git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
bugfix db ref retrieve routine so it removes dead query strings properly
[jalview.git]
/
src
/
jalview
/
ws
/
DBRefFetcher.java
diff --git
a/src/jalview/ws/DBRefFetcher.java
b/src/jalview/ws/DBRefFetcher.java
index
76e73e4
..
96ac7e8
100644
(file)
--- a/
src/jalview/ws/DBRefFetcher.java
+++ b/
src/jalview/ws/DBRefFetcher.java
@@
-213,27
+213,30
@@
public class DBRefFetcher implements Runnable
{
\r
// Still queries to make for current seqIndex
\r
StringBuffer queryString = new StringBuffer("");
\r
{
\r
// Still queries to make for current seqIndex
\r
StringBuffer queryString = new StringBuffer("");
\r
- int nqSize = (maxqlen > queries.size()) ? queries.size()
\r
+ int numq=0,nqSize = (maxqlen > queries.size()) ? queries.size()
\r
: maxqlen;
\r
: maxqlen;
\r
- for (int nq = 0, numq = 0; nq < nqSize; nq++)
\r
+
\r
+ while (queries.size()>0 && numq < nqSize)
\r
{
\r
{
\r
- String query = (String) queries.elementAt(nq);
\r
+ String query = (String) queries.elementAt(0);
\r
if (dbsource.isValidReference(query))
\r
{
\r
if (dbsource.isValidReference(query))
\r
{
\r
- queryString.append((nq == 0) ? "" : dbsource
\r
+ queryString.append((numq == 0) ? "" : dbsource
\r
.getAccessionSeparator());
\r
queryString.append(query);
\r
numq++;
\r
}
\r
.getAccessionSeparator());
\r
queryString.append(query);
\r
numq++;
\r
}
\r
- }
\r
- for (int nq = 0; nq < nqSize; nq++)
\r
- {
\r
+ // remove the extracted query string
\r
queries.removeElementAt(0);
\r
}
\r
// make the queries and process the response
\r
AlignmentI retrieved = null;
\r
try
\r
{
\r
queries.removeElementAt(0);
\r
}
\r
// make the queries and process the response
\r
AlignmentI retrieved = null;
\r
try
\r
{
\r
+ if (jalview.bin.Cache.log.isDebugEnabled())
\r
+ {
\r
+ jalview.bin.Cache.log.debug("Querying "+dbsource.getDbName()+" with : '"+queryString.toString()+"'");
\r
+ }
\r
retrieved = dbsource.getSequenceRecords(queryString.toString());
\r
} catch (Exception ex)
\r
{
\r
retrieved = dbsource.getSequenceRecords(queryString.toString());
\r
} catch (Exception ex)
\r
{
\r
@@
-259,7
+262,7
@@
public class DBRefFetcher implements Runnable
{ dbSources[db] }); // jalview.datamodel.DBRefSource.UNIPROT
\r
// });
\r
// check for existing dbrefs to use
\r
{ dbSources[db] }); // jalview.datamodel.DBRefSource.UNIPROT
\r
// });
\r
// check for existing dbrefs to use
\r
- if (uprefs != null)
\r
+ if (uprefs != null && uprefs.length>0)
\r
{
\r
for (int j = 0; j < uprefs.length; j++)
\r
{
\r
{
\r
for (int j = 0; j < uprefs.length; j++)
\r
{
\r