refactored gap insert/visible view modification code from JPredThread

diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java
index 98f2645..5d734c1 100644 (file)
--- a/src/jalview/ws/jws1/JPredThread.java
+++ b/src/jalview/ws/jws1/JPredThread.java
@@ -197,7 +197,7 @@ class JPredThread extends JWS1Thread implements WSClientI
           {
             // Adjust input view for gaps
             // propagate insertions into profile
-            alcsel = propagateInsertions(profileseq, al, input);
+            alcsel = ColumnSelection.propagateInsertions(profileseq, al, input);
           }
         }
       }
@@ -255,98 +255,6 @@ class JPredThread extends JWS1Thread implements WSClientI
       }
     }
 
-    /**
-     * Add gaps into the sequences aligned to profileseq under the given
-     * AlignmentView
-     * 
-     * @param profileseq
-     * @param al
-     * @param input
-     */
-    private ColumnSelection propagateInsertions(SequenceI profileseq,
-            Alignment al, AlignmentView input)
-    {
-      char gc = al.getGapCharacter();
-      Object[] alandcolsel = input.getAlignmentAndColumnSelection(gc);
-      ColumnSelection nview = (ColumnSelection) alandcolsel[1];
-      SequenceI origseq;
-      nview.pruneDeletions(ShiftList
-              .parseMap((origseq = ((SequenceI[]) alandcolsel[0])[0])
-                      .gapMap())); // recover original prediction sequence's
-      // mapping to view.
-      int[] viscontigs = nview.getVisibleContigs(0, profileseq.getLength());
-      int spos = 0;
-      int offset = 0;
-      // input.pruneDeletions(ShiftList.parseMap(((SequenceI[])
-      // alandcolsel[0])[0].gapMap()))
-      // add profile to visible contigs
-      for (int v = 0; v < viscontigs.length; v += 2)
-      {
-        if (viscontigs[v] > spos)
-        {
-          StringBuffer sb = new StringBuffer();
-          for (int s = 0, ns = viscontigs[v] - spos; s < ns; s++)
-          {
-            sb.append(gc);
-          }
-          for (int s = 0, ns = al.getHeight(); s < ns; s++)
-          {
-            SequenceI sqobj = al.getSequenceAt(s);
-            if (sqobj != profileseq)
-            {
-              String sq = al.getSequenceAt(s).getSequenceAsString();
-              if (sq.length() <= spos + offset)
-              {
-                // pad sequence
-                int diff = spos + offset - sq.length() - 1;
-                if (diff > 0)
-                {
-                  // pad gaps
-                  sq = sq + sb;
-                  while ((diff = spos + offset - sq.length() - 1) > 0)
-                  {
-                    sq = sq
-                            + ((diff >= sb.length()) ? sb.toString() : sb
-                                    .substring(0, diff));
-                  }
-                }
-                sq += sb.toString();
-              }
-              else
-              {
-                al.getSequenceAt(s).setSequence(
-                        sq.substring(0, spos + offset) + sb.toString()
-                                + sq.substring(spos + offset));
-              }
-            }
-          }
-          // offset+=sb.length();
-        }
-        spos = viscontigs[v + 1] + 1;
-      }
-      if ((offset + spos) < profileseq.getLength())
-      {
-        StringBuffer sb = new StringBuffer();
-        for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++)
-        {
-          sb.append(gc);
-        }
-        for (int s = 1, ns = al.getHeight(); s < ns; s++)
-        {
-          String sq = al.getSequenceAt(s).getSequenceAsString();
-          // pad sequence
-          int diff = origseq.getLength() - sq.length();
-          while (diff > 0)
-          {
-            sq = sq
-                    + ((diff >= sb.length()) ? sb.toString() : sb
-                            .substring(0, diff));
-            diff = origseq.getLength() - sq.length();
-          }
-        }
-      }
-      return nview;
-    }
 
     public JPredJob(Hashtable SequenceInfo, SequenceI seq, int[] delMap)
     {