X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=6a42a651fea4a368c845a34853625f0995977990;hb=e2bf8bf31acb32852fc7ded8706d35f16698b07f;hp=52bd1210f73b309871fc2a7ca03d15fa86d47a65;hpb=38d52319e75f1882278928184066da1033aef332;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 52bd121..6a42a65 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -23,13 +23,16 @@ package jalview.gui; import jalview.analysis.AAFrequency; import jalview.analysis.AlignmentSorter; import jalview.analysis.AlignmentUtils; +import jalview.analysis.AlignmentUtils.MappingResult; 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.analysis.ScoreModelI; import jalview.bin.Cache; import jalview.commands.CommandI; @@ -52,13 +55,14 @@ 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; import jalview.io.FeaturesFile; import jalview.io.FileLoader; import jalview.io.FormatAdapter; -import jalview.io.HTMLOutput; +import jalview.io.HtmlSvgOutput; import jalview.io.IdentifyFile; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; @@ -84,7 +88,9 @@ 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.jws1.Discoverer; import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.jabaws2.Jws2Instance; @@ -106,6 +112,8 @@ 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; @@ -116,9 +124,12 @@ 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; @@ -146,19 +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 @@ -337,7 +349,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, buildSortByAnnotationScoresMenu(); buildTreeMenu(); - if (viewport.wrapAlignment) + if (viewport.getWrapAlignment()) { wrapMenuItem_actionPerformed(null); } @@ -349,6 +361,40 @@ 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) + { + origview.get(0) + .getAlignViewport() + .setViewStyle( + selviews.get(0).getAlignViewport() + .getViewStyle()); + origview.get(0).updateLayout(); + origview.get(0).setSelected(true); + origview.get(0).alignFrame.setMenusForViewport(); + } + } + }); + formatMenu.add(vsel); + } /** @@ -367,6 +413,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, reload.setEnabled(true); } + /** + * Add a KeyListener with handlers for various KeyPressed and KeyReleased + * events + */ void addKeyListener() { addKeyListener(new KeyAdapter() @@ -380,7 +430,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getKeyCode() <= KeyEvent.VK_NUMPAD9)) && Character.isDigit(evt.getKeyChar())) { - alignPanel.seqPanel.numberPressed(evt.getKeyChar()); + alignPanel.getSeqPanel().numberPressed(evt.getKeyChar()); } switch (evt.getKeyCode()) @@ -398,7 +448,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport.cursorMode) { - alignPanel.seqPanel.moveCursor(0, 1); + alignPanel.getSeqPanel().moveCursor(0, 1); } break; @@ -409,7 +459,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport.cursorMode) { - alignPanel.seqPanel.moveCursor(0, -1); + alignPanel.getSeqPanel().moveCursor(0, -1); } break; @@ -417,11 +467,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_LEFT: if (evt.isAltDown() || !viewport.cursorMode) { - slideSequences(false, alignPanel.seqPanel.getKeyboardNo1()); + slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1()); } else { - alignPanel.seqPanel.moveCursor(-1, 0); + alignPanel.getSeqPanel().moveCursor(-1, 0); } break; @@ -429,18 +479,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_RIGHT: if (evt.isAltDown() || !viewport.cursorMode) { - slideSequences(true, alignPanel.seqPanel.getKeyboardNo1()); + slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1()); } else { - alignPanel.seqPanel.moveCursor(1, 0); + alignPanel.getSeqPanel().moveCursor(1, 0); } break; case KeyEvent.VK_SPACE: if (viewport.cursorMode) { - alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown() + alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown() || evt.isShiftDown() || evt.isAltDown()); } break; @@ -464,7 +514,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown() + alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown() || evt.isAltDown()); } @@ -473,19 +523,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_S: if (viewport.cursorMode) { - alignPanel.seqPanel.setCursorRow(); + alignPanel.getSeqPanel().setCursorRow(); } break; case KeyEvent.VK_C: if (viewport.cursorMode && !evt.isControlDown()) { - alignPanel.seqPanel.setCursorColumn(); + alignPanel.getSeqPanel().setCursorColumn(); } break; case KeyEvent.VK_P: if (viewport.cursorMode) { - alignPanel.seqPanel.setCursorPosition(); + alignPanel.getSeqPanel().setCursorPosition(); } break; @@ -493,20 +543,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_COMMA: if (viewport.cursorMode) { - alignPanel.seqPanel.setCursorRowAndColumn(); + alignPanel.getSeqPanel().setCursorRowAndColumn(); } break; case KeyEvent.VK_Q: if (viewport.cursorMode) { - alignPanel.seqPanel.setSelectionAreaAtCursor(true); + alignPanel.getSeqPanel().setSelectionAreaAtCursor(true); } break; case KeyEvent.VK_M: if (viewport.cursorMode) { - alignPanel.seqPanel.setSelectionAreaAtCursor(false); + alignPanel.getSeqPanel().setSelectionAreaAtCursor(false); } break; @@ -517,10 +567,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { (viewport.cursorMode ? "on" : "off") })); if (viewport.cursorMode) { - alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; - alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; + alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes; + alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq; } - alignPanel.seqPanel.seqCanvas.repaint(); + alignPanel.getSeqPanel().seqCanvas.repaint(); break; case KeyEvent.VK_F1: @@ -540,7 +590,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, break; } case KeyEvent.VK_PAGE_UP: - if (viewport.wrapAlignment) + if (viewport.getWrapAlignment()) { alignPanel.scrollUp(true); } @@ -551,7 +601,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } break; case KeyEvent.VK_PAGE_DOWN: - if (viewport.wrapAlignment) + if (viewport.getWrapAlignment()) { alignPanel.scrollUp(false); } @@ -595,7 +645,7 @@ 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()); @@ -638,7 +688,7 @@ 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); } @@ -702,21 +752,102 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void setGUINucleotide(boolean nucleotide) { showTranslation.setVisible(nucleotide); + cdna.setVisible(!nucleotide); conservationMenuItem.setEnabled(!nucleotide); modifyConservation.setEnabled(!nucleotide); showGroupConservation.setEnabled(!nucleotide); rnahelicesColour.setEnabled(nucleotide); purinePyrimidineColour.setEnabled(nucleotide); - // Remember AlignFrame always starts as protein - // if (!nucleotide) - // { - // showTr - // calculateMenu.remove(calculateMenu.getItemCount() - 2); - // } } /** - * set up menus for the currently viewport. This may be called after any + * Builds codon mappings from this (protein) alignment to any compatible + * nucleotide alignments. Mappings are built between sequences with the same + * name and compatible lengths. Also makes the cDNA alignment a + * CommandListener for the protein alignment so that edits are mirrored. + */ + @Override + protected void linkCdna_actionPerformed() + { + int linkedCount = 0; + int alreadyLinkedCount = 0; + final AlignmentI thisAlignment = this.alignPanel.getAlignment(); + + for (AlignFrame af : Desktop.getAlignFrames()) + { + if (af.alignPanel != null) + { + final AlignmentI thatAlignment = af.alignPanel.getAlignment(); + if (thatAlignment.isNucleotide()) + { + MappingResult mapped = AlignmentUtils.mapProteinToCdna( + thisAlignment, thatAlignment); + if (mapped == MappingResult.AlreadyMapped) + { + alreadyLinkedCount++; + } + else if (mapped == MappingResult.Mapped) + { + final StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + ssm.addMappings(thisAlignment.getCodonFrames()); + // enable the next line to enable linked editing + // ssm.addCommandListener(af.getViewport()); + linkedCount++; + } + } + } + } + String msg = ""; + if (linkedCount == 0 && alreadyLinkedCount == 0) + { + msg = MessageManager.getString("label.no_cdna"); + } + else if (linkedCount > 0) + { + msg = MessageManager.formatMessage("label.linked_cdna", linkedCount); + } + else + { + msg = MessageManager.formatMessage("label.cdna_all_linked", + alreadyLinkedCount); + } + setStatus(msg); + } + + /** + * Align any linked cDNA to match the alignment of this (protein) alignment. + * Any mapped sequence regions will be realigned, unmapped sequences are not + * affected. + */ + @Override + protected void alignCdna_actionPerformed() + { + int seqCount = 0; + int alignCount = 0; + final AlignmentI thisAlignment = this.alignPanel.getAlignment(); + for (AlignFrame af : Desktop.getAlignFrames()) + { + if (af.alignPanel != null) + { + final AlignmentI thatAlignment = af.alignPanel.getAlignment(); + if (thatAlignment.isNucleotide()) + { + int seqsAligned = thatAlignment.alignAs(thisAlignment); + seqCount += seqsAligned; + if (seqsAligned > 0) + { + af.alignPanel.alignmentChanged(); + alignCount++; + } + } + } + } + setStatus(MessageManager.formatMessage("label.cdna_aligned", seqCount, + alignCount)); + } + /** + * 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. */ @@ -735,18 +866,18 @@ 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.rightAlignIds); - centreColumnLabelsMenuItem.setState(av.centreColumnLabels); - renderGapsMenuItem.setSelected(av.renderGaps); - wrapMenuItem.setSelected(av.wrapAlignment); - scaleAbove.setVisible(av.wrapAlignment); - scaleLeft.setVisible(av.wrapAlignment); - scaleRight.setVisible(av.wrapAlignment); - annotationPanelMenuItem.setState(av.showAnnotation); + idRightAlign.setSelected(av.isRightAlignIds()); + 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 */ @@ -754,8 +885,8 @@ 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()); @@ -766,11 +897,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, setColourSelected(ColourSchemeProperty.getColourName(av .getGlobalColourScheme())); - showSeqFeatures.setSelected(av.showSequenceFeatures); - hiddenMarkers.setState(av.showHiddenMarkers); + showSeqFeatures.setSelected(av.isShowSequenceFeatures()); + 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); @@ -860,7 +991,7 @@ 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); @@ -897,7 +1028,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public FeatureRenderer getFeatureRenderer() { - return alignPanel.seqPanel.seqCanvas.getFeatureRenderer(); + return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer(); } @Override @@ -1031,7 +1162,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (value == JalviewFileChooser.APPROVE_OPTION) { currentFileFormat = chooser.getSelectedFormat(); - if (currentFileFormat == null) + while (currentFileFormat == null) { JOptionPane .showInternalMessageDialog( @@ -1041,8 +1172,12 @@ 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(); @@ -1074,10 +1209,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .lastIndexOf(java.io.File.separatorChar) + 1); } - success = new Jalview2XML().SaveAlignment(this, file, shortName); + /* + * First save any linked Chimera session. + */ + Desktop.instance.saveChimeraSessions(file); + + success = new Jalview2XML().saveAlignment(this, file, shortName); statusBar.setText(MessageManager.formatMessage( - "label.successfully_saved_to_file_in_format", new String[] + "label.successfully_saved_to_file_in_format", new Object[] { fileName, format })); } @@ -1134,7 +1274,7 @@ 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) { @@ -1147,7 +1287,7 @@ 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); @@ -1209,7 +1349,7 @@ 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) { @@ -1228,16 +1368,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void htmlMenuItem_actionPerformed(ActionEvent e) { - new HTMLOutput(alignPanel, - alignPanel.seqPanel.seqCanvas.getSequenceRenderer(), - alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); + // new HTMLOutput(alignPanel, + // alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(), + // alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()); + new HtmlSvgOutput(null, alignPanel); } @Override public void bioJSMenuItem_actionPerformed(ActionEvent e) { new BioJsHTMLOutput(alignPanel, - alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); + alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()); } public void createImageMap(File file, String image) { @@ -1302,11 +1443,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void exportAnnotations_actionPerformed(ActionEvent e) { - new AnnotationExporter().exportAnnotations(alignPanel, - viewport.showAnnotation ? viewport.getAlignment() - .getAlignmentAnnotation() : null, viewport - .getAlignment().getGroups(), ((Alignment) viewport - .getAlignment()).alignmentProperties); + new AnnotationExporter().exportAnnotations(alignPanel); } @Override @@ -1358,7 +1495,7 @@ 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(); } } @@ -1388,7 +1525,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { int index = tabbedPane.getSelectedIndex(); int closedindex = tabbedPane.indexOfComponent(alignPanel2); - alignPanels.removeElement(alignPanel2); + alignPanels.remove(alignPanel2); // Unnecessary // if (viewport == alignPanel2.av) // { @@ -1415,12 +1552,12 @@ 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 @@ -1429,13 +1566,13 @@ 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 @@ -1449,8 +1586,8 @@ 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 @@ -1468,11 +1605,11 @@ 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; } @@ -1493,15 +1630,15 @@ 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) @@ -1531,16 +1668,16 @@ 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) @@ -1562,9 +1699,9 @@ 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 @@ -1573,16 +1710,16 @@ 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; } } @@ -1621,15 +1758,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.getAlignment().moveSelectedSequencesByOne(sg, viewport.getHiddenRepSequences(), up); alignPanel.paintAlignment(true); + + final AlignViewportI peer = viewport.getCodingComplement(); + if (peer != null) + { + final SequenceGroup selectionGroup = peer.getSelectionGroup(); + if (selectionGroup != null) + { + peer.getAlignment().moveSelectedSequencesByOne( + peer.getSelectionGroup(), peer.getHiddenRepSequences(), up); + ((AlignViewport) peer).getAlignPanel().paintAlignment(true); + } + } } synchronized void slideSequences(boolean right, int size) { - List sg = new Vector(); + List sg = new ArrayList(); if (viewport.cursorMode) { sg.add(viewport.getAlignment().getSequenceAt( - alignPanel.seqPanel.seqCanvas.cursorY)); + alignPanel.getSeqPanel().seqCanvas.cursorY)); } else if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() != viewport @@ -1644,13 +1793,13 @@ 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); } } @@ -1659,7 +1808,7 @@ 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; @@ -1679,7 +1828,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (viewport.cursorMode) { - alignPanel.seqPanel.moveCursor(size, 0); + alignPanel.getSeqPanel().moveCursor(size, 0); } else { @@ -1690,7 +1839,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (viewport.cursorMode) { - alignPanel.seqPanel.moveCursor(-size, 0); + alignPanel.getSeqPanel().moveCursor(-size, 0); } else { @@ -1707,11 +1856,13 @@ 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()); } @@ -1768,20 +1919,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - Vector hiddenColumns = null; + ArrayList hiddenColumns = null; if (viewport.hasHiddenColumns()) { - hiddenColumns = new Vector(); + hiddenColumns = new ArrayList(); int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport .getSelectionGroup().getEndRes(); - for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns() - .size(); i++) + for (int[] region : viewport.getColumnSelection().getHiddenColumns()) { - int[] region = (int[]) viewport.getColumnSelection() - .getHiddenColumns().elementAt(i); if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff) { - hiddenColumns.addElement(new int[] + hiddenColumns.add(new int[] { region[0] - hiddenOffset, region[1] - hiddenOffset }); } } @@ -1790,7 +1938,7 @@ 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() })); } @@ -2088,7 +2236,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignment.getSequences()); if (alignPanels != null) { - for (AlignmentPanel ap : ((Vector) alignPanels)) + for (AlignmentPanel ap : alignPanels) { ap.validateAnnotationDimensions(false); } @@ -2108,19 +2256,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[2] != null) { - Vector hc = (Vector) Desktop.jalviewClipboard[2]; - for (int i = 0; i < hc.size(); i++) + List hc = (List) Desktop.jalviewClipboard[2]; + for (int[] region : hc) { - int[] region = (int[]) hc.elementAt(i); af.viewport.hideColumns(region[0], region[1]); } } // >>>This is a fix for the moment, until a better solution is // found!!<<< - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer() + af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() .transferSettings( - alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); + alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()); // TODO: maintain provenance of an alignment, rather than just make the // title a concatenation of operations. @@ -2168,19 +2315,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[2] != null) { - Vector hc = (Vector) Desktop.jalviewClipboard[2]; - for (int i = 0; i < hc.size(); i++) + List hc = (List) Desktop.jalviewClipboard[2]; + for (int region[] : hc) { - int[] region = (int[]) hc.elementAt(i); af.viewport.hideColumns(region[0], region[1]); } } // >>>This is a fix for the moment, until a better solution is // found!!<<< - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer() + af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() .transferSettings( - alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); + alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()); // TODO: maintain provenance of an alignment, rather than just make the // title a concatenation of operations. @@ -2344,14 +2490,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (viewport.cursorMode) { - alignPanel.seqPanel.keyboardNo1 = null; - alignPanel.seqPanel.keyboardNo2 = null; + alignPanel.getSeqPanel().keyboardNo1 = null; + alignPanel.getSeqPanel().keyboardNo2 = null; } viewport.setSelectionGroup(null); viewport.getColumnSelection().clear(); viewport.setSelectionGroup(null); - alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); - alignPanel.idPanel.idCanvas.searchResults = null; + alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null); + alignPanel.getIdPanel().getIdCanvas().searchResults = null; alignPanel.paintAlignment(true); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); @@ -2512,7 +2658,7 @@ 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 @@ -2583,16 +2729,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getSequences()); } - // else - { - // if (justifySeqs>0) - { - // alignment.justify(justifySeqs!=RIGHT_JUSTIFY); - } - } - - // } - /** * DOCUMENT ME! * @@ -2605,74 +2741,105 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new Finder(); } + /** + * Create a new view of the current alignment. + */ @Override public void newView_actionPerformed(ActionEvent e) { - newView(true); - } + /* + * Note if the current view has a protein/cdna complementary view + */ + AlignViewportI linkedView = this.viewport.getCodingComplement(); - /** - * - * @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); - } + AlignmentPanel newPanel = newView(null, true); - /** - * - * @param viewTitle - * title of newly created view - * @return new alignment panel, already displayed. - */ - public AlignmentPanel newView(String viewTitle) - { - return newView(viewTitle, true); + /* + * If the original view has a protein/cdna linked view, make and link a new + * view there also. + */ + // TODO refactor the hell out of this - move to a controller, lose the casts + // and direct member access, etc + if (linkedView != null) + { + AlignFrame linkedAlignFrame = ((AlignViewport) linkedView) + .getAlignPanel().alignFrame; + AlignmentPanel newLinkedPanel = linkedAlignFrame.newView(null, true); + newLinkedPanel.av.viewName = newPanel.av.viewName; + newPanel.av.setCodingComplement(newLinkedPanel.av); + final StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + ssm.addCommandListener(newPanel.av); + ssm.addCommandListener(newLinkedPanel.av); + + } } /** + * 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; 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.gatherViewsHere = 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) { @@ -2684,45 +2851,55 @@ 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) { @@ -2752,7 +2929,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.setShowJVSuffix(seqLimits.isSelected()); - alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel + alignPanel.getIdPanel().getIdCanvas().setPreferredSize(alignPanel .calculateIdWidth()); alignPanel.paintAlignment(true); } @@ -2760,14 +2937,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void idRightAlign_actionPerformed(ActionEvent e) { - viewport.rightAlignIds = idRightAlign.isSelected(); + viewport.setRightAlignIds(idRightAlign.isSelected()); alignPanel.paintAlignment(true); } @Override public void centreColumnLabels_actionPerformed(ActionEvent e) { - viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState(); + viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState()); alignPanel.paintAlignment(true); } @@ -2782,7 +2959,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport.followHighlight = this.followHighlightMenuItem.getState()) { alignPanel.scrollToPosition( - alignPanel.seqPanel.seqCanvas.searchResults, false); + alignPanel.getSeqPanel().seqCanvas.searchResults, false); } } @@ -2812,7 +2989,7 @@ 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 @@ -3089,7 +3266,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight .isSelected()); - if (viewport.getShowSequenceFeaturesHeight()) + if (viewport.isShowSequenceFeaturesHeight()) { // ensure we're actually displaying features viewport.setShowSequenceFeatures(true); @@ -3116,11 +3293,11 @@ 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 @@ -3131,13 +3308,13 @@ 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); } @@ -3159,7 +3336,7 @@ 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); @@ -3322,6 +3499,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } @Override + public void annotationColumn_actionPerformed(ActionEvent e) + { + new AnnotationColumnChooser(viewport, alignPanel); + } + + @Override public void rnahelicesColour_actionPerformed(ActionEvent e) { new RNAHelicesColourChooser(viewport, alignPanel); @@ -3356,11 +3539,11 @@ 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()) @@ -3423,7 +3606,7 @@ 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()), @@ -3431,7 +3614,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); + sg.cs.setThreshold(0, viewport.isIgnoreGapsConsensus()); } if (viewport.getConservationSelected()) @@ -3560,8 +3743,8 @@ 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")) @@ -3822,7 +4005,7 @@ 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"); } /** @@ -3834,7 +4017,7 @@ 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"); } /** @@ -3846,7 +4029,7 @@ 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"); } /** @@ -3858,7 +4041,7 @@ 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"); } /** @@ -3871,7 +4054,7 @@ 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; @@ -3962,7 +4145,7 @@ 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() { @@ -4086,7 +4269,7 @@ 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); @@ -4102,7 +4285,7 @@ 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); @@ -4112,21 +4295,18 @@ 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; @@ -4134,17 +4314,15 @@ 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)); } @@ -4194,28 +4372,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, else if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() == 1) { - int option = JOptionPane - .showConfirmDialog( -this, - "More than one sequece group selection is required for this Job, click \n'Cancel' to edit your selection or 'Ok' to submit the entire sequence.", - "Invalid selection", - JOptionPane.OK_CANCEL_OPTION); + int option = JOptionPane.showConfirmDialog(this, + MessageManager.getString("warn.oneseq_msainput_selection"), + MessageManager.getString("label.invalid_selection"), + JOptionPane.OK_CANCEL_OPTION); if (option == JOptionPane.OK_OPTION) { msa = viewport.getAlignmentView(false); } - } else { - /* - * Vector seqs = viewport.getAlignment().getSequences(); - * - * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()]; - * - * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI) - * seqs.elementAt(i); } } - */ msa = viewport.getAlignmentView(false); } return msa; @@ -4395,7 +4562,6 @@ this, } catch (Exception e) { } - ; } final AlignFrame me = this; buildingMenu = true; @@ -4550,14 +4716,11 @@ this, .debug("Exception during web service menu building process.", e); } - ; } }); } catch (Exception e) { } - ; - buildingMenu = false; } }).start(); @@ -4703,7 +4866,7 @@ this, public void run() { final long sttime = System.currentTimeMillis(); - ths.setProgressBar(MessageManager.formatMessage("status.searching_for_sequences_from", new String[]{fsrc}), sttime); + ths.setProgressBar(MessageManager.formatMessage("status.searching_for_sequences_from", new Object[]{fsrc}), sttime); try { Alignment ds = ths.getViewport().getAlignment().getDataset(); // update @@ -4727,12 +4890,11 @@ this, 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); @@ -4759,7 +4921,7 @@ this, jalview.bin.Cache.log.error("Error when finding crossreferences", e); } - ths.setProgressBar(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new String[]{fsrc}), + ths.setProgressBar(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new Object[]{fsrc}), sttime); } @@ -4785,92 +4947,49 @@ this, } } - @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 cDNA 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[] + "label.translation_of_params", new Object[] { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT); + // enable next line for linked editing + // viewport.getStructureSelectionManager().addCommandListener(viewport); } } @@ -4889,8 +5008,8 @@ this, try { featuresFile = new FeaturesFile(file, type).parse(viewport - .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas - .getFeatureRenderer().featureColours, false, + .getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas + .getFeatureRenderer().getFeatureColours(), false, jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false)); } catch (Exception ex) { @@ -4899,12 +5018,12 @@ this, if (featuresFile) { - viewport.showSequenceFeatures = true; + viewport.setShowSequenceFeatures(true); showSeqFeatures.setSelected(true); - if (alignPanel.seqPanel.seqCanvas.fr != null) + if (alignPanel.getSeqPanel().seqCanvas.fr != null) { // update the min/max ranges where necessary - alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true); + alignPanel.getSeqPanel().seqCanvas.fr.findAllFeatures(true); } if (featureSettings != null) { @@ -5066,7 +5185,7 @@ this, MessageManager .formatMessage( "label.automatically_associate_pdb_files_with_sequences_same_name", - new String[] + new Object[] { Integer.valueOf( filesmatched .size()) @@ -5109,7 +5228,7 @@ this, ""+MessageManager .formatMessage( "label.ignore_unmatched_dropped_files_info", - new String[] + new Object[] { Integer.valueOf( filesnotmatched .size()) @@ -5156,7 +5275,7 @@ this, // try to parse as annotation. boolean isAnnotation = (format == null || format .equalsIgnoreCase("PFAM")) ? new AnnotationFile() - .readAnnotationFile(viewport.getAlignment(), file, protocol) + .annotateAlignmentView(viewport, file, protocol) : false; if (!isAnnotation) @@ -5217,7 +5336,8 @@ this, { 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); isAnnotation = true; } @@ -5289,31 +5409,38 @@ this, } } + /** + * 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); } } + /** + * 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); } } @@ -5353,7 +5480,7 @@ this, @Override protected void showDbRefs_actionPerformed(ActionEvent e) { - viewport.setShowDbRefs(showDbRefsMenuitem.isSelected()); + viewport.setShowDBRefs(showDbRefsMenuitem.isSelected()); } /* @@ -5365,7 +5492,7 @@ this, @Override protected void showNpFeats_actionPerformed(ActionEvent e) { - viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected()); + viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected()); } /** @@ -5374,7 +5501,7 @@ this, * * @param av */ - public boolean closeView(AlignViewport av) + public boolean closeView(AlignmentViewport av) { if (viewport == av) { @@ -5520,7 +5647,7 @@ this, } }); - 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++; } @@ -5531,7 +5658,7 @@ this, // 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() { @@ -5553,11 +5680,11 @@ this, } }); - 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; @@ -5570,7 +5697,7 @@ this, 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 = @@ -5597,7 +5724,7 @@ this, }); 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())) @@ -5761,6 +5888,16 @@ this, alignPanel.paintAlignment(true); } } + public void clearAlignmentSeqRep() + { + // TODO refactor alignmentseqrep to controller + if (viewport.getAlignment().hasSeqrep()) { + viewport.getAlignment().setSeqrep(null); + PaintRefresher.Refresh(this, viewport.getSequenceSetId()); + alignPanel.updateAnnotation(); + alignPanel.paintAlignment(true); + } + } @Override protected void createGroup_actionPerformed(ActionEvent e) @@ -5793,7 +5930,8 @@ this, 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)); @@ -5838,6 +5976,64 @@ this, .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); alignPanel.paintAlignment(true); } + + /** + * + * @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. + */ + @Override + protected void viewAsCdna_actionPerformed() + { + 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); + + } } class PrintThread extends Thread