/*\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
import org.exolab.castor.xml.Unmarshaller;\r
\r
/**\r
- * This is annotation over the coordinate frame\r
- * defined by all the columns in the alignment.\r
- * \r
+ * This is annotation over the coordinate frame defined by all the columns in\r
+ * the alignment.\r
+ * \r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class AlignmentAnnotation extends uk.ac.vamsas.objects.core.RangeAnnotation \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * TODO: decide if this flag is\r
- * redundant - when true it would suggest that\r
- * the annotationElement values together form a\r
- * graph \r
- */\r
- private boolean _graph;\r
-\r
- /**\r
- * keeps track of state for field: _graph\r
- */\r
- private boolean _has_graph;\r
-\r
- /**\r
- * annotation is associated with\r
- * a range on a particular group of alignment\r
- * sequences\r
- */\r
- private java.util.Vector _seqrefs;\r
-\r
- /**\r
- * Field _provenance.\r
- */\r
- private uk.ac.vamsas.objects.core.Provenance _provenance;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public AlignmentAnnotation() {\r
- super();\r
- this._seqrefs = new java.util.Vector();\r
- }\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vSeqrefs\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addSeqrefs(\r
- final java.lang.Object vSeqrefs)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._seqrefs.addElement(vSeqrefs);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vSeqrefs\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addSeqrefs(\r
- final int index,\r
- final java.lang.Object vSeqrefs)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._seqrefs.add(index, vSeqrefs);\r
- }\r
-\r
- /**\r
- */\r
- public void deleteGraph(\r
- ) {\r
- this._has_graph= false;\r
- }\r
-\r
- /**\r
- * Method enumerateSeqrefs.\r
- * \r
- * @return an Enumeration over all java.lang.Object elements\r
- */\r
- public java.util.Enumeration enumerateSeqrefs(\r
- ) {\r
- return this._seqrefs.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
+public class AlignmentAnnotation extends\r
+ uk.ac.vamsas.objects.core.RangeAnnotation implements java.io.Serializable {\r
+\r
+ // --------------------------/\r
+ // - Class/Member Variables -/\r
+ // --------------------------/\r
+\r
+ /**\r
+ * TODO: decide if this flag is redundant - when true it would suggest that\r
+ * the annotationElement values together form a graph\r
+ */\r
+ private boolean _graph;\r
+\r
+ /**\r
+ * keeps track of state for field: _graph\r
+ */\r
+ private boolean _has_graph;\r
+\r
+ /**\r
+ * annotation is associated with a range on a particular group of alignment\r
+ * sequences\r
+ */\r
+ private java.util.Vector _seqrefs;\r
+\r
+ /**\r
+ * Field _provenance.\r
+ */\r
+ private uk.ac.vamsas.objects.core.Provenance _provenance;\r
+\r
+ // ----------------/\r
+ // - Constructors -/\r
+ // ----------------/\r
+\r
+ public AlignmentAnnotation() {\r
+ super();\r
+ this._seqrefs = new java.util.Vector();\r
+ }\r
+\r
+ // -----------/\r
+ // - Methods -/\r
+ // -----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vSeqrefs\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addSeqrefs(final java.lang.Object vSeqrefs)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._seqrefs.addElement(vSeqrefs);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vSeqrefs\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addSeqrefs(final int index, final java.lang.Object vSeqrefs)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._seqrefs.add(index, vSeqrefs);\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteGraph() {\r
+ this._has_graph = false;\r
+ }\r
+\r
+ /**\r
+ * Method enumerateSeqrefs.\r
+ * \r
+ * @return an Enumeration over all java.lang.Object elements\r
+ */\r
+ public java.util.Enumeration enumerateSeqrefs() {\r
+ return this._seqrefs.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(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 AlignmentAnnotation) {\r
+\r
+ AlignmentAnnotation temp = (AlignmentAnnotation) obj;\r
+ boolean thcycle;\r
+ boolean tmcycle;\r
+ if (this._graph != temp._graph)\r
+ return false;\r
+ if (this._has_graph != temp._has_graph)\r
+ return false;\r
+ if (this._seqrefs != null) {\r
+ if (temp._seqrefs == null)\r
+ return false;\r
+ if (this._seqrefs != temp._seqrefs) {\r
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._seqrefs);\r
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._seqrefs);\r
+ if (thcycle != tmcycle) {\r
+ if (!thcycle) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._seqrefs);\r
+ }\r
+ ;\r
+ if (!tmcycle) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqrefs);\r
+ }\r
+ ;\r
return false;\r
- \r
- if (obj instanceof AlignmentAnnotation) {\r
- \r
- AlignmentAnnotation temp = (AlignmentAnnotation)obj;\r
- boolean thcycle;\r
- boolean tmcycle;\r
- if (this._graph != temp._graph)\r
- return false;\r
- if (this._has_graph != temp._has_graph)\r
- return false;\r
- if (this._seqrefs != null) {\r
- if (temp._seqrefs == null) return false;\r
- if (this._seqrefs != temp._seqrefs) {\r
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._seqrefs);\r
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._seqrefs);\r
- if (thcycle!=tmcycle) {\r
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._seqrefs); };\r
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqrefs); };\r
- return false;\r
- }\r
- if (!thcycle) {\r
- if (!this._seqrefs.equals(temp._seqrefs)) {\r
- org.castor.util.CycleBreaker.releaseCycleHandle(this._seqrefs);\r
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqrefs);\r
- return false;\r
- }\r
- org.castor.util.CycleBreaker.releaseCycleHandle(this._seqrefs);\r
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqrefs);\r
- }\r
- }\r
- } else if (temp._seqrefs != null)\r
- return false;\r
- if (this._provenance != null) {\r
- if (temp._provenance == null) return false;\r
- if (this._provenance != temp._provenance) {\r
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._provenance);\r
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._provenance);\r
- if (thcycle!=tmcycle) {\r
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); };\r
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); };\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
+ if (!thcycle) {\r
+ if (!this._seqrefs.equals(temp._seqrefs)) {\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._seqrefs);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqrefs);\r
+ return false;\r
+ }\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._seqrefs);\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqrefs);\r
+ }\r
}\r
+ } else if (temp._seqrefs != null)\r
return false;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'graph'. The field 'graph' has\r
- * the following description: TODO: decide if this flag is\r
- * redundant - when true it would suggest that\r
- * the annotationElement values together form a\r
- * graph \r
- * \r
- * @return the value of field 'Graph'.\r
- */\r
- public boolean getGraph(\r
- ) {\r
- return this._graph;\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 getSeqrefs.\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 java.lang.Object at the given index\r
- */\r
- public java.lang.Object getSeqrefs(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._seqrefs.size()) {\r
- throw new IndexOutOfBoundsException("getSeqrefs: Index value '" + index + "' not in range [0.." + (this._seqrefs.size() - 1) + "]");\r
- }\r
- \r
- return _seqrefs.get(index);\r
- }\r
-\r
- /**\r
- * Method getSeqrefs.Returns the contents of the collection in\r
- * 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 java.lang.Object[] getSeqrefs(\r
- ) {\r
- java.lang.Object[] array = new java.lang.Object[0];\r
- return (java.lang.Object[]) this._seqrefs.toArray(array);\r
- }\r
-\r
- /**\r
- * Method getSeqrefsAsReference.Returns a reference to\r
- * '_seqrefs'. 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 getSeqrefsAsReference(\r
- ) {\r
- return this._seqrefs;\r
- }\r
-\r
- /**\r
- * Method getSeqrefsCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getSeqrefsCount(\r
- ) {\r
- return this._seqrefs.size();\r
- }\r
-\r
- /**\r
- * Method hasGraph.\r
- * \r
- * @return true if at least one Graph has been added\r
- */\r
- public boolean hasGraph(\r
- ) {\r
- return this._has_graph;\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
- result = 37 * result + (_graph?0:1);\r
- if (_seqrefs != null\r
- && !org.castor.util.CycleBreaker.startingToCycle(_seqrefs)) {\r
- result = 37 * result + _seqrefs.hashCode();\r
- org.castor.util.CycleBreaker.releaseCycleHandle(_seqrefs);\r
- }\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
- return result;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'graph'. The field 'graph' has\r
- * the following description: TODO: decide if this flag is\r
- * redundant - when true it would suggest that\r
- * the annotationElement values together form a\r
- * graph \r
- * \r
- * @return the value of field 'Graph'.\r
- */\r
- public boolean isGraph(\r
- ) {\r
- return this._graph;\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._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
- 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 removeAllSeqrefs(\r
- ) {\r
- this._seqrefs.clear();\r
- }\r
-\r
- /**\r
- * Method removeSeqrefs.\r
- * \r
- * @param vSeqrefs\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeSeqrefs(\r
- final java.lang.Object vSeqrefs) {\r
- boolean removed = _seqrefs.remove(vSeqrefs);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeSeqrefsAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public java.lang.Object removeSeqrefsAt(\r
- final int index) {\r
- java.lang.Object obj = this._seqrefs.remove(index);\r
- return obj;\r
+ } else if (temp._provenance != null)\r
+ return false;\r
+ return true;\r
}\r
-\r
- /**\r
- * Sets the value of field 'graph'. The field 'graph' has the\r
- * following description: TODO: decide if this flag is\r
- * redundant - when true it would suggest that\r
- * the annotationElement values together form a\r
- * graph \r
- * \r
- * @param graph the value of field 'graph'.\r
- */\r
- public void setGraph(\r
- final boolean graph) {\r
- this._graph = graph;\r
- this._has_graph = true;\r
+ return false;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'graph'. The field 'graph' has the following\r
+ * description: TODO: decide if this flag is redundant - when true it would\r
+ * suggest that the annotationElement values together form a graph\r
+ * \r
+ * @return the value of field 'Graph'.\r
+ */\r
+ public boolean getGraph() {\r
+ return this._graph;\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
+ * Method getSeqrefs.\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 java.lang.Object at the given index\r
+ */\r
+ public java.lang.Object getSeqrefs(final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._seqrefs.size()) {\r
+ throw new IndexOutOfBoundsException("getSeqrefs: Index value '" + index\r
+ + "' not in range [0.." + (this._seqrefs.size() - 1) + "]");\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
+ return _seqrefs.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getSeqrefs.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 java.lang.Object[] getSeqrefs() {\r
+ java.lang.Object[] array = new java.lang.Object[0];\r
+ return (java.lang.Object[]) this._seqrefs.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getSeqrefsAsReference.Returns a reference to '_seqrefs'. No type\r
+ * checking is performed on any modifications to the Vector.\r
+ * \r
+ * @return a reference to the Vector backing this class\r
+ */\r
+ public java.util.Vector getSeqrefsAsReference() {\r
+ return this._seqrefs;\r
+ }\r
+\r
+ /**\r
+ * Method getSeqrefsCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getSeqrefsCount() {\r
+ return this._seqrefs.size();\r
+ }\r
+\r
+ /**\r
+ * Method hasGraph.\r
+ * \r
+ * @return true if at least one Graph has been added\r
+ */\r
+ public boolean hasGraph() {\r
+ return this._has_graph;\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
+ result = 37 * result + (_graph ? 0 : 1);\r
+ if (_seqrefs != null\r
+ && !org.castor.util.CycleBreaker.startingToCycle(_seqrefs)) {\r
+ result = 37 * result + _seqrefs.hashCode();\r
+ org.castor.util.CycleBreaker.releaseCycleHandle(_seqrefs);\r
}\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vSeqrefs\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void setSeqrefs(\r
- final int index,\r
- final java.lang.Object vSeqrefs)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._seqrefs.size()) {\r
- throw new IndexOutOfBoundsException("setSeqrefs: Index value '" + index + "' not in range [0.." + (this._seqrefs.size() - 1) + "]");\r
- }\r
- \r
- this._seqrefs.set(index, vSeqrefs);\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
- * @param vSeqrefsArray\r
- */\r
- public void setSeqrefs(\r
- final java.lang.Object[] vSeqrefsArray) {\r
- //-- copy array\r
- _seqrefs.clear();\r
- \r
- for (int i = 0; i < vSeqrefsArray.length; i++) {\r
- this._seqrefs.add(vSeqrefsArray[i]);\r
- }\r
+ return result;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'graph'. The field 'graph' has the following\r
+ * description: TODO: decide if this flag is redundant - when true it would\r
+ * suggest that the annotationElement values together form a graph\r
+ * \r
+ * @return the value of field 'Graph'.\r
+ */\r
+ public boolean isGraph() {\r
+ return this._graph;\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
-\r
- /**\r
- * Sets the value of '_seqrefs' by copying the given Vector.\r
- * All elements will be checked for type safety.\r
- * \r
- * @param vSeqrefsList the Vector to copy.\r
- */\r
- public void setSeqrefs(\r
- final java.util.Vector vSeqrefsList) {\r
- // copy vector\r
- this._seqrefs.clear();\r
- \r
- this._seqrefs.addAll(vSeqrefsList);\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
+ */\r
+ public void removeAllSeqrefs() {\r
+ this._seqrefs.clear();\r
+ }\r
+\r
+ /**\r
+ * Method removeSeqrefs.\r
+ * \r
+ * @param vSeqrefs\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeSeqrefs(final java.lang.Object vSeqrefs) {\r
+ boolean removed = _seqrefs.remove(vSeqrefs);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeSeqrefsAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public java.lang.Object removeSeqrefsAt(final int index) {\r
+ java.lang.Object obj = this._seqrefs.remove(index);\r
+ return obj;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'graph'. The field 'graph' has the following\r
+ * description: TODO: decide if this flag is redundant - when true it would\r
+ * suggest that the annotationElement values together form a graph\r
+ * \r
+ * @param graph\r
+ * the value of field 'graph'.\r
+ */\r
+ public void setGraph(final boolean graph) {\r
+ this._graph = graph;\r
+ this._has_graph = true;\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
+ * \r
+ * \r
+ * @param index\r
+ * @param vSeqrefs\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void setSeqrefs(final int index, final java.lang.Object vSeqrefs)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._seqrefs.size()) {\r
+ throw new IndexOutOfBoundsException("setSeqrefs: Index value '" + index\r
+ + "' not in range [0.." + (this._seqrefs.size() - 1) + "]");\r
}\r
\r
- /**\r
- * Sets the value of '_seqrefs' by setting it to the given\r
- * Vector. No type checking is performed.\r
- * @deprecated\r
- * \r
- * @param seqrefsVector the Vector to set.\r
- */\r
- public void setSeqrefsAsReference(\r
- final java.util.Vector seqrefsVector) {\r
- this._seqrefs = seqrefsVector;\r
- }\r
+ this._seqrefs.set(index, vSeqrefs);\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 uk.ac.vamsas.objects.core.RangeType\r
- */\r
- public static uk.ac.vamsas.objects.core.RangeType 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.RangeType) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.AlignmentAnnotation.class, reader);\r
- }\r
+ /**\r
+ * \r
+ * \r
+ * @param vSeqrefsArray\r
+ */\r
+ public void setSeqrefs(final java.lang.Object[] vSeqrefsArray) {\r
+ // -- copy array\r
+ _seqrefs.clear();\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
+ for (int i = 0; i < vSeqrefsArray.length; i++) {\r
+ this._seqrefs.add(vSeqrefsArray[i]);\r
}\r
+ }\r
+\r
+ /**\r
+ * Sets the value of '_seqrefs' by copying the given Vector. All elements will\r
+ * be checked for type safety.\r
+ * \r
+ * @param vSeqrefsList\r
+ * the Vector to copy.\r
+ */\r
+ public void setSeqrefs(final java.util.Vector vSeqrefsList) {\r
+ // copy vector\r
+ this._seqrefs.clear();\r
+\r
+ this._seqrefs.addAll(vSeqrefsList);\r
+ }\r
+\r
+ /**\r
+ * Sets the value of '_seqrefs' by setting it to the given Vector. No type\r
+ * checking is performed.\r
+ * \r
+ * @deprecated\r
+ * \r
+ * @param seqrefsVector\r
+ * the Vector to set.\r
+ */\r
+ public void setSeqrefsAsReference(final java.util.Vector seqrefsVector) {\r
+ this._seqrefs = seqrefsVector;\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.RangeType\r
+ */\r
+ public static uk.ac.vamsas.objects.core.RangeType 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.RangeType) Unmarshaller.unmarshal(\r
+ uk.ac.vamsas.objects.core.AlignmentAnnotation.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