Stack redoList = new Stack();\r
\r
void updateEditMenuBar()\r
- {\r
- if(historyList.size()>0)\r
+ {\r
+ if(historyList.size()>0)\r
+ {\r
+ undoMenuItem.setEnabled(true);\r
+ HistoryItem hi = (HistoryItem)historyList.peek();\r
+ undoMenuItem.setLabel("Undo "+hi.getDescription());\r
+ }\r
+ else\r
{\r
- undoMenuItem.setEnabled(true);\r
- Object [] history = (Object[])historyList.elementAt(0);\r
- undoMenuItem.setLabel("Undo "+history[0]);\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setLabel("Undo");\r
}\r
- else\r
- {\r
- undoMenuItem.setEnabled(false);\r
- undoMenuItem.setLabel("Undo");\r
- }\r
\r
- if(redoList.size()>0)\r
+ if(redoList.size()>0)\r
+ {\r
+ redoMenuItem.setEnabled(true);\r
+ HistoryItem hi = (HistoryItem)redoList.peek();\r
+ redoMenuItem.setLabel("Redo "+hi.getDescription());\r
+ }\r
+ else\r
{\r
- redoMenuItem.setEnabled(true);\r
- Object [] history = (Object[])redoList.elementAt(0);\r
- redoMenuItem.setLabel("Redo "+history[0]);\r
+ redoMenuItem.setEnabled(false);\r
+ redoMenuItem.setLabel("Redo");\r
}\r
- else\r
- {\r
- redoMenuItem.setEnabled(false);\r
- redoMenuItem.setLabel("Redo");\r
- }\r
- }\r
+ }\r
\r
- public void addHistoryItem(String type)\r
- {\r
- // must make sure we add new sequence objects her, not refs to the existing sequences\r
- redoList.removeAllElements();\r
- SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
- for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
- {\r
- seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
- viewport.getAlignment().getSequenceAt(i).getSequence());\r
- }\r
+ public void addHistoryItem(HistoryItem hi)\r
+ {\r
+ historyList.push(hi);\r
+ updateEditMenuBar();\r
+ }\r
\r
- historyList.addElement(new Object[]{type, seq} );\r
- updateEditMenuBar();\r
- }\r
+ protected void undoMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ HistoryItem hi = (HistoryItem)historyList.pop();\r
+ redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, HistoryItem.HIDE));\r
+ restoreHistoryItem(hi);\r
+ }\r
\r
- protected void undoMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- Object [] history = (Object[])historyList.elementAt(0);\r
- historyList.removeElementAt(0);\r
- // add the redo state before continuing!!\r
- SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
- for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
- {\r
- seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
- viewport.getAlignment().getSequenceAt(i).\r
- getSequence());\r
- }\r
- /////////\r
+ protected void redoMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ HistoryItem hi = (HistoryItem)redoList.pop();\r
+ restoreHistoryItem(hi);\r
+ updateEditMenuBar();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
+ alignPanel.repaint();\r
+ }\r
\r
- redoList.addElement(new Object[] {history[0], seq});\r
\r
- seq = (SequenceI[]) history[1];\r
+ // used by undo and redo\r
+ void restoreHistoryItem(HistoryItem hi)\r
+ {\r
+ if(hi.getType()== HistoryItem.SORT)\r
+ {\r
+ for(int i=0; i<hi.getSequences().size(); i++)\r
+ viewport.alignment.getSequences().setElementAt(hi.getSequences().elementAt(i), i);\r
+ }\r
+ else\r
+ {\r
+ for (int i = 0; i < hi.getSequences().size(); i++)\r
+ {\r
+ SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
+ if(restore.getLength()==0)\r
+ {\r
+ System.out.println(hi.getHidden().elementAt(i));\r
+ restore.setSequence(hi.getHidden().elementAt(i).toString());\r
+ viewport.alignment.getSequences().insertElementAt(\r
+ restore,\r
+ hi.getAlignIndex(i));\r
+ }\r
+ else\r
+ restore.setSequence(hi.getHidden().elementAt(i).toString());\r
+ }\r
+ if(hi.getType()==HistoryItem.PASTE)\r
+ {\r
+ for(int i=viewport.alignment.getHeight()-1;i>hi.getSequences().size()-1; i--)\r
+ viewport.alignment.deleteSequence(i);\r
+ }\r
+ }\r
\r
- AlignmentAnnotation[] old = viewport.alignment.getAlignmentAnnotation();\r
- viewport.setAlignment(new Alignment(seq));\r
- updateEditMenuBar();\r
- for (int i = 0; i < old.length; i++)\r
- viewport.alignment.addAnnotation(old[i]);\r
+ updateEditMenuBar();\r
+\r
+ viewport.updateConsensus();\r
+ viewport.updateConservation();\r
+ alignPanel.repaint();\r
+ }\r
\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
- }\r
\r
public void moveSelectedSequences(boolean up)\r
{\r
\r
protected void pasteThis_actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem("Paste");\r
+ addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, HistoryItem.PASTE));\r
paste(false);\r
}\r
\r
\r
protected void delete_actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem("Delete");\r
+ addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));\r
if (viewport.getSelectionGroup() == null)\r
return;\r
\r
\r
\r
\r
- protected void redoMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- Object [] history = (Object[])redoList.pop();\r
- SequenceI[] seq = (SequenceI[]) history[1];\r
-\r
- AlignmentAnnotation[] old = viewport.alignment.getAlignmentAnnotation();\r
- viewport.setAlignment(new Alignment(seq));\r
- for (int i = 0; i < old.length; i++)\r
- viewport.alignment.addAnnotation(old[i]);\r
-\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- updateEditMenuBar();\r
- alignPanel.repaint();\r
- }\r
-\r
-\r
protected void deleteGroups_actionPerformed(ActionEvent e)\r
{\r
viewport.alignment.deleteAllGroups();\r
\r
public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem("delete columns");\r
ColumnSelection colSel = viewport.getColumnSelection();\r
if (colSel.size() > 0)\r
{\r
+ addHistoryItem(new HistoryItem("Remove Left",viewport.alignment,\r
+ HistoryItem.HIDE));\r
int min = colSel.getMin();\r
viewport.getAlignment().trimLeft(min);\r
colSel.compensateForEdit(0,min);\r
\r
public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem("delete columns");\r
ColumnSelection colSel = viewport.getColumnSelection();\r
if (colSel.size() > 0)\r
{\r
+ addHistoryItem(new HistoryItem("Remove Right",viewport.alignment,\r
+ HistoryItem.HIDE));\r
int max = colSel.getMax();\r
viewport.getAlignment().trimRight(max);\r
if(viewport.getSelectionGroup()!=null)\r
\r
public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem("delete gapped columns");\r
+ addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
+ viewport.alignment,\r
+ HistoryItem.HIDE));\r
viewport.getAlignment().removeGaps();\r
viewport.updateConservation();\r
viewport.updateConsensus();\r
\r
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem("delete all gaps");\r
+ addHistoryItem(new HistoryItem("Remove Gaps",\r
+ viewport.alignment,\r
+ HistoryItem.HIDE));\r
SequenceI current;\r
int jSize;\r
for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
\r
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem("sort");\r
+ addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, HistoryItem.SORT));\r
AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
alignPanel.repaint();\r
}\r
\r
public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem("sort");\r
+ addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, HistoryItem.SORT));\r
AlignmentSorter.sortByID( viewport.getAlignment() );\r
alignPanel.repaint();\r
}\r
\r
public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem("sort");\r
+ addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, HistoryItem.SORT));\r
AlignmentSorter.sortByGroup(viewport.getAlignment());\r
AlignmentSorter.sortGroups(viewport.getAlignment());\r
alignPanel.repaint();\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem("sort");\r
+ addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
+ HistoryItem.SORT));\r
AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
alignPanel.repaint();\r
}\r
\r
protected int lastres;\r
protected int startseq;\r
+ int startEdit=-1;\r
+ int endEdit=-1;\r
\r
protected AlignViewport av;\r
\r
ScrollThread scrollThread = null;\r
boolean mouseDragging = false;\r
\r
+ boolean editingSeqs = false;\r
+ boolean groupEditing = false;\r
+\r
+\r
\r
public SeqPanel(AlignViewport avp, AlignmentPanel p) {\r
this.av = avp;\r
{\r
if(av.getWrapAlignment())\r
return;\r
- if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
+ if( editingSeqs )\r
doMouseDragged(evt);\r
else\r
doMouseDraggedDefineMode(evt);\r
{\r
if(av.getWrapAlignment())\r
return;\r
- if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
+ if(editingSeqs)\r
doMouseReleased(evt);\r
else\r
doMouseReleasedDefineMode(evt);\r
+\r
}\r
public void mousePressed(MouseEvent evt)\r
{\r
if(av.getWrapAlignment())\r
return;\r
+ System.out.println("here");\r
if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
+ {\r
+ if(evt.isAltDown() || evt.isControlDown())\r
+ groupEditing = true;\r
+\r
+ editingSeqs = true;\r
doMousePressed(evt);\r
+ }\r
else\r
doMousePressedDefineMode(evt);\r
}\r
public void mouseExited(MouseEvent evt)\r
{\r
- if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||\r
- evt.isControlDown())\r
+ if (av.getWrapAlignment() || editingSeqs)\r
return;\r
doMouseExitedDefineMode(evt);\r
\r
}\r
public void mouseEntered(MouseEvent evt)\r
{\r
- if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||\r
- evt.isControlDown())\r
+ if (av.getWrapAlignment() || editingSeqs)\r
return;\r
doMouseEnteredDefineMode(evt);\r
}\r
\r
public void doMouseReleased(MouseEvent evt) {\r
\r
- startseq = -1;\r
- lastres = -1;\r
if(seqEditOccurred>-1)\r
- updateConservation(seqEditOccurred);\r
+ editOccurred(seqEditOccurred);\r
\r
+ startseq = -1;\r
+ lastres = -1;\r
seqEditOccurred = -1;\r
-\r
+ editingSeqs = false;\r
+ groupEditing = false;\r
ap.repaint();\r
}\r
\r
public void doMousePressed(MouseEvent evt) {\r
- ap.alignFrame.addHistoryItem("sequence edit");\r
+ ap.alignFrame.addHistoryItem( new HistoryItem(\r
+ "Edit Sequence",av.alignment, HistoryItem.EDIT));\r
int seq;\r
int res;\r
\r
\r
\r
if (res != lastres)\r
- {\r
- // Group editing\r
- if (evt.isAltDown() || evt.isControlDown())\r
- {\r
- SequenceGroup sg = av.getSelectionGroup();\r
- if(sg==null)\r
- {\r
- lastres=-1;\r
- return;\r
- }\r
-\r
- // drag to right\r
- if(dragRight)\r
- sg.setEndRes(sg.getEndRes() + (res-lastres));\r
-\r
- // drag to left\r
- else\r
- {\r
- /// Are we able to delete?\r
- // ie are all columns blank?\r
- boolean deleteAllowed = false;\r
- for (int s = 0; s < sg.getSize(); s++)\r
- {\r
- SequenceI seq = sg.getSequenceAt(s);\r
- for (int j=res; j<lastres; j++)\r
- {\r
- if(seq.getSequence().length()<=j)\r
- continue;\r
-\r
- if(!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))\r
- {\r
- // Not a gap, block edit not valid\r
- res=j+1;\r
- deleteAllowed = false;\r
- continue;\r
- }\r
- deleteAllowed = true;\r
- }\r
- }\r
-\r
- if(!deleteAllowed)\r
- {\r
- lastres = -1;\r
- return;\r
- }\r
-\r
- sg.setEndRes(sg.getEndRes() - (lastres-res));\r
- }\r
-\r
-\r
- for (int i = 0; i < sg.getSize(); i++)\r
- {\r
- SequenceI s = sg.getSequenceAt(i);\r
- int k = av.alignment.findIndex(s);\r
-\r
- // drag to right\r
- if (dragRight)\r
- for (int j = lastres; j < res; j++)\r
- insertChar(j, k);\r
-\r
- // drag to left\r
- else\r
- {\r
- for (int j = res; j < lastres; j++)\r
- {\r
- if(s.getLength()>j)\r
- deleteChar(res, k);\r
- }\r
- }\r
- }\r
- }\r
- else /////Editing a single sequence///////////\r
- {\r
- if (res < av.getAlignment().getWidth() && res > lastres)\r
- {\r
- // dragging to the right\r
- for (int j = lastres; j < res; j++)\r
- insertChar(j, startseq);\r
- }\r
- else if (res < av.getAlignment().getWidth() && res < lastres)\r
- {\r
- // dragging to the left\r
- for (int j = lastres; j > res; j--)\r
- {\r
- deleteChar(res, startseq);\r
- }\r
- }\r
-\r
- }\r
- }\r
+ {\r
+ // Group editing\r
+ if (groupEditing)\r
+ {\r
+ SequenceGroup sg = av.getSelectionGroup();\r
+ if(sg==null)\r
+ {\r
+ lastres=-1;\r
+ return;\r
+ }\r
\r
- lastres = res;\r
+ // drag to right\r
+ if(dragRight)\r
+ sg.setEndRes(sg.getEndRes() + (res-lastres));\r
+\r
+ // drag to left\r
+ else\r
+ {\r
+ /// Are we able to delete?\r
+ // ie are all columns blank?\r
+ boolean deleteAllowed = false;\r
+ for (int s = 0; s < sg.getSize(); s++)\r
+ {\r
+ SequenceI seq = sg.getSequenceAt(s);\r
+ for (int j=res; j<lastres; j++)\r
+ {\r
+ if(seq.getSequence().length()<=j)\r
+ continue;\r
+\r
+ if(!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))\r
+ {\r
+ // Not a gap, block edit not valid\r
+ res=j+1;\r
+ deleteAllowed = false;\r
+ continue;\r
+ }\r
+ deleteAllowed = true;\r
+ }\r
+ }\r
+\r
+ if(!deleteAllowed)\r
+ {\r
+ lastres = -1;\r
+ return;\r
+ }\r
+\r
+ sg.setEndRes(sg.getEndRes() - (lastres-res));\r
+ }\r
+\r
+\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
+ SequenceI s = sg.getSequenceAt(i);\r
+ int k = av.alignment.findIndex(s);\r
+\r
+ // drag to right\r
+ if (dragRight)\r
+ for (int j = lastres; j < res; j++)\r
+ insertChar(j, k);\r
+\r
+ // drag to left\r
+ else\r
+ {\r
+ for (int j = res; j < lastres; j++)\r
+ {\r
+ if(s.getLength()>j)\r
+ deleteChar(res, k);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ else /////Editing a single sequence///////////\r
+ {\r
+ if (res < av.getAlignment().getWidth() && res > lastres)\r
+ {\r
+ // dragging to the right\r
+ for (int j = lastres; j < res; j++)\r
+ insertChar(j, startseq);\r
+ }\r
+ else if (res < av.getAlignment().getWidth() && res < lastres)\r
+ {\r
+ // dragging to the left\r
+ for (int j = lastres; j > res; j--)\r
+ {\r
+ if( jalview.util.Comparison.isGap(\r
+ av.alignment.getSequenceAt(startseq).getSequence().charAt(res)))\r
+\r
+ deleteChar(res, startseq);\r
+ else\r
+ {\r
+\r
+ break;\r
+ }\r
+ }\r
+ }\r
+\r
+ }\r
+ }\r
+\r
+ endEdit = res;\r
+ lastres = res;\r
seqCanvas.repaint();\r
}\r
\r
public void deleteChar(int j, int seq)\r
{\r
\r
- if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))\r
- av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
-\r
+ av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
+ seqEditOccurred=seq;\r
av.alignment.getWidth();\r
repaint();\r
- seqEditOccurred=seq;\r
}\r
\r
\r
- void updateConservation(int i)\r
+ void editOccurred(int i)\r
{\r
+ if(endEdit==startEdit)\r
+ {\r
+ ap.alignFrame.historyList.pop();\r
+ ap.alignFrame.updateEditMenuBar();\r
+ }\r
+\r
av.updateConservation();\r
av.updateConsensus();\r
\r
cs = new ClustalxColourScheme(av.alignment.getSequences(), av.alignment.getWidth());\r
\r
ap.alignFrame.changeColour(cs);\r
+\r
}\r
\r
//////////////////////////////////////////\r
--- /dev/null
+package jalview.datamodel;\r
+\r
+import java.util.*;\r
+\r
+public class HistoryItem\r
+{\r
+ public static final int EDIT = 0;\r
+ public static final int SORT = 1;\r
+ public static final int HIDE = 2;\r
+ public static final int PASTE= 3;\r
+\r
+ final int type;\r
+ Vector sequences;\r
+ Vector alignIndex;\r
+ String description;\r
+ Vector hiddenSeqs;\r
+\r
+ public HistoryItem(String description, AlignmentI al, int type)\r
+ {\r
+ this.type = type;\r
+ this.description = description;\r
+ sequences = new Vector();\r
+ alignIndex = new Vector();\r
+ hiddenSeqs = new Vector();\r
+\r
+ for (int i = 0; i < al.getHeight(); i++)\r
+ {\r
+ SequenceI seq = al.getSequenceAt(i);\r
+ sequences.addElement(seq);\r
+ alignIndex.addElement(i + "");\r
+ hiddenSeqs.addElement(seq.getSequence().toString());\r
+ }\r
+ }\r
+\r
+ public int getType()\r
+ {return type;}\r
+\r
+ public Vector getSequences()\r
+ {return sequences;}\r
+\r
+ public String getDescription()\r
+ {return description; }\r
+\r
+ public Vector getHidden()\r
+ { return hiddenSeqs; }\r
+\r
+ public int getAlignIndex(int seq)\r
+ {\r
+ return Integer.parseInt(alignIndex.elementAt(seq).toString());\r
+ }\r
+\r
+}\r
Stack redoList = new Stack();
void updateEditMenuBar()
- {
- if(historyList.size()>0)
+ {
+ if(historyList.size()>0)
+ {
+ undoMenuItem.setEnabled(true);
+ HistoryItem hi = (HistoryItem)historyList.peek();
+ undoMenuItem.setText("Undo "+hi.getDescription());
+ }
+ else
{
- undoMenuItem.setEnabled(true);
- Object [] history = (Object[])historyList.get(0);
- undoMenuItem.setText("Undo "+history[0]);
+ undoMenuItem.setEnabled(false);
+ undoMenuItem.setText("Undo");
}
- else
- {
- undoMenuItem.setEnabled(false);
- undoMenuItem.setText("Undo");
- }
- if(redoList.size()>0)
+ if(redoList.size()>0)
+ {
+ redoMenuItem.setEnabled(true);
+ HistoryItem hi = (HistoryItem)redoList.peek();
+ redoMenuItem.setText("Redo "+hi.getDescription());
+ }
+ else
{
- redoMenuItem.setEnabled(true);
- Object [] history = (Object[])redoList.get(0);
- redoMenuItem.setText("Redo "+history[0]);
+ redoMenuItem.setEnabled(false);
+ redoMenuItem.setText("Redo");
}
- else
- {
- redoMenuItem.setEnabled(false);
- redoMenuItem.setText("Redo");
- }
- }
-
- public void addHistoryItem(String type)
- {
- // must make sure we add new sequence objects her, not refs to the existing sequences
- redoList.clear();
-
- SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
- for(int i=0; i<viewport.getAlignment().getHeight(); i++)
- {
- seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
- viewport.getAlignment().getSequenceAt(i).getSequence());
- }
-
+ }
- historyList.add(0, new Object[]{type, seq} );
- updateEditMenuBar();
- }
+ public void addHistoryItem(HistoryItem hi)
+ {
+ historyList.push(hi);
+ updateEditMenuBar();
+ }
- protected void undoMenuItem_actionPerformed(ActionEvent e)
- {
- Object [] history = (Object[])historyList.remove(0);
- // add the redo state before continuing!!
- SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
- for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
- {
- seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
- viewport.getAlignment().getSequenceAt(i).
- getSequence());
- }
- /////////
+ protected void undoMenuItem_actionPerformed(ActionEvent e)
+ {
+ HistoryItem hi = (HistoryItem)historyList.pop();
+ redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, HistoryItem.HIDE));
+ restoreHistoryItem(hi);
+ }
- redoList.add(0, new Object[] {history[0], seq});
- seq = (SequenceI[]) history[1];
- AlignmentAnnotation [] old = viewport.alignment.getAlignmentAnnotation();
- viewport.setAlignment( new Alignment(seq) );
- viewport.alignment.setGapCharacter( Preferences.gapSymbol );
+ protected void redoMenuItem_actionPerformed(ActionEvent e)
+ {
+ HistoryItem hi = (HistoryItem)redoList.pop();
+ restoreHistoryItem(hi);
updateEditMenuBar();
- for(int i=0; i<old.length; i++)
- viewport.alignment.addAnnotation(old[i]);
viewport.updateConsensus();
- viewport.updateConservation();
alignPanel.repaint();
- }
+ alignPanel.repaint();
+ }
+
+
+ // used by undo and redo
+ void restoreHistoryItem(HistoryItem hi)
+ {
+ if(hi.getType()== HistoryItem.SORT)
+ {
+ for(int i=0; i<hi.getSequences().size(); i++)
+ viewport.alignment.getSequences().setElementAt(hi.getSequences().elementAt(i), i);
+ }
+ else
+ {
+ for (int i = 0; i < hi.getSequences().size(); i++)
+ {
+ SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
+ if(restore.getLength()==0)
+ {
+ System.out.println(hi.getHidden().elementAt(i));
+ restore.setSequence(hi.getHidden().elementAt(i).toString());
+ viewport.alignment.getSequences().insertElementAt(
+ restore,
+ hi.getAlignIndex(i));
+ }
+ else
+ restore.setSequence(hi.getHidden().elementAt(i).toString());
+ }
+ if(hi.getType()==HistoryItem.PASTE)
+ {
+ for(int i=viewport.alignment.getHeight()-1;i>hi.getSequences().size()-1; i--)
+ viewport.alignment.deleteSequence(i);
+ }
+ }
+
+ updateEditMenuBar();
+
+ viewport.updateConsensus();
+ viewport.updateConservation();
+ alignPanel.repaint();
+ }
public void moveSelectedSequences(boolean up)
{
protected void pasteThis_actionPerformed(ActionEvent e)
{
- addHistoryItem("Paste");
+ addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, HistoryItem.PASTE));
paste(false);
}
protected void delete_actionPerformed(ActionEvent e)
{
- addHistoryItem("Delete");
+ addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));
+
if (viewport.getSelectionGroup() == null)
return;
}
-
- protected void redoMenuItem_actionPerformed(ActionEvent e)
- {
- Object [] history = (Object[])redoList.remove(0);
- SequenceI[] seq = (SequenceI[]) history[1];
- viewport.setAlignment( new Alignment(seq) );
- viewport.alignment.setGapCharacter( Preferences.gapSymbol );
- updateEditMenuBar();
- viewport.updateConsensus();
- alignPanel.repaint();
- alignPanel.repaint();
- }
-
-
protected void deleteGroups_actionPerformed(ActionEvent e)
{
viewport.alignment.deleteAllGroups();
public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
{
- addHistoryItem("delete columns");
ColumnSelection colSel = viewport.getColumnSelection();
if (colSel.size() > 0)
{
+ addHistoryItem(new HistoryItem("Remove Left",viewport.alignment,
+ HistoryItem.HIDE));
int min = colSel.getMin();
viewport.getAlignment().trimLeft(min);
colSel.compensateForEdit(0,min);
public void remove2RightMenuItem_actionPerformed(ActionEvent e)
{
- addHistoryItem("delete columns");
ColumnSelection colSel = viewport.getColumnSelection();
if (colSel.size() > 0)
{
+ addHistoryItem(new HistoryItem("Remove Right",viewport.alignment,
+ HistoryItem.HIDE));
+
int max = colSel.getMax();
viewport.getAlignment().trimRight(max);
if(viewport.getSelectionGroup()!=null)
public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
{
- addHistoryItem("delete gapped columns");
+ addHistoryItem(new HistoryItem("Remove Gapped Columns",
+ viewport.alignment,
+ HistoryItem.HIDE));
viewport.getAlignment().removeGaps();
viewport.updateConservation();
viewport.updateConsensus();
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
{
- addHistoryItem("delete all gaps");
+ addHistoryItem(new HistoryItem("Remove Gaps",
+ viewport.alignment,
+ HistoryItem.HIDE));
SequenceI current;
int jSize;
for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
- addHistoryItem("sort");
+ addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, HistoryItem.SORT));
AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
alignPanel.repaint();
}
public void sortIDMenuItem_actionPerformed(ActionEvent e)
{
- addHistoryItem("sort");
+ addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, HistoryItem.SORT));
AlignmentSorter.sortByID( viewport.getAlignment() );
alignPanel.repaint();
}
public void sortGroupMenuItem_actionPerformed(ActionEvent e)
{
- addHistoryItem("sort");
+ addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, HistoryItem.SORT));
AlignmentSorter.sortByGroup(viewport.getAlignment());
AlignmentSorter.sortGroups(viewport.getAlignment());
alignPanel.repaint();
{
public void actionPerformed(ActionEvent e)
{
- addHistoryItem("sort");
+ addHistoryItem(new HistoryItem("Sort", viewport.alignment,
+ HistoryItem.SORT));
// TODO: JBPNote - have to map order entries to curent SequenceI pointers
AlignmentSorter.sortBy(viewport.getAlignment(), order);
alignPanel.repaint();
{
public void actionPerformed(ActionEvent e)
{
- addHistoryItem("sort");
+ addHistoryItem(new HistoryItem("Tree Sort", viewport.alignment,
+ HistoryItem.SORT));
AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
alignPanel.repaint();
}
\r
protected int lastres;\r
protected int startseq;\r
+ int startEdit=-1;\r
+ int endEdit=-1;\r
\r
protected AlignViewport av;\r
\r
ScrollThread scrollThread = null;\r
boolean mouseDragging = false;\r
\r
+ boolean editingSeqs = false;\r
+ boolean groupEditing = false;\r
+\r
\r
public SeqPanel(AlignViewport avp, AlignmentPanel p) {\r
this.av = avp;\r
{\r
if(av.getWrapAlignment())\r
return;\r
- if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
+ if( editingSeqs )\r
doMouseDragged(evt);\r
else\r
doMouseDraggedDefineMode(evt);\r
{\r
if(av.getWrapAlignment())\r
return;\r
- if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
+ if(editingSeqs)\r
doMouseReleased(evt);\r
else\r
doMouseReleasedDefineMode(evt);\r
+\r
}\r
public void mousePressed(MouseEvent evt)\r
{\r
if(av.getWrapAlignment())\r
return;\r
if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
+ {\r
+ if(evt.isAltDown() || evt.isControlDown())\r
+ groupEditing = true;\r
+\r
+ editingSeqs = true;\r
doMousePressed(evt);\r
+ }\r
else\r
doMousePressedDefineMode(evt);\r
}\r
public void mouseExited(MouseEvent evt)\r
{\r
- if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||\r
- evt.isControlDown())\r
+ if (av.getWrapAlignment() || editingSeqs)\r
return;\r
doMouseExitedDefineMode(evt);\r
\r
}\r
public void mouseEntered(MouseEvent evt)\r
{\r
- if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||\r
- evt.isControlDown())\r
+ if (av.getWrapAlignment() || editingSeqs)\r
return;\r
doMouseEnteredDefineMode(evt);\r
}\r
\r
public void doMouseReleased(MouseEvent evt) {\r
\r
- startseq = -1;\r
- lastres = -1;\r
if(seqEditOccurred>-1)\r
- updateConservation(seqEditOccurred);\r
+ editOccurred(seqEditOccurred);\r
\r
+ startseq = -1;\r
+ lastres = -1;\r
seqEditOccurred = -1;\r
+ editingSeqs = false;\r
+ groupEditing = false;\r
\r
ap.repaint();\r
}\r
\r
public void doMousePressed(MouseEvent evt) {\r
- ap.alignFrame.addHistoryItem("sequence edit");\r
+\r
+ ap.alignFrame.addHistoryItem( new HistoryItem(\r
+ "Edit Sequence",av.alignment, HistoryItem.EDIT));\r
+\r
int seq;\r
int res;\r
\r
if (seq < av.getAlignment().getHeight() &&\r
res < av.getAlignment().getSequenceAt(seq).getLength())\r
{\r
- //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);\r
- // Find the residue's position in the sequence (res is the position\r
- // in the alignment\r
-\r
startseq = seq;\r
-\r
lastres = res;\r
-\r
}\r
else\r
{\r
lastres = -1;\r
}\r
\r
+ startEdit = lastres;\r
+ endEdit = lastres;\r
+\r
return;\r
}\r
\r
\r
if (res != lastres)\r
{\r
- // Group editing\r
- if (evt.isAltDown() || evt.isControlDown())\r
+ // Group editing\r
+ if (groupEditing)\r
{\r
- SequenceGroup sg = av.getSelectionGroup();\r
+ SequenceGroup sg = av.getSelectionGroup();\r
if(sg==null)\r
{\r
lastres=-1;\r
// dragging to the left\r
for (int j = lastres; j > res; j--)\r
{\r
+ if( jalview.util.Comparison.isGap(\r
+ av.alignment.getSequenceAt(startseq).getSequence().charAt(res)))\r
+\r
deleteChar(res, startseq);\r
+ else\r
+ {\r
+\r
+ break;\r
+ }\r
}\r
- }\r
+ }\r
\r
- }\r
+ }\r
}\r
\r
+ endEdit = res;\r
lastres = res;\r
repaint();\r
}\r
\r
public void deleteChar(int j, int seq)\r
{\r
+ av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
+ seqEditOccurred=seq;\r
\r
- if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))\r
- { av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
-\r
- }\r
- else System.out.println("err "+seq+" "+j);\r
av.alignment.getWidth();\r
repaint();\r
- seqEditOccurred=seq;\r
-\r
}\r
\r
\r
- void updateConservation(int i)\r
+ void editOccurred(int i)\r
{\r
+ if(endEdit==startEdit)\r
+ {\r
+ ap.alignFrame.historyList.pop();\r
+ ap.alignFrame.updateEditMenuBar();\r
+ }\r
+\r
av.updateConservation();\r
av.updateConsensus();\r
\r
// Edit end res position of selected group\r
changeStartRes = true;\r
\r
+ stretchGroup.getWidth();\r
\r
repaint();\r
\r
git://source.jalview.org / jalview.git / commitdiff