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