AlignmentPanel ap;\r
Stack historyList = new Stack(); // simpler than synching with alignFrame.\r
float [] redundancy;\r
- Vector originalSequences;\r
- Hashtable originalColours;\r
+ SequenceI [] originalSequences;\r
JInternalFrame frame;\r
+ Vector redundantSeqs;\r
\r
/**\r
* Creates a new RedundancyPanel object.\r
* @param ap DOCUMENT ME!\r
* @param af DOCUMENT ME!\r
*/\r
- public RedundancyPanel(AlignmentPanel ap, AlignFrame af)\r
+ public RedundancyPanel(final AlignmentPanel ap, AlignFrame af)\r
{\r
this.ap = ap;\r
this.af = af;\r
+ redundantSeqs = new Vector();\r
\r
slider.addChangeListener(new ChangeListener()\r
{\r
\r
applyButton.setText("Remove");\r
allGroupsCheck.setVisible(false);\r
- slider.setMinimum(60);\r
+ slider.setMinimum(0);\r
slider.setMaximum(100);\r
slider.setValue(100);\r
\r
{\r
public void internalFrameClosing(InternalFrameEvent evt)\r
{\r
- resetColours();\r
+ ap.idPanel.idCanvas.setHighlighted(null);\r
}\r
}\r
);\r
\r
validate();\r
\r
- Vector sel = new Vector();\r
+ String[] omitHidden = null;\r
+\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
int height;\r
- originalSequences = new Vector();\r
- originalColours = new Hashtable();\r
+\r
+ int start, end;\r
\r
if ( (sg != null) && (sg.getSize(false) >= 1))\r
{\r
- height = sg.getSize(false);\r
- for (int i = 0; i < sg.getSize(false); i++)\r
- {\r
- sel.addElement(sg.getSequenceAt(i));\r
- }\r
+ originalSequences = sg.getSequencesInOrder(ap.av.alignment);\r
+ start = sg.getStartRes();\r
+ end = sg.getEndRes();\r
}\r
else\r
{\r
- height = ap.av.alignment.getHeight();\r
- for (int i = 0; i < ap.av.alignment.getHeight(); i++)\r
- {\r
- sel.addElement(ap.av.alignment.getSequenceAt(i));\r
- }\r
+ originalSequences = ap.av.alignment.getSequencesArray();\r
+ start = 0;\r
+ end = ap.av.alignment.getWidth();\r
}\r
\r
+ height = originalSequences.length;\r
+\r
redundancy = new float[height];\r
for (int i = 0; i < height; i++)\r
{\r
redundancy[i] = 0f;\r
}\r
\r
+ if (ap.av.hasHiddenColumns)\r
+ {\r
+ omitHidden = ap.av.getViewAsString(sg!=null);\r
+ }\r
+\r
\r
// long start = System.currentTimeMillis();\r
\r
float pid;\r
- SequenceI seqi, seqj;\r
- for (int i = 0; i < sel.size(); i++)\r
+ String seqi, seqj;\r
+ for (int i = 0; i < height; i++)\r
{\r
- originalSequences.addElement(sel.elementAt(i));\r
- originalColours.put(sel.elementAt(i),\r
- ((SequenceI) sel.elementAt(i)).getColor());\r
\r
for (int j = 0; j < i; j++)\r
{\r
if(i==j)\r
continue;\r
\r
- seqi = (SequenceI) sel.elementAt(i);\r
- seqj = (SequenceI) sel.elementAt(j);\r
-\r
- if (sg != null)\r
- pid = Comparison.PID( seqi,\r
- seqj,\r
- sg.getStartRes(), sg.getEndRes());\r
+ if(omitHidden==null)\r
+ {\r
+ seqi = originalSequences[i].getSequence(start, end);\r
+ seqj = originalSequences[j].getSequence(start, end);\r
+ }\r
else\r
- pid = Comparison.PID( seqi, seqj );\r
+ {\r
+ seqi = omitHidden[i];\r
+ seqj = omitHidden[j];\r
+ }\r
\r
+ pid = Comparison.PID( seqi, seqj );\r
\r
- if(seqj.getLength() < seqi.getLength())\r
+ if(seqj.length() < seqi.length())\r
redundancy[j] = Math.max(pid, redundancy[j]);\r
else\r
redundancy[i] = Math.max(pid, redundancy[i]);\r
}\r
}\r
\r
-\r
progress.setIndeterminate(false);\r
progress.setVisible(false);\r
progress = null;\r
valueField.setVisible(true);\r
\r
validate();\r
- // System.out.println("blob done "+ (System.currentTimeMillis()-start));\r
+ // System.out.println((System.currentTimeMillis()-start));\r
}\r
\r
void sliderValueChanged()\r
for(int i=0; i<redundancy.length; i++)\r
{\r
if (value > redundancy[i])\r
- ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.white);\r
- else\r
- ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.red);\r
- }\r
+ redundantSeqs.remove(originalSequences[i]);\r
+ else if(!redundantSeqs.contains(originalSequences[i]))\r
+ redundantSeqs.add(originalSequences[i]);\r
\r
- PaintRefresher.Refresh(null,ap.av.alignment);\r
+ }\r
\r
+ ap.idPanel.idCanvas.setHighlighted(redundantSeqs);\r
}\r
\r
/**\r
{\r
if (value <= redundancy[i])\r
{\r
- SequenceI seq = (SequenceI) originalSequences.elementAt(i);\r
+ SequenceI seq = originalSequences[i];\r
ap.av.alignment.deleteSequence(seq);\r
del.add(seq);\r
if (sg != null)\r
af.updateEditMenuBar();\r
}\r
\r
- void resetColours()\r
- {\r
- for(int i=0; i<originalSequences.size(); i++)\r
- {\r
- SequenceI seq = (SequenceI)originalSequences.elementAt(i);\r
- seq.setColor( (java.awt.Color)originalColours.get(seq));\r
- }\r
-\r
- PaintRefresher.Refresh(ap.av.alignment);\r
- }\r
\r
/**\r
* DOCUMENT ME!\r