X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Fcore%2FDataSetAnnotations.java;h=43bc9f98f7db6f941369a7a2bab95a3b2d78d028;hb=844ccad5a3fcbedec17b2af66d460f31abc7cff1;hp=0507d371c3bd35aef4e81530f18d99886a0ca8a3;hpb=667c5f732b74c1a0e0ac50cd26d93634811663ee;p=vamsas.git
diff --git a/src/uk/ac/vamsas/objects/core/DataSetAnnotations.java b/src/uk/ac/vamsas/objects/core/DataSetAnnotations.java
index 0507d37..43bc9f9 100644
--- a/src/uk/ac/vamsas/objects/core/DataSetAnnotations.java
+++ b/src/uk/ac/vamsas/objects/core/DataSetAnnotations.java
@@ -1,217 +1,448 @@
/*
- * This class was automatically generated with
- * Castor 0.9.9M2, using an XML
- * Schema.
- * $Id$
+ * This file is part of the Vamsas Client version 0.1.
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite,
+ * Andrew Waterhouse and Dominik Lindner.
+ *
+ * Earlier versions have also been incorporated into Jalview version 2.4
+ * since 2008, and TOPALi version 2 since 2007.
+ *
+ * The Vamsas Client is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * The Vamsas Client is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the Vamsas Client. If not, see .
*/
-
package uk.ac.vamsas.objects.core;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- 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 DataSetAnnotations.
*
- * @version $Revision$ $Date$
+ * @version $Revision$ $Date: 2007-06-28 14:51:44 +0100 (Thu, 28 Jun 2007)
+ * $
*/
-public class DataSetAnnotations extends uk.ac.vamsas.objects.core.RangeAnnotation
-implements java.io.Serializable
-{
+public class DataSetAnnotations extends
+ uk.ac.vamsas.objects.core.RangeAnnotation implements java.io.Serializable {
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
+ /**
+ * annotation is associated with a particular dataset sequence
+ */
+ private java.util.Vector _seqRef;
- /**
- * annotation is associated with a
- * particular dataset sequence
- */
- private java.lang.Object _seqRef;
+ /**
+ * Field _provenance.
+ */
+ private uk.ac.vamsas.objects.core.Provenance _provenance;
- /**
- * Field _provenance
- */
- private uk.ac.vamsas.objects.core.Provenance _provenance;
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+ public DataSetAnnotations() {
+ super();
+ this._seqRef = new java.util.Vector();
+ }
- //----------------/
- //- Constructors -/
- //----------------/
+ // -----------/
+ // - Methods -/
+ // -----------/
- public DataSetAnnotations()
- {
- super();
- } //-- uk.ac.vamsas.objects.core.DataSetAnnotations()
+ /**
+ *
+ *
+ * @param vSeqRef
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSeqRef(final java.lang.Object vSeqRef)
+ throws java.lang.IndexOutOfBoundsException {
+ this._seqRef.addElement(vSeqRef);
+ }
+ /**
+ *
+ *
+ * @param index
+ * @param vSeqRef
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSeqRef(final int index, final java.lang.Object vSeqRef)
+ throws java.lang.IndexOutOfBoundsException {
+ this._seqRef.add(index, vSeqRef);
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ /**
+ * Method enumerateSeqRef.
+ *
+ * @return an Enumeration over all java.lang.Object elements
+ */
+ public java.util.Enumeration enumerateSeqRef() {
+ return this._seqRef.elements();
+ }
- /**
- * 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 DataSetAnnotations) {
-
- DataSetAnnotations temp = (DataSetAnnotations)obj;
- if (this._seqRef != null) {
- if (temp._seqRef == null) return false;
- else if (!(this._seqRef.equals(temp._seqRef)))
- return false;
+ /**
+ * Overrides the java.lang.Object.equals method.
+ *
+ * @param obj
+ * @return true if the objects are equal.
+ */
+ public boolean equals(final java.lang.Object obj) {
+ if (this == obj)
+ return true;
+
+ if (super.equals(obj) == false)
+ return false;
+
+ if (obj instanceof DataSetAnnotations) {
+
+ DataSetAnnotations temp = (DataSetAnnotations) obj;
+ boolean thcycle;
+ boolean tmcycle;
+ if (this._seqRef != null) {
+ if (temp._seqRef == null)
+ return false;
+ if (this._seqRef != temp._seqRef) {
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._seqRef);
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._seqRef);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._seqRef);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqRef);
}
- else if (temp._seqRef != null)
- return false;
- if (this._provenance != null) {
- if (temp._provenance == null) return false;
- else if (!(this._provenance.equals(temp._provenance)))
- return false;
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._seqRef.equals(temp._seqRef)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._seqRef);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqRef);
+ return false;
}
- else if (temp._provenance != null)
- return false;
- return true;
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._seqRef);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqRef);
+ }
}
+ } else if (temp._seqRef != null)
return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Returns the value of field 'provenance'.
- *
- * @return Provenance
- * @return the value of field 'provenance'.
- */
- public uk.ac.vamsas.objects.core.Provenance getProvenance()
- {
- return this._provenance;
- } //-- uk.ac.vamsas.objects.core.Provenance getProvenance()
-
- /**
- * Returns the value of field 'seqRef'. The field 'seqRef' has
- * the following description: annotation is associated with a
- * particular dataset sequence
- *
- * @return Object
- * @return the value of field 'seqRef'.
- */
- public java.lang.Object getSeqRef()
- {
- return this._seqRef;
- } //-- java.lang.Object getSeqRef()
-
- /**
- * Method isValid
- *
- *
- *
- * @return boolean
- */
- public boolean isValid()
- {
- try {
- validate();
- }
- catch (org.exolab.castor.xml.ValidationException vex) {
+ if (this._provenance != null) {
+ if (temp._provenance == null)
+ return false;
+ if (this._provenance != temp._provenance) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._provenance);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._provenance);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
+ }
+ ;
return false;
+ }
+ if (!thcycle) {
+ if (!this._provenance.equals(temp._provenance)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
+ }
}
- 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 'provenance'.
- *
- * @param provenance the value of field 'provenance'.
- */
- public void setProvenance(uk.ac.vamsas.objects.core.Provenance provenance)
- {
- this._provenance = provenance;
- } //-- void setProvenance(uk.ac.vamsas.objects.core.Provenance)
-
- /**
- * Sets the value of field 'seqRef'. The field 'seqRef' has the
- * following description: annotation is associated with a
- * particular dataset sequence
- *
- * @param seqRef the value of field 'seqRef'.
- */
- public void setSeqRef(java.lang.Object seqRef)
- {
- this._seqRef = seqRef;
- } //-- void setSeqRef(java.lang.Object)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return RangeType
- */
- public static uk.ac.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (uk.ac.vamsas.objects.core.DataSetAnnotations) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.DataSetAnnotations.class, reader);
- } //-- uk.ac.vamsas.objects.core.RangeType unmarshal(java.io.Reader)
-
- /**
- * Method validate
- *
+ } else if (temp._provenance != null)
+ return false;
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Returns the value of field 'provenance'.
+ *
+ * @return the value of field 'Provenance'.
+ */
+ public uk.ac.vamsas.objects.core.Provenance getProvenance() {
+ return this._provenance;
+ }
+
+ /**
+ * Method getSeqRef.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the java.lang.Object at the given index
+ */
+ public java.lang.Object getSeqRef(final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._seqRef.size()) {
+ throw new IndexOutOfBoundsException("getSeqRef: Index value '" + index
+ + "' not in range [0.." + (this._seqRef.size() - 1) + "]");
+ }
+
+ return _seqRef.get(index);
+ }
+
+ /**
+ * Method getSeqRef.Returns the contents of the collection in an Array.
+ *
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * know that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public java.lang.Object[] getSeqRef() {
+ java.lang.Object[] array = new java.lang.Object[0];
+ return (java.lang.Object[]) this._seqRef.toArray(array);
+ }
+
+ /**
+ * Method getSeqRefAsReference.Returns a reference to '_seqRef'. No type
+ * checking is performed on any modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getSeqRefAsReference() {
+ return this._seqRef;
+ }
+
+ /**
+ * Method getSeqRefCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSeqRefCount() {
+ return this._seqRef.size();
+ }
+
+ /**
+ * Overrides the java.lang.Object.hashCode method.
+ *
+ * The following steps came from Effective Java Programming Language
+ * Guide by Joshua Bloch, Chapter 3
+ *
+ * @return a hash code value for the object.
+ */
+ public int hashCode() {
+ int result = super.hashCode();
+
+ long tmp;
+ if (_seqRef != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_seqRef)) {
+ result = 37 * result + _seqRef.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_seqRef);
+ }
+ if (_provenance != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {
+ result = 37 * result + _provenance.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_provenance);
+ }
+
+ return result;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid() {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
*/
- 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()
+ public void removeAllSeqRef() {
+ this._seqRef.clear();
+ }
+
+ /**
+ * Method removeSeqRef.
+ *
+ * @param vSeqRef
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSeqRef(final java.lang.Object vSeqRef) {
+ boolean removed = _seqRef.remove(vSeqRef);
+ return removed;
+ }
+
+ /**
+ * Method removeSeqRefAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public java.lang.Object removeSeqRefAt(final int index) {
+ java.lang.Object obj = this._seqRef.remove(index);
+ return obj;
+ }
+
+ /**
+ * Sets the value of field 'provenance'.
+ *
+ * @param provenance
+ * the value of field 'provenance'.
+ */
+ public void setProvenance(
+ final uk.ac.vamsas.objects.core.Provenance provenance) {
+ this._provenance = provenance;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSeqRef
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setSeqRef(final int index, final java.lang.Object vSeqRef)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._seqRef.size()) {
+ throw new IndexOutOfBoundsException("setSeqRef: Index value '" + index
+ + "' not in range [0.." + (this._seqRef.size() - 1) + "]");
+ }
+
+ this._seqRef.set(index, vSeqRef);
+ }
+
+ /**
+ *
+ *
+ * @param vSeqRefArray
+ */
+ public void setSeqRef(final java.lang.Object[] vSeqRefArray) {
+ // -- copy array
+ _seqRef.clear();
+
+ for (int i = 0; i < vSeqRefArray.length; i++) {
+ this._seqRef.add(vSeqRefArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_seqRef' by copying the given Vector. All elements will
+ * be checked for type safety.
+ *
+ * @param vSeqRefList
+ * the Vector to copy.
+ */
+ public void setSeqRef(final java.util.Vector vSeqRefList) {
+ // copy vector
+ this._seqRef.clear();
+
+ this._seqRef.addAll(vSeqRefList);
+ }
+
+ /**
+ * Sets the value of '_seqRef' by setting it to the given Vector. No type
+ * checking is performed.
+ *
+ * @deprecated
+ *
+ * @param seqRefVector
+ * the Vector to set.
+ */
+ public void setSeqRefAsReference(final java.util.Vector seqRefVector) {
+ this._seqRef = seqRefVector;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled uk.ac.vamsas.objects.core.RangeType
+ */
+ public static uk.ac.vamsas.objects.core.RangeType unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ return (uk.ac.vamsas.objects.core.RangeType) Unmarshaller.unmarshal(
+ uk.ac.vamsas.objects.core.DataSetAnnotations.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}