/*\r
- * This class was automatically generated with \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
*/\r
\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+*\r
+* This program 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 2\r
+* of the License, or (at your option) any later version.\r
+*\r
+* This program is distributed in the hope that it will be useful,\r
+* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+* GNU General Public License for more details.\r
+*\r
+* You should have received a copy of the GNU General Public License\r
+* along with this program; if not, write to the Free Software\r
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+*/\r
+\r
package jalview.binding;\r
\r
//---------------------------------/\r
\r
/**\r
* Class JGroup.\r
- * \r
+ *\r
* @version $Revision$ $Date$\r
*/\r
public class JGroup implements java.io.Serializable {\r
\r
/**\r
* Method addSeq\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param vSeq\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
+ } //-- void addSeq(int)\r
\r
/**\r
* Method addSeq\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vSeq\r
*/\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_seqList.insertElementAt(new java.lang.Integer(vSeq), index);\r
- } //-- void addSeq(int, int) \r
+ } //-- void addSeq(int, int)\r
\r
/**\r
* Method deleteColourText\r
- * \r
+ *\r
*/\r
public void deleteColourText()\r
{\r
this._has_colourText= false;\r
- } //-- void deleteColourText() \r
+ } //-- void deleteColourText()\r
\r
/**\r
* Method deleteConsThreshold\r
- * \r
+ *\r
*/\r
public void deleteConsThreshold()\r
{\r
this._has_consThreshold= false;\r
- } //-- void deleteConsThreshold() \r
+ } //-- void deleteConsThreshold()\r
\r
/**\r
* Method deleteDisplayBoxes\r
- * \r
+ *\r
*/\r
public void deleteDisplayBoxes()\r
{\r
this._has_displayBoxes= false;\r
- } //-- void deleteDisplayBoxes() \r
+ } //-- void deleteDisplayBoxes()\r
\r
/**\r
* Method deleteDisplayText\r
- * \r
+ *\r
*/\r
public void deleteDisplayText()\r
{\r
this._has_displayText= false;\r
- } //-- void deleteDisplayText() \r
+ } //-- void deleteDisplayText()\r
\r
/**\r
* Method deleteEnd\r
- * \r
+ *\r
*/\r
public void deleteEnd()\r
{\r
this._has_end= false;\r
- } //-- void deleteEnd() \r
+ } //-- void deleteEnd()\r
\r
/**\r
* Method deleteOutlineColour\r
- * \r
+ *\r
*/\r
public void deleteOutlineColour()\r
{\r
this._has_outlineColour= false;\r
- } //-- void deleteOutlineColour() \r
+ } //-- void deleteOutlineColour()\r
\r
/**\r
* Method deletePidThreshold\r
- * \r
+ *\r
*/\r
public void deletePidThreshold()\r
{\r
this._has_pidThreshold= false;\r
- } //-- void deletePidThreshold() \r
+ } //-- void deletePidThreshold()\r
\r
/**\r
* Method deleteStart\r
- * \r
+ *\r
*/\r
public void deleteStart()\r
{\r
this._has_start= false;\r
- } //-- void deleteStart() \r
+ } //-- void deleteStart()\r
\r
/**\r
* Method enumerateSeq\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return Enumeration\r
*/\r
public java.util.Enumeration enumerateSeq()\r
{\r
return _seqList.elements();\r
- } //-- java.util.Enumeration enumerateSeq() \r
+ } //-- java.util.Enumeration enumerateSeq()\r
\r
/**\r
* Returns the value of field 'colour'.\r
- * \r
+ *\r
* @return String\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
+ } //-- java.lang.String getColour()\r
\r
/**\r
* Returns the value of field 'colourText'.\r
- * \r
+ *\r
* @return boolean\r
* @return the value of field 'colourText'.\r
*/\r
public boolean getColourText()\r
{\r
return this._colourText;\r
- } //-- boolean getColourText() \r
+ } //-- boolean getColourText()\r
\r
/**\r
* Returns the value of field 'consThreshold'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'consThreshold'.\r
*/\r
public int getConsThreshold()\r
{\r
return this._consThreshold;\r
- } //-- int getConsThreshold() \r
+ } //-- int getConsThreshold()\r
\r
/**\r
* Returns the value of field 'displayBoxes'.\r
- * \r
+ *\r
* @return boolean\r
* @return the value of field 'displayBoxes'.\r
*/\r
public boolean getDisplayBoxes()\r
{\r
return this._displayBoxes;\r
- } //-- boolean getDisplayBoxes() \r
+ } //-- boolean getDisplayBoxes()\r
\r
/**\r
* Returns the value of field 'displayText'.\r
- * \r
+ *\r
* @return boolean\r
* @return the value of field 'displayText'.\r
*/\r
public boolean getDisplayText()\r
{\r
return this._displayText;\r
- } //-- boolean getDisplayText() \r
+ } //-- boolean getDisplayText()\r
\r
/**\r
* Returns the value of field 'end'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'end'.\r
*/\r
public int getEnd()\r
{\r
return this._end;\r
- } //-- int getEnd() \r
+ } //-- int getEnd()\r
\r
/**\r
* Returns the value of field 'name'.\r
- * \r
+ *\r
* @return String\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
+ } //-- java.lang.String getName()\r
\r
/**\r
* Returns the value of field 'outlineColour'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'outlineColour'.\r
*/\r
public int getOutlineColour()\r
{\r
return this._outlineColour;\r
- } //-- int getOutlineColour() \r
+ } //-- int getOutlineColour()\r
\r
/**\r
* Returns the value of field 'pidThreshold'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'pidThreshold'.\r
*/\r
public int getPidThreshold()\r
{\r
return this._pidThreshold;\r
- } //-- int getPidThreshold() \r
+ } //-- int getPidThreshold()\r
\r
/**\r
* Method getSeq\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return int\r
*/\r
if ((index < 0) || (index > _seqList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
- \r
+\r
return ((java.lang.Integer)_seqList.elementAt(index)).intValue();\r
- } //-- int getSeq(int) \r
+ } //-- int getSeq(int)\r
\r
/**\r
* Method getSeq\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return int\r
*/\r
public int[] getSeq()\r
mArray[index] = ((java.lang.Integer)_seqList.elementAt(index)).intValue();\r
}\r
return mArray;\r
- } //-- int[] getSeq() \r
+ } //-- int[] getSeq()\r
\r
/**\r
* Method getSeqCount\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return int\r
*/\r
public int getSeqCount()\r
{\r
return _seqList.size();\r
- } //-- int getSeqCount() \r
+ } //-- int getSeqCount()\r
\r
/**\r
* Returns the value of field 'start'.\r
- * \r
+ *\r
* @return int\r
* @return the value of field 'start'.\r
*/\r
public int getStart()\r
{\r
return this._start;\r
- } //-- int getStart() \r
+ } //-- int getStart()\r
\r
/**\r
* Method hasColourText\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasColourText()\r
{\r
return this._has_colourText;\r
- } //-- boolean hasColourText() \r
+ } //-- boolean hasColourText()\r
\r
/**\r
* Method hasConsThreshold\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasConsThreshold()\r
{\r
return this._has_consThreshold;\r
- } //-- boolean hasConsThreshold() \r
+ } //-- boolean hasConsThreshold()\r
\r
/**\r
* Method hasDisplayBoxes\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasDisplayBoxes()\r
{\r
return this._has_displayBoxes;\r
- } //-- boolean hasDisplayBoxes() \r
+ } //-- boolean hasDisplayBoxes()\r
\r
/**\r
* Method hasDisplayText\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasDisplayText()\r
{\r
return this._has_displayText;\r
- } //-- boolean hasDisplayText() \r
+ } //-- boolean hasDisplayText()\r
\r
/**\r
* Method hasEnd\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasEnd()\r
{\r
return this._has_end;\r
- } //-- boolean hasEnd() \r
+ } //-- boolean hasEnd()\r
\r
/**\r
* Method hasOutlineColour\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasOutlineColour()\r
{\r
return this._has_outlineColour;\r
- } //-- boolean hasOutlineColour() \r
+ } //-- boolean hasOutlineColour()\r
\r
/**\r
* Method hasPidThreshold\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasPidThreshold()\r
{\r
return this._has_pidThreshold;\r
- } //-- boolean hasPidThreshold() \r
+ } //-- boolean hasPidThreshold()\r
\r
/**\r
* Method hasStart\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean hasStart()\r
{\r
return this._has_start;\r
- } //-- boolean hasStart() \r
+ } //-- boolean hasStart()\r
\r
/**\r
* Method isValid\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @return boolean\r
*/\r
public boolean isValid()\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid() \r
+ } //-- boolean isValid()\r
\r
/**\r
* Method marshal\r
- * \r
- * \r
- * \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
+\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
+ } //-- void marshal(java.io.Writer)\r
\r
/**\r
* Method marshal\r
- * \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, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
+ } //-- void marshal(org.xml.sax.ContentHandler)\r
\r
/**\r
* Method removeAllSeq\r
- * \r
+ *\r
*/\r
public void removeAllSeq()\r
{\r
_seqList.removeAllElements();\r
- } //-- void removeAllSeq() \r
+ } //-- void removeAllSeq()\r
\r
/**\r
* Method removeSeq\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @return int\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
+ } //-- int removeSeq(int)\r
\r
/**\r
* Sets the value of field 'colour'.\r
- * \r
+ *\r
* @param colour the value of field 'colour'.\r
*/\r
public void setColour(java.lang.String colour)\r
{\r
this._colour = colour;\r
- } //-- void setColour(java.lang.String) \r
+ } //-- void setColour(java.lang.String)\r
\r
/**\r
* Sets the value of field 'colourText'.\r
- * \r
+ *\r
* @param colourText the value of field 'colourText'.\r
*/\r
public void setColourText(boolean colourText)\r
{\r
this._colourText = colourText;\r
this._has_colourText = true;\r
- } //-- void setColourText(boolean) \r
+ } //-- void setColourText(boolean)\r
\r
/**\r
* Sets the value of field 'consThreshold'.\r
- * \r
+ *\r
* @param consThreshold the value of field 'consThreshold'.\r
*/\r
public void setConsThreshold(int consThreshold)\r
{\r
this._consThreshold = consThreshold;\r
this._has_consThreshold = true;\r
- } //-- void setConsThreshold(int) \r
+ } //-- void setConsThreshold(int)\r
\r
/**\r
* Sets the value of field 'displayBoxes'.\r
- * \r
+ *\r
* @param displayBoxes the value of field 'displayBoxes'.\r
*/\r
public void setDisplayBoxes(boolean displayBoxes)\r
{\r
this._displayBoxes = displayBoxes;\r
this._has_displayBoxes = true;\r
- } //-- void setDisplayBoxes(boolean) \r
+ } //-- void setDisplayBoxes(boolean)\r
\r
/**\r
* Sets the value of field 'displayText'.\r
- * \r
+ *\r
* @param displayText the value of field 'displayText'.\r
*/\r
public void setDisplayText(boolean displayText)\r
{\r
this._displayText = displayText;\r
this._has_displayText = true;\r
- } //-- void setDisplayText(boolean) \r
+ } //-- void setDisplayText(boolean)\r
\r
/**\r
* Sets the value of field 'end'.\r
- * \r
+ *\r
* @param end the value of field 'end'.\r
*/\r
public void setEnd(int end)\r
{\r
this._end = end;\r
this._has_end = true;\r
- } //-- void setEnd(int) \r
+ } //-- void setEnd(int)\r
\r
/**\r
* Sets the value of field 'name'.\r
- * \r
+ *\r
* @param name the value of field 'name'.\r
*/\r
public void setName(java.lang.String name)\r
{\r
this._name = name;\r
- } //-- void setName(java.lang.String) \r
+ } //-- void setName(java.lang.String)\r
\r
/**\r
* Sets the value of field 'outlineColour'.\r
- * \r
+ *\r
* @param outlineColour the value of field 'outlineColour'.\r
*/\r
public void setOutlineColour(int outlineColour)\r
{\r
this._outlineColour = outlineColour;\r
this._has_outlineColour = true;\r
- } //-- void setOutlineColour(int) \r
+ } //-- void setOutlineColour(int)\r
\r
/**\r
* Sets the value of field 'pidThreshold'.\r
- * \r
+ *\r
* @param pidThreshold the value of field 'pidThreshold'.\r
*/\r
public void setPidThreshold(int pidThreshold)\r
{\r
this._pidThreshold = pidThreshold;\r
this._has_pidThreshold = true;\r
- } //-- void setPidThreshold(int) \r
+ } //-- void setPidThreshold(int)\r
\r
/**\r
* Method setSeq\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param index\r
* @param vSeq\r
*/\r
throw new IndexOutOfBoundsException();\r
}\r
_seqList.setElementAt(new java.lang.Integer(vSeq), index);\r
- } //-- void setSeq(int, int) \r
+ } //-- void setSeq(int, int)\r
\r
/**\r
* Method setSeq\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param seqArray\r
*/\r
public void setSeq(int[] seqArray)\r
for (int i = 0; i < seqArray.length; i++) {\r
_seqList.addElement(new java.lang.Integer(seqArray[i]));\r
}\r
- } //-- void setSeq(int) \r
+ } //-- void setSeq(int)\r
\r
/**\r
* Sets the value of field 'start'.\r
- * \r
+ *\r
* @param start the value of field 'start'.\r
*/\r
public void setStart(int start)\r
{\r
this._start = start;\r
this._has_start = true;\r
- } //-- void setStart(int) \r
+ } //-- void setStart(int)\r
\r
/**\r
* Method unmarshal\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param reader\r
* @return Object\r
*/\r
throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
{\r
return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
+ } //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
- * \r
+ *\r
*/\r
public void validate()\r
throws org.exolab.castor.xml.ValidationException\r
{\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate() \r
+ } //-- void validate()\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff