git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-4366 provide options for updating (or not) the linked alignment or existing align...
[jalview.git]
/
src
/
jalview
/
gui
/
PairwiseAlignPanel.java
diff --git
a/src/jalview/gui/PairwiseAlignPanel.java
b/src/jalview/gui/PairwiseAlignPanel.java
index
d081794
..
2c65bcc
100755
(executable)
--- a/
src/jalview/gui/PairwiseAlignPanel.java
+++ b/
src/jalview/gui/PairwiseAlignPanel.java
@@
-21,6
+21,9
@@
package jalview.gui;
import jalview.analysis.AlignSeq;
package jalview.gui;
import jalview.analysis.AlignSeq;
+import jalview.analysis.scoremodels.ScoreMatrix;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SequenceGroup;
@@
-51,10
+54,22
@@
public class PairwiseAlignPanel extends GPairwiseAlignPanel
* Creates a new PairwiseAlignPanel object.
*
* @param viewport
* Creates a new PairwiseAlignPanel object.
*
* @param viewport
- * DOCUMENT ME!
+ * contains selected sequences to align
*/
public PairwiseAlignPanel(AlignmentViewport viewport)
{
*/
public PairwiseAlignPanel(AlignmentViewport viewport)
{
+ this(viewport,null);
+ }
+
+ /**
+ * Creates a new PairwiseAlignPanel object.
+ *
+ * @param viewport
+ * contains selected sequences to align
+ */
+
+ public PairwiseAlignPanel(AlignmentViewport viewport, ScoreMatrix params)
+ {
super();
this.av = viewport;
super();
this.av = viewport;
@@
-65,14
+80,14
@@
public class PairwiseAlignPanel extends GPairwiseAlignPanel
&& selectionGroup.getSize() > 0;
AlignmentView view = viewport.getAlignmentView(isSelection);
// String[] seqStrings = viewport.getViewAsString(true);
&& selectionGroup.getSize() > 0;
AlignmentView view = viewport.getAlignmentView(isSelection);
// String[] seqStrings = viewport.getViewAsString(true);
- String[] seqStrings = view.getSequenceStrings(viewport
- .getGapCharacter());
+ String[] seqStrings = view
+ .getSequenceStrings(viewport.getGapCharacter());
SequenceI[] seqs;
if (isSelection)
{
SequenceI[] seqs;
if (isSelection)
{
- seqs = (SequenceI[]) view.getAlignmentAndHiddenColumns(viewport
- .getGapCharacter())[0];
+ seqs = (SequenceI[]) view
+ .getAlignmentAndHiddenColumns(viewport.getGapCharacter())[0];
}
else
{
}
else
{
@@
-98,19
+113,21
@@
public class PairwiseAlignPanel extends GPairwiseAlignPanel
{
continue;
}
{
continue;
}
-
+ if (params!=null)
+ {
+ as.setScoreMatrix(params);
+ }
as.calcScoreMatrix();
as.traceAlignment();
if (!first)
{
as.calcScoreMatrix();
as.traceAlignment();
if (!first)
{
- System.out.println(DASHES);
+ jalview.bin.Console.outPrintln(DASHES);
textarea.append(DASHES);
}
first = false;
as.printAlignment(System.out);
textarea.append(DASHES);
}
first = false;
as.printAlignment(System.out);
- scores[i][j] = as.getMaxScore()
- / as.getASeq1().length;
+ scores[i][j] = as.getMaxScore() / as.getASeq1().length;
totscore = totscore + scores[i][j];
textarea.append(as.getOutput());
totscore = totscore + scores[i][j];
textarea.append(as.getOutput());
@@
-140,8
+157,8
@@
public class PairwiseAlignPanel extends GPairwiseAlignPanel
for (int i = 0; i < seqs.length; i++)
{
for (int i = 0; i < seqs.length; i++)
{
- System.out.println(String.format("%3d %s", i + 1,
- seqs[i].getDisplayId(true)));
+ jalview.bin.Console.outPrintln(
+ String.format("%3d %s", i + 1, seqs[i].getDisplayId(true)));
}
/*
}
/*
@@
-152,7
+169,7
@@
public class PairwiseAlignPanel extends GPairwiseAlignPanel
{
System.out.print(String.format("%7d", i + 1));
}
{
System.out.print(String.format("%7d", i + 1));
}
- System.out.println();
+ jalview.bin.Console.outPrintln();
for (int i = 0; i < seqs.length; i++)
{
for (int i = 0; i < seqs.length; i++)
{
@@
-164,10
+181,10
@@
public class PairwiseAlignPanel extends GPairwiseAlignPanel
*/
System.out.print(String.format("%7.3f", scores[i][j] / totscore));
}
*/
System.out.print(String.format("%7.3f", scores[i][j] / totscore));
}
- System.out.println();
+ jalview.bin.Console.outPrintln();
}
}
- System.out.println("\n");
+ jalview.bin.Console.outPrintln("\n");
}
/**
}
/**