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Back to org.biojava
[jalview.git]
/
src
/
jalview
/
analysis
/
AlignmentSorter.java
diff --git
a/src/jalview/analysis/AlignmentSorter.java
b/src/jalview/analysis/AlignmentSorter.java
index
20101dc
..
27d1e7b
100755
(executable)
--- a/
src/jalview/analysis/AlignmentSorter.java
+++ b/
src/jalview/analysis/AlignmentSorter.java
@@
-52,7
+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), s);
\r
+ scores[i] = Comparison.PID(align.getSequenceAt(i).getSequence(),
\r
+ s.getSequence());
\r
seqs[i] = align.getSequenceAt(i);
\r
}
\r
\r
seqs[i] = align.getSequenceAt(i);
\r
}
\r
\r
@@
-184,7
+185,7
@@
public class AlignmentSorter
{
\r
SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);
\r
\r
{
\r
SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);
\r
\r
- if (sg.getSize() > sg2.getSize())
\r
+ if (sg.getSize(false) > sg2.getSize(false))
\r
{
\r
groups.insertElementAt(sg, j);
\r
\r
{
\r
groups.insertElementAt(sg, j);
\r
\r