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better check for molecule type when identifying internal sequence cross-references
author
jprocter
<Jim Procter>
Tue, 19 Aug 2008 09:38:38 +0000
(09:38 +0000)
committer
jprocter
<Jim Procter>
Tue, 19 Aug 2008 09:38:38 +0000
(09:38 +0000)
src/jalview/analysis/CrossRef.java
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diff --git
a/src/jalview/analysis/CrossRef.java
b/src/jalview/analysis/CrossRef.java
index
d063eed
..
159d96a
100644
(file)
--- a/
src/jalview/analysis/CrossRef.java
+++ b/
src/jalview/analysis/CrossRef.java
@@
-445,6
+445,7
@@
public class CrossRef
boolean direct, boolean dna)
\r
{
\r
boolean found = false;
\r
boolean direct, boolean dna)
\r
{
\r
boolean found = false;
\r
+ SequenceI[] typer=new SequenceI[1];
\r
if (dataset == null)
\r
return false;
\r
if (dataset.getSequences() == null)
\r
if (dataset == null)
\r
return false;
\r
if (dataset.getSequences() == null)
\r
@@
-465,6
+466,17
@@
public class CrossRef
}
\r
if (nxt != sequenceI && nxt != sequenceI.getDatasetSequence())
\r
{
\r
}
\r
if (nxt != sequenceI && nxt != sequenceI.getDatasetSequence())
\r
{
\r
+ // check if this is the correct sequence type
\r
+ {
\r
+ typer[0] = nxt;
\r
+ boolean isDna = jalview.util.Comparison.isNucleotide(typer);
\r
+ if ((direct && isDna == dna) || (!direct && isDna!=dna))
\r
+ {
\r
+ // skip this sequence because it is same molecule type
\r
+ continue;
\r
+ }
\r
+ }
\r
+
\r
// look for direct or indirect references in common
\r
DBRefEntry[] poss = null, cands = null;
\r
if (direct)
\r
// look for direct or indirect references in common
\r
DBRefEntry[] poss = null, cands = null;
\r
if (direct)
\r