/*\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
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 java.io.IOException;\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
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\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 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
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public JSeq() {\r
+ super();\r
+ _featuresList = new Vector();\r
+ _pdbidsList = new Vector();\r
+ _hiddenSequencesList = new Vector();\r
+ } //-- jalview.schemabinding.version2.JSeq()\r
+\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, 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), 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, 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
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.Features) _featuresList.elementAt(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.schemabinding.version2.Features[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.schemabinding.version2.Features) _featuresList.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
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ \r
+ return ((java.lang.Integer)_hiddenSequencesList.elementAt(index)).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
+ mArray[index] = ((java.lang.Integer)_hiddenSequencesList.elementAt(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
+ 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.version2.Pdbids[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.schemabinding.version2.Pdbids) _pdbidsList.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
+ validate();\r
+ }\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\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, 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, 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, jalview.schemabinding.version2.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.schemabinding.version2.Features) \r
+\r
+ /**\r
+ * Method setFeatures\r
+ * \r
+ * \r
+ * \r
+ * @param featuresArray\r
+ */\r
+ public void setFeatures(jalview.schemabinding.version2.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.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
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ _hiddenSequencesList.setElementAt(new java.lang.Integer(vHiddenSequences), 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
+ _hiddenSequencesList.addElement(new java.lang.Integer(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, jalview.schemabinding.version2.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.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
+ _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, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal(jalview.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.Validator();\r
+ validator.validate(this);\r
+ } //-- void validate() \r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff