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JAL-2426 JAL-1270 report Xfam download URL used if debug enabled
author
Jim Procter
<jprocter@issues.jalview.org>
Wed, 9 Aug 2017 18:32:05 +0000
(19:32 +0100)
committer
Jim Procter
<jprocter@issues.jalview.org>
Wed, 9 Aug 2017 18:32:05 +0000
(19:32 +0100)
src/jalview/ws/dbsources/Xfam.java
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diff --git
a/src/jalview/ws/dbsources/Xfam.java
b/src/jalview/ws/dbsources/Xfam.java
index
3554f01
..
b0bea88
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;
@@
-56,9
+57,17
@@
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(),