X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=445e967ea5e1e16a5ac809a6f73e8bcee041473f;hb=c437fc72420baf7b045d417fb6cabcebe87987c5;hp=3644b28691d0fddff130add1c80773c72656cf4c;hpb=483e7163b1fb8d4bcb9393014816c944befce328;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 3644b28..445e967 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -59,6 +59,7 @@ import jalview.datamodel.SeqCigar; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.gui.ColourMenuHelper.ColourChangeListener; import jalview.gui.ViewSelectionMenu.ViewSetProvider; import jalview.io.AlignmentProperties; import jalview.io.AnnotationFile; @@ -66,6 +67,7 @@ import jalview.io.BioJsHTMLOutput; import jalview.io.DataSourceType; import jalview.io.FileFormat; import jalview.io.FileFormatI; +import jalview.io.FileFormats; import jalview.io.FileLoader; import jalview.io.FormatAdapter; import jalview.io.HtmlSvgOutput; @@ -75,29 +77,16 @@ 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.jbgui.GAlignFrame; -import jalview.schemes.Blosum62ColourScheme; -import jalview.schemes.BuriedColourScheme; -import jalview.schemes.ClustalxColourScheme; import jalview.schemes.ColourSchemeI; -import jalview.schemes.ColourSchemeProperty; -import jalview.schemes.HelixColourScheme; -import jalview.schemes.HydrophobicColourScheme; -import jalview.schemes.NucleotideColourScheme; -import jalview.schemes.PIDColourScheme; -import jalview.schemes.PurinePyrimidineColourScheme; -import jalview.schemes.RNAHelicesColourChooser; +import jalview.schemes.ColourSchemes; +import jalview.schemes.ResidueColourScheme; import jalview.schemes.ResidueProperties; -import jalview.schemes.StrandColourScheme; import jalview.schemes.TCoffeeColourScheme; -import jalview.schemes.TaylorColourScheme; -import jalview.schemes.TurnColourScheme; -import jalview.schemes.UserColourScheme; -import jalview.schemes.ZappoColourScheme; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.ViewportRanges; import jalview.ws.DBRefFetcher; import jalview.ws.DBRefFetcher.FetchFinishedListenerI; import jalview.ws.jws1.Discoverer; @@ -126,12 +115,13 @@ import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.awt.event.KeyAdapter; import java.awt.event.KeyEvent; -import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.awt.print.PageFormat; import java.awt.print.PrinterJob; import java.beans.PropertyChangeEvent; import java.io.File; +import java.io.FileWriter; +import java.io.PrintWriter; import java.net.URL; import java.util.ArrayList; import java.util.Arrays; @@ -147,8 +137,6 @@ import javax.swing.JInternalFrame; import javax.swing.JLayeredPane; import javax.swing.JMenu; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; -import javax.swing.JRadioButtonMenuItem; import javax.swing.JScrollPane; import javax.swing.SwingUtilities; @@ -159,7 +147,7 @@ import javax.swing.SwingUtilities; * @version $Revision$ */ public class AlignFrame extends GAlignFrame implements DropTargetListener, - IProgressIndicator, AlignViewControllerGuiI + IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener { public static final int DEFAULT_WIDTH = 700; @@ -173,6 +161,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignViewport viewport; + ViewportRanges vpRanges; + public AlignViewControllerI avc; List alignPanels = new ArrayList(); @@ -344,11 +334,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, progressBar = new ProgressBar(this.statusPanel, this.statusBar); } + vpRanges = viewport.getRanges(); avc = new jalview.controller.AlignViewController(this, viewport, alignPanel); if (viewport.getAlignmentConservationAnnotation() == null) { - BLOSUM62Colour.setEnabled(false); + // BLOSUM62Colour.setEnabled(false); conservationMenuItem.setEnabled(false); modifyConservation.setEnabled(false); // PIDColour.setEnabled(false); @@ -368,19 +359,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sortPairwiseMenuItem_actionPerformed(null); } - if (Desktop.desktop != null) - { - this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); - addServiceListeners(); - setGUINucleotide(viewport.getAlignment().isNucleotide()); - } - this.alignPanel.av .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); setMenusFromViewport(viewport); buildSortByAnnotationScoresMenu(); buildTreeMenu(); + buildColourMenu(); + + if (Desktop.desktop != null) + { + this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); + addServiceListeners(); + setGUINucleotide(); + } if (viewport.getWrapAlignment()) { @@ -652,8 +644,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new String[] { (viewport.cursorMode ? "on" : "off") })); if (viewport.cursorMode) { - alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes; - alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq; + alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges + .getStartRes(); + alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges + .getStartSeq(); } alignPanel.getSeqPanel().seqCanvas.repaint(); break; @@ -691,8 +685,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.setScrollValues(viewport.startRes, viewport.startSeq - - viewport.endSeq + viewport.startSeq); + alignPanel.setScrollValues(vpRanges.getStartRes(), + 2 * vpRanges.getStartSeq() - vpRanges.getEndSeq()); } break; case KeyEvent.VK_PAGE_DOWN: @@ -702,8 +696,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.setScrollValues(viewport.startRes, viewport.startSeq - + viewport.endSeq - viewport.startSeq); + alignPanel.setScrollValues(vpRanges.getStartRes(), + vpRanges.getEndSeq()); } break; } @@ -847,25 +841,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Configure menu items that vary according to whether the alignment is * nucleotide or protein - * - * @param nucleotide */ - public void setGUINucleotide(boolean nucleotide) + public void setGUINucleotide() { + AlignmentI al = getViewport().getAlignment(); + boolean nucleotide = al.isNucleotide(); + showTranslation.setVisible(nucleotide); showReverse.setVisible(nucleotide); showReverseComplement.setVisible(nucleotide); conservationMenuItem.setEnabled(!nucleotide); - modifyConservation.setEnabled(!nucleotide); + modifyConservation.setEnabled(!nucleotide + && conservationMenuItem.isSelected()); showGroupConservation.setEnabled(!nucleotide); - rnahelicesColour.setEnabled(nucleotide); - purinePyrimidineColour.setEnabled(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")); } /** @@ -891,7 +883,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, padGapsMenuitem.setSelected(av.isPadGaps()); colourTextMenuItem.setSelected(av.isShowColourText()); abovePIDThreshold.setSelected(av.getAbovePIDThreshold()); + modifyPID.setEnabled(abovePIDThreshold.isSelected()); conservationMenuItem.setSelected(av.getConservationSelected()); + modifyConservation.setEnabled(conservationMenuItem.isSelected()); seqLimits.setSelected(av.getShowJVSuffix()); idRightAlign.setSelected(av.isRightAlignIds()); centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels()); @@ -917,8 +911,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showSequenceLogo.setSelected(av.isShowSequenceLogo()); normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo()); - setColourSelected(ColourSchemeProperty.getColourName(av - .getGlobalColourScheme())); + ColourMenuHelper.setColourSelected(colourMenu, + av.getGlobalColourScheme()); showSeqFeatures.setSelected(av.isShowSequenceFeatures()); hiddenMarkers.setState(av.getShowHiddenMarkers()); @@ -928,9 +922,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, autoCalculate.setSelected(av.autoCalculateConsensus); sortByTree.setSelected(av.sortByTree); listenToViewSelections.setSelected(av.followSelection); - rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure()); - rnahelicesColour - .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour); showProducts.setEnabled(canShowProducts()); setGroovyEnabled(Desktop.getGroovyConsole() != null); @@ -1114,11 +1105,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void saveAs_actionPerformed(ActionEvent e) { + String format = currentFileFormat == null ? null : currentFileFormat + .getName(); JalviewFileChooser chooser = JalviewFileChooser.forWrite( - Cache.getProperty("LAST_DIRECTORY"), - // AppletFormatAdapter.WRITABLE_EXTENSIONS, - // AppletFormatAdapter.WRITABLE_FNAMES, - currentFileFormat.toString(), false); + Cache.getProperty("LAST_DIRECTORY"), format); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager @@ -1150,8 +1140,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, fileName = chooser.getSelectedFile().getPath(); - Cache.setProperty("DEFAULT_FILE_FORMAT", - currentFileFormat.toString()); + Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName()); Cache.setProperty("LAST_DIRECTORY", fileName); saveAlignment(fileName, currentFileFormat); @@ -1181,17 +1170,6 @@ 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; - // } - AlignmentExportData exportData = getAlignmentForExport(format, viewport, null); if (exportData.getSettings().isCancelled()) @@ -1216,15 +1194,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { try { - java.io.PrintWriter out = new java.io.PrintWriter( - new java.io.FileWriter(file)); + PrintWriter out = new PrintWriter(new FileWriter(file)); out.print(output); out.close(); this.setTitle(file); statusBar.setText(MessageManager.formatMessage( "label.successfully_saved_to_file_in_format", - new Object[] { fileName, format })); + new Object[] { fileName, format.getName() })); } catch (Exception ex) { success = false; @@ -1269,8 +1246,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void outputText_actionPerformed(ActionEvent e) { - - FileFormatI fileFormat = FileFormat.forName(e.getActionCommand()); + FileFormatI fileFormat = FileFormats.getInstance().forName( + e.getActionCommand()); AlignmentExportData exportData = getAlignmentForExport(fileFormat, viewport, null); if (exportData.getSettings().isCancelled()) @@ -1283,8 +1260,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { FileFormatI format = fileFormat; cap.setText(new FormatAdapter(alignPanel, exportData.getSettings()) - .formatSequences(format, - exportData.getAlignment(), + .formatSequences(format, exportData.getAlignment(), exportData.getOmitHidden(), exportData.getStartEndPostions(), viewport.getColumnSelection())); @@ -1875,8 +1851,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } String output = new FormatAdapter().formatSequences(FileFormat.Fasta, - seqs, - omitHidden, null); + seqs, omitHidden, null); StringSelection ss = new StringSelection(output); @@ -2172,7 +2147,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // propagate alignment changed. - viewport.setEndSeq(alignment.getHeight()); + vpRanges.setEndSeq(alignment.getHeight()); if (annotationAdded) { // Duplicate sequence annotation in all views. @@ -2576,7 +2551,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { trimRegion = new TrimRegionCommand("Remove Left", true, seqs, column, viewport.getAlignment()); - viewport.setStartRes(0); + vpRanges.setStartRes(0); } else { @@ -2643,13 +2618,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // This is to maintain viewport position on first residue // of first sequence SequenceI seq = viewport.getAlignment().getSequenceAt(0); - int startRes = seq.findPosition(viewport.startRes); + int startRes = seq.findPosition(vpRanges.getStartRes()); // ShiftList shifts; // viewport.getAlignment().removeGaps(shifts=new ShiftList()); // edit.alColumnChanges=shifts.getInverse(); // if (viewport.hasHiddenColumns) // viewport.getColumnSelection().compensateForEdits(shifts); - viewport.setStartRes(seq.findIndex(startRes) - 1); + vpRanges.setStartRes(seq.findIndex(startRes) - 1); viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); @@ -2682,12 +2657,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // This is to maintain viewport position on first residue // of first sequence SequenceI seq = viewport.getAlignment().getSequenceAt(0); - int startRes = seq.findPosition(viewport.startRes); + int startRes = seq.findPosition(vpRanges.getStartRes()); addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, viewport.getAlignment())); - viewport.setStartRes(seq.findIndex(startRes) - 1); + vpRanges.setStartRes(seq.findIndex(startRes) - 1); viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); @@ -3301,146 +3276,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } @Override - public void textColour_actionPerformed(ActionEvent e) + public void textColour_actionPerformed() { new TextColourChooser().chooseColour(alignPanel, null); } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - protected void noColourmenuItem_actionPerformed(ActionEvent e) - { - changeColour(null); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void clustalColour_actionPerformed(ActionEvent e) - { - changeColour(new ClustalxColourScheme(viewport.getAlignment(), - viewport.getHiddenRepSequences())); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void zappoColour_actionPerformed(ActionEvent e) - { - changeColour(new ZappoColourScheme()); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void taylorColour_actionPerformed(ActionEvent e) - { - changeColour(new TaylorColourScheme()); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void hydrophobicityColour_actionPerformed(ActionEvent e) - { - changeColour(new HydrophobicColourScheme()); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void helixColour_actionPerformed(ActionEvent e) - { - changeColour(new HelixColourScheme()); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void strandColour_actionPerformed(ActionEvent e) - { - changeColour(new StrandColourScheme()); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void turnColour_actionPerformed(ActionEvent e) - { - changeColour(new TurnColourScheme()); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void buriedColour_actionPerformed(ActionEvent e) - { - changeColour(new BuriedColourScheme()); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void nucleotideColour_actionPerformed(ActionEvent e) - { - changeColour(new NucleotideColourScheme()); - } - - @Override - public void purinePyrimidineColour_actionPerformed(ActionEvent e) - { - changeColour(new PurinePyrimidineColourScheme()); - } - /* - * public void covariationColour_actionPerformed(ActionEvent e) { + * public void covariationColour_actionPerformed() { * changeColour(new * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation * ()[0])); } */ @Override - public void annotationColour_actionPerformed(ActionEvent e) + public void annotationColour_actionPerformed() { new AnnotationColourChooser(viewport, alignPanel); } @@ -3451,55 +3299,58 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new AnnotationColumnChooser(viewport, alignPanel); } + /** + * Action on the user checking or unchecking the option to apply the selected + * colour scheme to all groups. If unchecked, groups may have their own + * independent colour schemes. + * + * @param selected + */ @Override - public void rnahelicesColour_actionPerformed(ActionEvent e) + public void applyToAllGroups_actionPerformed(boolean selected) { - new RNAHelicesColourChooser(viewport, alignPanel); + viewport.setColourAppliesToAllGroups(selected); } /** - * DOCUMENT ME! + * Action on user selecting a colour from the colour menu * - * @param e - * DOCUMENT ME! + * @param name + * the name (not the menu item label!) of the colour scheme */ @Override - protected void applyToAllGroups_actionPerformed(ActionEvent e) + public void changeColour_actionPerformed(String name) { - viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected()); + /* + * 'User Defined' opens a panel to configure or load a + * user-defined colour scheme + */ + if (ResidueColourScheme.USER_DEFINED.equals(name)) + { + new UserDefinedColours(alignPanel, null); + return; + } + + /* + * otherwise set the chosen colour scheme (or null for 'None') + */ + ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name, + viewport.getAlignment(), viewport.getHiddenRepSequences()); + changeColour(cs); } /** - * DOCUMENT ME! + * Actions on setting or changing the alignment colour scheme * * @param cs - * DOCUMENT ME! */ @Override public void changeColour(ColourSchemeI cs) { // TODO: pull up to controller method - if (cs != null) { - // Make sure viewport is up to date w.r.t. any sliders - if (viewport.getAbovePIDThreshold()) - { - int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, - "Background"); - viewport.setThreshold(threshold); - } - - if (viewport.getConservationSelected()) - { - cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, - cs, "Background")); - } - if (cs instanceof TCoffeeColourScheme) - { - tcoffeeColour.setEnabled(true); - tcoffeeColour.setSelected(true); - } + ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName()); } viewport.setGlobalColourScheme(cs); @@ -3508,190 +3359,70 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Show the PID threshold slider panel */ @Override - protected void modifyPID_actionPerformed(ActionEvent e) + protected void modifyPID_actionPerformed() { - if (viewport.getAbovePIDThreshold() - && viewport.getGlobalColourScheme() != null) - { - SliderPanel.setPIDSliderSource(alignPanel, - viewport.getGlobalColourScheme(), "Background"); - SliderPanel.showPIDSlider(); - } + SliderPanel.setPIDSliderSource(alignPanel, + viewport.getResidueShading(), alignPanel.getViewName()); + SliderPanel.showPIDSlider(); } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Show the Conservation slider panel */ @Override - protected void modifyConservation_actionPerformed(ActionEvent e) + protected void modifyConservation_actionPerformed() { - if (viewport.getConservationSelected() - && viewport.getGlobalColourScheme() != null) - { - SliderPanel.setConservationSlider(alignPanel, - viewport.getGlobalColourScheme(), "Background"); - SliderPanel.showConservationSlider(); - } + SliderPanel.setConservationSlider(alignPanel, + viewport.getResidueShading(), alignPanel.getViewName()); + SliderPanel.showConservationSlider(); } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Action on selecting or deselecting (Colour) By Conservation */ @Override - protected void conservationMenuItem_actionPerformed(ActionEvent e) + public void conservationMenuItem_actionPerformed(boolean selected) { - viewport.setConservationSelected(conservationMenuItem.isSelected()); - - viewport.setAbovePIDThreshold(false); - abovePIDThreshold.setSelected(false); + modifyConservation.setEnabled(selected); + viewport.setConservationSelected(selected); + viewport.getResidueShading().setConservationApplied(selected); changeColour(viewport.getGlobalColourScheme()); - - modifyConservation_actionPerformed(null); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void abovePIDThreshold_actionPerformed(ActionEvent e) - { - viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected()); - - conservationMenuItem.setSelected(false); - viewport.setConservationSelected(false); - - changeColour(viewport.getGlobalColourScheme()); - - modifyPID_actionPerformed(null); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void userDefinedColour_actionPerformed(ActionEvent e) - { - if (e.getActionCommand().equals( - MessageManager.getString("action.user_defined"))) + if (selected) { - new UserDefinedColours(alignPanel, null); + modifyConservation_actionPerformed(); } else { - UserColourScheme udc = (UserColourScheme) UserDefinedColours - .getUserColourSchemes().get(e.getActionCommand()); - - changeColour(udc); + SliderPanel.hideConservationSlider(); } } - public void updateUserColourMenu() + /** + * Action on selecting or deselecting (Colour) Above PID Threshold + */ + @Override + public void abovePIDThreshold_actionPerformed(boolean selected) { + modifyPID.setEnabled(selected); + viewport.setAbovePIDThreshold(selected); + if (!selected) + { + viewport.getResidueShading().setThreshold(0, + viewport.isIgnoreGapsConsensus()); + } - Component[] menuItems = colourMenu.getMenuComponents(); - int iSize = menuItems.length; - for (int i = 0; i < iSize; i++) + changeColour(viewport.getGlobalColourScheme()); + if (selected) { - if (menuItems[i].getName() != null - && menuItems[i].getName().equals("USER_DEFINED")) - { - colourMenu.remove(menuItems[i]); - iSize--; - } + modifyPID_actionPerformed(); } - if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) + else { - java.util.Enumeration userColours = jalview.gui.UserDefinedColours - .getUserColourSchemes().keys(); - - while (userColours.hasMoreElements()) - { - final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem( - userColours.nextElement().toString()); - radioItem.setName("USER_DEFINED"); - radioItem.addMouseListener(new MouseAdapter() - { - @Override - public void mousePressed(MouseEvent evt) - { - if (evt.isPopupTrigger()) // Mac - { - offerRemoval(radioItem); - } - } - - @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() - { - @Override - public void actionPerformed(ActionEvent evt) - { - userDefinedColour_actionPerformed(evt); - } - }); - } - } - }); - radioItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent evt) - { - userDefinedColour_actionPerformed(evt); - } - }); - - colourMenu.insert(radioItem, 15); - colours.add(radioItem); - } + SliderPanel.hidePIDSlider(); } } @@ -3702,30 +3433,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void PIDColour_actionPerformed(ActionEvent e) - { - changeColour(new PIDColourScheme()); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void BLOSUM62Colour_actionPerformed(ActionEvent e) - { - changeColour(new Blosum62ColourScheme()); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); @@ -4353,12 +4060,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } - @Override - protected void tcoffeeColorScheme_actionPerformed(ActionEvent e) - { - changeColour(new TCoffeeColourScheme(alignPanel.getAlignment())); - } - public TreePanel ShowNewickTree(NewickFile nf, String title) { return ShowNewickTree(nf, title, 600, 500, 4, 5); @@ -4899,13 +4600,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { type = null; } - if (type != null) + if (type != null && type.isStructureFile()) { - if (FileFormat.PDB.equals(type) || FileFormat.MMCif.equals(type)) - { - filesmatched.add(new Object[] { file, protocol, mtch }); - continue; - } + filesmatched.add(new Object[] { file, protocol, mtch }); + continue; } } // File wasn't named like one of the sequences or wasn't a PDB file. @@ -5027,8 +4725,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (tcf.annotateAlignment(viewport.getAlignment(), true)) { - tcoffeeColour.setEnabled(true); - tcoffeeColour.setSelected(true); + buildColourMenu(); changeColour(new TCoffeeColourScheme(viewport.getAlignment())); isAnnotation = true; statusBar @@ -5072,8 +4769,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (FileFormat.Jnet.equals(format)) { - JPredFile predictions = new JPredFile( - file, sourceType); + JPredFile predictions = new JPredFile(file, sourceType); new JnetAnnotationMaker(); JnetAnnotationMaker.add_annotation(predictions, viewport.getAlignment(), 0, false); @@ -5143,6 +4839,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /* + * 'focus' any colour slider that is open to the selected viewport + */ + if (viewport.getConservationSelected()) + { + SliderPanel.setConservationSlider(alignPanel, + viewport.getResidueShading(), alignPanel.getViewName()); + } + else + { + SliderPanel.hideConservationSlider(); + } + if (viewport.getAbovePIDThreshold()) + { + SliderPanel.setPIDSliderSource(alignPanel, + viewport.getResidueShading(), alignPanel.getViewName()); + } + else + { + SliderPanel.hidePIDSlider(); + } + + /* * If there is a frame linked to this one in a SplitPane, switch it to the * same view tab index. No infinite recursion of calls should happen, since * tabSelectionChanged() should not get invoked on setting the selected @@ -5842,7 +5560,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs .size()])); - AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH, + GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); cdna.alignAs(alignment); String newtitle = "cDNA " + MessageManager.getString("label.for") + " " @@ -5958,6 +5676,52 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, true, (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0); } + + /** + * Rebuilds the Colour menu, including any user-defined colours which have + * been loaded either on startup or during the session + */ + public void buildColourMenu() + { + colourMenu.removeAll(); + + colourMenu.add(applyToAllGroups); + colourMenu.add(textColour); + colourMenu.addSeparator(); + + ColourMenuHelper.addMenuItems(colourMenu, this, + viewport.getAlignment(), false); + + colourMenu.addSeparator(); + colourMenu.add(conservationMenuItem); + colourMenu.add(modifyConservation); + colourMenu.add(abovePIDThreshold); + colourMenu.add(modifyPID); + colourMenu.add(annotationColour); + + ColourSchemeI colourScheme = viewport.getGlobalColourScheme(); + String schemeName = colourScheme == null ? null : colourScheme + .getSchemeName(); + + ColourMenuHelper.setColourSelected(colourMenu, schemeName); + } + + /** + * Disable inapplicable items in the Select menu when it is clicked + */ + @Override + protected void configureSelectMenu() + { + createGroup.setEnabled(false); + unGroup.setEnabled(false); + SequenceGroup sg = viewport.getSelectionGroup(); + if (sg != null) + { + List groups = viewport.getAlignment().getGroups(); + createGroup.setEnabled(groups == null || !groups.contains(sg)); + unGroup.setEnabled(groups != null && groups.contains(sg)); + } + } } class PrintThread extends Thread