boolean embedded)\r
{\r
\r
- jalviewServletURL = applet.getParameter("APPLICATION_URL");\r
+ if (applet != null)\r
+ jalviewServletURL = applet.getParameter("APPLICATION_URL");\r
\r
try{\r
jbInit();\r
}\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
\r
if(toggleSeqs)\r
{\r
- if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())\r
+ if (sg != null && sg.getSize() != viewport.alignment.getHeight())\r
{\r
hide = true;\r
viewport.hideAllSelectedSeqs();\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
loadTree_actionPerformed();\r
else if(source==loadApplication)\r
launchFullApplication();\r
+ else if (source == loadAnnotations)\r
+ loadAnnotations();\r
+ else if (source == outputAnnotations)\r
+ outputAnnotations(true);\r
+ else if(source == outputFeatures)\r
+ outputFeatures(true, "Jalview");\r
else if(source==closeMenuItem)\r
closeMenuItem_actionPerformed();\r
else if(source==copy)\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
"Alignment output - " + e.getActionCommand(),\r
600, 500);\r
cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),\r
- viewport.getAlignment().getSequences(),\r
+ viewport.getAlignment(),\r
viewport.showJVSuffix));\r
}\r
\r
+ public void loadAnnotations()\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
+ cap.setText("Paste your features / annotations file here.");\r
+ cap.setAnnotationImport();\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);\r
+\r
+ }\r
+\r
+ public String outputAnnotations(boolean displayTextbox)\r
+ {\r
+ String annotation = new AnnotationFile().printAnnotations(\r
+ viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,\r
+ viewport.alignment.getGroups());\r
+\r
+ if(displayTextbox)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame,\r
+ "Annotations",\r
+ 600, 500);\r
+ cap.setText(annotation);\r
+ }\r
+\r
+ return annotation;\r
+ }\r
+\r
+ public String outputFeatures(boolean displayTextbox, String format)\r
+ {\r
+ String features;\r
+ if (format.equalsIgnoreCase("Jalview"))\r
+ features = new FeaturesFile().printJalviewFormat(\r
+ viewport.alignment.getSequencesArray(),\r
+ viewport.featuresDisplayed);\r
+ else\r
+ features = new FeaturesFile().printGFFFormat(\r
+ viewport.alignment.getSequencesArray(),\r
+ viewport.featuresDisplayed);\r
+\r
+\r
+ if(displayTextbox)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame,\r
+ "Features",\r
+ 600, 500);\r
+\r
+ cap.setText(features);\r
+ }\r
+\r
+ return features;\r
+ }\r
+\r
void launchFullApplication()\r
{\r
StringBuffer url = new StringBuffer(jalviewServletURL);\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,originalSource.alignment.getSequences());\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, originalSource.alignment.getSequences());\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
for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
{\r
SequenceI seq = viewport.alignment.getSequenceAt(i);\r
- if (!sg.getSequences(false).contains(seq))\r
+ if (!sg.getSequences(null).contains(seq))\r
{\r
continue;\r
}\r
\r
SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
- if (sg.getSequences(false).contains(temp))\r
+ if (sg.getSequences(null).contains(temp))\r
{\r
continue;\r
}\r
for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
{\r
SequenceI seq = viewport.alignment.getSequenceAt(i);\r
- if (!sg.getSequences(true).contains(seq))\r
+ if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))\r
{\r
continue;\r
}\r
\r
SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
- if (sg.getSequences(true).contains(temp))\r
+ if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))\r
{\r
continue;\r
}\r
SequenceGroup sg = viewport.getSelectionGroup();\r
copiedSequences = new StringBuffer();\r
Hashtable orderedSeqs = new Hashtable();\r
- for (int i = 0; i < sg.getSize(false); i++)\r
+ for (int i = 0; i < sg.getSize(); i++)\r
{\r
SequenceI seq = sg.getSequenceAt(i);\r
int index = viewport.alignment.findIndex(seq);\r
copiedHiddenColumns = null;\r
\r
\r
- for (int i = 0; i < sg.getSize(false); i++)\r
+ for (int i = 0; i < sg.getSize(); i++)\r
{\r
SequenceI seq = null;\r
\r
copiedSequences.append(seq.getName() + "\t" +\r
startRes + "\t" +\r
endRes + "\t" +\r
- seq.getSequence(sg.getStartRes(),\r
+ seq.getSequenceAsString(sg.getStartRes(),\r
sg.getEndRes() + 1) + "\n");\r
}\r
\r
{\r
try\r
{\r
+\r
if (copiedSequences == null)\r
{\r
return;\r
}\r
else\r
{\r
- //!newAlignment\r
- addHistoryItem(new EditCommand(\r
- "Add sequences",\r
- EditCommand.PASTE,\r
- newSeqs,\r
- 0,\r
- viewport.alignment.getWidth(),\r
- viewport.alignment)\r
- );\r
-\r
- viewport.setEndSeq(viewport.alignment.getHeight());\r
- viewport.alignment.getWidth();\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ addSequences(newSeqs);\r
}\r
\r
}\r
\r
}\r
\r
+ void addSequences(SequenceI[] seqs)\r
+ {\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ viewport.alignment.addSequence(seqs[i]);\r
+ }\r
+\r
+ //!newAlignment\r
+ addHistoryItem(new EditCommand(\r
+ "Add sequences",\r
+ EditCommand.PASTE,\r
+ seqs,\r
+ 0,\r
+ viewport.alignment.getWidth(),\r
+ viewport.alignment)\r
+ );\r
+\r
+ viewport.setEndSeq(viewport.alignment.getHeight());\r
+ viewport.alignment.getWidth();\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.alignment.getSequences());\r
+\r
+ }\r
+\r
protected void cut_actionPerformed()\r
{\r
copy_actionPerformed();\r
\r
Vector seqs = new Vector();\r
SequenceI seq;\r
- for (int i = 0; i < sg.getSize(false); i++)\r
+ for (int i = 0; i < sg.getSize(); i++)\r
{\r
seq = sg.getSequenceAt(i);\r
seqs.addElement(seq);\r
\r
\r
// If the cut affects all sequences, remove highlighted columns\r
- if (sg.getSize(false) == viewport.alignment.getHeight())\r
+ if (sg.getSize() == viewport.alignment.getHeight())\r
{\r
viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
sg.getEndRes() + 1);\r
\r
SequenceI [] seqs;\r
if(viewport.getSelectionGroup()!=null)\r
- seqs = viewport.getSelectionGroup().getSequencesAsArray(true);\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);\r
else\r
seqs = viewport.alignment.getSequencesArray();\r
\r
SequenceI[] seqs;\r
if (viewport.getSelectionGroup() != null)\r
{\r
- seqs = viewport.getSelectionGroup().getSequencesAsArray(true);\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);\r
start = viewport.getSelectionGroup().getStartRes();\r
end = viewport.getSelectionGroup().getEndRes();\r
}\r
new RemoveGapColCommand("Remove Gapped Columns",\r
seqs,\r
start, end,\r
- viewport.getGapCharacter());\r
+ viewport.alignment);\r
\r
addHistoryItem(removeGapCols);\r
\r
SequenceI[] seqs;\r
if (viewport.getSelectionGroup() != null)\r
{\r
- seqs = viewport.getSelectionGroup().getSequencesAsArray(true);\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);\r
start = viewport.getSelectionGroup().getStartRes();\r
end = viewport.getSelectionGroup().getEndRes();\r
}\r
addHistoryItem(new RemoveGapsCommand("Remove Gaps",\r
seqs,\r
start, end,\r
- viewport.getGapCharacter()));\r
+ viewport.alignment));\r
\r
viewport.setStartRes(seq.findIndex(startRes)-1);\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
+ if(viewport.alignment.getAlignmentAnnotation()!=null)\r
+ {\r
+ for(int i=0; i<viewport.alignment.getAlignmentAnnotation().length; i++)\r
+ {\r
+ if(!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)\r
+ {\r
+ newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);\r
+ }\r
+ }\r
+ }\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
frame.add(overview);\r
// +50 must allow for applet frame window\r
jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
- overview.preferredSize().width,\r
- overview.preferredSize().height + 50);\r
+ overview.getPreferredSize().width,\r
+ overview.getPreferredSize().height + 50);\r
\r
frame.pack();\r
frame.addWindowListener(new WindowAdapter()\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
}\r
if (cs instanceof ClustalxColourScheme)\r
{\r
- sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());\r
+ sg.cs = new ClustalxColourScheme(\r
+ sg.getSequences(viewport.hiddenRepSequences),\r
+ sg.getWidth());\r
}\r
else\r
{\r
|| cs instanceof Blosum62ColourScheme)\r
{\r
sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));\r
+ sg.cs.setConsensus(AAFrequency.calculate(\r
+ sg.getSequences(viewport.hiddenRepSequences), 0, sg.getWidth()));\r
}\r
else\r
sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
{\r
Conservation c = new Conservation("Group",\r
ResidueProperties.propHash, 3,\r
- sg.getSequences(true), 0,\r
+ sg.getSequences(viewport.hiddenRepSequences), 0,\r
viewport.alignment.getWidth() - 1);\r
c.calculate();\r
c.verdict(false, viewport.ConsPercGaps);\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
public void pairwiseAlignmentMenuItem_actionPerformed()\r
{\r
if (viewport.getSelectionGroup()!=null\r
- && viewport.getSelectionGroup().getSize(false) > 1)\r
+ && viewport.getSelectionGroup().getSize() > 1)\r
{\r
Frame frame = new Frame();\r
frame.add(new PairwiseAlignPanel(alignPanel));\r
}\r
\r
if ( (viewport.getSelectionGroup() != null &&\r
- viewport.getSelectionGroup().getSize(false) < 4 &&\r
- viewport.getSelectionGroup().getSize(false) > 0)\r
+ viewport.getSelectionGroup().getSize() < 4 &&\r
+ viewport.getSelectionGroup().getSize() > 0)\r
|| viewport.getAlignment().getHeight() < 4)\r
{\r
return;\r
\r
protected void avTreeBlosumMenuItem_actionPerformed()\r
{\r
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
+ NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");\r
}\r
\r
void NewTreePanel(String type, String pwType, String title)\r
}\r
\r
if ( (viewport.getSelectionGroup() != null &&\r
- viewport.getSelectionGroup().getSize(false) > 1)\r
+ viewport.getSelectionGroup().getSize() > 1)\r
|| (viewport.getSelectionGroup() == null\r
&& viewport.alignment.getHeight() > 1))\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
protected MenuBar alignFrameMenuBar = new MenuBar();\r
protected Menu fileMenu = new Menu("File");\r
protected MenuItem loadApplication = new MenuItem("View in Full Application");\r
- protected MenuItem loadTree = new MenuItem("Load Associated Tree");\r
+ protected MenuItem loadTree = new MenuItem("Load Associated Tree ...");\r
+ protected MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");\r
+ protected MenuItem outputFeatures = new MenuItem("Export Features ...");\r
+ protected MenuItem outputAnnotations = new MenuItem("Export Annotations ...");\r
+\r
protected MenuItem closeMenuItem = new MenuItem("Close");\r
protected Menu editMenu = new Menu("Edit");\r
protected Menu viewMenu = new Menu("View");\r
loadApplication.addActionListener(this);\r
\r
loadTree.addActionListener(this);\r
+ loadAnnotations.addActionListener(this);\r
+ outputFeatures.addActionListener(this);\r
+ outputAnnotations.addActionListener(this);\r
selectAllSequenceMenuItem.addActionListener(this);\r
deselectAllSequenceMenuItem.addActionListener(this);\r
invertSequenceMenuItem.addActionListener(this);\r
averageDistanceTreeMenuItem.addActionListener(this);\r
neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
neighbourTreeMenuItem.addActionListener(this);\r
- alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
statusBar.setBackground(Color.white);\r
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
statusBar.setText("Status bar");\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
alignFrameMenuBar.add(colourMenu);\r
alignFrameMenuBar.add(calculateMenu);\r
alignFrameMenuBar.add(helpMenu);\r
+\r
fileMenu.add(inputText);\r
+ fileMenu.add(loadTree);\r
+ fileMenu.add(loadAnnotations);\r
+\r
+ fileMenu.addSeparator();\r
fileMenu.add(outputTextboxMenu);\r
+ fileMenu.add(outputFeatures);\r
+ fileMenu.add(outputAnnotations);\r
+\r
if(jalviewServletURL!=null)\r
fileMenu.add(loadApplication);\r
+\r
fileMenu.addSeparator();\r
- fileMenu.add(loadTree);\r
fileMenu.add(closeMenuItem);\r
+\r
editMenu.add(undoMenuItem);\r
editMenu.add(redoMenuItem);\r
editMenu.add(cut);\r
editMenu.add(copy);\r
editMenu.add(pasteMenu);\r
editMenu.add(delete);\r
- editMenu.addSeparator();\r
+ editMenu.addSeparator();\r
editMenu.add(remove2LeftMenuItem);\r
editMenu.add(remove2RightMenuItem);\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
embeddedCalculate.addMouseListener(this);\r
embeddedHelp.addMouseListener(this);\r
\r
- // setVisible(false);\r
fileMenu.remove(closeMenuItem);\r
fileMenu.remove(3); // Seperator\r
\r
viewport.applet.setLayout(new BorderLayout());\r
viewport.applet.add(embeddedMenu, BorderLayout.NORTH);\r
viewport.applet.add(statusBar, BorderLayout.SOUTH);\r
- // viewport.applet.validate();\r
\r
- alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height\r
+ alignPanel.setSize(viewport.applet.getSize().width, viewport.applet.getSize().height\r
- embeddedMenu.HEIGHT - statusBar.HEIGHT);\r
\r
viewport.applet.add(alignPanel, BorderLayout.CENTER);\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