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
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
} //-- 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
* @return int\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
* @return int\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
* @return int\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
* @param colour the value of field 'colour'.\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
* @param id the value of field 'id'.\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
* @param start the value of field 'start'.\r