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
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 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
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
+\r
+ if (viewport.historyList.size() > 0)\r
+ {\r
+ undoMenuItem.setEnabled(true);\r
+ CommandI command = (CommandI) viewport.historyList.peek();\r
+ undoMenuItem.setLabel("Undo " + command.getDescription());\r
+ }\r
+ else\r
+ {\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setLabel("Undo");\r
+ }\r
+\r
+ if (viewport.redoList.size() > 0)\r
+ {\r
+ redoMenuItem.setEnabled(true);\r
+\r
+ CommandI command = (CommandI) viewport.redoList.peek();\r
+ redoMenuItem.setLabel("Redo " + command.getDescription());\r
+ }\r
+ else\r
+ {\r
+ redoMenuItem.setEnabled(false);\r
+ redoMenuItem.setLabel("Redo");\r
+ }\r
}\r
\r
+ public void addHistoryItem(CommandI command)\r
+ {\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
protected void undoMenuItem_actionPerformed()\r
{\r
+ CommandI command = (CommandI)viewport.historyList.pop();\r
+ viewport.redoList.push(command);\r
+ command.undoCommand();\r
+\r
+ viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
+ updateEditMenuBar();\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
}\r
\r
protected void redoMenuItem_actionPerformed()\r
{\r
+ CommandI command = (CommandI) viewport.redoList.pop();\r
+ viewport.historyList.push(command);\r
+ command.doCommand();\r
+ viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;\r
\r
+ updateEditMenuBar();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
- // used by undo and redo\r
- void restoreHistoryItem(CommandI command)\r
- {\r
- }\r
\r
public void moveSelectedSequences(boolean up)\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
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
else\r
{\r
+ //!newAlignment\r
+ addHistoryItem(new EditCommand(\r
+ "Add sequences",\r
+ EditCommand.PASTE,\r
+ newSeqs,\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, viewport.getAlignment().getSequences());\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.clear();\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
- }\r
+ ColumnSelection colSel = viewport.getColumnSelection();\r
+ int column;\r
\r
- public void remove2RightMenuItem_actionPerformed()\r
- {\r
- }\r
+ if (colSel.size() > 0)\r
+ {\r
+ if(trimLeft)\r
+ column = colSel.getMin();\r
+ else\r
+ column = colSel.getMax();\r
\r
- public void removeGappedColumnMenuItem_actionPerformed()\r
- {\r
- }\r
+ SequenceI [] seqs;\r
+ if(viewport.getSelectionGroup()!=null)\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(true);\r
+ else\r
+ seqs = viewport.alignment.getSequencesArray();\r
\r
- public void removeAllGapsMenuItem_actionPerformed()\r
- {\r
+\r
+ TrimRegionCommand trimRegion;\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
+ 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
+\r
+ if ( (trimLeft && !sg.adjustForRemoveLeft(column))\r
+ || (!trimLeft && !sg.adjustForRemoveRight(column)))\r
+ {\r
+ viewport.alignment.deleteGroup(sg);\r
+ }\r
+ }\r
+\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
+ }\r
}\r
\r
- public void alignmentChanged()\r
+\r
+ public void removeGappedColumnMenuItem_actionPerformed()\r
{\r
- viewport.alignment.padGaps();\r
- if(viewport.autocalculateConsensus)\r
+ int start = 0, end = viewport.alignment.getWidth()-1;\r
+\r
+ SequenceI[] seqs;\r
+ if (viewport.getSelectionGroup() != null)\r
{\r
- viewport.updateConsensus();\r
- viewport.updateConservation();\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
- resetAllColourSchemes();\r
- if(alignPanel.overviewPanel!=null)\r
- alignPanel.overviewPanel.updateOverviewImage();\r
\r
- viewport.alignment.adjustSequenceAnnotations();\r
- alignPanel.repaint();\r
+ RemoveGapColCommand removeGapCols =\r
+ new RemoveGapColCommand("Remove Gapped Columns",\r
+ seqs,\r
+ start, end,\r
+ viewport.getGapCharacter());\r
+\r
+ addHistoryItem(removeGapCols);\r
+\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
}\r
\r
- void resetAllColourSchemes()\r
+ public void removeAllGapsMenuItem_actionPerformed()\r
{\r
- ColourSchemeI cs = viewport.globalColourScheme;\r
- if(cs!=null)\r
+ int start = 0, end = viewport.alignment.getWidth()-1;\r
+\r
+ SequenceI[] seqs;\r
+ if (viewport.getSelectionGroup() != null)\r
{\r
- if (cs instanceof ClustalxColourScheme)\r
- {\r
- ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
- resetClustalX(viewport.alignment.getSequences(),\r
- viewport.alignment.getWidth());\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
- cs.setConsensus(viewport.hconsensus);\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
+ //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
- cs.setConservation(c);\r
- }\r
- }\r
+ addHistoryItem(new RemoveGapsCommand("Remove Gaps",\r
+ seqs,\r
+ start, end,\r
+ viewport.getGapCharacter()));\r
\r
- int s, sSize = viewport.alignment.getGroups().size();\r
- for(s=0; s<sSize; s++)\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
- }\r
- }\r
+ viewport.setStartRes(seq.findIndex(startRes)-1);\r
\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
\r
+ }\r
\r
public void findMenuItem_actionPerformed()\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
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
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
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
fileMenu.add(inputText);\r
editMenu.add(copy);\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.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(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("Label");\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
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
\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 = viewPopup = genPopupMenu(viewPopup, formatMenu);\r
+ }\r
else if(source==embeddedColour)\r
{\r
popup = colourPopup = genPopupMenu(colourPopup, colourMenu);\r
git://source.jalview.org / jalview.git / blobdiff