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[jalview.git]
/
src
/
jalview
/
analysis
/
AlignmentSorter.java
diff --git
a/src/jalview/analysis/AlignmentSorter.java
b/src/jalview/analysis/AlignmentSorter.java
index
c80c326
..
778142c
100755
(executable)
--- a/
src/jalview/analysis/AlignmentSorter.java
+++ b/
src/jalview/analysis/AlignmentSorter.java
@@
-52,8
+52,8
@@
public class AlignmentSorter
\r
for (int i = 0; i < nSeq; i++)
\r
{
\r
\r
for (int i = 0; i < nSeq; i++)
\r
{
\r
- scores[i] = Comparison.PID(align.getSequenceAt(i).getSequence(),
\r
- s.getSequence());
\r
+ scores[i] = Comparison.PID(align.getSequenceAt(i).getSequenceAsString(),
\r
+ s.getSequenceAsString());
\r
seqs[i] = align.getSequenceAt(i);
\r
}
\r
\r
seqs[i] = align.getSequenceAt(i);
\r
}
\r
\r
@@
-121,7
+121,7
@@
public class AlignmentSorter
tmp.addElement(seqs[i]);
\r
}
\r
\r
tmp.addElement(seqs[i]);
\r
}
\r
\r
- algn.clear();
\r
+ algn.removeAllElements();
\r
//User may have hidden seqs, then clicked undo or redo
\r
for (int i = 0; i < tmp.size(); i++)
\r
{
\r
//User may have hidden seqs, then clicked undo or redo
\r
for (int i = 0; i < tmp.size(); i++)
\r
{
\r
@@
-198,7
+198,7
@@
public class AlignmentSorter
{
\r
SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);
\r
\r
{
\r
SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);
\r
\r
- if (sg.getSize(false) > sg2.getSize(false))
\r
+ if (sg.getSize() > sg2.getSize())
\r
{
\r
groups.insertElementAt(sg, j);
\r
\r
{
\r
groups.insertElementAt(sg, j);
\r
\r