/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\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
Stack historyList = new Stack(); // simpler than synching with alignFrame.\r
float [] redundancy;\r
SequenceI [] originalSequences;\r
- Hashtable originalColours;\r
Frame frame;\r
+ Vector redundantSeqs;\r
\r
public RedundancyPanel(AlignmentPanel ap)\r
{\r
super(ap, 0, false, null);\r
\r
+ redundantSeqs = new Vector();\r
this.ap = ap;\r
undoButton.setVisible(true);\r
applyButton.setVisible(true);\r
valueField.setText("100");\r
\r
slider.setVisibleAmount(1);\r
- slider.setMinimum(40);\r
+ slider.setMinimum(0);\r
slider.setMaximum(100+slider.getVisibleAmount());\r
slider.setValue(100);\r
\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
int height;\r
\r
- originalColours = new Hashtable();\r
int start, end;\r
\r
if ( (sg != null) && (sg.getSize(false) >= 1))\r
String seqi, seqj;\r
for (int i = 0; i < height; i++)\r
{\r
- originalColours.put(originalSequences[i],\r
- originalSequences[i].getColor());\r
-\r
for (int j = 0; j < i; j++)\r
{\r
if(i==j)\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
for(int i=0; i<redundancy.length; i++)\r
{\r
if (value > redundancy[i])\r
- originalSequences[i].setColor(java.awt.Color.white);\r
- else\r
- originalSequences[i].setColor(java.awt.Color.red);\r
+ redundantSeqs.removeElement(originalSequences[i]);\r
+ else if(!redundantSeqs.contains(originalSequences[i]))\r
+ redundantSeqs.addElement(originalSequences[i]);\r
}\r
\r
- PaintRefresher.Refresh(null,ap.av.alignment);\r
+ ap.idPanel.idCanvas.setHighlighted(redundantSeqs);\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.alignFrame.addHistoryItem(cut);\r
\r
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());\r
- ap.alignFrame.updateEditMenuBar();\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
public void windowClosing(WindowEvent evt)\r
{\r
- for(int i=0; i<originalSequences.length; i++)\r
- {\r
- SequenceI seq = originalSequences[i];\r
- seq.setColor( (java.awt.Color)originalColours.get(seq));\r
- }\r
-\r
- PaintRefresher.Refresh(ap.av.alignment);\r
+ ap.idPanel.idCanvas.setHighlighted(null);\r
}\r
\r
public void windowClosed(WindowEvent evt)\r
git://source.jalview.org / jalview.git / blobdiff