/*\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
+ int DEFAULT_WIDTH = 700;\r
+ int DEFAULT_HEIGHT = 500;\r
\r
String jalviewServletURL;\r
\r
boolean embedded)\r
{\r
\r
- jalviewServletURL = applet.getParameter("APPLICATION_URL");\r
+ if (applet != null)\r
+ jalviewServletURL = applet.getParameter("APPLICATION_URL");\r
\r
try{\r
jbInit();\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
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
alignPanel.scalePanel.addKeyListener(this);\r
alignPanel.annotationPanel.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
if(embedded)\r
{\r
else\r
{\r
add(alignPanel, BorderLayout.CENTER);\r
- jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH,\r
- NEW_WINDOW_HEIGHT);\r
+ jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,\r
+ DEFAULT_HEIGHT);\r
}\r
alignPanel.validate();\r
alignPanel.repaint();\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
case KeyEvent.VK_SPACE:\r
if(viewport.cursorMode)\r
{\r
- alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown());\r
+ alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()\r
+ || evt.isShiftDown()\r
+ || evt.isAltDown()\r
+ );\r
}\r
break;\r
\r
case KeyEvent.VK_BACK_SPACE:\r
if(viewport.cursorMode)\r
{\r
- alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown());\r
+ alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()\r
+ || evt.isShiftDown()\r
+ || evt.isAltDown());\r
}\r
else\r
{\r
alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;\r
alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;\r
}\r
- alignPanel.seqPanel.seqCanvas.repaint();\r
break;\r
\r
case KeyEvent.VK_F:\r
findMenuItem_actionPerformed();\r
}\r
break;\r
+\r
case KeyEvent.VK_H:\r
{\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
+ boolean toggleSeqs = !evt.isControlDown();\r
+ boolean toggleCols = !evt.isShiftDown();\r
boolean hide = false;\r
- if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+\r
+ if(toggleSeqs)\r
{\r
- hide = true;\r
- viewport.hideAllSelectedSeqs();\r
+ if (sg != null && sg.getSize(false) != 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
- else if (viewport.colSel.getSelected().size() < 1)\r
- viewport.showAllHiddenSeqs();\r
\r
- if (viewport.colSel.getSelected().size() > 0)\r
- viewport.hideSelectedColumns();\r
- else if (!hide)\r
- viewport.showAllHiddenColumns();\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
- alignPanel.repaint();\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
+ }\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
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
loadTree_actionPerformed();\r
else if(source==loadApplication)\r
launchFullApplication();\r
+ else if (source == loadAnnotations)\r
+ loadAnnotations();\r
+ else if (source == outputAnnotations)\r
+ outputAnnotations();\r
+ else if(source == outputFeatures)\r
+ outputFeatures();\r
else if(source==closeMenuItem)\r
closeMenuItem_actionPerformed();\r
else if(source==copy)\r
else if(source==invertColSel)\r
{ viewport.invertColumnSelection(); alignPanel.repaint(); }\r
else if(source==remove2LeftMenuItem)\r
- remove2LeftMenuItem_actionPerformed();\r
+ trimAlignment(true);\r
else if(source==remove2RightMenuItem)\r
- remove2RightMenuItem_actionPerformed();\r
+ trimAlignment(false);\r
else if(source==removeGappedColumnMenuItem)\r
removeGappedColumnMenuItem_actionPerformed();\r
else if(source==removeAllGapsMenuItem)\r
else if(source==findMenuItem)\r
findMenuItem_actionPerformed();\r
else if(source==font)\r
- font_actionPerformed();\r
+ new FontChooser(alignPanel);\r
+ else if (source == newView)\r
+ newView();\r
else if(source==showColumns)\r
{\r
viewport.showAllHiddenColumns(); alignPanel.repaint();\r
viewport.hideAllSelectedSeqs();\r
}\r
else if(source==featureSettings)\r
- featureSettings_actionPerformed();\r
+ new FeatureSettings(alignPanel);\r
else if(source==overviewMenuItem)\r
overviewMenuItem_actionPerformed();\r
else if(source==noColourmenuItem)\r
- noColourmenuItem_actionPerformed();\r
+ changeColour(null);\r
else if(source==clustalColour)\r
- clustalColour_actionPerformed();\r
+ {\r
+ abovePIDThreshold.setState(false);\r
+ changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
+ viewport.alignment.getWidth()));\r
+ }\r
else if(source==zappoColour)\r
- zappoColour_actionPerformed();\r
+ changeColour(new ZappoColourScheme());\r
else if(source==taylorColour)\r
- taylorColour_actionPerformed();\r
+ changeColour(new TaylorColourScheme());\r
else if(source==hydrophobicityColour)\r
- hydrophobicityColour_actionPerformed();\r
+ changeColour(new HydrophobicColourScheme());\r
else if(source==helixColour)\r
- helixColour_actionPerformed();\r
+ changeColour(new HelixColourScheme());\r
else if(source==strandColour)\r
- strandColour_actionPerformed();\r
+ changeColour(new StrandColourScheme());\r
else if(source==turnColour)\r
- turnColour_actionPerformed();\r
+ changeColour(new TurnColourScheme());\r
else if(source==buriedColour)\r
- buriedColour_actionPerformed();\r
+ changeColour(new BuriedColourScheme());\r
else if(source==nucleotideColour)\r
- nucleotideColour_actionPerformed();\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
- userDefinedColour_actionPerformed();\r
+ new UserDefinedColours(alignPanel, null);\r
else if(source==PIDColour)\r
- PIDColour_actionPerformed();\r
+ changeColour(new PIDColourScheme());\r
else if(source==BLOSUM62Colour)\r
- BLOSUM62Colour_actionPerformed();\r
+ changeColour(new Blosum62ColourScheme());\r
else if(source==annotationColour)\r
new AnnotationColourChooser(viewport, alignPanel);\r
else if(source==sortPairwiseMenuItem)\r
\r
protected void outputText_actionPerformed(ActionEvent e)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
Frame frame = new Frame();\r
frame.add(cap);\r
jalview.bin.JalviewLite.addFrame(frame,\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 void outputAnnotations()\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame,\r
+ "Annotations",\r
+ 600, 500);\r
+ cap.setText( new AnnotationFile().printAnnotations(\r
+ viewport.alignment.getAlignmentAnnotation() ) );\r
+ }\r
+\r
+ public void outputFeatures()\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, 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(new FeaturesFile().printJalviewFormat(\r
+ viewport.alignment.getSequencesArray(),\r
+ viewport.featuresDisplayed));\r
+ }\r
+\r
void launchFullApplication()\r
{\r
StringBuffer url = new StringBuffer(jalviewServletURL);\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
\r
public void closeMenuItem_actionPerformed()\r
{\r
- PaintRefresher.components.remove(viewport.alignment);\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
- hi.restore();\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
+ 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
+ if (comps.elementAt(i) instanceof AlignmentPanel)\r
+ {\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
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
\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
-\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
- boolean allSequences = false;\r
- if(sg.getSize(false)==viewport.alignment.getHeight())\r
- allSequences = true;\r
-\r
+ Vector seqs = new Vector();\r
+ SequenceI seq;\r
for (int i = 0; i < sg.getSize(false); i++)\r
{\r
- SequenceI seq = sg.getSequenceAt(i);\r
- int index = viewport.getAlignment().findIndex(seq);\r
- seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
+ seq = sg.getSequenceAt(i);\r
+ seqs.addElement(seq);\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
+ // If the cut affects all sequences, remove highlighted columns\r
+ if (sg.getSize(false) == 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
+\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
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(true);\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(true);\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.getGapCharacter());\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().getSequences(false) != null\r
- && viewport.getSelectionGroup().getSize(false)>0)\r
+ SequenceI[] seqs;\r
+ if (viewport.getSelectionGroup() != null)\r
{\r
- seqs = viewport.getSelectionGroup().getSequences(true);\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(true);\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.getGapCharacter()));\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.alignment.padGaps();\r
- if(viewport.autocalculateConsensus)\r
- {\r
- viewport.updateConsensus();\r
- viewport.updateConservation();\r
- }\r
-\r
- resetAllColourSchemes();\r
- if(alignPanel.overviewPanel!=null)\r
- alignPanel.overviewPanel.updateOverviewImage();\r
-\r
- viewport.alignment.adjustSequenceAnnotations();\r
- alignPanel.repaint();\r
+ new Finder(alignPanel);\r
}\r
\r
- void resetAllColourSchemes()\r
+ public void newView()\r
{\r
- ColourSchemeI cs = viewport.globalColourScheme;\r
- if(cs!=null)\r
- {\r
- if (cs instanceof ClustalxColourScheme)\r
- {\r
- ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
- resetClustalX(viewport.alignment.getSequences(),\r
- viewport.alignment.getWidth());\r
- }\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
- 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
- int s, sSize = viewport.alignment.getGroups().size();\r
- for(s=0; s<sSize; s++)\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
+ 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(\r
- sg.getSequences(true), 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
}\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 featureSettings_actionPerformed()\r
- {\r
- new FeatureSettings(viewport, alignPanel);\r
- }\r
-\r
public void overviewMenuItem_actionPerformed()\r
{\r
if (alignPanel.overviewPanel != null)\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
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
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
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
cap.setText("Paste your Newick tree file here.");\r
- cap.treeImport = true;\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
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 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 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 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 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
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
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
showSeqs.addActionListener(this);\r
hideColumns.addActionListener(this);\r
hideSequences.addActionListener(this);\r
-\r
-\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(loadTree);\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(invertColSel);\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(newView);\r
+ viewMenu.addSeparator();\r
viewMenu.add(menu1);\r
viewMenu.add(menu2);\r
viewMenu.addSeparator();\r
- viewMenu.add(wrapMenuItem);\r
- viewMenu.add(scaleAbove);\r
- viewMenu.add(scaleLeft);\r
- viewMenu.add(scaleRight);\r
- viewMenu.addSeparator();\r
- viewMenu.add(seqLimits);\r
- viewMenu.add(viewBoxesMenuItem);\r
- viewMenu.add(viewTextMenuItem);\r
- viewMenu.add(colourTextMenuItem);\r
- viewMenu.add(renderGapsMenuItem);\r
- viewMenu.add(annotationPanelMenuItem);\r
+ viewMenu.add(annotationPanelMenuItem);\r
viewMenu.addSeparator();\r
viewMenu.add(sequenceFeatures);\r
viewMenu.add(featureSettings);\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(3); // Seperator\r
\r
viewport.applet.setLayout(new BorderLayout());\r
viewport.applet.add(embeddedMenu, BorderLayout.NORTH);\r
viewport.applet.add(statusBar, BorderLayout.SOUTH);\r
- // viewport.applet.validate();\r
\r
alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height\r
- embeddedMenu.HEIGHT - statusBar.HEIGHT);\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
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
git://source.jalview.org / jalview.git / blobdiff