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Merge branch 'feature/JAL-2587' into documentation/JAL-2675_release2102b1
[jalview.git]
/
src
/
jalview
/
ws
/
dbsources
/
Xfam.java
diff --git
a/src/jalview/ws/dbsources/Xfam.java
b/src/jalview/ws/dbsources/Xfam.java
index
3554f01
..
26291eb
100644
(file)
--- a/
src/jalview/ws/dbsources/Xfam.java
+++ b/
src/jalview/ws/dbsources/Xfam.java
@@
-20,6
+20,7
@@
*/
package jalview.ws.dbsources;
*/
package jalview.ws.dbsources;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.io.DataSourceType;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.io.DataSourceType;
@@
-56,19
+57,26
@@
public abstract class Xfam extends DbSourceProxyImpl
// retrieved.
startQuery();
// TODO: trap HTTP 404 exceptions and return null
// retrieved.
startQuery();
// TODO: trap HTTP 404 exceptions and return null
- AlignmentI rcds = new FormatAdapter().readFile(getXFAMURL()
- + queries.trim().toUpperCase() + getXFAMURLSUFFIX(),
+ String xfamUrl = getXFAMURL() + queries.trim().toUpperCase()
+ + getXFAMURLSUFFIX();
+
+ if (Cache.log != null)
+ {
+ Cache.log.debug("XFAM URL for retrieval is: " + xfamUrl);
+ }
+
+ AlignmentI rcds = new FormatAdapter().readFile(xfamUrl,
DataSourceType.URL, FileFormat.Stockholm);
DataSourceType.URL, FileFormat.Stockholm);
+
for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
{
rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getXfamSource(),
for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
{
rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getXfamSource(),
- // getDbSource(),
+ // getDbSource(),
getDbVersion(), queries.trim().toUpperCase()));
if (!getDbSource().equals(getXfamSource()))
{ // add the specific ref too
getDbVersion(), queries.trim().toUpperCase()));
if (!getDbSource().equals(getXfamSource()))
{ // add the specific ref too
- rcds.getSequenceAt(s).addDBRef(
- new DBRefEntry(getDbSource(), getDbVersion(), queries
- .trim().toUpperCase()));
+ rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getDbSource(),
+ getDbVersion(), queries.trim().toUpperCase()));
}
}
stopQuery();
}
}
stopQuery();