/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
- * Schema.\r
- * $Id$\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
-\r
package jalview.schemabinding.version2;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
//---------------------------------/\r
\r
import org.exolab.castor.xml.Marshaller;\r
/**\r
* developed after mapRangeType from\r
* http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes\r
- * \r
- * This effectively represents a java.util.MapList object\r
- * \r
+ * \r
+ * This effectively represents a java.util.MapList object\r
+ * \r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class MapListType implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * number of dictionary symbol widths involved in each\r
- * mapped position on this sequence (for example, 3 for a dna\r
- * sequence exon\r
- * region that is being mapped to a protein sequence). This is\r
- * optional,\r
- * since the unit can be usually be inferred from the\r
- * dictionary type of\r
- * each sequence involved in the mapping. \r
- */\r
- private long _mapFromUnit;\r
-\r
- /**\r
- * keeps track of state for field: _mapFromUnit\r
- */\r
- private boolean _has_mapFromUnit;\r
-\r
- /**\r
- * number of dictionary symbol widths involved in each\r
- * mapped position on this sequence (for example, 3 for a dna\r
- * sequence exon\r
- * region that is being mapped to a protein sequence). This is\r
- * optional,\r
- * since the unit can be usually be inferred from the\r
- * dictionary type of\r
- * each sequence involved in the mapping. \r
- */\r
- private long _mapToUnit;\r
-\r
- /**\r
- * keeps track of state for field: _mapToUnit\r
- */\r
- private boolean _has_mapToUnit;\r
-\r
- /**\r
- * a region from start to end inclusive\r
- */\r
- private java.util.Vector _mapListFromList;\r
-\r
- /**\r
- * a region from start to end inclusive\r
- */\r
- private java.util.Vector _mapListToList;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public MapListType() {\r
- super();\r
- this._mapListFromList = new java.util.Vector();\r
- this._mapListToList = new java.util.Vector();\r
- }\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vMapListFrom\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addMapListFrom(\r
- final jalview.schemabinding.version2.MapListFrom vMapListFrom)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._mapListFromList.addElement(vMapListFrom);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vMapListFrom\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addMapListFrom(\r
- final int index,\r
- final jalview.schemabinding.version2.MapListFrom vMapListFrom)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._mapListFromList.add(index, vMapListFrom);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vMapListTo\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addMapListTo(\r
- final jalview.schemabinding.version2.MapListTo vMapListTo)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._mapListToList.addElement(vMapListTo);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vMapListTo\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addMapListTo(\r
- final int index,\r
- final jalview.schemabinding.version2.MapListTo vMapListTo)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._mapListToList.add(index, vMapListTo);\r
- }\r
-\r
- /**\r
- */\r
- public void deleteMapFromUnit(\r
- ) {\r
- this._has_mapFromUnit= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteMapToUnit(\r
- ) {\r
- this._has_mapToUnit= false;\r
- }\r
-\r
- /**\r
- * Method enumerateMapListFrom.\r
- * \r
- * @return an Enumeration over all\r
- * jalview.schemabinding.version2.MapListFrom elements\r
- */\r
- public java.util.Enumeration enumerateMapListFrom(\r
- ) {\r
- return this._mapListFromList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateMapListTo.\r
- * \r
- * @return an Enumeration over all\r
- * jalview.schemabinding.version2.MapListTo elements\r
- */\r
- public java.util.Enumeration enumerateMapListTo(\r
- ) {\r
- return this._mapListToList.elements();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'mapFromUnit'. The field\r
- * 'mapFromUnit' has the following description: number of\r
- * dictionary symbol widths involved in each\r
- * mapped position on this sequence (for example, 3 for a dna\r
- * sequence exon\r
- * region that is being mapped to a protein sequence). This is\r
- * optional,\r
- * since the unit can be usually be inferred from the\r
- * dictionary type of\r
- * each sequence involved in the mapping. \r
- * \r
- * @return the value of field 'MapFromUnit'.\r
- */\r
- public long getMapFromUnit(\r
- ) {\r
- return this._mapFromUnit;\r
- }\r
-\r
- /**\r
- * Method getMapListFrom.\r
- * \r
- * @param index\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- * @return the value of the\r
- * jalview.schemabinding.version2.MapListFrom at the given index\r
- */\r
- public jalview.schemabinding.version2.MapListFrom getMapListFrom(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._mapListFromList.size()) {\r
- throw new IndexOutOfBoundsException("getMapListFrom: Index value '" + index + "' not in range [0.." + (this._mapListFromList.size() - 1) + "]");\r
- }\r
- \r
- return (jalview.schemabinding.version2.MapListFrom) _mapListFromList.get(index);\r
- }\r
-\r
- /**\r
- * Method getMapListFrom.Returns the contents of the collection\r
- * in an Array. <p>Note: Just in case the collection contents\r
- * are changing in another thread, we pass a 0-length Array of\r
- * the correct type into the API call. This way we <i>know</i>\r
- * that the Array returned is of exactly the correct length.\r
- * \r
- * @return this collection as an Array\r
- */\r
- public jalview.schemabinding.version2.MapListFrom[] getMapListFrom(\r
- ) {\r
- jalview.schemabinding.version2.MapListFrom[] array = new jalview.schemabinding.version2.MapListFrom[0];\r
- return (jalview.schemabinding.version2.MapListFrom[]) this._mapListFromList.toArray(array);\r
- }\r
-\r
- /**\r
- * Method getMapListFromCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getMapListFromCount(\r
- ) {\r
- return this._mapListFromList.size();\r
- }\r
-\r
- /**\r
- * Method getMapListTo.\r
- * \r
- * @param index\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- * @return the value of the\r
- * jalview.schemabinding.version2.MapListTo at the given index\r
- */\r
- public jalview.schemabinding.version2.MapListTo getMapListTo(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._mapListToList.size()) {\r
- throw new IndexOutOfBoundsException("getMapListTo: Index value '" + index + "' not in range [0.." + (this._mapListToList.size() - 1) + "]");\r
- }\r
- \r
- return (jalview.schemabinding.version2.MapListTo) _mapListToList.get(index);\r
- }\r
-\r
- /**\r
- * Method getMapListTo.Returns the contents of the collection\r
- * in an Array. <p>Note: Just in case the collection contents\r
- * are changing in another thread, we pass a 0-length Array of\r
- * the correct type into the API call. This way we <i>know</i>\r
- * that the Array returned is of exactly the correct length.\r
- * \r
- * @return this collection as an Array\r
- */\r
- public jalview.schemabinding.version2.MapListTo[] getMapListTo(\r
- ) {\r
- jalview.schemabinding.version2.MapListTo[] array = new jalview.schemabinding.version2.MapListTo[0];\r
- return (jalview.schemabinding.version2.MapListTo[]) this._mapListToList.toArray(array);\r
- }\r
-\r
- /**\r
- * Method getMapListToCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getMapListToCount(\r
- ) {\r
- return this._mapListToList.size();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'mapToUnit'. The field\r
- * 'mapToUnit' has the following description: number of\r
- * dictionary symbol widths involved in each\r
- * mapped position on this sequence (for example, 3 for a dna\r
- * sequence exon\r
- * region that is being mapped to a protein sequence). This is\r
- * optional,\r
- * since the unit can be usually be inferred from the\r
- * dictionary type of\r
- * each sequence involved in the mapping. \r
- * \r
- * @return the value of field 'MapToUnit'.\r
- */\r
- public long getMapToUnit(\r
- ) {\r
- return this._mapToUnit;\r
- }\r
-\r
- /**\r
- * Method hasMapFromUnit.\r
- * \r
- * @return true if at least one MapFromUnit has been added\r
- */\r
- public boolean hasMapFromUnit(\r
- ) {\r
- return this._has_mapFromUnit;\r
- }\r
-\r
- /**\r
- * Method hasMapToUnit.\r
- * \r
- * @return true if at least one MapToUnit has been added\r
- */\r
- public boolean hasMapToUnit(\r
- ) {\r
- return this._has_mapToUnit;\r
- }\r
-\r
- /**\r
- * Method isValid.\r
- * \r
- * @return true if this object is valid according to the schema\r
- */\r
- public boolean isValid(\r
- ) {\r
- try {\r
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param out\r
- * @throws org.exolab.castor.xml.MarshalException if object is\r
- * null or if any SAXException is thrown during marshaling\r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- */\r
- public void marshal(\r
- final java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
- Marshaller.marshal(this, out);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param handler\r
- * @throws java.io.IOException if an IOException occurs during\r
- * marshaling\r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- * @throws org.exolab.castor.xml.MarshalException if object is\r
- * null or if any SAXException is thrown during marshaling\r
- */\r
- public void marshal(\r
- final org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
- Marshaller.marshal(this, handler);\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllMapListFrom(\r
- ) {\r
- this._mapListFromList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllMapListTo(\r
- ) {\r
- this._mapListToList.clear();\r
- }\r
-\r
- /**\r
- * Method removeMapListFrom.\r
- * \r
- * @param vMapListFrom\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeMapListFrom(\r
- final jalview.schemabinding.version2.MapListFrom vMapListFrom) {\r
- boolean removed = _mapListFromList.remove(vMapListFrom);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeMapListFromAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.MapListFrom removeMapListFromAt(\r
- final int index) {\r
- java.lang.Object obj = this._mapListFromList.remove(index);\r
- return (jalview.schemabinding.version2.MapListFrom) obj;\r
- }\r
-\r
- /**\r
- * Method removeMapListTo.\r
- * \r
- * @param vMapListTo\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeMapListTo(\r
- final jalview.schemabinding.version2.MapListTo vMapListTo) {\r
- boolean removed = _mapListToList.remove(vMapListTo);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeMapListToAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.MapListTo removeMapListToAt(\r
- final int index) {\r
- java.lang.Object obj = this._mapListToList.remove(index);\r
- return (jalview.schemabinding.version2.MapListTo) obj;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'mapFromUnit'. The field\r
- * 'mapFromUnit' has the following description: number of\r
- * dictionary symbol widths involved in each\r
- * mapped position on this sequence (for example, 3 for a dna\r
- * sequence exon\r
- * region that is being mapped to a protein sequence). This is\r
- * optional,\r
- * since the unit can be usually be inferred from the\r
- * dictionary type of\r
- * each sequence involved in the mapping. \r
- * \r
- * @param mapFromUnit the value of field 'mapFromUnit'.\r
- */\r
- public void setMapFromUnit(\r
- final long mapFromUnit) {\r
- this._mapFromUnit = mapFromUnit;\r
- this._has_mapFromUnit = true;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vMapListFrom\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void setMapListFrom(\r
- final int index,\r
- final jalview.schemabinding.version2.MapListFrom vMapListFrom)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._mapListFromList.size()) {\r
- throw new IndexOutOfBoundsException("setMapListFrom: Index value '" + index + "' not in range [0.." + (this._mapListFromList.size() - 1) + "]");\r
- }\r
- \r
- this._mapListFromList.set(index, vMapListFrom);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vMapListFromArray\r
- */\r
- public void setMapListFrom(\r
- final jalview.schemabinding.version2.MapListFrom[] vMapListFromArray) {\r
- //-- copy array\r
- _mapListFromList.clear();\r
- \r
- for (int i = 0; i < vMapListFromArray.length; i++) {\r
- this._mapListFromList.add(vMapListFromArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vMapListTo\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void setMapListTo(\r
- final int index,\r
- final jalview.schemabinding.version2.MapListTo vMapListTo)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._mapListToList.size()) {\r
- throw new IndexOutOfBoundsException("setMapListTo: Index value '" + index + "' not in range [0.." + (this._mapListToList.size() - 1) + "]");\r
- }\r
- \r
- this._mapListToList.set(index, vMapListTo);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vMapListToArray\r
- */\r
- public void setMapListTo(\r
- final jalview.schemabinding.version2.MapListTo[] vMapListToArray) {\r
- //-- copy array\r
- _mapListToList.clear();\r
- \r
- for (int i = 0; i < vMapListToArray.length; i++) {\r
- this._mapListToList.add(vMapListToArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * Sets the value of field 'mapToUnit'. The field 'mapToUnit'\r
- * has the following description: number of dictionary symbol\r
- * widths involved in each\r
- * mapped position on this sequence (for example, 3 for a dna\r
- * sequence exon\r
- * region that is being mapped to a protein sequence). This is\r
- * optional,\r
- * since the unit can be usually be inferred from the\r
- * dictionary type of\r
- * each sequence involved in the mapping. \r
- * \r
- * @param mapToUnit the value of field 'mapToUnit'.\r
- */\r
- public void setMapToUnit(\r
- final long mapToUnit) {\r
- this._mapToUnit = mapToUnit;\r
- this._has_mapToUnit = true;\r
- }\r
-\r
- /**\r
- * Method unmarshal.\r
- * \r
- * @param reader\r
- * @throws org.exolab.castor.xml.MarshalException if object is\r
- * null or if any SAXException is thrown during marshaling\r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- * @return the unmarshaled\r
- * jalview.schemabinding.version2.MapListType\r
- */\r
- public static jalview.schemabinding.version2.MapListType unmarshal(\r
- final java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
- return (jalview.schemabinding.version2.MapListType) Unmarshaller.unmarshal(jalview.schemabinding.version2.MapListType.class, reader);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- */\r
- public void validate(\r
- )\r
- throws org.exolab.castor.xml.ValidationException {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- }\r
+public class MapListType implements java.io.Serializable\r
+{\r
+\r
+ // --------------------------/\r
+ // - Class/Member Variables -/\r
+ // --------------------------/\r
+\r
+ /**\r
+ * number of dictionary symbol widths involved in each mapped position on this\r
+ * sequence (for example, 3 for a dna sequence exon region that is being\r
+ * mapped to a protein sequence). This is optional, since the unit can be\r
+ * usually be inferred from the dictionary type of each sequence involved in\r
+ * the mapping.\r
+ */\r
+ private long _mapFromUnit;\r
+\r
+ /**\r
+ * keeps track of state for field: _mapFromUnit\r
+ */\r
+ private boolean _has_mapFromUnit;\r
+\r
+ /**\r
+ * number of dictionary symbol widths involved in each mapped position on this\r
+ * sequence (for example, 3 for a dna sequence exon region that is being\r
+ * mapped to a protein sequence). This is optional, since the unit can be\r
+ * usually be inferred from the dictionary type of each sequence involved in\r
+ * the mapping.\r
+ */\r
+ private long _mapToUnit;\r
+\r
+ /**\r
+ * keeps track of state for field: _mapToUnit\r
+ */\r
+ private boolean _has_mapToUnit;\r
+\r
+ /**\r
+ * a region from start to end inclusive\r
+ */\r
+ private java.util.Vector _mapListFromList;\r
+\r
+ /**\r
+ * a region from start to end inclusive\r
+ */\r
+ private java.util.Vector _mapListToList;\r
+\r
+ // ----------------/\r
+ // - Constructors -/\r
+ // ----------------/\r
+\r
+ public MapListType()\r
+ {\r
+ super();\r
+ this._mapListFromList = new java.util.Vector();\r
+ this._mapListToList = new java.util.Vector();\r
+ }\r
+\r
+ // -----------/\r
+ // - Methods -/\r
+ // -----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vMapListFrom\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addMapListFrom(\r
+ final jalview.schemabinding.version2.MapListFrom vMapListFrom)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._mapListFromList.addElement(vMapListFrom);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vMapListFrom\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addMapListFrom(final int index,\r
+ final jalview.schemabinding.version2.MapListFrom vMapListFrom)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._mapListFromList.add(index, vMapListFrom);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vMapListTo\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addMapListTo(\r
+ final jalview.schemabinding.version2.MapListTo vMapListTo)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._mapListToList.addElement(vMapListTo);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vMapListTo\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addMapListTo(final int index,\r
+ final jalview.schemabinding.version2.MapListTo vMapListTo)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._mapListToList.add(index, vMapListTo);\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteMapFromUnit()\r
+ {\r
+ this._has_mapFromUnit = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteMapToUnit()\r
+ {\r
+ this._has_mapToUnit = false;\r
+ }\r
+\r
+ /**\r
+ * Method enumerateMapListFrom.\r
+ * \r
+ * @return an Enumeration over all jalview.schemabinding.version2.MapListFrom\r
+ * elements\r
+ */\r
+ public java.util.Enumeration enumerateMapListFrom()\r
+ {\r
+ return this._mapListFromList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumerateMapListTo.\r
+ * \r
+ * @return an Enumeration over all jalview.schemabinding.version2.MapListTo\r
+ * elements\r
+ */\r
+ public java.util.Enumeration enumerateMapListTo()\r
+ {\r
+ return this._mapListToList.elements();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'mapFromUnit'. The field 'mapFromUnit' has the\r
+ * following description: number of dictionary symbol widths involved in each\r
+ * mapped position on this sequence (for example, 3 for a dna sequence exon\r
+ * region that is being mapped to a protein sequence). This is optional, since\r
+ * the unit can be usually be inferred from the dictionary type of each\r
+ * sequence involved in the mapping.\r
+ * \r
+ * @return the value of field 'MapFromUnit'.\r
+ */\r
+ public long getMapFromUnit()\r
+ {\r
+ return this._mapFromUnit;\r
+ }\r
+\r
+ /**\r
+ * Method getMapListFrom.\r
+ * \r
+ * @param index\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ * @return the value of the jalview.schemabinding.version2.MapListFrom at the\r
+ * given index\r
+ */\r
+ public jalview.schemabinding.version2.MapListFrom getMapListFrom(\r
+ final int index) throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._mapListFromList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException("getMapListFrom: Index value '"\r
+ + index + "' not in range [0.."\r
+ + (this._mapListFromList.size() - 1) + "]");\r
+ }\r
+\r
+ return (jalview.schemabinding.version2.MapListFrom) _mapListFromList\r
+ .get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getMapListFrom.Returns the contents of the collection in an Array.\r
+ * <p>\r
+ * Note: Just in case the collection contents are changing in another thread,\r
+ * we pass a 0-length Array of the correct type into the API call. This way we\r
+ * <i>know</i> that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.MapListFrom[] getMapListFrom()\r
+ {\r
+ jalview.schemabinding.version2.MapListFrom[] array = new jalview.schemabinding.version2.MapListFrom[0];\r
+ return (jalview.schemabinding.version2.MapListFrom[]) this._mapListFromList\r
+ .toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getMapListFromCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getMapListFromCount()\r
+ {\r
+ return this._mapListFromList.size();\r
+ }\r
+\r
+ /**\r
+ * Method getMapListTo.\r
+ * \r
+ * @param index\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ * @return the value of the jalview.schemabinding.version2.MapListTo at the\r
+ * given index\r
+ */\r
+ public jalview.schemabinding.version2.MapListTo getMapListTo(\r
+ final int index) throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._mapListToList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException("getMapListTo: Index value '"\r
+ + index + "' not in range [0.."\r
+ + (this._mapListToList.size() - 1) + "]");\r
+ }\r
+\r
+ return (jalview.schemabinding.version2.MapListTo) _mapListToList\r
+ .get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getMapListTo.Returns the contents of the collection in an Array.\r
+ * <p>\r
+ * Note: Just in case the collection contents are changing in another thread,\r
+ * we pass a 0-length Array of the correct type into the API call. This way we\r
+ * <i>know</i> that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.MapListTo[] getMapListTo()\r
+ {\r
+ jalview.schemabinding.version2.MapListTo[] array = new jalview.schemabinding.version2.MapListTo[0];\r
+ return (jalview.schemabinding.version2.MapListTo[]) this._mapListToList\r
+ .toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getMapListToCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getMapListToCount()\r
+ {\r
+ return this._mapListToList.size();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'mapToUnit'. The field 'mapToUnit' has the\r
+ * following description: number of dictionary symbol widths involved in each\r
+ * mapped position on this sequence (for example, 3 for a dna sequence exon\r
+ * region that is being mapped to a protein sequence). This is optional, since\r
+ * the unit can be usually be inferred from the dictionary type of each\r
+ * sequence involved in the mapping.\r
+ * \r
+ * @return the value of field 'MapToUnit'.\r
+ */\r
+ public long getMapToUnit()\r
+ {\r
+ return this._mapToUnit;\r
+ }\r
+\r
+ /**\r
+ * Method hasMapFromUnit.\r
+ * \r
+ * @return true if at least one MapFromUnit has been added\r
+ */\r
+ public boolean hasMapFromUnit()\r
+ {\r
+ return this._has_mapFromUnit;\r
+ }\r
+\r
+ /**\r
+ * Method hasMapToUnit.\r
+ * \r
+ * @return true if at least one MapToUnit has been added\r
+ */\r
+ public boolean hasMapToUnit()\r
+ {\r
+ return this._has_mapToUnit;\r
+ }\r
+\r
+ /**\r
+ * Method isValid.\r
+ * \r
+ * @return true if this object is valid according to the schema\r
+ */\r
+ public boolean isValid()\r
+ {\r
+ try\r
+ {\r
+ validate();\r
+ } catch (org.exolab.castor.xml.ValidationException vex)\r
+ {\r
+ return false;\r
+ }\r
+ return true;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param out\r
+ * @throws org.exolab.castor.xml.MarshalException\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException\r
+ {\r
+ Marshaller.marshal(this, out);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param handler\r
+ * @throws java.io.IOException\r
+ * if an IOException occurs during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
+ */\r
+ public void marshal(final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException,\r
+ org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException\r
+ {\r
+ Marshaller.marshal(this, handler);\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllMapListFrom()\r
+ {\r
+ this._mapListFromList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllMapListTo()\r
+ {\r
+ this._mapListToList.clear();\r
+ }\r
+\r
+ /**\r
+ * Method removeMapListFrom.\r
+ * \r
+ * @param vMapListFrom\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeMapListFrom(\r
+ final jalview.schemabinding.version2.MapListFrom vMapListFrom)\r
+ {\r
+ boolean removed = _mapListFromList.remove(vMapListFrom);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeMapListFromAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.MapListFrom removeMapListFromAt(\r
+ final int index)\r
+ {\r
+ java.lang.Object obj = this._mapListFromList.remove(index);\r
+ return (jalview.schemabinding.version2.MapListFrom) obj;\r
+ }\r
+\r
+ /**\r
+ * Method removeMapListTo.\r
+ * \r
+ * @param vMapListTo\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeMapListTo(\r
+ final jalview.schemabinding.version2.MapListTo vMapListTo)\r
+ {\r
+ boolean removed = _mapListToList.remove(vMapListTo);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeMapListToAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.MapListTo removeMapListToAt(\r
+ final int index)\r
+ {\r
+ java.lang.Object obj = this._mapListToList.remove(index);\r
+ return (jalview.schemabinding.version2.MapListTo) obj;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'mapFromUnit'. The field 'mapFromUnit' has the\r
+ * following description: number of dictionary symbol widths involved in each\r
+ * mapped position on this sequence (for example, 3 for a dna sequence exon\r
+ * region that is being mapped to a protein sequence). This is optional, since\r
+ * the unit can be usually be inferred from the dictionary type of each\r
+ * sequence involved in the mapping.\r
+ * \r
+ * @param mapFromUnit\r
+ * the value of field 'mapFromUnit'.\r
+ */\r
+ public void setMapFromUnit(final long mapFromUnit)\r
+ {\r
+ this._mapFromUnit = mapFromUnit;\r
+ this._has_mapFromUnit = true;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vMapListFrom\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void setMapListFrom(final int index,\r
+ final jalview.schemabinding.version2.MapListFrom vMapListFrom)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._mapListFromList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException("setMapListFrom: Index value '"\r
+ + index + "' not in range [0.."\r
+ + (this._mapListFromList.size() - 1) + "]");\r
+ }\r
+\r
+ this._mapListFromList.set(index, vMapListFrom);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vMapListFromArray\r
+ */\r
+ public void setMapListFrom(\r
+ final jalview.schemabinding.version2.MapListFrom[] vMapListFromArray)\r
+ {\r
+ // -- copy array\r
+ _mapListFromList.clear();\r
+\r
+ for (int i = 0; i < vMapListFromArray.length; i++)\r
+ {\r
+ this._mapListFromList.add(vMapListFromArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vMapListTo\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void setMapListTo(final int index,\r
+ final jalview.schemabinding.version2.MapListTo vMapListTo)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._mapListToList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException("setMapListTo: Index value '"\r
+ + index + "' not in range [0.."\r
+ + (this._mapListToList.size() - 1) + "]");\r
+ }\r
+\r
+ this._mapListToList.set(index, vMapListTo);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vMapListToArray\r
+ */\r
+ public void setMapListTo(\r
+ final jalview.schemabinding.version2.MapListTo[] vMapListToArray)\r
+ {\r
+ // -- copy array\r
+ _mapListToList.clear();\r
+\r
+ for (int i = 0; i < vMapListToArray.length; i++)\r
+ {\r
+ this._mapListToList.add(vMapListToArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'mapToUnit'. The field 'mapToUnit' has the\r
+ * following description: number of dictionary symbol widths involved in each\r
+ * mapped position on this sequence (for example, 3 for a dna sequence exon\r
+ * region that is being mapped to a protein sequence). This is optional, since\r
+ * the unit can be usually be inferred from the dictionary type of each\r
+ * sequence involved in the mapping.\r
+ * \r
+ * @param mapToUnit\r
+ * the value of field 'mapToUnit'.\r
+ */\r
+ public void setMapToUnit(final long mapToUnit)\r
+ {\r
+ this._mapToUnit = mapToUnit;\r
+ this._has_mapToUnit = true;\r
+ }\r
+\r
+ /**\r
+ * Method unmarshal.\r
+ * \r
+ * @param reader\r
+ * @throws org.exolab.castor.xml.MarshalException\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
+ * @return the unmarshaled jalview.schemabinding.version2.MapListType\r
+ */\r
+ public static jalview.schemabinding.version2.MapListType unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.schemabinding.version2.MapListType) Unmarshaller\r
+ .unmarshal(jalview.schemabinding.version2.MapListType.class,\r
+ reader);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
+ */\r
+ public void validate() throws org.exolab.castor.xml.ValidationException\r
+ {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ }\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff