X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FMapListType.java;h=a43e7971479af640999ff34b476de76213feb977;hb=47168f025aefdaa044802bd5f8f510ffe43a4808;hp=efb1bc58905d2a64375ec8c25d463288a3095dad;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/schemabinding/version2/MapListType.java b/src/jalview/schemabinding/version2/MapListType.java index efb1bc5..a43e797 100644 --- a/src/jalview/schemabinding/version2/MapListType.java +++ b/src/jalview/schemabinding/version2/MapListType.java @@ -1,612 +1,610 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ -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 2.8.2)
+ * 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); + } + +}