/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
import jalview.datamodel.*;\r
import jalview.analysis.*;\r
import jalview.io.*;\r
+import jalview.commands.*;\r
import java.awt.*;\r
import java.awt.event.*;\r
import java.util.*;\r
{\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
+ int DEFAULT_WIDTH = 700;\r
+ int DEFAULT_HEIGHT = 500;\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
+ if (applet != null)\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
+ viewport.updateConservation(alignPanel);\r
+ viewport.updateConsensus(alignPanel);\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
if (param != null)\r
{\r
int width = Integer.parseInt(param);\r
- NEW_WINDOW_WIDTH = width;\r
+ DEFAULT_WIDTH = width;\r
}\r
param = applet.getParameter("windowHeight");\r
if (param != null)\r
{\r
int height = Integer.parseInt(param);\r
- NEW_WINDOW_HEIGHT = height;\r
+ DEFAULT_HEIGHT = height;\r
}\r
}\r
catch (Exception ex)\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
- public void propertyChange(java.beans.PropertyChangeEvent evt)\r
- {\r
- if (evt.getPropertyName().equals("alignment"))\r
- {\r
- alignmentChanged();\r
- }\r
- }\r
- });\r
-\r
-\r
- add(alignPanel, BorderLayout.CENTER);\r
- jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
-\r
+ alignPanel.scalePanel.addKeyListener(this);\r
+ alignPanel.annotationPanel.addKeyListener(this);\r
+\r
+\r
+ if(embedded)\r
+ {\r
+ setEmbedded();\r
+ }\r
+ else\r
+ {\r
+ add(alignPanel, BorderLayout.CENTER);\r
+ jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,\r
+ DEFAULT_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_V:\r
- if (evt.isControlDown() || evt.isMetaDown())\r
+ if (evt.isControlDown())\r
{\r
- paste(true);\r
+ paste(evt.isShiftDown());\r
}\r
break;\r
case KeyEvent.VK_A:\r
}\r
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
+ || evt.isShiftDown()\r
+ || evt.isAltDown()\r
+ );\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
+ || evt.isShiftDown()\r
+ || evt.isAltDown());\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
+ 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
+\r
+ case KeyEvent.VK_H:\r
+ {\r
+ boolean toggleSeqs = !evt.isControlDown();\r
+ boolean toggleCols = !evt.isShiftDown();\r
+ boolean hide = false;\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+\r
+ if(toggleSeqs)\r
+ {\r
+ if (sg != null && sg.getSize() != viewport.alignment.getHeight())\r
+ {\r
+ hide = true;\r
+ viewport.hideAllSelectedSeqs();\r
+ }\r
+ else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))\r
+ viewport.showAllHiddenSeqs();\r
+ }\r
+\r
+ if(toggleCols)\r
+ {\r
+ if (viewport.colSel.getSelected().size() > 0)\r
+ {\r
+ viewport.hideSelectedColumns();\r
+ if(!toggleSeqs)\r
+ viewport.selectionGroup = sg;\r
+ }\r
+ else if (!hide)\r
+ viewport.showAllHiddenColumns();\r
+ }\r
break;\r
- }\r
+ }\r
+\r
+ case KeyEvent.VK_PAGE_UP:\r
+ if (viewport.wrapAlignment)\r
+ alignPanel.scrollUp(true);\r
+ else\r
+ alignPanel.setScrollValues(viewport.startRes,\r
+ viewport.startSeq\r
+ - viewport.endSeq + viewport.startSeq);\r
+ break;\r
+\r
+ case KeyEvent.VK_PAGE_DOWN:\r
+ if (viewport.wrapAlignment)\r
+ alignPanel.scrollUp(false);\r
+ else\r
+ alignPanel.setScrollValues(viewport.startRes,\r
+ viewport.startSeq\r
+ + viewport.endSeq - viewport.startSeq);\r
+ break;\r
+\r
+ case KeyEvent.VK_Z:\r
+ if (evt.isControlDown())\r
+ {\r
+ undoMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_Y:\r
+ if (evt.isControlDown())\r
+ {\r
+ redoMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_L:\r
+ if (evt.isControlDown())\r
+ {\r
+ trimAlignment(true);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_R:\r
+ if (evt.isControlDown())\r
+ {\r
+ trimAlignment(false);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_E:\r
+ if (evt.isControlDown())\r
+ {\r
+ if (evt.isShiftDown())\r
+ this.removeAllGapsMenuItem_actionPerformed();\r
+ else\r
+ removeGappedColumnMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_I:\r
+ if (evt.isControlDown())\r
+ {\r
+ if (evt.isAltDown())\r
+ viewport.invertColumnSelection();\r
+ else\r
+ this.invertSequenceMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_U:\r
+ if (evt.isControlDown())\r
+ {\r
+ this.deleteGroups_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_T:\r
+ if (evt.isControlDown())\r
+ {\r
+ newView();\r
+ }\r
+ break;\r
+\r
+\r
+ }\r
+ alignPanel.repaint();\r
}\r
public void keyReleased(KeyEvent evt)\r
{}\r
else if(evt.getSource()==wrapMenuItem)\r
wrapMenuItem_actionPerformed();\r
else if(evt.getSource()==scaleAbove)\r
- scaleAbove_actionPerformed();\r
+ viewport.setScaleAboveWrapped(scaleAbove.getState());\r
else if(evt.getSource()==scaleLeft)\r
- scaleLeft_actionPerformed();\r
+ viewport.setScaleLeftWrapped(scaleLeft.getState());\r
else if(evt.getSource()==scaleRight)\r
- scaleRight_actionPerformed();\r
+ viewport.setScaleRightWrapped(scaleRight.getState());\r
else if(evt.getSource()==seqLimits)\r
seqLimits_itemStateChanged();\r
else if(evt.getSource()==viewBoxesMenuItem)\r
- viewBoxesMenuItem_actionPerformed();\r
+ viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
else if(evt.getSource()==viewTextMenuItem)\r
- viewTextMenuItem_actionPerformed();\r
+ viewport.setShowText(viewTextMenuItem.getState());\r
else if(evt.getSource()==renderGapsMenuItem)\r
- renderGapsMenuItem_actionPerformed();\r
+ viewport.setRenderGaps(renderGapsMenuItem.getState());\r
else if(evt.getSource()==annotationPanelMenuItem)\r
- annotationPanelMenuItem_actionPerformed();\r
+ {\r
+ viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
+ alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
+ }\r
+ else if(evt.getSource()==sequenceFeatures)\r
+ {\r
+ viewport.showSequenceFeatures(sequenceFeatures.getState());\r
+ 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()==applyToAllGroups)\r
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
+ else if(evt.getSource()==autoCalculate)\r
+ viewport.autocalculateConsensus = autoCalculate.getState();\r
+\r
+ alignPanel.repaint();\r
}\r
public void actionPerformed(ActionEvent evt)\r
{\r
- 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 == loadAnnotations)\r
+ loadAnnotations();\r
+ else if (source == outputAnnotations)\r
+ outputAnnotations(true);\r
+ else if(source == outputFeatures)\r
+ outputFeatures(true, "Jalview");\r
+ else if(source==closeMenuItem)\r
closeMenuItem_actionPerformed();\r
- else if(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
- remove2LeftMenuItem_actionPerformed();\r
- else if(evt.getSource()==remove2RightMenuItem)\r
- remove2RightMenuItem_actionPerformed();\r
- else if(evt.getSource()==removeGappedColumnMenuItem)\r
+ else if(source==invertColSel)\r
+ { viewport.invertColumnSelection(); alignPanel.repaint(); }\r
+ else if(source==remove2LeftMenuItem)\r
+ trimAlignment(true);\r
+ else if(source==remove2RightMenuItem)\r
+ trimAlignment(false);\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
- font_actionPerformed();\r
- else if(evt.getSource()==overviewMenuItem)\r
+ else if(source==font)\r
+ new FontChooser(alignPanel);\r
+ else if (source == newView)\r
+ newView();\r
+ else if(source==showColumns)\r
+ {\r
+ viewport.showAllHiddenColumns(); alignPanel.repaint();\r
+ }\r
+ else if(source==showSeqs)\r
+ {\r
+ viewport.showAllHiddenSeqs();\r
+ }\r
+ else if(source == hideColumns)\r
+ {\r
+ viewport.hideSelectedColumns(); alignPanel.repaint();\r
+ }\r
+ else if(source == hideSequences && viewport.getSelectionGroup()!=null)\r
+ {\r
+ viewport.hideAllSelectedSeqs();\r
+ }\r
+ else if(source==featureSettings)\r
+ new FeatureSettings(alignPanel);\r
+ else if(source==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
+ else if(source==noColourmenuItem)\r
+ changeColour(null);\r
+ else if(source==clustalColour)\r
+ {\r
+ abovePIDThreshold.setState(false);\r
+ changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
+ viewport.alignment.getWidth()));\r
+ }\r
+ else if(source==zappoColour)\r
+ changeColour(new ZappoColourScheme());\r
+ else if(source==taylorColour)\r
+ changeColour(new TaylorColourScheme());\r
+ else if(source==hydrophobicityColour)\r
+ changeColour(new HydrophobicColourScheme());\r
+ else if(source==helixColour)\r
+ changeColour(new HelixColourScheme());\r
+ else if(source==strandColour)\r
+ changeColour(new StrandColourScheme());\r
+ else if(source==turnColour)\r
+ changeColour(new TurnColourScheme());\r
+ else if(source==buriedColour)\r
+ changeColour(new BuriedColourScheme());\r
+ else if(source==nucleotideColour)\r
+ changeColour(new NucleotideColourScheme());\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
- 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()==sortPairwiseMenuItem)\r
+ else if(source==userDefinedColour)\r
+ new UserDefinedColours(alignPanel, null);\r
+ else if(source==PIDColour)\r
+ changeColour(new PIDColourScheme());\r
+ else if(source==BLOSUM62Colour)\r
+ changeColour(new Blosum62ColourScheme());\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(true, this);\r
Frame frame = new Frame();\r
frame.add(cap);\r
jalview.bin.JalviewLite.addFrame(frame,\r
"Alignment output - " + e.getActionCommand(),\r
600, 500);\r
cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),\r
- viewport.getAlignment().getSequences(),\r
+ viewport.getAlignment(),\r
viewport.showJVSuffix));\r
}\r
\r
+ public void loadAnnotations()\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
+ cap.setText("Paste your features / annotations file here.");\r
+ cap.setAnnotationImport();\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);\r
+\r
+ }\r
+\r
+ public String outputAnnotations(boolean displayTextbox)\r
+ {\r
+ String annotation = new AnnotationFile().printAnnotations(\r
+ viewport.alignment.getAlignmentAnnotation() );\r
+\r
+ if(displayTextbox)\r
+ {\r
+\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame,\r
+ "Annotations",\r
+ 600, 500);\r
+ cap.setText(annotation);\r
+ }\r
+\r
+ return annotation;\r
+ }\r
+\r
+ public String outputFeatures(boolean displayTextbox, String format)\r
+ {\r
+ String features;\r
+ if (format.equalsIgnoreCase("Jalview"))\r
+ features = new FeaturesFile().printJalviewFormat(\r
+ viewport.alignment.getSequencesArray(),\r
+ viewport.featuresDisplayed);\r
+ else\r
+ features = new FeaturesFile().printGFFFormat(\r
+ viewport.alignment.getSequencesArray(),\r
+ viewport.featuresDisplayed);\r
+\r
+\r
+ if(displayTextbox)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame,\r
+ "Features",\r
+ 600, 500);\r
+\r
+ cap.setText(features);\r
+ }\r
+\r
+ return features;\r
+ }\r
+\r
+ void launchFullApplication()\r
+ {\r
+ StringBuffer url = new StringBuffer(jalviewServletURL);\r
+\r
+ 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("jnetfile")!=null)\r
+ {\r
+ url.append( "&annotations=" );\r
+ url.append( appendProtocol( viewport.applet.getParameter("jnetfile") ) );\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
+ PaintRefresher.RemoveComponent(alignPanel);\r
+ PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);\r
+ PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);\r
+\r
+ if(PaintRefresher.components.size()==0 && viewport.applet==null)\r
System.exit(0);\r
\r
this.dispose();\r
}\r
\r
- Stack historyList = new Stack();\r
- Stack redoList = new Stack();\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
void updateEditMenuBar()\r
{\r
- if (historyList.size() > 0)\r
+\r
+ if (viewport.historyList.size() > 0)\r
{\r
undoMenuItem.setEnabled(true);\r
- HistoryItem hi = (HistoryItem) historyList.peek();\r
- undoMenuItem.setLabel("Undo " + hi.getDescription());\r
+ CommandI command = (CommandI) viewport.historyList.peek();\r
+ undoMenuItem.setLabel("Undo " + command.getDescription());\r
}\r
else\r
{\r
undoMenuItem.setLabel("Undo");\r
}\r
\r
- if (redoList.size() > 0)\r
+ if (viewport.redoList.size() > 0)\r
{\r
redoMenuItem.setEnabled(true);\r
- HistoryItem hi = (HistoryItem) redoList.peek();\r
- redoMenuItem.setLabel("Redo " + hi.getDescription());\r
+\r
+ CommandI command = (CommandI) viewport.redoList.peek();\r
+ redoMenuItem.setLabel("Redo " + command.getDescription());\r
}\r
else\r
{\r
}\r
}\r
\r
- public void addHistoryItem(HistoryItem hi)\r
+ public void addHistoryItem(CommandI command)\r
{\r
- historyList.push(hi);\r
- updateEditMenuBar();\r
+ if(command.getSize()>0)\r
+ {\r
+ viewport.historyList.push(command);\r
+ viewport.redoList.removeAllElements();\r
+ updateEditMenuBar();\r
+ viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
+ }\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void undoMenuItem_actionPerformed()\r
{\r
- HistoryItem hi = (HistoryItem) historyList.pop();\r
- redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
- HistoryItem.HIDE));\r
- restoreHistoryItem(hi);\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ if(viewport.historyList.size()<1)\r
+ return;\r
+\r
+ CommandI command = (CommandI)viewport.historyList.pop();\r
+ viewport.redoList.push(command);\r
+ command.undoCommand();\r
+\r
+ AlignViewport originalSource = getOriginatingSource(command);\r
+\r
+ originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
+ updateEditMenuBar();\r
+ originalSource.firePropertyChange("alignment", null,originalSource.alignment.getSequences());\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void redoMenuItem_actionPerformed()\r
{\r
- HistoryItem hi = (HistoryItem) redoList.pop();\r
- restoreHistoryItem(hi);\r
+ if(viewport.redoList.size()<1)\r
+ return;\r
+\r
+ CommandI command = (CommandI) viewport.redoList.pop();\r
+ viewport.historyList.push(command);\r
+ command.doCommand();\r
+\r
+ AlignViewport originalSource = getOriginatingSource(command);\r
+ originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;\r
+\r
updateEditMenuBar();\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ originalSource.firePropertyChange("alignment", null, originalSource.alignment.getSequences());\r
}\r
\r
- // used by undo and redo\r
- void restoreHistoryItem(HistoryItem hi)\r
+ AlignViewport getOriginatingSource(CommandI command)\r
{\r
- if (hi.getType() == HistoryItem.SORT)\r
+ AlignViewport originalSource = null;\r
+ //For sequence removal and addition, we need to fire\r
+ //the property change event FROM the viewport where the\r
+ //original alignment was altered\r
+ AlignmentI al = null;\r
+ if (command instanceof EditCommand)\r
{\r
- 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
+ EditCommand editCommand = (EditCommand) command;\r
+ al = editCommand.getAlignment();\r
+ Vector comps = (Vector) PaintRefresher.components\r
+ .get(viewport.getSequenceSetId());\r
+ for (int i = 0; i < comps.size(); i++)\r
{\r
- for (int i = viewport.alignment.getHeight() - 1;\r
- i > hi.getSequences().size() - 1; i--)\r
+ if (comps.elementAt(i) instanceof AlignmentPanel)\r
{\r
- viewport.alignment.deleteSequence(i);\r
+ if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)\r
+ {\r
+ originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;\r
+ break;\r
+ }\r
}\r
}\r
}\r
\r
- updateEditMenuBar();\r
+ if (originalSource == null)\r
+ {\r
+ //The original view is closed, we must validate\r
+ //the current view against the closed view first\r
+ if (al != null)\r
+ PaintRefresher.validateSequences(al, viewport.alignment);\r
\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ originalSource = viewport;\r
+ }\r
+\r
+\r
+ return originalSource;\r
}\r
\r
public void moveSelectedSequences(boolean up)\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(null).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(null).contains(temp))\r
{\r
continue;\r
}\r
for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
{\r
SequenceI seq = viewport.alignment.getSequenceAt(i);\r
- if (!sg.sequences.contains(seq))\r
+ if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))\r
{\r
continue;\r
}\r
\r
SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
- if (sg.sequences.contains(temp))\r
+ if (sg.getSequences(viewport.hiddenRepSequences).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
orderedSeqs.put(index + "", seq);\r
}\r
\r
- int index = 0, startRes, endRes;\r
- char ch;\r
+ int index = 0, startRes, endRes;\r
+ char ch;\r
+\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(); i++)\r
{\r
copiedSequences.append(seq.getName() + "\t" +\r
startRes + "\t" +\r
endRes + "\t" +\r
- seq.getSequence(sg.getStartRes(),\r
+ seq.getSequenceAsString(sg.getStartRes(),\r
sg.getEndRes() + 1) + "\n");\r
}\r
\r
\r
protected void pasteThis_actionPerformed()\r
{\r
- addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
- HistoryItem.PASTE));\r
paste(false);\r
}\r
\r
{\r
try\r
{\r
+\r
if (copiedSequences == null)\r
{\r
return;\r
String name = st.nextToken();\r
int start = Integer.parseInt(st.nextToken());\r
int end = Integer.parseInt(st.nextToken());\r
- Sequence sequence = new Sequence(name, st.nextToken(), start, end);\r
-\r
- if (!newAlignment)\r
- {\r
- viewport.alignment.addSequence(sequence);\r
- }\r
- else\r
- {\r
- seqs.addElement(sequence);\r
- }\r
+ seqs.addElement(new Sequence(name, st.nextToken(), start, end));\r
+ }\r
+ SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
}\r
\r
if (newAlignment)\r
{\r
- SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
- for (int i = 0; i < seqs.size(); i++)\r
- {\r
- newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
- }\r
-\r
String newtitle = new String("Copied sequences");\r
if (getTitle().startsWith("Copied sequences"))\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
+ jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,\r
+ DEFAULT_HEIGHT);\r
}\r
else\r
{\r
- viewport.setEndSeq(viewport.alignment.getHeight());\r
- viewport.alignment.getWidth();\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ addSequences(newSeqs);\r
}\r
\r
}\r
\r
}\r
\r
+ void addSequences(SequenceI[] seqs)\r
+ {\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ viewport.alignment.addSequence(seqs[i]);\r
+ }\r
+\r
+ //!newAlignment\r
+ addHistoryItem(new EditCommand(\r
+ "Add sequences",\r
+ EditCommand.PASTE,\r
+ seqs,\r
+ 0,\r
+ viewport.alignment.getWidth(),\r
+ viewport.alignment)\r
+ );\r
+\r
+ viewport.setEndSeq(viewport.alignment.getHeight());\r
+ viewport.alignment.getWidth();\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.alignment.getSequences());\r
+\r
+ }\r
+\r
protected void cut_actionPerformed()\r
{\r
copy_actionPerformed();\r
\r
protected void delete_actionPerformed()\r
{\r
- addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
- HistoryItem.HIDE));\r
- if (viewport.getSelectionGroup() == null)\r
+\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+ if (sg == null)\r
{\r
return;\r
}\r
\r
+ Vector seqs = new Vector();\r
+ SequenceI seq;\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
+ seq = sg.getSequenceAt(i);\r
+ seqs.addElement(seq);\r
+ }\r
\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
- boolean allSequences = false;\r
- if(sg.sequences.size()==viewport.alignment.getHeight())\r
- allSequences = true;\r
\r
- for (int i = 0; i < sg.sequences.size(); i++)\r
- {\r
- SequenceI seq = sg.getSequenceAt(i);\r
- int index = viewport.getAlignment().findIndex(seq);\r
- seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
+ // If the cut affects all sequences, remove highlighted columns\r
+ if (sg.getSize() == viewport.alignment.getHeight())\r
+ {\r
+ viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
+ sg.getEndRes() + 1);\r
+ }\r
\r
- // If the cut affects all sequences, remove highlighted columns\r
- if (allSequences)\r
- {\r
- viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
- sg.getEndRes() + 1);\r
- }\r
\r
+ SequenceI [] cut = new SequenceI[seqs.size()];\r
+ for(int i=0; i<seqs.size(); i++)\r
+ cut[i] = (SequenceI)seqs.elementAt(i);\r
+\r
+\r
+ /*\r
+ //ADD HISTORY ITEM\r
+ */\r
+ addHistoryItem(new EditCommand("Cut Sequences",\r
+ EditCommand.CUT,\r
+ cut,\r
+ sg.getStartRes(),\r
+ sg.getEndRes()-sg.getStartRes()+1,\r
+ viewport.alignment));\r
\r
- if (seq.getSequence().length() < 1)\r
- {\r
- viewport.getAlignment().deleteSequence(seq);\r
- }\r
- else\r
- {\r
- viewport.getAlignment().getSequences().setElementAt(seq, index);\r
- }\r
- }\r
\r
viewport.setSelectionGroup(null);\r
viewport.alignment.deleteGroup(sg);\r
- viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);\r
+\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
+\r
if (viewport.getAlignment().getHeight() < 1)\r
{\r
- try\r
- {\r
this.setVisible(false);\r
- }\r
- catch (Exception ex)\r
- {}\r
}\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
-\r
}\r
\r
protected void deleteGroups_actionPerformed()\r
{\r
viewport.alignment.deleteAllGroups();\r
+ viewport.sequenceColours=null;\r
viewport.setSelectionGroup(null);\r
\r
alignPanel.repaint();\r
sg.setEndRes(viewport.alignment.getWidth()-1);\r
viewport.setSelectionGroup(sg);\r
alignPanel.repaint();\r
- PaintRefresher.Refresh(null, viewport.alignment);\r
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\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
+ alignPanel.idPanel.idCanvas.searchResults = null;\r
alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
alignPanel.repaint();\r
- PaintRefresher.Refresh(null, viewport.alignment);\r
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
}\r
\r
public void invertSequenceMenuItem_actionPerformed()\r
sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
}\r
\r
- PaintRefresher.Refresh(null, viewport.alignment);\r
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
}\r
\r
- public void remove2LeftMenuItem_actionPerformed()\r
+ void trimAlignment(boolean trimLeft)\r
{\r
ColumnSelection colSel = viewport.getColumnSelection();\r
+ int column;\r
+\r
if (colSel.size() > 0)\r
{\r
- addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
- HistoryItem.HIDE));\r
- int min = colSel.getMin();\r
- viewport.getAlignment().trimLeft(min);\r
- colSel.compensateForEdit(0, min);\r
+ if(trimLeft)\r
+ column = colSel.getMin();\r
+ else\r
+ column = colSel.getMax();\r
\r
- if (viewport.getSelectionGroup() != null)\r
- {\r
- viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
- }\r
+ SequenceI [] seqs;\r
+ if(viewport.getSelectionGroup()!=null)\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);\r
+ else\r
+ seqs = viewport.alignment.getSequencesArray();\r
\r
- Vector groups = viewport.alignment.getGroups();\r
- for (int i = 0; i < groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
- if (!sg.adjustForRemoveLeft(min))\r
- {\r
- viewport.alignment.deleteGroup(sg);\r
- }\r
- }\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
- }\r
- }\r
\r
- public void remove2RightMenuItem_actionPerformed()\r
- {\r
- ColumnSelection colSel = viewport.getColumnSelection();\r
- if (colSel.size() > 0)\r
- {\r
- addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
- HistoryItem.HIDE));\r
- int max = colSel.getMax();\r
- viewport.getAlignment().trimRight(max);\r
- if (viewport.getSelectionGroup() != null)\r
+ TrimRegionCommand trimRegion;\r
+ if(trimLeft)\r
{\r
- viewport.getSelectionGroup().adjustForRemoveRight(max);\r
+ trimRegion = new TrimRegionCommand("Remove Left",\r
+ TrimRegionCommand.TRIM_LEFT,\r
+ seqs,\r
+ column,\r
+ viewport.alignment,\r
+ viewport.colSel,\r
+ viewport.selectionGroup);\r
+ viewport.setStartRes(0);\r
}\r
+ else\r
+ {\r
+ trimRegion = new TrimRegionCommand("Remove Right",\r
+ TrimRegionCommand.TRIM_RIGHT,\r
+ seqs,\r
+ column,\r
+ viewport.alignment,\r
+ viewport.colSel,\r
+ viewport.selectionGroup);\r
+ }\r
+\r
+ statusBar.setText("Removed "+trimRegion.getSize()+" columns.");\r
+\r
+\r
+ addHistoryItem(trimRegion);\r
\r
Vector groups = viewport.alignment.getGroups();\r
+\r
for (int i = 0; i < groups.size(); i++)\r
{\r
SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
- if (!sg.adjustForRemoveRight(max))\r
+\r
+ if ( (trimLeft && !sg.adjustForRemoveLeft(column))\r
+ || (!trimLeft && !sg.adjustForRemoveRight(column)))\r
{\r
viewport.alignment.deleteGroup(sg);\r
}\r
}\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
- }\r
\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
+ }\r
}\r
\r
+\r
public void removeGappedColumnMenuItem_actionPerformed()\r
{\r
- addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
- viewport.alignment,\r
- HistoryItem.HIDE));\r
+ int start = 0, end = viewport.alignment.getWidth()-1;\r
\r
- //This is to maintain viewport position on first residue\r
- //of first sequence\r
- SequenceI seq = viewport.alignment.getSequenceAt(0);\r
- int startRes = seq.findPosition(viewport.startRes);\r
+ SequenceI[] seqs;\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);\r
+ start = viewport.getSelectionGroup().getStartRes();\r
+ end = viewport.getSelectionGroup().getEndRes();\r
+ }\r
+ else\r
+ seqs = viewport.alignment.getSequencesArray();\r
\r
- viewport.getAlignment().removeGaps();\r
\r
- viewport.setStartRes(seq.findIndex(startRes)-1);\r
+ RemoveGapColCommand removeGapCols =\r
+ new RemoveGapColCommand("Remove Gapped Columns",\r
+ seqs,\r
+ start, end,\r
+ viewport.alignment);\r
\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
- }\r
+ addHistoryItem(removeGapCols);\r
\r
- public void removeAllGapsMenuItem_actionPerformed()\r
- {\r
- addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
- HistoryItem.HIDE));\r
+ statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");\r
\r
//This is to maintain viewport position on first residue\r
//of first sequence\r
SequenceI seq = viewport.alignment.getSequenceAt(0);\r
int startRes = seq.findPosition(viewport.startRes);\r
+ // ShiftList shifts;\r
+ // viewport.getAlignment().removeGaps(shifts=new ShiftList());\r
+ // edit.alColumnChanges=shifts.getInverse();\r
+ // if (viewport.hasHiddenColumns)\r
+ // viewport.getColumnSelection().compensateForEdits(shifts);\r
+ viewport.setStartRes(seq.findIndex(startRes)-1);\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
\r
- SequenceI current;\r
- int jSize;\r
-\r
- Vector seqs=null;\r
+ }\r
\r
- int start=0, end = viewport.alignment.getWidth();\r
+ public void removeAllGapsMenuItem_actionPerformed()\r
+ {\r
+ int start = 0, end = viewport.alignment.getWidth()-1;\r
\r
- if (viewport.getSelectionGroup() != null\r
- && viewport.getSelectionGroup().sequences != null\r
- && viewport.getSelectionGroup().sequences.size()>0)\r
+ SequenceI[] seqs;\r
+ if (viewport.getSelectionGroup() != null)\r
{\r
- seqs = viewport.getSelectionGroup().sequences;\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);\r
start = viewport.getSelectionGroup().getStartRes();\r
- end = viewport.getSelectionGroup().getEndRes()+1;\r
+ end = viewport.getSelectionGroup().getEndRes();\r
}\r
else\r
- seqs = viewport.alignment.getSequences();\r
+ seqs = viewport.alignment.getSequencesArray();\r
\r
- for (int i = 0; i < seqs.size(); i++)\r
- {\r
- current = (SequenceI) seqs.elementAt(i);\r
- jSize = current.getLength();\r
+ //This is to maintain viewport position on first residue\r
+ //of first sequence\r
+ SequenceI seq = viewport.alignment.getSequenceAt(0);\r
+ int startRes = seq.findPosition(viewport.startRes);\r
\r
- // Removing a range is much quicker than removing gaps\r
- // one by one for long sequences\r
- int j = start;\r
- int rangeStart=-1, rangeEnd=-1;\r
+ addHistoryItem(new RemoveGapsCommand("Remove Gaps",\r
+ seqs,\r
+ start, end,\r
+ viewport.alignment));\r
\r
- do\r
- {\r
- if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
- {\r
- if(rangeStart==-1)\r
- {\r
- rangeStart = j;\r
- rangeEnd = j+1;\r
- }\r
- else\r
- {\r
- rangeEnd++;\r
- }\r
- j++;\r
- }\r
- else\r
- {\r
- if(rangeStart>-1)\r
- {\r
- current.deleteChars(rangeStart, rangeEnd);\r
- j-=rangeEnd-rangeStart;\r
- jSize-=rangeEnd-rangeStart;\r
- rangeStart = -1;\r
- rangeEnd = -1;\r
- }\r
- else\r
- j++;\r
- }\r
- }\r
- while (j < end && j < jSize);\r
- if(rangeStart>-1)\r
- {\r
- current.deleteChars(rangeStart, rangeEnd);\r
- }\r
- }\r
viewport.setStartRes(seq.findIndex(startRes)-1);\r
+\r
viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+\r
}\r
\r
- public void alignmentChanged()\r
+ public void findMenuItem_actionPerformed()\r
{\r
- viewport.updateConsensus();\r
- viewport.updateConservation ();\r
- resetAllColourSchemes();\r
- if(alignPanel.overviewPanel!=null)\r
- alignPanel.overviewPanel.updateOverviewImage();\r
- alignPanel.repaint();\r
+ new Finder(alignPanel);\r
}\r
\r
- void resetAllColourSchemes()\r
+ public void newView()\r
{\r
- ColourSchemeI cs = viewport.globalColourScheme;\r
- if(cs!=null)\r
+ AlignmentI newal;\r
+ if (viewport.hasHiddenRows)\r
+ newal = new Alignment(viewport.getAlignment().\r
+ getHiddenSequences()\r
+ .getFullAlignment().\r
+ getSequencesArray());\r
+ else\r
+ newal = new Alignment(viewport.alignment.getSequencesArray());\r
+\r
+ if(viewport.alignment.getAlignmentAnnotation()!=null)\r
{\r
- if (cs instanceof ClustalxColourScheme)\r
+ for(int i=0; i<viewport.alignment.getAlignmentAnnotation().length; i++)\r
{\r
- ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
- resetClustalX(viewport.alignment.getSequences(),\r
- viewport.alignment.getWidth());\r
+ if(!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)\r
+ {\r
+ newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);\r
+ }\r
}\r
+ }\r
\r
- cs.setConsensus(viewport.vconsensus);\r
- if (cs.conservationApplied())\r
- {\r
- Alignment al = (Alignment) viewport.alignment;\r
- Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3,\r
- al.getSequences(), 0,\r
- al.getWidth() - 1);\r
- c.calculate();\r
- c.verdict(false, viewport.ConsPercGaps);\r
+ AlignFrame newaf = new AlignFrame(newal,\r
+ viewport.applet,\r
+ "",\r
+ false);\r
\r
- cs.setConservation(c);\r
- }\r
- }\r
+ newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();\r
+ PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());\r
+ PaintRefresher.Register(newaf.alignPanel,\r
+ newaf.alignPanel.av.getSequenceSetId());\r
+\r
+ PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,\r
+ newaf.alignPanel.av.getSequenceSetId());\r
+ PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,\r
+ newaf.alignPanel.av.getSequenceSetId());\r
\r
- int s, sSize = viewport.alignment.getGroups().size();\r
- for(s=0; s<sSize; s++)\r
+ Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());\r
+ int viewSize = -1;\r
+ for (int i = 0; i < comps.size(); i++)\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
- }\r
- sg.recalcConservation();\r
+ if (comps.elementAt(i) instanceof AlignmentPanel)\r
+ viewSize++;\r
}\r
- }\r
\r
+ String title = new String(this.getTitle());\r
+ if (title.indexOf("(View") > -1)\r
+ title = title.substring(0, title.indexOf("(View"));\r
\r
+ title+= "(View "+viewSize+")";\r
\r
- public void findMenuItem_actionPerformed()\r
- {\r
- new Finder(alignPanel);\r
- }\r
+ newaf.setTitle(title.toString());\r
\r
- public void font_actionPerformed()\r
- {\r
- new FontChooser(alignPanel);\r
- }\r
+\r
+ newaf.viewport.historyList = viewport.historyList;\r
+ newaf.viewport.redoList = viewport.redoList;\r
+\r
+ }\r
\r
\r
public void seqLimits_itemStateChanged()\r
alignPanel.repaint();\r
}\r
\r
- protected void scaleAbove_actionPerformed()\r
- {\r
- viewport.setScaleAboveWrapped(scaleAbove.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void scaleLeft_actionPerformed()\r
- {\r
- viewport.setScaleLeftWrapped(scaleLeft.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void scaleRight_actionPerformed()\r
- {\r
- viewport.setScaleRightWrapped(scaleRight.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- public void viewBoxesMenuItem_actionPerformed()\r
- {\r
- viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- public void viewTextMenuItem_actionPerformed()\r
- {\r
- viewport.setShowText(viewTextMenuItem.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void renderGapsMenuItem_actionPerformed()\r
- {\r
- viewport.setRenderGaps(renderGapsMenuItem.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- public void annotationPanelMenuItem_actionPerformed()\r
- {\r
- viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
- alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
- }\r
\r
public void overviewMenuItem_actionPerformed()\r
{\r
\r
}\r
\r
- protected void noColourmenuItem_actionPerformed()\r
- {\r
- changeColour(null);\r
- }\r
-\r
- public void clustalColour_actionPerformed()\r
- {\r
- abovePIDThreshold.setState(false);\r
- changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
- viewport.alignment.getWidth()));\r
- }\r
-\r
- public void zappoColour_actionPerformed()\r
- {\r
- changeColour(new ZappoColourScheme());\r
- }\r
-\r
- public void taylorColour_actionPerformed()\r
- {\r
- changeColour(new TaylorColourScheme());\r
- }\r
-\r
- public void hydrophobicityColour_actionPerformed()\r
- {\r
- changeColour(new HydrophobicColourScheme());\r
- }\r
-\r
- public void helixColour_actionPerformed()\r
- {\r
- changeColour(new HelixColourScheme());\r
- }\r
-\r
- public void strandColour_actionPerformed()\r
- {\r
- changeColour(new StrandColourScheme());\r
- }\r
-\r
- public void turnColour_actionPerformed()\r
- {\r
- changeColour(new TurnColourScheme());\r
- }\r
-\r
- public void buriedColour_actionPerformed()\r
- {\r
- changeColour(new BuriedColourScheme());\r
- }\r
-\r
- public void nucleotideColour_actionPerformed()\r
- {\r
- changeColour(new NucleotideColourScheme());\r
- }\r
-\r
- protected void applyToAllGroups_actionPerformed()\r
- {\r
- viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
- }\r
\r
void changeColour(ColourSchemeI cs)\r
{\r
cs.setConservation(null);\r
}\r
\r
- cs.setConsensus(viewport.vconsensus);\r
+ cs.setConsensus(viewport.hconsensus);\r
\r
}\r
viewport.setGlobalColourScheme(cs);\r
}\r
if (cs instanceof ClustalxColourScheme)\r
{\r
- sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
+ sg.cs = new ClustalxColourScheme(\r
+ sg.getSequences(viewport.hiddenRepSequences),\r
+ sg.getWidth());\r
}\r
else\r
{\r
|| cs instanceof Blosum62ColourScheme)\r
{\r
sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
+ sg.cs.setConsensus(AAFrequency.calculate(\r
+ sg.getSequences(viewport.hiddenRepSequences), 0, sg.getWidth()));\r
}\r
else\r
sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
{\r
Conservation c = new Conservation("Group",\r
ResidueProperties.propHash, 3,\r
- sg.sequences, 0,\r
+ sg.getSequences(viewport.hiddenRepSequences), 0,\r
viewport.alignment.getWidth() - 1);\r
c.calculate();\r
c.verdict(false, viewport.ConsPercGaps);\r
modifyPID_actionPerformed();\r
}\r
\r
- public void userDefinedColour_actionPerformed()\r
- {\r
- new UserDefinedColours(alignPanel, null);\r
- }\r
-\r
- public void PIDColour_actionPerformed()\r
- {\r
- changeColour(new PIDColourScheme());\r
- }\r
\r
- public void BLOSUM62Colour_actionPerformed()\r
- {\r
- changeColour(new Blosum62ColourScheme());\r
- }\r
\r
public void sortPairwiseMenuItem_actionPerformed()\r
{\r
- addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
- HistoryItem.SORT));\r
+ SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();\r
AlignmentSorter.sortByPID(viewport.getAlignment(),\r
viewport.getAlignment().getSequenceAt(0));\r
+ addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));\r
alignPanel.repaint();\r
}\r
\r
public void sortIDMenuItem_actionPerformed()\r
{\r
- addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
- HistoryItem.SORT));\r
+ // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
+ // HistoryItem.SORT));\r
AlignmentSorter.sortByID(viewport.getAlignment());\r
alignPanel.repaint();\r
}\r
\r
public void sortGroupMenuItem_actionPerformed()\r
{\r
- addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
- HistoryItem.SORT));\r
+ // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
+ // HistoryItem.SORT));\r
AlignmentSorter.sortByGroup(viewport.getAlignment());\r
alignPanel.repaint();\r
\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() > 1)\r
{\r
Frame frame = new Frame();\r
frame.add(new PairwiseAlignPanel(alignPanel));\r
\r
protected void avTreeBlosumMenuItem_actionPerformed()\r
{\r
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
+ NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");\r
}\r
\r
void NewTreePanel(String type, String pwType, String title)\r
\r
}\r
\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() > 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.setTreeImport();\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
{\r
public void actionPerformed(ActionEvent evt)\r
{\r
- addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
- HistoryItem.SORT));\r
+ // addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
+ // HistoryItem.SORT));\r
AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
alignPanel.repaint();\r
}\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 loadAnnotations = new MenuItem("Load Features/Annotations ...");\r
+ protected MenuItem outputFeatures = new MenuItem("Export Features ...");\r
+ protected MenuItem outputAnnotations = new MenuItem("Export Annotations ...");\r
+\r
+ protected MenuItem closeMenuItem = new MenuItem("Close");\r
+ protected Menu editMenu = new Menu("Edit");\r
+ protected Menu viewMenu = new Menu("View");\r
+ 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 wrapMenuItem = new CheckboxMenuItem();\r
protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
MenuItem findMenuItem = new MenuItem();\r
- Menu searchMenu = new Menu();\r
- protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
protected MenuItem nucleotideColour = new MenuItem();\r
MenuItem deleteGroups = new MenuItem();\r
MenuItem delete = 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
protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
Panel embeddedMenu;\r
Label embeddedEdit;\r
- Label embeddedSearch;\r
+ Label embeddedSelect;\r
Label embeddedView;\r
+ Label embeddedFormat;\r
Label embeddedColour;\r
Label embeddedFile;\r
Label embeddedHelp;\r
MenuItem item;\r
\r
// dynamically fill save as menu with available formats\r
- for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++)\r
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)\r
{\r
\r
- item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.\r
- elementAt(\r
- i));\r
+ item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);\r
+\r
item.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\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
+ loadAnnotations.addActionListener(this);\r
+ outputFeatures.addActionListener(this);\r
+ outputAnnotations.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
averageDistanceTreeMenuItem.addActionListener(this);\r
neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
neighbourTreeMenuItem.addActionListener(this);\r
- alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
statusBar.setBackground(Color.white);\r
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
statusBar.setText("Status bar");\r
renderGapsMenuItem.addItemListener(this);\r
findMenuItem.setLabel("Find...");\r
findMenuItem.addActionListener(this);\r
- searchMenu.setLabel("Search");\r
-\r
- abovePIDThreshold.setLabel("Above Identity Threshold");\r
+ abovePIDThreshold.setLabel("Above Identity Threshold");\r
abovePIDThreshold.addItemListener(this);\r
nucleotideColour.setLabel("Nucleotide");\r
nucleotideColour.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
-\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
+ formatMenu.setLabel("Format");\r
+ selectMenu.setLabel("Select");\r
+ newView.setLabel("New View");\r
+ newView.addActionListener(this);\r
alignFrameMenuBar.add(fileMenu);\r
alignFrameMenuBar.add(editMenu);\r
- alignFrameMenuBar.add(searchMenu);\r
- alignFrameMenuBar.add(viewMenu);\r
- alignFrameMenuBar.add(colourMenu);\r
+ alignFrameMenuBar.add(selectMenu);\r
+ alignFrameMenuBar.add(viewMenu);\r
+ alignFrameMenuBar.add(formatMenu);\r
+ alignFrameMenuBar.add(colourMenu);\r
alignFrameMenuBar.add(calculateMenu);\r
alignFrameMenuBar.add(helpMenu);\r
+\r
fileMenu.add(inputText);\r
+ fileMenu.add(loadTree);\r
+ fileMenu.add(loadAnnotations);\r
+\r
+ fileMenu.addSeparator();\r
fileMenu.add(outputTextboxMenu);\r
+ fileMenu.add(outputFeatures);\r
+ fileMenu.add(outputAnnotations);\r
+\r
+ if(jalviewServletURL!=null)\r
+ fileMenu.add(loadApplication);\r
+\r
fileMenu.addSeparator();\r
fileMenu.add(closeMenuItem);\r
+\r
editMenu.add(undoMenuItem);\r
editMenu.add(redoMenuItem);\r
editMenu.add(cut);\r
editMenu.add(pasteMenu);\r
editMenu.add(delete);\r
editMenu.addSeparator();\r
- editMenu.add(selectAllSequenceMenuItem);\r
- editMenu.add(deselectAllSequenceMenuItem);\r
- editMenu.add(invertSequenceMenuItem);\r
- editMenu.add(deleteGroups);\r
- editMenu.addSeparator();\r
editMenu.add(remove2LeftMenuItem);\r
editMenu.add(remove2RightMenuItem);\r
editMenu.add(removeGappedColumnMenuItem);\r
editMenu.add(removeAllGapsMenuItem);\r
editMenu.add(removeRedundancyMenuItem);\r
- searchMenu.add(findMenuItem);\r
- viewMenu.add(font);\r
- viewMenu.addSeparator();\r
- viewMenu.add(seqLimits);\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(viewBoxesMenuItem);\r
- viewMenu.add(viewTextMenuItem);\r
- viewMenu.add(colourTextMenuItem);\r
- viewMenu.add(renderGapsMenuItem);\r
- viewMenu.add(annotationPanelMenuItem);\r
- viewMenu.addSeparator();\r
+ viewMenu.add(newView);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(menu1);\r
+ viewMenu.add(menu2);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(annotationPanelMenuItem);\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
+ formatMenu.add(font);\r
+ formatMenu.add(seqLimits);\r
+ formatMenu.add(wrapMenuItem);\r
+ formatMenu.add(scaleAbove);\r
+ formatMenu.add(scaleLeft);\r
+ formatMenu.add(scaleRight);\r
+ formatMenu.add(viewBoxesMenuItem);\r
+ formatMenu.add(viewTextMenuItem);\r
+ formatMenu.add(colourTextMenuItem);\r
+ formatMenu.add(renderGapsMenuItem);\r
+ selectMenu.add(findMenuItem);\r
+ selectMenu.addSeparator();\r
+ selectMenu.add(selectAllSequenceMenuItem);\r
+ selectMenu.add(deselectAllSequenceMenuItem);\r
+ selectMenu.add(invertSequenceMenuItem);\r
+ selectMenu.add(invertColSel);\r
+ selectMenu.add(deleteGroups);\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
+ embeddedEdit = new Label("Edit");\r
+ embeddedSelect = new Label("Select");\r
+ embeddedView = new Label("View");\r
+ embeddedFormat = new Label("Format");\r
+ embeddedColour = new Label("Colour");\r
+ embeddedFile = new Label("File");\r
+ embeddedHelp = new Label("Help");\r
+ embeddedCalculate = new Label("Calculate");\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
+ embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
- embeddedColour.setText("Colour");\r
+ embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\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(embeddedSelect);\r
embeddedMenu.add(embeddedView);\r
+ embeddedMenu.add(embeddedFormat);\r
embeddedMenu.add(embeddedColour);\r
embeddedMenu.add(embeddedCalculate);\r
embeddedMenu.add(embeddedHelp);\r
flowLayout1.setVgap(0);\r
embeddedFile.addMouseListener(this);\r
embeddedEdit.addMouseListener(this);\r
- embeddedSearch.addMouseListener(this);\r
+ embeddedSelect.addMouseListener(this);\r
embeddedView.addMouseListener(this);\r
+ embeddedFormat.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(2); // Seperator\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
+ viewport.applet.setLayout(new BorderLayout());\r
+ viewport.applet.add(embeddedMenu, BorderLayout.NORTH);\r
+ viewport.applet.add(statusBar, BorderLayout.SOUTH);\r
\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
+ viewPopup, formatPopup, 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
+ Menu formatMenu = new Menu();\r
+ Menu selectMenu = new Menu();\r
+ MenuItem newView = new MenuItem();\r
\r
public void mousePressed(MouseEvent evt)\r
{\r
{\r
popup = editPopup = genPopupMenu(editPopup, editMenu);\r
}\r
- else if(source==embeddedSearch)\r
+ else if(source==embeddedSelect)\r
{\r
- popup = searchPopup = genPopupMenu(searchPopup, searchMenu);\r
+ popup = searchPopup = genPopupMenu(searchPopup, selectMenu);\r
}\r
else if(source==embeddedView)\r
{\r
popup = viewPopup = genPopupMenu(viewPopup, viewMenu);\r
}\r
+ else if (source ==embeddedFormat)\r
+ {\r
+ popup = formatPopup = genPopupMenu(formatPopup, formatMenu);\r
+ }\r
else if(source==embeddedColour)\r
{\r
popup = colourPopup = genPopupMenu(colourPopup, colourMenu);\r