X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FCigarArray.java;h=529891f6dacfdd3a1ae14fb8eca77600fa4f7df7;hb=2e7da637a195ff484f92a333675284f071657cd6;hp=9b60e566929ade7150328476a74cacf45f8557dd;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index 9b60e56..529891f 100644
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -1,206 +1,399 @@
-/*
- * 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;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.Vector;
+
+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;
+        }
+      }
+    }
+  }
+
+  /**
+   * 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
+   */
+  public CigarArray(AlignmentI alignment, ColumnSelection columnSelection,
+          SequenceGroup selectionGroup)
+  {
+    this(constructSeqCigarArray(alignment, selectionGroup));
+    constructFromAlignment(alignment,
+            columnSelection != null ? columnSelection.getHiddenColumns()
+                    : null, 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 columnSelection
+   *          - vector of visible regions as returned from
+   *          columnSelection.getHiddenColumns()
+   * @param selectionGroup
+   */
+  private void constructFromAlignment(AlignmentI alignment,
+          Vector columnSelection, SequenceGroup selectionGroup)
+  {
+    int[] _startend = _calcStartEndBounds(alignment, selectionGroup);
+    int start = _startend[1], end = _startend[2];
+    // now construct the CigarArray operations
+    if (columnSelection != null)
+    {
+      int[] region;
+      int hideStart, hideEnd;
+      int last = start;
+      for (int j = 0; last < end & j < columnSelection.size(); j++)
+      {
+        region = (int[]) columnSelection.elementAt(j);
+        hideStart = region[0];
+        hideEnd = region[1];
+        // edit hidden regions to selection range
+        if (hideStart < last)
+        {
+          if (hideEnd > last)
+          {
+            hideStart = last;
+          }
+          else
+          {
+            continue;
+          }
+        }
+
+        if (hideStart > end)
+        {
+          break;
+        }
+
+        if (hideEnd > end)
+        {
+          hideEnd = end;
+        }
+
+        if (hideStart > hideEnd)
+        {
+          break;
+        }
+        /**
+         * form operations...
+         */
+        if (last < hideStart)
+        {
+          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);
+      }
+    }
+    else
+    {
+      addOperation(CigarArray.M, end - start + 1);
+    }
+  }
+
+  /**
+   * @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;
+  }
+}