\r
}\r
\r
- final TreePanel tp;\r
- if (viewport.getSelectionGroup() != null &&\r
- viewport.getSelectionGroup().getSize(false) > 3)\r
- {\r
- tp = new TreePanel(viewport,\r
- viewport.getSelectionGroup().getSequences(false),\r
+ final TreePanel tp = new TreePanel(viewport,\r
type,\r
- pwType,\r
- 0, viewport.alignment.getWidth());\r
- }\r
- else\r
- {\r
- tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
- type, pwType, 0, viewport.alignment.getWidth());\r
- }\r
+ pwType);\r
\r
addTreeMenuItem(tp, title);\r
\r
public void loadTree(jalview.io.NewickFile tree, String treeFile)\r
{\r
TreePanel tp = new TreePanel(viewport,\r
- viewport.getAlignment().getSequences(),\r
- tree, "From File - ", treeFile);\r
+ treeFile,\r
+ "From File - ",\r
+ tree);\r
jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
addTreeMenuItem(tp, treeFile);\r
}\r
*/\r
public void run()\r
{\r
- pca = new PCA(seqs);\r
+ pca = null;//new PCA(seqs);\r
pca.run();\r
\r
// Now find the component coordinates\r
AlignmentPanel ap;\r
\r
Stack historyList = new Stack(); // simpler than synching with alignFrame.\r
- Vector originalSequences;\r
- Hashtable originalColours;\r
- SequenceI[] oldAlignment;\r
float [] redundancy;\r
+ SequenceI [] originalSequences;\r
+ Hashtable originalColours;\r
Frame frame;\r
\r
public RedundancyPanel(AlignmentPanel ap)\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
+\r
originalColours = new Hashtable();\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.getSelectionAsString();\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
+ originalColours.put(originalSequences[i],\r
+ originalSequences[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
+ if(omitHidden==null)\r
{\r
- pid = jalview.util.Comparison.PID(seqi,\r
- seqj,\r
- sg.getStartRes(), sg.getEndRes());\r
+ seqi = originalSequences[i].getSequence(start, end);\r
+ seqj = originalSequences[j].getSequence(start, end);\r
}\r
else\r
- pid = jalview.util.Comparison.PID( seqi, seqj );\r
+ {\r
+ seqi = omitHidden[i];\r
+ seqj = omitHidden[j];\r
+ }\r
\r
+ pid = jalview.util.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
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
+ originalSequences[i].setColor(java.awt.Color.white);\r
else\r
- ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.red);\r
+ originalSequences[i].setColor(java.awt.Color.red);\r
}\r
\r
PaintRefresher.Refresh(null,ap.av.alignment);\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.addElement(seq);\r
if (sg != null)\r
\r
public void windowClosing(WindowEvent evt)\r
{\r
- for(int i=0; i<originalSequences.size(); i++)\r
+ for(int i=0; i<originalSequences.length; i++)\r
{\r
- SequenceI seq = (SequenceI)originalSequences.elementAt(i);\r
+ SequenceI seq = originalSequences[i];\r
seq.setColor( (java.awt.Color)originalColours.get(seq));\r
}\r
\r
* @param s DOCUMENT ME!\r
* @param e DOCUMENT ME!\r
*/\r
- public TreePanel(AlignViewport av, Vector seqVector, String type,\r
- String pwtype, int s, int e)\r
+ public TreePanel(AlignViewport av, String type, String pwtype)\r
{\r
try\r
{\r
ex.printStackTrace();\r
}\r
\r
- initTreePanel(av, seqVector, type, pwtype, s, e, null);\r
+ initTreePanel(av, type, pwtype, null);\r
}\r
\r
/**\r
* @param type DOCUMENT ME!\r
* @param pwtype DOCUMENT ME!\r
*/\r
- public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,\r
- String type, String pwtype)\r
+ public TreePanel(AlignViewport av,\r
+ String type,\r
+ String pwtype,\r
+ NewickFile newtree)\r
{\r
try\r
{\r
e.printStackTrace();\r
}\r
\r
- initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);\r
+ initTreePanel(av, type, pwtype, newtree);\r
}\r
\r
\r
- void initTreePanel(AlignViewport av, Vector seqVector, String type,\r
- String pwtype, int s, int e, NewickFile newTree)\r
+ void initTreePanel(AlignViewport av,\r
+ String type,\r
+ String pwtype,\r
+ NewickFile newTree)\r
{\r
\r
this.av = av;\r
this.type = type;\r
this.pwtype = pwtype;\r
\r
- start = s;\r
- end = e;\r
-\r
- seq = new Sequence[seqVector.size()];\r
- for(int i=0; i<seqVector.size(); i++)\r
- seq[i] = (SequenceI)seqVector.elementAt(i);\r
-\r
-\r
treeCanvas = new TreeCanvas(av, scrollPane);\r
scrollPane.add(treeCanvas);\r
\r
\r
public void run()\r
{\r
- if(newtree!=null)\r
- tree = new NJTree(seq, newtree);\r
+ if (newtree != null)\r
+ tree = new NJTree(av.alignment.getSequencesArray(),\r
+ newtree);\r
else\r
- tree = new NJTree(seq, type, pwtype, start, end);\r
+ {\r
+ int start, end;\r
+ SequenceI [] seqs;\r
+ String [] seqStrings = null;\r
+ // if (av.hasHiddenColumns)\r
+ {\r
+ // seqStrings = av.getSelectionAsString();\r
+ }\r
+\r
+ if(av.getSelectionGroup()==null)\r
+ {\r
+ start = 0;\r
+ end = av.alignment.getWidth();\r
+ seqs = av.alignment.getSequencesArray();\r
+ }\r
+ else\r
+ {\r
+ start = av.getSelectionGroup().getStartRes();\r
+ end = av.getSelectionGroup().getEndRes()+1;\r
+ seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);\r
+ }\r
+\r
+ tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);\r
+ }\r
\r
tree.reCount(tree.getTopNode());\r
tree.findHeight(tree.getTopNode());\r
}\r
\r
\r
+\r
+\r
BorderLayout borderLayout1 = new BorderLayout();\r
protected ScrollPane scrollPane = new ScrollPane();\r
MenuBar jMenuBar1 = new MenuBar();\r