/*\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
catch (Exception e)\r
{\r
e.printStackTrace();\r
- }\r
+ }\r
this.ap = ap;\r
- float scores[][] = new float[ap.av.alignment.getHeight()][ap.av.alignment.\r
- getHeight()];\r
+ sequences = new Vector();\r
+\r
+ SequenceI[] seqs;\r
+ String[] seqStrings = ap.av.getViewAsString(true);\r
+\r
+ if (ap.av.getSelectionGroup() == null)\r
+ {\r
+ seqs = ap.av.alignment.getSequencesArray();\r
+ }\r
+ else\r
+ {\r
+ seqs = ap.av.getSelectionGroup().getSequencesInOrder(ap.av.alignment);\r
+ }\r
+\r
+ float scores[][] = new float[seqs.length][seqs.length];\r
double totscore = 0;\r
- int count = ap.av.getSelectionGroup().getSize();\r
+ int count = ap.av.getSelectionGroup().getSize(false);\r
+\r
+ Sequence seq;\r
\r
- int acount = 0;\r
for (int i = 1; i < count; i++)\r
{\r
for (int j = 0; j < i; j++)\r
{\r
- acount++;\r
- AlignSeq as = new AlignSeq(ap.av.getSelectionGroup().getSequenceAt(i),\r
- ap.av.getSelectionGroup().getSequenceAt(j),\r
- "pep");\r
+\r
+ AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],\r
+ seqs[j], seqStrings[j], "pep");\r
+\r
+ if (as.s1str.length() == 0 || as.s2str.length() == 0)\r
+ {\r
+ continue;\r
+ }\r
\r
as.calcScoreMatrix();\r
as.traceAlignment();\r
+\r
as.printAlignment(System.out);\r
scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;\r
totscore = totscore + scores[i][j];\r
\r
textarea.append(as.getOutput());\r
- sequences.addElement(new Sequence(as.getS1().getName(), as.getAStr1()));\r
- sequences.addElement(new Sequence(as.getS2().getName(), as.getAStr2()));\r
-\r
+ seq = new Sequence(as.getS1().getName(),\r
+ as.getAStr1(),\r
+ as.getS1().getStart(),\r
+ as.getS1().getEnd()\r
+ );\r
+ sequences.addElement(seq);\r
+\r
+ seq = new Sequence(as.getS2().getName(),\r
+ as.getAStr2(),\r
+ as.getS2().getStart(),\r
+ as.getS2().getEnd());\r
+ sequences.addElement(seq);\r
}\r
}\r
\r
if (count > 2)\r
{\r
+ System.out.println(\r
+ "Pairwise alignment scaled similarity score matrix\n");\r
+\r
+ for (int i = 0; i < count; i++)\r
+ {\r
+ jalview.util.Format.print(System.out, "%s \n",\r
+ ("" + i) + " " +\r
+ seqs[i].getName());\r
+ }\r
+\r
+ System.out.println("\n");\r
+\r
for (int i = 0; i < count; i++)\r
{\r
for (int j = 0; j < i; j++)\r
scores[i][j] / totscore);\r
}\r
}\r
+\r
+ System.out.println("\n");\r
}\r
}\r
-\r
public void actionPerformed(ActionEvent evt)\r
{\r
if(evt.getSource()==viewInEditorButton)\r
}\r
\r
new AlignFrame(new Alignment(seq),\r
- ap.alignFrame.applet,\r
+ ap.av.applet,\r
"Pairwise Aligned Sequences",\r
false);\r
\r