JAL-3446 unused imports removed

[jalview.git] / src / jalview / analysis / CrossRef.java

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 4f01cea..1044802 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -20,6 +20,10 @@
  */
 package jalview.analysis;
 
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -31,12 +35,7 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
-import jalview.ws.SequenceFetcherFactory;
-import jalview.ws.seqfetcher.ASequenceFetcher;
-
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
+import jalview.ws.SequenceFetcher;
 
 /**
  * Functions for cross-referencing sequence databases.
@@ -402,7 +401,6 @@ public class CrossRef
   private void retrieveCrossRef(List<DBRefEntry> sourceRefs, SequenceI seq,
           List<DBRefEntry> xrfs, boolean fromDna, AlignedCodonFrame cf)
   {
-    ASequenceFetcher sftch = SequenceFetcherFactory.getSequenceFetcher();
     SequenceI[] retrieved = null;
     SequenceI dss = seq.getDatasetSequence() == null ? seq
             : seq.getDatasetSequence();
@@ -418,7 +416,7 @@ public class CrossRef
     }
     try
     {
-      retrieved = sftch.getSequences(sourceRefs, !fromDna);
+      retrieved = SequenceFetcher.getInstance().getSequences(sourceRefs, !fromDna);
     } catch (Exception e)
     {
       System.err.println(
@@ -483,9 +481,9 @@ public class CrossRef
   private void removeAlreadyRetrievedSeqs(List<DBRefEntry> sourceRefs,
           boolean fromDna)
   {
-    List<DBRefEntry> dbrSourceSet = new ArrayList<DBRefEntry>(sourceRefs);
+    List<DBRefEntry> dbrSourceSet = new ArrayList<>(sourceRefs);
     List<SequenceI> dsSeqs = dataset.getSequences();
-    for (int ids = dsSeqs.size(); --ids >= 0;)
+    for (int ids = 0, nds = dsSeqs.size(); ids < nds; ids++)
     {
       SequenceI sq = dsSeqs.get(ids);
       boolean dupeFound = false;
@@ -494,11 +492,11 @@ public class CrossRef
       if (sq.isProtein() == fromDna)
       {
        List<DBRefEntry> sqdbrefs = sq.getPrimaryDBRefs();
-        for (int idb = sqdbrefs.size(); --idb >= 0;)
+        for (int idb = 0, ndb = sqdbrefs.size(); idb < ndb; idb++)
         {
           DBRefEntry dbr = sqdbrefs.get(idb);  
           List<DBRefEntry> searchrefs = DBRefUtils.searchRefs(dbrSourceSet, dbr, DBRefUtils.SEARCH_MODE_FULL);
-          for (int isr = searchrefs.size(); --isr >= 0;)
+          for (int isr = 0, nsr = searchrefs.size(); isr < nsr; isr++)
           {
             sourceRefs.remove(searchrefs.get(isr));
             dupeFound = true;
@@ -929,7 +927,7 @@ public class CrossRef
 
     if (fromDna)
     {
-      AlignmentUtils.computeProteinFeatures(mapFrom, mapTo, mapping);
+      // AlignmentUtils.computeProteinFeatures(mapFrom, mapTo, mapping);
       mappings.addMap(mapFrom, mapTo, mapping);
     }
     else