-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 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
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
-package jalview.gui;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.jbgui.GPairwiseAlignPanel;\r
-import jalview.analysis.*;\r
-import java.awt.event.*;\r
-import javax.swing.*;\r
-import java.util.*;\r
-\r
-\r
-public class PairwiseAlignPanel extends GPairwiseAlignPanel\r
-{\r
- Vector sequences = new Vector();\r
- AlignViewport av;\r
-\r
- public PairwiseAlignPanel(AlignViewport av)\r
- {\r
- super();\r
- this.av = av;\r
- Vector selsubset = new Vector();\r
- for (int i=0, j=av.getSelectionGroup().getSize(); i<j; i++)\r
- if (av.getAlignment().getSequences().contains(av.getSelectionGroup().getSequenceAt(i)))\r
- selsubset.add(av.getSelectionGroup().getSequenceAt(i));\r
- float scores[][] = new float[selsubset.size()][selsubset.size()];\r
- double totscore = 0;\r
- int count = selsubset.size();\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( (SequenceI) selsubset.elementAt(i),\r
- (SequenceI) selsubset.elementAt(j), "pep");\r
- as.calcScoreMatrix();\r
- as.traceAlignment();\r
- as.printAlignment();\r
- scores[i][j] = (float) as.getMaxScore() /\r
- (float) as.getASeq1().length;\r
- totscore = totscore + scores[i][j];\r
-\r
- textarea.append(as.getOutput());\r
- sequences.add(new Sequence(as.getS1().getName(), as.getAStr1()));\r
- sequences.add(new Sequence(as.getS2().getName(), as.getAStr2()));\r
- }\r
- }\r
- if (count > 2)\r
- {\r
- System.out.println("Pairwise alignment scaled similarity score matrix\n");\r
- for (int i = 0; i < count;i++)\r
- jalview.util.Format.print(System.out, "%s \n", (""+i)+" "+((SequenceI) selsubset.elementAt(i)).getName());\r
- System.out.println("\n");\r
- for (int i = 0; i < count;i++)\r
- for (int j = 0; j < i; j++)\r
- jalview.util.Format.print(System.out,"%7.3f",scores[i][j]/totscore);\r
- System.out.println("\n");\r
-\r
- }\r
- }\r
-\r
-\r
- protected void viewInEditorButton_actionPerformed(ActionEvent e)\r
- {\r
-\r
- Sequence [] seq = new Sequence[sequences.size()];\r
-\r
- for (int i=0;i<sequences.size();i++)\r
- seq[i] = (Sequence) sequences.elementAt(i);\r
-\r
-\r
- AlignFrame af = new AlignFrame(new Alignment(seq));\r
- Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",\r
- AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\r
-\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.gui;
+
+import jalview.analysis.*;
+
+import jalview.datamodel.*;
+
+import jalview.jbgui.*;
+
+import java.awt.event.*;
+
+import java.util.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class PairwiseAlignPanel extends GPairwiseAlignPanel
+{
+
+ AlignViewport av;
+ Vector sequences;
+
+ /**
+ * Creates a new PairwiseAlignPanel object.
+ *
+ * @param av DOCUMENT ME!
+ */
+ public PairwiseAlignPanel(AlignViewport av)
+ {
+ super();
+ this.av = av;
+
+ sequences = new Vector();
+
+ SequenceI [] seqs;
+ String [] seqStrings = av.getViewAsString(true);
+
+ if(av.getSelectionGroup()==null)
+ {
+ seqs = av.alignment.getSequencesArray();
+ }
+ else
+ {
+ seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+ }
+
+ String type=(av.alignment.isNucleotide()) ? AlignSeq.DNA : AlignSeq.PEP;
+
+ float[][] scores = new float[seqs.length][seqs.length];
+ double totscore = 0;
+ int count = seqs.length;
+
+ Sequence seq;
+
+ for (int i = 1; i < count; i++)
+ {
+ for (int j = 0; j < i; j++)
+ {
+
+ AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],
+ seqs[j], seqStrings[j], type);
+
+ if(as.s1str.length()==0 || as.s2str.length()==0)
+ {
+ continue;
+ }
+
+ as.calcScoreMatrix();
+ as.traceAlignment();
+
+
+ as.printAlignment(System.out);
+ scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;
+ totscore = totscore + scores[i][j];
+
+ textarea.append(as.getOutput());
+ seq = new Sequence(as.getS1().getName(),
+ as.getAStr1(),
+ as.getS1().getStart(),
+ as.getS1().getEnd()
+ );
+ sequences.add(seq);
+
+ seq = new Sequence(as.getS2().getName(),
+ as.getAStr2(),
+ as.getS2().getStart(),
+ as.getS2().getEnd() );
+ sequences.add(seq);
+ }
+ }
+
+ if (count > 2)
+ {
+ System.out.println(
+ "Pairwise alignment scaled similarity score matrix\n");
+
+ for (int i = 0; i < count; i++)
+ {
+ jalview.util.Format.print(System.out, "%s \n",
+ ("" + i) + " " +
+ seqs[i].getName());
+ }
+
+ System.out.println("\n");
+
+ for (int i = 0; i < count; i++)
+ {
+ for (int j = 0; j < i; j++)
+ {
+ jalview.util.Format.print(System.out, "%7.3f",
+ scores[i][j] / totscore);
+ }
+ }
+
+ System.out.println("\n");
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void viewInEditorButton_actionPerformed(ActionEvent e)
+ {
+ Sequence[] seq = new Sequence[sequences.size()];
+
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ seq[i] = (Sequence) sequences.elementAt(i);
+ }
+
+ AlignFrame af = new AlignFrame(new Alignment(seq),
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+
+ Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ }
+}