git://source.jalview.org
/
jalview.git
/ commitdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
| commitdiff |
tree
raw
|
patch
|
inline
| side by side (parent:
a5a70dd
)
fix crossRef retrieval so either protein OR nucleotide
author
jprocter
<Jim Procter>
Wed, 25 Jul 2007 17:17:56 +0000
(17:17 +0000)
committer
jprocter
<Jim Procter>
Wed, 25 Jul 2007 17:17:56 +0000
(17:17 +0000)
src/jalview/analysis/CrossRef.java
patch
|
blob
|
history
diff --git
a/src/jalview/analysis/CrossRef.java
b/src/jalview/analysis/CrossRef.java
index
9e69ca4
..
9e99c7c
100644
(file)
--- a/
src/jalview/analysis/CrossRef.java
+++ b/
src/jalview/analysis/CrossRef.java
@@
-196,7
+196,7
@@
public class CrossRef
{
\r
Vector rseqs = new Vector();
\r
Alignment ral = null;
\r
{
\r
Vector rseqs = new Vector();
\r
Alignment ral = null;
\r
- AlignedCodonFrame cf=new AlignedCodonFrame(dataset.getWidth()); // nominal width
\r
+ AlignedCodonFrame cf=new AlignedCodonFrame(0); // nominal width
\r
for (int s = 0; s < seqs.length; s++)
\r
{
\r
SequenceI dss = seqs[s];
\r
for (int s = 0; s < seqs.length; s++)
\r
{
\r
SequenceI dss = seqs[s];
\r
@@
-210,6
+210,7
@@
public class CrossRef
{
\r
System.out.println("Attempting to find ds Xrefs refs.");
\r
DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seqs[s].getDBRef()); // less ambiguous would be a 'find primary dbRefEntry' method.
\r
{
\r
System.out.println("Attempting to find ds Xrefs refs.");
\r
DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seqs[s].getDBRef()); // less ambiguous would be a 'find primary dbRefEntry' method.
\r
+ // filter for desired source xref here
\r
found = CrossRef.searchDatasetXrefs(dss, !dna, lrfs, dataset, rseqs, cf);
\r
}
\r
for (int r = 0; xrfs!=null && r < xrfs.length; r++)
\r
found = CrossRef.searchDatasetXrefs(dss, !dna, lrfs, dataset, rseqs, cf);
\r
}
\r
for (int r = 0; xrfs!=null && r < xrfs.length; r++)
\r
@@
-244,6
+245,8
@@
public class CrossRef
if (dataset != null)
\r
{
\r
found = searchDataset(dss, xrfs[r], dataset, rseqs, cf);
\r
if (dataset != null)
\r
{
\r
found = searchDataset(dss, xrfs[r], dataset, rseqs, cf);
\r
+ if (found)
\r
+ xrfs[r] = null; // we've recovered seqs for this one.
\r
}
\r
}
\r
}
\r
}
\r
}
\r
}
\r
@@
-262,8
+265,8
@@
public class CrossRef
for (int r = 0; r < xrfs.length; r++)
\r
{
\r
// filter out any irrelevant or irretrievable references
\r
for (int r = 0; r < xrfs.length; r++)
\r
{
\r
// filter out any irrelevant or irretrievable references
\r
- if ((source != null && !source.equals(xrfs[r].getSource()))
\r
- || !sftch.isFetchable(xrfs[r].getSource()))
\r
+ if (xrfs[r]==null || ((source != null && !source.equals(xrfs[r].getSource()))
\r
+ || !sftch.isFetchable(xrfs[r].getSource())))
\r
{
\r
l--;
\r
xrfs[r] = null;
\r
{
\r
l--;
\r
xrfs[r] = null;
\r
@@
-347,10
+350,9
@@
public class CrossRef
*
\r
* @param sequenceI
\r
* @param xrf
\r
*
\r
* @param sequenceI
\r
* @param xrf
\r
- * @param dna
\r
* @param dataset
\r
* @param rseqs
\r
* @param dataset
\r
* @param rseqs
\r
- * @param cf
\r
+ * @param cf
\r
* @return true if sequences were found and added
\r
*/
\r
public static boolean searchDataset(SequenceI sequenceI, DBRefEntry xrf,
\r
* @return true if sequences were found and added
\r
*/
\r
public static boolean searchDataset(SequenceI sequenceI, DBRefEntry xrf,
\r
@@
-422,10
+424,10
@@
public class CrossRef
}
\r
}
\r
}
\r
}
\r
}
\r
}
\r
+ // TODO: add mapping between sequences if necessary
\r
+ found = true;
\r
}
\r
\r
}
\r
\r
- // TODO: add mapping between sequences if necessary
\r
- found = true;
\r
}
\r
}
\r
}
\r
}
\r
}
\r
}
\r