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
}\r
break;\r
case KeyEvent.VK_V:\r
- if (evt.isControlDown() || evt.isMetaDown())\r
+ if (evt.isControlDown())\r
{\r
- paste(true);\r
+ paste(evt.isShiftDown());\r
}\r
break;\r
case KeyEvent.VK_A:\r
{\r
alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()\r
|| evt.isShiftDown()\r
- || evt.isAltDown()\r
- );\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
boolean toggleSeqs = !evt.isControlDown();\r
else if (!hide)\r
viewport.showAllHiddenColumns();\r
}\r
-\r
- alignPanel.repaint();\r
break;\r
}\r
+\r
case KeyEvent.VK_PAGE_UP:\r
if (viewport.wrapAlignment)\r
alignPanel.scrollUp(true);\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
viewport.startSeq\r
+ viewport.endSeq - viewport.startSeq);\r
break;\r
+\r
+ case KeyEvent.VK_Z:\r
+ if (evt.isControlDown())\r
+ {\r
+ undoMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_Y:\r
+ if (evt.isControlDown())\r
+ {\r
+ redoMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_L:\r
+ if (evt.isControlDown())\r
+ {\r
+ trimAlignment(true);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_R:\r
+ if (evt.isControlDown())\r
+ {\r
+ trimAlignment(false);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_E:\r
+ if (evt.isControlDown())\r
+ {\r
+ if (evt.isShiftDown())\r
+ this.removeAllGapsMenuItem_actionPerformed();\r
+ else\r
+ removeGappedColumnMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_I:\r
+ if (evt.isControlDown())\r
+ {\r
+ if (evt.isAltDown())\r
+ viewport.invertColumnSelection();\r
+ else\r
+ this.invertSequenceMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_U:\r
+ if (evt.isControlDown())\r
+ {\r
+ this.deleteGroups_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_T:\r
+ if (evt.isControlDown())\r
+ {\r
+ newView();\r
}\r
+ break;\r
+\r
+\r
+ }\r
+ alignPanel.repaint();\r
}\r
public void keyReleased(KeyEvent evt)\r
{}\r
else if(evt.getSource()==wrapMenuItem)\r
wrapMenuItem_actionPerformed();\r
else if(evt.getSource()==scaleAbove)\r
- scaleAbove_actionPerformed();\r
+ viewport.setScaleAboveWrapped(scaleAbove.getState());\r
else if(evt.getSource()==scaleLeft)\r
- scaleLeft_actionPerformed();\r
+ viewport.setScaleLeftWrapped(scaleLeft.getState());\r
else if(evt.getSource()==scaleRight)\r
- scaleRight_actionPerformed();\r
+ viewport.setScaleRightWrapped(scaleRight.getState());\r
else if(evt.getSource()==seqLimits)\r
seqLimits_itemStateChanged();\r
else if(evt.getSource()==viewBoxesMenuItem)\r
- viewBoxesMenuItem_actionPerformed();\r
+ viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
else if(evt.getSource()==viewTextMenuItem)\r
- viewTextMenuItem_actionPerformed();\r
+ viewport.setShowText(viewTextMenuItem.getState());\r
else if(evt.getSource()==renderGapsMenuItem)\r
- renderGapsMenuItem_actionPerformed();\r
+ viewport.setRenderGaps(renderGapsMenuItem.getState());\r
else if(evt.getSource()==annotationPanelMenuItem)\r
- annotationPanelMenuItem_actionPerformed();\r
+ {\r
+ viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
+ alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
+ }\r
else if(evt.getSource()==sequenceFeatures)\r
{\r
viewport.showSequenceFeatures(sequenceFeatures.getState());\r
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
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
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
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void undoMenuItem_actionPerformed()\r
{\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,null);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void redoMenuItem_actionPerformed()\r
{\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
+ originalSource.firePropertyChange("alignment", null, null);\r
}\r
\r
- // used by undo and redo\r
- void restoreHistoryItem(CommandI command)\r
+ AlignViewport getOriginatingSource(CommandI command)\r
{\r
+ AlignViewport originalSource = viewport;\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
+ if (command instanceof EditCommand)\r
+ {\r
+ EditCommand editCommand = (EditCommand) command;\r
+ AlignmentI 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
+ return originalSource;\r
}\r
\r
public void moveSelectedSequences(boolean up)\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
else\r
{\r
+ for (int i = 0; i < newSeqs.length; i++)\r
+ {\r
+ viewport.alignment.addSequence(newSeqs[i]);\r
+ }\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
+ viewport.firePropertyChange("alignment", null, null);\r
}\r
\r
}\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
- 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
+ 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
\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
- }\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
new Finder(alignPanel);\r
}\r
\r
- public void font_actionPerformed()\r
+ public void newView()\r
{\r
- new FontChooser(alignPanel);\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
+\r
+\r
+ AlignFrame newaf = new AlignFrame(newal,\r
+ viewport.applet,\r
+ this.getTitle()+" (New View)",\r
+ false);\r
+\r
+ newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();\r
+ PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());\r
+ PaintRefresher.Register(newaf.alignPanel,\r
+ newaf.alignPanel.av.getSequenceSetId());\r
+\r
+ PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,\r
+ newaf.alignPanel.av.getSequenceSetId());\r
+ PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,\r
+ newaf.alignPanel.av.getSequenceSetId());\r
+\r
+ 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
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
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
+ 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
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(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
\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