X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FMapping.java;h=69555e6f87ab63d29bb6aa357a0762979694c690;hb=59d682209891099d46b960509907c79e3fb276fe;hp=4daf7d4ac40198c37acbcfdab0c0a0ce242276e5;hpb=1698842ec6755d1995dae7c1a590efbfc8f6e4d5;p=jalview.git

diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java
index 4daf7d4..69555e6 100644
--- a/src/jalview/datamodel/Mapping.java
+++ b/src/jalview/datamodel/Mapping.java
@@ -1,201 +1,455 @@
-package jalview.datamodel;
-
-import jalview.util.MapList;
-
-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
-   */
-  MapList map=null;
-  /**
-   * The seuqence that map maps the associated seuqence to (if any).
-   */
-  SequenceI to=null;
-  public Mapping(MapList map) {
-    super();
-    this.map = map;
-  }
-  /**
-   * create a new mapping from
-   * @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)
-  {
-    map = new MapList(exon, is, i, j);
-  }
-
-  /**
-   * @return the map
-   */
-  public MapList getMap() {
-    return map;
-  }
-
-  /**
-   * @param map the map to set
-   */
-  public void setMap(MapList map) {
-    this.map = map;
-  }
-  public boolean equals(Mapping other) {
-    if (other==null)
-      return false;
-    if (other==this)
-      return true;
-    if ((map!=null && other.map==null) || (map==null && other.map!=null))
-      return false;
-    if (map.equals(other.map))
-      return true;
-    return false;
-  }
-  /**
-   * get the 'initial' position in the associated
-   * sequence for a position in the mapped reference frame
-   * @param mpos
-   * @return
-   */
-  public int getPosition(int mpos) 
-  {
-    if (map!=null) {
-      int[] mp = map.shiftTo(mpos);
-      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)}; 
-      }
-    }
-    return null;
-  }
-  /**
-   * width of mapped unit in associated sequence 
-   * 
-   */
-  public int getWidth() {
-    if (map!=null) {
-      return map.getFromRatio();
-    }
-    return 1;
-  }
-
-  /**
-   * width of unit in mapped reference frame
-   * @return
-   */
-  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.
-   * @param pos
-   * @return
-   */
-  public int getMappedPosition(int pos) {
-    if (map!=null) {
-      int[] mp = map.shiftFrom(pos);
-      if (mp!=null)
-      {
-        return mp[0];
-      }
-    }
-    return pos;
-  }
-  public int[] getMappedWord(int pos) {
-    if (map!=null) {
-      int[] mp = map.shiftFrom(pos);
-      if (mp!=null)
-      {
-        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 
-   * @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) {
-        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) {
-          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);
-        }
-        return vf;
-      }
-    }
-    if (false){
-      int[] word = getWord(f.getBegin());
-      if (word[0]<word[1]) 
-      {
-        f.setBegin(word[0]);
-      } else {
-        f.setBegin(word[1]);
-      }
-      word = getWord(f.getEnd());
-      if (word[0]>word[1]) 
-      {
-        f.setEnd(word[0]);
-      } 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
-   * @param from
-   * @param to
-   * @return
-   */
-  public int[] locateRange(int from, int to) {
-    //TODO
-    return null;
-  }
-  /**
-   * return a series of contigs on the mapped reference frame corresponding to
-   * the from,to interval on the associated sequence
-   * @param from
-   * @param to
-   * @return
-   */
-  public int[] locateMappedRange(int from, int to) {
-    //TODO 
-    return null;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 
+ * 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/>.
+ */
+package jalview.datamodel;
+
+import java.util.Vector;
+
+import jalview.util.MapList;
+
+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
+   */
+  MapList map = null;
+
+  /**
+   * The seuqence that map maps the associated seuqence to (if any).
+   */
+  SequenceI to = null;
+
+  public Mapping(MapList map)
+  {
+    super();
+    this.map = 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
+   */
+  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.
+   * 
+   * @param map2
+   */
+  public Mapping(Mapping map2)
+  {
+    if (map2 != this && map2 != null)
+    {
+      if (map2.map != null)
+      {
+        map = new MapList(map2.map);
+      }
+      to = map2.to;
+    }
+  }
+
+  /**
+   * @return the map
+   */
+  public MapList getMap()
+  {
+    return map;
+  }
+
+  /**
+   * @param map
+   *          the map to set
+   */
+  public void setMap(MapList map)
+  {
+    this.map = map;
+  }
+
+  /**
+   * Equals that compares both the to references and MapList mappings.
+   * 
+   * @param other
+   * @return
+   */
+  public boolean equals(Mapping other)
+  {
+    if (other == null)
+      return false;
+    if (other == this)
+      return true;
+    if (other.to != to)
+      return false;
+    if ((map != null && other.map == null)
+            || (map == null && other.map != null))
+      return false;
+    if (map.equals(other.map))
+      return true;
+    return false;
+  }
+
+  /**
+   * get the 'initial' position in the associated sequence for a position in the
+   * mapped reference frame
+   * 
+   * @param mpos
+   * @return
+   */
+  public int getPosition(int mpos)
+  {
+    if (map != null)
+    {
+      int[] mp = map.shiftTo(mpos);
+      if (mp != null)
+      {
+        return mp[0];
+      }
+    }
+    return mpos;
+  }
+
+  /**
+   * 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
+   * 
+   */
+  public int getWidth()
+  {
+    if (map != null)
+    {
+      return map.getFromRatio();
+    }
+    return 1;
+  }
+
+  /**
+   * width of unit in mapped reference frame
+   * 
+   * @return
+   */
+  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.
+   * 
+   * @param pos
+   * @return
+   */
+  public int getMappedPosition(int pos)
+  {
+    if (map != null)
+    {
+      int[] mp = map.shiftFrom(pos);
+      if (mp != null)
+      {
+        return mp[0];
+      }
+    }
+    return pos;
+  }
+
+  public int[] getMappedWord(int pos)
+  {
+    if (map != null)
+    {
+      int[] mp = map.shiftFrom(pos);
+      if (mp != null)
+      {
+        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
+   * 
+   * @param f
+   * @return one or more features corresponding to f
+   */
+  public SequenceFeature[] locateFeature(SequenceFeature f)
+  {
+    if (true)
+    { // f.getBegin()!=f.getEnd()) {
+      if (map != null)
+      {
+        int[] frange = map.locateInFrom(f.getBegin(), f.getEnd());
+        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 + 1));
+        }
+        return vf;
+      }
+    }
+    if (false) // else
+    {
+      int[] word = getWord(f.getBegin());
+      if (word[0] < word[1])
+      {
+        f.setBegin(word[0]);
+      }
+      else
+      {
+        f.setBegin(word[1]);
+      }
+      word = getWord(f.getEnd());
+      if (word[0] > word[1])
+      {
+        f.setEnd(word[0]);
+      }
+      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
+   * 
+   * @param from
+   * @param to
+   * @return int[] { from_i, to_i for i=1 to n contiguous regions in the
+   *         associated sequence}
+   */
+  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 mapped contigs mapped from a range on the associated
+   * sequence
+   * 
+   * @param from
+   * @param to
+   * @return
+   */
+  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;
+  }
+
+  public static void main(String[] args)
+  {
+    /**
+     * trite test of the intersectVisContigs method for a simple DNA -> Protein
+     * exon map and a range of visContigs
+     */
+    MapList fk = new MapList(new int[]
+    { 1, 6, 8, 13, 15, 23 }, new int[]
+    { 1, 7 }, 3, 1);
+    Mapping m = new Mapping(fk);
+    Mapping m_1 = m.intersectVisContigs(new int[]
+    { fk.getFromLowest(), fk.getFromHighest() });
+    Mapping m_2 = m.intersectVisContigs(new int[]
+    { 1, 7, 11, 20 });
+    System.out.println("" + m_1.map.getFromRanges());
+
+  }
+
+  /**
+   * 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();
+  }
+
+}