public AlignViewport viewport;\r
int NEW_WINDOW_WIDTH = 700;\r
int NEW_WINDOW_HEIGHT = 500;\r
- jalview.bin.JalviewLite applet;\r
\r
+ String jalviewServletURL;\r
\r
- public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title)\r
+\r
+ public AlignFrame(AlignmentI al,\r
+ jalview.bin.JalviewLite applet,\r
+ String title,\r
+ boolean embedded)\r
{\r
+\r
+ jalviewServletURL = applet.getParameter("APPLICATION_URL");\r
+\r
try{\r
jbInit();\r
}catch(Exception ex)\r
ex.printStackTrace();\r
}\r
\r
- this.applet = applet;\r
viewport = new AlignViewport(al, applet);\r
alignPanel = new AlignmentPanel(this, viewport);\r
\r
annotationPanelMenuItem.setState(viewport.showAnnotation);\r
\r
+ seqLimits.setState(viewport.showJVSuffix);\r
+\r
if(applet!=null)\r
{\r
String param = applet.getParameter("sortBy");\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 && !evt.isControlDown())\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
+ Object source = evt.getSource();\r
+\r
+ if(source==inputText)\r
inputText_actionPerformed();\r
- else if(evt.getSource()==closeMenuItem)\r
+ else if(source==loadTree)\r
+ loadTree_actionPerformed();\r
+ else if(source==loadApplication)\r
+ launchFullApplication();\r
+ else if(source==closeMenuItem)\r
closeMenuItem_actionPerformed();\r
- else if(evt.getSource()==copy)\r
+ else if(source==copy)\r
copy_actionPerformed();\r
- else if(evt.getSource()==undoMenuItem)\r
+ else if(source==undoMenuItem)\r
undoMenuItem_actionPerformed();\r
- else if(evt.getSource()==redoMenuItem)\r
+ else if(source==redoMenuItem)\r
redoMenuItem_actionPerformed();\r
- else if(evt.getSource()==inputText)\r
+ else if(source==inputText)\r
inputText_actionPerformed();\r
- else if(evt.getSource()==closeMenuItem)\r
+ else if(source==closeMenuItem)\r
closeMenuItem_actionPerformed();\r
- else if(evt.getSource()==undoMenuItem)\r
+ else if(source==undoMenuItem)\r
undoMenuItem_actionPerformed();\r
- else if(evt.getSource()==redoMenuItem)\r
+ else if(source==redoMenuItem)\r
redoMenuItem_actionPerformed();\r
- else if(evt.getSource()==copy)\r
+ else if(source==copy)\r
copy_actionPerformed();\r
- else if(evt.getSource()==pasteNew)\r
+ else if(source==pasteNew)\r
pasteNew_actionPerformed();\r
- else if(evt.getSource()==pasteThis)\r
+ else if(source==pasteThis)\r
pasteThis_actionPerformed();\r
- else if(evt.getSource()==cut)\r
+ else if(source==cut)\r
cut_actionPerformed();\r
- else if(evt.getSource()==delete)\r
+ else if(source==delete)\r
delete_actionPerformed();\r
- else if(evt.getSource()==deleteGroups)\r
+ else if(source==deleteGroups)\r
deleteGroups_actionPerformed();\r
- else if(evt.getSource()==selectAllSequenceMenuItem)\r
+ else if(source==selectAllSequenceMenuItem)\r
selectAllSequenceMenuItem_actionPerformed();\r
- else if(evt.getSource()==deselectAllSequenceMenuItem)\r
+ else if(source==deselectAllSequenceMenuItem)\r
deselectAllSequenceMenuItem_actionPerformed();\r
- else if(evt.getSource()==invertSequenceMenuItem)\r
+ else if(source==invertSequenceMenuItem)\r
invertSequenceMenuItem_actionPerformed();\r
- else if(evt.getSource()==remove2LeftMenuItem)\r
+ else if(source==invertColSel)\r
+ { viewport.invertColumnSelection(); alignPanel.repaint(); }\r
+ else if(source==remove2LeftMenuItem)\r
remove2LeftMenuItem_actionPerformed();\r
- else if(evt.getSource()==remove2RightMenuItem)\r
+ else if(source==remove2RightMenuItem)\r
remove2RightMenuItem_actionPerformed();\r
- else if(evt.getSource()==removeGappedColumnMenuItem)\r
+ else if(source==removeGappedColumnMenuItem)\r
removeGappedColumnMenuItem_actionPerformed();\r
- else if(evt.getSource()==removeAllGapsMenuItem)\r
+ else if(source==removeAllGapsMenuItem)\r
removeAllGapsMenuItem_actionPerformed();\r
- else if(evt.getSource()==findMenuItem)\r
+ else if(source==findMenuItem)\r
findMenuItem_actionPerformed();\r
- else if(evt.getSource()==font)\r
+ else if(source==font)\r
font_actionPerformed();\r
- else if(evt.getSource()==overviewMenuItem)\r
+ else if(source==showColumns)\r
+ {\r
+ viewport.showAllHiddenColumns(); alignPanel.repaint();\r
+ }\r
+ else if(source==showSeqs)\r
+ {\r
+ viewport.showAllHiddenSeqs(); alignPanel.repaint();\r
+ }\r
+ else if(source == hideColumns)\r
+ {\r
+ viewport.hideSelectedColumns(); alignPanel.repaint();\r
+ }\r
+ else if(source == hideSequences && viewport.getSelectionGroup()!=null)\r
+ {\r
+ SequenceI[] seqs = viewport.getSelectionGroup().getSequencesInOrder(\r
+ viewport.alignment\r
+ );\r
+\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ viewport.hideSequence(seqs[i]);\r
+ }\r
+\r
+ alignPanel.repaint();\r
+ }\r
+ else if(source==featureSettings)\r
+ featureSettings_actionPerformed();\r
+ else if(source==overviewMenuItem)\r
overviewMenuItem_actionPerformed();\r
- else if(evt.getSource()==noColourmenuItem)\r
+ else if(source==noColourmenuItem)\r
noColourmenuItem_actionPerformed();\r
- else if(evt.getSource()==clustalColour)\r
+ else if(source==clustalColour)\r
clustalColour_actionPerformed();\r
- else if(evt.getSource()==zappoColour)\r
+ else if(source==zappoColour)\r
zappoColour_actionPerformed();\r
- else if(evt.getSource()==taylorColour)\r
+ else if(source==taylorColour)\r
taylorColour_actionPerformed();\r
- else if(evt.getSource()==hydrophobicityColour)\r
+ else if(source==hydrophobicityColour)\r
hydrophobicityColour_actionPerformed();\r
- else if(evt.getSource()==helixColour)\r
+ else if(source==helixColour)\r
helixColour_actionPerformed();\r
- else if(evt.getSource()==strandColour)\r
+ else if(source==strandColour)\r
strandColour_actionPerformed();\r
- else if(evt.getSource()==turnColour)\r
+ else if(source==turnColour)\r
turnColour_actionPerformed();\r
- else if(evt.getSource()==buriedColour)\r
+ else if(source==buriedColour)\r
buriedColour_actionPerformed();\r
- else if(evt.getSource()==nucleotideColour)\r
+ else if(source==nucleotideColour)\r
nucleotideColour_actionPerformed();\r
- else if(evt.getSource()==modifyPID)\r
+ else if(source==modifyPID)\r
modifyPID_actionPerformed();\r
- else if(evt.getSource()==modifyConservation)\r
+ else if(source==modifyConservation)\r
modifyConservation_actionPerformed();\r
- else if(evt.getSource()==userDefinedColour)\r
+ else if(source==userDefinedColour)\r
userDefinedColour_actionPerformed();\r
- else if(evt.getSource()==PIDColour)\r
+ else if(source==PIDColour)\r
PIDColour_actionPerformed();\r
- else if(evt.getSource()==BLOSUM62Colour)\r
+ else if(source==BLOSUM62Colour)\r
BLOSUM62Colour_actionPerformed();\r
- else if(evt.getSource()==sortPairwiseMenuItem)\r
+ else if(source==annotationColour)\r
+ new AnnotationColourChooser(viewport, alignPanel);\r
+ else if(source==sortPairwiseMenuItem)\r
sortPairwiseMenuItem_actionPerformed();\r
- else if(evt.getSource()==sortIDMenuItem)\r
+ else if(source==sortIDMenuItem)\r
sortIDMenuItem_actionPerformed();\r
- else if(evt.getSource()==sortGroupMenuItem)\r
+ else if(source==sortGroupMenuItem)\r
sortGroupMenuItem_actionPerformed();\r
- else if(evt.getSource()==removeRedundancyMenuItem)\r
+ else if(source==removeRedundancyMenuItem)\r
removeRedundancyMenuItem_actionPerformed();\r
- else if(evt.getSource()==pairwiseAlignmentMenuItem)\r
+ else if(source==pairwiseAlignmentMenuItem)\r
pairwiseAlignmentMenuItem_actionPerformed();\r
- else if(evt.getSource()==PCAMenuItem)\r
+ else if(source==PCAMenuItem)\r
PCAMenuItem_actionPerformed();\r
- else if(evt.getSource()==averageDistanceTreeMenuItem)\r
+ else if(source==averageDistanceTreeMenuItem)\r
averageDistanceTreeMenuItem_actionPerformed();\r
- else if(evt.getSource()==neighbourTreeMenuItem)\r
+ else if(source==neighbourTreeMenuItem)\r
neighbourTreeMenuItem_actionPerformed();\r
- else if(evt.getSource()==njTreeBlosumMenuItem)\r
+ else if(source==njTreeBlosumMenuItem)\r
njTreeBlosumMenuItem_actionPerformed();\r
- else if(evt.getSource()==avDistanceTreeBlosumMenuItem)\r
+ else if(source==avDistanceTreeBlosumMenuItem)\r
avTreeBlosumMenuItem_actionPerformed();\r
- else if(evt.getSource()==documentation)\r
+ else if(source==documentation)\r
documentation_actionPerformed();\r
- else if(evt.getSource()==about)\r
+ else if(source==about)\r
about_actionPerformed();\r
\r
}\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
viewport.showJVSuffix));\r
}\r
\r
+ void launchFullApplication()\r
+ {\r
+ StringBuffer url = new StringBuffer(jalviewServletURL);\r
+\r
+ url.append("?open="+\r
+ appendProtocol( viewport.applet.getParameter("file") ) );\r
+\r
+ if(viewport.applet.getParameter("features")!=null)\r
+ {\r
+ url.append( "&features=" );\r
+ url.append( appendProtocol( viewport.applet.getParameter("features") ) );\r
+ }\r
+\r
+ if(viewport.applet.getParameter("annotations")!=null)\r
+ {\r
+ url.append( "&annotations=" );\r
+ url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );\r
+ }\r
+\r
+ if(viewport.applet.getParameter("defaultColour")!=null)\r
+ {\r
+ url.append("&colour=" +\r
+ removeWhiteSpace(viewport.applet.getParameter("defaultColour"))\r
+ );\r
+ }\r
+\r
+ if(viewport.applet.getParameter("userDefinedColour")!=null)\r
+ {\r
+ url.append( "&colour=" +\r
+ removeWhiteSpace( viewport.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 = viewport.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
+ if(PaintRefresher.components.size()==0 && viewport.applet==null)\r
System.exit(0);\r
\r
this.dispose();\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
alignPanel.repaint();\r
}\r
\r
- StringBuffer copiedSequences;\r
+ static StringBuffer copiedSequences;\r
+ static Vector copiedHiddenColumns;\r
protected void copy_actionPerformed()\r
{\r
if (viewport.getSelectionGroup() == null)\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
+ if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)\r
+ {\r
+ copiedHiddenColumns = new Vector();\r
+ int hiddenOffset = viewport.getSelectionGroup().getStartRes();\r
+ for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();\r
+ i++)\r
+ {\r
+ int[] region = (int[])\r
+ viewport.getColumnSelection().getHiddenColumns().elementAt(i);\r
+\r
+ copiedHiddenColumns.addElement(new int[]\r
+ {region[0] - hiddenOffset,\r
+ region[1] - hiddenOffset});\r
+ }\r
+ }\r
+ else\r
+ copiedHiddenColumns = null;\r
+\r
+\r
+ for (int i = 0; i < sg.getSize(false); i++)\r
{\r
SequenceI seq = null;\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
+ viewport.applet,\r
+ newtitle,\r
+ false);\r
+ if (copiedHiddenColumns != null)\r
+ {\r
+ for (int i = 0; i < copiedHiddenColumns.size(); i++)\r
+ {\r
+ int[] region = (int[]) copiedHiddenColumns.elementAt(i);\r
+ af.viewport.hideColumns(region[0], region[1]);\r
+ }\r
+ }\r
+\r
\r
jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
NEW_WINDOW_HEIGHT);\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
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
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
alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
}\r
\r
+ public void featureSettings_actionPerformed()\r
+ {\r
+ new FeatureSettings(viewport, alignPanel);\r
+ }\r
+\r
public void overviewMenuItem_actionPerformed()\r
{\r
if (alignPanel.overviewPanel != null)\r
}\r
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
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()\r
{\r
- if (viewport.getSelectionGroup().getSize() > 1)\r
+ if (viewport.getSelectionGroup()!=null\r
+ && viewport.getSelectionGroup().getSize(false) > 1)\r
{\r
Frame frame = new Frame();\r
frame.add(new PairwiseAlignPanel(alignPanel));\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
- final TreePanel tp;\r
- if (viewport.getSelectionGroup() != null &&\r
- viewport.getSelectionGroup().getSize() > 3)\r
- {\r
- tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
- pwType,\r
- 0, viewport.alignment.getWidth());\r
- }\r
- else\r
+ if ( (viewport.getSelectionGroup() != null &&\r
+ viewport.getSelectionGroup().getSize(false) > 1)\r
+ || (viewport.getSelectionGroup() == null\r
+ && viewport.alignment.getHeight() > 1))\r
{\r
- tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
- type, pwType, 0, viewport.alignment.getWidth());\r
+ final TreePanel tp = new TreePanel(viewport,\r
+ type,\r
+ pwType);\r
+\r
+ addTreeMenuItem(tp, title);\r
+\r
+ jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
}\r
+ }\r
\r
- addTreeMenuItem(tp, title);\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
- jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
+ public void loadTree(jalview.io.NewickFile tree, String treeFile)\r
+ {\r
+ TreePanel tp = new TreePanel(viewport,\r
+ treeFile,\r
+ "From File - ",\r
+ tree);\r
+ jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
+ addTreeMenuItem(tp, treeFile);\r
}\r
\r
- public void addTreeMenuItem(final TreePanel treePanel, String title)\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
\r
public void showURL(String url, String target)\r
{\r
- if (applet == null)\r
+ if (viewport.applet == null)\r
{\r
System.out.println("Not running as applet - no browser available.");\r
}\r
{\r
try\r
{\r
- applet.getAppletContext().showDocument(new java.net.URL(url),\r
+ System.out.println("Show url: "+url);\r
+ viewport.applet.getAppletContext().showDocument(new java.net.URL(url),\r
target);\r
}\r
catch (Exception ex)\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
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
+ loadApplication.addActionListener(this);\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
font.addActionListener(this);\r
scaleAbove.setLabel("Scale Above");\r
scaleAbove.setState(true);\r
+ scaleAbove.setEnabled(false);\r
scaleAbove.addItemListener(this);\r
scaleLeft.setEnabled(false);\r
scaleLeft.setState(true);\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
+ invertSequenceMenuItem.setLabel("Invert Sequence Selection");\r
+ invertColSel.setLabel("Invert Column Selection");\r
+ menu1.setLabel("Show");\r
+ showColumns.setLabel("All Columns ");\r
+ showSeqs.setLabel("All Sequences");\r
+ menu2.setLabel("Hide");\r
+ hideColumns.setLabel("Selected Columns");\r
+ hideSequences.setLabel("Selected Sequences");\r
+ invertColSel.addActionListener(this);\r
+ showColumns.addActionListener(this);\r
+ showSeqs.addActionListener(this);\r
+ hideColumns.addActionListener(this);\r
+ hideSequences.addActionListener(this);\r
+\r
\r
alignFrameMenuBar.add(fileMenu);\r
alignFrameMenuBar.add(editMenu);\r
alignFrameMenuBar.add(helpMenu);\r
fileMenu.add(inputText);\r
fileMenu.add(outputTextboxMenu);\r
+ if(jalviewServletURL!=null)\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(selectAllSequenceMenuItem);\r
editMenu.add(deselectAllSequenceMenuItem);\r
editMenu.add(invertSequenceMenuItem);\r
- editMenu.add(deleteGroups);\r
+ editMenu.add(invertColSel);\r
+ editMenu.add(deleteGroups);\r
editMenu.addSeparator();\r
editMenu.add(remove2LeftMenuItem);\r
editMenu.add(remove2RightMenuItem);\r
searchMenu.add(findMenuItem);\r
viewMenu.add(font);\r
viewMenu.addSeparator();\r
- viewMenu.add(seqLimits);\r
- viewMenu.addSeparator();\r
+ viewMenu.add(menu1);\r
+ viewMenu.add(menu2);\r
+ viewMenu.addSeparator();\r
viewMenu.add(wrapMenuItem);\r
viewMenu.add(scaleAbove);\r
viewMenu.add(scaleLeft);\r
viewMenu.add(scaleRight);\r
viewMenu.addSeparator();\r
+ viewMenu.add(seqLimits);\r
viewMenu.add(viewBoxesMenuItem);\r
viewMenu.add(viewTextMenuItem);\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
calculate.add(njTreeBlosumMenuItem);\r
helpMenu.add(documentation);\r
helpMenu.add(about);\r
+ menu1.add(showColumns);\r
+ menu1.add(showSeqs);\r
+ menu2.add(hideColumns);\r
+ menu2.add(hideSequences);\r
}\r
\r
public void setEmbedded()\r
embeddedMenu.setBackground(Color.lightGray);\r
embeddedMenu.setLayout(flowLayout1);\r
embeddedEdit.setText("Edit");\r
- embeddedEdit.setAlignment(Label.CENTER);\r
embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
embeddedSearch.setText("Search");\r
- embeddedSearch.setAlignment(Label.CENTER);\r
embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
embeddedView.setText("View");\r
- embeddedView.setAlignment(Label.CENTER);\r
embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
embeddedColour.setText("Colour");\r
- embeddedColour.setAlignment(Label.CENTER);\r
embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
- embeddedFile.setAlignment(Label.CENTER);\r
embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
embeddedFile.setText("File");\r
- embeddedHelp.setAlignment(Label.CENTER);\r
embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
embeddedHelp.setText("Help");\r
- embeddedCalculate.setAlignment(Label.CENTER);\r
embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
embeddedCalculate.setText("Calculate");\r
embeddedMenu.add(embeddedFile);\r
embeddedMenu.add(embeddedCalculate);\r
embeddedMenu.add(embeddedHelp);\r
flowLayout1.setAlignment(FlowLayout.LEFT);\r
- flowLayout1.setHgap(0);\r
+ flowLayout1.setHgap(2);\r
flowLayout1.setVgap(0);\r
embeddedFile.addMouseListener(this);\r
embeddedEdit.addMouseListener(this);\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
+ 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(applet.size().width, applet.size().height\r
+ alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height\r
- embeddedMenu.HEIGHT - statusBar.HEIGHT);\r
\r
- applet.add(alignPanel, BorderLayout.CENTER);\r
- applet.validate();\r
+ viewport.applet.add(alignPanel, BorderLayout.CENTER);\r
+ viewport.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
+ MenuItem invertColSel = new MenuItem();\r
+ Menu menu1 = new Menu();\r
+ MenuItem showColumns = new MenuItem();\r
+ MenuItem showSeqs = new MenuItem();\r
+ Menu menu2 = new Menu();\r
+ MenuItem hideColumns = new MenuItem();\r
+ MenuItem hideSequences = new MenuItem();\r
\r
public void mousePressed(MouseEvent evt)\r
{\r
git://source.jalview.org / jalview.git / blobdiff