X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FCigarBase.java;h=0dfa84d2d177767ec994b795b09e3ef2a246a2f6;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=1e0705acc43dda0e01fcccac8c30ead4a9bdd13e;hpb=108d9a136d1794445f2169c04d80b7662085390d;p=jalview.git

diff --git a/src/jalview/datamodel/CigarBase.java b/src/jalview/datamodel/CigarBase.java
index 1e0705a..0dfa84d 100644
--- a/src/jalview/datamodel/CigarBase.java
+++ b/src/jalview/datamodel/CigarBase.java
@@ -1,13 +1,34 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
+import jalview.util.MessageManager;
+
 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
+   * 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()
@@ -16,93 +37,117 @@ public abstract class CigarBase
   }
 
   protected int length = 0;
-  protected int _inc_length = 10; // extension range for addition of new operations
+
+  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';
+  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
+   * 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 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;
+    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();
+    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++)
+      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(GapChar);
-            alcursor++;
+            sq.append(reference.substring(cursor, rlength));
+            while (sbend-- >= rlength)
+            {
+              sq.append(GapChar);
+            }
           }
-          break;
-        case M:
-          consecutive_del = false;
-          if (modstart)
+          else
           {
-            start = cursor;
-            startpos=alcursor;
-            modstart = false;
+            sq.append(reference.substring(cursor, sbend));
           }
-          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] + "'");
+        }
+        alcursor += range[i];
+        cursor += range[i];
+        end = cursor - 1;
+        endpos = alcursor;
+        break;
+      default:
+        throw new Error(MessageManager.formatMessage(
+                "error.unknown_seq_cigar_operation",
+                new String[] { new StringBuffer(operation[i]).toString() }));
       }
     }
     if (++delcount > 0)
@@ -111,46 +156,57 @@ public abstract class CigarBase
       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};
+    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)
+
+  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) {
+    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 {
+      }
+      else
+      {
         last = operation[i++];
       }
     }
   }
+
   /**
    * turn a cigar string into a series of operation range pairs
-   * @param cigarString String
+   * 
+   * @param cigarString
+   *          String
    * @return object[] {char[] operation, int[] range}
-   * @throws java.lang.Exception for improperly formated cigar strings or ones with unknown operations
+   * @throws java.lang.Exception
+   *           for improperly formated cigar strings or ones with unknown
+   *           operations
    */
   public static Object[] parseCigarString(String cigarString)
-      throws Exception
+          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))
+      if (c == M || c == (M - _case_shift) || c == I
+              || c == (I - _case_shift) || c == D || c == (D - _case_shift))
       {
         ops++;
       }
@@ -166,46 +222,50 @@ public abstract class CigarBase
       do
       {
         c = cigarString.charAt(j++);
-      }
-      while (c >= '0' && c <= '9' && j < l);
+      } while (c >= '0' && c <= '9' && j < l);
       if (j >= l && c >= '0' && c <= '9')
       {
-        throw new Exception("Unterminated cigar string.");
+        throw new Exception(
+                MessageManager
+                        .getString("exception.unterminated_cigar_string"));
       }
       try
       {
         String rangeint = cigarString.substring(i, j - 1);
         range[op] = Integer.parseInt(rangeint);
         i = j;
-      }
-      catch (Exception e)
+      } catch (Exception e)
       {
-        throw new Error("Implementation bug in parseCigarString");
+        throw new Error(
+                MessageManager
+                        .getString("error.implementation_bug_parse_cigar_string"));
       }
       if (c >= 'a' && c <= 'z')
       {
         c -= _case_shift;
       }
-      if ( (c == M || c == I || c == D))
+      if ((c == M || c == I || c == D))
       {
         operation[op++] = c;
       }
       else
       {
-        throw new Exception("Unexpected operation '" + c +
-                            "' in cigar string (position " + i + " in '" +
-                            cigarString + "'");
+        throw new Exception(MessageManager.formatMessage(
+                "exception.unexpected_operation_cigar_string_pos",
+                new String[] { new StringBuffer(c).toString(),
+                    Integer.valueOf(i).toString(), cigarString }));
       }
     }
-    return new Object[]
-        {
-        operation, range};
+    return new Object[] { operation, range };
   }
 
   /**
    * add an operation to cigar string
-   * @param op char
-   * @param range int
+   * 
+   * @param op
+   *          char
+   * @param range
+   *          int
    */
   public void addOperation(char op, int range)
   {
@@ -215,10 +275,19 @@ public abstract class CigarBase
     }
     if (op != M && op != D && op != I)
     {
-      throw new Error("Implementation error. Invalid operation string.");
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_invalid_operation_string"));
+    }
+    if (range == 0)
+    {
+      return; // No Operation to add.
+    }
+    if (range < 0)
+    {
+      throw new Error(
+              MessageManager.getString("error.invalid_range_string"));
     }
-    if (range<=0)
-      throw new Error("Invalid range string (must be non-zero positive number)");
     int lngth = 0;
     if (operation == null)
     {
@@ -236,234 +305,206 @@ public abstract class CigarBase
       System.arraycopy(rng, 0, this.range, 0, length);
       rng = null;
     }
-    if ((length>0) && (operation[length-1]==op))
+    if ((length > 0) && (operation[length - 1] == op))
+    {
       length--; // modify existing operation.
+    }
     else
-      this.range[length]=0; // reset range
+    {
+      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)->"
-   *
+   * 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++;
-      }
-    }
-  }
-**/
+   * 
+   * @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
+   * 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) {
+  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.");
+    if (start < 0 || start > end)
+    {
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_delete_range_out_of_bounds"));
+    }
     // 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 rlength = 1 + end - start; // number of positions to delete
+    int oldlen = length;
     int o = 0;
-    boolean editing=false;
+    boolean editing = false;
     char[] oldops = operation;
     int[] oldrange = range;
-    length=0;
+    length = 0;
     operation = null;
     range = null;
     compact_operations();
-    while (o<oldlen && cursor<=end && rlength>0) {
-      if (oldops[o] == D) {
+    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)
+      if (!editing)
+      {
+        if ((cursor + remain) <= start)
         {
-          addOperation(oldops[o],oldrange[o]);
-          cursor+=oldrange[o++];
+          addOperation(oldops[o], oldrange[o]);
+          cursor += oldrange[o++];
           continue; // next operation
         }
-        editing=true;
+        editing = true;
         // add operations before hidden region
-        if (start-cursor>0) {
-          addOperation(oldops[o], start- cursor);
+        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;
+      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.
             }
-            break;
-          case D:
-            throw new Error("Implementation error."); // do nothing;
-          default:
-            throw new Error("Implementation Error! Unknown operation '"+oldops[o]+"'");
+            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(
+                  MessageManager.getString("error.implementation_error")); // do
+                                                                           // nothing;
+        default:
+          throw new Error(MessageManager.formatMessage(
+                  "error.implementation_error_unknown_operation",
+                  new String[] { new StringBuffer(oldops[o]).toString() }));
         }
-        rlength-=remain;
+        rlength -= remain;
         remain = oldrange[++o]; // number of op characters left to edit
       }
     }
     // add remaining
-    while (o<oldlen) {
-      addOperation(oldops[o],oldrange[o++]);
+    while (o < oldlen)
+    {
+      addOperation(oldops[o], oldrange[o++]);
     }
-    //if (cursor<(start+1)) {
-      // ran out of ops - nothing to do here ?
-     // addInsertion(start-cursor);
-    //}
+    // 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).
+   * 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++)
+    for (int i = 0; i < length; i++)
     {
       if (operation[i] == D)
       {
@@ -472,41 +513,54 @@ public abstract class CigarBase
     }
     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)
+  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];
+    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)
+    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];
+    }
+    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
+   * 
+   * @return int number of residues hidden, matched, or gaps inserted into
+   *         sequence
    */
   public int getFullWidth()
   {
@@ -523,6 +577,7 @@ public abstract class CigarBase
 
   /**
    * Visible length of aligned sequence
+   * 
    * @return int length of including gaps and less hidden regions
    */
   public int getWidth()
@@ -540,9 +595,12 @@ public abstract class CigarBase
     }
     return w;
   }
+
   /**
    * mark a range of inserted residues
-   * @param range int
+   * 
+   * @param range
+   *          int
    */
   public void addInsertion(int range)
   {
@@ -551,7 +609,9 @@ public abstract class CigarBase
 
   /**
    * mark the next range residues as hidden (not aligned) or deleted
-   * @param range int
+   * 
+   * @param range
+   *          int
    */
   public void addDeleted(int range)
   {
@@ -561,64 +621,30 @@ public abstract class CigarBase
   /**
    * 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;
-  }
-*/
+   * 
+   * @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 an ENSEMBL style cigar string where D may indicates excluded parts
+   * of seq
+   * 
    * @return String of form ([0-9]+[IMD])+
    */
   public String getCigarstring()