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 (file)
--- 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;
 \r
 import java.util.Vector;\r
 \r
-\r
+import uk.ac.vamsas.objects.core.Local;\r
+import uk.ac.vamsas.objects.core.MapType;\r
+import uk.ac.vamsas.objects.core.Mapped;\r
 import uk.ac.vamsas.objects.core.RangeType;\r
 import uk.ac.vamsas.objects.core.Seg;\r
 \r
+/**\r
+ * Utilities for working with RangeType and MapType objects.\r
+ * Derived from bitter experience.\r
+ * @author JimP\r
+ *\r
+ */\r
 public class Range {\r
 \r
   /**\r
@@ -143,4 +151,134 @@ public class Range {
     }\r
     return null;\r
   }\r
+\r
+  public static int[] getIntervals(RangeType range)\r
+  {\r
+    int[] intervals=null;\r
+    Vector posList = new Vector();\r
+    if (range != null)\r
+    {\r
+      int[] se = null;\r
+      if (range.getSegCount() > 0 && range.getPosCount() > 0)\r
+      {\r
+        throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");\r
 }\r
+      if (range.getSegCount() > 0)\r
+      {\r
+        for (int s = 0, sSize = range.getSegCount(); s < sSize; s++)\r
+        {\r
+          se = getSegRange(range.getSeg(s), false);\r
+          posList.addElement(new Integer(se[0]));\r
+          posList.addElement(new Integer(se[1]));\r
+        }\r
+      }\r
+      else if (range.getPosCount() > 0)\r
+      {\r
+        int pos = range.getPos(0).getI();\r
+        for (int p = 0, pSize = range.getPosCount(); p < pSize; p++)\r
+        {\r
+          pos = range.getPos(p).getI();\r
+          posList.add(new Integer(pos));\r
+          posList.add(new Integer(pos));\r
+        }\r
+      }\r
+    }\r
+    if (posList != null && posList.size() > 0)\r
+    {\r
+      intervals=new int[posList.size()];\r
+      java.util.Enumeration e = posList.elements();\r
+      int i=0;\r
+      while (e.hasMoreElements())\r
+      {\r
+        intervals[i++] = ((Integer)e.nextElement()).intValue();\r
+      }\r
+    }\r
+    return intervals;\r
+  }\r
+  /**\r
+   * initialise a range type object from a set of start/end inclusive intervals\r
+   * @param mrt\r
+   * @param range\r
+   */\r
+  public static void initRangeType(RangeType mrt, int[] range)\r
+  {\r
+    for (int i=0; i<range.length; i+=2)\r
+    {\r
+      Seg vSeg = new Seg();\r
+      vSeg.setStart(range[i]);\r
+      vSeg.setEnd(range[i+1]);\r
+      vSeg.setInclusive(true);\r
+      mrt.addSeg(vSeg);\r
+    }\r
+  }\r
+\r
+  /**\r
+   * \r
+   * @param maprange where the from range is the local mapped range, and the to range is the 'mapped' range in the MapRangeType\r
+   * @param default unit for local\r
+   * @param default unit for mapped\r
+   * @return MapList\r
+   */\r
+  public static MapList parsemapType(MapType maprange, int localu, int mappedu)\r
+  {\r
+    MapList ml = null;\r
+    int[] localRange = getIntervals(maprange.getLocal());\r
+    int[] mappedRange = getIntervals(maprange.getMapped());\r
+    long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit() : localu;\r
+    long mu = maprange.getMapped().hasUnit() ? maprange.getMapped().getUnit() : mappedu;\r
+    ml = new MapList(localRange, mappedRange, (int)lu, (int)mu);\r
+    return ml;\r
+  }\r
+  /**\r
+   * Parse map with default units of 1,1\r
+   * @param map\r
+   * @return MapList representing map\r
+   */\r
+  public static MapList parsemapType(MapType map)\r
+  {\r
+    return parsemapType(map, 1, 1); \r
+  }\r
+\r
+  /**\r
+   * initialise a MapType object from a MapList object.\r
+   * @param maprange\r
+   * @param ml\r
+   * @param setUnits\r
+   */\r
+  public static void initMapType(MapType maprange, MapList ml, boolean setUnits)\r
+  {\r
+    initMapType(maprange, ml, setUnits, false);\r
+  }\r
+  /**\r
+   * \r
+   * @param maprange\r
+   * @param ml\r
+   * @param setUnits\r
+   * @param reverse - reverse MapList mapping for Local and Mapped ranges and units \r
+   */\r
+  public static void initMapType(MapType maprange, MapList ml, boolean setUnits, boolean reverse)\r
+  {\r
+    maprange.setLocal(new Local());\r
+    maprange.setMapped(new Mapped());\r
+    if (!reverse)\r
+      {\r
+      initRangeType(maprange.getLocal(), ml.getFromRanges());\r
+      initRangeType(maprange.getMapped(), ml.getToRanges());\r
+      } else {\r
+        initRangeType(maprange.getLocal(), ml.getToRanges());\r
+        initRangeType(maprange.getMapped(), ml.getFromRanges());\r
+      }\r
+    if (setUnits)\r
+    {\r
+      if (!reverse)\r
+      { \r
+        maprange.getLocal().setUnit(ml.getFromRatio());\r
+        maprange.getMapped().setUnit(ml.getToRatio());\r
+      } else {\r
+        maprange.getLocal().setUnit(ml.getToRatio());\r
+        maprange.getMapped().setUnit(ml.getFromRatio());\r
+      }\r
+    }\r
+  }\r
+\r
+}
\ No newline at end of file