\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
if(omitHidden==null)\r
{\r
- seqi = originalSequences[i].getSequence(start, end);\r
- seqj = originalSequences[j].getSequence(start, end);\r
+ seqi = originalSequences[i].getSequenceAsString(start, end);\r
+ seqj = originalSequences[j].getSequenceAsString(start, end);\r
}\r
else\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