package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
/**
* developed after mapRangeType from
* http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
- *
- * This effectively represents a java.util.MapList object
- *
+ *
+ * This effectively represents a java.util.MapList object
+ *
*
* @version $Revision$ $Date$
*/
-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. <p>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 <i>know</i>
- * 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. <p>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 <i>know</i>
- * 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.
+ * <p>
+ * 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
+ * <i>know</i> 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.
+ * <p>
+ * 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
+ * <i>know</i> 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);
+ }
}
git://source.jalview.org / jalview.git / blobdiff