\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
- AlignViewport av;\r
+ AlignmentPanel ap;\r
\r
- public PairwiseAlignPanel(AlignViewport av)\r
+ public PairwiseAlignPanel(AlignmentPanel ap)\r
{\r
- super();\r
- this.av = av;\r
- float scores[][] = new float[av.getAlignment().getHeight()][av.getAlignment().\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 = av.getSelectionGroup().getSize();\r
+ int count = ap.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
acount++;\r
- AlignSeq as = new AlignSeq(av.getSelectionGroup().getSequenceAt(i),\r
- av.getSelectionGroup().getSequenceAt(j),\r
+ AlignSeq as = new AlignSeq(ap.av.getSelectionGroup().getSequenceAt(i),\r
+ ap.av.getSelectionGroup().getSequenceAt(j),\r
"pep");\r
\r
as.calcScoreMatrix();\r
as.traceAlignment();\r
- as.printAlignment();\r
+ as.printAlignment(System.out);\r
scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;\r
totscore = totscore + scores[i][j];\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
+ 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));\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
\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