From 108d9a136d1794445f2169c04d80b7662085390d Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 9 Aug 2006 16:19:24 +0000
Subject: [PATCH] refactored hidden regions methods and made an AlignmentView
 preserve the alignment in hidden regions.

---
 src/jalview/datamodel/AlignmentView.java |    5 +-
 src/jalview/datamodel/CigarArray.java    |   28 ++++++++---
 src/jalview/datamodel/CigarBase.java     |   81 ++++++++++++++++++++++++++++--
 src/jalview/datamodel/CigarSimple.java   |    1 +
 src/jalview/datamodel/SeqCigar.java      |   39 ++++++--------
 5 files changed, 119 insertions(+), 35 deletions(-)

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 15309b7..727bc76 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -23,7 +23,8 @@ public class AlignmentView
   {
     if (!seqcigararray.isSeqCigarArray())
       throw new Error("Implementation Error - can only make an alignment view from a CigarArray of sequences.");
-    contigs = seqcigararray.applyDeletions();
+    //contigs = seqcigararray.applyDeletions();
+    contigs = seqcigararray.getDeletedRegions();
     sequences = seqcigararray.getSeqCigarArray();
   }
 
@@ -49,7 +50,7 @@ public class AlignmentView
   public Object[] getAlignmentAndColumnSelection(char gapCharacter) {
     ColumnSelection colsel = new ColumnSelection();
 
-    return new Object[] { SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel), colsel};
+    return new Object[] { SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel, contigs), colsel};
   }
   /**
    * getSequenceStrings
diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index b8cdf52..33e91a8 100644
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -118,7 +118,7 @@ public class CigarArray extends CigarBase
    * applyDeletions
    * edits underlying refCigars to propagate deleted regions, and removes deletion
    * operations from CigarArray operation list.
-   * @return int[] position where deletion occured in cigarArray or null if none occured
+   * @return int[] position after deletion occured and range of deletion in cigarArray or null if none occured
    */
   public int[] applyDeletions()
   {
@@ -127,31 +127,45 @@ public class CigarArray extends CigarBase
       return null;
     int cursor=0; // range counter for deletions
     int vcursor=0; // visible column index
-    for (int i=0; i<length; i++) {
+    int offset=0; // shift in visible column index as deletions are made
+    int i=0;
+    while (i<length) {
       if (operation[i]!=D) {
         if (operation[i]==M)
           cursor+=range[i];
-        vcursor+=range[i];
+        vcursor+=range[i++];
       }
       else
       {
         if (delpos==null)
           delpos=new java.util.Vector();
         int delstart=cursor, delend=cursor+range[i]-1; // inclusive
-        delpos.addElement(new Integer(vcursor-1)); // index of left hand column of hidden region boundary
+        delpos.addElement(new int[] { vcursor+offset, range[i]}); // index of right hand column after hidden region boundary
+        offset+=range[i]-1; // shift in visible column coordinates
         System.arraycopy(operation, i+1, operation, i, length-i);
         System.arraycopy(range, i+1, range, i, length-i);
         length--;
+        /*        int dmax=0;
+         for (int s=0; s<refCigars.length; s++) {
+           int d = refCigars[s].deleteRange(delstart, delend);
+           if (d>dmax)
+             dmax=d;
+         }
+         offset+=dmax; // shift in visible column coordinates
+         */
         for (int s=0; s<refCigars.length; s++) {
-          refCigars[s].deleteRange(delstart, delend);
+          int d = refCigars[s].deleteRange(delstart, delend);
         }
+
       }
     }
     if (delpos!=null)
     {
-      int[] pos=new int[delpos.size()];
+      int[] pos=new int[delpos.size()*2];
       for (int k = 0, l = delpos.size(); k < l; k++) {
-        pos[k] = ((Integer) delpos.elementAt(k)).intValue();
+        int[] dr = ((int[]) delpos.elementAt(k));
+        pos[k*2] = dr[0];
+        pos[k*2+1] = dr[1];
         delpos.setElementAt(null,k);
       }
       delpos=null;
diff --git a/src/jalview/datamodel/CigarBase.java b/src/jalview/datamodel/CigarBase.java
index 31aae1f..1e0705a 100644
--- a/src/jalview/datamodel/CigarBase.java
+++ b/src/jalview/datamodel/CigarBase.java
@@ -1,5 +1,7 @@
 package jalview.datamodel;
 
+import java.util.Vector;
+
 public abstract class CigarBase
 {
   /**
@@ -115,7 +117,25 @@ public abstract class CigarBase
         new int[] {
         start, startpos, end, endpos}, trunc_deletions};
   }
-
+  protected void compact_operations() {
+    int i=1;
+    if (operation==null)
+      return;
+    char last = operation[0];
+    while (i<length) {
+      if (last==operation[i]) {
+        range[i-1]+=range[i];
+        int r = length-i;
+        if (r>0) {
+          System.arraycopy(range, i + 1, range, i, r);
+          System.arraycopy(operation, i + 1, operation, i, r);
+        }
+        length--;
+      } else {
+        last = operation[i++];
+      }
+    }
+  }
   /**
    * turn a cigar string into a series of operation range pairs
    * @param cigarString String
@@ -349,11 +369,13 @@ public abstract class CigarBase
    * Mark residues from start to end (inclusive) as deleted from the alignment, and removes any insertions.
    * @param start int
    * @param end int
+   * @return deleted int - number of symbols marked as deleted
    */
-  public void deleteRange(int start, int end) {
+  public int deleteRange(int start, int end) {
+    int deleted=0;
     if (length==0) {
       // nothing to do here
-      return;
+      return deleted;
     }
     if (start<0 || start>end)
       throw new Error("Implementation Error: deleteRange out of bounds: start must be non-negative and less than end.");
@@ -368,6 +390,7 @@ public abstract class CigarBase
     length=0;
     operation = null;
     range = null;
+    compact_operations();
     while (o<oldlen && cursor<=end && rlength>0) {
       if (oldops[o] == D) {
         // absorbed into new deleted region.
@@ -396,7 +419,9 @@ public abstract class CigarBase
           case M:
             if (rlength>remain) {
               addDeleted(remain);
+              deleted+=remain;
             } else {
+              deleted+=rlength;
               addDeleted(rlength);
               if (remain-rlength>0)
                 this.addOperation(M,remain-rlength); // add remaining back.
@@ -428,6 +453,56 @@ public abstract class CigarBase
       // ran out of ops - nothing to do here ?
      // addInsertion(start-cursor);
     //}
+    return deleted;
+  }
+
+  /**
+   * Deleted regions mean that there will be discontinuous sequence numbering in the
+   * sequence returned by getSeq(char).
+   * @return true if there deletions
+   */
+  public boolean hasDeletedRegions()
+  {
+    for (int i = 0; i<length ; i++)
+    {
+      if (operation[i] == D)
+      {
+        return true;
+      }
+    }
+    return false;
+  }
+  /**
+   * enumerate the ranges on seq that are marked as deleted in this cigar
+   * @return int[] { vis_start, sym_start, length }
+   */
+  public int[] getDeletedRegions() {
+    if (length==0)
+      return null;
+    Vector dr = new Vector();
+    int cursor=0, vcursor=0;
+    for (int i=0;i<length;i++) {
+      switch (operation[i]) {
+        case M:
+          cursor+=range[i];
+        case I:
+          vcursor+=range[i];
+          break;
+        case D:
+          dr.add(new int[] { vcursor, cursor, range[i]});
+          cursor+=range[i];
+      }
+    }
+    if (dr.size()==0)
+      return null;
+    int[] delregions = new int[dr.size()*3];
+    for (int i=0,l=dr.size(); i<l; i++) {
+      int[] reg = (int[]) dr.get(i);
+      delregions[i*3] = reg[0];
+      delregions[i*3+1] = reg[1];
+      delregions[i*3+2] = reg[2];
+    }
+    return delregions;
   }
   /**
    * sum of ranges in cigar string
diff --git a/src/jalview/datamodel/CigarSimple.java b/src/jalview/datamodel/CigarSimple.java
index 4db24a6..4752669 100644
--- a/src/jalview/datamodel/CigarSimple.java
+++ b/src/jalview/datamodel/CigarSimple.java
@@ -21,4 +21,5 @@ public abstract class CigarSimple
      * @return String
      */
     public abstract String getSequenceString(char GapChar);
+
 }
diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index c9b737d..0203383 100644
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -218,24 +218,6 @@ public class SeqCigar
   {
     this.addOperation(M, range);
   }
-
-  /**
-   * Deleted regions mean that there will be discontinuous sequence numbering in the
-   * sequence returned by getSeq(char).
-   * @return true if there deletions
-   */
-  public boolean hasDeletedRegions()
-  {
-    for (int i = 0, l = length; i < l; i++)
-    {
-      if (operation[i] == D)
-      {
-        return true;
-      }
-    }
-    return false;
-  }
-
   /**
    * Adds
    * insertion and match operations based on seq to the cigar up to
@@ -365,10 +347,9 @@ public class SeqCigar
    * @return SequenceI[]
    */
   public static SequenceI[] createAlignmentSequences(SeqCigar[] alseqs,
-      char gapCharacter, ColumnSelection colsel)
+      char gapCharacter, ColumnSelection colsel, int[] segments)
   {
     SequenceI[] seqs = new SequenceI[alseqs.length];
-    Vector hiddenRegions=new Vector();
     StringBuffer[] g_seqs = new StringBuffer[alseqs.length];
     String[] alseqs_string=new String[alseqs.length];
     Object[] gs_regions = new Object[alseqs.length];
@@ -384,7 +365,7 @@ public class SeqCigar
       }
       g_seqs[i] = new StringBuffer( (String) ( (Object[]) gs_regions[i])[0]); // the visible gapped sequence
     }
-    // Now account for insertions.
+    // Now account for insertions. (well - deletions)
     // this is complicated because we must keep track of shifted positions in each sequence
     ShiftList shifts = new ShiftList();
     for (int i = 0; i < alseqs.length; i++)
@@ -423,7 +404,9 @@ public class SeqCigar
             }
           }
           shifts.addShift(region[2], insert.length); // update shift in alignment frame of reference
-          colsel.hideColumns(inspos, inspos+insert.length-1);
+          if (segments==null)
+            // add a hidden column for this deletion
+            colsel.hideColumns(inspos, inspos+insert.length-1);
         }
       }
     }
@@ -436,6 +419,15 @@ public class SeqCigar
                              ref.getStart() + alseqs[i].start+bounds[2]);
       seqs[i].setDatasetSequence(ref);
     }
+    if (segments!=null) {
+      int delshift=0; // need to shift the segments to their absolute positions in the sequence cigar frame.
+      for (int i=0; i<segments.length; i+=3) {
+        //int start=shifts.shift(segments[i]-1)+1;
+        //int end=shifts.shift(segments[i]+segments[i+1]-1)-1;
+        colsel.hideColumns(delshift+segments[i], delshift+segments[i]+segments[i+2]-1);
+        delshift+=segments[i+2];
+      }
+    }
     return seqs;
   }
 
@@ -546,13 +538,14 @@ public class SeqCigar
     {
       sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
       int sl = sub_se_gp.getWidth();
-      int st = sl - r - r;
+      int st = sl - 1 - r;
       for (int rs = 0; rs < 10; rs++)
       {
         int e = st + rs;
         sub_se_gp.deleteRange(st, e);
         String ssgapedseq = sub_se_gp.getSeq('-').getSequence();
         System.out.println(st + "," + e + "\t:" + ssgapedseq);
+        st -=3;
       }
     }
     {
-- 
1.7.10.2