\r
import jalview.analysis.*;\r
import jalview.datamodel.*;\r
-import jalview.jbappletgui.*;\r
+import java.awt.*;\r
\r
public class PairwiseAlignPanel\r
- extends GPairwiseAlignPanel\r
+ extends Panel implements ActionListener\r
{\r
Vector sequences = new Vector();\r
AlignmentPanel ap;\r
\r
public PairwiseAlignPanel(AlignmentPanel ap)\r
{\r
- super();\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
+ 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
- as.printAlignment();\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
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ if(evt.getSource()==viewInEditorButton)\r
+ viewInEditorButton_actionPerformed();\r
+ }\r
\r
- protected void viewInEditorButton_actionPerformed(ActionEvent e)\r
+ protected void viewInEditorButton_actionPerformed()\r
{\r
\r
Sequence[] seq = new Sequence[sequences.size()];\r
seq[i] = (Sequence) sequences.elementAt(i);\r
}\r
\r
- AlignFrame af = new AlignFrame(new Alignment(seq), ap.alignFrame.applet);\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.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