StringTokenizer st;\r
SequenceFeature sf;\r
FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
- int lineNo = 0;\r
- String featureGroup = null;\r
+ String featureGroup = null, groupLink = null;\r
+ Hashtable typeLink = new Hashtable();\r
+\r
while ( (line = in.readLine()) != null)\r
{\r
- lineNo++;\r
st = new StringTokenizer(line, "\t");\r
- if (st.countTokens() == 2)\r
+ if(!st.hasMoreTokens())\r
+ continue;\r
+\r
+ if (st.countTokens() < 4)\r
{\r
type = st.nextToken();\r
if(type.equalsIgnoreCase("startgroup"))\r
{\r
featureGroup = st.nextToken();\r
+ if (st.hasMoreElements())\r
+ {\r
+ groupLink = st.nextToken();\r
+ fr.addFeatureLink(featureGroup, groupLink);\r
+ }\r
}\r
else if(type.equalsIgnoreCase("endgroup"))\r
{\r
//but at present theres no way of showing more than 1 group\r
st.nextToken();\r
featureGroup = null;\r
+ groupLink = null;\r
}\r
else\r
{\r
UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
fr.setColour(type, ucs.findColour("A"));\r
+ if (st.hasMoreElements())\r
+ {\r
+ String link = st.nextToken();\r
+ typeLink.put(type, link);\r
+ fr.addFeatureLink(type, link);\r
+ }\r
+\r
}\r
continue;\r
}\r
while (st.hasMoreElements())\r
{\r
desc = st.nextToken();\r
+\r
token = st.nextToken();\r
if (!token.equals("ID_NOT_SPECIFIED"))\r
{\r
fr.setColour(type, ucs.findColour("A"));\r
}\r
\r
- sf = new SequenceFeature(type, desc, "", start, end, featureGroup);\r
-\r
+ sf = new SequenceFeature(type, desc, start, end, 0f, featureGroup);\r
seq.addSequenceFeature(sf);\r
+\r
+ if(groupLink!=null)\r
+ {\r
+ sf.addLink(groupLink);\r
+ sf.description += "%LINK%";\r
+ }\r
+ if(typeLink.containsKey(type))\r
+ {\r
+ sf.addLink(typeLink.get(type).toString());\r
+ sf.description += "%LINK%";\r
+ }\r
+\r
+ parseDescriptionHTML(sf);\r
}\r
}\r
\r
}\r
}\r
\r
+ void parseDescriptionHTML(SequenceFeature sf)\r
+ {\r
+ StringBuffer sb = new StringBuffer();\r
+ StringTokenizer st = new StringTokenizer(sf.getDescription(), "<");\r
+ String token, link;\r
+ while(st.hasMoreElements())\r
+ {\r
+ token = st.nextToken("<>");\r
+ if(token.equalsIgnoreCase("html") || token.startsWith("/"))\r
+ continue;\r
+\r
+ if(token.startsWith("a href="))\r
+ {\r
+ link = token.substring(token.indexOf("\"")+1, token.length()-1);\r
+ String label = st.nextToken("<>");\r
+ sf.addLink(label+"|"+link);\r
+ sb.append(label+"%LINK%");\r
+ }\r
+ else if(token.equalsIgnoreCase("br"))\r
+ sb.append("\n");\r
+ else\r
+ sb.append(token);\r
+ }\r
+\r
+ sf.description = sb.toString();\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
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
\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
\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
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
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
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
git://source.jalview.org / jalview.git / blobdiff