import javax.swing.WindowConstants;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
import org.forester.analysis.TaxonomyDataManager;
import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
-import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
import org.forester.io.parsers.tol.TolParser;
import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.writers.SequenceWriter;
public final class MainFrameApplication extends MainFrame {
- private final static int FRAME_X_SIZE = 800;
- private final static int FRAME_Y_SIZE = 800;
+ private final static int FRAME_X_SIZE = 900;
+ private final static int FRAME_Y_SIZE = 900;
// Filters for the file-open dialog (classes defined in this file)
private static final long serialVersionUID = -799735726778865234L;
private static final boolean PREPROCESS_TREES = false;
setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
// The window listener
setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
- addWindowListener( new WindowAdapter() {
+ addFrameListener( new FrameAdapter() {
@Override
- public void windowClosing( final WindowEvent e ) {
+ public void FrameClosing () {
+
exit();
}
} );
_contentpane.repaint();
}
+
+
private MainFrameApplication( final Phylogeny[] phys, final Configuration config, final String title ) {
this( phys, config, title, null );
}
-
- private MainFrameApplication( final Phylogeny[] phys,
+
+ private MainFrameApplication(final Phylogeny[] phys,
final Configuration config,
final String title,
- final File current_dir ) {
- super();
+ final File current_dir,
+ final boolean isEmbedded) {
+ super(isEmbedded);
_configuration = config;
if ( _configuration == null ) {
throw new IllegalArgumentException( "configuration is null" );
// } );
// The window listener
setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
- addWindowListener( new WindowAdapter() {
+
+ addFrameListener( new FrameAdapter() {
@Override
- public void windowClosing( final WindowEvent e ) {
+ public void FrameClosing( ) {
+ if (MainFrameApplication.this.getParent() == null) {
if ( isUnsavedDataPresent() ) {
- final int r = JOptionPane.showConfirmDialog( null,
- "Exit despite potentially unsaved changes?",
- "Exit?",
+ final int r = JOptionPane.showConfirmDialog( _mainpanel,
+ "Close Archaeopteryx despite potentially unsaved changes?",
+ "Close viewer?",
JOptionPane.YES_NO_OPTION );
if ( r != JOptionPane.YES_OPTION ) {
return;
}
}
else {
- final int r = JOptionPane.showConfirmDialog( null,
- "Exit Archaeopteryx?",
- "Exit?",
- JOptionPane.YES_NO_OPTION );
+ final int r = JOptionPane
+ .showConfirmDialog( null, "Exit Archaeopteryx?", "Exit?", JOptionPane.YES_NO_OPTION );
if ( r != JOptionPane.YES_OPTION ) {
return;
}
- }
+ }}
exit();
- }
- } );
+
+ } });
// The component listener
addComponentListener( new ComponentAdapter() {
@Override
public void componentResized( final ComponentEvent e ) {
if ( _mainpanel.getCurrentTreePanel() != null ) {
- _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()
- .getWidth(),
- _mainpanel.getCurrentTreePanel()
- .getHeight() );
+ _mainpanel.getCurrentTreePanel()
+ .calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
+ _mainpanel.getCurrentTreePanel().getHeight() );
}
}
} );
// ...and its children
_contentpane.repaint();
System.gc();
+
+ }
+
+ private MainFrameApplication( final Phylogeny[] phys,
+ final Configuration config,
+ final String title,
+ final File current_dir ) {
+ this(phys,config,title,current_dir,false);
}
private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) {
}
collapseBelowThreshold();
}
+
else if ( o == _collapse_below_branch_length ) {
if ( isSubtreeDisplayed() ) {
return;
msa = FastaParser.parseMsa( is );
}
else {
- msa = GeneralMsaParser.parse( is );
+ msa = GeneralMsaParser.parseMsa( is );
}
}
catch ( final MsaFormatException e ) {
setArrowCursor();
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
e.getLocalizedMessage(),
"Multiple sequence alignment format error",
JOptionPane.ERROR_MESSAGE );
}
catch ( final IOException e ) {
setArrowCursor();
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
e.getLocalizedMessage(),
"Failed to read multiple sequence alignment",
JOptionPane.ERROR_MESSAGE );
}
catch ( final IllegalArgumentException e ) {
setArrowCursor();
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
e.getLocalizedMessage(),
"Unexpected error during reading of multiple sequence alignment",
JOptionPane.ERROR_MESSAGE );
catch ( final Exception e ) {
setArrowCursor();
e.printStackTrace();
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
e.getLocalizedMessage(),
"Unexpected error during reading of multiple sequence alignment",
JOptionPane.ERROR_MESSAGE );
return;
}
if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
"Multiple sequence alignment is empty",
"Illegal Multiple Sequence Alignment",
JOptionPane.ERROR_MESSAGE );
return;
}
if ( msa.getNumberOfSequences() < 4 ) {
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
"Multiple sequence alignment needs to contain at least 3 sequences",
"Illegal multiple sequence alignment",
JOptionPane.ERROR_MESSAGE );
return;
}
if ( msa.getLength() < 2 ) {
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
"Multiple sequence alignment needs to contain at least 2 residues",
"Illegal multiple sequence alignment",
JOptionPane.ERROR_MESSAGE );
}
catch ( final MsaFormatException e ) {
setArrowCursor();
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
e.getLocalizedMessage(),
"Multiple sequence file format error",
JOptionPane.ERROR_MESSAGE );
}
catch ( final IOException e ) {
setArrowCursor();
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
e.getLocalizedMessage(),
"Failed to read multiple sequence file",
JOptionPane.ERROR_MESSAGE );
}
catch ( final IllegalArgumentException e ) {
setArrowCursor();
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
e.getLocalizedMessage(),
"Unexpected error during reading of multiple sequence file",
JOptionPane.ERROR_MESSAGE );
catch ( final Exception e ) {
setArrowCursor();
e.printStackTrace();
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
e.getLocalizedMessage(),
"Unexpected error during reading of multiple sequence file",
JOptionPane.ERROR_MESSAGE );
return;
}
if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
"Multiple sequence file is empty",
"Illegal multiple sequence file",
JOptionPane.ERROR_MESSAGE );
return;
}
if ( seqs.size() < 4 ) {
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
"Multiple sequence file needs to contain at least 3 sequences",
"Illegal multiple sequence file",
JOptionPane.ERROR_MESSAGE );
private void addExpressionValuesFromFile() {
if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
"Need to load evolutionary tree first",
"Can Not Read Expression Values",
JOptionPane.WARNING_MESSAGE );
}
}
catch ( final IOException e ) {
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
e.getMessage(),
"Could Not Read Expression Value Table",
JOptionPane.ERROR_MESSAGE );
return;
}
if ( t.getNumberOfColumns() < 2 ) {
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
"Table contains " + t.getNumberOfColumns() + " column(s)",
"Problem with Expression Value Table",
JOptionPane.ERROR_MESSAGE );
return;
}
if ( t.getNumberOfRows() < 1 ) {
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
"Table contains zero rows",
"Problem with Expression Value Table",
JOptionPane.ERROR_MESSAGE );
}
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
"Table contains " + t.getNumberOfRows() + " rows, but tree contains "
+ phy.getNumberOfExternalNodes() + " external nodes",
- "Warning",
- JOptionPane.WARNING_MESSAGE );
+ "Warning",
+ JOptionPane.WARNING_MESSAGE );
}
final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
int not_found = 0;
row = t.findRow( node_name );
}
catch ( final IllegalArgumentException e ) {
- JOptionPane
- .showMessageDialog( this,
- e.getMessage(),
- "Error Mapping Node Identifiers to Expression Value Identifiers",
- JOptionPane.ERROR_MESSAGE );
+ JOptionPane.showMessageDialog( getThisFrame(),
+ e.getMessage(),
+ "Error Mapping Node Identifiers to Expression Value Identifiers",
+ JOptionPane.ERROR_MESSAGE );
return;
}
if ( row < 0 ) {
d = Double.parseDouble( t.getValueAsString( col, row ) );
}
catch ( final NumberFormatException e ) {
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
"Could not parse \"" + t.getValueAsString( col, row )
- + "\" into a decimal value",
+ + "\" into a decimal value",
"Issue with Expression Value Table",
JOptionPane.ERROR_MESSAGE );
return;
l.add( d );
}
if ( !l.isEmpty() ) {
- if ( node.getNodeData().getProperties() != null ) {
- node.getNodeData().getProperties()
- .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
- }
+
node.getNodeData().setVector( l );
}
}
}
if ( not_found > 0 ) {
- JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found
- + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );
+ JOptionPane
+ .showMessageDialog( getThisFrame(),
+ "Could not fine expression values for " + not_found + " external node(s)",
+ "Warning",
+ JOptionPane.WARNING_MESSAGE );
}
getCurrentTreePanel().setStatisticsForExpressionValues( stats );
}
private void addSequencesFromFile() {
if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
"Need to load evolutionary tree first",
"Can Not Read Sequences",
JOptionPane.WARNING_MESSAGE );
seqs = FastaParser.parse( fis2 );
try {
fis2.close();
- }
- catch ( final Exception e ) {
- // Ignore.
- }
+ }
+ catch ( final Exception e ) {
+ // Ignore.
+ }
}
else {
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
"Format does not appear to be Fasta",
"Multiple sequence file format error",
JOptionPane.ERROR_MESSAGE );
fis1.close();
}
catch ( final Exception e ) {
- // Ignore.
+ // Ignore.
}
}
catch ( final MsaFormatException e ) {
setArrowCursor();
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
e.getLocalizedMessage(),
"Multiple sequence file format error",
JOptionPane.ERROR_MESSAGE );
}
catch ( final IOException e ) {
setArrowCursor();
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
e.getLocalizedMessage(),
"Failed to read multiple sequence file",
JOptionPane.ERROR_MESSAGE );
catch ( final Exception e ) {
setArrowCursor();
e.printStackTrace();
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
e.getLocalizedMessage(),
"Unexpected error during reading of multiple sequence file",
JOptionPane.ERROR_MESSAGE );
return;
}
if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
"Multiple sequence file is empty",
"Empty multiple sequence file",
JOptionPane.ERROR_MESSAGE );
nodes = phy.getNodes( seq_name );
}
if ( nodes.size() > 1 ) {
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
"Sequence name \"" + seq_name + "\" is not unique",
"Sequence name not unique",
JOptionPane.ERROR_MESSAGE );
nodes = phy.getNodes( seq_name_split );
}
if ( nodes.size() > 1 ) {
- JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split
- + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Split sequence name \"" + seq_name_split
+ + "\" is not unique",
+ "Sequence name not unique",
+ JOptionPane.ERROR_MESSAGE );
setArrowCursor();
return;
}
+ " external nodes now have a molecular sequence attached to them.";
}
if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) {
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
"Attached all " + total_counter + " sequences to tree nodes.\n" + s,
"All sequences attached",
JOptionPane.INFORMATION_MESSAGE );
}
else {
- JOptionPane.showMessageDialog( this, "Attached " + attached_counter
- + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter
- + " sequences attached", JOptionPane.WARNING_MESSAGE );
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Attached " + attached_counter + " sequences out of a total of "
+ + total_counter + " sequences.\n" + s,
+ attached_counter + " sequences attached",
+ JOptionPane.WARNING_MESSAGE );
}
}
else {
- JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter
- + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "No maching tree node for any of the " + total_counter + " sequences",
+ "Could not attach any sequences",
+ JOptionPane.ERROR_MESSAGE );
}
}
}
private void closeCurrentPane() {
if ( getMainPanel().getCurrentTreePanel() != null ) {
if ( getMainPanel().getCurrentTreePanel().isEdited() ) {
- final int r = JOptionPane.showConfirmDialog( this,
+ final int r = JOptionPane.showConfirmDialog( getThisFrame(),
"Close tab despite potentially unsaved changes?",
"Close Tab?",
JOptionPane.YES_NO_OPTION );
}
}
- private void collapse( final Phylogeny phy ) {
+ private void collapseBelowThreshold( final Phylogeny phy ) {
final PhylogenyNodeIterator it = phy.iteratorPostorder();
final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
double min_support = Double.MAX_VALUE;
repaint();
}
if ( to_be_removed.size() > 0 ) {
- JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
- + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "
- + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Collapsed " + to_be_removed.size()
+ + " branches with\nconfidence values below "
+ + getMinNotCollapseConfidenceValue(),
+ "Collapsed " + to_be_removed.size() + " branches",
+ JOptionPane.INFORMATION_MESSAGE );
}
else {
- JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "
- + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "No branch collapsed,\nminimum confidence value per branch is "
+ + min_support,
+ "No branch collapsed",
+ JOptionPane.INFORMATION_MESSAGE );
}
}
else {
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
"No branch collapsed because no confidence values present",
"No confidence values present",
JOptionPane.INFORMATION_MESSAGE );
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
- final String s = ( String ) JOptionPane
- .showInputDialog( this,
- "Please enter the minimum branch length value\n",
- "Minimal Branch Length Value",
- JOptionPane.QUESTION_MESSAGE,
- null,
- null,
- getMinNotCollapseBlValue() );
+ final String s = ( String ) JOptionPane.showInputDialog( getThisFrame(),
+ "Please enter the minimum branch length value\n",
+ "Minimal Branch Length Value",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ null,
+ getMinNotCollapseBlValue() );
if ( !ForesterUtil.isEmpty( s ) ) {
boolean success = true;
double m = 0.0;
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
- final String s = ( String ) JOptionPane.showInputDialog( this,
+ final String s = ( String ) JOptionPane.showInputDialog( getThisFrame(),
"Please enter the minimum confidence value\n",
"Minimal Confidence Value",
JOptionPane.QUESTION_MESSAGE,
}
if ( success && ( m >= 0.0 ) ) {
setMinNotCollapseConfidenceValue( m );
- collapse( phy );
+ collapseBelowThreshold( phy );
}
}
}
repaint();
}
if ( to_be_removed.size() > 0 ) {
- JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
- + " branches with\nbranch length values below " + getMinNotCollapseBlValue(), "Collapsed "
- + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Collapsed " + to_be_removed.size()
+ + " branches with\nbranch length values below "
+ + getMinNotCollapseBlValue(),
+ "Collapsed " + to_be_removed.size() + " branches",
+ JOptionPane.INFORMATION_MESSAGE );
}
else {
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
"No branch collapsed,\nminimum branch length is " + min_bl,
"No branch collapsed",
JOptionPane.INFORMATION_MESSAGE );
}
}
else {
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
"No branch collapsed because no branch length values present",
"No branch length values present",
JOptionPane.INFORMATION_MESSAGE );
xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
}
catch ( final Exception e ) {
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
e.getLocalizedMessage(),
"failed to create validating XML parser",
JOptionPane.WARNING_MESSAGE );
if ( getMsa() != null ) {
final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),
getPhylogeneticInferenceOptions()
- .copy(), this );
+ .copy(),
+ this );
new Thread( inferrer ).start();
}
else {
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
"No multiple sequence alignment selected",
"Phylogenetic Inference Not Launched",
JOptionPane.WARNING_MESSAGE );
if ( getSeqs() != null ) {
final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),
getPhylogeneticInferenceOptions()
- .copy(), this );
+ .copy(),
+ this );
new Thread( inferrer ).start();
}
else {
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
"No input sequences selected",
"Phylogenetic Inference Not Launched",
JOptionPane.WARNING_MESSAGE );
String all = "all ";
if ( counter_failed > 0 ) {
all = "";
- failed = "\nCould not extract taxonomic data for " + counter_failed
- + " named external nodes:\n" + sb_failed;
+ failed = "\nCould not extract taxonomic data for " + counter_failed + " named external nodes:\n"
+ + sb_failed;
}
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
"Extracted taxonomic data from " + all + counter
- + " named external nodes:\n" + sb.toString() + failed,
+ + " named external nodes:\n" + sb.toString() + failed,
"Taxonomic Data Extraction Completed",
counter_failed > 0 ? JOptionPane.WARNING_MESSAGE
: JOptionPane.INFORMATION_MESSAGE );
}
else {
- JOptionPane
- .showMessageDialog( this,
- "Could not extract any taxonomic data.\nMaybe node names are empty\n"
- + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"
- + "or nodes already have taxonomic data?\n",
- "No Taxonomic Data Extracted",
- JOptionPane.ERROR_MESSAGE );
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Could not extract any taxonomic data.\nMaybe node names are empty\n"
+ + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"
+ + "or nodes already have taxonomic data?\n",
+ "No Taxonomic Data Extracted",
+ JOptionPane.ERROR_MESSAGE );
}
}
}
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
- PhylogenyMethods
- .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );
+ PhylogenyMethods.transferNodeNameToField( phy,
+ PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME,
+ false );
}
}
}
_mainpanel.getControlPanel().showWhole();
_mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
_mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
- if ( getMainPanel().getMainFrame() == null ) {
- // Must be "E" applet version.
- ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
- .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
- }
- else {
- getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
- }
+
+ getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
+
activateSaveAllIfNeeded();
System.gc();
}
else {
try {
final PhylogenyParser parser = ParserUtils
- .createParserDependingOnFileType( file, getConfiguration()
- .isValidatePhyloXmlAgainstSchema() );
+ .createParserDependingOnFileType( file,
+ getConfiguration()
+ .isValidatePhyloXmlAgainstSchema() );
if ( parser instanceof NexusPhylogeniesParser ) {
final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
setSpecialOptionsForNexParser( nex );
getMainPanel() );
_mainpanel.getControlPanel().showWhole();
if ( nhx_or_nexus && one_desc ) {
- JOptionPane
- .showMessageDialog( this,
- "One or more trees contain (a) node(s) with one descendant, "
- + ForesterUtil.LINE_SEPARATOR
- + "possibly indicating illegal parentheses within node names.",
- "Warning: Possible Error in New Hampshire Formatted Data",
- JOptionPane.WARNING_MESSAGE );
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "One or more trees contain (a) node(s) with one descendant, "
+ + ForesterUtil.LINE_SEPARATOR
+ + "possibly indicating illegal parentheses within node names.",
+ "Warning: Possible Error in New Hampshire Formatted Data",
+ JOptionPane.WARNING_MESSAGE );
}
}
}
if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.xmlfilter ) {
try {
- final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
- .createPhyloXmlParserXsdValidating(), file );
+ final Phylogeny[] trees = PhylogenyMethods
+ .readPhylogenies( PhyloXmlParser.createPhyloXmlParserXsdValidating(), file );
t = trees[ 0 ];
}
catch ( final Exception e ) {
// "*.*":
else {
try {
- final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
- .createPhyloXmlParserXsdValidating(), file );
+ final Phylogeny[] trees = PhylogenyMethods
+ .readPhylogenies( PhyloXmlParser.createPhyloXmlParserXsdValidating(), file );
t = trees[ 0 ];
}
catch ( final Exception e ) {
if ( !exception && ( t != null ) && !t.isRooted() ) {
exception = true;
t = null;
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
"Species tree is not rooted",
"Species tree not loaded",
JOptionPane.ERROR_MESSAGE );
if ( !node.getNodeData().isHasTaxonomy() ) {
exception = true;
t = null;
- JOptionPane
- .showMessageDialog( this,
- "Species tree contains external node(s) without taxonomy information",
- "Species tree not loaded",
- JOptionPane.ERROR_MESSAGE );
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Species tree contains external node(s) without taxonomy information",
+ "Species tree not loaded",
+ JOptionPane.ERROR_MESSAGE );
break;
}
else {
if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {
exception = true;
t = null;
- JOptionPane.showMessageDialog( this,
- "Taxonomy ["
- + node.getNodeData().getTaxonomy().asSimpleText()
- + "] is not unique in species tree",
- "Species tree not loaded",
- JOptionPane.ERROR_MESSAGE );
+ JOptionPane
+ .showMessageDialog( getThisFrame(),
+ "Taxonomy [" + node.getNodeData().getTaxonomy().asSimpleText()
+ + "] is not unique in species tree",
+ "Species tree not loaded",
+ JOptionPane.ERROR_MESSAGE );
break;
}
else {
}
if ( !exception && ( t != null ) ) {
setSpeciesTree( t );
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
"Species tree successfully loaded",
"Species tree loaded",
JOptionPane.INFORMATION_MESSAGE );
_file_jmenu.addSeparator();
final WebservicesManager webservices_manager = WebservicesManager.getInstance();
_load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager
- .getAvailablePhylogeniesWebserviceClients().size() ];
+ .getAvailablePhylogeniesWebserviceClients().size() ];
for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );
_load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );
_save_all_item.setEnabled( false );
_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" ) ) {
+ 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.addSeparator();
_file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
customizeJMenuItem( _open_item );
- _open_item
- .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );
+ _open_item.setFont( new Font( _open_item.getFont().getFontName(),
+ Font.BOLD,
+ _open_item.getFont().getSize() + 4 ) );
customizeJMenuItem( _open_url_item );
for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );
public void stateChanged( final ChangeEvent e ) {
MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
- MainFrame
- .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
- MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
- .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
- // MainFrame.setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
+ MainFrame.setTextMinSupportMenuItem( _choose_minimal_confidence_mi,
+ getOptions(),
+ getCurrentTreePanel() );
+ MainFrame.setTextForFontChooserMenuItem( _choose_font_mi,
+ MainFrame.createCurrentFontDesc( getMainPanel()
+ .getTreeFontSet() ) );
+ // MainFrame.setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
MainFrame.setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
} );
_options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );
_options_jmenu
- .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
- _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
+ .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
_options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( 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 );
- _radio_group_1.add( _non_lined_up_cladograms_rbmi );
+ _radio_group_1.add( _non_lined_up_cladograms_rbmi );
_options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
_options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
_options_jmenu
- .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );
+ .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );
+ _options_jmenu
+ .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );
_options_jmenu
- .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );
+ .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
+
_options_jmenu
- .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 ) );
+ .add( _collapsed_with_average_height_cbmi = new JCheckBoxMenuItem( "Proportional Height of Collapsed Subtrees" ) );
+
+
+ _options_jmenu
+ .add( _show_abbreviated_labels_for_collapsed_nodes_cbmi = new JCheckBoxMenuItem( "Add Abbreviated Labels to Collapsed Subtrees" ) );
+
+
+
+ _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( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
_options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
}
_options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_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( INVERSE_SEARCH_RESULT_LABEL ) );
- _options_jmenu.add( _color_all_found_nodes_when_coloring_subtree_cbmi = new JCheckBoxMenuItem( "Colorize All Found Nodes When Colorizing Subtree(s)" ) );
+ _options_jmenu
+ .add( _color_all_found_nodes_when_coloring_subtree_cbmi = new JCheckBoxMenuItem( "Colorize All Found Nodes When Colorizing Subtree(s)" ) );
_options_jmenu.addSeparator();
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
- getConfiguration() ) );
+ _options_jmenu
+ .add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ), getConfiguration() ) );
_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( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') 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" ) );
_options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
_options_jmenu.addSeparator();
_options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Read:" ), getConfiguration() ) );
_options_jmenu
- .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
+ .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
_options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
- _options_jmenu.add( _parse_beast_style_extended_nexus_tags_cbmi = new JCheckBoxMenuItem( "Parse BEAST-style extended Newick/Nexus tags" ) );
-
- _parse_beast_style_extended_nexus_tags_cbmi.setToolTipText( "to parse elements in the form of \"[&!color=#800080]\" in Newick/Nexus formatted trees" );
-
-
_options_jmenu
- .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );
+ .add( _parse_beast_style_extended_nexus_tags_cbmi = new JCheckBoxMenuItem( "Parse BEAST-style extended Newick/Nexus tags" ) );
+ _parse_beast_style_extended_nexus_tags_cbmi
+ .setToolTipText( "to parse elements in the form of \"[&!color=#800080]\" in Newick/Nexus formatted trees" );
+ _options_jmenu
+ .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );
_options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );
_options_jmenu
- .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );
+ .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );
_options_jmenu
- .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) );
+ .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) );
_options_jmenu
- .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) );
+ .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) );
_extract_taxonomy_pfam_strict_rbmi
- .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" );
+ .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" );
_extract_taxonomy_pfam_relaxed_rbmi
- .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" );
+ .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" );
_extract_taxonomy_agressive_rbmi
- .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\"" );
+ .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\"" );
_radio_group_2 = new ButtonGroup();
_radio_group_2.add( _extract_taxonomy_no_rbmi );
_radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );
_radio_group_2.add( _extract_taxonomy_agressive_rbmi );
_options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Save:" ), getConfiguration() ) );
_options_jmenu
- .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
+ .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
_use_brackets_for_conf_in_nh_export_cbmi
- .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
+ .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
_options_jmenu
- .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
+ .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
customizeJMenuItem( _choose_font_mi );
customizeJMenuItem( _choose_minimal_confidence_mi );
customizeJMenuItem( _switch_colors_mi );
customizeJMenuItem( _choose_pdf_width_mi );
customizeJMenuItem( _overview_placment_mi );
- customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
- .isShowDefaultNodeShapesExternal() );
- customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
- .isShowDefaultNodeShapesInternal() );
- customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()
- .isShowDefaultNodeShapesForMarkedNodes() );
+ customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi,
+ getOptions().isShowDefaultNodeShapesExternal() );
+ customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi,
+ getOptions().isShowDefaultNodeShapesInternal() );
+ customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi,
+ getOptions().isShowDefaultNodeShapesForMarkedNodes() );
customizeJMenuItem( _cycle_node_shape_mi );
customizeJMenuItem( _cycle_node_fill_mi );
customizeJMenuItem( _choose_node_size_mi );
customizeJMenuItem( _cycle_data_return );
- customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
+ customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch,
+ getOptions().isColorLabelsSameAsParentBranch() );
customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
+ customizeCheckBoxMenuItem( _collapsed_with_average_height_cbmi, getOptions().isCollapsedWithAverageHeigh() );
+ customizeCheckBoxMenuItem( _show_abbreviated_labels_for_collapsed_nodes_cbmi, getOptions().isShowAbbreviatedLabelsForCollapsedNodes() );
+
customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
- customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
- getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
- getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
+ getOptions().getCladogramType() == CLADOGRAM_TYPE.LINED_UP );
customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
customizeCheckBoxMenuItem( _label_direction_cbmi,
getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
- customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()
- .isInternalNumberAreConfidenceForNhParsing() );
+ customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi,
+ getOptions().isInternalNumberAreConfidenceForNhParsing() );
customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,
getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );
customizeRadioButtonMenuItem( _extract_taxonomy_pfam_strict_rbmi,
customizeRadioButtonMenuItem( _extract_taxonomy_agressive_rbmi,
getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE );
customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
- customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi, getOptions()
- .isReplaceUnderscoresInNhParsing() );
+ customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi,
+ getOptions().isReplaceUnderscoresInNhParsing() );
customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );
customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
- customizeCheckBoxMenuItem( _color_all_found_nodes_when_coloring_subtree_cbmi, getOptions().isColorAllFoundNodesWhenColoringSubtree() );
- customizeCheckBoxMenuItem( _parse_beast_style_extended_nexus_tags_cbmi, getOptions().isParseBeastStyleExtendedNexusTags() );
-
+ customizeCheckBoxMenuItem( _color_all_found_nodes_when_coloring_subtree_cbmi,
+ getOptions().isColorAllFoundNodesWhenColoringSubtree() );
+ customizeCheckBoxMenuItem( _parse_beast_style_extended_nexus_tags_cbmi,
+ getOptions().isParseBeastStyleExtendedNexusTags() );
customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
- customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()
- .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
- customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()
- .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
+ customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi,
+ getOptions()
+ .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
+ customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi,
+ getOptions()
+ .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
_jmenubar.add( _options_jmenu );
_inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
customizeJMenuItem( _inference_from_seqs_item );
_inference_from_seqs_item
- .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
+ .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
}
else {
_inference_menu
- .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );
+ .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );
customizeJMenuItem( _inference_from_seqs_item );
_inference_from_seqs_item.setEnabled( false );
}
_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" );
_delete_not_selected_nodes_item.setToolTipText( "To delete all not selected external nodes" );
customizeJMenuItem( _delete_not_selected_nodes_item );
_tools_menu.addSeparator();
- _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
+ _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Single Taxonomy-Subtrees" ) );
customizeJMenuItem( _collapse_species_specific_subtrees );
- _collapse_species_specific_subtrees.setToolTipText( "To (reversibly) collapse species-specific subtrees" );
+ _collapse_species_specific_subtrees.setToolTipText( "To (reversibly) collapse subtrees associated with only one taxonomy (such as species specific subtrees)" );
_tools_menu
- .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
+ .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
customizeJMenuItem( _collapse_below_threshold );
_collapse_below_threshold
- .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)" );
+ .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)" );
//
_tools_menu
- .add( _collapse_below_branch_length = new JMenuItem( "Collapse Branches with Branch Lengths Below Threshold into Multifurcations" ) );
+ .add( _collapse_below_branch_length = new JMenuItem( "Collapse Branches with Branch Lengths Below Threshold into Multifurcations" ) );
customizeJMenuItem( _collapse_below_branch_length );
_collapse_below_branch_length
- .setToolTipText( "To (permanently) collapse branches with branches with branch lengths below a threshold into multifurcations" );
+ .setToolTipText( "To (permanently) collapse branches with branches with branch lengths below a threshold into multifurcations" );
//
_tools_menu.addSeparator();
_tools_menu
- .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );
+ .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );
customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
_extract_tax_code_from_node_names_jmi
- .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'" );
+ .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'" );
_tools_menu
- .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
+ .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
customizeJMenuItem( _move_node_names_to_tax_sn_jmi );
_move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );
_tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );
customizeJMenuItem( _obtain_seq_information_jmi );
_obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );
_tools_menu
- .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
+ .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
_obtain_detailed_taxonomic_information_jmi
- .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
+ .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
_tools_menu
- .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
+ .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
_obtain_detailed_taxonomic_information_deleting_jmi
- .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
+ .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
_tools_menu.addSeparator();
_tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) );
customizeJMenuItem( _read_values_jmi );
_tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) );
customizeJMenuItem( _read_seqs_jmi );
_read_seqs_jmi
- .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );
+ .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );
_jmenubar.add( _tools_menu );
}
@Override
void close() {
if ( isUnsavedDataPresent() ) {
- final int r = JOptionPane.showConfirmDialog( this,
+ final int r = JOptionPane.showConfirmDialog( getThisFrame(),
"Exit despite potentially unsaved changes?",
"Exit?",
JOptionPane.YES_NO_OPTION );
URL url = null;
Phylogeny[] phys = null;
final String message = "Please enter a complete URL, for example \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\"";
- final String url_string = JOptionPane.showInputDialog( this,
- message,
- "Use URL/webservice to obtain a phylogeny",
- JOptionPane.QUESTION_MESSAGE );
+ final String url_string = JOptionPane
+ .showInputDialog( getThisFrame(),
+ message,
+ "Use URL/webservice to obtain a phylogeny",
+ JOptionPane.QUESTION_MESSAGE );
boolean nhx_or_nexus = false;
if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
try {
parser = new TolParser();
}
else {
- parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()
- .isValidatePhyloXmlAgainstSchema() );
+ parser = ParserUtils
+ .createParserDependingOnUrlContents( url,
+ getConfiguration().isValidatePhyloXmlAgainstSchema() );
}
if ( parser instanceof NexusPhylogeniesParser ) {
nhx_or_nexus = true;
phys = factory.create( url.openStream(), parser );
}
catch ( final MalformedURLException e ) {
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
"Malformed URL: " + url + "\n" + e.getLocalizedMessage(),
"Malformed URL",
JOptionPane.ERROR_MESSAGE );
}
catch ( final IOException e ) {
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
"Could not read from " + url + "\n"
+ ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
- "Failed to read URL",
- JOptionPane.ERROR_MESSAGE );
+ "Failed to read URL",
+ JOptionPane.ERROR_MESSAGE );
}
catch ( final Exception e ) {
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
"Unexpected Exception",
JOptionPane.ERROR_MESSAGE );
static void warnIfNotPhyloXmlValidation( final Configuration c ) {
if ( !c.isValidatePhyloXmlAgainstSchema() ) {
- JOptionPane
- .showMessageDialog( null,
- ForesterUtil
- .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
- 80 ),
+ JOptionPane.showMessageDialog( null,
+ ForesterUtil.wordWrap(
+ "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
+ 80 ),
"Warning",
JOptionPane.WARNING_MESSAGE );
}
git://source.jalview.org / jalview.git / blobdiff