import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureSettingsControllerI;
-import jalview.api.FeatureSettingsModelI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
import jalview.api.analysis.ScoreModelI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.DBRefSource;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SeqCigar;
import jalview.io.JalviewFileView;
import jalview.io.JnetAnnotationMaker;
import jalview.io.NewickFile;
+import jalview.io.StructureFile;
import jalview.io.TCoffeeScoreFile;
-import jalview.io.gff.SequenceOntologyI;
import jalview.jbgui.GAlignFrame;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.TurnColourScheme;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ZappoColourScheme;
-import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.DBRefFetcher;
import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
-import jalview.ws.SequenceFetcher;
import jalview.ws.jws1.Discoverer;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import java.awt.datatransfer.DataFlavor;
import java.awt.datatransfer.StringSelection;
import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
import java.awt.dnd.DropTargetDragEvent;
import java.awt.dnd.DropTargetDropEvent;
import java.awt.dnd.DropTargetEvent;
toggleHiddenRegions(toggleSeqs, toggleCols);
break;
}
+ case KeyEvent.VK_B:
+ {
+ boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
+ boolean modifyExisting = true; // always modify, don't clear
+ // evt.isShiftDown();
+ boolean invertHighlighted = evt.isAltDown();
+ avc.markHighlightedColumns(invertHighlighted, modifyExisting,
+ toggleSel);
+ break;
+ }
case KeyEvent.VK_PAGE_UP:
if (viewport.getWrapAlignment())
{
// originating file's format
// TODO: work out how to recover feature settings for correct view(s) when
// file is reloaded.
- if (currentFileFormat == FileFormat.Jalview)
+ if (FileFormat.Jalview.equals(currentFileFormat))
{
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
for (int i = 0; i < frames.length; i++)
currentFileFormat = chooser.getSelectedFormat();
while (currentFileFormat == null)
{
- JOptionPane
+ JvOptionPane
.showInternalMessageDialog(
Desktop.desktop,
MessageManager
.getString("label.select_file_format_before_saving"),
MessageManager
.getString("label.file_format_not_specified"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
currentFileFormat = chooser.getSelectedFormat();
value = chooser.showSaveDialog(this);
if (value != JalviewFileChooser.APPROVE_OPTION)
{
boolean success = true;
- if (format == FileFormat.Jalview)
+ if (FileFormat.Jalview.equals(format))
{
String shortName = title;
if (!success)
{
- JOptionPane.showInternalMessageDialog(this, MessageManager
+ JvOptionPane.showInternalMessageDialog(this, MessageManager
.formatMessage("label.couldnt_save_file",
new Object[] { fileName }), MessageManager
.getString("label.error_saving_file"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
return success;
}
else
{
- JOptionPane.showInternalMessageDialog(this, warning, title,
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showInternalMessageDialog(this, warning, title,
+ JvOptionPane.WARNING_MESSAGE);
}
return;
}
@Override
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
- new HtmlSvgOutput(null, alignPanel);
+ HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
+ htmlSVG.exportHTML(null);
}
@Override
public void bioJSMenuItem_actionPerformed(ActionEvent e)
{
- BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
- bjs.exportJalviewAlignmentAsBioJsHtmlFile();
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
+ bjs.exportHTML(null);
}
public void createImageMap(File file, String image)
.getAlignment().getWidth()) ? true : false;
if (isEntireAlignWidth)
{
- int confirm = JOptionPane.showConfirmDialog(this,
+ int confirm = JvOptionPane.showConfirmDialog(this,
MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
MessageManager.getString("label.delete_all"), // $NON-NLS-1$
- JOptionPane.OK_CANCEL_OPTION);
+ JvOptionPane.OK_CANCEL_OPTION);
- if (confirm == JOptionPane.CANCEL_OPTION
- || confirm == JOptionPane.CLOSED_OPTION)
+ if (confirm == JvOptionPane.CANCEL_OPTION
+ || confirm == JvOptionPane.CLOSED_OPTION)
{
return;
}
viewport.setFollowHighlight(state);
if (state)
{
- alignPanel.scrollToPosition(
- alignPanel.getSeqPanel().seqCanvas.searchResults, false);
+ alignPanel.scrollToPosition(viewport.getSearchResults(), false);
}
}
// Hide everything by the current selection - this is a hack - we do the
// invert and then hide
// first check that there will be visible columns after the invert.
- if ((viewport.getColumnSelection() != null
- && viewport.getColumnSelection().getSelected() != null && viewport
- .getColumnSelection().getSelected().size() > 0)
+ if (viewport.hasSelectedColumns()
|| (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
.getEndRes()))
{
hideSelSequences_actionPerformed(null);
hide = true;
}
- else if (!(toggleCols && viewport.getColumnSelection().getSelected()
- .size() > 0))
+ else if (!(toggleCols && viewport.hasSelectedColumns()))
{
showAllSeqs_actionPerformed(null);
}
if (toggleCols)
{
- if (viewport.getColumnSelection().getSelected().size() > 0)
+ if (viewport.hasSelectedColumns())
{
hideSelColumns_actionPerformed(null);
if (!toggleSeqs)
@Override
public void mousePressed(MouseEvent evt)
{
- if (evt.isPopupTrigger())
+ if (evt.isPopupTrigger()) // Mac
{
- radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+ offerRemoval(radioItem);
+ }
+ }
- int option = JOptionPane.showInternalConfirmDialog(
- jalview.gui.Desktop.desktop,
- MessageManager
- .getString("label.remove_from_default_list"),
- MessageManager
- .getString("label.remove_user_defined_colour"),
- JOptionPane.YES_NO_OPTION);
- if (option == JOptionPane.YES_OPTION)
- {
- jalview.gui.UserDefinedColours
- .removeColourFromDefaults(radioItem.getText());
- colourMenu.remove(radioItem);
- }
- else
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ if (evt.isPopupTrigger()) // Windows
+ {
+ offerRemoval(radioItem);
+ }
+ }
+
+ /**
+ * @param radioItem
+ */
+ void offerRemoval(final JRadioButtonMenuItem radioItem)
+ {
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+ int option = JvOptionPane.showInternalConfirmDialog(
+ jalview.gui.Desktop.desktop, MessageManager
+ .getString("label.remove_from_default_list"),
+ MessageManager
+ .getString("label.remove_user_defined_colour"),
+ JvOptionPane.YES_NO_OPTION);
+ if (option == JvOptionPane.YES_OPTION)
+ {
+ jalview.gui.UserDefinedColours
+ .removeColourFromDefaults(radioItem.getText());
+ colourMenu.remove(radioItem);
+ }
+ else
+ {
+ radioItem.addActionListener(new ActionListener()
{
- radioItem.addActionListener(new ActionListener()
+ @Override
+ public void actionPerformed(ActionEvent evt)
{
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- }
+ userDefinedColour_actionPerformed(evt);
+ }
+ });
}
}
});
if ((viewport.getSelectionGroup() == null)
|| (viewport.getSelectionGroup().getSize() < 2))
{
- JOptionPane.showInternalMessageDialog(this, MessageManager
+ JvOptionPane.showInternalMessageDialog(this, MessageManager
.getString("label.you_must_select_least_two_sequences"),
MessageManager.getString("label.invalid_selection"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
else
{
.getSelectionGroup().getSize() > 0))
|| (viewport.getAlignment().getHeight() < 4))
{
- JOptionPane
+ JvOptionPane
.showInternalMessageDialog(
this,
MessageManager
.getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
MessageManager
.getString("label.sequence_selection_insufficient"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
{
if (viewport.getSelectionGroup().getSize() < 3)
{
- JOptionPane
+ JvOptionPane
.showMessageDialog(
Desktop.desktop,
MessageManager
.getString("label.you_need_more_two_sequences_selected_build_tree"),
MessageManager
.getString("label.not_enough_sequences"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
{
if (_s.getLength() < sg.getEndRes())
{
- JOptionPane
+ JvOptionPane
.showMessageDialog(
Desktop.desktop,
MessageManager
.getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
MessageManager
.getString("label.sequences_selection_not_aligned"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
// are the visible sequences aligned?
if (!viewport.getAlignment().isAligned(false))
{
- JOptionPane
+ JvOptionPane
.showMessageDialog(
Desktop.desktop,
MessageManager
.getString("label.sequences_must_be_aligned_before_creating_tree"),
MessageManager
.getString("label.sequences_not_aligned"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
else if (viewport.getSelectionGroup() != null
&& viewport.getSelectionGroup().getSize() == 1)
{
- int option = JOptionPane.showConfirmDialog(this,
+ int option = JvOptionPane.showConfirmDialog(this,
MessageManager.getString("warn.oneseq_msainput_selection"),
MessageManager.getString("label.invalid_selection"),
- JOptionPane.OK_CANCEL_OPTION);
- if (option == JOptionPane.OK_OPTION)
+ JvOptionPane.OK_CANCEL_OPTION);
+ if (option == JvOptionPane.OK_OPTION)
{
msa = viewport.getAlignmentView(false);
}
viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
} catch (Exception ex)
{
- JOptionPane
+ JvOptionPane
.showMessageDialog(
Desktop.desktop,
ex.getMessage(),
MessageManager
.getString("label.problem_reading_tree_file"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
if (fin != null && fin.hasWarningMessage())
{
- JOptionPane.showMessageDialog(Desktop.desktop, fin
+ JvOptionPane.showMessageDialog(Desktop.desktop, fin
.getWarningMessage(), MessageManager
.getString("label.possible_problem_with_tree_file"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
}
}
{
SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
AlignmentI dataset = viewport.getAlignment().getDataset();
+
+ showProducts.removeAll();
+ final boolean dna = viewport.getAlignment().isNucleotide();
+
+ if (seqs == null || seqs.length == 0)
+ {
+ // nothing to see here.
+ return false;
+ }
+
boolean showp = false;
try
{
- showProducts.removeAll();
- final boolean dna = viewport.getAlignment().isNucleotide();
- List<String> ptypes = (seqs == null || seqs.length == 0) ? null
- : new CrossRef(seqs, dataset)
- .findXrefSourcesForSequences(dna);
+ List<String> ptypes = new CrossRef(seqs, dataset)
+ .findXrefSourcesForSequences(dna);
for (final String source : ptypes)
{
protected void showProductsFor(final SequenceI[] sel,
final boolean _odna, final String source)
{
- Runnable foo = new Runnable()
- {
-
- @Override
- public void run()
- {
- final long sttime = System.currentTimeMillis();
- AlignFrame.this.setProgressBar(MessageManager.formatMessage(
- "status.searching_for_sequences_from",
- new Object[] { source }), sttime);
- try
- {
- AlignmentI alignment = AlignFrame.this.getViewport()
- .getAlignment();
- AlignmentI dataset = alignment.getDataset() == null ? alignment
- : alignment.getDataset();
- boolean dna = alignment.isNucleotide();
- if (_odna != dna)
- {
- System.err
- .println("Conflict: showProducts for alignment originally "
- + "thought to be "
- + (_odna ? "DNA" : "Protein")
- + " now searching for "
- + (dna ? "DNA" : "Protein") + " Context.");
- }
- AlignmentI xrefs = new CrossRef(sel, dataset).findXrefSequences(
- source, dna);
- if (xrefs == null)
- {
- return;
- }
- /*
- * get display scheme (if any) to apply to features
- */
- FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
- .getFeatureColourScheme(source);
-
- AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
- xrefs);
- if (!dna)
- {
- xrefsAlignment = AlignmentUtils.makeCdsAlignment(
- xrefsAlignment.getSequencesArray(), dataset, sel);
- xrefsAlignment.alignAs(alignment);
- }
-
- /*
- * If we are opening a splitframe, make a copy of this alignment (sharing the same dataset
- * sequences). If we are DNA, drop introns and update mappings
- */
- AlignmentI copyAlignment = null;
-
- if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
- {
- boolean copyAlignmentIsAligned = false;
- if (dna)
- {
- copyAlignment = AlignmentUtils.makeCdsAlignment(sel, dataset,
- xrefsAlignment.getSequencesArray());
- if (copyAlignment.getHeight() == 0)
- {
- JOptionPane.showMessageDialog(AlignFrame.this,
- MessageManager.getString("label.cant_map_cds"),
- MessageManager.getString("label.operation_failed"),
- JOptionPane.OK_OPTION);
- System.err.println("Failed to make CDS alignment");
- }
-
- /*
- * pending getting Embl transcripts to 'align',
- * we are only doing this for Ensembl
- */
- // TODO proper criteria for 'can align as cdna'
- if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
- || AlignmentUtils.looksLikeEnsembl(alignment))
- {
- copyAlignment.alignAs(alignment);
- copyAlignmentIsAligned = true;
- }
- }
- else
- {
- copyAlignment = AlignmentUtils.makeCopyAlignment(sel,
- xrefs.getSequencesArray(), dataset);
- }
- copyAlignment.setGapCharacter(AlignFrame.this.viewport
- .getGapCharacter());
-
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
-
- /*
- * register any new mappings for sequence mouseover etc
- * (will not duplicate any previously registered mappings)
- */
- ssm.registerMappings(dataset.getCodonFrames());
-
- if (copyAlignment.getHeight() <= 0)
- {
- System.err.println("No Sequences generated for xRef type "
- + source);
- return;
- }
- /*
- * align protein to dna
- */
- if (dna && copyAlignmentIsAligned)
- {
- xrefsAlignment.alignAs(copyAlignment);
- }
- else
- {
- /*
- * align cdna to protein - currently only if
- * fetching and aligning Ensembl transcripts!
- */
- // TODO: generalise for other sources of locus/transcript/cds data
- if (dna && DBRefSource.ENSEMBL.equalsIgnoreCase(source))
- {
- copyAlignment.alignAs(xrefsAlignment);
- }
- }
- }
- /*
- * build AlignFrame(s) according to available alignment data
- */
- AlignFrame newFrame = new AlignFrame(xrefsAlignment,
- DEFAULT_WIDTH, DEFAULT_HEIGHT);
- if (Cache.getDefault("HIDE_INTRONS", true))
- {
- newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
- }
- String newtitle = String.format("%s %s %s",
- dna ? MessageManager.getString("label.proteins")
- : MessageManager.getString("label.nucleotides"),
- MessageManager.getString("label.for"), getTitle());
- newFrame.setTitle(newtitle);
-
- if (copyAlignment == null)
- {
- /*
- * split frame display is turned off in preferences file
- */
- Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
- return; // via finally clause
- }
- AlignFrame copyThis = new AlignFrame(copyAlignment,
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- copyThis.setTitle(AlignFrame.this.getTitle());
-
- boolean showSequenceFeatures = viewport.isShowSequenceFeatures();
- newFrame.setShowSeqFeatures(showSequenceFeatures);
- copyThis.setShowSeqFeatures(showSequenceFeatures);
- FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
- .getFeatureRenderer();
-
- /*
- * copy feature rendering settings to split frame
- */
- newFrame.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
- .transferSettings(myFeatureStyling);
- copyThis.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
- .transferSettings(myFeatureStyling);
-
- /*
- * apply 'database source' feature configuration
- * if any was found
- */
- // TODO is this the feature colouring for the original
- // alignment or the fetched xrefs? either could be Ensembl
- newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
- copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
-
- SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
- dna ? newFrame : copyThis);
- newFrame.setVisible(true);
- copyThis.setVisible(true);
- String linkedTitle = MessageManager
- .getString("label.linked_view_title");
- Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
- sf.adjustDivider();
- } catch (OutOfMemoryError e)
- {
- new OOMWarning("whilst fetching crossreferences", e);
- } catch (Throwable e)
- {
- Cache.log.error("Error when finding crossreferences", e);
- } finally
- {
- AlignFrame.this.setProgressBar(MessageManager.formatMessage(
- "status.finished_searching_for_sequences_from",
- new Object[] { source }), sttime);
- }
- }
-
- /**
- * Makes an alignment containing the given sequences, and adds them to the
- * given dataset, which is also set as the dataset for the new alignment
- *
- * TODO: refactor to DatasetI method
- *
- * @param dataset
- * @param seqs
- * @return
- */
- protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,
- AlignmentI seqs)
- {
- SequenceI[] sprods = new SequenceI[seqs.getHeight()];
- for (int s = 0; s < sprods.length; s++)
- {
- sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
- if (dataset.getSequences() == null
- || !dataset.getSequences().contains(
- sprods[s].getDatasetSequence()))
- {
- dataset.addSequence(sprods[s].getDatasetSequence());
- }
- sprods[s].updatePDBIds();
- }
- Alignment al = new Alignment(sprods);
- al.setDataset(dataset);
- return al;
- }
-
- };
- Thread frunner = new Thread(foo);
- frunner.start();
+ new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
+ .start();
}
/**
final String errorTitle = MessageManager
.getString("label.implementation_error")
+ MessageManager.getString("label.translation_failed");
- JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
+ JvOptionPane.ERROR_MESSAGE);
return;
}
if (al == null || al.getHeight() == 0)
.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
final String errorTitle = MessageManager
.getString("label.translation_failed");
- JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
+ JvOptionPane.WARNING_MESSAGE);
}
else
{
@Override
public void drop(DropTargetDropEvent evt)
{
+ // JAL-1552 - acceptDrop required before getTransferable call for
+ // Java's Transferable for native dnd
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
Transferable t = evt.getTransferable();
List<String> files = new ArrayList<String>();
List<DataSourceType> protocols = new ArrayList<DataSourceType>();
}
if (type != null)
{
- if (type == FileFormat.PDB)
+ if (FileFormat.PDB.equals(type) || FileFormat.MMCif.equals(type))
{
filesmatched.add(new Object[] { file, protocol, mtch });
continue;
if (filesmatched.size() > 0)
{
if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
- || JOptionPane
+ || JvOptionPane
.showConfirmDialog(
this,
MessageManager
.formatMessage(
- "label.automatically_associate_pdb_files_with_sequences_same_name",
+ "label.automatically_associate_structure_files_with_sequences_same_name",
new Object[] { Integer
.valueOf(
filesmatched
.size())
.toString() }),
MessageManager
- .getString("label.automatically_associate_pdb_files_by_name"),
- JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
+ .getString("label.automatically_associate_structure_files_by_name"),
+ JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
{
for (Object[] fm : filesmatched)
{
if (assocfiles > 0
&& (Cache.getDefault(
- "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
+ "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
.showConfirmDialog(
this,
"<html>"
+ "</html>",
MessageManager
.getString("label.ignore_unmatched_dropped_files"),
- JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
+ JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
{
return;
}
// if the file isn't identified, or not positively identified as some
// other filetype (PFAM is default unidentified alignment file type) then
// try to parse as annotation.
- boolean isAnnotation = (format == null || format == FileFormat.Pfam) ? new AnnotationFile()
+ boolean isAnnotation = (format == null || FileFormat.Pfam
+ .equals(format)) ? new AnnotationFile()
.annotateAlignmentView(viewport, file, sourceType) : false;
if (!isAnnotation)
{
// some problem - if no warning its probable that the ID matching
// process didn't work
- JOptionPane
+ JvOptionPane
.showMessageDialog(
Desktop.desktop,
tcf.getWarningMessage() == null ? MessageManager
: tcf.getWarningMessage(),
MessageManager
.getString("label.problem_reading_tcoffee_score_file"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
}
else
{
format = new IdentifyFile().identify(file, sourceType);
}
- if (format == FileFormat.Jnet)
+ if (FileFormat.Jnet.equals(format))
{
JPredFile predictions = new JPredFile(
file, sourceType);
viewport.setColumnSelection(cs);
isAnnotation = true;
}
- else if (IdentifyFile.FeaturesFile.equals(format))
+ // else if (IdentifyFile.FeaturesFile.equals(format))
+ else if (FileFormat.Features.equals(format))
{
if (parseFeaturesFile(file, sourceType))
{
if (e.isPopupTrigger())
{
String msg = MessageManager.getString("label.enter_view_name");
- String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
- JOptionPane.QUESTION_MESSAGE);
+ String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
+ JvOptionPane.QUESTION_MESSAGE);
if (reply != null)
{
} catch (Exception ex)
{
System.err.println((ex.toString()));
- JOptionPane
+ JvOptionPane
.showInternalMessageDialog(Desktop.desktop, MessageManager
.getString("label.couldnt_run_groovy_script"),
MessageManager
.getString("label.groovy_support_failed"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
}
else
}
return false;
}
+
+ @Override
+ protected void selectHighlightedColumns_actionPerformed(
+ ActionEvent actionEvent)
+ {
+ // include key modifier check in case user selects from menu
+ avc.markHighlightedColumns(
+ (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
+ true,
+ (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
+ }
}
class PrintThread extends Thread
git://source.jalview.org / jalview.git / blobdiff