/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 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
\r
package jalview.appletgui;\r
\r
-import jalview.schemes.*;\r
-import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
-import jalview.io.*;\r
-import jalview.commands.*;\r
+import java.io.*;\r
+import java.net.*;\r
+import java.util.*;\r
+\r
import java.awt.*;\r
import java.awt.event.*;\r
-import java.util.*;\r
-import java.io.InputStreamReader;\r
-import java.io.BufferedReader;\r
-import java.net.URL;\r
\r
+import jalview.analysis.*;\r
+import jalview.commands.*;\r
+import jalview.datamodel.*;\r
+import jalview.io.*;\r
+import jalview.schemes.*;\r
\r
-public class AlignFrame extends Frame implements ActionListener,\r
+public class AlignFrame\r
+ extends Frame implements ActionListener,\r
ItemListener, KeyListener, MouseListener\r
{\r
public AlignmentPanel alignPanel;\r
\r
String jalviewServletURL;\r
\r
-\r
- public AlignFrame(AlignmentI al,\r
- jalview.bin.JalviewLite applet,\r
- String title,\r
- boolean embedded)\r
+ public AlignFrame(AlignmentI al,\r
+ jalview.bin.JalviewLite applet,\r
+ String title,\r
+ boolean embedded)\r
{\r
\r
if (applet != null)\r
+ {\r
jalviewServletURL = applet.getParameter("APPLICATION_URL");\r
+ }\r
\r
- try{\r
+ try\r
+ {\r
jbInit();\r
- }catch(Exception ex)\r
+ }\r
+ catch (Exception ex)\r
{\r
ex.printStackTrace();\r
}\r
\r
seqLimits.setState(viewport.showJVSuffix);\r
\r
- if(applet!=null)\r
+ if (applet != null)\r
{\r
String param = applet.getParameter("sortBy");\r
if (param != null)\r
{\r
if (param.equalsIgnoreCase("Id"))\r
+ {\r
sortIDMenuItem_actionPerformed();\r
+ }\r
else if (param.equalsIgnoreCase("Pairwise Identity"))\r
+ {\r
sortPairwiseMenuItem_actionPerformed();\r
+ }\r
}\r
\r
param = applet.getParameter("wrap");\r
\r
}\r
\r
- //Some JVMS send keyevents to Top frame or lowest panel,\r
- //Havent worked out why yet. So add to both this frame and seqCanvas for now\r
- this.addKeyListener(this);\r
- alignPanel.seqPanel.seqCanvas.addKeyListener(this);\r
- alignPanel.idPanel.idCanvas.addKeyListener(this);\r
- alignPanel.scalePanel.addKeyListener(this);\r
- alignPanel.annotationPanel.addKeyListener(this);\r
+ //Some JVMS send keyevents to Top frame or lowest panel,\r
+ //Havent worked out why yet. So add to both this frame and seqCanvas for now\r
+ this.addKeyListener(this);\r
+ alignPanel.seqPanel.seqCanvas.addKeyListener(this);\r
+ alignPanel.idPanel.idCanvas.addKeyListener(this);\r
+ 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
+ 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
+\r
public AlignViewport getAlignViewport()\r
{\r
return viewport;\r
return alignPanel.seqPanel.seqCanvas;\r
}\r
\r
-\r
/**\r
* DOCUMENT ME!\r
*\r
{\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
+ try\r
+ {\r
+ featuresFile = new jalview.io.FeaturesFile(file,\r
+ type).parse(viewport.alignment,\r
+ alignPanel.seqPanel.seqCanvas.\r
+ getFeatureRenderer().featureColours,\r
+ featureLinks,\r
+ true);\r
}\r
- catch(Exception ex)\r
+ catch (Exception ex)\r
{\r
ex.printStackTrace();\r
}\r
\r
- if(featuresFile)\r
+ if (featuresFile)\r
{\r
- if(featureLinks.size()>0)\r
+ if (featureLinks.size() > 0)\r
+ {\r
alignPanel.seqPanel.seqCanvas\r
.getFeatureRenderer().featureLinks = featureLinks;\r
+ }\r
viewport.showSequenceFeatures = true;\r
sequenceFeatures.setState(true);\r
alignPanel.repaint();\r
\r
}\r
\r
-\r
public void keyPressed(KeyEvent evt)\r
{\r
if (viewport.cursorMode\r
}\r
break;\r
case KeyEvent.VK_DOWN:\r
- if(viewport.cursorMode)\r
+ if (viewport.cursorMode)\r
{\r
- alignPanel.seqPanel.moveCursor(0,1);\r
+ alignPanel.seqPanel.moveCursor(0, 1);\r
}\r
else\r
+ {\r
moveSelectedSequences(false);\r
+ }\r
break;\r
\r
case KeyEvent.VK_UP:\r
if (viewport.cursorMode)\r
{\r
- alignPanel.seqPanel.moveCursor(0,-1);\r
+ alignPanel.seqPanel.moveCursor(0, -1);\r
}\r
else\r
+ {\r
moveSelectedSequences(true);\r
+ }\r
break;\r
\r
case KeyEvent.VK_LEFT:\r
- if(viewport.cursorMode)\r
+ if (viewport.cursorMode)\r
{\r
- alignPanel.seqPanel.moveCursor(-1,0);\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
+ alignPanel.seqPanel.moveCursor(1, 0);\r
}\r
break;\r
case KeyEvent.VK_SPACE:\r
- if(viewport.cursorMode)\r
+ if (viewport.cursorMode)\r
{\r
alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()\r
|| evt.isShiftDown()\r
\r
case KeyEvent.VK_DELETE:\r
case KeyEvent.VK_BACK_SPACE:\r
- if(viewport.cursorMode)\r
+ if (viewport.cursorMode)\r
{\r
alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()\r
|| evt.isShiftDown()\r
|| evt.isAltDown());\r
}\r
- else\r
+ else\r
{\r
cut_actionPerformed();\r
alignPanel.seqPanel.seqCanvas.repaint();\r
break;\r
\r
case KeyEvent.VK_S:\r
- if(viewport.cursorMode)\r
+ if (viewport.cursorMode)\r
{\r
alignPanel.seqPanel.setCursorRow();\r
}\r
break;\r
case KeyEvent.VK_P:\r
- if(viewport.cursorMode)\r
+ if (viewport.cursorMode)\r
{\r
alignPanel.seqPanel.setCursorPosition();\r
}\r
\r
case KeyEvent.VK_ENTER:\r
case KeyEvent.VK_COMMA:\r
- if(viewport.cursorMode)\r
+ if (viewport.cursorMode)\r
{\r
alignPanel.seqPanel.setCursorRowAndColumn();\r
}\r
break;\r
\r
case KeyEvent.VK_Q:\r
- if(viewport.cursorMode)\r
+ if (viewport.cursorMode)\r
{\r
alignPanel.seqPanel.setSelectionAreaAtCursor(true);\r
}\r
break;\r
case KeyEvent.VK_M:\r
- if(viewport.cursorMode)\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
+ 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
boolean hide = false;\r
SequenceGroup sg = viewport.getSelectionGroup();\r
\r
- if(toggleSeqs)\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
+ else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))\r
+ {\r
viewport.showAllHiddenSeqs();\r
+ }\r
}\r
\r
- if(toggleCols)\r
+ if (toggleCols)\r
{\r
if (viewport.colSel.getSelected().size() > 0)\r
{\r
viewport.hideSelectedColumns();\r
- if(!toggleSeqs)\r
- viewport.selectionGroup = sg;\r
+ if (!toggleSeqs)\r
+ {\r
+ viewport.selectionGroup = sg;\r
+ }\r
}\r
else if (!hide)\r
+ {\r
viewport.showAllHiddenColumns();\r
+ }\r
}\r
break;\r
}\r
\r
case KeyEvent.VK_PAGE_UP:\r
if (viewport.wrapAlignment)\r
+ {\r
alignPanel.scrollUp(true);\r
+ }\r
else\r
+ {\r
alignPanel.setScrollValues(viewport.startRes,\r
viewport.startSeq\r
- viewport.endSeq + viewport.startSeq);\r
+ }\r
break;\r
\r
case KeyEvent.VK_PAGE_DOWN:\r
if (viewport.wrapAlignment)\r
+ {\r
alignPanel.scrollUp(false);\r
+ }\r
else\r
+ {\r
alignPanel.setScrollValues(viewport.startRes,\r
viewport.startSeq\r
+ viewport.endSeq - viewport.startSeq);\r
+ }\r
break;\r
\r
case KeyEvent.VK_Z:\r
if (evt.isControlDown())\r
{\r
if (evt.isShiftDown())\r
+ {\r
this.removeAllGapsMenuItem_actionPerformed();\r
+ }\r
else\r
+ {\r
removeGappedColumnMenuItem_actionPerformed();\r
+ }\r
}\r
break;\r
case KeyEvent.VK_I:\r
if (evt.isControlDown())\r
{\r
if (evt.isAltDown())\r
+ {\r
viewport.invertColumnSelection();\r
+ }\r
else\r
+ {\r
this.invertSequenceMenuItem_actionPerformed();\r
+ }\r
}\r
break;\r
\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
+ break;\r
\r
+ case KeyEvent.VK_T:\r
+ if (evt.isControlDown())\r
+ {\r
+ newView();\r
+ }\r
+ break;\r
\r
- }\r
- alignPanel.repaint();\r
+ }\r
+ alignPanel.repaint();\r
}\r
+\r
public void keyReleased(KeyEvent evt)\r
{}\r
+\r
public void keyTyped(KeyEvent evt)\r
{}\r
\r
-public void itemStateChanged(ItemEvent evt)\r
- {\r
- if(evt.getSource()==colourTextMenuItem)\r
- colourTextMenuItem_actionPerformed();\r
- else if(evt.getSource()==wrapMenuItem)\r
- wrapMenuItem_actionPerformed();\r
- else if(evt.getSource()==scaleAbove)\r
- viewport.setScaleAboveWrapped(scaleAbove.getState());\r
- else if(evt.getSource()==scaleLeft)\r
- viewport.setScaleLeftWrapped(scaleLeft.getState());\r
- else if(evt.getSource()==scaleRight)\r
- viewport.setScaleRightWrapped(scaleRight.getState());\r
- else if(evt.getSource()==seqLimits)\r
+ public void itemStateChanged(ItemEvent evt)\r
+ {\r
+ if (evt.getSource() == colourTextMenuItem)\r
+ {\r
+ colourTextMenuItem_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == wrapMenuItem)\r
+ {\r
+ wrapMenuItem_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == scaleAbove)\r
+ {\r
+ viewport.setScaleAboveWrapped(scaleAbove.getState());\r
+ }\r
+ else if (evt.getSource() == scaleLeft)\r
+ {\r
+ viewport.setScaleLeftWrapped(scaleLeft.getState());\r
+ }\r
+ else if (evt.getSource() == scaleRight)\r
+ {\r
+ viewport.setScaleRightWrapped(scaleRight.getState());\r
+ }\r
+ else if (evt.getSource() == seqLimits)\r
+ {\r
seqLimits_itemStateChanged();\r
- else if(evt.getSource()==viewBoxesMenuItem)\r
- viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
- else if(evt.getSource()==viewTextMenuItem)\r
- viewport.setShowText(viewTextMenuItem.getState());\r
- else if(evt.getSource()==renderGapsMenuItem)\r
- viewport.setRenderGaps(renderGapsMenuItem.getState());\r
- else if(evt.getSource()==annotationPanelMenuItem)\r
+ }\r
+ else if (evt.getSource() == viewBoxesMenuItem)\r
+ {\r
+ viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
+ }\r
+ else if (evt.getSource() == viewTextMenuItem)\r
+ {\r
+ viewport.setShowText(viewTextMenuItem.getState());\r
+ }\r
+ else if (evt.getSource() == renderGapsMenuItem)\r
+ {\r
+ viewport.setRenderGaps(renderGapsMenuItem.getState());\r
+ }\r
+ else if (evt.getSource() == annotationPanelMenuItem)\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
- viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
- else if(evt.getSource()==autoCalculate)\r
- viewport.autocalculateConsensus = autoCalculate.getState();\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
+ {\r
+ conservationMenuItem_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == abovePIDThreshold)\r
+ {\r
+ abovePIDThreshold_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == applyToAllGroups)\r
+ {\r
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
+ }\r
+ else if (evt.getSource() == autoCalculate)\r
+ {\r
+ viewport.autocalculateConsensus = autoCalculate.getState();\r
+ }\r
\r
- alignPanel.repaint();\r
+ alignPanel.repaint();\r
}\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
+\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
Object source = evt.getSource();\r
\r
- if(source==inputText)\r
+ if (source == inputText)\r
+ {\r
inputText_actionPerformed();\r
- else if(source==loadTree)\r
+ }\r
+ else if (source == loadTree)\r
+ {\r
loadTree_actionPerformed();\r
- else if(source==loadApplication)\r
+ }\r
+ else if (source == loadApplication)\r
+ {\r
launchFullApplication();\r
+ }\r
else if (source == loadAnnotations)\r
+ {\r
loadAnnotations();\r
+ }\r
else if (source == outputAnnotations)\r
+ {\r
outputAnnotations(true);\r
- else if(source == outputFeatures)\r
+ }\r
+ else if (source == outputFeatures)\r
+ {\r
outputFeatures(true, "Jalview");\r
- else if(source==closeMenuItem)\r
+ }\r
+ else if (source == closeMenuItem)\r
+ {\r
closeMenuItem_actionPerformed();\r
- else if(source==copy)\r
+ }\r
+ else if (source == copy)\r
+ {\r
copy_actionPerformed();\r
- else if(source==undoMenuItem)\r
+ }\r
+ else if (source == undoMenuItem)\r
+ {\r
undoMenuItem_actionPerformed();\r
- else if(source==redoMenuItem)\r
+ }\r
+ else if (source == redoMenuItem)\r
+ {\r
redoMenuItem_actionPerformed();\r
- else if(source==inputText)\r
- inputText_actionPerformed();\r
- else if(source==closeMenuItem)\r
- closeMenuItem_actionPerformed();\r
- else if(source==undoMenuItem)\r
- undoMenuItem_actionPerformed();\r
- else if(source==redoMenuItem)\r
- redoMenuItem_actionPerformed();\r
- else if(source==copy)\r
- copy_actionPerformed();\r
- else if(source==pasteNew)\r
- pasteNew_actionPerformed();\r
- else if(source==pasteThis)\r
- pasteThis_actionPerformed();\r
- else if(source==cut)\r
- cut_actionPerformed();\r
- else if(source==delete)\r
- delete_actionPerformed();\r
- else if(source==deleteGroups)\r
- deleteGroups_actionPerformed();\r
- else if(source==selectAllSequenceMenuItem)\r
- selectAllSequenceMenuItem_actionPerformed();\r
- else if(source==deselectAllSequenceMenuItem)\r
- deselectAllSequenceMenuItem_actionPerformed();\r
- else if(source==invertSequenceMenuItem)\r
- invertSequenceMenuItem_actionPerformed();\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(source==removeAllGapsMenuItem)\r
- removeAllGapsMenuItem_actionPerformed();\r
- else if(source==findMenuItem)\r
- findMenuItem_actionPerformed();\r
- else if(source==font)\r
- new FontChooser(alignPanel);\r
+ }\r
+ else if (source == inputText)\r
+ {\r
+ inputText_actionPerformed();\r
+ }\r
+ else if (source == closeMenuItem)\r
+ {\r
+ closeMenuItem_actionPerformed();\r
+ }\r
+ else if (source == undoMenuItem)\r
+ {\r
+ undoMenuItem_actionPerformed();\r
+ }\r
+ else if (source == redoMenuItem)\r
+ {\r
+ redoMenuItem_actionPerformed();\r
+ }\r
+ else if (source == copy)\r
+ {\r
+ copy_actionPerformed();\r
+ }\r
+ else if (source == pasteNew)\r
+ {\r
+ pasteNew_actionPerformed();\r
+ }\r
+ else if (source == pasteThis)\r
+ {\r
+ pasteThis_actionPerformed();\r
+ }\r
+ else if (source == cut)\r
+ {\r
+ cut_actionPerformed();\r
+ }\r
+ else if (source == delete)\r
+ {\r
+ delete_actionPerformed();\r
+ }\r
+ else if (source == deleteGroups)\r
+ {\r
+ deleteGroups_actionPerformed();\r
+ }\r
+ else if (source == selectAllSequenceMenuItem)\r
+ {\r
+ selectAllSequenceMenuItem_actionPerformed();\r
+ }\r
+ else if (source == deselectAllSequenceMenuItem)\r
+ {\r
+ deselectAllSequenceMenuItem_actionPerformed();\r
+ }\r
+ else if (source == invertSequenceMenuItem)\r
+ {\r
+ invertSequenceMenuItem_actionPerformed();\r
+ }\r
+ else if (source == invertColSel)\r
+ {\r
+ viewport.invertColumnSelection();\r
+ alignPanel.repaint();\r
+ }\r
+ else if (source == remove2LeftMenuItem)\r
+ {\r
+ trimAlignment(true);\r
+ }\r
+ else if (source == remove2RightMenuItem)\r
+ {\r
+ trimAlignment(false);\r
+ }\r
+ else if (source == removeGappedColumnMenuItem)\r
+ {\r
+ removeGappedColumnMenuItem_actionPerformed();\r
+ }\r
+ else if (source == removeAllGapsMenuItem)\r
+ {\r
+ removeAllGapsMenuItem_actionPerformed();\r
+ }\r
+ else if (source == findMenuItem)\r
+ {\r
+ findMenuItem_actionPerformed();\r
+ }\r
+ else if (source == font)\r
+ {\r
+ new FontChooser(alignPanel);\r
+ }\r
else if (source == newView)\r
+ {\r
newView();\r
- else if(source==showColumns)\r
+ }\r
+ else if (source == showColumns)\r
{\r
- viewport.showAllHiddenColumns(); alignPanel.repaint();\r
+ viewport.showAllHiddenColumns();\r
+ alignPanel.repaint();\r
}\r
- else if(source==showSeqs)\r
+ else if (source == showSeqs)\r
{\r
viewport.showAllHiddenSeqs();\r
}\r
- else if(source == hideColumns)\r
+ else if (source == hideColumns)\r
{\r
- viewport.hideSelectedColumns(); alignPanel.repaint();\r
+ viewport.hideSelectedColumns();\r
+ alignPanel.repaint();\r
}\r
- else if(source == hideSequences && viewport.getSelectionGroup()!=null)\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(source==noColourmenuItem)\r
- changeColour(null);\r
- else if(source==clustalColour)\r
+ else if (source == featureSettings)\r
+ {\r
+ new FeatureSettings(alignPanel);\r
+ }\r
+ else if (source == overviewMenuItem)\r
+ {\r
+ overviewMenuItem_actionPerformed();\r
+ }\r
+ else if (source == noColourmenuItem)\r
+ {\r
+ changeColour(null);\r
+ }\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
+ {\r
+ changeColour(new ZappoColourScheme());\r
+ }\r
+ else if (source == taylorColour)\r
+ {\r
+ changeColour(new TaylorColourScheme());\r
+ }\r
+ else if (source == hydrophobicityColour)\r
+ {\r
+ changeColour(new HydrophobicColourScheme());\r
+ }\r
+ else if (source == helixColour)\r
+ {\r
+ changeColour(new HelixColourScheme());\r
+ }\r
+ else if (source == strandColour)\r
+ {\r
+ changeColour(new StrandColourScheme());\r
+ }\r
+ else if (source == turnColour)\r
+ {\r
+ changeColour(new TurnColourScheme());\r
+ }\r
+ else if (source == buriedColour)\r
+ {\r
+ changeColour(new BuriedColourScheme());\r
+ }\r
+ else if (source == nucleotideColour)\r
+ {\r
+ changeColour(new NucleotideColourScheme());\r
+ }\r
+ else if (source == modifyPID)\r
+ {\r
+ modifyPID_actionPerformed();\r
+ }\r
+ else if (source == modifyConservation)\r
+ {\r
+ modifyConservation_actionPerformed();\r
+ }\r
+ else if (source == userDefinedColour)\r
+ {\r
+ new UserDefinedColours(alignPanel, null);\r
+ }\r
+ else if (source == PIDColour)\r
+ {\r
+ changeColour(new PIDColourScheme());\r
+ }\r
+ else if (source == BLOSUM62Colour)\r
+ {\r
+ changeColour(new Blosum62ColourScheme());\r
+ }\r
+ else if (source == annotationColour)\r
+ {\r
+ new AnnotationColourChooser(viewport, alignPanel);\r
+ }\r
+ else if (source == sortPairwiseMenuItem)\r
+ {\r
+ sortPairwiseMenuItem_actionPerformed();\r
+ }\r
+ else if (source == sortIDMenuItem)\r
+ {\r
+ sortIDMenuItem_actionPerformed();\r
+ }\r
+ else if (source == sortGroupMenuItem)\r
+ {\r
+ sortGroupMenuItem_actionPerformed();\r
+ }\r
+ else if (source == removeRedundancyMenuItem)\r
+ {\r
+ removeRedundancyMenuItem_actionPerformed();\r
+ }\r
+ else if (source == pairwiseAlignmentMenuItem)\r
+ {\r
+ pairwiseAlignmentMenuItem_actionPerformed();\r
+ }\r
+ else if (source == PCAMenuItem)\r
+ {\r
+ PCAMenuItem_actionPerformed();\r
+ }\r
+ else if (source == averageDistanceTreeMenuItem)\r
+ {\r
+ averageDistanceTreeMenuItem_actionPerformed();\r
+ }\r
+ else if (source == neighbourTreeMenuItem)\r
+ {\r
+ neighbourTreeMenuItem_actionPerformed();\r
+ }\r
+ else if (source == njTreeBlosumMenuItem)\r
+ {\r
+ njTreeBlosumMenuItem_actionPerformed();\r
+ }\r
+ else if (source == avDistanceTreeBlosumMenuItem)\r
+ {\r
+ avTreeBlosumMenuItem_actionPerformed();\r
+ }\r
+ else if (source == documentation)\r
+ {\r
+ documentation_actionPerformed();\r
+ }\r
+ else if (source == about)\r
+ {\r
+ about_actionPerformed();\r
+ }\r
+\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(source==modifyConservation)\r
- modifyConservation_actionPerformed();\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(source==sortIDMenuItem)\r
- sortIDMenuItem_actionPerformed();\r
- else if(source==sortGroupMenuItem)\r
- sortGroupMenuItem_actionPerformed();\r
- else if(source==removeRedundancyMenuItem)\r
- removeRedundancyMenuItem_actionPerformed();\r
- else if(source==pairwiseAlignmentMenuItem)\r
- pairwiseAlignmentMenuItem_actionPerformed();\r
- else if(source==PCAMenuItem)\r
- PCAMenuItem_actionPerformed();\r
- else if(source==averageDistanceTreeMenuItem)\r
- averageDistanceTreeMenuItem_actionPerformed();\r
- else if(source==neighbourTreeMenuItem)\r
- neighbourTreeMenuItem_actionPerformed();\r
- else if(source==njTreeBlosumMenuItem)\r
- njTreeBlosumMenuItem_actionPerformed();\r
- else if(source==avDistanceTreeBlosumMenuItem)\r
- avTreeBlosumMenuItem_actionPerformed();\r
- else if(source==documentation)\r
- documentation_actionPerformed();\r
- else if(source==about)\r
- about_actionPerformed();\r
-\r
- }\r
\r
public void inputText_actionPerformed()\r
{\r
"Alignment output - " + e.getActionCommand(),\r
600, 500);\r
cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),\r
- viewport.getAlignment(),\r
- viewport.showJVSuffix));\r
+ viewport.getAlignment(),\r
+ viewport.showJVSuffix));\r
}\r
\r
public void loadAnnotations()\r
cap.setAnnotationImport();\r
Frame frame = new Frame();\r
frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);\r
\r
}\r
\r
viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,\r
viewport.alignment.getGroups());\r
\r
- if(displayTextbox)\r
+ if (displayTextbox)\r
{\r
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
Frame frame = new Frame();\r
{\r
String features;\r
if (format.equalsIgnoreCase("Jalview"))\r
+ {\r
features = new FeaturesFile().printJalviewFormat(\r
- viewport.alignment.getSequencesArray(),\r
- viewport.featuresDisplayed);\r
+ viewport.alignment.getSequencesArray(),\r
+ viewport.featuresDisplayed);\r
+ }\r
else\r
+ {\r
features = new FeaturesFile().printGFFFormat(\r
- viewport.alignment.getSequencesArray(),\r
- viewport.featuresDisplayed);\r
-\r
+ viewport.alignment.getSequencesArray(),\r
+ viewport.featuresDisplayed);\r
+ }\r
\r
- if(displayTextbox)\r
+ if (displayTextbox)\r
{\r
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
Frame frame = new Frame();\r
{\r
StringBuffer url = new StringBuffer(jalviewServletURL);\r
\r
- url.append("?open="+\r
- appendProtocol( viewport.applet.getParameter("file") ) );\r
+ url.append("?open=" +\r
+ appendProtocol(viewport.applet.getParameter("file")));\r
\r
- if(viewport.applet.getParameter("features")!=null)\r
+ if (viewport.applet.getParameter("features") != null)\r
{\r
- url.append( "&features=" );\r
- url.append( appendProtocol( viewport.applet.getParameter("features") ) );\r
+ url.append("&features=");\r
+ url.append(appendProtocol(viewport.applet.getParameter("features")));\r
}\r
\r
- if(viewport.applet.getParameter("annotations")!=null)\r
+ if (viewport.applet.getParameter("annotations") != null)\r
{\r
- url.append( "&annotations=" );\r
- url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );\r
+ url.append("&annotations=");\r
+ url.append(appendProtocol(viewport.applet.getParameter("annotations")));\r
}\r
\r
- if(viewport.applet.getParameter("jnetfile")!=null)\r
+ if (viewport.applet.getParameter("jnetfile") != null)\r
{\r
- url.append( "&annotations=" );\r
- url.append( appendProtocol( viewport.applet.getParameter("jnetfile") ) );\r
+ url.append("&annotations=");\r
+ url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));\r
}\r
\r
- if(viewport.applet.getParameter("defaultColour")!=null)\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
+ if (viewport.applet.getParameter("userDefinedColour") != null)\r
{\r
- url.append( "&colour=" +\r
- removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )\r
- );\r
+ url.append("&colour=" +\r
+ removeWhiteSpace(viewport.applet.getParameter(\r
+ "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
+ {\r
sb.append("%20");\r
+ }\r
else\r
+ {\r
sb.append(colour.charAt(i));\r
+ }\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
+ try\r
+ {\r
+ new URL(url);\r
+ }\r
+ catch (java.net.MalformedURLException ex)\r
{\r
- url = viewport.applet.getCodeBase()+url;\r
+ url = viewport.applet.getCodeBase() + url;\r
}\r
return url;\r
}\r
PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);\r
PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);\r
\r
- if(PaintRefresher.components.size()==0 && viewport.applet==null)\r
+ if (PaintRefresher.components.size() == 0 && viewport.applet == null)\r
+ {\r
System.exit(0);\r
+ }\r
\r
this.dispose();\r
}\r
\r
-\r
/**\r
* DOCUMENT ME!\r
*/\r
\r
public void addHistoryItem(CommandI command)\r
{\r
- if(command.getSize()>0)\r
+ if (command.getSize() > 0)\r
{\r
viewport.historyList.push(command);\r
viewport.redoList.removeAllElements();\r
*/\r
protected void undoMenuItem_actionPerformed()\r
{\r
- if(viewport.historyList.size()<1)\r
+ if (viewport.historyList.size() < 1)\r
+ {\r
return;\r
+ }\r
\r
- CommandI command = (CommandI)viewport.historyList.pop();\r
+ CommandI command = (CommandI) viewport.historyList.pop();\r
viewport.redoList.push(command);\r
command.undoCommand();\r
\r
\r
originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
updateEditMenuBar();\r
- originalSource.firePropertyChange("alignment", null,originalSource.alignment.getSequences());\r
+ originalSource.firePropertyChange("alignment", null,\r
+ originalSource.alignment.getSequences());\r
}\r
\r
/**\r
*/\r
protected void redoMenuItem_actionPerformed()\r
{\r
- if(viewport.redoList.size()<1)\r
+ if (viewport.redoList.size() < 1)\r
+ {\r
return;\r
+ }\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
+ originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
\r
updateEditMenuBar();\r
- originalSource.firePropertyChange("alignment", null, originalSource.alignment.getSequences());\r
+ originalSource.firePropertyChange("alignment", null,\r
+ originalSource.alignment.getSequences());\r
}\r
\r
AlignViewport getOriginatingSource(CommandI command)\r
{\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
+ //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
EditCommand editCommand = (EditCommand) command;\r
//The original view is closed, we must validate\r
//the current view against the closed view first\r
if (al != null)\r
+ {\r
PaintRefresher.validateSequences(al, viewport.alignment);\r
+ }\r
\r
originalSource = viewport;\r
}\r
\r
-\r
return originalSource;\r
}\r
\r
viewport.getColumnSelection().getHiddenColumns().elementAt(i);\r
\r
copiedHiddenColumns.addElement(new int[]\r
- {region[0] - hiddenOffset,\r
- region[1] - hiddenOffset});\r
+ {region[0] - hiddenOffset,\r
+ region[1] - hiddenOffset});\r
}\r
}\r
else\r
+ {\r
copiedHiddenColumns = null;\r
-\r
+ }\r
\r
for (int i = 0; i < sg.getSize(); i++)\r
{\r
- SequenceI seq = null;\r
+ SequenceI seq = null;\r
\r
- while (seq == null)\r
+ while (seq == null)\r
+ {\r
+ if (orderedSeqs.containsKey(index + ""))\r
{\r
- if (orderedSeqs.containsKey(index + ""))\r
- {\r
- seq = (SequenceI) orderedSeqs.get(index + "");\r
- index++;\r
+ seq = (SequenceI) orderedSeqs.get(index + "");\r
+ index++;\r
\r
- break;\r
- }\r
- else\r
- {\r
- index++;\r
- }\r
+ break;\r
+ }\r
+ else\r
+ {\r
+ index++;\r
}\r
+ }\r
\r
- //FIND START RES\r
- //Returns residue following index if gap\r
- startRes = seq.findPosition(sg.getStartRes());\r
+ //FIND START RES\r
+ //Returns residue following index if gap\r
+ startRes = seq.findPosition(sg.getStartRes());\r
\r
- //FIND END RES\r
- //Need to find the residue preceeding index if gap\r
- endRes = 0;\r
+ //FIND END RES\r
+ //Need to find the residue preceeding index if gap\r
+ endRes = 0;\r
\r
- for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
+ for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)\r
+ {\r
+ ch = seq.getCharAt(j);\r
+ if (!jalview.util.Comparison.isGap( (ch)))\r
{\r
- ch = seq.getCharAt(j);\r
- if (!jalview.util.Comparison.isGap( (ch)))\r
- {\r
- endRes++;\r
- }\r
+ endRes++;\r
}\r
+ }\r
\r
- if(endRes>0)\r
- {\r
- endRes += seq.getStart() -1;\r
- }\r
+ if (endRes > 0)\r
+ {\r
+ endRes += seq.getStart() - 1;\r
+ }\r
\r
- copiedSequences.append(seq.getName() + "\t" +\r
- startRes + "\t" +\r
- endRes + "\t" +\r
- seq.getSequenceAsString(sg.getStartRes(),\r
- sg.getEndRes() + 1) + "\n");\r
+ copiedSequences.append(seq.getName() + "\t" +\r
+ startRes + "\t" +\r
+ endRes + "\t" +\r
+ seq.getSequenceAsString(sg.getStartRes(),\r
+ sg.getEndRes() + 1) + "\n");\r
}\r
\r
}\r
}\r
}\r
\r
-\r
jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,\r
DEFAULT_HEIGHT);\r
}\r
seqs.addElement(seq);\r
}\r
\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 (sg.getSize() == viewport.alignment.getHeight())\r
- {\r
- viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
- sg.getEndRes() + 1);\r
- }\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
+ SequenceI[] cut = new SequenceI[seqs.size()];\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ cut[i] = (SequenceI) seqs.elementAt(i);\r
+ }\r
\r
/*\r
- //ADD HISTORY ITEM\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
+ EditCommand.CUT,\r
+ cut,\r
+ sg.getStartRes(),\r
+ sg.getEndRes() - sg.getStartRes() + 1,\r
+ viewport.alignment));\r
\r
viewport.setSelectionGroup(null);\r
viewport.alignment.deleteGroup(sg);\r
\r
viewport.firePropertyChange("alignment", null,\r
- viewport.getAlignment().getSequences());\r
+ viewport.getAlignment().getSequences());\r
\r
if (viewport.getAlignment().getHeight() < 1)\r
{\r
- this.setVisible(false);\r
+ this.setVisible(false);\r
}\r
}\r
\r
protected void deleteGroups_actionPerformed()\r
{\r
viewport.alignment.deleteAllGroups();\r
- viewport.sequenceColours=null;\r
+ viewport.sequenceColours = null;\r
viewport.setSelectionGroup(null);\r
\r
alignPanel.repaint();\r
{\r
sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
}\r
- sg.setEndRes(viewport.alignment.getWidth()-1);\r
+ sg.setEndRes(viewport.alignment.getWidth() - 1);\r
viewport.setSelectionGroup(sg);\r
alignPanel.repaint();\r
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
\r
public void deselectAllSequenceMenuItem_actionPerformed()\r
{\r
- if(viewport.cursorMode)\r
+ if (viewport.cursorMode)\r
{\r
- alignPanel.seqPanel.keyboardNo1=null;\r
- alignPanel.seqPanel.keyboardNo2=null;\r
+ alignPanel.seqPanel.keyboardNo1 = null;\r
+ alignPanel.seqPanel.keyboardNo2 = null;\r
}\r
viewport.setSelectionGroup(null);\r
viewport.getColumnSelection().clear();\r
\r
if (colSel.size() > 0)\r
{\r
- if(trimLeft)\r
+ if (trimLeft)\r
+ {\r
column = colSel.getMin();\r
+ }\r
else\r
+ {\r
column = colSel.getMax();\r
+ }\r
\r
- SequenceI [] seqs;\r
- if(viewport.getSelectionGroup()!=null)\r
- seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);\r
+ SequenceI[] seqs;\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.\r
+ hiddenRepSequences);\r
+ }\r
else\r
+ {\r
seqs = viewport.alignment.getSequencesArray();\r
-\r
+ }\r
\r
TrimRegionCommand trimRegion;\r
- if(trimLeft)\r
+ if (trimLeft)\r
{\r
trimRegion = new TrimRegionCommand("Remove Left",\r
- TrimRegionCommand.TRIM_LEFT,\r
- seqs,\r
- column,\r
- viewport.alignment,\r
- viewport.colSel,\r
- viewport.selectionGroup);\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
+ 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
addHistoryItem(trimRegion);\r
\r
}\r
}\r
\r
-\r
public void removeGappedColumnMenuItem_actionPerformed()\r
{\r
- int start = 0, end = viewport.alignment.getWidth()-1;\r
+ int start = 0, end = viewport.alignment.getWidth() - 1;\r
\r
SequenceI[] seqs;\r
if (viewport.getSelectionGroup() != null)\r
{\r
- seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.\r
+ hiddenRepSequences);\r
start = viewport.getSelectionGroup().getStartRes();\r
end = viewport.getSelectionGroup().getEndRes();\r
}\r
else\r
+ {\r
seqs = viewport.alignment.getSequencesArray();\r
-\r
+ }\r
\r
RemoveGapColCommand removeGapCols =\r
new RemoveGapColCommand("Remove Gapped Columns",\r
\r
addHistoryItem(removeGapCols);\r
\r
- statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");\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
+ // 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,\r
+ viewport.getAlignment().getSequences());\r
\r
}\r
\r
public void removeAllGapsMenuItem_actionPerformed()\r
{\r
- int start = 0, end = viewport.alignment.getWidth()-1;\r
+ int start = 0, end = viewport.alignment.getWidth() - 1;\r
\r
SequenceI[] seqs;\r
if (viewport.getSelectionGroup() != null)\r
{\r
- seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.\r
+ hiddenRepSequences);\r
start = viewport.getSelectionGroup().getStartRes();\r
end = viewport.getSelectionGroup().getEndRes();\r
}\r
else\r
+ {\r
seqs = viewport.alignment.getSequencesArray();\r
+ }\r
\r
//This is to maintain viewport position on first residue\r
//of first sequence\r
int startRes = seq.findPosition(viewport.startRes);\r
\r
addHistoryItem(new RemoveGapsCommand("Remove Gaps",\r
- seqs,\r
- start, end,\r
- viewport.alignment));\r
+ seqs,\r
+ start, end,\r
+ viewport.alignment));\r
\r
- viewport.setStartRes(seq.findIndex(startRes)-1);\r
+ viewport.setStartRes(seq.findIndex(startRes) - 1);\r
\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
\r
}\r
\r
{\r
AlignmentI newal;\r
if (viewport.hasHiddenRows)\r
+ {\r
newal = new Alignment(viewport.getAlignment().\r
getHiddenSequences()\r
.getFullAlignment().\r
getSequencesArray());\r
+ }\r
else\r
+ {\r
newal = new Alignment(viewport.alignment.getSequencesArray());\r
+ }\r
\r
- if(viewport.alignment.getAlignmentAnnotation()!=null)\r
+ if (viewport.alignment.getAlignmentAnnotation() != null)\r
{\r
- for(int i=0; i<viewport.alignment.getAlignmentAnnotation().length; i++)\r
+ for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)\r
{\r
- if(!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)\r
+ if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)\r
{\r
newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);\r
}\r
PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,\r
newaf.alignPanel.av.getSequenceSetId());\r
\r
- Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());\r
+ Vector comps = (Vector) PaintRefresher.components.get(viewport.\r
+ getSequenceSetId());\r
int viewSize = -1;\r
for (int i = 0; i < comps.size(); i++)\r
{\r
if (comps.elementAt(i) instanceof AlignmentPanel)\r
+ {\r
viewSize++;\r
+ }\r
}\r
\r
String title = new String(this.getTitle());\r
if (title.indexOf("(View") > -1)\r
+ {\r
title = title.substring(0, title.indexOf("(View"));\r
+ }\r
\r
- title+= "(View "+viewSize+")";\r
+ title += "(View " + viewSize + ")";\r
\r
newaf.setTitle(title.toString());\r
\r
-\r
newaf.viewport.historyList = viewport.historyList;\r
newaf.viewport.redoList = viewport.redoList;\r
\r
- }\r
-\r
+ }\r
\r
public void seqLimits_itemStateChanged()\r
{\r
alignPanel.repaint();\r
}\r
\r
-\r
protected void colourTextMenuItem_actionPerformed()\r
{\r
viewport.setColourText(colourTextMenuItem.getState());\r
alignPanel.repaint();\r
}\r
\r
-\r
public void overviewMenuItem_actionPerformed()\r
{\r
if (alignPanel.overviewPanel != null)\r
\r
}\r
\r
-\r
void changeColour(ColourSchemeI cs)\r
{\r
int threshold = 0;\r
\r
- if(cs!=null)\r
+ if (cs != null)\r
{\r
if (viewport.getAbovePIDThreshold())\r
{\r
{\r
SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
\r
- if(cs==null)\r
+ if (cs == null)\r
{\r
sg.cs = null;\r
continue;\r
sg.getSequences(viewport.hiddenRepSequences), 0, sg.getWidth()));\r
}\r
else\r
+ {\r
sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
+ }\r
\r
if (viewport.getConservationSelected())\r
{\r
Conservation c = new Conservation("Group",\r
ResidueProperties.propHash, 3,\r
- sg.getSequences(viewport.hiddenRepSequences), 0,\r
+ sg.getSequences(viewport.\r
+ hiddenRepSequences), 0,\r
viewport.alignment.getWidth() - 1);\r
c.calculate();\r
c.verdict(false, viewport.ConsPercGaps);\r
}\r
}\r
\r
-\r
if (alignPanel.getOverviewPanel() != null)\r
{\r
alignPanel.getOverviewPanel().updateOverviewImage();\r
alignPanel.repaint();\r
}\r
\r
-\r
-\r
protected void modifyPID_actionPerformed()\r
{\r
- if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
+ if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme != null)\r
{\r
SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
"Background");\r
\r
protected void modifyConservation_actionPerformed()\r
{\r
- if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
+ if (viewport.getConservationSelected() && viewport.globalColourScheme != null)\r
{\r
SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
"Background");\r
modifyPID_actionPerformed();\r
}\r
\r
-\r
-\r
public void sortPairwiseMenuItem_actionPerformed()\r
{\r
- SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();\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
+ addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,\r
+ 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
- new RedundancyPanel(alignPanel);\r
+ new RedundancyPanel(alignPanel);\r
}\r
\r
public void pairwiseAlignmentMenuItem_actionPerformed()\r
{\r
- if (viewport.getSelectionGroup()!=null\r
+ if (viewport.getSelectionGroup() != null\r
&& viewport.getSelectionGroup().getSize() > 1)\r
{\r
Frame frame = new Frame();\r
\r
if ( (viewport.getSelectionGroup() != null &&\r
viewport.getSelectionGroup().getSize() > 1)\r
- || (viewport.getSelectionGroup() == null\r
- && viewport.alignment.getHeight() > 1))\r
+ || (viewport.getSelectionGroup() == null\r
+ && viewport.alignment.getHeight() > 1))\r
{\r
final TreePanel tp = new TreePanel(viewport,\r
type,\r
\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
+ 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
public void loadTree(jalview.io.NewickFile tree, String treeFile)\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
protected void about_actionPerformed()\r
{\r
\r
- class AboutPanel extends Canvas\r
+ class AboutPanel\r
+ extends Canvas\r
{\r
String version;\r
public AboutPanel(String version)\r
- { this.version = version; }\r
+ {\r
+ this.version = version;\r
+ }\r
\r
public void paint(Graphics g)\r
{\r
int y = 5, x = 7;\r
g.setColor(Color.black);\r
g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
- g.drawString("Jalview - Release "+version, 200, y += fh);\r
+ g.drawString("Jalview - Release " + version, 200, y += fh);\r
g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
x, y += fh * 2);\r
}\r
}\r
\r
-\r
Frame frame = new Frame();\r
frame.add(new AboutPanel(version));\r
jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
{\r
try\r
{\r
- System.out.println("Show url: "+url);\r
+ System.out.println("Show url: " + url);\r
viewport.applet.getAppletContext().showDocument(new java.net.URL(url),\r
- target);\r
+ target);\r
}\r
catch (Exception ex)\r
{\r
}\r
}\r
\r
-\r
//////////////////////////////////////////////////////////////////////////////////\r
//JBuilder Graphics here\r
\r
- protected MenuBar alignFrameMenuBar = new MenuBar();\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 MenuItem removeAllGapsMenuItem = new MenuItem();\r
- protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
- protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
- protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
- protected MenuItem sortIDMenuItem = new MenuItem();\r
- protected MenuItem sortGroupMenuItem = new MenuItem();\r
- protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
- protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
- protected MenuItem PCAMenuItem = new MenuItem();\r
- protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
- protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- public Label statusBar = new Label();\r
- protected Menu outputTextboxMenu = new Menu();\r
- protected MenuItem clustalColour = new MenuItem();\r
- protected MenuItem zappoColour = new MenuItem();\r
- protected MenuItem taylorColour = new MenuItem();\r
- protected MenuItem hydrophobicityColour = new MenuItem();\r
- protected MenuItem helixColour = new MenuItem();\r
- protected MenuItem strandColour = new MenuItem();\r
- protected MenuItem turnColour = new MenuItem();\r
- protected MenuItem buriedColour = new MenuItem();\r
- protected MenuItem userDefinedColour = new MenuItem();\r
- protected MenuItem PIDColour = new MenuItem();\r
- protected MenuItem BLOSUM62Colour = new MenuItem();\r
- MenuItem njTreeBlosumMenuItem = new MenuItem();\r
- MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
- protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
- protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
- MenuItem overviewMenuItem = new MenuItem();\r
- protected MenuItem undoMenuItem = new MenuItem();\r
- protected MenuItem redoMenuItem = new MenuItem();\r
- protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
- MenuItem noColourmenuItem = new MenuItem();\r
- protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
- protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
- MenuItem findMenuItem = new MenuItem();\r
+ protected MenuBar alignFrameMenuBar = new MenuBar();\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(\r
+ "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 MenuItem removeAllGapsMenuItem = new MenuItem();\r
+ protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
+ protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
+ protected MenuItem sortIDMenuItem = new MenuItem();\r
+ protected MenuItem sortGroupMenuItem = new MenuItem();\r
+ protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
+ protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
+ protected MenuItem PCAMenuItem = new MenuItem();\r
+ protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
+ protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ public Label statusBar = new Label();\r
+ protected Menu outputTextboxMenu = new Menu();\r
+ protected MenuItem clustalColour = new MenuItem();\r
+ protected MenuItem zappoColour = new MenuItem();\r
+ protected MenuItem taylorColour = new MenuItem();\r
+ protected MenuItem hydrophobicityColour = new MenuItem();\r
+ protected MenuItem helixColour = new MenuItem();\r
+ protected MenuItem strandColour = new MenuItem();\r
+ protected MenuItem turnColour = new MenuItem();\r
+ protected MenuItem buriedColour = new MenuItem();\r
+ protected MenuItem userDefinedColour = new MenuItem();\r
+ protected MenuItem PIDColour = new MenuItem();\r
+ protected MenuItem BLOSUM62Colour = new MenuItem();\r
+ MenuItem njTreeBlosumMenuItem = new MenuItem();\r
+ MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
+ protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
+ MenuItem overviewMenuItem = new MenuItem();\r
+ protected MenuItem undoMenuItem = new MenuItem();\r
+ protected MenuItem redoMenuItem = new MenuItem();\r
+ protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
+ MenuItem noColourmenuItem = new MenuItem();\r
+ protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
+ MenuItem findMenuItem = new MenuItem();\r
protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
- protected MenuItem nucleotideColour = new MenuItem();\r
- MenuItem deleteGroups = new MenuItem();\r
- MenuItem delete = new MenuItem();\r
- MenuItem copy = new MenuItem();\r
- MenuItem cut = new MenuItem();\r
- Menu pasteMenu = new Menu();\r
- MenuItem pasteNew = new MenuItem();\r
- MenuItem pasteThis = new MenuItem();\r
- protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
- protected MenuItem font = new MenuItem();\r
- protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
- protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
- protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
- MenuItem modifyPID = new MenuItem();\r
- MenuItem modifyConservation = new MenuItem();\r
- protected CheckboxMenuItem autoCalculate\r
- = new CheckboxMenuItem("Autocalculate Consensus", true);\r
- protected Menu sortByTreeMenu = new Menu();\r
- Menu sort = new Menu();\r
- Menu calculate = new Menu();\r
- MenuItem inputText = new MenuItem();\r
- Menu helpMenu = new Menu();\r
- MenuItem documentation = new MenuItem();\r
- MenuItem about = new MenuItem();\r
- protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
+ protected MenuItem nucleotideColour = new MenuItem();\r
+ MenuItem deleteGroups = new MenuItem();\r
+ MenuItem delete = new MenuItem();\r
+ MenuItem copy = new MenuItem();\r
+ MenuItem cut = new MenuItem();\r
+ Menu pasteMenu = new Menu();\r
+ MenuItem pasteNew = new MenuItem();\r
+ MenuItem pasteThis = new MenuItem();\r
+ protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
+ protected MenuItem font = new MenuItem();\r
+ protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
+ MenuItem modifyPID = new MenuItem();\r
+ MenuItem modifyConservation = new MenuItem();\r
+ protected CheckboxMenuItem autoCalculate\r
+ = new CheckboxMenuItem("Autocalculate Consensus", true);\r
+ protected Menu sortByTreeMenu = new Menu();\r
+ Menu sort = new Menu();\r
+ Menu calculate = new Menu();\r
+ MenuItem inputText = new MenuItem();\r
+ Menu helpMenu = new Menu();\r
+ MenuItem documentation = new MenuItem();\r
+ MenuItem about = new MenuItem();\r
+ protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
Panel embeddedMenu;\r
Label embeddedEdit;\r
Label embeddedSelect;\r
Label embeddedCalculate;\r
FlowLayout flowLayout1;\r
\r
- private void jbInit() throws Exception {\r
+ private void jbInit()\r
+ throws Exception\r
+ {\r
\r
- setMenuBar(alignFrameMenuBar);\r
+ setMenuBar(alignFrameMenuBar);\r
\r
- MenuItem item;\r
+ MenuItem item;\r
\r
- // dynamically fill save as menu with available formats\r
- for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)\r
- {\r
+ // dynamically fill save as menu with available formats\r
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length;\r
+ i++)\r
+ {\r
\r
- item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);\r
+ item = new MenuItem(jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);\r
\r
- item.addActionListener(new java.awt.event.ActionListener()\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
{\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- outputText_actionPerformed(e);\r
- }\r
- });\r
-\r
- outputTextboxMenu.add(item);\r
- }\r
- closeMenuItem.addActionListener(this);\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.addActionListener(this);\r
- invertSequenceMenuItem.addActionListener(this);\r
- remove2LeftMenuItem.setLabel("Remove Left");\r
- remove2LeftMenuItem.addActionListener(this);\r
- remove2RightMenuItem.setLabel("Remove Right");\r
- remove2RightMenuItem.addActionListener(this);\r
- removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
- removeGappedColumnMenuItem.addActionListener(this);\r
- removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
- removeAllGapsMenuItem.addActionListener(this);\r
- viewBoxesMenuItem.setLabel("Boxes");\r
- viewBoxesMenuItem.setState(true);\r
- viewBoxesMenuItem.addItemListener(this);\r
- viewTextMenuItem.setLabel("Text");\r
- viewTextMenuItem.setState(true);\r
- viewTextMenuItem.addItemListener(this);\r
- sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
- sortPairwiseMenuItem.addActionListener(this);\r
- sortIDMenuItem.setLabel("by ID");\r
- sortIDMenuItem.addActionListener(this);\r
- sortGroupMenuItem.setLabel("by Group");\r
- sortGroupMenuItem.addActionListener(this);\r
- removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
- removeRedundancyMenuItem.addActionListener(this);\r
- pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
- pairwiseAlignmentMenuItem.addActionListener(this);\r
- PCAMenuItem.setLabel("Principal Component Analysis");\r
- PCAMenuItem.addActionListener(this);\r
- averageDistanceTreeMenuItem.setLabel(\r
- "Average Distance Using % Identity");\r
- averageDistanceTreeMenuItem.addActionListener(this);\r
- neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
- neighbourTreeMenuItem.addActionListener(this);\r
- statusBar.setBackground(Color.white);\r
- statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
- statusBar.setText("Status bar");\r
- outputTextboxMenu.setLabel("Output to Textbox");\r
- clustalColour.setLabel("Clustalx");\r
-\r
- clustalColour.addActionListener(this);\r
- zappoColour.setLabel("Zappo");\r
- zappoColour.addActionListener(this);\r
- taylorColour.setLabel("Taylor");\r
- taylorColour.addActionListener(this);\r
- hydrophobicityColour.setLabel("Hydrophobicity");\r
- hydrophobicityColour.addActionListener(this);\r
- helixColour.setLabel("Helix Propensity");\r
- helixColour.addActionListener(this);\r
- strandColour.setLabel("Strand Propensity");\r
- strandColour.addActionListener(this);\r
- turnColour.setLabel("Turn Propensity");\r
- turnColour.addActionListener(this);\r
- buriedColour.setLabel("Buried Index");\r
- buriedColour.addActionListener(this);\r
- userDefinedColour.setLabel("User Defined...");\r
- userDefinedColour.addActionListener(this);\r
- PIDColour.setLabel("Percentage Identity");\r
- PIDColour.addActionListener(this);\r
- BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
- BLOSUM62Colour.addActionListener(this);\r
- avDistanceTreeBlosumMenuItem.setLabel(\r
- "Average Distance Using BLOSUM62");\r
- avDistanceTreeBlosumMenuItem.addActionListener(this);\r
- njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
- njTreeBlosumMenuItem.addActionListener(this);\r
- annotationPanelMenuItem.setLabel("Show Annotations");\r
- annotationPanelMenuItem.addItemListener(this);\r
- colourTextMenuItem.setLabel("Colour Text");\r
- colourTextMenuItem.addItemListener(this);\r
- overviewMenuItem.setLabel("Overview Window");\r
- overviewMenuItem.addActionListener(this);\r
- undoMenuItem.setEnabled(false);\r
- undoMenuItem.setLabel("Undo");\r
- undoMenuItem.addActionListener(this);\r
- redoMenuItem.setEnabled(false);\r
- redoMenuItem.setLabel("Redo");\r
- redoMenuItem.addActionListener(this);\r
- conservationMenuItem.setLabel("by Conservation");\r
- conservationMenuItem.addItemListener(this);\r
- noColourmenuItem.setLabel("None");\r
- noColourmenuItem.addActionListener(this);\r
- wrapMenuItem.setLabel("Wrap");\r
- wrapMenuItem.addItemListener(this);\r
- renderGapsMenuItem.setLabel("Show Gaps");\r
- renderGapsMenuItem.setState(true);\r
- renderGapsMenuItem.addItemListener(this);\r
- findMenuItem.setLabel("Find...");\r
- findMenuItem.addActionListener(this);\r
+ outputText_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ outputTextboxMenu.add(item);\r
+ }\r
+ closeMenuItem.addActionListener(this);\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.addActionListener(this);\r
+ invertSequenceMenuItem.addActionListener(this);\r
+ remove2LeftMenuItem.setLabel("Remove Left");\r
+ remove2LeftMenuItem.addActionListener(this);\r
+ remove2RightMenuItem.setLabel("Remove Right");\r
+ remove2RightMenuItem.addActionListener(this);\r
+ removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
+ removeGappedColumnMenuItem.addActionListener(this);\r
+ removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
+ removeAllGapsMenuItem.addActionListener(this);\r
+ viewBoxesMenuItem.setLabel("Boxes");\r
+ viewBoxesMenuItem.setState(true);\r
+ viewBoxesMenuItem.addItemListener(this);\r
+ viewTextMenuItem.setLabel("Text");\r
+ viewTextMenuItem.setState(true);\r
+ viewTextMenuItem.addItemListener(this);\r
+ sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
+ sortPairwiseMenuItem.addActionListener(this);\r
+ sortIDMenuItem.setLabel("by ID");\r
+ sortIDMenuItem.addActionListener(this);\r
+ sortGroupMenuItem.setLabel("by Group");\r
+ sortGroupMenuItem.addActionListener(this);\r
+ removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
+ removeRedundancyMenuItem.addActionListener(this);\r
+ pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
+ pairwiseAlignmentMenuItem.addActionListener(this);\r
+ PCAMenuItem.setLabel("Principal Component Analysis");\r
+ PCAMenuItem.addActionListener(this);\r
+ averageDistanceTreeMenuItem.setLabel(\r
+ "Average Distance Using % Identity");\r
+ averageDistanceTreeMenuItem.addActionListener(this);\r
+ neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
+ neighbourTreeMenuItem.addActionListener(this);\r
+ statusBar.setBackground(Color.white);\r
+ statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ statusBar.setText("Status bar");\r
+ outputTextboxMenu.setLabel("Output to Textbox");\r
+ clustalColour.setLabel("Clustalx");\r
+\r
+ clustalColour.addActionListener(this);\r
+ zappoColour.setLabel("Zappo");\r
+ zappoColour.addActionListener(this);\r
+ taylorColour.setLabel("Taylor");\r
+ taylorColour.addActionListener(this);\r
+ hydrophobicityColour.setLabel("Hydrophobicity");\r
+ hydrophobicityColour.addActionListener(this);\r
+ helixColour.setLabel("Helix Propensity");\r
+ helixColour.addActionListener(this);\r
+ strandColour.setLabel("Strand Propensity");\r
+ strandColour.addActionListener(this);\r
+ turnColour.setLabel("Turn Propensity");\r
+ turnColour.addActionListener(this);\r
+ buriedColour.setLabel("Buried Index");\r
+ buriedColour.addActionListener(this);\r
+ userDefinedColour.setLabel("User Defined...");\r
+ userDefinedColour.addActionListener(this);\r
+ PIDColour.setLabel("Percentage Identity");\r
+ PIDColour.addActionListener(this);\r
+ BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
+ BLOSUM62Colour.addActionListener(this);\r
+ avDistanceTreeBlosumMenuItem.setLabel(\r
+ "Average Distance Using BLOSUM62");\r
+ avDistanceTreeBlosumMenuItem.addActionListener(this);\r
+ njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
+ njTreeBlosumMenuItem.addActionListener(this);\r
+ annotationPanelMenuItem.setLabel("Show Annotations");\r
+ annotationPanelMenuItem.addItemListener(this);\r
+ colourTextMenuItem.setLabel("Colour Text");\r
+ colourTextMenuItem.addItemListener(this);\r
+ overviewMenuItem.setLabel("Overview Window");\r
+ overviewMenuItem.addActionListener(this);\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setLabel("Undo");\r
+ undoMenuItem.addActionListener(this);\r
+ redoMenuItem.setEnabled(false);\r
+ redoMenuItem.setLabel("Redo");\r
+ redoMenuItem.addActionListener(this);\r
+ conservationMenuItem.setLabel("by Conservation");\r
+ conservationMenuItem.addItemListener(this);\r
+ noColourmenuItem.setLabel("None");\r
+ noColourmenuItem.addActionListener(this);\r
+ wrapMenuItem.setLabel("Wrap");\r
+ wrapMenuItem.addItemListener(this);\r
+ renderGapsMenuItem.setLabel("Show Gaps");\r
+ renderGapsMenuItem.setState(true);\r
+ renderGapsMenuItem.addItemListener(this);\r
+ findMenuItem.setLabel("Find...");\r
+ findMenuItem.addActionListener(this);\r
abovePIDThreshold.setLabel("Above Identity Threshold");\r
- abovePIDThreshold.addItemListener(this);\r
- nucleotideColour.setLabel("Nucleotide");\r
- nucleotideColour.addActionListener(this);\r
- deleteGroups.setLabel("Undefine Groups");\r
- deleteGroups.addActionListener(this);\r
- copy.setLabel("Copy");\r
- copy.addActionListener(this);\r
- cut.setLabel("Cut");\r
- cut.addActionListener(this);\r
- delete.setLabel("Delete");\r
- delete.addActionListener(this);\r
- pasteMenu.setLabel("Paste");\r
- pasteNew.setLabel("To New Alignment");\r
- pasteNew.addActionListener(this);\r
- pasteThis.setLabel("Add To This Alignment");\r
- pasteThis.addActionListener(this);\r
- applyToAllGroups.setLabel("Apply Colour To All Groups");\r
- applyToAllGroups.setState(true);\r
- applyToAllGroups.addItemListener(this);\r
- font.setLabel("Font...");\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
- scaleLeft.setLabel("Scale Left");\r
- scaleLeft.addItemListener(this);\r
- scaleRight.setEnabled(false);\r
- scaleRight.setState(true);\r
- scaleRight.setLabel("Scale Right");\r
- scaleRight.addItemListener(this);\r
- modifyPID.setLabel("Modify Identity Threshold...");\r
- modifyPID.addActionListener(this);\r
- modifyConservation.setLabel("Modify Conservation Threshold...");\r
- modifyConservation.addActionListener(this);\r
- sortByTreeMenu.setLabel("By Tree Order");\r
- sort.setLabel("Sort");\r
- calculate.setLabel("Calculate Tree");\r
- autoCalculate.addItemListener(this);\r
- inputText.setLabel("Input from textbox");\r
- inputText.addActionListener(this);\r
-\r
- helpMenu.setLabel("Help");\r
- documentation.setLabel("Documentation");\r
- documentation.addActionListener(this);\r
-\r
- about.setLabel("About...");\r
- about.addActionListener(this);\r
- seqLimits.setState(true);\r
+ abovePIDThreshold.addItemListener(this);\r
+ nucleotideColour.setLabel("Nucleotide");\r
+ nucleotideColour.addActionListener(this);\r
+ deleteGroups.setLabel("Undefine Groups");\r
+ deleteGroups.addActionListener(this);\r
+ copy.setLabel("Copy");\r
+ copy.addActionListener(this);\r
+ cut.setLabel("Cut");\r
+ cut.addActionListener(this);\r
+ delete.setLabel("Delete");\r
+ delete.addActionListener(this);\r
+ pasteMenu.setLabel("Paste");\r
+ pasteNew.setLabel("To New Alignment");\r
+ pasteNew.addActionListener(this);\r
+ pasteThis.setLabel("Add To This Alignment");\r
+ pasteThis.addActionListener(this);\r
+ applyToAllGroups.setLabel("Apply Colour To All Groups");\r
+ applyToAllGroups.setState(true);\r
+ applyToAllGroups.addItemListener(this);\r
+ font.setLabel("Font...");\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
+ scaleLeft.setLabel("Scale Left");\r
+ scaleLeft.addItemListener(this);\r
+ scaleRight.setEnabled(false);\r
+ scaleRight.setState(true);\r
+ scaleRight.setLabel("Scale Right");\r
+ scaleRight.addItemListener(this);\r
+ modifyPID.setLabel("Modify Identity Threshold...");\r
+ modifyPID.addActionListener(this);\r
+ modifyConservation.setLabel("Modify Conservation Threshold...");\r
+ modifyConservation.addActionListener(this);\r
+ sortByTreeMenu.setLabel("By Tree Order");\r
+ sort.setLabel("Sort");\r
+ calculate.setLabel("Calculate Tree");\r
+ autoCalculate.addItemListener(this);\r
+ inputText.setLabel("Input from textbox");\r
+ inputText.addActionListener(this);\r
+\r
+ helpMenu.setLabel("Help");\r
+ documentation.setLabel("Documentation");\r
+ documentation.addActionListener(this);\r
+\r
+ about.setLabel("About...");\r
+ about.addActionListener(this);\r
+ seqLimits.setState(true);\r
seqLimits.setLabel("Show Sequence Limits");\r
seqLimits.addItemListener(this);\r
featureSettings.setLabel("Feature Settings...");\r
newView.setLabel("New View");\r
newView.addActionListener(this);\r
alignFrameMenuBar.add(fileMenu);\r
- alignFrameMenuBar.add(editMenu);\r
+ alignFrameMenuBar.add(editMenu);\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(copy);\r
- editMenu.add(pasteMenu);\r
- editMenu.add(delete);\r
- editMenu.addSeparator();\r
- editMenu.add(remove2LeftMenuItem);\r
- editMenu.add(remove2RightMenuItem);\r
- editMenu.add(removeGappedColumnMenuItem);\r
- editMenu.add(removeAllGapsMenuItem);\r
- editMenu.add(removeRedundancyMenuItem);\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
+ {\r
+ fileMenu.add(loadApplication);\r
+ }\r
+\r
+ fileMenu.addSeparator();\r
+ fileMenu.add(closeMenuItem);\r
+\r
+ editMenu.add(undoMenuItem);\r
+ editMenu.add(redoMenuItem);\r
+ editMenu.add(cut);\r
+ editMenu.add(copy);\r
+ editMenu.add(pasteMenu);\r
+ editMenu.add(delete);\r
+ editMenu.addSeparator();\r
+ editMenu.add(remove2LeftMenuItem);\r
+ editMenu.add(remove2RightMenuItem);\r
+ editMenu.add(removeGappedColumnMenuItem);\r
+ editMenu.add(removeAllGapsMenuItem);\r
+ editMenu.add(removeRedundancyMenuItem);\r
viewMenu.add(newView);\r
viewMenu.addSeparator();\r
viewMenu.add(menu1);\r
viewMenu.addSeparator();\r
viewMenu.add(annotationPanelMenuItem);\r
viewMenu.addSeparator();\r
- viewMenu.add(sequenceFeatures);\r
- viewMenu.add(featureSettings);\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(noColourmenuItem);\r
- colourMenu.add(clustalColour);\r
- colourMenu.add(BLOSUM62Colour);\r
- colourMenu.add(PIDColour);\r
- colourMenu.add(zappoColour);\r
- colourMenu.add(taylorColour);\r
- colourMenu.add(hydrophobicityColour);\r
- colourMenu.add(helixColour);\r
- colourMenu.add(strandColour);\r
- colourMenu.add(turnColour);\r
- colourMenu.add(buriedColour);\r
- colourMenu.add(nucleotideColour);\r
- colourMenu.add(userDefinedColour);\r
- colourMenu.addSeparator();\r
- colourMenu.add(conservationMenuItem);\r
- colourMenu.add(modifyConservation);\r
- colourMenu.add(abovePIDThreshold);\r
- colourMenu.add(modifyPID);\r
+ viewMenu.add(overviewMenuItem);\r
+ colourMenu.add(applyToAllGroups);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(noColourmenuItem);\r
+ colourMenu.add(clustalColour);\r
+ colourMenu.add(BLOSUM62Colour);\r
+ colourMenu.add(PIDColour);\r
+ colourMenu.add(zappoColour);\r
+ colourMenu.add(taylorColour);\r
+ colourMenu.add(hydrophobicityColour);\r
+ colourMenu.add(helixColour);\r
+ colourMenu.add(strandColour);\r
+ colourMenu.add(turnColour);\r
+ colourMenu.add(buriedColour);\r
+ colourMenu.add(nucleotideColour);\r
+ colourMenu.add(userDefinedColour);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(conservationMenuItem);\r
+ colourMenu.add(modifyConservation);\r
+ colourMenu.add(abovePIDThreshold);\r
+ colourMenu.add(modifyPID);\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
- sort.add(sortIDMenuItem);\r
- sort.add(sortByTreeMenu);\r
- sort.add(sortGroupMenuItem);\r
- sort.add(sortPairwiseMenuItem);\r
- calculate.add(averageDistanceTreeMenuItem);\r
- calculate.add(neighbourTreeMenuItem);\r
- calculate.add(avDistanceTreeBlosumMenuItem);\r
- calculate.add(njTreeBlosumMenuItem);\r
- helpMenu.add(documentation);\r
- helpMenu.add(about);\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
+ sort.add(sortIDMenuItem);\r
+ sort.add(sortByTreeMenu);\r
+ sort.add(sortGroupMenuItem);\r
+ sort.add(sortPairwiseMenuItem);\r
+ calculate.add(averageDistanceTreeMenuItem);\r
+ calculate.add(neighbourTreeMenuItem);\r
+ calculate.add(avDistanceTreeBlosumMenuItem);\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
viewport.applet.add(embeddedMenu, BorderLayout.NORTH);\r
viewport.applet.add(statusBar, BorderLayout.SOUTH);\r
\r
- alignPanel.setSize(viewport.applet.getSize().width, viewport.applet.getSize().height\r
+ alignPanel.setSize(viewport.applet.getSize().width,\r
+ viewport.applet.getSize().height\r
- embeddedMenu.HEIGHT - statusBar.HEIGHT);\r
\r
- viewport.applet.add(alignPanel, BorderLayout.CENTER);\r
- viewport.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, formatPopup, 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
public void mousePressed(MouseEvent evt)\r
{\r
PopupMenu popup = null;\r
- Label source = (Label)evt.getSource();\r
- if(source==embeddedFile)\r
+ Label source = (Label) evt.getSource();\r
+ if (source == embeddedFile)\r
{\r
popup = filePopup = genPopupMenu(filePopup, fileMenu);\r
}\r
- else if(source==embeddedEdit)\r
+ else if (source == embeddedEdit)\r
{\r
popup = editPopup = genPopupMenu(editPopup, editMenu);\r
}\r
- else if(source==embeddedSelect)\r
+ else if (source == embeddedSelect)\r
{\r
popup = searchPopup = genPopupMenu(searchPopup, selectMenu);\r
}\r
- else if(source==embeddedView)\r
+ else if (source == embeddedView)\r
{\r
popup = viewPopup = genPopupMenu(viewPopup, viewMenu);\r
}\r
- else if (source ==embeddedFormat)\r
+ else if (source == embeddedFormat)\r
{\r
popup = formatPopup = genPopupMenu(formatPopup, formatMenu);\r
}\r
- else if(source==embeddedColour)\r
+ else if (source == embeddedColour)\r
{\r
popup = colourPopup = genPopupMenu(colourPopup, colourMenu);\r
}\r
- else if(source==embeddedCalculate)\r
+ else if (source == embeddedCalculate)\r
{\r
popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);\r
}\r
- else if(source==embeddedHelp)\r
+ else if (source == embeddedHelp)\r
{\r
popup = helpPopup = genPopupMenu(helpPopup, helpMenu);\r
}\r
\r
PopupMenu genPopupMenu(PopupMenu popup, Menu original)\r
{\r
- if(popup!=null)\r
+ if (popup != null)\r
{\r
return popup;\r
}\r
popup = new PopupMenu();\r
int m, mSize = original.getItemCount();\r
- for(m=0; m<mSize; m++)\r
+ for (m = 0; m < mSize; m++)\r
{\r
popup.add(original.getItem(m));\r
mSize--;\r
\r
return popup;\r
}\r
+\r
public void mouseClicked(MouseEvent evt)\r
{}\r
+\r
public void mouseReleased(MouseEvent evt)\r
{}\r
+\r
public void mouseEntered(MouseEvent evt)\r
{}\r
+\r
public void mouseExited(MouseEvent evt)\r
{}\r
\r
}\r
-\r
git://source.jalview.org / jalview.git / blobdiff