private java.lang.String _gapChar;\r
\r
/**\r
+ * reference to set where jalview will gather the dataset\r
+ * sequences for all 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
private java.util.Vector _sequenceSetPropertiesList;\r
\r
+ /**\r
+ * Field _alcodonFrameList.\r
+ */\r
+ private java.util.Vector _alcodonFrameList;\r
+\r
\r
//----------------/\r
//- Constructors -/\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
/**\r
* \r
* \r
+ * @param vAlcodonFrame\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * 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
+ this._alcodonFrameList.addElement(vAlcodonFrame);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAlcodonFrame\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addAlcodonFrame(\r
+ final int index,\r
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._alcodonFrameList.add(index, vAlcodonFrame);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
* @param vAnnotation\r
* @throws java.lang.IndexOutOfBoundsException if the index\r
* given is outside the bounds of the collection\r
}\r
\r
/**\r
+ * Method enumerateAlcodonFrame.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.AlcodonFrame 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\r
}\r
\r
/**\r
+ * Method getAlcodonFrame.\r
+ * \r
+ * @param index\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.AlcodonFrame at the given inde\r
+ */\r
+ public jalview.schemabinding.version2.AlcodonFrame getAlcodonFrame(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._alcodonFrameList.size()) {\r
+ throw new IndexOutOfBoundsException("getAlcodonFrame: Index value '" + index + "' not in range [0.." + (this._alcodonFrameList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.AlcodonFrame) _alcodonFrameList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getAlcodonFrame.Returns the contents of the\r
+ * collection in an Array. <p>Note: Just in case the\r
+ * collection contents are changing in another thread, we pass\r
+ * a 0-length Array of the correct type into the API call. \r
+ * This way we <i>know</i> that the Array returned is of\r
+ * exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.AlcodonFrame[] getAlcodonFrame(\r
+ ) {\r
+ jalview.schemabinding.version2.AlcodonFrame[] array = new jalview.schemabinding.version2.AlcodonFrame[0];\r
+ return (jalview.schemabinding.version2.AlcodonFrame[]) this._alcodonFrameList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getAlcodonFrameCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getAlcodonFrameCount(\r
+ ) {\r
+ return this._alcodonFrameList.size();\r
+ }\r
+\r
+ /**\r
* Method getAnnotation.\r
* \r
* @param index\r
}\r
\r
/**\r
+ * Returns the value of field 'datasetId'. The field\r
+ * 'datasetId' has the following description: reference to set\r
+ * where jalview will gather the dataset sequences for all\r
+ * sequences in the set. \r
+ * \r
+ * \r
+ * @return the value of field 'DatasetId'.\r
+ */\r
+ public java.lang.String getDatasetId(\r
+ ) {\r
+ return this._datasetId;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'gapChar'.\r
* \r
* @return the value of field 'GapChar'.\r
}\r
\r
/**\r
+ * Method removeAlcodonFrame.\r
+ * \r
+ * @param vAlcodonFrame\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeAlcodonFrame(\r
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) {\r
+ boolean removed = _alcodonFrameList.remove(vAlcodonFrame);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeAlcodonFrameAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.AlcodonFrame removeAlcodonFrameAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._alcodonFrameList.remove(index);\r
+ return (jalview.schemabinding.version2.AlcodonFrame) obj;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllAlcodonFrame(\r
+ ) {\r
+ this._alcodonFrameList.clear();\r
+ }\r
+\r
+ /**\r
*/\r
public void removeAllAnnotation(\r
) {\r
* \r
* \r
* @param index\r
+ * @param vAlcodonFrame\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setAlcodonFrame(\r
+ final int index,\r
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._alcodonFrameList.size()) {\r
+ throw new IndexOutOfBoundsException("setAlcodonFrame: Index value '" + index + "' not in range [0.." + (this._alcodonFrameList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._alcodonFrameList.set(index, vAlcodonFrame);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vAlcodonFrameArray\r
+ */\r
+ public void setAlcodonFrame(\r
+ final jalview.schemabinding.version2.AlcodonFrame[] vAlcodonFrameArray) {\r
+ //-- copy array\r
+ _alcodonFrameList.clear();\r
+ \r
+ for (int i = 0; i < vAlcodonFrameArray.length; i++) {\r
+ this._alcodonFrameList.add(vAlcodonFrameArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
* @param vAnnotation\r
* @throws java.lang.IndexOutOfBoundsException if the index\r
* given is outside the bounds of the collection\r
}\r
\r
/**\r
+ * Sets the value of field 'datasetId'. The field 'datasetId'\r
+ * has the following description: reference to set where\r
+ * jalview will gather the dataset sequences for all sequences\r
+ * in the set. \r
+ * \r
+ * \r
+ * @param datasetId the value of field 'datasetId'.\r
+ */\r
+ public void setDatasetId(\r
+ final java.lang.String datasetId) {\r
+ this._datasetId = datasetId;\r
+ }\r
+\r
+ /**\r
* Sets the value of field 'gapChar'.\r
* \r
* @param gapChar the value of field 'gapChar'.\r
git://source.jalview.org / jalview.git / blobdiff