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JAL-629 Change all stdout and stderr output to use Console.outPrintln and Console...
[jalview.git]
/
src
/
jalview
/
ws
/
seqfetcher
/
ASequenceFetcher.java
diff --git
a/src/jalview/ws/seqfetcher/ASequenceFetcher.java
b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
index
9284f82
..
374147a
100644
(file)
--- a/
src/jalview/ws/seqfetcher/ASequenceFetcher.java
+++ b/
src/jalview/ws/seqfetcher/ASequenceFetcher.java
@@
-21,7
+21,7
@@
package jalview.ws.seqfetcher;
import jalview.api.FeatureSettingsModelI;
package jalview.ws.seqfetcher;
import jalview.api.FeatureSettingsModelI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceI;
@@
-112,7
+112,7
@@
public class ASequenceFetcher
return true;
}
}
return true;
}
}
- Cache.log.warn("isFetchable doesn't know about '" + source + "'");
+ Console.warn("isFetchable doesn't know about '" + source + "'");
return false;
}
return false;
}
@@
-191,9
+191,9
@@
public class ASequenceFetcher
seqset = fetcher.getSequenceRecords(qsb.toString());
} catch (Exception ex)
{
seqset = fetcher.getSequenceRecords(qsb.toString());
} catch (Exception ex)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Failed to retrieve the following from " + db);
"Failed to retrieve the following from " + db);
- System.err.println(qsb);
+ jalview.bin.Console.errPrintln(qsb);
ex.printStackTrace(System.err);
}
// TODO: Merge alignment together - perhaps
ex.printStackTrace(System.err);
}
// TODO: Merge alignment together - perhaps
@@
-205,9
+205,11
@@
public class ASequenceFetcher
for (int is = 0; is < seqs.length; is++)
{
rseqs.addElement(seqs[is]);
for (int is = 0; is < seqs.length; is++)
{
rseqs.addElement(seqs[is]);
+ // BH 2015.01.25 check about version/accessid being null here
List<DBRefEntry> frefs = DBRefUtils.searchRefs(
seqs[is].getDBRefs(),
List<DBRefEntry> frefs = DBRefUtils.searchRefs(
seqs[is].getDBRefs(),
- new DBRefEntry(db, null, null));
+ new DBRefEntry(db, null, null),
+ DBRefUtils.SEARCH_MODE_FULL);
for (DBRefEntry dbr : frefs)
{
queriesFound.add(dbr.getAccessionId());
for (DBRefEntry dbr : frefs)
{
queriesFound.add(dbr.getAccessionId());
@@
-220,7
+222,7
@@
public class ASequenceFetcher
{
if (fetcher.getRawRecords() != null)
{
{
if (fetcher.getRawRecords() != null)
{
- System.out.println(
+ jalview.bin.Console.outPrintln(
"# Retrieved from " + db + ":" + qsb.toString());
StringBuffer rrb = fetcher.getRawRecords();
/*
"# Retrieved from " + db + ":" + qsb.toString());
StringBuffer rrb = fetcher.getRawRecords();
/*
@@
-233,12
+235,12
@@
public class ASequenceFetcher
/*
* } else { hdr = "# part "+rr; }
*/
/*
* } else { hdr = "# part "+rr; }
*/
- System.out.println(hdr);
+ jalview.bin.Console.outPrintln(hdr);
if (rrb != null)
{
if (rrb != null)
{
- System.out.println(rrb);
+ jalview.bin.Console.outPrintln(rrb);
}
}
- System.out.println("# end of " + hdr);
+ jalview.bin.Console.outPrintln("# end of " + hdr);
}
}
}
}
@@
-251,7
+253,7
@@
public class ASequenceFetcher
}
if (queriesMade.size() > 0)
{
}
if (queriesMade.size() > 0)
{
- System.out.println("# Adding " + queriesMade.size()
+ jalview.bin.Console.outPrintln("# Adding " + queriesMade.size()
+ " ids back to queries list for searching again (" + db
+ ")");
queriesLeft.addAll(queriesMade);
+ " ids back to queries list for searching again (" + db
+ ")");
queriesLeft.addAll(queriesMade);
@@
-277,7
+279,7
@@
public class ASequenceFetcher
Exception ex)
{
Exception ex)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Failed to retrieve the following references from " + db);
int n = 0;
for (String qv : queriesMade)
"Failed to retrieve the following references from " + db);
int n = 0;
for (String qv : queriesMade)
@@
-285,11
+287,11
@@
public class ASequenceFetcher
System.err.print(" " + qv + ";");
if (n++ > 10)
{
System.err.print(" " + qv + ";");
if (n++ > 10)
{
- System.err.println();
+ jalview.bin.Console.errPrintln();
n = 0;
}
}
n = 0;
}
}
- System.err.println();
+ jalview.bin.Console.errPrintln();
ex.printStackTrace();
}
ex.printStackTrace();
}
@@
-364,8
+366,7
@@
public class ASequenceFetcher
.get(proxy.getDbSource());
if (slist == null)
{
.get(proxy.getDbSource());
if (slist == null)
{
- fetchableDbs.put(proxy.getDbSource(),
- slist = new Hashtable<>());
+ fetchableDbs.put(proxy.getDbSource(), slist = new Hashtable<>());
}
slist.put(proxy.getDbName(), proxy);
}
}
slist.put(proxy.getDbName(), proxy);
}