X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FSequence.java;h=531ca6659ac177c7e4e6d430927aae0001296c2e;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=14137d895bedfa0a66c6e4facd3cc931f52021bc;hpb=619cc880371f3228e6a1fb33c6bfb6e7a7e2622c;p=jalview.git diff --git a/src/jalview/schemabinding/version2/Sequence.java b/src/jalview/schemabinding/version2/Sequence.java index 14137d8..531ca66 100644 --- a/src/jalview/schemabinding/version2/Sequence.java +++ b/src/jalview/schemabinding/version2/Sequence.java @@ -7,8 +7,8 @@ package jalview.schemabinding.version2; - //---------------------------------/ - //- Imported classes and packages -/ +//---------------------------------/ +//- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -19,293 +19,310 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class Sequence extends jalview.schemabinding.version2.SequenceType -implements java.io.Serializable +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(); + // --------------------------/ + // - 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) + "]"); } - /** - * 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); + 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; } - - /** - * 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 + 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 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); + 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) + "]"); } - /** - * 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); + 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); + } }