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
\r
\r
- add(alignPanel, BorderLayout.CENTER);\r
- jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\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
* @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
- URL url = new URL(file);\r
-\r
- BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));\r
- SequenceI seq = null;\r
- String line, type, desc, token;\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
- type = st.nextToken();\r
- UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
- fr.setColour(type, ucs.findColour("A"));\r
- continue;\r
- }\r
-\r
- while (st.hasMoreElements())\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
-\r
- start = Integer.parseInt(st.nextToken());\r
- end = Integer.parseInt(st.nextToken());\r
-\r
- seq = viewport.alignment.getSequenceAt(index);\r
- start = seq.findIndex(start) - 1;\r
- end = seq.findIndex(end) - 1;\r
-\r
- type = st.nextToken();\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
-\r
- sf = new SequenceFeature(type, desc, "", start, end);\r
-\r
- seq.addSequenceFeature(sf);\r
- }\r
- }\r
+ ex.printStackTrace();\r
+ }\r
\r
+ if(featuresFile)\r
+ {\r
+ if(featureLinks.size()>0)\r
+ alignPanel.seqPanel.seqCanvas\r
+ .getFeatureRenderer().featureLinks = featureLinks;\r
viewport.showSequenceFeatures = true;\r
-\r
+ sequenceFeatures.setState(true);\r
alignPanel.repaint();\r
-\r
- }\r
- catch (Exception ex)\r
- {\r
- System.out.println("Error parsing groups file: " + ex);\r
}\r
+\r
}\r
\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
}\r
break;\r
case KeyEvent.VK_C:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setCursorColumn();\r
+ }\r
if (evt.isControlDown() || evt.isMetaDown())\r
{\r
copy_actionPerformed();\r
}\r
break;\r
case KeyEvent.VK_DOWN:\r
- moveSelectedSequences(false);\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.moveCursor(0,1);\r
+ }\r
+ else\r
+ moveSelectedSequences(false);\r
break;\r
+\r
case KeyEvent.VK_UP:\r
- moveSelectedSequences(true);\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.moveCursor(0,-1);\r
+ }\r
+ else\r
+ moveSelectedSequences(true);\r
+ break;\r
+\r
+ case KeyEvent.VK_LEFT:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.moveCursor(-1,0);\r
+ }\r
+ break;\r
+\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
+ 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
+ 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
+ case KeyEvent.VK_ENTER:\r
+ case KeyEvent.VK_COMMA:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setCursorRowAndColumn();\r
+ }\r
+ break;\r
+\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
+ 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
case KeyEvent.VK_F:\r
if (evt.isControlDown())\r
{\r
findMenuItem_actionPerformed();\r
}\r
break;\r
- case KeyEvent.VK_BACK_SPACE:\r
- case KeyEvent.VK_DELETE:\r
- cut_actionPerformed();\r
- break;\r
}\r
}\r
public void keyReleased(KeyEvent evt)\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()==closeMenuItem)\r
closeMenuItem_actionPerformed();\r
else if(evt.getSource()==copy)\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
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
\r
public void inputText_actionPerformed()\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);\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
// 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
{\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
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
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
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
jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
}\r
\r
- public void addTreeMenuItem(final TreePanel treePanel, String title)\r
+ void loadTree_actionPerformed()\r
+ {\r
+ TreePanel tp = null;\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
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
//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 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
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
\r
outputTextboxMenu.add(item);\r
}\r
-\r
- fileMenu.setLabel("File");\r
- closeMenuItem.setLabel("Close");\r
closeMenuItem.addActionListener(this);\r
- editMenu.setLabel("Edit");\r
- viewMenu.setLabel("View");\r
- colourMenu.setLabel("Colour");\r
- calculateMenu.setLabel("Calculate");\r
- selectAllSequenceMenuItem.setLabel("Select all");\r
+\r
+ loadTree.addActionListener(this);\r
selectAllSequenceMenuItem.addActionListener(this);\r
- deselectAllSequenceMenuItem.setLabel("Deselect All");\r
deselectAllSequenceMenuItem.addActionListener(this);\r
- invertSequenceMenuItem.setLabel("Invert Selection");\r
invertSequenceMenuItem.addActionListener(this);\r
remove2LeftMenuItem.setLabel("Remove Left");\r
remove2LeftMenuItem.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(this);\r
\r
seqLimits.setState(true);\r
seqLimits.setLabel("Show Sequence Limits");\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
fileMenu.add(inputText);\r
fileMenu.add(outputTextboxMenu);\r
fileMenu.addSeparator();\r
+ fileMenu.add(loadTree);\r
fileMenu.add(closeMenuItem);\r
editMenu.add(undoMenuItem);\r
editMenu.add(redoMenuItem);\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
pasteMenu.add(pasteNew);\r
pasteMenu.add(pasteThis);\r
embeddedCalculate.addMouseListener(this);\r
embeddedHelp.addMouseListener(this);\r
\r
- setVisible(false);\r
+ // setVisible(false);\r
fileMenu.remove(closeMenuItem);\r
fileMenu.remove(2); // Seperator\r
\r
applet.setLayout(new BorderLayout());\r
applet.add(embeddedMenu, BorderLayout.NORTH);\r
applet.add(statusBar, BorderLayout.SOUTH);\r
- applet.validate();\r
-\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
git://source.jalview.org / jalview.git / blobdiff