Menu
▾
▴
[Jsbml-svn] SF.net SVN: jsbml:[2408] trunk/extensions
|
From: <nik...@us...> - 2015-11-27 10:59:37
|
Revision: 2408
http://sourceforge.net/p/jsbml/code/2408
Author: niko-rodrigue
Date: 2015-11-27 10:59:35 +0000 (Fri, 27 Nov 2015)
Log Message:
-----------
update to the group package to support the latest specs, version 0.7 (2015-11-24). Mainly removed/commented the MemberConstraint list on the Group class.
Modified Paths:
--------------
trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java
trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/ListOfMemberConstraint.java
trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/MemberConstraint.java
trunk/extensions/groups/src/org/sbml/jsbml/xml/parsers/GroupsParser.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/BindingStatus.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/DenotedSpeciesTypeComponentIndex.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/OutwardBindingSite.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesType.java
trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualitativeSpecies.java
Modified: trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java
===================================================================
--- trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java 2015-11-26 16:32:15 UTC (rev 2407)
+++ trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java 2015-11-27 10:59:35 UTC (rev 2408)
@@ -30,7 +30,6 @@
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.SBMLException;
import org.sbml.jsbml.UniqueNamedSBase;
-import org.sbml.jsbml.util.filters.NameFilter;
/**
*
@@ -43,23 +42,27 @@
/**
* This is a collection of possible values for the {@code kind} attribute within
- * a {@link Group}. It has been defined in version 3 of the Groups proposal.
+ * a {@link Group}.
*
- * @author Clemens Wrzodek
- * @since 3.0
- * @version $Rev$
*/
public enum Kind {
/**
- * the group is a class, and its members have an <i>is-a</i> relationship to the group
+ * The group represents a class, and its members have an <i>is-a</i> relationship to the group. For example, the
+ * group could represent a type of molecule such as ATP, and the members could be species located in different
+ * compartments, thereby establishing that the species are pools of the same molecule in different locations.
*/
classification,
/**
- * the group is a collection of parts, and its members have a <i>part-of</i> relationship to the group
+ * The group represents a collection of parts, and its members have a <i>part-of</i> relationship to the group. For ex-ample,
+ * the group could represent a cellular structure, and individual compartments could be made members
+ * of the group to indicate they represent subparts of that cellular structure
*/
partonomy,
/**
- * the grouping is one of convenience, without an implied relationship
+ * The grouping is merely a collection for convenience, without an implied relationship between the members.
+ * For example, the group could be used to collect together multiple disparate components of a model—species,
+ * reactions, events—involved in a particular phenotype, and apply a common annotation rather than having to
+ * copy the same annotation to each component individually.
*/
collection
}
@@ -70,7 +73,7 @@
private static final long serialVersionUID = 2361503116934849753L;
/**
- * Defined in version 3 of the groups proposal.
+ * This attribute is used to indicate the nature of the group
*/
private Kind kind = null;
@@ -82,7 +85,7 @@
/**
*
*/
- private ListOfMemberConstraint listOfMemberConstraints = null;
+// removed as unsupported but could be added again in the future private ListOfMemberConstraint listOfMemberConstraints = null;
/**
*
@@ -105,9 +108,11 @@
if (group.isSetKind()) {
setKind(group.getKind());
}
- if (group.isSetListOfMemberConstraints()) {
- setListOfMemberConstraints(group.getListOfMemberConstraints().clone());
- }
+
+ // removed as unsupported but could be added again in the future
+ // if (group.isSetListOfMemberConstraints()) {
+// setListOfMemberConstraints(group.getListOfMemberConstraints().clone());
+// }
}
/**
@@ -214,12 +219,13 @@
position++;
}
- if (isSetListOfMemberConstraints()) {
- if (position == index) {
- return getListOfMemberConstraints();
- }
- position++;
- }
+ // removed as unsupported but could be added again in the future
+// if (isSetListOfMemberConstraints()) {
+// if (position == index) {
+// return getListOfMemberConstraints();
+// }
+// position++;
+// }
throw new IndexOutOfBoundsException(MessageFormat.format(
resourceBundle.getString("IndexExceedsBoundsException"), index,
@@ -237,9 +243,10 @@
if (isSetListOfMembers()) {
childCount++;
}
- if (isSetListOfMemberConstraints()) {
- childCount++;
- }
+ // removed as unsupported but could be added again in the future
+// if (isSetListOfMemberConstraints()) {
+// childCount++;
+// }
return childCount;
}
@@ -453,14 +460,15 @@
return isSetListOfMembers() ? getListOfMembers().size() : 0;
}
- /**
- * Returns the number of {@link MemberConstraint}s of this {@link Group}.
- *
- * @return the number of {@link MemberConstraint}s of this {@link Group}.
- */
- public int getMemberConstraintCount() {
- return isSetListOfMemberConstraints() ? getListOfMemberConstraints().size() : 0;
- }
+ // removed as unsupported but could be added again in the future
+// /**
+// * Returns the number of {@link MemberConstraint}s of this {@link Group}.
+// *
+// * @return the number of {@link MemberConstraint}s of this {@link Group}.
+// */
+// public int getMemberConstraintCount() {
+// return isSetListOfMemberConstraints() ? getListOfMemberConstraints().size() : 0;
+// }
/**
* Returns the number of {@link Member}s of this {@link Group}.
@@ -472,15 +480,16 @@
return getMemberCount();
}
- /**
- * Returns the number of {@link MemberConstraint}s of this {@link Group}.
- *
- * @return the number of {@link MemberConstraint}s of this {@link Group}.
- * @libsbml.deprecated same as {@link #getMemberConstraintCount()}
- */
- public int getNumMemberConstraints() {
- return getMemberConstraintCount();
- }
+ // removed as unsupported but could be added again in the future
+// /**
+// * Returns the number of {@link MemberConstraint}s of this {@link Group}.
+// *
+// * @return the number of {@link MemberConstraint}s of this {@link Group}.
+// * @libsbml.deprecated same as {@link #getMemberConstraintCount()}
+// */
+// public int getNumMemberConstraints() {
+// return getMemberConstraintCount();
+// }
/**
*
@@ -506,140 +515,142 @@
public boolean isSetKind() {
return kind!=null;
}
+
+
+//
+// /**
+// * Returns {@code true}, if listOfMemberConstraints is not null.
+// *
+// * @return {@code true}, if listOfMemberConstraints is not null,
+// * otherwise {@code false}
+// */
+// public boolean isSetListOfMemberConstraints() {
+// return listOfMemberConstraints != null;
+// }
+//
+// /**
+// * Returns the listOfMemberConstraints. Creates it if it is not already existing.
+// *
+// * @return the listOfMemberConstraints
+// */
+// public ListOfMemberConstraint getListOfMemberConstraints() {
+// if (!isSetListOfMemberConstraints()) {
+// listOfMemberConstraints = new ListOfMemberConstraint(getLevel(), getVersion());
+// listOfMemberConstraints.setPackageVersion(-1);
+// // changing the ListOf package name from 'core' to 'groups'
+// listOfMemberConstraints.setPackageName(null);
+// listOfMemberConstraints.setPackageName(GroupsConstants.shortLabel);
+// listOfMemberConstraints.setSBaseListType(ListOf.Type.other);
+// registerChild(listOfMemberConstraints);
+// }
+// return listOfMemberConstraints;
+// }
+//
+// /**
+// * Sets the given {@code ListOf<MemberConstraint>}. If listOfMemberConstraints
+// * was defined before and contains some elements, they are all unset.
+// *
+// * @param listOfMemberConstraints
+// */
+// public void setListOfMemberConstraints(ListOfMemberConstraint listOfMemberConstraints) {
+// unsetListOfMemberConstraints();
+// this.listOfMemberConstraints = listOfMemberConstraints;
+//
+// if (listOfMemberConstraints != null) {
+// listOfMemberConstraints.setPackageVersion(-1);
+// // changing the ListOf package name from 'core' to 'groups'
+// listOfMemberConstraints.setPackageName(null);
+// listOfMemberConstraints.setPackageName(GroupsConstants.shortLabel);
+// listOfMemberConstraints.setSBaseListType(ListOf.Type.other);
+//
+// registerChild(this.listOfMemberConstraints);
+// }
+// }
+//
+// /**
+// * Returns {@code true}, if listOfMemberConstraints contain at least one element,
+// * otherwise {@code false}
+// *
+// * @return {@code true}, if listOfMemberConstraints contain at least one element,
+// * otherwise {@code false}
+// */
+// public boolean unsetListOfMemberConstraints() {
+// if (isSetListOfMemberConstraints()) {
+// ListOf<MemberConstraint> oldMemberConstraints = listOfMemberConstraints;
+// listOfMemberConstraints = null;
+// oldMemberConstraints.fireNodeRemovedEvent();
+// return true;
+// }
+// return false;
+// }
+//
+// /**
+// * Adds a new {@link MemberConstraint} to the listOfMemberConstraints.
+// * <p>The listOfMemberConstraints is initialized if necessary.
+// *
+// * @param memberConstraint the element to add to the list
+// * @return true (as specified by {@link java.util.Collection#add})
+// */
+// public boolean addMemberConstraint(MemberConstraint memberConstraint) {
+// return getListOfMemberConstraints().add(memberConstraint);
+// }
+//
+// /**
+// * Removes an element from the listOfMemberConstraints.
+// *
+// * @param memberConstraint the element to be removed from the list
+// * @return true if the list contained the specified element
+// * @see java.util.List#remove(Object)
+// */
+// public boolean removeMemberConstraint(MemberConstraint memberConstraint) {
+// if (isSetListOfMemberConstraints()) {
+// return getListOfMemberConstraints().remove(memberConstraint);
+// }
+// return false;
+// }
+//
+// /**
+// * Removes an element from the listOfMemberConstraints at the given index.
+// *
+// * @param i the index where to remove the {@link MemberConstraint}
+// * @throws IndexOutOfBoundsException if the listOf is not set or
+// * if the index is out of bound (index < 0 || index > list.size)
+// */
+// public void removeMemberConstraint(int i) {
+// if (!isSetListOfMemberConstraints()) {
+// throw new IndexOutOfBoundsException(Integer.toString(i));
+// }
+// getListOfMemberConstraints().remove(i);
+// }
+//
+// /**
+// * @param id
+// */
+// public void removeMemberConstraint(String id) {
+// getListOfMemberConstraints().removeFirst(new NameFilter(id));
+// }
+//
+// /**
+// * Creates a new MemberConstraint element and adds it to the ListOfMemberConstraints list
+// * @return
+// */
+// public MemberConstraint createMemberConstraint() {
+// return createMemberConstraint(null);
+// }
+//
+// /**
+// * Creates a new {@link MemberConstraint} element and adds it to the ListOfMemberConstraints list
+// * @param id
+// *
+// * @return a new {@link MemberConstraint} element
+// */
+// public MemberConstraint createMemberConstraint(String id) {
+// MemberConstraint MemberConstraint = new MemberConstraint(id, getLevel(), getVersion());
+// addMemberConstraint(MemberConstraint);
+// return MemberConstraint;
+// }
- /**
- * Returns {@code true}, if listOfMemberConstraints is not null.
- *
- * @return {@code true}, if listOfMemberConstraints is not null,
- * otherwise {@code false}
- */
- public boolean isSetListOfMemberConstraints() {
- return listOfMemberConstraints != null;
- }
- /**
- * Returns the listOfMemberConstraints. Creates it if it is not already existing.
- *
- * @return the listOfMemberConstraints
- */
- public ListOfMemberConstraint getListOfMemberConstraints() {
- if (!isSetListOfMemberConstraints()) {
- listOfMemberConstraints = new ListOfMemberConstraint(getLevel(), getVersion());
- listOfMemberConstraints.setPackageVersion(-1);
- // changing the ListOf package name from 'core' to 'groups'
- listOfMemberConstraints.setPackageName(null);
- listOfMemberConstraints.setPackageName(GroupsConstants.shortLabel);
- listOfMemberConstraints.setSBaseListType(ListOf.Type.other);
- registerChild(listOfMemberConstraints);
- }
- return listOfMemberConstraints;
- }
-
- /**
- * Sets the given {@code ListOf<MemberConstraint>}. If listOfMemberConstraints
- * was defined before and contains some elements, they are all unset.
- *
- * @param listOfMemberConstraints
- */
- public void setListOfMemberConstraints(ListOfMemberConstraint listOfMemberConstraints) {
- unsetListOfMemberConstraints();
- this.listOfMemberConstraints = listOfMemberConstraints;
-
- if (listOfMemberConstraints != null) {
- listOfMemberConstraints.setPackageVersion(-1);
- // changing the ListOf package name from 'core' to 'groups'
- listOfMemberConstraints.setPackageName(null);
- listOfMemberConstraints.setPackageName(GroupsConstants.shortLabel);
- listOfMemberConstraints.setSBaseListType(ListOf.Type.other);
-
- registerChild(this.listOfMemberConstraints);
- }
- }
-
- /**
- * Returns {@code true}, if listOfMemberConstraints contain at least one element,
- * otherwise {@code false}
- *
- * @return {@code true}, if listOfMemberConstraints contain at least one element,
- * otherwise {@code false}
- */
- public boolean unsetListOfMemberConstraints() {
- if (isSetListOfMemberConstraints()) {
- ListOf<MemberConstraint> oldMemberConstraints = listOfMemberConstraints;
- listOfMemberConstraints = null;
- oldMemberConstraints.fireNodeRemovedEvent();
- return true;
- }
- return false;
- }
-
- /**
- * Adds a new {@link MemberConstraint} to the listOfMemberConstraints.
- * <p>The listOfMemberConstraints is initialized if necessary.
- *
- * @param memberConstraint the element to add to the list
- * @return true (as specified by {@link java.util.Collection#add})
- */
- public boolean addMemberConstraint(MemberConstraint memberConstraint) {
- return getListOfMemberConstraints().add(memberConstraint);
- }
-
- /**
- * Removes an element from the listOfMemberConstraints.
- *
- * @param memberConstraint the element to be removed from the list
- * @return true if the list contained the specified element
- * @see java.util.List#remove(Object)
- */
- public boolean removeMemberConstraint(MemberConstraint memberConstraint) {
- if (isSetListOfMemberConstraints()) {
- return getListOfMemberConstraints().remove(memberConstraint);
- }
- return false;
- }
-
- /**
- * Removes an element from the listOfMemberConstraints at the given index.
- *
- * @param i the index where to remove the {@link MemberConstraint}
- * @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
- */
- public void removeMemberConstraint(int i) {
- if (!isSetListOfMemberConstraints()) {
- throw new IndexOutOfBoundsException(Integer.toString(i));
- }
- getListOfMemberConstraints().remove(i);
- }
-
- /**
- * @param id
- */
- public void removeMemberConstraint(String id) {
- getListOfMemberConstraints().removeFirst(new NameFilter(id));
- }
-
- /**
- * Creates a new MemberConstraint element and adds it to the ListOfMemberConstraints list
- * @return
- */
- public MemberConstraint createMemberConstraint() {
- return createMemberConstraint(null);
- }
-
- /**
- * Creates a new {@link MemberConstraint} element and adds it to the ListOfMemberConstraints list
- * @param id
- *
- * @return a new {@link MemberConstraint} element
- */
- public MemberConstraint createMemberConstraint(String id) {
- MemberConstraint MemberConstraint = new MemberConstraint(id, getLevel(), getVersion());
- addMemberConstraint(MemberConstraint);
- return MemberConstraint;
- }
-
-
/* (non-Javadoc)
* @see org.sbml.jsbml.element.SBase#readAttribute(String attributeName, String prefix, String value)
*/
@@ -717,10 +728,11 @@
final int prime = 31;
int result = super.hashCode();
result = prime * result + ((kind == null) ? 0 : kind.hashCode());
- result = prime
- * result
- + ((listOfMemberConstraints == null) ? 0
- : listOfMemberConstraints.hashCode());
+ // removed as unsupported but could be added again in the future
+// result = prime
+// * result
+// + ((listOfMemberConstraints == null) ? 0
+// : listOfMemberConstraints.hashCode());
result = prime * result
+ ((listOfMembers == null) ? 0 : listOfMembers.hashCode());
return result;
@@ -744,13 +756,14 @@
if (kind != other.kind) {
return false;
}
- if (listOfMemberConstraints == null) {
- if (other.listOfMemberConstraints != null) {
- return false;
- }
- } else if (!listOfMemberConstraints.equals(other.listOfMemberConstraints)) {
- return false;
- }
+ // removed as unsupported but could be added again in the future
+// if (listOfMemberConstraints == null) {
+// if (other.listOfMemberConstraints != null) {
+// return false;
+// }
+// } else if (!listOfMemberConstraints.equals(other.listOfMemberConstraints)) {
+// return false;
+// }
if (listOfMembers == null) {
if (other.listOfMembers != null) {
return false;
Modified: trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/ListOfMemberConstraint.java
===================================================================
--- trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/ListOfMemberConstraint.java 2015-11-26 16:32:15 UTC (rev 2407)
+++ trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/ListOfMemberConstraint.java 2015-11-27 10:59:35 UTC (rev 2408)
@@ -35,11 +35,13 @@
import org.sbml.jsbml.validator.SyntaxChecker;
/**
+ * This class was removed from the specifications as of version 0.7 (2015-11-24) as
+ * no software wanted to implement support for it.
+ * It might be added back in a future version of the specifications if somebody want to implement it.
*
* @author Nicolas Rodriguez
* @version $Rev$
* @since 1.0
- * @date 2013-11-14
*/
public class ListOfMemberConstraint extends ListOf<MemberConstraint> implements NamedSBase, UniqueNamedSBase {
Modified: trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/MemberConstraint.java
===================================================================
--- trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/MemberConstraint.java 2015-11-26 16:32:15 UTC (rev 2407)
+++ trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/MemberConstraint.java 2015-11-27 10:59:35 UTC (rev 2408)
@@ -28,11 +28,13 @@
import org.sbml.jsbml.UniqueNamedSBase;
/**
+ * This class was removed from the specifications as of version 0.7 (2015-11-24) as
+ * no software wanted to implement support for it.
+ * It might be added back in a future version of the specifications if somebody want to implement it.
*
* @author Nicolas Rodriguez
* @version $Rev$
* @since 1.0
- * @date 2013-11-18
*/
public class MemberConstraint extends AbstractNamedSBase implements UniqueNamedSBase {
Modified: trunk/extensions/groups/src/org/sbml/jsbml/xml/parsers/GroupsParser.java
===================================================================
--- trunk/extensions/groups/src/org/sbml/jsbml/xml/parsers/GroupsParser.java 2015-11-26 16:32:15 UTC (rev 2407)
+++ trunk/extensions/groups/src/org/sbml/jsbml/xml/parsers/GroupsParser.java 2015-11-27 10:59:35 UTC (rev 2408)
@@ -108,7 +108,9 @@
}
else if (elementName.equals("listOfMemberConstraints")) {
- return group.getListOfMemberConstraints();
+ // removed in version 0.7 of the specs but could be added again in the future
+ // return group.getListOfMemberConstraints();
+ logger.warn("Your model make use of listOfMemberConstraints which was removed in version 0.7 of the groups specification !");
}
}
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/BindingStatus.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/BindingStatus.java 2015-11-26 16:32:15 UTC (rev 2407)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/BindingStatus.java 2015-11-27 10:59:35 UTC (rev 2408)
@@ -5,7 +5,7 @@
* This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
* for the latest version of JSBML and more information about SBML.
*
- * Copyright (C) 2009-2014 jointly by the following organizations:
+ * Copyright (C) 2009-2015 jointly by the following organizations:
* 1. The University of Tuebingen, Germany
* 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
* 3. The California Institute of Technology, Pasadena, CA, USA
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/DenotedSpeciesTypeComponentIndex.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/DenotedSpeciesTypeComponentIndex.java 2015-11-26 16:32:15 UTC (rev 2407)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/DenotedSpeciesTypeComponentIndex.java 2015-11-27 10:59:35 UTC (rev 2408)
@@ -41,7 +41,9 @@
*/
private String speciesTypeComponentIndex;
+ // TODO - missing the reference attribute although the whole class might be removed from the specs.
+
/**
* Creates an DenotedSpeciesTypeComponentIndex instance
*/
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/OutwardBindingSite.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/OutwardBindingSite.java 2015-11-26 16:32:15 UTC (rev 2407)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/OutwardBindingSite.java 2015-11-27 10:59:35 UTC (rev 2408)
@@ -5,7 +5,7 @@
* This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
* for the latest version of JSBML and more information about SBML.
*
- * Copyright (C) 2009-2014 jointly by the following organizations:
+ * Copyright (C) 2009-2015 jointly by the following organizations:
* 1. The University of Tuebingen, Germany
* 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
* 3. The California Institute of Technology, Pasadena, CA, USA
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesType.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesType.java 2015-11-26 16:32:15 UTC (rev 2407)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesType.java 2015-11-27 10:59:35 UTC (rev 2408)
@@ -854,7 +854,7 @@
/**
- * Initializes the default values using the namespace.
+ * Initializes the default values.
*/
public void initDefaults() {
packageName = MultiConstants.shortLabel;
Modified: trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualitativeSpecies.java
===================================================================
--- trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualitativeSpecies.java 2015-11-26 16:32:15 UTC (rev 2407)
+++ trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualitativeSpecies.java 2015-11-27 10:59:35 UTC (rev 2408)
@@ -60,8 +60,7 @@
/**
*
*/
- private Boolean constant; // TODO: extends/implements the jsbml interface
- // that has the constant attribute.
+ private Boolean constant; // TODO: extends/implements the jsbml interface that has the constant attribute?
/**
*
*/
@@ -184,6 +183,7 @@
@Override
public boolean equals(Object object) {
boolean equals = super.equals(object);
+
if (equals) {
QualitativeSpecies qs = (QualitativeSpecies) object;
equals &= qs.isSetConstant() == isSetConstant();
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|