X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FCigarArray.java;h=c17e01eecbbb9b336a63369fb0c306d6c9e2535d;hb=449db06a788539e8ea7463ff4b56f012280994d0;hp=447b4d016ed31087d81502042ae89e1ebc0ebd25;hpb=95789943eb181b1768a081e779a044bf595b6bf6;p=jalview.git

diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index 447b4d0..c17e01e 100644
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -1,117 +1,244 @@
-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[] {};
-  }
-}
+/*
+ * 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
+{
+  /**
+   * 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;
+  }
+}