/*\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
+/*\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
+\r
package jalview.binding;\r
\r
//---------------------------------/\r
\r
/**\r
* Class SequenceSet.\r
- * \r
+ *\r
* @version $Revision$ $Date$\r
*/\r
public class SequenceSet implements java.io.Serializable {\r
\r
/**\r
* Method addAnnotation\r
- * \r
- * \r
- * \r
+ *\r
+ *\r
+ *\r
* @param vAnnotation\r
*/\r
public void addAnnotation(jalview.binding.Annotation vAnnotation)\r
throws java.lang.IndexOutOfBoundsException\r
{\r
_annotationList.addElement(vAnnotation);\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
throws java.lang.IndexOutOfBoundsException\r
{\r
_annotationList.insertElementAt(vAnnotation, index);\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
{\r
_sequenceList.addElement(vSequence);\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
throws java.lang.IndexOutOfBoundsException\r
{\r
_sequenceList.insertElementAt(vSequence, index);\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
{\r
this._has_aligned= false;\r
- } //-- void deleteAligned() \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
{\r
return _annotationList.elements();\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
{\r
return _sequenceList.elements();\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
{\r
return this._aligned;\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
if ((index < 0) || (index > _annotationList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
- \r
+\r
return (jalview.binding.Annotation) _annotationList.elementAt(index);\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
mArray[index] = (jalview.binding.Annotation) _annotationList.elementAt(index);\r
}\r
return mArray;\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
{\r
return _annotationList.size();\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
{\r
return this._gapChar;\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
if ((index < 0) || (index > _sequenceList.size())) {\r
throw new IndexOutOfBoundsException();\r
}\r
- \r
+\r
return (jalview.binding.Sequence) _sequenceList.elementAt(index);\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
mArray[index] = (jalview.binding.Sequence) _sequenceList.elementAt(index);\r
}\r
return mArray;\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
{\r
return _sequenceList.size();\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
{\r
return this._has_aligned;\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
return false;\r
}\r
return true;\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, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, out);\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, org.exolab.castor.xml.ValidationException\r
{\r
- \r
+\r
Marshaller.marshal(this, handler);\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
{\r
_annotationList.removeAllElements();\r
- } //-- void removeAllAnnotation() \r
+ } //-- void removeAllAnnotation()\r
\r
/**\r
* Method removeAllSequence\r
- * \r
+ *\r
*/\r
public void removeAllSequence()\r
{\r
_sequenceList.removeAllElements();\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
java.lang.Object obj = _annotationList.elementAt(index);\r
_annotationList.removeElementAt(index);\r
return (jalview.binding.Annotation) obj;\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
java.lang.Object obj = _sequenceList.elementAt(index);\r
_sequenceList.removeElementAt(index);\r
return (jalview.binding.Sequence) obj;\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
{\r
this._aligned = aligned;\r
this._has_aligned = true;\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
throw new IndexOutOfBoundsException();\r
}\r
_annotationList.setElementAt(vAnnotation, index);\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
for (int i = 0; i < annotationArray.length; i++) {\r
_annotationList.addElement(annotationArray[i]);\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
{\r
this._gapChar = gapChar;\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
throw new IndexOutOfBoundsException();\r
}\r
_sequenceList.setElementAt(vSequence, index);\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
for (int i = 0; i < sequenceArray.length; i++) {\r
_sequenceList.addElement(sequenceArray[i]);\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
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
+ } //-- java.lang.Object unmarshal(java.io.Reader)\r
\r
/**\r
* Method validate\r
- * \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
+ } //-- void validate()\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff