refactoring org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@282 be28352e-c001-0410-b1a7-c7978e42abec

diff --git a/src/org/vamsas/test/objects/Core.java b/src/org/vamsas/test/objects/Core.java
index 0436736..794eefe 100644 (file)
--- a/src/org/vamsas/test/objects/Core.java
+++ b/src/org/vamsas/test/objects/Core.java
@@ -5,11 +5,11 @@ package org.vamsas.test.objects;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.vamsas.objects.utils.*;
-import org.vamsas.objects.utils.document.*;
 import org.vamsas.test.simpleclient.ArchiveReports;
 
 import uk.ac.vamsas.objects.core.*;
+import uk.ac.vamsas.objects.utils.*;
+import uk.ac.vamsas.objects.utils.document.*;
 
 /**
  * @author jim

diff --git a/src/org/vamsas/test/simpleclient/ArchiveClient.java b/src/org/vamsas/test/simpleclient/ArchiveClient.java
index 0681c0f..dec872a 100644 (file)
--- a/src/org/vamsas/test/simpleclient/ArchiveClient.java
+++ b/src/org/vamsas/test/simpleclient/ArchiveClient.java
@@ -13,11 +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.utils.AppDataReference;
-import org.vamsas.objects.utils.DocumentStuff;
-import org.vamsas.objects.utils.ProvenanceStuff;
-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;
@@ -39,6 +34,11 @@ 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;
+import uk.ac.vamsas.objects.utils.AppDataReference;
+import uk.ac.vamsas.objects.utils.DocumentStuff;
+import uk.ac.vamsas.objects.utils.ProvenanceStuff;
+import uk.ac.vamsas.objects.utils.SeqSet;
+import uk.ac.vamsas.objects.utils.document.VersionEntries;
 
 /**
  * @author jimp

diff --git a/src/org/vamsas/test/simpleclient/ClientDoc.java b/src/org/vamsas/test/simpleclient/ClientDoc.java
index 80b5f6e..0e88c1d 100644 (file)
--- a/src/org/vamsas/test/simpleclient/ClientDoc.java
+++ b/src/org/vamsas/test/simpleclient/ClientDoc.java
@@ -5,7 +5,6 @@ import java.util.Vector;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.vamsas.objects.utils.ProvenanceStuff;
 
 import uk.ac.vamsas.client.IClientAppdata;
 import uk.ac.vamsas.client.Vobject;
@@ -16,6 +15,7 @@ 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;
+import uk.ac.vamsas.objects.utils.ProvenanceStuff;
 
 // simple holder to pass to client.
 public class ClientDoc extends uk.ac.vamsas.client.ClientDocument {

diff --git a/src/org/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java b/src/org/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java
index 8581ba7..9140a7f 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.utils.DocumentStuff;\r
 import org.vamsas.test.simpleclient.ClientDoc;\r
 \r
 \r
@@ -36,6 +35,7 @@ import org.exolab.castor.mapping.Mapping;
 import uk.ac.vamsas.client.Vobject;\r
 import uk.ac.vamsas.client.VorbaId;\r
 import uk.ac.vamsas.objects.core.*;\r
+import uk.ac.vamsas.objects.utils.DocumentStuff;\r
 \r
 /*\r
  * \r

diff --git a/src/uk/ac/vamsas/client/simpleclient/ClientDocument.java b/src/uk/ac/vamsas/client/simpleclient/ClientDocument.java
index f853937..b38b64a 100644 (file)
--- a/src/uk/ac/vamsas/client/simpleclient/ClientDocument.java
+++ b/src/uk/ac/vamsas/client/simpleclient/ClientDocument.java
@@ -8,7 +8,6 @@ import java.util.Vector;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.vamsas.objects.utils.AppDataReference;
 import org.vamsas.test.objects.Core;
 
 import uk.ac.vamsas.client.ClientHandle;
@@ -21,6 +20,7 @@ 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;
+import uk.ac.vamsas.objects.utils.AppDataReference;
 
 /**
  * Maintains a collection of vamsas objects, appdatas and states, and provides api for a SimpleClient's client.

diff --git a/src/uk/ac/vamsas/client/simpleclient/IdFactory.java b/src/uk/ac/vamsas/client/simpleclient/IdFactory.java
index a5f3879..dff2fe4 100644 (file)
--- a/src/uk/ac/vamsas/client/simpleclient/IdFactory.java
+++ b/src/uk/ac/vamsas/client/simpleclient/IdFactory.java
@@ -5,7 +5,6 @@ package uk.ac.vamsas.client.simpleclient;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.vamsas.objects.utils.document.VersionEntries;
 
 import uk.ac.vamsas.client.ClientHandle;
 import uk.ac.vamsas.client.SessionHandle;
@@ -13,6 +12,7 @@ import uk.ac.vamsas.client.UserHandle;
 import uk.ac.vamsas.client.Vobject;
 import uk.ac.vamsas.client.VorbaId;
 import uk.ac.vamsas.client.VorbaIdFactory;
+import uk.ac.vamsas.objects.utils.document.VersionEntries;
 
 import java.util.Hashtable;
 import java.util.zip.CRC32;

diff --git a/src/uk/ac/vamsas/client/simpleclient/SimpleClient.java b/src/uk/ac/vamsas/client/simpleclient/SimpleClient.java
index 06b7744..b2b1757 100644 (file)
--- a/src/uk/ac/vamsas/client/simpleclient/SimpleClient.java
+++ b/src/uk/ac/vamsas/client/simpleclient/SimpleClient.java
@@ -19,9 +19,6 @@ import java.util.Vector;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.vamsas.objects.utils.AppDataReference;
-import org.vamsas.objects.utils.ProvenanceStuff;
-import org.vamsas.objects.utils.document.VersionEntries;
 
 import uk.ac.vamsas.client.ClientHandle;
 import uk.ac.vamsas.client.Events;
@@ -35,6 +32,9 @@ 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;
+import uk.ac.vamsas.objects.utils.AppDataReference;
+import uk.ac.vamsas.objects.utils.ProvenanceStuff;
+import uk.ac.vamsas.objects.utils.document.VersionEntries;
 
 /**
  * @author jimp

diff --git a/src/uk/ac/vamsas/client/simpleclient/SimpleClientAppdata.java b/src/uk/ac/vamsas/client/simpleclient/SimpleClientAppdata.java
index 7d47759..18f7d2e 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.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;
+import uk.ac.vamsas.objects.utils.AppDataReference;
 
 /**
  * @author jimp

diff --git a/src/uk/ac/vamsas/client/simpleclient/SimpleDocBinding.java b/src/uk/ac/vamsas/client/simpleclient/SimpleDocBinding.java
index 789a238..b65d00b 100644 (file)
--- a/src/uk/ac/vamsas/client/simpleclient/SimpleDocBinding.java
+++ b/src/uk/ac/vamsas/client/simpleclient/SimpleDocBinding.java
@@ -7,16 +7,16 @@ import java.io.InputStreamReader;
 import java.util.Vector;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.vamsas.objects.utils.AppDataReference;
-import org.vamsas.objects.utils.DocumentStuff;
-import org.vamsas.objects.utils.ProvenanceStuff;
-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;
+import uk.ac.vamsas.objects.utils.AppDataReference;
+import uk.ac.vamsas.objects.utils.DocumentStuff;
+import uk.ac.vamsas.objects.utils.ProvenanceStuff;
+import uk.ac.vamsas.objects.utils.document.VersionEntries;
 
 /**
  * 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 b6854cf..d8c64c3 100644 (file)
--- a/src/uk/ac/vamsas/client/simpleclient/VamsasArchive.java
+++ b/src/uk/ac/vamsas/client/simpleclient/VamsasArchive.java
@@ -19,10 +19,6 @@ import java.util.jar.Manifest;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.vamsas.objects.utils.AppDataReference;
-import org.vamsas.objects.utils.DocumentStuff;
-import org.vamsas.objects.utils.ProvenanceStuff;
-import org.vamsas.objects.utils.document.VersionEntries;
 
 import uk.ac.vamsas.client.ClientHandle;
 import uk.ac.vamsas.client.IVorbaIdFactory;
@@ -34,6 +30,10 @@ 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;
+import uk.ac.vamsas.objects.utils.AppDataReference;
+import uk.ac.vamsas.objects.utils.DocumentStuff;
+import uk.ac.vamsas.objects.utils.ProvenanceStuff;
+import uk.ac.vamsas.objects.utils.document.VersionEntries;
 
 /**
  * Class for high-level io and Jar manipulation involved in creating 

diff --git a/src/uk/ac/vamsas/client/simpleclient/VamsasArchiveReader.java b/src/uk/ac/vamsas/client/simpleclient/VamsasArchiveReader.java
index e8df789..291a28a 100644 (file)
--- a/src/uk/ac/vamsas/client/simpleclient/VamsasArchiveReader.java
+++ b/src/uk/ac/vamsas/client/simpleclient/VamsasArchiveReader.java
@@ -19,7 +19,8 @@ import java.util.zip.ZipInputStream;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.vamsas.objects.utils.document.VersionEntries;
+
+import uk.ac.vamsas.objects.utils.document.VersionEntries;
 /**
  * Basic methods for accessing an existing Vamsas Archive, 
  * and Jar entry names for creating new vamsas archives.