/*\r
- * This class was automatically generated with\r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
- * Schema.\r
- * $Id$\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
-\r
package jalview.schemabinding.version2;\r
\r
//---------------------------------/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.util.*;\r
-\r
-import org.exolab.castor.xml.*;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
\r
/**\r
* Class JGroup.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
-public class JGroup\r
- implements java.io.Serializable\r
+public class JGroup implements java.io.Serializable\r
{\r
\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
+ // --------------------------/\r
+ // - Class/Member Variables -/\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 alignment)\r
+ * \r
+ */\r
+ private java.lang.String _id;\r
+\r
+ /**\r
+ * Field _seqList.\r
*/\r
private java.util.Vector _seqList;\r
\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
+ // ----------------/\r
+ // - Constructors -/\r
+ // ----------------/\r
\r
public JGroup()\r
{\r
super();\r
- _seqList = new Vector();\r
- } //-- jalview.schemabinding.version2.JGroup()\r
+ this._seqList = new java.util.Vector();\r
+ }\r
\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
+ // -----------/\r
+ // - Methods -/\r
+ // -----------/\r
\r
/**\r
- * Method addSeq\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
* @param vSeq\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
*/\r
- public void addSeq(int vSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
+ public void addSeq(final java.lang.String vSeq)\r
+ throws java.lang.IndexOutOfBoundsException\r
{\r
- _seqList.addElement(new java.lang.Integer(vSeq));\r
- } //-- void addSeq(int)\r
+ this._seqList.addElement(vSeq);\r
+ }\r
\r
/**\r
- * Method addSeq\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
* @param index\r
* @param vSeq\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
*/\r
- public void addSeq(int index, int vSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
+ public void addSeq(final int index, final java.lang.String vSeq)\r
+ throws java.lang.IndexOutOfBoundsException\r
{\r
- _seqList.insertElementAt(new java.lang.Integer(vSeq), index);\r
- } //-- void addSeq(int, int)\r
+ this._seqList.add(index, vSeq);\r
+ }\r
\r
/**\r
- * Method deleteColourText\r
- *\r
- */\r
+ */\r
public void deleteColourText()\r
{\r
this._has_colourText = false;\r
- } //-- void deleteColourText()\r
+ }\r
\r
/**\r
- * Method deleteConsThreshold\r
- *\r
- */\r
+ */\r
public void deleteConsThreshold()\r
{\r
this._has_consThreshold = false;\r
- } //-- void deleteConsThreshold()\r
+ }\r
\r
/**\r
- * Method deleteDisplayBoxes\r
- *\r
- */\r
+ */\r
public void deleteDisplayBoxes()\r
{\r
this._has_displayBoxes = false;\r
- } //-- void deleteDisplayBoxes()\r
+ }\r
\r
/**\r
- * Method deleteDisplayText\r
- *\r
- */\r
+ */\r
public void deleteDisplayText()\r
{\r
this._has_displayText = false;\r
- } //-- void deleteDisplayText()\r
+ }\r
\r
/**\r
- * Method deleteEnd\r
- *\r
- */\r
+ */\r
public void deleteEnd()\r
{\r
this._has_end = false;\r
- } //-- void deleteEnd()\r
+ }\r
\r
/**\r
- * Method deleteOutlineColour\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
- } //-- void deleteOutlineColour()\r
+ }\r
\r
/**\r
- * Method deletePidThreshold\r
- *\r
- */\r
+ */\r
public void deletePidThreshold()\r
{\r
this._has_pidThreshold = false;\r
- } //-- void deletePidThreshold()\r
+ }\r
\r
/**\r
- * Method deleteStart\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
- } //-- void deleteStart()\r
+ }\r
\r
/**\r
- * Method deleteTextCol1\r
- *\r
- */\r
+ */\r
public void deleteTextCol1()\r
{\r
this._has_textCol1 = false;\r
- } //-- void deleteTextCol1()\r
+ }\r
\r
/**\r
- * Method deleteTextCol2\r
- *\r
- */\r
+ */\r
public void deleteTextCol2()\r
{\r
this._has_textCol2 = false;\r
- } //-- void deleteTextCol2()\r
+ }\r
\r
/**\r
- * Method deleteTextColThreshold\r
- *\r
- */\r
+ */\r
public void deleteTextColThreshold()\r
{\r
this._has_textColThreshold = false;\r
- } //-- void deleteTextColThreshold()\r
+ }\r
\r
/**\r
- * Method enumerateSeq\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
+ * Method enumerateSeq.\r
+ * \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
+ 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
+ * \r
+ * @return the value of field 'Colour'.\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
+ * \r
+ * @return the value of field 'ColourText'.\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
+ * \r
+ * @return the value of field 'ConsThreshold'.\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
+ * \r
+ * @return the value of field 'DisplayBoxes'.\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
+ * \r
+ * @return the value of field 'DisplayText'.\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
+ * \r
+ * @return the value of field 'End'.\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 following\r
+ * description: Optional sequence group ID (only needs to be unique for this\r
+ * 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
+ * \r
+ * @return the value of field 'Name'.\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
+ * \r
+ * @return the value of field 'OutlineColour'.\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
+ * \r
+ * @return the value of field 'PidThreshold'.\r
*/\r
public int getPidThreshold()\r
{\r
return this._pidThreshold;\r
- } //-- int getPidThreshold()\r
+ }\r
\r
/**\r
- * Method getSeq\r
- *\r
- *\r
- *\r
+ * Method getSeq.\r
+ * \r
* @param index\r
- * @return int\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ * @return the value of the java.lang.String at the given index\r
*/\r
- public int getSeq(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
+ public java.lang.String getSeq(final int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
{\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _seqList.size()))\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._seqList.size())\r
{\r
- throw new IndexOutOfBoundsException();\r
+ throw new IndexOutOfBoundsException("getSeq: Index value '" + index\r
+ + "' 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
- *\r
- *\r
- * @return int\r
+ * Method getSeq.Returns the contents of the collection in an Array.\r
+ * <p>\r
+ * Note: Just in case the collection contents are changing in another thread,\r
+ * we pass a 0-length Array of the correct type into the API call. This way we\r
+ * <i>know</i> 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 = _seqList.size();\r
- int[] mArray = new int[size];\r
- for (int index = 0; index < size; index++)\r
- {\r
- mArray[index] = ( (java.lang.Integer) _seqList.elementAt(index)).intValue();\r
- }\r
- return mArray;\r
- } //-- int[] getSeq()\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
- *\r
- *\r
- * @return int\r
+ * Method getSeqCount.\r
+ * \r
+ * @return the size of this collection\r
*/\r
public int getSeqCount()\r
{\r
- return _seqList.size();\r
- } //-- int getSeqCount()\r
+ return this._seqList.size();\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 int\r
- * @return the value of field 'start'.\r
+ * \r
+ * @return the value of field 'Start'.\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
+ * \r
+ * @return the value of field 'TextCol1'.\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
+ * \r
+ * @return the value of field 'TextCol2'.\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
+ * \r
+ * @return the value of field 'TextColThreshold'.\r
*/\r
public int getTextColThreshold()\r
{\r
return this._textColThreshold;\r
- } //-- int getTextColThreshold()\r
+ }\r
\r
/**\r
- * Method hasColourText\r
- *\r
- *\r
- *\r
- * @return boolean\r
+ * Method hasColourText.\r
+ * \r
+ * @return true if at least one ColourText has been added\r
*/\r
public boolean hasColourText()\r
{\r
return this._has_colourText;\r
- } //-- boolean hasColourText()\r
+ }\r
\r
/**\r
- * Method hasConsThreshold\r
- *\r
- *\r
- *\r
- * @return boolean\r
+ * Method hasConsThreshold.\r
+ * \r
+ * @return true if at least one ConsThreshold has been added\r
*/\r
public boolean hasConsThreshold()\r
{\r
return this._has_consThreshold;\r
- } //-- boolean hasConsThreshold()\r
+ }\r
\r
/**\r
- * Method hasDisplayBoxes\r
- *\r
- *\r
- *\r
- * @return boolean\r
+ * Method hasDisplayBoxes.\r
+ * \r
+ * @return true if at least one DisplayBoxes has been added\r
*/\r
public boolean hasDisplayBoxes()\r
{\r
return this._has_displayBoxes;\r
- } //-- boolean hasDisplayBoxes()\r
+ }\r
\r
/**\r
- * Method hasDisplayText\r
- *\r
- *\r
- *\r
- * @return boolean\r
+ * Method hasDisplayText.\r
+ * \r
+ * @return true if at least one DisplayText has been added\r
*/\r
public boolean hasDisplayText()\r
{\r
return this._has_displayText;\r
- } //-- boolean hasDisplayText()\r
+ }\r
\r
/**\r
- * Method hasEnd\r
- *\r
- *\r
- *\r
- * @return boolean\r
+ * Method hasEnd.\r
+ * \r
+ * @return true if at least one End has been added\r
*/\r
public boolean hasEnd()\r
{\r
return this._has_end;\r
- } //-- boolean hasEnd()\r
+ }\r
\r
/**\r
- * Method hasOutlineColour\r
- *\r
- *\r
- *\r
- * @return boolean\r
+ * Method hasIgnoreGapsinConsensus.\r
+ * \r
+ * @return true if at least one IgnoreGapsinConsensus has been 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
public boolean hasOutlineColour()\r
{\r
return this._has_outlineColour;\r
- } //-- boolean hasOutlineColour()\r
+ }\r
\r
/**\r
- * Method hasPidThreshold\r
- *\r
- *\r
- *\r
- * @return boolean\r
+ * Method hasPidThreshold.\r
+ * \r
+ * @return true if at least one PidThreshold has been added\r
*/\r
public boolean hasPidThreshold()\r
{\r
return this._has_pidThreshold;\r
- } //-- boolean hasPidThreshold()\r
+ }\r
\r
/**\r
- * Method hasStart\r
- *\r
- *\r
- *\r
- * @return boolean\r
+ * Method hasShowConsensusHistogram.\r
+ * \r
+ * @return true if at least one ShowConsensusHistogram has been 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
public boolean hasStart()\r
{\r
return this._has_start;\r
- } //-- boolean hasStart()\r
+ }\r
\r
/**\r
- * Method hasTextCol1\r
- *\r
- *\r
- *\r
- * @return boolean\r
+ * Method hasTextCol1.\r
+ * \r
+ * @return true if at least one TextCol1 has been added\r
*/\r
public boolean hasTextCol1()\r
{\r
return this._has_textCol1;\r
- } //-- boolean hasTextCol1()\r
+ }\r
\r
/**\r
- * Method hasTextCol2\r
- *\r
- *\r
- *\r
- * @return boolean\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
- } //-- boolean hasTextCol2()\r
+ }\r
\r
/**\r
- * Method hasTextColThreshold\r
- *\r
- *\r
- *\r
- * @return boolean\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
- } //-- boolean hasTextColThreshold()\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 the value of field 'DisplayBoxes'.\r
+ */\r
+ public boolean isDisplayBoxes()\r
+ {\r
+ return this._displayBoxes;\r
+ }\r
+\r
+ /**\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 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
- *\r
- *\r
- * @return boolean\r
+ * Method isValid.\r
+ * \r
+ * @return true if this object is valid according to the schema\r
*/\r
public boolean isValid()\r
{\r
try\r
{\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
+ } catch (org.exolab.castor.xml.ValidationException vex)\r
{\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid()\r
+ }\r
\r
/**\r
- * Method marshal\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
* @param out\r
+ * @throws org.exolab.castor.xml.MarshalException\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
*/\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
+ public void marshal(final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException\r
{\r
-\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
+ }\r
\r
/**\r
- * Method marshal\r
- *\r
- *\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,\r
- org.exolab.castor.xml.ValidationException\r
+ * @throws java.io.IOException\r
+ * if an IOException occurs during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
+ */\r
+ public void marshal(final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException,\r
+ org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException\r
{\r
-\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
+ }\r
\r
/**\r
- * Method removeAllSeq\r
- *\r
- */\r
+ */\r
public void removeAllSeq()\r
{\r
- _seqList.removeAllElements();\r
- } //-- void removeAllSeq()\r
+ this._seqList.clear();\r
+ }\r
+\r
+ /**\r
+ * Method removeSeq.\r
+ * \r
+ * @param vSeq\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeSeq(final java.lang.String vSeq)\r
+ {\r
+ boolean removed = _seqList.remove(vSeq);\r
+ return removed;\r
+ }\r
\r
/**\r
- * Method removeSeq\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
+ public java.lang.String removeSeqAt(final 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
+ 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
+ * @param colour\r
+ * the value of field 'colour'.\r
*/\r
- public void setColour(java.lang.String colour)\r
+ public void setColour(final java.lang.String colour)\r
{\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
+ * @param colourText\r
+ * the value of field 'colourText'.\r
*/\r
- public void setColourText(boolean colourText)\r
+ public void setColourText(final boolean colourText)\r
{\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
+ * @param consThreshold\r
+ * the value of field 'consThreshold'.\r
*/\r
- public void setConsThreshold(int consThreshold)\r
+ public void setConsThreshold(final int consThreshold)\r
{\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
+ * @param displayBoxes\r
+ * the value of field 'displayBoxes'.\r
*/\r
- public void setDisplayBoxes(boolean displayBoxes)\r
+ public void setDisplayBoxes(final boolean displayBoxes)\r
{\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
+ * @param displayText\r
+ * the value of field 'displayText'.\r
*/\r
- public void setDisplayText(boolean displayText)\r
+ public void setDisplayText(final boolean displayText)\r
{\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
+ * @param end\r
+ * the value of field 'end'.\r
*/\r
- public void setEnd(int end)\r
+ public void setEnd(final int end)\r
{\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 following description:\r
+ * Optional sequence group ID (only needs to be unique for this alignment)\r
+ * \r
+ * \r
+ * @param id\r
+ * the value of field 'id'.\r
+ */\r
+ public void setId(final java.lang.String id)\r
+ {\r
+ this._id = id;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'ignoreGapsinConsensus'.\r
+ * \r
+ * @param ignoreGapsinConsensus\r
+ * the value of field 'ignoreGapsinConsensus'.\r
+ */\r
+ public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus)\r
+ {\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
+ * @param name\r
+ * the value of field 'name'.\r
*/\r
- public void setName(java.lang.String name)\r
+ public void setName(final java.lang.String name)\r
{\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
+ * @param outlineColour\r
+ * the value of field 'outlineColour'.\r
*/\r
- public void setOutlineColour(int outlineColour)\r
+ public void setOutlineColour(final int outlineColour)\r
{\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
+ * @param pidThreshold\r
+ * the value of field 'pidThreshold'.\r
*/\r
- public void setPidThreshold(int pidThreshold)\r
+ public void setPidThreshold(final int pidThreshold)\r
{\r
this._pidThreshold = pidThreshold;\r
this._has_pidThreshold = true;\r
- } //-- void setPidThreshold(int)\r
+ }\r
\r
/**\r
- * Method setSeq\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
* @param index\r
* @param vSeq\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
*/\r
- public void setSeq(int index, int vSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
+ public void setSeq(final int index, final java.lang.String vSeq)\r
+ throws java.lang.IndexOutOfBoundsException\r
{\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _seqList.size()))\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._seqList.size())\r
{\r
- throw new IndexOutOfBoundsException();\r
+ throw new IndexOutOfBoundsException("setSeq: Index value '" + index\r
+ + "' 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
+ * \r
+ * \r
+ * @param vSeqArray\r
*/\r
- public void setSeq(int[] seqArray)\r
+ public void setSeq(final java.lang.String[] vSeqArray)\r
{\r
- //-- copy array\r
- _seqList.removeAllElements();\r
- for (int i = 0; i < seqArray.length; i++)\r
+ // -- copy array\r
+ _seqList.clear();\r
+\r
+ for (int i = 0; i < vSeqArray.length; i++)\r
{\r
- _seqList.addElement(new java.lang.Integer(seqArray[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\r
+ * the value of field 'showConsensusHistogram'.\r
+ */\r
+ public void setShowConsensusHistogram(final boolean showConsensusHistogram)\r
+ {\r
+ this._showConsensusHistogram = showConsensusHistogram;\r
+ this._has_showConsensusHistogram = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showSequenceLogo'.\r
+ * \r
+ * @param showSequenceLogo\r
+ * the value of field 'showSequenceLogo'\r
+ */\r
+ public void setShowSequenceLogo(final boolean showSequenceLogo)\r
+ {\r
+ this._showSequenceLogo = showSequenceLogo;\r
+ this._has_showSequenceLogo = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'showUnconserved'.\r
+ * \r
+ * @param showUnconserved\r
+ * the value of field 'showUnconserved'.\r
+ */\r
+ public void setShowUnconserved(final boolean showUnconserved)\r
+ {\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
+ * @param start\r
+ * the value of field 'start'.\r
*/\r
- public void setStart(int start)\r
+ public void setStart(final int start)\r
{\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
+ * @param textCol1\r
+ * the value of field 'textCol1'.\r
*/\r
- public void setTextCol1(int textCol1)\r
+ public void setTextCol1(final int textCol1)\r
{\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
+ * @param textCol2\r
+ * the value of field 'textCol2'.\r
*/\r
- public void setTextCol2(int textCol2)\r
+ public void setTextCol2(final int textCol2)\r
{\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
+ * @param textColThreshold\r
+ * the value of field 'textColThreshold'\r
*/\r
- public void setTextColThreshold(int textColThreshold)\r
+ public void setTextColThreshold(final int textColThreshold)\r
{\r
this._textColThreshold = textColThreshold;\r
this._has_textColThreshold = true;\r
- } //-- void setTextColThreshold(int)\r
+ }\r
\r
/**\r
- * Method unmarshal\r
- *\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,\r
- org.exolab.castor.xml.ValidationException\r
+ * @throws org.exolab.castor.xml.MarshalException\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this 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,\r
+ org.exolab.castor.xml.ValidationException\r
{\r
return (jalview.schemabinding.version2.JGroup) Unmarshaller.unmarshal(\r
- jalview.schemabinding.version2.JGroup.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
+ jalview.schemabinding.version2.JGroup.class, reader);\r
+ }\r
\r
/**\r
- * Method validate\r
- *\r
+ * \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
+ public void validate() throws org.exolab.castor.xml.ValidationException\r
{\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
- Validator();\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