X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=3644b28691d0fddff130add1c80773c72656cf4c;hb=483e7163b1fb8d4bcb9393014816c944befce328;hp=477d1133c8b124b3a6a0fa4e7303c68e9da170d2;hpb=65675b2d016736f8ca4dfb2493863c4d53cec591;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 477d113..3644b28 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -23,7 +23,6 @@ package jalview.gui; import jalview.analysis.AlignmentSorter; import jalview.analysis.AlignmentUtils; import jalview.analysis.CrossRef; -import jalview.analysis.CrossRefs; import jalview.analysis.Dna; import jalview.analysis.ParseProperties; import jalview.analysis.SequenceIdMatcher; @@ -33,7 +32,6 @@ import jalview.api.AlignViewControllerI; 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; @@ -55,7 +53,6 @@ import jalview.datamodel.AlignmentI; 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; @@ -66,16 +63,20 @@ import jalview.gui.ViewSelectionMenu.ViewSetProvider; import jalview.io.AlignmentProperties; import jalview.io.AnnotationFile; import jalview.io.BioJsHTMLOutput; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; +import jalview.io.FileFormatI; import jalview.io.FileLoader; import jalview.io.FormatAdapter; import jalview.io.HtmlSvgOutput; import jalview.io.IdentifyFile; +import jalview.io.JPredFile; import jalview.io.JalviewFileChooser; 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; @@ -95,12 +96,10 @@ import jalview.schemes.TaylorColourScheme; 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; @@ -114,6 +113,7 @@ import java.awt.datatransfer.Clipboard; 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; @@ -180,7 +180,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Last format used to load or save alignments in this window */ - String currentFileFormat = null; + FileFormatI currentFileFormat = null; /** * Current filename for this alignment @@ -474,7 +474,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void focusGained(FocusEvent e) { - Desktop.setCurrentAlignFrame(AlignFrame.this); + Jalview.setCurrentAlignFrame(AlignFrame.this); } }); @@ -489,7 +489,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param format * format of file */ - public void setFileName(String file, String format) + public void setFileName(String file, FileFormatI format) { fileName = file; setFileFormat(format); @@ -674,6 +674,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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()) { @@ -850,8 +860,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showGroupConservation.setEnabled(!nucleotide); rnahelicesColour.setEnabled(nucleotide); purinePyrimidineColour.setEnabled(nucleotide); - showComplementMenuItem.setText(MessageManager - .getString(nucleotide ? "label.protein" : "label.nucleotide")); + showComplementMenuItem.setText(nucleotide ? MessageManager + .getString("label.protein") : MessageManager + .getString("label.nucleotide")); setColourSelected(jalview.bin.Cache.getDefault( nucleotide ? Preferences.DEFAULT_COLOUR_NUC : Preferences.DEFAULT_COLOUR_PROT, "None")); @@ -1007,7 +1018,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // originating file's format // TODO: work out how to recover feature settings for correct view(s) when // file is reloaded. - if (currentFileFormat.equals("Jalview")) + if (FileFormat.Jalview.equals(currentFileFormat)) { JInternalFrame[] frames = Desktop.desktop.getAllFrames(); for (int i = 0; i < frames.length; i++) @@ -1029,7 +1040,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Desktop.instance.closeAssociatedWindows(); FileLoader loader = new FileLoader(); - String protocol = fileName.startsWith("http:") ? "URL" : "File"; + DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL + : DataSourceType.FILE; loader.LoadFile(viewport, fileName, protocol, currentFileFormat); } else @@ -1037,7 +1049,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Rectangle bounds = this.getBounds(); FileLoader loader = new FileLoader(); - String protocol = fileName.startsWith("http:") ? "URL" : "File"; + DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL + : DataSourceType.FILE; AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName, protocol, currentFileFormat); @@ -1081,9 +1094,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void save_actionPerformed(ActionEvent e) { - if (fileName == null - || (currentFileFormat == null || !jalview.io.FormatAdapter - .isValidIOFormat(currentFileFormat, true)) + if (fileName == null || (currentFileFormat == null) || fileName.startsWith("http")) { saveAs_actionPerformed(null); @@ -1103,11 +1114,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void saveAs_actionPerformed(ActionEvent e) { - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), - jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS, - jalview.io.AppletFormatAdapter.WRITABLE_FNAMES, - currentFileFormat, false); + JalviewFileChooser chooser = JalviewFileChooser.forWrite( + Cache.getProperty("LAST_DIRECTORY"), + // AppletFormatAdapter.WRITABLE_EXTENSIONS, + // AppletFormatAdapter.WRITABLE_FNAMES, + currentFileFormat.toString(), false); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager @@ -1121,14 +1132,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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) @@ -1139,24 +1150,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, fileName = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", - currentFileFormat); + Cache.setProperty("DEFAULT_FILE_FORMAT", + currentFileFormat.toString()); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName); - if (currentFileFormat.indexOf(" ") > -1) - { - currentFileFormat = currentFileFormat.substring(0, - currentFileFormat.indexOf(" ")); - } + Cache.setProperty("LAST_DIRECTORY", fileName); saveAlignment(fileName, currentFileFormat); } } - public boolean saveAlignment(String file, String format) + public boolean saveAlignment(String file, FileFormatI format) { boolean success = true; - if (format.equalsIgnoreCase("Jalview")) + if (FileFormat.Jalview.equals(format)) { String shortName = title; @@ -1175,16 +1181,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true)) - { - warningMessage("Cannot save file " + fileName + " using format " - + format, "Alignment output format not supported"); - if (!Jalview.isHeadlessMode()) - { - saveAs_actionPerformed(null); - } - return false; - } + // if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true)) + // { + // warningMessage("Cannot save file " + fileName + " using format " + // + format, "Alignment output format not supported"); + // if (!Jalview.isHeadlessMode()) + // { + // saveAs_actionPerformed(null); + // } + // return false; + // } AlignmentExportData exportData = getAlignmentForExport(format, viewport, null); @@ -1229,11 +1235,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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; @@ -1248,8 +1254,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - JOptionPane.showInternalMessageDialog(this, warning, title, - JOptionPane.WARNING_MESSAGE); + JvOptionPane.showInternalMessageDialog(this, warning, title, + JvOptionPane.WARNING_MESSAGE); } return; } @@ -1264,8 +1270,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void outputText_actionPerformed(ActionEvent e) { - AlignmentExportData exportData = getAlignmentForExport( - e.getActionCommand(), viewport, null); + FileFormatI fileFormat = FileFormat.forName(e.getActionCommand()); + AlignmentExportData exportData = getAlignmentForExport(fileFormat, + viewport, null); if (exportData.getSettings().isCancelled()) { return; @@ -1274,8 +1281,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, cap.setForInput(null); try { + FileFormatI format = fileFormat; cap.setText(new FormatAdapter(alignPanel, exportData.getSettings()) - .formatSequences(e.getActionCommand(), + .formatSequences(format, exportData.getAlignment(), exportData.getOmitHidden(), exportData.getStartEndPostions(), @@ -1292,7 +1300,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } public static AlignmentExportData getAlignmentForExport( - String exportFormat, AlignViewportI viewport, + FileFormatI format, AlignViewportI viewport, AlignExportSettingI exportSettings) { AlignmentI alignmentToExport = null; @@ -1308,7 +1316,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (settings == null) { settings = new AlignExportSettings(hasHiddenSeqs, - viewport.hasHiddenColumns(), exportFormat); + viewport.hasHiddenColumns(), format); } // settings.isExportAnnotations(); @@ -1326,10 +1334,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, else { alignmentToExport = viewport.getAlignment(); - alignmentStartEnd = viewport.getAlignment() - .getVisibleStartAndEndIndex( - viewport.getColumnSelection().getHiddenColumns()); } + alignmentStartEnd = alignmentToExport + .getVisibleStartAndEndIndex(viewport.getColumnSelection() + .getHiddenColumns()); AlignmentExportData ed = new AlignmentExportData(alignmentToExport, omitHidden, alignmentStartEnd, settings); return ed; @@ -1344,14 +1352,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @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) @@ -1865,7 +1874,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, omitHidden = viewport.getViewAsString(true); } - String output = new FormatAdapter().formatSequences("Fasta", seqs, + String output = new FormatAdapter().formatSequences(FileFormat.Fasta, + seqs, omitHidden, null); StringSelection ss = new StringSelection(output); @@ -1952,7 +1962,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - String str, format; + String str; + FileFormatI format; try { str = (String) contents.getTransferData(DataFlavor.stringFlavor); @@ -1961,7 +1972,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - format = new IdentifyFile().identify(str, "Paste"); + format = new IdentifyFile().identify(str, DataSourceType.PASTE); } catch (OutOfMemoryError er) { @@ -1991,7 +2002,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, else { // parse the clipboard as an alignment. - alignment = new FormatAdapter().readFile(str, "Paste", format); + alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE, + format); sequences = alignment.getSequencesArray(); } @@ -2360,13 +2372,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .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; } @@ -2435,7 +2447,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sg.setEndRes(viewport.getAlignment().getWidth() - 1); viewport.setSelectionGroup(sg); viewport.sendSelection(); - alignPanel.paintAlignment(true); + // JAL-2034 - should delegate to + // alignPanel to decide if overview needs + // updating. + alignPanel.paintAlignment(false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); } @@ -2458,7 +2473,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setSelectionGroup(null); alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null); alignPanel.getIdPanel().getIdCanvas().searchResults = null; - alignPanel.paintAlignment(true); + // JAL-2034 - should delegate to + // alignPanel to decide if overview needs + // updating. + alignPanel.paintAlignment(false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } @@ -2485,6 +2503,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false); } + // JAL-2034 - should delegate to + // alignPanel to decide if overview needs + // updating. alignPanel.paintAlignment(true); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); @@ -2832,7 +2853,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void expandViews_actionPerformed(ActionEvent e) { - Desktop.instance.explodeViews(this); + Desktop.explodeViews(this); } /** @@ -2902,8 +2923,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setFollowHighlight(state); if (state) { - alignPanel.scrollToPosition( - alignPanel.getSeqPanel().seqCanvas.searchResults, false); + alignPanel.scrollToPosition(viewport.getSearchResults(), false); } } @@ -2973,9 +2993,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // 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())) { @@ -3003,8 +3021,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, hideSelSequences_actionPerformed(null); hide = true; } - else if (!(toggleCols && viewport.getColumnSelection().getSelected() - .size() > 0)) + else if (!(toggleCols && viewport.hasSelectedColumns())) { showAllSeqs_actionPerformed(null); } @@ -3012,7 +3029,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (toggleCols) { - if (viewport.getColumnSelection().getSelected().size() > 0) + if (viewport.hasSelectedColumns()) { hideSelColumns_actionPerformed(null); if (!toggleSeqs) @@ -3211,30 +3228,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * Set or clear 'Show Sequence Features' - * - * @param evt - * DOCUMENT ME! - */ - @Override - public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt) - { - viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight - .isSelected()); - if (viewport.isShowSequenceFeaturesHeight()) - { - // ensure we're actually displaying features - viewport.setShowSequenceFeatures(true); - showSeqFeatures.setSelected(true); - } - alignPanel.paintAlignment(true); - if (alignPanel.getOverviewPanel() != null) - { - alignPanel.getOverviewPanel().updateOverviewImage(); - } - } - - /** * Action on toggle of the 'Show annotations' menu item. This shows or hides * the annotations panel as a whole. * @@ -3640,34 +3633,50 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void mousePressed(MouseEvent evt) { - if (evt.isPopupTrigger()) + if (evt.isPopupTrigger()) // Mac + { + offerRemoval(radioItem); + } + } + + @Override + public void mouseReleased(MouseEvent evt) + { + if (evt.isPopupTrigger()) // Windows { - 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 + /** + * @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); + } + }); } } }); @@ -3800,10 +3809,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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 { @@ -3829,14 +3838,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .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; } @@ -3934,14 +3943,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { 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; } @@ -3952,14 +3961,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { 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; } @@ -3973,14 +3982,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // 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; } @@ -4245,11 +4254,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); } @@ -4321,25 +4330,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, jalview.io.NewickFile fin = null; try { - fin = new jalview.io.NewickFile(choice, "File"); + fin = new NewickFile(choice, DataSourceType.FILE); 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); } } } @@ -4459,22 +4468,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // object broker mechanism. final Vector wsmenu = new Vector(); final IProgressIndicator af = me; + + /* + * do not i18n these strings - they are hard-coded in class + * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and + * SequenceAnnotationWSClient.initSequenceAnnotationWSClient() + */ final JMenu msawsmenu = new JMenu("Alignment"); final JMenu secstrmenu = new JMenu( "Secondary Structure Prediction"); final JMenu seqsrchmenu = new JMenu("Sequence Database Search"); final JMenu analymenu = new JMenu("Analysis"); final JMenu dismenu = new JMenu("Protein Disorder"); - // final JMenu msawsmenu = new - // JMenu(MessageManager.getString("label.alignment")); - // final JMenu secstrmenu = new - // JMenu(MessageManager.getString("label.secondary_structure_prediction")); - // final JMenu seqsrchmenu = new - // JMenu(MessageManager.getString("label.sequence_database_search")); - // final JMenu analymenu = new - // JMenu(MessageManager.getString("label.analysis")); - // final JMenu dismenu = new - // JMenu(MessageManager.getString("label.protein_disorder")); // JAL-940 - only show secondary structure prediction services from // the legacy server if (// Cache.getDefault("SHOW_JWS1_SERVICES", true) @@ -4634,22 +4639,32 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * Searches selected sequences for xRef products and builds the Show - * Cross-References menu (formerly called Show Products) + * Searches the alignment sequences for xRefs and builds the Show + * Cross-References menu (formerly called Show Products), with database + * sources for which cross-references are found (protein sources for a + * nucleotide alignment and vice versa) * - * @return true if Show Cross-references menu should be enabled. + * @return true if Show Cross-references menu should be enabled */ public boolean canShowProducts() { - SequenceI[] selection = viewport.getSequenceSelection(); + 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 ptypes = (selection == null || selection.length == 0) ? null - : CrossRef.findXrefSourcesForSequences(dna, selection, dataset); + List ptypes = new CrossRef(seqs, dataset) + .findXrefSourcesForSequences(dna); for (final String source : ptypes) { @@ -4689,233 +4704,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param source * the database to show cross-references for */ - protected void showProductsFor(final SequenceI[] sel, final boolean dna, - final String source) + 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 xrefs = CrossRefs.findXrefSequences(sel, dna, source, - alignment); - if (xrefs != null) - { - /* - * get display scheme (if any) to apply to features - */ - FeatureSettingsModelI featureColourScheme = new SequenceFetcher() - .getFeatureColourScheme(source); - - AlignmentI al = makeCrossReferencesAlignment( - alignment.getDataset(), xrefs); - - AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH, - DEFAULT_HEIGHT); - if (Cache.getDefault("HIDE_INTRONS", true)) - { - newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false); - } - String newtitle = String.format("%s %s %s", - MessageManager.getString(dna ? "label.proteins" - : "label.nucleotides"), MessageManager - .getString("label.for"), getTitle()); - newFrame.setTitle(newtitle); - - if (!Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true)) - { - /* - * split frame display is turned off in preferences file - */ - Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH, - DEFAULT_HEIGHT); - return; // via finally clause - } - - /* - * Make a copy of this alignment (sharing the same dataset - * sequences). If we are DNA, drop introns and update mappings - */ - AlignmentI copyAlignment = null; - final SequenceI[] sequenceSelection = AlignFrame.this.viewport - .getSequenceSelection(); - List cf = xrefs.getCodonFrames(); - boolean copyAlignmentIsAligned = false; - if (dna) - { - copyAlignment = AlignmentUtils.makeCdsAlignment( - sequenceSelection, cf, alignment); - if (copyAlignment.getHeight() == 0) - { - System.err.println("Failed to make CDS alignment"); - } - al.getCodonFrames().clear(); - al.addCodonFrames(copyAlignment.getCodonFrames()); - al.addCodonFrames(cf); - - /* - * 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( - sequenceSelection, xrefs.getSequencesArray()); - copyAlignment.addCodonFrames(cf); - al.addCodonFrames(copyAlignment.getCodonFrames()); - al.addCodonFrames(cf); - } - copyAlignment.setGapCharacter(AlignFrame.this.viewport - .getGapCharacter()); - - StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); - ssm.registerMappings(cf); - - if (copyAlignment.getHeight() <= 0) - { - System.err.println("No Sequences generated for xRef type " - + source); - return; - } - /* - * align protein to dna - */ - if (dna && copyAlignmentIsAligned) - { - al.alignAs(copyAlignment); - } - else - { - /* - * align cdna to protein - currently only if - * fetching and aligning Ensembl transcripts! - */ - if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)) - { - copyAlignment.alignAs(al); - } - } - - 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 (Exception e) - { - Cache.log.error("Exception when finding crossreferences", e); - } 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. If this is of the - * same type as the given dataset (nucleotide/protein), then the new - * alignment shares the same dataset, and its dataset sequences are added - * to it. Otherwise a new dataset sequence is created for the - * cross-references. - * - * @param dataset - * @param seqs - * @return - */ - protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset, - AlignmentI seqs) - { - boolean sameType = dataset.isNucleotide() == seqs.isNucleotide(); - - SequenceI[] sprods = new SequenceI[seqs.getHeight()]; - for (int s = 0; s < sprods.length; s++) - { - sprods[s] = (seqs.getSequenceAt(s)).deriveSequence(); - if (sameType) - { - if (dataset.getSequences() == null - || !dataset.getSequences().contains( - sprods[s].getDatasetSequence())) - { - dataset.addSequence(sprods[s].getDatasetSequence()); - } - } - sprods[s].updatePDBIds(); - } - Alignment al = new Alignment(sprods); - if (sameType) - { - al.setDataset((Alignment) dataset); - } - else - { - al.createDatasetAlignment(); - } - return al; - } - - }; - Thread frunner = new Thread(foo); - frunner.start(); + new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this)) + .start(); } /** @@ -4940,8 +4733,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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) @@ -4950,8 +4743,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .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 { @@ -4977,11 +4770,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Set the file format * - * @param fileFormat + * @param format */ - public void setFileFormat(String fileFormat) + public void setFileFormat(FileFormatI format) { - this.currentFileFormat = fileFormat; + this.currentFileFormat = format; } /** @@ -4989,14 +4782,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param file * contents or path to retrieve file - * @param type + * @param sourceType * access mode of file (see jalview.io.AlignFile) * @return true if features file was parsed correctly. */ - public boolean parseFeaturesFile(String file, String type) + public boolean parseFeaturesFile(String file, DataSourceType sourceType) { - return avc.parseFeaturesFile(file, type, - jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false)); + return avc.parseFeaturesFile(file, sourceType, + Cache.getDefault("RELAXEDSEQIDMATCHING", false)); } @@ -5037,8 +4830,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @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(); - java.util.List files = new ArrayList(), protocols = new ArrayList(); + List files = new ArrayList(); + List protocols = new ArrayList(); try { @@ -5064,13 +4861,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { String file = files.get(i).toString(); String pdbfn = ""; - String protocol = FormatAdapter.checkProtocol(file); - if (protocol == jalview.io.FormatAdapter.FILE) + DataSourceType protocol = FormatAdapter.checkProtocol(file); + if (protocol == DataSourceType.FILE) { File fl = new File(file); pdbfn = fl.getName(); } - else if (protocol == jalview.io.FormatAdapter.URL) + else if (protocol == DataSourceType.URL) { URL url = new URL(file); pdbfn = url.getFile(); @@ -5094,7 +4891,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (mtch != null) { - String type = null; + FileFormatI type = null; try { type = new IdentifyFile().identify(file, protocol); @@ -5104,7 +4901,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (type != null) { - if (type.equalsIgnoreCase("PDB")) + if (FileFormat.PDB.equals(type) || FileFormat.MMCif.equals(type)) { filesmatched.add(new Object[] { file, protocol, mtch }); continue; @@ -5119,20 +4916,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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) @@ -5144,7 +4941,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { PDBEntry pe = new AssociatePdbFileWithSeq() .associatePdbWithSeq((String) fm[0], - (String) fm[1], toassoc, false, + (DataSourceType) fm[1], toassoc, false, Desktop.instance); if (pe != null) { @@ -5162,7 +4959,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (assocfiles > 0 && (Cache.getDefault( - "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane + "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane .showConfirmDialog( this, "" @@ -5177,7 +4974,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, + "", MessageManager .getString("label.ignore_unmatched_dropped_files"), - JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)) + JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)) { return; } @@ -5203,21 +5000,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param file * either a filename or a URL string. */ - public void loadJalviewDataFile(String file, String protocol, - String format, SequenceI assocSeq) + public void loadJalviewDataFile(String file, DataSourceType sourceType, + FileFormatI format, SequenceI assocSeq) { try { - if (protocol == null) + if (sourceType == null) { - protocol = FormatAdapter.checkProtocol(file); + sourceType = FormatAdapter.checkProtocol(file); } // 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 - .equalsIgnoreCase("PFAM")) ? new AnnotationFile() - .annotateAlignmentView(viewport, file, protocol) : false; + boolean isAnnotation = (format == null || FileFormat.Pfam + .equals(format)) ? new AnnotationFile() + .annotateAlignmentView(viewport, file, sourceType) : false; if (!isAnnotation) { @@ -5225,7 +5022,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, TCoffeeScoreFile tcf = null; try { - tcf = new TCoffeeScoreFile(file, protocol); + tcf = new TCoffeeScoreFile(file, sourceType); if (tcf.isValid()) { if (tcf.annotateAlignment(viewport.getAlignment(), true)) @@ -5242,7 +5039,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // some problem - if no warning its probable that the ID matching // process didn't work - JOptionPane + JvOptionPane .showMessageDialog( Desktop.desktop, tcf.getWarningMessage() == null ? MessageManager @@ -5250,7 +5047,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, : tcf.getWarningMessage(), MessageManager .getString("label.problem_reading_tcoffee_score_file"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } } else @@ -5271,12 +5068,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // try to parse it as a features file if (format == null) { - format = new IdentifyFile().identify(file, protocol); + format = new IdentifyFile().identify(file, sourceType); } - if (format.equalsIgnoreCase("JnetFile")) + if (FileFormat.Jnet.equals(format)) { - jalview.io.JPredFile predictions = new jalview.io.JPredFile( - file, protocol); + JPredFile predictions = new JPredFile( + file, sourceType); new JnetAnnotationMaker(); JnetAnnotationMaker.add_annotation(predictions, viewport.getAlignment(), 0, false); @@ -5287,16 +5084,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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, protocol)) + if (parseFeaturesFile(file, sourceType)) { alignPanel.paintAlignment(true); } } else { - new FileLoader().LoadFile(viewport, file, protocol, format); + new FileLoader().LoadFile(viewport, file, sourceType, format); } } } @@ -5321,8 +5119,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } new OOMWarning( "loading data " - + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard." - : "using " + protocol + " from " + file) + + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard." + : "using " + sourceType + " from " + file) : ".") + (format != null ? "(parsing as '" + format + "' file)" : ""), oom, Desktop.desktop); @@ -5371,8 +5169,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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) { @@ -5958,8 +5756,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void setAnnotationsVisibility(boolean visible, boolean forSequences, boolean forAlignment) { - for (AlignmentAnnotation aa : alignPanel.getAlignment() - .getAlignmentAnnotation()) + AlignmentAnnotation[] anns = alignPanel.getAlignment() + .getAlignmentAnnotation(); + if (anns == null) + { + return; + } + for (AlignmentAnnotation aa : anns) { /* * don't display non-positional annotations on an alignment @@ -6096,7 +5899,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void runGroovy_actionPerformed() { - Desktop.setCurrentAlignFrame(this); + Jalview.setCurrentAlignFrame(this); groovy.ui.Console console = Desktop.getGroovyConsole(); if (console != null) { @@ -6106,12 +5909,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } 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 @@ -6144,6 +5947,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } 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