private boolean _has_textColThreshold;\r
\r
/**\r
+ * Field _showUnconserved.\r
+ */\r
+ private boolean _showUnconserved;\r
+\r
+ /**\r
+ * keeps track of state for field: _showUnconserved\r
+ */\r
+ private boolean _has_showUnconserved;\r
+\r
+ /**\r
+ * Field _ignoreGapsinConsensus.\r
+ */\r
+ private boolean _ignoreGapsinConsensus = true;\r
+\r
+ /**\r
+ * keeps track of state for field: _ignoreGapsinConsensus\r
+ */\r
+ private boolean _has_ignoreGapsinConsensus;\r
+\r
+ /**\r
+ * Field _showConsensusHistogram.\r
+ */\r
+ private boolean _showConsensusHistogram = true;\r
+\r
+ /**\r
+ * keeps track of state for field: _showConsensusHistogram\r
+ */\r
+ private boolean _has_showConsensusHistogram;\r
+\r
+ /**\r
+ * Field _showSequenceLogo.\r
+ */\r
+ private boolean _showSequenceLogo = false;\r
+\r
+ /**\r
+ * keeps track of state for field: _showSequenceLogo\r
+ */\r
+ private boolean _has_showSequenceLogo;\r
+\r
+ /**\r
+ * Optional sequence group ID (only needs to be unique for this\r
+ * alignment)\r
+ * \r
+ */\r
+ private java.lang.String _id;\r
+\r
+ /**\r
* Field _seqList.\r
*/\r
private java.util.Vector _seqList;\r
* given is outside the bounds of the collection\r
*/\r
public void addSeq(\r
- final int vSeq)\r
+ final java.lang.String vSeq)\r
throws java.lang.IndexOutOfBoundsException {\r
- this._seqList.addElement(new java.lang.Integer(vSeq));\r
+ this._seqList.addElement(vSeq);\r
}\r
\r
/**\r
*/\r
public void addSeq(\r
final int index,\r
- final int vSeq)\r
+ final java.lang.String vSeq)\r
throws java.lang.IndexOutOfBoundsException {\r
- this._seqList.add(index, new java.lang.Integer(vSeq));\r
+ this._seqList.add(index, vSeq);\r
}\r
\r
/**\r
\r
/**\r
*/\r
+ public void deleteIgnoreGapsinConsensus(\r
+ ) {\r
+ this._has_ignoreGapsinConsensus= false;\r
+ }\r
+\r
+ /**\r
+ */\r
public void deleteOutlineColour(\r
) {\r
this._has_outlineColour= false;\r
\r
/**\r
*/\r
+ public void deleteShowConsensusHistogram(\r
+ ) {\r
+ this._has_showConsensusHistogram= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowSequenceLogo(\r
+ ) {\r
+ this._has_showSequenceLogo= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteShowUnconserved(\r
+ ) {\r
+ this._has_showUnconserved= false;\r
+ }\r
+\r
+ /**\r
+ */\r
public void deleteStart(\r
) {\r
this._has_start= false;\r
/**\r
* Method enumerateSeq.\r
* \r
- * @return an Enumeration over all int elements\r
+ * @return an Enumeration over all java.lang.String elements\r
*/\r
public java.util.Enumeration enumerateSeq(\r
) {\r
}\r
\r
/**\r
+ * Returns the value of field 'id'. The field 'id' has the\r
+ * following description: Optional sequence group ID (only\r
+ * needs to be unique for this alignment)\r
+ * \r
+ * \r
+ * @return the value of field 'Id'.\r
+ */\r
+ public java.lang.String getId(\r
+ ) {\r
+ return this._id;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'ignoreGapsinConsensus'.\r
+ * \r
+ * @return the value of field 'IgnoreGapsinConsensus'.\r
+ */\r
+ public boolean getIgnoreGapsinConsensus(\r
+ ) {\r
+ return this._ignoreGapsinConsensus;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'name'.\r
* \r
* @return the value of field 'Name'.\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 int at the given index\r
+ * @return the value of the java.lang.String at the given index\r
*/\r
- public int getSeq(\r
+ public java.lang.String getSeq(\r
final int index)\r
throws java.lang.IndexOutOfBoundsException {\r
// check bounds for index\r
throw new IndexOutOfBoundsException("getSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");\r
}\r
\r
- return ((java.lang.Integer) _seqList.get(index)).intValue();\r
+ return (java.lang.String) _seqList.get(index);\r
}\r
\r
/**\r
* Method getSeq.Returns the contents of the collection in an\r
- * Array. \r
+ * Array. <p>Note: Just in case the collection contents are\r
+ * changing in another thread, we pass a 0-length Array of the\r
+ * correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
* \r
* @return this collection as an Array\r
*/\r
- public int[] getSeq(\r
+ public java.lang.String[] getSeq(\r
) {\r
- int size = this._seqList.size();\r
- int[] array = new int[size];\r
- java.util.Iterator iter = _seqList.iterator();\r
- for (int index = 0; index < size; index++) {\r
- array[index] = ((java.lang.Integer) iter.next()).intValue();\r
- }\r
- return array;\r
+ java.lang.String[] array = new java.lang.String[0];\r
+ return (java.lang.String[]) this._seqList.toArray(array);\r
}\r
\r
/**\r
}\r
\r
/**\r
+ * Returns the value of field 'showConsensusHistogram'.\r
+ * \r
+ * @return the value of field 'ShowConsensusHistogram'.\r
+ */\r
+ public boolean getShowConsensusHistogram(\r
+ ) {\r
+ return this._showConsensusHistogram;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showSequenceLogo'.\r
+ * \r
+ * @return the value of field 'ShowSequenceLogo'.\r
+ */\r
+ public boolean getShowSequenceLogo(\r
+ ) {\r
+ return this._showSequenceLogo;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showUnconserved'.\r
+ * \r
+ * @return the value of field 'ShowUnconserved'.\r
+ */\r
+ public boolean getShowUnconserved(\r
+ ) {\r
+ return this._showUnconserved;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'start'.\r
* \r
* @return the value of field 'Start'.\r
}\r
\r
/**\r
+ * Method hasIgnoreGapsinConsensus.\r
+ * \r
+ * @return true if at least one IgnoreGapsinConsensus has been\r
+ * added\r
+ */\r
+ public boolean hasIgnoreGapsinConsensus(\r
+ ) {\r
+ return this._has_ignoreGapsinConsensus;\r
+ }\r
+\r
+ /**\r
* Method hasOutlineColour.\r
* \r
* @return true if at least one OutlineColour has been added\r
}\r
\r
/**\r
+ * Method hasShowConsensusHistogram.\r
+ * \r
+ * @return true if at least one ShowConsensusHistogram has been\r
+ * added\r
+ */\r
+ public boolean hasShowConsensusHistogram(\r
+ ) {\r
+ return this._has_showConsensusHistogram;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowSequenceLogo.\r
+ * \r
+ * @return true if at least one ShowSequenceLogo has been added\r
+ */\r
+ public boolean hasShowSequenceLogo(\r
+ ) {\r
+ return this._has_showSequenceLogo;\r
+ }\r
+\r
+ /**\r
+ * Method hasShowUnconserved.\r
+ * \r
+ * @return true if at least one ShowUnconserved has been added\r
+ */\r
+ public boolean hasShowUnconserved(\r
+ ) {\r
+ return this._has_showUnconserved;\r
+ }\r
+\r
+ /**\r
* Method hasStart.\r
* \r
* @return true if at least one Start has been added\r
}\r
\r
/**\r
+ * Returns the value of field 'ignoreGapsinConsensus'.\r
+ * \r
+ * @return the value of field 'IgnoreGapsinConsensus'.\r
+ */\r
+ public boolean isIgnoreGapsinConsensus(\r
+ ) {\r
+ return this._ignoreGapsinConsensus;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showConsensusHistogram'.\r
+ * \r
+ * @return the value of field 'ShowConsensusHistogram'.\r
+ */\r
+ public boolean isShowConsensusHistogram(\r
+ ) {\r
+ return this._showConsensusHistogram;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showSequenceLogo'.\r
+ * \r
+ * @return the value of field 'ShowSequenceLogo'.\r
+ */\r
+ public boolean isShowSequenceLogo(\r
+ ) {\r
+ return this._showSequenceLogo;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'showUnconserved'.\r
+ * \r
+ * @return the value of field 'ShowUnconserved'.\r
+ */\r
+ public boolean isShowUnconserved(\r
+ ) {\r
+ return this._showUnconserved;\r
+ }\r
+\r
+ /**\r
* Method isValid.\r
* \r
* @return true if this object is valid according to the schema\r
* @return true if the object was removed from the collection.\r
*/\r
public boolean removeSeq(\r
- final int vSeq) {\r
- boolean removed = _seqList.remove(new java.lang.Integer(vSeq));\r
+ final java.lang.String vSeq) {\r
+ boolean removed = _seqList.remove(vSeq);\r
return removed;\r
}\r
\r
* @param index\r
* @return the element removed from the collection\r
*/\r
- public int removeSeqAt(\r
+ public java.lang.String removeSeqAt(\r
final int index) {\r
java.lang.Object obj = this._seqList.remove(index);\r
- return ((java.lang.Integer) obj).intValue();\r
+ return (java.lang.String) obj;\r
}\r
\r
/**\r
}\r
\r
/**\r
+ * Sets the value of field 'id'. The field 'id' has the\r
+ * following description: Optional sequence group ID (only\r
+ * needs to be unique for this alignment)\r
+ * \r
+ * \r
+ * @param id the value of field 'id'.\r
+ */\r
+ public void setId(\r
+ final java.lang.String id) {\r
+ this._id = id;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'ignoreGapsinConsensus'.\r
+ * \r
+ * @param ignoreGapsinConsensus the value of field\r
+ * 'ignoreGapsinConsensus'.\r
+ */\r
+ public void setIgnoreGapsinConsensus(\r
+ final boolean ignoreGapsinConsensus) {\r
+ this._ignoreGapsinConsensus = ignoreGapsinConsensus;\r
+ this._has_ignoreGapsinConsensus = true;\r
+ }\r
+\r
+ /**\r
* Sets the value of field 'name'.\r
* \r
* @param name the value of field 'name'.\r
*/\r
public void setSeq(\r
final int index,\r
- final int vSeq)\r
+ final java.lang.String vSeq)\r
throws java.lang.IndexOutOfBoundsException {\r
// check bounds for index\r
if (index < 0 || index >= this._seqList.size()) {\r
throw new IndexOutOfBoundsException("setSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");\r
}\r
\r
- this._seqList.set(index, new java.lang.Integer(vSeq));\r
+ this._seqList.set(index, vSeq);\r
}\r
\r
/**\r
* @param vSeqArray\r
*/\r
public void setSeq(\r
- final int[] vSeqArray) {\r
+ final java.lang.String[] vSeqArray) {\r
//-- copy array\r
_seqList.clear();\r
\r
for (int i = 0; i < vSeqArray.length; i++) {\r
- this._seqList.add(new java.lang.Integer(vSeqArray[i]));\r
+ this._seqList.add(vSeqArray[i]);\r
}\r
}\r
\r
/**\r
+ * Sets the value of field 'showConsensusHistogram'.\r
+ * \r
+ * @param showConsensusHistogram the value of field\r
+ * 'showConsensusHistogram'.\r
+ */\r
+ public void setShowConsensusHistogram(\r
+ final boolean showConsensusHistogram) {\r
+ this._showConsensusHistogram = showConsensusHistogram;\r
+ this._has_showConsensusHistogram = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showSequenceLogo'.\r
+ * \r
+ * @param showSequenceLogo the value of field 'showSequenceLogo'\r
+ */\r
+ public void setShowSequenceLogo(\r
+ final boolean showSequenceLogo) {\r
+ this._showSequenceLogo = showSequenceLogo;\r
+ this._has_showSequenceLogo = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showUnconserved'.\r
+ * \r
+ * @param showUnconserved the value of field 'showUnconserved'.\r
+ */\r
+ public void setShowUnconserved(\r
+ final boolean showUnconserved) {\r
+ this._showUnconserved = showUnconserved;\r
+ this._has_showUnconserved = true;\r
+ }\r
+\r
+ /**\r
* Sets the value of field 'start'.\r
* \r
* @param start the value of field 'start'.\r
git://source.jalview.org / jalview.git / blobdiff