/*\r
* This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
* Schema.\r
* $Id$\r
*/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\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 JGroup.\r
//--------------------------/\r
\r
/**\r
- * Field _start\r
+ * Field _start.\r
*/\r
private int _start;\r
\r
private boolean _has_start;\r
\r
/**\r
- * Field _end\r
+ * Field _end.\r
*/\r
private int _end;\r
\r
private boolean _has_end;\r
\r
/**\r
- * Field _name\r
+ * Field _name.\r
*/\r
private java.lang.String _name;\r
\r
/**\r
- * Field _colour\r
+ * Field _colour.\r
*/\r
private java.lang.String _colour;\r
\r
/**\r
- * Field _consThreshold\r
+ * Field _consThreshold.\r
*/\r
private int _consThreshold;\r
\r
private boolean _has_consThreshold;\r
\r
/**\r
- * Field _pidThreshold\r
+ * Field _pidThreshold.\r
*/\r
private int _pidThreshold;\r
\r
private boolean _has_pidThreshold;\r
\r
/**\r
- * Field _outlineColour\r
+ * Field _outlineColour.\r
*/\r
private int _outlineColour;\r
\r
private boolean _has_outlineColour;\r
\r
/**\r
- * Field _displayBoxes\r
+ * Field _displayBoxes.\r
*/\r
private boolean _displayBoxes;\r
\r
private boolean _has_displayBoxes;\r
\r
/**\r
- * Field _displayText\r
+ * Field _displayText.\r
*/\r
private boolean _displayText;\r
\r
private boolean _has_displayText;\r
\r
/**\r
- * Field _colourText\r
+ * Field _colourText.\r
*/\r
private boolean _colourText;\r
\r
private boolean _has_colourText;\r
\r
/**\r
- * Field _textCol1\r
+ * Field _textCol1.\r
*/\r
private int _textCol1;\r
\r
private boolean _has_textCol1;\r
\r
/**\r
- * Field _textCol2\r
+ * Field _textCol2.\r
*/\r
private int _textCol2;\r
\r
private boolean _has_textCol2;\r
\r
/**\r
- * Field _textColThreshold\r
+ * Field _textColThreshold.\r
*/\r
private int _textColThreshold;\r
\r
private boolean _has_textColThreshold;\r
\r
/**\r
- * Field _seqList\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
\r
\r
public JGroup() {\r
super();\r
- _seqList = new Vector();\r
- } //-- jalview.schemabinding.version2.JGroup()\r
+ this._seqList = new java.util.Vector();\r
+ }\r
\r
\r
//-----------/\r
//-----------/\r
\r
/**\r
- * Method addSeq\r
- * \r
* \r
* \r
* @param vSeq\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addSeq(int vSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _seqList.addElement(new java.lang.Integer(vSeq));\r
- } //-- void addSeq(int) \r
+ public void addSeq(\r
+ final java.lang.String vSeq)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._seqList.addElement(vSeq);\r
+ }\r
\r
/**\r
- * Method addSeq\r
- * \r
* \r
* \r
* @param index\r
* @param vSeq\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
*/\r
- public void addSeq(int index, int vSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _seqList.insertElementAt(new java.lang.Integer(vSeq), index);\r
- } //-- void addSeq(int, int) \r
+ public void addSeq(\r
+ final int index,\r
+ final java.lang.String vSeq)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._seqList.add(index, vSeq);\r
+ }\r
\r
/**\r
- * Method deleteColourText\r
- * \r
*/\r
- public void deleteColourText()\r
- {\r
+ public void deleteColourText(\r
+ ) {\r
this._has_colourText= false;\r
- } //-- void deleteColourText() \r
+ }\r
\r
/**\r
- * Method deleteConsThreshold\r
- * \r
*/\r
- public void deleteConsThreshold()\r
- {\r
+ public void deleteConsThreshold(\r
+ ) {\r
this._has_consThreshold= false;\r
- } //-- void deleteConsThreshold() \r
+ }\r
\r
/**\r
- * Method deleteDisplayBoxes\r
- * \r
*/\r
- public void deleteDisplayBoxes()\r
- {\r
+ public void deleteDisplayBoxes(\r
+ ) {\r
this._has_displayBoxes= false;\r
- } //-- void deleteDisplayBoxes() \r
+ }\r
\r
/**\r
- * Method deleteDisplayText\r
- * \r
*/\r
- public void deleteDisplayText()\r
- {\r
+ public void deleteDisplayText(\r
+ ) {\r
this._has_displayText= false;\r
- } //-- void deleteDisplayText() \r
+ }\r
\r
/**\r
- * Method deleteEnd\r
- * \r
*/\r
- public void deleteEnd()\r
- {\r
+ public void deleteEnd(\r
+ ) {\r
this._has_end= false;\r
- } //-- void deleteEnd() \r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteIgnoreGapsinConsensus(\r
+ ) {\r
+ this._has_ignoreGapsinConsensus= false;\r
+ }\r
\r
/**\r
- * Method deleteOutlineColour\r
- * \r
*/\r
- public void deleteOutlineColour()\r
- {\r
+ public void deleteOutlineColour(\r
+ ) {\r
this._has_outlineColour= false;\r
- } //-- void deleteOutlineColour() \r
+ }\r
\r
/**\r
- * Method deletePidThreshold\r
- * \r
*/\r
- public void deletePidThreshold()\r
- {\r
+ public void deletePidThreshold(\r
+ ) {\r
this._has_pidThreshold= false;\r
- } //-- void deletePidThreshold() \r
+ }\r
\r
/**\r
- * Method deleteStart\r
- * \r
*/\r
- public void deleteStart()\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
- } //-- void deleteStart() \r
+ }\r
\r
/**\r
- * Method deleteTextCol1\r
- * \r
*/\r
- public void deleteTextCol1()\r
- {\r
+ public void deleteTextCol1(\r
+ ) {\r
this._has_textCol1= false;\r
- } //-- void deleteTextCol1() \r
+ }\r
\r
/**\r
- * Method deleteTextCol2\r
- * \r
*/\r
- public void deleteTextCol2()\r
- {\r
+ public void deleteTextCol2(\r
+ ) {\r
this._has_textCol2= false;\r
- } //-- void deleteTextCol2() \r
+ }\r
\r
/**\r
- * Method deleteTextColThreshold\r
- * \r
*/\r
- public void deleteTextColThreshold()\r
- {\r
+ public void deleteTextColThreshold(\r
+ ) {\r
this._has_textColThreshold= false;\r
- } //-- void deleteTextColThreshold() \r
+ }\r
\r
/**\r
- * Method enumerateSeq\r
- * \r
- * \r
+ * Method enumerateSeq.\r
* \r
- * @return Enumeration\r
+ * @return an Enumeration over all java.lang.String elements\r
*/\r
- public java.util.Enumeration enumerateSeq()\r
- {\r
- return _seqList.elements();\r
- } //-- java.util.Enumeration enumerateSeq() \r
+ public java.util.Enumeration enumerateSeq(\r
+ ) {\r
+ return this._seqList.elements();\r
+ }\r
\r
/**\r
* Returns the value of field 'colour'.\r
* \r
- * @return String\r
- * @return the value of field 'colour'.\r
+ * @return the value of field 'Colour'.\r
*/\r
- public java.lang.String getColour()\r
- {\r
+ public java.lang.String getColour(\r
+ ) {\r
return this._colour;\r
- } //-- java.lang.String getColour() \r
+ }\r
\r
/**\r
* Returns the value of field 'colourText'.\r
* \r
- * @return boolean\r
- * @return the value of field 'colourText'.\r
+ * @return the value of field 'ColourText'.\r
*/\r
- public boolean getColourText()\r
- {\r
+ public boolean getColourText(\r
+ ) {\r
return this._colourText;\r
- } //-- boolean getColourText() \r
+ }\r
\r
/**\r
* Returns the value of field 'consThreshold'.\r
* \r
- * @return int\r
- * @return the value of field 'consThreshold'.\r
+ * @return the value of field 'ConsThreshold'.\r
*/\r
- public int getConsThreshold()\r
- {\r
+ public int getConsThreshold(\r
+ ) {\r
return this._consThreshold;\r
- } //-- int getConsThreshold() \r
+ }\r
\r
/**\r
* Returns the value of field 'displayBoxes'.\r
* \r
- * @return boolean\r
- * @return the value of field 'displayBoxes'.\r
+ * @return the value of field 'DisplayBoxes'.\r
*/\r
- public boolean getDisplayBoxes()\r
- {\r
+ public boolean getDisplayBoxes(\r
+ ) {\r
return this._displayBoxes;\r
- } //-- boolean getDisplayBoxes() \r
+ }\r
\r
/**\r
* Returns the value of field 'displayText'.\r
* \r
- * @return boolean\r
- * @return the value of field 'displayText'.\r
+ * @return the value of field 'DisplayText'.\r
*/\r
- public boolean getDisplayText()\r
- {\r
+ public boolean getDisplayText(\r
+ ) {\r
return this._displayText;\r
- } //-- boolean getDisplayText() \r
+ }\r
\r
/**\r
* Returns the value of field 'end'.\r
* \r
- * @return int\r
- * @return the value of field 'end'.\r
+ * @return the value of field 'End'.\r
*/\r
- public int getEnd()\r
- {\r
+ public int getEnd(\r
+ ) {\r
return this._end;\r
- } //-- int getEnd() \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 String\r
- * @return the value of field 'name'.\r
+ * @return the value of field 'Name'.\r
*/\r
- public java.lang.String getName()\r
- {\r
+ public java.lang.String getName(\r
+ ) {\r
return this._name;\r
- } //-- java.lang.String getName() \r
+ }\r
\r
/**\r
* Returns the value of field 'outlineColour'.\r
* \r
- * @return int\r
- * @return the value of field 'outlineColour'.\r
+ * @return the value of field 'OutlineColour'.\r
*/\r
- public int getOutlineColour()\r
- {\r
+ public int getOutlineColour(\r
+ ) {\r
return this._outlineColour;\r
- } //-- int getOutlineColour() \r
+ }\r
\r
/**\r
* Returns the value of field 'pidThreshold'.\r
* \r
- * @return int\r
- * @return the value of field 'pidThreshold'.\r
+ * @return the value of field 'PidThreshold'.\r
*/\r
- public int getPidThreshold()\r
- {\r
+ public int getPidThreshold(\r
+ ) {\r
return this._pidThreshold;\r
- } //-- int getPidThreshold() \r
+ }\r
\r
/**\r
- * Method getSeq\r
- * \r
- * \r
+ * Method getSeq.\r
* \r
* @param index\r
- * @return int\r
- */\r
- public int getSeq(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _seqList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the java.lang.String at the given index\r
+ */\r
+ public java.lang.String getSeq(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._seqList.size()) {\r
+ throw new IndexOutOfBoundsException("getSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");\r
}\r
\r
- return ((java.lang.Integer)_seqList.elementAt(index)).intValue();\r
- } //-- int getSeq(int) \r
+ return (java.lang.String) _seqList.get(index);\r
+ }\r
\r
/**\r
- * Method getSeq\r
- * \r
+ * Method getSeq.Returns the contents of the collection in an\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 java.lang.String[] getSeq(\r
+ ) {\r
+ java.lang.String[] array = new java.lang.String[0];\r
+ return (java.lang.String[]) this._seqList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getSeqCount.\r
* \r
- * @return int\r
+ * @return the size of this collection\r
*/\r
- public int[] getSeq()\r
- {\r
- int size = _seqList.size();\r
- int[] mArray = new int[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = ((java.lang.Integer)_seqList.elementAt(index)).intValue();\r
- }\r
- return mArray;\r
- } //-- int[] getSeq() \r
+ public int getSeqCount(\r
+ ) {\r
+ return this._seqList.size();\r
+ }\r
\r
/**\r
- * Method getSeqCount\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 int\r
+ * @return the value of field 'ShowUnconserved'.\r
*/\r
- public int getSeqCount()\r
- {\r
- return _seqList.size();\r
- } //-- int getSeqCount() \r
+ public boolean getShowUnconserved(\r
+ ) {\r
+ return this._showUnconserved;\r
+ }\r
\r
/**\r
* Returns the value of field 'start'.\r
* \r
- * @return int\r
- * @return the value of field 'start'.\r
+ * @return the value of field 'Start'.\r
*/\r
- public int getStart()\r
- {\r
+ public int getStart(\r
+ ) {\r
return this._start;\r
- } //-- int getStart() \r
+ }\r
\r
/**\r
* Returns the value of field 'textCol1'.\r
* \r
- * @return int\r
- * @return the value of field 'textCol1'.\r
+ * @return the value of field 'TextCol1'.\r
*/\r
- public int getTextCol1()\r
- {\r
+ public int getTextCol1(\r
+ ) {\r
return this._textCol1;\r
- } //-- int getTextCol1() \r
+ }\r
\r
/**\r
* Returns the value of field 'textCol2'.\r
* \r
- * @return int\r
- * @return the value of field 'textCol2'.\r
+ * @return the value of field 'TextCol2'.\r
*/\r
- public int getTextCol2()\r
- {\r
+ public int getTextCol2(\r
+ ) {\r
return this._textCol2;\r
- } //-- int getTextCol2() \r
+ }\r
\r
/**\r
* Returns the value of field 'textColThreshold'.\r
* \r
- * @return int\r
- * @return the value of field 'textColThreshold'.\r
+ * @return the value of field 'TextColThreshold'.\r
*/\r
- public int getTextColThreshold()\r
- {\r
+ public int getTextColThreshold(\r
+ ) {\r
return this._textColThreshold;\r
- } //-- int getTextColThreshold() \r
+ }\r
\r
/**\r
- * Method hasColourText\r
- * \r
+ * Method hasColourText.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one ColourText has been added\r
*/\r
- public boolean hasColourText()\r
- {\r
+ public boolean hasColourText(\r
+ ) {\r
return this._has_colourText;\r
- } //-- boolean hasColourText() \r
+ }\r
\r
/**\r
- * Method hasConsThreshold\r
- * \r
+ * Method hasConsThreshold.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one ConsThreshold has been added\r
*/\r
- public boolean hasConsThreshold()\r
- {\r
+ public boolean hasConsThreshold(\r
+ ) {\r
return this._has_consThreshold;\r
- } //-- boolean hasConsThreshold() \r
+ }\r
\r
/**\r
- * Method hasDisplayBoxes\r
- * \r
- * \r
+ * Method hasDisplayBoxes.\r
* \r
- * @return boolean\r
+ * @return true if at least one DisplayBoxes has been added\r
*/\r
- public boolean hasDisplayBoxes()\r
- {\r
+ public boolean hasDisplayBoxes(\r
+ ) {\r
return this._has_displayBoxes;\r
- } //-- boolean hasDisplayBoxes() \r
+ }\r
\r
/**\r
- * Method hasDisplayText\r
+ * Method hasDisplayText.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if at least one DisplayText has been added\r
*/\r
- public boolean hasDisplayText()\r
- {\r
+ public boolean hasDisplayText(\r
+ ) {\r
return this._has_displayText;\r
- } //-- boolean hasDisplayText() \r
+ }\r
\r
/**\r
- * Method hasEnd\r
- * \r
+ * Method hasEnd.\r
* \r
- * \r
- * @return boolean\r
+ * @return true if at least one End has been added\r
*/\r
- public boolean hasEnd()\r
- {\r
+ public boolean hasEnd(\r
+ ) {\r
return this._has_end;\r
- } //-- boolean hasEnd() \r
+ }\r
\r
/**\r
- * Method hasOutlineColour\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 boolean\r
+ * @return true if at least one OutlineColour has been added\r
*/\r
- public boolean hasOutlineColour()\r
- {\r
+ public boolean hasOutlineColour(\r
+ ) {\r
return this._has_outlineColour;\r
- } //-- boolean hasOutlineColour() \r
+ }\r
\r
/**\r
- * Method hasPidThreshold\r
+ * Method hasPidThreshold.\r
* \r
- * \r
- * \r
- * @return boolean\r
+ * @return true if at least one PidThreshold has been added\r
*/\r
- public boolean hasPidThreshold()\r
- {\r
+ public boolean hasPidThreshold(\r
+ ) {\r
return this._has_pidThreshold;\r
- } //-- boolean hasPidThreshold() \r
+ }\r
\r
/**\r
- * Method hasStart\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 boolean\r
+ * @return true if at least one ShowSequenceLogo has been added\r
*/\r
- public boolean hasStart()\r
- {\r
- return this._has_start;\r
- } //-- boolean hasStart() \r
+ public boolean hasShowSequenceLogo(\r
+ ) {\r
+ return this._has_showSequenceLogo;\r
+ }\r
\r
/**\r
- * Method hasTextCol1\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
+ public boolean hasStart(\r
+ ) {\r
+ return this._has_start;\r
+ }\r
+\r
+ /**\r
+ * Method hasTextCol1.\r
* \r
- * @return boolean\r
+ * @return true if at least one TextCol1 has been added\r
*/\r
- public boolean hasTextCol1()\r
- {\r
+ public boolean hasTextCol1(\r
+ ) {\r
return this._has_textCol1;\r
- } //-- boolean hasTextCol1() \r
+ }\r
\r
/**\r
- * Method hasTextCol2\r
+ * Method hasTextCol2.\r
* \r
+ * @return true if at least one TextCol2 has been added\r
+ */\r
+ public boolean hasTextCol2(\r
+ ) {\r
+ return this._has_textCol2;\r
+ }\r
+\r
+ /**\r
+ * Method hasTextColThreshold.\r
+ * \r
+ * @return true if at least one TextColThreshold has been added\r
+ */\r
+ public boolean hasTextColThreshold(\r
+ ) {\r
+ return this._has_textColThreshold;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'colourText'.\r
* \r
+ * @return the value of field 'ColourText'.\r
+ */\r
+ public boolean isColourText(\r
+ ) {\r
+ return this._colourText;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'displayBoxes'.\r
* \r
- * @return boolean\r
+ * @return the value of field 'DisplayBoxes'.\r
*/\r
- public boolean hasTextCol2()\r
- {\r
- return this._has_textCol2;\r
- } //-- boolean hasTextCol2() \r
+ public boolean isDisplayBoxes(\r
+ ) {\r
+ return this._displayBoxes;\r
+ }\r
\r
/**\r
- * Method hasTextColThreshold\r
+ * Returns the value of field 'displayText'.\r
* \r
+ * @return the value of field 'DisplayText'.\r
+ */\r
+ public boolean isDisplayText(\r
+ ) {\r
+ return this._displayText;\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 boolean\r
+ * @return the value of field 'ShowConsensusHistogram'.\r
*/\r
- public boolean hasTextColThreshold()\r
- {\r
- return this._has_textColThreshold;\r
- } //-- boolean hasTextColThreshold() \r
+ public boolean isShowConsensusHistogram(\r
+ ) {\r
+ return this._showConsensusHistogram;\r
+ }\r
\r
/**\r
- * Method isValid\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 boolean\r
+ * @return true if this object is valid according to the schema\r
*/\r
- public boolean isValid()\r
- {\r
+ public boolean isValid(\r
+ ) {\r
try {\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ }\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
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ }\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
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ */\r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ }\r
\r
/**\r
- * Method removeAllSeq\r
- * \r
*/\r
- public void removeAllSeq()\r
- {\r
- _seqList.removeAllElements();\r
- } //-- void removeAllSeq() \r
+ public void removeAllSeq(\r
+ ) {\r
+ this._seqList.clear();\r
+ }\r
\r
/**\r
- * Method removeSeq\r
- * \r
+ * Method removeSeq.\r
* \r
+ * @param vSeq\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeSeq(\r
+ final java.lang.String vSeq) {\r
+ boolean removed = _seqList.remove(vSeq);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeSeqAt.\r
* \r
* @param index\r
- * @return int\r
+ * @return the element removed from the collection\r
*/\r
- public int removeSeq(int index)\r
- {\r
- java.lang.Object obj = _seqList.elementAt(index);\r
- _seqList.removeElementAt(index);\r
- return ((java.lang.Integer)obj).intValue();\r
- } //-- int removeSeq(int) \r
+ public java.lang.String removeSeqAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._seqList.remove(index);\r
+ return (java.lang.String) obj;\r
+ }\r
\r
/**\r
* Sets the value of field 'colour'.\r
* \r
* @param colour the value of field 'colour'.\r
*/\r
- public void setColour(java.lang.String colour)\r
- {\r
+ public void setColour(\r
+ final java.lang.String colour) {\r
this._colour = colour;\r
- } //-- void setColour(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'colourText'.\r
* \r
* @param colourText the value of field 'colourText'.\r
*/\r
- public void setColourText(boolean colourText)\r
- {\r
+ public void setColourText(\r
+ final boolean colourText) {\r
this._colourText = colourText;\r
this._has_colourText = true;\r
- } //-- void setColourText(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'consThreshold'.\r
* \r
* @param consThreshold the value of field 'consThreshold'.\r
*/\r
- public void setConsThreshold(int consThreshold)\r
- {\r
+ public void setConsThreshold(\r
+ final int consThreshold) {\r
this._consThreshold = consThreshold;\r
this._has_consThreshold = true;\r
- } //-- void setConsThreshold(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'displayBoxes'.\r
* \r
* @param displayBoxes the value of field 'displayBoxes'.\r
*/\r
- public void setDisplayBoxes(boolean displayBoxes)\r
- {\r
+ public void setDisplayBoxes(\r
+ final boolean displayBoxes) {\r
this._displayBoxes = displayBoxes;\r
this._has_displayBoxes = true;\r
- } //-- void setDisplayBoxes(boolean) \r
+ }\r
\r
/**\r
* Sets the value of field 'displayText'.\r
* \r
* @param displayText the value of field 'displayText'.\r
*/\r
- public void setDisplayText(boolean displayText)\r
- {\r
+ public void setDisplayText(\r
+ final boolean displayText) {\r
this._displayText = displayText;\r
this._has_displayText = true;\r
- } //-- void setDisplayText(boolean) \r
+ }\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
+ public void setEnd(\r
+ final int end) {\r
this._end = end;\r
this._has_end = true;\r
- } //-- void setEnd(int) \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 setName(java.lang.String name)\r
- {\r
+ public void setName(\r
+ final java.lang.String name) {\r
this._name = name;\r
- } //-- void setName(java.lang.String) \r
+ }\r
\r
/**\r
* Sets the value of field 'outlineColour'.\r
* \r
* @param outlineColour the value of field 'outlineColour'.\r
*/\r
- public void setOutlineColour(int outlineColour)\r
- {\r
+ public void setOutlineColour(\r
+ final int outlineColour) {\r
this._outlineColour = outlineColour;\r
this._has_outlineColour = true;\r
- } //-- void setOutlineColour(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'pidThreshold'.\r
* \r
* @param pidThreshold the value of field 'pidThreshold'.\r
*/\r
- public void setPidThreshold(int pidThreshold)\r
- {\r
+ public void setPidThreshold(\r
+ final int pidThreshold) {\r
this._pidThreshold = pidThreshold;\r
this._has_pidThreshold = true;\r
- } //-- void setPidThreshold(int) \r
+ }\r
\r
/**\r
- * Method setSeq\r
- * \r
* \r
* \r
* @param index\r
* @param vSeq\r
- */\r
- public void setSeq(int index, int vSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _seqList.size())) {\r
- throw new IndexOutOfBoundsException();\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setSeq(\r
+ final int index,\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
- _seqList.setElementAt(new java.lang.Integer(vSeq), index);\r
- } //-- void setSeq(int, int) \r
+ \r
+ this._seqList.set(index, vSeq);\r
+ }\r
\r
/**\r
- * Method setSeq\r
- * \r
* \r
* \r
- * @param seqArray\r
+ * @param vSeqArray\r
*/\r
- public void setSeq(int[] seqArray)\r
- {\r
+ public void setSeq(\r
+ final java.lang.String[] vSeqArray) {\r
//-- copy array\r
- _seqList.removeAllElements();\r
- for (int i = 0; i < seqArray.length; i++) {\r
- _seqList.addElement(new java.lang.Integer(seqArray[i]));\r
+ _seqList.clear();\r
+ \r
+ for (int i = 0; i < vSeqArray.length; i++) {\r
+ this._seqList.add(vSeqArray[i]);\r
}\r
- } //-- void setSeq(int) \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
*/\r
- public void setStart(int start)\r
- {\r
+ public void setStart(\r
+ final int start) {\r
this._start = start;\r
this._has_start = true;\r
- } //-- void setStart(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'textCol1'.\r
* \r
* @param textCol1 the value of field 'textCol1'.\r
*/\r
- public void setTextCol1(int textCol1)\r
- {\r
+ public void setTextCol1(\r
+ final int textCol1) {\r
this._textCol1 = textCol1;\r
this._has_textCol1 = true;\r
- } //-- void setTextCol1(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'textCol2'.\r
* \r
* @param textCol2 the value of field 'textCol2'.\r
*/\r
- public void setTextCol2(int textCol2)\r
- {\r
+ public void setTextCol2(\r
+ final int textCol2) {\r
this._textCol2 = textCol2;\r
this._has_textCol2 = true;\r
- } //-- void setTextCol2(int) \r
+ }\r
\r
/**\r
* Sets the value of field 'textColThreshold'.\r
* \r
* @param textColThreshold the value of field 'textColThreshold'\r
*/\r
- public void setTextColThreshold(int textColThreshold)\r
- {\r
+ public void setTextColThreshold(\r
+ final int textColThreshold) {\r
this._textColThreshold = textColThreshold;\r
this._has_textColThreshold = true;\r
- } //-- void setTextColThreshold(int) \r
+ }\r
\r
/**\r
- * Method unmarshal\r
- * \r
- * \r
+ * Method unmarshal.\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
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled jalview.schemabinding.version2.JGroup\r
+ */\r
+ public static jalview.schemabinding.version2.JGroup unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
return (jalview.schemabinding.version2.JGroup) Unmarshaller.unmarshal(jalview.schemabinding.version2.JGroup.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ }\r
\r
/**\r
- * Method validate\r
* \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ }\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff