X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FCigarArray.java;fp=src%2Fjalview%2Fdatamodel%2FCigarArray.java;h=9b60e566929ade7150328476a74cacf45f8557dd;hb=0f71bfca98457c30f1051f142c31b6aaa3e23ead;hp=0000000000000000000000000000000000000000;hpb=072fc418c393cbd2a40dfa1d3e46f90178b79572;p=jalview.git

diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
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+++ b/src/jalview/datamodel/CigarArray.java
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+/*
+ * 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
+ */
+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() {
+    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[]
+   */
+  public CigarArray(CigarSimple[] cigars) {
+    super();
+    seqcigararray = true;
+    if (cigars != null && cigars.length > 0)
+    {
+      refCigars = new CigarSimple[cigars.length];
+      for (int c = 0; c < cigars.length; c++)
+      {
+        refCigars[c] = cigars[c];
+        if (! ( (cigars[c] instanceof SeqCigar)
+               || cigars[c] instanceof CigarCigar))
+        {
+          seqcigararray = false;
+        }
+      }
+    }
+  }
+  /**
+   * @see Cigar.getSequenceAndDeletions
+   * @param GapChar char
+   * @return Object[][]
+   */
+  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);
+        } else {
+          sqanddels[c] = null;
+        }
+      }
+      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 '\n' separated strings (empty results included as \n\n)
+   */
+  public String getSequenceString(char GapChar)
+  {
+    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]);
+        sqanddels[c][0] = null;
+      }
+      seqStrings.append('\n');
+    }
+    return seqStrings.toString();
+  }
+  /**
+   * return string results of applying cigar string to all reference cigars
+   * @param GapChar char
+   * @return String[]
+   */
+  public String[] getSequenceStrings(char GapChar) {
+
+    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++) {
+      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[] {};
+  }
+*/
+  /**
+   * 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)
+      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++];
+      }
+      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);
+        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
+         */
+        for (int s=0; s<refCigars.length; s++) {
+          int d = refCigars[s].deleteRange(delstart, delend);
+        }
+
+      }
+    }
+    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);
+      }
+      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() {
+    if (!isSeqCigarArray())
+      return null;
+    SeqCigar[] sa = new SeqCigar[refCigars.length];
+    for (int i=0; i<refCigars.length; i++)
+      sa[i] = (SeqCigar) refCigars[i];
+    return sa;
+  }
+}