Jalview 2.8 Source Header

[jalview.git] / src / jalview / util / MapList.java

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index 943705a..e584a13 100644 (file)
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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 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 file is part of Jalview.
  * 
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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.util;
 
@@ -333,20 +332,21 @@ public class MapList
    * addShift
    * 
    * @param pos
-   *                start position for shift (in original reference frame)
+   *          start position for shift (in original reference frame)
    * @param shift
-   *                length of shift
+   *          length of shift
    * 
-   * public void addShift(int pos, int shift) { int sidx = 0; int[] rshift=null;
-   * while (sidx<shifts.size() && (rshift=(int[]) shifts.elementAt(sidx))[0]<pos)
-   * sidx++; if (sidx==shifts.size()) shifts.insertElementAt(new int[] { pos,
-   * shift}, sidx); else rshift[1]+=shift; }
+   *          public void addShift(int pos, int shift) { int sidx = 0; int[]
+   *          rshift=null; while (sidx<shifts.size() && (rshift=(int[])
+   *          shifts.elementAt(sidx))[0]<pos) sidx++; if (sidx==shifts.size())
+   *          shifts.insertElementAt(new int[] { pos, shift}, sidx); else
+   *          rshift[1]+=shift; }
    */
   /**
    * shift from pos to To(pos)
    * 
    * @param pos
-   *                int
+   *          int
    * @return int shifted position in To, frameshift in From, direction of mapped
    *         symbol in To
    */
@@ -359,7 +359,7 @@ public class MapList
    * inverse of shiftFrom - maps pos in To to a position in From
    * 
    * @param pos
-   *                (in To)
+   *          (in To)
    * @return shifted position in From, frameshift in To, direction of mapped
    *         symbol in From
    */
@@ -484,9 +484,9 @@ public class MapList
    * find series of intervals mapping from start-end in the From map.
    * 
    * @param start
-   *                position in to map
+   *          position in to map
    * @param end
-   *                position in to map
+   *          position in to map
    * @return series of ranges in from map
    */
   public int[] locateInFrom(int start, int end)
@@ -505,9 +505,9 @@ public class MapList
    * find series of intervals mapping from start-end in the to map.
    * 
    * @param start
-   *                position in from map
+   *          position in from map
    * @param end
-   *                position in from map
+   *          position in from map
    * @return series of ranges in to map
    */
   public int[] locateInTo(int start, int end)
@@ -570,7 +570,7 @@ public class MapList
             {
               fe = i;
               endpos = endpos + endindx; // end of end token is within this
-                                          // interval
+              // interval
             }
             else
             {
@@ -597,7 +597,7 @@ public class MapList
             {
               fe = i;
               endpos = endpos - endindx; // end of end token is within this
-                                          // interval
+              // interval
             }
             else
             {
@@ -686,7 +686,7 @@ public class MapList
    * get the 'initial' position of mpos in To
    * 
    * @param mpos
-   *                position in from
+   *          position in from
    * @return position of first word in to reference frame
    */
   public int getToPosition(int mpos)
@@ -703,7 +703,7 @@ public class MapList
    * get range of positions in To frame for the mpos word in From
    * 
    * @param mpos
-   *                position in From
+   *          position in From
    * @return null or int[] first position in To for mpos, last position in to
    *         for Mpos
    */
@@ -973,4 +973,28 @@ public class MapList
     return new MapList(getToRanges(), getFromRanges(), getToRatio(),
             getFromRatio());
   }
+
+  /**
+   * test for containment rather than equivalence to another mapping
+   * 
+   * @param map
+   *          to be tested for containment
+   * @return true if local or mapped range map contains or is contained by this
+   *         mapping
+   */
+  public boolean containsEither(boolean local, MapList map)
+  {
+    if (local)
+    {
+      return ((getFromLowest() >= map.getFromLowest() && getFromHighest() <= map
+              .getFromHighest()) || (getFromLowest() <= map.getFromLowest() && getFromHighest() >= map
+              .getFromHighest()));
+    }
+    else
+    {
+      return ((getToLowest() >= map.getToLowest() && getToHighest() <= map
+              .getToHighest()) || (getToLowest() <= map.getToLowest() && getToHighest() >= map
+              .getToHighest()));
+    }
+  }
 }