/*\r
- * This class was automatically generated with\r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
- * Schema.\r
- * $Id$\r
+ * Jalview - A Sequence Alignment Editor and Viewer (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
-\r
package jalview.schemabinding.version2;\r
\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.util.*;\r
-\r
-import org.exolab.castor.xml.*;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
\r
/**\r
* Class JSeq.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
-public class JSeq\r
- implements java.io.Serializable\r
-{\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _colour\r
- */\r
- private int _colour;\r
-\r
- /**\r
- * keeps track of state for field: _colour\r
- */\r
- private boolean _has_colour;\r
-\r
- /**\r
- * Field _start\r
- */\r
- private int _start;\r
-\r
- /**\r
- * keeps track of state for field: _start\r
- */\r
- private boolean _has_start;\r
-\r
- /**\r
- * Field _end\r
- */\r
- private int _end;\r
-\r
- /**\r
- * keeps track of state for field: _end\r
- */\r
- private boolean _has_end;\r
-\r
- /**\r
- * Field _id\r
- */\r
- private int _id;\r
-\r
- /**\r
- * keeps track of state for field: _id\r
- */\r
- private boolean _has_id;\r
-\r
- /**\r
- * Field _hidden\r
- */\r
- private boolean _hidden;\r
-\r
- /**\r
- * keeps track of state for field: _hidden\r
- */\r
- private boolean _has_hidden;\r
-\r
- /**\r
- * Field _featuresList\r
- */\r
- private java.util.Vector _featuresList;\r
-\r
- /**\r
- * Field _pdbidsList\r
- */\r
- private java.util.Vector _pdbidsList;\r
-\r
- /**\r
- * Field _hiddenSequencesList\r
- */\r
- private java.util.Vector _hiddenSequencesList;\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public JSeq()\r
- {\r
- super();\r
- _featuresList = new Vector();\r
- _pdbidsList = new Vector();\r
- _hiddenSequencesList = new Vector();\r
- } //-- jalview.schemabinding.version2.JSeq()\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addFeatures\r
- *\r
- *\r
- *\r
- * @param vFeatures\r
- */\r
- public void addFeatures(jalview.schemabinding.version2.Features vFeatures)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _featuresList.addElement(vFeatures);\r
- } //-- void addFeatures(jalview.schemabinding.version2.Features)\r
-\r
- /**\r
- * Method addFeatures\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vFeatures\r
- */\r
- public void addFeatures(int index,\r
- jalview.schemabinding.version2.Features vFeatures)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _featuresList.insertElementAt(vFeatures, index);\r
- } //-- void addFeatures(int, jalview.schemabinding.version2.Features)\r
-\r
- /**\r
- * Method addHiddenSequences\r
- *\r
- *\r
- *\r
- * @param vHiddenSequences\r
- */\r
- public void addHiddenSequences(int vHiddenSequences)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _hiddenSequencesList.addElement(new java.lang.Integer(vHiddenSequences));\r
- } //-- void addHiddenSequences(int)\r
-\r
- /**\r
- * Method addHiddenSequences\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vHiddenSequences\r
- */\r
- public void addHiddenSequences(int index, int vHiddenSequences)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _hiddenSequencesList.insertElementAt(new java.lang.Integer(vHiddenSequences),\r
- index);\r
- } //-- void addHiddenSequences(int, int)\r
-\r
- /**\r
- * Method addPdbids\r
- *\r
- *\r
- *\r
- * @param vPdbids\r
- */\r
- public void addPdbids(jalview.schemabinding.version2.Pdbids vPdbids)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _pdbidsList.addElement(vPdbids);\r
- } //-- void addPdbids(jalview.schemabinding.version2.Pdbids)\r
-\r
- /**\r
- * Method addPdbids\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vPdbids\r
- */\r
- public void addPdbids(int index,\r
- jalview.schemabinding.version2.Pdbids vPdbids)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _pdbidsList.insertElementAt(vPdbids, index);\r
- } //-- void addPdbids(int, jalview.schemabinding.version2.Pdbids)\r
-\r
- /**\r
- * Method deleteColour\r
- *\r
- */\r
- public void deleteColour()\r
- {\r
- this._has_colour = false;\r
- } //-- void deleteColour()\r
-\r
- /**\r
- * Method deleteEnd\r
- *\r
- */\r
- public void deleteEnd()\r
- {\r
- this._has_end = false;\r
- } //-- void deleteEnd()\r
-\r
- /**\r
- * Method deleteHidden\r
- *\r
- */\r
- public void deleteHidden()\r
- {\r
- this._has_hidden = false;\r
- } //-- void deleteHidden()\r
-\r
- /**\r
- * Method deleteId\r
- *\r
- */\r
- public void deleteId()\r
- {\r
- this._has_id = false;\r
- } //-- void deleteId()\r
-\r
- /**\r
- * Method deleteStart\r
- *\r
- */\r
- public void deleteStart()\r
- {\r
- this._has_start = false;\r
- } //-- void deleteStart()\r
-\r
- /**\r
- * Method enumerateFeatures\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateFeatures()\r
- {\r
- return _featuresList.elements();\r
- } //-- java.util.Enumeration enumerateFeatures()\r
-\r
- /**\r
- * Method enumerateHiddenSequences\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateHiddenSequences()\r
- {\r
- return _hiddenSequencesList.elements();\r
- } //-- java.util.Enumeration enumerateHiddenSequences()\r
-\r
- /**\r
- * Method enumeratePdbids\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumeratePdbids()\r
- {\r
- return _pdbidsList.elements();\r
- } //-- java.util.Enumeration enumeratePdbids()\r
-\r
- /**\r
- * Returns the value of field 'colour'.\r
- *\r
- * @return int\r
- * @return the value of field 'colour'.\r
- */\r
- public int getColour()\r
- {\r
- return this._colour;\r
- } //-- int getColour()\r
-\r
- /**\r
- * Returns the value of field 'end'.\r
- *\r
- * @return int\r
- * @return the value of field 'end'.\r
- */\r
- public int getEnd()\r
- {\r
- return this._end;\r
- } //-- int getEnd()\r
-\r
- /**\r
- * Method getFeatures\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return Features\r
- */\r
- public jalview.schemabinding.version2.Features getFeatures(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _featuresList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
-\r
- return (jalview.schemabinding.version2.Features) _featuresList.elementAt(\r
- index);\r
- } //-- jalview.schemabinding.version2.Features getFeatures(int)\r
-\r
- /**\r
- * Method getFeatures\r
- *\r
- *\r
- *\r
- * @return Features\r
- */\r
- public jalview.schemabinding.version2.Features[] getFeatures()\r
- {\r
- int size = _featuresList.size();\r
- jalview.schemabinding.version2.Features[] mArray = new jalview.\r
- schemabinding.version2.Features[size];\r
- for (int index = 0; index < size; index++)\r
- {\r
- mArray[index] = (jalview.schemabinding.version2.Features) _featuresList.\r
- elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.Features[] getFeatures()\r
-\r
- /**\r
- * Method getFeaturesCount\r
- *\r
- *\r
- *\r
- * @return int\r
- */\r
- public int getFeaturesCount()\r
- {\r
- return _featuresList.size();\r
- } //-- int getFeaturesCount()\r
-\r
- /**\r
- * Returns the value of field 'hidden'.\r
- *\r
- * @return boolean\r
- * @return the value of field 'hidden'.\r
- */\r
- public boolean getHidden()\r
- {\r
- return this._hidden;\r
- } //-- boolean getHidden()\r
-\r
- /**\r
- * Method getHiddenSequences\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return int\r
- */\r
- public int getHiddenSequences(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _hiddenSequencesList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
-\r
- return ( (java.lang.Integer) _hiddenSequencesList.elementAt(index)).\r
- intValue();\r
- } //-- int getHiddenSequences(int)\r
-\r
- /**\r
- * Method getHiddenSequences\r
- *\r
- *\r
- *\r
- * @return int\r
- */\r
- public int[] getHiddenSequences()\r
- {\r
- int size = _hiddenSequencesList.size();\r
- int[] mArray = new int[size];\r
- for (int index = 0; index < size; index++)\r
- {\r
- mArray[index] = ( (java.lang.Integer) _hiddenSequencesList.elementAt(\r
- index)).intValue();\r
- }\r
- return mArray;\r
- } //-- int[] getHiddenSequences()\r
-\r
- /**\r
- * Method getHiddenSequencesCount\r
- *\r
- *\r
- *\r
- * @return int\r
- */\r
- public int getHiddenSequencesCount()\r
- {\r
- return _hiddenSequencesList.size();\r
- } //-- int getHiddenSequencesCount()\r
-\r
- /**\r
- * Returns the value of field 'id'.\r
- *\r
- * @return int\r
- * @return the value of field 'id'.\r
- */\r
- public int getId()\r
- {\r
- return this._id;\r
- } //-- int getId()\r
-\r
- /**\r
- * Method getPdbids\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return Pdbids\r
- */\r
- public jalview.schemabinding.version2.Pdbids getPdbids(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _pdbidsList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
-\r
- return (jalview.schemabinding.version2.Pdbids) _pdbidsList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.Pdbids getPdbids(int)\r
-\r
- /**\r
- * Method getPdbids\r
- *\r
- *\r
- *\r
- * @return Pdbids\r
- */\r
- public jalview.schemabinding.version2.Pdbids[] getPdbids()\r
- {\r
- int size = _pdbidsList.size();\r
- jalview.schemabinding.version2.Pdbids[] mArray = new jalview.schemabinding.\r
- version2.Pdbids[size];\r
- for (int index = 0; index < size; index++)\r
- {\r
- mArray[index] = (jalview.schemabinding.version2.Pdbids) _pdbidsList.\r
- elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.Pdbids[] getPdbids()\r
-\r
- /**\r
- * Method getPdbidsCount\r
- *\r
- *\r
- *\r
- * @return int\r
- */\r
- public int getPdbidsCount()\r
- {\r
- return _pdbidsList.size();\r
- } //-- int getPdbidsCount()\r
-\r
- /**\r
- * Returns the value of field 'start'.\r
- *\r
- * @return int\r
- * @return the value of field 'start'.\r
- */\r
- public int getStart()\r
- {\r
- return this._start;\r
- } //-- int getStart()\r
-\r
- /**\r
- * Method hasColour\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasColour()\r
- {\r
- return this._has_colour;\r
- } //-- boolean hasColour()\r
-\r
- /**\r
- * Method hasEnd\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasEnd()\r
- {\r
- return this._has_end;\r
- } //-- boolean hasEnd()\r
-\r
- /**\r
- * Method hasHidden\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasHidden()\r
- {\r
- return this._has_hidden;\r
- } //-- boolean hasHidden()\r
-\r
- /**\r
- * Method hasId\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasId()\r
- {\r
- return this._has_id;\r
- } //-- boolean hasId()\r
-\r
- /**\r
- * Method hasStart\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasStart()\r
- {\r
- return this._has_start;\r
- } //-- boolean hasStart()\r
-\r
- /**\r
- * Method isValid\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try\r
- {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid()\r
-\r
- /**\r
- * Method marshal\r
- *\r
- *\r
- *\r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
- {\r
-\r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
-\r
- /**\r
- * Method marshal\r
- *\r
- *\r
- *\r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
- {\r
-\r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
- /**\r
- * Method removeAllFeatures\r
- *\r
- */\r
- public void removeAllFeatures()\r
- {\r
- _featuresList.removeAllElements();\r
- } //-- void removeAllFeatures()\r
-\r
- /**\r
- * Method removeAllHiddenSequences\r
- *\r
- */\r
- public void removeAllHiddenSequences()\r
- {\r
- _hiddenSequencesList.removeAllElements();\r
- } //-- void removeAllHiddenSequences()\r
-\r
- /**\r
- * Method removeAllPdbids\r
- *\r
- */\r
- public void removeAllPdbids()\r
- {\r
- _pdbidsList.removeAllElements();\r
- } //-- void removeAllPdbids()\r
-\r
- /**\r
- * Method removeFeatures\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return Features\r
- */\r
- public jalview.schemabinding.version2.Features removeFeatures(int index)\r
- {\r
- java.lang.Object obj = _featuresList.elementAt(index);\r
- _featuresList.removeElementAt(index);\r
- return (jalview.schemabinding.version2.Features) obj;\r
- } //-- jalview.schemabinding.version2.Features removeFeatures(int)\r
-\r
- /**\r
- * Method removeHiddenSequences\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return int\r
- */\r
- public int removeHiddenSequences(int index)\r
- {\r
- java.lang.Object obj = _hiddenSequencesList.elementAt(index);\r
- _hiddenSequencesList.removeElementAt(index);\r
- return ( (java.lang.Integer) obj).intValue();\r
- } //-- int removeHiddenSequences(int)\r
-\r
- /**\r
- * Method removePdbids\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return Pdbids\r
- */\r
- public jalview.schemabinding.version2.Pdbids removePdbids(int index)\r
- {\r
- java.lang.Object obj = _pdbidsList.elementAt(index);\r
- _pdbidsList.removeElementAt(index);\r
- return (jalview.schemabinding.version2.Pdbids) obj;\r
- } //-- jalview.schemabinding.version2.Pdbids removePdbids(int)\r
-\r
- /**\r
- * Sets the value of field 'colour'.\r
- *\r
- * @param colour the value of field 'colour'.\r
- */\r
- public void setColour(int colour)\r
- {\r
- this._colour = colour;\r
- this._has_colour = true;\r
- } //-- void setColour(int)\r
-\r
- /**\r
- * Sets the value of field 'end'.\r
- *\r
- * @param end the value of field 'end'.\r
- */\r
- public void setEnd(int end)\r
- {\r
- this._end = end;\r
- this._has_end = true;\r
- } //-- void setEnd(int)\r
-\r
- /**\r
- * Method setFeatures\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vFeatures\r
- */\r
- public void setFeatures(int index,\r
- jalview.schemabinding.version2.Features vFeatures)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _featuresList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _featuresList.setElementAt(vFeatures, index);\r
- } //-- void setFeatures(int, jalview.schemabinding.version2.Features)\r
-\r
- /**\r
- * Method setFeatures\r
- *\r
- *\r
- *\r
- * @param featuresArray\r
- */\r
- public void setFeatures(jalview.schemabinding.version2.Features[]\r
- featuresArray)\r
- {\r
- //-- copy array\r
- _featuresList.removeAllElements();\r
- for (int i = 0; i < featuresArray.length; i++)\r
- {\r
- _featuresList.addElement(featuresArray[i]);\r
- }\r
- } //-- void setFeatures(jalview.schemabinding.version2.Features)\r
-\r
- /**\r
- * Sets the value of field 'hidden'.\r
- *\r
- * @param hidden the value of field 'hidden'.\r
- */\r
- public void setHidden(boolean hidden)\r
- {\r
- this._hidden = hidden;\r
- this._has_hidden = true;\r
- } //-- void setHidden(boolean)\r
-\r
- /**\r
- * Method setHiddenSequences\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vHiddenSequences\r
- */\r
- public void setHiddenSequences(int index, int vHiddenSequences)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _hiddenSequencesList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _hiddenSequencesList.setElementAt(new java.lang.Integer(vHiddenSequences),\r
- index);\r
- } //-- void setHiddenSequences(int, int)\r
-\r
- /**\r
- * Method setHiddenSequences\r
- *\r
- *\r
- *\r
- * @param hiddenSequencesArray\r
- */\r
- public void setHiddenSequences(int[] hiddenSequencesArray)\r
- {\r
- //-- copy array\r
- _hiddenSequencesList.removeAllElements();\r
- for (int i = 0; i < hiddenSequencesArray.length; i++)\r
- {\r
- _hiddenSequencesList.addElement(new java.lang.Integer(\r
- hiddenSequencesArray[i]));\r
- }\r
- } //-- void setHiddenSequences(int)\r
-\r
- /**\r
- * Sets the value of field 'id'.\r
- *\r
- * @param id the value of field 'id'.\r
- */\r
- public void setId(int id)\r
- {\r
- this._id = id;\r
- this._has_id = true;\r
- } //-- void setId(int)\r
-\r
- /**\r
- * Method setPdbids\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vPdbids\r
- */\r
- public void setPdbids(int index,\r
- jalview.schemabinding.version2.Pdbids vPdbids)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _pdbidsList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _pdbidsList.setElementAt(vPdbids, index);\r
- } //-- void setPdbids(int, jalview.schemabinding.version2.Pdbids)\r
-\r
- /**\r
- * Method setPdbids\r
- *\r
- *\r
- *\r
- * @param pdbidsArray\r
- */\r
- public void setPdbids(jalview.schemabinding.version2.Pdbids[] pdbidsArray)\r
- {\r
- //-- copy array\r
- _pdbidsList.removeAllElements();\r
- for (int i = 0; i < pdbidsArray.length; i++)\r
- {\r
- _pdbidsList.addElement(pdbidsArray[i]);\r
- }\r
- } //-- void setPdbids(jalview.schemabinding.version2.Pdbids)\r
-\r
- /**\r
- * Sets the value of field 'start'.\r
- *\r
- * @param start the value of field 'start'.\r
- */\r
- public void setStart(int start)\r
- {\r
- this._start = start;\r
- this._has_start = true;\r
- } //-- void setStart(int)\r
-\r
- /**\r
- * Method unmarshal\r
- *\r
- *\r
- *\r
- * @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal(jalview.\r
- schemabinding.version2.JSeq.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
- /**\r
- * Method validate\r
- *\r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
- Validator();\r
- validator.validate(this);\r
- } //-- void validate()\r
+public class JSeq implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _colour.\r
+ */\r
+ private int _colour;\r
+\r
+ /**\r
+ * keeps track of state for field: _colour\r
+ */\r
+ private boolean _has_colour;\r
+\r
+ /**\r
+ * Field _start.\r
+ */\r
+ private int _start;\r
+\r
+ /**\r
+ * keeps track of state for field: _start\r
+ */\r
+ private boolean _has_start;\r
+\r
+ /**\r
+ * Field _end.\r
+ */\r
+ private int _end;\r
+\r
+ /**\r
+ * keeps track of state for field: _end\r
+ */\r
+ private boolean _has_end;\r
+\r
+ /**\r
+ * Field _id.\r
+ */\r
+ private java.lang.String _id;\r
+\r
+ /**\r
+ * Field _hidden.\r
+ */\r
+ private boolean _hidden;\r
+\r
+ /**\r
+ * keeps track of state for field: _hidden\r
+ */\r
+ private boolean _has_hidden;\r
+\r
+ /**\r
+ * Field _featuresList.\r
+ */\r
+ private java.util.Vector _featuresList;\r
+\r
+ /**\r
+ * Field _pdbidsList.\r
+ */\r
+ private java.util.Vector _pdbidsList;\r
+\r
+ /**\r
+ * Field _hiddenSequencesList.\r
+ */\r
+ private java.util.Vector _hiddenSequencesList;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public JSeq() {\r
+ super();\r
+ this._featuresList = new java.util.Vector();\r
+ this._pdbidsList = new java.util.Vector();\r
+ this._hiddenSequencesList = new java.util.Vector();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vFeatures\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addFeatures(\r
+ final jalview.schemabinding.version2.Features vFeatures)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._featuresList.addElement(vFeatures);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vFeatures\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addFeatures(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Features vFeatures)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._featuresList.add(index, vFeatures);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vHiddenSequences\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addHiddenSequences(\r
+ final int vHiddenSequences)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._hiddenSequencesList.addElement(new java.lang.Integer(vHiddenSequences));\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vHiddenSequences\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addHiddenSequences(\r
+ final int index,\r
+ final int vHiddenSequences)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._hiddenSequencesList.add(index, new java.lang.Integer(vHiddenSequences));\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vPdbids\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addPdbids(\r
+ final jalview.schemabinding.version2.Pdbids vPdbids)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._pdbidsList.addElement(vPdbids);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vPdbids\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addPdbids(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Pdbids vPdbids)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._pdbidsList.add(index, vPdbids);\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteColour(\r
+ ) {\r
+ this._has_colour= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteEnd(\r
+ ) {\r
+ this._has_end= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteHidden(\r
+ ) {\r
+ this._has_hidden= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteStart(\r
+ ) {\r
+ this._has_start= false;\r
+ }\r
+\r
+ /**\r
+ * Method enumerateFeatures.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.Features elements\r
+ */\r
+ public java.util.Enumeration enumerateFeatures(\r
+ ) {\r
+ return this._featuresList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumerateHiddenSequences.\r
+ * \r
+ * @return an Enumeration over all int elements\r
+ */\r
+ public java.util.Enumeration enumerateHiddenSequences(\r
+ ) {\r
+ return this._hiddenSequencesList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumeratePdbids.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.Pdbids elements\r
+ */\r
+ public java.util.Enumeration enumeratePdbids(\r
+ ) {\r
+ return this._pdbidsList.elements();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'colour'.\r
+ * \r
+ * @return the value of field 'Colour'.\r
+ */\r
+ public int getColour(\r
+ ) {\r
+ return this._colour;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'end'.\r
+ * \r
+ * @return the value of field 'End'.\r
+ */\r
+ public int getEnd(\r
+ ) {\r
+ return this._end;\r
+ }\r
+\r
+ /**\r
+ * Method getFeatures.\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.Features at the given index\r
+ */\r
+ public jalview.schemabinding.version2.Features getFeatures(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._featuresList.size()) {\r
+ throw new IndexOutOfBoundsException("getFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.Features) _featuresList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getFeatures.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 jalview.schemabinding.version2.Features[] getFeatures(\r
+ ) {\r
+ jalview.schemabinding.version2.Features[] array = new jalview.schemabinding.version2.Features[0];\r
+ return (jalview.schemabinding.version2.Features[]) this._featuresList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getFeaturesCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getFeaturesCount(\r
+ ) {\r
+ return this._featuresList.size();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'hidden'.\r
+ * \r
+ * @return the value of field 'Hidden'.\r
+ */\r
+ public boolean getHidden(\r
+ ) {\r
+ return this._hidden;\r
+ }\r
+\r
+ /**\r
+ * Method getHiddenSequences.\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 int at the given index\r
+ */\r
+ public int getHiddenSequences(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._hiddenSequencesList.size()) {\r
+ throw new IndexOutOfBoundsException("getHiddenSequences: Index value '" + index + "' not in range [0.." + (this._hiddenSequencesList.size() - 1) + "]");\r
+ }\r
+ \r
+ return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue();\r
+ }\r
+\r
+ /**\r
+ * Method getHiddenSequences.Returns the contents of the\r
+ * collection in an Array. \r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public int[] getHiddenSequences(\r
+ ) {\r
+ int size = this._hiddenSequencesList.size();\r
+ int[] array = new int[size];\r
+ java.util.Iterator iter = _hiddenSequencesList.iterator();\r
+ for (int index = 0; index < size; index++) {\r
+ array[index] = ((java.lang.Integer) iter.next()).intValue();\r
+ }\r
+ return array;\r
+ }\r
+\r
+ /**\r
+ * Method getHiddenSequencesCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getHiddenSequencesCount(\r
+ ) {\r
+ return this._hiddenSequencesList.size();\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
+ * Method getPdbids.\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.Pdbids at the given index\r
+ */\r
+ public jalview.schemabinding.version2.Pdbids getPdbids(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._pdbidsList.size()) {\r
+ throw new IndexOutOfBoundsException("getPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.Pdbids) _pdbidsList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getPdbids.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 jalview.schemabinding.version2.Pdbids[] getPdbids(\r
+ ) {\r
+ jalview.schemabinding.version2.Pdbids[] array = new jalview.schemabinding.version2.Pdbids[0];\r
+ return (jalview.schemabinding.version2.Pdbids[]) this._pdbidsList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getPdbidsCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getPdbidsCount(\r
+ ) {\r
+ return this._pdbidsList.size();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'start'.\r
+ * \r
+ * @return the value of field 'Start'.\r
+ */\r
+ public int getStart(\r
+ ) {\r
+ return this._start;\r
+ }\r
+\r
+ /**\r
+ * Method hasColour.\r
+ * \r
+ * @return true if at least one Colour has been added\r
+ */\r
+ public boolean hasColour(\r
+ ) {\r
+ return this._has_colour;\r
+ }\r
+\r
+ /**\r
+ * Method hasEnd.\r
+ * \r
+ * @return true if at least one End has been added\r
+ */\r
+ public boolean hasEnd(\r
+ ) {\r
+ return this._has_end;\r
+ }\r
+\r
+ /**\r
+ * Method hasHidden.\r
+ * \r
+ * @return true if at least one Hidden has been added\r
+ */\r
+ public boolean hasHidden(\r
+ ) {\r
+ return this._has_hidden;\r
+ }\r
+\r
+ /**\r
+ * Method hasStart.\r
+ * \r
+ * @return true if at least one Start has been added\r
+ */\r
+ public boolean hasStart(\r
+ ) {\r
+ return this._has_start;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'hidden'.\r
+ * \r
+ * @return the value of field 'Hidden'.\r
+ */\r
+ public boolean isHidden(\r
+ ) {\r
+ return this._hidden;\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 removeAllFeatures(\r
+ ) {\r
+ this._featuresList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllHiddenSequences(\r
+ ) {\r
+ this._hiddenSequencesList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllPdbids(\r
+ ) {\r
+ this._pdbidsList.clear();\r
+ }\r
+\r
+ /**\r
+ * Method removeFeatures.\r
+ * \r
+ * @param vFeatures\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeFeatures(\r
+ final jalview.schemabinding.version2.Features vFeatures) {\r
+ boolean removed = _featuresList.remove(vFeatures);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeFeaturesAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.Features removeFeaturesAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._featuresList.remove(index);\r
+ return (jalview.schemabinding.version2.Features) obj;\r
+ }\r
+\r
+ /**\r
+ * Method removeHiddenSequences.\r
+ * \r
+ * @param vHiddenSequences\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeHiddenSequences(\r
+ final int vHiddenSequences) {\r
+ boolean removed = _hiddenSequencesList.remove(new java.lang.Integer(vHiddenSequences));\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeHiddenSequencesAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public int removeHiddenSequencesAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._hiddenSequencesList.remove(index);\r
+ return ((java.lang.Integer) obj).intValue();\r
+ }\r
+\r
+ /**\r
+ * Method removePdbids.\r
+ * \r
+ * @param vPdbids\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removePdbids(\r
+ final jalview.schemabinding.version2.Pdbids vPdbids) {\r
+ boolean removed = _pdbidsList.remove(vPdbids);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removePdbidsAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.Pdbids removePdbidsAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._pdbidsList.remove(index);\r
+ return (jalview.schemabinding.version2.Pdbids) obj;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'colour'.\r
+ * \r
+ * @param colour the value of field 'colour'.\r
+ */\r
+ public void setColour(\r
+ final int colour) {\r
+ this._colour = colour;\r
+ this._has_colour = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'end'.\r
+ * \r
+ * @param end the value of field 'end'.\r
+ */\r
+ public void setEnd(\r
+ final int end) {\r
+ this._end = end;\r
+ this._has_end = true;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vFeatures\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setFeatures(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Features vFeatures)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._featuresList.size()) {\r
+ throw new IndexOutOfBoundsException("setFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._featuresList.set(index, vFeatures);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vFeaturesArray\r
+ */\r
+ public void setFeatures(\r
+ final jalview.schemabinding.version2.Features[] vFeaturesArray) {\r
+ //-- copy array\r
+ _featuresList.clear();\r
+ \r
+ for (int i = 0; i < vFeaturesArray.length; i++) {\r
+ this._featuresList.add(vFeaturesArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'hidden'.\r
+ * \r
+ * @param hidden the value of field 'hidden'.\r
+ */\r
+ public void setHidden(\r
+ final boolean hidden) {\r
+ this._hidden = hidden;\r
+ this._has_hidden = true;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vHiddenSequences\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setHiddenSequences(\r
+ final int index,\r
+ final int vHiddenSequences)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._hiddenSequencesList.size()) {\r
+ throw new IndexOutOfBoundsException("setHiddenSequences: Index value '" + index + "' not in range [0.." + (this._hiddenSequencesList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._hiddenSequencesList.set(index, new java.lang.Integer(vHiddenSequences));\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vHiddenSequencesArray\r
+ */\r
+ public void setHiddenSequences(\r
+ final int[] vHiddenSequencesArray) {\r
+ //-- copy array\r
+ _hiddenSequencesList.clear();\r
+ \r
+ for (int i = 0; i < vHiddenSequencesArray.length; i++) {\r
+ this._hiddenSequencesList.add(new java.lang.Integer(vHiddenSequencesArray[i]));\r
+ }\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
+ * \r
+ * \r
+ * @param index\r
+ * @param vPdbids\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setPdbids(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Pdbids vPdbids)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._pdbidsList.size()) {\r
+ throw new IndexOutOfBoundsException("setPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._pdbidsList.set(index, vPdbids);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vPdbidsArray\r
+ */\r
+ public void setPdbids(\r
+ final jalview.schemabinding.version2.Pdbids[] vPdbidsArray) {\r
+ //-- copy array\r
+ _pdbidsList.clear();\r
+ \r
+ for (int i = 0; i < vPdbidsArray.length; i++) {\r
+ this._pdbidsList.add(vPdbidsArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'start'.\r
+ * \r
+ * @param start the value of field 'start'.\r
+ */\r
+ public void setStart(\r
+ final int start) {\r
+ this._start = start;\r
+ this._has_start = 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 jalview.schemabinding.version2.JSeq\r
+ */\r
+ public static jalview.schemabinding.version2.JSeq unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal(jalview.schemabinding.version2.JSeq.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
git://source.jalview.org / jalview.git / blobdiff