X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FCigarArray.java;h=6fef9a41527181cce7fe7bd239d34a3c469aff8d;hb=9e9b624ed84ec54b959e05a0ab8554416525f4e2;hp=9b60e566929ade7150328476a74cacf45f8557dd;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index 9b60e56..6fef9a4 100644
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -1,53 +1,60 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * 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/>.
  */
 package jalview.datamodel;
 
 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();
   }
 
   /**
    * isSeqCigarArray()
+   * 
    * @return boolean true if all refCigars resolve to a SeqCigar or a CigarCigar
    */
   public boolean isSeqCigarArray()
   {
     return seqcigararray;
   }
+
   /**
-   * Apply CIGAR operations to several cigars in parallel
-   * will throw an error if any of cigar are actually CigarArrays.
-   * @param cigar Cigar[]
+   * 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)
@@ -56,151 +63,190 @@ public class CigarArray extends CigarBase
       for (int c = 0; c < cigars.length; c++)
       {
         refCigars[c] = cigars[c];
-        if (! ( (cigars[c] instanceof SeqCigar)
-               || cigars[c] instanceof CigarCigar))
+        if (!((cigars[c] instanceof SeqCigar) || cigars[c] instanceof CigarCigar))
         {
           seqcigararray = false;
         }
       }
     }
   }
+
   /**
    * @see Cigar.getSequenceAndDeletions
-   * @param GapChar char
+   * @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.
-   * @param GapChar char
+   * 
+   * @return String formed by newline concatenated results of applying CIGAR
+   *         operations to each reference object in turn.
+   * @param GapChar
+   *          char
    * @return '\n' separated strings (empty results included as \n\n)
    */
   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) {
-        seqStrings.append( (String) sqanddels[c][0]);
+    for (int c = 0; c < refCigars.length; c++)
+    {
+      if (sqanddels[c] != null)
+      {
+        seqStrings.append((String) sqanddels[c][0]);
         sqanddels[c][0] = null;
       }
       seqStrings.append('\n');
     }
     return seqStrings.toString();
   }
+
   /**
    * return string results of applying cigar string to all reference cigars
-   * @param GapChar char
+   * 
+   * @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() {
-
-    return new CigarBase[] {};
-  }
-*/
+   * 
+   *         public CigarBase[] getEditedCigars() {
+   * 
+   *         return new CigarBase[] {}; }
+   */
   /**
-   * applyDeletions
-   * edits underlying refCigars to propagate deleted regions, and removes deletion
-   * operations from CigarArray operation list.
-   * @return int[] position after deletion occured and range of deletion in cigarArray or null if none occured
+   * applyDeletions edits underlying refCigars to propagate deleted regions, and
+   * removes deletion operations from CigarArray operation list.
+   * 
+   * @return int[] position after deletion occured and range of deletion in
+   *         cigarArray or null if none occured
    */
   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++) {
-           int d = refCigars[s].deleteRange(delstart, delend);
-           if (d>dmax)
-             dmax=d;
-         }
-         offset+=dmax; // shift in visible column coordinates
+        /*
+         * int dmax=0; for (int s=0; s<refCigars.length; s++) { int d =
+         * refCigars[s].deleteRange(delstart, delend); if (d>dmax) dmax=d; }
+         * offset+=dmax; // shift in visible column coordinates
          */
-        for (int s=0; s<refCigars.length; s++) {
+        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[] 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);
+        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)
+   * 
+   * @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;
   }
 }