// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// Copyright (C) 2003-2007 Ethalinda K.S. Cannon
// All rights reserved
-//
+//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
-//
+//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.swing.filechooser.FileFilter;
+import javax.swing.plaf.synth.SynthLookAndFeel;
import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
import org.forester.archaeopteryx.Util.GraphicsExportType;
+import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
+import org.forester.archaeopteryx.tools.GoAnnotation;
+import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
+import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
+import org.forester.archaeopteryx.tools.PhylogeneticInferrer;
+import org.forester.archaeopteryx.tools.SequenceDataRetriver;
+import org.forester.archaeopteryx.tools.TaxonomyDataObtainer;
import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
import org.forester.archaeopteryx.webservices.WebservicesManager;
import org.forester.io.parsers.FastaParser;
import org.forester.util.BasicTableParser;
import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterUtil;
-import org.forester.util.WindowsUtils;
import org.forester.util.ForesterUtil.PhylogenyNodeField;
import org.forester.util.ForesterUtil.TAXONOMY_EXTRACTION;
+import org.forester.util.WindowsUtils;
class DefaultFilter extends FileFilter {
throw new IllegalArgumentException( "configuration is null" );
}
try {
- if ( _configuration.isUseNativeUI() ) {
- UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
+ boolean synth_exception = false;
+ if ( Constants.__SYNTH_LF ) {
+ try {
+ final SynthLookAndFeel synth = new SynthLookAndFeel();
+ synth.load( MainFrameApplication.class.getResourceAsStream( "/resources/synth_look_and_feel_1.xml" ),
+ MainFrameApplication.class );
+ UIManager.setLookAndFeel( synth );
+ }
+ catch ( Exception ex ) {
+ synth_exception = true;
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME,
+ "could not create synth look and feel: "
+ + ex.getLocalizedMessage() );
+ }
}
- else {
- UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
+ if ( !Constants.__SYNTH_LF || synth_exception ) {
+ if ( _configuration.isUseNativeUI() ) {
+ UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
+ }
+ else {
+ UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
+ }
}
+ //UIManager.setLookAndFeel( "com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel" );
}
catch ( final UnsupportedLookAndFeelException e ) {
- Util.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
+ Util.dieWithSystemError( "unsupported look and feel: " + e.toString() );
}
catch ( final ClassNotFoundException e ) {
- Util.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
+ Util.dieWithSystemError( "class not found exception: " + e.toString() );
}
catch ( final InstantiationException e ) {
- Util.dieWithSystemError( "InstantiationException: " + e.toString() );
+ Util.dieWithSystemError( "instantiation exception: " + e.toString() );
}
catch ( final IllegalAccessException e ) {
- Util.dieWithSystemError( "IllegalAccessException: " + e.toString() );
+ Util.dieWithSystemError( "illegal access exception: " + e.toString() );
}
catch ( final Exception e ) {
Util.dieWithSystemError( e.toString() );
}
obtainDetailedTaxonomicInformation();
}
+ else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ obtainDetailedTaxonomicInformationDelete();
+ }
+ else if ( o == _obtain_uniprot_seq_information_jmi ) {
+ obtainUniProtSequenceInformation();
+ }
else if ( o == _read_values_jmi ) {
if ( isSubtreeDisplayed() ) {
return;
@Override
public void stateChanged( final ChangeEvent e ) {
- MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getCurrentTreePanel() );
+ MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
MainFrame
.setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
_uniform_cladograms_rbmi,
_ext_node_dependent_cladogram_rbmi,
_label_direction_cbmi );
+ MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
+ MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
+ MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
}
} );
_options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );
_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 );
- _options_jmenu.add( _show_node_boxes_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL ) );
+ _options_jmenu.add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL ) );
+ _options_jmenu
+ .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
+ _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
+ _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
+ _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
_options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
_options_jmenu
.add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
customizeJMenuItem( _print_size_mi );
customizeJMenuItem( _choose_pdf_width_mi );
customizeJMenuItem( _overview_placment_mi );
- customizeCheckBoxMenuItem( _show_node_boxes_cbmi, getOptions().isShowNodeBoxes() );
+ customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
+ customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
+ customizeJMenuItem( _cycle_node_shape_mi );
+ customizeJMenuItem( _cycle_node_fill_mi );
+ customizeJMenuItem( _choose_node_size_mi );
customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
_obtain_detailed_taxonomic_information_jmi
.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!)" ) );
+ 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)" );
+ _tools_menu
+ .add( _obtain_uniprot_seq_information_jmi = new JMenuItem( "Obtain Sequence Information (from UniProt)" ) );
+ customizeJMenuItem( _obtain_uniprot_seq_information_jmi );
+ _obtain_uniprot_seq_information_jmi.setToolTipText( "To add additional sequence information (from UniProt)" );
_tools_menu.addSeparator();
if ( !Constants.__RELEASE ) {
_tools_menu.add( _function_analysis = new JMenuItem( "Add UniProtKB Annotations" ) );
if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
return;
}
- final MainPanelEdit a = new MainPanelEdit( this, _mainpanel.getCurrentTreePanel(), _mainpanel
- .getCurrentPhylogeny() );
+ final GoAnnotation a = new GoAnnotation( this,
+ _mainpanel.getCurrentTreePanel(),
+ _mainpanel.getCurrentPhylogeny() );
new Thread( a ).start();
}
JOptionPane.ERROR_MESSAGE );
return;
}
- final Phylogeny phy = _mainpanel.getCurrentPhylogeny().copy();
- final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this, _mainpanel
- .getCurrentTreePanel(), phy );
+ final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,
+ _mainpanel.getCurrentTreePanel(),
+ _mainpanel.getCurrentPhylogeny()
+ .copy() );
new Thread( inferrer ).start();
}
if ( getMsa() != null ) {
final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),
getPhylogeneticInferenceOptions()
- .copy(),
- this );
+ .copy(), this );
new Thread( inferrer ).start();
}
else {
if ( getSeqs() != null ) {
final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),
getPhylogeneticInferenceOptions()
- .copy(),
- this );
+ .copy(), this );
new Thread( inferrer ).start();
}
else {
}
@Override
- MainPanel getMainPanel() {
+ public MainPanel getMainPanel() {
return _mainpanel;
}
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
- final TaxonomyDataObtainer t = new TaxonomyDataObtainer( this, _mainpanel.getCurrentTreePanel(), phy
- .copy() );
+ final TaxonomyDataObtainer t = new TaxonomyDataObtainer( this,
+ _mainpanel.getCurrentTreePanel(),
+ phy.copy() );
new Thread( t ).start();
}
}
}
+ private void obtainDetailedTaxonomicInformationDelete() {
+ if ( getCurrentTreePanel() != null ) {
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
+ if ( ( phy != null ) && !phy.isEmpty() ) {
+ final TaxonomyDataObtainer t = new TaxonomyDataObtainer( this,
+ _mainpanel.getCurrentTreePanel(),
+ phy.copy(),
+ true );
+ new Thread( t ).start();
+ }
+ }
+ }
+
+ private void obtainUniProtSequenceInformation() {
+ if ( getCurrentTreePanel() != null ) {
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
+ if ( ( phy != null ) && !phy.isEmpty() ) {
+ final SequenceDataRetriver u = new SequenceDataRetriver( this,
+ _mainpanel.getCurrentTreePanel(),
+ phy.copy() );
+ new Thread( u ).start();
+ }
+ }
+ }
+
private void print() {
if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null )
|| getCurrentTreePanel().getPhylogeny().isEmpty() ) {
try {
final NHXParser nhx = new NHXParser();
setSpecialOptionsForNhxParser( nhx );
- phys = Util.readPhylogenies( nhx, file );
+ phys = ForesterUtil.readPhylogenies( nhx, file );
nhx_or_nexus = true;
}
catch ( final Exception e ) {
warnIfNotPhyloXmlValidation( getConfiguration() );
try {
final PhyloXmlParser xml_parser = createPhyloXmlParser();
- phys = Util.readPhylogenies( xml_parser, file );
+ phys = ForesterUtil.readPhylogenies( xml_parser, file );
}
catch ( final Exception e ) {
exception = true;
}
else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) {
try {
- phys = Util.readPhylogenies( new TolParser(), file );
+ phys = ForesterUtil.readPhylogenies( new TolParser(), file );
}
catch ( final Exception e ) {
exception = true;
try {
final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
setSpecialOptionsForNexParser( nex );
- phys = Util.readPhylogenies( nex, file );
+ phys = ForesterUtil.readPhylogenies( nex, file );
nhx_or_nexus = true;
}
catch ( final Exception e ) {
else if ( parser instanceof PhyloXmlParser ) {
warnIfNotPhyloXmlValidation( getConfiguration() );
}
- phys = Util.readPhylogenies( parser, file );
+ phys = ForesterUtil.readPhylogenies( parser, file );
}
catch ( final Exception e ) {
exception = true;
System.gc();
}
- void readSeqsFromFile() {
+ public void readSeqsFromFile() {
// Set an initial directory if none set yet
final File my_dir = getCurrentDir();
_seqs_filechooser.setMultiSelectionEnabled( false );
}
}
- void readMsaFromFile() {
+ public void readMsaFromFile() {
// Set an initial directory if none set yet
final File my_dir = getCurrentDir();
_msa_filechooser.setMultiSelectionEnabled( false );
ForesterUtil.transferInternalNodeNamesToConfidence( phy );
}
}
- Util.addPhylogeniesToTabs( phys, new File( url.getFile() ).getName(), new File( url.getFile() )
- .toString(), getConfiguration(), getMainPanel() );
+ Util.addPhylogeniesToTabs( phys,
+ new File( url.getFile() ).getName(),
+ new File( url.getFile() ).toString(),
+ getConfiguration(),
+ getMainPanel() );
_mainpanel.getControlPanel().showWhole();
}
}
if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {
try {
- final Phylogeny[] trees = Util.readPhylogenies( new PhyloXmlParser(), file );
+ final Phylogeny[] trees = ForesterUtil.readPhylogenies( new PhyloXmlParser(), file );
t = trees[ 0 ];
}
catch ( final Exception e ) {
}
else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) {
try {
- final Phylogeny[] trees = Util.readPhylogenies( new TolParser(), file );
+ final Phylogeny[] trees = ForesterUtil.readPhylogenies( new TolParser(), file );
t = trees[ 0 ];
}
catch ( final Exception e ) {
// "*.*":
else {
try {
- final Phylogeny[] trees = Util.readPhylogenies( new PhyloXmlParser(), file );
+ final Phylogeny[] trees = ForesterUtil.readPhylogenies( new PhyloXmlParser(), file );
t = trees[ 0 ];
}
catch ( final Exception e ) {
}
}
if ( !exception ) {
+ getMainPanel().setTitleOfSelectedTab( file.getName() );
getMainPanel().getCurrentTreePanel().setTreeFile( file );
getMainPanel().getCurrentTreePanel().setEdited( false );
}
return _phylogenetic_inference_options;
}
- Msa getMsa() {
+ public Msa getMsa() {
return _msa;
}
_msa_file = msa_file;
}
- File getMsaFile() {
+ public File getMsaFile() {
return _msa_file;
}
- List<Sequence> getSeqs() {
+ public List<Sequence> getSeqs() {
return _seqs;
}
_seqs_file = seqs_file;
}
- File getSeqsFile() {
+ public File getSeqsFile() {
return _seqs_file;
}
} // MainFrameApplication.
public boolean accept( final File f ) {
final String file_name = f.getName().trim().toLowerCase();
return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f
- .isDirectory() )
- && ( !file_name.endsWith( ".xml.zip" ) );
+ .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );
}
@Override
git://source.jalview.org / jalview.git / blobdiff