X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FCigarArray.java;h=c17e01eecbbb9b336a63369fb0c306d6c9e2535d;hb=449db06a788539e8ea7463ff4b56f012280994d0;hp=33e91a889315f4d0f89e7b61618c59e03e302500;hpb=108d9a136d1794445f2169c04d80b7662085390d;p=jalview.git

diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index 33e91a8..c17e01e 100644
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -1,18 +1,38 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel;
 
-public class CigarArray extends CigarBase
+public class CigarArray
+    extends CigarBase
 {
-    /**
-     * Do CIGAR operations on a set of sequences from many other cigars
-     * BAD THINGS WILL HAPPEN IF A CIGARARRAY IS PASSED TO A CIGARARRAY
-     * or a CIGARCIGAR is given a CIGARARRAY to insert gaps into.
-     */
-    /**
-     * array of subject cigars
-     */
-    public CigarSimple refCigars[]=null;
-    private boolean seqcigararray=false;
-  private CigarArray() {
+  /**
+   * Do CIGAR operations on a set of sequences from many other cigars
+   * BAD THINGS WILL HAPPEN IF A CIGARARRAY IS PASSED TO A CIGARARRAY
+   * or a CIGARCIGAR is given a CIGARARRAY to insert gaps into.
+   */
+  /**
+   * array of subject cigars
+   */
+  public CigarSimple refCigars[] = null;
+  private boolean seqcigararray = false;
+  private CigarArray()
+  {
     super();
   }
 
@@ -24,12 +44,14 @@ public class CigarArray extends CigarBase
   {
     return seqcigararray;
   }
+
   /**
    * Apply CIGAR operations to several cigars in parallel
    * will throw an error if any of cigar are actually CigarArrays.
    * @param cigar Cigar[]
    */
-  public CigarArray(CigarSimple[] cigars) {
+  public CigarArray(CigarSimple[] cigars)
+  {
     super();
     seqcigararray = true;
     if (cigars != null && cigars.length > 0)
@@ -46,27 +68,34 @@ public class CigarArray extends CigarBase
       }
     }
   }
+
   /**
    * @see Cigar.getSequenceAndDeletions
    * @param GapChar char
    * @return Object[][]
    */
-  protected Object[][] getArrayofSequenceAndDeletions(char GapChar) {
-      if (refCigars == null || refCigars.length == 0 || length == 0) {
-        return null;
+  protected Object[][] getArrayofSequenceAndDeletions(char GapChar)
+  {
+    if (refCigars == null || refCigars.length == 0 || length == 0)
+    {
+      return null;
+    }
+    Object[][] sqanddels = new Object[refCigars.length][];
+    for (int c = 0; c < refCigars.length; c++)
+    {
+      String refString = refCigars[c].getSequenceString(GapChar);
+      if (refString != null)
+      {
+        sqanddels[c] = getSequenceAndDeletions(refString, GapChar);
       }
-      Object[][] sqanddels = new Object[refCigars.length][];
-      for (int c=0; c<refCigars.length; c++) {
-        String refString = refCigars[c].getSequenceString(GapChar);
-        if (refString != null)
-        {
-          sqanddels[c] = getSequenceAndDeletions(refString, GapChar);
-        } else {
-          sqanddels[c] = null;
-        }
+      else
+      {
+        sqanddels[c] = null;
       }
-      return sqanddels;
     }
+    return sqanddels;
+  }
+
   /**
    * NOTE: this is an improper sequence string function
    * @return String formed by newline concatenated results of applying CIGAR operations to each reference object in turn.
@@ -75,12 +104,16 @@ public class CigarArray extends CigarBase
    */
   public String getSequenceString(char GapChar)
   {
-    if (length==0 || refCigars==null)
+    if (length == 0 || refCigars == null)
+    {
       return "";
+    }
     StringBuffer seqStrings = new StringBuffer();
     Object[][] sqanddels = getArrayofSequenceAndDeletions(GapChar);
-    for (int c=0; c<refCigars.length; c++) {
-      if (sqanddels[c]!=null) {
+    for (int c = 0; c < refCigars.length; c++)
+    {
+      if (sqanddels[c] != null)
+      {
         seqStrings.append( (String) sqanddels[c][0]);
         sqanddels[c][0] = null;
       }
@@ -88,32 +121,38 @@ public class CigarArray extends CigarBase
     }
     return seqStrings.toString();
   }
+
   /**
    * return string results of applying cigar string to all reference cigars
    * @param GapChar char
    * @return String[]
    */
-  public String[] getSequenceStrings(char GapChar) {
+  public String[] getSequenceStrings(char GapChar)
+  {
 
-    if (length==0 || refCigars==null || refCigars.length==0)
+    if (length == 0 || refCigars == null || refCigars.length == 0)
+    {
       return null;
+    }
     Object[][] sqanddels = getArrayofSequenceAndDeletions(GapChar);
     String[] seqs = new String[sqanddels.length];
-    for (int c=0; c<refCigars.length; c++) {
+    for (int c = 0; c < refCigars.length; c++)
+    {
       seqs[c] = (String) sqanddels[c][0];
     }
     return seqs;
   }
+
   /**
    * Combines the CigarArray cigar operations with the operations in each
    * reference cigar - creating a new reference cigar
    * @return Cigar[]
 
-  public CigarBase[] getEditedCigars() {
+     public CigarBase[] getEditedCigars() {
 
     return new CigarBase[] {};
-  }
-*/
+     }
+   */
   /**
    * applyDeletions
    * edits underlying refCigars to propagate deleted regions, and removes deletion
@@ -122,28 +161,37 @@ public class CigarArray extends CigarBase
    */
   public int[] applyDeletions()
   {
-    java.util.Vector delpos=null;
-    if (length==0)
+    java.util.Vector delpos = null;
+    if (length == 0)
+    {
       return null;
-    int cursor=0; // range counter for deletions
-    int vcursor=0; // visible column index
-    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++];
+    }
+    int cursor = 0; // range counter for deletions
+    int vcursor = 0; // visible column index
+    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++];
       }
       else
       {
-        if (delpos==null)
-          delpos=new java.util.Vector();
-        int delstart=cursor, delend=cursor+range[i]-1; // inclusive
-        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);
+        if (delpos == null)
+        {
+          delpos = new java.util.Vector();
+        }
+        int delstart = cursor, delend = cursor + range[i] - 1; // inclusive
+        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++) {
@@ -153,36 +201,44 @@ public class CigarArray extends CigarBase
          }
          offset+=dmax; // shift in visible column coordinates
          */
-        for (int s=0; s<refCigars.length; s++) {
+        for (int s = 0; s < refCigars.length; s++)
+        {
           int d = refCigars[s].deleteRange(delstart, delend);
         }
 
       }
     }
-    if (delpos!=null)
+    if (delpos != null)
     {
-      int[] pos=new int[delpos.size()*2];
-      for (int k = 0, l = delpos.size(); k < l; k++) {
-        int[] dr = ((int[]) delpos.elementAt(k));
-        pos[k*2] = dr[0];
-        pos[k*2+1] = dr[1];
-        delpos.setElementAt(null,k);
+      int[] pos = new int[delpos.size() * 2];
+      for (int k = 0, l = delpos.size(); k < l; k++)
+      {
+        int[] dr = ( (int[]) delpos.elementAt(k));
+        pos[k * 2] = dr[0];
+        pos[k * 2 + 1] = dr[1];
+        delpos.setElementAt(null, k);
       }
-      delpos=null;
+      delpos = null;
       return pos;
     }
     return null;
   }
+
   /**
    *
    * @return SeqCigar[] or null if CigarArray is not a SeqCigarArray (ie it does not resolve to set of seqCigars)
    */
-  public SeqCigar[] getSeqCigarArray() {
+  public SeqCigar[] getSeqCigarArray()
+  {
     if (!isSeqCigarArray())
+    {
       return null;
+    }
     SeqCigar[] sa = new SeqCigar[refCigars.length];
-    for (int i=0; i<refCigars.length; i++)
+    for (int i = 0; i < refCigars.length; i++)
+    {
       sa[i] = (SeqCigar) refCigars[i];
+    }
     return sa;
   }
 }