refactoring org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@277 be28352e-c001-0410-b1a7-c7978e42abec

diff --git a/src/org/vamsas/objects/utils/AppDataReference.java b/src/org/vamsas/objects/utils/AppDataReference.java
index 2afbd6e..c0e8109 100644 (file)
--- a/src/org/vamsas/objects/utils/AppDataReference.java
+++ b/src/org/vamsas/objects/utils/AppDataReference.java
@@ -4,12 +4,12 @@
 package org.vamsas.objects.utils;
 import java.util.Vector;
 
-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;
+import uk.ac.vamsas.objects.core.*;
 /**
  * Form, accessors and validation for ApplicationData references in
  * vamsas document.
@@ -62,7 +62,7 @@ public class AppDataReference {
    * @param doc
    * @param test interface implemented by the filter selecting particular AppDatas.
    * @param cascade if true only User objects for ApplicationData objects that test.process returned true will be tested.
-   * @return set of org.vamsas.objects.core.AppData objects for which test.process returned true
+   * @return set of uk.ac.vamsas.objects.core.AppData objects for which test.process returned true
    */
   static public Vector searchAppDatas(VamsasDocument doc, IAppDSearch test, boolean cascade) {
     if ((doc!=null) && (doc.getApplicationDataCount()>0)) {
@@ -112,9 +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, uk.ac.vamsas.client.UserHandle)
+   * @see AppDataReference.equals(uk.ac.vamsas.objects.core.User, uk.ac.vamsas.client.UserHandle)
    * @param app
-   * @see AppDataReference.equals(org.vamsas.objects.core.ApplicationData, uk.ac.vamsas.client.ClientHandle)
+   * @see AppDataReference.equals(uk.ac.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/objects/utils/DocumentStuff.java b/src/org/vamsas/objects/utils/DocumentStuff.java
index 825a3ae..dcf3edb 100644 (file)
--- a/src/org/vamsas/objects/utils/DocumentStuff.java
+++ b/src/org/vamsas/objects/utils/DocumentStuff.java
@@ -1,8 +1,9 @@
 package org.vamsas.objects.utils;
 
-import org.vamsas.objects.core.*;
 import org.vamsas.objects.utils.document.VersionEntries;
 
+import uk.ac.vamsas.objects.core.*;
+
 /**
  * various vamsas-client independent helpers 
  * for creating and manipulating the vamsasDocument Vobject

diff --git a/src/org/vamsas/objects/utils/GlyphDictionary.java b/src/org/vamsas/objects/utils/GlyphDictionary.java
index 1ed7b20..88134bf 100644 (file)
--- a/src/org/vamsas/objects/utils/GlyphDictionary.java
+++ b/src/org/vamsas/objects/utils/GlyphDictionary.java
@@ -1,7 +1,7 @@
 package org.vamsas.objects.utils;\r
 \r
 /**\r
- * dict attribute values for glyph symbol sets found in org.vamsas.objects.core.AnnotationElement\r
+ * dict attribute values for glyph symbol sets found in uk.ac.vamsas.objects.core.AnnotationElement\r
  * TODO: add validators and multilength symbols.\r
  * @author JimP\r
  *\r

diff --git a/src/org/vamsas/objects/utils/ProvenanceStuff.java b/src/org/vamsas/objects/utils/ProvenanceStuff.java
index 2e813f7..9d668d5 100644 (file)
--- a/src/org/vamsas/objects/utils/ProvenanceStuff.java
+++ b/src/org/vamsas/objects/utils/ProvenanceStuff.java
@@ -4,8 +4,9 @@ import java.util.Date;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.vamsas.objects.core.Entry;
-import org.vamsas.objects.core.Provenance;
+
+import uk.ac.vamsas.objects.core.Entry;
+import uk.ac.vamsas.objects.core.Provenance;
 
 public class ProvenanceStuff {
 

diff --git a/src/org/vamsas/objects/utils/Seq.java b/src/org/vamsas/objects/utils/Seq.java
index b1955a1..7785050 100644 (file)
--- a/src/org/vamsas/objects/utils/Seq.java
+++ b/src/org/vamsas/objects/utils/Seq.java
@@ -12,9 +12,9 @@ import java.io.OutputStream;
 import java.io.OutputStreamWriter;
 import java.util.regex.Pattern;
 
-import org.vamsas.objects.core.AlignmentSequence;
-import org.vamsas.objects.core.Sequence;
-import org.vamsas.objects.core.SequenceType;
+import uk.ac.vamsas.objects.core.AlignmentSequence;
+import uk.ac.vamsas.objects.core.Sequence;
+import uk.ac.vamsas.objects.core.SequenceType;
 
 /**
  * @author jimp

diff --git a/src/org/vamsas/objects/utils/SeqAln.java b/src/org/vamsas/objects/utils/SeqAln.java
index 5e351f9..b76d8ce 100644 (file)
--- a/src/org/vamsas/objects/utils/SeqAln.java
+++ b/src/org/vamsas/objects/utils/SeqAln.java
@@ -17,7 +17,7 @@ import java.util.StringTokenizer;
 import java.util.Vector;
 import java.util.regex.Pattern;
 
-import org.vamsas.objects.core.*;
+import uk.ac.vamsas.objects.core.*;
 
 /**
  * @author jimp
@@ -25,7 +25,7 @@ import org.vamsas.objects.core.*;
  * TODO To change the template for this generated type comment go to Window -
  * Preferences - Java - Code Style - Code Templates
  */
-public class SeqAln extends org.vamsas.objects.core.Alignment {
+public class SeqAln extends uk.ac.vamsas.objects.core.Alignment {
 
   public static Sequence[] ReadClustalFile(InputStream os) throws Exception {
     System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method

diff --git a/src/org/vamsas/objects/utils/SeqSet.java b/src/org/vamsas/objects/utils/SeqSet.java
index 294ce43..88e5345 100644 (file)
--- a/src/org/vamsas/objects/utils/SeqSet.java
+++ b/src/org/vamsas/objects/utils/SeqSet.java
@@ -18,7 +18,7 @@ import java.util.Hashtable;
 import java.util.Vector;
 import java.util.regex.Pattern;
 
-import org.vamsas.objects.core.*;
+import uk.ac.vamsas.objects.core.*;
 
 /**
  * @author jimp

diff --git a/src/org/vamsas/test/objects/Core.java b/src/org/vamsas/test/objects/Core.java
index ffc8a23..0436736 100644 (file)
--- a/src/org/vamsas/test/objects/Core.java
+++ b/src/org/vamsas/test/objects/Core.java
@@ -5,14 +5,15 @@ package org.vamsas.test.objects;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.vamsas.objects.core.*;
 import org.vamsas.objects.utils.*;
 import org.vamsas.objects.utils.document.*;
 import org.vamsas.test.simpleclient.ArchiveReports;
 
+import uk.ac.vamsas.objects.core.*;
+
 /**
  * @author jim
- * test XSD-Java binding classes in org.vamsas.objects.core
+ * test XSD-Java binding classes in uk.ac.vamsas.objects.core
  */
 public class Core {
   static Log log = LogFactory.getLog(Core.class);

diff --git a/src/org/vamsas/test/simpleclient/ArchiveClient.java b/src/org/vamsas/test/simpleclient/ArchiveClient.java
index fdc6898..0681c0f 100644 (file)
--- a/src/org/vamsas/test/simpleclient/ArchiveClient.java
+++ b/src/org/vamsas/test/simpleclient/ArchiveClient.java
@@ -13,10 +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.objects.core.AppData;
-import org.vamsas.objects.core.ApplicationData;
-import org.vamsas.objects.core.User;
-import org.vamsas.objects.core.VamsasDocument;
 import org.vamsas.objects.utils.AppDataReference;
 import org.vamsas.objects.utils.DocumentStuff;
 import org.vamsas.objects.utils.ProvenanceStuff;
@@ -39,6 +35,10 @@ 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;
+import uk.ac.vamsas.objects.core.AppData;
+import uk.ac.vamsas.objects.core.ApplicationData;
+import uk.ac.vamsas.objects.core.User;
+import uk.ac.vamsas.objects.core.VamsasDocument;
 
 /**
  * @author jimp

diff --git a/src/org/vamsas/test/simpleclient/ArchiveReader.java b/src/org/vamsas/test/simpleclient/ArchiveReader.java
index 5f88d71..971bfa0 100644 (file)
--- a/src/org/vamsas/test/simpleclient/ArchiveReader.java
+++ b/src/org/vamsas/test/simpleclient/ArchiveReader.java
@@ -5,10 +5,10 @@ import java.io.File;
 import java.io.InputStream;
 import java.io.InputStreamReader;
 
-import org.vamsas.objects.core.VAMSAS;
-import org.vamsas.objects.core.VamsasDocument;
 
 import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
+import uk.ac.vamsas.objects.core.VAMSAS;
+import uk.ac.vamsas.objects.core.VamsasDocument;
 
 public class ArchiveReader {
   /**

diff --git a/src/org/vamsas/test/simpleclient/ArchiveReports.java b/src/org/vamsas/test/simpleclient/ArchiveReports.java
index 26175a7..a2a2dfe 100644 (file)
--- a/src/org/vamsas/test/simpleclient/ArchiveReports.java
+++ b/src/org/vamsas/test/simpleclient/ArchiveReports.java
@@ -4,21 +4,21 @@ import java.io.InputStream;
 import java.io.PrintStream;
 import java.io.PrintWriter;
 
-import org.vamsas.objects.core.Alignment;
-import org.vamsas.objects.core.AppData;
-import org.vamsas.objects.core.ApplicationData;
-import org.vamsas.objects.core.DataSet;
-import org.vamsas.objects.core.Entry;
-import org.vamsas.objects.core.Instance;
-import org.vamsas.objects.core.Provenance;
-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;
+import uk.ac.vamsas.objects.core.Alignment;
+import uk.ac.vamsas.objects.core.AppData;
+import uk.ac.vamsas.objects.core.ApplicationData;
+import uk.ac.vamsas.objects.core.DataSet;
+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.Tree;
+import uk.ac.vamsas.objects.core.User;
+import uk.ac.vamsas.objects.core.VAMSAS;
+import uk.ac.vamsas.objects.core.VamsasDocument;
 /**
  * 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 82037a5..c1f9b58 100644 (file)
--- a/src/org/vamsas/test/simpleclient/ArchiveStreamReader.java
+++ b/src/org/vamsas/test/simpleclient/ArchiveStreamReader.java
@@ -5,12 +5,12 @@ import java.io.File;
 import java.io.InputStream;
 import java.io.InputStreamReader;
 
-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;
+import uk.ac.vamsas.objects.core.VAMSAS;
+import uk.ac.vamsas.objects.core.VamsasDocument;
 
 public class ArchiveStreamReader {
   /**

diff --git a/src/org/vamsas/test/simpleclient/ArchiveWatcher.java b/src/org/vamsas/test/simpleclient/ArchiveWatcher.java
index 98aa4d0..08a6522 100644 (file)
--- a/src/org/vamsas/test/simpleclient/ArchiveWatcher.java
+++ b/src/org/vamsas/test/simpleclient/ArchiveWatcher.java
@@ -4,7 +4,6 @@ import java.io.File;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.vamsas.objects.core.VamsasDocument;
 
 import uk.ac.vamsas.client.ClientHandle;
 import uk.ac.vamsas.client.simpleclient.FileWatcher;
@@ -12,6 +11,7 @@ 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;
+import uk.ac.vamsas.objects.core.VamsasDocument;
 /**
  * demo of archive watching process - should mimic the clientsfileTest watcher/monitor process.
  * @author jimp

diff --git a/src/org/vamsas/test/simpleclient/ClientDoc.java b/src/org/vamsas/test/simpleclient/ClientDoc.java
index 9ff7ee3..80b5f6e 100644 (file)
--- a/src/org/vamsas/test/simpleclient/ClientDoc.java
+++ b/src/org/vamsas/test/simpleclient/ClientDoc.java
@@ -5,9 +5,6 @@ import java.util.Vector;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-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;
@@ -16,6 +13,9 @@ 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;
+import uk.ac.vamsas.objects.core.Entry;
+import uk.ac.vamsas.objects.core.VAMSAS;
+import uk.ac.vamsas.objects.core.VamsasDocument;
 
 // simple holder to pass to client.
 public class ClientDoc extends uk.ac.vamsas.client.ClientDocument {
@@ -28,7 +28,7 @@ public class ClientDoc extends uk.ac.vamsas.client.ClientDocument {
   protected boolean isModified=false;
   private Log log = LogFactory.getLog(ClientDoc.class);
   protected VamsasDocument doc;
-  public org.vamsas.objects.core.VAMSAS[] _VamsasRoots;
+  public uk.ac.vamsas.objects.core.VAMSAS[] _VamsasRoots;
   protected VamsasArchive iohandler=null;
   protected VamsasArchiveReader reader=null;
   private String user=null;
@@ -203,7 +203,7 @@ public class ClientDoc extends uk.ac.vamsas.client.ClientDocument {
   
   /* (non-Javadoc)
    * LATER: decide: this affects the next call to getVamsasRoots()
-   * @see uk.ac.vamsas.client.IClientDocument#addVamsasRoot(org.vamsas.objects.core.VAMSAS)
+   * @see uk.ac.vamsas.client.IClientDocument#addVamsasRoot(uk.ac.vamsas.objects.core.VAMSAS)
    */
   public void addVamsasRoot(VAMSAS newroot) {
     if (doc==null) {

diff --git a/src/org/vamsas/test/simpleclient/VamsasArchive.java b/src/org/vamsas/test/simpleclient/VamsasArchive.java
index 651979c..c98b4b7 100644 (file)
--- a/src/org/vamsas/test/simpleclient/VamsasArchive.java
+++ b/src/org/vamsas/test/simpleclient/VamsasArchive.java
@@ -5,10 +5,6 @@ import java.io.ObjectOutputStream;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-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;
@@ -16,6 +12,10 @@ 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;
+import uk.ac.vamsas.objects.core.ApplicationData;
+import uk.ac.vamsas.objects.core.User;
+import uk.ac.vamsas.objects.core.VAMSAS;
+import uk.ac.vamsas.objects.core.VamsasDocument;
 
 public class VamsasArchive {
   /**

diff --git a/src/org/vamsas/test/simpleclient/simpleapp/VamsasClient.java b/src/org/vamsas/test/simpleclient/simpleapp/VamsasClient.java
index 338bc70..71beb89 100644 (file)
--- a/src/org/vamsas/test/simpleclient/simpleapp/VamsasClient.java
+++ b/src/org/vamsas/test/simpleclient/simpleapp/VamsasClient.java
@@ -14,8 +14,6 @@ import java.util.jar.JarOutputStream;
 
 import javax.swing.JInternalFrame;
 
-import org.vamsas.objects.core.Entry;
-import org.vamsas.objects.core.VamsasDocument;
 import org.vamsas.test.simpleclient.ArchiveClient;
 import org.vamsas.test.simpleclient.ClientDoc;
 
@@ -23,6 +21,8 @@ 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;
+import uk.ac.vamsas.objects.core.Entry;
+import uk.ac.vamsas.objects.core.VamsasDocument;
 
 /**
  * @author jimp
@@ -119,7 +119,7 @@ public class VamsasClient extends ArchiveClient {
    * @return a base provenance entry used by the VamsasDatastore object to get attributes from. this isn't particularly elegant either.
    */
        private Entry baseProvEntry() {
-    org.vamsas.objects.core.Entry pentry = new org.vamsas.objects.core.Entry();
+    uk.ac.vamsas.objects.core.Entry pentry = new uk.ac.vamsas.objects.core.Entry();
     pentry.setUser(this.getProvenanceUser());
     pentry.setApp(this.getClientHandle().getClientName());
     pentry.setDate(new org.exolab.castor.types.Date(new java.util.Date()));

diff --git a/src/org/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java b/src/org/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java
index d0b5a2a..8581ba7 100644 (file)
--- a/src/org/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java
+++ b/src/org/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java
@@ -19,7 +19,6 @@
 \r
 package org.vamsas.test.simpleclient.simpleapp;\r
 \r
-import org.vamsas.objects.core.*;\r
 import org.vamsas.objects.utils.DocumentStuff;\r
 import org.vamsas.test.simpleclient.ClientDoc;\r
 \r
@@ -36,6 +35,7 @@ import org.exolab.castor.mapping.Mapping;
 \r
 import uk.ac.vamsas.client.Vobject;\r
 import uk.ac.vamsas.client.VorbaId;\r
+import uk.ac.vamsas.objects.core.*;\r
 \r
 /*\r
  * \r

diff --git a/src/uk/ac/vamsas/client/ClientDocument.java b/src/uk/ac/vamsas/client/ClientDocument.java
index a66ed9d..49f949c 100644 (file)
--- a/src/uk/ac/vamsas/client/ClientDocument.java
+++ b/src/uk/ac/vamsas/client/ClientDocument.java
@@ -7,7 +7,8 @@ import java.util.Hashtable;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.vamsas.objects.core.VAMSAS;
+
+import uk.ac.vamsas.objects.core.VAMSAS;
 
 /**
  * skeleton abstract class to allow client implementations 

diff --git a/src/uk/ac/vamsas/client/IClientDocument.java b/src/uk/ac/vamsas/client/IClientDocument.java
index 1a58d2f..5244849 100644 (file)
--- a/src/uk/ac/vamsas/client/IClientDocument.java
+++ b/src/uk/ac/vamsas/client/IClientDocument.java
@@ -6,7 +6,7 @@
  */
 package uk.ac.vamsas.client;
 
-import org.vamsas.objects.core.VAMSAS;
+import uk.ac.vamsas.objects.core.VAMSAS;
 
 
 /**
@@ -76,7 +76,7 @@ public interface IClientDocument {
    * 
    * Note: An Vobject with valid VorbaId will not be reregistered.
    * Advice: Calling this method for a high-level Vobject 
-   * (such as org.vamsas.objects.core.VAMSAS) will 
+   * (such as uk.ac.vamsas.objects.core.VAMSAS) will 
    * register all its component objects too.
    * 
    * @param unregistered unregistered vamsas Vobject

diff --git a/src/uk/ac/vamsas/client/VorbaXmlBinder.java b/src/uk/ac/vamsas/client/VorbaXmlBinder.java
index 330372a..1834e95 100644 (file)
--- a/src/uk/ac/vamsas/client/VorbaXmlBinder.java
+++ b/src/uk/ac/vamsas/client/VorbaXmlBinder.java
@@ -24,7 +24,8 @@ import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.UnmarshalListener;
 import org.exolab.castor.xml.Unmarshaller;
 import org.exolab.castor.xml.ValidationException;
-import org.vamsas.objects.core.VamsasDocument;
+
+import uk.ac.vamsas.objects.core.VamsasDocument;
 /**
  * Implements the Vamsas Vobject ID machinery for translating 
  * between non-volatile XML IDs and Vobject references. Use the
@@ -193,7 +194,7 @@ public class VorbaXmlBinder implements UnmarshalListener {
      * obtained from the VorbaIdFactory's VorbaId, Vobject.get__last_Hash() pairs (if any) 
      * @param instream - the XML input stream 
    * @param factory - the SimpleClient's properly configured VorbaId factory to make new references.
-   * @param root the root element's org.vamsas.objects.core Vobject.
+   * @param root the root element's uk.ac.vamsas.objects.core Vobject.
      * @return null or {(Object) VamsasDocument Vobject, (Object) Hashtable of Vobject references, (Object) Boolean(sync), (Object) Vector of updated objects in document }
      */
   public static Object[] getVamsasObjects(Reader instream,

diff --git a/src/uk/ac/vamsas/client/simpleclient/ClientDocument.java b/src/uk/ac/vamsas/client/simpleclient/ClientDocument.java
index 86294be..f853937 100644 (file)
--- a/src/uk/ac/vamsas/client/simpleclient/ClientDocument.java
+++ b/src/uk/ac/vamsas/client/simpleclient/ClientDocument.java
@@ -8,10 +8,6 @@ import java.util.Vector;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-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.objects.utils.AppDataReference;
 import org.vamsas.test.objects.Core;
 
@@ -21,6 +17,10 @@ import uk.ac.vamsas.client.IClientDocument;
 import uk.ac.vamsas.client.UserHandle;
 import uk.ac.vamsas.client.Vobject;
 import uk.ac.vamsas.client.VorbaId;
+import uk.ac.vamsas.objects.core.ApplicationData;
+import uk.ac.vamsas.objects.core.User;
+import uk.ac.vamsas.objects.core.VAMSAS;
+import uk.ac.vamsas.objects.core.VamsasDocument;
 
 /**
  * Maintains a collection of vamsas objects, appdatas and states, and provides api for a SimpleClient's client.
@@ -293,7 +293,7 @@ public class ClientDocument extends uk.ac.vamsas.client.ClientDocument implement
   
   /* (non-Javadoc)
    * LATER: decide: this affects the next call to getVamsasRoots()
-   * @see uk.ac.vamsas.client.IClientDocument#addVamsasRoot(org.vamsas.objects.core.VAMSAS)
+   * @see uk.ac.vamsas.client.IClientDocument#addVamsasRoot(uk.ac.vamsas.objects.core.VAMSAS)
    */
   public void addVamsasRoot(VAMSAS newroot) {
     if (doc==null) {

diff --git a/src/uk/ac/vamsas/client/simpleclient/SimpleClient.java b/src/uk/ac/vamsas/client/simpleclient/SimpleClient.java
index e93df6c..06b7744 100644 (file)
--- a/src/uk/ac/vamsas/client/simpleclient/SimpleClient.java
+++ b/src/uk/ac/vamsas/client/simpleclient/SimpleClient.java
@@ -19,10 +19,6 @@ import java.util.Vector;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.vamsas.objects.core.ApplicationData;
-import org.vamsas.objects.core.Entry;
-import org.vamsas.objects.core.LockFile;
-import org.vamsas.objects.core.VamsasDocument;
 import org.vamsas.objects.utils.AppDataReference;
 import org.vamsas.objects.utils.ProvenanceStuff;
 import org.vamsas.objects.utils.document.VersionEntries;
@@ -35,6 +31,10 @@ import uk.ac.vamsas.client.IObjectUpdate;
 import uk.ac.vamsas.client.InvalidSessionUrnException;
 import uk.ac.vamsas.client.SessionHandle;
 import uk.ac.vamsas.client.UserHandle;
+import uk.ac.vamsas.objects.core.ApplicationData;
+import uk.ac.vamsas.objects.core.Entry;
+import uk.ac.vamsas.objects.core.LockFile;
+import uk.ac.vamsas.objects.core.VamsasDocument;
 
 /**
  * @author jimp

diff --git a/src/uk/ac/vamsas/client/simpleclient/SimpleClientAppdata.java b/src/uk/ac/vamsas/client/simpleclient/SimpleClientAppdata.java
index 705f024..7d47759 100644 (file)
--- a/src/uk/ac/vamsas/client/simpleclient/SimpleClientAppdata.java
+++ b/src/uk/ac/vamsas/client/simpleclient/SimpleClientAppdata.java
@@ -21,12 +21,12 @@ import java.util.jar.JarOutputStream;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.vamsas.objects.core.AppData;
-import org.vamsas.objects.core.ApplicationData;
-import org.vamsas.objects.core.User;
 import org.vamsas.objects.utils.AppDataReference;
 
 import uk.ac.vamsas.client.IClientAppdata;
+import uk.ac.vamsas.objects.core.AppData;
+import uk.ac.vamsas.objects.core.ApplicationData;
+import uk.ac.vamsas.objects.core.User;
 
 /**
  * @author jimp
@@ -87,7 +87,7 @@ public class SimpleClientAppdata implements IClientAppdata {
    * gets appropriate app data for the application, if it exists in this dataset
    * Called by every accessor to ensure data has been retrieved from document.
    */
-  private void extractAppData(org.vamsas.objects.core.VamsasDocument doc) {
+  private void extractAppData(uk.ac.vamsas.objects.core.VamsasDocument doc) {
     if (doc==null) {
       log.debug("extractAppData called for null document object");
       return;

diff --git a/src/uk/ac/vamsas/client/simpleclient/SimpleDocBinding.java b/src/uk/ac/vamsas/client/simpleclient/SimpleDocBinding.java
index 1790572..789a238 100644 (file)
--- a/src/uk/ac/vamsas/client/simpleclient/SimpleDocBinding.java
+++ b/src/uk/ac/vamsas/client/simpleclient/SimpleDocBinding.java
@@ -7,8 +7,6 @@ import java.io.InputStreamReader;
 import java.util.Vector;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.vamsas.objects.core.VAMSAS;
-import org.vamsas.objects.core.VamsasDocument;
 import org.vamsas.objects.utils.AppDataReference;
 import org.vamsas.objects.utils.DocumentStuff;
 import org.vamsas.objects.utils.ProvenanceStuff;
@@ -17,6 +15,8 @@ import org.vamsas.objects.utils.document.VersionEntries;
 import uk.ac.vamsas.client.Vobject;
 import uk.ac.vamsas.client.VorbaIdFactory;
 import uk.ac.vamsas.client.VorbaXmlBinder;
+import uk.ac.vamsas.objects.core.VAMSAS;
+import uk.ac.vamsas.objects.core.VamsasDocument;
 
 /**
  * Base class for SimpleClient Vamsas Document Object Manipulation

diff --git a/src/uk/ac/vamsas/client/simpleclient/VamsasArchive.java b/src/uk/ac/vamsas/client/simpleclient/VamsasArchive.java
index 4f875e3..b6854cf 100644 (file)
--- a/src/uk/ac/vamsas/client/simpleclient/VamsasArchive.java
+++ b/src/uk/ac/vamsas/client/simpleclient/VamsasArchive.java
@@ -19,9 +19,6 @@ import java.util.jar.Manifest;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.vamsas.objects.core.ApplicationData;
-import org.vamsas.objects.core.VAMSAS;
-import org.vamsas.objects.core.VamsasDocument;
 import org.vamsas.objects.utils.AppDataReference;
 import org.vamsas.objects.utils.DocumentStuff;
 import org.vamsas.objects.utils.ProvenanceStuff;
@@ -34,6 +31,9 @@ import uk.ac.vamsas.client.UserHandle;
 import uk.ac.vamsas.client.Vobject;
 import uk.ac.vamsas.client.VorbaIdFactory;
 import uk.ac.vamsas.client.VorbaXmlBinder;
+import uk.ac.vamsas.objects.core.ApplicationData;
+import uk.ac.vamsas.objects.core.VAMSAS;
+import uk.ac.vamsas.objects.core.VamsasDocument;
 
 /**
  * Class for high-level io and Jar manipulation involved in creating 

diff --git a/src/uk/ac/vamsas/client/simpleclient/VamsasFile.java b/src/uk/ac/vamsas/client/simpleclient/VamsasFile.java
index c30e5e6..e5841ff 100644 (file)
--- a/src/uk/ac/vamsas/client/simpleclient/VamsasFile.java
+++ b/src/uk/ac/vamsas/client/simpleclient/VamsasFile.java
@@ -14,7 +14,7 @@ import java.util.jar.JarFile;
 import java.util.jar.JarInputStream;
 import java.util.jar.JarOutputStream;
 
-import org.vamsas.objects.core.LockFileDescriptor;
+import uk.ac.vamsas.objects.core.LockFileDescriptor;
 
 /**
  * low level vamsas document management routines