X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=c7792a5398d2eb011b94ee08adf58058ba9fd364;hb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;hp=7e451aa1d1f9607f467ff77b5fd9789ec2c984ab;hpb=0846d23b8e3bd33b2120a0f724299bf05c175f32;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 7e451aa..c7792a5 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -20,17 +20,71 @@ */ package jalview.gui; +import java.awt.BorderLayout; +import java.awt.Component; +import java.awt.GridLayout; +import java.awt.Rectangle; +import java.awt.Toolkit; +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; +import java.awt.dnd.DropTargetListener; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +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.net.URL; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Deque; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.List; +import java.util.Set; +import java.util.Vector; + +import javax.swing.JButton; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JEditorPane; +import javax.swing.JInternalFrame; +import javax.swing.JLabel; +import javax.swing.JLayeredPane; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.JPanel; +import javax.swing.JProgressBar; +import javax.swing.JRadioButtonMenuItem; +import javax.swing.JScrollPane; +import javax.swing.SwingUtilities; + import jalview.analysis.AAFrequency; import jalview.analysis.AlignmentSorter; import jalview.analysis.AlignmentUtils; import jalview.analysis.Conservation; import jalview.analysis.CrossRef; -import jalview.analysis.NJTree; +import jalview.analysis.Dna; import jalview.analysis.ParseProperties; import jalview.analysis.SequenceIdMatcher; import jalview.api.AlignViewControllerGuiI; import jalview.api.AlignViewControllerI; +import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; +import jalview.api.SplitContainerI; +import jalview.api.ViewStyleI; import jalview.api.analysis.ScoreModelI; import jalview.bin.Cache; import jalview.commands.CommandI; @@ -53,6 +107,7 @@ import jalview.datamodel.SeqCigar; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.gui.ViewSelectionMenu.ViewSetProvider; import jalview.io.AlignmentProperties; import jalview.io.AnnotationFile; import jalview.io.BioJsHTMLOutput; @@ -86,58 +141,12 @@ import jalview.schemes.TurnColourScheme; import jalview.schemes.UserColourScheme; import jalview.schemes.ZappoColourScheme; import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; import jalview.ws.jws1.Discoverer; import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.jabaws2.Jws2Instance; import jalview.ws.seqfetcher.DbSourceProxy; -import java.awt.BorderLayout; -import java.awt.Component; -import java.awt.GridLayout; -import java.awt.Rectangle; -import java.awt.Toolkit; -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; -import java.awt.dnd.DropTargetListener; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -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.net.URL; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Enumeration; -import java.util.Hashtable; -import java.util.List; -import java.util.Vector; - -import javax.swing.JButton; -import javax.swing.JCheckBoxMenuItem; -import javax.swing.JEditorPane; -import javax.swing.JInternalFrame; -import javax.swing.JLabel; -import javax.swing.JLayeredPane; -import javax.swing.JMenu; -import javax.swing.JMenuItem; -import javax.swing.JOptionPane; -import javax.swing.JPanel; -import javax.swing.JProgressBar; -import javax.swing.JRadioButtonMenuItem; -import javax.swing.JScrollPane; -import javax.swing.SwingUtilities; - /** * DOCUMENT ME! * @@ -148,19 +157,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, IProgressIndicator, AlignViewControllerGuiI { - /** DOCUMENT ME!! */ public static final int DEFAULT_WIDTH = 700; - /** DOCUMENT ME!! */ public static final int DEFAULT_HEIGHT = 500; + /* + * The currently displayed panel (selected tabbed view if more than one) + */ public AlignmentPanel alignPanel; AlignViewport viewport; public AlignViewControllerI avc; - Vector alignPanels = new Vector(); + List alignPanels = new ArrayList(); /** * Last format used to load or save alignments in this window @@ -339,7 +349,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, buildSortByAnnotationScoresMenu(); buildTreeMenu(); - if (viewport.wrapAlignment) + if (viewport.getWrapAlignment()) { wrapMenuItem_actionPerformed(null); } @@ -351,6 +361,59 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addKeyListener(); + final List selviews = new ArrayList(); + final List origview = new ArrayList(); + ViewSelectionMenu vsel = new ViewSelectionMenu("Transfer colours from", + new ViewSetProvider() + { + + @Override + public AlignmentPanel[] getAllAlignmentPanels() + { + origview.clear(); + origview.add(alignPanel); + return Desktop.getAlignmentPanels(null); + } + }, selviews, new ItemListener() + { + + @Override + public void itemStateChanged(ItemEvent e) + { + if (origview.size() > 0) + { + ViewStyleI vs = selviews.get(0).getAlignViewport() + .getViewStyle(); + origview.get(0).getAlignViewport().setViewStyle(vs); + AlignViewportI complement = origview.get(0) + .getAlignViewport().getCodingComplement(); + if (complement != null) + { + AlignFrame af = Desktop.getAlignFrameFor(complement); + if (complement.isNucleotide()) + { + complement.setViewStyle(vs); + vs.setCharWidth(vs.getCharWidth() / 3); + } + else + { + int rw = vs.getCharWidth(); + vs.setCharWidth(rw * 3); + complement.setViewStyle(vs); + vs.setCharWidth(rw); + } + af.alignPanel.updateLayout(); + af.setMenusForViewport(); + } + origview.get(0).updateLayout(); + origview.get(0).setSelected(true); + origview.get(0).alignFrame.setMenusForViewport(); + + } + } + }); + formatMenu.add(vsel); + } /** @@ -365,10 +428,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void setFileName(String file, String format) { fileName = file; - currentFileFormat = format; + setFileFormat(format); reload.setEnabled(true); } + /** + * Add a KeyListener with handlers for various KeyPressed and KeyReleased + * events + */ void addKeyListener() { addKeyListener(new KeyAdapter() @@ -542,7 +609,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, break; } case KeyEvent.VK_PAGE_UP: - if (viewport.wrapAlignment) + if (viewport.getWrapAlignment()) { alignPanel.scrollUp(true); } @@ -553,7 +620,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } break; case KeyEvent.VK_PAGE_DOWN: - if (viewport.wrapAlignment) + if (viewport.getWrapAlignment()) { alignPanel.scrollUp(false); } @@ -597,7 +664,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, avc = new jalview.controller.AlignViewController(this, viewport, alignPanel); - alignPanels.addElement(ap); + alignPanels.add(ap); PaintRefresher.Register(ap, ap.av.getSequenceSetId()); @@ -640,7 +707,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, expandViews.setEnabled(true); gatherViews.setEnabled(true); tabbedPane.setVisible(true); - AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement(); + AlignmentPanel first = alignPanels.get(0); tabbedPane.addTab(first.av.viewName, first); this.getContentPane().add(tabbedPane, BorderLayout.CENTER); } @@ -701,6 +768,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }).start(); } + /** + * Configure menu items that vary according to whether the alignment is + * nucleotide or protein + * + * @param nucleotide + */ public void setGUINucleotide(boolean nucleotide) { showTranslation.setVisible(nucleotide); @@ -709,16 +782,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showGroupConservation.setEnabled(!nucleotide); rnahelicesColour.setEnabled(nucleotide); purinePyrimidineColour.setEnabled(nucleotide); - // Remember AlignFrame always starts as protein - // if (!nucleotide) - // { - // showTr - // calculateMenu.remove(calculateMenu.getItemCount() - 2); - // } + showComplementMenuItem.setText(MessageManager + .getString(nucleotide ? "label.protein" : "label.nucleotide")); + setColourSelected(jalview.bin.Cache.getDefault( + nucleotide ? Preferences.DEFAULT_COLOUR_NUC + : Preferences.DEFAULT_COLOUR_PROT, "None")); } /** - * set up menus for the currently viewport. This may be called after any + * set up menus for the current viewport. This may be called after any * operation that affects the data in the current view (selection changed, * etc) to update the menus to reflect the new state. */ @@ -737,17 +809,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, void setMenusFromViewport(AlignViewport av) { padGapsMenuitem.setSelected(av.isPadGaps()); - colourTextMenuItem.setSelected(av.showColourText); + colourTextMenuItem.setSelected(av.isShowColourText()); abovePIDThreshold.setSelected(av.getAbovePIDThreshold()); conservationMenuItem.setSelected(av.getConservationSelected()); seqLimits.setSelected(av.getShowJVSuffix()); idRightAlign.setSelected(av.isRightAlignIds()); - centreColumnLabelsMenuItem.setState(av.centreColumnLabels); - renderGapsMenuItem.setSelected(av.renderGaps); - wrapMenuItem.setSelected(av.wrapAlignment); - scaleAbove.setVisible(av.wrapAlignment); - scaleLeft.setVisible(av.wrapAlignment); - scaleRight.setVisible(av.wrapAlignment); + centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels()); + renderGapsMenuItem.setSelected(av.isRenderGaps()); + wrapMenuItem.setSelected(av.getWrapAlignment()); + scaleAbove.setVisible(av.getWrapAlignment()); + scaleLeft.setVisible(av.getWrapAlignment()); + scaleRight.setVisible(av.getWrapAlignment()); annotationPanelMenuItem.setState(av.isShowAnnotation()); /* * Show/hide annotations only enabled if annotation panel is shown @@ -756,8 +828,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState()); showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState()); hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState()); - viewBoxesMenuItem.setSelected(av.showBoxes); - viewTextMenuItem.setSelected(av.showText); + viewBoxesMenuItem.setSelected(av.getShowBoxes()); + viewTextMenuItem.setSelected(av.getShowText()); showNonconservedMenuItem.setSelected(av.getShowUnconserved()); showGroupConsensus.setSelected(av.isShowGroupConsensus()); showGroupConservation.setSelected(av.isShowGroupConservation()); @@ -769,10 +841,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getGlobalColourScheme())); showSeqFeatures.setSelected(av.isShowSequenceFeatures()); - hiddenMarkers.setState(av.showHiddenMarkers); + hiddenMarkers.setState(av.getShowHiddenMarkers()); applyToAllGroups.setState(av.getColourAppliesToAllGroups()); - showNpFeatsMenuitem.setSelected(av.isShowNpFeats()); - showDbRefsMenuitem.setSelected(av.isShowDbRefs()); + showNpFeatsMenuitem.setSelected(av.isShowNPFeats()); + showDbRefsMenuitem.setSelected(av.isShowDBRefs()); autoCalculate.setSelected(av.autoCalculateConsensus); sortByTree.setSelected(av.sortByTree); listenToViewSelections.setSelected(av.followSelection); @@ -862,7 +934,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void actionPerformed(ActionEvent e) { handler.cancelActivity(id); - us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id); + us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new Object[]{((JLabel) progressPanel.getComponent(0)).getText()}), id); } }); progressPanel.add(cancel, BorderLayout.EAST); @@ -1033,7 +1105,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (value == JalviewFileChooser.APPROVE_OPTION) { currentFileFormat = chooser.getSelectedFormat(); - if (currentFileFormat == null) + while (currentFileFormat == null) { JOptionPane .showInternalMessageDialog( @@ -1043,8 +1115,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, MessageManager .getString("label.file_format_not_specified"), JOptionPane.WARNING_MESSAGE); + currentFileFormat = chooser.getSelectedFormat(); value = chooser.showSaveDialog(this); - return; + if (value != JalviewFileChooser.APPROVE_OPTION) + { + return; + } } fileName = chooser.getSelectedFile().getPath(); @@ -1141,7 +1217,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, this.setTitle(file); statusBar.setText(MessageManager.formatMessage( "label.successfully_saved_to_file_in_format", - new String[] + new Object[] { fileName, format })); } catch (Exception ex) { @@ -1154,7 +1230,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (!success) { JOptionPane.showInternalMessageDialog(this, MessageManager - .formatMessage("label.couldnt_save_file", new String[] + .formatMessage("label.couldnt_save_file", new Object[] { fileName }), MessageManager .getString("label.error_saving_file"), JOptionPane.WARNING_MESSAGE); @@ -1216,7 +1292,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.getAlignment(), omitHidden, viewport.getColumnSelection())); Desktop.addInternalFrame(cap, MessageManager.formatMessage( - "label.alignment_output_command", new String[] + "label.alignment_output_command", new Object[] { e.getActionCommand() }), 600, 500); } catch (OutOfMemoryError oom) { @@ -1362,7 +1438,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // setClosed(true) is called for (int i = 0; i < alignPanels.size(); i++) { - AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i); + AlignmentPanel ap = alignPanels.get(i); ap.closePanel(); } } @@ -1384,22 +1460,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * close alignPanel2 and shuffle tabs appropriately. + * Close the specified panel and close up tabs appropriately. * - * @param alignPanel2 + * @param panelToClose */ - public void closeView(AlignmentPanel alignPanel2) + public void closeView(AlignmentPanel panelToClose) { int index = tabbedPane.getSelectedIndex(); - int closedindex = tabbedPane.indexOfComponent(alignPanel2); - alignPanels.removeElement(alignPanel2); - // Unnecessary - // if (viewport == alignPanel2.av) - // { - // viewport = null; - // } - alignPanel2.closePanel(); - alignPanel2 = null; + int closedindex = tabbedPane.indexOfComponent(panelToClose); + alignPanels.remove(panelToClose); + panelToClose.closePanel(); + panelToClose = null; tabbedPane.removeTabAt(closedindex); tabbedPane.validate(); @@ -1419,12 +1490,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, void updateEditMenuBar() { - if (viewport.historyList.size() > 0) + if (viewport.getHistoryList().size() > 0) { undoMenuItem.setEnabled(true); - CommandI command = viewport.historyList.peek(); + CommandI command = viewport.getHistoryList().peek(); undoMenuItem.setText(MessageManager.formatMessage( - "label.undo_command", new String[] + "label.undo_command", new Object[] { command.getDescription() })); } else @@ -1433,13 +1504,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, undoMenuItem.setText(MessageManager.getString("action.undo")); } - if (viewport.redoList.size() > 0) + if (viewport.getRedoList().size() > 0) { redoMenuItem.setEnabled(true); - CommandI command = viewport.redoList.peek(); + CommandI command = viewport.getRedoList().peek(); redoMenuItem.setText(MessageManager.formatMessage( - "label.redo_command", new String[] + "label.redo_command", new Object[] { command.getDescription() })); } else @@ -1453,8 +1524,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (command.getSize() > 0) { - viewport.historyList.push(command); - viewport.redoList.clear(); + viewport.addToHistoryList(command); + viewport.clearRedoList(); updateEditMenuBar(); viewport.updateHiddenColumns(); // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null @@ -1472,11 +1543,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (alignPanels != null) { - Enumeration e = alignPanels.elements(); AlignmentI[] als = new AlignmentI[alignPanels.size()]; - for (int i = 0; e.hasMoreElements(); i++) + int i = 0; + for (AlignmentPanel ap : alignPanels) { - als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment(); + als[i++] = ap.av.getAlignment(); } return als; } @@ -1497,15 +1568,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void undoMenuItem_actionPerformed(ActionEvent e) { - if (viewport.historyList.empty()) + if (viewport.getHistoryList().isEmpty()) { return; } - CommandI command = viewport.historyList.pop(); - viewport.redoList.push(command); + CommandI command = viewport.getHistoryList().pop(); + viewport.addToRedoList(command); command.undoCommand(getViewAlignments()); - AlignViewport originalSource = getOriginatingSource(command); + AlignmentViewport originalSource = getOriginatingSource(command); updateEditMenuBar(); if (originalSource != null) @@ -1535,16 +1606,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void redoMenuItem_actionPerformed(ActionEvent e) { - if (viewport.redoList.size() < 1) + if (viewport.getRedoList().size() < 1) { return; } - CommandI command = viewport.redoList.pop(); - viewport.historyList.push(command); + CommandI command = viewport.getRedoList().pop(); + viewport.addToHistoryList(command); command.doCommand(getViewAlignments()); - AlignViewport originalSource = getOriginatingSource(command); + AlignmentViewport originalSource = getOriginatingSource(command); updateEditMenuBar(); if (originalSource != null) @@ -1566,9 +1637,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } - AlignViewport getOriginatingSource(CommandI command) + AlignmentViewport getOriginatingSource(CommandI command) { - AlignViewport originalSource = null; + AlignmentViewport originalSource = null; // For sequence removal and addition, we need to fire // the property change event FROM the viewport where the // original alignment was altered @@ -1577,16 +1648,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { EditCommand editCommand = (EditCommand) command; al = editCommand.getAlignment(); - Vector comps = (Vector) PaintRefresher.components.get(viewport + List comps = PaintRefresher.components.get(viewport .getSequenceSetId()); - for (int i = 0; i < comps.size(); i++) + for (Component comp : comps) { - if (comps.elementAt(i) instanceof AlignmentPanel) + if (comp instanceof AlignmentPanel) { - if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment()) + if (al == ((AlignmentPanel) comp).av.getAlignment()) { - originalSource = ((AlignmentPanel) comps.elementAt(i)).av; + originalSource = ((AlignmentPanel) comp).av; break; } } @@ -1629,7 +1700,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, synchronized void slideSequences(boolean right, int size) { - List sg = new Vector(); + List sg = new ArrayList(); if (viewport.cursorMode) { sg.add(viewport.getAlignment().getSequenceAt( @@ -1648,13 +1719,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - Vector invertGroup = new Vector(); + List invertGroup = new ArrayList(); - for (int i = 0; i < viewport.getAlignment().getHeight(); i++) + for (SequenceI seq : viewport.getAlignment().getSequences()) { - if (!sg.contains(viewport.getAlignment().getSequenceAt(i))) + if (!sg.contains(seq)) { - invertGroup.add(viewport.getAlignment().getSequenceAt(i)); + invertGroup.add(seq); } } @@ -1663,7 +1734,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SequenceI[] seqs2 = new SequenceI[invertGroup.size()]; for (int i = 0; i < invertGroup.size(); i++) { - seqs2[i] = (SequenceI) invertGroup.elementAt(i); + seqs2[i] = invertGroup.get(i); } SlideSequencesCommand ssc; @@ -1711,11 +1782,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } boolean appendHistoryItem = false; - if (viewport.historyList != null && viewport.historyList.size() > 0 - && viewport.historyList.peek() instanceof SlideSequencesCommand) + Deque historyList = viewport.getHistoryList(); + if (historyList != null + && historyList.size() > 0 + && historyList.peek() instanceof SlideSequencesCommand) { appendHistoryItem = ssc - .appendSlideCommand((SlideSequencesCommand) viewport.historyList + .appendSlideCommand((SlideSequencesCommand) historyList .peek()); } @@ -1791,7 +1864,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Desktop.jalviewClipboard = new Object[] { seqs, viewport.getAlignment().getDataset(), hiddenColumns }; statusBar.setText(MessageManager.formatMessage( - "label.copied_sequences_to_clipboard", new String[] + "label.copied_sequences_to_clipboard", new Object[] { Integer.valueOf(seqs.length).toString() })); } @@ -2089,7 +2162,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignment.getSequences()); if (alignPanels != null) { - for (AlignmentPanel ap : ((Vector) alignPanels)) + for (AlignmentPanel ap : alignPanels) { ap.validateAnnotationDimensions(false); } @@ -2236,15 +2309,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - List seqs = new ArrayList(sg.getSize()); - SequenceI seq; - for (int i = 0; i < sg.getSize(); i++) - { - seq = sg.getSequenceAt(i); - seqs.add(seq); - } - - // If the cut affects all sequences, warn, remove highlighted columns + /* + * If the cut affects all sequences, warn, remove highlighted columns + */ if (sg.getSize() == viewport.getAlignment().getHeight()) { int confirm = JOptionPane.showConfirmDialog(this, @@ -2261,15 +2328,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sg.getEndRes() + 1); } - SequenceI[] cut = new SequenceI[seqs.size()]; - for (int i = 0; i < seqs.size(); i++) - { - cut[i] = seqs.get(i); - } + SequenceI[] cut = sg.getSequences() + .toArray(new SequenceI[sg.getSize()]); - /* - * //ADD HISTORY ITEM - */ addHistoryItem(new EditCommand( MessageManager.getString("label.cut_sequences"), Action.CUT, cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, @@ -2511,7 +2572,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addHistoryItem(removeGapCols); statusBar.setText(MessageManager.formatMessage( - "label.removed_empty_columns", new String[] + "label.removed_empty_columns", new Object[] { Integer.valueOf(removeGapCols.getSize()).toString() })); // This is to maintain viewport position on first residue @@ -2582,16 +2643,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getSequences()); } - // else - { - // if (justifySeqs>0) - { - // alignment.justify(justifySeqs!=RIGHT_JUSTIFY); - } - } - - // } - /** * DOCUMENT ME! * @@ -2604,74 +2655,80 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new Finder(); } - @Override - public void newView_actionPerformed(ActionEvent e) - { - newView(true); - } - - /** - * - * @param copyAnnotation - * if true then duplicate all annnotation, groups and settings - * @return new alignment panel, already displayed. - */ - public AlignmentPanel newView(boolean copyAnnotation) - { - return newView(null, copyAnnotation); - } - /** - * - * @param viewTitle - * title of newly created view - * @return new alignment panel, already displayed. + * Create a new view of the current alignment. */ - public AlignmentPanel newView(String viewTitle) + @Override + public void newView_actionPerformed(ActionEvent e) { - return newView(viewTitle, true); + newView(null, true); } /** + * Creates and shows a new view of the current alignment. * * @param viewTitle - * title of newly created view + * title of newly created view; if null, one will be generated * @param copyAnnotation * if true then duplicate all annnotation, groups and settings * @return new alignment panel, already displayed. */ public AlignmentPanel newView(String viewTitle, boolean copyAnnotation) { + /* + * Create a new AlignmentPanel (with its own, new Viewport) + */ AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel, true); if (!copyAnnotation) { - // just remove all the current annotation except for the automatic stuff + /* + * remove all groups and annotation except for the automatic stuff + */ newap.av.getAlignment().deleteAllGroups(); - for (AlignmentAnnotation alan : newap.av.getAlignment() - .getAlignmentAnnotation()) - { - if (!alan.autoCalculated) - { - newap.av.getAlignment().deleteAnnotation(alan); - } - ; - } + newap.av.getAlignment().deleteAllAnnotations(false); } - newap.av.gatherViewsHere = false; + newap.av.setGatherViewsHere(false); if (viewport.viewName == null) { - viewport.viewName = "Original"; + viewport.viewName = MessageManager + .getString("label.view_name_original"); } - newap.av.historyList = viewport.historyList; - newap.av.redoList = viewport.redoList; + /* + * Views share the same edits, undo and redo stacks, mappings. + */ + newap.av.setHistoryList(viewport.getHistoryList()); + newap.av.setRedoList(viewport.getRedoList()); + newap.av.getAlignment().setCodonFrames( + viewport.getAlignment().getCodonFrames()); + + newap.av.viewName = getNewViewName(viewTitle); + addAlignmentPanel(newap, true); + newap.alignmentChanged(); + + if (alignPanels.size() == 2) + { + viewport.setGatherViewsHere(true); + } + tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1); + return newap; + } + + /** + * Make a new name for the view, ensuring it is unique within the current + * sequenceSetId. (This used to be essential for Jalview Project archives, but + * these now use viewId. Unique view names are still desirable for usability.) + * + * @param viewTitle + * @return + */ + protected String getNewViewName(String viewTitle) + { int index = Desktop.getViewCount(viewport.getSequenceSetId()); - // make sure the new view has a unique name - this is essential for Jalview - // 2 archives boolean addFirstIndex = false; if (viewTitle == null || viewTitle.trim().length() == 0) { @@ -2683,45 +2740,55 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, index = 1;// we count from 1 if given a specific name } String newViewName = viewTitle + ((addFirstIndex) ? " " + index : ""); - Vector comps = (Vector) PaintRefresher.components.get(viewport + + List comps = PaintRefresher.components.get(viewport .getSequenceSetId()); - Vector existingNames = new Vector(); - for (int i = 0; i < comps.size(); i++) - { - if (comps.elementAt(i) instanceof AlignmentPanel) - { - AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i); - if (!existingNames.contains(ap.av.viewName)) - { - existingNames.addElement(ap.av.viewName); - } - } - } + + List existingNames = getExistingViewNames(comps); while (existingNames.contains(newViewName)) { newViewName = viewTitle + " " + (++index); } + return newViewName; + } - newap.av.viewName = newViewName; - - addAlignmentPanel(newap, true); - newap.alignmentChanged(); - - if (alignPanels.size() == 2) + /** + * Returns a list of distinct view names found in the given list of + * components. View names are held on the viewport of an AlignmentPanel. + * + * @param comps + * @return + */ + protected List getExistingViewNames(List comps) + { + List existingNames = new ArrayList(); + for (Component comp : comps) { - viewport.gatherViewsHere = true; + if (comp instanceof AlignmentPanel) + { + AlignmentPanel ap = (AlignmentPanel) comp; + if (!existingNames.contains(ap.av.viewName)) + { + existingNames.add(ap.av.viewName); + } + } } - tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1); - return newap; + return existingNames; } + /** + * Explode tabbed views into separate windows. + */ @Override public void expandViews_actionPerformed(ActionEvent e) { Desktop.instance.explodeViews(this); } + /** + * Gather views in separate windows back into a tabbed presentation. + */ @Override public void gatherViews_actionPerformed(ActionEvent e) { @@ -2766,7 +2833,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void centreColumnLabels_actionPerformed(ActionEvent e) { - viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState(); + viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState()); alignPanel.paintAlignment(true); } @@ -2778,6 +2845,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void followHighlight_actionPerformed() { + /* + * Set the 'follow' flag on the Viewport (and scroll to position if now + * true). + */ if (viewport.followHighlight = this.followHighlightMenuItem.getState()) { alignPanel.scrollToPosition( @@ -2811,7 +2882,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, scaleLeft.setVisible(wrapMenuItem.isSelected()); scaleRight.setVisible(wrapMenuItem.isSelected()); viewport.setWrapAlignment(wrapMenuItem.isSelected()); - alignPanel.setWrapAlignment(wrapMenuItem.isSelected()); + alignPanel.updateLayout(); } @Override @@ -2831,7 +2902,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void hideSelSequences_actionPerformed(ActionEvent e) { viewport.hideAllSelectedSeqs(); - alignPanel.paintAlignment(true); +// alignPanel.paintAlignment(true); } /** @@ -3115,11 +3186,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { final boolean setVisible = annotationPanelMenuItem.isSelected(); viewport.setShowAnnotation(setVisible); - alignPanel.setAnnotationVisible(setVisible); this.showAllSeqAnnotations.setEnabled(setVisible); this.hideAllSeqAnnotations.setEnabled(setVisible); this.showAllAlAnnotations.setEnabled(setVisible); this.hideAllAlAnnotations.setEnabled(setVisible); + alignPanel.updateLayout(); } @Override @@ -3130,13 +3201,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, StringBuffer contents = new AlignmentProperties(viewport.getAlignment()) .formatAsHtml(); editPane.setText(MessageManager.formatMessage("label.html_content", - new String[] + new Object[] { contents.toString() })); JInternalFrame frame = new JInternalFrame(); frame.getContentPane().add(new JScrollPane(editPane)); - Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage( - "label.alignment_properties", new String[] + Desktop.addInternalFrame(frame, MessageManager.formatMessage( + "label.alignment_properties", new Object[] { getTitle() }), 500, 400); } @@ -3158,7 +3229,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, OverviewPanel overview = new OverviewPanel(alignPanel); frame.setContentPane(overview); Desktop.addInternalFrame(frame, MessageManager.formatMessage( - "label.overview_params", new String[] + "label.overview_params", new Object[] { this.getTitle() }), frame.getWidth(), frame.getHeight()); frame.pack(); frame.setLayer(JLayeredPane.PALETTE_LAYER); @@ -3361,11 +3432,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background"); - cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); + cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus()); } else { - cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); + cs.setThreshold(0, viewport.isIgnoreGapsConsensus()); } if (viewport.getConservationSelected()) @@ -3428,7 +3499,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, || cs instanceof PIDColourScheme || cs instanceof Blosum62ColourScheme) { - sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); + sg.cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus()); sg.cs.setConsensus(AAFrequency.calculate( sg.getSequences(viewport.getHiddenRepSequences()), @@ -3436,7 +3507,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); + sg.cs.setThreshold(0, viewport.isIgnoreGapsConsensus()); } if (viewport.getConservationSelected()) @@ -3565,8 +3636,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { Component[] menuItems = colourMenu.getMenuComponents(); - int i, iSize = menuItems.length; - for (i = 0; i < iSize; i++) + int iSize = menuItems.length; + for (int i = 0; i < iSize; i++) { if (menuItems[i].getName() != null && menuItems[i].getName().equals("USER_DEFINED")) @@ -3827,7 +3898,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) { - NewTreePanel("AV", "PID", "Average distance tree using PID"); + newTreePanel("AV", "PID", "Average distance tree using PID"); } /** @@ -3839,7 +3910,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void neighbourTreeMenuItem_actionPerformed(ActionEvent e) { - NewTreePanel("NJ", "PID", "Neighbour joining tree using PID"); + newTreePanel("NJ", "PID", "Neighbour joining tree using PID"); } /** @@ -3851,7 +3922,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) { - NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); + newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); } /** @@ -3863,7 +3934,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) { - NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); + newTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); } /** @@ -3876,7 +3947,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param title * DOCUMENT ME! */ - void NewTreePanel(String type, String pwType, String title) + void newTreePanel(String type, String pwType, String title) { TreePanel tp; @@ -3967,7 +4038,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void addSortByOrderMenuItem(String title, final AlignmentOrder order) { - final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new String[]{title})); + final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new Object[]{title})); sort.add(item); item.addActionListener(new java.awt.event.ActionListener() { @@ -4091,7 +4162,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { String treecalcnm = MessageManager.getString("label.tree_calc_" + type.toLowerCase()); - for (final Object pwtype : ResidueProperties.scoreMatrices.keySet()) + for (final String pwtype : ResidueProperties.scoreMatrices.keySet()) { JMenuItem tm = new JMenuItem(); ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype); @@ -4107,7 +4178,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void actionPerformed(ActionEvent e) { - NewTreePanel(type, (String) pwtype, title); + newTreePanel(type, pwtype, title); } }); calculateTree.add(tm); @@ -4117,21 +4188,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } sortByTreeMenu.removeAll(); - Vector comps = (Vector) PaintRefresher.components.get(viewport + List comps = PaintRefresher.components.get(viewport .getSequenceSetId()); - Vector treePanels = new Vector(); - int i, iSize = comps.size(); - for (i = 0; i < iSize; i++) + List treePanels = new ArrayList(); + for (Component comp : comps) { - if (comps.elementAt(i) instanceof TreePanel) + if (comp instanceof TreePanel) { - treePanels.add(comps.elementAt(i)); + treePanels.add((TreePanel) comp); } } - iSize = treePanels.size(); - - if (iSize < 1) + if (treePanels.size() < 1) { sortByTreeMenu.setVisible(false); return; @@ -4139,17 +4207,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sortByTreeMenu.setVisible(true); - for (i = 0; i < treePanels.size(); i++) + for (final TreePanel tp : treePanels) { - final TreePanel tp = (TreePanel) treePanels.elementAt(i); final JMenuItem item = new JMenuItem(tp.getTitle()); - final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree(); item.addActionListener(new java.awt.event.ActionListener() { @Override public void actionPerformed(ActionEvent e) { - tp.sortByTree_actionPerformed(null); + tp.sortByTree_actionPerformed(); addHistoryItem(tp.sortAlignmentIn(alignPanel)); } @@ -4257,7 +4323,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) + protected void loadTreeMenuItem_actionPerformed(ActionEvent e) { // Pick the tree file JalviewFileChooser chooser = new JalviewFileChooser( @@ -4389,7 +4455,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (Exception e) { } - ; } final AlignFrame me = this; buildingMenu = true; @@ -4544,14 +4609,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .debug("Exception during web service menu building process.", e); } - ; } }); } catch (Exception e) { } - ; - buildingMenu = false; } }).start(); @@ -4663,7 +4725,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void actionPerformed(ActionEvent e) { // TODO: new thread for this call with vis-delay - af.showProductsFor(af.viewport.getSequenceSelection(), ds, + af.showProductsFor(af.viewport.getSequenceSelection(), isRegSel, dna, source); } @@ -4682,14 +4744,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return showp; } - protected void showProductsFor(SequenceI[] sel, Alignment ds, - boolean isRegSel, boolean dna, String source) + protected void showProductsFor(final SequenceI[] sel, + final boolean isRegSel, final boolean dna, final String source) { - final boolean fisRegSel = isRegSel; - final boolean fdna = dna; - final String fsrc = source; - final AlignFrame ths = this; - final SequenceI[] fsel = sel; Runnable foo = new Runnable() { @@ -4697,15 +4754,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void run() { final long sttime = System.currentTimeMillis(); - ths.setProgressBar(MessageManager.formatMessage("status.searching_for_sequences_from", new String[]{fsrc}), sttime); + AlignFrame.this.setProgressBar(MessageManager.formatMessage( + "status.searching_for_sequences_from", new Object[] + { source }), sttime); try { - Alignment ds = ths.getViewport().getAlignment().getDataset(); // update - // our local - // dataset - // reference + // update our local dataset reference + Alignment ds = AlignFrame.this.getViewport().getAlignment() + .getDataset(); Alignment prods = CrossRef - .findXrefSequences(fsel, fdna, fsrc, ds); + .findXrefSequences(sel, dna, source, ds); if (prods != null) { SequenceI[] sprods = new SequenceI[prods.getHeight()]; @@ -4721,25 +4779,47 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sprods[s].updatePDBIds(); } Alignment al = new Alignment(sprods); - AlignedCodonFrame[] cf = prods.getCodonFrames(); + Set cf = prods.getCodonFrames(); al.setDataset(ds); - for (int s = 0; cf != null && s < cf.length; s++) + for (AlignedCodonFrame acf : cf) { - al.addCodonFrame(cf[s]); - cf[s] = null; + al.addCodonFrame(acf); } AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); - String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ") - + " for " + ((fisRegSel) ? "selected region of " : "") + String newtitle = "" + ((dna) ? "Proteins" : "Nucleotides") + + " for " + ((isRegSel) ? "selected region of " : "") + getTitle(); - Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH, - DEFAULT_HEIGHT); + naf.setTitle(newtitle); + + // remove this flag once confirmed we want a split view + boolean asSplitFrame = true; + if (asSplitFrame) + { + final Alignment copyAlignment = new Alignment(new Alignment( + AlignFrame.this.viewport.getSequenceSelection())); + AlignFrame copyThis = new AlignFrame(copyAlignment, + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + copyThis.setTitle(AlignFrame.this.getTitle()); + // SplitFrame with dna above, protein below + SplitFrame sf = new SplitFrame(dna ? copyThis : naf, + dna ? naf : copyThis); + naf.setVisible(true); + copyThis.setVisible(true); + String linkedTitle = MessageManager + .getString("label.linked_view_title"); + Desktop.addInternalFrame(sf, linkedTitle, -1, -1); + } + else + { + Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + } } else { System.err.println("No Sequences generated for xRef type " - + fsrc); + + source); } } catch (Exception e) { @@ -4753,7 +4833,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, jalview.bin.Cache.log.error("Error when finding crossreferences", e); } - ths.setProgressBar(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new String[]{fsrc}), + AlignFrame.this.setProgressBar(MessageManager.formatMessage( + "status.finished_searching_for_sequences_from", + new Object[] + { source }), sttime); } @@ -4779,96 +4862,66 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } - @Override - public void showProducts_actionPerformed(ActionEvent e) - { - // ///////////////////////////// - // Collect Data to be translated/transferred - - SequenceI[] selection = viewport.getSequenceSelection(); - AlignmentI al = null; - try - { - al = jalview.analysis.Dna.CdnaTranslate(selection, viewport - .getViewAsVisibleContigs(true), viewport.getGapCharacter(), - viewport.getAlignment().getDataset()); - } catch (Exception ex) - { - al = null; - jalview.bin.Cache.log.debug("Exception during translation.", ex); - } - if (al == null) - { - JOptionPane - .showMessageDialog( - Desktop.desktop, - MessageManager - .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"), - MessageManager.getString("label.translation_failed"), - JOptionPane.WARNING_MESSAGE); - } - else - { - AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); - Desktop.addInternalFrame(af, MessageManager.formatMessage( - "label.translation_of_params", new String[] - { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT); - } - } - + /** + * Construct and display a new frame containing the translation of this + * frame's DNA sequences to their aligned protein (amino acid) equivalents. + */ @Override public void showTranslation_actionPerformed(ActionEvent e) { - // ///////////////////////////// - // Collect Data to be translated/transferred - - SequenceI[] selection = viewport.getSequenceSelection(); - String[] seqstring = viewport.getViewAsString(true); AlignmentI al = null; try { - al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring, - viewport.getViewAsVisibleContigs(true), viewport - .getGapCharacter(), viewport.getAlignment() - .getAlignmentAnnotation(), viewport.getAlignment() - .getWidth(), viewport.getAlignment().getDataset()); + Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true)); + + al = dna.translateCdna(); } catch (Exception ex) { - al = null; jalview.bin.Cache.log.error( "Exception during translation. Please report this !", ex); - JOptionPane - .showMessageDialog( - Desktop.desktop, - MessageManager - .getString("label.error_when_translating_sequences_submit_bug_report"), - MessageManager - .getString("label.implementation_error") - + MessageManager - .getString("translation_failed"), - JOptionPane.ERROR_MESSAGE); + final String msg = MessageManager + .getString("label.error_when_translating_sequences_submit_bug_report"); + final String title = MessageManager + .getString("label.implementation_error") + + MessageManager.getString("translation_failed"); + JOptionPane.showMessageDialog(Desktop.desktop, msg, title, + JOptionPane.ERROR_MESSAGE); return; } - if (al == null) + if (al == null || al.getHeight() == 0) { - JOptionPane - .showMessageDialog( - Desktop.desktop, - MessageManager - .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"), - MessageManager.getString("label.translation_failed"), - JOptionPane.WARNING_MESSAGE); + final String msg = MessageManager + .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"); + final String title = MessageManager + .getString("label.translation_failed"); + JOptionPane.showMessageDialog(Desktop.desktop, msg, title, + JOptionPane.WARNING_MESSAGE); } else { AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); - Desktop.addInternalFrame(af, MessageManager.formatMessage( - "label.translation_of_params", new String[] - { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT); + af.setFileFormat(this.currentFileFormat); + final String newTitle = MessageManager.formatMessage( + "label.translation_of_params", new Object[] + { this.getTitle() }); + af.setTitle(newTitle); + final SequenceI[] seqs = viewport.getSelectionAsNewSequence(); + viewport.openSplitFrame(af, new Alignment(seqs), al.getCodonFrames()); + // Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH, DEFAULT_HEIGHT); } } /** + * Set the file format + * + * @param fileFormat + */ + public void setFileFormat(String fileFormat) + { + this.currentFileFormat = fileFormat; + } + + /** * Try to load a features file onto the alignment. * * @param file @@ -5060,7 +5113,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, MessageManager .formatMessage( "label.automatically_associate_pdb_files_with_sequences_same_name", - new String[] + new Object[] { Integer.valueOf( filesmatched .size()) @@ -5103,7 +5156,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, ""+MessageManager .formatMessage( "label.ignore_unmatched_dropped_files_info", - new String[] + new Object[] { Integer.valueOf( filesnotmatched .size()) @@ -5211,7 +5264,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { jalview.io.JPredFile predictions = new jalview.io.JPredFile( file, protocol); - new JnetAnnotationMaker().add_annotation(predictions, + new JnetAnnotationMaker(); + JnetAnnotationMaker.add_annotation(predictions, viewport.getAlignment(), 0, false); SequenceI repseq = viewport.getAlignment().getSequenceAt(0); viewport.getAlignment().setSeqrep(repseq); @@ -5288,31 +5342,55 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + /** + * Method invoked by the ChangeListener on the tabbed pane, in other words + * when a different tabbed pane is selected by the user or programmatically. + */ @Override public void tabSelectionChanged(int index) { if (index > -1) { - alignPanel = (AlignmentPanel) alignPanels.elementAt(index); + alignPanel = alignPanels.get(index); viewport = alignPanel.av; avc.setViewportAndAlignmentPanel(viewport, alignPanel); setMenusFromViewport(viewport); } + + /* + * 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 + * index to an unchanged value. Guard against setting an invalid index + * before the new view peer tab has been created. + */ + final AlignViewportI peer = viewport.getCodingComplement(); + if (peer != null) + { + AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame; + if (linkedAlignFrame.tabbedPane.getTabCount() > index) + { + linkedAlignFrame.tabbedPane.setSelectedIndex(index); + } + } } + /** + * On right mouse click on view tab, prompt for and set new view name. + */ @Override public void tabbedPane_mousePressed(MouseEvent e) { if (SwingUtilities.isRightMouseButton(e)) { - String reply = JOptionPane.showInternalInputDialog(this, - MessageManager.getString("label.enter_view_name"), - MessageManager.getString("label.enter_view_name"), + String msg = MessageManager.getString("label.enter_view_name"); + String reply = JOptionPane.showInternalInputDialog(this, msg, msg, JOptionPane.QUESTION_MESSAGE); if (reply != null) { viewport.viewName = reply; + // TODO warn if reply is in getExistingViewNames()? tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply); } } @@ -5352,7 +5430,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void showDbRefs_actionPerformed(ActionEvent e) { - viewport.setShowDbRefs(showDbRefsMenuitem.isSelected()); + viewport.setShowDBRefs(showDbRefsMenuitem.isSelected()); } /* @@ -5364,7 +5442,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void showNpFeats_actionPerformed(ActionEvent e) { - viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected()); + viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected()); } /** @@ -5373,7 +5451,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param av */ - public boolean closeView(AlignViewport av) + public boolean closeView(AlignViewportI av) { if (viewport == av) { @@ -5519,7 +5597,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } }); - fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{src.getDbName()}))); + fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{src.getDbName()}))); dfetch.add(fetchr); comp++; } @@ -5530,7 +5608,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // fetch all entry DbSourceProxy src = otherdb.get(0); fetchr = new JMenuItem(MessageManager.formatMessage( - "label.fetch_all_param", new String[] + "label.fetch_all_param", new Object[] { src.getDbSource() })); fetchr.addActionListener(new ActionListener() { @@ -5552,11 +5630,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } }); - fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new String[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()}))); + fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new Object[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()}))); dfetch.add(fetchr); comp++; // and then build the rest of the individual menus - ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new String[]{src.getDbSource()})); + ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new Object[]{src.getDbSource()})); icomp = 0; String imname = null; int i = 0; @@ -5569,7 +5647,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 0, 10) + "..." : dbname; if (imname == null) { - imname = MessageManager.formatMessage("label.from_msname", new String[]{sname}); + imname = MessageManager.formatMessage("label.from_msname", new Object[]{sname}); } fetchr = new JMenuItem(msname); final DbSourceProxy[] dassrc = @@ -5596,7 +5674,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }); fetchr.setToolTipText("" - + MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{dbname})); + + MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{dbname})); ifetch.add(fetchr); ++i; if (++icomp >= mcomp || i == (otherdb.size())) @@ -5802,7 +5880,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame")); } if (tabbedPane != null - & alignPanels.indexOf(alignmentPanel) != tabbedPane + && tabbedPane.getTabCount() > 0 + && alignPanels.indexOf(alignmentPanel) != tabbedPane .getSelectedIndex()) { tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel)); @@ -5850,11 +5929,74 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * - * @return alignment panels in this alignemnt frame + * @return alignment panels in this alignment frame + */ + public List getAlignPanels() + { + return alignPanels == null ? Arrays.asList(alignPanel) + : alignPanels; + } + + /** + * Open a new alignment window, with the cDNA associated with this (protein) + * alignment, aligned as is the protein. + */ + protected void viewAsCdna_actionPerformed() + { + // TODO no longer a menu action - refactor as required + final AlignmentI alignment = getViewport().getAlignment(); + Set mappings = alignment.getCodonFrames(); + if (mappings == null) + { + return; + } + List cdnaSeqs = new ArrayList(); + for (SequenceI aaSeq : alignment.getSequences()) { + for (AlignedCodonFrame acf : mappings) { + SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence()); + if (dnaSeq != null) + { + /* + * There is a cDNA mapping for this protein sequence - add to new + * alignment. It will share the same dataset sequence as other mapped + * cDNA (no new mappings need to be created). + */ + final Sequence newSeq = new Sequence(dnaSeq); + newSeq.setDatasetSequence(dnaSeq); + cdnaSeqs.add(newSeq); + } + } + } + if (cdnaSeqs.size() == 0) + { + // show a warning dialog no mapped cDNA + return; + } + AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs + .size()])); + AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + cdna.alignAs(alignment); + String newtitle = "cDNA " + MessageManager.getString("label.for") + " " + + this.title; + Desktop.addInternalFrame(alignFrame, newtitle, + AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + } + + /** + * Set visibility of dna/protein complement view (available when shown in a + * split frame). + * + * @param show */ - public List getAlignPanels() + @Override + protected void showComplement_actionPerformed(boolean show) { - return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels; + SplitContainerI sf = getSplitViewContainer(); + if (sf != null) { + sf.setComplementVisible(this, show); + } } }