/*\r
- * This class was automatically generated with\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
-* 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
-package jalview.binding;\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
-import org.xml.sax.ContentHandler;\r
+package jalview.binding;\r
\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\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
-\r
import java.util.Enumeration;\r
import java.util.Vector;\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
+import org.xml.sax.ContentHandler;\r
\r
/**\r
* Class SequenceSet.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
public class SequenceSet implements java.io.Serializable {\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
//--------------------------/\r
\r
/**\r
*/\r
private java.util.Vector _annotationList;\r
\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
//----------------/\r
- //- Constructors -/\r
- //----------------/\r
+\r
public SequenceSet() {\r
super();\r
_sequenceList = new Vector();\r
_annotationList = new Vector();\r
- }\r
- //-- jalview.binding.SequenceSet()\r
- //-----------/\r
+ } //-- jalview.binding.SequenceSet()\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
\r
+ /**\r
+ * Method addAnnotation\r
+ * \r
+ * \r
+ * \r
+ * @param vAnnotation\r
+ */\r
public void addAnnotation(jalview.binding.Annotation vAnnotation)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_annotationList.addElement(vAnnotation);\r
- }\r
- //-- void addAnnotation(jalview.binding.Annotation)\r
+ } //-- void addAnnotation(jalview.binding.Annotation) \r
\r
/**\r
* Method addAnnotation\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @param vAnnotation\r
*/\r
public void addAnnotation(int index, jalview.binding.Annotation vAnnotation)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_annotationList.insertElementAt(vAnnotation, index);\r
- }\r
- //-- void addAnnotation(int, jalview.binding.Annotation)\r
+ } //-- void addAnnotation(int, jalview.binding.Annotation) \r
\r
/**\r
* Method addSequence\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param vSequence\r
*/\r
public void addSequence(jalview.binding.Sequence vSequence)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_sequenceList.addElement(vSequence);\r
- }\r
- //-- void addSequence(jalview.binding.Sequence)\r
+ } //-- void addSequence(jalview.binding.Sequence) \r
\r
/**\r
* Method addSequence\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @param vSequence\r
*/\r
public void addSequence(int index, jalview.binding.Sequence vSequence)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
_sequenceList.insertElementAt(vSequence, index);\r
- }\r
- //-- void addSequence(int, jalview.binding.Sequence)\r
+ } //-- void addSequence(int, jalview.binding.Sequence) \r
\r
/**\r
* Method deleteAligned\r
- *\r
+ * \r
*/\r
- public void deleteAligned() {\r
- this._has_aligned = false;\r
- }\r
- //-- void deleteAligned()\r
+ public void deleteAligned()\r
+ {\r
+ this._has_aligned= false;\r
+ } //-- void deleteAligned() \r
\r
/**\r
* Method enumerateAnnotation\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateAnnotation() {\r
+ public java.util.Enumeration enumerateAnnotation()\r
+ {\r
return _annotationList.elements();\r
- }\r
- //-- java.util.Enumeration enumerateAnnotation()\r
+ } //-- java.util.Enumeration enumerateAnnotation() \r
\r
/**\r
* Method enumerateSequence\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Enumeration\r
*/\r
- public java.util.Enumeration enumerateSequence() {\r
+ public java.util.Enumeration enumerateSequence()\r
+ {\r
return _sequenceList.elements();\r
- }\r
- //-- java.util.Enumeration enumerateSequence()\r
+ } //-- java.util.Enumeration enumerateSequence() \r
\r
/**\r
* Returns the value of field 'aligned'.\r
- *\r
+ * \r
* @return boolean\r
* @return the value of field 'aligned'.\r
*/\r
- public boolean getAligned() {\r
+ public boolean getAligned()\r
+ {\r
return this._aligned;\r
- }\r
- //-- boolean getAligned()\r
+ } //-- boolean getAligned() \r
\r
/**\r
* Method getAnnotation\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return Annotation\r
*/\r
public jalview.binding.Annotation getAnnotation(int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _annotationList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
+ \r
return (jalview.binding.Annotation) _annotationList.elementAt(index);\r
- }\r
- //-- jalview.binding.Annotation getAnnotation(int)\r
+ } //-- jalview.binding.Annotation getAnnotation(int) \r
\r
/**\r
* Method getAnnotation\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Annotation\r
*/\r
- public jalview.binding.Annotation[] getAnnotation() {\r
+ public jalview.binding.Annotation[] getAnnotation()\r
+ {\r
int size = _annotationList.size();\r
jalview.binding.Annotation[] mArray = new jalview.binding.Annotation[size];\r
-\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.Annotation) _annotationList.elementAt(index);\r
}\r
-\r
return mArray;\r
- }\r
- //-- jalview.binding.Annotation[] getAnnotation()\r
+ } //-- jalview.binding.Annotation[] getAnnotation() \r
\r
/**\r
* Method getAnnotationCount\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return int\r
*/\r
- public int getAnnotationCount() {\r
+ public int getAnnotationCount()\r
+ {\r
return _annotationList.size();\r
- }\r
- //-- int getAnnotationCount()\r
+ } //-- int getAnnotationCount() \r
\r
/**\r
* Returns the value of field 'gapChar'.\r
- *\r
+ * \r
* @return String\r
* @return the value of field 'gapChar'.\r
*/\r
- public java.lang.String getGapChar() {\r
+ public java.lang.String getGapChar()\r
+ {\r
return this._gapChar;\r
- }\r
- //-- java.lang.String getGapChar()\r
+ } //-- java.lang.String getGapChar() \r
\r
/**\r
* Method getSequence\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return Sequence\r
*/\r
public jalview.binding.Sequence getSequence(int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _sequenceList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
+ \r
return (jalview.binding.Sequence) _sequenceList.elementAt(index);\r
- }\r
- //-- jalview.binding.Sequence getSequence(int)\r
+ } //-- jalview.binding.Sequence getSequence(int) \r
\r
/**\r
* Method getSequence\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return Sequence\r
*/\r
- public jalview.binding.Sequence[] getSequence() {\r
+ public jalview.binding.Sequence[] getSequence()\r
+ {\r
int size = _sequenceList.size();\r
jalview.binding.Sequence[] mArray = new jalview.binding.Sequence[size];\r
-\r
for (int index = 0; index < size; index++) {\r
mArray[index] = (jalview.binding.Sequence) _sequenceList.elementAt(index);\r
}\r
-\r
return mArray;\r
- }\r
- //-- jalview.binding.Sequence[] getSequence()\r
+ } //-- jalview.binding.Sequence[] getSequence() \r
\r
/**\r
* Method getSequenceCount\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return int\r
*/\r
- public int getSequenceCount() {\r
+ public int getSequenceCount()\r
+ {\r
return _sequenceList.size();\r
- }\r
- //-- int getSequenceCount()\r
+ } //-- int getSequenceCount() \r
\r
/**\r
* Method hasAligned\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean hasAligned() {\r
+ public boolean hasAligned()\r
+ {\r
return this._has_aligned;\r
- }\r
- //-- boolean hasAligned()\r
+ } //-- boolean hasAligned() \r
\r
/**\r
* Method isValid\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @return boolean\r
*/\r
- public boolean isValid() {\r
+ public boolean isValid()\r
+ {\r
try {\r
validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex) {\r
+ }\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
return false;\r
}\r
-\r
return true;\r
- }\r
- //-- boolean isValid()\r
+ } //-- boolean isValid() \r
\r
/**\r
* Method marshal\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param out\r
*/\r
public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, \r
- org.exolab.castor.xml.ValidationException {\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
Marshaller.marshal(this, out);\r
- }\r
- //-- void marshal(java.io.Writer)\r
+ } //-- void marshal(java.io.Writer) \r
\r
/**\r
* Method marshal\r
- *\r
- *\r
- *\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, \r
- org.exolab.castor.xml.ValidationException {\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
Marshaller.marshal(this, handler);\r
- }\r
- //-- void marshal(org.xml.sax.ContentHandler)\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
\r
/**\r
* Method removeAllAnnotation\r
- *\r
+ * \r
*/\r
- public void removeAllAnnotation() {\r
+ public void removeAllAnnotation()\r
+ {\r
_annotationList.removeAllElements();\r
- }\r
- //-- void removeAllAnnotation()\r
+ } //-- void removeAllAnnotation() \r
\r
/**\r
* Method removeAllSequence\r
- *\r
+ * \r
*/\r
- public void removeAllSequence() {\r
+ public void removeAllSequence()\r
+ {\r
_sequenceList.removeAllElements();\r
- }\r
- //-- void removeAllSequence()\r
+ } //-- void removeAllSequence() \r
\r
/**\r
* Method removeAnnotation\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return Annotation\r
*/\r
- public jalview.binding.Annotation removeAnnotation(int index) {\r
+ public jalview.binding.Annotation removeAnnotation(int index)\r
+ {\r
java.lang.Object obj = _annotationList.elementAt(index);\r
_annotationList.removeElementAt(index);\r
-\r
return (jalview.binding.Annotation) obj;\r
- }\r
- //-- jalview.binding.Annotation removeAnnotation(int)\r
+ } //-- jalview.binding.Annotation removeAnnotation(int) \r
\r
/**\r
* Method removeSequence\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @return Sequence\r
*/\r
- public jalview.binding.Sequence removeSequence(int index) {\r
+ public jalview.binding.Sequence removeSequence(int index)\r
+ {\r
java.lang.Object obj = _sequenceList.elementAt(index);\r
_sequenceList.removeElementAt(index);\r
-\r
return (jalview.binding.Sequence) obj;\r
- }\r
- //-- jalview.binding.Sequence removeSequence(int)\r
+ } //-- jalview.binding.Sequence removeSequence(int) \r
\r
/**\r
* Sets the value of field 'aligned'.\r
- *\r
+ * \r
* @param aligned the value of field 'aligned'.\r
*/\r
- public void setAligned(boolean aligned) {\r
+ public void setAligned(boolean aligned)\r
+ {\r
this._aligned = aligned;\r
this._has_aligned = true;\r
- }\r
- //-- void setAligned(boolean)\r
+ } //-- void setAligned(boolean) \r
\r
/**\r
* Method setAnnotation\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @param vAnnotation\r
*/\r
public void setAnnotation(int index, jalview.binding.Annotation vAnnotation)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _annotationList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
_annotationList.setElementAt(vAnnotation, index);\r
- }\r
- //-- void setAnnotation(int, jalview.binding.Annotation)\r
+ } //-- void setAnnotation(int, jalview.binding.Annotation) \r
\r
/**\r
* Method setAnnotation\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param annotationArray\r
*/\r
- public void setAnnotation(jalview.binding.Annotation[] annotationArray) {\r
+ public void setAnnotation(jalview.binding.Annotation[] annotationArray)\r
+ {\r
//-- copy array\r
_annotationList.removeAllElements();\r
-\r
for (int i = 0; i < annotationArray.length; i++) {\r
_annotationList.addElement(annotationArray[i]);\r
}\r
- }\r
- //-- void setAnnotation(jalview.binding.Annotation)\r
+ } //-- void setAnnotation(jalview.binding.Annotation) \r
\r
/**\r
* Sets the value of field 'gapChar'.\r
- *\r
+ * \r
* @param gapChar the value of field 'gapChar'.\r
*/\r
- public void setGapChar(java.lang.String gapChar) {\r
+ public void setGapChar(java.lang.String gapChar)\r
+ {\r
this._gapChar = gapChar;\r
- }\r
- //-- void setGapChar(java.lang.String)\r
+ } //-- void setGapChar(java.lang.String) \r
\r
/**\r
* Method setSequence\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param index\r
* @param vSequence\r
*/\r
public void setSequence(int index, jalview.binding.Sequence vSequence)\r
- throws java.lang.IndexOutOfBoundsException {\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
//-- check bounds for index\r
if ((index < 0) || (index > _sequenceList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
-\r
_sequenceList.setElementAt(vSequence, index);\r
- }\r
- //-- void setSequence(int, jalview.binding.Sequence)\r
+ } //-- void setSequence(int, jalview.binding.Sequence) \r
\r
/**\r
* Method setSequence\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * \r
* @param sequenceArray\r
*/\r
- public void setSequence(jalview.binding.Sequence[] sequenceArray) {\r
+ public void setSequence(jalview.binding.Sequence[] sequenceArray)\r
+ {\r
//-- copy array\r
_sequenceList.removeAllElements();\r
-\r
for (int i = 0; i < sequenceArray.length; i++) {\r
_sequenceList.addElement(sequenceArray[i]);\r
}\r
- }\r
- //-- void setSequence(jalview.binding.Sequence)\r
+ } //-- void setSequence(jalview.binding.Sequence) \r
\r
/**\r
* Method unmarshal\r
- *\r
- *\r
- *\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, \r
- org.exolab.castor.xml.ValidationException {\r
- return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.class,\r
- reader);\r
- }\r
- //-- java.lang.Object unmarshal(java.io.Reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.class, reader);\r
+ } //-- java.lang.Object unmarshal(java.io.Reader) \r
\r
/**\r
* Method validate\r
- *\r
+ * \r
*/\r
- public void validate() throws org.exolab.castor.xml.ValidationException {\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
- }\r
- //-- void validate()\r
+ } //-- void validate() \r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff