JAL-3187 removal of variant feature (non-virtual) transfer to protein

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

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 1a56393..40401fb 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -99,7 +99,7 @@ public class CrossRef
    */
   public List<String> findXrefSourcesForSequences(boolean dna)
   {
-    List<String> sources = new ArrayList<String>();
+    List<String> sources = new ArrayList<>();
     for (SequenceI seq : fromSeqs)
     {
       if (seq != null)
@@ -151,7 +151,7 @@ public class CrossRef
        * find sequence's direct (dna-to-dna, peptide-to-peptide) xrefs
        */
       DBRefEntry[] lrfs = DBRefUtils.selectDbRefs(fromDna, seq.getDBRefs());
-      List<SequenceI> foundSeqs = new ArrayList<SequenceI>();
+      List<SequenceI> foundSeqs = new ArrayList<>();
 
       /*
        * find sequences in the alignment which xref one of these DBRefs
@@ -218,7 +218,7 @@ public class CrossRef
   public Alignment findXrefSequences(String source, boolean fromDna)
   {
 
-    rseqs = new ArrayList<SequenceI>();
+    rseqs = new ArrayList<>();
     AlignedCodonFrame cf = new AlignedCodonFrame();
     matcher = new SequenceIdMatcher(dataset.getSequences());
 
@@ -430,8 +430,8 @@ public class CrossRef
     if (retrieved != null)
     {
       boolean addedXref = false;
-      List<SequenceI> newDsSeqs = new ArrayList<SequenceI>(),
-              doNotAdd = new ArrayList<SequenceI>();
+      List<SequenceI> newDsSeqs = new ArrayList<>(),
+              doNotAdd = new ArrayList<>();
 
       for (SequenceI retrievedSequence : retrieved)
       {
@@ -619,28 +619,25 @@ public class CrossRef
                  * duplication (e.g. same variation from two 
                  * transcripts)
                  */
-                SequenceFeature[] sfs = ms.getSequenceFeatures();
-                if (sfs != null)
+                List<SequenceFeature> sfs = ms.getFeatures()
+                        .getAllFeatures();
+                for (SequenceFeature feat : sfs)
                 {
-                  for (SequenceFeature feat : sfs)
+                  /*
+                   * make a flyweight feature object which ignores Parent
+                   * attribute in equality test; this avoids creating many
+                   * otherwise duplicate exon features on genomic sequence
+                   */
+                  SequenceFeature newFeature = new SequenceFeature(feat)
                   {
-                    /*
-                     * make a flyweight feature object which ignores Parent
-                     * attribute in equality test; this avoids creating many
-                     * otherwise duplicate exon features on genomic sequence
-                     */
-                    SequenceFeature newFeature = new SequenceFeature(feat)
+                    @Override
+                    public boolean equals(Object o)
                     {
-                      @Override
-                      public boolean equals(Object o)
-                      {
-                        return super.equals(o, true);
-                      }
-                    };
-                    matched.addSequenceFeature(newFeature);
-                  }
+                      return super.equals(o, true);
+                    }
+                  };
+                  matched.addSequenceFeature(newFeature);
                 }
-
               }
               cf.addMap(retrievedSequence, map.getTo(), map.getMap());
             } catch (Exception e)
@@ -785,15 +782,15 @@ public class CrossRef
     {
       return false;
     }
-    char[] c1 = seq1.getSequence();
-    char[] c2 = seq2.getSequence();
-    if (c1.length != c2.length)
+
+    if (seq1.getLength() != seq2.getLength())
     {
       return false;
     }
-    for (int i = 0; i < c1.length; i++)
+    int length = seq1.getLength();
+    for (int i = 0; i < length; i++)
     {
-      int diff = c1[i] - c2[i];
+      int diff = seq1.getCharAt(i) - seq2.getCharAt(i);
       /*
        * same char or differ in case only ('a'-'A' == 32)
        */
@@ -924,7 +921,7 @@ public class CrossRef
 
     if (fromDna)
     {
-      AlignmentUtils.computeProteinFeatures(mapFrom, mapTo, mapping);
+      // AlignmentUtils.computeProteinFeatures(mapFrom, mapTo, mapping);
       mappings.addMap(mapFrom, mapTo, mapping);
     }
     else