X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FCigarBase.java;h=d44d5993a881a4f546eaa3ac356dc76e2abcd8c2;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=a36bf76d717a628d1442f3ea561a06b4b2db39f1;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git

diff --git a/src/jalview/datamodel/CigarBase.java b/src/jalview/datamodel/CigarBase.java
index a36bf76..d44d599 100644
--- a/src/jalview/datamodel/CigarBase.java
+++ b/src/jalview/datamodel/CigarBase.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -18,7 +18,7 @@
  */
 package jalview.datamodel;
 
-import java.util.Vector;
+import java.util.*;
 
 public abstract class CigarBase
 {
@@ -58,18 +58,21 @@ public abstract class CigarBase
    */
   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++)
     {
@@ -99,22 +102,26 @@ public abstract class CigarBase
           if (modstart)
           {
             start = cursor;
-            startpos=alcursor;
+            startpos = alcursor;
             modstart = false;
           }
-          if (reference!=null) {
-            int sbend = cursor+range[i];
-            if (sbend>rlength) {
+          if (reference != null)
+          {
+            int sbend = cursor + range[i];
+            if (sbend > rlength)
+            {
               sq.append(reference.substring(cursor, rlength));
               while (sbend-- >= rlength)
               {
                 sq.append(GapChar);
               }
-            } else {
+            }
+            else
+            {
               sq.append(reference.substring(cursor, sbend));
             }
           }
-          alcursor+=range[i];
+          alcursor += range[i];
           cursor += range[i];
           end = cursor - 1;
           endpos = alcursor;
@@ -131,29 +138,40 @@ public abstract class CigarBase
     deletions = null;
     return new Object[]
         {
-        ((reference!=null) ? sq.toString() : null),
-        new int[] {
+        ( (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
@@ -235,8 +253,10 @@ public abstract class CigarBase
     {
       throw new Error("Implementation error. Invalid operation string.");
     }
-    if (range<=0)
+    if (range <= 0)
+    {
       throw new Error("Invalid range string (must be non-zero positive number)");
+    }
     int lngth = 0;
     if (operation == null)
     {
@@ -254,10 +274,14 @@ 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;
   }
@@ -284,9 +308,9 @@ public abstract class CigarBase
    * @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.
+     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)
@@ -373,7 +397,7 @@ public abstract class CigarBase
               }
           break;
         default:
-          throw new Error("Implementation Error: Unknown operation in addOperation!");
+   throw new Error("Implementation Error: Unknown operation in addOperation!");
       }
       // finally, add remaining ops.
       while (e_o<e_length) {
@@ -381,95 +405,113 @@ public abstract class CigarBase
         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) {
+  public int deleteRange(int start, int end)
+  {
+    int deleted = 0;
+    if (length == 0)
+    {
       // nothing to do here
       return deleted;
     }
-    if (start<0 || start>end)
+    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 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 (!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]) {
+      if (o < oldlen && editing && rlength > 0 && remain > 0)
+      {
+        switch (oldops[o])
+        {
           case M:
-            if (rlength>remain) {
+            if (rlength > remain)
+            {
               addDeleted(remain);
-              deleted+=remain;
-            } else {
-              deleted+=rlength;
+              deleted += remain;
+            }
+            else
+            {
+              deleted += rlength;
               addDeleted(rlength);
-              if (remain-rlength>0)
-                this.addOperation(M,remain-rlength); // add remaining back.
-              rlength=0;
-              remain=0;
+              if (remain - rlength > 0)
+              {
+                this.addOperation(M, remain - rlength); // add remaining back.
+              }
+              rlength = 0;
+              remain = 0;
             }
             break;
           case I:
-            if (remain-rlength>0) {
+            if (remain - rlength > 0)
+            {
               // only remove some gaps
-              addInsertion(remain-rlength);
-              rlength=0;
+              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]+"'");
+            throw new Error("Implementation Error! Unknown operation '" +
+                            oldops[o] + "'");
         }
-        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);
+    // ran out of ops - nothing to do here ?
+    // addInsertion(start-cursor);
     //}
     return deleted;
   }
@@ -481,7 +523,7 @@ public abstract class CigarBase
    */
   public boolean hasDeletedRegions()
   {
-    for (int i = 0; i<length ; i++)
+    for (int i = 0; i < length; i++)
     {
       if (operation[i] == D)
       {
@@ -490,38 +532,49 @@ 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]) {
+    int cursor = 0, vcursor = 0;
+    for (int i = 0; i < length; i++)
+    {
+      switch (operation[i])
+      {
         case M:
-          cursor+=range[i];
+          cursor += range[i];
         case I:
-          vcursor+=range[i];
+          vcursor += range[i];
           break;
         case D:
-          dr.addElement(new int[] { vcursor, cursor, range[i]});
-          cursor+=range[i];
+          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[] 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];
+      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
@@ -558,6 +611,7 @@ public abstract class CigarBase
     }
     return w;
   }
+
   /**
    * mark a range of inserted residues
    * @param range int
@@ -582,8 +636,8 @@ public abstract class CigarBase
    * @param start alignment column
    * @param end alignment column
    * @return boolean true if residues were marked as deleted.
-  public boolean deleteRange(int start, int end)
-  {
+     public boolean deleteRange(int start, int end)
+     {
     boolean deleted = false;
     int op = 0, prevop = -1, firstm = -1,
         lastm = -1, postop = -1;
@@ -633,8 +687,8 @@ public abstract class CigarBase
       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])+