JAL-1479 JAL- Fix to eradicate duplicate mapping output and further improvement for...

[jalview.git] / src / jalview / gui / StructureChooser.java

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 6471795..2972c69 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -407,7 +407,6 @@ public class StructureChooser extends GStructureChooser implements
           FTSRestRequest pdbRequest = new FTSRestRequest();
           if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
           {
-            System.out.println(">>>>>> Filtering with uniprot coverate");
             pdbRequest.setAllowEmptySeq(false);
             pdbRequest.setResponseSize(1);
             pdbRequest.setFieldToSearchBy("(");
@@ -862,45 +861,19 @@ public class StructureChooser extends GStructureChooser implements
       ArrayList<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
       for (SequenceI seq : sequences)
       {
-        if (seq.getSourceDBRef() == null)
+        if (seq.getSourceDBRef() == null && seq.getDBRefs() == null)
         {
-          if (seq.getDBRefs() == null)
-          {
             seqsWithoutSourceDBRef.add(seq);
             continue;
           }
-          for (DBRefEntry dbRef : seq.getDBRefs())
-          {
-            if (dbRef.getSource().equalsIgnoreCase("uniprot"))
-            {
-              seq.setSourceDBRef(dbRef);
-              break;
-            }
-          }
-          for (DBRefEntry dbRef : seq.getDBRefs())
-          {
-            if (dbRef.getSource().equalsIgnoreCase("pdb"))
-            {
-              seq.setSourceDBRef(dbRef);
-              break;
-            }
-          }
-          if (seq.getSourceDBRef() == null)
-          {
-            seqsWithoutSourceDBRef.add(seq);
-          }
-        }
       }
       if (!seqsWithoutSourceDBRef.isEmpty())
       {
         int y = seqsWithoutSourceDBRef.size();
         ssm.setProgressBar(null);
-        ssm.setProgressBar(">>>>> Fetching Database refs for " + y
-                + " sequence" + (y > 1 ? "s" : "")
-                + " with no valid uniprot or pdb ref for SIFTS mapping");
-        System.out.println(">>>>> Fetching Database refs for " + y
+        ssm.setProgressBar("Fetching db refs for " + y
                 + " sequence" + (y > 1 ? "s" : "")
-                + " with no valid uniprot or pdb ref for SIFTS mapping");
+                + " without valid db ref required for SIFTS mapping");
         SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
         int x = 0;
         for (SequenceI fSeq : seqsWithoutSourceDBRef)