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Merge branch 'develop' into patch/JAL-4110_stdout_for_tests
[jalview.git]
/
src
/
jalview
/
ws
/
DBRefFetcher.java
diff --git
a/src/jalview/ws/DBRefFetcher.java
b/src/jalview/ws/DBRefFetcher.java
index
d8858a9
..
0ebd3c3
100644
(file)
--- a/
src/jalview/ws/DBRefFetcher.java
+++ b/
src/jalview/ws/DBRefFetcher.java
@@
-302,7
+302,7
@@
public class DBRefFetcher implements Runnable
}
} catch (Exception e)
{
}
} catch (Exception e)
{
- System.err.println("Couldn't locate PICR service instance.\n");
+ jalview.bin.Console.errPrintln("Couldn't locate PICR service instance.\n");
e.printStackTrace();
}
e.printStackTrace();
}
@@
-316,7
+316,7
@@
public class DBRefFetcher implements Runnable
while (sdataset.size() > 0 && db < dbSources.length)
{
int maxqlen = 1; // default number of queries made at one time
while (sdataset.size() > 0 && db < dbSources.length)
{
int maxqlen = 1; // default number of queries made at one time
- System.out.println("Verifying against " + dbSources[db].getDbName());
+ jalview.bin.Console.outPrintln("Verifying against " + dbSources[db].getDbName());
// iterate through db for each remaining un-verified sequence
SequenceI[] currSeqs = new SequenceI[sdataset.size()];
// iterate through db for each remaining un-verified sequence
SequenceI[] currSeqs = new SequenceI[sdataset.size()];
@@
-425,7
+425,7
@@
public class DBRefFetcher implements Runnable
true);
} catch (Exception e)
{
true);
} catch (Exception e)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Exception with Picr for '" + token + "'\n");
e.printStackTrace();
}
"Exception with Picr for '" + token + "'\n");
e.printStackTrace();
}
@@
-438,7
+438,7
@@
public class DBRefFetcher implements Runnable
// present, and do a transferReferences
// otherwise transfer non sequence x-references directly.
}
// present, and do a transferReferences
// otherwise transfer non sequence x-references directly.
}
- System.out.println(
+ jalview.bin.Console.outPrintln(
"Validated ID against PICR... (for what its worth):"
+ token);
addSeqId(sequence, token);
"Validated ID against PICR... (for what its worth):"
+ token);
addSeqId(sequence, token);
@@
-447,7
+447,7
@@
public class DBRefFetcher implements Runnable
else
{
// if ()
else
{
// if ()
- // System.out.println("Not querying source with
+ // jalview.bin.Console.outPrintln("Not querying source with
// token="+token+"\n");
addSeqId(sequence, token);
queries.addElement(token.toUpperCase(Locale.ROOT));
// token="+token+"\n");
addSeqId(sequence, token);
queries.addElement(token.toUpperCase(Locale.ROOT));
@@
-512,7
+512,7
@@
public class DBRefFetcher implements Runnable
DbSourceProxy dbSourceProxy, AlignmentI retrievedAl,
boolean trimDatasetSeqs, List<String> warningMessages)
{
DbSourceProxy dbSourceProxy, AlignmentI retrievedAl,
boolean trimDatasetSeqs, List<String> warningMessages)
{
- // System.out.println("trimming ? " + trimDatasetSeqs);
+ // jalview.bin.Console.outPrintln("trimming ? " + trimDatasetSeqs);
if (retrievedAl == null || retrievedAl.getHeight() == 0)
{
return false;
if (retrievedAl == null || retrievedAl.getHeight() == 0)
{
return false;
@@
-678,7
+678,7
@@
public class DBRefFetcher implements Runnable
}
}
}
}
- System.out.println("Adding dbrefs to " + sequence.getName()
+ jalview.bin.Console.outPrintln("Adding dbrefs to " + sequence.getName()
+ " from " + dbSource + " sequence : "
+ retrievedSeq.getName());
sequence.transferAnnotation(retrievedSeq, mp);
+ " from " + dbSource + " sequence : "
+ retrievedSeq.getName());
sequence.transferAnnotation(retrievedSeq, mp);