From: jprocter Date: Thu, 14 Dec 2006 18:17:24 +0000 (+0000) Subject: refactoring org to uk X-Git-Tag: Release_0.2~243 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=63b0b269c333a317ddd018c70a336c4cf839a2ee;p=vamsas.git 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 --- 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 --- 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 --- 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; /** - * dict attribute values for glyph symbol sets found in org.vamsas.objects.core.AnnotationElement + * dict attribute values for glyph symbol sets found in uk.ac.vamsas.objects.core.AnnotationElement * TODO: add validators and multilength symbols. * @author JimP * diff --git a/src/org/vamsas/objects/utils/ProvenanceStuff.java b/src/org/vamsas/objects/utils/ProvenanceStuff.java index 2e813f7..9d668d5 100644 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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.core.*; 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.*; /* * diff --git a/src/uk/ac/vamsas/client/ClientDocument.java b/src/uk/ac/vamsas/client/ClientDocument.java index a66ed9d..49f949c 100644 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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