From 815d45c0c23f2309d93c3ca073d307f391927b11 Mon Sep 17 00:00:00 2001 From: jprocter Date: Thu, 14 Dec 2006 18:27:16 +0000 Subject: [PATCH] refactoring org to uk git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@282 be28352e-c001-0410-b1a7-c7978e42abec --- src/org/vamsas/test/objects/Core.java | 4 ++-- src/org/vamsas/test/simpleclient/ArchiveClient.java | 10 +++++----- src/org/vamsas/test/simpleclient/ClientDoc.java | 2 +- .../vamsas/test/simpleclient/simpleapp/VamsasDatastore.java | 2 +- src/uk/ac/vamsas/client/simpleclient/ClientDocument.java | 2 +- src/uk/ac/vamsas/client/simpleclient/IdFactory.java | 2 +- src/uk/ac/vamsas/client/simpleclient/SimpleClient.java | 6 +++--- .../ac/vamsas/client/simpleclient/SimpleClientAppdata.java | 2 +- src/uk/ac/vamsas/client/simpleclient/SimpleDocBinding.java | 8 ++++---- src/uk/ac/vamsas/client/simpleclient/VamsasArchive.java | 8 ++++---- .../ac/vamsas/client/simpleclient/VamsasArchiveReader.java | 3 ++- 11 files changed, 25 insertions(+), 24 deletions(-) diff --git a/src/org/vamsas/test/objects/Core.java b/src/org/vamsas/test/objects/Core.java index 0436736..794eefe 100644 --- 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 --- 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 --- 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 --- a/src/org/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java +++ b/src/org/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java @@ -19,7 +19,6 @@ package org.vamsas.test.simpleclient.simpleapp; -import org.vamsas.objects.utils.DocumentStuff; import org.vamsas.test.simpleclient.ClientDoc; @@ -36,6 +35,7 @@ import org.exolab.castor.mapping.Mapping; import uk.ac.vamsas.client.Vobject; import uk.ac.vamsas.client.VorbaId; import uk.ac.vamsas.objects.core.*; +import uk.ac.vamsas.objects.utils.DocumentStuff; /* * diff --git a/src/uk/ac/vamsas/client/simpleclient/ClientDocument.java b/src/uk/ac/vamsas/client/simpleclient/ClientDocument.java index f853937..b38b64a 100644 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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. -- 1.7.10.2