git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Formatted source
[jalview.git]
/
src
/
jalview
/
binding
/
Alignment.java
diff --git
a/src/jalview/binding/Alignment.java
b/src/jalview/binding/Alignment.java
index
644cd03
..
093ae6f
100755
(executable)
--- a/
src/jalview/binding/Alignment.java
+++ b/
src/jalview/binding/Alignment.java
@@
-4,7
+4,6
@@
* Schema.
\r
* $Id$
\r
*/
\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
* Jalview - A Sequence Alignment Editor and Viewer
\r
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
@@
-23,33
+22,32
@@
* 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
* 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
package jalview.binding;
\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 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.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
\r
import org.xml.sax.ContentHandler;
\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
+
\r
/**
\r
* Class Alignment.
\r
*
\r
* @version $Revision$ $Date$
\r
*/
\r
public class Alignment implements java.io.Serializable {
\r
/**
\r
* Class Alignment.
\r
*
\r
* @version $Revision$ $Date$
\r
*/
\r
public class Alignment implements java.io.Serializable {
\r
-
\r
-
\r
- //--------------------------/
\r
- //- Class/Member Variables -/
\r
+ //--------------------------/
\r
+ //- Class/Member Variables -/
\r
//--------------------------/
\r
\r
/**
\r
//--------------------------/
\r
\r
/**
\r
@@
-62,30
+60,19
@@
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
-
\r
+ //- Constructors -/
\r
+ //----------------/
\r
public Alignment() {
\r
super();
\r
public Alignment() {
\r
super();
\r
- } //-- jalview.binding.Alignment()
\r
-
\r
-
\r
- //-----------/
\r
- //- Methods -/
\r
- //-----------/
\r
+ }
\r
+ //-- jalview.binding.Alignment()
\r
+ //-----------/
\r
\r
\r
- /**
\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
+ public jalview.binding.Annotation getAnnotation() {
\r
return this._annotation;
\r
return this._annotation;
\r
- } //-- jalview.binding.Annotation getAnnotation()
\r
+ }
\r
+ //-- jalview.binding.Annotation getAnnotation()
\r
\r
/**
\r
* Returns the value of field 'sequenceSet'.
\r
\r
/**
\r
* Returns the value of field 'sequenceSet'.
\r
@@
-93,10
+80,10
@@
public class Alignment implements java.io.Serializable {
* @return SequenceSet
\r
* @return the value of field 'sequenceSet'.
\r
*/
\r
* @return SequenceSet
\r
* @return the value of field 'sequenceSet'.
\r
*/
\r
- public jalview.binding.SequenceSet getSequenceSet()
\r
- {
\r
+ public jalview.binding.SequenceSet getSequenceSet() {
\r
return this._sequenceSet;
\r
return this._sequenceSet;
\r
- } //-- jalview.binding.SequenceSet getSequenceSet()
\r
+ }
\r
+ //-- jalview.binding.SequenceSet getSequenceSet()
\r
\r
/**
\r
* Method isValid
\r
\r
/**
\r
* Method isValid
\r
@@
-105,16
+92,16
@@
public class Alignment implements java.io.Serializable {
*
\r
* @return boolean
\r
*/
\r
*
\r
* @return boolean
\r
*/
\r
- public boolean isValid()
\r
- {
\r
+ public boolean isValid() {
\r
try {
\r
validate();
\r
try {
\r
validate();
\r
- }
\r
- catch (org.exolab.castor.xml.ValidationException vex) {
\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {
\r
return false;
\r
}
\r
return false;
\r
}
\r
+
\r
return true;
\r
return true;
\r
- } //-- boolean isValid()
\r
+ }
\r
+ //-- boolean isValid()
\r
\r
/**
\r
* Method marshal
\r
\r
/**
\r
* Method marshal
\r
@@
-124,11
+111,11
@@
public class Alignment implements java.io.Serializable {
* @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, org.exolab.castor.xml.ValidationException
\r
- {
\r
-
\r
+ throws org.exolab.castor.xml.MarshalException,
\r
+ org.exolab.castor.xml.ValidationException {
\r
Marshaller.marshal(this, out);
\r
Marshaller.marshal(this, out);
\r
- } //-- void marshal(java.io.Writer)
\r
+ }
\r
+ //-- void marshal(java.io.Writer)
\r
\r
/**
\r
* Method marshal
\r
\r
/**
\r
* Method marshal
\r
@@
-138,31
+125,31
@@
public class Alignment implements java.io.Serializable {
* @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, org.exolab.castor.xml.ValidationException
\r
- {
\r
-
\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException,
\r
+ org.exolab.castor.xml.ValidationException {
\r
Marshaller.marshal(this, handler);
\r
Marshaller.marshal(this, handler);
\r
- } //-- void marshal(org.xml.sax.ContentHandler)
\r
+ }
\r
+ //-- void marshal(org.xml.sax.ContentHandler)
\r
\r
/**
\r
* Sets the value of field 'annotation'.
\r
*
\r
* @param annotation the value of field 'annotation'.
\r
*/
\r
\r
/**
\r
* Sets the value of field 'annotation'.
\r
*
\r
* @param annotation the value of field 'annotation'.
\r
*/
\r
- public void setAnnotation(jalview.binding.Annotation annotation)
\r
- {
\r
+ public void setAnnotation(jalview.binding.Annotation annotation) {
\r
this._annotation = annotation;
\r
this._annotation = annotation;
\r
- } //-- void setAnnotation(jalview.binding.Annotation)
\r
+ }
\r
+ //-- void setAnnotation(jalview.binding.Annotation)
\r
\r
/**
\r
* Sets the value of field 'sequenceSet'.
\r
*
\r
* @param sequenceSet the value of field 'sequenceSet'.
\r
*/
\r
\r
/**
\r
* Sets the value of field 'sequenceSet'.
\r
*
\r
* @param sequenceSet the value of field 'sequenceSet'.
\r
*/
\r
- public void setSequenceSet(jalview.binding.SequenceSet sequenceSet)
\r
- {
\r
+ public void setSequenceSet(jalview.binding.SequenceSet sequenceSet) {
\r
this._sequenceSet = sequenceSet;
\r
this._sequenceSet = sequenceSet;
\r
- } //-- void setSequenceSet(jalview.binding.SequenceSet)
\r
+ }
\r
+ //-- void setSequenceSet(jalview.binding.SequenceSet)
\r
\r
/**
\r
* Method unmarshal
\r
\r
/**
\r
* Method unmarshal
\r
@@
-173,20
+160,20
@@
public class Alignment implements java.io.Serializable {
* @return Object
\r
*/
\r
public static java.lang.Object unmarshal(java.io.Reader reader)
\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
- {
\r
- return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class, reader);
\r
- } //-- java.lang.Object unmarshal(java.io.Reader)
\r
+ throws org.exolab.castor.xml.MarshalException,
\r
+ org.exolab.castor.xml.ValidationException {
\r
+ return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class,
\r
+ reader);
\r
+ }
\r
+ //-- java.lang.Object unmarshal(java.io.Reader)
\r
\r
/**
\r
* Method validate
\r
*
\r
*/
\r
\r
/**
\r
* Method validate
\r
*
\r
*/
\r
- public void validate()
\r
- throws org.exolab.castor.xml.ValidationException
\r
- {
\r
+ public void validate() throws org.exolab.castor.xml.ValidationException {
\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
\r
validator.validate(this);
\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
}
\r