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.MapListFrom[] getMapListFrom( - ) { - jalview.schemabinding.version2.MapListFrom[] array = new jalview.schemabinding.version2.MapListFrom[0]; - return (jalview.schemabinding.version2.MapListFrom[]) this._mapListFromList.toArray(array); - } - - /** - * Method getMapListFromCount. - * - * @return the size of this collection - */ - public int getMapListFromCount( - ) { - return this._mapListFromList.size(); - } - - /** - * Method getMapListTo. - * - * @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.MapListTo at the given index - */ - public jalview.schemabinding.version2.MapListTo getMapListTo( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._mapListToList.size()) { - throw new IndexOutOfBoundsException("getMapListTo: Index value '" + index + "' not in range [0.." + (this._mapListToList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.MapListTo) _mapListToList.get(index); - } - - /** - * Method getMapListTo.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.MapListTo[] getMapListTo( - ) { - jalview.schemabinding.version2.MapListTo[] array = new jalview.schemabinding.version2.MapListTo[0]; - return (jalview.schemabinding.version2.MapListTo[]) this._mapListToList.toArray(array); - } - - /** - * Method getMapListToCount. - * - * @return the size of this collection - */ - public int getMapListToCount( - ) { - return this._mapListToList.size(); - } - - /** - * Returns the value of field 'mapToUnit'. The field - * 'mapToUnit' has the following description: number of - * dictionary symbol widths involved in each - * mapped position on this sequence (for example, 3 for a dna - * sequence exon - * region that is being mapped to a protein sequence). This is - * optional, - * since the unit can be usually be inferred from the - * dictionary type of - * each sequence involved in the mapping. - * - * @return the value of field 'MapToUnit'. - */ - public long getMapToUnit( - ) { - return this._mapToUnit; - } - - /** - * Method hasMapFromUnit. - * - * @return true if at least one MapFromUnit has been added - */ - public boolean hasMapFromUnit( - ) { - return this._has_mapFromUnit; - } - - /** - * Method hasMapToUnit. - * - * @return true if at least one MapToUnit has been added - */ - public boolean hasMapToUnit( - ) { - return this._has_mapToUnit; - } - - /** - * 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 removeAllMapListFrom( - ) { - this._mapListFromList.clear(); - } - - /** - */ - public void removeAllMapListTo( - ) { - this._mapListToList.clear(); - } - - /** - * Method removeMapListFrom. - * - * @param vMapListFrom - * @return true if the object was removed from the collection. - */ - public boolean removeMapListFrom( - final jalview.schemabinding.version2.MapListFrom vMapListFrom) { - boolean removed = _mapListFromList.remove(vMapListFrom); - return removed; - } - - /** - * Method removeMapListFromAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.MapListFrom removeMapListFromAt( - final int index) { - java.lang.Object obj = this._mapListFromList.remove(index); - return (jalview.schemabinding.version2.MapListFrom) obj; - } - - /** - * Method removeMapListTo. - * - * @param vMapListTo - * @return true if the object was removed from the collection. - */ - public boolean removeMapListTo( - final jalview.schemabinding.version2.MapListTo vMapListTo) { - boolean removed = _mapListToList.remove(vMapListTo); - return removed; - } - - /** - * Method removeMapListToAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.MapListTo removeMapListToAt( - final int index) { - java.lang.Object obj = this._mapListToList.remove(index); - return (jalview.schemabinding.version2.MapListTo) obj; - } - - /** - * Sets the value of field 'mapFromUnit'. The field - * 'mapFromUnit' has the following description: number of - * dictionary symbol widths involved in each - * mapped position on this sequence (for example, 3 for a dna - * sequence exon - * region that is being mapped to a protein sequence). This is - * optional, - * since the unit can be usually be inferred from the - * dictionary type of - * each sequence involved in the mapping. - * - * @param mapFromUnit the value of field 'mapFromUnit'. - */ - public void setMapFromUnit( - final long mapFromUnit) { - this._mapFromUnit = mapFromUnit; - this._has_mapFromUnit = true; - } - - /** - * - * - * @param index - * @param vMapListFrom - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setMapListFrom( - final int index, - final jalview.schemabinding.version2.MapListFrom vMapListFrom) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._mapListFromList.size()) { - throw new IndexOutOfBoundsException("setMapListFrom: Index value '" + index + "' not in range [0.." + (this._mapListFromList.size() - 1) + "]"); - } - - this._mapListFromList.set(index, vMapListFrom); - } - - /** - * - * - * @param vMapListFromArray - */ - public void setMapListFrom( - final jalview.schemabinding.version2.MapListFrom[] vMapListFromArray) { - //-- copy array - _mapListFromList.clear(); - - for (int i = 0; i < vMapListFromArray.length; i++) { - this._mapListFromList.add(vMapListFromArray[i]); - } - } - - /** - * - * - * @param index - * @param vMapListTo - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setMapListTo( - final int index, - final jalview.schemabinding.version2.MapListTo vMapListTo) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._mapListToList.size()) { - throw new IndexOutOfBoundsException("setMapListTo: Index value '" + index + "' not in range [0.." + (this._mapListToList.size() - 1) + "]"); - } - - this._mapListToList.set(index, vMapListTo); - } - - /** - * - * - * @param vMapListToArray - */ - public void setMapListTo( - final jalview.schemabinding.version2.MapListTo[] vMapListToArray) { - //-- copy array - _mapListToList.clear(); - - for (int i = 0; i < vMapListToArray.length; i++) { - this._mapListToList.add(vMapListToArray[i]); - } - } - - /** - * Sets the value of field 'mapToUnit'. The field 'mapToUnit' - * has the following description: number of dictionary symbol - * widths involved in each - * mapped position on this sequence (for example, 3 for a dna - * sequence exon - * region that is being mapped to a protein sequence). This is - * optional, - * since the unit can be usually be inferred from the - * dictionary type of - * each sequence involved in the mapping. - * - * @param mapToUnit the value of field 'mapToUnit'. - */ - public void setMapToUnit( - final long mapToUnit) { - this._mapToUnit = mapToUnit; - this._has_mapToUnit = true; - } - - /** - * 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.MapListType - */ - public static jalview.schemabinding.version2.MapListType unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.MapListType) Unmarshaller.unmarshal(jalview.schemabinding.version2.MapListType.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); - } +public class MapListType implements java.io.Serializable +{ + + // --------------------------/ + // - Class/Member Variables -/ + // --------------------------/ + + /** + * number of dictionary symbol widths involved in each mapped position on this + * sequence (for example, 3 for a dna sequence exon region that is being + * mapped to a protein sequence). This is optional, since the unit can be + * usually be inferred from the dictionary type of each sequence involved in + * the mapping. + */ + private long _mapFromUnit; + + /** + * keeps track of state for field: _mapFromUnit + */ + private boolean _has_mapFromUnit; + + /** + * number of dictionary symbol widths involved in each mapped position on this + * sequence (for example, 3 for a dna sequence exon region that is being + * mapped to a protein sequence). This is optional, since the unit can be + * usually be inferred from the dictionary type of each sequence involved in + * the mapping. + */ + private long _mapToUnit; + + /** + * keeps track of state for field: _mapToUnit + */ + private boolean _has_mapToUnit; + + /** + * a region from start to end inclusive + */ + private java.util.Vector _mapListFromList; + + /** + * a region from start to end inclusive + */ + private java.util.Vector _mapListToList; + + // ----------------/ + // - Constructors -/ + // ----------------/ + + public MapListType() + { + super(); + this._mapListFromList = new java.util.Vector(); + this._mapListToList = new java.util.Vector(); + } + + // -----------/ + // - Methods -/ + // -----------/ + + /** + * + * + * @param vMapListFrom + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addMapListFrom( + final jalview.schemabinding.version2.MapListFrom vMapListFrom) + throws java.lang.IndexOutOfBoundsException + { + this._mapListFromList.addElement(vMapListFrom); + } + + /** + * + * + * @param index + * @param vMapListFrom + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addMapListFrom(final int index, + final jalview.schemabinding.version2.MapListFrom vMapListFrom) + throws java.lang.IndexOutOfBoundsException + { + this._mapListFromList.add(index, vMapListFrom); + } + + /** + * + * + * @param vMapListTo + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addMapListTo( + final jalview.schemabinding.version2.MapListTo vMapListTo) + throws java.lang.IndexOutOfBoundsException + { + this._mapListToList.addElement(vMapListTo); + } + + /** + * + * + * @param index + * @param vMapListTo + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addMapListTo(final int index, + final jalview.schemabinding.version2.MapListTo vMapListTo) + throws java.lang.IndexOutOfBoundsException + { + this._mapListToList.add(index, vMapListTo); + } + + /** + */ + public void deleteMapFromUnit() + { + this._has_mapFromUnit = false; + } + + /** + */ + public void deleteMapToUnit() + { + this._has_mapToUnit = false; + } + + /** + * Method enumerateMapListFrom. + * + * @return an Enumeration over all jalview.schemabinding.version2.MapListFrom + * elements + */ + public java.util.Enumeration enumerateMapListFrom() + { + return this._mapListFromList.elements(); + } + + /** + * Method enumerateMapListTo. + * + * @return an Enumeration over all jalview.schemabinding.version2.MapListTo + * elements + */ + public java.util.Enumeration enumerateMapListTo() + { + return this._mapListToList.elements(); + } + + /** + * Returns the value of field 'mapFromUnit'. The field 'mapFromUnit' has the + * following description: number of dictionary symbol widths involved in each + * mapped position on this sequence (for example, 3 for a dna sequence exon + * region that is being mapped to a protein sequence). This is optional, since + * the unit can be usually be inferred from the dictionary type of each + * sequence involved in the mapping. + * + * @return the value of field 'MapFromUnit'. + */ + public long getMapFromUnit() + { + return this._mapFromUnit; + } + + /** + * Method getMapListFrom. + * + * @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.MapListFrom at the + * given index + */ + public jalview.schemabinding.version2.MapListFrom getMapListFrom( + final int index) throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._mapListFromList.size()) + { + throw new IndexOutOfBoundsException("getMapListFrom: Index value '" + + index + "' not in range [0.." + + (this._mapListFromList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.MapListFrom) _mapListFromList + .get(index); + } + + /** + * Method getMapListFrom.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.MapListFrom[] getMapListFrom() + { + jalview.schemabinding.version2.MapListFrom[] array = new jalview.schemabinding.version2.MapListFrom[0]; + return (jalview.schemabinding.version2.MapListFrom[]) this._mapListFromList + .toArray(array); + } + + /** + * Method getMapListFromCount. + * + * @return the size of this collection + */ + public int getMapListFromCount() + { + return this._mapListFromList.size(); + } + + /** + * Method getMapListTo. + * + * @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.MapListTo at the + * given index + */ + public jalview.schemabinding.version2.MapListTo getMapListTo( + final int index) throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._mapListToList.size()) + { + throw new IndexOutOfBoundsException("getMapListTo: Index value '" + + index + "' not in range [0.." + + (this._mapListToList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.MapListTo) _mapListToList + .get(index); + } + + /** + * Method getMapListTo.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.MapListTo[] getMapListTo() + { + jalview.schemabinding.version2.MapListTo[] array = new jalview.schemabinding.version2.MapListTo[0]; + return (jalview.schemabinding.version2.MapListTo[]) this._mapListToList + .toArray(array); + } + + /** + * Method getMapListToCount. + * + * @return the size of this collection + */ + public int getMapListToCount() + { + return this._mapListToList.size(); + } + + /** + * Returns the value of field 'mapToUnit'. The field 'mapToUnit' has the + * following description: number of dictionary symbol widths involved in each + * mapped position on this sequence (for example, 3 for a dna sequence exon + * region that is being mapped to a protein sequence). This is optional, since + * the unit can be usually be inferred from the dictionary type of each + * sequence involved in the mapping. + * + * @return the value of field 'MapToUnit'. + */ + public long getMapToUnit() + { + return this._mapToUnit; + } + + /** + * Method hasMapFromUnit. + * + * @return true if at least one MapFromUnit has been added + */ + public boolean hasMapFromUnit() + { + return this._has_mapFromUnit; + } + + /** + * Method hasMapToUnit. + * + * @return true if at least one MapToUnit has been added + */ + public boolean hasMapToUnit() + { + return this._has_mapToUnit; + } + + /** + * 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 removeAllMapListFrom() + { + this._mapListFromList.clear(); + } + + /** + */ + public void removeAllMapListTo() + { + this._mapListToList.clear(); + } + + /** + * Method removeMapListFrom. + * + * @param vMapListFrom + * @return true if the object was removed from the collection. + */ + public boolean removeMapListFrom( + final jalview.schemabinding.version2.MapListFrom vMapListFrom) + { + boolean removed = _mapListFromList.remove(vMapListFrom); + return removed; + } + + /** + * Method removeMapListFromAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.MapListFrom removeMapListFromAt( + final int index) + { + java.lang.Object obj = this._mapListFromList.remove(index); + return (jalview.schemabinding.version2.MapListFrom) obj; + } + + /** + * Method removeMapListTo. + * + * @param vMapListTo + * @return true if the object was removed from the collection. + */ + public boolean removeMapListTo( + final jalview.schemabinding.version2.MapListTo vMapListTo) + { + boolean removed = _mapListToList.remove(vMapListTo); + return removed; + } + + /** + * Method removeMapListToAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.MapListTo removeMapListToAt( + final int index) + { + java.lang.Object obj = this._mapListToList.remove(index); + return (jalview.schemabinding.version2.MapListTo) obj; + } + + /** + * Sets the value of field 'mapFromUnit'. The field 'mapFromUnit' has the + * following description: number of dictionary symbol widths involved in each + * mapped position on this sequence (for example, 3 for a dna sequence exon + * region that is being mapped to a protein sequence). This is optional, since + * the unit can be usually be inferred from the dictionary type of each + * sequence involved in the mapping. + * + * @param mapFromUnit + * the value of field 'mapFromUnit'. + */ + public void setMapFromUnit(final long mapFromUnit) + { + this._mapFromUnit = mapFromUnit; + this._has_mapFromUnit = true; + } + + /** + * + * + * @param index + * @param vMapListFrom + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setMapListFrom(final int index, + final jalview.schemabinding.version2.MapListFrom vMapListFrom) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._mapListFromList.size()) + { + throw new IndexOutOfBoundsException("setMapListFrom: Index value '" + + index + "' not in range [0.." + + (this._mapListFromList.size() - 1) + "]"); + } + + this._mapListFromList.set(index, vMapListFrom); + } + + /** + * + * + * @param vMapListFromArray + */ + public void setMapListFrom( + final jalview.schemabinding.version2.MapListFrom[] vMapListFromArray) + { + // -- copy array + _mapListFromList.clear(); + + for (int i = 0; i < vMapListFromArray.length; i++) + { + this._mapListFromList.add(vMapListFromArray[i]); + } + } + + /** + * + * + * @param index + * @param vMapListTo + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setMapListTo(final int index, + final jalview.schemabinding.version2.MapListTo vMapListTo) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._mapListToList.size()) + { + throw new IndexOutOfBoundsException("setMapListTo: Index value '" + + index + "' not in range [0.." + + (this._mapListToList.size() - 1) + "]"); + } + + this._mapListToList.set(index, vMapListTo); + } + + /** + * + * + * @param vMapListToArray + */ + public void setMapListTo( + final jalview.schemabinding.version2.MapListTo[] vMapListToArray) + { + // -- copy array + _mapListToList.clear(); + + for (int i = 0; i < vMapListToArray.length; i++) + { + this._mapListToList.add(vMapListToArray[i]); + } + } + + /** + * Sets the value of field 'mapToUnit'. The field 'mapToUnit' has the + * following description: number of dictionary symbol widths involved in each + * mapped position on this sequence (for example, 3 for a dna sequence exon + * region that is being mapped to a protein sequence). This is optional, since + * the unit can be usually be inferred from the dictionary type of each + * sequence involved in the mapping. + * + * @param mapToUnit + * the value of field 'mapToUnit'. + */ + public void setMapToUnit(final long mapToUnit) + { + this._mapToUnit = mapToUnit; + this._has_mapToUnit = true; + } + + /** + * 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.MapListType + */ + public static jalview.schemabinding.version2.MapListType unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException + { + return (jalview.schemabinding.version2.MapListType) Unmarshaller + .unmarshal(jalview.schemabinding.version2.MapListType.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); + } }