-public class SequenceSet\r
- implements java.io.Serializable\r
-{\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _gapChar\r
- */\r
- private java.lang.String _gapChar;\r
-\r
- /**\r
- * Field _sequenceList\r
- */\r
- private java.util.Vector _sequenceList;\r
-\r
- /**\r
- * Field _annotationList\r
- */\r
- private java.util.Vector _annotationList;\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public SequenceSet()\r
- {\r
- super();\r
- _sequenceList = new Vector();\r
- _annotationList = new Vector();\r
- } //-- jalview.schemabinding.version2.SequenceSet()\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addAnnotation\r
- *\r
- *\r
- *\r
- * @param vAnnotation\r
- */\r
- public void addAnnotation(jalview.schemabinding.version2.Annotation\r
- vAnnotation)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _annotationList.addElement(vAnnotation);\r
- } //-- void addAnnotation(jalview.schemabinding.version2.Annotation)\r
-\r
- /**\r
- * Method addAnnotation\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vAnnotation\r
- */\r
- public void addAnnotation(int index,\r
- jalview.schemabinding.version2.Annotation\r
- vAnnotation)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _annotationList.insertElementAt(vAnnotation, index);\r
- } //-- void addAnnotation(int, jalview.schemabinding.version2.Annotation)\r
-\r
- /**\r
- * Method addSequence\r
- *\r
- *\r
- *\r
- * @param vSequence\r
- */\r
- public void addSequence(jalview.schemabinding.version2.Sequence vSequence)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _sequenceList.addElement(vSequence);\r
- } //-- void addSequence(jalview.schemabinding.version2.Sequence)\r
-\r
- /**\r
- * Method addSequence\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vSequence\r
- */\r
- public void addSequence(int index,\r
- jalview.schemabinding.version2.Sequence vSequence)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _sequenceList.insertElementAt(vSequence, index);\r
- } //-- void addSequence(int, jalview.schemabinding.version2.Sequence)\r
-\r
- /**\r
- * Method enumerateAnnotation\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateAnnotation()\r
- {\r
- return _annotationList.elements();\r
- } //-- java.util.Enumeration enumerateAnnotation()\r
-\r
- /**\r
- * Method enumerateSequence\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateSequence()\r
- {\r
- return _sequenceList.elements();\r
- } //-- java.util.Enumeration enumerateSequence()\r
-\r
- /**\r
- * Method getAnnotation\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return Annotation\r
- */\r
- public jalview.schemabinding.version2.Annotation getAnnotation(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _annotationList.size()))\r
+public class SequenceSet implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _gapChar\r
+ */\r
+ private java.lang.String _gapChar;\r
+\r
+ /**\r
+ * Field _sequenceList\r
+ */\r
+ private java.util.Vector _sequenceList;\r
+\r
+ /**\r
+ * Field _annotationList\r
+ */\r
+ private java.util.Vector _annotationList;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public SequenceSet() {\r
+ super();\r
+ _sequenceList = new Vector();\r
+ _annotationList = new Vector();\r
+ } //-- jalview.schemabinding.version2.SequenceSet()\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method addAnnotation\r
+ * \r
+ * \r
+ * \r
+ * @param vAnnotation\r
+ */\r
+ public void addAnnotation(jalview.schemabinding.version2.Annotation vAnnotation)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _annotationList.addElement(vAnnotation);\r
+ } //-- void addAnnotation(jalview.schemabinding.version2.Annotation) \r
+\r
+ /**\r
+ * Method addAnnotation\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAnnotation\r
+ */\r
+ public void addAnnotation(int index, jalview.schemabinding.version2.Annotation vAnnotation)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _annotationList.insertElementAt(vAnnotation, index);\r
+ } //-- void addAnnotation(int, jalview.schemabinding.version2.Annotation) \r
+\r
+ /**\r
+ * Method addSequence\r
+ * \r
+ * \r
+ * \r
+ * @param vSequence\r
+ */\r
+ public void addSequence(jalview.schemabinding.version2.Sequence vSequence)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _sequenceList.addElement(vSequence);\r
+ } //-- void addSequence(jalview.schemabinding.version2.Sequence) \r
+\r
+ /**\r
+ * Method addSequence\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vSequence\r
+ */\r
+ public void addSequence(int index, jalview.schemabinding.version2.Sequence vSequence)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _sequenceList.insertElementAt(vSequence, index);\r
+ } //-- void addSequence(int, jalview.schemabinding.version2.Sequence) \r
+\r
+ /**\r
+ * Method enumerateAnnotation\r
+ * \r
+ * \r
+ * \r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumerateAnnotation()\r
+ {\r
+ return _annotationList.elements();\r
+ } //-- java.util.Enumeration enumerateAnnotation() \r
+\r
+ /**\r
+ * Method enumerateSequence\r
+ * \r
+ * \r
+ * \r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumerateSequence()\r
+ {\r
+ return _sequenceList.elements();\r
+ } //-- java.util.Enumeration enumerateSequence() \r
+\r
+ /**\r
+ * Method getAnnotation\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Annotation\r
+ */\r
+ public jalview.schemabinding.version2.Annotation getAnnotation(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _annotationList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.Annotation) _annotationList.elementAt(index);\r
+ } //-- jalview.schemabinding.version2.Annotation getAnnotation(int) \r
+\r
+ /**\r
+ * Method getAnnotation\r
+ * \r
+ * \r
+ * \r
+ * @return Annotation\r
+ */\r
+ public jalview.schemabinding.version2.Annotation[] getAnnotation()\r
+ {\r
+ int size = _annotationList.size();\r
+ jalview.schemabinding.version2.Annotation[] mArray = new jalview.schemabinding.version2.Annotation[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.schemabinding.version2.Annotation) _annotationList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- jalview.schemabinding.version2.Annotation[] getAnnotation() \r
+\r
+ /**\r
+ * Method getAnnotationCount\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int getAnnotationCount()\r
+ {\r
+ return _annotationList.size();\r
+ } //-- int getAnnotationCount() \r
+\r
+ /**\r
+ * Returns the value of field 'gapChar'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'gapChar'.\r
+ */\r
+ public java.lang.String getGapChar()\r
+ {\r
+ return this._gapChar;\r
+ } //-- java.lang.String getGapChar() \r
+\r
+ /**\r
+ * Method getSequence\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Sequence\r
+ */\r
+ public jalview.schemabinding.version2.Sequence getSequence(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _sequenceList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.Sequence) _sequenceList.elementAt(index);\r
+ } //-- jalview.schemabinding.version2.Sequence getSequence(int) \r
+\r
+ /**\r
+ * Method getSequence\r
+ * \r
+ * \r
+ * \r
+ * @return Sequence\r
+ */\r
+ public jalview.schemabinding.version2.Sequence[] getSequence()\r
+ {\r
+ int size = _sequenceList.size();\r
+ jalview.schemabinding.version2.Sequence[] mArray = new jalview.schemabinding.version2.Sequence[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.schemabinding.version2.Sequence) _sequenceList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- jalview.schemabinding.version2.Sequence[] getSequence() \r
+\r
+ /**\r
+ * Method getSequenceCount\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int getSequenceCount()\r
+ {\r
+ return _sequenceList.size();\r
+ } //-- int getSequenceCount() \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 removeAllAnnotation\r
+ * \r
+ */\r
+ public void removeAllAnnotation()\r
+ {\r
+ _annotationList.removeAllElements();\r
+ } //-- void removeAllAnnotation() \r
+\r
+ /**\r
+ * Method removeAllSequence\r
+ * \r
+ */\r
+ public void removeAllSequence()\r