-/*\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 java.util.*;\r
-\r
-import java.awt.event.*;\r
-\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
-import java.awt.*;\r
-\r
-public class PairwiseAlignPanel\r
- extends Panel implements ActionListener\r
-{\r
- Vector sequences = new Vector();\r
- AlignmentPanel ap;\r
-\r
- public PairwiseAlignPanel(AlignmentPanel ap)\r
- {\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
- this.ap = ap;\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(false);\r
-\r
- Sequence seq;\r
-\r
- for (int i = 1; i < count; i++)\r
- {\r
- for (int j = 0; j < i; j++)\r
- {\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
- 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
- {\r
- jalview.util.Format.print(System.out, "%7.3f",\r
- scores[i][j] / totscore);\r
- }\r
- }\r
-\r
- System.out.println("\n");\r
- }\r
- }\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- if(evt.getSource()==viewInEditorButton)\r
- viewInEditorButton_actionPerformed();\r
- }\r
-\r
- protected void viewInEditorButton_actionPerformed()\r
- {\r
-\r
- Sequence[] seq = new Sequence[sequences.size()];\r
-\r
- for (int i = 0; i < sequences.size(); i++)\r
- {\r
- seq[i] = (Sequence) sequences.elementAt(i);\r
- }\r
-\r
- new AlignFrame(new Alignment(seq),\r
- ap.av.applet,\r
- "Pairwise Aligned Sequences",\r
- false);\r
-\r
- }\r
- protected ScrollPane scrollPane = new ScrollPane();\r
- protected TextArea textarea = new TextArea();\r
- protected Button viewInEditorButton = new Button();\r
- Panel jPanel1 = new Panel();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
-\r
- private void jbInit() throws Exception {\r
- this.setLayout(borderLayout1);\r
- textarea.setFont(new java.awt.Font("Monospaced", 0, 12));\r
- textarea.setText("");\r
- viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));\r
- viewInEditorButton.setLabel("View in alignment editor");\r
- viewInEditorButton.addActionListener(this);\r
- this.add(scrollPane, BorderLayout.CENTER);\r
- scrollPane.add(textarea);\r
- this.add(jPanel1, BorderLayout.SOUTH);\r
- jPanel1.add(viewInEditorButton, null);\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
+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