/*\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
+ * This file is part of the Vamsas Client version 0.1. \r
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite, \r
+ * Andrew Waterhouse and Dominik Lindner.\r
+ * \r
+ * Earlier versions have also been incorporated into Jalview version 2.4 \r
+ * since 2008, and TOPALi version 2 since 2007.\r
+ * \r
+ * The Vamsas Client is free software: you can redistribute it and/or modify\r
+ * it under the terms of the GNU Lesser General Public License as published by\r
+ * the Free Software Foundation, either version 3 of the License, or\r
+ * (at your option) any later version.\r
+ * \r
+ * The Vamsas Client 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 Lesser General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU Lesser General Public License\r
+ * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
-\r
package uk.ac.vamsas.objects.core;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
//---------------------------------/\r
\r
import org.exolab.castor.xml.Marshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class SequenceMapping extends uk.ac.vamsas.client.Vobject \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _sequenceA.\r
- */\r
- private java.lang.Object _sequenceA;\r
-\r
- /**\r
- * Field _sequenceB.\r
- */\r
- private java.lang.Object _sequenceB;\r
-\r
- /**\r
- * Field _id.\r
- */\r
- private java.lang.String _id;\r
-\r
- /**\r
- * Field _rangeList.\r
- */\r
- private java.util.Vector _rangeList;\r
-\r
- /**\r
- * Field _provenance.\r
- */\r
- private uk.ac.vamsas.objects.core.Provenance _provenance;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public SequenceMapping() {\r
- super();\r
- this._rangeList = new java.util.Vector();\r
- }\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vRange\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addRange(\r
- final uk.ac.vamsas.objects.core.Range vRange)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._rangeList.addElement(vRange);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vRange\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addRange(\r
- final int index,\r
- final uk.ac.vamsas.objects.core.Range vRange)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._rangeList.add(index, vRange);\r
- }\r
-\r
- /**\r
- * Method enumerateRange.\r
- * \r
- * @return an Enumeration over all\r
- * uk.ac.vamsas.objects.core.Range elements\r
- */\r
- public java.util.Enumeration enumerateRange(\r
- ) {\r
- return this._rangeList.elements();\r
- }\r
-\r
- /**\r
- * Overrides the java.lang.Object.equals method.\r
- * \r
- * @param obj\r
- * @return true if the objects are equal.\r
- */\r
- public boolean equals(\r
- final java.lang.Object obj) {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof SequenceMapping) {\r
- \r
- SequenceMapping temp = (SequenceMapping)obj;\r
- if (this._sequenceA != null) {\r
- if (temp._sequenceA == null) return false;\r
- else if (!(this._sequenceA.equals(temp._sequenceA))) \r
- return false;\r
+public class SequenceMapping extends uk.ac.vamsas.objects.core.MapType\r
+ implements java.io.Serializable {\r
+\r
+ // --------------------------/\r
+ // - Class/Member Variables -/\r
+ // --------------------------/\r
+\r
+ /**\r
+ * Object on which the local range is defined.\r
+ */\r
+ private java.lang.Object _loc;\r
+\r
+ /**\r
+ * Object on which the mapped range is defined.\r
+ */\r
+ private java.lang.Object _map;\r
+\r
+ /**\r
+ * Field _id.\r
+ */\r
+ private java.lang.String _id;\r
+\r
+ /**\r
+ * Field _provenance.\r
+ */\r
+ private uk.ac.vamsas.objects.core.Provenance _provenance;\r
+\r
+ // ----------------/\r
+ // - Constructors -/\r
+ // ----------------/\r
+\r
+ public SequenceMapping() {\r
+ super();\r
+ }\r
+\r
+ // -----------/\r
+ // - Methods -/\r
+ // -----------/\r
+\r
+ /**\r
+ * Overrides the java.lang.Object.equals method.\r
+ * \r
+ * @param obj\r
+ * @return true if the objects are equal.\r
+ */\r
+ public boolean equals(final java.lang.Object obj) {\r
+ if (this == obj)\r
+ return true;\r
+\r
+ if (super.equals(obj) == false)\r
+ return false;\r
+\r
+ if (obj instanceof SequenceMapping) {\r
+\r
+ SequenceMapping temp = (SequenceMapping) obj;\r
+ boolean thcycle;\r
+ boolean tmcycle;\r
+ if (this._loc != null) {\r
+ if (temp._loc == null)\r
+ return false;\r
+ if (this._loc != temp._loc) {\r
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._loc);\r
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._loc);\r
+ if (thcycle != tmcycle) {\r
+ if (!thcycle) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._loc);\r
}\r
- else if (temp._sequenceA != null)\r
- return false;\r
- if (this._sequenceB != null) {\r
- if (temp._sequenceB == null) return false;\r
- else if (!(this._sequenceB.equals(temp._sequenceB))) \r
- return false;\r
+ ;\r
+ if (!tmcycle) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._loc);\r
}\r
- else if (temp._sequenceB != null)\r
- return false;\r
- if (this._id != null) {\r
- if (temp._id == null) return false;\r
- else if (!(this._id.equals(temp._id))) \r
- return false;\r
+ ;\r
+ return false;\r
+ }\r
+ if (!thcycle) {\r
+ if (!this._loc.equals(temp._loc)) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._loc);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._loc);\r
+ return false;\r
}\r
- else if (temp._id != null)\r
- return false;\r
- if (this._rangeList != null) {\r
- if (temp._rangeList == null) return false;\r
- else if (!(this._rangeList.equals(temp._rangeList))) \r
- return false;\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._loc);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._loc);\r
+ }\r
+ }\r
+ } else if (temp._loc != null)\r
+ return false;\r
+ if (this._map != null) {\r
+ if (temp._map == null)\r
+ return false;\r
+ if (this._map != temp._map) {\r
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._map);\r
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._map);\r
+ if (thcycle != tmcycle) {\r
+ if (!thcycle) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._map);\r
}\r
- else if (temp._rangeList != null)\r
- return false;\r
- if (this._provenance != null) {\r
- if (temp._provenance == null) return false;\r
- else if (!(this._provenance.equals(temp._provenance))) \r
- return false;\r
+ ;\r
+ if (!tmcycle) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._map);\r
}\r
- else if (temp._provenance != null)\r
- return false;\r
- return true;\r
+ ;\r
+ return false;\r
+ }\r
+ if (!thcycle) {\r
+ if (!this._map.equals(temp._map)) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._map);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._map);\r
+ return false;\r
+ }\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._map);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._map);\r
+ }\r
}\r
+ } else if (temp._map != null)\r
return false;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'id'.\r
- * \r
- * @return the value of field 'Id'.\r
- */\r
- public java.lang.String getId(\r
- ) {\r
- return this._id;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'provenance'.\r
- * \r
- * @return the value of field 'Provenance'.\r
- */\r
- public uk.ac.vamsas.objects.core.Provenance getProvenance(\r
- ) {\r
- return this._provenance;\r
- }\r
-\r
- /**\r
- * Method getRange.\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 uk.ac.vamsas.objects.core.Range at\r
- * the given index\r
- */\r
- public uk.ac.vamsas.objects.core.Range getRange(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._rangeList.size()) {\r
- throw new IndexOutOfBoundsException("getRange: Index value '" + index + "' not in range [0.." + (this._rangeList.size() - 1) + "]");\r
- }\r
- \r
- return (uk.ac.vamsas.objects.core.Range) _rangeList.get(index);\r
- }\r
-\r
- /**\r
- * Method getRange.Returns the contents of the collection in an\r
- * Array. <p>Note: Just in case the collection contents are\r
- * changing in another thread, we pass a 0-length Array of the\r
- * 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 uk.ac.vamsas.objects.core.Range[] getRange(\r
- ) {\r
- uk.ac.vamsas.objects.core.Range[] array = new uk.ac.vamsas.objects.core.Range[0];\r
- return (uk.ac.vamsas.objects.core.Range[]) this._rangeList.toArray(array);\r
- }\r
-\r
- /**\r
- * Method getRangeAsReference.Returns a reference to\r
- * '_rangeList'. No type checking is performed on any\r
- * modifications to the Vector.\r
- * \r
- * @return a reference to the Vector backing this class\r
- */\r
- public java.util.Vector getRangeAsReference(\r
- ) {\r
- return this._rangeList;\r
- }\r
-\r
- /**\r
- * Method getRangeCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getRangeCount(\r
- ) {\r
- return this._rangeList.size();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'sequenceA'.\r
- * \r
- * @return the value of field 'SequenceA'.\r
- */\r
- public java.lang.Object getSequenceA(\r
- ) {\r
- return this._sequenceA;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'sequenceB'.\r
- * \r
- * @return the value of field 'SequenceB'.\r
- */\r
- public java.lang.Object getSequenceB(\r
- ) {\r
- return this._sequenceB;\r
- }\r
-\r
- /**\r
- * Overrides the java.lang.Object.hashCode method.\r
- * <p>\r
- * The following steps came from <b>Effective Java Programming\r
- * Language Guide</b> by Joshua Bloch, Chapter 3\r
- * \r
- * @return a hash code value for the object.\r
- */\r
- public int hashCode(\r
- ) {\r
- int result = super.hashCode();\r
- \r
- long tmp;\r
- if (_sequenceA != null) {\r
- result = 37 * result + _sequenceA.hashCode();\r
- }\r
- if (_sequenceB != null) {\r
- result = 37 * result + _sequenceB.hashCode();\r
- }\r
- if (_id != null) {\r
- result = 37 * result + _id.hashCode();\r
- }\r
- if (_rangeList != null) {\r
- result = 37 * result + _rangeList.hashCode();\r
- }\r
- if (_provenance != null) {\r
- result = 37 * result + _provenance.hashCode();\r
- }\r
- \r
- return result;\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
+ if (this._id != null) {\r
+ if (temp._id == null)\r
+ return false;\r
+ if (this._id != temp._id) {\r
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);\r
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);\r
+ if (thcycle != tmcycle) {\r
+ if (!thcycle) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);\r
+ }\r
+ ;\r
+ if (!tmcycle) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);\r
+ }\r
+ ;\r
return false;\r
+ }\r
+ if (!thcycle) {\r
+ if (!this._id.equals(temp._id)) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);\r
+ return false;\r
+ }\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);\r
+ }\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 removeAllRange(\r
- ) {\r
- this._rangeList.clear();\r
- }\r
-\r
- /**\r
- * Method removeRange.\r
- * \r
- * @param vRange\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeRange(\r
- final uk.ac.vamsas.objects.core.Range vRange) {\r
- boolean removed = _rangeList.remove(vRange);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeRangeAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public uk.ac.vamsas.objects.core.Range removeRangeAt(\r
- final int index) {\r
- java.lang.Object obj = this._rangeList.remove(index);\r
- return (uk.ac.vamsas.objects.core.Range) obj;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'id'.\r
- * \r
- * @param id the value of field 'id'.\r
- */\r
- public void setId(\r
- final java.lang.String id) {\r
- this._id = id;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'provenance'.\r
- * \r
- * @param provenance the value of field 'provenance'.\r
- */\r
- public void setProvenance(\r
- final uk.ac.vamsas.objects.core.Provenance provenance) {\r
- this._provenance = provenance;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vRange\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void setRange(\r
- final int index,\r
- final uk.ac.vamsas.objects.core.Range vRange)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._rangeList.size()) {\r
- throw new IndexOutOfBoundsException("setRange: Index value '" + index + "' not in range [0.." + (this._rangeList.size() - 1) + "]");\r
- }\r
- \r
- this._rangeList.set(index, vRange);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vRangeArray\r
- */\r
- public void setRange(\r
- final uk.ac.vamsas.objects.core.Range[] vRangeArray) {\r
- //-- copy array\r
- _rangeList.clear();\r
- \r
- for (int i = 0; i < vRangeArray.length; i++) {\r
- this._rangeList.add(vRangeArray[i]);\r
+ } else if (temp._id != null)\r
+ return false;\r
+ if (this._provenance != null) {\r
+ if (temp._provenance == null)\r
+ return false;\r
+ if (this._provenance != temp._provenance) {\r
+ thcycle = org.castor.util.CycleBreaker\r
+ .startingToCycle(this._provenance);\r
+ tmcycle = org.castor.util.CycleBreaker\r
+ .startingToCycle(temp._provenance);\r
+ if (thcycle != tmcycle) {\r
+ if (!thcycle) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);\r
+ }\r
+ ;\r
+ if (!tmcycle) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);\r
+ }\r
+ ;\r
+ return false;\r
+ }\r
+ if (!thcycle) {\r
+ if (!this._provenance.equals(temp._provenance)) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);\r
+ return false;\r
+ }\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);\r
+ }\r
}\r
+ } else if (temp._provenance != null)\r
+ return false;\r
+ return true;\r
}\r
-\r
- /**\r
- * Sets the value of '_rangeList' by copying the given Vector.\r
- * All elements will be checked for type safety.\r
- * \r
- * @param vRangeList the Vector to copy.\r
- */\r
- public void setRange(\r
- final java.util.Vector vRangeList) {\r
- // copy vector\r
- this._rangeList.clear();\r
- \r
- this._rangeList.addAll(vRangeList);\r
- }\r
-\r
- /**\r
- * Sets the value of '_rangeList' by setting it to the given\r
- * Vector. No type checking is performed.\r
- * @deprecated\r
- * \r
- * @param rangeVector the Vector to set.\r
- */\r
- public void setRangeAsReference(\r
- final java.util.Vector rangeVector) {\r
- this._rangeList = rangeVector;\r
+ return false;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'id'.\r
+ * \r
+ * @return the value of field 'Id'.\r
+ */\r
+ public java.lang.String getId() {\r
+ return this._id;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'loc'. The field 'loc' has the following\r
+ * description: Object on which the local range is defined.\r
+ * \r
+ * @return the value of field 'Loc'.\r
+ */\r
+ public java.lang.Object getLoc() {\r
+ return this._loc;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'map'. The field 'map' has the following\r
+ * description: Object on which the mapped range is defined.\r
+ * \r
+ * @return the value of field 'Map'.\r
+ */\r
+ public java.lang.Object getMap() {\r
+ return this._map;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'provenance'.\r
+ * \r
+ * @return the value of field 'Provenance'.\r
+ */\r
+ public uk.ac.vamsas.objects.core.Provenance getProvenance() {\r
+ return this._provenance;\r
+ }\r
+\r
+ /**\r
+ * Overrides the java.lang.Object.hashCode method.\r
+ * <p>\r
+ * The following steps came from <b>Effective Java Programming Language\r
+ * Guide</b> by Joshua Bloch, Chapter 3\r
+ * \r
+ * @return a hash code value for the object.\r
+ */\r
+ public int hashCode() {\r
+ int result = super.hashCode();\r
+\r
+ long tmp;\r
+ if (_loc != null && !org.castor.util.CycleBreaker.startingToCycle(_loc)) {\r
+ result = 37 * result + _loc.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_loc);\r
}\r
-\r
- /**\r
- * Sets the value of field 'sequenceA'.\r
- * \r
- * @param sequenceA the value of field 'sequenceA'.\r
- */\r
- public void setSequenceA(\r
- final java.lang.Object sequenceA) {\r
- this._sequenceA = sequenceA;\r
+ if (_map != null && !org.castor.util.CycleBreaker.startingToCycle(_map)) {\r
+ result = 37 * result + _map.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_map);\r
}\r
-\r
- /**\r
- * Sets the value of field 'sequenceB'.\r
- * \r
- * @param sequenceB the value of field 'sequenceB'.\r
- */\r
- public void setSequenceB(\r
- final java.lang.Object sequenceB) {\r
- this._sequenceB = sequenceB;\r
+ if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {\r
+ result = 37 * result + _id.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_id);\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
- * uk.ac.vamsas.objects.core.SequenceMapping\r
- */\r
- public static uk.ac.vamsas.objects.core.SequenceMapping unmarshal(\r
- final java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
- return (uk.ac.vamsas.objects.core.SequenceMapping) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.SequenceMapping.class, reader);\r
+ if (_provenance != null\r
+ && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {\r
+ result = 37 * result + _provenance.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_provenance);\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
+ return result;\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
+ 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\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
+ 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, org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException {\r
+ Marshaller.marshal(this, handler);\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'id'.\r
+ * \r
+ * @param id\r
+ * the value of field 'id'.\r
+ */\r
+ public void setId(final java.lang.String id) {\r
+ this._id = id;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'loc'. The field 'loc' has the following\r
+ * description: Object on which the local range is defined.\r
+ * \r
+ * @param loc\r
+ * the value of field 'loc'.\r
+ */\r
+ public void setLoc(final java.lang.Object loc) {\r
+ this._loc = loc;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'map'. The field 'map' has the following\r
+ * description: Object on which the mapped range is defined.\r
+ * \r
+ * @param map\r
+ * the value of field 'map'.\r
+ */\r
+ public void setMap(final java.lang.Object map) {\r
+ this._map = map;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'provenance'.\r
+ * \r
+ * @param provenance\r
+ * the value of field 'provenance'.\r
+ */\r
+ public void setProvenance(\r
+ final uk.ac.vamsas.objects.core.Provenance provenance) {\r
+ this._provenance = provenance;\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 uk.ac.vamsas.objects.core.MapType\r
+ */\r
+ public static uk.ac.vamsas.objects.core.MapType unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException {\r
+ return (uk.ac.vamsas.objects.core.MapType) Unmarshaller.unmarshal(\r
+ uk.ac.vamsas.objects.core.SequenceMapping.class, 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
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ }\r
\r
}\r
git://source.jalview.org / vamsas.git / blobdiff