-/*\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.appletgui;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.jbappletgui.GPairwiseAlignPanel;\r
-import jalview.analysis.*;\r
-import java.awt.event.*;\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
- float scores[][] = new float[av.getAlignment().getHeight()][av.getAlignment().getHeight()];\r
- double totscore = 0;\r
- int count = av.getSelectionGroup().getSize();\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(av.getSelectionGroup().getSequenceAt(i),\r
- av.getSelectionGroup().getSequenceAt(j),"pep");\r
-\r
- as.calcScoreMatrix();\r
- as.traceAlignment();\r
- as.printAlignment();\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
-\r
- }\r
- }\r
-\r
- if (count > 2)\r
- {\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
- }\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
- jalview.bin.JalviewLite.addFrame(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 (Development Version 2.4.1)
+ * Copyright (C) 2009 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.appletgui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+
+public class PairwiseAlignPanel extends Panel implements ActionListener
+{
+ Vector sequences = new Vector();
+
+ AlignmentPanel ap;
+
+ public PairwiseAlignPanel(AlignmentPanel ap)
+ {
+ try
+ {
+ jbInit();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ this.ap = ap;
+ sequences = new Vector();
+
+ SequenceI[] seqs;
+ String[] seqStrings = ap.av.getViewAsString(true);
+
+ if (ap.av.getSelectionGroup() == null)
+ {
+ seqs = ap.av.alignment.getSequencesArray();
+ }
+ else
+ {
+ seqs = ap.av.getSelectionGroup().getSequencesInOrder(ap.av.alignment);
+ }
+
+ float scores[][] = new float[seqs.length][seqs.length];
+ double totscore = 0;
+ int count = ap.av.getSelectionGroup().getSize();
+ String type = (ap.av.alignment.isNucleotide()) ? AlignSeq.DNA
+ : AlignSeq.PEP;
+ 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.addElement(seq);
+
+ seq = new Sequence(as.getS2().getName(), as.getAStr2(), as.getS2()
+ .getStart(), as.getS2().getEnd());
+ sequences.addElement(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");
+ }
+ }
+
+ public void actionPerformed(ActionEvent evt)
+ {
+ if (evt.getSource() == viewInEditorButton)
+ {
+ viewInEditorButton_actionPerformed();
+ }
+ }
+
+ protected void viewInEditorButton_actionPerformed()
+ {
+
+ Sequence[] seq = new Sequence[sequences.size()];
+
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ seq[i] = (Sequence) sequences.elementAt(i);
+ }
+
+ new AlignFrame(new Alignment(seq), ap.av.applet,
+ "Pairwise Aligned Sequences", false);
+
+ }
+
+ protected ScrollPane scrollPane = new ScrollPane();
+
+ protected TextArea textarea = new TextArea();
+
+ protected Button viewInEditorButton = new Button();
+
+ Panel jPanel1 = new Panel();
+
+ BorderLayout borderLayout1 = new BorderLayout();
+
+ private void jbInit() throws Exception
+ {
+ this.setLayout(borderLayout1);
+ textarea.setFont(new java.awt.Font("Monospaced", 0, 12));
+ textarea.setText("");
+ viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));
+ viewInEditorButton.setLabel("View in alignment editor");
+ viewInEditorButton.addActionListener(this);
+ this.add(scrollPane, BorderLayout.CENTER);
+ scrollPane.add(textarea);
+ this.add(jPanel1, BorderLayout.SOUTH);
+ jPanel1.add(viewInEditorButton, null);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff