X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FSequence.java;h=14137d895bedfa0a66c6e4facd3cc931f52021bc;hb=a23cc416cd520ac6dec6052591575b264f5d25bc;hp=7a1533276062ff12ab51c19652ebaecdc2494e5a;hpb=65df62f4b048a1615d32ea2c3576082ad2b63af8;p=jalview.git diff --git a/src/jalview/schemabinding/version2/Sequence.java b/src/jalview/schemabinding/version2/Sequence.java old mode 100755 new mode 100644 index 7a15332..14137d8 --- a/src/jalview/schemabinding/version2/Sequence.java +++ b/src/jalview/schemabinding/version2/Sequence.java @@ -1,118 +1,311 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - - //---------------------------------/ - //- 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 Sequence. - * - * @version $Revision$ $Date$ - */ -public class Sequence extends SequenceType -implements java.io.Serializable -{ - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Sequence() { - super(); - } //-- jalview.schemabinding.version2.Sequence() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * 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) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Sequence) Unmarshaller.unmarshal(jalview.schemabinding.version2.Sequence.class, reader); - } //-- java.lang.Object 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() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class Sequence. + * + * @version $Revision$ $Date$ + */ +public class Sequence extends jalview.schemabinding.version2.SequenceType +implements java.io.Serializable +{ + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * dataset sequence id for this sequence. Will be created as + * union of sequences. + * + */ + private java.lang.String _dsseqid; + + /** + * Field _DBRefList. + */ + private java.util.Vector _DBRefList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Sequence() { + super(); + this._DBRefList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vDBRef + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addDBRef( + final jalview.schemabinding.version2.DBRef vDBRef) + throws java.lang.IndexOutOfBoundsException { + this._DBRefList.addElement(vDBRef); + } + + /** + * + * + * @param index + * @param vDBRef + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addDBRef( + final int index, + final jalview.schemabinding.version2.DBRef vDBRef) + throws java.lang.IndexOutOfBoundsException { + this._DBRefList.add(index, vDBRef); + } + + /** + * Method enumerateDBRef. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.DBRef elements + */ + public java.util.Enumeration enumerateDBRef( + ) { + return this._DBRefList.elements(); + } + + /** + * Method getDBRef. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.DBRef at the given index + */ + public jalview.schemabinding.version2.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 (jalview.schemabinding.version2.DBRef) _DBRefList.get(index); + } + + /** + * 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 this collection as an Array + */ + public jalview.schemabinding.version2.DBRef[] getDBRef( + ) { + jalview.schemabinding.version2.DBRef[] array = new jalview.schemabinding.version2.DBRef[0]; + return (jalview.schemabinding.version2.DBRef[]) this._DBRefList.toArray(array); + } + + /** + * Method getDBRefCount. + * + * @return the size of this collection + */ + public int getDBRefCount( + ) { + return this._DBRefList.size(); + } + + /** + * Returns the value of field 'dsseqid'. The field 'dsseqid' + * has the following description: dataset sequence id for this + * sequence. Will be created as union of sequences. + * + * + * @return the value of field 'Dsseqid'. + */ + public java.lang.String getDsseqid( + ) { + return this._dsseqid; + } + + /** + * 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 removeAllDBRef( + ) { + this._DBRefList.clear(); + } + + /** + * Method removeDBRef. + * + * @param vDBRef + * @return true if the object was removed from the collection. + */ + public boolean removeDBRef( + final jalview.schemabinding.version2.DBRef vDBRef) { + boolean removed = _DBRefList.remove(vDBRef); + return removed; + } + + /** + * Method removeDBRefAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.DBRef removeDBRefAt( + final int index) { + java.lang.Object obj = this._DBRefList.remove(index); + return (jalview.schemabinding.version2.DBRef) obj; + } + + /** + * + * + * @param index + * @param vDBRef + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setDBRef( + final int index, + final jalview.schemabinding.version2.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) + "]"); + } + + this._DBRefList.set(index, vDBRef); + } + + /** + * + * + * @param vDBRefArray + */ + public void setDBRef( + final jalview.schemabinding.version2.DBRef[] vDBRefArray) { + //-- copy array + _DBRefList.clear(); + + for (int i = 0; i < vDBRefArray.length; i++) { + this._DBRefList.add(vDBRefArray[i]); + } + } + + /** + * Sets the value of field 'dsseqid'. The field 'dsseqid' has + * the following description: dataset sequence id for this + * sequence. Will be created as union of sequences. + * + * + * @param dsseqid the value of field 'dsseqid'. + */ + public void setDsseqid( + final java.lang.String dsseqid) { + this._dsseqid = dsseqid; + } + + /** + * 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 + * jalview.schemabinding.version2.SequenceType + */ + public static jalview.schemabinding.version2.SequenceType unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.SequenceType) Unmarshaller.unmarshal(jalview.schemabinding.version2.Sequence.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); + } + +}