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Merge branch 'JAL-1956_featureStyles' into features/JAL-653_JAL-1766_htslib_refseqsupport
[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
7d88414
..
2ed3263
100644
(file)
--- a/
src/jalview/ws/seqfetcher/ASequenceFetcher.java
+++ b/
src/jalview/ws/seqfetcher/ASequenceFetcher.java
@@
-157,7
+157,8
@@
public class ASequenceFetcher
Stack<String> queriesLeft = new Stack<String>();
queriesLeft.addAll(query);
Stack<String> queriesLeft = new Stack<String>();
queriesLeft.addAll(query);
- for (DbSourceProxy fetcher : getSourceProxy(db))
+ List<DbSourceProxy> proxies = getSourceProxy(db);
+ for (DbSourceProxy fetcher : proxies)
{
List<String> queriesMade = new ArrayList<String>();
HashSet<String> queriesFound = new HashSet<String>();
{
List<String> queriesMade = new ArrayList<String>();
HashSet<String> queriesFound = new HashSet<String>();
@@
-167,8
+168,7
@@
public class ASequenceFetcher
{
continue; // wrong sort of data
}
{
continue; // wrong sort of data
}
- boolean doMultiple = fetcher.getAccessionSeparator() != null;
- // No separator - no Multiple Queries
+ boolean doMultiple = fetcher.getMaximumQueryCount() > 1;
while (!queriesLeft.isEmpty())
{
StringBuffer qsb = new StringBuffer();
while (!queriesLeft.isEmpty())
{
StringBuffer qsb = new StringBuffer();
@@
-187,8
+187,7
@@
public class ASequenceFetcher
try
{
// create a fetcher and go to it
try
{
// create a fetcher and go to it
- seqset = fetcher.getSequenceRecords(qsb.toString()); // ,
- // queriesFailed);
+ seqset = fetcher.getSequenceRecords(qsb.toString());
} catch (Exception ex)
{
System.err.println("Failed to retrieve the following from "
} catch (Exception ex)
{
System.err.println("Failed to retrieve the following from "
@@
-255,7
+254,7
@@
public class ASequenceFetcher
{
System.out.println("# Adding " + queriesMade.size()
+ " ids back to queries list for searching again (" + db
{
System.out.println("# Adding " + queriesMade.size()
+ " ids back to queries list for searching again (" + db
- + ".");
+ + ")");
queriesLeft.addAll(queriesMade);
}
}
queriesLeft.addAll(queriesMade);
}
}