X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FCigarArray.java;h=17e9ea6fc65e17faad9b7f76656fa0f1a30cdf68;hb=2eea4e73351d902cd88923d863e9780fa57a0ee7;hp=8961425031ee64d06dfc87116c4b0234f95f1798;hpb=7570956d4b58f313d402cdd0507737c0628f1544;p=jalview.git

diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index 8961425..17e9ea6 100644
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -1,35 +1,65 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
+import java.util.Iterator;
+
 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)
@@ -38,137 +68,324 @@ 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
-   * @return Object[][]
+   * construct a cigar array from the current alignment, or just the subset of
+   * the current alignment specified by selectionGroup. Any columns marked as
+   * hidden in columnSelection will be marked as deleted in the array.
+   * 
+   * @param alignment
+   * @param columnSelection
+   * @param selectionGroup
    */
-  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)
+  public CigarArray(AlignmentI alignment, HiddenColumns hidden,
+          SequenceGroup selectionGroup)
+  {
+    this(constructSeqCigarArray(alignment, selectionGroup));
+    constructFromAlignment(alignment, hidden, selectionGroup);
+  }
+
+  private static int[] _calcStartEndBounds(AlignmentI alignment,
+          SequenceGroup selectionGroup)
+  {
+    int[] startend = new int[] { 0, 0, 0 };
+    if (selectionGroup != null)
+    {
+      startend[0] = selectionGroup.getSize();
+      startend[1] = selectionGroup.getStartRes();
+      startend[2] = selectionGroup.getEndRes(); // inclusive for start and end
+                                                // in
+      // SeqCigar constructor
+    }
+    else
+    {
+      startend[0] = alignment.getHeight();
+      startend[2] = alignment.getWidth() - 1;
+    }
+    return startend;
+  }
+
+  public static SeqCigar[] constructSeqCigarArray(AlignmentI alignment,
+          SequenceGroup selectionGroup)
+  {
+    SequenceI[] seqs = null;
+    int i, iSize;
+    int _startend[] = _calcStartEndBounds(alignment, selectionGroup);
+    int start = _startend[1], end = _startend[2];
+    if (selectionGroup != null)
+    {
+      iSize = selectionGroup.getSize();
+      seqs = selectionGroup.getSequencesInOrder(alignment);
+      start = selectionGroup.getStartRes();
+      end = selectionGroup.getEndRes(); // inclusive for start and end in
+      // SeqCigar constructor
+    }
+    else
+    {
+      iSize = alignment.getHeight();
+      seqs = alignment.getSequencesArray();
+      end = alignment.getWidth() - 1;
+    }
+    SeqCigar[] selseqs = new SeqCigar[iSize];
+    for (i = 0; i < iSize; i++)
+    {
+      selseqs[i] = new SeqCigar(seqs[i], start, end);
+    }
+    return selseqs;
+  }
+
+  /**
+   * internal constructor function - called by CigarArray(AlignmentI, ...);
+   * 
+   * @param alignment
+   * @param list
+   *          - vector of visible regions as returned from
+   *          columnSelection.getHiddenColumns()
+   * @param selectionGroup
+   */
+  private void constructFromAlignment(AlignmentI alignment,
+          HiddenColumns hidden, SequenceGroup selectionGroup)
+  {
+    int[] _startend = _calcStartEndBounds(alignment, selectionGroup);
+    int start = _startend[1];
+    int end = _startend[2];
+    // now construct the CigarArray operations
+    if (hidden != null)
+    {
+      int[] region;
+      int hideStart;
+      int hideEnd;
+      int last = start;
+
+      Iterator<int[]> regions = hidden.getBoundedIterator(start, end);
+      while (regions.hasNext())
+      {
+        region = regions.next();
+        hideStart = region[0];
+        hideEnd = region[1];
+
+        // truncate region at start if last falls in region
+        if ((hideStart < last) && (hideEnd >= last))
+        {
+          hideStart = last;
+        }
+
+        // truncate region at end if end falls in region
+        if (hideEnd > end) // already checked that hideStart<=end
+        {
+          hideEnd = end;
+        }
+
+        /**
+         * form operations...
+         */
+        if (last < hideStart)
         {
-          sqanddels[c] = getSequenceAndDeletions(refString, GapChar);
-        } else {
-          sqanddels[c] = null;
+          addOperation(CigarArray.M, hideStart - last);
         }
+        addOperation(CigarArray.D, 1 + hideEnd - hideStart);
+        last = hideEnd + 1;
+      }
+
+      // Final match if necessary.
+      if (last <= end)
+      {
+        addOperation(CigarArray.M, end - last + 1);
       }
-      return sqanddels;
     }
+    else
+    {
+      addOperation(CigarArray.M, end - start + 1);
+    }
+  }
+
+  /**
+   * @see CigarBase.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 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 where deletion occured 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
-    for (int i=0; i<length; i++) {
-      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.add(new Integer(vcursor-1)); // index of left hand column of hidden region boundary
-        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--;
-        for (int s=0; s<refCigars.length; s++) {
-          refCigars[s].deleteRange(delstart, delend);
+        /*
+         * 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)
+    if (delpos != null)
     {
-      int[] pos=new int[delpos.size()];
-      for (int k = 0, l = delpos.size(); k < l; k++) {
-        pos[k] = ((Integer) delpos.get(k)).intValue();
-        delpos.set(k,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;
+      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;
   }
 }