-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- * \r
- * This program 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 2\r
- * of the License, or (at your option) any later version.\r
- * \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.schemabinding.version2;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-\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
- * @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
-\r
-}\r
+/*******************************************************************************
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ ******************************************************************************/
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, 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.
+ * <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