfidence, confidenceX, pos_y, g );
- x += CONFIDENCE_LEFT_MARGIN + confidenceWidth;
- }
- }
- if ( ( x + nodeTextBoundsWidth ) > 0 ) /* we only underline if there is something displayed */
- {
- if ( nodeTextBoundsWidth == 0 ) {
- nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */
- }
- else {
- nodeTextBoundsWidth += 2;
- }
- g.drawLine( ( int ) linePosX + 1, 3 + ( int ) pos_y, ( int ) linePosX + x
- + nodeTextBoundsWidth, 3 + ( int ) pos_y );
- break;
- }
- }
+ while ( ( getLongestExtNodeInfo() < ( x * 0.6 ) )
+ && ( getTreeFontSet().getLargeFont().getSize() <= ( getTreeFontSet().getLargeFontMemory()
+ .getSize() - TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) ) {
+ getMainPanel().getTreeFontSet().increaseFontSize();
+ calculateLongestExtNodeInfo();
}
}
- }
- if ( sb_str.length() > 0 ) {
- TreePanel.drawString( sb_str, pos_x, pos_y, g );
- }
- // GUILHEM_END _____________
- if ( _sb.length() > 0 ) {
- if ( !using_visual_font && !is_in_found_nodes ) {
- x += getFontMetricsForLargeDefaultFont().stringWidth( _sb.toString() ) + 5;
+ //_length_of_longest_text = calcLengthOfLongestText();
+ int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
+ final int max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
+ if ( ext_nodes == 1 ) {
+ ext_nodes = max_depth;
+ if ( ext_nodes < 1 ) {
+ ext_nodes = 1;
+ }
}
- else {
- x += getFontMetrics( g.getFont() ).stringWidth( _sb.toString() ) + 5;
+ updateOvSizes();
+ float xdist = 0;
+ float ov_xdist = 0;
+ if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
+ xdist = ( float ) ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( ext_nodes + 3.0 ) );
+ ov_xdist = ( float ) ( getOvMaxWidth() / ( ext_nodes + 3.0 ) );
}
- }
- if ( getControlPanel().isShowAnnotation() && node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getAnnotations() != null )
- && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
- final SortedSet<Annotation> ann = node.getNodeData().getSequence().getAnnotations();
- if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- g.setColor( Color.BLACK );
+ else {
+ xdist = ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( max_depth + 1 ) );
+ ov_xdist = ( getOvMaxWidth() / ( max_depth + 1 ) );
}
- else if ( getControlPanel().isColorAccordingToAnnotation() ) {
- g.setColor( calculateColorForAnnotation( ann ) );
+ float ydist = ( float ) ( ( y - TreePanel.MOVE ) / ( ext_nodes * 2.0 ) );
+ if ( xdist < 0.0 ) {
+ xdist = 0.0f;
}
- final String ann_str = TreePanelUtil.createAnnotationString( ann, getOptions().isShowAnnotationRefSource() );
- TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord()
- + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ), g );
- _sb.setLength( 0 );
- _sb.append( ann_str );
- if ( _sb.length() > 0 ) {
- if ( !using_visual_font && !is_in_found_nodes ) {
- x += getFontMetricsForLargeDefaultFont().stringWidth( _sb.toString() ) + 5;
- }
- else {
- x += getFontMetrics( g.getFont() ).stringWidth( _sb.toString() ) + 5;
- }
+ if ( ov_xdist < 0.0 ) {
+ ov_xdist = 0.0f;
}
- }
- if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
- || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
- || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
- if ( ( getControlPanel().isShowBinaryCharacters() || getControlPanel().isShowBinaryCharacterCounts() )
- && node.getNodeData().isHasBinaryCharacters() ) {
- if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- g.setColor( Color.BLACK );
- }
- else {
- g.setColor( getTreeColorSet().getBinaryDomainCombinationsColor() );
- }
- if ( getControlPanel().isShowBinaryCharacters() ) {
- TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()
- .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord()
- + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ), g );
- paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters()
- .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters()
- .getLostCharactersAsStringBuffer().toString() );
- }
- else {
- TreePanel
- .drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
- node.getXcoord() + x + 4 + half_box_size,
- node.getYcoord()
- + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ),
- g );
- paintGainedAndLostCharacters( g, node, "+"
- + node.getNodeData().getBinaryCharacters().getGainedCount(), "-"
- + node.getNodeData().getBinaryCharacters().getLostCount() );
- }
+ if ( ydist < 0.0 ) {
+ ydist = 0.0f;
}
- }
- return x;
- }
-
- final private void paintNodeDataUnrootedCirc( final Graphics2D g,
- final PhylogenyNode node,
- final boolean to_pdf,
- final boolean to_graphics_file,
- final boolean radial_labels,
- final double ur_angle,
- final boolean is_in_found_nodes ) {
- if ( isNodeDataInvisibleUnrootedCirc( node ) && !to_graphics_file && !to_pdf ) {
- return;
- }
- _sb.setLength( 0 );
- _sb.append( " " );
- if ( node.getNodeData().isHasTaxonomy()
- && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
- .isShowTaxonomyCommonNames() ) ) {
- final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
- if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
- _sb.append( taxonomy.getTaxonomyCode() );
- _sb.append( " " );
- }
- if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
- if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
- && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
- _sb.append( taxonomy.getScientificName() );
- _sb.append( " (" );
- _sb.append( taxonomy.getCommonName() );
- _sb.append( ") " );
- }
- else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
- _sb.append( taxonomy.getScientificName() );
- _sb.append( " " );
- }
- else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
- _sb.append( taxonomy.getCommonName() );
- _sb.append( " " );
- }
+ setXdistance( xdist );
+ setYdistance( ydist );
+ setOvXDistance( ov_xdist );
+ final double height = _phylogeny.getHeight();
+ if ( height > 0 ) {
+ final float corr = ( float ) ( ( x - TreePanel.MOVE - getLongestExtNodeInfo() - getXdistance() ) / height );
+ setXcorrectionFactor( corr > 0 ? corr : 0 );
+ final float ov_corr = ( float ) ( ( getOvMaxWidth() - getOvXDistance() ) / height );
+ setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
}
- else if ( _control_panel.isShowTaxonomyScientificNames() ) {
- if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
- _sb.append( taxonomy.getScientificName() );
- _sb.append( " " );
- }
+ else {
+ setXcorrectionFactor( 0 );
+ setOvXcorrectionFactor( 0 );
}
- else if ( _control_panel.isShowTaxonomyCommonNames() ) {
- if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
- _sb.append( taxonomy.getCommonName() );
- _sb.append( " " );
- }
+ _circ_max_depth = max_depth;
+ setUpUrtFactor();
+ //
+ if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
+ && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
+ // int dynamic_hiding_factor = calcDynamicHidingFactor();
+ // if ( dynamic_hiding_factor > 1 ) {
+ // while ( dynamic_hiding_factor > 1
+ // && getTreeFontSet()._fm_large.getHeight() > TreeFontSet.SMALL_FONTS_BASE ) {
+ // getTreeFontSet().decreaseFontSize( 1, true );
+ // dynamic_hiding_factor = calcDynamicHidingFactor();
+ // }
+ // }
+ // else if ( getTreeFontSet().isDecreasedSizeBySystem() ) {
+ // while ( dynamic_hiding_factor < 1 && getTreeFontSet()._fm_large.getHeight() < 12 ) {
+ // getTreeFontSet().increaseFontSize();
+ // dynamic_hiding_factor = calcDynamicHidingFactor();
+ // }
+ // }
}
+ //
}
- if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
- _sb.append( " [" );
- _sb.append( node.getAllExternalDescendants().size() );
- _sb.append( "]" );
+ }
+
+ final void calculateLongestExtNodeInfo() {
+ if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
+ return;
}
- if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
- if ( _sb.length() > 0 ) {
- _sb.append( " " );
- }
- _sb.append( node.getName() );
+ int max_length = ForesterUtil.roundToInt( ( getSize().getWidth() - MOVE )
+ * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO );
+ if ( max_length < 40 ) {
+ max_length = 40;
}
- if ( node.getNodeData().isHasSequence() ) {
- if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
- if ( _sb.length() > 0 ) {
- _sb.append( " " );
- }
- if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
- _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
- _sb.append( ":" );
- }
- _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
+ int longest = 30;
+ int longest_txt = 0;
+ _longest_domain = 0;
+ PhylogenyNode longest_txt_node = _phylogeny.getFirstExternalNode();
+ for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
+ int sum = 0;
+ if ( node.isCollapse() ) {
+ continue;
}
- if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
- if ( _sb.length() > 0 ) {
- _sb.append( " " );
- }
- _sb.append( node.getNodeData().getSequence().getName() );
+ final StringBuilder sb = new StringBuilder();
+ nodeDataAsSB( node, sb );
+ if ( node.getNodeData().isHasTaxonomy() ) {
+ nodeTaxonomyDataAsSB( node.getNodeData().getTaxonomy(), sb );
}
- }
- //g.setFont( getTreeFontSet().getLargeFont() );
- //if ( is_in_found_nodes ) {
- // g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
- // }
- if ( _sb.length() > 1 ) {
- setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getSequenceColor() );
- final boolean using_visual_font = setFont( g, node, is_in_found_nodes );
- final String sb_str = _sb.toString();
- double m = 0;
- if ( _graphics_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
- m = _urt_nodeid_angle_map.get( node.getId() ) % TWO_PI;
+ final int txt = sb.length();
+ if ( txt > longest_txt ) {
+ longest_txt = txt;
+ longest_txt_node = node;
}
- else {
- m = ( float ) ( ur_angle % TWO_PI );
+ boolean use_vis = false;
+ final Graphics2D g = ( Graphics2D ) getGraphics();
+ if ( getControlPanel().isUseVisualStyles() ) {
+ use_vis = setFont( g, node, false );
}
- _at = g.getTransform();
- boolean need_to_reset = false;
- final float x_coord = node.getXcoord();
- float y_coord;
- if ( !using_visual_font ) {
- y_coord = node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent() / 3.0f );
+ if ( !use_vis ) {
+ sum = getFontMetricsForLargeDefaultFont().stringWidth( sb.toString() );
}
else {
- y_coord = node.getYcoord() + ( getFontMetrics( g.getFont() ).getAscent() / 3.0f );
+ sum = getFontMetrics( g.getFont() ).stringWidth( sb.toString() );
}
- if ( radial_labels ) {
- need_to_reset = true;
- boolean left = false;
- if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
- m -= PI;
- left = true;
+ if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
+ sum += getFontMetricsForLargeDefaultFont().stringWidth( node.getNodeData().getBinaryCharacters()
+ .getGainedCharactersAsStringBuffer().toString() );
+ }
+ if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
+ && ( node.getNodeData().getVector().size() > 0 ) ) {
+ if ( getConfiguration() != null ) {
+ sum += getConfiguration().getVectorDataWidth() + 10;
}
- g.rotate( m, x_coord, node.getYcoord() );
- if ( left ) {
- if ( !using_visual_font ) {
- g.translate( -( getFontMetricsForLargeDefaultFont().getStringBounds( sb_str, g ).getWidth() ),
- 0 );
- }
- else {
- g.translate( -( getFontMetrics( g.getFont() ).getStringBounds( sb_str, g ).getWidth() ), 0 );
- }
+ else {
+ sum += RenderableVector.VECTOR_DEFAULT_WIDTH + 10;
}
}
- else {
- if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
- need_to_reset = true;
- if ( !using_visual_font ) {
- g.translate( -getFontMetricsForLargeDefaultFont().getStringBounds( sb_str, g ).getWidth(), 0 );
- }
- else {
- g.translate( -getFontMetrics( g.getFont() ).getStringBounds( sb_str, g ).getWidth(), 0 );
- }
+ if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
+ // FIXME
+ // TODO this might need some clean up
+ final DomainArchitecture d = node.getNodeData().getSequence().getDomainArchitecture();
+ sum += ( ( _domain_structure_width / ( ( RenderableDomainArchitecture ) d ).getOriginalSize()
+ .getWidth() ) * d.getTotalLength() ) + 10;
+ if ( d.getTotalLength() > _longest_domain ) {
+ _longest_domain = d.getTotalLength();
}
}
- TreePanel.drawString( sb_str, x_coord, y_coord, g );
- if ( need_to_reset ) {
- g.setTransform( _at );
+ if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() )
+ && ( node.getNodeData().getSequence().isMolecularSequenceAligned() )
+ && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) {
+ // FIXME
+ sum += RenderableMsaSequence.DEFAULT_WIDTH + 30;
}
+ if ( sum >= max_length ) {
+ _longest_ext_node_info = max_length;
+ // return; //FIXME why?
+ }
+ if ( sum > longest ) {
+ longest = sum;
+ }
+ }
+ _ext_node_with_longest_txt_info = longest_txt_node;
+ if ( longest >= max_length ) {
+ _longest_ext_node_info = max_length;
+ }
+ else {
+ _longest_ext_node_info = longest;
}
+ _length_of_longest_text = calcLengthOfLongestText();
}
- final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) {
- if ( node.isCollapse() ) {
- if ( !node.isRoot() && !node.getParent().isCollapse() ) {
- paintCollapsedNode( g, node, false, false, false );
- }
+ final void calculateScaleDistance() {
+ if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
return;
}
- if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
- g.setColor( getColorForFoundNode( node ) );
- drawRectFilled( node.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, node.getYSecondary()
- - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g );
+ final double height = getMaxDistanceToRoot();
+ if ( height > 0 ) {
+ if ( ( height <= 0.5 ) ) {
+ setScaleDistance( 0.01 );
+ }
+ else if ( height <= 5.0 ) {
+ setScaleDistance( 0.1 );
+ }
+ else if ( height <= 50.0 ) {
+ setScaleDistance( 1 );
+ }
+ else if ( height <= 500.0 ) {
+ setScaleDistance( 10 );
+ }
+ else {
+ setScaleDistance( 100 );
+ }
}
- float new_x = 0;
- if ( !node.isExternal() && !node.isCollapse() ) {
- boolean first_child = true;
- float y2 = 0.0f;
- final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
- for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
- final PhylogenyNode child_node = node.getChildNode( i );
- int factor_x;
- if ( !isUniformBranchLengthsForCladogram() ) {
- factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
- }
- else {
- factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
- }
- if ( first_child ) {
- first_child = false;
- y2 = node.getYSecondary()
- - ( getOvYDistance() * ( node.getNumberOfExternalNodes() - child_node
- .getNumberOfExternalNodes() ) );
- }
- else {
- y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
- }
- final float x2 = calculateOvBranchLengthToParent( child_node, factor_x );
- new_x = x2 + node.getXSecondary();
- final float diff_y = node.getYSecondary() - y2;
- final float diff_x = node.getXSecondary() - new_x;
- if ( ( diff_y > 2 ) || ( diff_y < -2 ) || ( diff_x > 2 ) || ( diff_x < -2 ) ) {
- paintBranchLite( g, node.getXSecondary(), new_x, node.getYSecondary(), y2, child_node );
- }
- child_node.setXSecondary( new_x );
- child_node.setYSecondary( y2 );
- y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
- }
+ else {
+ setScaleDistance( 0.0 );
+ }
+ String scale_label = String.valueOf( getScaleDistance() );
+ if ( !ForesterUtil.isEmpty( _phylogeny.getDistanceUnit() ) ) {
+ scale_label += " [" + _phylogeny.getDistanceUnit() + "]";
}
+ setScaleLabel( scale_label );
}
- final private void paintNodeRectangular( final Graphics2D g,
- final PhylogenyNode node,
- final boolean to_pdf,
- final boolean dynamically_hide,
- final int dynamic_hiding_factor,
- final boolean to_graphics_file,
- final boolean disallow_shortcutting ) {
- final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node );
- if ( node.isCollapse() ) {
- if ( ( !node.isRoot() && !node.getParent().isCollapse() ) ) {
- paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
- }
- return;
- }
- if ( node.isExternal() ) {
- ++_external_node_index;
+ final Color calculateSequenceBasedColor( final Sequence seq ) {
+ if ( ForesterUtil.isEmpty( seq.getName() ) ) {
+ return getTreeColorSet().getSequenceColor();
}
- // Confidence values
- if ( getControlPanel().isShowConfidenceValues()
- && !node.isExternal()
- && !node.isRoot()
- && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
- || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
- && node.getBranchData().isHasConfidences() ) {
- paintConfidenceValues( g, node, to_pdf, to_graphics_file );
+ Color c = null;
+ final String seq_name = seq.getName();
+ c = getControlPanel().getSequenceColors().get( seq_name );
+ if ( c == null ) {
+ c = AptxUtil.calculateColorFromString( seq_name, false );
+ getControlPanel().getSequenceColors().put( seq_name, c );
}
- // Draw a line to root:
- if ( node.isRoot() && _phylogeny.isRooted() ) {
- paintRootBranch( g, node.getXcoord(), node.getYcoord(), node, to_pdf, to_graphics_file );
+ return c;
+ }
+
+ final Color calculateTaxonomyBasedColor( final Taxonomy tax ) {
+ if ( getOptions().isColorByTaxonomicGroup() ) {
+ if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
+ boolean ex = false;
+ String group = null;
+ try {
+ group = TaxonomyUtil.getTaxGroupByTaxCode( tax.getTaxonomyCode() );
+ }
+ catch ( final Exception e ) {
+ ex = true;
+ }
+ if ( !ex && !ForesterUtil.isEmpty( group ) ) {
+ final Color c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( group );
+ if ( c != null ) {
+ return c;
+ }
+ }
+ }
+ return getTreeColorSet().getTaxonomyColor();
}
- float new_x = 0;
- float new_x_min = Float.MAX_VALUE;
- float min_dist = 1.5f;
- if ( !disallow_shortcutting ) {
- if ( dynamic_hiding_factor > 4000 ) {
- min_dist = 4;
+ else {
+ if ( ForesterUtil.isEmpty( tax.getTaxonomyCode() ) && ForesterUtil.isEmpty( tax.getScientificName() ) ) {
+ return getTreeColorSet().getTaxonomyColor();
}
- else if ( dynamic_hiding_factor > 1000 ) {
- min_dist = 3;
+ Color c = null;
+ if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
+ c = getControlPanel().getSpeciesColors().get( tax.getTaxonomyCode() );
}
- else if ( dynamic_hiding_factor > 100 ) {
- min_dist = 2;
+ if ( ( c == null ) && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
+ c = getControlPanel().getSpeciesColors().get( tax.getScientificName() );
}
- }
- if ( !node.isExternal() && !node.isCollapse() ) {
- boolean first_child = true;
- float y2 = 0.0f;
- final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
- for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
- final PhylogenyNode child_node = node.getChildNode( i );
- int factor_x;
- if ( !isUniformBranchLengthsForCladogram() ) {
- factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
- }
- else {
- factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
- }
- if ( first_child ) {
- first_child = false;
- y2 = node.getYcoord()
- - ( _y_distance * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) );
+ if ( c == null ) {
+ if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
+ c = AptxUtil.calculateColorFromString( tax.getTaxonomyCode(), true );
+ getControlPanel().getSpeciesColors().put( tax.getTaxonomyCode(), c );
}
else {
- y2 += _y_distance * child_node.getNumberOfExternalNodes();
+ c = AptxUtil.calculateColorFromString( tax.getScientificName(), true );
+ getControlPanel().getSpeciesColors().put( tax.getScientificName(), c );
}
- final float x2 = calculateBranchLengthToParent( child_node, factor_x );
- new_x = x2 + node.getXcoord();
- if ( dynamically_hide && ( x2 < new_x_min ) ) {
- new_x_min = x2;
+ }
+ return c;
+ }
+ }
+
+ void checkForVectorProperties( final Phylogeny phy ) {
+ final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+ final PhylogenyNode node = iter.next();
+ if ( node.getNodeData().getProperties() != null ) {
+ final PropertiesMap pm = node.getNodeData().getProperties();
+ final double[] vector = new double[ pm.getProperties().size() ];
+ int counter = 0;
+ for( final String ref : pm.getProperties().keySet() ) {
+ if ( ref.startsWith( PhyloXmlUtil.VECTOR_PROPERTY_REF ) ) {
+ final Property p = pm.getProperty( ref );
+ final String value_str = p.getValue();
+ final String index_str = ref
+ .substring( PhyloXmlUtil.VECTOR_PROPERTY_REF.length(), ref.length() );
+ double d = -100;
+ try {
+ d = Double.parseDouble( value_str );
+ }
+ catch ( final NumberFormatException e ) {
+ JOptionPane.showMessageDialog( this, "Could not parse \"" + value_str
+ + "\" into a decimal value", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ int i = -1;
+ try {
+ i = Integer.parseInt( index_str );
+ }
+ catch ( final NumberFormatException e ) {
+ JOptionPane.showMessageDialog( this,
+ "Could not parse \"" + index_str
+ + "\" into index for vector data",
+ "Problem with Vector Data",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ if ( i < 0 ) {
+ JOptionPane.showMessageDialog( this,
+ "Attempt to use negative index for vector data",
+ "Problem with Vector Data",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ vector[ i ] = d;
+ ++counter;
+ stats.addValue( d );
+ }
}
- final float diff_y = node.getYcoord() - y2;
- final float diff_x = node.getXcoord() - new_x;
- if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist )
- || ( diff_x < -min_dist ) ) {
- paintBranchRectangular( g,
- node.getXcoord(),
- new_x,
- node.getYcoord(),
- y2,
- child_node,
- to_pdf,
- to_graphics_file );
+ final List<Double> vector_l = new ArrayList<Double>( counter );
+ for( int i = 0; i < counter; ++i ) {
+ vector_l.add( vector[ i ] );
}
- child_node.setXcoord( new_x );
- child_node.setYcoord( y2 );
- y2 += _y_distance * child_node.getNumberOfExternalNodes();
+ node.getNodeData().setVector( vector_l );
}
- paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file );
}
- if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() )
- && ( node.getNodeData().getSequence().isMolecularSequenceAligned() )
- && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) {
- paintMolecularSequences( g, node, to_pdf );
- }
- if ( dynamically_hide
- && !is_in_found_nodes
- && ( ( node.isExternal() && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) ) || ( !node
- .isExternal() && ( ( new_x_min < 20 ) || ( ( _y_distance * node.getNumberOfExternalNodes() ) < getFontMetricsForLargeDefaultFont()
- .getHeight() ) ) ) ) ) {
- return;
+ if ( stats.getN() > 0 ) {
+ _statistics_for_vector_data = stats;
}
- final int x = paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
- paintNodeWithRenderableData( x, g, node, to_graphics_file, to_pdf );
}
- final private void paintNodeWithRenderableData( final int x,
- final Graphics2D g,
- final PhylogenyNode node,
- final boolean to_graphics_file,
- final boolean to_pdf ) {
- if ( isNodeDataInvisible( node ) && !( to_graphics_file || to_pdf ) ) {
- return;
- }
- if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) {
+ void clearCurrentExternalNodesDataBuffer() {
+ setCurrentExternalNodesDataBuffer( new StringBuilder() );
+ }
+
+ /**
+ * Collapse the tree from the given node
+ *
+ * @param node
+ * a PhylogenyNode
+ */
+ final void collapse( final PhylogenyNode node ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot collapse in unrooted display type",
+ "Attempt to collapse in unrooted display",
+ JOptionPane.WARNING_MESSAGE );
return;
}
- if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getDomainArchitecture() != null )
- && ( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
- RenderableDomainArchitecture rds = null;
- try {
- rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
- }
- catch ( final ClassCastException cce ) {
- cce.printStackTrace();
- }
- if ( rds != null ) {
- final int default_height = 7;
- float y = getYdistance();
- if ( getControlPanel().isDynamicallyHideData() ) {
- y = getTreeFontSet().getFontMetricsLarge().getHeight();
- }
- final int h = y < default_height ? ForesterUtil.roundToInt( y ) : default_height;
- rds.setRenderingHeight( h > 1 ? h : 2 );
- if ( getControlPanel().isDrawPhylogram() ) {
- if ( getOptions().isLineUpRendarableNodeData() ) {
- if ( getOptions().isRightLineUpDomains() ) {
- rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() )
- + _length_of_longest_text + ( ( _longest_domain - rds.getTotalLength() ) * rds
- .getRenderingFactorWidth() ) ), node.getYcoord() - ( h / 2.0f ), g, this, to_pdf );
- }
- else {
- rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + _length_of_longest_text ),
- node.getYcoord() - ( h / 2.0f ),
- g,
- this,
- to_pdf );
- }
- }
- else {
- rds.render( node.getXcoord() + x, node.getYcoord() - ( h / 2.0f ), g, this, to_pdf );
- }
- }
- else {
- if ( getOptions().isRightLineUpDomains() ) {
- rds.render( ( ( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text ) - 20 )
- + ( ( _longest_domain - rds.getTotalLength() ) * rds
- .getRenderingFactorWidth() ),
- node.getYcoord() - ( h / 2.0f ),
- g,
- this,
- to_pdf );
- }
- else {
- rds.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text,
- node.getYcoord() - ( h / 2.0f ),
- g,
- this,
- to_pdf );
- }
- }
- }
+ if ( !node.isExternal() && !node.isRoot() ) {
+ final boolean collapse = !node.isCollapse();
+ TreePanelUtil.collapseSubtree( node, collapse );
+ updateSetOfCollapsedExternalNodes();
+ _phylogeny.recalculateNumberOfExternalDescendants( true );
+ resetNodeIdToDistToLeafMap();
+ calculateLongestExtNodeInfo();
+ setNodeInPreorderToNull();
+ _control_panel.displayedPhylogenyMightHaveChanged( true );
+ resetPreferredSize();
+ updateOvSizes();
+ _main_panel.adjustJScrollPane();
+ repaint();
}
- if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
- && ( node.getNodeData().getVector().size() > 0 ) && ( getStatisticsForExpressionValues() != null ) ) {
- final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(),
- getStatisticsForExpressionValues(),
- getConfiguration() );
- if ( rv != null ) {
- double domain_add = 0;
- if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
- domain_add = _domain_structure_width + 10;
- }
- if ( getControlPanel().isDrawPhylogram() ) {
- rv.render( ( float ) ( node.getXcoord() + x + domain_add ), node.getYcoord() - 3, g, this, to_pdf );
- }
- else {
- rv.render( ( float ) ( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text + domain_add ),
- node.getYcoord() - 3,
- g,
- this,
- to_pdf );
- }
- }
+ }
+
+ final void collapseSpeciesSpecificSubtrees() {
+ if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
+ return;
}
-
- //if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() )
- // && ( node.getNodeData().getSequence().isMolecularSequenceAligned() )
- // && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) {
- // paintMolecularSequences( g, node, to_pdf );
- //}
+ setWaitCursor();
+ TreePanelUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
+ updateSetOfCollapsedExternalNodes();
+ _phylogeny.recalculateNumberOfExternalDescendants( true );
+ resetNodeIdToDistToLeafMap();
+ calculateLongestExtNodeInfo();
+ setNodeInPreorderToNull();
+ resetPreferredSize();
+ _main_panel.adjustJScrollPane();
+ setArrowCursor();
+ repaint();
}
- private void paintMolecularSequences( final Graphics2D g, final PhylogenyNode node, final boolean to_pdf ) {
- final RenderableMsaSequence rs = RenderableMsaSequence.createInstance( node.getNodeData().getSequence()
- .getMolecularSequence(), node.getNodeData().getSequence().getType(), getConfiguration() );
- if ( rs != null ) {
- final int default_height = 8;
- float y = getYdistance();
-
- final int h = ( y / 2) < default_height ? ForesterUtil.roundToInt( y * 2 ) : default_height;
- rs.setRenderingHeight( h > 1 ? h : 1 );
-
- if ( getControlPanel().isDrawPhylogram() ) {
- rs.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + _length_of_longest_text ),
- node.getYcoord() - ( h / 2.0f ),
- g,
- this,
- to_pdf );
+ final void colorRank( final String rank ) {
+ if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
+ return;
+ }
+ setWaitCursor();
+ AptxUtil.removeBranchColors( _phylogeny );
+ final int colorizations = TreePanelUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
+ if ( colorizations > 0 ) {
+ _control_panel.setColorBranches( true );
+ if ( _control_panel.getUseVisualStylesCb() != null ) {
+ _control_panel.getUseVisualStylesCb().setSelected( true );
}
- else {
- rs.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text,
- node.getYcoord() - ( h / 2.0f ),
- g,
- this,
- to_pdf );
+ if ( _control_panel.getColorAccSpeciesCb() != null ) {
+ _control_panel.getColorAccSpeciesCb().setSelected( false );
+ }
+ _options.setColorLabelsSameAsParentBranch( true );
+ if ( getMainPanel().getMainFrame()._color_labels_same_as_parent_branch != null ) {
+ getMainPanel().getMainFrame()._color_labels_same_as_parent_branch.setSelected( true );
}
+ _control_panel.repaint();
}
- }
-
- final private int calcLengthOfLongestText() {
- final StringBuilder sb = new StringBuilder();
- if ( _ext_node_with_longest_txt_info != null ) {
- nodeDataAsSB( _ext_node_with_longest_txt_info, sb );
- if ( _ext_node_with_longest_txt_info.getNodeData().isHasTaxonomy() ) {
- nodeTaxonomyDataAsSB( _ext_node_with_longest_txt_info.getNodeData().getTaxonomy(), sb );
+ setArrowCursor();
+ repaint();
+ if ( colorizations > 0 ) {
+ String msg = "Taxonomy colorization via " + rank + " completed:\n";
+ if ( colorizations > 1 ) {
+ msg += "colorized " + colorizations + " subtrees";
+ }
+ else {
+ msg += "colorized one subtree";
}
+ setEdited( true );
+ JOptionPane.showMessageDialog( this,
+ msg,
+ "Taxonomy Colorization Completed (" + rank + ")",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ else {
+ String msg = "Could not taxonomy colorize any subtree via " + rank + ".\n";
+ msg += "Possible solutions (given that suitable taxonomic information is present):\n";
+ msg += "select a different rank (e.g. phylum, genus, ...)\n";
+ msg += " and/or\n";
+ msg += "execute:\n";
+ msg += "1. \"" + MainFrameApplication.OBTAIN_DETAILED_TAXONOMIC_INFORMATION + "\" (Tools)\n";
+ msg += "2. \"" + MainFrameApplication.INFER_ANCESTOR_TAXONOMIES + "\" (Analysis)";
+ JOptionPane.showMessageDialog( this, msg, "Taxonomy Colorization Failed", JOptionPane.WARNING_MESSAGE );
}
- return getFontMetricsForLargeDefaultFont().stringWidth( sb.toString() );
}
- final private void paintOvRectangle( final Graphics2D g ) {
- final float w_ratio = ( ( float ) getWidth() ) / getVisibleRect().width;
- final float h_ratio = ( ( float ) getHeight() ) / getVisibleRect().height;
- final float x_ratio = ( ( float ) getWidth() ) / getVisibleRect().x;
- final float y_ratio = ( ( float ) getHeight() ) / getVisibleRect().y;
- final float width = getOvMaxWidth() / w_ratio;
- final float height = getOvMaxHeight() / h_ratio;
- final float x = getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / x_ratio );
- final float y = getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / y_ratio );
- g.setColor( getTreeColorSet().getFoundColor0() );
- getOvRectangle().setRect( x, y, width, height );
- final Stroke s = g.getStroke();
- g.setStroke( STROKE_1 );
- if ( ( width < 6 ) && ( height < 6 ) ) {
- drawRectFilled( x, y, 6, 6, g );
- getOvVirtualRectangle().setRect( x, y, 6, 6 );
- }
- else if ( width < 6 ) {
- drawRectFilled( x, y, 6, height, g );
- getOvVirtualRectangle().setRect( x, y, 6, height );
- }
- else if ( height < 6 ) {
- drawRectFilled( x, y, width, 6, g );
- getOvVirtualRectangle().setRect( x, y, width, 6 );
+ final void confColor() {
+ if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
+ return;
}
- else {
- drawRect( x, y, width, height, g );
- if ( isInOvRect() ) {
- drawRect( x + 1, y + 1, width - 2, height - 2, g );
- }
- getOvVirtualRectangle().setRect( x, y, width, height );
+ setWaitCursor();
+ AptxUtil.removeBranchColors( _phylogeny );
+ TreePanelUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
+ _control_panel.setColorBranches( true );
+ if ( _control_panel.getUseVisualStylesCb() != null ) {
+ _control_panel.getUseVisualStylesCb().setSelected( true );
}
- g.setStroke( s );
+ setArrowCursor();
+ repaint();
}
- final private void paintPhylogenyLite( final Graphics2D g ) {
- _phylogeny
- .getRoot()
- .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle()
- .getWidth() ) ) ) );
- _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
- final Stroke s = g.getStroke();
- g.setStroke( STROKE_05 );
- for( final PhylogenyNode element : _nodes_in_preorder ) {
- paintNodeLite( g, element );
+ final void decreaseDomainStructureEvalueThresholdExp() {
+ if ( _domain_structure_e_value_thr_exp > -20 ) {
+ _domain_structure_e_value_thr_exp -= 1;
}
- g.setStroke( s );
- paintOvRectangle( g );
}
/**
- * Paint the root branch. (Differs from others because it will always be a
- * single horizontal line).
- * @param to_graphics_file
+ * Find the node, if any, at the given location
*
- * @return new x1 value
+ * @param x
+ * @param y
+ * @return pointer to the node at x,y, null if not found
*/
- final private void paintRootBranch( final Graphics2D g,
- final float x1,
- final float y1,
- final PhylogenyNode root,
- final boolean to_pdf,
- final boolean to_graphics_file ) {
- assignGraphicsForBranchWithColorForParentBranch( root, false, g, to_pdf, to_graphics_file );
- float d = getXdistance();
- if ( getControlPanel().isDrawPhylogram() && ( root.getDistanceToParent() > 0.0 ) ) {
- d = ( float ) ( getXcorrectionFactor() * root.getDistanceToParent() );
- }
- if ( d < MIN_ROOT_LENGTH ) {
- d = MIN_ROOT_LENGTH;
+ final PhylogenyNode findNode( final int x, final int y ) {
+ if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
+ return null;
}
- if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( root ) == 1 ) ) {
- drawLine( x1 - d, root.getYcoord(), x1, root.getYcoord(), g );
+ final int half_box_size_plus_wiggle = ( getOptions().getDefaultNodeShapeSize() / 2 ) + WIGGLE;
+ for( final PhylogenyNodeIterator iter = _phylogeny.iteratorPostorder(); iter.hasNext(); ) {
+ final PhylogenyNode node = iter.next();
+ if ( ( _phylogeny.isRooted() || !node.isRoot() || ( node.getNumberOfDescendants() > 2 ) )
+ && ( ( node.getXcoord() - half_box_size_plus_wiggle ) <= x )
+ && ( ( node.getXcoord() + half_box_size_plus_wiggle ) >= x )
+ && ( ( node.getYcoord() - half_box_size_plus_wiggle ) <= y )
+ && ( ( node.getYcoord() + half_box_size_plus_wiggle ) >= y ) ) {
+ return node;
+ }
}
- else {
- final double w = PhylogenyMethods.getBranchWidthValue( root );
- drawRectFilled( x1 - d, root.getYcoord() - ( w / 2 ), d, w, g );
- }
- paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file );
+ return null;
}
- final private void paintScale( final Graphics2D g,
- int x1,
- int y1,
- final boolean to_pdf,
- final boolean to_graphics_file ) {
- x1 += MOVE;
- final double x2 = x1 + ( getScaleDistance() * getXcorrectionFactor() );
- y1 -= 12;
- final int y2 = y1 - 8;
- final int y3 = y1 - 4;
- g.setFont( getTreeFontSet().getSmallFont() );
- if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- g.setColor( Color.BLACK );
- }
- else {
- g.setColor( getTreeColorSet().getBranchLengthColor() );
+ final Configuration getConfiguration() {
+ return _configuration;
+ }
+
+ final ControlPanel getControlPanel() {
+ return _control_panel;
+ }
+
+ String getCurrentExternalNodesDataBufferAsString() {
+ return _current_external_nodes_data_buffer.toString();
+ }
+
+ int getCurrentExternalNodesDataBufferChangeCounter() {
+ return _current_external_nodes_data_buffer_change_counter;
+ }
+
+ final int getDomainStructureEvalueThresholdExp() {
+ return _domain_structure_e_value_thr_exp;
+ }
+
+ final Set<Long> getFoundNodes0() {
+ return _found_nodes_0;
+ }
+
+ final Set<Long> getFoundNodes1() {
+ return _found_nodes_1;
+ }
+
+ List<PhylogenyNode> getFoundNodesAsListOfPhylogenyNodes() {
+ final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
+ if ( getFoundNodes0() != null ) {
+ for( final Long id : getFoundNodes0() ) {
+ final PhylogenyNode n = _phylogeny.getNode( id );
+ if ( n != null ) {
+ additional_nodes.add( n );
+ }
+ }
}
- final Stroke s = g.getStroke();
- g.setStroke( STROKE_1 );
- drawLine( x1, y1, x1, y2, g );
- drawLine( x2, y1, x2, y2, g );
- drawLine( x1, y3, x2, y3, g );
- if ( getScaleLabel() != null ) {
- g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 );
+ if ( getFoundNodes1() != null ) {
+ for( final Long id : getFoundNodes1() ) {
+ if ( ( getFoundNodes0() == null ) || !getFoundNodes0().contains( id ) ) {
+ final PhylogenyNode n = _phylogeny.getNode( id );
+ if ( n != null ) {
+ additional_nodes.add( n );
+ }
+ }
+ }
}
- g.setStroke( s );
+ return additional_nodes;
}
- final private int paintTaxonomy( final Graphics2D g,
- final PhylogenyNode node,
- final boolean is_in_found_nodes,
- final boolean to_pdf,
- final boolean to_graphics_file,
- final float x_shift ) {
- final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
- final boolean using_visual_font = setFont( g, node, is_in_found_nodes );
- setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getTaxonomyColor() );
- final float start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift;
- float start_y;
- if ( !using_visual_font ) {
- start_y = node.getYcoord()
- + ( getFontMetricsForLargeDefaultFont().getAscent() / ( node.getNumberOfDescendants() == 1 ? 1
- : 3.0f ) );
+ final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) {
+ if ( getControlPanel().isUseVisualStyles() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
+ return ( PhylogenyMethods.getBranchColorValue( node ) );
}
else {
- start_y = node.getYcoord()
- + ( getFontMetrics( g.getFont() ).getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0f ) );
+ return ( getTreeColorSet().getBranchColor() );
}
- _sb.setLength( 0 );
- nodeTaxonomyDataAsSB( taxonomy, _sb );
- final String label = _sb.toString();
- /* GUILHEM_BEG */
- if ( _control_panel.isShowSequenceRelations() && ( label.length() > 0 )
- && ( node.getNodeData().isHasSequence() ) && node.getNodeData().getSequence().equals( _query_sequence ) ) {
- // invert font color and background color to show that this is the query sequence
- final Rectangle2D nodeTextBounds = new TextLayout( label, g.getFont(), new FontRenderContext( null,
- false,
- false ) )
- .getBounds();
- g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 );
- g.setColor( getTreeColorSet().getBackgroundColor() );
+ }
+
+ final int getLongestExtNodeInfo() {
+ return _longest_ext_node_info;
+ }
+
+ final Options getOptions() {
+ if ( _options == null ) {
+ _options = getControlPanel().getOptions();
}
- /* GUILHEM_END */
- TreePanel.drawString( label, start_x, start_y, g );
- if ( !using_visual_font && !is_in_found_nodes ) {
- return getFontMetricsForLargeDefaultFont().stringWidth( label );
+ return _options;
+ }
+
+ final Rectangle2D getOvRectangle() {
+ return _ov_rectangle;
+ }
+
+ final Rectangle getOvVirtualRectangle() {
+ return _ov_virtual_rectangle;
+ }
+
+ final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
+ return _graphics_type;
+ }
+
+ final Color getSequenceBasedColor( final PhylogenyNode node ) {
+ if ( node.getNodeData().isHasSequence() ) {
+ return calculateSequenceBasedColor( node.getNodeData().getSequence() );
}
- return getFontMetrics( g.getFont() ).stringWidth( label );
+ // return non-colorized color
+ return getTreeColorSet().getSequenceColor();
}
- final private void paintUnrooted( final PhylogenyNode n,
- final double low_angle,
- final double high_angle,
- final boolean radial_labels,
- final Graphics2D g,
- final boolean to_pdf,
- final boolean to_graphics_file ) {
- if ( n.isRoot() ) {
- n.setXcoord( getWidth() / 2 );
- n.setYcoord( getHeight() / 2 );
+ final double getStartingAngle() {
+ return _urt_starting_angle;
+ }
+
+ DescriptiveStatistics getStatisticsForExpressionValues() {
+ return _statistics_for_vector_data;
+ }
+
+ final Color getTaxonomyBasedColor( final PhylogenyNode node ) {
+ if ( node.isExternal() && node.getNodeData().isHasTaxonomy() ) {
+ return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() );
}
- if ( n.isExternal() ) {
- paintNodeDataUnrootedCirc( g,
- n,
- to_pdf,
- to_graphics_file,
- radial_labels,
- ( high_angle + low_angle ) / 2,
- isInFoundNodes( n ) || isInCurrentExternalNodes( n ) );
+ // return non-colorized color
+ return getTreeColorSet().getTaxonomyColor();
+ }
+
+ final File getTreeFile() {
+ return _treefile;
+ }
+
+ final float getXcorrectionFactor() {
+ return _x_correction_factor;
+ }
+
+ final float getXdistance() {
+ return _x_distance;
+ }
+
+ final float getYdistance() {
+ return _y_distance;
+ }
+
+ final void increaseDomainStructureEvalueThresholdExp() {
+ if ( _domain_structure_e_value_thr_exp < 3 ) {
+ _domain_structure_e_value_thr_exp += 1;
+ }
+ }
+
+ final void initNodeData() {
+ if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
return;
}
- final float num_enclosed = n.getNumberOfExternalNodes();
- final float x = n.getXcoord();
- final float y = n.getYcoord();
- double current_angle = low_angle;
- // final boolean n_below = n.getYcoord() < getVisibleRect().getMinY() - 20;
- // final boolean n_above = n.getYcoord() > getVisibleRect().getMaxY() + 20;
- // final boolean n_left = n.getXcoord() < getVisibleRect().getMinX() - 20;
- // final boolean n_right = n.getXcoord() > getVisibleRect().getMaxX() + 20;
- for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
- final PhylogenyNode desc = n.getChildNode( i );
- /// if ( ( ( n_below ) & ( desc.getYcoord() < getVisibleRect().getMinY() - 20 ) )
- // || ( ( n_above ) & ( desc.getYcoord() > getVisibleRect().getMaxY() + 20 ) )
- // || ( ( n_left ) & ( desc.getXcoord() < getVisibleRect().getMinX() - 20 ) )
- // || ( ( n_right ) & ( desc.getXcoord() > getVisibleRect().getMaxX() + 20 ) ) ) {
- // continue;
- // }
- //if ( ( desc.getYcoord() > n.getYcoord() ) && ( n.getYcoord() > getVisibleRect().getMaxY() - 20 ) ) {
- // continue;
- //}
- //if ( ( desc.getYcoord() < n.getYcoord() ) && ( n.getYcoord() < getVisibleRect().getMinY() + 20 ) ) {
- // continue;
- // }
- final int desc_num_enclosed = desc.getNumberOfExternalNodes();
- final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
- float length;
- if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
- if ( desc.getDistanceToParent() < 0 ) {
- length = 0;
+ double _max_original_domain_structure_width = 0.0;
+ for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
+ if ( node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
+ RenderableDomainArchitecture rds = null;
+ if ( !( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
+ if ( SPECIAL_DOMAIN_COLORING ) {
+ rds = new RenderableDomainArchitecture( node.getNodeData().getSequence()
+ .getDomainArchitecture(), node.getName() );
+ }
+ else {
+ rds = new RenderableDomainArchitecture( node.getNodeData().getSequence()
+ .getDomainArchitecture() );
+ }
+ node.getNodeData().getSequence().setDomainArchitecture( rds );
}
else {
- length = ( float ) ( desc.getDistanceToParent() * getUrtFactor() );
+ rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
+ }
+ if ( getControlPanel().isShowDomainArchitectures() ) {
+ final double dsw = rds.getOriginalSize().getWidth();
+ if ( dsw > _max_original_domain_structure_width ) {
+ _max_original_domain_structure_width = dsw;
+ }
}
}
- else {
- length = getUrtFactor();
- }
- final double mid_angle = current_angle + ( arc_size / 2 );
- final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
- final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );
- desc.setXcoord( new_x );
- desc.setYcoord( new_y );
- paintUnrooted( desc, current_angle, current_angle + arc_size, radial_labels, g, to_pdf, to_graphics_file );
- current_angle += arc_size;
- assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file );
- drawLine( x, y, new_x, new_y, g );
- paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file );
- }
- if ( n.isRoot() ) {
- paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file );
- }
- }
-
- final private void paintUnrootedLite( final PhylogenyNode n,
- final double low_angle,
- final double high_angle,
- final Graphics2D g,
- final float urt_ov_factor ) {
- if ( n.isRoot() ) {
- final int x_pos = ( int ) ( getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / 2 ) );
- final int y_pos = ( int ) ( getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / 2 ) );
- n.setXSecondary( x_pos );
- n.setYSecondary( y_pos );
- }
- if ( n.isExternal() ) {
- return;
}
- final float num_enclosed = n.getNumberOfExternalNodes();
- final float x = n.getXSecondary();
- final float y = n.getYSecondary();
- double current_angle = low_angle;
- for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
- final PhylogenyNode desc = n.getChildNode( i );
- final int desc_num_enclosed = desc.getNumberOfExternalNodes();
- final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
- float length;
- if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
- if ( desc.getDistanceToParent() < 0 ) {
- length = 0;
- }
- else {
- length = ( float ) ( desc.getDistanceToParent() * urt_ov_factor );
+ if ( getControlPanel().isShowDomainArchitectures() ) {
+ final float ds_factor_width = ( float ) ( _domain_structure_width / _max_original_domain_structure_width );
+ for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
+ if ( node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
+ final RenderableDomainArchitecture rds = ( RenderableDomainArchitecture ) node.getNodeData()
+ .getSequence().getDomainArchitecture();
+ rds.setRenderingFactorWidth( ds_factor_width );
+ rds.setParameter( _domain_structure_e_value_thr_exp );
}
}
- else {
- length = urt_ov_factor;
- }
- final double mid_angle = current_angle + ( arc_size / 2 );
- final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
- final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );
- desc.setXSecondary( new_x );
- desc.setYSecondary( new_y );
- if ( isInFoundNodes( desc ) || isInCurrentExternalNodes( desc ) ) {
- g.setColor( getColorForFoundNode( desc ) );
- drawRectFilled( desc.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF,
- desc.getYSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF,
- OVERVIEW_FOUND_NODE_BOX_SIZE,
- OVERVIEW_FOUND_NODE_BOX_SIZE,
- g );
- g.setColor( getTreeColorSet().getOvColor() );
- }
- paintUnrootedLite( desc, current_angle, current_angle + arc_size, g, urt_ov_factor );
- current_angle += arc_size;
- drawLine( x, y, new_x, new_y, g );
}
}
- final private void pasteSubtree( final PhylogenyNode node ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- errorMessageNoCutCopyPasteInUnrootedDisplay();
- return;
- }
- if ( ( getCutOrCopiedTree() == null ) || getCutOrCopiedTree().isEmpty() ) {
- JOptionPane.showMessageDialog( this,
- "No tree in buffer (need to copy or cut a subtree first)",
- "Attempt to paste with empty buffer",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- final String label = createASimpleTextRepresentationOfANode( getCutOrCopiedTree().getRoot() );
- final Object[] options = { "As sibling", "As descendant", "Cancel" };
- final int r = JOptionPane.showOptionDialog( this,
- "How to paste subtree" + label + "?",
- "Paste Subtree",
- JOptionPane.CLOSED_OPTION,
- JOptionPane.QUESTION_MESSAGE,
- null,
- options,
- options[ 2 ] );
- boolean paste_as_sibling = true;
- if ( r == 1 ) {
- paste_as_sibling = false;
- }
- else if ( r != 0 ) {
- return;
- }
- final Phylogeny buffer_phy = getCutOrCopiedTree().copy();
- buffer_phy.setAllNodesToNotCollapse();
- PhylogenyMethods.preOrderReId( buffer_phy );
- buffer_phy.setRooted( true );
- boolean need_to_show_whole = false;
- if ( paste_as_sibling ) {
- if ( node.isRoot() ) {
- JOptionPane.showMessageDialog( this,
- "Cannot paste sibling to root",
- "Attempt to paste sibling to root",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- buffer_phy.addAsSibling( node );
- }
- else {
- if ( ( node.getNumberOfExternalNodes() == 1 ) && node.isRoot() ) {
- need_to_show_whole = true;
- _phylogeny = buffer_phy;
- }
- else {
- buffer_phy.addAsChild( node );
- }
- }
- if ( getCopiedAndPastedNodes() == null ) {
- setCopiedAndPastedNodes( new HashSet<Long>() );
- }
- final List<PhylogenyNode> nodes = PhylogenyMethods.obtainAllNodesAsList( buffer_phy );
- final Set<Long> node_ids = new HashSet<Long>( nodes.size() );
- for( final PhylogenyNode n : nodes ) {
- node_ids.add( n.getId() );
- }
- node_ids.add( node.getId() );
- getCopiedAndPastedNodes().addAll( node_ids );
- setNodeInPreorderToNull();
- _phylogeny.externalNodesHaveChanged();
- _phylogeny.clearHashIdToNodeMap();
- _phylogeny.recalculateNumberOfExternalDescendants( true );
- resetNodeIdToDistToLeafMap();
- setEdited( true );
- if ( need_to_show_whole ) {
- getControlPanel().showWhole();
- }
- repaint();
+ final boolean inOv( final MouseEvent e ) {
+ return ( ( e.getX() > ( getVisibleRect().x + getOvXPosition() + 1 ) )
+ && ( e.getX() < ( ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() ) - 1 ) )
+ && ( e.getY() > ( getVisibleRect().y + getOvYPosition() + 1 ) ) && ( e.getY() < ( ( getVisibleRect().y
+ + getOvYPosition() + getOvMaxHeight() ) - 1 ) ) );
}
- private final StringBuffer propertiesToString( final PhylogenyNode node ) {
- final PropertiesMap properties = node.getNodeData().getProperties();
- final StringBuffer sb = new StringBuffer();
- boolean first = true;
- for( final String ref : properties.getPropertyRefs() ) {
- if ( first ) {
- first = false;
- }
- else {
- sb.append( " " );
- }
- final Property p = properties.getProperty( ref );
- sb.append( TreePanelUtil.getPartAfterColon( p.getRef() ) );
- sb.append( "=" );
- sb.append( p.getValue() );
- if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
- sb.append( TreePanelUtil.getPartAfterColon( p.getUnit() ) );
- }
- }
- return sb;
+ final boolean inOvRectangle( final MouseEvent e ) {
+ return ( ( e.getX() >= ( getOvRectangle().getX() - 1 ) )
+ && ( e.getX() <= ( getOvRectangle().getX() + getOvRectangle().getWidth() + 1 ) )
+ && ( e.getY() >= ( getOvRectangle().getY() - 1 ) ) && ( e.getY() <= ( getOvRectangle().getY()
+ + getOvRectangle().getHeight() + 1 ) ) );
}
- private void setColor( final Graphics2D g,
- final PhylogenyNode node,
- final boolean to_graphics_file,
- final boolean to_pdf,
- final boolean is_in_found_nodes,
- final Color default_color ) {
- if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- g.setColor( Color.BLACK );
- }
- else if ( is_in_found_nodes ) {
- g.setColor( getColorForFoundNode( node ) );
- }
- else if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null )
- && ( node.getNodeData().getNodeVisualData().getFontColor() != null ) ) {
- g.setColor( node.getNodeData().getNodeVisualData().getFontColor() );
- }
- else if ( getControlPanel().isColorAccordingToSequence() ) {
- g.setColor( getSequenceBasedColor( node ) );
- }
- 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().getAnnotations() ) );
- }
- else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isUseVisualStyles()
- && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
- g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
- }
- else if ( to_pdf ) {
- g.setColor( Color.BLACK );
- }
- else {
- g.setColor( default_color );
- }
+ final boolean isApplet() {
+ return getMainPanel() instanceof MainPanelApplets;
}
- final private void setCopiedAndPastedNodes( final Set<Long> nodeIds ) {
- getMainPanel().setCopiedAndPastedNodes( nodeIds );
+ final boolean isCanCollapse() {
+ return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
}
- final private void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) {
- getMainPanel().setCutOrCopiedTree( cut_or_copied_tree );
+ final boolean isCanColorSubtree() {
+ return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
}
- private boolean setFont( final Graphics2D g, final PhylogenyNode node, final boolean is_in_found_nodes ) {
- Font visual_font = null;
- if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null ) ) {
- visual_font = node.getNodeData().getNodeVisualData().getFont();
- g.setFont( visual_font != null ? visual_font : getTreeFontSet().getLargeFont() );
- }
- else {
- g.setFont( getTreeFontSet().getLargeFont() );
- }
- if ( is_in_found_nodes ) {
- g.setFont( g.getFont().deriveFont( Font.BOLD ) );
- }
- return visual_font != null;
+ final boolean isCanCopy() {
+ return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
}
- final private void setInOv( final boolean in_ov ) {
- _in_ov = in_ov;
+ final boolean isCanCut( final PhylogenyNode node ) {
+ return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() && !node
+ .isRoot() );
}
- final private void setOvMaxHeight( final float ov_max_height ) {
- _ov_max_height = ov_max_height;
+ final boolean isCanDelete() {
+ return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
}
- final private void setOvMaxWidth( final float ov_max_width ) {
- _ov_max_width = ov_max_width;
+ final boolean isCanPaste() {
+ return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable()
+ && ( getCutOrCopiedTree() != null ) && !getCutOrCopiedTree().isEmpty() );
}
- final private void setOvXcorrectionFactor( final float f ) {
- _ov_x_correction_factor = f;
+ final boolean isCanReroot() {
+ return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( _subtree_index < 1 ) );
}
- final private void setOvXDistance( final float ov_x_distance ) {
- _ov_x_distance = ov_x_distance;
+ final boolean isCanSubtree( final PhylogenyNode node ) {
+ return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && !node.isExternal() && ( !node
+ .isRoot() || ( _subtree_index > 0 ) ) );
}
- final private void setOvXPosition( final int ov_x_position ) {
- _ov_x_position = ov_x_position;
+ final boolean isCurrentTreeIsSubtree() {
+ return ( _subtree_index > 0 );
}
- final private void setOvYDistance( final float ov_y_distance ) {
- _ov_y_distance = ov_y_distance;
+ final boolean isEdited() {
+ return _edited;
}
- final private void setOvYPosition( final int ov_y_position ) {
- _ov_y_position = ov_y_position;
+ final boolean isInOvRect() {
+ return _in_ov_rect;
}
- final private void setOvYStart( final int ov_y_start ) {
- _ov_y_start = ov_y_start;
+ final boolean isOvOn() {
+ return _ov_on;
}
- final private void setScaleDistance( final double scale_distance ) {
- _scale_distance = scale_distance;
+ final boolean isPhyHasBranchLengths() {
+ return _phy_has_branch_lengths;
}
- final private void setScaleLabel( final String scale_label ) {
- _scale_label = scale_label;
+ final void midpointRoot() {
+ if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
+ return;
+ }
+ if ( !_phylogeny.isRerootable() ) {
+ JOptionPane.showMessageDialog( this,
+ "This is not rerootable",
+ "Not rerootable",
+ JOptionPane.WARNING_MESSAGE );
+ return;
+ }
+ setNodeInPreorderToNull();
+ setWaitCursor();
+ PhylogenyMethods.midpointRoot( _phylogeny );
+ resetNodeIdToDistToLeafMap();
+ setArrowCursor();
+ setEdited( true );
+ repaint();
}
- private final void setupStroke( final Graphics2D g ) {
- if ( getYdistance() < 0.0001 ) {
- g.setStroke( STROKE_0025 );
+ final void mouseClicked( final MouseEvent e ) {
+ if ( getOptions().isShowOverview() && isOvOn() && isInOv() ) {
+ final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
+ final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
+ double x = ( e.getX() - getVisibleRect().x - getOvXPosition() - ( getOvRectangle().getWidth() / 2.0 ) )
+ * w_ratio;
+ double y = ( e.getY() - getVisibleRect().y - getOvYPosition() - ( getOvRectangle().getHeight() / 2.0 ) )
+ * h_ratio;
+ if ( x < 0 ) {
+ x = 0;
+ }
+ if ( y < 0 ) {
+ y = 0;
+ }
+ final double max_x = getWidth() - getVisibleRect().width;
+ final double max_y = getHeight() - getVisibleRect().height;
+ if ( x > max_x ) {
+ x = max_x;
+ }
+ if ( y > max_y ) {
+ y = max_y;
+ }
+ getMainPanel().getCurrentScrollPane().getViewport()
+ .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) );
+ setInOvRect( true );
+ repaint();
}
- if ( getYdistance() < 0.001 ) {
- g.setStroke( STROKE_005 );
+ else {
+ final PhylogenyNode node = findNode( e.getX(), e.getY() );
+ if ( node != null ) {
+ if ( !node.isRoot() && node.getParent().isCollapse() ) {
+ return;
+ }
+ _highlight_node = node;
+ // Check if shift key is down
+ if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) {
+ // Yes, so add to _found_nodes
+ if ( getFoundNodes0() == null ) {
+ setFoundNodes0( new HashSet<Long>() );
+ }
+ getFoundNodes0().add( node.getId() );
+ // Check if control key is down
+ }
+ else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) {
+ // Yes, so pop-up menu
+ displayNodePopupMenu( node, e.getX(), e.getY() );
+ // Handle unadorned click
+ }
+ else {
+ // Check for right mouse button
+ if ( e.getModifiers() == 4 ) {
+ displayNodePopupMenu( node, e.getX(), e.getY() );
+ }
+ else {
+ // if not in _found_nodes, clear _found_nodes
+ handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
+ }
+ }
+ }
+ else {
+ // no node was clicked
+ _highlight_node = null;
+ }
}
- else if ( getYdistance() < 0.01 ) {
- g.setStroke( STROKE_01 );
+ repaint();
+ }
+
+ final void mouseDragInBrowserPanel( final MouseEvent e ) {
+ setCursor( MOVE_CURSOR );
+ final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
+ scroll_position.x -= ( e.getX() - getLastDragPointX() );
+ scroll_position.y -= ( e.getY() - getLastDragPointY() );
+ if ( scroll_position.x < 0 ) {
+ scroll_position.x = 0;
}
- else if ( getYdistance() < 0.5 ) {
- g.setStroke( STROKE_025 );
+ else {
+ final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
+ - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
+ if ( scroll_position.x > max_x ) {
+ scroll_position.x = max_x;
+ }
}
- else if ( getYdistance() < 1 ) {
- g.setStroke( STROKE_05 );
+ if ( scroll_position.y < 0 ) {
+ scroll_position.y = 0;
}
- else if ( getYdistance() < 2 ) {
- g.setStroke( STROKE_075 );
+ else {
+ final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
+ - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
+ if ( scroll_position.y > max_y ) {
+ scroll_position.y = max_y;
+ }
}
- else if ( ( getYdistance() < 20 ) || !getConfiguration().isAllowThickStrokes() ) {
- g.setStroke( STROKE_1 );
+ if ( isOvOn() || getOptions().isShowScale() ) {
+ repaint();
+ }
+ getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
+ }
+
+ final void mouseDragInOvRectangle( final MouseEvent e ) {
+ setCursor( HAND_CURSOR );
+ final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
+ final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
+ final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
+ double dx = ( ( w_ratio * e.getX() ) - ( w_ratio * getLastDragPointX() ) );
+ double dy = ( ( h_ratio * e.getY() ) - ( h_ratio * getLastDragPointY() ) );
+ scroll_position.x = ForesterUtil.roundToInt( scroll_position.x + dx );
+ scroll_position.y = ForesterUtil.roundToInt( scroll_position.y + dy );
+ if ( scroll_position.x <= 0 ) {
+ scroll_position.x = 0;
+ dx = 0;
}
else {
- g.setStroke( STROKE_2 );
+ final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
+ - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
+ if ( scroll_position.x >= max_x ) {
+ dx = 0;
+ scroll_position.x = max_x;
+ }
+ }
+ if ( scroll_position.y <= 0 ) {
+ dy = 0;
+ scroll_position.y = 0;
+ }
+ else {
+ final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
+ - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
+ if ( scroll_position.y >= max_y ) {
+ dy = 0;
+ scroll_position.y = max_y;
+ }
}
+ repaint();
+ getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
+ setLastMouseDragPointX( ( float ) ( e.getX() + dx ) );
+ setLastMouseDragPointY( ( float ) ( e.getY() + dy ) );
}
- final private void setUpUrtFactor() {
- final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width
- : getVisibleRect().height;
- if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
- setUrtFactor( ( float ) ( d / ( 2 * getMaxDistanceToRoot() ) ) );
+ final void mouseMoved( final MouseEvent e ) {
+ requestFocusInWindow();
+ if ( _current_external_nodes != null ) {
+ _current_external_nodes = null;
+ repaint();
+ }
+ if ( getControlPanel().isNodeDescPopup() ) {
+ if ( _node_desc_popup != null ) {
+ _node_desc_popup.hide();
+ _node_desc_popup = null;
+ }
+ }
+ if ( getOptions().isShowOverview() && isOvOn() ) {
+ if ( inOvVirtualRectangle( e ) ) {
+ if ( !isInOvRect() ) {
+ setInOvRect( true );
+ repaint();
+ }
+ }
+ else {
+ if ( isInOvRect() ) {
+ setInOvRect( false );
+ repaint();
+ }
+ }
+ }
+ if ( inOv( e ) && getOptions().isShowOverview() && isOvOn() ) {
+ if ( !isInOv() ) {
+ setInOv( true );
+ }
}
else {
- final int max_depth = _circ_max_depth;
- if ( max_depth > 0 ) {
- setUrtFactor( d / ( 2 * max_depth ) );
+ if ( isInOv() ) {
+ setInOv( false );
+ }
+ final PhylogenyNode node = findNode( e.getX(), e.getY() );
+ if ( ( node != null ) && ( node.isRoot() || !node.getParent().isCollapse() ) ) {
+ if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.GET_EXT_DESC_DATA ) ) {
+ for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
+ addToCurrentExternalNodes( n.getId() );
+ }
+ setCursor( HAND_CURSOR );
+ repaint();
+ }
+ else if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.CUT_SUBTREE )
+ || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.COPY_SUBTREE )
+ || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.PASTE_SUBTREE )
+ || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.DELETE_NODE_OR_SUBTREE )
+ || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.REROOT )
+ || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.ADD_NEW_NODE ) ) {
+ setCursor( CUT_CURSOR );
+ }
+ else {
+ setCursor( HAND_CURSOR );
+ if ( getControlPanel().isNodeDescPopup() ) {
+ showNodeDataPopup( e, node );
+ }
+ }
}
else {
- setUrtFactor( d / 2 );
+ setCursor( ARROW_CURSOR );
}
}
- setUrtFactorOv( getUrtFactor() );
}
- final private void setUrtFactor( final float urt_factor ) {
- _urt_factor = urt_factor;
+ final void mouseReleasedInBrowserPanel( final MouseEvent e ) {
+ setCursor( ARROW_CURSOR );
}
- final private void setUrtFactorOv( final float urt_factor_ov ) {
- _urt_factor_ov = urt_factor_ov;
+ final void multiplyUrtFactor( final float f ) {
+ _urt_factor *= f;
}
- private void showExtDescNodeData( final PhylogenyNode node ) {
- final List<String> data = new ArrayList<String>();
- final List<PhylogenyNode> nodes = node.getAllExternalDescendants();
- if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
- for( final PhylogenyNode n : getFoundNodesAsListOfPhylogenyNodes() ) {
- if ( !nodes.contains( n ) ) {
- nodes.add( n );
- }
- }
+ final JApplet obtainApplet() {
+ return ( ( MainPanelApplets ) getMainPanel() ).getApplet();
+ }
+
+ final void paintBranchCircular( final PhylogenyNode p,
+ final PhylogenyNode c,
+ final Graphics2D g,
+ final boolean radial_labels,
+ final boolean to_pdf,
+ final boolean to_graphics_file ) {
+ final double angle = _urt_nodeid_angle_map.get( c.getId() );
+ final double root_x = _root.getXcoord();
+ final double root_y = _root.getYcoord();
+ final double dx = root_x - p.getXcoord();
+ final double dy = root_y - p.getYcoord();
+ final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) );
+ final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
+ assignGraphicsForBranchWithColorForParentBranch( c, false, g, to_pdf, to_graphics_file );
+ if ( ( c.isFirstChildNode() || c.isLastChildNode() )
+ && ( ( Math.abs( parent_radius * arc ) > 1.5 ) || to_pdf || to_graphics_file ) ) {
+ final double r2 = 2.0 * parent_radius;
+ drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
}
- for( final PhylogenyNode n : nodes ) {
- switch ( getOptions().getExtDescNodeDataToReturn() ) {
- case NODE_NAME:
- if ( !ForesterUtil.isEmpty( n.getName() ) ) {
- data.add( n.getName() );
- }
- break;
- case SEQUENCE_NAME:
- if ( n.getNodeData().isHasSequence()
- && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
- data.add( n.getNodeData().getSequence().getName() );
- }
- break;
- case GENE_NAME:
- if ( n.getNodeData().isHasSequence()
- && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) {
- data.add( n.getNodeData().getSequence().getGeneName() );
- }
- break;
- case SEQUENCE_SYMBOL:
- if ( n.getNodeData().isHasSequence()
- && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
- data.add( n.getNodeData().getSequence().getSymbol() );
- }
- break;
- case SEQUENCE_MOL_SEQ_FASTA:
- final StringBuilder sb = new StringBuilder();
- if ( n.getNodeData().isHasSequence()
- && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
- final StringBuilder ann = new StringBuilder();
- if ( !ForesterUtil.isEmpty( n.getName() ) ) {
- ann.append( n.getName() );
- ann.append( "|" );
- }
- if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
- ann.append( "SYM=" );
- ann.append( n.getNodeData().getSequence().getSymbol() );
- ann.append( "|" );
- }
- if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
- ann.append( "NAME=" );
- ann.append( n.getNodeData().getSequence().getName() );
- ann.append( "|" );
- }
- if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) {
- ann.append( "GN=" );
- ann.append( n.getNodeData().getSequence().getGeneName() );
- ann.append( "|" );
- }
- if ( n.getNodeData().getSequence().getAccession() != null ) {
- ann.append( "ACC=" );
- ann.append( n.getNodeData().getSequence().getAccession().asText() );
- ann.append( "|" );
- }
- if ( n.getNodeData().isHasTaxonomy() ) {
- if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
- ann.append( "TAXID=" );
- ann.append( n.getNodeData().getTaxonomy().getTaxonomyCode() );
- ann.append( "|" );
- }
- if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
- ann.append( "SN=" );
- ann.append( n.getNodeData().getTaxonomy().getScientificName() );
- ann.append( "|" );
- }
- }
- String ann_str;
- if ( ann.charAt( ann.length() - 1 ) == '|' ) {
- ann_str = ann.substring( 0, ann.length() - 1 );
- }
- else {
- ann_str = ann.toString();
- }
- sb.append( SequenceWriter.toFasta( ann_str, n.getNodeData().getSequence()
- .getMolecularSequence(), 60 ) );
- data.add( sb.toString() );
- }
- break;
- case SEQUENCE_ACC:
- if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null )
- && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().toString() ) ) {
- data.add( n.getNodeData().getSequence().getAccession().toString() );
- }
- break;
- case TAXONOMY_SCIENTIFIC_NAME:
- if ( n.getNodeData().isHasTaxonomy()
- && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
- data.add( n.getNodeData().getTaxonomy().getScientificName() );
- }
- break;
- case TAXONOMY_CODE:
- if ( n.getNodeData().isHasTaxonomy()
- && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
- data.add( n.getNodeData().getTaxonomy().getTaxonomyCode() );
- }
- break;
- case DOMAINS_ALL:
- case DOMAINS_COLLAPSED_PER_PROTEIN:
- if ( n.getNodeData().isHasSequence()
- && ( n.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
- final DomainArchitecture da = n.getNodeData().getSequence().getDomainArchitecture();
- final Set<String> s = new HashSet<String>();
- for( int i = 0; i < da.getDomains().size(); ++i ) {
- final ProteinDomain d = da.getDomain( i );
- if ( d.getConfidence() <= Math.pow( 10, getDomainStructureEvalueThresholdExp() ) ) {
- final String name = d.getName();
- if ( !( s.contains( name ) ) ) {
- data.add( name );
- if ( getOptions().getExtDescNodeDataToReturn() == NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN ) {
- s.add( name );
- }
- }
- }
- }
- }
- break;
- case SEQ_ANNOTATIONS:
- if ( n.getNodeData().isHasSequence() ) {
- if ( n.getNodeData().isHasSequence()
- && ( n.getNodeData().getSequence().getAnnotations() != null ) ) {
- final SortedSet<Annotation> a = n.getNodeData().getSequence().getAnnotations();
- for( int i = 0; i < a.size(); ++i ) {
- data.add( n.getNodeData().getSequence().getAnnotation( i ).toString() );
- }
- }
- }
- break;
- case GO_TERM_IDS:
- if ( n.getNodeData().isHasSequence() ) {
- if ( n.getNodeData().isHasSequence()
- && ( n.getNodeData().getSequence().getAnnotations() != null ) ) {
- final SortedSet<Annotation> a = n.getNodeData().getSequence().getAnnotations();
- for( int i = 0; i < a.size(); ++i ) {
- final Annotation ann = n.getNodeData().getSequence().getAnnotation( i );
- final String ref = ann.getRef();
- if ( ref.toUpperCase().startsWith( "GO:" ) ) {
- data.add( ref );
- }
- }
- }
- }
- break;
- case UNKNOWN:
- TreePanelUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data );
- break;
- default:
- throw new IllegalArgumentException( "unknown data element: "
- + getOptions().getExtDescNodeDataToReturn() );
- }
- } // for loop
- final StringBuilder sb = new StringBuilder();
- final int size = TreePanelUtil.nodeDataIntoStringBuffer( data, getOptions(), sb );
- if ( ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE )
- || ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ) ) {
- if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
- System.out.println( sb );
+ drawLine( c.getXcoord(),
+ c.getYcoord(),
+ root_x + ( Math.cos( angle ) * parent_radius ),
+ root_y + ( Math.sin( angle ) * parent_radius ),
+ g );
+ paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file );
+ if ( c.isExternal() ) {
+ final boolean is_in_found_nodes = isInFoundNodes0( c ) || isInFoundNodes1( c )
+ || isInCurrentExternalNodes( c );
+ if ( ( _dynamic_hiding_factor > 1 ) && !is_in_found_nodes
+ && ( ( _urt_nodeid_index_map.get( c.getId() ) % _dynamic_hiding_factor ) != 1 ) ) {
+ return;
}
- if ( sb.length() < 1 ) {
- clearCurrentExternalNodesDataBuffer();
+ paintNodeDataUnrootedCirc( g, c, to_pdf, to_graphics_file, radial_labels, 0, is_in_found_nodes );
+ }
+ }
+
+ final void paintBranchCircularLite( final PhylogenyNode p, final PhylogenyNode c, final Graphics2D g ) {
+ final double angle = _urt_nodeid_angle_map.get( c.getId() );
+ final double root_x = _root.getXSecondary();
+ final double root_y = _root.getYSecondary();
+ final double dx = root_x - p.getXSecondary();
+ final double dy = root_y - p.getYSecondary();
+ final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
+ final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) );
+ g.setColor( getTreeColorSet().getOvColor() );
+ if ( ( c.isFirstChildNode() || c.isLastChildNode() ) && ( Math.abs( arc ) > 0.02 ) ) {
+ final double r2 = 2.0 * parent_radius;
+ drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
+ }
+ drawLine( c.getXSecondary(),
+ c.getYSecondary(),
+ root_x + ( Math.cos( angle ) * parent_radius ),
+ root_y + ( Math.sin( angle ) * parent_radius ),
+ g );
+ if ( isInFoundNodes( c ) || isInCurrentExternalNodes( c ) ) {
+ g.setColor( getColorForFoundNode( c ) );
+ drawRectFilled( c.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, c.getYSecondary()
+ - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g );
+ }
+ }
+
+ final void paintCircular( final Phylogeny phy,
+ final double starting_angle,
+ final int center_x,
+ final int center_y,
+ final int radius,
+ final Graphics2D g,
+ final boolean to_pdf,
+ final boolean to_graphics_file ) {
+ final int circ_num_ext_nodes = phy.getNumberOfExternalNodes() - _collapsed_external_nodeid_set.size();
+ System.out.println( "# collapsed external = " + _collapsed_external_nodeid_set.size() );
+ _root = phy.getRoot();
+ _root.setXcoord( center_x );
+ _root.setYcoord( center_y );
+ final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
+ double current_angle = starting_angle;
+ int i = 0;
+ for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
+ final PhylogenyNode n = it.next();
+ if ( !n.isCollapse() ) {
+ n.setXcoord( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
+ n.setYcoord( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
+ _urt_nodeid_angle_map.put( n.getId(), current_angle );
+ _urt_nodeid_index_map.put( n.getId(), i++ );
+ current_angle += ( TWO_PI / circ_num_ext_nodes );
}
else {
- setCurrentExternalNodesDataBuffer( sb );
+ //TODO remove me
+ System.out.println( "is collapse" + n.getName() );
}
}
- else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) {
- if ( sb.length() < 1 ) {
- TreePanelUtil.showInformationMessage( this, "No Appropriate Data (" + obtainTitleForExtDescNodeData()
- + ")", "Descendants of selected node do not contain selected data" );
- clearCurrentExternalNodesDataBuffer();
+ paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file );
+ paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file );
+ }
+
+ final void paintCircularLite( final Phylogeny phy,
+ final double starting_angle,
+ final int center_x,
+ final int center_y,
+ final int radius,
+ final Graphics2D g ) {
+ final int circ_num_ext_nodes = phy.getNumberOfExternalNodes();
+ _root = phy.getRoot();
+ _root.setXSecondary( center_x );
+ _root.setYSecondary( center_y );
+ double current_angle = starting_angle;
+ for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
+ final PhylogenyNode n = it.next();
+ n.setXSecondary( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
+ n.setYSecondary( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
+ _urt_nodeid_angle_map.put( n.getId(), current_angle );
+ current_angle += ( TWO_PI / circ_num_ext_nodes );
+ }
+ paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g );
+ }
+
+ final void paintPhylogeny( final Graphics2D g,
+ final boolean to_pdf,
+ final boolean to_graphics_file,
+ final int graphics_file_width,
+ final int graphics_file_height,
+ final int graphics_file_x,
+ final int graphics_file_y ) {
+ if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
+ return;
+ }
+ if ( _control_panel.isShowSequenceRelations() ) {
+ _query_sequence = _control_panel.getSelectedQuerySequence();
+ }
+ // Color the background
+ if ( !to_pdf ) {
+ final Rectangle r = getVisibleRect();
+ if ( !getOptions().isBackgroundColorGradient() || getOptions().isPrintBlackAndWhite() ) {
+ g.setColor( getTreeColorSet().getBackgroundColor() );
+ if ( !to_graphics_file ) {
+ g.fill( r );
+ }
+ else {
+ if ( getOptions().isPrintBlackAndWhite() ) {
+ g.setColor( Color.WHITE );
+ }
+ g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
+ }
}
else {
- setCurrentExternalNodesDataBuffer( sb );
- String title;
- if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) {
- title = ( getOptions().getExtDescNodeDataToReturn() == NodeDataField.UNKNOWN ? "Data"
- : obtainTitleForExtDescNodeData() )
- + " for "
- + data.size()
- + " nodes, unique entries: "
- + size;
+ if ( !to_graphics_file ) {
+ g.setPaint( new GradientPaint( r.x, r.y, getTreeColorSet().getBackgroundColor(), r.x, r.y
+ + r.height, getTreeColorSet().getBackgroundColorGradientBottom() ) );
+ g.fill( r );
}
else {
- title = ( getOptions().getExtDescNodeDataToReturn() == NodeDataField.UNKNOWN ? "Data"
- : obtainTitleForExtDescNodeData() )
- + " for "
- + data.size()
- + "/"
- + node.getNumberOfExternalNodes()
- + " external descendats of node "
- + node
- + ", unique entries: " + size;
+ g.setPaint( new GradientPaint( graphics_file_x,
+ graphics_file_y,
+ getTreeColorSet().getBackgroundColor(),
+ graphics_file_x,
+ graphics_file_y + graphics_file_height,
+ getTreeColorSet().getBackgroundColorGradientBottom() ) );
+ g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
}
- final String s = sb.toString().trim();
- if ( getMainPanel().getMainFrame() == null ) {
- // Must be "E" applet version.
- final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
- ae.showTextFrame( s, title );
+ }
+ setupStroke( g );
+ }
+ else {
+ g.setStroke( new BasicStroke( getOptions().getPrintLineWidth() ) );
+ }
+ if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
+ && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
+ _external_node_index = 0;
+ // Position starting X of tree
+ if ( !_phylogeny.isRooted() /*|| ( _subtree_index > 0 )*/) {
+ _phylogeny.getRoot().setXcoord( TreePanel.MOVE );
+ }
+ else if ( ( _phylogeny.getRoot().getDistanceToParent() > 0.0 ) && getControlPanel().isDrawPhylogram() ) {
+ _phylogeny.getRoot().setXcoord( ( float ) ( TreePanel.MOVE + ( _phylogeny.getRoot()
+ .getDistanceToParent() * getXcorrectionFactor() ) ) );
+ }
+ else {
+ _phylogeny.getRoot().setXcoord( TreePanel.MOVE + getXdistance() );
+ }
+ // Position starting Y of tree
+ _phylogeny.getRoot().setYcoord( ( getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes() )
+ + ( TreePanel.MOVE / 2.0f ) );
+ final int dynamic_hiding_factor = calcDynamicHidingFactor();
+ if ( getControlPanel().isDynamicallyHideData() ) {
+ if ( dynamic_hiding_factor > 1 ) {
+ getControlPanel().setDynamicHidingIsOn( true );
}
else {
- getMainPanel().getMainFrame().showTextFrame( s, title );
+ getControlPanel().setDynamicHidingIsOn( false );
+ }
+ }
+ if ( _nodes_in_preorder == null ) {
+ _nodes_in_preorder = new PhylogenyNode[ _phylogeny.getNodeCount() ];
+ int i = 0;
+ for( final PhylogenyNodeIterator it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
+ _nodes_in_preorder[ i++ ] = it.next();
+ }
+ }
+ final boolean disallow_shortcutting = ( dynamic_hiding_factor < 40 )
+ || getControlPanel().isUseVisualStyles() || getOptions().isShowDefaultNodeShapesForMarkedNodes()
+ || ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() )
+ || ( ( getFoundNodes1() != null ) && !getFoundNodes1().isEmpty() )
+ || ( ( getCurrentExternalNodes() != null ) && !getCurrentExternalNodes().isEmpty() )
+ || to_graphics_file || to_pdf;
+ for( final PhylogenyNode element : _nodes_in_preorder ) {
+ paintNodeRectangular( g,
+ element,
+ to_pdf,
+ getControlPanel().isDynamicallyHideData() && ( dynamic_hiding_factor > 1 ),
+ dynamic_hiding_factor,
+ to_graphics_file,
+ disallow_shortcutting );
+ }
+ if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) {
+ if ( !( to_graphics_file || to_pdf ) ) {
+ paintScale( g,
+ getVisibleRect().x,
+ getVisibleRect().y + getVisibleRect().height,
+ to_pdf,
+ to_graphics_file );
+ }
+ else {
+ paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
+ }
+ }
+ if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
+ paintPhylogenyLite( g );
+ }
+ }
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ if ( getControlPanel().getDynamicallyHideData() != null ) {
+ getControlPanel().setDynamicHidingIsOn( false );
+ }
+ final double angle = getStartingAngle();
+ final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
+ _dynamic_hiding_factor = 0;
+ if ( getControlPanel().isDynamicallyHideData() ) {
+ _dynamic_hiding_factor = ( int ) ( ( getFontMetricsForLargeDefaultFont().getHeight() * 1.5 * getPhylogeny()
+ .getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) );
+ }
+ if ( getControlPanel().getDynamicallyHideData() != null ) {
+ if ( _dynamic_hiding_factor > 1 ) {
+ getControlPanel().setDynamicHidingIsOn( true );
+ }
+ else {
+ getControlPanel().setDynamicHidingIsOn( false );
+ }
+ }
+ paintUnrooted( _phylogeny.getRoot(),
+ angle,
+ ( float ) ( angle + ( 2 * Math.PI ) ),
+ radial_labels,
+ g,
+ to_pdf,
+ to_graphics_file );
+ if ( getOptions().isShowScale() ) {
+ if ( !( to_graphics_file || to_pdf ) ) {
+ paintScale( g,
+ getVisibleRect().x,
+ getVisibleRect().y + getVisibleRect().height,
+ to_pdf,
+ to_graphics_file );
+ }
+ else {
+ paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
+ }
+ }
+ if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
+ g.setColor( getTreeColorSet().getOvColor() );
+ paintUnrootedLite( _phylogeny.getRoot(),
+ angle,
+ angle + ( 2 * Math.PI ),
+ g,
+ ( getUrtFactorOv() / ( getVisibleRect().width / getOvMaxWidth() ) ) );
+ paintOvRectangle( g );
+ }
+ }
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
+ final int radius = ( int ) ( ( Math.min( getPreferredSize().getWidth(), getPreferredSize().getHeight() ) / 2 ) - ( MOVE + getLongestExtNodeInfo() ) );
+ final int d = radius + MOVE + getLongestExtNodeInfo();
+ _dynamic_hiding_factor = 0;
+ if ( getControlPanel().isDynamicallyHideData() && ( radius > 0 ) ) {
+ _dynamic_hiding_factor = ( int ) ( ( getFontMetricsForLargeDefaultFont().getHeight() * 1.5 * getPhylogeny()
+ .getNumberOfExternalNodes() ) / ( TWO_PI * radius ) );
+ }
+ if ( getControlPanel().getDynamicallyHideData() != null ) {
+ if ( _dynamic_hiding_factor > 1 ) {
+ getControlPanel().setDynamicHidingIsOn( true );
+ }
+ else {
+ getControlPanel().setDynamicHidingIsOn( false );
+ }
+ }
+ paintCircular( _phylogeny, getStartingAngle(), d, d, radius > 0 ? radius : 0, g, to_pdf, to_graphics_file );
+ if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
+ final int radius_ov = ( int ) ( getOvMaxHeight() < getOvMaxWidth() ? getOvMaxHeight() / 2
+ : getOvMaxWidth() / 2 );
+ double x_scale = 1.0;
+ double y_scale = 1.0;
+ int x_pos = getVisibleRect().x + getOvXPosition();
+ int y_pos = getVisibleRect().y + getOvYPosition();
+ if ( getWidth() > getHeight() ) {
+ x_scale = ( double ) getHeight() / getWidth();
+ x_pos = ForesterUtil.roundToInt( x_pos / x_scale );
+ }
+ else {
+ y_scale = ( double ) getWidth() / getHeight();
+ y_pos = ForesterUtil.roundToInt( y_pos / y_scale );
}
+ _at = g.getTransform();
+ g.scale( x_scale, y_scale );
+ paintCircularLite( _phylogeny,
+ getStartingAngle(),
+ x_pos + radius_ov,
+ y_pos + radius_ov,
+ ( int ) ( radius_ov - ( getLongestExtNodeInfo() / ( getVisibleRect().width / getOvRectangle()
+ .getWidth() ) ) ),
+ g );
+ g.setTransform( _at );
+ paintOvRectangle( g );
}
}
}
- final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) {
- try {
- if ( ( node.getName().length() > 0 )
- || ( node.getNodeData().isHasTaxonomy() && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData()
- .getTaxonomy() ) )
- || ( node.getNodeData().isHasSequence() && !TreePanelUtil.isSequenceEmpty( node.getNodeData()
- .getSequence() ) ) || ( node.getNodeData().isHasDate() )
- || ( node.getNodeData().isHasDistribution() ) || node.getBranchData().isHasConfidences() ) {
- _popup_buffer.setLength( 0 );
- short lines = 0;
- if ( node.getName().length() > 0 ) {
- lines++;
- _popup_buffer.append( node.getName() );
- }
- if ( node.getNodeData().isHasTaxonomy()
- && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) {
- lines++;
- boolean enc_data = false;
- final Taxonomy tax = node.getNodeData().getTaxonomy();
- if ( _popup_buffer.length() > 0 ) {
- _popup_buffer.append( "\n" );
- }
- if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
- _popup_buffer.append( "[" );
- _popup_buffer.append( tax.getTaxonomyCode() );
- _popup_buffer.append( "]" );
- enc_data = true;
- }
- if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
- if ( enc_data ) {
- _popup_buffer.append( " " );
- }
- _popup_buffer.append( tax.getScientificName() );
- enc_data = true;
- }
- if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
- if ( enc_data ) {
- _popup_buffer.append( " (" );
- }
- else {
- _popup_buffer.append( "(" );
- }
- _popup_buffer.append( tax.getCommonName() );
- _popup_buffer.append( ")" );
- enc_data = true;
- }
- if ( !ForesterUtil.isEmpty( tax.getAuthority() ) ) {
- if ( enc_data ) {
- _popup_buffer.append( " (" );
- }
- else {
- _popup_buffer.append( "(" );
- }
- _popup_buffer.append( tax.getAuthority() );
- _popup_buffer.append( ")" );
- enc_data = true;
- }
- if ( !ForesterUtil.isEmpty( tax.getRank() ) ) {
- if ( enc_data ) {
- _popup_buffer.append( " [" );
- }
- else {
- _popup_buffer.append( "[" );
- }
- _popup_buffer.append( tax.getRank() );
- _popup_buffer.append( "]" );
- enc_data = true;
- }
- if ( tax.getSynonyms().size() > 0 ) {
- if ( enc_data ) {
- _popup_buffer.append( " " );
- }
- _popup_buffer.append( "[" );
- int counter = 1;
- for( final String syn : tax.getSynonyms() ) {
- if ( !ForesterUtil.isEmpty( syn ) ) {
- enc_data = true;
- _popup_buffer.append( syn );
- if ( counter < tax.getSynonyms().size() ) {
- _popup_buffer.append( ", " );
- }
- }
- counter++;
- }
- _popup_buffer.append( "]" );
- }
- if ( !enc_data ) {
- if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
- if ( !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
- _popup_buffer.append( "[" );
- _popup_buffer.append( tax.getIdentifier().getProvider() );
- _popup_buffer.append( "] " );
- }
- _popup_buffer.append( tax.getIdentifier().getValue() );
- }
- }
- }
- if ( node.getNodeData().isHasSequence()
- && !TreePanelUtil.isSequenceEmpty( node.getNodeData().getSequence() ) ) {
- lines++;
- boolean enc_data = false;
- if ( _popup_buffer.length() > 0 ) {
- _popup_buffer.append( "\n" );
- }
- final Sequence seq = node.getNodeData().getSequence();
- if ( seq.getAccession() != null ) {
- _popup_buffer.append( "[" );
- if ( !ForesterUtil.isEmpty( seq.getAccession().getSource() ) ) {
- _popup_buffer.append( seq.getAccession().getSource() );
- _popup_buffer.append( ":" );
- }
- _popup_buffer.append( seq.getAccession().getValue() );
- _popup_buffer.append( "]" );
- enc_data = true;
- }
- if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
- if ( enc_data ) {
- _popup_buffer.append( " [" );
- }
- else {
- _popup_buffer.append( "[" );
- }
- _popup_buffer.append( seq.getSymbol() );
- _popup_buffer.append( "]" );
- enc_data = true;
- }
- if ( !ForesterUtil.isEmpty( seq.getGeneName() ) ) {
- if ( enc_data ) {
- _popup_buffer.append( " [" );
- }
- else {
- _popup_buffer.append( "[" );
- }
- _popup_buffer.append( seq.getGeneName() );
- _popup_buffer.append( "]" );
- enc_data = true;
- }
- if ( !ForesterUtil.isEmpty( seq.getName() ) ) {
- if ( enc_data ) {
- _popup_buffer.append( " " );
- }
- _popup_buffer.append( seq.getName() );
- }
- }
- if ( node.getNodeData().isHasDate() ) {
- lines++;
- if ( _popup_buffer.length() > 0 ) {
- _popup_buffer.append( "\n" );
- }
- _popup_buffer.append( node.getNodeData().getDate().asSimpleText() );
- }
- if ( node.getNodeData().isHasDistribution() ) {
- lines++;
- if ( _popup_buffer.length() > 0 ) {
- _popup_buffer.append( "\n" );
- }
- _popup_buffer.append( node.getNodeData().getDistribution().asSimpleText() );
- }
- if ( node.getBranchData().isHasConfidences() ) {
- final List<Confidence> confs = node.getBranchData().getConfidences();
- for( final Confidence confidence : confs ) {
- lines++;
- if ( _popup_buffer.length() > 0 ) {
- _popup_buffer.append( "\n" );
- }
- if ( !ForesterUtil.isEmpty( confidence.getType() ) ) {
- _popup_buffer.append( "[" );
- _popup_buffer.append( confidence.getType() );
- _popup_buffer.append( "] " );
- }
- _popup_buffer
- .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(),
- getOptions()
- .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
- if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
- _popup_buffer.append( " (sd=" );
- _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence
- .getStandardDeviation(), getOptions()
- .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
- _popup_buffer.append( ")" );
- }
- }
- }
- if ( node.getNodeData().isHasProperties() ) {
- final PropertiesMap properties = node.getNodeData().getProperties();
- for( final String ref : properties.getPropertyRefs() ) {
- _popup_buffer.append( "\n" );
- final Property p = properties.getProperty( ref );
- _popup_buffer.append( TreePanelUtil.getPartAfterColon( p.getRef() ) );
- _popup_buffer.append( "=" );
- _popup_buffer.append( p.getValue() );
- if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
- _popup_buffer.append( TreePanelUtil.getPartAfterColon( p.getUnit() ) );
- }
- }
- }
- if ( _popup_buffer.length() > 0 ) {
- if ( !getConfiguration().isUseNativeUI() ) {
- _rollover_popup
- .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
- _rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() );
- if ( isInFoundNodes0( node ) && !isInFoundNodes1( node ) ) {
- _rollover_popup.setForeground( getTreeColorSet().getFoundColor0() );
- }
- else if ( !isInFoundNodes0( node ) && isInFoundNodes1( node ) ) {
- _rollover_popup.setForeground( getTreeColorSet().getFoundColor1() );
- }
- else if ( isInFoundNodes0( node ) && isInFoundNodes1( node ) ) {
- _rollover_popup.setForeground( getTreeColorSet().getFoundColor0and1() );
- }
- else {
- _rollover_popup.setForeground( getTreeColorSet().getSequenceColor() );
- }
- }
- else {
- _rollover_popup.setBorder( BorderFactory.createLineBorder( Color.BLACK ) );
- }
- _rollover_popup.setText( _popup_buffer.toString() );
- _node_desc_popup = PopupFactory.getSharedInstance().getPopup( null,
- _rollover_popup,
- e.getLocationOnScreen().x + 10,
- e.getLocationOnScreen().y
- - ( lines * 20 ) );
- _node_desc_popup.show();
- }
+ final void recalculateMaxDistanceToRoot() {
+ _max_distance_to_root = PhylogenyMethods.calculateMaxDistanceToRoot( getPhylogeny() );
+ }
+
+ /**
+ * Remove all edit-node frames
+ */
+ final void removeAllEditNodeJFrames() {
+ for( int i = 0; i <= ( TreePanel.MAX_NODE_FRAMES - 1 ); i++ ) {
+ if ( _node_frames[ i ] != null ) {
+ _node_frames[ i ].dispose();
+ _node_frames[ i ] = null;
+ }
+ }
+ _node_frame_index = 0;
+ }
+
+ /**
+ * Remove a node-edit frame.
+ */
+ final void removeEditNodeFrame( final int i ) {
+ _node_frame_index--;
+ _node_frames[ i ] = null;
+ if ( i < _node_frame_index ) {
+ for( int j = 0; j < ( _node_frame_index - 1 ); j++ ) {
+ _node_frames[ j ] = _node_frames[ j + 1 ];
+ }
+ _node_frames[ _node_frame_index ] = null;
+ }
+ }
+
+ final void reRoot( final PhylogenyNode node ) {
+ if ( !getPhylogeny().isRerootable() ) {
+ JOptionPane.showMessageDialog( this,
+ "This is not rerootable",
+ "Not rerootable",
+ JOptionPane.WARNING_MESSAGE );
+ return;
+ }
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot reroot in unrooted display type",
+ "Attempt to reroot tree in unrooted display",
+ JOptionPane.WARNING_MESSAGE );
+ return;
+ }
+ getPhylogeny().reRoot( node );
+ getPhylogeny().recalculateNumberOfExternalDescendants( true );
+ resetNodeIdToDistToLeafMap();
+ setNodeInPreorderToNull();
+ resetPreferredSize();
+ getMainPanel().adjustJScrollPane();
+ setEdited( true );
+ repaint();
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
+ getControlPanel().showWhole();
+ }
+ }
+
+ final void resetNodeIdToDistToLeafMap() {
+ _nodeid_dist_to_leaf = new HashMap<Long, Short>();
+ }
+
+ final void resetPreferredSize() {
+ if ( ( getPhylogeny() == null ) || getPhylogeny().isEmpty() ) {
+ return;
+ }
+ int x = 0;
+ int y = 0;
+ y = TreePanel.MOVE
+ + ForesterUtil.roundToInt( getYdistance() * getPhylogeny().getRoot().getNumberOfExternalNodes() * 2 );
+ if ( getControlPanel().isDrawPhylogram() ) {
+ x = TreePanel.MOVE
+ + getLongestExtNodeInfo()
+ + ForesterUtil
+ .roundToInt( ( getXcorrectionFactor() * getPhylogeny().getHeight() ) + getXdistance() );
+ }
+ else {
+ if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
+ x = TreePanel.MOVE
+ + getLongestExtNodeInfo()
+ + ForesterUtil.roundToInt( getXdistance()
+ * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) );
+ }
+ else {
+ x = TreePanel.MOVE
+ + getLongestExtNodeInfo()
+ + ForesterUtil.roundToInt( getXdistance()
+ * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) );
+ }
+ }
+ setPreferredSize( new Dimension( x, y ) );
+ }
+
+ final void selectNode( final PhylogenyNode node ) {
+ if ( ( getFoundNodes0() != null ) && getFoundNodes0().contains( node.getId() ) ) {
+ getFoundNodes0().remove( node.getId() );
+ getControlPanel().setSearchFoundCountsOnLabel0( getFoundNodes0().size() );
+ if ( getFoundNodes0().size() < 1 ) {
+ getControlPanel().searchReset0();
+ }
+ }
+ else {
+ getControlPanel().getSearchFoundCountsLabel0().setVisible( true );
+ getControlPanel().getSearchResetButton0().setEnabled( true );
+ getControlPanel().getSearchResetButton0().setVisible( true );
+ if ( getFoundNodes0() == null ) {
+ setFoundNodes0( new HashSet<Long>() );
+ }
+ getFoundNodes0().add( node.getId() );
+ getControlPanel().setSearchFoundCountsOnLabel0( getFoundNodes0().size() );
+ }
+ }
+
+ final void setArrowCursor() {
+ setCursor( ARROW_CURSOR );
+ repaint();
+ }
+
+ final void setControlPanel( final ControlPanel atv_control ) {
+ _control_panel = atv_control;
+ }
+
+ void setCurrentExternalNodesDataBuffer( final StringBuilder sb ) {
+ increaseCurrentExternalNodesDataBufferChangeCounter();
+ _current_external_nodes_data_buffer = sb;
+ }
+
+ final void setFoundNodes0( final Set<Long> found_nodes ) {
+ _found_nodes_0 = found_nodes;
+ }
+
+ final void setFoundNodes1( final Set<Long> found_nodes ) {
+ _found_nodes_1 = found_nodes;
+ }
+
+ final void setInOvRect( final boolean in_ov_rect ) {
+ _in_ov_rect = in_ov_rect;
+ }
+
+ final void setLargeFonts() {
+ getTreeFontSet().largeFonts();
+ }
+
+ final void setLastMouseDragPointX( final float x ) {
+ _last_drag_point_x = x;
+ }
+
+ final void setLastMouseDragPointY( final float y ) {
+ _last_drag_point_y = y;
+ }
+
+ final void setMediumFonts() {
+ getTreeFontSet().mediumFonts();
+ }
+
+ final void setNodeInPreorderToNull() {
+ _nodes_in_preorder = null;
+ }
+
+ final void setOvOn( final boolean ov_on ) {
+ _ov_on = ov_on;
+ }
+
+ final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE graphics_type ) {
+ _graphics_type = graphics_type;
+ setTextAntialias();
+ }
+
+ final void setSmallFonts() {
+ getTreeFontSet().smallFonts();
+ }
+
+ final void setStartingAngle( final double starting_angle ) {
+ _urt_starting_angle = starting_angle;
+ }
+
+ void setStatisticsForExpressionValues( final DescriptiveStatistics statistics_for_expression_values ) {
+ _statistics_for_vector_data = statistics_for_expression_values;
+ }
+
+ final void setSuperTinyFonts() {
+ getTreeFontSet().superTinyFonts();
+ }
+
+ final void setTextAntialias() {
+ if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
+ if ( _phylogeny.getNumberOfExternalNodes() <= LIMIT_FOR_HQ_RENDERING ) {
+ _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY );
}
+ else {
+ _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED );
+ }
+ }
+ if ( getMainPanel().getOptions().isAntialiasScreen() ) {
+ _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
+ // try {
+ _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB );
+ // }
+ // catch ( final Throwable e ) {
+ // _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_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 void setTinyFonts() {
+ getTreeFontSet().tinyFonts();
+ }
+
+ final void setTreeFile( final File treefile ) {
+ _treefile = treefile;
+ }
+
+ final void setXcorrectionFactor( final float f ) {
+ _x_correction_factor = f;
+ }
+
+ final void setXdistance( final float x ) {
+ _x_distance = x;
+ }
+
+ final void setYdistance( final float y ) {
+ _y_distance = y;
+ }
+
+ final void sortDescendants( final PhylogenyNode node ) {
+ if ( !node.isExternal() ) {
+ DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
+ if ( getControlPanel().isShowTaxonomyScientificNames() || getControlPanel().isShowTaxonomyCode() ) {
+ pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
+ }
+ else if ( getControlPanel().isShowSeqNames() || getControlPanel().isShowSeqSymbols()
+ || getControlPanel().isShowGeneNames() ) {
+ pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
+ }
+ PhylogenyMethods.sortNodeDescendents( node, pri );
+ setNodeInPreorderToNull();
+ _phylogeny.externalNodesHaveChanged();
+ _phylogeny.clearHashIdToNodeMap();
+ _phylogeny.recalculateNumberOfExternalDescendants( true );
+ resetNodeIdToDistToLeafMap();
+ setEdited( true );
+ }
+ repaint();
+ }
+
+ final void subTree( final PhylogenyNode node ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot get a sub/super tree in unrooted display",
+ "Attempt to get sub/super tree in unrooted display",
+ JOptionPane.WARNING_MESSAGE );
+ return;
+ }
+ if ( node.isExternal() ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot get a subtree of a external node",
+ "Attempt to get subtree of external node",
+ JOptionPane.WARNING_MESSAGE );
+ return;
+ }
+ if ( node.isRoot() && !isCurrentTreeIsSubtree() ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot get a subtree of the root node",
+ "Attempt to get subtree of root node",
+ JOptionPane.WARNING_MESSAGE );
+ return;
}
- catch ( final Exception ex ) {
- // Do nothing.
+ setNodeInPreorderToNull();
+ if ( !node.isExternal() && !node.isRoot() && ( _subtree_index <= ( TreePanel.MAX_SUBTREES - 1 ) ) ) {
+ _sub_phylogenies[ _subtree_index ] = _phylogeny;
+ _sub_phylogenies_temp_roots[ _subtree_index ] = node;
+ ++_subtree_index;
+ _phylogeny = TreePanelUtil.subTree( node, _phylogeny );
+ updateSubSuperTreeButton();
+ }
+ else if ( node.isRoot() && isCurrentTreeIsSubtree() ) {
+ superTree();
}
+ _main_panel.getControlPanel().showWhole();
+ repaint();
}
- final private void showNodeEditFrame( final PhylogenyNode n ) {
- if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
- // pop up edit box for single node
- _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index, "" );
- _node_frame_index++;
+ final void superTree() {
+ setNodeInPreorderToNull();
+ final PhylogenyNode temp_root = _sub_phylogenies_temp_roots[ _subtree_index - 1 ];
+ for( final PhylogenyNode n : temp_root.getDescendants() ) {
+ n.setParent( temp_root );
}
- else {
- JOptionPane.showMessageDialog( this, "too many node windows are open" );
+ _sub_phylogenies[ _subtree_index ] = null;
+ _sub_phylogenies_temp_roots[ _subtree_index ] = null;
+ _phylogeny = _sub_phylogenies[ --_subtree_index ];
+ updateSubSuperTreeButton();
+ }
+
+ final void swap( final PhylogenyNode node ) {
+ if ( node.isExternal() || ( node.getNumberOfDescendants() < 2 ) ) {
+ return;
+ }
+ if ( node.getNumberOfDescendants() > 2 ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot swap descendants of nodes with more than 2 descendants",
+ "Cannot swap descendants",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ if ( !node.isExternal() ) {
+ node.swapChildren();
+ setNodeInPreorderToNull();
+ _phylogeny.externalNodesHaveChanged();
+ _phylogeny.clearHashIdToNodeMap();
+ _phylogeny.recalculateNumberOfExternalDescendants( true );
+ resetNodeIdToDistToLeafMap();
+ setEdited( true );
}
+ repaint();
}
- final private void showNodeFrame( final PhylogenyNode n ) {
- if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
- // pop up edit box for single node
- _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index );
- _node_frame_index++;
+ final void taxColor() {
+ if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
+ return;
}
- else {
- JOptionPane.showMessageDialog( this, "too many node windows are open" );
+ setWaitCursor();
+ TreePanelUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
+ _control_panel.setColorBranches( true );
+ if ( _control_panel.getUseVisualStylesCb() != null ) {
+ _control_panel.getUseVisualStylesCb().setSelected( true );
}
+ setEdited( true );
+ setArrowCursor();
+ repaint();
}
- final private void switchDisplaygetPhylogenyGraphicsType() {
- switch ( getPhylogenyGraphicsType() ) {
- case RECTANGULAR:
- setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
- getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
- break;
- case EURO_STYLE:
- setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
- getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
- break;
- case ROUNDED:
- setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
- getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
- break;
- case CURVED:
- setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
- getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
- break;
- case TRIANGULAR:
- setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
- getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
- break;
- case CONVEX:
- setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
- getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
+ final void updateOvSettings() {
+ switch ( getOptions().getOvPlacement() ) {
+ case LOWER_LEFT:
+ setOvXPosition( OV_BORDER );
+ setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
+ setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
break;
- case UNROOTED:
- setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
- getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
+ case LOWER_RIGHT:
+ setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
+ setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
+ setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
break;
- case CIRCULAR:
- setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
- getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
+ case UPPER_RIGHT:
+ setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
+ setOvYPosition( OV_BORDER );
+ setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
break;
default:
- throw new RuntimeException( "unkwnown display type: " + getPhylogenyGraphicsType() );
+ setOvXPosition( OV_BORDER );
+ setOvYPosition( OV_BORDER );
+ setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
+ break;
}
- if ( getControlPanel().getDynamicallyHideData() != null ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- getControlPanel().getDynamicallyHideData().setEnabled( false );
+ }
+
+ final void updateOvSizes() {
+ if ( ( getWidth() > ( 1.05 * getVisibleRect().width ) ) || ( getHeight() > ( 1.05 * getVisibleRect().height ) ) ) {
+ setOvOn( true );
+ float l = getLongestExtNodeInfo();
+ final float w_ratio = getOvMaxWidth() / getWidth();
+ l *= w_ratio;
+ final int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
+ setOvYDistance( getOvMaxHeight() / ( 2 * ext_nodes ) );
+ float ov_xdist = 0;
+ if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
+ ov_xdist = ( ( getOvMaxWidth() - l ) / ( ext_nodes ) );
}
else {
- getControlPanel().getDynamicallyHideData().setEnabled( true );
+ ov_xdist = ( ( getOvMaxWidth() - l ) / ( PhylogenyMethods.calculateMaxDepth( _phylogeny ) ) );
+ }
+ float ydist = ( float ) ( ( getOvMaxWidth() / ( ext_nodes * 2.0 ) ) );
+ if ( ov_xdist < 0.0 ) {
+ ov_xdist = 0.0f;
+ }
+ if ( ydist < 0.0 ) {
+ ydist = 0.0f;
+ }
+ setOvXDistance( ov_xdist );
+ final double height = _phylogeny.getHeight();
+ if ( height > 0 ) {
+ final float ov_corr = ( float ) ( ( ( getOvMaxWidth() - l ) - getOvXDistance() ) / height );
+ setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
+ }
+ else {
+ setOvXcorrectionFactor( 0 );
}
- }
- if ( isPhyHasBranchLengths() && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
- getControlPanel().setDrawPhylogramEnabled( true );
}
else {
- getControlPanel().setDrawPhylogramEnabled( false );
+ setOvOn( false );
}
- if ( getMainPanel().getMainFrame() == null ) {
- // Must be "E" applet version.
- ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
- .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
+ }
+
+ void updateSetOfCollapsedExternalNodes() {
+ final Phylogeny phy = getPhylogeny();
+ _collapsed_external_nodeid_set.clear();
+ if ( phy != null ) {
+ E: for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
+ final PhylogenyNode ext_node = it.next();
+ PhylogenyNode n = ext_node;
+ while ( !n.isRoot() ) {
+ if ( n.isCollapse() ) {
+ _collapsed_external_nodeid_set.add( ext_node.getId() );
+ ext_node.setCollapse( true );
+ continue E;
+ }
+ n = n.getParent();
+ }
+ }
+ }
+ }
+
+ final void updateSubSuperTreeButton() {
+ if ( _subtree_index < 1 ) {
+ getControlPanel().deactivateButtonToReturnToSuperTree();
}
else {
- getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
+ getControlPanel().activateButtonToReturnToSuperTree( _subtree_index );
+ }
+ }
+
+ final void zoomInDomainStructure() {
+ if ( _domain_structure_width < 2000 ) {
+ _domain_structure_width *= 1.2;
+ }
+ }
+
+ final void zoomOutDomainStructure() {
+ if ( _domain_structure_width > 20 ) {
+ _domain_structure_width *= 0.8;
}
}
return ( ( key_code == KeyEvent.VK_ADD ) || ( key_code == KeyEvent.VK_PLUS )
|| ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON ) || ( key_code == KeyEvent.VK_1 ) );
}
-
- final private class NodeColorizationActionListener implements ActionListener {
-
- List<PhylogenyNode> _additional_nodes = null;
- JColorChooser _chooser = null;
- PhylogenyNode _node = null;
-
- NodeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
- _chooser = chooser;
- _node = node;
- }
-
- NodeColorizationActionListener( final JColorChooser chooser,
- final PhylogenyNode node,
- final List<PhylogenyNode> additional_nodes ) {
- _chooser = chooser;
- _node = node;
- _additional_nodes = additional_nodes;
- }
-
- @Override
- public void actionPerformed( final ActionEvent e ) {
- final Color c = _chooser.getColor();
- if ( c != null ) {
- colorizeNodes( c, _node, _additional_nodes );
- }
- }
- }
-
- final private class SubtreeColorizationActionListener implements ActionListener {
-
- List<PhylogenyNode> _additional_nodes = null;
- JColorChooser _chooser = null;
- PhylogenyNode _node = null;
-
- SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
- _chooser = chooser;
- _node = node;
- }
-
- SubtreeColorizationActionListener( final JColorChooser chooser,
- final PhylogenyNode node,
- final List<PhylogenyNode> additional_nodes ) {
- _chooser = chooser;
- _node = node;
- _additional_nodes = additional_nodes;
- }
-
- @Override
- public void actionPerformed( final ActionEvent e ) {
- final Color c = _chooser.getColor();
- if ( c != null ) {
- colorizeSubtree( c, _node, _additional_nodes );
- }
- }
- }
}
if ( cp.isShowSeqSymbols() && node.getNodeData().isHasSequence()
&& !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) {
TreePanelUtil
- .showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getSymbol(), sb );
+ .showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getSymbol(), sb );
}
if ( cp.isShowGeneNames() && node.getNodeData().isHasSequence()
&& !ForesterUtil.isEmpty( node.getNodeData().getSequence().getGeneName() ) ) {
&& ( node.getNodeData().getSequence().getAccession() != null )
&& !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().toString() ) ) {
TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getAccession()
- .toString(), sb );
+ .toString(), sb );
}
if ( cp.isShowTaxonomyCode() && node.getNodeData().isHasTaxonomy()
&& !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy()
- .getTaxonomyCode(), sb );
+ .getTaxonomyCode(), sb );
}
if ( cp.isShowTaxonomyScientificNames() && node.getNodeData().isHasTaxonomy()
&& !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) {
TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy()
- .getScientificName(), sb );
+ .getScientificName(), sb );
}
if ( cp.isShowTaxonomyCommonNames() && node.getNodeData().isHasTaxonomy()
&& !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) {
TreePanelUtil
- .showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getCommonName(), sb );
- }
-// if ( ( cp.isShowSeqNames() || cp.isShowSeqSymbols() || cp.isShowSequenceAcc() )
-// && node.getNodeData().isHasSequence()
-// && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
-// TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence()
-// .getMolecularSequence(), sb );
-// }
+ .showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getCommonName(), sb );
+ }
+ // if ( ( cp.isShowSeqNames() || cp.isShowSeqSymbols() || cp.isShowSequenceAcc() )
+ // && node.getNodeData().isHasSequence()
+ // && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
+ // TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence()
+ // .getMolecularSequence(), sb );
+ // }
final String s = sb.toString().trim();
if ( !ForesterUtil.isEmpty( s ) ) {
data.add( s );
TreePanelUtil.collapseSubtree( n, true );
if ( !n.getNodeData().isHasTaxonomy() ) {
n.getNodeData().setTaxonomy( ( Taxonomy ) n.getAllExternalDescendants().get( 0 ).getNodeData()
- .getTaxonomy().copy() );
+ .getTaxonomy().copy() );
}
inferred = true;
}
final List<PhylogenyNode> descs = PhylogenyMethods.getAllDescendants( n );
for( final PhylogenyNode desc : descs ) {
desc.getBranchData()
- .setBranchColor( new BranchColor( tree_panel.calculateTaxonomyBasedColor( tax ) ) );
+ .setBranchColor( new BranchColor( tree_panel.calculateTaxonomyBasedColor( tax ) ) );
}
}
}
if ( n.getNodeData().isHasTaxonomy()
&& ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() )
|| !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) || !ForesterUtil
- .isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
+ .isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() )
&& n.getNodeData().getTaxonomy().getRank().equalsIgnoreCase( rank ) ) {
final BranchColor c = new BranchColor( tree_panel.calculateTaxonomyBasedColor( n.getNodeData()
- .getTaxonomy() ) );
+ .getTaxonomy() ) );
TreePanelUtil.colorizeSubtree( n, c );
++colorizations;
if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
for( final String lin : node.getNodeData().getTaxonomy().getLineage() ) {
if ( true_lineage_to_color_map.containsKey( lin ) ) {
TreePanelUtil
- .colorizeSubtree( node, new BranchColor( true_lineage_to_color_map.get( lin ) ) );
+ .colorizeSubtree( node, new BranchColor( true_lineage_to_color_map.get( lin ) ) );
++colorizations;
success = true;
break;
case PFAM:
parser = new NHXParser();
( ( NHXParser ) parser )
- .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
( ( NHXParser ) parser ).setReplaceUnderscores( false );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
}
_main_frame.getMainPanel().getCurrentTreePanel().setTreeFile( new File( my_name_for_file ) );
AptxUtil.lookAtSomeTreePropertiesForAptxControlSettings( phylogeny, _main_frame.getMainPanel()
- .getControlPanel(), _main_frame.getConfiguration() );
+ .getControlPanel(), _main_frame.getConfiguration() );
_main_frame.getMainPanel().getControlPanel().showWhole();
}
}
}
else if ( !exception ) {
JOptionPane.showMessageDialog( null, ForesterUtil.wordWrap( "Failed to read in tree(s) from [" + url
- + "]", 80 ), "Error", JOptionPane.ERROR_MESSAGE );
+ + "]", 80 ), "Error", JOptionPane.ERROR_MESSAGE );
}
_main_frame.getContentPane().repaint();
if ( ( trees != null ) && ( trees.length > 0 ) ) {
try {
JOptionPane.showMessageDialog( null,
ForesterUtil.wordWrap( "Successfully read in " + trees.length
- + " tree(s) from [" + url + "]", 80 ),
- "Success",
- JOptionPane.INFORMATION_MESSAGE );
+ + " tree(s) from [" + url + "]", 80 ),
+ "Success",
+ JOptionPane.INFORMATION_MESSAGE );
}
catch ( final Exception e ) {
// Not important if this fails, do nothing.
git://source.jalview.org / jalview.git / commitdiff