JAL-674 refactor method to match and transfer annotation between aligned

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

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 4460985..9815b97 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1024,6 +1024,87 @@ public class AlignSeq
   }
 
   /**
+   * matches ochains against al and populates seqs with the best match between
+   * each ochain and the set in al
+   * 
+   * @param ochains
+   * @param al
+   * @param dnaOrProtein
+   * @param removeOldAnnots when true, old annotation is cleared before new annotation transferred
+   */
+  public static void replaceMatchingSeqsWith(List<SequenceI> seqs, List<AlignmentAnnotation> annotations, List<SequenceI> ochains,
+          AlignmentI al, String dnaOrProtein, boolean removeOldAnnots)
+  {
+    if (al != null && al.getHeight() > 0)
+    {
+      ArrayList<SequenceI> matches = new ArrayList<SequenceI>();
+      ArrayList<AlignSeq> aligns = new ArrayList<AlignSeq>();
+  
+      for (SequenceI sq : ochains)
+      {
+        SequenceI bestm = null;
+        AlignSeq bestaseq = null;
+        int bestscore = 0;
+        for (SequenceI msq : al.getSequences())
+        {
+          AlignSeq aseq = doGlobalNWAlignment(msq, sq,
+                  dnaOrProtein);
+          if (bestm == null || aseq.getMaxScore() > bestscore)
+          {
+            bestscore = aseq.getMaxScore();
+            bestaseq = aseq;
+            bestm = msq;
+          }
+        }
+        System.out.println("Best Score for " + (matches.size() + 1) + " :"
+                + bestscore);
+        matches.add(bestm);
+        aligns.add(bestaseq);
+        al.deleteSequence(bestm);
+      }
+      for (int p = 0, pSize = seqs.size(); p < pSize; p++)
+      {
+        SequenceI sq, sp = seqs.get(p);
+        int q;
+        if ((q = ochains.indexOf(sp)) > -1)
+        {
+          seqs.set(p, sq = matches.get(q));
+          sq.setName(sp.getName());
+          sq.setDescription(sp.getDescription());
+          Mapping sp2sq;
+          sq.transferAnnotation(sp, sp2sq = aligns.get(q).getMappingFromS1(false));
+          int inspos = -1;
+          for (int ap = 0; ap < annotations.size();)
+          {
+            if (annotations.get(ap).sequenceRef == sp)
+            {
+              if (inspos == -1)
+              {
+                inspos = ap;
+              }
+              if (removeOldAnnots) {
+                annotations.remove(ap);
+              } else {
+                AlignmentAnnotation alan = annotations.get(ap);
+                alan.liftOver(sq, sp2sq);
+                alan.setSequenceRef(sq);
+              }
+            }
+            else
+            {
+              ap++;
+            }
+          }
+          if (sq.getAnnotation() != null)
+          {
+            annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
+          }
+        }
+      }
+    }
+  }
+
+  /**
    * compute the PID vector used by the redundancy filter.
    * 
    * @param originalSequences