refactored org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@273 be28352e-c001-0410-b1a7-c7978e42abec

diff --git a/src/org/vamsas/objects/core/Alignment.java b/src/org/vamsas/objects/core/Alignment.java
index bf70f4e..f824e1f 100644 (file)
--- a/src/org/vamsas/objects/core/Alignment.java
+++ b/src/org/vamsas/objects/core/Alignment.java
@@ -2,7 +2,7 @@
  * This class was automatically generated with 
  * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
  * Schema.
- * $Id$
+ * $Id:Alignment.java 264 2006-12-14 17:42:54Z JimP $
  */
 
 package org.vamsas.objects.core;
@@ -26,9 +26,9 @@ import org.xml.sax.ContentHandler;
 /**
  * Class Alignment.
  * 
- * @version $Revision$ $Date$
+ * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
  */
-public class Alignment extends org.vamsas.client.Vobject 
+public class Alignment extends uk.ac.vamsas.client.Vobject 
 implements java.io.Serializable
 {
 

diff --git a/src/org/vamsas/objects/core/AnnotationElement.java b/src/org/vamsas/objects/core/AnnotationElement.java
index b2ed9c5..e4edd8d 100644 (file)
--- a/src/org/vamsas/objects/core/AnnotationElement.java
+++ b/src/org/vamsas/objects/core/AnnotationElement.java
@@ -2,7 +2,7 @@
  * This class was automatically generated with 
  * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
  * Schema.
- * $Id$
+ * $Id:AnnotationElement.java 264 2006-12-14 17:42:54Z JimP $
  */
 
 package org.vamsas.objects.core;
@@ -26,9 +26,9 @@ import org.xml.sax.ContentHandler;
 /**
  * Class AnnotationElement.
  * 
- * @version $Revision$ $Date$
+ * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
  */
-public class AnnotationElement extends org.vamsas.client.Vobject 
+public class AnnotationElement extends uk.ac.vamsas.client.Vobject 
 implements java.io.Serializable
 {
 

diff --git a/src/org/vamsas/objects/core/AppData.java b/src/org/vamsas/objects/core/AppData.java
index 168bc6b..b5c574f 100644 (file)
--- a/src/org/vamsas/objects/core/AppData.java
+++ b/src/org/vamsas/objects/core/AppData.java
@@ -26,7 +26,7 @@ import org.xml.sax.ContentHandler;
  * \r
  * @version $Revision$ $Date$\r
  */\r
-public class AppData extends org.vamsas.client.Vobject \r
+public class AppData extends uk.ac.vamsas.client.Vobject \r
 implements java.io.Serializable\r
 {\r
 \r

diff --git a/src/org/vamsas/objects/core/DataSet.java b/src/org/vamsas/objects/core/DataSet.java
index e6d064e..25f92a6 100644 (file)
--- a/src/org/vamsas/objects/core/DataSet.java
+++ b/src/org/vamsas/objects/core/DataSet.java
@@ -2,7 +2,7 @@
  * This class was automatically generated with 
  * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
  * Schema.
- * $Id$
+ * $Id:DataSet.java 264 2006-12-14 17:42:54Z JimP $
  */
 
 package org.vamsas.objects.core;
@@ -26,9 +26,9 @@ import org.xml.sax.ContentHandler;
 /**
  * Class DataSet.
  * 
- * @version $Revision$ $Date$
+ * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
  */
-public class DataSet extends org.vamsas.client.Vobject 
+public class DataSet extends uk.ac.vamsas.client.Vobject 
 implements java.io.Serializable
 {
 

diff --git a/src/org/vamsas/objects/core/DbRef.java b/src/org/vamsas/objects/core/DbRef.java
index 3be5671..d26993d 100644 (file)
--- a/src/org/vamsas/objects/core/DbRef.java
+++ b/src/org/vamsas/objects/core/DbRef.java
@@ -2,7 +2,7 @@
  * This class was automatically generated with 
  * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
  * Schema.
- * $Id$
+ * $Id:DbRef.java 264 2006-12-14 17:42:54Z JimP $
  */
 
 package org.vamsas.objects.core;
@@ -28,9 +28,9 @@ import org.xml.sax.ContentHandler;
  *  for this sequence record - with optional mapping
  *  from database sequence to the given sequence record 
  * 
- * @version $Revision$ $Date$
+ * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
  */
-public class DbRef extends org.vamsas.client.Vobject 
+public class DbRef extends uk.ac.vamsas.client.Vobject 
 implements java.io.Serializable
 {
 

diff --git a/src/org/vamsas/objects/core/Entry.java b/src/org/vamsas/objects/core/Entry.java
index dcf3c5e..2a65ca5 100644 (file)
--- a/src/org/vamsas/objects/core/Entry.java
+++ b/src/org/vamsas/objects/core/Entry.java
@@ -2,7 +2,7 @@
  * This class was automatically generated with 
  * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
  * Schema.
- * $Id$
+ * $Id:Entry.java 264 2006-12-14 17:42:54Z JimP $
  */
 
 package org.vamsas.objects.core;
@@ -26,9 +26,9 @@ import org.xml.sax.ContentHandler;
 /**
  * Class Entry.
  * 
- * @version $Revision$ $Date$
+ * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
  */
-public class Entry extends org.vamsas.client.Vobject 
+public class Entry extends uk.ac.vamsas.client.Vobject 
 implements java.io.Serializable
 {
 

diff --git a/src/org/vamsas/objects/core/Glyph.java b/src/org/vamsas/objects/core/Glyph.java
index f5d9362..1fe61c7 100644 (file)
--- a/src/org/vamsas/objects/core/Glyph.java
+++ b/src/org/vamsas/objects/core/Glyph.java
@@ -27,7 +27,7 @@ import org.xml.sax.ContentHandler;
  * \r
  * @version $Revision$ $Date$\r
  */\r
-public class Glyph extends org.vamsas.client.Vobject \r
+public class Glyph extends uk.ac.vamsas.client.Vobject \r
 implements java.io.Serializable\r
 {\r
 \r

diff --git a/src/org/vamsas/objects/core/Link.java b/src/org/vamsas/objects/core/Link.java
index 1330cff..4d4eeca 100644 (file)
--- a/src/org/vamsas/objects/core/Link.java
+++ b/src/org/vamsas/objects/core/Link.java
@@ -26,7 +26,7 @@ import org.xml.sax.ContentHandler;
  * \r
  * @version $Revision$ $Date$\r
  */\r
-public class Link extends org.vamsas.client.Vobject \r
+public class Link extends uk.ac.vamsas.client.Vobject \r
 implements java.io.Serializable\r
 {\r
 \r

diff --git a/src/org/vamsas/objects/core/LockFile.java b/src/org/vamsas/objects/core/LockFile.java
index a26bbe2..e9b5baf 100644 (file)
--- a/src/org/vamsas/objects/core/LockFile.java
+++ b/src/org/vamsas/objects/core/LockFile.java
@@ -2,7 +2,7 @@
  * This class was automatically generated with 
  * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
  * Schema.
- * $Id$
+ * $Id:LockFile.java 264 2006-12-14 17:42:54Z JimP $
  */
 
 package org.vamsas.objects.core;
@@ -24,9 +24,9 @@ import org.xml.sax.ContentHandler;
 /**
  * Class LockFile.
  * 
- * @version $Revision$ $Date$
+ * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
  */
-public class LockFile extends org.vamsas.client.Vobject 
+public class LockFile extends uk.ac.vamsas.client.Vobject 
 implements java.io.Serializable
 {
 

diff --git a/src/org/vamsas/objects/core/MapList.java b/src/org/vamsas/objects/core/MapList.java
index 608ee58..7ab23ea 100644 (file)
--- a/src/org/vamsas/objects/core/MapList.java
+++ b/src/org/vamsas/objects/core/MapList.java
@@ -26,7 +26,7 @@ import org.xml.sax.ContentHandler;
  * \r
  * @version $Revision$ $Date$\r
  */\r
-public class MapList extends org.vamsas.client.Vobject \r
+public class MapList extends uk.ac.vamsas.client.Vobject \r
 implements java.io.Serializable\r
 {\r
 \r

diff --git a/src/org/vamsas/objects/core/Newick.java b/src/org/vamsas/objects/core/Newick.java
index 2c60f61..34d4351 100644 (file)
--- a/src/org/vamsas/objects/core/Newick.java
+++ b/src/org/vamsas/objects/core/Newick.java
@@ -2,7 +2,7 @@
  * This class was automatically generated with 
  * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
  * Schema.
- * $Id$
+ * $Id:Newick.java 264 2006-12-14 17:42:54Z JimP $
  */
 
 package org.vamsas.objects.core;
@@ -24,9 +24,9 @@ import org.xml.sax.ContentHandler;
 /**
  * Class Newick.
  * 
- * @version $Revision$ $Date$
+ * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
  */
-public class Newick extends org.vamsas.client.Vobject 
+public class Newick extends uk.ac.vamsas.client.Vobject 
 implements java.io.Serializable
 {
 

diff --git a/src/org/vamsas/objects/core/Param.java b/src/org/vamsas/objects/core/Param.java
index b7c2ab5..701af66 100644 (file)
--- a/src/org/vamsas/objects/core/Param.java
+++ b/src/org/vamsas/objects/core/Param.java
@@ -26,7 +26,7 @@ import org.xml.sax.ContentHandler;
  * \r
  * @version $Revision$ $Date$\r
  */\r
-public class Param extends org.vamsas.client.Vobject \r
+public class Param extends uk.ac.vamsas.client.Vobject \r
 implements java.io.Serializable\r
 {\r
 \r

diff --git a/src/org/vamsas/objects/core/Pos.java b/src/org/vamsas/objects/core/Pos.java
index 5053f98..80252f0 100644 (file)
--- a/src/org/vamsas/objects/core/Pos.java
+++ b/src/org/vamsas/objects/core/Pos.java
@@ -27,7 +27,7 @@ import org.xml.sax.ContentHandler;
  * \r
  * @version $Revision$ $Date$\r
  */\r
-public class Pos extends org.vamsas.client.Vobject \r
+public class Pos extends uk.ac.vamsas.client.Vobject \r
 implements java.io.Serializable\r
 {\r
 \r

diff --git a/src/org/vamsas/objects/core/Property.java b/src/org/vamsas/objects/core/Property.java
index fb4aacc..e832f72 100644 (file)
--- a/src/org/vamsas/objects/core/Property.java
+++ b/src/org/vamsas/objects/core/Property.java
@@ -26,7 +26,7 @@ import org.xml.sax.ContentHandler;
  * \r
  * @version $Revision$ $Date$\r
  */\r
-public class Property extends org.vamsas.client.Vobject \r
+public class Property extends uk.ac.vamsas.client.Vobject \r
 implements java.io.Serializable\r
 {\r
 \r

diff --git a/src/org/vamsas/objects/core/Provenance.java b/src/org/vamsas/objects/core/Provenance.java
index e1f6b85..ac71d23 100644 (file)
--- a/src/org/vamsas/objects/core/Provenance.java
+++ b/src/org/vamsas/objects/core/Provenance.java
@@ -2,7 +2,7 @@
  * This class was automatically generated with 
  * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
  * Schema.
- * $Id$
+ * $Id:Provenance.java 264 2006-12-14 17:42:54Z JimP $
  */
 
 package org.vamsas.objects.core;
@@ -26,9 +26,9 @@ import org.xml.sax.ContentHandler;
 /**
  * Class Provenance.
  * 
- * @version $Revision$ $Date$
+ * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
  */
-public class Provenance extends org.vamsas.client.Vobject 
+public class Provenance extends uk.ac.vamsas.client.Vobject 
 implements java.io.Serializable
 {
 

diff --git a/src/org/vamsas/objects/core/RangeType.java b/src/org/vamsas/objects/core/RangeType.java
index c0d6571..4a5e0a8 100644 (file)
--- a/src/org/vamsas/objects/core/RangeType.java
+++ b/src/org/vamsas/objects/core/RangeType.java
@@ -31,7 +31,7 @@ import org.exolab.castor.xml.ValidationException;
  * \r
  * @version $Revision$ $Date$\r
  */\r
-public abstract class RangeType extends org.vamsas.client.Vobject \r
+public abstract class RangeType extends uk.ac.vamsas.clientnt.Vobject \r
 implements java.io.Serializable\r
 {\r
 \r
@@ -67,7 +67,7 @@ implements java.io.Serializable
         super();\r
         _posList = new Vector();\r
         _segList = new Vector();\r
-    } //-- org.vamsas.objects.core.RangeType()\r
+    } //-- uk.ac.vamsas.objects.core.RangeType()\r
 \r
 \r
       //-----------/\r
@@ -81,11 +81,11 @@ implements java.io.Serializable
      * \r
      * @param vPos\r
      */\r
-    public void addPos(org.vamsas.objects.core.Pos vPos)\r
+    public void addPos(uk.ac.vamsas.objects.core.Pos vPos)\r
         throws java.lang.IndexOutOfBoundsException\r
     {\r
         _posList.addElement(vPos);\r
-    } //-- void addPos(org.vamsas.objects.core.Pos) \r
+    } //-- void addPos(uk.ac.vamsas.objects.core.Pos) \r
 \r
     /**\r
      * Method addPos\r
@@ -95,11 +95,11 @@ implements java.io.Serializable
      * @param index\r
      * @param vPos\r
      */\r
-    public void addPos(int index, org.vamsas.objects.core.Pos vPos)\r
+    public void addPos(int index, uk.ac.vamsas.objects.core.Pos vPos)\r
         throws java.lang.IndexOutOfBoundsException\r
     {\r
         _posList.insertElementAt(vPos, index);\r
-    } //-- void addPos(int, org.vamsas.objects.core.Pos) \r
+    } //-- void addPos(int, uk.ac.vamsas.objects.core.Pos) \r
 \r
     /**\r
      * Method addSeg\r
@@ -108,11 +108,11 @@ implements java.io.Serializable
      * \r
      * @param vSeg\r
      */\r
-    public void addSeg(org.vamsas.objects.core.Seg vSeg)\r
+    public void addSeg(uk.ac.vamsas.objects.core.Seg vSeg)\r
         throws java.lang.IndexOutOfBoundsException\r
     {\r
         _segList.addElement(vSeg);\r
-    } //-- void addSeg(org.vamsas.objects.core.Seg) \r
+    } //-- void addSeg(uk.ac.vamsas.objects.core.Seg) \r
 \r
     /**\r
      * Method addSeg\r
@@ -122,11 +122,11 @@ implements java.io.Serializable
      * @param index\r
      * @param vSeg\r
      */\r
-    public void addSeg(int index, org.vamsas.objects.core.Seg vSeg)\r
+    public void addSeg(int index, uk.ac.vamsas.objects.core.Seg vSeg)\r
         throws java.lang.IndexOutOfBoundsException\r
     {\r
         _segList.insertElementAt(vSeg, index);\r
-    } //-- void addSeg(int, org.vamsas.objects.core.Seg) \r
+    } //-- void addSeg(int, uk.ac.vamsas.objects.core.Seg) \r
 \r
     /**\r
      * Method enumeratePos\r
@@ -216,7 +216,7 @@ implements java.io.Serializable
      * @param index\r
      * @return Pos\r
      */\r
-    public org.vamsas.objects.core.Pos getPos(int index)\r
+    public uk.ac.vamsas.objects.core.Pos getPos(int index)\r
         throws java.lang.IndexOutOfBoundsException\r
     {\r
         //-- check bounds for index\r
@@ -224,8 +224,8 @@ implements java.io.Serializable
             throw new IndexOutOfBoundsException("getPos: Index value '"+index+"' not in range [0.."+_posList.size()+ "]");\r
         }\r
         \r
-        return (org.vamsas.objects.core.Pos) _posList.elementAt(index);\r
-    } //-- org.vamsas.objects.core.Pos getPos(int) \r
+        return (uk.ac.vamsas.objects.core.Pos) _posList.elementAt(index);\r
+    } //-- uk.ac.vamsas.objects.core.Pos getPos(int) \r
 \r
     /**\r
      * Method getPos\r
@@ -234,15 +234,15 @@ implements java.io.Serializable
      * \r
      * @return Pos\r
      */\r
-    public org.vamsas.objects.core.Pos[] getPos()\r
+    public uk.ac.vamsas.objects.core.Pos[] getPos()\r
     {\r
         int size = _posList.size();\r
-        org.vamsas.objects.core.Pos[] mArray = new org.vamsas.objects.core.Pos[size];\r
+        uk.ac.vamsas.objects.core.Pos[] mArray = new uk.ac.vamsas.objects.core.Pos[size];\r
         for (int index = 0; index < size; index++) {\r
-            mArray[index] = (org.vamsas.objects.core.Pos) _posList.elementAt(index);\r
+            mArray[index] = (uk.ac.vamsas.objects.core.Pos) _posList.elementAt(index);\r
         }\r
         return mArray;\r
-    } //-- org.vamsas.objects.core.Pos[] getPos() \r
+    } //-- uk.ac.vamsas.objects.core.Pos[] getPos() \r
 \r
     /**\r
      * Method getPosCount\r
@@ -264,7 +264,7 @@ implements java.io.Serializable
      * @param index\r
      * @return Seg\r
      */\r
-    public org.vamsas.objects.core.Seg getSeg(int index)\r
+    public uk.ac.vamsas.objects.core.Seg getSeg(int index)\r
         throws java.lang.IndexOutOfBoundsException\r
     {\r
         //-- check bounds for index\r
@@ -272,8 +272,8 @@ implements java.io.Serializable
             throw new IndexOutOfBoundsException("getSeg: Index value '"+index+"' not in range [0.."+_segList.size()+ "]");\r
         }\r
         \r
-        return (org.vamsas.objects.core.Seg) _segList.elementAt(index);\r
-    } //-- org.vamsas.objects.core.Seg getSeg(int) \r
+        return (uk.ac.vamsas.objects.core.Seg) _segList.elementAt(index);\r
+    } //-- uk.ac.vamsas.objects.core.Seg getSeg(int) \r
 \r
     /**\r
      * Method getSeg\r
@@ -282,15 +282,15 @@ implements java.io.Serializable
      * \r
      * @return Seg\r
      */\r
-    public org.vamsas.objects.core.Seg[] getSeg()\r
+    public uk.ac.vamsas.objects.core.Seg[] getSeg()\r
     {\r
         int size = _segList.size();\r
-        org.vamsas.objects.core.Seg[] mArray = new org.vamsas.objects.core.Seg[size];\r
+        uk.ac.vamsas.objects.core.Seg[] mArray = new uk.ac.vamsas.objects.core.Seg[size];\r
         for (int index = 0; index < size; index++) {\r
-            mArray[index] = (org.vamsas.objects.core.Seg) _segList.elementAt(index);\r
+            mArray[index] = (uk.ac.vamsas.objects.core.Seg) _segList.elementAt(index);\r
         }\r
         return mArray;\r
-    } //-- org.vamsas.objects.core.Seg[] getSeg() \r
+    } //-- uk.ac.vamsas.objects.core.Seg[] getSeg() \r
 \r
     /**\r
      * Method getSegCount\r
@@ -348,12 +348,12 @@ implements java.io.Serializable
      * @param index\r
      * @return Pos\r
      */\r
-    public org.vamsas.objects.core.Pos removePos(int index)\r
+    public uk.ac.vamsas.objects.core.Pos removePos(int index)\r
     {\r
         java.lang.Object obj = _posList.elementAt(index);\r
         _posList.removeElementAt(index);\r
-        return (org.vamsas.objects.core.Pos) obj;\r
-    } //-- org.vamsas.objects.core.Pos removePos(int) \r
+        return (uk.ac.vamsas.objects.core.Pos) obj;\r
+    } //-- uk.ac.vamsas.objects.core.Pos removePos(int) \r
 \r
     /**\r
      * Method removeSeg\r
@@ -363,12 +363,12 @@ implements java.io.Serializable
      * @param index\r
      * @return Seg\r
      */\r
-    public org.vamsas.objects.core.Seg removeSeg(int index)\r
+    public uk.ac.vamsas.objects.core.Seg removeSeg(int index)\r
     {\r
         java.lang.Object obj = _segList.elementAt(index);\r
         _segList.removeElementAt(index);\r
-        return (org.vamsas.objects.core.Seg) obj;\r
-    } //-- org.vamsas.objects.core.Seg removeSeg(int) \r
+        return (uk.ac.vamsas.objects.core.Seg) obj;\r
+    } //-- uk.ac.vamsas.objects.core.Seg removeSeg(int) \r
 \r
     /**\r
      * Method setPos\r
@@ -378,7 +378,7 @@ implements java.io.Serializable
      * @param index\r
      * @param vPos\r
      */\r
-    public void setPos(int index, org.vamsas.objects.core.Pos vPos)\r
+    public void setPos(int index, uk.ac.vamsas.objects.core.Pos vPos)\r
         throws java.lang.IndexOutOfBoundsException\r
     {\r
         //-- check bounds for index\r
@@ -386,7 +386,7 @@ implements java.io.Serializable
             throw new IndexOutOfBoundsException("setPos: Index value '"+index+"' not in range [0.."+_posList.size()+ "]");\r
         }\r
         _posList.setElementAt(vPos, index);\r
-    } //-- void setPos(int, org.vamsas.objects.core.Pos) \r
+    } //-- void setPos(int, uk.ac.vamsas.objects.core.Pos) \r
 \r
     /**\r
      * Method setPos\r
@@ -395,14 +395,14 @@ implements java.io.Serializable
      * \r
      * @param posArray\r
      */\r
-    public void setPos(org.vamsas.objects.core.Pos[] posArray)\r
+    public void setPos(uk.ac.vamsas.objects.core.Pos[] posArray)\r
     {\r
         //-- copy array\r
         _posList.removeAllElements();\r
         for (int i = 0; i < posArray.length; i++) {\r
             _posList.addElement(posArray[i]);\r
         }\r
-    } //-- void setPos(org.vamsas.objects.core.Pos) \r
+    } //-- void setPos(uk.ac.vamsas.objects.core.Pos) \r
 \r
     /**\r
      * Method setSeg\r
@@ -412,7 +412,7 @@ implements java.io.Serializable
      * @param index\r
      * @param vSeg\r
      */\r
-    public void setSeg(int index, org.vamsas.objects.core.Seg vSeg)\r
+    public void setSeg(int index, uk.ac.vamsas.objects.core.Seg vSeg)\r
         throws java.lang.IndexOutOfBoundsException\r
     {\r
         //-- check bounds for index\r
@@ -420,7 +420,7 @@ implements java.io.Serializable
             throw new IndexOutOfBoundsException("setSeg: Index value '"+index+"' not in range [0.."+_segList.size()+ "]");\r
         }\r
         _segList.setElementAt(vSeg, index);\r
-    } //-- void setSeg(int, org.vamsas.objects.core.Seg) \r
+    } //-- void setSeg(int, uk.ac.vamsas.objects.core.Seg) \r
 \r
     /**\r
      * Method setSeg\r
@@ -429,14 +429,14 @@ implements java.io.Serializable
      * \r
      * @param segArray\r
      */\r
-    public void setSeg(org.vamsas.objects.core.Seg[] segArray)\r
+    public void setSeg(uk.ac.vamsas.objects.core.Seg[] segArray)\r
     {\r
         //-- copy array\r
         _segList.removeAllElements();\r
         for (int i = 0; i < segArray.length; i++) {\r
             _segList.addElement(segArray[i]);\r
         }\r
-    } //-- void setSeg(org.vamsas.objects.core.Seg) \r
+    } //-- void setSeg(uk.ac.vamsas.objects.core.Seg) \r
 \r
     /**\r
      * Method validate\r

diff --git a/src/org/vamsas/objects/core/Score.java b/src/org/vamsas/objects/core/Score.java
index cb294f3..c0e6ec5 100644 (file)
--- a/src/org/vamsas/objects/core/Score.java
+++ b/src/org/vamsas/objects/core/Score.java
@@ -27,7 +27,7 @@ import org.xml.sax.ContentHandler;
  * \r
  * @version $Revision$ $Date$\r
  */\r
-public class Score extends org.vamsas.client.Vobject \r
+public class Score extends uk.ac.vamsas.client.Vobject \r
 implements java.io.Serializable\r
 {\r
 \r

diff --git a/src/org/vamsas/objects/core/Seg.java b/src/org/vamsas/objects/core/Seg.java
index 5e36703..92f1c6b 100644 (file)
--- a/src/org/vamsas/objects/core/Seg.java
+++ b/src/org/vamsas/objects/core/Seg.java
@@ -27,7 +27,7 @@ import org.xml.sax.ContentHandler;
  * \r
  * @version $Revision$ $Date$\r
  */\r
-public class Seg extends org.vamsas.client.Vobject \r
+public class Seg extends uk.ac.vamsas.client.Vobject \r
 implements java.io.Serializable\r
 {\r
 \r

diff --git a/src/org/vamsas/objects/core/SequenceType.java b/src/org/vamsas/objects/core/SequenceType.java
index 96fba5b..ce66db6 100644 (file)
--- a/src/org/vamsas/objects/core/SequenceType.java
+++ b/src/org/vamsas/objects/core/SequenceType.java
@@ -2,7 +2,7 @@
  * This class was automatically generated with 
  * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
  * Schema.
- * $Id$
+ * $Id:SequenceType.java 264 2006-12-14 17:42:54Z JimP $
  */
 
 package org.vamsas.objects.core;
@@ -26,9 +26,9 @@ import org.xml.sax.ContentHandler;
 /**
  * Class SequenceType.
  * 
- * @version $Revision$ $Date$
+ * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
  */
-public class SequenceType extends org.vamsas.client.Vobject 
+public class SequenceType extends uk.ac.vamsas.client.Vobject 
 implements java.io.Serializable
 {
 

diff --git a/src/org/vamsas/objects/core/Tree.java b/src/org/vamsas/objects/core/Tree.java
index 5b9ea99..b23a5dc 100644 (file)
--- a/src/org/vamsas/objects/core/Tree.java
+++ b/src/org/vamsas/objects/core/Tree.java
@@ -2,7 +2,7 @@
  * This class was automatically generated with 
  * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
  * Schema.
- * $Id$
+ * $Id:Tree.java 264 2006-12-14 17:42:54Z JimP $
  */
 
 package org.vamsas.objects.core;
@@ -26,9 +26,9 @@ import org.xml.sax.ContentHandler;
 /**
  * Class Tree.
  * 
- * @version $Revision$ $Date$
+ * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
  */
-public class Tree extends org.vamsas.client.Vobject 
+public class Tree extends uk.ac.vamsas.client.Vobject 
 implements java.io.Serializable
 {
 

diff --git a/src/org/vamsas/objects/core/VAMSAS.java b/src/org/vamsas/objects/core/VAMSAS.java
index c359593..94ab365 100644 (file)
--- a/src/org/vamsas/objects/core/VAMSAS.java
+++ b/src/org/vamsas/objects/core/VAMSAS.java
@@ -2,7 +2,7 @@
  * This class was automatically generated with 
  * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
  * Schema.
- * $Id$
+ * $Id:VAMSAS.java 264 2006-12-14 17:42:54Z JimP $
  */
 
 package org.vamsas.objects.core;
@@ -27,9 +27,9 @@ import org.xml.sax.ContentHandler;
  * contains unassociated trees and a number of analysis sets
  *  
  * 
- * @version $Revision$ $Date$
+ * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
  */
-public class VAMSAS extends org.vamsas.client.Vobject 
+public class VAMSAS extends uk.ac.vamsas.client.Vobject 
 implements java.io.Serializable
 {
 

diff --git a/src/org/vamsas/objects/core/VamsasDocument.java b/src/org/vamsas/objects/core/VamsasDocument.java
index f8df822..ebe6353 100644 (file)
--- a/src/org/vamsas/objects/core/VamsasDocument.java
+++ b/src/org/vamsas/objects/core/VamsasDocument.java
@@ -2,7 +2,7 @@
  * This class was automatically generated with 
  * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
  * Schema.
- * $Id$
+ * $Id:VamsasDocument.java 264 2006-12-14 17:42:54Z JimP $
  */
 
 package org.vamsas.objects.core;
@@ -26,9 +26,9 @@ import org.xml.sax.ContentHandler;
 /**
  * Class VamsasDocument.
  * 
- * @version $Revision$ $Date$
+ * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
  */
-public class VamsasDocument extends org.vamsas.client.Vobject 
+public class VamsasDocument extends uk.ac.vamsas.client.Vobject 
 implements java.io.Serializable
 {
 

diff --git a/src/org/vamsas/objects/utils/AppDataReference.java b/src/org/vamsas/objects/utils/AppDataReference.java
index 414c8da..2afbd6e 100644 (file)
--- a/src/org/vamsas/objects/utils/AppDataReference.java
+++ b/src/org/vamsas/objects/utils/AppDataReference.java
@@ -4,11 +4,12 @@
 package org.vamsas.objects.utils;
 import java.util.Vector;
 
-import org.vamsas.client.ClientHandle;
-import org.vamsas.client.UserHandle;
-import org.vamsas.client.simpleclient.VamsasArchive;
-import org.vamsas.client.simpleclient.VamsasArchiveReader;
 import org.vamsas.objects.core.*;
+
+import uk.ac.vamsas.client.ClientHandle;
+import uk.ac.vamsas.client.UserHandle;
+import uk.ac.vamsas.client.simpleclient.VamsasArchive;
+import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
 /**
  * Form, accessors and validation for ApplicationData references in
  * vamsas document.
@@ -111,9 +112,9 @@ public class AppDataReference {
    * Searches document appData structure for particular combinations of client and user data
    * @param doc the data 
    * @param user template user data to match against
-   * @see AppDataReference.equals(org.vamsas.objects.core.User, org.vamsas.client.UserHandle)
+   * @see AppDataReference.equals(org.vamsas.objects.core.User, uk.ac.vamsas.client.UserHandle)
    * @param app
-   * @see AppDataReference.equals(org.vamsas.objects.core.ApplicationData, org.vamsas.client.ClientHandle)
+   * @see AppDataReference.equals(org.vamsas.objects.core.ApplicationData, uk.ac.vamsas.client.ClientHandle)
    * @return set of matching client app datas for this client and user combination
    */
   static public Vector getUserandApplicationsData(VamsasDocument doc, UserHandle user, ClientHandle app) {

diff --git a/src/org/vamsas/test/ExampleApplication.java b/src/org/vamsas/test/ExampleApplication.java
index 071d20d..b6597be 100644 (file)
--- a/src/org/vamsas/test/ExampleApplication.java
+++ b/src/org/vamsas/test/ExampleApplication.java
@@ -6,7 +6,7 @@
  */
 package org.vamsas.test;
 
-import org.vamsas.client.*;
+import uk.ac.vamsas.client.*;
 
 import java.awt.Event;
 import java.beans.PropertyChangeEvent;
@@ -105,7 +105,7 @@ public class ExampleApplication {
 
     // get IClientFactory
     try {
-      clientfactory = new org.vamsas.client.simpleclient.SimpleClientFactory(args[0]);
+      clientfactory = new uk.ac.vamsas.client.simpleclient.SimpleClientFactory(args[0]);
     } catch (IOException e) {
       System.err.println(e+"\n"+Usage);
       System.exit(1);

diff --git a/src/org/vamsas/test/simpleclient/ArchiveClient.java b/src/org/vamsas/test/simpleclient/ArchiveClient.java
index c681fe0..fdc6898 100644 (file)
--- a/src/org/vamsas/test/simpleclient/ArchiveClient.java
+++ b/src/org/vamsas/test/simpleclient/ArchiveClient.java
@@ -13,21 +13,6 @@ import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.exolab.castor.xml.MarshalException;
 import org.exolab.castor.xml.ValidationException;
-import org.vamsas.client.ClientHandle;
-import org.vamsas.client.IVorbaIdFactory;
-import org.vamsas.client.SessionHandle;
-import org.vamsas.client.UserHandle;
-import org.vamsas.client.Vobject;
-import org.vamsas.client.VorbaId;
-import org.vamsas.client.simpleclient.AppDataOutputStream;
-import org.vamsas.client.simpleclient.FileWatcher;
-import org.vamsas.client.simpleclient.IdFactory;
-import org.vamsas.client.simpleclient.SessionFile;
-import org.vamsas.client.simpleclient.SimpleDocBinding;
-import org.vamsas.client.simpleclient.SimpleDocument;
-import org.vamsas.client.simpleclient.VamsasArchive;
-import org.vamsas.client.simpleclient.VamsasArchiveReader;
-import org.vamsas.client.simpleclient.VamsasFile;
 import org.vamsas.objects.core.AppData;
 import org.vamsas.objects.core.ApplicationData;
 import org.vamsas.objects.core.User;
@@ -39,6 +24,22 @@ import org.vamsas.objects.utils.SeqSet;
 import org.vamsas.objects.utils.document.VersionEntries;
 import org.vamsas.test.objects.Core;
 
+import uk.ac.vamsas.client.ClientHandle;
+import uk.ac.vamsas.client.IVorbaIdFactory;
+import uk.ac.vamsas.client.SessionHandle;
+import uk.ac.vamsas.client.UserHandle;
+import uk.ac.vamsas.client.Vobject;
+import uk.ac.vamsas.client.VorbaId;
+import uk.ac.vamsas.client.simpleclient.AppDataOutputStream;
+import uk.ac.vamsas.client.simpleclient.FileWatcher;
+import uk.ac.vamsas.client.simpleclient.IdFactory;
+import uk.ac.vamsas.client.simpleclient.SessionFile;
+import uk.ac.vamsas.client.simpleclient.SimpleDocBinding;
+import uk.ac.vamsas.client.simpleclient.SimpleDocument;
+import uk.ac.vamsas.client.simpleclient.VamsasArchive;
+import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
+import uk.ac.vamsas.client.simpleclient.VamsasFile;
+
 /**
  * @author jimp
  *  test the VamsasFile routines for watching, reading and updating a vamsas document jar file.
@@ -101,7 +102,7 @@ public class ArchiveClient extends IdFactory {
     watchForChange=true;
     long endtime=System.currentTimeMillis()+time;
     try {
-      org.vamsas.client.simpleclient.Lock doclock;
+      uk.ac.vamsas.client.simpleclient.Lock doclock;
       do {
         doclock=watcher.getChangedState();
         if (doclock==null)
@@ -177,7 +178,7 @@ public class ArchiveClient extends IdFactory {
   public ClientDoc getUpdateable() {
     return getUpdateable(null);
   }
-  public ClientDoc getUpdateable(org.vamsas.client.simpleclient.Lock lock) {
+  public ClientDoc getUpdateable(uk.ac.vamsas.client.simpleclient.Lock lock) {
     getVorbaIdHash().clear();
     valid();
     try {
@@ -283,7 +284,7 @@ public class ArchiveClient extends IdFactory {
     }
     System.out.println("Finished at "+new Date());
   }
-  public org.vamsas.client.Vobject getObject(VorbaId id) {
+  public uk.ac.vamsas.client.Vobject getObject(VorbaId id) {
     Hashtable idhash = this.getVorbaIdHash();
     if (idhash!=null && idhash.containsKey(id))
       return (Vobject) idhash.get(id);

diff --git a/src/org/vamsas/test/simpleclient/ArchiveReader.java b/src/org/vamsas/test/simpleclient/ArchiveReader.java
index d7959b4..5f88d71 100644 (file)
--- a/src/org/vamsas/test/simpleclient/ArchiveReader.java
+++ b/src/org/vamsas/test/simpleclient/ArchiveReader.java
@@ -5,10 +5,11 @@ import java.io.File;
 import java.io.InputStream;
 import java.io.InputStreamReader;
 
-import org.vamsas.client.simpleclient.VamsasArchiveReader;
 import org.vamsas.objects.core.VAMSAS;
 import org.vamsas.objects.core.VamsasDocument;
 
+import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
+
 public class ArchiveReader {
   /**
    * tests VamsasArchiveReader archive reader on a vamsas jar file

diff --git a/src/org/vamsas/test/simpleclient/ArchiveReports.java b/src/org/vamsas/test/simpleclient/ArchiveReports.java
index 4a3a284..26175a7 100644 (file)
--- a/src/org/vamsas/test/simpleclient/ArchiveReports.java
+++ b/src/org/vamsas/test/simpleclient/ArchiveReports.java
@@ -4,9 +4,6 @@ import java.io.InputStream;
 import java.io.PrintStream;
 import java.io.PrintWriter;
 
-import org.vamsas.client.ClientDocument;
-import org.vamsas.client.Vobject;
-import org.vamsas.client.simpleclient.VamsasArchiveReader;
 import org.vamsas.objects.core.Alignment;
 import org.vamsas.objects.core.AppData;
 import org.vamsas.objects.core.ApplicationData;
@@ -18,6 +15,10 @@ import org.vamsas.objects.core.Tree;
 import org.vamsas.objects.core.User;
 import org.vamsas.objects.core.VAMSAS;
 import org.vamsas.objects.core.VamsasDocument;
+
+import uk.ac.vamsas.client.ClientDocument;
+import uk.ac.vamsas.client.Vobject;
+import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
 /**
  * this class contains static methods for writing info to stdout about a vamsas document
  * Methods have a 'cascade' switch to indicate if sub-objects should have info printed on them.

diff --git a/src/org/vamsas/test/simpleclient/ArchiveStreamReader.java b/src/org/vamsas/test/simpleclient/ArchiveStreamReader.java
index 1415731..82037a5 100644 (file)
--- a/src/org/vamsas/test/simpleclient/ArchiveStreamReader.java
+++ b/src/org/vamsas/test/simpleclient/ArchiveStreamReader.java
@@ -5,12 +5,13 @@ import java.io.File;
 import java.io.InputStream;
 import java.io.InputStreamReader;
 
-import org.vamsas.client.simpleclient.SessionFile;
-import org.vamsas.client.simpleclient.VamsasArchiveReader;
-import org.vamsas.client.simpleclient.VamsasFile;
 import org.vamsas.objects.core.VAMSAS;
 import org.vamsas.objects.core.VamsasDocument;
 
+import uk.ac.vamsas.client.simpleclient.SessionFile;
+import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
+import uk.ac.vamsas.client.simpleclient.VamsasFile;
+
 public class ArchiveStreamReader {
   /**
    * tests VamsasArchiveReader archive reader on a vamsas jar file opened as a stream

diff --git a/src/org/vamsas/test/simpleclient/ArchiveWatcher.java b/src/org/vamsas/test/simpleclient/ArchiveWatcher.java
index c1c7422..98aa4d0 100644 (file)
--- a/src/org/vamsas/test/simpleclient/ArchiveWatcher.java
+++ b/src/org/vamsas/test/simpleclient/ArchiveWatcher.java
@@ -4,13 +4,14 @@ import java.io.File;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.vamsas.client.ClientHandle;
-import org.vamsas.client.simpleclient.FileWatcher;
-import org.vamsas.client.simpleclient.Lock;
-import org.vamsas.client.simpleclient.SimpleDocument;
-import org.vamsas.client.simpleclient.VamsasArchiveReader;
-import org.vamsas.client.simpleclient.VamsasFile;
 import org.vamsas.objects.core.VamsasDocument;
+
+import uk.ac.vamsas.client.ClientHandle;
+import uk.ac.vamsas.client.simpleclient.FileWatcher;
+import uk.ac.vamsas.client.simpleclient.Lock;
+import uk.ac.vamsas.client.simpleclient.SimpleDocument;
+import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
+import uk.ac.vamsas.client.simpleclient.VamsasFile;
 /**
  * demo of archive watching process - should mimic the clientsfileTest watcher/monitor process.
  * @author jimp

diff --git a/src/org/vamsas/test/simpleclient/ArchiveWriter.java b/src/org/vamsas/test/simpleclient/ArchiveWriter.java
index d6f8ee9..f99f400 100644 (file)
--- a/src/org/vamsas/test/simpleclient/ArchiveWriter.java
+++ b/src/org/vamsas/test/simpleclient/ArchiveWriter.java
@@ -11,16 +11,18 @@ import java.util.Vector;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.vamsas.client.simpleclient.VamsasArchive;
-import org.vamsas.client.simpleclient.VamsasArchiveReader;
-import org.vamsas.objects.core.Alignment;
-import org.vamsas.objects.core.ApplicationData;
-import org.vamsas.objects.core.Entry;
-import org.vamsas.objects.core.Instance;
-import org.vamsas.objects.core.Provenance;
-import org.vamsas.objects.core.VAMSAS;
-import org.vamsas.objects.core.VamsasDocument;
-import org.vamsas.objects.utils.ProvenanceStuff;
+der;
+import uk.ac.vamsas.objects.core.Alignment;
+import uk.ac.vamsas.objects.core.ApplicationData;
+import uk.ac.vamsas.objects.core.Entry;
+import uk.ac.vamsas.objects.core.Instance;
+import uk.ac.vamsas.objects.core.Provenance;
+import uk.ac.vamsas.objects.core.VAMSAS;
+import uk.ac.vamsas.objects.core.VamsasDocument;
+import uk.ac.vamsas.objects.ut
+import uk.ac.vamsas.client.simpleclient.VamsasArchive;
+import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
+ils.ProvenanceStuff;
 
 public class ArchiveWriter {
   

diff --git a/src/org/vamsas/test/simpleclient/ClientDoc.java b/src/org/vamsas/test/simpleclient/ClientDoc.java
index da05e00..9ff7ee3 100644 (file)
--- a/src/org/vamsas/test/simpleclient/ClientDoc.java
+++ b/src/org/vamsas/test/simpleclient/ClientDoc.java
@@ -5,21 +5,22 @@ import java.util.Vector;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.vamsas.client.IClientAppdata;
-import org.vamsas.client.Vobject;
-import org.vamsas.client.VorbaId;
-import org.vamsas.client.simpleclient.ClientDocument;
-import org.vamsas.client.simpleclient.VamsasArchive;
-import org.vamsas.client.simpleclient.VamsasArchiveReader;
 import org.vamsas.objects.core.Entry;
 import org.vamsas.objects.core.VAMSAS;
 import org.vamsas.objects.core.VamsasDocument;
 import org.vamsas.objects.utils.ProvenanceStuff;
 
+import uk.ac.vamsas.client.IClientAppdata;
+import uk.ac.vamsas.client.Vobject;
+import uk.ac.vamsas.client.VorbaId;
+import uk.ac.vamsas.client.simpleclient.ClientDocument;
+import uk.ac.vamsas.client.simpleclient.VamsasArchive;
+import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
+
 // simple holder to pass to client.
-public class ClientDoc extends org.vamsas.client.ClientDocument {
+public class ClientDoc extends uk.ac.vamsas.client.ClientDocument {
   /* (non-Javadoc)
-   * @see org.vamsas.client.IClientDocument#getClientAppdata()
+   * @see uk.ac.vamsas.client.IClientDocument#getClientAppdata()
    */
   public IClientAppdata getClientAppdata() {
     throw new Error("Appdata access is not implemented in the test.simpleclient.ClientDoc instance."); // TODO Auto-generated method stub
@@ -202,7 +203,7 @@ public class ClientDoc extends org.vamsas.client.ClientDocument {
   
   /* (non-Javadoc)
    * LATER: decide: this affects the next call to getVamsasRoots()
-   * @see org.vamsas.client.IClientDocument#addVamsasRoot(org.vamsas.objects.core.VAMSAS)
+   * @see uk.ac.vamsas.client.IClientDocument#addVamsasRoot(org.vamsas.objects.core.VAMSAS)
    */
   public void addVamsasRoot(VAMSAS newroot) {
     if (doc==null) {
@@ -269,7 +270,7 @@ public class ClientDoc extends org.vamsas.client.ClientDocument {
     return null;
   }
   /* (non-Javadoc)
-   * @see org.vamsas.client.IClientDocument#registerObject(org.vamsas.client.Vobject)
+   * @see uk.ac.vamsas.client.IClientDocument#registerObject(uk.ac.vamsas.client.Vobject)
    */
   public VorbaId registerObject(Vobject unregistered) {
     if (doc==null) {
@@ -296,7 +297,7 @@ public class ClientDoc extends org.vamsas.client.ClientDocument {
   /*
    * (non-Javadoc)
    * 
-   * @see org.vamsas.client.IClientDocument#getObject(org.vamsas.client.VorbaId)
+   * @see uk.ac.vamsas.client.IClientDocument#getObject(uk.ac.vamsas.client.VorbaId)
    */
   public Vobject getObject(VorbaId id) {
     if (objrefs==null) {
@@ -312,7 +313,7 @@ public class ClientDoc extends org.vamsas.client.ClientDocument {
   /*
    * (non-Javadoc)
    * 
-   * @see org.vamsas.client.IClientDocument#getObjects(org.vamsas.client.VorbaId[])
+   * @see uk.ac.vamsas.client.IClientDocument#getObjects(uk.ac.vamsas.client.VorbaId[])
    */
   public Vobject[] getObjects(VorbaId[] ids) {
     if (objrefs==null) {

diff --git a/src/org/vamsas/test/simpleclient/ClientsFileTest.java b/src/org/vamsas/test/simpleclient/ClientsFileTest.java
index 46fbfd7..1a2ab35 100644 (file)
--- a/src/org/vamsas/test/simpleclient/ClientsFileTest.java
+++ b/src/org/vamsas/test/simpleclient/ClientsFileTest.java
@@ -4,10 +4,11 @@ import java.io.File;
 import java.util.Iterator;
 import java.util.Vector;
 
-import org.vamsas.client.ClientHandle;
-import org.vamsas.client.simpleclient.ClientsFile;
-import org.vamsas.client.simpleclient.FileWatcher;
-import org.vamsas.client.simpleclient.Lock;
+
+import uk.ac.vamsas.client.ClientHandle;
+import uk.ac.vamsas.client.simpleclient.ClientsFile;
+import uk.ac.vamsas.client.simpleclient.FileWatcher;
+import uk.ac.vamsas.client.simpleclient.Lock;
 
 public class ClientsFileTest {
   private static CommandProcessor cproc;

diff --git a/src/org/vamsas/test/simpleclient/VamsasArchive.java b/src/org/vamsas/test/simpleclient/VamsasArchive.java
index 09ddf34..651979c 100644 (file)
--- a/src/org/vamsas/test/simpleclient/VamsasArchive.java
+++ b/src/org/vamsas/test/simpleclient/VamsasArchive.java
@@ -5,23 +5,24 @@ import java.io.ObjectOutputStream;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.vamsas.client.simpleclient.Lock;
-import org.vamsas.client.simpleclient.SessionFile;
-import org.vamsas.client.simpleclient.SimpleDocument;
-import org.vamsas.client.simpleclient.VamsasArchiveReader;
-import org.vamsas.client.simpleclient.VamsasFile;
 import org.vamsas.objects.core.ApplicationData;
 import org.vamsas.objects.core.User;
 import org.vamsas.objects.core.VAMSAS;
 import org.vamsas.objects.core.VamsasDocument;
 import org.vamsas.test.objects.Core;
 
+import uk.ac.vamsas.client.simpleclient.Lock;
+import uk.ac.vamsas.client.simpleclient.SessionFile;
+import uk.ac.vamsas.client.simpleclient.SimpleDocument;
+import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
+import uk.ac.vamsas.client.simpleclient.VamsasFile;
+
 public class VamsasArchive {
   /**
    * test the org.vamsas.simpleclient.vamsasArchive class
    */
   static Log log = LogFactory.getLog(VamsasArchive.class);
-  public static ApplicationData makeDemoAppdata(org.vamsas.client.simpleclient.VamsasArchive va, String apname, String userName, String userOrg) {
+  public static ApplicationData makeDemoAppdata(uk.ac.vamsas.client.simpleclient.VamsasArchive va, String apname, String userName, String userOrg) {
     if (va==null)
       return null;
     VamsasArchiveReader vread=null;
@@ -98,7 +99,7 @@ public class VamsasArchive {
       else
         av = new File("test/vamsas.zip");
       log.info("Opening archive "+av);
-      org.vamsas.client.simpleclient.VamsasArchive varchive = new org.vamsas.client.simpleclient.VamsasArchive(av, true);
+      uk.ac.vamsas.client.simpleclient.VamsasArchive varchive = new uk.ac.vamsas.client.simpleclient.VamsasArchive(av, true);
       
       VAMSAS[] roots = (VAMSAS[]) varchive.getOriginalRoots();
       
@@ -131,12 +132,12 @@ public class VamsasArchive {
       }
         
       log.info("Now writing new Archive into "+newf.getAbsolutePath());
-      org.vamsas.client.simpleclient.VamsasArchive va=null;
+      uk.ac.vamsas.client.simpleclient.VamsasArchive va=null;
       { // hold lock over deletion and write of new archive.
         //Lock wlock = sfile.getLock();
         //newf.delete(); // clear out old file.
         sfile.getLock();
-        va = new org.vamsas.client.simpleclient.VamsasArchive(newf, true, true, sfile);
+        va = new uk.ac.vamsas.client.simpleclient.VamsasArchive(newf, true, true, sfile);
         // open another and...
         ApplicationData appdata = makeDemoAppdata(va, 
             "org.vamsas.test.simpleclient.VamsasArchive", "arnold Bugger esq", "disOrganised");
@@ -170,7 +171,7 @@ public class VamsasArchive {
         log.info("Didn't cancel.");
       long t=System.currentTimeMillis()+200; while (t>System.currentTimeMillis());
       log.info("Now testing archive update.");
-      va = new org.vamsas.client.simpleclient.VamsasArchive(newf, false, true, sfile);
+      va = new uk.ac.vamsas.client.simpleclient.VamsasArchive(newf, false, true, sfile);
       doc = va.getVamsasDocument();
       doc.addVAMSAS(Core.getDemoVamsas());
       doc.addApplicationData(makeDemoAppdata(va, 

diff --git a/src/org/vamsas/test/simpleclient/simpleapp/VamsasClient.java b/src/org/vamsas/test/simpleclient/simpleapp/VamsasClient.java
index 2b70a0a..338bc70 100644 (file)
--- a/src/org/vamsas/test/simpleclient/simpleapp/VamsasClient.java
+++ b/src/org/vamsas/test/simpleclient/simpleapp/VamsasClient.java
@@ -14,15 +14,16 @@ import java.util.jar.JarOutputStream;
 
 import javax.swing.JInternalFrame;
 
-import org.vamsas.client.UserHandle;
-import org.vamsas.client.simpleclient.FileWatcher;
-import org.vamsas.client.simpleclient.VamsasArchive;
-import org.vamsas.client.simpleclient.VamsasFile;
 import org.vamsas.objects.core.Entry;
 import org.vamsas.objects.core.VamsasDocument;
 import org.vamsas.test.simpleclient.ArchiveClient;
 import org.vamsas.test.simpleclient.ClientDoc;
 
+import uk.ac.vamsas.client.UserHandle;
+import uk.ac.vamsas.client.simpleclient.FileWatcher;
+import uk.ac.vamsas.client.simpleclient.VamsasArchive;
+import uk.ac.vamsas.client.simpleclient.VamsasFile;
+
 /**
  * @author jimp
  *

diff --git a/src/org/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java b/src/org/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java
index 9114e88..d0b5a2a 100644 (file)
--- a/src/org/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java
+++ b/src/org/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java
@@ -19,8 +19,6 @@
 \r
 package org.vamsas.test.simpleclient.simpleapp;\r
 \r
-import org.vamsas.client.Vobject;\r
-import org.vamsas.client.VorbaId;\r
 import org.vamsas.objects.core.*;\r
 import org.vamsas.objects.utils.DocumentStuff;\r
 import org.vamsas.test.simpleclient.ClientDoc;\r
@@ -36,6 +34,9 @@ import java.util.jar.*;
 import org.exolab.castor.xml.*;\r
 import org.exolab.castor.mapping.Mapping;\r
 \r
+import uk.ac.vamsas.client.Vobject;\r
+import uk.ac.vamsas.client.VorbaId;\r
+\r
 /*\r
  * \r
  * static {\r
@@ -96,7 +97,7 @@ public class VamsasDatastore {
    * @param vobj\r
    * @return Jalview datamodel object bound to the vamsas document object\r
    */\r
-  protected Object getvObj2jv(org.vamsas.client.Vobject vobj) {\r
+  protected Object getvObj2jv(uk.ac.vamsas.client.Vobject vobj) {\r
     VorbaId id = vobj.getVorbaId();\r
     if (id == null)\r
     {\r
@@ -110,7 +111,7 @@ public class VamsasDatastore {
     return null;\r
   }\r
 \r
-  protected void bindjvvobj(Object jvobj, org.vamsas.client.Vobject vobj) {\r
+  protected void bindjvvobj(Object jvobj, uk.ac.vamsas.client.Vobject vobj) {\r
     VorbaId id = vobj.getVorbaId();\r
     if (id == null)\r
     {\r