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Sends gapChar to seqData
[jalview.git]
/
src
/
jalview
/
binding
/
Alignment.java
diff --git
a/src/jalview/binding/Alignment.java
b/src/jalview/binding/Alignment.java
index
78fff89
..
9a38f10
100755
(executable)
--- a/
src/jalview/binding/Alignment.java
+++ b/
src/jalview/binding/Alignment.java
@@
-1,36
+1,36
@@
/*
\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 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 Alignment.
\r
\r
/**
\r
* Class Alignment.
\r
- *
\r
+ *
\r
* @version $Revision$ $Date$
\r
*/
\r
* @version $Revision$ $Date$
\r
*/
\r
-public class Alignment implements java.io.Serializable
\r
-{
\r
- //--------------------------/
\r
- //- Class/Member Variables -/
\r
+public class Alignment implements java.io.Serializable {
\r
+
\r
+
\r
+ //--------------------------/
\r
+ //- Class/Member Variables -/
\r
//--------------------------/
\r
\r
/**
\r
//--------------------------/
\r
\r
/**
\r
@@
-43,148
+43,131
@@
public class Alignment implements java.io.Serializable
*/
\r
private jalview.binding.SequenceSet _sequenceSet;
\r
\r
*/
\r
private jalview.binding.SequenceSet _sequenceSet;
\r
\r
+
\r
+ //----------------/
\r
+ //- Constructors -/
\r
//----------------/
\r
//----------------/
\r
- //- Constructors -/
\r
- //----------------/
\r
- public Alignment()
\r
- {
\r
+
\r
+ public Alignment() {
\r
super();
\r
super();
\r
- }
\r
+ } //-- jalview.binding.Alignment()
\r
\r
\r
- //-- jalview.binding.Alignment()
\r
+
\r
+ //-----------/
\r
+ //- Methods -/
\r
//-----------/
\r
\r
/**
\r
//-----------/
\r
\r
/**
\r
- * DOCUMENT ME!
\r
- *
\r
- * @return DOCUMENT ME!
\r
+ * Returns the value of field 'annotation'.
\r
+ *
\r
+ * @return Annotation
\r
+ * @return the value of field 'annotation'.
\r
*/
\r
public jalview.binding.Annotation getAnnotation()
\r
{
\r
return this._annotation;
\r
*/
\r
public jalview.binding.Annotation getAnnotation()
\r
{
\r
return this._annotation;
\r
- }
\r
-
\r
- //-- jalview.binding.Annotation getAnnotation()
\r
+ } //-- jalview.binding.Annotation getAnnotation()
\r
\r
/**
\r
* Returns the value of field 'sequenceSet'.
\r
\r
/**
\r
* Returns the value of field 'sequenceSet'.
\r
- *
\r
+ *
\r
* @return SequenceSet
\r
* @return the value of field 'sequenceSet'.
\r
*/
\r
public jalview.binding.SequenceSet getSequenceSet()
\r
{
\r
return this._sequenceSet;
\r
* @return SequenceSet
\r
* @return the value of field 'sequenceSet'.
\r
*/
\r
public jalview.binding.SequenceSet getSequenceSet()
\r
{
\r
return this._sequenceSet;
\r
- }
\r
-
\r
- //-- jalview.binding.SequenceSet getSequenceSet()
\r
+ } //-- jalview.binding.SequenceSet getSequenceSet()
\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
* Sets the value of field 'annotation'.
\r
\r
/**
\r
* Sets the value of field 'annotation'.
\r
- *
\r
+ *
\r
* @param annotation the value of field 'annotation'.
\r
*/
\r
public void setAnnotation(jalview.binding.Annotation annotation)
\r
{
\r
this._annotation = annotation;
\r
* @param annotation the value of field 'annotation'.
\r
*/
\r
public void setAnnotation(jalview.binding.Annotation annotation)
\r
{
\r
this._annotation = annotation;
\r
- }
\r
-
\r
- //-- void setAnnotation(jalview.binding.Annotation)
\r
+ } //-- void setAnnotation(jalview.binding.Annotation)
\r
\r
/**
\r
* Sets the value of field 'sequenceSet'.
\r
\r
/**
\r
* Sets the value of field 'sequenceSet'.
\r
- *
\r
+ *
\r
* @param sequenceSet the value of field 'sequenceSet'.
\r
*/
\r
public void setSequenceSet(jalview.binding.SequenceSet sequenceSet)
\r
{
\r
this._sequenceSet = sequenceSet;
\r
* @param sequenceSet the value of field 'sequenceSet'.
\r
*/
\r
public void setSequenceSet(jalview.binding.SequenceSet sequenceSet)
\r
{
\r
this._sequenceSet = sequenceSet;
\r
- }
\r
-
\r
- //-- void setSequenceSet(jalview.binding.SequenceSet)
\r
+ } //-- void setSequenceSet(jalview.binding.SequenceSet)
\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.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class,
\r
- reader);
\r
- }
\r
-
\r
- //-- java.lang.Object unmarshal(java.io.Reader)
\r
+ return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.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