X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenColumns.java;h=2edb3f1d8905aa6a30854b146329200fcc5d72b8;hb=d4c27a996e22436dd4c4d8f64f6341d5315ff621;hp=f6102d422bf1a2478e4f87297b7c4b81ad4fac39;hpb=460c037bef9ec113c2a46010c443d85e73347592;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index f6102d4..2edb3f1 100644
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -1,6 +1,7 @@
 package jalview.datamodel;
 
 import jalview.util.Comparison;
+import jalview.util.ShiftList;
 
 import java.util.ArrayList;
 import java.util.Collections;
@@ -1054,7 +1055,197 @@ public class HiddenColumns
   }
 
   /**
-   * Returns a hashCode built from selected columns and hidden column ranges
+   * Add gaps into the sequences aligned to profileseq under the given
+   * AlignmentView
+   * 
+   * @param profileseq
+   * @param al
+   *          - alignment to have gaps inserted into it
+   * @param input
+   *          - alignment view where sequence corresponding to profileseq is
+   *          first entry
+   * @return new HiddenColumns for new alignment view, with insertions into
+   *         profileseq marked as hidden.
+   */
+  public static HiddenColumns propagateInsertions(SequenceI profileseq,
+          AlignmentI al, AlignmentView input)
+  {
+    int profsqpos = 0;
+
+    char gc = al.getGapCharacter();
+    Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc);
+    HiddenColumns nview = (HiddenColumns) alandhidden[1];
+    SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos];
+    nview.propagateInsertions(profileseq, al, origseq);
+    return nview;
+  }
+
+  /**
+   * 
+   * @param profileseq
+   *          - sequence in al which corresponds to origseq
+   * @param al
+   *          - alignment which is to have gaps inserted into it
+   * @param origseq
+   *          - sequence corresponding to profileseq which defines gap map for
+   *          modifying al
+   */
+  private void propagateInsertions(SequenceI profileseq, AlignmentI al,
+          SequenceI origseq)
+  {
+    char gc = al.getGapCharacter();
+    // recover mapping between sequence's non-gap positions and positions
+    // mapping to view.
+    pruneDeletions(ShiftList.parseMap(origseq.gapMap()));
+    int[] viscontigs = al.getHiddenColumns().getVisibleContigs(0,
+            profileseq.getLength());
+    int spos = 0;
+    int offset = 0;
+
+    // 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));
+                  if (diff >= sb.length())
+                  {
+                    sq += sb.toString();
+                  }
+                  else
+                  {
+                    char[] buf = new char[diff];
+                    sb.getChars(0, diff, buf, 0);
+                    sq += buf.toString();
+                  }
+                }
+              }
+              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())
+    {
+      // pad the final region with gaps.
+      StringBuffer sb = new StringBuffer();
+      for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++)
+      {
+        sb.append(gc);
+      }
+      for (int s = 0, ns = al.getHeight(); s < ns; s++)
+      {
+        SequenceI sqobj = al.getSequenceAt(s);
+        if (sqobj == profileseq)
+        {
+          continue;
+        }
+        String sq = sqobj.getSequenceAsString();
+        // pad sequence
+        int diff = origseq.getLength() - sq.length();
+        while (diff > 0)
+        {
+          // sq = sq
+          // + ((diff >= sb.length()) ? sb.toString() : sb
+          // .substring(0, diff));
+          if (diff >= sb.length())
+          {
+            sq += sb.toString();
+          }
+          else
+          {
+            char[] buf = new char[diff];
+            sb.getChars(0, diff, buf, 0);
+            sq += buf.toString();
+          }
+          diff = origseq.getLength() - sq.length();
+        }
+      }
+    }
+  }
+
+  /**
+   * remove any hiddenColumns or selected columns and shift remaining based on a
+   * series of position, range deletions.
+   * 
+   * @param deletions
+   */
+  private void pruneDeletions(ShiftList deletions)
+  {
+    if (deletions != null)
+    {
+      final List<int[]> shifts = deletions.getShifts();
+      if (shifts != null && shifts.size() > 0)
+      {
+        pruneDeletions(shifts);
+
+        // and shift the rest.
+        this.compensateForEdits(deletions);
+      }
+    }
+  }
+
+  /**
+   * Adjust hidden column boundaries based on a series of column additions or
+   * deletions in visible regions.
+   * 
+   * @param shiftrecord
+   * @return
+   */
+  private ShiftList compensateForEdits(ShiftList shiftrecord)
+  {
+    if (shiftrecord != null)
+    {
+      final List<int[]> shifts = shiftrecord.getShifts();
+      if (shifts != null && shifts.size() > 0)
+      {
+        int shifted = 0;
+        for (int i = 0, j = shifts.size(); i < j; i++)
+        {
+          int[] sh = shifts.get(i);
+          compensateForDelEdits(shifted + sh[0], sh[1]);
+          shifted -= sh[1];
+        }
+      }
+      return shiftrecord.getInverse();
+    }
+    return null;
+  }
+
+  /**
+   * Returns a hashCode built from hidden column ranges
    */
   public int hashCode(int hc)
   {