/*\r
- * This class was automatically generated with\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
*/\r
\r
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 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.binding;\r
\r
//---------------------------------/\r
import java.io.Reader;\r
import java.io.Serializable;\r
import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
import org.exolab.castor.xml.MarshalException;\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 implements java.io.Serializable {\r
*/\r
private boolean _has_id;\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
//----------------/\r
//- Constructors -/\r
\r
public JSeq() {\r
super();\r
+ _featuresList = new Vector();\r
+ _pdbidsList = new Vector();\r
} //-- jalview.binding.JSeq()\r
\r
\r
//-----------/\r
\r
/**\r
+ * Method addFeatures\r
+ * \r
+ * \r
+ * \r
+ * @param vFeatures\r
+ */\r
+ public void addFeatures(jalview.binding.Features vFeatures)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _featuresList.addElement(vFeatures);\r
+ } //-- void addFeatures(jalview.binding.Features) \r
+\r
+ /**\r
+ * Method addFeatures\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vFeatures\r
+ */\r
+ public void addFeatures(int index, jalview.binding.Features vFeatures)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _featuresList.insertElementAt(vFeatures, index);\r
+ } //-- void addFeatures(int, jalview.binding.Features) \r
+\r
+ /**\r
+ * Method addPdbids\r
+ * \r
+ * \r
+ * \r
+ * @param vPdbids\r
+ */\r
+ public void addPdbids(jalview.binding.Pdbids vPdbids)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _pdbidsList.addElement(vPdbids);\r
+ } //-- void addPdbids(jalview.binding.Pdbids) \r
+\r
+ /**\r
+ * Method addPdbids\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vPdbids\r
+ */\r
+ public void addPdbids(int index, jalview.binding.Pdbids vPdbids)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _pdbidsList.insertElementAt(vPdbids, index);\r
+ } //-- void addPdbids(int, jalview.binding.Pdbids) \r
+\r
+ /**\r
* Method deleteColour\r
- *\r
+ * \r
*/\r
public void deleteColour()\r
{\r
this._has_colour= false;\r
- } //-- void deleteColour()\r
+ } //-- void deleteColour() \r
\r
/**\r
* Method deleteEnd\r
- *\r
+ * \r
*/\r
public void deleteEnd()\r
{\r
this._has_end= false;\r
- } //-- void deleteEnd()\r
+ } //-- void deleteEnd() \r
\r
/**\r
* Method deleteId\r
- *\r
+ * \r
*/\r
public void deleteId()\r
{\r
this._has_id= false;\r
- } //-- void deleteId()\r
+ } //-- void deleteId() \r
\r
/**\r
* Method deleteStart\r
- *\r
+ * \r
*/\r
public void deleteStart()\r
{\r
this._has_start= false;\r
- } //-- void deleteStart()\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 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
+ * \r
* @return int\r
* @return the value of field 'colour'.\r
*/\r
public int getColour()\r
{\r
return this._colour;\r
- } //-- int getColour()\r
+ } //-- int getColour() \r
\r
/**\r
* Returns the value of field 'end'.\r
- *\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
+ } //-- int getEnd() \r
+\r
+ /**\r
+ * Method getFeatures\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Features\r
+ */\r
+ public jalview.binding.Features getFeatures(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _featuresList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ \r
+ return (jalview.binding.Features) _featuresList.elementAt(index);\r
+ } //-- jalview.binding.Features getFeatures(int) \r
+\r
+ /**\r
+ * Method getFeatures\r
+ * \r
+ * \r
+ * \r
+ * @return Features\r
+ */\r
+ public jalview.binding.Features[] getFeatures()\r
+ {\r
+ int size = _featuresList.size();\r
+ jalview.binding.Features[] mArray = new jalview.binding.Features[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.binding.Features) _featuresList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- jalview.binding.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 'id'.\r
- *\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
+ } //-- int getId() \r
+\r
+ /**\r
+ * Method getPdbids\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Pdbids\r
+ */\r
+ public jalview.binding.Pdbids getPdbids(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _pdbidsList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ \r
+ return (jalview.binding.Pdbids) _pdbidsList.elementAt(index);\r
+ } //-- jalview.binding.Pdbids getPdbids(int) \r
+\r
+ /**\r
+ * Method getPdbids\r
+ * \r
+ * \r
+ * \r
+ * @return Pdbids\r
+ */\r
+ public jalview.binding.Pdbids[] getPdbids()\r
+ {\r
+ int size = _pdbidsList.size();\r
+ jalview.binding.Pdbids[] mArray = new jalview.binding.Pdbids[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.binding.Pdbids) _pdbidsList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- jalview.binding.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
+ * \r
* @return int\r
* @return the value of field 'start'.\r
*/\r
public int getStart()\r
{\r
return this._start;\r
- } //-- int getStart()\r
+ } //-- int getStart() \r
\r
/**\r
* Method hasColour\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasColour()\r
{\r
return this._has_colour;\r
- } //-- boolean hasColour()\r
+ } //-- boolean hasColour() \r
\r
/**\r
* Method hasEnd\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasEnd()\r
{\r
return this._has_end;\r
- } //-- boolean hasEnd()\r
+ } //-- boolean hasEnd() \r
\r
/**\r
* Method hasId\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasId()\r
{\r
return this._has_id;\r
- } //-- boolean hasId()\r
+ } //-- boolean hasId() \r
\r
/**\r
* Method hasStart\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean hasStart()\r
{\r
return this._has_start;\r
- } //-- boolean hasStart()\r
+ } //-- boolean hasStart() \r
\r
/**\r
* Method isValid\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
public boolean isValid()\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid()\r
+ } //-- boolean isValid() \r
\r
/**\r
* Method marshal\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
-\r
+ \r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
+ } //-- void marshal(java.io.Writer) \r
\r
/**\r
* Method marshal\r
- *\r
- *\r
- *\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, org.exolab.castor.xml.ValidationException\r
{\r
-\r
+ \r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\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 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.binding.Features removeFeatures(int index)\r
+ {\r
+ java.lang.Object obj = _featuresList.elementAt(index);\r
+ _featuresList.removeElementAt(index);\r
+ return (jalview.binding.Features) obj;\r
+ } //-- jalview.binding.Features removeFeatures(int) \r
+\r
+ /**\r
+ * Method removePdbids\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Pdbids\r
+ */\r
+ public jalview.binding.Pdbids removePdbids(int index)\r
+ {\r
+ java.lang.Object obj = _pdbidsList.elementAt(index);\r
+ _pdbidsList.removeElementAt(index);\r
+ return (jalview.binding.Pdbids) obj;\r
+ } //-- jalview.binding.Pdbids removePdbids(int) \r
\r
/**\r
* Sets the value of field 'colour'.\r
- *\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
+ } //-- void setColour(int) \r
\r
/**\r
* Sets the value of field 'end'.\r
- *\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
+ } //-- void setEnd(int) \r
+\r
+ /**\r
+ * Method setFeatures\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vFeatures\r
+ */\r
+ public void setFeatures(int index, jalview.binding.Features vFeatures)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _featuresList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ _featuresList.setElementAt(vFeatures, index);\r
+ } //-- void setFeatures(int, jalview.binding.Features) \r
+\r
+ /**\r
+ * Method setFeatures\r
+ * \r
+ * \r
+ * \r
+ * @param featuresArray\r
+ */\r
+ public void setFeatures(jalview.binding.Features[] featuresArray)\r
+ {\r
+ //-- copy array\r
+ _featuresList.removeAllElements();\r
+ for (int i = 0; i < featuresArray.length; i++) {\r
+ _featuresList.addElement(featuresArray[i]);\r
+ }\r
+ } //-- void setFeatures(jalview.binding.Features) \r
\r
/**\r
* Sets the value of field 'id'.\r
- *\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
+ } //-- void setId(int) \r
+\r
+ /**\r
+ * Method setPdbids\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vPdbids\r
+ */\r
+ public void setPdbids(int index, jalview.binding.Pdbids vPdbids)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _pdbidsList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ _pdbidsList.setElementAt(vPdbids, index);\r
+ } //-- void setPdbids(int, jalview.binding.Pdbids) \r
+\r
+ /**\r
+ * Method setPdbids\r
+ * \r
+ * \r
+ * \r
+ * @param pdbidsArray\r
+ */\r
+ public void setPdbids(jalview.binding.Pdbids[] pdbidsArray)\r
+ {\r
+ //-- copy array\r
+ _pdbidsList.removeAllElements();\r
+ for (int i = 0; i < pdbidsArray.length; i++) {\r
+ _pdbidsList.addElement(pdbidsArray[i]);\r
+ }\r
+ } //-- void setPdbids(jalview.binding.Pdbids) \r
\r
/**\r
* Sets the value of field 'start'.\r
- *\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
+ } //-- void setStart(int) \r
\r
/**\r
* Method unmarshal\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param reader\r
* @return Object\r
*/\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
return (jalview.binding.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
+ } //-- java.lang.Object unmarshal(java.io.Reader) \r
\r
/**\r
* Method validate\r
- *\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.Validator();\r
validator.validate(this);\r
- } //-- void validate()\r
+ } //-- void validate() \r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff