--- /dev/null
+/*\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
+package jalview.binding;\r
+\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
+ * @version $Revision$ $Date$\r
+ */\r
+public class JGroup implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _start\r
+ */\r
+ private int _start;\r
+\r
+ /**\r
+ * keeps track of state for field: _start\r
+ */\r
+ private boolean _has_start;\r
+\r
+ /**\r
+ * Field _end\r
+ */\r
+ private int _end;\r
+\r
+ /**\r
+ * keeps track of state for field: _end\r
+ */\r
+ private boolean _has_end;\r
+\r
+ /**\r
+ * Field _name\r
+ */\r
+ private java.lang.String _name;\r
+\r
+ /**\r
+ * Field _colour\r
+ */\r
+ private java.lang.String _colour;\r
+\r
+ /**\r
+ * Field _consThreshold\r
+ */\r
+ private int _consThreshold;\r
+\r
+ /**\r
+ * keeps track of state for field: _consThreshold\r
+ */\r
+ private boolean _has_consThreshold;\r
+\r
+ /**\r
+ * Field _pidThreshold\r
+ */\r
+ private int _pidThreshold;\r
+\r
+ /**\r
+ * keeps track of state for field: _pidThreshold\r
+ */\r
+ private boolean _has_pidThreshold;\r
+\r
+ /**\r
+ * Field _outlineColour\r
+ */\r
+ private int _outlineColour;\r
+\r
+ /**\r
+ * keeps track of state for field: _outlineColour\r
+ */\r
+ private boolean _has_outlineColour;\r
+\r
+ /**\r
+ * Field _displayBoxes\r
+ */\r
+ private boolean _displayBoxes;\r
+\r
+ /**\r
+ * keeps track of state for field: _displayBoxes\r
+ */\r
+ private boolean _has_displayBoxes;\r
+\r
+ /**\r
+ * Field _displayText\r
+ */\r
+ private boolean _displayText;\r
+\r
+ /**\r
+ * keeps track of state for field: _displayText\r
+ */\r
+ private boolean _has_displayText;\r
+\r
+ /**\r
+ * Field _colourText\r
+ */\r
+ private boolean _colourText;\r
+\r
+ /**\r
+ * keeps track of state for field: _colourText\r
+ */\r
+ private boolean _has_colourText;\r
+\r
+ /**\r
+ * Field _seqList\r
+ */\r
+ private java.util.Vector _seqList;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public JGroup() {\r
+ super();\r
+ _seqList = new Vector();\r
+ } //-- jalview.binding.JGroup()\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method addSeq\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
+\r
+ /**\r
+ * Method addSeq\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vSeq\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
+\r
+ /**\r
+ * Method deleteColourText\r
+ * \r
+ */\r
+ public void deleteColourText()\r
+ {\r
+ this._has_colourText= false;\r
+ } //-- void deleteColourText() \r
+\r
+ /**\r
+ * Method deleteConsThreshold\r
+ * \r
+ */\r
+ public void deleteConsThreshold()\r
+ {\r
+ this._has_consThreshold= false;\r
+ } //-- void deleteConsThreshold() \r
+\r
+ /**\r
+ * Method deleteDisplayBoxes\r
+ * \r
+ */\r
+ public void deleteDisplayBoxes()\r
+ {\r
+ this._has_displayBoxes= false;\r
+ } //-- void deleteDisplayBoxes() \r
+\r
+ /**\r
+ * Method deleteDisplayText\r
+ * \r
+ */\r
+ public void deleteDisplayText()\r
+ {\r
+ this._has_displayText= false;\r
+ } //-- void deleteDisplayText() \r
+\r
+ /**\r
+ * Method deleteEnd\r
+ * \r
+ */\r
+ public void deleteEnd()\r
+ {\r
+ this._has_end= false;\r
+ } //-- void deleteEnd() \r
+\r
+ /**\r
+ * Method deleteOutlineColour\r
+ * \r
+ */\r
+ public void deleteOutlineColour()\r
+ {\r
+ this._has_outlineColour= false;\r
+ } //-- void deleteOutlineColour() \r
+\r
+ /**\r
+ * Method deletePidThreshold\r
+ * \r
+ */\r
+ public void deletePidThreshold()\r
+ {\r
+ this._has_pidThreshold= false;\r
+ } //-- void deletePidThreshold() \r
+\r
+ /**\r
+ * Method deleteStart\r
+ * \r
+ */\r
+ public void deleteStart()\r
+ {\r
+ this._has_start= false;\r
+ } //-- void deleteStart() \r
+\r
+ /**\r
+ * Method enumerateSeq\r
+ * \r
+ * \r
+ * \r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumerateSeq()\r
+ {\r
+ return _seqList.elements();\r
+ } //-- java.util.Enumeration enumerateSeq() \r
+\r
+ /**\r
+ * Returns the value of field 'colour'.\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
+\r
+ /**\r
+ * Returns the value of field 'colourText'.\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
+\r
+ /**\r
+ * Returns the value of field 'consThreshold'.\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
+\r
+ /**\r
+ * Returns the value of field 'displayBoxes'.\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
+\r
+ /**\r
+ * Returns the value of field 'displayText'.\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
+\r
+ /**\r
+ * Returns the value of field 'end'.\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
+\r
+ /**\r
+ * Returns the value of field 'name'.\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
+\r
+ /**\r
+ * Returns the value of field 'outlineColour'.\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
+\r
+ /**\r
+ * Returns the value of field 'pidThreshold'.\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
+\r
+ /**\r
+ * Method getSeq\r
+ * \r
+ * \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
+ }\r
+ \r
+ return ((java.lang.Integer)_seqList.elementAt(index)).intValue();\r
+ } //-- int getSeq(int) \r
+\r
+ /**\r
+ * Method getSeq\r
+ * \r
+ * \r
+ * \r
+ * @return int\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
+\r
+ /**\r
+ * Method getSeqCount\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int getSeqCount()\r
+ {\r
+ return _seqList.size();\r
+ } //-- int getSeqCount() \r
+\r
+ /**\r
+ * Returns the value of field 'start'.\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
+\r
+ /**\r
+ * Method hasColourText\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasColourText()\r
+ {\r
+ return this._has_colourText;\r
+ } //-- boolean hasColourText() \r
+\r
+ /**\r
+ * Method hasConsThreshold\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasConsThreshold()\r
+ {\r
+ return this._has_consThreshold;\r
+ } //-- boolean hasConsThreshold() \r
+\r
+ /**\r
+ * Method hasDisplayBoxes\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasDisplayBoxes()\r
+ {\r
+ return this._has_displayBoxes;\r
+ } //-- boolean hasDisplayBoxes() \r
+\r
+ /**\r
+ * Method hasDisplayText\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasDisplayText()\r
+ {\r
+ return this._has_displayText;\r
+ } //-- boolean hasDisplayText() \r
+\r
+ /**\r
+ * Method hasEnd\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasEnd()\r
+ {\r
+ return this._has_end;\r
+ } //-- boolean hasEnd() \r
+\r
+ /**\r
+ * Method hasOutlineColour\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasOutlineColour()\r
+ {\r
+ return this._has_outlineColour;\r
+ } //-- boolean hasOutlineColour() \r
+\r
+ /**\r
+ * Method hasPidThreshold\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasPidThreshold()\r
+ {\r
+ return this._has_pidThreshold;\r
+ } //-- boolean hasPidThreshold() \r
+\r
+ /**\r
+ * Method hasStart\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasStart()\r
+ {\r
+ return this._has_start;\r
+ } //-- boolean hasStart() \r
+\r
+ /**\r
+ * Method isValid\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean isValid()\r
+ {\r
+ try {\r
+ validate();\r
+ }\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ } //-- boolean isValid() \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
+ Marshaller.marshal(this, out);\r
+ } //-- void marshal(java.io.Writer) \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
+ Marshaller.marshal(this, handler);\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+ /**\r
+ * Method removeAllSeq\r
+ * \r
+ */\r
+ public void removeAllSeq()\r
+ {\r
+ _seqList.removeAllElements();\r
+ } //-- void removeAllSeq() \r
+\r
+ /**\r
+ * Method removeSeq\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return int\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
+\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
+ this._colour = colour;\r
+ } //-- void setColour(java.lang.String) \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
+ this._colourText = colourText;\r
+ this._has_colourText = true;\r
+ } //-- void setColourText(boolean) \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
+ this._consThreshold = consThreshold;\r
+ this._has_consThreshold = true;\r
+ } //-- void setConsThreshold(int) \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
+ this._displayBoxes = displayBoxes;\r
+ this._has_displayBoxes = true;\r
+ } //-- void setDisplayBoxes(boolean) \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
+ this._displayText = displayText;\r
+ this._has_displayText = true;\r
+ } //-- void setDisplayText(boolean) \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
+ this._end = end;\r
+ this._has_end = true;\r
+ } //-- void setEnd(int) \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
+ this._name = name;\r
+ } //-- void setName(java.lang.String) \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
+ this._outlineColour = outlineColour;\r
+ this._has_outlineColour = true;\r
+ } //-- void setOutlineColour(int) \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
+ this._pidThreshold = pidThreshold;\r
+ this._has_pidThreshold = true;\r
+ } //-- void setPidThreshold(int) \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
+ }\r
+ _seqList.setElementAt(new java.lang.Integer(vSeq), index);\r
+ } //-- void setSeq(int, int) \r
+\r
+ /**\r
+ * Method setSeq\r
+ * \r
+ * \r
+ * \r
+ * @param seqArray\r
+ */\r
+ public void setSeq(int[] seqArray)\r
+ {\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
+ }\r
+ } //-- void setSeq(int) \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
+ this._start = start;\r
+ this._has_start = true;\r
+ } //-- void setStart(int) \r
+\r
+ /**\r
+ * Method unmarshal\r
+ * \r
+ * \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
+ return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.class, reader);\r
+ } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+ /**\r
+ * Method validate\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
+\r
+}\r
git://source.jalview.org / jalview.git / blobdiff