X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FMapListType.java;h=04de49762709412e882e2cd1c30c2935280d35f6;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=21d56e7b14d9bad35af5c4ae756b726b08b13a0d;hpb=a96d51f58325f8429c5792ae554243de5628d62a;p=jalview.git diff --git a/src/jalview/schemabinding/version2/MapListType.java b/src/jalview/schemabinding/version2/MapListType.java index 21d56e7..04de497 100644 --- a/src/jalview/schemabinding/version2/MapListType.java +++ b/src/jalview/schemabinding/version2/MapListType.java @@ -1,582 +1,616 @@ -/* - * 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; - -/** - * developed after mapRangeType from - * http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes - * - * 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.
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);
- }
-
-}
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview.
+ * If not, see
+ * 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); + } + +}