-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
+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
+ * reference to set where jalview will gather the dataset sequences for all\r
+ * sequences in the set.\r
+ * \r
+ */\r
+ private java.lang.String _datasetId;\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
+ * Field _sequenceSetPropertiesList.\r
+ */\r
+ private java.util.Vector _sequenceSetPropertiesList;\r
+\r
+ /**\r
+ * Field _alcodonFrameList.\r
+ */\r
+ private java.util.Vector _alcodonFrameList;\r
+\r
+ // ----------------/\r
+ // - Constructors -/\r
+ // ----------------/\r
+\r
+ public SequenceSet()\r
+ {\r
+ super();\r
+ this._sequenceList = new java.util.Vector();\r
+ this._annotationList = new java.util.Vector();\r
+ this._sequenceSetPropertiesList = new java.util.Vector();\r
+ this._alcodonFrameList = new java.util.Vector();\r
+ }\r
+\r
+ // -----------/\r
+ // - Methods -/\r
+ // -----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vAlcodonFrame\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addAlcodonFrame(\r
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._alcodonFrameList.addElement(vAlcodonFrame);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAlcodonFrame\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addAlcodonFrame(final int index,\r
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._alcodonFrameList.add(index, vAlcodonFrame);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vAnnotation\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addAnnotation(\r
+ final jalview.schemabinding.version2.Annotation vAnnotation)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._annotationList.addElement(vAnnotation);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAnnotation\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addAnnotation(final int index,\r
+ final jalview.schemabinding.version2.Annotation vAnnotation)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._annotationList.add(index, vAnnotation);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vSequence\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addSequence(\r
+ final jalview.schemabinding.version2.Sequence vSequence)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._sequenceList.addElement(vSequence);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vSequence\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addSequence(final int index,\r
+ final jalview.schemabinding.version2.Sequence vSequence)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._sequenceList.add(index, vSequence);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vSequenceSetProperties\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addSequenceSetProperties(\r
+ final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._sequenceSetPropertiesList.addElement(vSequenceSetProperties);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vSequenceSetProperties\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addSequenceSetProperties(\r
+ final int index,\r
+ final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._sequenceSetPropertiesList.add(index, vSequenceSetProperties);\r
+ }\r
+\r
+ /**\r
+ * Method enumerateAlcodonFrame.\r
+ * \r
+ * @return an Enumeration over all jalview.schemabinding.version2.AlcodonFrame\r
+ * elements\r
+ */\r
+ public java.util.Enumeration enumerateAlcodonFrame()\r
+ {\r
+ return this._alcodonFrameList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumerateAnnotation.\r
+ * \r
+ * @return an Enumeration over all jalview.schemabinding.version2.Annotation\r
+ * elements\r
+ */\r
+ public java.util.Enumeration enumerateAnnotation()\r
+ {\r
+ return this._annotationList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumerateSequence.\r
+ * \r
+ * @return an Enumeration over all jalview.schemabinding.version2.Sequence\r
+ * elements\r
+ */\r
+ public java.util.Enumeration enumerateSequence()\r
+ {\r
+ return this._sequenceList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumerateSequenceSetProperties.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.SequenceSetProperties elements\r
+ */\r
+ public java.util.Enumeration enumerateSequenceSetProperties()\r
+ {\r
+ return this._sequenceSetPropertiesList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method getAlcodonFrame.\r
+ * \r
+ * @param index\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ * @return the value of the jalview.schemabinding.version2.AlcodonFrame at the\r
+ * given inde\r
+ */\r
+ public jalview.schemabinding.version2.AlcodonFrame getAlcodonFrame(\r
+ final int index) throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._alcodonFrameList.size())\r