From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 28 Jun 2007 20:12:32 +0000 (+0000)
Subject: added mapType utilities.
X-Git-Tag: Release_0.2~99
X-Git-Url: http://source.jalview.org/gitweb/?p=vamsas.git;a=commitdiff_plain;h=d6f378ff4d767169376e6f2489a00b75d8a36e39

added mapType utilities.


git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@421 be28352e-c001-0410-b1a7-c7978e42abec
---

diff --git a/src/uk/ac/vamsas/objects/utils/Range.java b/src/uk/ac/vamsas/objects/utils/Range.java
index b20cb5b..f66df31 100644
--- a/src/uk/ac/vamsas/objects/utils/Range.java
+++ b/src/uk/ac/vamsas/objects/utils/Range.java
@@ -2,10 +2,18 @@ package uk.ac.vamsas.objects.utils;
 
 import java.util.Vector;
 
-
+import uk.ac.vamsas.objects.core.Local;
+import uk.ac.vamsas.objects.core.MapType;
+import uk.ac.vamsas.objects.core.Mapped;
 import uk.ac.vamsas.objects.core.RangeType;
 import uk.ac.vamsas.objects.core.Seg;
 
+/**
+ * Utilities for working with RangeType and MapType objects.
+ * Derived from bitter experience.
+ * @author JimP
+ *
+ */
 public class Range {
 
   /**
@@ -143,4 +151,134 @@ public class Range {
     }
     return null;
   }
+
+  public static int[] getIntervals(RangeType range)
+  {
+    int[] intervals=null;
+    Vector posList = new Vector();
+    if (range != null)
+    {
+      int[] se = null;
+      if (range.getSegCount() > 0 && range.getPosCount() > 0)
+      {
+        throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
 }
+      if (range.getSegCount() > 0)
+      {
+        for (int s = 0, sSize = range.getSegCount(); s < sSize; s++)
+        {
+          se = getSegRange(range.getSeg(s), false);
+          posList.addElement(new Integer(se[0]));
+          posList.addElement(new Integer(se[1]));
+        }
+      }
+      else if (range.getPosCount() > 0)
+      {
+        int pos = range.getPos(0).getI();
+        for (int p = 0, pSize = range.getPosCount(); p < pSize; p++)
+        {
+          pos = range.getPos(p).getI();
+          posList.add(new Integer(pos));
+          posList.add(new Integer(pos));
+        }
+      }
+    }
+    if (posList != null && posList.size() > 0)
+    {
+      intervals=new int[posList.size()];
+      java.util.Enumeration e = posList.elements();
+      int i=0;
+      while (e.hasMoreElements())
+      {
+        intervals[i++] = ((Integer)e.nextElement()).intValue();
+      }
+    }
+    return intervals;
+  }
+  /**
+   * initialise a range type object from a set of start/end inclusive intervals
+   * @param mrt
+   * @param range
+   */
+  public static void initRangeType(RangeType mrt, int[] range)
+  {
+    for (int i=0; i<range.length; i+=2)
+    {
+      Seg vSeg = new Seg();
+      vSeg.setStart(range[i]);
+      vSeg.setEnd(range[i+1]);
+      vSeg.setInclusive(true);
+      mrt.addSeg(vSeg);
+    }
+  }
+
+  /**
+   * 
+   * @param maprange where the from range is the local mapped range, and the to range is the 'mapped' range in the MapRangeType
+   * @param default unit for local
+   * @param default unit for mapped
+   * @return MapList
+   */
+  public static MapList parsemapType(MapType maprange, int localu, int mappedu)
+  {
+    MapList ml = null;
+    int[] localRange = getIntervals(maprange.getLocal());
+    int[] mappedRange = getIntervals(maprange.getMapped());
+    long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit() : localu;
+    long mu = maprange.getMapped().hasUnit() ? maprange.getMapped().getUnit() : mappedu;
+    ml = new MapList(localRange, mappedRange, (int)lu, (int)mu);
+    return ml;
+  }
+  /**
+   * Parse map with default units of 1,1
+   * @param map
+   * @return MapList representing map
+   */
+  public static MapList parsemapType(MapType map)
+  {
+    return parsemapType(map, 1, 1); 
+  }
+
+  /**
+   * initialise a MapType object from a MapList object.
+   * @param maprange
+   * @param ml
+   * @param setUnits
+   */
+  public static void initMapType(MapType maprange, MapList ml, boolean setUnits)
+  {
+    initMapType(maprange, ml, setUnits, false);
+  }
+  /**
+   * 
+   * @param maprange
+   * @param ml
+   * @param setUnits
+   * @param reverse - reverse MapList mapping for Local and Mapped ranges and units 
+   */
+  public static void initMapType(MapType maprange, MapList ml, boolean setUnits, boolean reverse)
+  {
+    maprange.setLocal(new Local());
+    maprange.setMapped(new Mapped());
+    if (!reverse)
+      {
+      initRangeType(maprange.getLocal(), ml.getFromRanges());
+      initRangeType(maprange.getMapped(), ml.getToRanges());
+      } else {
+        initRangeType(maprange.getLocal(), ml.getToRanges());
+        initRangeType(maprange.getMapped(), ml.getFromRanges());
+      }
+    if (setUnits)
+    {
+      if (!reverse)
+      { 
+        maprange.getLocal().setUnit(ml.getFromRatio());
+        maprange.getMapped().setUnit(ml.getToRatio());
+      } else {
+        maprange.getLocal().setUnit(ml.getToRatio());
+        maprange.getMapped().setUnit(ml.getFromRatio());
+      }
+    }
+  }
+
+}
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