X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Forg%2Fvamsas%2Fobjects%2Fcore%2FRangeType.java;h=4a5e0a8ba3a73c8894e70d935e727da7490ab621;hb=b2c76f76a8c9040e0d70c0d0a30a04aac962c2c7;hp=070af2accdf95a286bf4faf64e4bd74dfb22d7fa;hpb=8102c1325cac1288977f498c87924264d3037151;p=vamsas.git

diff --git a/src/org/vamsas/objects/core/RangeType.java b/src/org/vamsas/objects/core/RangeType.java
index 070af2a..4a5e0a8 100644
--- a/src/org/vamsas/objects/core/RangeType.java
+++ b/src/org/vamsas/objects/core/RangeType.java
@@ -23,16 +23,15 @@ import org.exolab.castor.xml.ValidationException;
 /**
  * Specify an ordered set of positions and/or regions on the
  * principle
- *  dimension of some associated vamsas object
- *  
- *  Keeping to jaxb-1.0 specification for the moment - this
- *  choice should become a substitution group when we use
- *  jaxb-2.0 capable bindings
+ *  dimension of some associated vamsas object Keeping to jaxb-1.0
+ * specification for the moment - this choice should
+ *  become a substitution group when we use jaxb-2.0 capable
+ * bindings
  *  
  * 
  * @version $Revision$ $Date$
  */
-public abstract class RangeType extends org.vamsas.client.Vobject 
+public abstract class RangeType extends uk.ac.vamsas.clientnt.Vobject 
 implements java.io.Serializable
 {
 
@@ -47,16 +46,14 @@ implements java.io.Serializable
     private java.lang.Object _choiceValue;
 
     /**
-     * a position within the associated object's
-     *  coordinate system
+     * a position within the associated object's coordinate system
      *  
      */
     private java.util.Vector _posList;
 
     /**
-     * a region from start to end, with flag for
-     *  inclusivity of terminii
-     *  
+     * a region from start to end, with flag for inclusivity of
+     *  terminii 
      */
     private java.util.Vector _segList;
 
@@ -70,7 +67,7 @@ implements java.io.Serializable
         super();
         _posList = new Vector();
         _segList = new Vector();
-    } //-- org.vamsas.objects.core.RangeType()
+    } //-- uk.ac.vamsas.objects.core.RangeType()
 
 
       //-----------/
@@ -84,11 +81,11 @@ implements java.io.Serializable
      * 
      * @param vPos
      */
-    public void addPos(org.vamsas.objects.core.Pos vPos)
+    public void addPos(uk.ac.vamsas.objects.core.Pos vPos)
         throws java.lang.IndexOutOfBoundsException
     {
         _posList.addElement(vPos);
-    } //-- void addPos(org.vamsas.objects.core.Pos) 
+    } //-- void addPos(uk.ac.vamsas.objects.core.Pos) 
 
     /**
      * Method addPos
@@ -98,11 +95,11 @@ implements java.io.Serializable
      * @param index
      * @param vPos
      */
-    public void addPos(int index, org.vamsas.objects.core.Pos vPos)
+    public void addPos(int index, uk.ac.vamsas.objects.core.Pos vPos)
         throws java.lang.IndexOutOfBoundsException
     {
         _posList.insertElementAt(vPos, index);
-    } //-- void addPos(int, org.vamsas.objects.core.Pos) 
+    } //-- void addPos(int, uk.ac.vamsas.objects.core.Pos) 
 
     /**
      * Method addSeg
@@ -111,11 +108,11 @@ implements java.io.Serializable
      * 
      * @param vSeg
      */
-    public void addSeg(org.vamsas.objects.core.Seg vSeg)
+    public void addSeg(uk.ac.vamsas.objects.core.Seg vSeg)
         throws java.lang.IndexOutOfBoundsException
     {
         _segList.addElement(vSeg);
-    } //-- void addSeg(org.vamsas.objects.core.Seg) 
+    } //-- void addSeg(uk.ac.vamsas.objects.core.Seg) 
 
     /**
      * Method addSeg
@@ -125,11 +122,11 @@ implements java.io.Serializable
      * @param index
      * @param vSeg
      */
-    public void addSeg(int index, org.vamsas.objects.core.Seg vSeg)
+    public void addSeg(int index, uk.ac.vamsas.objects.core.Seg vSeg)
         throws java.lang.IndexOutOfBoundsException
     {
         _segList.insertElementAt(vSeg, index);
-    } //-- void addSeg(int, org.vamsas.objects.core.Seg) 
+    } //-- void addSeg(int, uk.ac.vamsas.objects.core.Seg) 
 
     /**
      * Method enumeratePos
@@ -219,7 +216,7 @@ implements java.io.Serializable
      * @param index
      * @return Pos
      */
-    public org.vamsas.objects.core.Pos getPos(int index)
+    public uk.ac.vamsas.objects.core.Pos getPos(int index)
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
@@ -227,8 +224,8 @@ implements java.io.Serializable
             throw new IndexOutOfBoundsException("getPos: Index value '"+index+"' not in range [0.."+_posList.size()+ "]");
         }
         
-        return (org.vamsas.objects.core.Pos) _posList.elementAt(index);
-    } //-- org.vamsas.objects.core.Pos getPos(int) 
+        return (uk.ac.vamsas.objects.core.Pos) _posList.elementAt(index);
+    } //-- uk.ac.vamsas.objects.core.Pos getPos(int) 
 
     /**
      * Method getPos
@@ -237,15 +234,15 @@ implements java.io.Serializable
      * 
      * @return Pos
      */
-    public org.vamsas.objects.core.Pos[] getPos()
+    public uk.ac.vamsas.objects.core.Pos[] getPos()
     {
         int size = _posList.size();
-        org.vamsas.objects.core.Pos[] mArray = new org.vamsas.objects.core.Pos[size];
+        uk.ac.vamsas.objects.core.Pos[] mArray = new uk.ac.vamsas.objects.core.Pos[size];
         for (int index = 0; index < size; index++) {
-            mArray[index] = (org.vamsas.objects.core.Pos) _posList.elementAt(index);
+            mArray[index] = (uk.ac.vamsas.objects.core.Pos) _posList.elementAt(index);
         }
         return mArray;
-    } //-- org.vamsas.objects.core.Pos[] getPos() 
+    } //-- uk.ac.vamsas.objects.core.Pos[] getPos() 
 
     /**
      * Method getPosCount
@@ -267,7 +264,7 @@ implements java.io.Serializable
      * @param index
      * @return Seg
      */
-    public org.vamsas.objects.core.Seg getSeg(int index)
+    public uk.ac.vamsas.objects.core.Seg getSeg(int index)
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
@@ -275,8 +272,8 @@ implements java.io.Serializable
             throw new IndexOutOfBoundsException("getSeg: Index value '"+index+"' not in range [0.."+_segList.size()+ "]");
         }
         
-        return (org.vamsas.objects.core.Seg) _segList.elementAt(index);
-    } //-- org.vamsas.objects.core.Seg getSeg(int) 
+        return (uk.ac.vamsas.objects.core.Seg) _segList.elementAt(index);
+    } //-- uk.ac.vamsas.objects.core.Seg getSeg(int) 
 
     /**
      * Method getSeg
@@ -285,15 +282,15 @@ implements java.io.Serializable
      * 
      * @return Seg
      */
-    public org.vamsas.objects.core.Seg[] getSeg()
+    public uk.ac.vamsas.objects.core.Seg[] getSeg()
     {
         int size = _segList.size();
-        org.vamsas.objects.core.Seg[] mArray = new org.vamsas.objects.core.Seg[size];
+        uk.ac.vamsas.objects.core.Seg[] mArray = new uk.ac.vamsas.objects.core.Seg[size];
         for (int index = 0; index < size; index++) {
-            mArray[index] = (org.vamsas.objects.core.Seg) _segList.elementAt(index);
+            mArray[index] = (uk.ac.vamsas.objects.core.Seg) _segList.elementAt(index);
         }
         return mArray;
-    } //-- org.vamsas.objects.core.Seg[] getSeg() 
+    } //-- uk.ac.vamsas.objects.core.Seg[] getSeg() 
 
     /**
      * Method getSegCount
@@ -351,12 +348,12 @@ implements java.io.Serializable
      * @param index
      * @return Pos
      */
-    public org.vamsas.objects.core.Pos removePos(int index)
+    public uk.ac.vamsas.objects.core.Pos removePos(int index)
     {
         java.lang.Object obj = _posList.elementAt(index);
         _posList.removeElementAt(index);
-        return (org.vamsas.objects.core.Pos) obj;
-    } //-- org.vamsas.objects.core.Pos removePos(int) 
+        return (uk.ac.vamsas.objects.core.Pos) obj;
+    } //-- uk.ac.vamsas.objects.core.Pos removePos(int) 
 
     /**
      * Method removeSeg
@@ -366,12 +363,12 @@ implements java.io.Serializable
      * @param index
      * @return Seg
      */
-    public org.vamsas.objects.core.Seg removeSeg(int index)
+    public uk.ac.vamsas.objects.core.Seg removeSeg(int index)
     {
         java.lang.Object obj = _segList.elementAt(index);
         _segList.removeElementAt(index);
-        return (org.vamsas.objects.core.Seg) obj;
-    } //-- org.vamsas.objects.core.Seg removeSeg(int) 
+        return (uk.ac.vamsas.objects.core.Seg) obj;
+    } //-- uk.ac.vamsas.objects.core.Seg removeSeg(int) 
 
     /**
      * Method setPos
@@ -381,7 +378,7 @@ implements java.io.Serializable
      * @param index
      * @param vPos
      */
-    public void setPos(int index, org.vamsas.objects.core.Pos vPos)
+    public void setPos(int index, uk.ac.vamsas.objects.core.Pos vPos)
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
@@ -389,7 +386,7 @@ implements java.io.Serializable
             throw new IndexOutOfBoundsException("setPos: Index value '"+index+"' not in range [0.."+_posList.size()+ "]");
         }
         _posList.setElementAt(vPos, index);
-    } //-- void setPos(int, org.vamsas.objects.core.Pos) 
+    } //-- void setPos(int, uk.ac.vamsas.objects.core.Pos) 
 
     /**
      * Method setPos
@@ -398,14 +395,14 @@ implements java.io.Serializable
      * 
      * @param posArray
      */
-    public void setPos(org.vamsas.objects.core.Pos[] posArray)
+    public void setPos(uk.ac.vamsas.objects.core.Pos[] posArray)
     {
         //-- copy array
         _posList.removeAllElements();
         for (int i = 0; i < posArray.length; i++) {
             _posList.addElement(posArray[i]);
         }
-    } //-- void setPos(org.vamsas.objects.core.Pos) 
+    } //-- void setPos(uk.ac.vamsas.objects.core.Pos) 
 
     /**
      * Method setSeg
@@ -415,7 +412,7 @@ implements java.io.Serializable
      * @param index
      * @param vSeg
      */
-    public void setSeg(int index, org.vamsas.objects.core.Seg vSeg)
+    public void setSeg(int index, uk.ac.vamsas.objects.core.Seg vSeg)
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
@@ -423,7 +420,7 @@ implements java.io.Serializable
             throw new IndexOutOfBoundsException("setSeg: Index value '"+index+"' not in range [0.."+_segList.size()+ "]");
         }
         _segList.setElementAt(vSeg, index);
-    } //-- void setSeg(int, org.vamsas.objects.core.Seg) 
+    } //-- void setSeg(int, uk.ac.vamsas.objects.core.Seg) 
 
     /**
      * Method setSeg
@@ -432,14 +429,14 @@ implements java.io.Serializable
      * 
      * @param segArray
      */
-    public void setSeg(org.vamsas.objects.core.Seg[] segArray)
+    public void setSeg(uk.ac.vamsas.objects.core.Seg[] segArray)
     {
         //-- copy array
         _segList.removeAllElements();
         for (int i = 0; i < segArray.length; i++) {
             _segList.addElement(segArray[i]);
         }
-    } //-- void setSeg(org.vamsas.objects.core.Seg) 
+    } //-- void setSeg(uk.ac.vamsas.objects.core.Seg) 
 
     /**
      * Method validate