X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Futils%2FRange.java;h=8e4c314df620d64cd7e3065bd8a256409ff4a361;hb=844ccad5a3fcbedec17b2af66d460f31abc7cff1;hp=f66df316f8d31fa7f1927a3fcf4fc593f6787006;hpb=d6f378ff4d767169376e6f2489a00b75d8a36e39;p=vamsas.git

diff --git a/src/uk/ac/vamsas/objects/utils/Range.java b/src/uk/ac/vamsas/objects/utils/Range.java
index f66df31..8e4c314 100644
--- a/src/uk/ac/vamsas/objects/utils/Range.java
+++ b/src/uk/ac/vamsas/objects/utils/Range.java
@@ -1,3 +1,24 @@
+/*
+ * This file is part of the Vamsas Client version 0.1. 
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite, 
+ *  Andrew Waterhouse and Dominik Lindner.
+ * 
+ * Earlier versions have also been incorporated into Jalview version 2.4 
+ * since 2008, and TOPALi version 2 since 2007.
+ * 
+ * The Vamsas Client is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *  
+ * The Vamsas Client 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 Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the Vamsas Client.  If not, see <http://www.gnu.org/licenses/>.
+ */
 package uk.ac.vamsas.objects.utils;
 
 import java.util.Vector;
@@ -9,89 +30,80 @@ 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.
+ * Utilities for working with RangeType and MapType objects. Derived from bitter
+ * experience.
+ * 
  * @author JimP
- *
+ * 
  */
 public class Range {
+  static org.apache.commons.logging.Log log = org.apache.commons.logging.LogFactory
+      .getFactory().getLog(Range.class);
 
   /**
    * get start<end range of segment, adjusting for inclusivity flag and
    * polarity.
-   *
+   * 
    * @param visSeg
-   * @param ensureDirection when true - always ensure start is less than end.
-   * @return int[] { start, end, direction} where direction==1 for range running from end to start.
+   * @param ensureDirection
+   *          when true - always ensure start is less than end.
+   * @return int[] { start, end, direction} where direction==1 for range running
+   *         from end to start.
    */
-  public static int[] getSegRange(Seg visSeg, boolean ensureDirection)
-  {
+  public static int[] getSegRange(Seg visSeg, boolean ensureDirection) {
     boolean incl = visSeg.getInclusive();
     // adjust for inclusive flag.
     int pol = (visSeg.getStart() <= visSeg.getEnd()) ? 1 : -1; // polarity of
     // region.
     int start = visSeg.getStart() + (incl ? 0 : pol);
     int end = visSeg.getEnd() + (incl ? 0 : -pol);
-    if (ensureDirection && pol == -1)
-    {
+    if (ensureDirection && pol == -1) {
       // jalview doesn't deal with inverted ranges, yet.
       int t = end;
       end = start;
       start = t;
     }
-    return new int[]
-        {
-        start, end, pol < 0 ? 1 : 0};
+    return new int[] { start, end, pol < 0 ? 1 : 0 };
   }
 
   /**
    * get real bounds of a RangeType's specification. start and end are an
-   * inclusive range within which all segments and positions lie.
-   * TODO: refactor to vamsas utils
+   * inclusive range within which all segments and positions lie. TODO: refactor
+   * to vamsas utils
+   * 
    * @param dseta
    * @return int[] { start, end}
    */
-  public static int[] getBounds(RangeType dseta)
-  {
-    if (dseta != null)
-    {
+  public static int[] getBounds(RangeType dseta) {
+    if (dseta != null) {
       int[] se = null;
-      if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
-      {
-        throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+      if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0) {
+        throw new Error(
+            "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
       }
-      if (dseta.getSegCount() > 0)
-      {
+      if (dseta.getSegCount() > 0) {
         se = getSegRange(dseta.getSeg(0), true);
-        for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++)
-        {
+        for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++) {
           int nse[] = getSegRange(dseta.getSeg(s), true);
-          if (se[0] > nse[0])
-          {
+          if (se[0] > nse[0]) {
             se[0] = nse[0];
           }
-          if (se[1] < nse[1])
-          {
+          if (se[1] < nse[1]) {
             se[1] = nse[1];
           }
         }
       }
-      if (dseta.getPosCount() > 0)
-      {
-        // could do a polarity for pos range too. and pass back indication of discontinuities.
+      if (dseta.getPosCount() > 0) {
+        // could do a polarity for pos range too. and pass back indication of
+        // discontinuities.
         int pos = dseta.getPos(0).getI();
-        se = new int[]
-            {
-            pos, pos};
-        for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
-        {
+        se = new int[] { pos, pos };
+        for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++) {
           pos = dseta.getPos(p).getI();
-          if (se[0] > pos)
-          {
+          if (se[0] > pos) {
             se[0] = pos;
           }
-          if (se[1] < pos)
-          {
+          if (se[1] < pos) {
             se[1] = pos;
           }
         }
@@ -102,49 +114,41 @@ public class Range {
   }
 
   /**
-   * map from a rangeType's internal frame to the referenced object's coordinate frame.
+   * map from a rangeType's internal frame to the referenced object's coordinate
+   * frame.
+   * 
    * @param dseta
    * @return int [] { ref(pos)...} for all pos in rangeType's frame.
    */
-  public static int[] getMapping(RangeType dseta)
-  {
+  public static int[] getMapping(RangeType dseta) {
     Vector posList = new Vector();
-    if (dseta != null)
-    {
+    if (dseta != null) {
       int[] se = null;
-      if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
-      {
-        throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+      if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0) {
+        throw new Error(
+            "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
       }
-      if (dseta.getSegCount() > 0)
-      {
-        for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++)
-        {
+      if (dseta.getSegCount() > 0) {
+        for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++) {
           se = getSegRange(dseta.getSeg(s), false);
           int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1);
-          for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1)
-          {
+          for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1) {
             posList.add(new Integer(p));
           }
         }
-      }
-      else if (dseta.getPosCount() > 0)
-      {
+      } else if (dseta.getPosCount() > 0) {
         int pos = dseta.getPos(0).getI();
 
-        for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
-        {
+        for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++) {
           pos = dseta.getPos(p).getI();
           posList.add(new Integer(pos));
         }
       }
     }
-    if (posList != null && posList.size() > 0)
-    {
+    if (posList != null && posList.size() > 0) {
       int[] range = new int[posList.size()];
-      for (int i = 0; i < range.length; i++)
-      {
-        range[i] = ( (Integer) posList.elementAt(i)).intValue();
+      for (int i = 0; i < range.length; i++) {
+        range[i] = ((Integer) posList.elementAt(i)).intValue();
       }
       posList.clear();
       return range;
@@ -152,61 +156,52 @@ public class Range {
     return null;
   }
 
-  public static int[] getIntervals(RangeType range)
-  {
-    int[] intervals=null;
+  public static int[] getIntervals(RangeType range) {
+    int[] intervals = null;
     Vector posList = new Vector();
-    if (range != null)
-    {
+    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++)
-        {
+      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)
-      {
+      } else if (range.getPosCount() > 0) {
         int pos = range.getPos(0).getI();
-        for (int p = 0, pSize = range.getPosCount(); p < pSize; p++)
-        {
+        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()];
+    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();
+      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)
-    {
+  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.setEnd(range[i + 1]);
       vSeg.setInclusive(true);
       mrt.addSeg(vSeg);
     }
@@ -214,64 +209,74 @@ public class Range {
 
   /**
    * 
-   * @param maprange where the from range is the local mapped range, and the to range is the 'mapped' range in the MapRangeType
+   * @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)
-  {
+  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);
+    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); 
+  public static MapList parsemapType(MapType map) {
+    if (!map.getLocal().hasUnit() || !map.getMapped().hasUnit()) {
+      if (log.isDebugEnabled()) {
+        log.debug("using default mapping length of 1:1 for map "
+            + (map.isRegistered() ? map.getVorbaId().toString()
+                : ("<no Id registered> " + map.toString())));
+      }
+    }
+    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)
-  {
+  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 
+   * @param reverse
+   *          - reverse MapList mapping for Local and Mapped ranges and units
    */
-  public static void initMapType(MapType maprange, MapList ml, boolean setUnits, boolean reverse)
-  {
+  public static void initMapType(MapType maprange, MapList ml,
+      boolean setUnits, boolean reverse) {
     maprange.setLocal(new Local());
     maprange.setMapped(new Mapped());
-    if (!reverse)
-      {
+    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)
-      { 
+    } 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 {
@@ -281,4 +286,4 @@ public class Range {
     }
   }
 
-}
\ No newline at end of file
+}