X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FMapping.java;h=7f2c24c99b22d706ebeea602df4a2d40908768fc;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=705cb15987292d9153f37480a5c994994230fa15;hpb=a878db688154da91ca7cc75a90c75d39bd193b3c;p=jalview.git

diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java
index 705cb15..7f2c24c 100644
--- a/src/jalview/datamodel/Mapping.java
+++ b/src/jalview/datamodel/Mapping.java
@@ -1,119 +1,436 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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 jalview.util.MapList;
 
-public class Mapping {
+import java.util.Iterator;
+import java.util.NoSuchElementException;
+import java.util.Vector;
+
+public class Mapping
+{
   /**
-   * Contains the
-   * start-end pairs mapping from 
-   * the associated sequence to the 
-   * sequence in the database 
-   * coordinate system
-   * it also takes care of step difference between coordinate systems
+   * An iterator that serves the aligned codon positions (with their protein
+   * products).
+   * 
+   * @author gmcarstairs
+   *
    */
-  MapList map=null;
+  public class AlignedCodonIterator implements Iterator<AlignedCodon>
+  {
+    /*
+     * The gap character used in the aligned sequence
+     */
+    private final char gap;
+
+    /*
+     * The characters of the aligned sequence e.g. "-cGT-ACgTG-"
+     */
+    private final char[] alignedSeq;
+
+    /*
+     * the sequence start residue
+     */
+    private int start;
+
+    /*
+     * Next position (base 0) in the aligned sequence
+     */
+    private int alignedColumn = 0;
+
+    /*
+     * Count of bases up to and including alignedColumn position
+     */
+    private int alignedBases = 0;
+
+    /*
+     * [start, end] from ranges (base 1)
+     */
+    private Iterator<int[]> fromRanges;
+
+    /*
+     * [start, end] to ranges (base 1)
+     */
+    private Iterator<int[]> toRanges;
+
+    /*
+     * The current [start, end] (base 1) from range
+     */
+    private int[] currentFromRange = null;
+
+    /*
+     * The current [start, end] (base 1) to range
+     */
+    private int[] currentToRange = null;
+
+    /*
+     * The next 'from' position (base 1) to process
+     */
+    private int fromPosition = 0;
+
+    /*
+     * The next 'to' position (base 1) to process
+     */
+    private int toPosition = 0;
+
+    /**
+     * Constructor
+     * 
+     * @param seq
+     *          the aligned sequence
+     * @param gapChar
+     */
+    public AlignedCodonIterator(SequenceI seq, char gapChar)
+    {
+      this.alignedSeq = seq.getSequence();
+      this.start = seq.getStart();
+      this.gap = gapChar;
+      fromRanges = map.getFromRanges().iterator();
+      toRanges = map.getToRanges().iterator();
+      if (fromRanges.hasNext())
+      {
+        currentFromRange = fromRanges.next();
+        fromPosition = currentFromRange[0];
+      }
+      if (toRanges.hasNext())
+      {
+        currentToRange = toRanges.next();
+        toPosition = currentToRange[0];
+      }
+    }
+
+    /**
+     * Returns true unless we have already traversed the whole mapping.
+     */
+    @Override
+    public boolean hasNext()
+    {
+      if (fromRanges.hasNext())
+      {
+        return true;
+      }
+      if (currentFromRange == null || fromPosition >= currentFromRange[1])
+      {
+        return false;
+      }
+      return true;
+    }
+
+    /**
+     * Returns the next codon's aligned positions, and translated value.
+     * 
+     * @throws NoSuchElementException
+     *           if hasNext() would have returned false
+     * @throws IncompleteCodonException
+     *           if not enough mapped bases are left to make up a codon
+     */
+    @Override
+    public AlignedCodon next() throws IncompleteCodonException
+    {
+      if (!hasNext())
+      {
+        throw new NoSuchElementException();
+      }
+
+      int[] codon = getNextCodon();
+      int[] alignedCodon = getAlignedCodon(codon);
+
+      String peptide = getPeptide();
+      return new AlignedCodon(alignedCodon[0], alignedCodon[1],
+              alignedCodon[2], peptide);
+    }
+
+    /**
+     * Retrieve the translation as the 'mapped to' position in the mapped to
+     * sequence.
+     * 
+     * @return
+     */
+    private String getPeptide()
+    {
+      // TODO should ideally handle toRatio other than 1 as well...
+      // i.e. code like getNextCodon()
+      if (toPosition <= currentToRange[1])
+      {
+        SequenceI seq = Mapping.this.to;
+        char pep = seq.getSequence()[toPosition - seq.getStart()];
+        toPosition++;
+        return String.valueOf(pep);
+      }
+      if (!toRanges.hasNext())
+      {
+        throw new NoSuchElementException("Ran out of peptide at position "
+                + toPosition);
+      }
+      currentToRange = toRanges.next();
+      toPosition = currentToRange[0];
+      return getPeptide();
+    }
+
+    /**
+     * Get the (base 1) dataset positions for the next codon in the mapping.
+     * 
+     * @throws IncompleteCodonException
+     *           if less than 3 remaining bases are mapped
+     */
+    private int[] getNextCodon()
+    {
+      int[] codon = new int[3];
+      int codonbase = 0;
+
+      while (codonbase < 3)
+      {
+        if (fromPosition <= currentFromRange[1])
+        {
+          /*
+           * Add next position from the current start-end range
+           */
+          codon[codonbase++] = fromPosition++;
+        }
+        else
+        {
+          /*
+           * Move to the next range - if there is one
+           */
+          if (!fromRanges.hasNext())
+          {
+            throw new IncompleteCodonException();
+          }
+          currentFromRange = fromRanges.next();
+          fromPosition = currentFromRange[0];
+        }
+      }
+      return codon;
+    }
+
+    /**
+     * Get the aligned column positions (base 0) for the given sequence
+     * positions (base 1), by counting ungapped characters in the aligned
+     * sequence.
+     * 
+     * @param codon
+     * @return
+     */
+    private int[] getAlignedCodon(int[] codon)
+    {
+      int[] aligned = new int[codon.length];
+      for (int i = 0; i < codon.length; i++)
+      {
+        aligned[i] = getAlignedColumn(codon[i]);
+      }
+      return aligned;
+    }
+
+    /**
+     * Get the aligned column position (base 0) for the given sequence position
+     * (base 1).
+     * 
+     * @param sequencePos
+     * @return
+     */
+    private int getAlignedColumn(int sequencePos)
+    {
+      /*
+       * allow for offset e.g. treat pos 8 as 2 if sequence starts at 7
+       */
+      int truePos = sequencePos - (start - 1);
+      while (alignedBases < truePos && alignedColumn < alignedSeq.length)
+      {
+        if (alignedSeq[alignedColumn++] != gap)
+        {
+          alignedBases++;
+        }
+      }
+      return alignedColumn - 1;
+    }
+
+    @Override
+    public void remove()
+    {
+      // ignore
+    }
+
+  }
+
+  /**
+   * Contains the start-end pairs mapping from the associated sequence to the
+   * sequence in the database coordinate system. It also takes care of step
+   * difference between coordinate systems.
+   */
+  MapList map = null;
+
   /**
-   * The seuqence that map maps the associated seuqence to (if any).
+   * The sequence that map maps the associated sequence to (if any).
    */
-  SequenceI to=null;
-  public Mapping(MapList map) {
+  SequenceI to = null;
+
+  public Mapping(MapList map)
+  {
     super();
     this.map = map;
   }
-  public Mapping(SequenceI to, MapList map) {
+
+  public Mapping(SequenceI to, MapList map)
+  {
     this(map);
     this.to = to;
   }
+
   /**
    * create a new mapping from
-   * @param to the sequence being mapped
-   * @param exon int[] {start,end,start,end} series on associated sequence
-   * @param is int[] {start,end,...} ranges on the reference frame being mapped to
-   * @param i step size on associated sequence
-   * @param j step size on mapped frame
+   * 
+   * @param to
+   *          the sequence being mapped
+   * @param exon
+   *          int[] {start,end,start,end} series on associated sequence
+   * @param is
+   *          int[] {start,end,...} ranges on the reference frame being mapped
+   *          to
+   * @param i
+   *          step size on associated sequence
+   * @param j
+   *          step size on mapped frame
    */
   public Mapping(SequenceI to, int[] exon, int[] is, int i, int j)
   {
     this(to, new MapList(exon, is, i, j));
   }
+
   /**
-   * create a duplicate (and independent) mapping object with 
-   * the same reference to any SequenceI being mapped to.
+   * create a duplicate (and independent) mapping object with the same reference
+   * to any SequenceI being mapped to.
+   * 
    * @param map2
    */
   public Mapping(Mapping map2)
   {
-    if (map2!=this && map2!=null) {
-      if (map2.map!=null) 
+    if (map2 != this && map2 != null)
+    {
+      if (map2.map != null)
       {
-        map=new MapList(map2.map);
+        map = new MapList(map2.map);
       }
       to = map2.to;
     }
   }
+
   /**
    * @return the map
    */
-  public MapList getMap() {
+  public MapList getMap()
+  {
     return map;
   }
 
   /**
-   * @param map the map to set
+   * @param map
+   *          the map to set
    */
-  public void setMap(MapList map) {
+  public void setMap(MapList map)
+  {
     this.map = map;
   }
+
   /**
    * Equals that compares both the to references and MapList mappings.
+   * 
    * @param other
-   * @return 
+   * @return
    */
-  public boolean equals(Mapping other) {
-    if (other==null)
+  @Override
+  public boolean equals(Object o)
+  {
+    // TODO should override Object.hashCode() to ensure that equal objects have
+    // equal hashcodes
+    if (o == null || !(o instanceof Mapping))
+    {
       return false;
-    if (other==this)
+    }
+    Mapping other = (Mapping) o;
+    if (other == this)
+    {
       return true;
-    if (other.to!=to)
+    }
+    if (other.to != to)
+    {
       return false;
-    if ((map!=null && other.map==null) || (map==null && other.map!=null))
+    }
+    if ((map != null && other.map == null)
+            || (map == null && other.map != null))
+    {
       return false;
-    if (map.equals(other.map))
+    }
+    if ((map == null && other.map == null) || map.equals(other.map))
+    {
       return true;
+    }
     return false;
   }
+
   /**
-   * get the 'initial' position in the associated
-   * sequence for a position in the mapped reference frame
+   * get the 'initial' position in the associated sequence for a position in the
+   * mapped reference frame
+   * 
    * @param mpos
    * @return
    */
-  public int getPosition(int mpos) 
+  public int getPosition(int mpos)
   {
-    if (map!=null) {
+    if (map != null)
+    {
       int[] mp = map.shiftTo(mpos);
-      if (mp!=null)
+      if (mp != null)
       {
         return mp[0];
       }
     }
     return mpos;
   }
-  public int[] getWord(int mpos) {
-    if (map!=null) {
-      int[] mp=map.shiftTo(mpos);
-      if (mp!=null) {
-        return new int[] {mp[0], mp[0]+mp[2]*(map.getFromRatio()-1)}; 
-      }
+
+  /**
+   * gets boundary in direction of mapping
+   * 
+   * @param position
+   *          in mapped reference frame
+   * @return int{start, end} positions in associated sequence (in direction of
+   *         mapped word)
+   */
+  public int[] getWord(int mpos)
+  {
+    if (map != null)
+    {
+      return map.getToWord(mpos);
     }
     return null;
   }
+
   /**
-   * width of mapped unit in associated sequence 
+   * width of mapped unit in associated sequence
    * 
    */
-  public int getWidth() {
-    if (map!=null) {
+  public int getWidth()
+  {
+    if (map != null)
+    {
       return map.getFromRatio();
     }
     return 1;
@@ -121,107 +438,271 @@ public class Mapping {
 
   /**
    * width of unit in mapped reference frame
+   * 
    * @return
    */
-  public int getMappedWidth() {
-    if (map!=null) {
+  public int getMappedWidth()
+  {
+    if (map != null)
+    {
       return map.getToRatio();
     }
     return 1;
   }
+
   /**
-   * get mapped position in the associated
-   * reference frame for position pos in the
-   * associated sequence.
+   * get mapped position in the associated reference frame for position pos in
+   * the associated sequence.
+   * 
    * @param pos
    * @return
    */
-  public int getMappedPosition(int pos) {
-    if (map!=null) {
+  public int getMappedPosition(int pos)
+  {
+    if (map != null)
+    {
       int[] mp = map.shiftFrom(pos);
-      if (mp!=null)
+      if (mp != null)
       {
         return mp[0];
       }
     }
     return pos;
   }
-  public int[] getMappedWord(int pos) {
-    if (map!=null) {
+
+  public int[] getMappedWord(int pos)
+  {
+    if (map != null)
+    {
       int[] mp = map.shiftFrom(pos);
-      if (mp!=null)
+      if (mp != null)
       {
-        return new int[] { mp[0], mp[0]+mp[2]*(map.getToRatio()-1)};
+        return new int[] { mp[0], mp[0] + mp[2] * (map.getToRatio() - 1) };
       }
     }
     return null;
   }
+
   /**
-   * locates the region of feature f in the associated sequence's reference frame 
+   * locates the region of feature f in the associated sequence's reference
+   * frame
+   * 
    * @param f
    * @return one or more features corresponding to f
    */
   public SequenceFeature[] locateFeature(SequenceFeature f)
   {
-    // this is a stopgap - features broken over exon boundaries will not be
-    // broken into a collection of feature fragments.
-    // TODO: implement creation of several features from a single feature on a discontinuously mapped seuqence
-    // need a function like int [] fromrange = map.getRange(from,to)
-    // need to make subgrouped sequence features.
-    if (true) {
-      if (map!=null) {
+    if (true)
+    { // f.getBegin()!=f.getEnd()) {
+      if (map != null)
+      {
         int[] frange = map.locateInFrom(f.getBegin(), f.getEnd());
-        SequenceFeature[] vf = new SequenceFeature[frange.length/2];
-        for (int i=0,v=0;i<frange.length;i+=2) {
+        if (frange == null)
+        {
+          // JBPNote - this isprobably not the right thing to doJBPHack
+          return null;
+        }
+        SequenceFeature[] vf = new SequenceFeature[frange.length / 2];
+        for (int i = 0, v = 0; i < frange.length; i += 2, v++)
+        {
           vf[v] = new SequenceFeature(f);
           vf[v].setBegin(frange[i]);
-          vf[v].setEnd(frange[i+1]);
-          if (frange.length>2)
-            vf[v].setDescription(f.getDescription() +"\nPart "+v);
+          vf[v].setEnd(frange[i + 1]);
+          if (frange.length > 2)
+          {
+            vf[v].setDescription(f.getDescription() + "\nPart " + (v + 1));
+          }
         }
         return vf;
       }
     }
-    if (false){
+    if (false) // else
+    {
       int[] word = getWord(f.getBegin());
-      if (word[0]<word[1]) 
+      if (word[0] < word[1])
       {
         f.setBegin(word[0]);
-      } else {
+      }
+      else
+      {
         f.setBegin(word[1]);
       }
       word = getWord(f.getEnd());
-      if (word[0]>word[1]) 
+      if (word[0] > word[1])
       {
         f.setEnd(word[0]);
-      } else {
+      }
+      else
+      {
         f.setEnd(word[1]);
       }
     }
     // give up and just return the feature.
     return new SequenceFeature[] { f };
   }
-      
-    /**
-   * return a series of contigs on the associated sequence corresponding to
-   * the from,to interval on the mapped reference frame
+
+  /**
+   * return a series of contigs on the associated sequence corresponding to the
+   * from,to interval on the mapped reference frame
+   * 
    * @param from
    * @param to
-   * @return
+   * @return int[] { from_i, to_i for i=1 to n contiguous regions in the
+   *         associated sequence}
    */
-  public int[] locateRange(int from, int to) {
-    //TODO
-    return null;
+  public int[] locateRange(int from, int to)
+  {
+    if (map != null)
+    {
+      if (from <= to)
+      {
+        from = (map.getToLowest() < from) ? from : map.getToLowest();
+        to = (map.getToHighest() > to) ? to : map.getToHighest();
+        if (from > to)
+        {
+          return null;
+        }
+      }
+      else
+      {
+        from = (map.getToHighest() > from) ? from : map.getToHighest();
+        to = (map.getToLowest() < to) ? to : map.getToLowest();
+        if (from < to)
+        {
+          return null;
+        }
+      }
+      return map.locateInFrom(from, to);
+    }
+    return new int[] { from, to };
   }
+
   /**
-   * return a series of contigs on the mapped reference frame corresponding to
-   * the from,to interval on the associated sequence
+   * return a series of mapped contigs mapped from a range on the associated
+   * sequence
+   * 
    * @param from
    * @param to
    * @return
    */
-  public int[] locateMappedRange(int from, int to) {
-    //TODO 
-    return null;
+  public int[] locateMappedRange(int from, int to)
+  {
+    if (map != null)
+    {
+
+      if (from <= to)
+      {
+        from = (map.getFromLowest() < from) ? from : map.getFromLowest();
+        to = (map.getFromHighest() > to) ? to : map.getFromHighest();
+        if (from > to)
+        {
+          return null;
+        }
+      }
+      else
+      {
+        from = (map.getFromHighest() > from) ? from : map.getFromHighest();
+        to = (map.getFromLowest() < to) ? to : map.getFromLowest();
+        if (from < to)
+        {
+          return null;
+        }
+      }
+      return map.locateInTo(from, to);
+    }
+    return new int[] { from, to };
+  }
+
+  /**
+   * return a new mapping object with a maplist modifed to only map the visible
+   * regions defined by viscontigs.
+   * 
+   * @param viscontigs
+   * @return
+   */
+  public Mapping intersectVisContigs(int[] viscontigs)
+  {
+    Mapping copy = new Mapping(this);
+    if (map != null)
+    {
+      int vpos = 0;
+      int apos = 0;
+      Vector toRange = new Vector();
+      Vector fromRange = new Vector();
+      for (int vc = 0; vc < viscontigs.length; vc += 2)
+      {
+        // find a mapped range in this visible region
+        int[] mpr = locateMappedRange(1 + viscontigs[vc],
+                viscontigs[vc + 1] - 1);
+        if (mpr != null)
+        {
+          for (int m = 0; m < mpr.length; m += 2)
+          {
+            toRange.addElement(new int[] { mpr[m], mpr[m + 1] });
+            int[] xpos = locateRange(mpr[m], mpr[m + 1]);
+            for (int x = 0; x < xpos.length; x += 2)
+            {
+              fromRange.addElement(new int[] { xpos[x], xpos[x + 1] });
+            }
+          }
+        }
+      }
+      int[] from = new int[fromRange.size() * 2];
+      int[] to = new int[toRange.size() * 2];
+      int[] r;
+      for (int f = 0, fSize = fromRange.size(); f < fSize; f++)
+      {
+        r = (int[]) fromRange.elementAt(f);
+        from[f * 2] = r[0];
+        from[f * 2 + 1] = r[1];
+      }
+      for (int f = 0, fSize = toRange.size(); f < fSize; f++)
+      {
+        r = (int[]) toRange.elementAt(f);
+        to[f * 2] = r[0];
+        to[f * 2 + 1] = r[1];
+      }
+      copy.setMap(new MapList(from, to, map.getFromRatio(), map
+              .getToRatio()));
+    }
+    return copy;
+  }
+
+  /**
+   * get the sequence being mapped to - if any
+   * 
+   * @return null or a dataset sequence
+   */
+  public SequenceI getTo()
+  {
+    return to;
+  }
+
+  /**
+   * set the dataset sequence being mapped to if any
+   * 
+   * @param tto
+   */
+  public void setTo(SequenceI tto)
+  {
+    to = tto;
   }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see java.lang.Object#finalize()
+   */
+  protected void finalize() throws Throwable
+  {
+    map = null;
+    to = null;
+    super.finalize();
+  }
+
+  public Iterator<AlignedCodon> getCodonIterator(SequenceI seq, char gapChar)
+  {
+    return new AlignedCodonIterator(seq, gapChar);
+  }
+
 }