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Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git...
[jalview.git]
/
src
/
jalview
/
datamodel
/
HiddenSequences.java
diff --git
a/src/jalview/datamodel/HiddenSequences.java
b/src/jalview/datamodel/HiddenSequences.java
index
ed07290
..
b5efeb4
100755
(executable)
--- a/
src/jalview/datamodel/HiddenSequences.java
+++ b/
src/jalview/datamodel/HiddenSequences.java
@@
-157,9
+157,10
@@
public class HiddenSequences
int absAlignmentIndex = alignment.findIndex(sequence);
int alignmentIndex = adjustForHiddenSeqs(absAlignmentIndex);
int absAlignmentIndex = alignment.findIndex(sequence);
int alignmentIndex = adjustForHiddenSeqs(absAlignmentIndex);
- if (hiddenSequences[alignmentIndex] != null)
+ if (alignmentIndex < 0 || hiddenSequences[alignmentIndex] != null)
{
System.out.println("ERROR!!!!!!!!!!!");
{
System.out.println("ERROR!!!!!!!!!!!");
+ return;
}
hiddenSequences[alignmentIndex] = sequence;
}
hiddenSequences[alignmentIndex] = sequence;
@@
-221,8
+222,8
@@
public class HiddenSequences
end = hiddenSequences.length - 1;
}
end = hiddenSequences.length - 1;
}
- List<SequenceI> asequences;
- synchronized (asequences = alignment.getSequences())
+ List<SequenceI> asequences = alignment.getSequences();
+ synchronized (asequences)
{
for (int index = end; index > start; index--)
{
{
for (int index = end; index > start; index--)
{
@@
-238,8
+239,8
@@
public class HiddenSequences
}
else
{
}
else
{
- System.out.println(seq.getName()
- + " has been deleted whilst hidden");
+ System.out.println(
+ seq.getName() + " has been deleted whilst hidden");
}
}
}
}
}
}
@@
-253,7
+254,8
@@
public class HiddenSequences
}
/**
}
/**
- * Convert absolute alignment index to visible alignment index
+ * Convert absolute alignment index to visible alignment index (or -1 if
+ * before the first visible sequence)
*
* @param alignmentIndex
* @return
*
* @param alignmentIndex
* @return