From 2e92d5449226c6b2423129d779977df26fe74ec6 Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 20 Sep 2005 16:33:50 +0000 Subject: [PATCH] latest schema. git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@38 be28352e-c001-0410-b1a7-c7978e42abec --- schemas/vamsas15_9.xsd | 66 +++-- src/org/vamsas/client/SimpleClientFactory.java | 32 ++- src/org/vamsas/client/object.java | 11 + src/org/vamsas/objects/core/.castor.cdr | 23 +- src/org/vamsas/objects/core/Alignment.java | 33 +++ .../vamsas/objects/core/AlignmentDescriptor.java | 34 +++ src/org/vamsas/objects/core/AlignmentSequence.java | 33 +++ .../objects/core/AlignmentSequenceDescriptor.java | 34 +++ src/org/vamsas/objects/core/Application.java | 65 +++-- .../vamsas/objects/core/ApplicationDescriptor.java | 49 +++- src/org/vamsas/objects/core/Newick.java | 248 +++++++++++++++++ src/org/vamsas/objects/core/NewickDescriptor.java | 278 +++++++++++++++++++ src/org/vamsas/objects/core/Provenance.java | 128 ++++----- .../vamsas/objects/core/ProvenanceDescriptor.java | 19 +- src/org/vamsas/objects/core/Sequence.java | 193 ++++++++++++++ .../vamsas/objects/core/SequenceDescriptor.java | 72 +++++ .../objects/core/SequenceSetAnnotations.java | 155 +++++++++-- .../core/SequenceSetAnnotationsDescriptor.java | 13 +- src/org/vamsas/objects/core/SequenceType.java | 193 -------------- .../objects/core/SequenceTypeDescriptor.java | 69 ----- src/org/vamsas/objects/core/Tree.java | 161 ++++++----- src/org/vamsas/objects/core/TreeDescriptor.java | 50 +++- src/org/vamsas/objects/core/User.java | 245 +++++++++++++++++ src/org/vamsas/objects/core/UserDescriptor.java | 282 ++++++++++++++++++++ 24 files changed, 1994 insertions(+), 492 deletions(-) create mode 100644 src/org/vamsas/objects/core/Newick.java create mode 100644 src/org/vamsas/objects/core/NewickDescriptor.java create mode 100644 src/org/vamsas/objects/core/User.java create mode 100644 src/org/vamsas/objects/core/UserDescriptor.java diff --git a/schemas/vamsas15_9.xsd b/schemas/vamsas15_9.xsd index 1a5ba63..dd12108 100644 --- a/schemas/vamsas15_9.xsd +++ b/schemas/vamsas15_9.xsd @@ -13,33 +13,44 @@ - + - + + + + + + + + + + + - + - - + + - + + @@ -47,6 +58,17 @@ + + + + + + + + + + + @@ -58,13 +80,13 @@ - + - + @@ -79,7 +101,7 @@ - + @@ -87,6 +109,7 @@ + @@ -94,6 +117,7 @@ + @@ -101,7 +125,7 @@ - + @@ -119,34 +143,34 @@ - + - - - - - - - - - + + + + + + + + + - + diff --git a/src/org/vamsas/client/SimpleClientFactory.java b/src/org/vamsas/client/SimpleClientFactory.java index 5a53bd2..5b9346f 100644 --- a/src/org/vamsas/client/SimpleClientFactory.java +++ b/src/org/vamsas/client/SimpleClientFactory.java @@ -1,28 +1,38 @@ package org.vamsas.client; + +import java.io.File; +import java.io.IOException; + /** * TODO document type SimpleClientFactory * @author jimp * */ public class SimpleClientFactory implements IClientFactory { - static SimpleClientFactory singleton = null; - - static private void CreateClientFactory() { - if (singleton != null) { - - } else { - // Create singleton class. - - } + + File sessionArena; + + /** + * default constructor - called by CreateClientFactory only. + * + */ + public SimpleClientFactory() { + sessionArena = null; } /** * Create a client factory that works with sessions at the given * path. * @param path */ - public SimpleClientFactory(String path) { + public SimpleClientFactory(String path) throws IOException { // Check path is valid and read/writeable. - // make housekeeping files... + File newarena = new File(path); + if (newarena.isDirectory() && newarena.canRead() && newarena.canWrite()) { + sessionArena = newarena; + } else { + sessionArena = null; + throw(new IOException("Cannot read and write to a directory called "+path)); + } } /* (non-Javadoc) * @see org.vamsas.client.IClientFactory#getIClient(org.vamsas.client.ClientHandle) diff --git a/src/org/vamsas/client/object.java b/src/org/vamsas/client/object.java index 4f19c26..e1384a4 100644 --- a/src/org/vamsas/client/object.java +++ b/src/org/vamsas/client/object.java @@ -18,6 +18,7 @@ public abstract class object { * to any object in the vamsas document */ protected boolean __stored_in_document=false; + protected long __last_hash=0; protected VorbaId vorbaId=null; protected IVorbaIdFactory __vorba=null; /** @@ -68,4 +69,14 @@ public abstract class object { protected void set__stored_in_document(boolean __stored_in_document) { this.__stored_in_document = __stored_in_document; } + /** + * __last_hash is the hash value computed + * when the object was last checked against + * a IClientDocument generated by the + * object's parent IClient instance. + * @return Returns the __last_hash. + */ + public long get__last_hash() { + return __last_hash; + } } diff --git a/src/org/vamsas/objects/core/.castor.cdr b/src/org/vamsas/objects/core/.castor.cdr index ce4c376..ffd7903 100644 --- a/src/org/vamsas/objects/core/.castor.cdr +++ b/src/org/vamsas/objects/core/.castor.cdr @@ -1,18 +1,19 @@ -- listing properties -- -org.vamsas.objects.core.ProvenanceItem=org.vamsas.objects.core.ProvenanceIte... -org.vamsas.objects.core.AlignmentAnnotations=org.vamsas.objects.core.AlignmentAnno... org.vamsas.objects.core.Tree=org.vamsas.objects.core.TreeDescriptor -org.vamsas.objects.core.Sequence=org.vamsas.objects.core.SequenceDescr... +org.vamsas.objects.core.Provenance=org.vamsas.objects.core.ProvenanceDes... +org.vamsas.objects.core.SequenceType=org.vamsas.objects.core.SequenceTypeD... +org.vamsas.objects.core.Newick=org.vamsas.objects.core.NewickDescriptor org.vamsas.objects.core.AnnotationElement=org.vamsas.objects.core.AnnotationEle... +org.vamsas.objects.core.AlignmentSequence=org.vamsas.objects.core.AlignmentSequ... +org.vamsas.objects.core.Alignment=org.vamsas.objects.core.AlignmentDesc... +org.vamsas.objects.core.DbRef=org.vamsas.objects.core.DbRefDescriptor +org.vamsas.objects.core.User=org.vamsas.objects.core.UserDescriptor +org.vamsas.objects.core.SequenceSetAnnotations=org.vamsas.objects.core.SequenceSetAn... +org.vamsas.objects.core.Application=org.vamsas.objects.core.ApplicationDe... +org.vamsas.objects.core.VAMSAS=org.vamsas.objects.core.VAMSASDescriptor +org.vamsas.objects.core.Sequence=org.vamsas.objects.core.SequenceDescr... org.vamsas.objects.core.LockFile=org.vamsas.objects.core.LockFileDescr... org.vamsas.objects.core.Entry=org.vamsas.objects.core.EntryDescriptor -org.vamsas.objects.core.SequenceType=org.vamsas.objects.core.SequenceTypeD... -org.vamsas.objects.core.VAMSAS=org.vamsas.objects.core.VAMSASDescriptor org.vamsas.objects.core.SequenceSet=org.vamsas.objects.core.SequenceSetDe... -org.vamsas.objects.core.DbRef=org.vamsas.objects.core.DbRefDescriptor org.vamsas.objects.core.ApplicationData=org.vamsas.objects.core.ApplicationDa... -org.vamsas.objects.core.Application=org.vamsas.objects.core.ApplicationDe... -org.vamsas.objects.core.Provenance=org.vamsas.objects.core.ProvenanceDes... -org.vamsas.objects.core.AlignmentSequence=org.vamsas.objects.core.AlignmentSequ... -org.vamsas.objects.core.Alignment=org.vamsas.objects.core.AlignmentDesc... -org.vamsas.objects.core.SequenceSetAnnotations=org.vamsas.objects.core.SequenceSetAn... +org.vamsas.objects.core.AlignmentAnnotations=org.vamsas.objects.core.AlignmentAnno... diff --git a/src/org/vamsas/objects/core/Alignment.java b/src/org/vamsas/objects/core/Alignment.java index b9fa81c..9a6d432 100644 --- a/src/org/vamsas/objects/core/Alignment.java +++ b/src/org/vamsas/objects/core/Alignment.java @@ -38,6 +38,11 @@ implements java.io.Serializable //--------------------------/ /** + * Field _id + */ + private java.lang.String _id; + + /** * Field _alignmentAnnotations */ private org.vamsas.objects.core.AlignmentAnnotations _alignmentAnnotations; @@ -169,6 +174,13 @@ implements java.io.Serializable if (obj instanceof Alignment) { Alignment temp = (Alignment)obj; + if (this._id != null) { + if (temp._id == null) return false; + else if (!(this._id.equals(temp._id))) + return false; + } + else if (temp._id != null) + return false; if (this._alignmentAnnotations != null) { if (temp._alignmentAnnotations == null) return false; else if (!(this._alignmentAnnotations.equals(temp._alignmentAnnotations))) @@ -262,6 +274,17 @@ implements java.io.Serializable } //-- int getAlignmentSequenceCount() /** + * Returns the value of field 'id'. + * + * @return String + * @return the value of field 'id'. + */ + public java.lang.String getId() + { + return this._id; + } //-- java.lang.String getId() + + /** * Returns the value of field 'provenance'. * * @return Provenance @@ -460,6 +483,16 @@ implements java.io.Serializable } //-- void setAlignmentSequence(org.vamsas.objects.core.AlignmentSequence) /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId(java.lang.String id) + { + this._id = id; + } //-- void setId(java.lang.String) + + /** * Sets the value of field 'provenance'. * * @param provenance the value of field 'provenance'. diff --git a/src/org/vamsas/objects/core/AlignmentDescriptor.java b/src/org/vamsas/objects/core/AlignmentDescriptor.java index 684f619..4d65fe1 100644 --- a/src/org/vamsas/objects/core/AlignmentDescriptor.java +++ b/src/org/vamsas/objects/core/AlignmentDescriptor.java @@ -66,6 +66,40 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc org.exolab.castor.xml.FieldValidator fieldValidator = null; //-- initialize attribute descriptors + //-- _id + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); + this.identity = desc; + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Alignment target = (Alignment) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Alignment target = (Alignment) object; + target.setId( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new java.lang.String(); + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); //-- initialize element descriptors //-- _alignmentAnnotations diff --git a/src/org/vamsas/objects/core/AlignmentSequence.java b/src/org/vamsas/objects/core/AlignmentSequence.java index 91fd691..6761934 100644 --- a/src/org/vamsas/objects/core/AlignmentSequence.java +++ b/src/org/vamsas/objects/core/AlignmentSequence.java @@ -36,6 +36,11 @@ implements java.io.Serializable //--------------------------/ /** + * Field _id + */ + private java.lang.String _id; + + /** * Field _refid */ private java.lang.Object _refid; @@ -72,6 +77,13 @@ implements java.io.Serializable if (obj instanceof AlignmentSequence) { AlignmentSequence temp = (AlignmentSequence)obj; + if (this._id != null) { + if (temp._id == null) return false; + else if (!(this._id.equals(temp._id))) + return false; + } + else if (temp._id != null) + return false; if (this._refid != null) { if (temp._refid == null) return false; else if (!(this._refid.equals(temp._refid))) @@ -85,6 +97,17 @@ implements java.io.Serializable } //-- boolean equals(java.lang.Object) /** + * Returns the value of field 'id'. + * + * @return String + * @return the value of field 'id'. + */ + public java.lang.String getId() + { + return this._id; + } //-- java.lang.String getId() + + /** * Returns the value of field 'refid'. * * @return Object @@ -142,6 +165,16 @@ implements java.io.Serializable } //-- void marshal(org.xml.sax.ContentHandler) /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId(java.lang.String id) + { + this._id = id; + } //-- void setId(java.lang.String) + + /** * Sets the value of field 'refid'. * * @param refid the value of field 'refid'. diff --git a/src/org/vamsas/objects/core/AlignmentSequenceDescriptor.java b/src/org/vamsas/objects/core/AlignmentSequenceDescriptor.java index b49e045..e219b2b 100644 --- a/src/org/vamsas/objects/core/AlignmentSequenceDescriptor.java +++ b/src/org/vamsas/objects/core/AlignmentSequenceDescriptor.java @@ -64,6 +64,40 @@ public class AlignmentSequenceDescriptor extends org.vamsas.objects.core.Sequenc org.exolab.castor.xml.FieldValidator fieldValidator = null; //-- initialize attribute descriptors + //-- _id + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); + this.identity = desc; + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AlignmentSequence target = (AlignmentSequence) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AlignmentSequence target = (AlignmentSequence) object; + target.setId( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new java.lang.String(); + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); //-- _refid desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_refid", "refid", org.exolab.castor.xml.NodeType.Attribute); desc.setReference(true); diff --git a/src/org/vamsas/objects/core/Application.java b/src/org/vamsas/objects/core/Application.java index 1b2659c..0567205 100644 --- a/src/org/vamsas/objects/core/Application.java +++ b/src/org/vamsas/objects/core/Application.java @@ -46,15 +46,20 @@ implements java.io.Serializable private java.lang.String _name; /** - * Field _session + * Field _urn */ - private java.lang.String _session; + private java.lang.String _urn; /** * Field _data */ private java.lang.String _data; + /** + * Field _user + */ + private org.vamsas.objects.core.User _user; + //----------------/ //- Constructors -/ @@ -101,12 +106,12 @@ implements java.io.Serializable } else if (temp._name != null) return false; - if (this._session != null) { - if (temp._session == null) return false; - else if (!(this._session.equals(temp._session))) + if (this._urn != null) { + if (temp._urn == null) return false; + else if (!(this._urn.equals(temp._urn))) return false; } - else if (temp._session != null) + else if (temp._urn != null) return false; if (this._data != null) { if (temp._data == null) return false; @@ -115,6 +120,13 @@ implements java.io.Serializable } else if (temp._data != null) return false; + if (this._user != null) { + if (temp._user == null) return false; + else if (!(this._user.equals(temp._user))) + return false; + } + else if (temp._user != null) + return false; return true; } return false; @@ -143,15 +155,26 @@ implements java.io.Serializable } //-- java.lang.String getName() /** - * Returns the value of field 'session'. + * Returns the value of field 'urn'. * * @return String - * @return the value of field 'session'. + * @return the value of field 'urn'. + */ + public java.lang.String getUrn() + { + return this._urn; + } //-- java.lang.String getUrn() + + /** + * Returns the value of field 'user'. + * + * @return User + * @return the value of field 'user'. */ - public java.lang.String getSession() + public org.vamsas.objects.core.User getUser() { - return this._session; - } //-- java.lang.String getSession() + return this._user; + } //-- org.vamsas.objects.core.User getUser() /** * Returns the value of field 'version'. @@ -231,14 +254,24 @@ implements java.io.Serializable } //-- void setName(java.lang.String) /** - * Sets the value of field 'session'. + * Sets the value of field 'urn'. + * + * @param urn the value of field 'urn'. + */ + public void setUrn(java.lang.String urn) + { + this._urn = urn; + } //-- void setUrn(java.lang.String) + + /** + * Sets the value of field 'user'. * - * @param session the value of field 'session'. + * @param user the value of field 'user'. */ - public void setSession(java.lang.String session) + public void setUser(org.vamsas.objects.core.User user) { - this._session = session; - } //-- void setSession(java.lang.String) + this._user = user; + } //-- void setUser(org.vamsas.objects.core.User) /** * Sets the value of field 'version'. diff --git a/src/org/vamsas/objects/core/ApplicationDescriptor.java b/src/org/vamsas/objects/core/ApplicationDescriptor.java index 7b3a6a6..0f956fa 100644 --- a/src/org/vamsas/objects/core/ApplicationDescriptor.java +++ b/src/org/vamsas/objects/core/ApplicationDescriptor.java @@ -58,6 +58,9 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe super(); nsURI = "http://www.vamsas.org"; xmlName = "Application"; + + //-- set grouping compositor + setCompositorAsSequence(); org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; org.exolab.castor.mapping.FieldHandler handler = null; org.exolab.castor.xml.FieldValidator fieldValidator = null; @@ -137,22 +140,22 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); - //-- _session - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_session", "session", org.exolab.castor.xml.NodeType.Attribute); + //-- _urn + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_urn", "urn", org.exolab.castor.xml.NodeType.Attribute); desc.setImmutable(true); handler = new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { Application target = (Application) object; - return target.getSession(); + return target.getUrn(); } public void setValue( java.lang.Object object, java.lang.Object value) throws IllegalStateException, IllegalArgumentException { try { Application target = (Application) object; - target.setSession( (java.lang.String) value); + target.setUrn( (java.lang.String) value); } catch (java.lang.Exception ex) { throw new IllegalStateException(ex.toString()); @@ -166,7 +169,7 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe desc.setMultivalued(false); addFieldDescriptor(desc); - //-- validation code for: _session + //-- validation code for: _urn fieldValidator = new org.exolab.castor.xml.FieldValidator(); { //-- local scope StringValidator typeValidator = new StringValidator(); @@ -213,6 +216,42 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe desc.setValidator(fieldValidator); //-- initialize element descriptors + //-- _user + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.User.class, "_user", "User", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Application target = (Application) object; + return target.getUser(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Application target = (Application) object; + target.setUser( (org.vamsas.objects.core.User) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new org.vamsas.objects.core.User(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _user + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + } + desc.setValidator(fieldValidator); } //-- org.vamsas.objects.core.ApplicationDescriptor() diff --git a/src/org/vamsas/objects/core/Newick.java b/src/org/vamsas/objects/core/Newick.java new file mode 100644 index 0000000..3d2bd2a --- /dev/null +++ b/src/org/vamsas/objects/core/Newick.java @@ -0,0 +1,248 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M2, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.objects.core; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import java.io.IOException; +import java.io.Reader; +import java.io.Serializable; +import java.io.Writer; +import org.exolab.castor.xml.MarshalException; +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; +import org.exolab.castor.xml.ValidationException; +import org.xml.sax.ContentHandler; + +/** + * Class Newick. + * + * @version $Revision$ $Date$ + */ +public class Newick extends org.vamsas.client.object +implements java.io.Serializable +{ + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * internal content storage + */ + private java.lang.String _content = ""; + + /** + * Field _title + */ + private java.lang.String _title; + + /** + * Field _id + */ + private java.lang.String _id; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Newick() + { + super(); + setContent(""); + } //-- org.vamsas.objects.core.Newick() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Note: hashCode() has not been overriden + * + * @param obj + * @return boolean + */ + public boolean equals(java.lang.Object obj) + { + if ( this == obj ) + return true; + + if (super.equals(obj)==false) + return false; + + if (obj instanceof Newick) { + + Newick temp = (Newick)obj; + if (this._content != null) { + if (temp._content == null) return false; + else if (!(this._content.equals(temp._content))) + return false; + } + else if (temp._content != null) + return false; + if (this._title != null) { + if (temp._title == null) return false; + else if (!(this._title.equals(temp._title))) + return false; + } + else if (temp._title != null) + return false; + if (this._id != null) { + if (temp._id == null) return false; + else if (!(this._id.equals(temp._id))) + return false; + } + else if (temp._id != null) + return false; + return true; + } + return false; + } //-- boolean equals(java.lang.Object) + + /** + * Returns the value of field 'content'. The field 'content' + * has the following description: internal content storage + * + * @return String + * @return the value of field 'content'. + */ + public java.lang.String getContent() + { + return this._content; + } //-- java.lang.String getContent() + + /** + * Returns the value of field 'id'. + * + * @return String + * @return the value of field 'id'. + */ + public java.lang.String getId() + { + return this._id; + } //-- java.lang.String getId() + + /** + * Returns the value of field 'title'. + * + * @return String + * @return the value of field 'title'. + */ + public java.lang.String getTitle() + { + return this._title; + } //-- java.lang.String getTitle() + + /** + * Method isValid + * + * + * + * @return boolean + */ + public boolean isValid() + { + try { + validate(); + } + catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } //-- boolean isValid() + + /** + * Method marshal + * + * + * + * @param out + */ + public void marshal(java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + + Marshaller.marshal(this, out); + } //-- void marshal(java.io.Writer) + + /** + * Method marshal + * + * + * + * @param handler + */ + public void marshal(org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + + Marshaller.marshal(this, handler); + } //-- void marshal(org.xml.sax.ContentHandler) + + /** + * Sets the value of field 'content'. The field 'content' has + * the following description: internal content storage + * + * @param content the value of field 'content'. + */ + public void setContent(java.lang.String content) + { + this._content = content; + } //-- void setContent(java.lang.String) + + /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId(java.lang.String id) + { + this._id = id; + } //-- void setId(java.lang.String) + + /** + * Sets the value of field 'title'. + * + * @param title the value of field 'title'. + */ + public void setTitle(java.lang.String title) + { + this._title = title; + } //-- void setTitle(java.lang.String) + + /** + * Method unmarshal + * + * + * + * @param reader + * @return Newick + */ + public static org.vamsas.objects.core.Newick unmarshal(java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + return (org.vamsas.objects.core.Newick) Unmarshaller.unmarshal(org.vamsas.objects.core.Newick.class, reader); + } //-- org.vamsas.objects.core.Newick unmarshal(java.io.Reader) + + /** + * Method validate + * + */ + public void validate() + throws org.exolab.castor.xml.ValidationException + { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } //-- void validate() + +} diff --git a/src/org/vamsas/objects/core/NewickDescriptor.java b/src/org/vamsas/objects/core/NewickDescriptor.java new file mode 100644 index 0000000..ee208f6 --- /dev/null +++ b/src/org/vamsas/objects/core/NewickDescriptor.java @@ -0,0 +1,278 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M2, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.objects.core; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.mapping.AccessMode; +import org.exolab.castor.xml.TypeValidator; +import org.exolab.castor.xml.XMLFieldDescriptor; +import org.exolab.castor.xml.validators.*; + +/** + * Class NewickDescriptor. + * + * @version $Revision$ $Date$ + */ +public class NewickDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field nsPrefix + */ + private java.lang.String nsPrefix; + + /** + * Field nsURI + */ + private java.lang.String nsURI; + + /** + * Field xmlName + */ + private java.lang.String xmlName; + + /** + * Field identity + */ + private org.exolab.castor.xml.XMLFieldDescriptor identity; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public NewickDescriptor() + { + super(); + nsURI = "http://www.vamsas.org"; + xmlName = "newick"; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- _content + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Newick target = (Newick) object; + return target.getContent(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Newick target = (Newick) object; + target.setContent( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + addFieldDescriptor(desc); + + //-- validation code for: _content + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + StringValidator typeValidator = new StringValidator(); + typeValidator.setWhiteSpace("preserve"); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- initialize attribute descriptors + + //-- _title + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Newick target = (Newick) object; + return target.getTitle(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Newick target = (Newick) object; + target.setTitle( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _title + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + StringValidator typeValidator = new StringValidator(); + typeValidator.setWhiteSpace("preserve"); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _id + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); + this.identity = desc; + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Newick target = (Newick) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Newick target = (Newick) object; + target.setId( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new java.lang.String(); + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + } //-- org.vamsas.objects.core.NewickDescriptor() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode + * + * + * + * @return AccessMode + */ + public org.exolab.castor.mapping.AccessMode getAccessMode() + { + return null; + } //-- org.exolab.castor.mapping.AccessMode getAccessMode() + + /** + * Method getExtends + * + * + * + * @return ClassDescriptor + */ + public org.exolab.castor.mapping.ClassDescriptor getExtends() + { + return null; + } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() + + /** + * Method getIdentity + * + * + * + * @return FieldDescriptor + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity() + { + return identity; + } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() + + /** + * Method getJavaClass + * + * + * + * @return Class + */ + public java.lang.Class getJavaClass() + { + return org.vamsas.objects.core.Newick.class; + } //-- java.lang.Class getJavaClass() + + /** + * Method getNameSpacePrefix + * + * + * + * @return String + */ + public java.lang.String getNameSpacePrefix() + { + return nsPrefix; + } //-- java.lang.String getNameSpacePrefix() + + /** + * Method getNameSpaceURI + * + * + * + * @return String + */ + public java.lang.String getNameSpaceURI() + { + return nsURI; + } //-- java.lang.String getNameSpaceURI() + + /** + * Method getValidator + * + * + * + * @return TypeValidator + */ + public org.exolab.castor.xml.TypeValidator getValidator() + { + return this; + } //-- org.exolab.castor.xml.TypeValidator getValidator() + + /** + * Method getXMLName + * + * + * + * @return String + */ + public java.lang.String getXMLName() + { + return xmlName; + } //-- java.lang.String getXMLName() + +} diff --git a/src/org/vamsas/objects/core/Provenance.java b/src/org/vamsas/objects/core/Provenance.java index 9f0adc5..3c3eb8d 100644 --- a/src/org/vamsas/objects/core/Provenance.java +++ b/src/org/vamsas/objects/core/Provenance.java @@ -38,9 +38,9 @@ implements java.io.Serializable //--------------------------/ /** - * Field _items + * Field _entryList */ - private java.util.Vector _items; + private java.util.Vector _entryList; //----------------/ @@ -50,7 +50,7 @@ implements java.io.Serializable public Provenance() { super(); - _items = new Vector(); + _entryList = new Vector(); } //-- org.vamsas.objects.core.Provenance() @@ -59,43 +59,43 @@ implements java.io.Serializable //-----------/ /** - * Method addProvenanceItem + * Method addEntry * * * - * @param vProvenanceItem + * @param vEntry */ - public void addProvenanceItem(org.vamsas.objects.core.ProvenanceItem vProvenanceItem) + public void addEntry(org.vamsas.objects.core.Entry vEntry) throws java.lang.IndexOutOfBoundsException { - _items.addElement(vProvenanceItem); - } //-- void addProvenanceItem(org.vamsas.objects.core.ProvenanceItem) + _entryList.addElement(vEntry); + } //-- void addEntry(org.vamsas.objects.core.Entry) /** - * Method addProvenanceItem + * Method addEntry * * * * @param index - * @param vProvenanceItem + * @param vEntry */ - public void addProvenanceItem(int index, org.vamsas.objects.core.ProvenanceItem vProvenanceItem) + public void addEntry(int index, org.vamsas.objects.core.Entry vEntry) throws java.lang.IndexOutOfBoundsException { - _items.insertElementAt(vProvenanceItem, index); - } //-- void addProvenanceItem(int, org.vamsas.objects.core.ProvenanceItem) + _entryList.insertElementAt(vEntry, index); + } //-- void addEntry(int, org.vamsas.objects.core.Entry) /** - * Method enumerateProvenanceItem + * Method enumerateEntry * * * * @return Enumeration */ - public java.util.Enumeration enumerateProvenanceItem() + public java.util.Enumeration enumerateEntry() { - return _items.elements(); - } //-- java.util.Enumeration enumerateProvenanceItem() + return _entryList.elements(); + } //-- java.util.Enumeration enumerateEntry() /** * Note: hashCode() has not been overriden @@ -114,12 +114,12 @@ implements java.io.Serializable if (obj instanceof Provenance) { Provenance temp = (Provenance)obj; - if (this._items != null) { - if (temp._items == null) return false; - else if (!(this._items.equals(temp._items))) + if (this._entryList != null) { + if (temp._entryList == null) return false; + else if (!(this._entryList.equals(temp._entryList))) return false; } - else if (temp._items != null) + else if (temp._entryList != null) return false; return true; } @@ -127,52 +127,52 @@ implements java.io.Serializable } //-- boolean equals(java.lang.Object) /** - * Method getProvenanceItem + * Method getEntry * * * * @param index - * @return ProvenanceItem + * @return Entry */ - public org.vamsas.objects.core.ProvenanceItem getProvenanceItem(int index) + public org.vamsas.objects.core.Entry getEntry(int index) throws java.lang.IndexOutOfBoundsException { //-- check bounds for index - if ((index < 0) || (index > _items.size())) { - throw new IndexOutOfBoundsException("getProvenanceItem: Index value '"+index+"' not in range [0.."+_items.size()+ "]"); + if ((index < 0) || (index > _entryList.size())) { + throw new IndexOutOfBoundsException("getEntry: Index value '"+index+"' not in range [0.."+_entryList.size()+ "]"); } - return (org.vamsas.objects.core.ProvenanceItem) _items.elementAt(index); - } //-- org.vamsas.objects.core.ProvenanceItem getProvenanceItem(int) + return (org.vamsas.objects.core.Entry) _entryList.elementAt(index); + } //-- org.vamsas.objects.core.Entry getEntry(int) /** - * Method getProvenanceItem + * Method getEntry * * * - * @return ProvenanceItem + * @return Entry */ - public org.vamsas.objects.core.ProvenanceItem[] getProvenanceItem() + public org.vamsas.objects.core.Entry[] getEntry() { - int size = _items.size(); - org.vamsas.objects.core.ProvenanceItem[] mArray = new org.vamsas.objects.core.ProvenanceItem[size]; + int size = _entryList.size(); + org.vamsas.objects.core.Entry[] mArray = new org.vamsas.objects.core.Entry[size]; for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.ProvenanceItem) _items.elementAt(index); + mArray[index] = (org.vamsas.objects.core.Entry) _entryList.elementAt(index); } return mArray; - } //-- org.vamsas.objects.core.ProvenanceItem[] getProvenanceItem() + } //-- org.vamsas.objects.core.Entry[] getEntry() /** - * Method getProvenanceItemCount + * Method getEntryCount * * * * @return int */ - public int getProvenanceItemCount() + public int getEntryCount() { - return _items.size(); - } //-- int getProvenanceItemCount() + return _entryList.size(); + } //-- int getEntryCount() /** * Method isValid @@ -221,62 +221,62 @@ implements java.io.Serializable } //-- void marshal(org.xml.sax.ContentHandler) /** - * Method removeAllProvenanceItem + * Method removeAllEntry * */ - public void removeAllProvenanceItem() + public void removeAllEntry() { - _items.removeAllElements(); - } //-- void removeAllProvenanceItem() + _entryList.removeAllElements(); + } //-- void removeAllEntry() /** - * Method removeProvenanceItem + * Method removeEntry * * * * @param index - * @return ProvenanceItem + * @return Entry */ - public org.vamsas.objects.core.ProvenanceItem removeProvenanceItem(int index) + public org.vamsas.objects.core.Entry removeEntry(int index) { - java.lang.Object obj = _items.elementAt(index); - _items.removeElementAt(index); - return (org.vamsas.objects.core.ProvenanceItem) obj; - } //-- org.vamsas.objects.core.ProvenanceItem removeProvenanceItem(int) + java.lang.Object obj = _entryList.elementAt(index); + _entryList.removeElementAt(index); + return (org.vamsas.objects.core.Entry) obj; + } //-- org.vamsas.objects.core.Entry removeEntry(int) /** - * Method setProvenanceItem + * Method setEntry * * * * @param index - * @param vProvenanceItem + * @param vEntry */ - public void setProvenanceItem(int index, org.vamsas.objects.core.ProvenanceItem vProvenanceItem) + public void setEntry(int index, org.vamsas.objects.core.Entry vEntry) throws java.lang.IndexOutOfBoundsException { //-- check bounds for index - if ((index < 0) || (index > _items.size())) { - throw new IndexOutOfBoundsException("setProvenanceItem: Index value '"+index+"' not in range [0.."+_items.size()+ "]"); + if ((index < 0) || (index > _entryList.size())) { + throw new IndexOutOfBoundsException("setEntry: Index value '"+index+"' not in range [0.."+_entryList.size()+ "]"); } - _items.setElementAt(vProvenanceItem, index); - } //-- void setProvenanceItem(int, org.vamsas.objects.core.ProvenanceItem) + _entryList.setElementAt(vEntry, index); + } //-- void setEntry(int, org.vamsas.objects.core.Entry) /** - * Method setProvenanceItem + * Method setEntry * * * - * @param provenanceItemArray + * @param entryArray */ - public void setProvenanceItem(org.vamsas.objects.core.ProvenanceItem[] provenanceItemArray) + public void setEntry(org.vamsas.objects.core.Entry[] entryArray) { //-- copy array - _items.removeAllElements(); - for (int i = 0; i < provenanceItemArray.length; i++) { - _items.addElement(provenanceItemArray[i]); + _entryList.removeAllElements(); + for (int i = 0; i < entryArray.length; i++) { + _entryList.addElement(entryArray[i]); } - } //-- void setProvenanceItem(org.vamsas.objects.core.ProvenanceItem) + } //-- void setEntry(org.vamsas.objects.core.Entry) /** * Method unmarshal diff --git a/src/org/vamsas/objects/core/ProvenanceDescriptor.java b/src/org/vamsas/objects/core/ProvenanceDescriptor.java index 71db58f..23b355d 100644 --- a/src/org/vamsas/objects/core/ProvenanceDescriptor.java +++ b/src/org/vamsas/objects/core/ProvenanceDescriptor.java @@ -56,7 +56,11 @@ public class ProvenanceDescriptor extends org.exolab.castor.xml.util.XMLClassDes public ProvenanceDescriptor() { super(); + nsURI = "http://www.vamsas.org"; xmlName = "Provenance"; + + //-- set grouping compositor + setCompositorAsSequence(); org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; org.exolab.castor.mapping.FieldHandler handler = null; org.exolab.castor.xml.FieldValidator fieldValidator = null; @@ -64,37 +68,36 @@ public class ProvenanceDescriptor extends org.exolab.castor.xml.util.XMLClassDes //-- initialize element descriptors - //-- _items - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.ProvenanceItem.class, "_items", (String)null, org.exolab.castor.xml.NodeType.Element); + //-- _entryList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Entry.class, "_entryList", "entry", org.exolab.castor.xml.NodeType.Element); handler = new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { Provenance target = (Provenance) object; - return target.getProvenanceItem(); + return target.getEntry(); } public void setValue( java.lang.Object object, java.lang.Object value) throws IllegalStateException, IllegalArgumentException { try { Provenance target = (Provenance) object; - target.addProvenanceItem( (org.vamsas.objects.core.ProvenanceItem) value); + target.addEntry( (org.vamsas.objects.core.Entry) value); } catch (java.lang.Exception ex) { throw new IllegalStateException(ex.toString()); } } public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.ProvenanceItem(); + return new org.vamsas.objects.core.Entry(); } }; desc.setHandler(handler); - desc.setContainer(true); - desc.setClassDescriptor(new org.vamsas.objects.core.ProvenanceItemDescriptor()); + desc.setNameSpaceURI("http://www.vamsas.org"); desc.setMultivalued(true); addFieldDescriptor(desc); - //-- validation code for: _items + //-- validation code for: _entryList fieldValidator = new org.exolab.castor.xml.FieldValidator(); fieldValidator.setMinOccurs(0); { //-- local scope diff --git a/src/org/vamsas/objects/core/Sequence.java b/src/org/vamsas/objects/core/Sequence.java index 5988d65..27a1d8d 100644 --- a/src/org/vamsas/objects/core/Sequence.java +++ b/src/org/vamsas/objects/core/Sequence.java @@ -15,6 +15,8 @@ import java.io.IOException; import java.io.Reader; import java.io.Serializable; import java.io.Writer; +import java.util.Enumeration; +import java.util.Vector; import org.exolab.castor.xml.MarshalException; import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -36,10 +38,20 @@ implements java.io.Serializable //--------------------------/ /** + * Field _id + */ + private java.lang.String _id; + + /** * Field _dictionary */ private java.lang.String _dictionary; + /** + * Field _dbRefList + */ + private java.util.Vector _dbRefList; + //----------------/ //- Constructors -/ @@ -48,6 +60,7 @@ implements java.io.Serializable public Sequence() { super(); + _dbRefList = new Vector(); } //-- org.vamsas.objects.core.Sequence() @@ -56,6 +69,45 @@ implements java.io.Serializable //-----------/ /** + * Method addDbRef + * + * + * + * @param vDbRef + */ + public void addDbRef(org.vamsas.objects.core.DbRef vDbRef) + throws java.lang.IndexOutOfBoundsException + { + _dbRefList.addElement(vDbRef); + } //-- void addDbRef(org.vamsas.objects.core.DbRef) + + /** + * Method addDbRef + * + * + * + * @param index + * @param vDbRef + */ + public void addDbRef(int index, org.vamsas.objects.core.DbRef vDbRef) + throws java.lang.IndexOutOfBoundsException + { + _dbRefList.insertElementAt(vDbRef, index); + } //-- void addDbRef(int, org.vamsas.objects.core.DbRef) + + /** + * Method enumerateDbRef + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateDbRef() + { + return _dbRefList.elements(); + } //-- java.util.Enumeration enumerateDbRef() + + /** * Note: hashCode() has not been overriden * * @param obj @@ -72,6 +124,13 @@ implements java.io.Serializable if (obj instanceof Sequence) { Sequence temp = (Sequence)obj; + if (this._id != null) { + if (temp._id == null) return false; + else if (!(this._id.equals(temp._id))) + return false; + } + else if (temp._id != null) + return false; if (this._dictionary != null) { if (temp._dictionary == null) return false; else if (!(this._dictionary.equals(temp._dictionary))) @@ -79,12 +138,67 @@ implements java.io.Serializable } else if (temp._dictionary != null) return false; + if (this._dbRefList != null) { + if (temp._dbRefList == null) return false; + else if (!(this._dbRefList.equals(temp._dbRefList))) + return false; + } + else if (temp._dbRefList != null) + return false; return true; } return false; } //-- boolean equals(java.lang.Object) /** + * Method getDbRef + * + * + * + * @param index + * @return DbRef + */ + public org.vamsas.objects.core.DbRef getDbRef(int index) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _dbRefList.size())) { + throw new IndexOutOfBoundsException("getDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]"); + } + + return (org.vamsas.objects.core.DbRef) _dbRefList.elementAt(index); + } //-- org.vamsas.objects.core.DbRef getDbRef(int) + + /** + * Method getDbRef + * + * + * + * @return DbRef + */ + public org.vamsas.objects.core.DbRef[] getDbRef() + { + int size = _dbRefList.size(); + org.vamsas.objects.core.DbRef[] mArray = new org.vamsas.objects.core.DbRef[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (org.vamsas.objects.core.DbRef) _dbRefList.elementAt(index); + } + return mArray; + } //-- org.vamsas.objects.core.DbRef[] getDbRef() + + /** + * Method getDbRefCount + * + * + * + * @return int + */ + public int getDbRefCount() + { + return _dbRefList.size(); + } //-- int getDbRefCount() + + /** * Returns the value of field 'dictionary'. * * @return String @@ -96,6 +210,17 @@ implements java.io.Serializable } //-- java.lang.String getDictionary() /** + * Returns the value of field 'id'. + * + * @return String + * @return the value of field 'id'. + */ + public java.lang.String getId() + { + return this._id; + } //-- java.lang.String getId() + + /** * Method isValid * * @@ -142,6 +267,64 @@ implements java.io.Serializable } //-- void marshal(org.xml.sax.ContentHandler) /** + * Method removeAllDbRef + * + */ + public void removeAllDbRef() + { + _dbRefList.removeAllElements(); + } //-- void removeAllDbRef() + + /** + * Method removeDbRef + * + * + * + * @param index + * @return DbRef + */ + public org.vamsas.objects.core.DbRef removeDbRef(int index) + { + java.lang.Object obj = _dbRefList.elementAt(index); + _dbRefList.removeElementAt(index); + return (org.vamsas.objects.core.DbRef) obj; + } //-- org.vamsas.objects.core.DbRef removeDbRef(int) + + /** + * Method setDbRef + * + * + * + * @param index + * @param vDbRef + */ + public void setDbRef(int index, org.vamsas.objects.core.DbRef vDbRef) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _dbRefList.size())) { + throw new IndexOutOfBoundsException("setDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]"); + } + _dbRefList.setElementAt(vDbRef, index); + } //-- void setDbRef(int, org.vamsas.objects.core.DbRef) + + /** + * Method setDbRef + * + * + * + * @param dbRefArray + */ + public void setDbRef(org.vamsas.objects.core.DbRef[] dbRefArray) + { + //-- copy array + _dbRefList.removeAllElements(); + for (int i = 0; i < dbRefArray.length; i++) { + _dbRefList.addElement(dbRefArray[i]); + } + } //-- void setDbRef(org.vamsas.objects.core.DbRef) + + /** * Sets the value of field 'dictionary'. * * @param dictionary the value of field 'dictionary'. @@ -152,6 +335,16 @@ implements java.io.Serializable } //-- void setDictionary(java.lang.String) /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId(java.lang.String id) + { + this._id = id; + } //-- void setId(java.lang.String) + + /** * Method unmarshal * * diff --git a/src/org/vamsas/objects/core/SequenceDescriptor.java b/src/org/vamsas/objects/core/SequenceDescriptor.java index 202b67f..7486c01 100644 --- a/src/org/vamsas/objects/core/SequenceDescriptor.java +++ b/src/org/vamsas/objects/core/SequenceDescriptor.java @@ -59,11 +59,48 @@ public class SequenceDescriptor extends org.vamsas.objects.core.SequenceTypeDesc setExtendsWithoutFlatten(new org.vamsas.objects.core.SequenceTypeDescriptor()); nsURI = "http://www.vamsas.org"; xmlName = "Sequence"; + + //-- set grouping compositor + setCompositorAsSequence(); org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; org.exolab.castor.mapping.FieldHandler handler = null; org.exolab.castor.xml.FieldValidator fieldValidator = null; //-- initialize attribute descriptors + //-- _id + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); + this.identity = desc; + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Sequence target = (Sequence) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Sequence target = (Sequence) object; + target.setId( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new java.lang.String(); + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); //-- _dictionary desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dictionary", "dictionary", org.exolab.castor.xml.NodeType.Attribute); desc.setImmutable(true); @@ -103,6 +140,41 @@ public class SequenceDescriptor extends org.vamsas.objects.core.SequenceTypeDesc desc.setValidator(fieldValidator); //-- initialize element descriptors + //-- _dbRefList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.DbRef.class, "_dbRefList", "dbRef", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Sequence target = (Sequence) object; + return target.getDbRef(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Sequence target = (Sequence) object; + target.addDbRef( (org.vamsas.objects.core.DbRef) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new org.vamsas.objects.core.DbRef(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _dbRefList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); } //-- org.vamsas.objects.core.SequenceDescriptor() diff --git a/src/org/vamsas/objects/core/SequenceSetAnnotations.java b/src/org/vamsas/objects/core/SequenceSetAnnotations.java index 347636c..04e249d 100644 --- a/src/org/vamsas/objects/core/SequenceSetAnnotations.java +++ b/src/org/vamsas/objects/core/SequenceSetAnnotations.java @@ -78,9 +78,9 @@ implements java.io.Serializable private java.util.Vector _annotationElementList; /** - * Field _provenance + * Field _provenanceList */ - private org.vamsas.objects.core.Provenance _provenance; + private java.util.Vector _provenanceList; //----------------/ @@ -91,6 +91,7 @@ implements java.io.Serializable { super(); _annotationElementList = new Vector(); + _provenanceList = new Vector(); } //-- org.vamsas.objects.core.SequenceSetAnnotations() @@ -126,6 +127,33 @@ implements java.io.Serializable } //-- void addAnnotationElement(int, org.vamsas.objects.core.AnnotationElement) /** + * Method addProvenance + * + * + * + * @param vProvenance + */ + public void addProvenance(org.vamsas.objects.core.Provenance vProvenance) + throws java.lang.IndexOutOfBoundsException + { + _provenanceList.addElement(vProvenance); + } //-- void addProvenance(org.vamsas.objects.core.Provenance) + + /** + * Method addProvenance + * + * + * + * @param index + * @param vProvenance + */ + public void addProvenance(int index, org.vamsas.objects.core.Provenance vProvenance) + throws java.lang.IndexOutOfBoundsException + { + _provenanceList.insertElementAt(vProvenance, index); + } //-- void addProvenance(int, org.vamsas.objects.core.Provenance) + + /** * Method enumerateAnnotationElement * * @@ -138,6 +166,18 @@ implements java.io.Serializable } //-- java.util.Enumeration enumerateAnnotationElement() /** + * Method enumerateProvenance + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateProvenance() + { + return _provenanceList.elements(); + } //-- java.util.Enumeration enumerateProvenance() + + /** * Note: hashCode() has not been overriden * * @param obj @@ -210,12 +250,12 @@ implements java.io.Serializable } else if (temp._annotationElementList != null) return false; - if (this._provenance != null) { - if (temp._provenance == null) return false; - else if (!(this._provenance.equals(temp._provenance))) + if (this._provenanceList != null) { + if (temp._provenanceList == null) return false; + else if (!(this._provenanceList.equals(temp._provenanceList))) return false; } - else if (temp._provenance != null) + else if (temp._provenanceList != null) return false; return true; } @@ -315,15 +355,52 @@ implements java.io.Serializable } //-- java.lang.String getId() /** - * Returns the value of field 'provenance'. + * Method getProvenance + * + * + * + * @param index + * @return Provenance + */ + public org.vamsas.objects.core.Provenance getProvenance(int index) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _provenanceList.size())) { + throw new IndexOutOfBoundsException("getProvenance: Index value '"+index+"' not in range [0.."+_provenanceList.size()+ "]"); + } + + return (org.vamsas.objects.core.Provenance) _provenanceList.elementAt(index); + } //-- org.vamsas.objects.core.Provenance getProvenance(int) + + /** + * Method getProvenance + * + * * * @return Provenance - * @return the value of field 'provenance'. */ - public org.vamsas.objects.core.Provenance getProvenance() + public org.vamsas.objects.core.Provenance[] getProvenance() { - return this._provenance; - } //-- org.vamsas.objects.core.Provenance getProvenance() + int size = _provenanceList.size(); + org.vamsas.objects.core.Provenance[] mArray = new org.vamsas.objects.core.Provenance[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (org.vamsas.objects.core.Provenance) _provenanceList.elementAt(index); + } + return mArray; + } //-- org.vamsas.objects.core.Provenance[] getProvenance() + + /** + * Method getProvenanceCount + * + * + * + * @return int + */ + public int getProvenanceCount() + { + return _provenanceList.size(); + } //-- int getProvenanceCount() /** * Returns the value of field 'seqRef'. @@ -414,6 +491,15 @@ implements java.io.Serializable } //-- void removeAllAnnotationElement() /** + * Method removeAllProvenance + * + */ + public void removeAllProvenance() + { + _provenanceList.removeAllElements(); + } //-- void removeAllProvenance() + + /** * Method removeAnnotationElement * * @@ -429,6 +515,21 @@ implements java.io.Serializable } //-- org.vamsas.objects.core.AnnotationElement removeAnnotationElement(int) /** + * Method removeProvenance + * + * + * + * @param index + * @return Provenance + */ + public org.vamsas.objects.core.Provenance removeProvenance(int index) + { + java.lang.Object obj = _provenanceList.elementAt(index); + _provenanceList.removeElementAt(index); + return (org.vamsas.objects.core.Provenance) obj; + } //-- org.vamsas.objects.core.Provenance removeProvenance(int) + + /** * Method setAnnotationElement * * @@ -503,13 +604,37 @@ implements java.io.Serializable } //-- void setId(java.lang.String) /** - * Sets the value of field 'provenance'. + * Method setProvenance + * + * + * + * @param index + * @param vProvenance + */ + public void setProvenance(int index, org.vamsas.objects.core.Provenance vProvenance) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _provenanceList.size())) { + throw new IndexOutOfBoundsException("setProvenance: Index value '"+index+"' not in range [0.."+_provenanceList.size()+ "]"); + } + _provenanceList.setElementAt(vProvenance, index); + } //-- void setProvenance(int, org.vamsas.objects.core.Provenance) + + /** + * Method setProvenance + * + * * - * @param provenance the value of field 'provenance'. + * @param provenanceArray */ - public void setProvenance(org.vamsas.objects.core.Provenance provenance) + public void setProvenance(org.vamsas.objects.core.Provenance[] provenanceArray) { - this._provenance = provenance; + //-- copy array + _provenanceList.removeAllElements(); + for (int i = 0; i < provenanceArray.length; i++) { + _provenanceList.addElement(provenanceArray[i]); + } } //-- void setProvenance(org.vamsas.objects.core.Provenance) /** diff --git a/src/org/vamsas/objects/core/SequenceSetAnnotationsDescriptor.java b/src/org/vamsas/objects/core/SequenceSetAnnotationsDescriptor.java index c270df7..6fc4a18 100644 --- a/src/org/vamsas/objects/core/SequenceSetAnnotationsDescriptor.java +++ b/src/org/vamsas/objects/core/SequenceSetAnnotationsDescriptor.java @@ -366,8 +366,8 @@ public class SequenceSetAnnotationsDescriptor extends org.exolab.castor.xml.util { //-- local scope } desc.setValidator(fieldValidator); - //-- _provenance - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element); + //-- _provenanceList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenanceList", "Provenance", org.exolab.castor.xml.NodeType.Element); handler = new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException @@ -380,7 +380,7 @@ public class SequenceSetAnnotationsDescriptor extends org.exolab.castor.xml.util { try { SequenceSetAnnotations target = (SequenceSetAnnotations) object; - target.setProvenance( (org.vamsas.objects.core.Provenance) value); + target.addProvenance( (org.vamsas.objects.core.Provenance) value); } catch (java.lang.Exception ex) { throw new IllegalStateException(ex.toString()); @@ -392,13 +392,12 @@ public class SequenceSetAnnotationsDescriptor extends org.exolab.castor.xml.util }; desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); + desc.setMultivalued(true); addFieldDescriptor(desc); - //-- validation code for: _provenance + //-- validation code for: _provenanceList fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); + fieldValidator.setMinOccurs(0); { //-- local scope } desc.setValidator(fieldValidator); diff --git a/src/org/vamsas/objects/core/SequenceType.java b/src/org/vamsas/objects/core/SequenceType.java index e6204d6..1adc80a 100644 --- a/src/org/vamsas/objects/core/SequenceType.java +++ b/src/org/vamsas/objects/core/SequenceType.java @@ -15,8 +15,6 @@ import java.io.IOException; import java.io.Reader; import java.io.Serializable; import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; import org.exolab.castor.xml.MarshalException; import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -58,11 +56,6 @@ implements java.io.Serializable private boolean _has_end; /** - * Field _id - */ - private java.lang.String _id; - - /** * Field _sequence */ private java.lang.String _sequence; @@ -72,11 +65,6 @@ implements java.io.Serializable */ private java.lang.String _name; - /** - * Field _dbRefList - */ - private java.util.Vector _dbRefList; - //----------------/ //- Constructors -/ @@ -85,7 +73,6 @@ implements java.io.Serializable public SequenceType() { super(); - _dbRefList = new Vector(); } //-- org.vamsas.objects.core.SequenceType() @@ -94,33 +81,6 @@ implements java.io.Serializable //-----------/ /** - * Method addDbRef - * - * - * - * @param vDbRef - */ - public void addDbRef(org.vamsas.objects.core.DbRef vDbRef) - throws java.lang.IndexOutOfBoundsException - { - _dbRefList.addElement(vDbRef); - } //-- void addDbRef(org.vamsas.objects.core.DbRef) - - /** - * Method addDbRef - * - * - * - * @param index - * @param vDbRef - */ - public void addDbRef(int index, org.vamsas.objects.core.DbRef vDbRef) - throws java.lang.IndexOutOfBoundsException - { - _dbRefList.insertElementAt(vDbRef, index); - } //-- void addDbRef(int, org.vamsas.objects.core.DbRef) - - /** * Method deleteEnd * */ @@ -139,18 +99,6 @@ implements java.io.Serializable } //-- void deleteStart() /** - * Method enumerateDbRef - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateDbRef() - { - return _dbRefList.elements(); - } //-- java.util.Enumeration enumerateDbRef() - - /** * Note: hashCode() has not been overriden * * @param obj @@ -175,13 +123,6 @@ implements java.io.Serializable return false; if (this._has_end != temp._has_end) return false; - if (this._id != null) { - if (temp._id == null) return false; - else if (!(this._id.equals(temp._id))) - return false; - } - else if (temp._id != null) - return false; if (this._sequence != null) { if (temp._sequence == null) return false; else if (!(this._sequence.equals(temp._sequence))) @@ -196,67 +137,12 @@ implements java.io.Serializable } else if (temp._name != null) return false; - if (this._dbRefList != null) { - if (temp._dbRefList == null) return false; - else if (!(this._dbRefList.equals(temp._dbRefList))) - return false; - } - else if (temp._dbRefList != null) - return false; return true; } return false; } //-- boolean equals(java.lang.Object) /** - * Method getDbRef - * - * - * - * @param index - * @return DbRef - */ - public org.vamsas.objects.core.DbRef getDbRef(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _dbRefList.size())) { - throw new IndexOutOfBoundsException("getDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]"); - } - - return (org.vamsas.objects.core.DbRef) _dbRefList.elementAt(index); - } //-- org.vamsas.objects.core.DbRef getDbRef(int) - - /** - * Method getDbRef - * - * - * - * @return DbRef - */ - public org.vamsas.objects.core.DbRef[] getDbRef() - { - int size = _dbRefList.size(); - org.vamsas.objects.core.DbRef[] mArray = new org.vamsas.objects.core.DbRef[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.DbRef) _dbRefList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.DbRef[] getDbRef() - - /** - * Method getDbRefCount - * - * - * - * @return int - */ - public int getDbRefCount() - { - return _dbRefList.size(); - } //-- int getDbRefCount() - - /** * Returns the value of field 'end'. * * @return int @@ -268,17 +154,6 @@ implements java.io.Serializable } //-- int getEnd() /** - * Returns the value of field 'id'. - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** * Returns the value of field 'name'. * * @return String @@ -382,64 +257,6 @@ implements java.io.Serializable } //-- void marshal(org.xml.sax.ContentHandler) /** - * Method removeAllDbRef - * - */ - public void removeAllDbRef() - { - _dbRefList.removeAllElements(); - } //-- void removeAllDbRef() - - /** - * Method removeDbRef - * - * - * - * @param index - * @return DbRef - */ - public org.vamsas.objects.core.DbRef removeDbRef(int index) - { - java.lang.Object obj = _dbRefList.elementAt(index); - _dbRefList.removeElementAt(index); - return (org.vamsas.objects.core.DbRef) obj; - } //-- org.vamsas.objects.core.DbRef removeDbRef(int) - - /** - * Method setDbRef - * - * - * - * @param index - * @param vDbRef - */ - public void setDbRef(int index, org.vamsas.objects.core.DbRef vDbRef) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _dbRefList.size())) { - throw new IndexOutOfBoundsException("setDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]"); - } - _dbRefList.setElementAt(vDbRef, index); - } //-- void setDbRef(int, org.vamsas.objects.core.DbRef) - - /** - * Method setDbRef - * - * - * - * @param dbRefArray - */ - public void setDbRef(org.vamsas.objects.core.DbRef[] dbRefArray) - { - //-- copy array - _dbRefList.removeAllElements(); - for (int i = 0; i < dbRefArray.length; i++) { - _dbRefList.addElement(dbRefArray[i]); - } - } //-- void setDbRef(org.vamsas.objects.core.DbRef) - - /** * Sets the value of field 'end'. * * @param end the value of field 'end'. @@ -451,16 +268,6 @@ implements java.io.Serializable } //-- void setEnd(int) /** - * Sets the value of field 'id'. - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** * Sets the value of field 'name'. * * @param name the value of field 'name'. diff --git a/src/org/vamsas/objects/core/SequenceTypeDescriptor.java b/src/org/vamsas/objects/core/SequenceTypeDescriptor.java index 3740da3..0c4ded0 100644 --- a/src/org/vamsas/objects/core/SequenceTypeDescriptor.java +++ b/src/org/vamsas/objects/core/SequenceTypeDescriptor.java @@ -150,40 +150,6 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); - //-- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); - this.identity = desc; - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceType target = (SequenceType) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceType target = (SequenceType) object; - target.setId( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.String(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); //-- initialize element descriptors //-- _sequence @@ -266,41 +232,6 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); - //-- _dbRefList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.DbRef.class, "_dbRefList", "dbRef", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceType target = (SequenceType) object; - return target.getDbRef(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceType target = (SequenceType) object; - target.addDbRef( (org.vamsas.objects.core.DbRef) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.DbRef(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _dbRefList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); } //-- org.vamsas.objects.core.SequenceTypeDescriptor() diff --git a/src/org/vamsas/objects/core/Tree.java b/src/org/vamsas/objects/core/Tree.java index ddb22b8..a6cbad3 100644 --- a/src/org/vamsas/objects/core/Tree.java +++ b/src/org/vamsas/objects/core/Tree.java @@ -43,9 +43,14 @@ implements java.io.Serializable private java.lang.String _id; /** - * Field _newickFormatList + * Field _title */ - private java.util.Vector _newickFormatList; + private java.lang.String _title; + + /** + * Field _newickList + */ + private java.util.Vector _newickList; /** * Field _provenance @@ -60,7 +65,7 @@ implements java.io.Serializable public Tree() { super(); - _newickFormatList = new Vector(); + _newickList = new Vector(); } //-- org.vamsas.objects.core.Tree() @@ -69,43 +74,43 @@ implements java.io.Serializable //-----------/ /** - * Method addNewickFormat + * Method addNewick * * * - * @param vNewickFormat + * @param vNewick */ - public void addNewickFormat(java.lang.String vNewickFormat) + public void addNewick(org.vamsas.objects.core.Newick vNewick) throws java.lang.IndexOutOfBoundsException { - _newickFormatList.addElement(vNewickFormat); - } //-- void addNewickFormat(java.lang.String) + _newickList.addElement(vNewick); + } //-- void addNewick(org.vamsas.objects.core.Newick) /** - * Method addNewickFormat + * Method addNewick * * * * @param index - * @param vNewickFormat + * @param vNewick */ - public void addNewickFormat(int index, java.lang.String vNewickFormat) + public void addNewick(int index, org.vamsas.objects.core.Newick vNewick) throws java.lang.IndexOutOfBoundsException { - _newickFormatList.insertElementAt(vNewickFormat, index); - } //-- void addNewickFormat(int, java.lang.String) + _newickList.insertElementAt(vNewick, index); + } //-- void addNewick(int, org.vamsas.objects.core.Newick) /** - * Method enumerateNewickFormat + * Method enumerateNewick * * * * @return Enumeration */ - public java.util.Enumeration enumerateNewickFormat() + public java.util.Enumeration enumerateNewick() { - return _newickFormatList.elements(); - } //-- java.util.Enumeration enumerateNewickFormat() + return _newickList.elements(); + } //-- java.util.Enumeration enumerateNewick() /** * Note: hashCode() has not been overriden @@ -131,12 +136,19 @@ implements java.io.Serializable } else if (temp._id != null) return false; - if (this._newickFormatList != null) { - if (temp._newickFormatList == null) return false; - else if (!(this._newickFormatList.equals(temp._newickFormatList))) + if (this._title != null) { + if (temp._title == null) return false; + else if (!(this._title.equals(temp._title))) + return false; + } + else if (temp._title != null) + return false; + if (this._newickList != null) { + if (temp._newickList == null) return false; + else if (!(this._newickList.equals(temp._newickList))) return false; } - else if (temp._newickFormatList != null) + else if (temp._newickList != null) return false; if (this._provenance != null) { if (temp._provenance == null) return false; @@ -162,52 +174,52 @@ implements java.io.Serializable } //-- java.lang.String getId() /** - * Method getNewickFormat + * Method getNewick * * * * @param index - * @return String + * @return Newick */ - public java.lang.String getNewickFormat(int index) + public org.vamsas.objects.core.Newick getNewick(int index) throws java.lang.IndexOutOfBoundsException { //-- check bounds for index - if ((index < 0) || (index > _newickFormatList.size())) { - throw new IndexOutOfBoundsException("getNewickFormat: Index value '"+index+"' not in range [0.."+_newickFormatList.size()+ "]"); + if ((index < 0) || (index > _newickList.size())) { + throw new IndexOutOfBoundsException("getNewick: Index value '"+index+"' not in range [0.."+_newickList.size()+ "]"); } - return (String)_newickFormatList.elementAt(index); - } //-- java.lang.String getNewickFormat(int) + return (org.vamsas.objects.core.Newick) _newickList.elementAt(index); + } //-- org.vamsas.objects.core.Newick getNewick(int) /** - * Method getNewickFormat + * Method getNewick * * * - * @return String + * @return Newick */ - public java.lang.String[] getNewickFormat() + public org.vamsas.objects.core.Newick[] getNewick() { - int size = _newickFormatList.size(); - java.lang.String[] mArray = new java.lang.String[size]; + int size = _newickList.size(); + org.vamsas.objects.core.Newick[] mArray = new org.vamsas.objects.core.Newick[size]; for (int index = 0; index < size; index++) { - mArray[index] = (String)_newickFormatList.elementAt(index); + mArray[index] = (org.vamsas.objects.core.Newick) _newickList.elementAt(index); } return mArray; - } //-- java.lang.String[] getNewickFormat() + } //-- org.vamsas.objects.core.Newick[] getNewick() /** - * Method getNewickFormatCount + * Method getNewickCount * * * * @return int */ - public int getNewickFormatCount() + public int getNewickCount() { - return _newickFormatList.size(); - } //-- int getNewickFormatCount() + return _newickList.size(); + } //-- int getNewickCount() /** * Returns the value of field 'provenance'. @@ -221,6 +233,17 @@ implements java.io.Serializable } //-- org.vamsas.objects.core.Provenance getProvenance() /** + * Returns the value of field 'title'. + * + * @return String + * @return the value of field 'title'. + */ + public java.lang.String getTitle() + { + return this._title; + } //-- java.lang.String getTitle() + + /** * Method isValid * * @@ -267,28 +290,28 @@ implements java.io.Serializable } //-- void marshal(org.xml.sax.ContentHandler) /** - * Method removeAllNewickFormat + * Method removeAllNewick * */ - public void removeAllNewickFormat() + public void removeAllNewick() { - _newickFormatList.removeAllElements(); - } //-- void removeAllNewickFormat() + _newickList.removeAllElements(); + } //-- void removeAllNewick() /** - * Method removeNewickFormat + * Method removeNewick * * * * @param index - * @return String + * @return Newick */ - public java.lang.String removeNewickFormat(int index) + public org.vamsas.objects.core.Newick removeNewick(int index) { - java.lang.Object obj = _newickFormatList.elementAt(index); - _newickFormatList.removeElementAt(index); - return (String)obj; - } //-- java.lang.String removeNewickFormat(int) + java.lang.Object obj = _newickList.elementAt(index); + _newickList.removeElementAt(index); + return (org.vamsas.objects.core.Newick) obj; + } //-- org.vamsas.objects.core.Newick removeNewick(int) /** * Sets the value of field 'id'. @@ -301,38 +324,38 @@ implements java.io.Serializable } //-- void setId(java.lang.String) /** - * Method setNewickFormat + * Method setNewick * * * * @param index - * @param vNewickFormat + * @param vNewick */ - public void setNewickFormat(int index, java.lang.String vNewickFormat) + public void setNewick(int index, org.vamsas.objects.core.Newick vNewick) throws java.lang.IndexOutOfBoundsException { //-- check bounds for index - if ((index < 0) || (index > _newickFormatList.size())) { - throw new IndexOutOfBoundsException("setNewickFormat: Index value '"+index+"' not in range [0.."+_newickFormatList.size()+ "]"); + if ((index < 0) || (index > _newickList.size())) { + throw new IndexOutOfBoundsException("setNewick: Index value '"+index+"' not in range [0.."+_newickList.size()+ "]"); } - _newickFormatList.setElementAt(vNewickFormat, index); - } //-- void setNewickFormat(int, java.lang.String) + _newickList.setElementAt(vNewick, index); + } //-- void setNewick(int, org.vamsas.objects.core.Newick) /** - * Method setNewickFormat + * Method setNewick * * * - * @param newickFormatArray + * @param newickArray */ - public void setNewickFormat(java.lang.String[] newickFormatArray) + public void setNewick(org.vamsas.objects.core.Newick[] newickArray) { //-- copy array - _newickFormatList.removeAllElements(); - for (int i = 0; i < newickFormatArray.length; i++) { - _newickFormatList.addElement(newickFormatArray[i]); + _newickList.removeAllElements(); + for (int i = 0; i < newickArray.length; i++) { + _newickList.addElement(newickArray[i]); } - } //-- void setNewickFormat(java.lang.String) + } //-- void setNewick(org.vamsas.objects.core.Newick) /** * Sets the value of field 'provenance'. @@ -345,6 +368,16 @@ implements java.io.Serializable } //-- void setProvenance(org.vamsas.objects.core.Provenance) /** + * Sets the value of field 'title'. + * + * @param title the value of field 'title'. + */ + public void setTitle(java.lang.String title) + { + this._title = title; + } //-- void setTitle(java.lang.String) + + /** * Method unmarshal * * diff --git a/src/org/vamsas/objects/core/TreeDescriptor.java b/src/org/vamsas/objects/core/TreeDescriptor.java index af3b115..a4c7d8d 100644 --- a/src/org/vamsas/objects/core/TreeDescriptor.java +++ b/src/org/vamsas/objects/core/TreeDescriptor.java @@ -102,22 +102,22 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto desc.setValidator(fieldValidator); //-- initialize element descriptors - //-- _newickFormatList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_newickFormatList", "newickFormat", org.exolab.castor.xml.NodeType.Element); + //-- _title + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Element); desc.setImmutable(true); handler = new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException { Tree target = (Tree) object; - return target.getNewickFormat(); + return target.getTitle(); } public void setValue( java.lang.Object object, java.lang.Object value) throws IllegalStateException, IllegalArgumentException { try { Tree target = (Tree) object; - target.addNewickFormat( (java.lang.String) value); + target.setTitle( (java.lang.String) value); } catch (java.lang.Exception ex) { throw new IllegalStateException(ex.toString()); @@ -129,19 +129,53 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto }; desc.setHandler(handler); desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(true); + desc.setMultivalued(false); addFieldDescriptor(desc); - //-- validation code for: _newickFormatList + //-- validation code for: _title fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); { //-- local scope StringValidator typeValidator = new StringValidator(); typeValidator.setWhiteSpace("preserve"); fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); + //-- _newickList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Newick.class, "_newickList", "newick", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + return target.getNewick(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + target.addNewick( (org.vamsas.objects.core.Newick) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return new org.vamsas.objects.core.Newick(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("http://www.vamsas.org"); + desc.setRequired(true); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _newickList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + } + desc.setValidator(fieldValidator); //-- _provenance desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element); handler = new org.exolab.castor.xml.XMLFieldHandler() { diff --git a/src/org/vamsas/objects/core/User.java b/src/org/vamsas/objects/core/User.java new file mode 100644 index 0000000..037d544 --- /dev/null +++ b/src/org/vamsas/objects/core/User.java @@ -0,0 +1,245 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M2, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.objects.core; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import java.io.IOException; +import java.io.Reader; +import java.io.Serializable; +import java.io.Writer; +import org.exolab.castor.xml.MarshalException; +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; +import org.exolab.castor.xml.ValidationException; +import org.xml.sax.ContentHandler; + +/** + * Class User. + * + * @version $Revision$ $Date$ + */ +public class User extends org.vamsas.client.object +implements java.io.Serializable +{ + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _fullname + */ + private java.lang.String _fullname; + + /** + * Field _organization + */ + private java.lang.String _organization; + + /** + * Field _data + */ + private java.lang.String _data; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public User() + { + super(); + } //-- org.vamsas.objects.core.User() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Note: hashCode() has not been overriden + * + * @param obj + * @return boolean + */ + public boolean equals(java.lang.Object obj) + { + if ( this == obj ) + return true; + + if (super.equals(obj)==false) + return false; + + if (obj instanceof User) { + + User temp = (User)obj; + if (this._fullname != null) { + if (temp._fullname == null) return false; + else if (!(this._fullname.equals(temp._fullname))) + return false; + } + else if (temp._fullname != null) + return false; + if (this._organization != null) { + if (temp._organization == null) return false; + else if (!(this._organization.equals(temp._organization))) + return false; + } + else if (temp._organization != null) + return false; + if (this._data != null) { + if (temp._data == null) return false; + else if (!(this._data.equals(temp._data))) + return false; + } + else if (temp._data != null) + return false; + return true; + } + return false; + } //-- boolean equals(java.lang.Object) + + /** + * Returns the value of field 'data'. + * + * @return String + * @return the value of field 'data'. + */ + public java.lang.String getData() + { + return this._data; + } //-- java.lang.String getData() + + /** + * Returns the value of field 'fullname'. + * + * @return String + * @return the value of field 'fullname'. + */ + public java.lang.String getFullname() + { + return this._fullname; + } //-- java.lang.String getFullname() + + /** + * Returns the value of field 'organization'. + * + * @return String + * @return the value of field 'organization'. + */ + public java.lang.String getOrganization() + { + return this._organization; + } //-- java.lang.String getOrganization() + + /** + * Method isValid + * + * + * + * @return boolean + */ + public boolean isValid() + { + try { + validate(); + } + catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } //-- boolean isValid() + + /** + * Method marshal + * + * + * + * @param out + */ + public void marshal(java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + + Marshaller.marshal(this, out); + } //-- void marshal(java.io.Writer) + + /** + * Method marshal + * + * + * + * @param handler + */ + public void marshal(org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + + Marshaller.marshal(this, handler); + } //-- void marshal(org.xml.sax.ContentHandler) + + /** + * Sets the value of field 'data'. + * + * @param data the value of field 'data'. + */ + public void setData(java.lang.String data) + { + this._data = data; + } //-- void setData(java.lang.String) + + /** + * Sets the value of field 'fullname'. + * + * @param fullname the value of field 'fullname'. + */ + public void setFullname(java.lang.String fullname) + { + this._fullname = fullname; + } //-- void setFullname(java.lang.String) + + /** + * Sets the value of field 'organization'. + * + * @param organization the value of field 'organization'. + */ + public void setOrganization(java.lang.String organization) + { + this._organization = organization; + } //-- void setOrganization(java.lang.String) + + /** + * Method unmarshal + * + * + * + * @param reader + * @return User + */ + public static org.vamsas.objects.core.User unmarshal(java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + return (org.vamsas.objects.core.User) Unmarshaller.unmarshal(org.vamsas.objects.core.User.class, reader); + } //-- org.vamsas.objects.core.User unmarshal(java.io.Reader) + + /** + * Method validate + * + */ + public void validate() + throws org.exolab.castor.xml.ValidationException + { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } //-- void validate() + +} diff --git a/src/org/vamsas/objects/core/UserDescriptor.java b/src/org/vamsas/objects/core/UserDescriptor.java new file mode 100644 index 0000000..c38181a --- /dev/null +++ b/src/org/vamsas/objects/core/UserDescriptor.java @@ -0,0 +1,282 @@ +/* + * This class was automatically generated with + * Castor 0.9.9M2, using an XML + * Schema. + * $Id$ + */ + +package org.vamsas.objects.core; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.mapping.AccessMode; +import org.exolab.castor.xml.TypeValidator; +import org.exolab.castor.xml.XMLFieldDescriptor; +import org.exolab.castor.xml.validators.*; + +/** + * Class UserDescriptor. + * + * @version $Revision$ $Date$ + */ +public class UserDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field nsPrefix + */ + private java.lang.String nsPrefix; + + /** + * Field nsURI + */ + private java.lang.String nsURI; + + /** + * Field xmlName + */ + private java.lang.String xmlName; + + /** + * Field identity + */ + private org.exolab.castor.xml.XMLFieldDescriptor identity; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public UserDescriptor() + { + super(); + nsURI = "http://www.vamsas.org"; + xmlName = "User"; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _fullname + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fullname", "fullname", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + User target = (User) object; + return target.getFullname(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + User target = (User) object; + target.setFullname( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _fullname + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + StringValidator typeValidator = new StringValidator(); + typeValidator.setWhiteSpace("preserve"); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _organization + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_organization", "organization", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + User target = (User) object; + return target.getOrganization(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + User target = (User) object; + target.setOrganization( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _organization + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + StringValidator typeValidator = new StringValidator(); + typeValidator.setWhiteSpace("preserve"); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _data + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_data", "data", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + User target = (User) object; + return target.getData(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + User target = (User) object; + target.setData( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _data + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + StringValidator typeValidator = new StringValidator(); + typeValidator.setWhiteSpace("preserve"); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + } //-- org.vamsas.objects.core.UserDescriptor() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode + * + * + * + * @return AccessMode + */ + public org.exolab.castor.mapping.AccessMode getAccessMode() + { + return null; + } //-- org.exolab.castor.mapping.AccessMode getAccessMode() + + /** + * Method getExtends + * + * + * + * @return ClassDescriptor + */ + public org.exolab.castor.mapping.ClassDescriptor getExtends() + { + return null; + } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() + + /** + * Method getIdentity + * + * + * + * @return FieldDescriptor + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity() + { + return identity; + } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() + + /** + * Method getJavaClass + * + * + * + * @return Class + */ + public java.lang.Class getJavaClass() + { + return org.vamsas.objects.core.User.class; + } //-- java.lang.Class getJavaClass() + + /** + * Method getNameSpacePrefix + * + * + * + * @return String + */ + public java.lang.String getNameSpacePrefix() + { + return nsPrefix; + } //-- java.lang.String getNameSpacePrefix() + + /** + * Method getNameSpaceURI + * + * + * + * @return String + */ + public java.lang.String getNameSpaceURI() + { + return nsURI; + } //-- java.lang.String getNameSpaceURI() + + /** + * Method getValidator + * + * + * + * @return TypeValidator + */ + public org.exolab.castor.xml.TypeValidator getValidator() + { + return this; + } //-- org.exolab.castor.xml.TypeValidator getValidator() + + /** + * Method getXMLName + * + * + * + * @return String + */ + public java.lang.String getXMLName() + { + return xmlName; + } //-- java.lang.String getXMLName() + +} -- 1.7.10.2