-/*\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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.binding;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.util.MessageManager;
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class JGroup.
+ *
+ * @version $Revision$ $Date$
+ */
+public class JGroup implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _start.
+ */
+ private int _start;
+
+ /**
+ * keeps track of state for field: _start
+ */
+ private boolean _has_start;
+
+ /**
+ * Field _end.
+ */
+ private int _end;
+
+ /**
+ * keeps track of state for field: _end
+ */
+ private boolean _has_end;
+
+ /**
+ * Field _name.
+ */
+ private java.lang.String _name;
+
+ /**
+ * Field _colour.
+ */
+ private java.lang.String _colour;
+
+ /**
+ * Field _consThreshold.
+ */
+ private int _consThreshold;
+
+ /**
+ * keeps track of state for field: _consThreshold
+ */
+ private boolean _has_consThreshold;
+
+ /**
+ * Field _pidThreshold.
+ */
+ private int _pidThreshold;
+
+ /**
+ * keeps track of state for field: _pidThreshold
+ */
+ private boolean _has_pidThreshold;
+
+ /**
+ * Field _outlineColour.
+ */
+ private int _outlineColour;
+
+ /**
+ * keeps track of state for field: _outlineColour
+ */
+ private boolean _has_outlineColour;
+
+ /**
+ * Field _displayBoxes.
+ */
+ private boolean _displayBoxes;
+
+ /**
+ * keeps track of state for field: _displayBoxes
+ */
+ private boolean _has_displayBoxes;
+
+ /**
+ * Field _displayText.
+ */
+ private boolean _displayText;
+
+ /**
+ * keeps track of state for field: _displayText
+ */
+ private boolean _has_displayText;
+
+ /**
+ * Field _colourText.
+ */
+ private boolean _colourText;
+
+ /**
+ * keeps track of state for field: _colourText
+ */
+ private boolean _has_colourText;
+
+ /**
+ * Field _seqList.
+ */
+ private java.util.Vector _seqList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public JGroup()
+ {
+ super();
+ this._seqList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vSeq
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSeq(final int vSeq)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._seqList.addElement(new java.lang.Integer(vSeq));
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSeq
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSeq(final int index, final int vSeq)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._seqList.add(index, new java.lang.Integer(vSeq));
+ }
+
+ /**
+ */
+ public void deleteColourText()
+ {
+ this._has_colourText = false;
+ }
+
+ /**
+ */
+ public void deleteConsThreshold()
+ {
+ this._has_consThreshold = false;
+ }
+
+ /**
+ */
+ public void deleteDisplayBoxes()
+ {
+ this._has_displayBoxes = false;
+ }
+
+ /**
+ */
+ public void deleteDisplayText()
+ {
+ this._has_displayText = false;
+ }
+
+ /**
+ */
+ public void deleteEnd()
+ {
+ this._has_end = false;
+ }
+
+ /**
+ */
+ public void deleteOutlineColour()
+ {
+ this._has_outlineColour = false;
+ }
+
+ /**
+ */
+ public void deletePidThreshold()
+ {
+ this._has_pidThreshold = false;
+ }
+
+ /**
+ */
+ public void deleteStart()
+ {
+ this._has_start = false;
+ }
+
+ /**
+ * Method enumerateSeq.
+ *
+ * @return an Enumeration over all int elements
+ */
+ public java.util.Enumeration enumerateSeq()
+ {
+ return this._seqList.elements();
+ }
+
+ /**
+ * Returns the value of field 'colour'.
+ *
+ * @return the value of field 'Colour'.
+ */
+ public java.lang.String getColour()
+ {
+ return this._colour;
+ }
+
+ /**
+ * Returns the value of field 'colourText'.
+ *
+ * @return the value of field 'ColourText'.
+ */
+ public boolean getColourText()
+ {
+ return this._colourText;
+ }
+
+ /**
+ * Returns the value of field 'consThreshold'.
+ *
+ * @return the value of field 'ConsThreshold'.
+ */
+ public int getConsThreshold()
+ {
+ return this._consThreshold;
+ }
+
+ /**
+ * Returns the value of field 'displayBoxes'.
+ *
+ * @return the value of field 'DisplayBoxes'.
+ */
+ public boolean getDisplayBoxes()
+ {
+ return this._displayBoxes;
+ }
+
+ /**
+ * Returns the value of field 'displayText'.
+ *
+ * @return the value of field 'DisplayText'.
+ */
+ public boolean getDisplayText()
+ {
+ return this._displayText;
+ }
+
+ /**
+ * Returns the value of field 'end'.
+ *
+ * @return the value of field 'End'.
+ */
+ public int getEnd()
+ {
+ return this._end;
+ }
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName()
+ {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'outlineColour'.
+ *
+ * @return the value of field 'OutlineColour'.
+ */
+ public int getOutlineColour()
+ {
+ return this._outlineColour;
+ }
+
+ /**
+ * Returns the value of field 'pidThreshold'.
+ *
+ * @return the value of field 'PidThreshold'.
+ */
+ public int getPidThreshold()
+ {
+ return this._pidThreshold;
+ }
+
+ /**
+ * Method getSeq.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the int at the given index
+ */
+ public int getSeq(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._seqList.size())
+ {
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getSeq",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._seqList.size() - 1)).toString()
+ }));
+ }
+
+ return ((java.lang.Integer) _seqList.get(index)).intValue();
+ }
+
+ /**
+ * Method getSeq.Returns the contents of the collection in an Array.
+ *
+ * @return this collection as an Array
+ */
+ public int[] getSeq()
+ {
+ int size = this._seqList.size();
+ int[] array = new int[size];
+ java.util.Iterator iter = _seqList.iterator();
+ for (int index = 0; index < size; index++)
+ {
+ array[index] = ((java.lang.Integer) iter.next()).intValue();
+ }
+ return array;
+ }
+
+ /**
+ * Method getSeqCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSeqCount()
+ {
+ return this._seqList.size();
+ }
+
+ /**
+ * Returns the value of field 'start'.
+ *
+ * @return the value of field 'Start'.
+ */
+ public int getStart()
+ {
+ return this._start;
+ }
+
+ /**
+ * Method hasColourText.
+ *
+ * @return true if at least one ColourText has been added
+ */
+ public boolean hasColourText()
+ {
+ return this._has_colourText;
+ }
+
+ /**
+ * Method hasConsThreshold.
+ *
+ * @return true if at least one ConsThreshold has been added
+ */
+ public boolean hasConsThreshold()
+ {
+ return this._has_consThreshold;
+ }
+
+ /**
+ * Method hasDisplayBoxes.
+ *
+ * @return true if at least one DisplayBoxes has been added
+ */
+ public boolean hasDisplayBoxes()
+ {
+ return this._has_displayBoxes;
+ }
+
+ /**
+ * Method hasDisplayText.
+ *
+ * @return true if at least one DisplayText has been added
+ */
+ public boolean hasDisplayText()
+ {
+ return this._has_displayText;
+ }
+
+ /**
+ * Method hasEnd.
+ *
+ * @return true if at least one End has been added
+ */
+ public boolean hasEnd()
+ {
+ return this._has_end;
+ }
+
+ /**
+ * Method hasOutlineColour.
+ *
+ * @return true if at least one OutlineColour has been added
+ */
+ public boolean hasOutlineColour()
+ {
+ return this._has_outlineColour;
+ }
+
+ /**
+ * Method hasPidThreshold.
+ *
+ * @return true if at least one PidThreshold has been added
+ */
+ public boolean hasPidThreshold()
+ {
+ return this._has_pidThreshold;
+ }
+
+ /**
+ * Method hasStart.
+ *
+ * @return true if at least one Start has been added
+ */
+ public boolean hasStart()
+ {
+ return this._has_start;
+ }
+
+ /**
+ * Returns the value of field 'colourText'.
+ *
+ * @return the value of field 'ColourText'.
+ */
+ public boolean isColourText()
+ {
+ return this._colourText;
+ }
+
+ /**
+ * Returns the value of field 'displayBoxes'.
+ *
+ * @return the value of field 'DisplayBoxes'.
+ */
+ public boolean isDisplayBoxes()
+ {
+ return this._displayBoxes;
+ }
+
+ /**
+ * Returns the value of field 'displayText'.
+ *
+ * @return the value of field 'DisplayText'.
+ */
+ public boolean isDisplayText()
+ {
+ return this._displayText;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllSeq()
+ {
+ this._seqList.clear();
+ }
+
+ /**
+ * Method removeSeq.
+ *
+ * @param vSeq
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSeq(final int vSeq)
+ {
+ boolean removed = _seqList.remove(new java.lang.Integer(vSeq));
+ return removed;
+ }
+
+ /**
+ * Method removeSeqAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public int removeSeqAt(final int index)
+ {
+ java.lang.Object obj = this._seqList.remove(index);
+ return ((java.lang.Integer) obj).intValue();
+ }
+
+ /**
+ * Sets the value of field 'colour'.
+ *
+ * @param colour
+ * the value of field 'colour'.
+ */
+ public void setColour(final java.lang.String colour)
+ {
+ this._colour = colour;
+ }
+
+ /**
+ * Sets the value of field 'colourText'.
+ *
+ * @param colourText
+ * the value of field 'colourText'.
+ */
+ public void setColourText(final boolean colourText)
+ {
+ this._colourText = colourText;
+ this._has_colourText = true;
+ }
+
+ /**
+ * Sets the value of field 'consThreshold'.
+ *
+ * @param consThreshold
+ * the value of field 'consThreshold'.
+ */
+ public void setConsThreshold(final int consThreshold)
+ {
+ this._consThreshold = consThreshold;
+ this._has_consThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'displayBoxes'.
+ *
+ * @param displayBoxes
+ * the value of field 'displayBoxes'.
+ */
+ public void setDisplayBoxes(final boolean displayBoxes)
+ {
+ this._displayBoxes = displayBoxes;
+ this._has_displayBoxes = true;
+ }
+
+ /**
+ * Sets the value of field 'displayText'.
+ *
+ * @param displayText
+ * the value of field 'displayText'.
+ */
+ public void setDisplayText(final boolean displayText)
+ {
+ this._displayText = displayText;
+ this._has_displayText = true;
+ }
+
+ /**
+ * Sets the value of field 'end'.
+ *
+ * @param end
+ * the value of field 'end'.
+ */
+ public void setEnd(final int end)
+ {
+ this._end = end;
+ this._has_end = true;
+ }
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name
+ * the value of field 'name'.
+ */
+ public void setName(final java.lang.String name)
+ {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'outlineColour'.
+ *
+ * @param outlineColour
+ * the value of field 'outlineColour'.
+ */
+ public void setOutlineColour(final int outlineColour)
+ {
+ this._outlineColour = outlineColour;
+ this._has_outlineColour = true;
+ }
+
+ /**
+ * Sets the value of field 'pidThreshold'.
+ *
+ * @param pidThreshold
+ * the value of field 'pidThreshold'.
+ */
+ public void setPidThreshold(final int pidThreshold)
+ {
+ this._pidThreshold = pidThreshold;
+ this._has_pidThreshold = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSeq
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setSeq(final int index, final int vSeq)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._seqList.size())
+ {
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setSeq",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._seqList.size() - 1)).toString()
+ }));
+ }
+
+ this._seqList.set(index, new java.lang.Integer(vSeq));
+ }
+
+ /**
+ *
+ *
+ * @param vSeqArray
+ */
+ public void setSeq(final int[] vSeqArray)
+ {
+ // -- copy array
+ _seqList.clear();
+
+ for (int i = 0; i < vSeqArray.length; i++)
+ {
+ this._seqList.add(new java.lang.Integer(vSeqArray[i]));
+ }
+ }
+
+ /**
+ * Sets the value of field 'start'.
+ *
+ * @param start
+ * the value of field 'start'.
+ */
+ public void setStart(final int start)
+ {
+ this._start = start;
+ this._has_start = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.JGroup
+ */
+ public static jalview.binding.JGroup unmarshal(final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.JGroup) Unmarshaller.unmarshal(
+ jalview.binding.JGroup.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff