X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Fcore%2FSequence.java;h=d4ff049c2e7203b944f1a98fd626206a02f929af;hb=81fe0e97b0e8b642fed42495cd61ea1c8526e6b5;hp=1a235122917fd6a40f728f2c1dc3cea8ace6f437;hpb=667c5f732b74c1a0e0ac50cd26d93634811663ee;p=vamsas.git diff --git a/src/uk/ac/vamsas/objects/core/Sequence.java b/src/uk/ac/vamsas/objects/core/Sequence.java index 1a23512..d4ff049 100644 --- a/src/uk/ac/vamsas/objects/core/Sequence.java +++ b/src/uk/ac/vamsas/objects/core/Sequence.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.9M2, using an XML + * Castor 1.1, using an XML * Schema. * $Id$ */ @@ -11,17 +11,8 @@ package uk.ac.vamsas.objects.core; //- Imported classes and packages -/ //---------------------------------/ -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; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; /** * Class Sequence. @@ -61,11 +52,10 @@ implements java.io.Serializable //- Constructors -/ //----------------/ - public Sequence() - { + public Sequence() { super(); - _dbRefList = new Vector(); - } //-- uk.ac.vamsas.objects.core.Sequence() + this._dbRefList = new java.util.Vector(); + } //-----------/ @@ -73,52 +63,52 @@ implements java.io.Serializable //-----------/ /** - * Method addDbRef - * * * * @param vDbRef + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection */ - public void addDbRef(uk.ac.vamsas.objects.core.DbRef vDbRef) - throws java.lang.IndexOutOfBoundsException - { - _dbRefList.addElement(vDbRef); - } //-- void addDbRef(uk.ac.vamsas.objects.core.DbRef) + public void addDbRef( + final uk.ac.vamsas.objects.core.DbRef vDbRef) + throws java.lang.IndexOutOfBoundsException { + this._dbRefList.addElement(vDbRef); + } /** - * Method addDbRef - * * * * @param index * @param vDbRef + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection */ - public void addDbRef(int index, uk.ac.vamsas.objects.core.DbRef vDbRef) - throws java.lang.IndexOutOfBoundsException - { - _dbRefList.insertElementAt(vDbRef, index); - } //-- void addDbRef(int, uk.ac.vamsas.objects.core.DbRef) + public void addDbRef( + final int index, + final uk.ac.vamsas.objects.core.DbRef vDbRef) + throws java.lang.IndexOutOfBoundsException { + this._dbRefList.add(index, vDbRef); + } /** - * Method enumerateDbRef - * - * + * Method enumerateDbRef. * - * @return Enumeration + * @return an Enumeration over all + * uk.ac.vamsas.objects.core.DbRef elements */ - public java.util.Enumeration enumerateDbRef() - { - return _dbRefList.elements(); - } //-- java.util.Enumeration enumerateDbRef() + public java.util.Enumeration enumerateDbRef( + ) { + return this._dbRefList.elements(); + } /** - * Note: hashCode() has not been overriden + * Overrides the java.lang.Object.equals method. * * @param obj - * @return boolean + * @return true if the objects are equal. */ - public boolean equals(java.lang.Object obj) - { + public boolean equals( + final java.lang.Object obj) { if ( this == obj ) return true; @@ -152,55 +142,64 @@ implements java.io.Serializable return true; } return false; - } //-- boolean equals(java.lang.Object) + } /** - * Method getDbRef - * - * + * Method getDbRef. * * @param index - * @return DbRef + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the uk.ac.vamsas.objects.core.DbRef at + * the given index */ - public uk.ac.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()+ "]"); + public uk.ac.vamsas.objects.core.DbRef getDbRef( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._dbRefList.size()) { + throw new IndexOutOfBoundsException("getDbRef: Index value '" + index + "' not in range [0.." + (this._dbRefList.size() - 1) + "]"); } - return (uk.ac.vamsas.objects.core.DbRef) _dbRefList.elementAt(index); - } //-- uk.ac.vamsas.objects.core.DbRef getDbRef(int) + return (uk.ac.vamsas.objects.core.DbRef) _dbRefList.get(index); + } /** - * Method getDbRef - * + * Method getDbRef.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 DbRef + * @return this collection as an Array */ - public uk.ac.vamsas.objects.core.DbRef[] getDbRef() - { - int size = _dbRefList.size(); - uk.ac.vamsas.objects.core.DbRef[] mArray = new uk.ac.vamsas.objects.core.DbRef[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (uk.ac.vamsas.objects.core.DbRef) _dbRefList.elementAt(index); - } - return mArray; - } //-- uk.ac.vamsas.objects.core.DbRef[] getDbRef() + public uk.ac.vamsas.objects.core.DbRef[] getDbRef( + ) { + uk.ac.vamsas.objects.core.DbRef[] array = new uk.ac.vamsas.objects.core.DbRef[0]; + return (uk.ac.vamsas.objects.core.DbRef[]) this._dbRefList.toArray(array); + } /** - * Method getDbRefCount - * + * Method getDbRefAsReference.Returns a reference to + * '_dbRefList'. No type checking is performed on any + * modifications to the Vector. * + * @return a reference to the Vector backing this class + */ + public java.util.Vector getDbRefAsReference( + ) { + return this._dbRefList; + } + + /** + * Method getDbRefCount. * - * @return int + * @return the size of this collection */ - public int getDbRefCount() - { - return _dbRefList.size(); - } //-- int getDbRefCount() + public int getDbRefCount( + ) { + return this._dbRefList.size(); + } /** * Returns the value of field 'dictionary'. The field @@ -208,13 +207,12 @@ implements java.io.Serializable * sequence * * - * @return String - * @return the value of field 'dictionary'. + * @return the value of field 'Dictionary'. */ - public java.lang.String getDictionary() - { + public java.lang.String getDictionary( + ) { return this._dictionary; - } //-- java.lang.String getDictionary() + } /** * Returns the value of field 'id'. The field 'id' has the @@ -222,117 +220,177 @@ implements java.io.Serializable * referencing * * - * @return String - * @return the value of field 'id'. + * @return the value of field 'Id'. */ - public java.lang.String getId() - { + public java.lang.String getId( + ) { return this._id; - } //-- java.lang.String getId() + } /** - * Method isValid - * + * 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 (_id != null) { + result = 37 * result + _id.hashCode(); + } + if (_dictionary != null) { + result = 37 * result + _dictionary.hashCode(); + } + if (_dbRefList != null) { + result = 37 * result + _dbRefList.hashCode(); + } + + return result; + } + + /** + * Method isValid. * - * @return boolean + * @return true if this object is valid according to the schema */ - public boolean isValid() - { + public boolean isValid( + ) { try { validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { + } catch (org.exolab.castor.xml.ValidationException vex) { return false; } return true; - } //-- boolean isValid() + } /** - * Method marshal - * * * * @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(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - + public void marshal( + final 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 + * @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(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - + 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); - } //-- void marshal(org.xml.sax.ContentHandler) + } /** - * Method removeAllDbRef - * */ - public void removeAllDbRef() - { - _dbRefList.removeAllElements(); - } //-- void removeAllDbRef() + public void removeAllDbRef( + ) { + this._dbRefList.clear(); + } /** - * Method removeDbRef - * + * Method removeDbRef. * + * @param vDbRef + * @return true if the object was removed from the collection. + */ + public boolean removeDbRef( + final uk.ac.vamsas.objects.core.DbRef vDbRef) { + boolean removed = _dbRefList.remove(vDbRef); + return removed; + } + + /** + * Method removeDbRefAt. * * @param index - * @return DbRef + * @return the element removed from the collection */ - public uk.ac.vamsas.objects.core.DbRef removeDbRef(int index) - { - java.lang.Object obj = _dbRefList.elementAt(index); - _dbRefList.removeElementAt(index); + public uk.ac.vamsas.objects.core.DbRef removeDbRefAt( + final int index) { + java.lang.Object obj = this._dbRefList.remove(index); return (uk.ac.vamsas.objects.core.DbRef) obj; - } //-- uk.ac.vamsas.objects.core.DbRef removeDbRef(int) + } /** - * Method setDbRef - * * * * @param index * @param vDbRef + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection */ - public void setDbRef(int index, uk.ac.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()+ "]"); + public void setDbRef( + final int index, + final uk.ac.vamsas.objects.core.DbRef vDbRef) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._dbRefList.size()) { + throw new IndexOutOfBoundsException("setDbRef: Index value '" + index + "' not in range [0.." + (this._dbRefList.size() - 1) + "]"); } - _dbRefList.setElementAt(vDbRef, index); - } //-- void setDbRef(int, uk.ac.vamsas.objects.core.DbRef) + + this._dbRefList.set(index, vDbRef); + } /** - * Method setDbRef - * * * - * @param dbRefArray + * @param vDbRefArray */ - public void setDbRef(uk.ac.vamsas.objects.core.DbRef[] dbRefArray) - { + public void setDbRef( + final uk.ac.vamsas.objects.core.DbRef[] vDbRefArray) { //-- copy array - _dbRefList.removeAllElements(); - for (int i = 0; i < dbRefArray.length; i++) { - _dbRefList.addElement(dbRefArray[i]); + _dbRefList.clear(); + + for (int i = 0; i < vDbRefArray.length; i++) { + this._dbRefList.add(vDbRefArray[i]); } - } //-- void setDbRef(uk.ac.vamsas.objects.core.DbRef) + } + + /** + * Sets the value of '_dbRefList' by copying the given Vector. + * All elements will be checked for type safety. + * + * @param vDbRefList the Vector to copy. + */ + public void setDbRef( + final java.util.Vector vDbRefList) { + // copy vector + this._dbRefList.clear(); + + this._dbRefList.addAll(vDbRefList); + } + + /** + * Sets the value of '_dbRefList' by setting it to the given + * Vector. No type checking is performed. + * @deprecated + * + * @param dbRefVector the Vector to set. + */ + public void setDbRefAsReference( + final java.util.Vector dbRefVector) { + this._dbRefList = dbRefVector; + } /** * Sets the value of field 'dictionary'. The field 'dictionary' @@ -341,10 +399,10 @@ implements java.io.Serializable * * @param dictionary the value of field 'dictionary'. */ - public void setDictionary(java.lang.String dictionary) - { + public void setDictionary( + final java.lang.String dictionary) { this._dictionary = dictionary; - } //-- void setDictionary(java.lang.String) + } /** * Sets the value of field 'id'. The field 'id' has the @@ -354,34 +412,38 @@ implements java.io.Serializable * * @param id the value of field 'id'. */ - public void setId(java.lang.String id) - { + public void setId( + final java.lang.String id) { this._id = id; - } //-- void setId(java.lang.String) + } /** - * Method unmarshal - * - * + * Method unmarshal. * * @param reader - * @return SequenceType + * @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.SequenceTyp */ - public static uk.ac.vamsas.objects.core.SequenceType unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (uk.ac.vamsas.objects.core.Sequence) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Sequence.class, reader); - } //-- uk.ac.vamsas.objects.core.SequenceType unmarshal(java.io.Reader) + public static uk.ac.vamsas.objects.core.SequenceType unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (uk.ac.vamsas.objects.core.SequenceType) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Sequence.class, reader); + } /** - * Method validate * + * + * @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 - { + 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() + } }