\r
Sequence seq;\r
MenuItem revealAll = new MenuItem();\r
+ MenuItem menuItem1 = new MenuItem();\r
+ Menu menu1 = new Menu();\r
\r
public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)\r
{\r
hideSeqs.setLabel("Hide Sequences");\r
repGroup.setLabel("Represent Group with");\r
revealAll.setLabel("Reveal All");\r
-\r
+ menuItem1.setLabel("Create Sequence Feature");\r
+ menu1.setLabel("Group");\r
add(groupMenu);\r
this.add(seqMenu);\r
this.add(hideSeqs);\r
this.add(revealAll);\r
groupMenu.add(editMenu);\r
groupMenu.add(outputmenu);\r
- groupMenu.addSeparator();\r
- groupMenu.add(unGroupMenuItem);\r
- groupMenu.add(colourMenu);\r
- groupMenu.add(showBoxes);\r
- groupMenu.add(showText);\r
- groupMenu.add(showColourText);\r
+ groupMenu.add(menuItem1);\r
+ groupMenu.add(menu1);\r
colourMenu.add(noColourmenuItem);\r
colourMenu.add(clustalColour);\r
colourMenu.add(BLOSUM62Colour);\r
editMenu.add(toggleCase);\r
seqMenu.add(pdb);\r
seqMenu.add(repGroup);\r
+ menu1.add(unGroupMenuItem);\r
+ menu1.add(colourMenu);\r
+ menu1.add(showBoxes);\r
+ menu1.add(showText);\r
+ menu1.add(showColourText);\r
toggleCase.addActionListener(this);\r
pdb.addActionListener(this);\r
hideSeqs.addActionListener(this);\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
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
\r
boolean MAC = false;\r
\r
+ Stack historyList = new Stack();\r
+ Stack redoList = new Stack();\r
+\r
+ String sequenceSetID;\r
+\r
public AlignViewport(AlignmentI al, JalviewLite applet)\r
{\r
this.applet = applet;\r
}\r
\r
}\r
- // We must set conservation and consensus before setting colour,\r
- // as Blosum and Clustal require this to be done\r
- updateConservation();\r
- updateConsensus();\r
-\r
\r
if (applet != null)\r
{\r
applet.getParameter("userDefinedColour"));\r
}\r
\r
+ if(hconsensus==null)\r
+ {\r
+ if(!alignment.isNucleotide())\r
+ {\r
+ conservation = new AlignmentAnnotation("Conservation",\r
+ "Conservation of total alignment less than " +\r
+ ConsPercGaps + "% gaps",\r
+ new Annotation[1], 0f,\r
+ 11f,\r
+ AlignmentAnnotation.BAR_GRAPH);\r
+ conservation.hasText = true;\r
+\r
+\r
+ if (showConservation)\r
+ {\r
+ alignment.addAnnotation(conservation);\r
+ }\r
+\r
+ if (showQuality)\r
+ {\r
+ quality = new AlignmentAnnotation("Quality",\r
+ "Alignment Quality based on Blosum62 scores",\r
+ new Annotation[1],\r
+ 0f,\r
+ 11f,\r
+ AlignmentAnnotation.BAR_GRAPH);\r
+ quality.hasText = true;\r
+\r
+ alignment.addAnnotation(quality);\r
+ }\r
+ }\r
\r
+ consensus = new AlignmentAnnotation("Consensus", "PID",\r
+ new Annotation[1], 0f, 100f,\r
+ AlignmentAnnotation.BAR_GRAPH);\r
+ consensus.hasText = true;\r
+\r
+ if (showConsensus)\r
+ {\r
+ alignment.addAnnotation(consensus);\r
+ }\r
+ }\r
}\r
}\r
\r
}\r
\r
\r
- public void updateConservation()\r
+ class ConservationThread extends Thread\r
{\r
- if(alignment.isNucleotide())\r
- return;\r
+ AlignmentPanel ap;\r
+ public ConservationThread(AlignmentPanel ap)\r
+ {\r
+ this.ap = ap;\r
+ }\r
\r
- Conservation cons = new jalview.analysis.Conservation("All",\r
- jalview.schemes.ResidueProperties.propHash, 3,\r
- alignment.getSequences(), 0,\r
- alignment.getWidth() - 1);\r
- cons.calculate();\r
- cons.verdict(false, ConsPercGaps);\r
- cons.findQuality();\r
- int alWidth = alignment.getWidth();\r
- Annotation[] annotations = new Annotation[alWidth];\r
- Annotation[] qannotations = new Annotation[alWidth];\r
- String sequence = cons.getConsSequence().getSequence();\r
- float minR, minG, minB, maxR, maxG, maxB;\r
- minR = 0.3f;\r
- minG = 0.0f;\r
- minB = 0f;\r
- maxR = 1.0f - minR;\r
- maxG = 0.9f - minG;\r
- maxB = 0f - minB; // scalable range for colouring both Conservation and Quality\r
- float min = 0f;\r
- float max = 11f;\r
- float qmin = cons.qualityRange[0].floatValue();\r
- float qmax = cons.qualityRange[1].floatValue();\r
-\r
- for (int i = 0; i < alWidth; i++)\r
+ public void run()\r
{\r
- float value = 0;\r
try\r
{\r
- value = Integer.parseInt(sequence.charAt(i) + "");\r
- }\r
- catch (Exception ex)\r
- {\r
- if (sequence.charAt(i) == '*')\r
+ updatingConservation = true;\r
+\r
+ while (UPDATING_CONSERVATION)\r
{\r
- value = 11;\r
+ try\r
+ {\r
+ if (ap != null)\r
+ {\r
+ ap.repaint();\r
+ }\r
+ Thread.sleep(200);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
}\r
- if (sequence.charAt(i) == '+')\r
+\r
+ UPDATING_CONSERVATION = true;\r
+\r
+\r
+ int alWidth = alignment.getWidth();\r
+ if(alWidth<0)\r
+ return;\r
+\r
+ Conservation cons = new jalview.analysis.Conservation("All",\r
+ jalview.schemes.ResidueProperties.propHash, 3,\r
+ alignment.getSequences(), 0, alWidth -1);\r
+\r
+ cons.calculate();\r
+ cons.verdict(false, ConsPercGaps);\r
+\r
+ if (quality!=null)\r
{\r
- value = 10;\r
+ cons.findQuality();\r
}\r
- }\r
- float vprop = value - min;\r
- vprop /= max;\r
-\r
- annotations[i] = new Annotation(sequence.charAt(i) + "",\r
- "", ' ', value,\r
- new Color(minR + maxR * vprop,\r
- minG + maxG * vprop,\r
- minB + maxB * vprop));\r
- // Quality calc\r
- value = ( (Double) cons.quality.elementAt(i)).floatValue();\r
- vprop = value - qmin;\r
- vprop /= qmax;\r
- qannotations[i] = new Annotation(" ",\r
- String.valueOf(value), ' ', value,\r
- new\r
- Color(minR + maxR * vprop,\r
- minG + maxG * vprop,\r
- minB + maxB * vprop));\r
- }\r
\r
- if (conservation == null)\r
- {\r
- conservation = new AlignmentAnnotation("Conservation",\r
- "Conservation of total alignment less than " +\r
- ConsPercGaps + "% gaps",\r
- annotations,\r
- 0f, // cons.qualityRange[0].floatValue(),\r
- 11f, // cons.qualityRange[1].floatValue()\r
- AlignmentAnnotation.BAR_GRAPH);\r
- if (showConservation)\r
+ String sequence = cons.getConsSequence().getSequence();\r
+ float minR;\r
+ float minG;\r
+ float minB;\r
+ float maxR;\r
+ float maxG;\r
+ float maxB;\r
+ minR = 0.3f;\r
+ minG = 0.0f;\r
+ minB = 0f;\r
+ maxR = 1.0f - minR;\r
+ maxG = 0.9f - minG;\r
+ maxB = 0f - minB; // scalable range for colouring both Conservation and Quality\r
+\r
+ float min = 0f;\r
+ float max = 11f;\r
+ float qmin = 0f;\r
+ float qmax = 0f;\r
+\r
+ char c;\r
+\r
+ conservation.annotations = new Annotation[alWidth];\r
+\r
+ if (quality!=null)\r
+ {\r
+ quality.graphMax = cons.qualityRange[1].floatValue();\r
+ quality.annotations = new Annotation[alWidth];\r
+ qmin = cons.qualityRange[0].floatValue();\r
+ qmax = cons.qualityRange[1].floatValue();\r
+ }\r
+\r
+ for (int i = 0; i < alWidth; i++)\r
+ {\r
+ float value = 0;\r
+\r
+ c = sequence.charAt(i);\r
+\r
+ if (Character.isDigit(c))\r
+ value = (int) (c - '0');\r
+ else if (c == '*')\r
+ value = 11;\r
+ else if (c == '+')\r
+ value = 10;\r
+\r
+ float vprop = value - min;\r
+ vprop /= max;\r
+ conservation.annotations[i] =\r
+ new Annotation(String.valueOf(c),\r
+ String.valueOf(value), ' ', value,\r
+ new Color(minR + (maxR * vprop),\r
+ minG + (maxG * vprop),\r
+ minB + (maxB * vprop)));\r
+\r
+ // Quality calc\r
+ if (quality!=null)\r
+ {\r
+ value = ( (Double) cons.quality.elementAt(i)).floatValue();\r
+ vprop = value - qmin;\r
+ vprop /= qmax;\r
+ quality.annotations[i] = new Annotation(" ", String.valueOf(value), ' ',\r
+ value,\r
+ new Color(minR + (maxR * vprop),\r
+ minG + (maxG * vprop),\r
+ minB + (maxB * vprop)));\r
+ }\r
+ }\r
+ }\r
+ catch (OutOfMemoryError error)\r
{\r
- alignment.addAnnotation(conservation);\r
+ System.out.println("Out of memory calculating conservation!!");\r
+ conservation = null;\r
+ quality = null;\r
+ System.gc();\r
}\r
- quality = new AlignmentAnnotation("Quality",\r
- "Alignment Quality based on Blosum62 scores",\r
- qannotations,\r
- cons.qualityRange[0].floatValue(),\r
- cons.qualityRange[1].floatValue(),\r
- AlignmentAnnotation.BAR_GRAPH);\r
- if (showQuality)\r
+\r
+ UPDATING_CONSERVATION = false;\r
+ updatingConservation = false;\r
+\r
+ if(ap!=null)\r
{\r
- alignment.addAnnotation(quality);\r
+ ap.repaint();\r
}\r
- }\r
- else\r
- {\r
- conservation.annotations = annotations;\r
- quality.annotations = qannotations;\r
- quality.graphMax = cons.qualityRange[1].floatValue();\r
- }\r
\r
+ }\r
}\r
\r
- public void updateConsensus()\r
- {\r
- // this routine prevents vconsensus becoming a new object each time\r
- // consenus is calculated. Important for speed of Blosum62\r
- // and PID colouring of alignment\r
- int aWidth = alignment.getWidth();\r
\r
- Annotation[] annotations = new Annotation[aWidth];\r
+ ConservationThread conservationThread;\r
\r
- hconsensus = new Hashtable[aWidth];\r
- AAFrequency.calculate(alignment.getSequencesArray(),\r
- 0, aWidth,\r
- hconsensus);\r
+ ConsensusThread consensusThread;\r
\r
- for (int i = 0; i < aWidth; i++)\r
- {\r
- float value = 0;\r
- if(ignoreGapsInConsensusCalculation)\r
- value = ((Float)hconsensus[i].get(AAFrequency.PID_NOGAPS)).floatValue();\r
- else\r
- value = ((Float)hconsensus[i].get(AAFrequency.PID_GAPS)).floatValue();\r
+ boolean consUpdateNeeded = false;\r
\r
- String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();\r
- String mouseOver = maxRes;\r
- if (maxRes.length() > 1)\r
- {\r
- mouseOver = "[" + maxRes + "] ";\r
- maxRes = "+";\r
- }\r
+ static boolean UPDATING_CONSENSUS = false;\r
\r
+ static boolean UPDATING_CONSERVATION = false;\r
\r
- mouseOver += (int) value + "%";\r
- annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);\r
+ boolean updatingConsensus = false;\r
\r
- }\r
+ boolean updatingConservation = false;\r
\r
- if (consensus == null)\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void updateConservation(final AlignmentPanel ap)\r
+ {\r
+ if (alignment.isNucleotide() || conservation==null)\r
+ return;\r
+\r
+ conservationThread = new ConservationThread(ap);\r
+ conservationThread.start();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void updateConsensus(final AlignmentPanel ap)\r
+ {\r
+ consensusThread = new ConsensusThread(ap);\r
+ consensusThread.start();\r
+ }\r
+\r
+\r
+ class ConsensusThread extends Thread\r
+ {\r
+ AlignmentPanel ap;\r
+ public ConsensusThread(AlignmentPanel ap)\r
{\r
- consensus = new AlignmentAnnotation("Consensus",\r
- "PID", annotations, 0f, 100f, AlignmentAnnotation.BAR_GRAPH);\r
- if (showConsensus)\r
- {\r
- alignment.addAnnotation(consensus);\r
- }\r
+ this.ap = ap;\r
}\r
- else\r
+ public void run()\r
{\r
- consensus.annotations = annotations;\r
- }\r
+ updatingConsensus = true;\r
+ while (UPDATING_CONSENSUS)\r
+ {\r
+ try\r
+ {\r
+ if (ap != null)\r
+ {\r
+ ap.repaint();\r
+ }\r
+\r
+ Thread.sleep(200);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+\r
+ UPDATING_CONSENSUS = true;\r
+\r
+ try\r
+ {\r
+ int aWidth = alignment.getWidth();\r
+ if(aWidth<0)\r
+ return;\r
+\r
+ consensus.annotations = null;\r
+ consensus.annotations = new Annotation[aWidth];\r
+\r
\r
- if(globalColourScheme!=null)\r
+ hconsensus = new Hashtable[aWidth];\r
+ AAFrequency.calculate(alignment.getSequencesArray(),\r
+ 0,\r
+ alignment.getWidth(),\r
+ hconsensus);\r
+\r
+ for (int i = 0; i < aWidth; i++)\r
+ {\r
+ float value = 0;\r
+ if (ignoreGapsInConsensusCalculation)\r
+ value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)).\r
+ floatValue();\r
+ else\r
+ value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).\r
+ floatValue();\r
+\r
+ String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();\r
+ String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";\r
+\r
+ if (maxRes.length() > 1)\r
+ {\r
+ mouseOver = "[" + maxRes + "] ";\r
+ maxRes = "+";\r
+ }\r
+\r
+ mouseOver += ( (int) value + "%");\r
+ consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);\r
+ }\r
+\r
+\r
+ if (globalColourScheme != null)\r
globalColourScheme.setConsensus(hconsensus);\r
\r
+ }\r
+ catch (OutOfMemoryError error)\r
+ {\r
+ alignment.deleteAnnotation(consensus);\r
+\r
+ consensus = null;\r
+ hconsensus = null;\r
+ System.out.println("Out of memory calculating consensus!!");\r
+ System.gc();\r
+ }\r
+ UPDATING_CONSENSUS = false;\r
+ updatingConsensus = false;\r
+\r
+ if (ap != null)\r
+ {\r
+ ap.repaint();\r
+ }\r
+ }\r
}\r
+\r
/**\r
* get the consensus sequence as displayed under the PID consensus annotation row.\r
* @return consensus sequence as a new sequence object\r
* get the consensus sequence as displayed under the PID consensus annotation row.\r
* @return consensus sequence as a new sequence object\r
*/\r
- public SequenceI getConsensusSeq() {\r
- if (consensus==null)\r
- updateConsensus();\r
+ public SequenceI getConsensusSeq()\r
+ {\r
if (consensus==null)\r
return null;\r
StringBuffer seqs=new StringBuffer();\r
public void setIgnoreGapsConsensus(boolean b)\r
{\r
ignoreGapsInConsensusCalculation = b;\r
- updateConsensus();\r
+ updateConsensus(null);\r
if (globalColourScheme!=null)\r
{\r
globalColourScheme.setThreshold(globalColourScheme.getThreshold(),\r
sequenceColours.put(seq, col);\r
}\r
\r
+ public String getSequenceSetId()\r
+ {\r
+ if (sequenceSetID == null)\r
+ sequenceSetID = alignment.hashCode() + "";\r
+\r
+ return sequenceSetID;\r
+ }\r
+\r
+ public void alignmentChanged(AlignmentPanel ap)\r
+ {\r
+ alignment.padGaps();\r
+\r
+ if (hconsensus != null && autocalculateConsensus)\r
+ {\r
+ updateConsensus(ap);\r
+ updateConservation(ap);\r
+ }\r
+\r
+ //Reset endRes of groups if beyond alignment width\r
+ int alWidth = alignment.getWidth();\r
+ Vector groups = alignment.getGroups();\r
+ if(groups!=null)\r
+ {\r
+ for(int i=0; i<groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
+ if(sg.getEndRes()>alWidth)\r
+ sg.setEndRes(alWidth-1);\r
+ }\r
+ }\r
+\r
+ if(selectionGroup!=null && selectionGroup.getEndRes()>alWidth)\r
+ selectionGroup.setEndRes(alWidth-1);\r
+\r
+ resetAllColourSchemes();\r
+\r
+ alignment.adjustSequenceAnnotations();\r
+ }\r
+\r
+ void resetAllColourSchemes()\r
+ {\r
+ ColourSchemeI cs = globalColourScheme;\r
+ if(cs!=null)\r
+ {\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ ( (ClustalxColourScheme) cs).\r
+ resetClustalX(alignment.getSequences(),\r
+ alignment.getWidth());\r
+ }\r
+\r
+ cs.setConsensus(hconsensus);\r
+ if (cs.conservationApplied())\r
+ {\r
+ Alignment al = (Alignment) 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, ConsPercGaps);\r
+\r
+ cs.setConservation(c);\r
+ }\r
+ }\r
+\r
+ int s, sSize = alignment.getGroups().size();\r
+ for(s=0; s<sSize; s++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup)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
+\r
+\r
}\r
annotationPanel.getSize().height);\r
alabels.setSize(d.width, annotationPanel.getSize().height);\r
\r
+ final AlignmentPanel ap = this;\r
+ av.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
+ {\r
+ public void propertyChange(java.beans.PropertyChangeEvent evt)\r
+ {\r
+ if (evt.getPropertyName().equals("alignment"))\r
+ {\r
+ PaintRefresher.Refresh(ap,\r
+ av.getSequenceSetId(),\r
+ true,\r
+ true);\r
+ alignmentChanged();\r
+ }\r
+ }\r
+ });\r
+\r
}\r
\r
\r
+ public void alignmentChanged()\r
+ {\r
+ av.alignmentChanged(this);\r
+\r
+ if (overviewPanel != null)\r
+ overviewPanel.updateOverviewImage();\r
+\r
+ alignFrame.updateEditMenuBar();\r
+\r
+ repaint();\r
+ }\r
+\r
public void fontChanged()\r
{\r
// set idCanvas bufferedImage to null\r
{\r
setLayout(null);\r
this.av = av;\r
- PaintRefresher.Register(this, av.alignment);\r
+ PaintRefresher.Register(this, av.getSequenceSetId());\r
}\r
\r
public void drawIdString(Graphics gg, SequenceI s, int i, int starty,\r
}\r
\r
seq = av.alignment.getSequenceAt(i);\r
+ if(seq==null)\r
+ continue;\r
\r
// Selected sequence colours\r
if ( (searchResults != null) &&\r
av.getSelectionGroup().recalcConservation();\r
\r
mouseDragging = false;\r
- PaintRefresher.Refresh(this, av.alignment);\r
+ PaintRefresher.Refresh(this, av.getSequenceSetId());\r
}\r
\r
public void highlightSearchResults(java.util.Vector found)\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
-\r
-\r
package jalview.appletgui;\r
\r
+import jalview.datamodel.*;\r
+\r
import java.awt.*;\r
+\r
import java.util.*;\r
-import jalview.datamodel.*;\r
\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
public class PaintRefresher\r
{\r
- static Hashtable components = new Hashtable();\r
+ static Hashtable components;\r
\r
- public static void Register(Component comp, AlignmentI al)\r
- {\r
- if(components.containsKey(al))\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param comp DOCUMENT ME!\r
+ * @param al DOCUMENT ME!\r
+ */\r
+ public static void Register(Component comp, String seqSetId)\r
{\r
- Vector comps = (Vector)components.get(al);\r
- comps.addElement(comp);\r
+ if (components == null)\r
+ components = new Hashtable();\r
+\r
+ if (components.containsKey(seqSetId))\r
+ {\r
+ Vector comps = (Vector) components.get(seqSetId);\r
+ if(!comps.contains(comp))\r
+ {\r
+ comps.addElement(comp);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ Vector vcoms = new Vector();\r
+ vcoms.addElement(comp);\r
+ components.put(seqSetId, vcoms);\r
+ }\r
}\r
- else\r
+\r
+ public static void RemoveComponent(Component comp)\r
{\r
- Vector vcoms = new Vector();\r
- vcoms.addElement(comp);\r
- components.put(al, vcoms);\r
+ if (components == null)\r
+ return;\r
+\r
+ Enumeration en = components.keys();\r
+ while(en.hasMoreElements())\r
+ {\r
+ String id = en.nextElement().toString();\r
+ Vector comps = (Vector) components.get(id);\r
+ comps.removeElement(comp);\r
+ if(comps.size()==0)\r
+ {\r
+ components.remove(id);\r
+ }\r
+ }\r
}\r
- }\r
-\r
- public static void Refresh(AlignmentI al)\r
- {\r
- Refresh(null, al);\r
- }\r
-\r
- public static void Refresh(Component c, AlignmentI al)\r
- {\r
- Component temp;\r
- Vector coms = (Vector)components.get(al);\r
- Enumeration e = coms.elements();\r
- while( e.hasMoreElements() )\r
+\r
+ public static void Refresh(Component source, String id)\r
{\r
- temp = (Component)e.nextElement();\r
+ Refresh( source, id, false, false);\r
+ }\r
\r
- if(!temp.isValid())\r
- coms.removeElement( temp );\r
- else if( temp == c )\r
- continue;\r
- else\r
- temp.repaint();\r
+ public static void Refresh(Component source,\r
+ String id,\r
+ boolean alignmentChanged,\r
+ boolean validateSequences)\r
+ {\r
+ if (components == null)\r
+ return;\r
+\r
+ Component comp;\r
+ Vector comps = (Vector) components.get(id);\r
+\r
+ if(comps==null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ Enumeration e = comps.elements();\r
+ while (e.hasMoreElements())\r
+ {\r
+ comp = (Component) e.nextElement();\r
+\r
+ if(comp==source)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (!comp.isValid())\r
+ {\r
+ comps.removeElement(comp);\r
+ }\r
+ else if(validateSequences\r
+ && comp instanceof AlignmentPanel\r
+ && source instanceof AlignmentPanel )\r
+ {\r
+ validateSequences( ((AlignmentPanel)source).av.alignment,\r
+ ((AlignmentPanel)comp).av.alignment);\r
+ }\r
+\r
+ if(comp instanceof AlignmentPanel && alignmentChanged)\r
+ {\r
+ ((AlignmentPanel)comp).alignmentChanged();\r
+ }\r
+\r
+ comp.repaint();\r
+ }\r
}\r
\r
- }\r
+ static void validateSequences(AlignmentI source, AlignmentI comp)\r
+ {\r
+ SequenceI[] a1;\r
+ if(source.getHiddenSequences().getSize()>0)\r
+ a1 = source.getHiddenSequences().getFullAlignment().getSequencesArray();\r
+ else\r
+ a1 = source.getSequencesArray();\r
\r
-}\r
+ SequenceI[] a2;\r
+ if (comp.getHiddenSequences().getSize() > 0)\r
+ a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();\r
+ else\r
+ a2 = comp.getSequencesArray();\r
\r
+ int i, iSize=a1.length, j, jSize=a2.length;\r
+ boolean exists = false;\r
+ for(i=0; i<iSize; i++)\r
+ {\r
+ exists = false;\r
+\r
+ for(j=0; j<jSize; j++)\r
+ if (a2[j]==a1[i] )\r
+ {\r
+ exists = true;\r
+ break;\r
+ }\r
+\r
+ if(!exists)\r
+ {\r
+ if (i < jSize)\r
+ comp.getSequences().insertElementAt(a1[i], i);\r
+ else\r
+ comp.addSequence(a1[i]);\r
+\r
+ jSize++;\r
+\r
+ if (comp.getHiddenSequences().getSize() > 0)\r
+ a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();\r
+ else\r
+ a2 = comp.getSequencesArray();\r
+ }\r
+ }\r
+\r
+ iSize=a1.length;\r
+ jSize=a2.length;\r
+\r
+ for(j=0; j<jSize; j++)\r
+ {\r
+ exists = false;\r
+ for(i=0; i<iSize; i++)\r
+ {\r
+ if (a2[j]==a1[i])\r
+ {\r
+ exists = true;\r
+ break;\r
+ }\r
+ }\r
+\r
+ if(!exists)\r
+ {\r
+ comp.deleteSequence(a2[j]);\r
+ }\r
+ }\r
+ }\r
+}\r
\r
import jalview.datamodel.*;\r
import jalview.appletgui.PaintRefresher;\r
+import jalview.commands.*;\r
\r
public class RedundancyPanel extends SliderPanel implements Runnable, WindowListener\r
{\r
}\r
\r
ap.idPanel.idCanvas.setHighlighted(redundantSeqs);\r
-\r
- PaintRefresher.Refresh(null,ap.av.alignment);\r
+ PaintRefresher.Refresh(this,\r
+ ap.av.getSequenceSetId(),\r
+ true,\r
+ true);\r
\r
}\r
public void applyButton_actionPerformed()\r
- {\r
- // historyList.push(new HistoryItem("Remove redundancy",\r
- // ap.av.alignment, HistoryItem.HIDE));\r
+ { Vector del = new Vector();\r
\r
- if ((historyList.size() == 1) ||\r
- !ap.alignFrame.historyList.contains(historyList.firstElement()))\r
- {\r
- // ap.alignFrame.addHistoryItem((HistoryItem) historyList.firstElement());\r
- // ap.alignFrame.updateEditMenuBar();\r
- }\r
+ undoButton.setEnabled(true);\r
\r
- Vector del = new Vector();\r
+ float value = slider.getValue();\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
\r
- undoButton.setEnabled(true);\r
+ for (int i = 0; i < redundancy.length; i++)\r
+ {\r
+ if (value <= redundancy[i])\r
+ {\r
+ del.addElement(originalSequences[i]);\r
+ }\r
+ }\r
\r
- float value = slider.getValue();\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
+ // This has to be done before the restoreHistoryItem method of alignFrame will\r
+ // actually restore these sequences.\r
+ if (del.size() > 0)\r
+ {\r
+ SequenceI [] deleted = new SequenceI[del.size()];\r
\r
- for (int i = 0; i < redundancy.length; i++)\r
- {\r
- if (value <= redundancy[i])\r
- {\r
- SequenceI seq = originalSequences[i];\r
- ap.av.alignment.deleteSequence(seq);\r
- del.addElement(seq);\r
- if (sg != null)\r
- {\r
- sg.deleteSequence(seq, false);\r
- }\r
- }\r
- }\r
+ int width = 0;\r
+ for (int i = 0; i < del.size(); i++)\r
+ {\r
+ deleted[i] = (SequenceI)del.elementAt(i);\r
+ if(deleted[i].getLength()>width)\r
+ width = deleted[i].getLength();\r
+ }\r
\r
+ EditCommand cut = new EditCommand("Remove Redundancy",\r
+ EditCommand.CUT, deleted,0,width,ap.av.alignment);\r
\r
- // This has to be done before the restoreHistoryItem method of alignFrame will\r
- // actually restore these sequences.\r
- if (del.size() > 0)\r
+ for (int i = 0; i < del.size(); i++)\r
+ {\r
+ ap.av.alignment.deleteSequence( deleted[i] );\r
+ PaintRefresher.Refresh(this,\r
+ ap.av.getSequenceSetId(),\r
+ true,\r
+ true);\r
+ if (sg != null)\r
{\r
- for (int i = 0, j = del.size(); i < j; i++)\r
- {\r
- SequenceI sq = (SequenceI) del.elementAt(i);\r
- sq.deleteChars(0, sq.getLength());\r
- }\r
+ sg.deleteSequence(deleted[i], false);\r
}\r
+ }\r
+\r
+ historyList.push(cut);\r
\r
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());\r
- ap.alignFrame.updateEditMenuBar();\r
+ ap.alignFrame.addHistoryItem(cut);\r
+\r
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());\r
+ }\r
\r
}\r
\r
public void undoButton_actionPerformed()\r
{\r
- // HistoryItem hi = (HistoryItem) historyList.pop();\r
- // ap.alignFrame.restoreHistoryItem(hi);\r
+ CommandI command = (CommandI) historyList.pop();\r
+ command.undoCommand();\r
+\r
+ if (ap.av.historyList.contains(command))\r
+ {\r
+ ap.av.historyList.removeElement(command);\r
+ ap.alignFrame.updateEditMenuBar();\r
+ }\r
+\r
+ ap.repaint();\r
\r
if (historyList.size() == 0)\r
{\r
undoButton.setEnabled(false);\r
- }\r
- ap.alignFrame.updateEditMenuBar();\r
+ }\r
}\r
\r
public void valueField_actionPerformed(ActionEvent e)\r
{\r
this.points = points;\r
this.npoint = npoint;\r
- PaintRefresher.Register(this, av.alignment);\r
+ PaintRefresher.Register(this, av.getSequenceSetId());\r
\r
prefsize = getPreferredSize();\r
orig = new float[npoint][3];\r
{\r
av.getSelectionGroup().addOrRemove(found, true);\r
av.getSelectionGroup().setEndRes(av.alignment.getWidth()-1);\r
- PaintRefresher.Refresh(this, av.alignment);\r
+ PaintRefresher.Refresh(this, av.getSequenceSetId());\r
}\r
else\r
{\r
this.av = av;\r
fr = new FeatureRenderer(av);\r
sr = new SequenceRenderer(av);\r
- PaintRefresher.Register(this, av.alignment);\r
+ PaintRefresher.Register(this, av.getSequenceSetId());\r
}\r
\r
public AlignViewport getViewport()\r
\r
import jalview.datamodel.*;\r
import jalview.schemes.*;\r
+import jalview.commands.*;\r
\r
import java.util.Vector;\r
\r
boolean mouseWheelPressed = false;\r
Point lastMousePress;\r
\r
+ EditCommand editCommand;\r
+\r
public SeqPanel(AlignViewport avp, AlignmentPanel p)\r
{\r
this.av = avp;\r
\r
void endEditing()\r
{\r
+ if (editCommand!=null && editCommand.getSize() > 0)\r
+ {\r
+ ap.alignFrame.addHistoryItem(editCommand);\r
+ av.firePropertyChange("alignment", null,\r
+ av.getAlignment().getSequences());\r
+ }\r
+\r
startseq = -1;\r
lastres = -1;\r
- seqEditOccurred = false;\r
editingSeqs = false;\r
groupEditing = false;\r
keyboardNo1 = null;\r
keyboardNo2 = null;\r
+ editCommand = null;\r
}\r
\r
void setCursorRow()\r
startseq = seqCanvas.cursorY;\r
lastres = seqCanvas.cursorX;\r
editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));\r
- editOccurred();\r
+ endEditing();\r
}\r
\r
void deleteGapAtCursor(boolean group)\r
startseq = seqCanvas.cursorY;\r
lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);\r
editSequence(false, seqCanvas.cursorX);\r
- editOccurred();\r
+ endEditing();\r
}\r
\r
void numberPressed(char value)\r
return;\r
}\r
\r
- editOccurred();\r
-\r
endEditing();\r
ap.repaint();\r
}\r
SequenceI seq = av.alignment.getSequenceAt(startseq);\r
StringBuffer message = new StringBuffer();\r
if (groupEditing)\r
- message.append("Edit group:");\r
+ {\r
+ message.append("Edit group:");\r
+ if (editCommand == null)\r
+ editCommand = new EditCommand("Edit Group");\r
+ }\r
else\r
- message.append("Edit sequence: "+seq.getName());\r
+ {\r
+ message.append("Edit sequence: " + seq.getName());\r
+ String label = seq.getName();\r
+ if(label.length()>10)\r
+ label = label.substring(0,10);\r
+ if(editCommand==null)\r
+ editCommand = new EditCommand("Edit "+label);\r
+ }\r
\r
if(insertGap)\r
message.append(" insert ");\r
}\r
\r
\r
-\r
if (groupEditing)\r
{\r
Vector vseqs = sg.getSequences(true);\r
}\r
}\r
\r
-\r
- for (g = 0; g < groupSize; g++)\r
- {\r
if (insertGap)\r
{\r
// dragging to the right\r
- for (int j = lastres; j < startres; j++)\r
+ if (fixedColumns && fixedRight != -1)\r
{\r
- if (fixedColumns && fixedRight != -1)\r
+ for (int j = lastres; j < startres; j++)\r
{\r
- insertChar(j, groupSeqs[g], fixedRight);\r
+ insertChar(j, groupSeqs, fixedRight);\r
}\r
- else\r
- insertChar(j, groupSeqs[g]);\r
+ }\r
+ else\r
+ {\r
+ editCommand.appendEdit(EditCommand.INSERT_GAP,\r
+ groupSeqs,\r
+ startres, startres-lastres,\r
+ av.getGapCharacter(),\r
+ true);\r
}\r
}\r
else\r
{\r
// dragging to the left\r
- for (int j = lastres; j > startres; j--)\r
+ if (fixedColumns && fixedRight != -1)\r
{\r
- if (fixedColumns && fixedRight != -1)\r
+ for (int j = lastres; j > startres; j--)\r
{\r
- deleteChar(startres, groupSeqs[g], fixedRight);\r
- }\r
- else\r
- {\r
- deleteChar(startres, groupSeqs[g]);\r
+ deleteChar(startres, groupSeqs, fixedRight);\r
}\r
}\r
+ else\r
+ editCommand.appendEdit(EditCommand.DELETE_GAP,\r
+ groupSeqs,\r
+ startres, lastres - startres,\r
+ av.getGapCharacter(),\r
+ true);\r
+\r
}\r
- }\r
- } else /////Editing a single sequence///////////\r
+ }\r
+ else /////Editing a single sequence///////////\r
{\r
if (insertGap)\r
{\r
// dragging to the right\r
- for (int j = lastres; j < startres; j++)\r
+ if (fixedColumns && fixedRight != -1)\r
{\r
- if (fixedColumns && fixedRight != -1)\r
+ for (int j = lastres; j < startres; j++)\r
{\r
- insertChar(j, seq, fixedRight);\r
+ insertChar(j, new SequenceI[]{seq}, fixedRight);\r
}\r
- else\r
- insertChar(j, seq);\r
+ }\r
+ else\r
+ {\r
+ editCommand.appendEdit(EditCommand.INSERT_GAP,\r
+ new SequenceI[]\r
+ {seq},\r
+ lastres, startres-lastres,\r
+ av.getGapCharacter(),\r
+ true);\r
}\r
}\r
else\r
{\r
// dragging to the left\r
- for (int j = lastres; j > startres; j--)\r
+ if (fixedColumns && fixedRight != -1)\r
{\r
- if (fixedColumns && fixedRight != -1)\r
+ for (int j = lastres; j > startres; j--)\r
+ {\r
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))\r
+ {\r
+ endEditing();\r
+ break;\r
+ }\r
+ deleteChar(startres, new SequenceI[]{seq}, fixedRight);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ //could be a keyboard edit trying to delete none gaps\r
+ int max=0;\r
+ for(int m = startres; m<lastres; m++)\r
{\r
- deleteChar(startres, seq, fixedRight);\r
+ if(!jalview.util.Comparison.isGap(seq.getCharAt(m)))\r
+ break;\r
+ max++;\r
}\r
- else\r
+\r
+ if (max>0)\r
{\r
- deleteChar(startres, seq);\r
+ editCommand.appendEdit(EditCommand.DELETE_GAP,\r
+ new SequenceI[]\r
+ {seq},\r
+ startres, max,\r
+ av.getGapCharacter(),\r
+ true);\r
}\r
}\r
}\r
}\r
\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param j DOCUMENT ME!\r
- * @param seq DOCUMENT ME!\r
- */\r
- void insertChar(int j, SequenceI seq)\r
- {\r
- seq.insertCharAt(j, av.getGapCharacter());\r
- seqEditOccurred = true;\r
- }\r
\r
- void insertChar(int j, SequenceI seq, int fixedColumn)\r
+ void insertChar(int j, SequenceI [] seq, int fixedColumn)\r
+ {\r
+ int blankColumn = fixedColumn;\r
+ for(int s=0; s<seq.length; s++)\r
{\r
//Find the next gap before the end of the visible region boundary\r
//If lastCol > j, theres a boundary after the gap insertion\r
- int blankColumn = fixedColumn;\r
+\r
for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)\r
{\r
- if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))\r
+ if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))\r
{\r
//Theres a space, so break and insert the gap\r
break;\r
\r
if (blankColumn <= j)\r
{\r
+ blankColumn = fixedColumn;\r
endEditing();\r
return;\r
}\r
-\r
- if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))\r
- {\r
- //Just Checking\r
- System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn));\r
- return;\r
- }\r
-\r
- seq.deleteCharAt(blankColumn);\r
- seq.insertCharAt(j, av.getGapCharacter());\r
- seqEditOccurred = true;\r
}\r
\r
- void deleteChar(int j, SequenceI seq, int fixedColumn)\r
- {\r
- if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))\r
- {\r
- ap.alignFrame.statusBar.setText(\r
- "End editing: Tried removing residue " + seq.getCharAt(j));\r
- return;\r
- }\r
- seq.deleteCharAt(j);\r
- seq.insertCharAt(fixedColumn, av.getGapCharacter());\r
- seqEditOccurred = true;\r
- }\r
+ editCommand.appendEdit(EditCommand.DELETE_GAP,\r
+ seq,\r
+ blankColumn, 1, av.getGapCharacter(), true);\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param j DOCUMENT ME!\r
- * @param seq DOCUMENT ME!\r
- */\r
- void deleteChar(int j, SequenceI seq)\r
- {\r
- if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))\r
- {\r
- ap.alignFrame.statusBar.setText(\r
- "End editing: Tried removing residue " + seq.getCharAt(j));\r
- return;\r
- }\r
+ editCommand.appendEdit(EditCommand.INSERT_GAP,\r
+ seq,\r
+ j, 1, av.getGapCharacter(),\r
+ true);\r
\r
- seq.deleteCharAt(j);\r
- seqEditOccurred = true;\r
- seqCanvas.repaint();\r
- }\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param i DOCUMENT ME!\r
- */\r
- void editOccurred()\r
- {\r
- if (!seqEditOccurred)\r
- {\r
- ap.alignFrame.historyList.pop();\r
- ap.alignFrame.updateEditMenuBar();\r
- }\r
+ void deleteChar(int j, SequenceI [] seq, int fixedColumn)\r
+ {\r
\r
- endEditing();\r
+ editCommand.appendEdit(EditCommand.DELETE_GAP,\r
+ seq,\r
+ j, 1, av.getGapCharacter(), true);\r
\r
- av.firePropertyChange("alignment", null,av.getAlignment().getSequences());\r
+ editCommand.appendEdit(EditCommand.INSERT_GAP,\r
+ seq,\r
+ fixedColumn, 1, av.getGapCharacter(), true);\r
+ }\r
\r
- }\r
\r
//////////////////////////////////////////\r
/////Everything below this is for defining the boundary of the rubberband\r
//////////////////////////////////////////\r
public void doMousePressedDefineMode(MouseEvent evt)\r
{\r
-\r
-\r
if (scrollThread != null)\r
{\r
scrollThread.running = false;\r
stretchGroup.getWidth());\r
}\r
\r
+ if (stretchGroup.cs instanceof Blosum62ColourScheme\r
+ || stretchGroup.cs instanceof PIDColourScheme\r
+ || stretchGroup.cs.conservationApplied()\r
+ || stretchGroup.cs.getThreshold() > 0)\r
+ stretchGroup.recalcConservation();\r
+\r
+\r
if (stretchGroup.cs.conservationApplied())\r
{\r
SliderPanel.setConservationSlider(ap, stretchGroup.cs,\r
changeEndRes = false;\r
changeStartRes = false;\r
stretchGroup = null;\r
- PaintRefresher.Refresh(av.alignment);\r
+ PaintRefresher.Refresh(ap, av.getSequenceSetId());\r
ap.repaint();\r
}\r
\r
public void drawSequence(SequenceI seq, SequenceGroup[] sg,\r
int start, int end, int y1)\r
{\r
+ if(seq==null)\r
+ return;\r
+\r
allGroups = sg;\r
\r
drawBoxes(seq, start, end, y1);\r
addMouseMotionListener(this);\r
setLayout(null);\r
\r
- PaintRefresher.Register(this, av.alignment);\r
+ PaintRefresher.Register(this, av.getSequenceSetId());\r
}\r
\r
public void treeSelectionChanged(SequenceI sequence)\r
}\r
}\r
\r
- PaintRefresher.Refresh(this, av.alignment);\r
+ PaintRefresher.Refresh(this, av.getSequenceSetId());\r
repaint();\r
}\r
}\r
if (ob instanceof SequenceI)\r
{\r
treeSelectionChanged( (Sequence) ob);\r
- PaintRefresher.Refresh(this, av.alignment);\r
+ PaintRefresher.Refresh(this, av.getSequenceSetId());\r
repaint();\r
return;\r
}\r
\r
av.setSelectionGroup(null);\r
av.alignment.deleteAllGroups();\r
- av.sequenceColours.clear();\r
+ av.sequenceColours=null;\r
\r
colourGroups();\r
\r
}\r
}\r
\r
- PaintRefresher.Refresh(this, av.alignment);\r
+ PaintRefresher.Refresh(this, av.getSequenceSetId());\r
repaint();\r
\r
}\r
git://source.jalview.org / jalview.git / commitdiff