JAL-1705 get xrefs only for dna/peptide; code tidy

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

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 95d2396..e96d9d7 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -244,29 +244,30 @@ public class CrossRef
       }
       for (int r = 0; xrfs != null && r < xrfs.length; r++)
       {
-        if (source != null && !source.equals(xrfs[r].getSource()))
+        DBRefEntry xref = xrfs[r];
+        if (source != null && !source.equals(xref.getSource()))
         {
           continue;
         }
-        if (xrfs[r].hasMap())
+        if (xref.hasMap())
         {
-          if (xrfs[r].getMap().getTo() != null)
+          if (xref.getMap().getTo() != null)
           {
-            SequenceI rsq = new Sequence(xrfs[r].getMap().getTo());
+            SequenceI rsq = new Sequence(xref.getMap().getTo());
             rseqs.add(rsq);
-            if (xrfs[r].getMap().getMap().getFromRatio() != xrfs[r]
+            if (xref.getMap().getMap().getFromRatio() != xref
                     .getMap().getMap().getToRatio())
             {
               // get sense of map correct for adding to product alignment.
               if (dna)
               {
                 // map is from dna seq to a protein product
-                cf.addMap(dss, rsq, xrfs[r].getMap().getMap());
+                cf.addMap(dss, rsq, xref.getMap().getMap());
               }
               else
               {
                 // map should be from protein seq to its coding dna
-                cf.addMap(rsq, dss, xrfs[r].getMap().getMap().getInverse());
+                cf.addMap(rsq, dss, xref.getMap().getMap().getInverse());
               }
             }
             found = true;
@@ -278,7 +279,7 @@ public class CrossRef
           // xrefs on this sequence.
           if (dataset != null)
           {
-            found |= searchDataset(dss, xrfs[r], dataset, rseqs, cf); // ,false,!dna);
+            found |= searchDataset(dss, xref, dataset, rseqs, cf); // ,false,!dna);
             if (found)
             {
               xrfs[r] = null; // we've recovered seqs for this one.
@@ -326,9 +327,8 @@ public class CrossRef
             xrfs = t;
             try
             {
-              retrieved = sftch.getSequences(xrfs); // problem here is we don't
-              // know which of xrfs
-              // resulted in which
+              retrieved = sftch.getSequences(xrfs, !dna);
+              // problem here is we don't know which of xrfs resulted in which
               // retrieved element
             } catch (Exception e)
             {
@@ -401,7 +401,7 @@ public class CrossRef
       SequenceI[] rsqs = new SequenceI[rseqs.size()];
       rseqs.toArray(rsqs);
       ral = new Alignment(rsqs);
-      if (cf != null && cf.getProtMappings() != null)
+      if (cf != null && !cf.isEmpty())
       {
         ral.addCodonFrame(cf);
       }