From: Jim Procter <j.procter@dundee.ac.uk>
Date: Mon, 20 Oct 2014 08:27:57 +0000 (+0100)
Subject: JAL-674 refactor method to match and transfer annotation between aligned
X-Git-Tag: Jalview_2_9~169^2~20
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=97e37bce240ce2430ca838bfb3060bd06dfe1711;p=jalview.git

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

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 086c4d9..19e13e7 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -279,7 +279,7 @@ public class PDBfile extends jalview.io.AlignFile
                 {}).invoke(jmf));
         cl.getMethod("addAnnotations", new Class[]
         { Alignment.class }).invoke(jmf, al);
-        replaceMatchingSeqsWith(seqs, annotations, prot, al, AlignSeq.PEP, false);
+        AlignSeq.replaceMatchingSeqsWith(seqs, annotations, prot, al, AlignSeq.PEP, false);
       }
     } catch (ClassNotFoundException q)
     {
@@ -307,7 +307,7 @@ public class PDBfile extends jalview.io.AlignFile
                 new Class[]
                 { FileParse.class }).invoke(annotate3d, new Object[]
         { new FileParse(getDataName(), type) }));
-        replaceMatchingSeqsWith(seqs, annotations, rna, al, AlignSeq.DNA, false);
+        AlignSeq.replaceMatchingSeqsWith(seqs, annotations, rna, al, AlignSeq.DNA, false);
       }
     } catch (ClassNotFoundException x)
     {
@@ -317,87 +317,6 @@ public class PDBfile extends jalview.io.AlignFile
   }
 
   /**
-   * 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 = AlignSeq.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()));
-          }
-        }
-      }
-    }
-  }
-
-  /**
    * make a friendly ID string.
    * 
    * @param dataName
diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 4460985..9815b97 100755
--- 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