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Forces init of alignPanel if annotations added
[jalview.git]
/
src
/
jalview
/
binding
/
SequenceSet.java
diff --git
a/src/jalview/binding/SequenceSet.java
b/src/jalview/binding/SequenceSet.java
index
a0d116e
..
7ed3b52
100755
(executable)
--- a/
src/jalview/binding/SequenceSet.java
+++ b/
src/jalview/binding/SequenceSet.java
@@
-1,39
+1,38
@@
/*
\r
/*
\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
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
\r
* Schema.
\r
* $Id$
\r
*/
\r
-package jalview.binding;
\r
\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
+ //---------------------------------/
\r
+ //- Imported classes and packages -/
\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.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 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
* Class SequenceSet.
\r
- *
\r
+ *
\r
* @version $Revision$ $Date$
\r
*/
\r
* @version $Revision$ $Date$
\r
*/
\r
-public class SequenceSet implements java.io.Serializable
\r
-{
\r
- //--------------------------/
\r
- //- Class/Member Variables -/
\r
+public class SequenceSet implements java.io.Serializable {
\r
+
\r
+
\r
+ //--------------------------/
\r
+ //- Class/Member Variables -/
\r
//--------------------------/
\r
\r
/**
\r
//--------------------------/
\r
\r
/**
\r
@@
-61,39
+60,40
@@
public class SequenceSet implements java.io.Serializable
*/
\r
private java.util.Vector _annotationList;
\r
\r
*/
\r
private java.util.Vector _annotationList;
\r
\r
+
\r
+ //----------------/
\r
+ //- Constructors -/
\r
//----------------/
\r
//----------------/
\r
- //- Constructors -/
\r
- //----------------/
\r
- public SequenceSet()
\r
- {
\r
+
\r
+ public SequenceSet() {
\r
super();
\r
_sequenceList = new Vector();
\r
_annotationList = new Vector();
\r
super();
\r
_sequenceList = new Vector();
\r
_annotationList = new Vector();
\r
- }
\r
+ } //-- jalview.binding.SequenceSet()
\r
+
\r
\r
\r
- //-- jalview.binding.SequenceSet()
\r
+ //-----------/
\r
+ //- Methods -/
\r
//-----------/
\r
\r
/**
\r
//-----------/
\r
\r
/**
\r
- * DOCUMENT ME!
\r
- *
\r
- * @param vAnnotation DOCUMENT ME!
\r
- *
\r
- * @throws java.lang.IndexOutOfBoundsException DOCUMENT ME!
\r
+ * Method addAnnotation
\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
*/
\r
public void addAnnotation(jalview.binding.Annotation vAnnotation)
\r
throws java.lang.IndexOutOfBoundsException
\r
{
\r
_annotationList.addElement(vAnnotation);
\r
- }
\r
-
\r
- //-- void addAnnotation(jalview.binding.Annotation)
\r
+ } //-- void addAnnotation(jalview.binding.Annotation)
\r
\r
/**
\r
* Method addAnnotation
\r
\r
/**
\r
* Method addAnnotation
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @param index
\r
* @param vAnnotation
\r
*/
\r
* @param index
\r
* @param vAnnotation
\r
*/
\r
@@
-101,30
+101,26
@@
public class SequenceSet implements java.io.Serializable
throws java.lang.IndexOutOfBoundsException
\r
{
\r
_annotationList.insertElementAt(vAnnotation, index);
\r
throws java.lang.IndexOutOfBoundsException
\r
{
\r
_annotationList.insertElementAt(vAnnotation, index);
\r
- }
\r
-
\r
- //-- void addAnnotation(int, jalview.binding.Annotation)
\r
+ } //-- void addAnnotation(int, jalview.binding.Annotation)
\r
\r
/**
\r
* Method addSequence
\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
* @param vSequence
\r
*/
\r
public void addSequence(jalview.binding.Sequence vSequence)
\r
throws java.lang.IndexOutOfBoundsException
\r
{
\r
_sequenceList.addElement(vSequence);
\r
- }
\r
-
\r
- //-- void addSequence(jalview.binding.Sequence)
\r
+ } //-- void addSequence(jalview.binding.Sequence)
\r
\r
/**
\r
* Method addSequence
\r
\r
/**
\r
* Method addSequence
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @param index
\r
* @param vSequence
\r
*/
\r
* @param index
\r
* @param vSequence
\r
*/
\r
@@
-132,67
+128,57
@@
public class SequenceSet implements java.io.Serializable
throws java.lang.IndexOutOfBoundsException
\r
{
\r
_sequenceList.insertElementAt(vSequence, index);
\r
throws java.lang.IndexOutOfBoundsException
\r
{
\r
_sequenceList.insertElementAt(vSequence, index);
\r
- }
\r
-
\r
- //-- void addSequence(int, jalview.binding.Sequence)
\r
+ } //-- void addSequence(int, jalview.binding.Sequence)
\r
\r
/**
\r
* Method deleteAligned
\r
\r
/**
\r
* Method deleteAligned
\r
- *
\r
+ *
\r
*/
\r
public void deleteAligned()
\r
{
\r
*/
\r
public void deleteAligned()
\r
{
\r
- this._has_aligned = false;
\r
- }
\r
-
\r
- //-- void deleteAligned()
\r
+ this._has_aligned= false;
\r
+ } //-- void deleteAligned()
\r
\r
/**
\r
* Method enumerateAnnotation
\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
* @return Enumeration
\r
*/
\r
public java.util.Enumeration enumerateAnnotation()
\r
{
\r
return _annotationList.elements();
\r
- }
\r
-
\r
- //-- java.util.Enumeration enumerateAnnotation()
\r
+ } //-- java.util.Enumeration enumerateAnnotation()
\r
\r
/**
\r
* Method enumerateSequence
\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
* @return Enumeration
\r
*/
\r
public java.util.Enumeration enumerateSequence()
\r
{
\r
return _sequenceList.elements();
\r
- }
\r
-
\r
- //-- java.util.Enumeration enumerateSequence()
\r
+ } //-- java.util.Enumeration enumerateSequence()
\r
\r
/**
\r
* Returns the value of field 'aligned'.
\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
* @return boolean
\r
* @return the value of field 'aligned'.
\r
*/
\r
public boolean getAligned()
\r
{
\r
return this._aligned;
\r
- }
\r
-
\r
- //-- boolean getAligned()
\r
+ } //-- boolean getAligned()
\r
\r
/**
\r
* Method getAnnotation
\r
\r
/**
\r
* Method getAnnotation
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @param index
\r
* @return Annotation
\r
*/
\r
* @param index
\r
* @return Annotation
\r
*/
\r
@@
-200,70
+186,58
@@
public class SequenceSet implements java.io.Serializable
throws java.lang.IndexOutOfBoundsException
\r
{
\r
//-- check bounds for index
\r
throws java.lang.IndexOutOfBoundsException
\r
{
\r
//-- check bounds for index
\r
- if ((index < 0) || (index > _annotationList.size()))
\r
- {
\r
+ if ((index < 0) || (index > _annotationList.size())) {
\r
throw new IndexOutOfBoundsException();
\r
}
\r
throw new IndexOutOfBoundsException();
\r
}
\r
-
\r
+
\r
return (jalview.binding.Annotation) _annotationList.elementAt(index);
\r
return (jalview.binding.Annotation) _annotationList.elementAt(index);
\r
- }
\r
-
\r
- //-- jalview.binding.Annotation getAnnotation(int)
\r
+ } //-- jalview.binding.Annotation getAnnotation(int)
\r
\r
/**
\r
* Method getAnnotation
\r
\r
/**
\r
* Method getAnnotation
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @return Annotation
\r
*/
\r
public jalview.binding.Annotation[] getAnnotation()
\r
{
\r
int size = _annotationList.size();
\r
jalview.binding.Annotation[] mArray = new jalview.binding.Annotation[size];
\r
* @return Annotation
\r
*/
\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
- {
\r
+ for (int index = 0; index < size; index++) {
\r
mArray[index] = (jalview.binding.Annotation) _annotationList.elementAt(index);
\r
}
\r
mArray[index] = (jalview.binding.Annotation) _annotationList.elementAt(index);
\r
}
\r
-
\r
return mArray;
\r
return mArray;
\r
- }
\r
-
\r
- //-- jalview.binding.Annotation[] getAnnotation()
\r
+ } //-- jalview.binding.Annotation[] getAnnotation()
\r
\r
/**
\r
* Method getAnnotationCount
\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
* @return int
\r
*/
\r
public int getAnnotationCount()
\r
{
\r
return _annotationList.size();
\r
- }
\r
-
\r
- //-- int getAnnotationCount()
\r
+ } //-- int getAnnotationCount()
\r
\r
/**
\r
* Returns the value of field 'gapChar'.
\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
* @return String
\r
* @return the value of field 'gapChar'.
\r
*/
\r
public java.lang.String getGapChar()
\r
{
\r
return this._gapChar;
\r
- }
\r
-
\r
- //-- java.lang.String getGapChar()
\r
+ } //-- java.lang.String getGapChar()
\r
\r
/**
\r
* Method getSequence
\r
\r
/**
\r
* Method getSequence
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @param index
\r
* @return Sequence
\r
*/
\r
* @param index
\r
* @return Sequence
\r
*/
\r
@@
-271,148
+245,123
@@
public class SequenceSet implements java.io.Serializable
throws java.lang.IndexOutOfBoundsException
\r
{
\r
//-- check bounds for index
\r
throws java.lang.IndexOutOfBoundsException
\r
{
\r
//-- check bounds for index
\r
- if ((index < 0) || (index > _sequenceList.size()))
\r
- {
\r
+ if ((index < 0) || (index > _sequenceList.size())) {
\r
throw new IndexOutOfBoundsException();
\r
}
\r
throw new IndexOutOfBoundsException();
\r
}
\r
-
\r
+
\r
return (jalview.binding.Sequence) _sequenceList.elementAt(index);
\r
return (jalview.binding.Sequence) _sequenceList.elementAt(index);
\r
- }
\r
-
\r
- //-- jalview.binding.Sequence getSequence(int)
\r
+ } //-- jalview.binding.Sequence getSequence(int)
\r
\r
/**
\r
* Method getSequence
\r
\r
/**
\r
* Method getSequence
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @return Sequence
\r
*/
\r
public jalview.binding.Sequence[] getSequence()
\r
{
\r
int size = _sequenceList.size();
\r
jalview.binding.Sequence[] mArray = new jalview.binding.Sequence[size];
\r
* @return Sequence
\r
*/
\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
- {
\r
+ for (int index = 0; index < size; index++) {
\r
mArray[index] = (jalview.binding.Sequence) _sequenceList.elementAt(index);
\r
}
\r
mArray[index] = (jalview.binding.Sequence) _sequenceList.elementAt(index);
\r
}
\r
-
\r
return mArray;
\r
return mArray;
\r
- }
\r
-
\r
- //-- jalview.binding.Sequence[] getSequence()
\r
+ } //-- jalview.binding.Sequence[] getSequence()
\r
\r
/**
\r
* Method getSequenceCount
\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
* @return int
\r
*/
\r
public int getSequenceCount()
\r
{
\r
return _sequenceList.size();
\r
- }
\r
-
\r
- //-- int getSequenceCount()
\r
+ } //-- int getSequenceCount()
\r
\r
/**
\r
* Method hasAligned
\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
* @return boolean
\r
*/
\r
public boolean hasAligned()
\r
{
\r
return this._has_aligned;
\r
- }
\r
-
\r
- //-- boolean hasAligned()
\r
+ } //-- boolean hasAligned()
\r
\r
/**
\r
* Method isValid
\r
\r
/**
\r
* Method isValid
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @return boolean
\r
*/
\r
public boolean isValid()
\r
{
\r
* @return boolean
\r
*/
\r
public boolean isValid()
\r
{
\r
- try
\r
- {
\r
+ try {
\r
validate();
\r
}
\r
validate();
\r
}
\r
- catch (org.exolab.castor.xml.ValidationException vex)
\r
- {
\r
+ catch (org.exolab.castor.xml.ValidationException vex) {
\r
return false;
\r
}
\r
return false;
\r
}
\r
-
\r
return true;
\r
return true;
\r
- }
\r
-
\r
- //-- boolean isValid()
\r
+ } //-- boolean isValid()
\r
\r
/**
\r
* Method marshal
\r
\r
/**
\r
* Method marshal
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @param out
\r
*/
\r
public void marshal(java.io.Writer out)
\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
+
\r
Marshaller.marshal(this, out);
\r
Marshaller.marshal(this, out);
\r
- }
\r
-
\r
- //-- void marshal(java.io.Writer)
\r
+ } //-- void marshal(java.io.Writer)
\r
\r
/**
\r
* Method marshal
\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
* @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
+
\r
Marshaller.marshal(this, handler);
\r
Marshaller.marshal(this, handler);
\r
- }
\r
-
\r
- //-- void marshal(org.xml.sax.ContentHandler)
\r
+ } //-- void marshal(org.xml.sax.ContentHandler)
\r
\r
/**
\r
* Method removeAllAnnotation
\r
\r
/**
\r
* Method removeAllAnnotation
\r
- *
\r
+ *
\r
*/
\r
public void removeAllAnnotation()
\r
{
\r
_annotationList.removeAllElements();
\r
*/
\r
public void removeAllAnnotation()
\r
{
\r
_annotationList.removeAllElements();
\r
- }
\r
-
\r
- //-- void removeAllAnnotation()
\r
+ } //-- void removeAllAnnotation()
\r
\r
/**
\r
* Method removeAllSequence
\r
\r
/**
\r
* Method removeAllSequence
\r
- *
\r
+ *
\r
*/
\r
public void removeAllSequence()
\r
{
\r
_sequenceList.removeAllElements();
\r
*/
\r
public void removeAllSequence()
\r
{
\r
_sequenceList.removeAllElements();
\r
- }
\r
-
\r
- //-- void removeAllSequence()
\r
+ } //-- void removeAllSequence()
\r
\r
/**
\r
* Method removeAnnotation
\r
\r
/**
\r
* Method removeAnnotation
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @param index
\r
* @return Annotation
\r
*/
\r
* @param index
\r
* @return Annotation
\r
*/
\r
@@
-420,17
+369,14
@@
public class SequenceSet implements java.io.Serializable
{
\r
java.lang.Object obj = _annotationList.elementAt(index);
\r
_annotationList.removeElementAt(index);
\r
{
\r
java.lang.Object obj = _annotationList.elementAt(index);
\r
_annotationList.removeElementAt(index);
\r
-
\r
return (jalview.binding.Annotation) obj;
\r
return (jalview.binding.Annotation) obj;
\r
- }
\r
-
\r
- //-- jalview.binding.Annotation removeAnnotation(int)
\r
+ } //-- jalview.binding.Annotation removeAnnotation(int)
\r
\r
/**
\r
* Method removeSequence
\r
\r
/**
\r
* Method removeSequence
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @param index
\r
* @return Sequence
\r
*/
\r
* @param index
\r
* @return Sequence
\r
*/
\r
@@
-438,30
+384,25
@@
public class SequenceSet implements java.io.Serializable
{
\r
java.lang.Object obj = _sequenceList.elementAt(index);
\r
_sequenceList.removeElementAt(index);
\r
{
\r
java.lang.Object obj = _sequenceList.elementAt(index);
\r
_sequenceList.removeElementAt(index);
\r
-
\r
return (jalview.binding.Sequence) obj;
\r
return (jalview.binding.Sequence) obj;
\r
- }
\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
* 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
* @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
- }
\r
-
\r
- //-- void setAligned(boolean)
\r
+ } //-- void setAligned(boolean)
\r
\r
/**
\r
* Method setAnnotation
\r
\r
/**
\r
* Method setAnnotation
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @param index
\r
* @param vAnnotation
\r
*/
\r
* @param index
\r
* @param vAnnotation
\r
*/
\r
@@
-469,53
+410,43
@@
public class SequenceSet implements java.io.Serializable
throws java.lang.IndexOutOfBoundsException
\r
{
\r
//-- check bounds for index
\r
throws java.lang.IndexOutOfBoundsException
\r
{
\r
//-- check bounds for index
\r
- if ((index < 0) || (index > _annotationList.size()))
\r
- {
\r
+ if ((index < 0) || (index > _annotationList.size())) {
\r
throw new IndexOutOfBoundsException();
\r
}
\r
throw new IndexOutOfBoundsException();
\r
}
\r
-
\r
_annotationList.setElementAt(vAnnotation, index);
\r
_annotationList.setElementAt(vAnnotation, index);
\r
- }
\r
-
\r
- //-- void setAnnotation(int, jalview.binding.Annotation)
\r
+ } //-- void setAnnotation(int, jalview.binding.Annotation)
\r
\r
/**
\r
* Method setAnnotation
\r
\r
/**
\r
* Method setAnnotation
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @param annotationArray
\r
*/
\r
public void setAnnotation(jalview.binding.Annotation[] annotationArray)
\r
{
\r
//-- copy array
\r
_annotationList.removeAllElements();
\r
* @param annotationArray
\r
*/
\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
- {
\r
+ for (int i = 0; i < annotationArray.length; i++) {
\r
_annotationList.addElement(annotationArray[i]);
\r
}
\r
_annotationList.addElement(annotationArray[i]);
\r
}
\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
* 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
* @param gapChar the value of field 'gapChar'.
\r
*/
\r
public void setGapChar(java.lang.String gapChar)
\r
{
\r
this._gapChar = gapChar;
\r
- }
\r
-
\r
- //-- void setGapChar(java.lang.String)
\r
+ } //-- void setGapChar(java.lang.String)
\r
\r
/**
\r
* Method setSequence
\r
\r
/**
\r
* Method setSequence
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @param index
\r
* @param vSequence
\r
*/
\r
* @param index
\r
* @param vSequence
\r
*/
\r
@@
-523,63
+454,51
@@
public class SequenceSet implements java.io.Serializable
throws java.lang.IndexOutOfBoundsException
\r
{
\r
//-- check bounds for index
\r
throws java.lang.IndexOutOfBoundsException
\r
{
\r
//-- check bounds for index
\r
- if ((index < 0) || (index > _sequenceList.size()))
\r
- {
\r
+ if ((index < 0) || (index > _sequenceList.size())) {
\r
throw new IndexOutOfBoundsException();
\r
}
\r
throw new IndexOutOfBoundsException();
\r
}
\r
-
\r
_sequenceList.setElementAt(vSequence, index);
\r
_sequenceList.setElementAt(vSequence, index);
\r
- }
\r
-
\r
- //-- void setSequence(int, jalview.binding.Sequence)
\r
+ } //-- void setSequence(int, jalview.binding.Sequence)
\r
\r
/**
\r
* Method setSequence
\r
\r
/**
\r
* Method setSequence
\r
- *
\r
- *
\r
- *
\r
+ *
\r
+ *
\r
+ *
\r
* @param sequenceArray
\r
*/
\r
public void setSequence(jalview.binding.Sequence[] sequenceArray)
\r
{
\r
//-- copy array
\r
_sequenceList.removeAllElements();
\r
* @param sequenceArray
\r
*/
\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
- {
\r
+ for (int i = 0; i < sequenceArray.length; i++) {
\r
_sequenceList.addElement(sequenceArray[i]);
\r
}
\r
_sequenceList.addElement(sequenceArray[i]);
\r
}
\r
- }
\r
-
\r
- //-- void setSequence(jalview.binding.Sequence)
\r
+ } //-- void setSequence(jalview.binding.Sequence)
\r
\r
/**
\r
* Method unmarshal
\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
* @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
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
\r
{
\r
{
\r
- return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.class,
\r
- reader);
\r
- }
\r
-
\r
- //-- java.lang.Object unmarshal(java.io.Reader)
\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
* Method validate
\r
- *
\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
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
\r
validator.validate(this);
\r
- }
\r
+ } //-- void validate()
\r
\r
\r
- //-- void validate()
\r
}
\r
}
\r