X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FSequence.java;h=531ca6659ac177c7e4e6d430927aae0001296c2e;hb=9885d5229311c88fc0ac67da9afb08f01269858b;hp=993ad23609b227ec32ae07d817e49cd2abed549c;hpb=48df59aa393e03aa7269b2df662ac1b8d58cbb25;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 993ad23..531ca66 --- a/src/jalview/schemabinding/version2/Sequence.java +++ b/src/jalview/schemabinding/version2/Sequence.java @@ -1,276 +1,328 @@ -/* - * 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 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. - * - * @version $Revision$ $Date$ - */ -public class Sequence extends jalview.schemabinding.version2.SequenceType -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _DBRefList - */ - private java.util.Vector _DBRefList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Sequence() { - super(); - _DBRefList = new Vector(); - } //-- jalview.schemabinding.version2.Sequence() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addDBRef - * - * - * - * @param vDBRef - */ - public void addDBRef(jalview.schemabinding.version2.DBRef vDBRef) - throws java.lang.IndexOutOfBoundsException - { - _DBRefList.addElement(vDBRef); - } //-- void addDBRef(jalview.schemabinding.version2.DBRef) - - /** - * Method addDBRef - * - * - * - * @param index - * @param vDBRef - */ - public void addDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef) - throws java.lang.IndexOutOfBoundsException - { - _DBRefList.insertElementAt(vDBRef, index); - } //-- void addDBRef(int, jalview.schemabinding.version2.DBRef) - - /** - * Method enumerateDBRef - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateDBRef() - { - return _DBRefList.elements(); - } //-- java.util.Enumeration enumerateDBRef() - - /** - * Method getDBRef - * - * - * - * @param index - * @return DBRef - */ - public jalview.schemabinding.version2.DBRef getDBRef(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _DBRefList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.schemabinding.version2.DBRef) _DBRefList.elementAt(index); - } //-- jalview.schemabinding.version2.DBRef getDBRef(int) - - /** - * Method getDBRef - * - * - * - * @return DBRef - */ - public jalview.schemabinding.version2.DBRef[] getDBRef() - { - int size = _DBRefList.size(); - jalview.schemabinding.version2.DBRef[] mArray = new jalview.schemabinding.version2.DBRef[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.schemabinding.version2.DBRef) _DBRefList.elementAt(index); - } - return mArray; - } //-- jalview.schemabinding.version2.DBRef[] getDBRef() - - /** - * Method getDBRefCount - * - * - * - * @return int - */ - public int getDBRefCount() - { - return _DBRefList.size(); - } //-- int getDBRefCount() - - /** - * 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 removeAllDBRef - * - */ - public void removeAllDBRef() - { - _DBRefList.removeAllElements(); - } //-- void removeAllDBRef() - - /** - * Method removeDBRef - * - * - * - * @param index - * @return DBRef - */ - public jalview.schemabinding.version2.DBRef removeDBRef(int index) - { - java.lang.Object obj = _DBRefList.elementAt(index); - _DBRefList.removeElementAt(index); - return (jalview.schemabinding.version2.DBRef) obj; - } //-- jalview.schemabinding.version2.DBRef removeDBRef(int) - - /** - * Method setDBRef - * - * - * - * @param index - * @param vDBRef - */ - public void setDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _DBRefList.size())) { - throw new IndexOutOfBoundsException(); - } - _DBRefList.setElementAt(vDBRef, index); - } //-- void setDBRef(int, jalview.schemabinding.version2.DBRef) - - /** - * Method setDBRef - * - * - * - * @param DBRefArray - */ - public void setDBRef(jalview.schemabinding.version2.DBRef[] DBRefArray) - { - //-- copy array - _DBRefList.removeAllElements(); - for (int i = 0; i < DBRefArray.length; i++) { - _DBRefList.addElement(DBRefArray[i]); - } - } //-- void setDBRef(jalview.schemabinding.version2.DBRef) - - /** - * 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); + } + +}