import java.net.URL;\r
\r
\r
-public class AlignFrame extends Frame\r
+public class AlignFrame extends Frame implements ActionListener,\r
+ ItemListener, KeyListener, MouseListener\r
{\r
- final AlignmentPanel alignPanel;\r
- public final AlignViewport viewport;\r
+ public AlignmentPanel alignPanel;\r
+ public AlignViewport viewport;\r
int NEW_WINDOW_WIDTH = 700;\r
int NEW_WINDOW_HEIGHT = 500;\r
jalview.bin.JalviewLite applet;\r
\r
\r
- public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title)\r
+ public AlignFrame(AlignmentI al,\r
+ jalview.bin.JalviewLite applet,\r
+ String title,\r
+ boolean embedded)\r
{\r
try{\r
jbInit();\r
{\r
ex.printStackTrace();\r
}\r
+\r
this.applet = applet;\r
viewport = new AlignViewport(al, applet);\r
alignPanel = new AlignmentPanel(this, viewport);\r
- add(alignPanel);\r
- alignPanel.validate();\r
\r
- if(applet!=null)\r
- {\r
- String treeFile = applet.getParameter("treeFile");\r
- if (treeFile != null)\r
- {\r
- try\r
- {\r
- jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.\r
- getCodeBase() + treeFile, "URL");\r
- fin.parse();\r
+ annotationPanelMenuItem.setState(viewport.showAnnotation);\r
\r
- if (fin.getTree() != null)\r
- {\r
- TreePanel tp = null;\r
- tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
- fin, "FromFile", applet.getCodeBase() + treeFile);\r
- jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
- addTreeMenuItem(tp, treeFile);\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
+ seqLimits.setState(viewport.showJVSuffix);\r
\r
+ if(applet!=null)\r
+ {\r
String param = applet.getParameter("sortBy");\r
if (param != null)\r
{\r
if (param.equalsIgnoreCase("Id"))\r
- sortIDMenuItem_actionPerformed(null);\r
+ sortIDMenuItem_actionPerformed();\r
else if (param.equalsIgnoreCase("Pairwise Identity"))\r
- sortPairwiseMenuItem_actionPerformed(null);\r
+ sortPairwiseMenuItem_actionPerformed();\r
}\r
\r
param = applet.getParameter("wrap");\r
if (param.equalsIgnoreCase("true"))\r
{\r
wrapMenuItem.setState(true);\r
- wrapMenuItem_actionPerformed(null);\r
+ wrapMenuItem_actionPerformed();\r
}\r
}\r
\r
\r
}\r
\r
- this.addWindowListener(new WindowAdapter()\r
- {\r
- public void windowClosing(WindowEvent e)\r
- {\r
- closeMenuItem_actionPerformed(null);\r
- }\r
- });\r
+ //Some JVMS send keyevents to Top frame or lowest panel,\r
+ //Havent worked out why yet. So add to both this frame and seqCanvas for now\r
+ this.addKeyListener(this);\r
+ alignPanel.seqPanel.seqCanvas.addKeyListener(this);\r
+ alignPanel.idPanel.idCanvas.addKeyListener(this);\r
\r
viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
{\r
}\r
});\r
\r
- jalview.bin.JalviewLite.addFrame(this, title,\r
- NEW_WINDOW_WIDTH,\r
- NEW_WINDOW_HEIGHT);\r
-\r
\r
+ if(embedded)\r
+ {\r
+ setEmbedded();\r
+ }\r
+ else\r
+ {\r
+ add(alignPanel, BorderLayout.CENTER);\r
+ jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH,\r
+ NEW_WINDOW_HEIGHT);\r
+ }\r
+ alignPanel.validate();\r
+ alignPanel.repaint();\r
}\r
-\r
public AlignViewport getAlignViewport()\r
{\r
return viewport;\r
* @param String DOCUMENT ME!\r
*/\r
\r
- public void parseFeaturesFile(String file)\r
+ public void parseFeaturesFile(String file, String type)\r
{\r
- try\r
+ Hashtable featureLinks = new Hashtable();\r
+ boolean featuresFile = false;\r
+ try{\r
+ featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment,\r
+ alignPanel.seqPanel.seqCanvas.\r
+ getFeatureRenderer().featureColours,\r
+ featureLinks,\r
+ true);\r
+ }\r
+ catch(Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ if(featuresFile)\r
{\r
- URL url = new URL(file);\r
+ if(featureLinks.size()>0)\r
+ alignPanel.seqPanel.seqCanvas\r
+ .getFeatureRenderer().featureLinks = featureLinks;\r
+ viewport.showSequenceFeatures = true;\r
+ sequenceFeatures.setState(true);\r
+ alignPanel.repaint();\r
+ }\r
\r
- BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));\r
- SequenceI seq = null;\r
- String line, type, desc, token;\r
+ }\r
\r
- int index, start, end;\r
- StringTokenizer st;\r
- SequenceFeature sf;\r
- FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
- int lineNo = 0;\r
- while ( (line = in.readLine()) != null)\r
- {\r
- lineNo++;\r
- st = new StringTokenizer(line, "\t");\r
- if (st.countTokens() == 2)\r
+\r
+ public void keyPressed(KeyEvent evt)\r
+ {\r
+ if (viewport.cursorMode\r
+ && evt.getKeyCode() >= KeyEvent.VK_0\r
+ && evt.getKeyCode() <= KeyEvent.VK_9)\r
+ {\r
+ alignPanel.seqPanel.numberPressed(evt.getKeyChar());\r
+ }\r
+\r
+ switch (evt.getKeyCode())\r
+ {\r
+ case 27: // escape key\r
+ deselectAllSequenceMenuItem_actionPerformed();\r
+ break;\r
+ case KeyEvent.VK_X:\r
+ if (evt.isControlDown() || evt.isMetaDown())\r
{\r
- type = st.nextToken();\r
- UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
- fr.setColour(type, ucs.findColour("A"));\r
- continue;\r
+ cut_actionPerformed();\r
}\r
-\r
- while (st.hasMoreElements())\r
+ break;\r
+ case KeyEvent.VK_C:\r
+ if (viewport.cursorMode && !evt.isControlDown())\r
{\r
- desc = st.nextToken();\r
- token = st.nextToken();\r
- if (!token.equals("ID_NOT_SPECIFIED"))\r
- {\r
- index = viewport.alignment.findIndex(viewport.alignment.findName(\r
- token));\r
- st.nextToken();\r
- }\r
- else\r
- {\r
- index = Integer.parseInt(st.nextToken());\r
- }\r
+ alignPanel.seqPanel.setCursorColumn();\r
+ }\r
+ if (evt.isControlDown() || evt.isMetaDown())\r
+ {\r
+ copy_actionPerformed();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_V:\r
+ if (evt.isControlDown() || evt.isMetaDown())\r
+ {\r
+ paste(true);\r
+ }\r
+ break;\r
+ case KeyEvent.VK_A:\r
+ if (evt.isControlDown() || evt.isMetaDown())\r
+ {\r
+ selectAllSequenceMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_DOWN:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.moveCursor(0,1);\r
+ }\r
+ else\r
+ moveSelectedSequences(false);\r
+ break;\r
\r
- start = Integer.parseInt(st.nextToken());\r
- end = Integer.parseInt(st.nextToken());\r
+ case KeyEvent.VK_UP:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.moveCursor(0,-1);\r
+ }\r
+ else\r
+ moveSelectedSequences(true);\r
+ break;\r
\r
- seq = viewport.alignment.getSequenceAt(index);\r
- start = seq.findIndex(start) - 1;\r
- end = seq.findIndex(end) - 1;\r
+ case KeyEvent.VK_LEFT:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.moveCursor(-1,0);\r
+ }\r
+ break;\r
\r
- type = st.nextToken();\r
+ case KeyEvent.VK_RIGHT:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.moveCursor(1,0);\r
+ }\r
+ break;\r
+ case KeyEvent.VK_SPACE:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown());\r
+ }\r
+ break;\r
\r
- if(fr.getColour(type)==null)\r
- {\r
- // Probably the old style groups file\r
- UserColourScheme ucs = new UserColourScheme(type);\r
- fr.setColour(type, ucs.findColour("A"));\r
- }\r
+ case KeyEvent.VK_DELETE:\r
+ case KeyEvent.VK_BACK_SPACE:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown());\r
+ }\r
+ else\r
+ {\r
+ cut_actionPerformed();\r
+ alignPanel.seqPanel.seqCanvas.repaint();\r
+ }\r
+ break;\r
\r
- sf = new SequenceFeature(type, desc, "", start, end);\r
+ case KeyEvent.VK_S:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setCursorRow();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_P:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setCursorPosition();\r
+ }\r
+ break;\r
\r
- seq.addSequenceFeature(sf);\r
+ case KeyEvent.VK_ENTER:\r
+ case KeyEvent.VK_COMMA:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setCursorRowAndColumn();\r
}\r
- }\r
+ break;\r
\r
- viewport.showSequenceFeatures = true;\r
+ case KeyEvent.VK_Q:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setSelectionAreaAtCursor(true);\r
+ }\r
+ break;\r
+ case KeyEvent.VK_M:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setSelectionAreaAtCursor(false);\r
+ }\r
+ break;\r
\r
- alignPanel.repaint();\r
+ case KeyEvent.VK_F2:\r
+ viewport.cursorMode = ! viewport.cursorMode;\r
+ statusBar.setText("Keyboard editing mode is "+\r
+ (viewport.cursorMode ? "on" : "off"));\r
+ if(viewport.cursorMode)\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
- }\r
- catch (Exception ex)\r
- {\r
- System.out.println("Error parsing groups file: " + ex);\r
+ case KeyEvent.VK_F:\r
+ if (evt.isControlDown())\r
+ {\r
+ findMenuItem_actionPerformed();\r
+ }\r
+ break;\r
}\r
}\r
-\r
-\r
- public void inputText_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);\r
+ public void keyReleased(KeyEvent evt)\r
+ {}\r
+ public void keyTyped(KeyEvent evt)\r
+ {}\r
+\r
+public void itemStateChanged(ItemEvent evt)\r
+ {\r
+ if(evt.getSource()==colourTextMenuItem)\r
+ colourTextMenuItem_actionPerformed();\r
+ else if(evt.getSource()==wrapMenuItem)\r
+ wrapMenuItem_actionPerformed();\r
+ else if(evt.getSource()==scaleAbove)\r
+ scaleAbove_actionPerformed();\r
+ else if(evt.getSource()==scaleLeft)\r
+ scaleLeft_actionPerformed();\r
+ else if(evt.getSource()==scaleRight)\r
+ scaleRight_actionPerformed();\r
+ else if(evt.getSource()==seqLimits)\r
+ seqLimits_itemStateChanged();\r
+ else if(evt.getSource()==viewBoxesMenuItem)\r
+ viewBoxesMenuItem_actionPerformed();\r
+ else if(evt.getSource()==viewTextMenuItem)\r
+ viewTextMenuItem_actionPerformed();\r
+ else if(evt.getSource()==renderGapsMenuItem)\r
+ renderGapsMenuItem_actionPerformed();\r
+ else if(evt.getSource()==annotationPanelMenuItem)\r
+ annotationPanelMenuItem_actionPerformed();\r
+ else if(evt.getSource()==sequenceFeatures)\r
+ {\r
+ viewport.showSequenceFeatures(sequenceFeatures.getState());\r
+ alignPanel.seqPanel.seqCanvas.repaint();\r
+ }\r
+ else if(evt.getSource()==conservationMenuItem)\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()==autoCalculate)\r
+ viewport.autocalculateConsensus = autoCalculate.getState();\r
+ }\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ if(evt.getSource()==inputText)\r
+ inputText_actionPerformed();\r
+ else if(evt.getSource()==loadTree)\r
+ loadTree_actionPerformed();\r
+ else if(evt.getSource()==loadApplication)\r
+ launchFullApplication();\r
+ else if(evt.getSource()==closeMenuItem)\r
+ closeMenuItem_actionPerformed();\r
+ else if(evt.getSource()==copy)\r
+ copy_actionPerformed();\r
+ else if(evt.getSource()==undoMenuItem)\r
+ undoMenuItem_actionPerformed();\r
+ else if(evt.getSource()==redoMenuItem)\r
+ redoMenuItem_actionPerformed();\r
+ else if(evt.getSource()==inputText)\r
+ inputText_actionPerformed();\r
+ else if(evt.getSource()==closeMenuItem)\r
+ closeMenuItem_actionPerformed();\r
+ else if(evt.getSource()==undoMenuItem)\r
+ undoMenuItem_actionPerformed();\r
+ else if(evt.getSource()==redoMenuItem)\r
+ redoMenuItem_actionPerformed();\r
+ else if(evt.getSource()==copy)\r
+ copy_actionPerformed();\r
+ else if(evt.getSource()==pasteNew)\r
+ pasteNew_actionPerformed();\r
+ else if(evt.getSource()==pasteThis)\r
+ pasteThis_actionPerformed();\r
+ else if(evt.getSource()==cut)\r
+ cut_actionPerformed();\r
+ else if(evt.getSource()==delete)\r
+ delete_actionPerformed();\r
+ else if(evt.getSource()==deleteGroups)\r
+ deleteGroups_actionPerformed();\r
+ else if(evt.getSource()==selectAllSequenceMenuItem)\r
+ selectAllSequenceMenuItem_actionPerformed();\r
+ else if(evt.getSource()==deselectAllSequenceMenuItem)\r
+ deselectAllSequenceMenuItem_actionPerformed();\r
+ else if(evt.getSource()==invertSequenceMenuItem)\r
+ invertSequenceMenuItem_actionPerformed();\r
+ else if(evt.getSource()==remove2LeftMenuItem)\r
+ remove2LeftMenuItem_actionPerformed();\r
+ else if(evt.getSource()==remove2RightMenuItem)\r
+ remove2RightMenuItem_actionPerformed();\r
+ else if(evt.getSource()==removeGappedColumnMenuItem)\r
+ removeGappedColumnMenuItem_actionPerformed();\r
+ else if(evt.getSource()==removeAllGapsMenuItem)\r
+ removeAllGapsMenuItem_actionPerformed();\r
+ else if(evt.getSource()==findMenuItem)\r
+ findMenuItem_actionPerformed();\r
+ else if(evt.getSource()==font)\r
+ font_actionPerformed();\r
+ else if(evt.getSource()==featureSettings)\r
+ featureSettings_actionPerformed();\r
+ else if(evt.getSource()==overviewMenuItem)\r
+ overviewMenuItem_actionPerformed();\r
+ else if(evt.getSource()==noColourmenuItem)\r
+ noColourmenuItem_actionPerformed();\r
+ else if(evt.getSource()==clustalColour)\r
+ clustalColour_actionPerformed();\r
+ else if(evt.getSource()==zappoColour)\r
+ zappoColour_actionPerformed();\r
+ else if(evt.getSource()==taylorColour)\r
+ taylorColour_actionPerformed();\r
+ else if(evt.getSource()==hydrophobicityColour)\r
+ hydrophobicityColour_actionPerformed();\r
+ else if(evt.getSource()==helixColour)\r
+ helixColour_actionPerformed();\r
+ else if(evt.getSource()==strandColour)\r
+ strandColour_actionPerformed();\r
+ else if(evt.getSource()==turnColour)\r
+ turnColour_actionPerformed();\r
+ else if(evt.getSource()==buriedColour)\r
+ buriedColour_actionPerformed();\r
+ else if(evt.getSource()==nucleotideColour)\r
+ nucleotideColour_actionPerformed();\r
+ else if(evt.getSource()==modifyPID)\r
+ modifyPID_actionPerformed();\r
+ else if(evt.getSource()==modifyConservation)\r
+ modifyConservation_actionPerformed();\r
+ else if(evt.getSource()==userDefinedColour)\r
+ userDefinedColour_actionPerformed();\r
+ else if(evt.getSource()==PIDColour)\r
+ PIDColour_actionPerformed();\r
+ else if(evt.getSource()==BLOSUM62Colour)\r
+ BLOSUM62Colour_actionPerformed();\r
+ else if(evt.getSource()==annotationColour)\r
+ new AnnotationColourChooser(viewport, alignPanel);\r
+ else if(evt.getSource()==sortPairwiseMenuItem)\r
+ sortPairwiseMenuItem_actionPerformed();\r
+ else if(evt.getSource()==sortIDMenuItem)\r
+ sortIDMenuItem_actionPerformed();\r
+ else if(evt.getSource()==sortGroupMenuItem)\r
+ sortGroupMenuItem_actionPerformed();\r
+ else if(evt.getSource()==removeRedundancyMenuItem)\r
+ removeRedundancyMenuItem_actionPerformed();\r
+ else if(evt.getSource()==pairwiseAlignmentMenuItem)\r
+ pairwiseAlignmentMenuItem_actionPerformed();\r
+ else if(evt.getSource()==PCAMenuItem)\r
+ PCAMenuItem_actionPerformed();\r
+ else if(evt.getSource()==averageDistanceTreeMenuItem)\r
+ averageDistanceTreeMenuItem_actionPerformed();\r
+ else if(evt.getSource()==neighbourTreeMenuItem)\r
+ neighbourTreeMenuItem_actionPerformed();\r
+ else if(evt.getSource()==njTreeBlosumMenuItem)\r
+ njTreeBlosumMenuItem_actionPerformed();\r
+ else if(evt.getSource()==avDistanceTreeBlosumMenuItem)\r
+ avTreeBlosumMenuItem_actionPerformed();\r
+ else if(evt.getSource()==documentation)\r
+ documentation_actionPerformed();\r
+ else if(evt.getSource()==about)\r
+ about_actionPerformed();\r
+\r
+ }\r
+\r
+ public void inputText_actionPerformed()\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
Frame frame = new Frame();\r
frame.add(cap);\r
jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
\r
protected void outputText_actionPerformed(ActionEvent e)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
Frame frame = new Frame();\r
frame.add(cap);\r
jalview.bin.JalviewLite.addFrame(frame,\r
viewport.showJVSuffix));\r
}\r
\r
- public void closeMenuItem_actionPerformed(ActionEvent e)\r
+ void launchFullApplication()\r
+ {\r
+ StringBuffer url = new StringBuffer("http://bug.compbio.dundee.ac.uk:8080/Jalview/jalview?");\r
+\r
+ url.append("open="+\r
+ appendProtocol( applet.getParameter("file") ) );\r
+\r
+ if(applet.getParameter("features")!=null)\r
+ {\r
+ url.append( "&features=" );\r
+ url.append( appendProtocol( applet.getParameter("features") ) );\r
+ }\r
+\r
+ if(applet.getParameter("defaultColour")!=null)\r
+ {\r
+ url.append("&colour=" +\r
+ removeWhiteSpace(applet.getParameter("defaultColour"))\r
+ );\r
+ }\r
+\r
+ if(applet.getParameter("userDefinedColour")!=null)\r
+ {\r
+ url.append( "&colour=" +\r
+ removeWhiteSpace( applet.getParameter("userDefinedColour") )\r
+ );\r
+ }\r
+\r
+ showURL(url.toString(), "FULL_APP");\r
+ }\r
+\r
+\r
+ String removeWhiteSpace(String colour)\r
+ {\r
+ StringBuffer sb = new StringBuffer();\r
+ for (int i = 0; i < colour.length(); i++)\r
+ {\r
+ if (Character.isWhitespace(colour.charAt(i)))\r
+ sb.append("%20");\r
+ else\r
+ sb.append(colour.charAt(i));\r
+ }\r
+\r
+ return sb.toString();\r
+ }\r
+\r
+\r
+ String appendProtocol(String url)\r
+ {\r
+ try{\r
+ new URL(url);\r
+ }catch(java.net.MalformedURLException ex)\r
+ {\r
+ url = applet.getCodeBase()+url;\r
+ }\r
+ return url;\r
+ }\r
+\r
+ public void closeMenuItem_actionPerformed()\r
{\r
PaintRefresher.components.remove(viewport.alignment);\r
if(PaintRefresher.components.size()==0 && applet==null)\r
System.exit(0);\r
+\r
+ this.dispose();\r
}\r
\r
Stack historyList = new Stack();\r
updateEditMenuBar();\r
}\r
\r
- protected void undoMenuItem_actionPerformed(ActionEvent e)\r
+ protected void undoMenuItem_actionPerformed()\r
{\r
HistoryItem hi = (HistoryItem) historyList.pop();\r
redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
- protected void redoMenuItem_actionPerformed(ActionEvent e)\r
+ protected void redoMenuItem_actionPerformed()\r
{\r
HistoryItem hi = (HistoryItem) redoList.pop();\r
restoreHistoryItem(hi);\r
// used by undo and redo\r
void restoreHistoryItem(HistoryItem hi)\r
{\r
- if (hi.getType() == HistoryItem.SORT)\r
- {\r
- for (int i = 0; i < hi.getSequences().size(); i++)\r
- {\r
- viewport.alignment.getSequences().setElementAt(hi.getSequences().\r
- elementAt(i), i);\r
- }\r
- }\r
- else\r
- {\r
- for (int i = 0; i < hi.getSequences().size(); i++)\r
- {\r
- SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
- if (restore.getLength() == 0)\r
- {\r
- // log.System.out.println(hi.getHidden().elementAt(i));\r
- restore.setSequence(hi.getHidden().elementAt(i).toString());\r
- viewport.alignment.getSequences().insertElementAt(\r
- restore,\r
- hi.getAlignIndex(i));\r
- }\r
- else\r
- {\r
- restore.setSequence(hi.getHidden().elementAt(i).toString());\r
- }\r
- }\r
- if (hi.getType() == HistoryItem.PASTE)\r
- {\r
- for (int i = viewport.alignment.getHeight() - 1;\r
- i > hi.getSequences().size() - 1; i--)\r
- {\r
- viewport.alignment.deleteSequence(i);\r
- }\r
- }\r
- }\r
+ hi.restore();\r
\r
updateEditMenuBar();\r
\r
for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
{\r
SequenceI seq = viewport.alignment.getSequenceAt(i);\r
- if (!sg.sequences.contains(seq))\r
+ if (!sg.getSequences(false).contains(seq))\r
{\r
continue;\r
}\r
\r
SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
- if (sg.sequences.contains(temp))\r
+ if (sg.getSequences(false).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.sequences.contains(seq))\r
+ if (!sg.getSequences(true).contains(seq))\r
{\r
continue;\r
}\r
\r
SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
- if (sg.sequences.contains(temp))\r
+ if (sg.getSequences(true).contains(temp))\r
{\r
continue;\r
}\r
}\r
\r
StringBuffer copiedSequences;\r
- protected void copy_actionPerformed(ActionEvent e)\r
+ protected void copy_actionPerformed()\r
{\r
if (viewport.getSelectionGroup() == null)\r
{\r
SequenceGroup sg = viewport.getSelectionGroup();\r
copiedSequences = new StringBuffer();\r
Hashtable orderedSeqs = new Hashtable();\r
- for (int i = 0; i < sg.getSize(); i++)\r
+ for (int i = 0; i < sg.getSize(false); i++)\r
{\r
SequenceI seq = sg.getSequenceAt(i);\r
int index = viewport.alignment.findIndex(seq);\r
int index = 0, startRes, endRes;\r
char ch;\r
\r
- for (int i = 0; i < sg.getSize(); i++)\r
+ for (int i = 0; i < sg.getSize(false); i++)\r
{\r
SequenceI seq = null;\r
\r
\r
}\r
\r
- protected void pasteNew_actionPerformed(ActionEvent e)\r
+ protected void pasteNew_actionPerformed()\r
{\r
paste(true);\r
}\r
\r
- protected void pasteThis_actionPerformed(ActionEvent e)\r
+ protected void pasteThis_actionPerformed()\r
{\r
addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
HistoryItem.PASTE));\r
{\r
newtitle = newtitle.concat("- from " + getTitle());\r
}\r
- AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle);\r
+ AlignFrame af = new AlignFrame(new Alignment(newSeqs),\r
+ applet,\r
+ newtitle,\r
+ false);\r
\r
jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
NEW_WINDOW_HEIGHT);\r
\r
}\r
\r
- protected void cut_actionPerformed(ActionEvent e)\r
+ protected void cut_actionPerformed()\r
{\r
- copy_actionPerformed(null);\r
- delete_actionPerformed(null);\r
+ copy_actionPerformed();\r
+ delete_actionPerformed();\r
}\r
\r
- protected void delete_actionPerformed(ActionEvent e)\r
+ protected void delete_actionPerformed()\r
{\r
addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
HistoryItem.HIDE));\r
\r
SequenceGroup sg = viewport.getSelectionGroup();\r
boolean allSequences = false;\r
- if(sg.sequences.size()==viewport.alignment.getHeight())\r
+ if(sg.getSize(false)==viewport.alignment.getHeight())\r
allSequences = true;\r
\r
- for (int i = 0; i < sg.sequences.size(); i++)\r
+ for (int i = 0; i < sg.getSize(false); i++)\r
{\r
SequenceI seq = sg.getSequenceAt(i);\r
int index = viewport.getAlignment().findIndex(seq);\r
\r
}\r
\r
- protected void deleteGroups_actionPerformed(ActionEvent e)\r
+ protected void deleteGroups_actionPerformed()\r
{\r
viewport.alignment.deleteAllGroups();\r
viewport.setSelectionGroup(null);\r
alignPanel.repaint();\r
}\r
\r
- public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ public void selectAllSequenceMenuItem_actionPerformed()\r
{\r
SequenceGroup sg = new SequenceGroup();\r
for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
PaintRefresher.Refresh(null, viewport.alignment);\r
}\r
\r
- public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ public void deselectAllSequenceMenuItem_actionPerformed()\r
{\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.keyboardNo1=null;\r
+ alignPanel.seqPanel.keyboardNo2=null;\r
+ }\r
viewport.setSelectionGroup(null);\r
viewport.getColumnSelection().clear();\r
viewport.setSelectionGroup(null);\r
+ alignPanel.idPanel.idCanvas.searchResults = null;\r
alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
alignPanel.repaint();\r
PaintRefresher.Refresh(null, viewport.alignment);\r
}\r
\r
- public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ public void invertSequenceMenuItem_actionPerformed()\r
{\r
SequenceGroup sg = viewport.getSelectionGroup();\r
for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
PaintRefresher.Refresh(null, viewport.alignment);\r
}\r
\r
- public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
+ public void remove2LeftMenuItem_actionPerformed()\r
{\r
ColumnSelection colSel = viewport.getColumnSelection();\r
if (colSel.size() > 0)\r
}\r
}\r
\r
- public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
+ public void remove2RightMenuItem_actionPerformed()\r
{\r
ColumnSelection colSel = viewport.getColumnSelection();\r
if (colSel.size() > 0)\r
\r
}\r
\r
- public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
+ public void removeGappedColumnMenuItem_actionPerformed()\r
{\r
addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
viewport.alignment,\r
viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
- public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
+ public void removeAllGapsMenuItem_actionPerformed()\r
{\r
addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
HistoryItem.HIDE));\r
int start=0, end = viewport.alignment.getWidth();\r
\r
if (viewport.getSelectionGroup() != null\r
- && viewport.getSelectionGroup().sequences != null\r
- && viewport.getSelectionGroup().sequences.size()>0)\r
+ && viewport.getSelectionGroup().getSequences(false) != null\r
+ && viewport.getSelectionGroup().getSize(false)>0)\r
{\r
- seqs = viewport.getSelectionGroup().sequences;\r
+ seqs = viewport.getSelectionGroup().getSequences(true);\r
start = viewport.getSelectionGroup().getStartRes();\r
end = viewport.getSelectionGroup().getEndRes()+1;\r
}\r
\r
public void alignmentChanged()\r
{\r
- viewport.updateConsensus();\r
- viewport.updateConservation ();\r
+ viewport.alignment.padGaps();\r
+ if(viewport.autocalculateConsensus)\r
+ {\r
+ viewport.updateConsensus();\r
+ viewport.updateConservation();\r
+ }\r
+\r
resetAllColourSchemes();\r
if(alignPanel.overviewPanel!=null)\r
alignPanel.overviewPanel.updateOverviewImage();\r
+\r
+ viewport.alignment.adjustSequenceAnnotations();\r
alignPanel.repaint();\r
}\r
\r
SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
{\r
- ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
+ ((ClustalxColourScheme)sg.cs).resetClustalX(\r
+ sg.getSequences(true), sg.getWidth());\r
}\r
sg.recalcConservation();\r
}\r
\r
\r
\r
- public void findMenuItem_actionPerformed(ActionEvent e)\r
+ public void findMenuItem_actionPerformed()\r
{\r
new Finder(alignPanel);\r
}\r
\r
- public void font_actionPerformed(ActionEvent e)\r
+ public void font_actionPerformed()\r
{\r
new FontChooser(alignPanel);\r
}\r
\r
\r
- public void seqLimits_itemStateChanged(ItemEvent e)\r
+ public void seqLimits_itemStateChanged()\r
{\r
viewport.setShowJVSuffix(seqLimits.getState());\r
alignPanel.fontChanged();\r
}\r
\r
\r
- protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
+ protected void colourTextMenuItem_actionPerformed()\r
{\r
viewport.setColourText(colourTextMenuItem.getState());\r
alignPanel.repaint();\r
}\r
\r
- protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
+ protected void wrapMenuItem_actionPerformed()\r
{\r
viewport.setWrapAlignment(wrapMenuItem.getState());\r
alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
alignPanel.repaint();\r
}\r
\r
- protected void scaleAbove_actionPerformed(ActionEvent e)\r
+ protected void scaleAbove_actionPerformed()\r
{\r
viewport.setScaleAboveWrapped(scaleAbove.getState());\r
alignPanel.repaint();\r
}\r
\r
- protected void scaleLeft_actionPerformed(ActionEvent e)\r
+ protected void scaleLeft_actionPerformed()\r
{\r
viewport.setScaleLeftWrapped(scaleLeft.getState());\r
alignPanel.repaint();\r
}\r
\r
- protected void scaleRight_actionPerformed(ActionEvent e)\r
+ protected void scaleRight_actionPerformed()\r
{\r
viewport.setScaleRightWrapped(scaleRight.getState());\r
alignPanel.repaint();\r
}\r
\r
- public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
+ public void viewBoxesMenuItem_actionPerformed()\r
{\r
viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
alignPanel.repaint();\r
}\r
\r
- public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
+ public void viewTextMenuItem_actionPerformed()\r
{\r
viewport.setShowText(viewTextMenuItem.getState());\r
alignPanel.repaint();\r
}\r
\r
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
+ protected void renderGapsMenuItem_actionPerformed()\r
{\r
viewport.setRenderGaps(renderGapsMenuItem.getState());\r
alignPanel.repaint();\r
}\r
\r
- public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
+ public void annotationPanelMenuItem_actionPerformed()\r
{\r
viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
}\r
\r
- public void overviewMenuItem_actionPerformed(ActionEvent e)\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
\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
+ protected void noColourmenuItem_actionPerformed()\r
{\r
changeColour(null);\r
}\r
\r
- public void clustalColour_actionPerformed(ActionEvent e)\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(ActionEvent e)\r
+ public void zappoColour_actionPerformed()\r
{\r
changeColour(new ZappoColourScheme());\r
}\r
\r
- public void taylorColour_actionPerformed(ActionEvent e)\r
+ public void taylorColour_actionPerformed()\r
{\r
changeColour(new TaylorColourScheme());\r
}\r
\r
- public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
+ public void hydrophobicityColour_actionPerformed()\r
{\r
changeColour(new HydrophobicColourScheme());\r
}\r
\r
- public void helixColour_actionPerformed(ActionEvent e)\r
+ public void helixColour_actionPerformed()\r
{\r
changeColour(new HelixColourScheme());\r
}\r
\r
- public void strandColour_actionPerformed(ActionEvent e)\r
+ public void strandColour_actionPerformed()\r
{\r
changeColour(new StrandColourScheme());\r
}\r
\r
- public void turnColour_actionPerformed(ActionEvent e)\r
+ public void turnColour_actionPerformed()\r
{\r
changeColour(new TurnColourScheme());\r
}\r
\r
- public void buriedColour_actionPerformed(ActionEvent e)\r
+ public void buriedColour_actionPerformed()\r
{\r
changeColour(new BuriedColourScheme());\r
}\r
\r
- public void nucleotideColour_actionPerformed(ActionEvent e)\r
+ public void nucleotideColour_actionPerformed()\r
{\r
changeColour(new NucleotideColourScheme());\r
}\r
\r
- protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
+ protected void applyToAllGroups_actionPerformed()\r
{\r
viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
}\r
}\r
if (cs instanceof ClustalxColourScheme)\r
{\r
- sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
+ sg.cs = new ClustalxColourScheme(sg.getSequences(true), 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.sequences, 0, sg.getWidth()));\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 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.sequences, 0,\r
+ sg.getSequences(true), 0,\r
viewport.alignment.getWidth() - 1);\r
c.calculate();\r
c.verdict(false, viewport.ConsPercGaps);\r
\r
\r
\r
- protected void modifyPID_actionPerformed(ActionEvent e)\r
+ protected void modifyPID_actionPerformed()\r
{\r
if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
{\r
}\r
}\r
\r
- protected void modifyConservation_actionPerformed(ActionEvent e)\r
+ protected void modifyConservation_actionPerformed()\r
{\r
if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
{\r
}\r
}\r
\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ protected void conservationMenuItem_actionPerformed()\r
{\r
viewport.setConservationSelected(conservationMenuItem.getState());\r
\r
\r
changeColour(viewport.getGlobalColourScheme());\r
\r
- modifyConservation_actionPerformed(null);\r
+ modifyConservation_actionPerformed();\r
}\r
\r
- public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
+ public void abovePIDThreshold_actionPerformed()\r
{\r
viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
\r
\r
changeColour(viewport.getGlobalColourScheme());\r
\r
- modifyPID_actionPerformed(null);\r
+ modifyPID_actionPerformed();\r
}\r
\r
- public void userDefinedColour_actionPerformed(ActionEvent e)\r
+ public void userDefinedColour_actionPerformed()\r
{\r
new UserDefinedColours(alignPanel, null);\r
}\r
\r
- public void PIDColour_actionPerformed(ActionEvent e)\r
+ public void PIDColour_actionPerformed()\r
{\r
changeColour(new PIDColourScheme());\r
}\r
\r
- public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
+ public void BLOSUM62Colour_actionPerformed()\r
{\r
changeColour(new Blosum62ColourScheme());\r
}\r
\r
- public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
+ public void sortPairwiseMenuItem_actionPerformed()\r
{\r
addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
HistoryItem.SORT));\r
alignPanel.repaint();\r
}\r
\r
- public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
+ public void sortIDMenuItem_actionPerformed()\r
{\r
addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
HistoryItem.SORT));\r
alignPanel.repaint();\r
}\r
\r
- public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
+ public void sortGroupMenuItem_actionPerformed()\r
{\r
addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
HistoryItem.SORT));\r
\r
}\r
\r
- public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
+ public void removeRedundancyMenuItem_actionPerformed()\r
{\r
- RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
- Frame frame = new Frame();\r
- frame.add(sp);\r
- jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",\r
- 400, 120);\r
-\r
+ new RedundancyPanel(alignPanel);\r
}\r
\r
- public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
+ public void pairwiseAlignmentMenuItem_actionPerformed()\r
{\r
- if (viewport.getSelectionGroup().getSize() > 1)\r
+ if (viewport.getSelectionGroup().getSize(false) > 1)\r
{\r
Frame frame = new Frame();\r
frame.add(new PairwiseAlignPanel(alignPanel));\r
}\r
}\r
\r
- public void PCAMenuItem_actionPerformed(ActionEvent e)\r
+ public void PCAMenuItem_actionPerformed()\r
{\r
//are the sequences aligned?\r
if (!viewport.alignment.isAligned())\r
}\r
\r
if ( (viewport.getSelectionGroup() != null &&\r
- viewport.getSelectionGroup().getSize() < 4 &&\r
- viewport.getSelectionGroup().getSize() > 0)\r
+ viewport.getSelectionGroup().getSize(false) < 4 &&\r
+ viewport.getSelectionGroup().getSize(false) > 0)\r
|| viewport.getAlignment().getHeight() < 4)\r
{\r
return;\r
\r
}\r
\r
- public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
+ public void averageDistanceTreeMenuItem_actionPerformed()\r
{\r
NewTreePanel("AV", "PID", "Average distance tree using PID");\r
}\r
\r
- public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
+ public void neighbourTreeMenuItem_actionPerformed()\r
{\r
NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
}\r
\r
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+ protected void njTreeBlosumMenuItem_actionPerformed()\r
{\r
NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
}\r
\r
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+ protected void avTreeBlosumMenuItem_actionPerformed()\r
{\r
NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
}\r
\r
final TreePanel tp;\r
if (viewport.getSelectionGroup() != null &&\r
- viewport.getSelectionGroup().getSize() > 3)\r
+ viewport.getSelectionGroup().getSize(false) > 3)\r
{\r
- tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
+ tp = new TreePanel(viewport,\r
+ viewport.getSelectionGroup().getSequences(false),\r
+ type,\r
pwType,\r
0, viewport.alignment.getWidth());\r
}\r
jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
}\r
\r
+ void loadTree_actionPerformed()\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
+ cap.setText("Paste your Newick tree file here.");\r
+ cap.treeImport = true;\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);\r
+ }\r
+\r
+ public void loadTree(jalview.io.NewickFile tree, String treeFile)\r
+ {\r
+ TreePanel tp = new TreePanel(viewport,\r
+ viewport.getAlignment().getSequences(),\r
+ tree, "From File - ", treeFile);\r
+ jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
+ addTreeMenuItem(tp, treeFile);\r
+ }\r
+\r
void addTreeMenuItem(final TreePanel treePanel, String title)\r
{\r
final MenuItem item = new MenuItem(title);\r
sortByTreeMenu.add(item);\r
item.addActionListener(new java.awt.event.ActionListener()\r
{\r
- public void actionPerformed(ActionEvent e)\r
+ public void actionPerformed(ActionEvent evt)\r
{\r
addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
HistoryItem.SORT));\r
});\r
}\r
\r
- protected void documentation_actionPerformed(ActionEvent e)\r
+ protected void documentation_actionPerformed()\r
{\r
- showURL("http://www.jalview.org/help.html");\r
+ showURL("http://www.jalview.org/help.html", "HELP");\r
}\r
\r
- protected void about_actionPerformed(ActionEvent e)\r
+ protected void about_actionPerformed()\r
{\r
\r
class AboutPanel extends Canvas\r
g.drawString("If you use JalView, please cite:", x, y += fh + 8);\r
g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
x, y += fh);\r
- g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh);\r
+ g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);\r
}\r
}\r
\r
\r
}\r
\r
- /**\r
- * Displays the given URL in a new browser window\r
- *\r
- * @param url URL to display in browser window.\r
- * <br>New window will be named "HELP_WINDOW"\r
- */\r
- public void showURL(String url)\r
- {\r
- showURL(url, "HELP");\r
- }\r
-\r
public void showURL(String url, String target)\r
{\r
if (applet == null)\r
{\r
try\r
{\r
+ System.out.println("Show url: "+url);\r
applet.getAppletContext().showDocument(new java.net.URL(url),\r
target);\r
}\r
//JBuilder Graphics here\r
\r
protected MenuBar alignFrameMenuBar = new MenuBar();\r
- protected Menu fileMenu = new Menu();\r
- protected MenuItem closeMenuItem = new MenuItem();\r
- protected Menu editMenu = new Menu();\r
- protected Menu viewMenu = new Menu();\r
- protected Menu colourMenu = new Menu();\r
- protected Menu calculateMenu = new Menu();\r
- protected MenuItem selectAllSequenceMenuItem = new MenuItem();\r
- protected MenuItem deselectAllSequenceMenuItem = new MenuItem();\r
- protected MenuItem invertSequenceMenuItem = new MenuItem();\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 closeMenuItem = new MenuItem("Close");\r
+ protected Menu editMenu = new Menu("Edit");\r
+ protected Menu viewMenu = new Menu("View");\r
+ protected Menu colourMenu = new Menu("Colour");\r
+ protected Menu calculateMenu = new Menu("Calculate");\r
+ protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
+ protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");\r
+ protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");\r
protected MenuItem remove2LeftMenuItem = new MenuItem();\r
protected MenuItem remove2RightMenuItem = new MenuItem();\r
protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
MenuItem delete = new MenuItem();\r
MenuItem copy = new MenuItem();\r
MenuItem cut = new MenuItem();\r
- Menu Menu1 = new Menu();\r
+ Menu pasteMenu = new Menu();\r
MenuItem pasteNew = new MenuItem();\r
MenuItem pasteThis = new MenuItem();\r
protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
MenuItem modifyPID = new MenuItem();\r
MenuItem modifyConservation = new MenuItem();\r
+ protected CheckboxMenuItem autoCalculate\r
+ = new CheckboxMenuItem("Autocalculate Consensus", true);\r
protected Menu sortByTreeMenu = new Menu();\r
Menu sort = new Menu();\r
Menu calculate = new Menu();\r
MenuItem documentation = new MenuItem();\r
MenuItem about = new MenuItem();\r
protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
-\r
- private void jbInit() throws Exception {\r
+ Panel embeddedMenu;\r
+ Label embeddedEdit;\r
+ Label embeddedSearch;\r
+ Label embeddedView;\r
+ Label embeddedColour;\r
+ Label embeddedFile;\r
+ Label embeddedHelp;\r
+ Label embeddedCalculate;\r
+ FlowLayout flowLayout1;\r
+\r
+ private void jbInit() throws Exception {\r
\r
setMenuBar(alignFrameMenuBar);\r
\r
\r
outputTextboxMenu.add(item);\r
}\r
+ closeMenuItem.addActionListener(this);\r
+ loadApplication.addActionListener(this);\r
\r
-\r
- fileMenu.setLabel("File");\r
- closeMenuItem.setLabel("Close");\r
- closeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- closeMenuItem_actionPerformed(e);\r
- }\r
- });\r
- editMenu.setLabel("Edit");\r
- viewMenu.setLabel("View");\r
- colourMenu.setLabel("Colour");\r
- calculateMenu.setLabel("Calculate");\r
- selectAllSequenceMenuItem.setLabel("Select all");\r
- selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- selectAllSequenceMenuItem_actionPerformed(e);\r
- }\r
- });\r
- deselectAllSequenceMenuItem.setLabel("Deselect All");\r
- deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- deselectAllSequenceMenuItem_actionPerformed(e);\r
- }\r
- });\r
- invertSequenceMenuItem.setLabel("Invert Selection");\r
- invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- invertSequenceMenuItem_actionPerformed(e);\r
- }\r
- });\r
+ loadTree.addActionListener(this);\r
+ selectAllSequenceMenuItem.addActionListener(this);\r
+ deselectAllSequenceMenuItem.addActionListener(this);\r
+ invertSequenceMenuItem.addActionListener(this);\r
remove2LeftMenuItem.setLabel("Remove Left");\r
- remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- remove2LeftMenuItem_actionPerformed(e);\r
- }\r
- });\r
+ remove2LeftMenuItem.addActionListener(this);\r
remove2RightMenuItem.setLabel("Remove Right");\r
- remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- remove2RightMenuItem_actionPerformed(e);\r
- }\r
- });\r
+ remove2RightMenuItem.addActionListener(this);\r
removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
- removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- removeGappedColumnMenuItem_actionPerformed(e);\r
- }\r
- });\r
+ removeGappedColumnMenuItem.addActionListener(this);\r
removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
- removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- removeAllGapsMenuItem_actionPerformed(e);\r
- }\r
- });\r
+ removeAllGapsMenuItem.addActionListener(this);\r
viewBoxesMenuItem.setLabel("Boxes");\r
viewBoxesMenuItem.setState(true);\r
- viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- viewBoxesMenuItem_actionPerformed(null);\r
- }\r
- });\r
+ viewBoxesMenuItem.addItemListener(this);\r
viewTextMenuItem.setLabel("Text");\r
viewTextMenuItem.setState(true);\r
- viewTextMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- viewTextMenuItem_actionPerformed(null);\r
- }\r
- });\r
+ viewTextMenuItem.addItemListener(this);\r
sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
- sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- sortPairwiseMenuItem_actionPerformed(e);\r
- }\r
- });\r
+ sortPairwiseMenuItem.addActionListener(this);\r
sortIDMenuItem.setLabel("by ID");\r
- sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- sortIDMenuItem_actionPerformed(e);\r
- }\r
- });\r
+ sortIDMenuItem.addActionListener(this);\r
sortGroupMenuItem.setLabel("by Group");\r
- sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- sortGroupMenuItem_actionPerformed(e);\r
- }\r
- });\r
+ sortGroupMenuItem.addActionListener(this);\r
removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
- removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- removeRedundancyMenuItem_actionPerformed(e);\r
- }\r
- });\r
+ removeRedundancyMenuItem.addActionListener(this);\r
pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
- pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- pairwiseAlignmentMenuItem_actionPerformed(e);\r
- }\r
- });\r
+ pairwiseAlignmentMenuItem.addActionListener(this);\r
PCAMenuItem.setLabel("Principal Component Analysis");\r
- PCAMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- PCAMenuItem_actionPerformed(e);\r
- }\r
- });\r
+ PCAMenuItem.addActionListener(this);\r
averageDistanceTreeMenuItem.setLabel(\r
"Average Distance Using % Identity");\r
- averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- averageDistanceTreeMenuItem_actionPerformed(e);\r
- }\r
- });\r
+ averageDistanceTreeMenuItem.addActionListener(this);\r
neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
- neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- neighbourTreeMenuItem_actionPerformed(e);\r
- }\r
- });\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
outputTextboxMenu.setLabel("Output to Textbox");\r
clustalColour.setLabel("Clustalx");\r
\r
- clustalColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- clustalColour_actionPerformed(e);\r
- }\r
- });\r
+ clustalColour.addActionListener(this);\r
zappoColour.setLabel("Zappo");\r
- zappoColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- zappoColour_actionPerformed(e);\r
- }\r
- });\r
+ zappoColour.addActionListener(this);\r
taylorColour.setLabel("Taylor");\r
- taylorColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- taylorColour_actionPerformed(e);\r
- }\r
- });\r
+ taylorColour.addActionListener(this);\r
hydrophobicityColour.setLabel("Hydrophobicity");\r
- hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- hydrophobicityColour_actionPerformed(e);\r
- }\r
- });\r
+ hydrophobicityColour.addActionListener(this);\r
helixColour.setLabel("Helix Propensity");\r
- helixColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- helixColour_actionPerformed(e);\r
- }\r
- });\r
+ helixColour.addActionListener(this);\r
strandColour.setLabel("Strand Propensity");\r
- strandColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- strandColour_actionPerformed(e);\r
- }\r
- });\r
+ strandColour.addActionListener(this);\r
turnColour.setLabel("Turn Propensity");\r
- turnColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- turnColour_actionPerformed(e);\r
- }\r
- });\r
+ turnColour.addActionListener(this);\r
buriedColour.setLabel("Buried Index");\r
- buriedColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- buriedColour_actionPerformed(e);\r
- }\r
- });\r
+ buriedColour.addActionListener(this);\r
userDefinedColour.setLabel("User Defined...");\r
- userDefinedColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- userDefinedColour_actionPerformed(e);\r
- }\r
- });\r
+ userDefinedColour.addActionListener(this);\r
PIDColour.setLabel("Percentage Identity");\r
- PIDColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- PIDColour_actionPerformed(e);\r
- }\r
- });\r
+ PIDColour.addActionListener(this);\r
BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- BLOSUM62Colour_actionPerformed(e);\r
- }\r
- });\r
+ BLOSUM62Colour.addActionListener(this);\r
avDistanceTreeBlosumMenuItem.setLabel(\r
"Average Distance Using BLOSUM62");\r
- avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- avTreeBlosumMenuItem_actionPerformed(e);\r
- }\r
- });\r
+ avDistanceTreeBlosumMenuItem.addActionListener(this);\r
njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
- njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- njTreeBlosumMenuItem_actionPerformed(e);\r
- }\r
- });\r
- annotationPanelMenuItem.setActionCommand("");\r
- annotationPanelMenuItem.setState(true);\r
+ njTreeBlosumMenuItem.addActionListener(this);\r
annotationPanelMenuItem.setLabel("Show Annotations");\r
- annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- annotationPanelMenuItem_actionPerformed(null);\r
- }\r
- });\r
+ annotationPanelMenuItem.addItemListener(this);\r
colourTextMenuItem.setLabel("Colour Text");\r
- colourTextMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- colourTextMenuItem_actionPerformed(null);\r
- }\r
- });\r
+ colourTextMenuItem.addItemListener(this);\r
overviewMenuItem.setLabel("Overview Window");\r
- overviewMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- overviewMenuItem_actionPerformed(e);\r
- }\r
- });\r
+ overviewMenuItem.addActionListener(this);\r
undoMenuItem.setEnabled(false);\r
undoMenuItem.setLabel("Undo");\r
- undoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- undoMenuItem_actionPerformed(e);\r
- }\r
- });\r
+ undoMenuItem.addActionListener(this);\r
redoMenuItem.setEnabled(false);\r
redoMenuItem.setLabel("Redo");\r
- redoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- redoMenuItem_actionPerformed(e);\r
- }\r
- });\r
+ redoMenuItem.addActionListener(this);\r
conservationMenuItem.setLabel("by Conservation");\r
- conservationMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- conservationMenuItem_actionPerformed(null);\r
- }\r
- });\r
+ conservationMenuItem.addItemListener(this);\r
noColourmenuItem.setLabel("None");\r
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- noColourmenuItem_actionPerformed(e);\r
- }\r
- });\r
+ noColourmenuItem.addActionListener(this);\r
wrapMenuItem.setLabel("Wrap");\r
- wrapMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- wrapMenuItem_actionPerformed(null);\r
- }\r
- });\r
+ wrapMenuItem.addItemListener(this);\r
renderGapsMenuItem.setLabel("Show Gaps");\r
renderGapsMenuItem.setState(true);\r
- renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- renderGapsMenuItem_actionPerformed(null);\r
- }\r
- });\r
+ renderGapsMenuItem.addItemListener(this);\r
findMenuItem.setLabel("Find...");\r
- findMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- findMenuItem_actionPerformed(e);\r
- }\r
- });\r
+ findMenuItem.addActionListener(this);\r
searchMenu.setLabel("Search");\r
\r
abovePIDThreshold.setLabel("Above Identity Threshold");\r
- abovePIDThreshold.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- abovePIDThreshold_actionPerformed(null);\r
- }\r
- });\r
+ abovePIDThreshold.addItemListener(this);\r
nucleotideColour.setLabel("Nucleotide");\r
- nucleotideColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- nucleotideColour_actionPerformed(e);\r
- }\r
- });\r
+ nucleotideColour.addActionListener(this);\r
deleteGroups.setLabel("Undefine Groups");\r
- deleteGroups.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- deleteGroups_actionPerformed(e);\r
- }\r
- });\r
+ deleteGroups.addActionListener(this);\r
copy.setLabel("Copy");\r
- copy.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- copy_actionPerformed(e);\r
- }\r
- });\r
+ copy.addActionListener(this);\r
cut.setLabel("Cut");\r
- cut.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- cut_actionPerformed(e);\r
- }\r
- });\r
+ cut.addActionListener(this);\r
delete.setLabel("Delete");\r
- delete.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- delete_actionPerformed(e);\r
- }\r
- });\r
- Menu1.setLabel("Paste");\r
+ delete.addActionListener(this);\r
+ pasteMenu.setLabel("Paste");\r
pasteNew.setLabel("To New Alignment");\r
- pasteNew.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- pasteNew_actionPerformed(e);\r
- }\r
- });\r
+ pasteNew.addActionListener(this);\r
pasteThis.setLabel("Add To This Alignment");\r
- pasteThis.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- pasteThis_actionPerformed(e);\r
- }\r
- });\r
+ pasteThis.addActionListener(this);\r
applyToAllGroups.setLabel("Apply Colour To All Groups");\r
applyToAllGroups.setState(true);\r
- applyToAllGroups.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- applyToAllGroups_actionPerformed(null);\r
- }\r
- });\r
+ applyToAllGroups.addItemListener(this);\r
font.setLabel("Font...");\r
- font.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- font_actionPerformed(e);\r
- }\r
- });\r
+ font.addActionListener(this);\r
scaleAbove.setLabel("Scale Above");\r
scaleAbove.setState(true);\r
- scaleAbove.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- scaleAbove_actionPerformed(null);\r
- }\r
- });\r
+ scaleAbove.setEnabled(false);\r
+ scaleAbove.addItemListener(this);\r
scaleLeft.setEnabled(false);\r
scaleLeft.setState(true);\r
scaleLeft.setLabel("Scale Left");\r
- scaleLeft.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- scaleLeft_actionPerformed(null);\r
- }\r
- });\r
+ scaleLeft.addItemListener(this);\r
scaleRight.setEnabled(false);\r
scaleRight.setState(true);\r
scaleRight.setLabel("Scale Right");\r
- scaleRight.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- scaleRight_actionPerformed(null);\r
- }\r
- });\r
+ scaleRight.addItemListener(this);\r
modifyPID.setLabel("Modify Identity Threshold...");\r
- modifyPID.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- modifyPID_actionPerformed(e);\r
- }\r
- });\r
+ modifyPID.addActionListener(this);\r
modifyConservation.setLabel("Modify Conservation Threshold...");\r
- modifyConservation.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- modifyConservation_actionPerformed(e);\r
- }\r
- });\r
+ modifyConservation.addActionListener(this);\r
sortByTreeMenu.setLabel("By Tree Order");\r
sort.setLabel("Sort");\r
calculate.setLabel("Calculate Tree");\r
+ autoCalculate.addItemListener(this);\r
inputText.setLabel("Input from textbox");\r
- inputText.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- inputText_actionPerformed(e);\r
- }\r
- });\r
+ inputText.addActionListener(this);\r
\r
helpMenu.setLabel("Help");\r
documentation.setLabel("Documentation");\r
- documentation.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- documentation_actionPerformed(e);\r
- }\r
- });\r
+ documentation.addActionListener(this);\r
\r
about.setLabel("About...");\r
- about.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- about_actionPerformed(e);\r
- }\r
- });\r
+ about.addActionListener(this);\r
seqLimits.setState(true);\r
seqLimits.setLabel("Show Sequence Limits");\r
- seqLimits.addItemListener(new ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- seqLimits_itemStateChanged(e);\r
- }\r
- });\r
+ seqLimits.addItemListener(this);\r
+ featureSettings.setLabel("Feature Settings...");\r
+ featureSettings.addActionListener(this);\r
+ sequenceFeatures.setLabel("Sequence Features");\r
+ sequenceFeatures.addItemListener(this);\r
+ sequenceFeatures.setState(false);\r
+ annotationColour.setLabel("by Annotation...");\r
+ annotationColour.addActionListener(this);\r
\r
alignFrameMenuBar.add(fileMenu);\r
alignFrameMenuBar.add(editMenu);\r
alignFrameMenuBar.add(helpMenu);\r
fileMenu.add(inputText);\r
fileMenu.add(outputTextboxMenu);\r
+ // fileMenu.add(loadApplication);\r
fileMenu.addSeparator();\r
+ fileMenu.add(loadTree);\r
fileMenu.add(closeMenuItem);\r
editMenu.add(undoMenuItem);\r
editMenu.add(redoMenuItem);\r
editMenu.add(cut);\r
editMenu.add(copy);\r
- editMenu.add(Menu1);\r
+ editMenu.add(pasteMenu);\r
editMenu.add(delete);\r
editMenu.addSeparator();\r
editMenu.add(selectAllSequenceMenuItem);\r
searchMenu.add(findMenuItem);\r
viewMenu.add(font);\r
viewMenu.addSeparator();\r
- viewMenu.add(seqLimits);\r
+ viewMenu.add(seqLimits);\r
viewMenu.addSeparator();\r
viewMenu.add(wrapMenuItem);\r
viewMenu.add(scaleAbove);\r
viewMenu.add(colourTextMenuItem);\r
viewMenu.add(renderGapsMenuItem);\r
viewMenu.add(annotationPanelMenuItem);\r
- viewMenu.addSeparator();\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(sequenceFeatures);\r
+ viewMenu.add(featureSettings);\r
+ viewMenu.addSeparator();\r
viewMenu.add(overviewMenuItem);\r
colourMenu.add(applyToAllGroups);\r
colourMenu.addSeparator();\r
colourMenu.add(modifyConservation);\r
colourMenu.add(abovePIDThreshold);\r
colourMenu.add(modifyPID);\r
- calculateMenu.add(sort);\r
+ colourMenu.add(annotationColour);\r
+ calculateMenu.add(sort);\r
calculateMenu.add(calculate);\r
calculateMenu.addSeparator();\r
calculateMenu.add(pairwiseAlignmentMenuItem);\r
calculateMenu.add(PCAMenuItem);\r
+ calculateMenu.add(autoCalculate);\r
this.add(statusBar, BorderLayout.SOUTH);\r
- Menu1.add(pasteNew);\r
- Menu1.add(pasteThis);\r
+ pasteMenu.add(pasteNew);\r
+ pasteMenu.add(pasteThis);\r
sort.add(sortIDMenuItem);\r
sort.add(sortByTreeMenu);\r
sort.add(sortGroupMenuItem);\r
calculate.add(njTreeBlosumMenuItem);\r
helpMenu.add(documentation);\r
helpMenu.add(about);\r
+ }\r
+\r
+ public void setEmbedded()\r
+ {\r
+\r
+ embeddedMenu = new Panel();\r
+ embeddedEdit = new Label();\r
+ embeddedSearch = new Label();\r
+ embeddedView = new Label();\r
+ embeddedColour = new Label();\r
+ embeddedFile = new Label();\r
+ embeddedHelp = new Label();\r
+ embeddedCalculate = new Label();\r
+ flowLayout1 = new FlowLayout();\r
+ embeddedMenu.setBackground(Color.lightGray);\r
+ embeddedMenu.setLayout(flowLayout1);\r
+ embeddedEdit.setText("Edit");\r
+ embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedSearch.setText("Search");\r
+ embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedView.setText("View");\r
+ embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedColour.setText("Colour");\r
+ embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedFile.setText("File");\r
+ embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedHelp.setText("Help");\r
+ embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedCalculate.setText("Calculate");\r
+ embeddedMenu.add(embeddedFile);\r
+ embeddedMenu.add(embeddedEdit);\r
+ embeddedMenu.add(embeddedSearch);\r
+ embeddedMenu.add(embeddedView);\r
+ embeddedMenu.add(embeddedColour);\r
+ embeddedMenu.add(embeddedCalculate);\r
+ embeddedMenu.add(embeddedHelp);\r
+ flowLayout1.setAlignment(FlowLayout.LEFT);\r
+ flowLayout1.setHgap(2);\r
+ flowLayout1.setVgap(0);\r
+ embeddedFile.addMouseListener(this);\r
+ embeddedEdit.addMouseListener(this);\r
+ embeddedSearch.addMouseListener(this);\r
+ embeddedView.addMouseListener(this);\r
+ embeddedColour.addMouseListener(this);\r
+ embeddedCalculate.addMouseListener(this);\r
+ embeddedHelp.addMouseListener(this);\r
+\r
+ // setVisible(false);\r
+ fileMenu.remove(closeMenuItem);\r
+ fileMenu.remove(3); // Seperator\r
+\r
+ applet.setLayout(new BorderLayout());\r
+ applet.add(embeddedMenu, BorderLayout.NORTH);\r
+ applet.add(statusBar, BorderLayout.SOUTH);\r
+ // applet.validate();\r
+\r
+ alignPanel.setSize(applet.size().width, applet.size().height\r
+ - embeddedMenu.HEIGHT - statusBar.HEIGHT);\r
+\r
+ applet.add(alignPanel, BorderLayout.CENTER);\r
+ applet.validate();\r
+\r
+ }\r
+\r
+\r
+\r
+ PopupMenu filePopup, editPopup, searchPopup,\r
+ viewPopup, colourPopup, calculatePopup, helpPopup;\r
+ MenuItem featureSettings = new MenuItem();\r
+ CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();\r
+ MenuItem annotationColour = new MenuItem();\r
+\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ PopupMenu popup = null;\r
+ Label source = (Label)evt.getSource();\r
+ if(source==embeddedFile)\r
+ {\r
+ popup = filePopup = genPopupMenu(filePopup, fileMenu);\r
+ }\r
+ else if(source==embeddedEdit)\r
+ {\r
+ popup = editPopup = genPopupMenu(editPopup, editMenu);\r
+ }\r
+ else if(source==embeddedSearch)\r
+ {\r
+ popup = searchPopup = genPopupMenu(searchPopup, searchMenu);\r
+ }\r
+ else if(source==embeddedView)\r
+ {\r
+ popup = viewPopup = genPopupMenu(viewPopup, viewMenu);\r
+ }\r
+ else if(source==embeddedColour)\r
+ {\r
+ popup = colourPopup = genPopupMenu(colourPopup, colourMenu);\r
+ }\r
+ else if(source==embeddedCalculate)\r
+ {\r
+ popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);\r
+ }\r
+ else if(source==embeddedHelp)\r
+ {\r
+ popup = helpPopup = genPopupMenu(helpPopup, helpMenu);\r
+ }\r
+\r
+ embeddedMenu.add(popup);\r
+ popup.show(embeddedMenu,\r
+ source.getBounds().x,\r
+ source.getBounds().y + source.getBounds().getSize().height);\r
+ }\r
+\r
+ PopupMenu genPopupMenu(PopupMenu popup, Menu original)\r
+ {\r
+ if(popup!=null)\r
+ {\r
+ return popup;\r
+ }\r
+ popup = new PopupMenu();\r
+ int m, mSize = original.getItemCount();\r
+ for(m=0; m<mSize; m++)\r
+ {\r
+ popup.add(original.getItem(m));\r
+ mSize--;\r
+ m--;\r
}\r
+\r
+ return popup;\r
+ }\r
+ public void mouseClicked(MouseEvent evt)\r
+ {}\r
+ public void mouseReleased(MouseEvent evt)\r
+ {}\r
+ public void mouseEntered(MouseEvent evt)\r
+ {}\r
+ public void mouseExited(MouseEvent evt)\r
+ {}\r
+\r
}\r
\r
git://source.jalview.org / jalview.git / blobdiff