From b2c76f76a8c9040e0d70c0d0a30a04aac962c2c7 Mon Sep 17 00:00:00 2001 From: jprocter Date: Thu, 14 Dec 2006 18:08:11 +0000 Subject: [PATCH] refactored org to uk git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@273 be28352e-c001-0410-b1a7-c7978e42abec --- src/org/vamsas/objects/core/Alignment.java | 6 +- src/org/vamsas/objects/core/AnnotationElement.java | 6 +- src/org/vamsas/objects/core/AppData.java | 2 +- src/org/vamsas/objects/core/DataSet.java | 6 +- src/org/vamsas/objects/core/DbRef.java | 6 +- src/org/vamsas/objects/core/Entry.java | 6 +- src/org/vamsas/objects/core/Glyph.java | 2 +- src/org/vamsas/objects/core/Link.java | 2 +- src/org/vamsas/objects/core/LockFile.java | 6 +- src/org/vamsas/objects/core/MapList.java | 2 +- src/org/vamsas/objects/core/Newick.java | 6 +- src/org/vamsas/objects/core/Param.java | 2 +- src/org/vamsas/objects/core/Pos.java | 2 +- src/org/vamsas/objects/core/Property.java | 2 +- src/org/vamsas/objects/core/Provenance.java | 6 +- src/org/vamsas/objects/core/RangeType.java | 76 ++++++++++---------- src/org/vamsas/objects/core/Score.java | 2 +- src/org/vamsas/objects/core/Seg.java | 2 +- src/org/vamsas/objects/core/SequenceType.java | 6 +- src/org/vamsas/objects/core/Tree.java | 6 +- src/org/vamsas/objects/core/VAMSAS.java | 6 +- src/org/vamsas/objects/core/VamsasDocument.java | 6 +- src/org/vamsas/objects/utils/AppDataReference.java | 13 ++-- src/org/vamsas/test/ExampleApplication.java | 4 +- .../vamsas/test/simpleclient/ArchiveClient.java | 37 +++++----- .../vamsas/test/simpleclient/ArchiveReader.java | 3 +- .../vamsas/test/simpleclient/ArchiveReports.java | 7 +- .../test/simpleclient/ArchiveStreamReader.java | 7 +- .../vamsas/test/simpleclient/ArchiveWatcher.java | 13 ++-- .../vamsas/test/simpleclient/ArchiveWriter.java | 22 +++--- src/org/vamsas/test/simpleclient/ClientDoc.java | 25 +++---- .../vamsas/test/simpleclient/ClientsFileTest.java | 9 +-- .../vamsas/test/simpleclient/VamsasArchive.java | 21 +++--- .../test/simpleclient/simpleapp/VamsasClient.java | 9 +-- .../simpleclient/simpleapp/VamsasDatastore.java | 9 +-- 35 files changed, 179 insertions(+), 166 deletions(-) diff --git a/src/org/vamsas/objects/core/Alignment.java b/src/org/vamsas/objects/core/Alignment.java index bf70f4e..f824e1f 100644 --- 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 * Castor 0.9.9M2, 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 --- 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 * Castor 0.9.9M2, 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 --- 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; * * @version $Revision$ $Date$ */ -public class AppData extends org.vamsas.client.Vobject +public class AppData extends uk.ac.vamsas.client.Vobject implements java.io.Serializable { diff --git a/src/org/vamsas/objects/core/DataSet.java b/src/org/vamsas/objects/core/DataSet.java index e6d064e..25f92a6 100644 --- 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 * Castor 0.9.9M2, 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 --- 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 * Castor 0.9.9M2, 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 --- 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 * Castor 0.9.9M2, 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 --- 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; * * @version $Revision$ $Date$ */ -public class Glyph extends org.vamsas.client.Vobject +public class Glyph extends uk.ac.vamsas.client.Vobject implements java.io.Serializable { diff --git a/src/org/vamsas/objects/core/Link.java b/src/org/vamsas/objects/core/Link.java index 1330cff..4d4eeca 100644 --- 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; * * @version $Revision$ $Date$ */ -public class Link extends org.vamsas.client.Vobject +public class Link extends uk.ac.vamsas.client.Vobject implements java.io.Serializable { diff --git a/src/org/vamsas/objects/core/LockFile.java b/src/org/vamsas/objects/core/LockFile.java index a26bbe2..e9b5baf 100644 --- 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 * Castor 0.9.9M2, 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 --- 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; * * @version $Revision$ $Date$ */ -public class MapList extends org.vamsas.client.Vobject +public class MapList extends uk.ac.vamsas.client.Vobject implements java.io.Serializable { diff --git a/src/org/vamsas/objects/core/Newick.java b/src/org/vamsas/objects/core/Newick.java index 2c60f61..34d4351 100644 --- 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 * Castor 0.9.9M2, 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 --- 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; * * @version $Revision$ $Date$ */ -public class Param extends org.vamsas.client.Vobject +public class Param extends uk.ac.vamsas.client.Vobject implements java.io.Serializable { diff --git a/src/org/vamsas/objects/core/Pos.java b/src/org/vamsas/objects/core/Pos.java index 5053f98..80252f0 100644 --- 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; * * @version $Revision$ $Date$ */ -public class Pos extends org.vamsas.client.Vobject +public class Pos extends uk.ac.vamsas.client.Vobject implements java.io.Serializable { diff --git a/src/org/vamsas/objects/core/Property.java b/src/org/vamsas/objects/core/Property.java index fb4aacc..e832f72 100644 --- 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; * * @version $Revision$ $Date$ */ -public class Property extends org.vamsas.client.Vobject +public class Property extends uk.ac.vamsas.client.Vobject implements java.io.Serializable { diff --git a/src/org/vamsas/objects/core/Provenance.java b/src/org/vamsas/objects/core/Provenance.java index e1f6b85..ac71d23 100644 --- 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 * Castor 0.9.9M2, 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 --- 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; * * @version $Revision$ $Date$ */ -public abstract class RangeType extends org.vamsas.client.Vobject +public abstract class RangeType extends uk.ac.vamsas.clientnt.Vobject implements java.io.Serializable { @@ -67,7 +67,7 @@ implements java.io.Serializable super(); _posList = new Vector(); _segList = new Vector(); - } //-- org.vamsas.objects.core.RangeType() + } //-- uk.ac.vamsas.objects.core.RangeType() //-----------/ @@ -81,11 +81,11 @@ implements java.io.Serializable * * @param vPos */ - public void addPos(org.vamsas.objects.core.Pos vPos) + public void addPos(uk.ac.vamsas.objects.core.Pos vPos) throws java.lang.IndexOutOfBoundsException { _posList.addElement(vPos); - } //-- void addPos(org.vamsas.objects.core.Pos) + } //-- void addPos(uk.ac.vamsas.objects.core.Pos) /** * Method addPos @@ -95,11 +95,11 @@ implements java.io.Serializable * @param index * @param vPos */ - public void addPos(int index, org.vamsas.objects.core.Pos vPos) + public void addPos(int index, uk.ac.vamsas.objects.core.Pos vPos) throws java.lang.IndexOutOfBoundsException { _posList.insertElementAt(vPos, index); - } //-- void addPos(int, org.vamsas.objects.core.Pos) + } //-- void addPos(int, uk.ac.vamsas.objects.core.Pos) /** * Method addSeg @@ -108,11 +108,11 @@ implements java.io.Serializable * * @param vSeg */ - public void addSeg(org.vamsas.objects.core.Seg vSeg) + public void addSeg(uk.ac.vamsas.objects.core.Seg vSeg) throws java.lang.IndexOutOfBoundsException { _segList.addElement(vSeg); - } //-- void addSeg(org.vamsas.objects.core.Seg) + } //-- void addSeg(uk.ac.vamsas.objects.core.Seg) /** * Method addSeg @@ -122,11 +122,11 @@ implements java.io.Serializable * @param index * @param vSeg */ - public void addSeg(int index, org.vamsas.objects.core.Seg vSeg) + public void addSeg(int index, uk.ac.vamsas.objects.core.Seg vSeg) throws java.lang.IndexOutOfBoundsException { _segList.insertElementAt(vSeg, index); - } //-- void addSeg(int, org.vamsas.objects.core.Seg) + } //-- void addSeg(int, uk.ac.vamsas.objects.core.Seg) /** * Method enumeratePos @@ -216,7 +216,7 @@ implements java.io.Serializable * @param index * @return Pos */ - public org.vamsas.objects.core.Pos getPos(int index) + public uk.ac.vamsas.objects.core.Pos getPos(int index) throws java.lang.IndexOutOfBoundsException { //-- check bounds for index @@ -224,8 +224,8 @@ implements java.io.Serializable throw new IndexOutOfBoundsException("getPos: Index value '"+index+"' not in range [0.."+_posList.size()+ "]"); } - return (org.vamsas.objects.core.Pos) _posList.elementAt(index); - } //-- org.vamsas.objects.core.Pos getPos(int) + return (uk.ac.vamsas.objects.core.Pos) _posList.elementAt(index); + } //-- uk.ac.vamsas.objects.core.Pos getPos(int) /** * Method getPos @@ -234,15 +234,15 @@ implements java.io.Serializable * * @return Pos */ - public org.vamsas.objects.core.Pos[] getPos() + public uk.ac.vamsas.objects.core.Pos[] getPos() { int size = _posList.size(); - org.vamsas.objects.core.Pos[] mArray = new org.vamsas.objects.core.Pos[size]; + uk.ac.vamsas.objects.core.Pos[] mArray = new uk.ac.vamsas.objects.core.Pos[size]; for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Pos) _posList.elementAt(index); + mArray[index] = (uk.ac.vamsas.objects.core.Pos) _posList.elementAt(index); } return mArray; - } //-- org.vamsas.objects.core.Pos[] getPos() + } //-- uk.ac.vamsas.objects.core.Pos[] getPos() /** * Method getPosCount @@ -264,7 +264,7 @@ implements java.io.Serializable * @param index * @return Seg */ - public org.vamsas.objects.core.Seg getSeg(int index) + public uk.ac.vamsas.objects.core.Seg getSeg(int index) throws java.lang.IndexOutOfBoundsException { //-- check bounds for index @@ -272,8 +272,8 @@ implements java.io.Serializable throw new IndexOutOfBoundsException("getSeg: Index value '"+index+"' not in range [0.."+_segList.size()+ "]"); } - return (org.vamsas.objects.core.Seg) _segList.elementAt(index); - } //-- org.vamsas.objects.core.Seg getSeg(int) + return (uk.ac.vamsas.objects.core.Seg) _segList.elementAt(index); + } //-- uk.ac.vamsas.objects.core.Seg getSeg(int) /** * Method getSeg @@ -282,15 +282,15 @@ implements java.io.Serializable * * @return Seg */ - public org.vamsas.objects.core.Seg[] getSeg() + public uk.ac.vamsas.objects.core.Seg[] getSeg() { int size = _segList.size(); - org.vamsas.objects.core.Seg[] mArray = new org.vamsas.objects.core.Seg[size]; + uk.ac.vamsas.objects.core.Seg[] mArray = new uk.ac.vamsas.objects.core.Seg[size]; for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Seg) _segList.elementAt(index); + mArray[index] = (uk.ac.vamsas.objects.core.Seg) _segList.elementAt(index); } return mArray; - } //-- org.vamsas.objects.core.Seg[] getSeg() + } //-- uk.ac.vamsas.objects.core.Seg[] getSeg() /** * Method getSegCount @@ -348,12 +348,12 @@ implements java.io.Serializable * @param index * @return Pos */ - public org.vamsas.objects.core.Pos removePos(int index) + public uk.ac.vamsas.objects.core.Pos removePos(int index) { java.lang.Object obj = _posList.elementAt(index); _posList.removeElementAt(index); - return (org.vamsas.objects.core.Pos) obj; - } //-- org.vamsas.objects.core.Pos removePos(int) + return (uk.ac.vamsas.objects.core.Pos) obj; + } //-- uk.ac.vamsas.objects.core.Pos removePos(int) /** * Method removeSeg @@ -363,12 +363,12 @@ implements java.io.Serializable * @param index * @return Seg */ - public org.vamsas.objects.core.Seg removeSeg(int index) + public uk.ac.vamsas.objects.core.Seg removeSeg(int index) { java.lang.Object obj = _segList.elementAt(index); _segList.removeElementAt(index); - return (org.vamsas.objects.core.Seg) obj; - } //-- org.vamsas.objects.core.Seg removeSeg(int) + return (uk.ac.vamsas.objects.core.Seg) obj; + } //-- uk.ac.vamsas.objects.core.Seg removeSeg(int) /** * Method setPos @@ -378,7 +378,7 @@ implements java.io.Serializable * @param index * @param vPos */ - public void setPos(int index, org.vamsas.objects.core.Pos vPos) + public void setPos(int index, uk.ac.vamsas.objects.core.Pos vPos) throws java.lang.IndexOutOfBoundsException { //-- check bounds for index @@ -386,7 +386,7 @@ implements java.io.Serializable throw new IndexOutOfBoundsException("setPos: Index value '"+index+"' not in range [0.."+_posList.size()+ "]"); } _posList.setElementAt(vPos, index); - } //-- void setPos(int, org.vamsas.objects.core.Pos) + } //-- void setPos(int, uk.ac.vamsas.objects.core.Pos) /** * Method setPos @@ -395,14 +395,14 @@ implements java.io.Serializable * * @param posArray */ - public void setPos(org.vamsas.objects.core.Pos[] posArray) + public void setPos(uk.ac.vamsas.objects.core.Pos[] posArray) { //-- copy array _posList.removeAllElements(); for (int i = 0; i < posArray.length; i++) { _posList.addElement(posArray[i]); } - } //-- void setPos(org.vamsas.objects.core.Pos) + } //-- void setPos(uk.ac.vamsas.objects.core.Pos) /** * Method setSeg @@ -412,7 +412,7 @@ implements java.io.Serializable * @param index * @param vSeg */ - public void setSeg(int index, org.vamsas.objects.core.Seg vSeg) + public void setSeg(int index, uk.ac.vamsas.objects.core.Seg vSeg) throws java.lang.IndexOutOfBoundsException { //-- check bounds for index @@ -420,7 +420,7 @@ implements java.io.Serializable throw new IndexOutOfBoundsException("setSeg: Index value '"+index+"' not in range [0.."+_segList.size()+ "]"); } _segList.setElementAt(vSeg, index); - } //-- void setSeg(int, org.vamsas.objects.core.Seg) + } //-- void setSeg(int, uk.ac.vamsas.objects.core.Seg) /** * Method setSeg @@ -429,14 +429,14 @@ implements java.io.Serializable * * @param segArray */ - public void setSeg(org.vamsas.objects.core.Seg[] segArray) + public void setSeg(uk.ac.vamsas.objects.core.Seg[] segArray) { //-- copy array _segList.removeAllElements(); for (int i = 0; i < segArray.length; i++) { _segList.addElement(segArray[i]); } - } //-- void setSeg(org.vamsas.objects.core.Seg) + } //-- void setSeg(uk.ac.vamsas.objects.core.Seg) /** * Method validate diff --git a/src/org/vamsas/objects/core/Score.java b/src/org/vamsas/objects/core/Score.java index cb294f3..c0e6ec5 100644 --- 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; * * @version $Revision$ $Date$ */ -public class Score extends org.vamsas.client.Vobject +public class Score extends uk.ac.vamsas.client.Vobject implements java.io.Serializable { diff --git a/src/org/vamsas/objects/core/Seg.java b/src/org/vamsas/objects/core/Seg.java index 5e36703..92f1c6b 100644 --- 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; * * @version $Revision$ $Date$ */ -public class Seg extends org.vamsas.client.Vobject +public class Seg extends uk.ac.vamsas.client.Vobject implements java.io.Serializable { diff --git a/src/org/vamsas/objects/core/SequenceType.java b/src/org/vamsas/objects/core/SequenceType.java index 96fba5b..ce66db6 100644 --- 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 * Castor 0.9.9M2, 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 --- 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 * Castor 0.9.9M2, 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 --- 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 * Castor 0.9.9M2, 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 --- 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 * Castor 0.9.9M2, 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- a/src/org/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java +++ b/src/org/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java @@ -19,8 +19,6 @@ package org.vamsas.test.simpleclient.simpleapp; -import org.vamsas.client.Vobject; -import org.vamsas.client.VorbaId; import org.vamsas.objects.core.*; import org.vamsas.objects.utils.DocumentStuff; import org.vamsas.test.simpleclient.ClientDoc; @@ -36,6 +34,9 @@ import java.util.jar.*; import org.exolab.castor.xml.*; import org.exolab.castor.mapping.Mapping; +import uk.ac.vamsas.client.Vobject; +import uk.ac.vamsas.client.VorbaId; + /* * * static { @@ -96,7 +97,7 @@ public class VamsasDatastore { * @param vobj * @return Jalview datamodel object bound to the vamsas document object */ - protected Object getvObj2jv(org.vamsas.client.Vobject vobj) { + protected Object getvObj2jv(uk.ac.vamsas.client.Vobject vobj) { VorbaId id = vobj.getVorbaId(); if (id == null) { @@ -110,7 +111,7 @@ public class VamsasDatastore { return null; } - protected void bindjvvobj(Object jvobj, org.vamsas.client.Vobject vobj) { + protected void bindjvvobj(Object jvobj, uk.ac.vamsas.client.Vobject vobj) { VorbaId id = vobj.getVorbaId(); if (id == null) { -- 1.7.10.2