+/*\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
+import java.awt.event.*;\r
+\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import java.awt.*;\r
\r
-public class PairwiseAlignPanel extends GPairwiseAlignPanel\r
+public class PairwiseAlignPanel\r
+ extends Panel implements ActionListener\r
{\r
- Vector sequences = new Vector();\r
- AlignViewport av;\r
+ Vector sequences = new Vector();\r
+ AlignmentPanel ap;\r
\r
- public PairwiseAlignPanel(AlignViewport av)\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
+ float scores[][] = new float[ap.av.alignment.getHeight()][ap.av.alignment.\r
+ getHeight()];\r
+ double totscore = 0;\r
+ int count = ap.av.getSelectionGroup().getSize(false);\r
+\r
+ Sequence seq;\r
+ for (int i = 1; i < count; i++)\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
+ for (int j = 0; j < i; j++)\r
+ {\r
+ AlignSeq as = new AlignSeq(ap.av.getSelectionGroup().getSequenceAt(i),\r
+ ap.av.getSelectionGroup().getSequenceAt(j),\r
+ "pep");\r
+\r
+ if (as.s1str.length() == 0 || as.s2str.length() == 0)\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
+ continue;\r
+ }\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
+ as.calcScoreMatrix();\r
+ as.traceAlignment();\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
+ textarea.append(as.getOutput());\r
\r
+ seq = new Sequence(as.getS1().getName(),\r
+ as.getAStr1(),\r
+ as.getS1().getStart(), as.getS1().getEnd()\r
+ );\r
+ sequences.addElement(seq);\r
\r
- }\r
- }\r
+ seq = new Sequence(as.getS2().getName(),\r
+ as.getAStr2(),\r
+ as.getS2().getStart(), as.getS2().getEnd()\r
+ );\r
\r
- if (count > 2)\r
+ sequences.addElement(seq);\r
+ }\r
+ }\r
+\r
+ if (count > 2)\r
+ {\r
+ for (int i = 0; i < count; i++)\r
+ {\r
+ for (int j = 0; j < i; j++)\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
+ jalview.util.Format.print(System.out, "%7.3f",\r
+ scores[i][j] / totscore);\r
}\r
}\r
+ }\r
+ }\r
\r
-\r
- protected void viewInEditorButton_actionPerformed(ActionEvent e)\r
+ public void actionPerformed(ActionEvent evt)\r
{\r
+ if(evt.getSource()==viewInEditorButton)\r
+ viewInEditorButton_actionPerformed();\r
+ }\r
\r
- Sequence [] seq = new Sequence[sequences.size()];\r
+ protected void viewInEditorButton_actionPerformed()\r
+ {\r
\r
- for (int i=0;i<sequences.size();i++)\r
- seq[i] = (Sequence) sequences.elementAt(i);\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
- 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
+ new AlignFrame(new Alignment(seq),\r
+ ap.alignFrame.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