From e2c91fd4e77e2be8942eb872e5b3a30cabb6a9bc Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 10 Aug 2006 09:50:14 +0000
Subject: [PATCH] 1.1 compatible

---
 src/jalview/datamodel/CigarBase.java | 1268 +++++++++++++++++-----------------
 1 file changed, 634 insertions(+), 634 deletions(-)

diff --git a/src/jalview/datamodel/CigarBase.java b/src/jalview/datamodel/CigarBase.java
index 1e0705a..24c568b 100644
--- a/src/jalview/datamodel/CigarBase.java
+++ b/src/jalview/datamodel/CigarBase.java
@@ -1,634 +1,634 @@
-package jalview.datamodel;
-
-import java.util.Vector;
-
-public abstract class CigarBase
-{
-  /**
-   * Base class for compact idiosyncratic representation of gaps and aligned residues
-   * Regards to Tom Oldfield for his DynamicArray class.
-   * 17th July 2006
-   * Not thread safe.
-   */
-  public CigarBase()
-  {
-    // nothing to be done (probably)
-  }
-
-  protected int length = 0;
-  protected int _inc_length = 10; // extension range for addition of new operations
-  protected char[] operation = null;
-  protected int[] range = null;
-  /**
-   * Range of Hidden residues in seq (translated as deleted in seq)
-   */
-  public static final char D = 'D'; /**
-  * Range of insertions to seq
-  */
- public static final char I = 'I'; /**
-  * Range of aligned residues
-  */
- public static final char M = 'M';
-  static protected final char _case_shift = 'a' - 'A';
-  /**
-   * Ugly function to get edited sequence string, start and end symbol positions and the deletion regions as an array of int pairs
-   * May return null for an empty cigar string.
-   * May return null for deletion ranges if there are none.
-   * @param reference - the symbol sequence to apply the cigar operations to (or null if no sequence)
-   * @param GapChar - the symbol to use for Insert operations
-   * @return Object[] { String, int[] {start, startcol, end, endcol}, int[][3] {start, end, col} or null} the gapped sequence, first and last residue index, and the deletion ranges on the reference sequence
-   */
-  public Object[] getSequenceAndDeletions(String reference, char GapChar)
-  {
-    int rlength=0;
-    int[][] deletions = new int[length][];
-    int[][] trunc_deletions = null;
-    StringBuffer sq = new StringBuffer();
-    int cursor = 0, alcursor=0,start = 0, startpos=0, end = 0, endpos=0, delcount = -1;
-    boolean consecutive_del = false;
-    if (length == 0)
-    {
-      return null;
-    }
-    if (reference!=null)
-      rlength=reference.length();
-    boolean modstart = true;
-    for (int i = 0; i < length; i++)
-    {
-      switch (operation[i])
-      {
-        case D:
-          if (!consecutive_del)
-          {
-            deletions[++delcount] = new int[]
-                {
-                cursor, 0, alcursor};
-          }
-          cursor += range[i];
-          deletions[delcount][1] = cursor - 1;
-          consecutive_del = true;
-          break;
-        case I:
-          consecutive_del = false;
-          for (int r = 0; r < range[i]; r++)
-          {
-            sq.append(GapChar);
-            alcursor++;
-          }
-          break;
-        case M:
-          consecutive_del = false;
-          if (modstart)
-          {
-            start = cursor;
-            startpos=alcursor;
-            modstart = false;
-          }
-          if (reference!=null) {
-            int sbend = cursor+range[i];
-            if (sbend>rlength) {
-              sq.append(reference.substring(cursor, rlength));
-              while (sbend-- >= rlength)
-              {
-                sq.append(GapChar);
-              }
-            } else {
-              sq.append(reference.substring(cursor, sbend));
-            }
-          }
-          alcursor+=range[i];
-          cursor += range[i];
-          end = cursor - 1;
-          endpos = alcursor;
-          break;
-        default:
-          throw new Error("Unknown SeqCigar operation '" + operation[i] + "'");
-      }
-    }
-    if (++delcount > 0)
-    {
-      trunc_deletions = new int[delcount][];
-      System.arraycopy(deletions, 0, trunc_deletions, 0, delcount);
-    }
-    deletions = null;
-    return new Object[]
-        {
-        ((reference!=null) ? sq.toString() : null),
-        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
-   * @return object[] {char[] operation, int[] range}
-   * @throws java.lang.Exception for improperly formated cigar strings or ones with unknown operations
-   */
-  public static Object[] parseCigarString(String cigarString)
-      throws Exception
-  {
-    int ops = 0;
-    for (int i = 0, l = cigarString.length(); i < l; i++)
-    {
-      char c = cigarString.charAt(i);
-      if (c == M || c == (M - _case_shift) || c == I || c == (I - _case_shift) ||
-          c == D || c == (D - _case_shift))
-      {
-        ops++;
-      }
-    }
-    char[] operation = new char[ops];
-    int[] range = new int[ops];
-    int op = 0;
-    int i = 0, l = cigarString.length();
-    while (i < l)
-    {
-      char c;
-      int j = i;
-      do
-      {
-        c = cigarString.charAt(j++);
-      }
-      while (c >= '0' && c <= '9' && j < l);
-      if (j >= l && c >= '0' && c <= '9')
-      {
-        throw new Exception("Unterminated cigar string.");
-      }
-      try
-      {
-        String rangeint = cigarString.substring(i, j - 1);
-        range[op] = Integer.parseInt(rangeint);
-        i = j;
-      }
-      catch (Exception e)
-      {
-        throw new Error("Implementation bug in parseCigarString");
-      }
-      if (c >= 'a' && c <= 'z')
-      {
-        c -= _case_shift;
-      }
-      if ( (c == M || c == I || c == D))
-      {
-        operation[op++] = c;
-      }
-      else
-      {
-        throw new Exception("Unexpected operation '" + c +
-                            "' in cigar string (position " + i + " in '" +
-                            cigarString + "'");
-      }
-    }
-    return new Object[]
-        {
-        operation, range};
-  }
-
-  /**
-   * add an operation to cigar string
-   * @param op char
-   * @param range int
-   */
-  public void addOperation(char op, int range)
-  {
-    if (op >= 'a' && op <= 'z')
-    {
-      op -= _case_shift;
-    }
-    if (op != M && op != D && op != I)
-    {
-      throw new Error("Implementation error. Invalid operation string.");
-    }
-    if (range<=0)
-      throw new Error("Invalid range string (must be non-zero positive number)");
-    int lngth = 0;
-    if (operation == null)
-    {
-      this.operation = new char[_inc_length];
-      this.range = new int[_inc_length];
-    }
-    if (length + 1 == operation.length)
-    {
-      char[] ops = this.operation;
-      this.operation = new char[length + 1 + _inc_length];
-      System.arraycopy(ops, 0, this.operation, 0, length);
-      ops = null;
-      int[] rng = this.range;
-      this.range = new int[length + 1 + _inc_length];
-      System.arraycopy(rng, 0, this.range, 0, length);
-      rng = null;
-    }
-    if ((length>0) && (operation[length-1]==op))
-      length--; // modify existing operation.
-    else
-      this.range[length]=0; // reset range
-    this.operation[length] = op;
-    this.range[length++] += range;
-  }
-
-  /**
-   * semi-efficient insert an operation on the current cigar string set at column pos (from 1)
-   * NOTE: Insertion operations simply extend width of cigar result - affecting registration of alignment
-   * Deletion ops will shorten length of result - and affect registration of alignment
-   * Match ops will also affect length of result - affecting registration of alignment
-   * (ie "10M".insert(4,I,3)->"4M3I3M") - (replace?)
-   * (ie "10M".insert(4,D,3)->"4M3D3M") - (shortens alignment)
-   * (ie "5I5M".insert(4,I,3)->"8I5M") - real insertion
-   * (ie "5I5M".insert(4,D,3)->"4I2D3M") - shortens aligment - I's are removed, Ms changed to Ds
-   * (ie "10M".insert(4,M,3)->"13M")  - lengthens - Is changed to M, Ds changed to M.
-   * (ie "5I5M".insert(4,M,3)->"4I8M") - effectively shifts sequence left by 1 residue and extends it by 3
-   * ( "10D5M".insert(-1,M,3)->"3M7D5M")
-   * ( "10D5M".insert(0,M,3)->"7D8M")
-   * ( "10D5M".insert(1,M,3)->"10D8M")
-   *
-   * ( "1M10D5M".insert(0,M,3)->"1M10D8M")
-   * ( "1M10D5M".insert(1,M,3)->"
-   *
-   * if pos is beyond width - I operations are added before the operation
-   * @param pos int -1, 0-length of visible region, or greater to append new ops (with insertions in between)
-   * @param op char
-   * @param range int
-  public void addOperationAt(int pos, char op, int range)
-  {
-    int cursor = -1; // mark the position for the current operation being edited.
-    int o = 0;
-    boolean last_d = false; // previous op was a deletion.
-    if (pos < -1)
-      throw new Error("pos<-1 is not supported.");
-    while (o<length) {
-      if (operation[o] != D)
-      {
-        if ( (cursor + this.range[o]) < pos)
-        {
-          cursor += this.range[o];
-          o++;
-          last_d=false;
-        }
-        else
-        {
-          break;
-        }
-      }
-      else {
-        last_d=true;
-        o++;
-      }
-    }
-    if (o==length) {
-      // must insert more operations before pos
-      if (pos-cursor>0)
-        addInsertion(pos-cursor);
-      // then just add the new operation. Regardless of what it is.
-      addOperation(op, range);
-    } else {
-      int diff = pos - cursor;
-
-      int e_length = length-o; // new edit operation array length.
-      // diff<0 - can only happen before first insertion or match. - affects op and all following
-      // dif==0 - only when at first position of existing op -
-      // diff>0 - must preserve some existing operations
-      int[] e_range = new int[e_length];
-      System.arraycopy(this.range, o, e_range, 0, e_length);
-      char[] e_op = new char[e_length];
-      System.arraycopy(this.operation, o, e_op, 0, e_length);
-      length = o; // can now use add_operation to extend list.
-      int e_o=0; // current operation being edited.
-      switch (op) {
-        case M:
-          switch (e_op[e_o])
-          {
-            case M:
-              if (last_d && diff <= 0)
-              {
-                // reduce D's, if possible
-                if (range<=this.range[o-1]) {
-                  this.range[o - 1] -= range;
-                } else {
-                  this.range[o-1]=0;
-                }
-                if (this.range[o-1]==0)
-                  o--; // lose this op.
-              }
-              e_range[e_o] += range; // just add more matched residues
-              break;
-            case I:
-              // change from insertion to match
-              if (last_d && diff<=0)
-              {
-                // reduce D's, if possible
-                if (range<=this.range[o-1]) {
-                  this.range[o - 1] -= range;
-                } else {
-                  this.range[o-1]=0;
-                }
-                if (this.range[o-1]==0)
-                  o--; // lose this op.
-              }
-              e_range[e_o]
-                    break;
-                default:
-                  throw new Inp
-                      }
-
-                      break;
-                case I:
-                  break;
-                case D:
-              }
-          break;
-        default:
-          throw new Error("Implementation Error: Unknown operation in addOperation!");
-      }
-      // finally, add remaining ops.
-      while (e_o<e_length) {
-        addOperation(e_op[e_o], e_range[e_o]);
-        e_o++;
-      }
-    }
-  }
-**/
-  /**
-   * 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 int deleteRange(int start, int end) {
-    int deleted=0;
-    if (length==0) {
-      // nothing to do here
-      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.");
-    // find beginning
-    int cursor = 0; // mark the position for the current operation being edited.
-    int rlength=1+end-start; // number of positions to delete
-    int oldlen=length;
-    int o = 0;
-    boolean editing=false;
-    char[] oldops = operation;
-    int[] oldrange = range;
-    length=0;
-    operation = null;
-    range = null;
-    compact_operations();
-    while (o<oldlen && cursor<=end && rlength>0) {
-      if (oldops[o] == D) {
-        // absorbed into new deleted region.
-        addDeleted(oldrange[o++]);
-        continue;
-      }
-
-      int remain = oldrange[o]; // number of op characters left to edit
-      if (!editing) {
-        if ( (cursor + remain) <= start)
-        {
-          addOperation(oldops[o],oldrange[o]);
-          cursor+=oldrange[o++];
-          continue; // next operation
-        }
-        editing=true;
-        // add operations before hidden region
-        if (start-cursor>0) {
-          addOperation(oldops[o], start- cursor);
-          remain -= start - cursor;
-        }
-      }
-      // start inserting new ops
-      if (o<oldlen && editing && rlength>0 && remain>0) {
-        switch (oldops[o]) {
-          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.
-              rlength=0;
-              remain=0;
-            }
-            break;
-          case I:
-            if (remain-rlength>0) {
-              // only remove some gaps
-              addInsertion(remain-rlength);
-              rlength=0;
-            }
-            break;
-          case D:
-            throw new Error("Implementation error."); // do nothing;
-          default:
-            throw new Error("Implementation Error! Unknown operation '"+oldops[o]+"'");
-        }
-        rlength-=remain;
-        remain = oldrange[++o]; // number of op characters left to edit
-      }
-    }
-    // add remaining
-    while (o<oldlen) {
-      addOperation(oldops[o],oldrange[o++]);
-    }
-    //if (cursor<(start+1)) {
-      // 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
-   * @return int number of residues hidden, matched, or gaps inserted into sequence
-   */
-  public int getFullWidth()
-  {
-    int w = 0;
-    if (range != null)
-    {
-      for (int i = 0; i < length; i++)
-      {
-        w += range[i];
-      }
-    }
-    return w;
-  }
-
-  /**
-   * Visible length of aligned sequence
-   * @return int length of including gaps and less hidden regions
-   */
-  public int getWidth()
-  {
-    int w = 0;
-    if (range != null)
-    {
-      for (int i = 0; i < length; i++)
-      {
-        if (operation[i] == M || operation[i] == I)
-        {
-          w += range[i];
-        }
-      }
-    }
-    return w;
-  }
-  /**
-   * mark a range of inserted residues
-   * @param range int
-   */
-  public void addInsertion(int range)
-  {
-    this.addOperation(I, range);
-  }
-
-  /**
-   * mark the next range residues as hidden (not aligned) or deleted
-   * @param range int
-   */
-  public void addDeleted(int range)
-  {
-    this.addOperation(D, range);
-  }
-
-  /**
-   * Modifies operation list to delete columns from start to end (inclusive)
-   * editing will remove insertion operations, and convert matches to deletions
-   * @param start alignment column
-   * @param end alignment column
-   * @return boolean true if residues were marked as deleted.
-  public boolean deleteRange(int start, int end)
-  {
-    boolean deleted = false;
-    int op = 0, prevop = -1, firstm = -1,
-        lastm = -1, postop = -1;
-    int width = 0; // zero'th column
-    if (length > 0)
-    {
-      // find operation bracketing start of the range
-      do
-      {
-        if (operation[op] != D)
-        {
-          width += range[prevop = op];
-        }
-        op++;
-      }
-      while (op < length && width < start);
-    }
-    if (width < start)
-    {
-      // run off end - add more operations up to deletion.
-      addInsertion(start - width);
-    }
-    else
-    {
-      // edit existing operations.
-      op = prevop;
-      width -= range[prevop];
-      int[] oldrange = range;
-      char[] oldops = operation;
-      range = new int[oldrange.length];
-      operation = new char[oldops.length];
-      if (op < length)
-      {
-        do
-        {
-          if (operation[op] != D)
-          {
-            width += range[postop = op];
-          }
-          op++;
-        }
-        while (op < length && width <= end);
-      }
-    }
-    if (deleted == true)
-    {
-      addDeleted(end - start + 1);
-    }
-    return deleted;
-  }
-*/
-  /**
-   * Return an ENSEMBL style cigar string where D may indicates excluded parts of seq
-   * @return String of form ([0-9]+[IMD])+
-   */
-  public String getCigarstring()
-  {
-    StringBuffer cigarString = new StringBuffer();
-    for (int i = 0; i < length; i++)
-    {
-      cigarString.append("" + range[i]);
-      cigarString.append(operation[i]);
-    }
-    return cigarString.toString();
-  }
-}
+package jalview.datamodel;
+
+import java.util.Vector;
+
+public abstract class CigarBase
+{
+  /**
+   * Base class for compact idiosyncratic representation of gaps and aligned residues
+   * Regards to Tom Oldfield for his DynamicArray class.
+   * 17th July 2006
+   * Not thread safe.
+   */
+  public CigarBase()
+  {
+    // nothing to be done (probably)
+  }
+
+  protected int length = 0;
+  protected int _inc_length = 10; // extension range for addition of new operations
+  protected char[] operation = null;
+  protected int[] range = null;
+  /**
+   * Range of Hidden residues in seq (translated as deleted in seq)
+   */
+  public static final char D = 'D'; /**
+  * Range of insertions to seq
+  */
+ public static final char I = 'I'; /**
+  * Range of aligned residues
+  */
+ public static final char M = 'M';
+  static protected final char _case_shift = 'a' - 'A';
+  /**
+   * Ugly function to get edited sequence string, start and end symbol positions and the deletion regions as an array of int pairs
+   * May return null for an empty cigar string.
+   * May return null for deletion ranges if there are none.
+   * @param reference - the symbol sequence to apply the cigar operations to (or null if no sequence)
+   * @param GapChar - the symbol to use for Insert operations
+   * @return Object[] { String, int[] {start, startcol, end, endcol}, int[][3] {start, end, col} or null} the gapped sequence, first and last residue index, and the deletion ranges on the reference sequence
+   */
+  public Object[] getSequenceAndDeletions(String reference, char GapChar)
+  {
+    int rlength=0;
+    int[][] deletions = new int[length][];
+    int[][] trunc_deletions = null;
+    StringBuffer sq = new StringBuffer();
+    int cursor = 0, alcursor=0,start = 0, startpos=0, end = 0, endpos=0, delcount = -1;
+    boolean consecutive_del = false;
+    if (length == 0)
+    {
+      return null;
+    }
+    if (reference!=null)
+      rlength=reference.length();
+    boolean modstart = true;
+    for (int i = 0; i < length; i++)
+    {
+      switch (operation[i])
+      {
+        case D:
+          if (!consecutive_del)
+          {
+            deletions[++delcount] = new int[]
+                {
+                cursor, 0, alcursor};
+          }
+          cursor += range[i];
+          deletions[delcount][1] = cursor - 1;
+          consecutive_del = true;
+          break;
+        case I:
+          consecutive_del = false;
+          for (int r = 0; r < range[i]; r++)
+          {
+            sq.append(GapChar);
+            alcursor++;
+          }
+          break;
+        case M:
+          consecutive_del = false;
+          if (modstart)
+          {
+            start = cursor;
+            startpos=alcursor;
+            modstart = false;
+          }
+          if (reference!=null) {
+            int sbend = cursor+range[i];
+            if (sbend>rlength) {
+              sq.append(reference.substring(cursor, rlength));
+              while (sbend-- >= rlength)
+              {
+                sq.append(GapChar);
+              }
+            } else {
+              sq.append(reference.substring(cursor, sbend));
+            }
+          }
+          alcursor+=range[i];
+          cursor += range[i];
+          end = cursor - 1;
+          endpos = alcursor;
+          break;
+        default:
+          throw new Error("Unknown SeqCigar operation '" + operation[i] + "'");
+      }
+    }
+    if (++delcount > 0)
+    {
+      trunc_deletions = new int[delcount][];
+      System.arraycopy(deletions, 0, trunc_deletions, 0, delcount);
+    }
+    deletions = null;
+    return new Object[]
+        {
+        ((reference!=null) ? sq.toString() : null),
+        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
+   * @return object[] {char[] operation, int[] range}
+   * @throws java.lang.Exception for improperly formated cigar strings or ones with unknown operations
+   */
+  public static Object[] parseCigarString(String cigarString)
+      throws Exception
+  {
+    int ops = 0;
+    for (int i = 0, l = cigarString.length(); i < l; i++)
+    {
+      char c = cigarString.charAt(i);
+      if (c == M || c == (M - _case_shift) || c == I || c == (I - _case_shift) ||
+          c == D || c == (D - _case_shift))
+      {
+        ops++;
+      }
+    }
+    char[] operation = new char[ops];
+    int[] range = new int[ops];
+    int op = 0;
+    int i = 0, l = cigarString.length();
+    while (i < l)
+    {
+      char c;
+      int j = i;
+      do
+      {
+        c = cigarString.charAt(j++);
+      }
+      while (c >= '0' && c <= '9' && j < l);
+      if (j >= l && c >= '0' && c <= '9')
+      {
+        throw new Exception("Unterminated cigar string.");
+      }
+      try
+      {
+        String rangeint = cigarString.substring(i, j - 1);
+        range[op] = Integer.parseInt(rangeint);
+        i = j;
+      }
+      catch (Exception e)
+      {
+        throw new Error("Implementation bug in parseCigarString");
+      }
+      if (c >= 'a' && c <= 'z')
+      {
+        c -= _case_shift;
+      }
+      if ( (c == M || c == I || c == D))
+      {
+        operation[op++] = c;
+      }
+      else
+      {
+        throw new Exception("Unexpected operation '" + c +
+                            "' in cigar string (position " + i + " in '" +
+                            cigarString + "'");
+      }
+    }
+    return new Object[]
+        {
+        operation, range};
+  }
+
+  /**
+   * add an operation to cigar string
+   * @param op char
+   * @param range int
+   */
+  public void addOperation(char op, int range)
+  {
+    if (op >= 'a' && op <= 'z')
+    {
+      op -= _case_shift;
+    }
+    if (op != M && op != D && op != I)
+    {
+      throw new Error("Implementation error. Invalid operation string.");
+    }
+    if (range<=0)
+      throw new Error("Invalid range string (must be non-zero positive number)");
+    int lngth = 0;
+    if (operation == null)
+    {
+      this.operation = new char[_inc_length];
+      this.range = new int[_inc_length];
+    }
+    if (length + 1 == operation.length)
+    {
+      char[] ops = this.operation;
+      this.operation = new char[length + 1 + _inc_length];
+      System.arraycopy(ops, 0, this.operation, 0, length);
+      ops = null;
+      int[] rng = this.range;
+      this.range = new int[length + 1 + _inc_length];
+      System.arraycopy(rng, 0, this.range, 0, length);
+      rng = null;
+    }
+    if ((length>0) && (operation[length-1]==op))
+      length--; // modify existing operation.
+    else
+      this.range[length]=0; // reset range
+    this.operation[length] = op;
+    this.range[length++] += range;
+  }
+
+  /**
+   * semi-efficient insert an operation on the current cigar string set at column pos (from 1)
+   * NOTE: Insertion operations simply extend width of cigar result - affecting registration of alignment
+   * Deletion ops will shorten length of result - and affect registration of alignment
+   * Match ops will also affect length of result - affecting registration of alignment
+   * (ie "10M".insert(4,I,3)->"4M3I3M") - (replace?)
+   * (ie "10M".insert(4,D,3)->"4M3D3M") - (shortens alignment)
+   * (ie "5I5M".insert(4,I,3)->"8I5M") - real insertion
+   * (ie "5I5M".insert(4,D,3)->"4I2D3M") - shortens aligment - I's are removed, Ms changed to Ds
+   * (ie "10M".insert(4,M,3)->"13M")  - lengthens - Is changed to M, Ds changed to M.
+   * (ie "5I5M".insert(4,M,3)->"4I8M") - effectively shifts sequence left by 1 residue and extends it by 3
+   * ( "10D5M".insert(-1,M,3)->"3M7D5M")
+   * ( "10D5M".insert(0,M,3)->"7D8M")
+   * ( "10D5M".insert(1,M,3)->"10D8M")
+   *
+   * ( "1M10D5M".insert(0,M,3)->"1M10D8M")
+   * ( "1M10D5M".insert(1,M,3)->"
+   *
+   * if pos is beyond width - I operations are added before the operation
+   * @param pos int -1, 0-length of visible region, or greater to append new ops (with insertions in between)
+   * @param op char
+   * @param range int
+  public void addOperationAt(int pos, char op, int range)
+  {
+    int cursor = -1; // mark the position for the current operation being edited.
+    int o = 0;
+    boolean last_d = false; // previous op was a deletion.
+    if (pos < -1)
+      throw new Error("pos<-1 is not supported.");
+    while (o<length) {
+      if (operation[o] != D)
+      {
+        if ( (cursor + this.range[o]) < pos)
+        {
+          cursor += this.range[o];
+          o++;
+          last_d=false;
+        }
+        else
+        {
+          break;
+        }
+      }
+      else {
+        last_d=true;
+        o++;
+      }
+    }
+    if (o==length) {
+      // must insert more operations before pos
+      if (pos-cursor>0)
+        addInsertion(pos-cursor);
+      // then just add the new operation. Regardless of what it is.
+      addOperation(op, range);
+    } else {
+      int diff = pos - cursor;
+
+      int e_length = length-o; // new edit operation array length.
+      // diff<0 - can only happen before first insertion or match. - affects op and all following
+      // dif==0 - only when at first position of existing op -
+      // diff>0 - must preserve some existing operations
+      int[] e_range = new int[e_length];
+      System.arraycopy(this.range, o, e_range, 0, e_length);
+      char[] e_op = new char[e_length];
+      System.arraycopy(this.operation, o, e_op, 0, e_length);
+      length = o; // can now use add_operation to extend list.
+      int e_o=0; // current operation being edited.
+      switch (op) {
+        case M:
+          switch (e_op[e_o])
+          {
+            case M:
+              if (last_d && diff <= 0)
+              {
+                // reduce D's, if possible
+                if (range<=this.range[o-1]) {
+                  this.range[o - 1] -= range;
+                } else {
+                  this.range[o-1]=0;
+                }
+                if (this.range[o-1]==0)
+                  o--; // lose this op.
+              }
+              e_range[e_o] += range; // just add more matched residues
+              break;
+            case I:
+              // change from insertion to match
+              if (last_d && diff<=0)
+              {
+                // reduce D's, if possible
+                if (range<=this.range[o-1]) {
+                  this.range[o - 1] -= range;
+                } else {
+                  this.range[o-1]=0;
+                }
+                if (this.range[o-1]==0)
+                  o--; // lose this op.
+              }
+              e_range[e_o]
+                    break;
+                default:
+                  throw new Inp
+                      }
+
+                      break;
+                case I:
+                  break;
+                case D:
+              }
+          break;
+        default:
+          throw new Error("Implementation Error: Unknown operation in addOperation!");
+      }
+      // finally, add remaining ops.
+      while (e_o<e_length) {
+        addOperation(e_op[e_o], e_range[e_o]);
+        e_o++;
+      }
+    }
+  }
+**/
+  /**
+   * 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 int deleteRange(int start, int end) {
+    int deleted=0;
+    if (length==0) {
+      // nothing to do here
+      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.");
+    // find beginning
+    int cursor = 0; // mark the position for the current operation being edited.
+    int rlength=1+end-start; // number of positions to delete
+    int oldlen=length;
+    int o = 0;
+    boolean editing=false;
+    char[] oldops = operation;
+    int[] oldrange = range;
+    length=0;
+    operation = null;
+    range = null;
+    compact_operations();
+    while (o<oldlen && cursor<=end && rlength>0) {
+      if (oldops[o] == D) {
+        // absorbed into new deleted region.
+        addDeleted(oldrange[o++]);
+        continue;
+      }
+
+      int remain = oldrange[o]; // number of op characters left to edit
+      if (!editing) {
+        if ( (cursor + remain) <= start)
+        {
+          addOperation(oldops[o],oldrange[o]);
+          cursor+=oldrange[o++];
+          continue; // next operation
+        }
+        editing=true;
+        // add operations before hidden region
+        if (start-cursor>0) {
+          addOperation(oldops[o], start- cursor);
+          remain -= start - cursor;
+        }
+      }
+      // start inserting new ops
+      if (o<oldlen && editing && rlength>0 && remain>0) {
+        switch (oldops[o]) {
+          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.
+              rlength=0;
+              remain=0;
+            }
+            break;
+          case I:
+            if (remain-rlength>0) {
+              // only remove some gaps
+              addInsertion(remain-rlength);
+              rlength=0;
+            }
+            break;
+          case D:
+            throw new Error("Implementation error."); // do nothing;
+          default:
+            throw new Error("Implementation Error! Unknown operation '"+oldops[o]+"'");
+        }
+        rlength-=remain;
+        remain = oldrange[++o]; // number of op characters left to edit
+      }
+    }
+    // add remaining
+    while (o<oldlen) {
+      addOperation(oldops[o],oldrange[o++]);
+    }
+    //if (cursor<(start+1)) {
+      // 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.addElement(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.elementAt(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
+   * @return int number of residues hidden, matched, or gaps inserted into sequence
+   */
+  public int getFullWidth()
+  {
+    int w = 0;
+    if (range != null)
+    {
+      for (int i = 0; i < length; i++)
+      {
+        w += range[i];
+      }
+    }
+    return w;
+  }
+
+  /**
+   * Visible length of aligned sequence
+   * @return int length of including gaps and less hidden regions
+   */
+  public int getWidth()
+  {
+    int w = 0;
+    if (range != null)
+    {
+      for (int i = 0; i < length; i++)
+      {
+        if (operation[i] == M || operation[i] == I)
+        {
+          w += range[i];
+        }
+      }
+    }
+    return w;
+  }
+  /**
+   * mark a range of inserted residues
+   * @param range int
+   */
+  public void addInsertion(int range)
+  {
+    this.addOperation(I, range);
+  }
+
+  /**
+   * mark the next range residues as hidden (not aligned) or deleted
+   * @param range int
+   */
+  public void addDeleted(int range)
+  {
+    this.addOperation(D, range);
+  }
+
+  /**
+   * Modifies operation list to delete columns from start to end (inclusive)
+   * editing will remove insertion operations, and convert matches to deletions
+   * @param start alignment column
+   * @param end alignment column
+   * @return boolean true if residues were marked as deleted.
+  public boolean deleteRange(int start, int end)
+  {
+    boolean deleted = false;
+    int op = 0, prevop = -1, firstm = -1,
+        lastm = -1, postop = -1;
+    int width = 0; // zero'th column
+    if (length > 0)
+    {
+      // find operation bracketing start of the range
+      do
+      {
+        if (operation[op] != D)
+        {
+          width += range[prevop = op];
+        }
+        op++;
+      }
+      while (op < length && width < start);
+    }
+    if (width < start)
+    {
+      // run off end - add more operations up to deletion.
+      addInsertion(start - width);
+    }
+    else
+    {
+      // edit existing operations.
+      op = prevop;
+      width -= range[prevop];
+      int[] oldrange = range;
+      char[] oldops = operation;
+      range = new int[oldrange.length];
+      operation = new char[oldops.length];
+      if (op < length)
+      {
+        do
+        {
+          if (operation[op] != D)
+          {
+            width += range[postop = op];
+          }
+          op++;
+        }
+        while (op < length && width <= end);
+      }
+    }
+    if (deleted == true)
+    {
+      addDeleted(end - start + 1);
+    }
+    return deleted;
+  }
+*/
+  /**
+   * Return an ENSEMBL style cigar string where D may indicates excluded parts of seq
+   * @return String of form ([0-9]+[IMD])+
+   */
+  public String getCigarstring()
+  {
+    StringBuffer cigarString = new StringBuffer();
+    for (int i = 0; i < length; i++)
+    {
+      cigarString.append("" + range[i]);
+      cigarString.append(operation[i]);
+    }
+    return cigarString.toString();
+  }
+}
-- 
1.7.10.2