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licencing and format applied (eclipse)
[jalview.git]
/
src
/
jalview
/
gui
/
PairwiseAlignPanel.java
diff --git
a/src/jalview/gui/PairwiseAlignPanel.java
b/src/jalview/gui/PairwiseAlignPanel.java
index
7347f0a
..
15c8c70
100755
(executable)
--- a/
src/jalview/gui/PairwiseAlignPanel.java
+++ b/
src/jalview/gui/PairwiseAlignPanel.java
@@
-28,21
+28,22
@@
import jalview.jbgui.*;
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
* @author $author$
* @version $Revision$
*/
-public class PairwiseAlignPanel
- extends GPairwiseAlignPanel
+public class PairwiseAlignPanel extends GPairwiseAlignPanel
{
AlignViewport av;
{
AlignViewport av;
+
Vector sequences;
/**
* Creates a new PairwiseAlignPanel object.
Vector sequences;
/**
* Creates a new PairwiseAlignPanel object.
- *
- * @param av DOCUMENT ME!
+ *
+ * @param av
+ * DOCUMENT ME!
*/
public PairwiseAlignPanel(AlignViewport av)
{
*/
public PairwiseAlignPanel(AlignViewport av)
{
@@
-63,7
+64,8
@@
public class PairwiseAlignPanel
seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
}
seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
}
- String type = (av.alignment.isNucleotide()) ? AlignSeq.DNA : AlignSeq.PEP;
+ String type = (av.alignment.isNucleotide()) ? AlignSeq.DNA
+ : AlignSeq.PEP;
float[][] scores = new float[seqs.length][seqs.length];
double totscore = 0;
float[][] scores = new float[seqs.length][seqs.length];
double totscore = 0;
@@
-76,8
+78,8
@@
public class PairwiseAlignPanel
for (int j = 0; j < i; j++)
{
for (int j = 0; j < i; j++)
{
- AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],
- seqs[j], seqStrings[j], type);
+ AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
+ seqStrings[j], type);
if (as.s1str.length() == 0 || as.s2str.length() == 0)
{
if (as.s1str.length() == 0 || as.s2str.length() == 0)
{
@@
-88,35
+90,30
@@
public class PairwiseAlignPanel
as.traceAlignment();
as.printAlignment(System.out);
as.traceAlignment();
as.printAlignment(System.out);
- scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;
+ scores[i][j] = (float) as.getMaxScore()
+ / (float) as.getASeq1().length;
totscore = totscore + scores[i][j];
textarea.append(as.getOutput());
totscore = totscore + scores[i][j];
textarea.append(as.getOutput());
- seq = new Sequence(as.getS1().getName(),
- as.getAStr1(),
- as.getS1().getStart(),
- as.getS1().getEnd()
- );
+ seq = new Sequence(as.getS1().getName(), as.getAStr1(), as.getS1()
+ .getStart(), as.getS1().getEnd());
sequences.add(seq);
sequences.add(seq);
- seq = new Sequence(as.getS2().getName(),
- as.getAStr2(),
- as.getS2().getStart(),
- as.getS2().getEnd());
+ seq = new Sequence(as.getS2().getName(), as.getAStr2(), as.getS2()
+ .getStart(), as.getS2().getEnd());
sequences.add(seq);
}
}
if (count > 2)
{
sequences.add(seq);
}
}
if (count > 2)
{
- System.out.println(
- "Pairwise alignment scaled similarity score matrix\n");
+ System.out
+ .println("Pairwise alignment scaled similarity score matrix\n");
for (int i = 0; i < count; i++)
{
for (int i = 0; i < count; i++)
{
- jalview.util.Format.print(System.out, "%s \n",
- ("" + i) + " " +
- seqs[i].getName());
+ jalview.util.Format.print(System.out, "%s \n", ("" + i) + " "
+ + seqs[i].getName());
}
System.out.println("\n");
}
System.out.println("\n");
@@
-125,8
+122,8
@@
public class PairwiseAlignPanel
{
for (int j = 0; j < i; j++)
{
{
for (int j = 0; j < i; j++)
{
- jalview.util.Format.print(System.out, "%7.3f",
- scores[i][j] / totscore);
+ jalview.util.Format.print(System.out, "%7.3f", scores[i][j]
+ / totscore);
}
}
}
}
@@
-136,8
+133,9
@@
public class PairwiseAlignPanel
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void viewInEditorButton_actionPerformed(ActionEvent e)
{
*/
protected void viewInEditorButton_actionPerformed(ActionEvent e)
{
@@
-149,11
+147,9
@@
public class PairwiseAlignPanel
}
AlignFrame af = new AlignFrame(new Alignment(seq),
}
AlignFrame af = new AlignFrame(new Alignment(seq),
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
}
}
}
}