[pkg-java] r15208 - in trunk/libvamsas-client-java/debian: . patches
Vincent Fourmond
fourmond at alioth.debian.org
Mon Oct 17 21:49:05 UTC 2011
Author: fourmond
Date: 2011-10-17 21:49:05 +0000 (Mon, 17 Oct 2011)
New Revision: 15208
Added:
trunk/libvamsas-client-java/debian/get-git-source
Modified:
trunk/libvamsas-client-java/debian/changelog
trunk/libvamsas-client-java/debian/copyright
trunk/libvamsas-client-java/debian/patches/castor-util-to-castor-core-utils.diff
Log:
[libvamsas-client-java] Now using the recently published git repository
Modified: trunk/libvamsas-client-java/debian/changelog
===================================================================
--- trunk/libvamsas-client-java/debian/changelog 2011-10-15 23:19:04 UTC (rev 15207)
+++ trunk/libvamsas-client-java/debian/changelog 2011-10-17 21:49:05 UTC (rev 15208)
@@ -1,4 +1,4 @@
-libvamsas-client-java (0.1+dfsg-1) unstable; urgency=low
+libvamsas-client-java (0.2~git2011.10.17+1b42648-1~java1) unstable; urgency=low
* Initial release. (Closes: #622811)
Modified: trunk/libvamsas-client-java/debian/copyright
===================================================================
--- trunk/libvamsas-client-java/debian/copyright 2011-10-15 23:19:04 UTC (rev 15207)
+++ trunk/libvamsas-client-java/debian/copyright 2011-10-17 21:49:05 UTC (rev 15208)
@@ -1,13 +1,10 @@
Format: http://svn.debian.org/wsvn/dep/web/deps/dep5.mdwn?op=file&rev=174
Upstream-Name: Vamsas
-Source: http://www.vamsas.ac.uk/
- The archive provided by Debian was repackaged from the
- "Complete Source and documentation JAR" link above and:
- * stripping already-generated API docs
- * removing all bundled JARS
+Source: http://source.jalview.org/git/vamsas.git
+ The source code used by Debian was obtained by cloning the above git
+ repository and stripping the tools/, lib/ and packages/ directories.
.
- The debian/new-upstream precisely does that, you can dig into it for
- more details.
+ The debian/get-git-source script does precisely that.
Files: *
Copyright: 2009, by Jim Procter, Iain Milne, Pierre Marguerite
Added: trunk/libvamsas-client-java/debian/get-git-source
===================================================================
--- trunk/libvamsas-client-java/debian/get-git-source (rev 0)
+++ trunk/libvamsas-client-java/debian/get-git-source 2011-10-17 21:49:05 UTC (rev 15208)
@@ -0,0 +1,44 @@
+#!/bin/sh
+
+# Script to export the source code of jsymphonic from its SVN
+# repository, and repackage that into a decent .orig tarball...
+
+version="$1"
+package="libvamsas-client-java"
+
+if [ -z "$version" ]; then
+ echo <<EOF
+Usage:
+
+ debian/get-git-source version
+EOF
+ exit 1;
+fi
+
+REP="http://source.jalview.org/git/vamsas.git"
+
+tmpdir=`mktemp -d `
+curdir=`pwd`
+
+cd $tmpdir;
+
+echo "Getting git code"
+git clone $REP
+cd vamsas
+rev=$(git rev-list --abbrev-commit HEAD | head -n1)
+fullrev=`date +%Y.%m.%d`+$rev
+fullversion="${version}~git$fullrev"
+tarball="${package}_${fullversion}.orig.tar.bz2"
+
+echo
+echo "Removing unnecessary files"
+rm -rf .git docs packages lib tools
+
+echo
+echo "Making tarball"
+cd ..
+tar cvjf "$curdir/../$tarball" vamsas
+
+echo "Cleaning up temporary files"
+cd $curdir
+rm -rf $tmpdir
\ No newline at end of file
Property changes on: trunk/libvamsas-client-java/debian/get-git-source
___________________________________________________________________
Added: svn:executable
+ *
Modified: trunk/libvamsas-client-java/debian/patches/castor-util-to-castor-core-utils.diff
===================================================================
--- trunk/libvamsas-client-java/debian/patches/castor-util-to-castor-core-utils.diff 2011-10-15 23:19:04 UTC (rev 15207)
+++ trunk/libvamsas-client-java/debian/patches/castor-util-to-castor-core-utils.diff 2011-10-17 21:49:05 UTC (rev 15208)
@@ -8,391 +8,10 @@
find src | perl -pi -e 's/castor\.util/castor.core.util/g'
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Alignment.java
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/AlignmentAnnotation.java
===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/Alignment.java 2011-04-14 23:01:23.920202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Alignment.java 2011-04-14 23:01:44.500202539 +0200
-@@ -282,27 +282,27 @@
- if (temp._gapChar == null)
- return false;
- if (this._gapChar != temp._gapChar) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._gapChar);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._gapChar);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._gapChar);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._gapChar);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._gapChar);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._gapChar);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._gapChar);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._gapChar);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._gapChar.equals(temp._gapChar)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._gapChar);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._gapChar);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._gapChar);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._gapChar);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._gapChar);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._gapChar);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._gapChar);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._gapChar);
- }
- }
- } else if (temp._gapChar != null)
-@@ -315,27 +315,27 @@
- if (temp._id == null)
- return false;
- if (this._id != temp._id) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._id.equals(temp._id)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- }
- }
- } else if (temp._id != null)
-@@ -344,29 +344,29 @@
- if (temp._modifiable == null)
- return false;
- if (this._modifiable != temp._modifiable) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._modifiable);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._modifiable);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._modifiable.equals(temp._modifiable)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
- }
- }
- } else if (temp._modifiable != null)
-@@ -375,18 +375,18 @@
- if (temp._alignmentAnnotationList == null)
- return false;
- if (this._alignmentAnnotationList != temp._alignmentAnnotationList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._alignmentAnnotationList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._alignmentAnnotationList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._alignmentAnnotationList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._alignmentAnnotationList);
- }
- ;
-@@ -395,15 +395,15 @@
- if (!thcycle) {
- if (!this._alignmentAnnotationList
- .equals(temp._alignmentAnnotationList)) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._alignmentAnnotationList);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._alignmentAnnotationList);
- return false;
- }
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._alignmentAnnotationList);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._alignmentAnnotationList);
- }
- }
-@@ -413,29 +413,29 @@
- if (temp._treeList == null)
- return false;
- if (this._treeList != temp._treeList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._treeList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._treeList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._treeList.equals(temp._treeList)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList);
- }
- }
- } else if (temp._treeList != null)
-@@ -444,18 +444,18 @@
- if (temp._alignmentSequenceList == null)
- return false;
- if (this._alignmentSequenceList != temp._alignmentSequenceList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._alignmentSequenceList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._alignmentSequenceList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._alignmentSequenceList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._alignmentSequenceList);
- }
- ;
-@@ -464,15 +464,15 @@
- if (!thcycle) {
- if (!this._alignmentSequenceList
- .equals(temp._alignmentSequenceList)) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._alignmentSequenceList);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._alignmentSequenceList);
- return false;
- }
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._alignmentSequenceList);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._alignmentSequenceList);
- }
- }
-@@ -482,18 +482,18 @@
- if (temp._propertyList == null)
- return false;
- if (this._propertyList != temp._propertyList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._propertyList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._propertyList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._propertyList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._propertyList);
- }
- ;
-@@ -501,14 +501,14 @@
- }
- if (!thcycle) {
- if (!this._propertyList.equals(temp._propertyList)) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._propertyList);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._propertyList);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._propertyList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
- }
- }
- } else if (temp._propertyList != null)
-@@ -517,29 +517,29 @@
- if (temp._provenance == null)
- return false;
- if (this._provenance != temp._provenance) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._provenance);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._provenance);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._provenance.equals(temp._provenance)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
- }
- }
- } else if (temp._provenance != null)
-@@ -841,46 +841,46 @@
-
- long tmp;
- if (_gapChar != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_gapChar)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_gapChar)) {
- result = 37 * result + _gapChar.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_gapChar);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_gapChar);
- }
- result = 37 * result + (_aligned ? 0 : 1);
-- if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
-+ if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) {
- result = 37 * result + _id.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_id);
- }
- if (_modifiable != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_modifiable)) {
- result = 37 * result + _modifiable.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_modifiable);
- }
- if (_alignmentAnnotationList != null
-- && !org.castor.util.CycleBreaker
-+ && !org.castor.core.util.CycleBreaker
- .startingToCycle(_alignmentAnnotationList)) {
- result = 37 * result + _alignmentAnnotationList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_alignmentAnnotationList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_alignmentAnnotationList);
- }
- if (_treeList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_treeList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_treeList)) {
- result = 37 * result + _treeList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_treeList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_treeList);
- }
- if (_alignmentSequenceList != null
-- && !org.castor.util.CycleBreaker
-+ && !org.castor.core.util.CycleBreaker
- .startingToCycle(_alignmentSequenceList)) {
- result = 37 * result + _alignmentSequenceList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_alignmentSequenceList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_alignmentSequenceList);
- }
- if (_propertyList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_propertyList)) {
- result = 37 * result + _propertyList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_propertyList);
- }
- if (_provenance != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_provenance)) {
- result = 37 * result + _provenance.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_provenance);
- }
-
- return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/AlignmentAnnotation.java
-===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/AlignmentAnnotation.java 2011-04-14 23:01:23.868202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/AlignmentAnnotation.java 2011-04-14 23:01:44.500202539 +0200
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/AlignmentAnnotation.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/AlignmentAnnotation.java 2011-10-17 23:43:32.628672117 +0200
@@ -143,27 +143,27 @@
if (temp._seqrefs == null)
return false;
@@ -486,155 +105,10 @@
}
return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/AlignmentSequence.java
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/AlignmentSequenceAnnotation.java
===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/AlignmentSequence.java 2011-04-14 23:01:23.764202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/AlignmentSequence.java 2011-04-14 23:01:44.496202539 +0200
-@@ -132,27 +132,27 @@
- if (temp._id == null)
- return false;
- if (this._id != temp._id) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._id.equals(temp._id)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- }
- }
- } else if (temp._id != null)
-@@ -161,27 +161,27 @@
- if (temp._refid == null)
- return false;
- if (this._refid != temp._refid) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._refid);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._refid);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._refid);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._refid);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._refid);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._refid);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._refid);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._refid);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._refid.equals(temp._refid)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._refid);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._refid);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._refid);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._refid);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._refid);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._refid);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._refid);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._refid);
- }
- }
- } else if (temp._refid != null)
-@@ -190,18 +190,18 @@
- if (temp._alignmentSequenceAnnotationList == null)
- return false;
- if (this._alignmentSequenceAnnotationList != temp._alignmentSequenceAnnotationList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._alignmentSequenceAnnotationList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._alignmentSequenceAnnotationList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._alignmentSequenceAnnotationList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._alignmentSequenceAnnotationList);
- }
- ;
-@@ -210,15 +210,15 @@
- if (!thcycle) {
- if (!this._alignmentSequenceAnnotationList
- .equals(temp._alignmentSequenceAnnotationList)) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._alignmentSequenceAnnotationList);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._alignmentSequenceAnnotationList);
- return false;
- }
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._alignmentSequenceAnnotationList);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._alignmentSequenceAnnotationList);
- }
- }
-@@ -323,19 +323,19 @@
- int result = super.hashCode();
-
- long tmp;
-- if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
-+ if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) {
- result = 37 * result + _id.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_id);
- }
-- if (_refid != null && !org.castor.util.CycleBreaker.startingToCycle(_refid)) {
-+ if (_refid != null && !org.castor.core.util.CycleBreaker.startingToCycle(_refid)) {
- result = 37 * result + _refid.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_refid);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_refid);
- }
- if (_alignmentSequenceAnnotationList != null
-- && !org.castor.util.CycleBreaker
-+ && !org.castor.core.util.CycleBreaker
- .startingToCycle(_alignmentSequenceAnnotationList)) {
- result = 37 * result + _alignmentSequenceAnnotationList.hashCode();
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(_alignmentSequenceAnnotationList);
- }
-
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/AlignmentSequenceAnnotation.java
-===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/AlignmentSequenceAnnotation.java 2011-04-14 23:01:23.752202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/AlignmentSequenceAnnotation.java 2011-04-14 23:01:44.496202539 +0200
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/AlignmentSequenceAnnotation.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/AlignmentSequenceAnnotation.java 2011-10-17 23:43:32.624672117 +0200
@@ -101,29 +101,29 @@
if (temp._provenance == null)
return false;
@@ -685,201 +159,10 @@
}
return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/AnnotationElement.java
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/AppData.java
===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/AnnotationElement.java 2011-04-14 23:01:23.952202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/AnnotationElement.java 2011-04-14 23:01:44.504202539 +0200
-@@ -213,27 +213,27 @@
- if (temp._id == null)
- return false;
- if (this._id != temp._id) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._id.equals(temp._id)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- }
- }
- } else if (temp._id != null)
-@@ -242,18 +242,18 @@
- if (temp._description == null)
- return false;
- if (this._description != temp._description) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._description);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._description);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._description);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._description);
- }
- ;
-@@ -261,14 +261,14 @@
- }
- if (!thcycle) {
- if (!this._description.equals(temp._description)) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._description);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._description);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._description);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._description);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._description);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._description);
- }
- }
- } else if (temp._description != null)
-@@ -277,29 +277,29 @@
- if (temp._glyphList == null)
- return false;
- if (this._glyphList != temp._glyphList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._glyphList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._glyphList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._glyphList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._glyphList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._glyphList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._glyphList);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._glyphList.equals(temp._glyphList)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._glyphList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._glyphList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._glyphList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._glyphList);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._glyphList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._glyphList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._glyphList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._glyphList);
- }
- }
- } else if (temp._glyphList != null)
-@@ -308,29 +308,29 @@
- if (temp._valueList == null)
- return false;
- if (this._valueList != temp._valueList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._valueList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._valueList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._valueList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._valueList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._valueList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._valueList);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._valueList.equals(temp._valueList)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._valueList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._valueList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._valueList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._valueList);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._valueList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._valueList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._valueList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._valueList);
- }
- }
- } else if (temp._valueList != null)
-@@ -519,24 +519,24 @@
- long tmp;
- result = 37 * result + (int) (_position ^ (_position >>> 32));
- result = 37 * result + (_after ? 0 : 1);
-- if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
-+ if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) {
- result = 37 * result + _id.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_id);
- }
- if (_description != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_description)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_description)) {
- result = 37 * result + _description.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_description);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_description);
- }
- if (_glyphList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_glyphList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_glyphList)) {
- result = 37 * result + _glyphList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_glyphList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_glyphList);
- }
- if (_valueList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_valueList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_valueList)) {
- result = 37 * result + _valueList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_valueList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_valueList);
- }
-
- return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/AppData.java
-===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/AppData.java 2011-04-14 23:01:24.112202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/AppData.java 2011-04-14 23:01:44.508202539 +0200
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/AppData.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/AppData.java 2011-10-17 23:43:32.644672117 +0200
@@ -89,18 +89,18 @@
if (temp._choiceValue == null)
return false;
@@ -1026,241 +309,10 @@
}
return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/ApplicationData.java
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Attachment.java
===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/ApplicationData.java 2011-04-14 23:01:23.784202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/ApplicationData.java 2011-04-14 23:01:44.496202539 +0200
-@@ -173,27 +173,27 @@
- if (temp._version == null)
- return false;
- if (this._version != temp._version) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._version);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._version);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._version);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._version);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._version.equals(temp._version)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version);
- }
- }
- } else if (temp._version != null)
-@@ -202,27 +202,27 @@
- if (temp._name == null)
- return false;
- if (this._name != temp._name) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._name);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._name);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._name);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._name);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._name);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._name);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._name.equals(temp._name)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._name);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._name);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._name);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._name);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name);
- }
- }
- } else if (temp._name != null)
-@@ -231,29 +231,29 @@
- if (temp._userList == null)
- return false;
- if (this._userList != temp._userList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._userList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._userList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._userList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._userList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._userList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._userList);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._userList.equals(temp._userList)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._userList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._userList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._userList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._userList);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._userList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._userList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._userList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._userList);
- }
- }
- } else if (temp._userList != null)
-@@ -262,27 +262,27 @@
- if (temp._common == null)
- return false;
- if (this._common != temp._common) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._common);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._common);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._common);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._common);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._common);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._common);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._common);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._common);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._common.equals(temp._common)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._common);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._common);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._common);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._common);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._common);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._common);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._common);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._common);
- }
- }
- } else if (temp._common != null)
-@@ -291,18 +291,18 @@
- if (temp._instanceList == null)
- return false;
- if (this._instanceList != temp._instanceList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._instanceList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._instanceList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._instanceList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._instanceList);
- }
- ;
-@@ -310,14 +310,14 @@
- }
- if (!thcycle) {
- if (!this._instanceList.equals(temp._instanceList)) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._instanceList);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._instanceList);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._instanceList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._instanceList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._instanceList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._instanceList);
- }
- }
- } else if (temp._instanceList != null)
-@@ -476,28 +476,28 @@
-
- long tmp;
- if (_version != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_version)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_version)) {
- result = 37 * result + _version.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_version);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_version);
- }
-- if (_name != null && !org.castor.util.CycleBreaker.startingToCycle(_name)) {
-+ if (_name != null && !org.castor.core.util.CycleBreaker.startingToCycle(_name)) {
- result = 37 * result + _name.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_name);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_name);
- }
- if (_userList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_userList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_userList)) {
- result = 37 * result + _userList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_userList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_userList);
- }
- if (_common != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_common)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_common)) {
- result = 37 * result + _common.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_common);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_common);
- }
- if (_instanceList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_instanceList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_instanceList)) {
- result = 37 * result + _instanceList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_instanceList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_instanceList);
- }
-
- return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Attachment.java
-===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/Attachment.java 2011-04-14 23:01:23.796202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Attachment.java 2011-04-14 23:01:44.496202539 +0200
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Attachment.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Attachment.java 2011-10-17 23:43:32.624672117 +0200
@@ -112,27 +112,27 @@
if (temp._type == null)
return false;
@@ -1396,1132 +448,10 @@
}
return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/DataSet.java
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Glyph.java
===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/DataSet.java 2011-04-14 23:01:24.092202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/DataSet.java 2011-04-14 23:01:44.508202539 +0200
-@@ -295,27 +295,27 @@
- if (temp._id == null)
- return false;
- if (this._id != temp._id) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._id.equals(temp._id)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- }
- }
- } else if (temp._id != null)
-@@ -324,18 +324,18 @@
- if (temp._sequenceList == null)
- return false;
- if (this._sequenceList != temp._sequenceList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._sequenceList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._sequenceList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._sequenceList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._sequenceList);
- }
- ;
-@@ -343,14 +343,14 @@
- }
- if (!thcycle) {
- if (!this._sequenceList.equals(temp._sequenceList)) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._sequenceList);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._sequenceList);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._sequenceList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequenceList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._sequenceList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._sequenceList);
- }
- }
- } else if (temp._sequenceList != null)
-@@ -359,18 +359,18 @@
- if (temp._sequenceMappingList == null)
- return false;
- if (this._sequenceMappingList != temp._sequenceMappingList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._sequenceMappingList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._sequenceMappingList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._sequenceMappingList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._sequenceMappingList);
- }
- ;
-@@ -378,15 +378,15 @@
- }
- if (!thcycle) {
- if (!this._sequenceMappingList.equals(temp._sequenceMappingList)) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._sequenceMappingList);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._sequenceMappingList);
- return false;
- }
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._sequenceMappingList);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._sequenceMappingList);
- }
- }
-@@ -396,18 +396,18 @@
- if (temp._dataSetAnnotationsList == null)
- return false;
- if (this._dataSetAnnotationsList != temp._dataSetAnnotationsList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._dataSetAnnotationsList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._dataSetAnnotationsList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._dataSetAnnotationsList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._dataSetAnnotationsList);
- }
- ;
-@@ -416,15 +416,15 @@
- if (!thcycle) {
- if (!this._dataSetAnnotationsList
- .equals(temp._dataSetAnnotationsList)) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._dataSetAnnotationsList);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._dataSetAnnotationsList);
- return false;
- }
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._dataSetAnnotationsList);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._dataSetAnnotationsList);
- }
- }
-@@ -434,18 +434,18 @@
- if (temp._alignmentList == null)
- return false;
- if (this._alignmentList != temp._alignmentList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._alignmentList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._alignmentList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._alignmentList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._alignmentList);
- }
- ;
-@@ -453,15 +453,15 @@
- }
- if (!thcycle) {
- if (!this._alignmentList.equals(temp._alignmentList)) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._alignmentList);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._alignmentList);
- return false;
- }
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._alignmentList);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._alignmentList);
- }
- }
-@@ -471,29 +471,29 @@
- if (temp._treeList == null)
- return false;
- if (this._treeList != temp._treeList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._treeList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._treeList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._treeList.equals(temp._treeList)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList);
- }
- }
- } else if (temp._treeList != null)
-@@ -502,29 +502,29 @@
- if (temp._provenance == null)
- return false;
- if (this._provenance != temp._provenance) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._provenance);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._provenance);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._provenance.equals(temp._provenance)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
- }
- }
- } else if (temp._provenance != null)
-@@ -842,40 +842,40 @@
- int result = super.hashCode();
-
- long tmp;
-- if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
-+ if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) {
- result = 37 * result + _id.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_id);
- }
- if (_sequenceList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_sequenceList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_sequenceList)) {
- result = 37 * result + _sequenceList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_sequenceList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_sequenceList);
- }
- if (_sequenceMappingList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_sequenceMappingList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_sequenceMappingList)) {
- result = 37 * result + _sequenceMappingList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_sequenceMappingList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_sequenceMappingList);
- }
- if (_dataSetAnnotationsList != null
-- && !org.castor.util.CycleBreaker
-+ && !org.castor.core.util.CycleBreaker
- .startingToCycle(_dataSetAnnotationsList)) {
- result = 37 * result + _dataSetAnnotationsList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_dataSetAnnotationsList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_dataSetAnnotationsList);
- }
- if (_alignmentList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_alignmentList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_alignmentList)) {
- result = 37 * result + _alignmentList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_alignmentList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_alignmentList);
- }
- if (_treeList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_treeList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_treeList)) {
- result = 37 * result + _treeList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_treeList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_treeList);
- }
- if (_provenance != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_provenance)) {
- result = 37 * result + _provenance.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_provenance);
- }
-
- return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/DataSetAnnotations.java
-===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/DataSetAnnotations.java 2011-04-14 23:01:23.976202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/DataSetAnnotations.java 2011-04-14 23:01:44.504202539 +0200
-@@ -120,27 +120,27 @@
- if (temp._seqRef == null)
- return false;
- if (this._seqRef != temp._seqRef) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._seqRef);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._seqRef);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._seqRef);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._seqRef);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._seqRef);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._seqRef);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqRef);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._seqRef);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._seqRef.equals(temp._seqRef)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._seqRef);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqRef);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._seqRef);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._seqRef);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._seqRef);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqRef);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._seqRef);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._seqRef);
- }
- }
- } else if (temp._seqRef != null)
-@@ -149,29 +149,29 @@
- if (temp._provenance == null)
- return false;
- if (this._provenance != temp._provenance) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._provenance);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._provenance);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._provenance.equals(temp._provenance)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
- }
- }
- } else if (temp._provenance != null)
-@@ -255,14 +255,14 @@
-
- long tmp;
- if (_seqRef != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_seqRef)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_seqRef)) {
- result = 37 * result + _seqRef.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_seqRef);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_seqRef);
- }
- if (_provenance != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_provenance)) {
- result = 37 * result + _provenance.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_provenance);
- }
-
- return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/DbRef.java
-===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/DbRef.java 2011-04-14 23:01:24.124202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/DbRef.java 2011-04-14 23:01:44.508202539 +0200
-@@ -231,27 +231,27 @@
- if (temp._source == null)
- return false;
- if (this._source != temp._source) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._source);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._source);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._source);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._source);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._source);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._source);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._source);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._source);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._source.equals(temp._source)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._source);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._source);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._source);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._source);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._source);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._source);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._source);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._source);
- }
- }
- } else if (temp._source != null)
-@@ -260,27 +260,27 @@
- if (temp._version == null)
- return false;
- if (this._version != temp._version) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._version);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._version);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._version);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._version);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._version.equals(temp._version)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version);
- }
- }
- } else if (temp._version != null)
-@@ -289,18 +289,18 @@
- if (temp._accessionId == null)
- return false;
- if (this._accessionId != temp._accessionId) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._accessionId);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._accessionId);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._accessionId);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._accessionId);
- }
- ;
-@@ -308,14 +308,14 @@
- }
- if (!thcycle) {
- if (!this._accessionId.equals(temp._accessionId)) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._accessionId);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._accessionId);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._accessionId);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._accessionId);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._accessionId);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._accessionId);
- }
- }
- } else if (temp._accessionId != null)
-@@ -324,27 +324,27 @@
- if (temp._id == null)
- return false;
- if (this._id != temp._id) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._id.equals(temp._id)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- }
- }
- } else if (temp._id != null)
-@@ -353,27 +353,27 @@
- if (temp._mapList == null)
- return false;
- if (this._mapList != temp._mapList) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._mapList);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._mapList);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._mapList);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._mapList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._mapList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._mapList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._mapList);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._mapList.equals(temp._mapList)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._mapList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._mapList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._mapList);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._mapList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._mapList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._mapList);
- }
- }
- } else if (temp._mapList != null)
-@@ -382,29 +382,29 @@
- if (temp._linkList == null)
- return false;
- if (this._linkList != temp._linkList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._linkList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._linkList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._linkList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._linkList);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._linkList.equals(temp._linkList)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._linkList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._linkList);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._linkList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._linkList);
- }
- }
- } else if (temp._linkList != null)
-@@ -413,18 +413,18 @@
- if (temp._propertyList == null)
- return false;
- if (this._propertyList != temp._propertyList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._propertyList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._propertyList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._propertyList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._propertyList);
- }
- ;
-@@ -432,14 +432,14 @@
- }
- if (!thcycle) {
- if (!this._propertyList.equals(temp._propertyList)) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._propertyList);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._propertyList);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._propertyList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
- }
- }
- } else if (temp._propertyList != null)
-@@ -666,38 +666,38 @@
-
- long tmp;
- if (_source != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_source)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_source)) {
- result = 37 * result + _source.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_source);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_source);
- }
- if (_version != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_version)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_version)) {
- result = 37 * result + _version.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_version);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_version);
- }
- if (_accessionId != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_accessionId)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_accessionId)) {
- result = 37 * result + _accessionId.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_accessionId);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_accessionId);
- }
-- if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
-+ if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) {
- result = 37 * result + _id.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_id);
- }
- if (_mapList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_mapList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_mapList)) {
- result = 37 * result + _mapList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_mapList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_mapList);
- }
- if (_linkList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_linkList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_linkList)) {
- result = 37 * result + _linkList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_linkList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_linkList);
- }
- if (_propertyList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_propertyList)) {
- result = 37 * result + _propertyList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_propertyList);
- }
-
- return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Entry.java
-===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/Entry.java 2011-04-14 23:01:24.004202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Entry.java 2011-04-14 23:01:44.504202539 +0200
-@@ -225,27 +225,27 @@
- if (temp._id == null)
- return false;
- if (this._id != temp._id) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._id.equals(temp._id)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- }
- }
- } else if (temp._id != null)
-@@ -254,27 +254,27 @@
- if (temp._user == null)
- return false;
- if (this._user != temp._user) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._user);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._user);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._user);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._user);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._user);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._user);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._user);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._user);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._user.equals(temp._user)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._user);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._user);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._user);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._user);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._user);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._user);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._user);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._user);
- }
- }
- } else if (temp._user != null)
-@@ -283,27 +283,27 @@
- if (temp._app == null)
- return false;
- if (this._app != temp._app) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._app);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._app);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._app);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._app);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._app);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._app);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._app);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._app);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._app.equals(temp._app)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._app);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._app);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._app);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._app);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._app);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._app);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._app);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._app);
- }
- }
- } else if (temp._app != null)
-@@ -312,27 +312,27 @@
- if (temp._action == null)
- return false;
- if (this._action != temp._action) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._action);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._action);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._action);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._action);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._action);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._action);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._action);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._action);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._action.equals(temp._action)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._action);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._action);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._action);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._action);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._action);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._action);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._action);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._action);
- }
- }
- } else if (temp._action != null)
-@@ -341,27 +341,27 @@
- if (temp._date == null)
- return false;
- if (this._date != temp._date) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._date);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._date);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._date);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._date);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._date);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._date);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._date);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._date);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._date.equals(temp._date)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._date);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._date);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._date);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._date);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._date);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._date);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._date);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._date);
- }
- }
- } else if (temp._date != null)
-@@ -370,18 +370,18 @@
- if (temp._propertyList == null)
- return false;
- if (this._propertyList != temp._propertyList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._propertyList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._propertyList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._propertyList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._propertyList);
- }
- ;
-@@ -389,14 +389,14 @@
- }
- if (!thcycle) {
- if (!this._propertyList.equals(temp._propertyList)) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._propertyList);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._propertyList);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._propertyList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
- }
- }
- } else if (temp._propertyList != null)
-@@ -405,29 +405,29 @@
- if (temp._paramList == null)
- return false;
- if (this._paramList != temp._paramList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._paramList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._paramList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._paramList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._paramList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._paramList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._paramList);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._paramList.equals(temp._paramList)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._paramList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._paramList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._paramList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._paramList);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._paramList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._paramList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._paramList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._paramList);
- }
- }
- } else if (temp._paramList != null)
-@@ -436,29 +436,29 @@
- if (temp._inputList == null)
- return false;
- if (this._inputList != temp._inputList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._inputList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._inputList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._inputList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._inputList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._inputList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._inputList);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._inputList.equals(temp._inputList)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._inputList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._inputList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._inputList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._inputList);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._inputList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._inputList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._inputList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._inputList);
- }
- }
- } else if (temp._inputList != null)
-@@ -689,41 +689,41 @@
- int result = super.hashCode();
-
- long tmp;
-- if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
-+ if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) {
- result = 37 * result + _id.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_id);
- }
-- if (_user != null && !org.castor.util.CycleBreaker.startingToCycle(_user)) {
-+ if (_user != null && !org.castor.core.util.CycleBreaker.startingToCycle(_user)) {
- result = 37 * result + _user.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_user);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_user);
- }
-- if (_app != null && !org.castor.util.CycleBreaker.startingToCycle(_app)) {
-+ if (_app != null && !org.castor.core.util.CycleBreaker.startingToCycle(_app)) {
- result = 37 * result + _app.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_app);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_app);
- }
- if (_action != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_action)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_action)) {
- result = 37 * result + _action.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_action);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_action);
- }
-- if (_date != null && !org.castor.util.CycleBreaker.startingToCycle(_date)) {
-+ if (_date != null && !org.castor.core.util.CycleBreaker.startingToCycle(_date)) {
- result = 37 * result + _date.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_date);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_date);
- }
- if (_propertyList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_propertyList)) {
- result = 37 * result + _propertyList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_propertyList);
- }
- if (_paramList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_paramList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_paramList)) {
- result = 37 * result + _paramList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_paramList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_paramList);
- }
- if (_inputList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_inputList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_inputList)) {
- result = 37 * result + _inputList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_inputList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_inputList);
- }
-
- return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Glyph.java
-===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/Glyph.java 2011-04-14 23:01:23.912202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Glyph.java 2011-04-14 23:01:44.500202539 +0200
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Glyph.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Glyph.java 2011-10-17 23:43:32.628672117 +0200
@@ -89,27 +89,27 @@
if (temp._content == null)
return false;
@@ -2612,10 +542,10 @@
}
return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Input.java
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Input.java
===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/Input.java 2011-04-14 23:01:23.996202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Input.java 2011-04-14 23:01:44.504202539 +0200
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Input.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Input.java 2011-10-17 23:43:32.640672117 +0200
@@ -120,27 +120,27 @@
if (temp._name == null)
return false;
@@ -2707,10 +637,10 @@
}
return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Instance.java
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Instance.java
===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/Instance.java 2011-04-14 23:01:24.020202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Instance.java 2011-04-14 23:01:44.504202539 +0200
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Instance.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Instance.java 2011-10-17 23:43:32.640672117 +0200
@@ -79,27 +79,27 @@
if (temp._urn == null)
return false;
@@ -2759,10 +689,10 @@
}
return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Link.java
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Link.java
===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/Link.java 2011-04-14 23:01:24.048202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Link.java 2011-04-14 23:01:44.504202539 +0200
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Link.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Link.java 2011-10-17 23:43:32.640672117 +0200
@@ -85,27 +85,27 @@
if (temp._content == null)
return false;
@@ -2853,62 +783,10 @@
}
return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/LockFile.java
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Map.java
===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/LockFile.java 2011-04-14 23:01:23.828202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/LockFile.java 2011-04-14 23:01:44.500202539 +0200
-@@ -81,27 +81,27 @@
- if (temp._content == null)
- return false;
- if (this._content != temp._content) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._content);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._content);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._content);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._content);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._content);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._content);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._content.equals(temp._content)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._content);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._content);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._content);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._content);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content);
- }
- }
- } else if (temp._content != null)
-@@ -134,9 +134,9 @@
-
- long tmp;
- if (_content != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_content)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_content)) {
- result = 37 * result + _content.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_content);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_content);
- }
-
- return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Map.java
-===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/Map.java 2011-04-14 23:01:23.860202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Map.java 2011-04-14 23:01:44.500202539 +0200
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Map.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Map.java 2011-10-17 23:43:32.628672117 +0200
@@ -85,27 +85,27 @@
if (temp._id == null)
return false;
@@ -2957,10 +835,10 @@
}
return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/MapType.java
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/MapType.java
===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/MapType.java 2011-04-14 23:01:23.964202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/MapType.java 2011-04-14 23:01:44.504202539 +0200
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/MapType.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/MapType.java 2011-10-17 23:43:32.632672117 +0200
@@ -83,27 +83,27 @@
if (temp._local == null)
return false;
@@ -3052,191 +930,10 @@
}
return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Newick.java
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/NodeType.java
===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/Newick.java 2011-04-14 23:01:23.888202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Newick.java 2011-04-14 23:01:44.500202539 +0200
-@@ -97,27 +97,27 @@
- if (temp._content == null)
- return false;
- if (this._content != temp._content) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._content);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._content);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._content);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._content);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._content);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._content);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._content.equals(temp._content)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._content);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._content);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._content);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._content);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content);
- }
- }
- } else if (temp._content != null)
-@@ -126,27 +126,27 @@
- if (temp._title == null)
- return false;
- if (this._title != temp._title) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._title);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._title);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._title);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._title);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._title);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._title);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._title);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._title);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._title.equals(temp._title)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._title);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._title);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._title);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._title);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._title);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._title);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._title);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._title);
- }
- }
- } else if (temp._title != null)
-@@ -155,27 +155,27 @@
- if (temp._id == null)
- return false;
- if (this._id != temp._id) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._id.equals(temp._id)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- }
- }
- } else if (temp._id != null)
-@@ -184,29 +184,29 @@
- if (temp._modifiable == null)
- return false;
- if (this._modifiable != temp._modifiable) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._modifiable);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._modifiable);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._modifiable.equals(temp._modifiable)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
- }
- }
- } else if (temp._modifiable != null)
-@@ -268,22 +268,22 @@
-
- long tmp;
- if (_content != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_content)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_content)) {
- result = 37 * result + _content.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_content);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_content);
- }
-- if (_title != null && !org.castor.util.CycleBreaker.startingToCycle(_title)) {
-+ if (_title != null && !org.castor.core.util.CycleBreaker.startingToCycle(_title)) {
- result = 37 * result + _title.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_title);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_title);
- }
-- if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
-+ if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) {
- result = 37 * result + _id.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_id);
- }
- if (_modifiable != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_modifiable)) {
- result = 37 * result + _modifiable.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_modifiable);
- }
-
- return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/NodeType.java
-===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/NodeType.java 2011-04-14 23:01:23.944202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/NodeType.java 2011-04-14 23:01:44.504202539 +0200
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/NodeType.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/NodeType.java 2011-10-17 23:43:32.628672117 +0200
@@ -176,27 +176,27 @@
if (temp._id == null)
return false;
@@ -3515,10 +1212,10 @@
}
return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Param.java
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Param.java
===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/Param.java 2011-04-14 23:01:23.848202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Param.java 2011-04-14 23:01:44.500202539 +0200
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Param.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Param.java 2011-10-17 23:43:32.628672117 +0200
@@ -92,27 +92,27 @@
if (temp._content == null)
return false;
@@ -3651,10 +1348,10 @@
}
return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Property.java
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Property.java
===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/Property.java 2011-04-14 23:01:23.900202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Property.java 2011-04-14 23:01:44.500202539 +0200
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Property.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Property.java 2011-10-17 23:43:32.628672117 +0200
@@ -92,27 +92,27 @@
if (temp._content == null)
return false;
@@ -3787,64 +1484,10 @@
}
return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Provenance.java
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/RangeAnnotation.java
===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/Provenance.java 2011-04-14 23:01:23.984202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Provenance.java 2011-04-14 23:01:44.504202539 +0200
-@@ -116,29 +116,29 @@
- if (temp._entryList == null)
- return false;
- if (this._entryList != temp._entryList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._entryList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._entryList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._entryList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._entryList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._entryList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._entryList);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._entryList.equals(temp._entryList)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._entryList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._entryList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._entryList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._entryList);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._entryList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._entryList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._entryList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._entryList);
- }
- }
- } else if (temp._entryList != null)
-@@ -213,9 +213,9 @@
-
- long tmp;
- if (_entryList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_entryList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_entryList)) {
- result = 37 * result + _entryList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_entryList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_entryList);
- }
-
- return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/RangeAnnotation.java
-===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/RangeAnnotation.java 2011-04-14 23:01:24.080202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/RangeAnnotation.java 2011-04-14 23:01:44.508202539 +0200
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/RangeAnnotation.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/RangeAnnotation.java 2011-10-17 23:43:32.644672117 +0200
@@ -288,27 +288,27 @@
if (temp._id == null)
return false;
@@ -4346,10 +1989,10 @@
}
return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/RangeType.java
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/RangeType.java
===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/RangeType.java 2011-04-14 23:01:24.104202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/RangeType.java 2011-04-14 23:01:44.508202539 +0200
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/RangeType.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/RangeType.java 2011-10-17 23:43:32.644672117 +0200
@@ -157,18 +157,18 @@
if (temp._choiceValue == null)
return false;
@@ -4490,10 +2133,10 @@
}
return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/ReferenceType.java
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/ReferenceType.java
===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/ReferenceType.java 2011-04-14 23:01:24.040202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/ReferenceType.java 2011-04-14 23:01:44.504202539 +0200
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/ReferenceType.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/ReferenceType.java 2011-10-17 23:43:32.640672117 +0200
@@ -128,27 +128,27 @@
if (temp._content == null)
return false;
@@ -4626,10 +2269,10 @@
}
return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Score.java
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Score.java
===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/Score.java 2011-04-14 23:01:23.932202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Score.java 2011-04-14 23:01:44.500202539 +0200
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Score.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Score.java 2011-10-17 23:43:32.628672117 +0200
@@ -100,27 +100,27 @@
if (temp._name == null)
return false;
@@ -4678,197 +2321,10 @@
}
return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Sequence.java
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/SequenceMapping.java
===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/Sequence.java 2011-04-14 23:01:24.028202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Sequence.java 2011-04-14 23:01:44.504202539 +0200
-@@ -170,27 +170,27 @@
- if (temp._id == null)
- return false;
- if (this._id != temp._id) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._id.equals(temp._id)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- }
- }
- } else if (temp._id != null)
-@@ -199,29 +199,29 @@
- if (temp._dictionary == null)
- return false;
- if (this._dictionary != temp._dictionary) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._dictionary);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._dictionary);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._dictionary);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._dictionary);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._dictionary);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._dictionary);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._dictionary.equals(temp._dictionary)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._dictionary);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._dictionary);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._dictionary);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._dictionary);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._dictionary);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._dictionary);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._dictionary);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._dictionary);
- }
- }
- } else if (temp._dictionary != null)
-@@ -230,29 +230,29 @@
- if (temp._dbRefList == null)
- return false;
- if (this._dbRefList != temp._dbRefList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._dbRefList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._dbRefList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._dbRefList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._dbRefList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._dbRefList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._dbRefList);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._dbRefList.equals(temp._dbRefList)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._dbRefList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._dbRefList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._dbRefList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._dbRefList);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._dbRefList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._dbRefList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._dbRefList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._dbRefList);
- }
- }
- } else if (temp._dbRefList != null)
-@@ -261,29 +261,29 @@
- if (temp._vxrefList == null)
- return false;
- if (this._vxrefList != temp._vxrefList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._vxrefList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._vxrefList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._vxrefList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._vxrefList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._vxrefList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._vxrefList);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._vxrefList.equals(temp._vxrefList)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._vxrefList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._vxrefList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._vxrefList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._vxrefList);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._vxrefList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._vxrefList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._vxrefList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._vxrefList);
- }
- }
- } else if (temp._vxrefList != null)
-@@ -431,24 +431,24 @@
- int result = super.hashCode();
-
- long tmp;
-- if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
-+ if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) {
- result = 37 * result + _id.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_id);
- }
- if (_dictionary != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_dictionary)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_dictionary)) {
- result = 37 * result + _dictionary.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_dictionary);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_dictionary);
- }
- if (_dbRefList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_dbRefList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_dbRefList)) {
- result = 37 * result + _dbRefList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_dbRefList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_dbRefList);
- }
- if (_vxrefList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_vxrefList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_vxrefList)) {
- result = 37 * result + _vxrefList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_vxrefList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_vxrefList);
- }
-
- return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/SequenceMapping.java
-===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/SequenceMapping.java 2011-04-14 23:01:23.880202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/SequenceMapping.java 2011-04-14 23:01:44.500202539 +0200
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/SequenceMapping.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/SequenceMapping.java 2011-10-17 23:43:32.628672117 +0200
@@ -94,27 +94,27 @@
if (temp._loc == null)
return false;
@@ -5046,531 +2502,10 @@
}
return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/SequenceType.java
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Treenode.java
===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/SequenceType.java 2011-04-14 23:01:23.776202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/SequenceType.java 2011-04-14 23:01:44.496202539 +0200
-@@ -171,29 +171,29 @@
- if (temp._sequence == null)
- return false;
- if (this._sequence != temp._sequence) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._sequence);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._sequence);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._sequence);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._sequence);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequence);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._sequence);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._sequence.equals(temp._sequence)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._sequence);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequence);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._sequence);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._sequence);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._sequence);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequence);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._sequence);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._sequence);
- }
- }
- } else if (temp._sequence != null)
-@@ -202,27 +202,27 @@
- if (temp._name == null)
- return false;
- if (this._name != temp._name) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._name);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._name);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._name);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._name);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._name);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._name);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._name.equals(temp._name)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._name);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._name);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._name);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._name);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name);
- }
- }
- } else if (temp._name != null)
-@@ -231,18 +231,18 @@
- if (temp._description == null)
- return false;
- if (this._description != temp._description) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._description);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._description);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._description);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._description);
- }
- ;
-@@ -250,14 +250,14 @@
- }
- if (!thcycle) {
- if (!this._description.equals(temp._description)) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._description);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._description);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._description);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._description);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._description);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._description);
- }
- }
- } else if (temp._description != null)
-@@ -266,18 +266,18 @@
- if (temp._propertyList == null)
- return false;
- if (this._propertyList != temp._propertyList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._propertyList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._propertyList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._propertyList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._propertyList);
- }
- ;
-@@ -285,14 +285,14 @@
- }
- if (!thcycle) {
- if (!this._propertyList.equals(temp._propertyList)) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._propertyList);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._propertyList);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._propertyList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
- }
- }
- } else if (temp._propertyList != null)
-@@ -434,23 +434,23 @@
- result = 37 * result + (int) (_start ^ (_start >>> 32));
- result = 37 * result + (int) (_end ^ (_end >>> 32));
- if (_sequence != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_sequence)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_sequence)) {
- result = 37 * result + _sequence.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_sequence);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_sequence);
- }
-- if (_name != null && !org.castor.util.CycleBreaker.startingToCycle(_name)) {
-+ if (_name != null && !org.castor.core.util.CycleBreaker.startingToCycle(_name)) {
- result = 37 * result + _name.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_name);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_name);
- }
- if (_description != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_description)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_description)) {
- result = 37 * result + _description.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_description);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_description);
- }
- if (_propertyList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_propertyList)) {
- result = 37 * result + _propertyList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_propertyList);
- }
-
- return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Tree.java
-===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/Tree.java 2011-04-14 23:01:23.816202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Tree.java 2011-04-14 23:01:44.500202539 +0200
-@@ -219,27 +219,27 @@
- if (temp._id == null)
- return false;
- if (this._id != temp._id) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._id.equals(temp._id)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- }
- }
- } else if (temp._id != null)
-@@ -248,29 +248,29 @@
- if (temp._modifiable == null)
- return false;
- if (this._modifiable != temp._modifiable) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._modifiable);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._modifiable);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._modifiable.equals(temp._modifiable)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
- }
- }
- } else if (temp._modifiable != null)
-@@ -279,27 +279,27 @@
- if (temp._title == null)
- return false;
- if (this._title != temp._title) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._title);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._title);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._title);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._title);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._title);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._title);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._title);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._title);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._title.equals(temp._title)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._title);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._title);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._title);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._title);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._title);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._title);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._title);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._title);
- }
- }
- } else if (temp._title != null)
-@@ -308,29 +308,29 @@
- if (temp._newickList == null)
- return false;
- if (this._newickList != temp._newickList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._newickList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._newickList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._newickList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._newickList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._newickList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._newickList);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._newickList.equals(temp._newickList)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._newickList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._newickList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._newickList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._newickList);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._newickList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._newickList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._newickList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._newickList);
- }
- }
- } else if (temp._newickList != null)
-@@ -339,18 +339,18 @@
- if (temp._treenodeList == null)
- return false;
- if (this._treenodeList != temp._treenodeList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._treenodeList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._treenodeList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._treenodeList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._treenodeList);
- }
- ;
-@@ -358,14 +358,14 @@
- }
- if (!thcycle) {
- if (!this._treenodeList.equals(temp._treenodeList)) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._treenodeList);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._treenodeList);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._treenodeList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._treenodeList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treenodeList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treenodeList);
- }
- }
- } else if (temp._treenodeList != null)
-@@ -374,18 +374,18 @@
- if (temp._propertyList == null)
- return false;
- if (this._propertyList != temp._propertyList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._propertyList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._propertyList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._propertyList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._propertyList);
- }
- ;
-@@ -393,14 +393,14 @@
- }
- if (!thcycle) {
- if (!this._propertyList.equals(temp._propertyList)) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._propertyList);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._propertyList);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._propertyList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
- }
- }
- } else if (temp._propertyList != null)
-@@ -409,29 +409,29 @@
- if (temp._provenance == null)
- return false;
- if (this._provenance != temp._provenance) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._provenance);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._provenance);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._provenance.equals(temp._provenance)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
- }
- }
- } else if (temp._provenance != null)
-@@ -651,38 +651,38 @@
- int result = super.hashCode();
-
- long tmp;
-- if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
-+ if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) {
- result = 37 * result + _id.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_id);
- }
- if (_modifiable != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_modifiable)) {
- result = 37 * result + _modifiable.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_modifiable);
- }
-- if (_title != null && !org.castor.util.CycleBreaker.startingToCycle(_title)) {
-+ if (_title != null && !org.castor.core.util.CycleBreaker.startingToCycle(_title)) {
- result = 37 * result + _title.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_title);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_title);
- }
- if (_newickList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_newickList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_newickList)) {
- result = 37 * result + _newickList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_newickList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_newickList);
- }
- if (_treenodeList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_treenodeList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_treenodeList)) {
- result = 37 * result + _treenodeList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_treenodeList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_treenodeList);
- }
- if (_propertyList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_propertyList)) {
- result = 37 * result + _propertyList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_propertyList);
- }
- if (_provenance != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_provenance)) {
- result = 37 * result + _provenance.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_provenance);
- }
-
- return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Treenode.java
-===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/Treenode.java 2011-04-14 23:01:23.836202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/Treenode.java 2011-04-14 23:01:44.500202539 +0200
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Treenode.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Treenode.java 2011-10-17 23:43:32.628672117 +0200
@@ -122,27 +122,27 @@
if (temp._treeId == null)
return false;
@@ -5664,597 +2599,3662 @@
}
return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/User.java
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java
===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/User.java 2011-04-14 23:01:24.060202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/User.java 2011-04-14 23:01:44.504202539 +0200
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java 2011-10-17 23:43:32.608672117 +0200
+@@ -40,7 +40,7 @@
+ /*
+ *
+ * static {
+- * org.exolab.castor.util.LocalConfiguration.getInstance().getProperties().setProperty(
++ * org.exolab.castor.core.util.LocalConfiguration.getInstance().getProperties().setProperty(
+ * "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer"); }
+ *
+ */
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Alignment.java
+===================================================================
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Alignment.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Alignment.java 2011-10-17 23:43:32.628672117 +0200
+@@ -282,27 +282,27 @@
+ if (temp._gapChar == null)
+ return false;
+ if (this._gapChar != temp._gapChar) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._gapChar);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._gapChar);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._gapChar);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._gapChar);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._gapChar);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._gapChar);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._gapChar);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._gapChar);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._gapChar.equals(temp._gapChar)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._gapChar);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._gapChar);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._gapChar);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._gapChar);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._gapChar);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._gapChar);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._gapChar);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._gapChar);
+ }
+ }
+ } else if (temp._gapChar != null)
+@@ -315,27 +315,27 @@
+ if (temp._id == null)
+ return false;
+ if (this._id != temp._id) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._id.equals(temp._id)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ }
+ } else if (temp._id != null)
+@@ -344,29 +344,29 @@
+ if (temp._modifiable == null)
+ return false;
+ if (this._modifiable != temp._modifiable) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._modifiable);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._modifiable);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._modifiable.equals(temp._modifiable)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
+ }
+ }
+ } else if (temp._modifiable != null)
+@@ -375,18 +375,18 @@
+ if (temp._alignmentAnnotationList == null)
+ return false;
+ if (this._alignmentAnnotationList != temp._alignmentAnnotationList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._alignmentAnnotationList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._alignmentAnnotationList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._alignmentAnnotationList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._alignmentAnnotationList);
+ }
+ ;
+@@ -395,15 +395,15 @@
+ if (!thcycle) {
+ if (!this._alignmentAnnotationList
+ .equals(temp._alignmentAnnotationList)) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._alignmentAnnotationList);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._alignmentAnnotationList);
+ return false;
+ }
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._alignmentAnnotationList);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._alignmentAnnotationList);
+ }
+ }
+@@ -413,29 +413,29 @@
+ if (temp._treeList == null)
+ return false;
+ if (this._treeList != temp._treeList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._treeList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._treeList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._treeList.equals(temp._treeList)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList);
+ }
+ }
+ } else if (temp._treeList != null)
+@@ -444,18 +444,18 @@
+ if (temp._alignmentSequenceList == null)
+ return false;
+ if (this._alignmentSequenceList != temp._alignmentSequenceList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._alignmentSequenceList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._alignmentSequenceList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._alignmentSequenceList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._alignmentSequenceList);
+ }
+ ;
+@@ -464,15 +464,15 @@
+ if (!thcycle) {
+ if (!this._alignmentSequenceList
+ .equals(temp._alignmentSequenceList)) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._alignmentSequenceList);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._alignmentSequenceList);
+ return false;
+ }
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._alignmentSequenceList);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._alignmentSequenceList);
+ }
+ }
+@@ -482,18 +482,18 @@
+ if (temp._propertyList == null)
+ return false;
+ if (this._propertyList != temp._propertyList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._propertyList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._propertyList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._propertyList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._propertyList);
+ }
+ ;
+@@ -501,14 +501,14 @@
+ }
+ if (!thcycle) {
+ if (!this._propertyList.equals(temp._propertyList)) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._propertyList);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._propertyList);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._propertyList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
+ }
+ }
+ } else if (temp._propertyList != null)
+@@ -517,29 +517,29 @@
+ if (temp._provenance == null)
+ return false;
+ if (this._provenance != temp._provenance) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._provenance);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._provenance);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._provenance.equals(temp._provenance)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
+ }
+ }
+ } else if (temp._provenance != null)
+@@ -841,46 +841,46 @@
+
+ long tmp;
+ if (_gapChar != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_gapChar)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_gapChar)) {
+ result = 37 * result + _gapChar.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_gapChar);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_gapChar);
+ }
+ result = 37 * result + (_aligned ? 0 : 1);
+- if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
++ if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) {
+ result = 37 * result + _id.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_id);
+ }
+ if (_modifiable != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_modifiable)) {
+ result = 37 * result + _modifiable.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_modifiable);
+ }
+ if (_alignmentAnnotationList != null
+- && !org.castor.util.CycleBreaker
++ && !org.castor.core.util.CycleBreaker
+ .startingToCycle(_alignmentAnnotationList)) {
+ result = 37 * result + _alignmentAnnotationList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_alignmentAnnotationList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_alignmentAnnotationList);
+ }
+ if (_treeList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_treeList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_treeList)) {
+ result = 37 * result + _treeList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_treeList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_treeList);
+ }
+ if (_alignmentSequenceList != null
+- && !org.castor.util.CycleBreaker
++ && !org.castor.core.util.CycleBreaker
+ .startingToCycle(_alignmentSequenceList)) {
+ result = 37 * result + _alignmentSequenceList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_alignmentSequenceList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_alignmentSequenceList);
+ }
+ if (_propertyList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_propertyList)) {
+ result = 37 * result + _propertyList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_propertyList);
+ }
+ if (_provenance != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_provenance)) {
+ result = 37 * result + _provenance.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_provenance);
+ }
+
+ return result;
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/AlignmentSequence.java
+===================================================================
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/AlignmentSequence.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/AlignmentSequence.java 2011-10-17 23:43:32.624672117 +0200
+@@ -132,27 +132,27 @@
+ if (temp._id == null)
+ return false;
+ if (this._id != temp._id) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._id.equals(temp._id)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ }
+ } else if (temp._id != null)
+@@ -161,27 +161,27 @@
+ if (temp._refid == null)
+ return false;
+ if (this._refid != temp._refid) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._refid);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._refid);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._refid);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._refid);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._refid);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._refid);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._refid);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._refid);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._refid.equals(temp._refid)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._refid);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._refid);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._refid);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._refid);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._refid);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._refid);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._refid);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._refid);
+ }
+ }
+ } else if (temp._refid != null)
+@@ -190,18 +190,18 @@
+ if (temp._alignmentSequenceAnnotationList == null)
+ return false;
+ if (this._alignmentSequenceAnnotationList != temp._alignmentSequenceAnnotationList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._alignmentSequenceAnnotationList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._alignmentSequenceAnnotationList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._alignmentSequenceAnnotationList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._alignmentSequenceAnnotationList);
+ }
+ ;
+@@ -210,15 +210,15 @@
+ if (!thcycle) {
+ if (!this._alignmentSequenceAnnotationList
+ .equals(temp._alignmentSequenceAnnotationList)) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._alignmentSequenceAnnotationList);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._alignmentSequenceAnnotationList);
+ return false;
+ }
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._alignmentSequenceAnnotationList);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._alignmentSequenceAnnotationList);
+ }
+ }
+@@ -323,19 +323,19 @@
+ int result = super.hashCode();
+
+ long tmp;
+- if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
++ if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) {
+ result = 37 * result + _id.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_id);
+ }
+- if (_refid != null && !org.castor.util.CycleBreaker.startingToCycle(_refid)) {
++ if (_refid != null && !org.castor.core.util.CycleBreaker.startingToCycle(_refid)) {
+ result = 37 * result + _refid.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_refid);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_refid);
+ }
+ if (_alignmentSequenceAnnotationList != null
+- && !org.castor.util.CycleBreaker
++ && !org.castor.core.util.CycleBreaker
+ .startingToCycle(_alignmentSequenceAnnotationList)) {
+ result = 37 * result + _alignmentSequenceAnnotationList.hashCode();
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(_alignmentSequenceAnnotationList);
+ }
+
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/AnnotationElement.java
+===================================================================
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/AnnotationElement.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/AnnotationElement.java 2011-10-17 23:43:32.632672117 +0200
+@@ -213,27 +213,27 @@
+ if (temp._id == null)
+ return false;
+ if (this._id != temp._id) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._id.equals(temp._id)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ }
+ } else if (temp._id != null)
+@@ -242,18 +242,18 @@
+ if (temp._description == null)
+ return false;
+ if (this._description != temp._description) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._description);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._description);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._description);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._description);
+ }
+ ;
+@@ -261,14 +261,14 @@
+ }
+ if (!thcycle) {
+ if (!this._description.equals(temp._description)) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._description);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._description);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._description);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._description);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._description);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._description);
+ }
+ }
+ } else if (temp._description != null)
+@@ -277,29 +277,29 @@
+ if (temp._glyphList == null)
+ return false;
+ if (this._glyphList != temp._glyphList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._glyphList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._glyphList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._glyphList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._glyphList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._glyphList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._glyphList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._glyphList.equals(temp._glyphList)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._glyphList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._glyphList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._glyphList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._glyphList);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._glyphList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._glyphList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._glyphList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._glyphList);
+ }
+ }
+ } else if (temp._glyphList != null)
+@@ -308,29 +308,29 @@
+ if (temp._valueList == null)
+ return false;
+ if (this._valueList != temp._valueList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._valueList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._valueList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._valueList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._valueList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._valueList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._valueList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._valueList.equals(temp._valueList)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._valueList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._valueList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._valueList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._valueList);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._valueList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._valueList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._valueList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._valueList);
+ }
+ }
+ } else if (temp._valueList != null)
+@@ -519,24 +519,24 @@
+ long tmp;
+ result = 37 * result + (int) (_position ^ (_position >>> 32));
+ result = 37 * result + (_after ? 0 : 1);
+- if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
++ if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) {
+ result = 37 * result + _id.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_id);
+ }
+ if (_description != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_description)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_description)) {
+ result = 37 * result + _description.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_description);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_description);
+ }
+ if (_glyphList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_glyphList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_glyphList)) {
+ result = 37 * result + _glyphList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_glyphList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_glyphList);
+ }
+ if (_valueList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_valueList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_valueList)) {
+ result = 37 * result + _valueList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_valueList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_valueList);
+ }
+
+ return result;
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/ApplicationData.java
+===================================================================
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/ApplicationData.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/ApplicationData.java 2011-10-17 23:43:32.624672117 +0200
+@@ -173,27 +173,27 @@
+ if (temp._version == null)
+ return false;
+ if (this._version != temp._version) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._version);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._version);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._version);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._version);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._version.equals(temp._version)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version);
+ }
+ }
+ } else if (temp._version != null)
+@@ -202,27 +202,27 @@
+ if (temp._name == null)
+ return false;
+ if (this._name != temp._name) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._name);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._name);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._name);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._name);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._name);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._name);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._name.equals(temp._name)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._name);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._name);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._name);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._name);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name);
+ }
+ }
+ } else if (temp._name != null)
+@@ -231,29 +231,29 @@
+ if (temp._userList == null)
+ return false;
+ if (this._userList != temp._userList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._userList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._userList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._userList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._userList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._userList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._userList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._userList.equals(temp._userList)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._userList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._userList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._userList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._userList);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._userList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._userList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._userList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._userList);
+ }
+ }
+ } else if (temp._userList != null)
+@@ -262,27 +262,27 @@
+ if (temp._common == null)
+ return false;
+ if (this._common != temp._common) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._common);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._common);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._common);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._common);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._common);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._common);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._common);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._common);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._common.equals(temp._common)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._common);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._common);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._common);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._common);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._common);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._common);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._common);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._common);
+ }
+ }
+ } else if (temp._common != null)
+@@ -291,18 +291,18 @@
+ if (temp._instanceList == null)
+ return false;
+ if (this._instanceList != temp._instanceList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._instanceList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._instanceList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._instanceList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._instanceList);
+ }
+ ;
+@@ -310,14 +310,14 @@
+ }
+ if (!thcycle) {
+ if (!this._instanceList.equals(temp._instanceList)) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._instanceList);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._instanceList);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._instanceList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._instanceList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._instanceList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._instanceList);
+ }
+ }
+ } else if (temp._instanceList != null)
+@@ -476,28 +476,28 @@
+
+ long tmp;
+ if (_version != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_version)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_version)) {
+ result = 37 * result + _version.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_version);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_version);
+ }
+- if (_name != null && !org.castor.util.CycleBreaker.startingToCycle(_name)) {
++ if (_name != null && !org.castor.core.util.CycleBreaker.startingToCycle(_name)) {
+ result = 37 * result + _name.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_name);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_name);
+ }
+ if (_userList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_userList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_userList)) {
+ result = 37 * result + _userList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_userList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_userList);
+ }
+ if (_common != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_common)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_common)) {
+ result = 37 * result + _common.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_common);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_common);
+ }
+ if (_instanceList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_instanceList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_instanceList)) {
+ result = 37 * result + _instanceList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_instanceList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_instanceList);
+ }
+
+ return result;
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/DataSet.java
+===================================================================
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/DataSet.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/DataSet.java 2011-10-17 23:43:32.644672117 +0200
+@@ -295,27 +295,27 @@
+ if (temp._id == null)
+ return false;
+ if (this._id != temp._id) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._id.equals(temp._id)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ }
+ } else if (temp._id != null)
+@@ -324,18 +324,18 @@
+ if (temp._sequenceList == null)
+ return false;
+ if (this._sequenceList != temp._sequenceList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._sequenceList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._sequenceList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._sequenceList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._sequenceList);
+ }
+ ;
+@@ -343,14 +343,14 @@
+ }
+ if (!thcycle) {
+ if (!this._sequenceList.equals(temp._sequenceList)) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._sequenceList);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._sequenceList);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._sequenceList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequenceList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._sequenceList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._sequenceList);
+ }
+ }
+ } else if (temp._sequenceList != null)
+@@ -359,18 +359,18 @@
+ if (temp._sequenceMappingList == null)
+ return false;
+ if (this._sequenceMappingList != temp._sequenceMappingList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._sequenceMappingList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._sequenceMappingList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._sequenceMappingList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._sequenceMappingList);
+ }
+ ;
+@@ -378,15 +378,15 @@
+ }
+ if (!thcycle) {
+ if (!this._sequenceMappingList.equals(temp._sequenceMappingList)) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._sequenceMappingList);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._sequenceMappingList);
+ return false;
+ }
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._sequenceMappingList);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._sequenceMappingList);
+ }
+ }
+@@ -396,18 +396,18 @@
+ if (temp._dataSetAnnotationsList == null)
+ return false;
+ if (this._dataSetAnnotationsList != temp._dataSetAnnotationsList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._dataSetAnnotationsList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._dataSetAnnotationsList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._dataSetAnnotationsList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._dataSetAnnotationsList);
+ }
+ ;
+@@ -416,15 +416,15 @@
+ if (!thcycle) {
+ if (!this._dataSetAnnotationsList
+ .equals(temp._dataSetAnnotationsList)) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._dataSetAnnotationsList);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._dataSetAnnotationsList);
+ return false;
+ }
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._dataSetAnnotationsList);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._dataSetAnnotationsList);
+ }
+ }
+@@ -434,18 +434,18 @@
+ if (temp._alignmentList == null)
+ return false;
+ if (this._alignmentList != temp._alignmentList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._alignmentList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._alignmentList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._alignmentList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._alignmentList);
+ }
+ ;
+@@ -453,15 +453,15 @@
+ }
+ if (!thcycle) {
+ if (!this._alignmentList.equals(temp._alignmentList)) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._alignmentList);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._alignmentList);
+ return false;
+ }
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._alignmentList);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._alignmentList);
+ }
+ }
+@@ -471,29 +471,29 @@
+ if (temp._treeList == null)
+ return false;
+ if (this._treeList != temp._treeList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._treeList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._treeList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._treeList.equals(temp._treeList)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList);
+ }
+ }
+ } else if (temp._treeList != null)
+@@ -502,29 +502,29 @@
+ if (temp._provenance == null)
+ return false;
+ if (this._provenance != temp._provenance) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._provenance);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._provenance);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._provenance.equals(temp._provenance)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
+ }
+ }
+ } else if (temp._provenance != null)
+@@ -842,40 +842,40 @@
+ int result = super.hashCode();
+
+ long tmp;
+- if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
++ if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) {
+ result = 37 * result + _id.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_id);
+ }
+ if (_sequenceList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_sequenceList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_sequenceList)) {
+ result = 37 * result + _sequenceList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_sequenceList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_sequenceList);
+ }
+ if (_sequenceMappingList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_sequenceMappingList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_sequenceMappingList)) {
+ result = 37 * result + _sequenceMappingList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_sequenceMappingList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_sequenceMappingList);
+ }
+ if (_dataSetAnnotationsList != null
+- && !org.castor.util.CycleBreaker
++ && !org.castor.core.util.CycleBreaker
+ .startingToCycle(_dataSetAnnotationsList)) {
+ result = 37 * result + _dataSetAnnotationsList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_dataSetAnnotationsList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_dataSetAnnotationsList);
+ }
+ if (_alignmentList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_alignmentList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_alignmentList)) {
+ result = 37 * result + _alignmentList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_alignmentList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_alignmentList);
+ }
+ if (_treeList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_treeList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_treeList)) {
+ result = 37 * result + _treeList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_treeList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_treeList);
+ }
+ if (_provenance != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_provenance)) {
+ result = 37 * result + _provenance.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_provenance);
+ }
+
+ return result;
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/DataSetAnnotations.java
+===================================================================
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/DataSetAnnotations.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/DataSetAnnotations.java 2011-10-17 23:43:32.640672117 +0200
+@@ -120,27 +120,27 @@
+ if (temp._seqRef == null)
+ return false;
+ if (this._seqRef != temp._seqRef) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._seqRef);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._seqRef);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._seqRef);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._seqRef);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._seqRef);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._seqRef);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqRef);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._seqRef);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._seqRef.equals(temp._seqRef)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._seqRef);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqRef);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._seqRef);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._seqRef);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._seqRef);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqRef);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._seqRef);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._seqRef);
+ }
+ }
+ } else if (temp._seqRef != null)
+@@ -149,29 +149,29 @@
+ if (temp._provenance == null)
+ return false;
+ if (this._provenance != temp._provenance) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._provenance);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._provenance);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._provenance.equals(temp._provenance)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
+ }
+ }
+ } else if (temp._provenance != null)
+@@ -255,14 +255,14 @@
+
+ long tmp;
+ if (_seqRef != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_seqRef)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_seqRef)) {
+ result = 37 * result + _seqRef.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_seqRef);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_seqRef);
+ }
+ if (_provenance != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_provenance)) {
+ result = 37 * result + _provenance.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_provenance);
+ }
+
+ return result;
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/DbRef.java
+===================================================================
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/DbRef.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/DbRef.java 2011-10-17 23:43:32.644672117 +0200
+@@ -231,27 +231,27 @@
+ if (temp._source == null)
+ return false;
+ if (this._source != temp._source) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._source);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._source);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._source);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._source);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._source);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._source);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._source);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._source);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._source.equals(temp._source)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._source);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._source);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._source);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._source);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._source);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._source);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._source);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._source);
+ }
+ }
+ } else if (temp._source != null)
+@@ -260,27 +260,27 @@
+ if (temp._version == null)
+ return false;
+ if (this._version != temp._version) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._version);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._version);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._version);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._version);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._version.equals(temp._version)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version);
+ }
+ }
+ } else if (temp._version != null)
+@@ -289,18 +289,18 @@
+ if (temp._accessionId == null)
+ return false;
+ if (this._accessionId != temp._accessionId) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._accessionId);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._accessionId);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._accessionId);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._accessionId);
+ }
+ ;
+@@ -308,14 +308,14 @@
+ }
+ if (!thcycle) {
+ if (!this._accessionId.equals(temp._accessionId)) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._accessionId);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._accessionId);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._accessionId);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._accessionId);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._accessionId);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._accessionId);
+ }
+ }
+ } else if (temp._accessionId != null)
+@@ -324,27 +324,27 @@
+ if (temp._id == null)
+ return false;
+ if (this._id != temp._id) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._id.equals(temp._id)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ }
+ } else if (temp._id != null)
+@@ -353,27 +353,27 @@
+ if (temp._mapList == null)
+ return false;
+ if (this._mapList != temp._mapList) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._mapList);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._mapList);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._mapList);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._mapList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._mapList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._mapList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._mapList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._mapList.equals(temp._mapList)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._mapList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._mapList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._mapList);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._mapList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._mapList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._mapList);
+ }
+ }
+ } else if (temp._mapList != null)
+@@ -382,29 +382,29 @@
+ if (temp._linkList == null)
+ return false;
+ if (this._linkList != temp._linkList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._linkList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._linkList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._linkList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._linkList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._linkList.equals(temp._linkList)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._linkList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._linkList);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._linkList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._linkList);
+ }
+ }
+ } else if (temp._linkList != null)
+@@ -413,18 +413,18 @@
+ if (temp._propertyList == null)
+ return false;
+ if (this._propertyList != temp._propertyList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._propertyList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._propertyList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._propertyList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._propertyList);
+ }
+ ;
+@@ -432,14 +432,14 @@
+ }
+ if (!thcycle) {
+ if (!this._propertyList.equals(temp._propertyList)) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._propertyList);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._propertyList);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._propertyList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
+ }
+ }
+ } else if (temp._propertyList != null)
+@@ -666,38 +666,38 @@
+
+ long tmp;
+ if (_source != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_source)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_source)) {
+ result = 37 * result + _source.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_source);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_source);
+ }
+ if (_version != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_version)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_version)) {
+ result = 37 * result + _version.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_version);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_version);
+ }
+ if (_accessionId != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_accessionId)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_accessionId)) {
+ result = 37 * result + _accessionId.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_accessionId);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_accessionId);
+ }
+- if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
++ if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) {
+ result = 37 * result + _id.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_id);
+ }
+ if (_mapList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_mapList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_mapList)) {
+ result = 37 * result + _mapList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_mapList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_mapList);
+ }
+ if (_linkList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_linkList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_linkList)) {
+ result = 37 * result + _linkList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_linkList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_linkList);
+ }
+ if (_propertyList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_propertyList)) {
+ result = 37 * result + _propertyList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_propertyList);
+ }
+
+ return result;
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Entry.java
+===================================================================
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Entry.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Entry.java 2011-10-17 23:43:32.640672117 +0200
+@@ -225,27 +225,27 @@
+ if (temp._id == null)
+ return false;
+ if (this._id != temp._id) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._id.equals(temp._id)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ }
+ } else if (temp._id != null)
+@@ -254,27 +254,27 @@
+ if (temp._user == null)
+ return false;
+ if (this._user != temp._user) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._user);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._user);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._user);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._user);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._user);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._user);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._user);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._user);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._user.equals(temp._user)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._user);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._user);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._user);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._user);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._user);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._user);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._user);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._user);
+ }
+ }
+ } else if (temp._user != null)
+@@ -283,27 +283,27 @@
+ if (temp._app == null)
+ return false;
+ if (this._app != temp._app) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._app);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._app);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._app);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._app);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._app);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._app);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._app);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._app);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._app.equals(temp._app)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._app);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._app);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._app);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._app);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._app);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._app);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._app);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._app);
+ }
+ }
+ } else if (temp._app != null)
+@@ -312,27 +312,27 @@
+ if (temp._action == null)
+ return false;
+ if (this._action != temp._action) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._action);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._action);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._action);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._action);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._action);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._action);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._action);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._action);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._action.equals(temp._action)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._action);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._action);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._action);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._action);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._action);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._action);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._action);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._action);
+ }
+ }
+ } else if (temp._action != null)
+@@ -341,27 +341,27 @@
+ if (temp._date == null)
+ return false;
+ if (this._date != temp._date) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._date);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._date);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._date);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._date);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._date);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._date);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._date);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._date);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._date.equals(temp._date)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._date);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._date);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._date);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._date);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._date);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._date);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._date);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._date);
+ }
+ }
+ } else if (temp._date != null)
+@@ -370,18 +370,18 @@
+ if (temp._propertyList == null)
+ return false;
+ if (this._propertyList != temp._propertyList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._propertyList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._propertyList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._propertyList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._propertyList);
+ }
+ ;
+@@ -389,14 +389,14 @@
+ }
+ if (!thcycle) {
+ if (!this._propertyList.equals(temp._propertyList)) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._propertyList);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._propertyList);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._propertyList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
+ }
+ }
+ } else if (temp._propertyList != null)
+@@ -405,29 +405,29 @@
+ if (temp._paramList == null)
+ return false;
+ if (this._paramList != temp._paramList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._paramList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._paramList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._paramList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._paramList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._paramList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._paramList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._paramList.equals(temp._paramList)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._paramList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._paramList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._paramList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._paramList);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._paramList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._paramList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._paramList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._paramList);
+ }
+ }
+ } else if (temp._paramList != null)
+@@ -436,29 +436,29 @@
+ if (temp._inputList == null)
+ return false;
+ if (this._inputList != temp._inputList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._inputList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._inputList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._inputList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._inputList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._inputList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._inputList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._inputList.equals(temp._inputList)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._inputList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._inputList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._inputList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._inputList);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._inputList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._inputList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._inputList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._inputList);
+ }
+ }
+ } else if (temp._inputList != null)
+@@ -689,41 +689,41 @@
+ int result = super.hashCode();
+
+ long tmp;
+- if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
++ if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) {
+ result = 37 * result + _id.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_id);
+ }
+- if (_user != null && !org.castor.util.CycleBreaker.startingToCycle(_user)) {
++ if (_user != null && !org.castor.core.util.CycleBreaker.startingToCycle(_user)) {
+ result = 37 * result + _user.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_user);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_user);
+ }
+- if (_app != null && !org.castor.util.CycleBreaker.startingToCycle(_app)) {
++ if (_app != null && !org.castor.core.util.CycleBreaker.startingToCycle(_app)) {
+ result = 37 * result + _app.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_app);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_app);
+ }
+ if (_action != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_action)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_action)) {
+ result = 37 * result + _action.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_action);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_action);
+ }
+- if (_date != null && !org.castor.util.CycleBreaker.startingToCycle(_date)) {
++ if (_date != null && !org.castor.core.util.CycleBreaker.startingToCycle(_date)) {
+ result = 37 * result + _date.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_date);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_date);
+ }
+ if (_propertyList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_propertyList)) {
+ result = 37 * result + _propertyList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_propertyList);
+ }
+ if (_paramList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_paramList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_paramList)) {
+ result = 37 * result + _paramList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_paramList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_paramList);
+ }
+ if (_inputList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_inputList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_inputList)) {
+ result = 37 * result + _inputList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_inputList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_inputList);
+ }
+
+ return result;
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/LockFile.java
+===================================================================
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/LockFile.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/LockFile.java 2011-10-17 23:43:32.624672117 +0200
+@@ -81,27 +81,27 @@
+ if (temp._content == null)
+ return false;
+ if (this._content != temp._content) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._content);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._content);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._content);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._content);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._content);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._content);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._content.equals(temp._content)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._content);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._content);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._content);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._content);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content);
+ }
+ }
+ } else if (temp._content != null)
+@@ -134,9 +134,9 @@
+
+ long tmp;
+ if (_content != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_content)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_content)) {
+ result = 37 * result + _content.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_content);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_content);
+ }
+
+ return result;
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Newick.java
+===================================================================
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Newick.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Newick.java 2011-10-17 23:43:32.628672117 +0200
+@@ -97,27 +97,27 @@
+ if (temp._content == null)
+ return false;
+ if (this._content != temp._content) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._content);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._content);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._content);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._content);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._content);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._content);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._content.equals(temp._content)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._content);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._content);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._content);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._content);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content);
+ }
+ }
+ } else if (temp._content != null)
+@@ -126,27 +126,27 @@
+ if (temp._title == null)
+ return false;
+ if (this._title != temp._title) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._title);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._title);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._title);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._title);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._title);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._title);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._title);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._title);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._title.equals(temp._title)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._title);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._title);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._title);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._title);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._title);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._title);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._title);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._title);
+ }
+ }
+ } else if (temp._title != null)
+@@ -155,27 +155,27 @@
+ if (temp._id == null)
+ return false;
+ if (this._id != temp._id) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._id.equals(temp._id)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ }
+ } else if (temp._id != null)
+@@ -184,29 +184,29 @@
+ if (temp._modifiable == null)
+ return false;
+ if (this._modifiable != temp._modifiable) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._modifiable);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._modifiable);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._modifiable.equals(temp._modifiable)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
+ }
+ }
+ } else if (temp._modifiable != null)
+@@ -268,22 +268,22 @@
+
+ long tmp;
+ if (_content != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_content)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_content)) {
+ result = 37 * result + _content.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_content);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_content);
+ }
+- if (_title != null && !org.castor.util.CycleBreaker.startingToCycle(_title)) {
++ if (_title != null && !org.castor.core.util.CycleBreaker.startingToCycle(_title)) {
+ result = 37 * result + _title.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_title);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_title);
+ }
+- if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
++ if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) {
+ result = 37 * result + _id.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_id);
+ }
+ if (_modifiable != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_modifiable)) {
+ result = 37 * result + _modifiable.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_modifiable);
+ }
+
+ return result;
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Provenance.java
+===================================================================
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Provenance.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Provenance.java 2011-10-17 23:43:32.640672117 +0200
+@@ -116,29 +116,29 @@
+ if (temp._entryList == null)
+ return false;
+ if (this._entryList != temp._entryList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._entryList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._entryList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._entryList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._entryList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._entryList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._entryList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._entryList.equals(temp._entryList)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._entryList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._entryList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._entryList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._entryList);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._entryList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._entryList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._entryList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._entryList);
+ }
+ }
+ } else if (temp._entryList != null)
+@@ -213,9 +213,9 @@
+
+ long tmp;
+ if (_entryList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_entryList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_entryList)) {
+ result = 37 * result + _entryList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_entryList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_entryList);
+ }
+
+ return result;
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Sequence.java
+===================================================================
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Sequence.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Sequence.java 2011-10-17 23:43:32.640672117 +0200
+@@ -170,27 +170,27 @@
+ if (temp._id == null)
+ return false;
+ if (this._id != temp._id) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._id.equals(temp._id)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ }
+ } else if (temp._id != null)
+@@ -199,29 +199,29 @@
+ if (temp._dictionary == null)
+ return false;
+ if (this._dictionary != temp._dictionary) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._dictionary);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._dictionary);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._dictionary);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._dictionary);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._dictionary);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._dictionary);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._dictionary.equals(temp._dictionary)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._dictionary);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._dictionary);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._dictionary);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._dictionary);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._dictionary);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._dictionary);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._dictionary);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._dictionary);
+ }
+ }
+ } else if (temp._dictionary != null)
+@@ -230,29 +230,29 @@
+ if (temp._dbRefList == null)
+ return false;
+ if (this._dbRefList != temp._dbRefList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._dbRefList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._dbRefList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._dbRefList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._dbRefList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._dbRefList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._dbRefList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._dbRefList.equals(temp._dbRefList)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._dbRefList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._dbRefList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._dbRefList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._dbRefList);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._dbRefList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._dbRefList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._dbRefList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._dbRefList);
+ }
+ }
+ } else if (temp._dbRefList != null)
+@@ -261,29 +261,29 @@
+ if (temp._vxrefList == null)
+ return false;
+ if (this._vxrefList != temp._vxrefList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._vxrefList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._vxrefList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._vxrefList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._vxrefList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._vxrefList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._vxrefList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._vxrefList.equals(temp._vxrefList)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._vxrefList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._vxrefList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._vxrefList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._vxrefList);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._vxrefList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._vxrefList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._vxrefList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._vxrefList);
+ }
+ }
+ } else if (temp._vxrefList != null)
+@@ -431,24 +431,24 @@
+ int result = super.hashCode();
+
+ long tmp;
+- if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
++ if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) {
+ result = 37 * result + _id.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_id);
+ }
+ if (_dictionary != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_dictionary)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_dictionary)) {
+ result = 37 * result + _dictionary.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_dictionary);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_dictionary);
+ }
+ if (_dbRefList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_dbRefList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_dbRefList)) {
+ result = 37 * result + _dbRefList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_dbRefList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_dbRefList);
+ }
+ if (_vxrefList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_vxrefList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_vxrefList)) {
+ result = 37 * result + _vxrefList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_vxrefList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_vxrefList);
+ }
+
+ return result;
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/SequenceType.java
+===================================================================
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/SequenceType.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/SequenceType.java 2011-10-17 23:43:32.624672117 +0200
+@@ -171,29 +171,29 @@
+ if (temp._sequence == null)
+ return false;
+ if (this._sequence != temp._sequence) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._sequence);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._sequence);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._sequence);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._sequence);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequence);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._sequence);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._sequence.equals(temp._sequence)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._sequence);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequence);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._sequence);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._sequence);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._sequence);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequence);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._sequence);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._sequence);
+ }
+ }
+ } else if (temp._sequence != null)
+@@ -202,27 +202,27 @@
+ if (temp._name == null)
+ return false;
+ if (this._name != temp._name) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._name);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._name);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._name);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._name);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._name);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._name);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._name.equals(temp._name)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._name);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._name);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._name);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._name);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name);
+ }
+ }
+ } else if (temp._name != null)
+@@ -231,18 +231,18 @@
+ if (temp._description == null)
+ return false;
+ if (this._description != temp._description) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._description);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._description);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._description);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._description);
+ }
+ ;
+@@ -250,14 +250,14 @@
+ }
+ if (!thcycle) {
+ if (!this._description.equals(temp._description)) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._description);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._description);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._description);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._description);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._description);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._description);
+ }
+ }
+ } else if (temp._description != null)
+@@ -266,18 +266,18 @@
+ if (temp._propertyList == null)
+ return false;
+ if (this._propertyList != temp._propertyList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._propertyList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._propertyList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._propertyList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._propertyList);
+ }
+ ;
+@@ -285,14 +285,14 @@
+ }
+ if (!thcycle) {
+ if (!this._propertyList.equals(temp._propertyList)) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._propertyList);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._propertyList);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._propertyList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
+ }
+ }
+ } else if (temp._propertyList != null)
+@@ -434,23 +434,23 @@
+ result = 37 * result + (int) (_start ^ (_start >>> 32));
+ result = 37 * result + (int) (_end ^ (_end >>> 32));
+ if (_sequence != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_sequence)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_sequence)) {
+ result = 37 * result + _sequence.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_sequence);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_sequence);
+ }
+- if (_name != null && !org.castor.util.CycleBreaker.startingToCycle(_name)) {
++ if (_name != null && !org.castor.core.util.CycleBreaker.startingToCycle(_name)) {
+ result = 37 * result + _name.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_name);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_name);
+ }
+ if (_description != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_description)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_description)) {
+ result = 37 * result + _description.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_description);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_description);
+ }
+ if (_propertyList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_propertyList)) {
+ result = 37 * result + _propertyList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_propertyList);
+ }
+
+ return result;
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Tree.java
+===================================================================
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Tree.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Tree.java 2011-10-17 23:43:32.624672117 +0200
+@@ -219,27 +219,27 @@
+ if (temp._id == null)
+ return false;
+ if (this._id != temp._id) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._id.equals(temp._id)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ }
+ } else if (temp._id != null)
+@@ -248,29 +248,29 @@
+ if (temp._modifiable == null)
+ return false;
+ if (this._modifiable != temp._modifiable) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._modifiable);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._modifiable);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._modifiable.equals(temp._modifiable)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
+ }
+ }
+ } else if (temp._modifiable != null)
+@@ -279,27 +279,27 @@
+ if (temp._title == null)
+ return false;
+ if (this._title != temp._title) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._title);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._title);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._title);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._title);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._title);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._title);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._title);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._title);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._title.equals(temp._title)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._title);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._title);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._title);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._title);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._title);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._title);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._title);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._title);
+ }
+ }
+ } else if (temp._title != null)
+@@ -308,29 +308,29 @@
+ if (temp._newickList == null)
+ return false;
+ if (this._newickList != temp._newickList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._newickList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._newickList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._newickList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._newickList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._newickList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._newickList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._newickList.equals(temp._newickList)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._newickList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._newickList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._newickList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._newickList);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._newickList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._newickList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._newickList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._newickList);
+ }
+ }
+ } else if (temp._newickList != null)
+@@ -339,18 +339,18 @@
+ if (temp._treenodeList == null)
+ return false;
+ if (this._treenodeList != temp._treenodeList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._treenodeList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._treenodeList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._treenodeList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._treenodeList);
+ }
+ ;
+@@ -358,14 +358,14 @@
+ }
+ if (!thcycle) {
+ if (!this._treenodeList.equals(temp._treenodeList)) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._treenodeList);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._treenodeList);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._treenodeList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._treenodeList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treenodeList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treenodeList);
+ }
+ }
+ } else if (temp._treenodeList != null)
+@@ -374,18 +374,18 @@
+ if (temp._propertyList == null)
+ return false;
+ if (this._propertyList != temp._propertyList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._propertyList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._propertyList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._propertyList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._propertyList);
+ }
+ ;
+@@ -393,14 +393,14 @@
+ }
+ if (!thcycle) {
+ if (!this._propertyList.equals(temp._propertyList)) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._propertyList);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._propertyList);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._propertyList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
+ }
+ }
+ } else if (temp._propertyList != null)
+@@ -409,29 +409,29 @@
+ if (temp._provenance == null)
+ return false;
+ if (this._provenance != temp._provenance) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._provenance);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._provenance);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._provenance.equals(temp._provenance)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
+ }
+ }
+ } else if (temp._provenance != null)
+@@ -651,38 +651,38 @@
+ int result = super.hashCode();
+
+ long tmp;
+- if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
++ if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) {
+ result = 37 * result + _id.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_id);
+ }
+ if (_modifiable != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_modifiable)) {
+ result = 37 * result + _modifiable.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_modifiable);
+ }
+- if (_title != null && !org.castor.util.CycleBreaker.startingToCycle(_title)) {
++ if (_title != null && !org.castor.core.util.CycleBreaker.startingToCycle(_title)) {
+ result = 37 * result + _title.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_title);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_title);
+ }
+ if (_newickList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_newickList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_newickList)) {
+ result = 37 * result + _newickList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_newickList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_newickList);
+ }
+ if (_treenodeList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_treenodeList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_treenodeList)) {
+ result = 37 * result + _treenodeList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_treenodeList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_treenodeList);
+ }
+ if (_propertyList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_propertyList)) {
+ result = 37 * result + _propertyList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_propertyList);
+ }
+ if (_provenance != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_provenance)) {
+ result = 37 * result + _provenance.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_provenance);
+ }
+
+ return result;
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/User.java
+===================================================================
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/User.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/User.java 2011-10-17 23:43:32.640672117 +0200
@@ -85,29 +85,29 @@
- if (temp._fullname == null)
- return false;
- if (this._fullname != temp._fullname) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._fullname);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._fullname);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._fullname);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._fullname);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._fullname);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._fullname);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._fullname.equals(temp._fullname)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._fullname);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._fullname);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._fullname);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._fullname);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._fullname);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._fullname);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._fullname);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._fullname);
- }
- }
- } else if (temp._fullname != null)
+ if (temp._fullname == null)
+ return false;
+ if (this._fullname != temp._fullname) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._fullname);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._fullname);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._fullname);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._fullname);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._fullname);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._fullname);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._fullname.equals(temp._fullname)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._fullname);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._fullname);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._fullname);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._fullname);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._fullname);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._fullname);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._fullname);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._fullname);
+ }
+ }
+ } else if (temp._fullname != null)
@@ -116,18 +116,18 @@
- if (temp._organization == null)
- return false;
- if (this._organization != temp._organization) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._organization);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._organization);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._organization);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._organization);
- }
- ;
+ if (temp._organization == null)
+ return false;
+ if (this._organization != temp._organization) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._organization);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._organization);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._organization);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._organization);
+ }
+ ;
@@ -135,14 +135,14 @@
- }
- if (!thcycle) {
- if (!this._organization.equals(temp._organization)) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._organization);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._organization);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._organization);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._organization);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._organization);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._organization);
- }
- }
- } else if (temp._organization != null)
+ }
+ if (!thcycle) {
+ if (!this._organization.equals(temp._organization)) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._organization);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._organization);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._organization);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._organization);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._organization);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._organization);
+ }
+ }
+ } else if (temp._organization != null)
@@ -183,14 +183,14 @@
-
- long tmp;
- if (_fullname != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_fullname)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_fullname)) {
- result = 37 * result + _fullname.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_fullname);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_fullname);
- }
- if (_organization != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_organization)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_organization)) {
- result = 37 * result + _organization.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_organization);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_organization);
- }
-
- return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/VAMSAS.java
+
+ long tmp;
+ if (_fullname != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_fullname)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_fullname)) {
+ result = 37 * result + _fullname.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_fullname);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_fullname);
+ }
+ if (_organization != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_organization)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_organization)) {
+ result = 37 * result + _organization.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_organization);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_organization);
+ }
+
+ return result;
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/VAMSAS.java
===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/VAMSAS.java 2011-04-14 23:01:23.808202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/VAMSAS.java 2011-04-14 23:01:44.500202539 +0200
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/VAMSAS.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/VAMSAS.java 2011-10-17 23:43:32.624672117 +0200
@@ -168,27 +168,27 @@
- if (temp._id == null)
- return false;
- if (this._id != temp._id) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._id.equals(temp._id)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
- }
- }
- } else if (temp._id != null)
+ if (temp._id == null)
+ return false;
+ if (this._id != temp._id) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._id.equals(temp._id)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ }
+ } else if (temp._id != null)
@@ -197,29 +197,29 @@
- if (temp._modifiable == null)
- return false;
- if (this._modifiable != temp._modifiable) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._modifiable);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._modifiable);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._modifiable.equals(temp._modifiable)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
- }
- }
- } else if (temp._modifiable != null)
+ if (temp._modifiable == null)
+ return false;
+ if (this._modifiable != temp._modifiable) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._modifiable);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._modifiable);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._modifiable.equals(temp._modifiable)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
+ }
+ }
+ } else if (temp._modifiable != null)
@@ -228,29 +228,29 @@
- if (temp._treeList == null)
- return false;
- if (this._treeList != temp._treeList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._treeList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._treeList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._treeList.equals(temp._treeList)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList);
- }
- }
- } else if (temp._treeList != null)
+ if (temp._treeList == null)
+ return false;
+ if (this._treeList != temp._treeList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._treeList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._treeList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._treeList.equals(temp._treeList)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList);
+ }
+ }
+ } else if (temp._treeList != null)
@@ -259,18 +259,18 @@
- if (temp._dataSetList == null)
- return false;
- if (this._dataSetList != temp._dataSetList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._dataSetList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._dataSetList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._dataSetList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._dataSetList);
- }
- ;
+ if (temp._dataSetList == null)
+ return false;
+ if (this._dataSetList != temp._dataSetList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._dataSetList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._dataSetList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._dataSetList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._dataSetList);
+ }
+ ;
@@ -278,14 +278,14 @@
- }
- if (!thcycle) {
- if (!this._dataSetList.equals(temp._dataSetList)) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._dataSetList);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._dataSetList);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._dataSetList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._dataSetList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._dataSetList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._dataSetList);
- }
- }
- } else if (temp._dataSetList != null)
+ }
+ if (!thcycle) {
+ if (!this._dataSetList.equals(temp._dataSetList)) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._dataSetList);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._dataSetList);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._dataSetList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._dataSetList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._dataSetList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._dataSetList);
+ }
+ }
+ } else if (temp._dataSetList != null)
@@ -432,24 +432,24 @@
- int result = super.hashCode();
-
- long tmp;
-- if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
-+ if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) {
- result = 37 * result + _id.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_id);
- }
- if (_modifiable != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_modifiable)) {
- result = 37 * result + _modifiable.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_modifiable);
- }
- if (_treeList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_treeList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_treeList)) {
- result = 37 * result + _treeList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_treeList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_treeList);
- }
- if (_dataSetList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_dataSetList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_dataSetList)) {
- result = 37 * result + _dataSetList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_dataSetList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_dataSetList);
- }
-
- return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/VamsasDocument.java
+ int result = super.hashCode();
+
+ long tmp;
+- if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
++ if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) {
+ result = 37 * result + _id.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_id);
+ }
+ if (_modifiable != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_modifiable)) {
+ result = 37 * result + _modifiable.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_modifiable);
+ }
+ if (_treeList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_treeList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_treeList)) {
+ result = 37 * result + _treeList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_treeList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_treeList);
+ }
+ if (_dataSetList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_dataSetList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_dataSetList)) {
+ result = 37 * result + _dataSetList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_dataSetList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_dataSetList);
+ }
+
+ return result;
+Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/VamsasDocument.java
===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/objects/core/VamsasDocument.java 2011-04-14 23:01:24.072202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/objects/core/VamsasDocument.java 2011-04-14 23:01:44.504202539 +0200
+--- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/VamsasDocument.java 2011-10-17 23:31:53.000000000 +0200
++++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/VamsasDocument.java 2011-10-17 23:43:32.644672117 +0200
@@ -218,27 +218,27 @@
- if (temp._version == null)
- return false;
- if (this._version != temp._version) {
-- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._version);
-- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._version);
-+ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._version);
-+ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._version);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._version.equals(temp._version)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version);
- }
- }
- } else if (temp._version != null)
+ if (temp._version == null)
+ return false;
+ if (this._version != temp._version) {
+- thcycle = org.castor.util.CycleBreaker.startingToCycle(this._version);
+- tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._version);
++ thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._version);
++ tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._version);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._version.equals(temp._version)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version);
+ }
+ }
+ } else if (temp._version != null)
@@ -247,29 +247,29 @@
- if (temp._lockFile == null)
- return false;
- if (this._lockFile != temp._lockFile) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._lockFile);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._lockFile);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._lockFile);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._lockFile);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._lockFile);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._lockFile);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._lockFile.equals(temp._lockFile)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._lockFile);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._lockFile);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._lockFile);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._lockFile);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._lockFile);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._lockFile);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._lockFile);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._lockFile);
- }
- }
- } else if (temp._lockFile != null)
+ if (temp._lockFile == null)
+ return false;
+ if (this._lockFile != temp._lockFile) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._lockFile);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._lockFile);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._lockFile);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._lockFile);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._lockFile);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._lockFile);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._lockFile.equals(temp._lockFile)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._lockFile);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._lockFile);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._lockFile);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._lockFile);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._lockFile);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._lockFile);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._lockFile);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._lockFile);
+ }
+ }
+ } else if (temp._lockFile != null)
@@ -278,29 +278,29 @@
- if (temp._provenance == null)
- return false;
- if (this._provenance != temp._provenance) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._provenance);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._provenance);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._provenance.equals(temp._provenance)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
- }
- }
- } else if (temp._provenance != null)
+ if (temp._provenance == null)
+ return false;
+ if (this._provenance != temp._provenance) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._provenance);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._provenance);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._provenance.equals(temp._provenance)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance);
+ }
+ }
+ } else if (temp._provenance != null)
@@ -309,29 +309,29 @@
- if (temp._VAMSASList == null)
- return false;
- if (this._VAMSASList != temp._VAMSASList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._VAMSASList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._VAMSASList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._VAMSASList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._VAMSASList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList);
- }
- ;
- return false;
- }
- if (!thcycle) {
- if (!this._VAMSASList.equals(temp._VAMSASList)) {
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._VAMSASList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._VAMSASList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList);
- return false;
- }
-- org.castor.util.CycleBreaker.releaseCycleHandle(this._VAMSASList);
-- org.castor.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._VAMSASList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList);
- }
- }
- } else if (temp._VAMSASList != null)
+ if (temp._VAMSASList == null)
+ return false;
+ if (this._VAMSASList != temp._VAMSASList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._VAMSASList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._VAMSASList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._VAMSASList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._VAMSASList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._VAMSASList.equals(temp._VAMSASList)) {
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._VAMSASList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._VAMSASList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList);
+ return false;
+ }
+- org.castor.util.CycleBreaker.releaseCycleHandle(this._VAMSASList);
+- org.castor.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(this._VAMSASList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList);
+ }
+ }
+ } else if (temp._VAMSASList != null)
@@ -340,18 +340,18 @@
- if (temp._applicationDataList == null)
- return false;
- if (this._applicationDataList != temp._applicationDataList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._applicationDataList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._applicationDataList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._applicationDataList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._applicationDataList);
- }
- ;
+ if (temp._applicationDataList == null)
+ return false;
+ if (this._applicationDataList != temp._applicationDataList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._applicationDataList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._applicationDataList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._applicationDataList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._applicationDataList);
+ }
+ ;
@@ -359,15 +359,15 @@
- }
- if (!thcycle) {
- if (!this._applicationDataList.equals(temp._applicationDataList)) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._applicationDataList);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._applicationDataList);
- return false;
- }
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._applicationDataList);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._applicationDataList);
- }
- }
+ }
+ if (!thcycle) {
+ if (!this._applicationDataList.equals(temp._applicationDataList)) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._applicationDataList);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._applicationDataList);
+ return false;
+ }
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._applicationDataList);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._applicationDataList);
+ }
+ }
@@ -377,18 +377,18 @@
- if (temp._attachmentList == null)
- return false;
- if (this._attachmentList != temp._attachmentList) {
-- thcycle = org.castor.util.CycleBreaker
-+ thcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(this._attachmentList);
-- tmcycle = org.castor.util.CycleBreaker
-+ tmcycle = org.castor.core.util.CycleBreaker
- .startingToCycle(temp._attachmentList);
- if (thcycle != tmcycle) {
- if (!thcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._attachmentList);
- }
- ;
- if (!tmcycle) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._attachmentList);
- }
- ;
+ if (temp._attachmentList == null)
+ return false;
+ if (this._attachmentList != temp._attachmentList) {
+- thcycle = org.castor.util.CycleBreaker
++ thcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(this._attachmentList);
+- tmcycle = org.castor.util.CycleBreaker
++ tmcycle = org.castor.core.util.CycleBreaker
+ .startingToCycle(temp._attachmentList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._attachmentList);
+ }
+ ;
+ if (!tmcycle) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._attachmentList);
+ }
+ ;
@@ -396,15 +396,15 @@
- }
- if (!thcycle) {
- if (!this._attachmentList.equals(temp._attachmentList)) {
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._attachmentList);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._attachmentList);
- return false;
- }
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(this._attachmentList);
-- org.castor.util.CycleBreaker
-+ org.castor.core.util.CycleBreaker
- .releaseCycleHandle(temp._attachmentList);
- }
- }
+ }
+ if (!thcycle) {
+ if (!this._attachmentList.equals(temp._attachmentList)) {
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._attachmentList);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._attachmentList);
+ return false;
+ }
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(this._attachmentList);
+- org.castor.util.CycleBreaker
++ org.castor.core.util.CycleBreaker
+ .releaseCycleHandle(temp._attachmentList);
+ }
+ }
@@ -622,34 +622,34 @@
-
- long tmp;
- if (_version != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_version)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_version)) {
- result = 37 * result + _version.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_version);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_version);
- }
- if (_lockFile != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_lockFile)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_lockFile)) {
- result = 37 * result + _lockFile.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_lockFile);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_lockFile);
- }
- if (_provenance != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_provenance)) {
- result = 37 * result + _provenance.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_provenance);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_provenance);
- }
- if (_VAMSASList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_VAMSASList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_VAMSASList)) {
- result = 37 * result + _VAMSASList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_VAMSASList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_VAMSASList);
- }
- if (_applicationDataList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_applicationDataList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_applicationDataList)) {
- result = 37 * result + _applicationDataList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_applicationDataList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_applicationDataList);
- }
- if (_attachmentList != null
-- && !org.castor.util.CycleBreaker.startingToCycle(_attachmentList)) {
-+ && !org.castor.core.util.CycleBreaker.startingToCycle(_attachmentList)) {
- result = 37 * result + _attachmentList.hashCode();
-- org.castor.util.CycleBreaker.releaseCycleHandle(_attachmentList);
-+ org.castor.core.util.CycleBreaker.releaseCycleHandle(_attachmentList);
- }
-
- return result;
-Index: libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java
-===================================================================
---- libvamsas-client-java-0.1+dfsg.orig/src/uk/ac/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java 2011-04-14 23:01:23.744202528 +0200
-+++ libvamsas-client-java-0.1+dfsg/src/uk/ac/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java 2011-04-14 23:01:44.496202539 +0200
-@@ -40,7 +40,7 @@
- /*
- *
- * static {
-- * org.exolab.castor.util.LocalConfiguration.getInstance().getProperties().setProperty(
-+ * org.exolab.castor.core.util.LocalConfiguration.getInstance().getProperties().setProperty(
- * "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer"); }
- *
- */
+
+ long tmp;
+ if (_version != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_version)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_version)) {
+ result = 37 * result + _version.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_version);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_version);
+ }
+ if (_lockFile != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_lockFile)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_lockFile)) {
+ result = 37 * result + _lockFile.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_lockFile);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_lockFile);
+ }
+ if (_provenance != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_provenance)) {
+ result = 37 * result + _provenance.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_provenance);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_provenance);
+ }
+ if (_VAMSASList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_VAMSASList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_VAMSASList)) {
+ result = 37 * result + _VAMSASList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_VAMSASList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_VAMSASList);
+ }
+ if (_applicationDataList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_applicationDataList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_applicationDataList)) {
+ result = 37 * result + _applicationDataList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_applicationDataList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_applicationDataList);
+ }
+ if (_attachmentList != null
+- && !org.castor.util.CycleBreaker.startingToCycle(_attachmentList)) {
++ && !org.castor.core.util.CycleBreaker.startingToCycle(_attachmentList)) {
+ result = 37 * result + _attachmentList.hashCode();
+- org.castor.util.CycleBreaker.releaseCycleHandle(_attachmentList);
++ org.castor.core.util.CycleBreaker.releaseCycleHandle(_attachmentList);
+ }
+
+ return result;
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