/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
- * Schema.\r
- * $Id$\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
+ * Copyright (C) 2008 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.schemabinding.version2;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
+// ---------------------------------/\r
+// - Imported classes and packages -/\r
+// ---------------------------------/\r
\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\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 _textCol1.\r
- */\r
- private int _textCol1;\r
-\r
- /**\r
- * keeps track of state for field: _textCol1\r
- */\r
- private boolean _has_textCol1;\r
-\r
- /**\r
- * Field _textCol2.\r
- */\r
- private int _textCol2;\r
-\r
- /**\r
- * keeps track of state for field: _textCol2\r
- */\r
- private boolean _has_textCol2;\r
-\r
- /**\r
- * Field _textColThreshold.\r
- */\r
- private int _textColThreshold;\r
-\r
- /**\r
- * keeps track of state for field: _textColThreshold\r
- */\r
- private boolean _has_textColThreshold;\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
- this._seqList = new java.util.Vector();\r
- }\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vSeq\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addSeq(\r
- final int vSeq)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._seqList.addElement(new java.lang.Integer(vSeq));\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vSeq\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addSeq(\r
- final int index,\r
- final int vSeq)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._seqList.add(index, new java.lang.Integer(vSeq));\r
- }\r
-\r
- /**\r
- */\r
- public void deleteColourText(\r
- ) {\r
- this._has_colourText= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteConsThreshold(\r
- ) {\r
- this._has_consThreshold= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteDisplayBoxes(\r
- ) {\r
- this._has_displayBoxes= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteDisplayText(\r
- ) {\r
- this._has_displayText= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteEnd(\r
- ) {\r
- this._has_end= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteOutlineColour(\r
- ) {\r
- this._has_outlineColour= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deletePidThreshold(\r
- ) {\r
- this._has_pidThreshold= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteStart(\r
- ) {\r
- this._has_start= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteTextCol1(\r
- ) {\r
- this._has_textCol1= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteTextCol2(\r
- ) {\r
- this._has_textCol2= false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteTextColThreshold(\r
- ) {\r
- this._has_textColThreshold= false;\r
- }\r
-\r
- /**\r
- * Method enumerateSeq.\r
- * \r
- * @return an Enumeration over all int elements\r
- */\r
- public java.util.Enumeration enumerateSeq(\r
- ) {\r
- return this._seqList.elements();\r
- }\r
-\r
- /**\r
- * Returns 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
- }\r
-\r
- /**\r
- * Returns the value of field 'colourText'.\r
- * \r
- * @return the value of field 'ColourText'.\r
- */\r
- public boolean getColourText(\r
- ) {\r
- return this._colourText;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'consThreshold'.\r
- * \r
- * @return the value of field 'ConsThreshold'.\r
- */\r
- public int getConsThreshold(\r
- ) {\r
- return this._consThreshold;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'displayBoxes'.\r
- * \r
- * @return the value of field 'DisplayBoxes'.\r
- */\r
- public boolean getDisplayBoxes(\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 getDisplayText(\r
- ) {\r
- return this._displayText;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'end'.\r
- * \r
- * @return the value of field 'End'.\r
- */\r
- public int getEnd(\r
- ) {\r
- return this._end;\r
- }\r
-\r
- /**\r
- * Returns 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
- }\r
-\r
- /**\r
- * Returns the value of field 'outlineColour'.\r
- * \r
- * @return the value of field 'OutlineColour'.\r
- */\r
- public int getOutlineColour(\r
- ) {\r
- return this._outlineColour;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'pidThreshold'.\r
- * \r
- * @return the value of field 'PidThreshold'.\r
- */\r
- public int getPidThreshold(\r
- ) {\r
- return this._pidThreshold;\r
- }\r
-\r
- /**\r
- * Method getSeq.\r
- * \r
- * @param index\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- * @return the value of the int at the given index\r
- */\r
- public int getSeq(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._seqList.size()) {\r
- throw new IndexOutOfBoundsException("getSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");\r
- }\r
- \r
- return ((java.lang.Integer) _seqList.get(index)).intValue();\r
- }\r
-\r
- /**\r
- * Method getSeq.Returns the contents of the collection in an\r
- * Array. \r
- * \r
- * @return this collection as an Array\r
- */\r
- public int[] getSeq(\r
- ) {\r
- int size = this._seqList.size();\r
- int[] array = new int[size];\r
- java.util.Iterator iter = _seqList.iterator();\r
- for (int index = 0; index < size; index++) {\r
- array[index] = ((java.lang.Integer) iter.next()).intValue();\r
- }\r
- return array;\r
- }\r
-\r
- /**\r
- * Method getSeqCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getSeqCount(\r
- ) {\r
- return this._seqList.size();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'start'.\r
- * \r
- * @return the value of field 'Start'.\r
- */\r
- public int getStart(\r
- ) {\r
- return this._start;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'textCol1'.\r
- * \r
- * @return the value of field 'TextCol1'.\r
- */\r
- public int getTextCol1(\r
- ) {\r
- return this._textCol1;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'textCol2'.\r
- * \r
- * @return the value of field 'TextCol2'.\r
- */\r
- public int getTextCol2(\r
- ) {\r
- return this._textCol2;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'textColThreshold'.\r
- * \r
- * @return the value of field 'TextColThreshold'.\r
- */\r
- public int getTextColThreshold(\r
- ) {\r
- return this._textColThreshold;\r
- }\r
-\r
- /**\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
- }\r
-\r
- /**\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
- }\r
-\r
- /**\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
- }\r
-\r
- /**\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
- }\r
-\r
- /**\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
- }\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
- }\r
-\r
- /**\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
- }\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
- }\r
-\r
- /**\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
- }\r
-\r
- /**\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
- }\r
-\r
- /**\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
- }\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
- * Method isValid.\r
- * \r
- * @return true if this object is valid according to the schema\r
- */\r
- public boolean isValid(\r
- ) {\r
- try {\r
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param out\r
- * @throws org.exolab.castor.xml.MarshalException if object is\r
- * null or if any SAXException is thrown during marshaling\r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- */\r
- public void marshal(\r
- final java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
- Marshaller.marshal(this, out);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param handler\r
- * @throws java.io.IOException if an IOException occurs during\r
- * marshaling\r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- * @throws org.exolab.castor.xml.MarshalException if object is\r
- * null or if any SAXException is thrown during marshaling\r
- */\r
- public void marshal(\r
- final org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
- Marshaller.marshal(this, handler);\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllSeq(\r
- ) {\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(\r
- final int vSeq) {\r
- boolean removed = _seqList.remove(new java.lang.Integer(vSeq));\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeSeqAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public int removeSeqAt(\r
- final int index) {\r
- java.lang.Object obj = this._seqList.remove(index);\r
- return ((java.lang.Integer) obj).intValue();\r
- }\r
-\r
- /**\r
- * Sets the value of field 'colour'.\r
- * \r
- * @param colour the value of field 'colour'.\r
- */\r
- public void setColour(\r
- final java.lang.String colour) {\r
- this._colour = colour;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'colourText'.\r
- * \r
- * @param colourText the value of field 'colourText'.\r
- */\r
- public void setColourText(\r
- final boolean colourText) {\r
- this._colourText = colourText;\r
- this._has_colourText = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'consThreshold'.\r
- * \r
- * @param consThreshold the value of field 'consThreshold'.\r
- */\r
- public void setConsThreshold(\r
- final int consThreshold) {\r
- this._consThreshold = consThreshold;\r
- this._has_consThreshold = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'displayBoxes'.\r
- * \r
- * @param displayBoxes the value of field 'displayBoxes'.\r
- */\r
- public void setDisplayBoxes(\r
- final boolean displayBoxes) {\r
- this._displayBoxes = displayBoxes;\r
- this._has_displayBoxes = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'displayText'.\r
- * \r
- * @param displayText the value of field 'displayText'.\r
- */\r
- public void setDisplayText(\r
- final boolean displayText) {\r
- this._displayText = displayText;\r
- this._has_displayText = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'end'.\r
- * \r
- * @param end the value of field 'end'.\r
- */\r
- public void setEnd(\r
- final int end) {\r
- this._end = end;\r
- this._has_end = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'name'.\r
- * \r
- * @param name the value of field 'name'.\r
- */\r
- public void setName(\r
- final java.lang.String name) {\r
- this._name = name;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'outlineColour'.\r
- * \r
- * @param outlineColour the value of field 'outlineColour'.\r
- */\r
- public void setOutlineColour(\r
- final int outlineColour) {\r
- this._outlineColour = outlineColour;\r
- this._has_outlineColour = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'pidThreshold'.\r
- * \r
- * @param pidThreshold the value of field 'pidThreshold'.\r
- */\r
- public void setPidThreshold(\r
- final int pidThreshold) {\r
- this._pidThreshold = pidThreshold;\r
- this._has_pidThreshold = true;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vSeq\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void setSeq(\r
- final int index,\r
- final int vSeq)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._seqList.size()) {\r
- throw new IndexOutOfBoundsException("setSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");\r
- }\r
- \r
- this._seqList.set(index, new java.lang.Integer(vSeq));\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vSeqArray\r
- */\r
- public void setSeq(\r
- final int[] vSeqArray) {\r
- //-- copy array\r
- _seqList.clear();\r
- \r
- for (int i = 0; i < vSeqArray.length; i++) {\r
- this._seqList.add(new java.lang.Integer(vSeqArray[i]));\r
- }\r
- }\r
-\r
- /**\r
- * Sets the value of field 'start'.\r
- * \r
- * @param start the value of field 'start'.\r
- */\r
- public void setStart(\r
- final int start) {\r
- this._start = start;\r
- this._has_start = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'textCol1'.\r
- * \r
- * @param textCol1 the value of field 'textCol1'.\r
- */\r
- public void setTextCol1(\r
- final int textCol1) {\r
- this._textCol1 = textCol1;\r
- this._has_textCol1 = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'textCol2'.\r
- * \r
- * @param textCol2 the value of field 'textCol2'.\r
- */\r
- public void setTextCol2(\r
- final int textCol2) {\r
- this._textCol2 = textCol2;\r
- this._has_textCol2 = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'textColThreshold'.\r
- * \r
- * @param textColThreshold the value of field 'textColThreshold'\r
- */\r
- public void setTextColThreshold(\r
- final int textColThreshold) {\r
- this._textColThreshold = textColThreshold;\r
- this._has_textColThreshold = true;\r
- }\r
-\r
- /**\r
- * Method unmarshal.\r
- * \r
- * @param reader\r
- * @throws org.exolab.castor.xml.MarshalException if object is\r
- * null or if any SAXException is thrown during marshaling\r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * 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, org.exolab.castor.xml.ValidationException {\r
- return (jalview.schemabinding.version2.JGroup) Unmarshaller.unmarshal(jalview.schemabinding.version2.JGroup.class, reader);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- */\r
- public void validate(\r
- )\r
- throws org.exolab.castor.xml.ValidationException {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\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 _textCol1.\r
+ */\r
+ private int _textCol1;\r
+\r
+ /**\r
+ * keeps track of state for field: _textCol1\r
+ */\r
+ private boolean _has_textCol1;\r
+\r
+ /**\r
+ * Field _textCol2.\r
+ */\r
+ private int _textCol2;\r
+\r
+ /**\r
+ * keeps track of state for field: _textCol2\r
+ */\r
+ private boolean _has_textCol2;\r
+\r
+ /**\r
+ * Field _textColThreshold.\r
+ */\r
+ private int _textColThreshold;\r
+\r
+ /**\r
+ * keeps track of state for field: _textColThreshold\r
+ */\r
+ private boolean _has_textColThreshold;\r
+\r
+ /**\r
+ * Field _seqList.\r
+ */\r
+ private java.util.Vector _seqList;\r
+\r
+ // ----------------/\r
+ // - Constructors -/\r
+ // ----------------/\r
+\r
+ public JGroup()\r
+ {\r
+ super();\r
+ this._seqList = new java.util.Vector();\r
+ }\r
+\r
+ // -----------/\r
+ // - Methods -/\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(final java.lang.String vSeq)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._seqList.addElement(vSeq);\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(final int index, final java.lang.String vSeq)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._seqList.add(index, vSeq);\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteColourText()\r
+ {\r
+ this._has_colourText = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteConsThreshold()\r
+ {\r
+ this._has_consThreshold = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteDisplayBoxes()\r
+ {\r
+ this._has_displayBoxes = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteDisplayText()\r
+ {\r
+ this._has_displayText = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteEnd()\r
+ {\r
+ this._has_end = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteOutlineColour()\r
+ {\r
+ this._has_outlineColour = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deletePidThreshold()\r
+ {\r
+ this._has_pidThreshold = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteStart()\r
+ {\r
+ this._has_start = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteTextCol1()\r
+ {\r
+ this._has_textCol1 = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteTextCol2()\r
+ {\r
+ this._has_textCol2 = false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteTextColThreshold()\r
+ {\r
+ this._has_textColThreshold = false;\r
+ }\r
+\r
+ /**\r
+ * Method enumerateSeq.\r
+ * \r
+ * @return an Enumeration over all java.lang.String elements\r
+ */\r
+ public java.util.Enumeration enumerateSeq()\r
+ {\r
+ return this._seqList.elements();\r
+ }\r
+\r
+ /**\r
+ * Returns 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
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'colourText'.\r
+ * \r
+ * @return the value of field 'ColourText'.\r
+ */\r
+ public boolean getColourText()\r
+ {\r
+ return this._colourText;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'consThreshold'.\r
+ * \r
+ * @return the value of field 'ConsThreshold'.\r
+ */\r
+ public int getConsThreshold()\r
+ {\r
+ return this._consThreshold;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'displayBoxes'.\r
+ * \r
+ * @return the value of field 'DisplayBoxes'.\r
+ */\r
+ public boolean getDisplayBoxes()\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 getDisplayText()\r
+ {\r
+ return this._displayText;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'end'.\r
+ * \r
+ * @return the value of field 'End'.\r
+ */\r
+ public int getEnd()\r
+ {\r
+ return this._end;\r
+ }\r
+\r
+ /**\r
+ * Returns 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
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'outlineColour'.\r
+ * \r
+ * @return the value of field 'OutlineColour'.\r
+ */\r
+ public int getOutlineColour()\r
+ {\r
+ return this._outlineColour;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'pidThreshold'.\r
+ * \r
+ * @return the value of field 'PidThreshold'.\r
+ */\r
+ public int getPidThreshold()\r
+ {\r
+ return this._pidThreshold;\r
+ }\r
+\r
+ /**\r
+ * Method getSeq.\r
+ * \r
+ * @param index\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 java.lang.String getSeq(final int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._seqList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException("getSeq: Index value '" + index\r
+ + "' not in range [0.." + (this._seqList.size() - 1) + "]");\r
+ }\r
+\r
+ return (java.lang.String) _seqList.get(index);\r
+ }\r
+\r
+ /**\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 java.lang.String[] getSeq()\r
+ {\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
+ * @return the size of this collection\r
+ */\r
+ public int getSeqCount()\r
+ {\r
+ return this._seqList.size();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'start'.\r
+ * \r
+ * @return the value of field 'Start'.\r
+ */\r
+ public int getStart()\r
+ {\r
+ return this._start;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'textCol1'.\r
+ * \r
+ * @return the value of field 'TextCol1'.\r
+ */\r
+ public int getTextCol1()\r
+ {\r
+ return this._textCol1;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'textCol2'.\r
+ * \r
+ * @return the value of field 'TextCol2'.\r
+ */\r
+ public int getTextCol2()\r
+ {\r
+ return this._textCol2;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'textColThreshold'.\r
+ * \r
+ * @return the value of field 'TextColThreshold'.\r
+ */\r
+ public int getTextColThreshold()\r
+ {\r
+ return this._textColThreshold;\r
+ }\r
+\r
+ /**\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
+ }\r
+\r
+ /**\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
+ }\r
+\r
+ /**\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
+ }\r
+\r
+ /**\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
+ }\r
+\r
+ /**\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
+ }\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
+ }\r
+\r
+ /**\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
+ }\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
+ }\r
+\r
+ /**\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
+ }\r
+\r
+ /**\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
+ }\r
+\r
+ /**\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
+ }\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
+ * 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
+ } catch (org.exolab.castor.xml.ValidationException vex)\r
+ {\r
+ return false;\r
+ }\r
+ return true;\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\r
+ * schema\r
+ */\r
+ public void marshal(final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException\r
+ {\r
+ Marshaller.marshal(this, out);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param handler\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\r
+ * 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
+ Marshaller.marshal(this, handler);\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllSeq()\r
+ {\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 removeSeqAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public java.lang.String removeSeqAt(final int index)\r
+ {\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\r
+ * the value of field 'colour'.\r
+ */\r
+ public void setColour(final java.lang.String colour)\r
+ {\r
+ this._colour = colour;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'colourText'.\r
+ * \r
+ * @param colourText\r
+ * the value of field 'colourText'.\r
+ */\r
+ public void setColourText(final boolean colourText)\r
+ {\r
+ this._colourText = colourText;\r
+ this._has_colourText = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'consThreshold'.\r
+ * \r
+ * @param consThreshold\r
+ * the value of field 'consThreshold'.\r
+ */\r
+ public void setConsThreshold(final int consThreshold)\r
+ {\r
+ this._consThreshold = consThreshold;\r
+ this._has_consThreshold = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'displayBoxes'.\r
+ * \r
+ * @param displayBoxes\r
+ * the value of field 'displayBoxes'.\r
+ */\r
+ public void setDisplayBoxes(final boolean displayBoxes)\r
+ {\r
+ this._displayBoxes = displayBoxes;\r
+ this._has_displayBoxes = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'displayText'.\r
+ * \r
+ * @param displayText\r
+ * the value of field 'displayText'.\r
+ */\r
+ public void setDisplayText(final boolean displayText)\r
+ {\r
+ this._displayText = displayText;\r
+ this._has_displayText = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'end'.\r
+ * \r
+ * @param end\r
+ * the value of field 'end'.\r
+ */\r
+ public void setEnd(final int end)\r
+ {\r
+ this._end = end;\r
+ this._has_end = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'name'.\r
+ * \r
+ * @param name\r
+ * the value of field 'name'.\r
+ */\r
+ public void setName(final java.lang.String name)\r
+ {\r
+ this._name = name;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'outlineColour'.\r
+ * \r
+ * @param outlineColour\r
+ * the value of field 'outlineColour'.\r
+ */\r
+ public void setOutlineColour(final int outlineColour)\r
+ {\r
+ this._outlineColour = outlineColour;\r
+ this._has_outlineColour = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'pidThreshold'.\r
+ * \r
+ * @param pidThreshold\r
+ * the value of field 'pidThreshold'.\r
+ */\r
+ public void setPidThreshold(final int pidThreshold)\r
+ {\r
+ this._pidThreshold = pidThreshold;\r
+ this._has_pidThreshold = true;\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(final int index, final java.lang.String vSeq)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._seqList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException("setSeq: Index value '" + index\r
+ + "' not in range [0.." + (this._seqList.size() - 1) + "]");\r
+ }\r
+\r
+ this._seqList.set(index, vSeq);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vSeqArray\r
+ */\r
+ public void setSeq(final java.lang.String[] vSeqArray)\r
+ {\r
+ // -- copy array\r
+ _seqList.clear();\r
+\r
+ for (int i = 0; i < vSeqArray.length; i++)\r
+ {\r
+ this._seqList.add(vSeqArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'start'.\r
+ * \r
+ * @param start\r
+ * the value of field 'start'.\r
+ */\r
+ public void setStart(final int start)\r
+ {\r
+ this._start = start;\r
+ this._has_start = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'textCol1'.\r
+ * \r
+ * @param textCol1\r
+ * the value of field 'textCol1'.\r
+ */\r
+ public void setTextCol1(final int textCol1)\r
+ {\r
+ this._textCol1 = textCol1;\r
+ this._has_textCol1 = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'textCol2'.\r
+ * \r
+ * @param textCol2\r
+ * the value of field 'textCol2'.\r
+ */\r
+ public void setTextCol2(final int textCol2)\r
+ {\r
+ this._textCol2 = textCol2;\r
+ this._has_textCol2 = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'textColThreshold'.\r
+ * \r
+ * @param textColThreshold\r
+ * the value of field 'textColThreshold'\r
+ */\r
+ public void setTextColThreshold(final int textColThreshold)\r
+ {\r
+ this._textColThreshold = textColThreshold;\r
+ this._has_textColThreshold = true;\r
+ }\r
+\r
+ /**\r
+ * Method unmarshal.\r
+ * \r
+ * @param reader\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\r
+ * 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
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the\r
+ * schema\r
+ */\r
+ public void validate() 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
+ }\r
\r
}\r
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