- 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.schemabinding.version2.JGroup) Unmarshaller.unmarshal(jalview.schemabinding.version2.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