}\r
break;\r
case KeyEvent.VK_V:\r
- if (evt.isControlDown() || evt.isMetaDown())\r
+ if (evt.isControlDown())\r
{\r
- paste(true);\r
+ paste(evt.isShiftDown());\r
}\r
break;\r
case KeyEvent.VK_A:\r
{\r
alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()\r
|| evt.isShiftDown()\r
- || evt.isAltDown()\r
- );\r
+ || evt.isAltDown());\r
}\r
else\r
{\r
alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;\r
alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;\r
}\r
- alignPanel.seqPanel.seqCanvas.repaint();\r
break;\r
\r
case KeyEvent.VK_F:\r
findMenuItem_actionPerformed();\r
}\r
break;\r
+\r
case KeyEvent.VK_H:\r
{\r
boolean toggleSeqs = !evt.isControlDown();\r
else if (!hide)\r
viewport.showAllHiddenColumns();\r
}\r
-\r
- alignPanel.repaint();\r
break;\r
}\r
+\r
case KeyEvent.VK_PAGE_UP:\r
if (viewport.wrapAlignment)\r
alignPanel.scrollUp(true);\r
viewport.startSeq\r
- viewport.endSeq + viewport.startSeq);\r
break;\r
+\r
case KeyEvent.VK_PAGE_DOWN:\r
if (viewport.wrapAlignment)\r
alignPanel.scrollUp(false);\r
viewport.startSeq\r
+ viewport.endSeq - viewport.startSeq);\r
break;\r
+\r
+ case KeyEvent.VK_Z:\r
+ if (evt.isControlDown())\r
+ {\r
+ undoMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_Y:\r
+ if (evt.isControlDown())\r
+ {\r
+ redoMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_L:\r
+ if (evt.isControlDown())\r
+ {\r
+ trimAlignment(true);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_R:\r
+ if (evt.isControlDown())\r
+ {\r
+ trimAlignment(false);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_E:\r
+ if (evt.isControlDown())\r
+ {\r
+ if (evt.isShiftDown())\r
+ this.removeAllGapsMenuItem_actionPerformed();\r
+ else\r
+ removeGappedColumnMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_I:\r
+ if (evt.isControlDown())\r
+ {\r
+ if (evt.isAltDown())\r
+ viewport.invertColumnSelection();\r
+ else\r
+ this.invertSequenceMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_U:\r
+ if (evt.isControlDown())\r
+ {\r
+ this.deleteGroups_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_T:\r
+ if (evt.isControlDown())\r
+ {\r
+ newView();\r
}\r
+ break;\r
+\r
+\r
+ }\r
+ alignPanel.repaint();\r
}\r
public void keyReleased(KeyEvent evt)\r
{}\r
else if(evt.getSource()==wrapMenuItem)\r
wrapMenuItem_actionPerformed();\r
else if(evt.getSource()==scaleAbove)\r
- scaleAbove_actionPerformed();\r
+ viewport.setScaleAboveWrapped(scaleAbove.getState());\r
else if(evt.getSource()==scaleLeft)\r
- scaleLeft_actionPerformed();\r
+ viewport.setScaleLeftWrapped(scaleLeft.getState());\r
else if(evt.getSource()==scaleRight)\r
- scaleRight_actionPerformed();\r
+ viewport.setScaleRightWrapped(scaleRight.getState());\r
else if(evt.getSource()==seqLimits)\r
seqLimits_itemStateChanged();\r
else if(evt.getSource()==viewBoxesMenuItem)\r
- viewBoxesMenuItem_actionPerformed();\r
+ viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
else if(evt.getSource()==viewTextMenuItem)\r
- viewTextMenuItem_actionPerformed();\r
+ viewport.setShowText(viewTextMenuItem.getState());\r
else if(evt.getSource()==renderGapsMenuItem)\r
- renderGapsMenuItem_actionPerformed();\r
+ viewport.setRenderGaps(renderGapsMenuItem.getState());\r
else if(evt.getSource()==annotationPanelMenuItem)\r
- annotationPanelMenuItem_actionPerformed();\r
+ {\r
+ viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
+ alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
+ }\r
else if(evt.getSource()==sequenceFeatures)\r
{\r
viewport.showSequenceFeatures(sequenceFeatures.getState());\r
conservationMenuItem_actionPerformed();\r
else if(evt.getSource()==abovePIDThreshold)\r
abovePIDThreshold_actionPerformed();\r
- else if(evt.getSource()==applyToAllGroups)\r
- applyToAllGroups_actionPerformed();\r
+ else if(evt.getSource()==applyToAllGroups)\r
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
else if(evt.getSource()==autoCalculate)\r
viewport.autocalculateConsensus = autoCalculate.getState();\r
+\r
+ alignPanel.repaint();\r
}\r
public void actionPerformed(ActionEvent evt)\r
{\r
else if(source==findMenuItem)\r
findMenuItem_actionPerformed();\r
else if(source==font)\r
- font_actionPerformed();\r
+ new FontChooser(alignPanel);\r
+ else if (source == newView)\r
+ newView();\r
else if(source==showColumns)\r
{\r
viewport.showAllHiddenColumns(); alignPanel.repaint();\r
viewport.hideAllSelectedSeqs();\r
}\r
else if(source==featureSettings)\r
- featureSettings_actionPerformed();\r
+ new FeatureSettings(alignPanel);\r
else if(source==overviewMenuItem)\r
overviewMenuItem_actionPerformed();\r
else if(source==noColourmenuItem)\r
- noColourmenuItem_actionPerformed();\r
+ changeColour(null);\r
else if(source==clustalColour)\r
- clustalColour_actionPerformed();\r
+ {\r
+ abovePIDThreshold.setState(false);\r
+ changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
+ viewport.alignment.getWidth()));\r
+ }\r
else if(source==zappoColour)\r
- zappoColour_actionPerformed();\r
+ changeColour(new ZappoColourScheme());\r
else if(source==taylorColour)\r
- taylorColour_actionPerformed();\r
+ changeColour(new TaylorColourScheme());\r
else if(source==hydrophobicityColour)\r
- hydrophobicityColour_actionPerformed();\r
+ changeColour(new HydrophobicColourScheme());\r
else if(source==helixColour)\r
- helixColour_actionPerformed();\r
+ changeColour(new HelixColourScheme());\r
else if(source==strandColour)\r
- strandColour_actionPerformed();\r
+ changeColour(new StrandColourScheme());\r
else if(source==turnColour)\r
- turnColour_actionPerformed();\r
+ changeColour(new TurnColourScheme());\r
else if(source==buriedColour)\r
- buriedColour_actionPerformed();\r
+ changeColour(new BuriedColourScheme());\r
else if(source==nucleotideColour)\r
- nucleotideColour_actionPerformed();\r
+ changeColour(new NucleotideColourScheme());\r
else if(source==modifyPID)\r
modifyPID_actionPerformed();\r
else if(source==modifyConservation)\r
modifyConservation_actionPerformed();\r
else if(source==userDefinedColour)\r
- userDefinedColour_actionPerformed();\r
+ new UserDefinedColours(alignPanel, null);\r
else if(source==PIDColour)\r
- PIDColour_actionPerformed();\r
+ changeColour(new PIDColourScheme());\r
else if(source==BLOSUM62Colour)\r
- BLOSUM62Colour_actionPerformed();\r
+ changeColour(new Blosum62ColourScheme());\r
else if(source==annotationColour)\r
new AnnotationColourChooser(viewport, alignPanel);\r
else if(source==sortPairwiseMenuItem)\r
\r
public void closeMenuItem_actionPerformed()\r
{\r
- PaintRefresher.components.remove(viewport.alignment);\r
+ PaintRefresher.RemoveComponent(alignPanel);\r
+ PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);\r
+ PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);\r
+\r
if(PaintRefresher.components.size()==0 && viewport.applet==null)\r
System.exit(0);\r
\r
}\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void undoMenuItem_actionPerformed()\r
{\r
+ if(viewport.historyList.size()<1)\r
+ return;\r
+\r
CommandI command = (CommandI)viewport.historyList.pop();\r
viewport.redoList.push(command);\r
command.undoCommand();\r
\r
- viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
+ AlignViewport originalSource = getOriginatingSource(command);\r
+\r
+ originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
updateEditMenuBar();\r
- viewport.firePropertyChange("alignment", null,\r
- viewport.getAlignment().getSequences());\r
+ originalSource.firePropertyChange("alignment", null,null);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void redoMenuItem_actionPerformed()\r
{\r
+ if(viewport.redoList.size()<1)\r
+ return;\r
+\r
CommandI command = (CommandI) viewport.redoList.pop();\r
viewport.historyList.push(command);\r
command.doCommand();\r
- viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;\r
+\r
+ AlignViewport originalSource = getOriginatingSource(command);\r
+ originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;\r
\r
updateEditMenuBar();\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ originalSource.firePropertyChange("alignment", null, null);\r
}\r
\r
+ AlignViewport getOriginatingSource(CommandI command)\r
+ {\r
+ AlignViewport originalSource = null;\r
+ //For sequence removal and addition, we need to fire\r
+ //the property change event FROM the viewport where the\r
+ //original alignment was altered\r
+ AlignmentI al = null;\r
+ if (command instanceof EditCommand)\r
+ {\r
+ EditCommand editCommand = (EditCommand) command;\r
+ al = editCommand.getAlignment();\r
+ Vector comps = (Vector) PaintRefresher.components\r
+ .get(viewport.getSequenceSetId());\r
+ for (int i = 0; i < comps.size(); i++)\r
+ {\r
+ if (comps.elementAt(i) instanceof AlignmentPanel)\r
+ {\r
+ if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)\r
+ {\r
+ originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ if (originalSource == null)\r
+ {\r
+ //The original view is closed, we must validate\r
+ //the current view against the closed view first\r
+ if (al != null)\r
+ PaintRefresher.validateSequences(al, viewport.alignment);\r
+\r
+ originalSource = viewport;\r
+ }\r
+\r
+\r
+ return originalSource;\r
+ }\r
\r
public void moveSelectedSequences(boolean up)\r
{\r
{\r
try\r
{\r
+\r
if (copiedSequences == null)\r
{\r
return;\r
}\r
else\r
{\r
+ for (int i = 0; i < newSeqs.length; i++)\r
+ {\r
+ viewport.alignment.addSequence(newSeqs[i]);\r
+ }\r
+\r
//!newAlignment\r
addHistoryItem(new EditCommand(\r
"Add sequences",\r
\r
viewport.setEndSeq(viewport.alignment.getHeight());\r
viewport.alignment.getWidth();\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ viewport.firePropertyChange("alignment", null, null);\r
}\r
\r
}\r
new Finder(alignPanel);\r
}\r
\r
- public void font_actionPerformed()\r
+ public void newView()\r
{\r
- new FontChooser(alignPanel);\r
- }\r
+ AlignmentI newal;\r
+ if (viewport.hasHiddenRows)\r
+ newal = new Alignment(viewport.getAlignment().\r
+ getHiddenSequences()\r
+ .getFullAlignment().\r
+ getSequencesArray());\r
+ else\r
+ newal = new Alignment(viewport.alignment.getSequencesArray());\r
+\r
+ AlignFrame newaf = new AlignFrame(newal,\r
+ viewport.applet,\r
+ "",\r
+ false);\r
+\r
+ newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();\r
+ PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());\r
+ PaintRefresher.Register(newaf.alignPanel,\r
+ newaf.alignPanel.av.getSequenceSetId());\r
+\r
+ PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,\r
+ newaf.alignPanel.av.getSequenceSetId());\r
+ PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,\r
+ newaf.alignPanel.av.getSequenceSetId());\r
+\r
+ Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());\r
+ int viewSize = -1;\r
+ for (int i = 0; i < comps.size(); i++)\r
+ {\r
+ if (comps.elementAt(i) instanceof AlignmentPanel)\r
+ viewSize++;\r
+ }\r
+\r
+ String title = new String(this.getTitle());\r
+ if (title.indexOf("(View") > -1)\r
+ title = title.substring(0, title.indexOf("(View"));\r
+\r
+ title+= "(View "+viewSize+")";\r
+\r
+ newaf.setTitle(title.toString());\r
+\r
+\r
+ newaf.viewport.historyList = viewport.historyList;\r
+ newaf.viewport.redoList = viewport.redoList;\r
+\r
+ }\r
\r
\r
public void seqLimits_itemStateChanged()\r
}\r
\r
\r
- protected void scaleAbove_actionPerformed()\r
- {\r
- viewport.setScaleAboveWrapped(scaleAbove.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void scaleLeft_actionPerformed()\r
- {\r
- viewport.setScaleLeftWrapped(scaleLeft.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void scaleRight_actionPerformed()\r
- {\r
- viewport.setScaleRightWrapped(scaleRight.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- public void viewBoxesMenuItem_actionPerformed()\r
- {\r
- viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- public void viewTextMenuItem_actionPerformed()\r
- {\r
- viewport.setShowText(viewTextMenuItem.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void renderGapsMenuItem_actionPerformed()\r
- {\r
- viewport.setRenderGaps(renderGapsMenuItem.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- public void annotationPanelMenuItem_actionPerformed()\r
- {\r
- viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
- alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
- }\r
-\r
- public void featureSettings_actionPerformed()\r
- {\r
- new FeatureSettings(viewport, alignPanel);\r
- }\r
-\r
public void overviewMenuItem_actionPerformed()\r
{\r
if (alignPanel.overviewPanel != null)\r
\r
}\r
\r
- protected void noColourmenuItem_actionPerformed()\r
- {\r
- changeColour(null);\r
- }\r
-\r
- public void clustalColour_actionPerformed()\r
- {\r
- abovePIDThreshold.setState(false);\r
- changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
- viewport.alignment.getWidth()));\r
- }\r
-\r
- public void zappoColour_actionPerformed()\r
- {\r
- changeColour(new ZappoColourScheme());\r
- }\r
-\r
- public void taylorColour_actionPerformed()\r
- {\r
- changeColour(new TaylorColourScheme());\r
- }\r
-\r
- public void hydrophobicityColour_actionPerformed()\r
- {\r
- changeColour(new HydrophobicColourScheme());\r
- }\r
-\r
- public void helixColour_actionPerformed()\r
- {\r
- changeColour(new HelixColourScheme());\r
- }\r
-\r
- public void strandColour_actionPerformed()\r
- {\r
- changeColour(new StrandColourScheme());\r
- }\r
-\r
- public void turnColour_actionPerformed()\r
- {\r
- changeColour(new TurnColourScheme());\r
- }\r
-\r
- public void buriedColour_actionPerformed()\r
- {\r
- changeColour(new BuriedColourScheme());\r
- }\r
-\r
- public void nucleotideColour_actionPerformed()\r
- {\r
- changeColour(new NucleotideColourScheme());\r
- }\r
-\r
- protected void applyToAllGroups_actionPerformed()\r
- {\r
- viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
- }\r
\r
void changeColour(ColourSchemeI cs)\r
{\r
modifyPID_actionPerformed();\r
}\r
\r
- public void userDefinedColour_actionPerformed()\r
- {\r
- new UserDefinedColours(alignPanel, null);\r
- }\r
\r
- public void PIDColour_actionPerformed()\r
- {\r
- changeColour(new PIDColourScheme());\r
- }\r
-\r
- public void BLOSUM62Colour_actionPerformed()\r
- {\r
- changeColour(new Blosum62ColourScheme());\r
- }\r
\r
public void sortPairwiseMenuItem_actionPerformed()\r
{\r
{\r
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
cap.setText("Paste your Newick tree file here.");\r
- cap.treeImport = true;\r
+ cap.setTreeImport();\r
Frame frame = new Frame();\r
frame.add(cap);\r
jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);\r
hideSequences.addActionListener(this);\r
formatMenu.setLabel("Format");\r
selectMenu.setLabel("Select");\r
+ newView.setLabel("New View");\r
+ newView.addActionListener(this);\r
alignFrameMenuBar.add(fileMenu);\r
alignFrameMenuBar.add(editMenu);\r
alignFrameMenuBar.add(selectMenu);\r
editMenu.add(removeGappedColumnMenuItem);\r
editMenu.add(removeAllGapsMenuItem);\r
editMenu.add(removeRedundancyMenuItem);\r
+ viewMenu.add(newView);\r
+ viewMenu.addSeparator();\r
viewMenu.add(menu1);\r
viewMenu.add(menu2);\r
viewMenu.addSeparator();\r
embeddedEdit = new Label("Edit");\r
embeddedSelect = new Label("Select");\r
embeddedView = new Label("View");\r
- embeddedFormat = new Label("Label");\r
+ embeddedFormat = new Label("Format");\r
embeddedColour = new Label("Colour");\r
embeddedFile = new Label("File");\r
embeddedHelp = new Label("Help");\r
\r
\r
PopupMenu filePopup, editPopup, searchPopup,\r
- viewPopup, colourPopup, calculatePopup, helpPopup;\r
+ viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup;\r
MenuItem featureSettings = new MenuItem();\r
CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();\r
MenuItem annotationColour = new MenuItem();\r
MenuItem hideSequences = new MenuItem();\r
Menu formatMenu = new Menu();\r
Menu selectMenu = new Menu();\r
+ MenuItem newView = new MenuItem();\r
\r
public void mousePressed(MouseEvent evt)\r
{\r
}\r
else if (source ==embeddedFormat)\r
{\r
- popup = viewPopup = genPopupMenu(viewPopup, formatMenu);\r
+ popup = formatPopup = genPopupMenu(formatPopup, formatMenu);\r
}\r
else if(source==embeddedColour)\r
{\r
git://source.jalview.org / jalview.git / blobdiff