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Formatted source
[jalview.git]
/
src
/
jalview
/
binding
/
AnnotationElement.java
diff --git
a/src/jalview/binding/AnnotationElement.java
b/src/jalview/binding/AnnotationElement.java
index
211810d
..
3c6eba4
100755
(executable)
--- a/
src/jalview/binding/AnnotationElement.java
+++ b/
src/jalview/binding/AnnotationElement.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 AnnotationElement.
\r
*
\r
* @version $Revision$ $Date$
\r
*/
\r
public class AnnotationElement implements java.io.Serializable {
\r
/**
\r
* Class AnnotationElement.
\r
*
\r
* @version $Revision$ $Date$
\r
*/
\r
public class AnnotationElement implements java.io.Serializable {
\r
-
\r
-
\r
- //--------------------------/
\r
- //- Class/Member Variables -/
\r
+ //--------------------------/
\r
+ //- Class/Member Variables -/
\r
//--------------------------/
\r
\r
/**
\r
//--------------------------/
\r
\r
/**
\r
@@
-87,37
+85,28
@@
public class AnnotationElement implements java.io.Serializable {
*/
\r
private boolean _has_value;
\r
\r
*/
\r
private boolean _has_value;
\r
\r
-
\r
- //----------------/
\r
- //- Constructors -/
\r
//----------------/
\r
//----------------/
\r
-
\r
+ //- Constructors -/
\r
+ //----------------/
\r
public AnnotationElement() {
\r
super();
\r
public AnnotationElement() {
\r
super();
\r
- } //-- jalview.binding.AnnotationElement()
\r
-
\r
-
\r
- //-----------/
\r
- //- Methods -/
\r
- //-----------/
\r
+ }
\r
+ //-- jalview.binding.AnnotationElement()
\r
+ //-----------/
\r
\r
\r
- /**
\r
- * Method deletePosition
\r
- *
\r
- */
\r
- public void deletePosition()
\r
- {
\r
- this._has_position= false;
\r
- } //-- void deletePosition()
\r
+ public void deletePosition() {
\r
+ this._has_position = false;
\r
+ }
\r
+ //-- void deletePosition()
\r
\r
/**
\r
* Method deleteValue
\r
*
\r
*/
\r
\r
/**
\r
* Method deleteValue
\r
*
\r
*/
\r
- public void deleteValue()
\r
- {
\r
- this._has_value= false;
\r
- } //-- void deleteValue()
\r
+ public void deleteValue() {
\r
+ this._has_value = false;
\r
+ }
\r
+ //-- void deleteValue()
\r
\r
/**
\r
* Returns the value of field 'description'.
\r
\r
/**
\r
* Returns the value of field 'description'.
\r
@@
-125,10
+114,10
@@
public class AnnotationElement implements java.io.Serializable {
* @return String
\r
* @return the value of field 'description'.
\r
*/
\r
* @return String
\r
* @return the value of field 'description'.
\r
*/
\r
- public java.lang.String getDescription()
\r
- {
\r
+ public java.lang.String getDescription() {
\r
return this._description;
\r
return this._description;
\r
- } //-- java.lang.String getDescription()
\r
+ }
\r
+ //-- java.lang.String getDescription()
\r
\r
/**
\r
* Returns the value of field 'displayCharacter'.
\r
\r
/**
\r
* Returns the value of field 'displayCharacter'.
\r
@@
-136,10
+125,10
@@
public class AnnotationElement implements java.io.Serializable {
* @return String
\r
* @return the value of field 'displayCharacter'.
\r
*/
\r
* @return String
\r
* @return the value of field 'displayCharacter'.
\r
*/
\r
- public java.lang.String getDisplayCharacter()
\r
- {
\r
+ public java.lang.String getDisplayCharacter() {
\r
return this._displayCharacter;
\r
return this._displayCharacter;
\r
- } //-- java.lang.String getDisplayCharacter()
\r
+ }
\r
+ //-- java.lang.String getDisplayCharacter()
\r
\r
/**
\r
* Returns the value of field 'position'.
\r
\r
/**
\r
* Returns the value of field 'position'.
\r
@@
-147,10
+136,10
@@
public class AnnotationElement implements java.io.Serializable {
* @return int
\r
* @return the value of field 'position'.
\r
*/
\r
* @return int
\r
* @return the value of field 'position'.
\r
*/
\r
- public int getPosition()
\r
- {
\r
+ public int getPosition() {
\r
return this._position;
\r
return this._position;
\r
- } //-- int getPosition()
\r
+ }
\r
+ //-- int getPosition()
\r
\r
/**
\r
* Returns the value of field 'secondaryStructure'.
\r
\r
/**
\r
* Returns the value of field 'secondaryStructure'.
\r
@@
-158,10
+147,10
@@
public class AnnotationElement implements java.io.Serializable {
* @return String
\r
* @return the value of field 'secondaryStructure'.
\r
*/
\r
* @return String
\r
* @return the value of field 'secondaryStructure'.
\r
*/
\r
- public java.lang.String getSecondaryStructure()
\r
- {
\r
+ public java.lang.String getSecondaryStructure() {
\r
return this._secondaryStructure;
\r
return this._secondaryStructure;
\r
- } //-- java.lang.String getSecondaryStructure()
\r
+ }
\r
+ //-- java.lang.String getSecondaryStructure()
\r
\r
/**
\r
* Returns the value of field 'value'.
\r
\r
/**
\r
* Returns the value of field 'value'.
\r
@@
-169,10
+158,10
@@
public class AnnotationElement implements java.io.Serializable {
* @return float
\r
* @return the value of field 'value'.
\r
*/
\r
* @return float
\r
* @return the value of field 'value'.
\r
*/
\r
- public float getValue()
\r
- {
\r
+ public float getValue() {
\r
return this._value;
\r
return this._value;
\r
- } //-- float getValue()
\r
+ }
\r
+ //-- float getValue()
\r
\r
/**
\r
* Method hasPosition
\r
\r
/**
\r
* Method hasPosition
\r
@@
-181,10
+170,10
@@
public class AnnotationElement implements java.io.Serializable {
*
\r
* @return boolean
\r
*/
\r
*
\r
* @return boolean
\r
*/
\r
- public boolean hasPosition()
\r
- {
\r
+ public boolean hasPosition() {
\r
return this._has_position;
\r
return this._has_position;
\r
- } //-- boolean hasPosition()
\r
+ }
\r
+ //-- boolean hasPosition()
\r
\r
/**
\r
* Method hasValue
\r
\r
/**
\r
* Method hasValue
\r
@@
-193,10
+182,10
@@
public class AnnotationElement implements java.io.Serializable {
*
\r
* @return boolean
\r
*/
\r
*
\r
* @return boolean
\r
*/
\r
- public boolean hasValue()
\r
- {
\r
+ public boolean hasValue() {
\r
return this._has_value;
\r
return this._has_value;
\r
- } //-- boolean hasValue()
\r
+ }
\r
+ //-- boolean hasValue()
\r
\r
/**
\r
* Method isValid
\r
\r
/**
\r
* Method isValid
\r
@@
-205,16
+194,16
@@
public class AnnotationElement 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
@@
-224,11
+213,11
@@
public class AnnotationElement 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
@@
-238,42
+227,42
@@
public class AnnotationElement 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 'description'.
\r
*
\r
* @param description the value of field 'description'.
\r
*/
\r
\r
/**
\r
* Sets the value of field 'description'.
\r
*
\r
* @param description the value of field 'description'.
\r
*/
\r
- public void setDescription(java.lang.String description)
\r
- {
\r
+ public void setDescription(java.lang.String description) {
\r
this._description = description;
\r
this._description = description;
\r
- } //-- void setDescription(java.lang.String)
\r
+ }
\r
+ //-- void setDescription(java.lang.String)
\r
\r
/**
\r
* Sets the value of field 'displayCharacter'.
\r
*
\r
* @param displayCharacter the value of field 'displayCharacter'
\r
*/
\r
\r
/**
\r
* Sets the value of field 'displayCharacter'.
\r
*
\r
* @param displayCharacter the value of field 'displayCharacter'
\r
*/
\r
- public void setDisplayCharacter(java.lang.String displayCharacter)
\r
- {
\r
+ public void setDisplayCharacter(java.lang.String displayCharacter) {
\r
this._displayCharacter = displayCharacter;
\r
this._displayCharacter = displayCharacter;
\r
- } //-- void setDisplayCharacter(java.lang.String)
\r
+ }
\r
+ //-- void setDisplayCharacter(java.lang.String)
\r
\r
/**
\r
* Sets the value of field 'position'.
\r
*
\r
* @param position the value of field 'position'.
\r
*/
\r
\r
/**
\r
* Sets the value of field 'position'.
\r
*
\r
* @param position the value of field 'position'.
\r
*/
\r
- public void setPosition(int position)
\r
- {
\r
+ public void setPosition(int position) {
\r
this._position = position;
\r
this._has_position = true;
\r
this._position = position;
\r
this._has_position = true;
\r
- } //-- void setPosition(int)
\r
+ }
\r
+ //-- void setPosition(int)
\r
\r
/**
\r
* Sets the value of field 'secondaryStructure'.
\r
\r
/**
\r
* Sets the value of field 'secondaryStructure'.
\r
@@
-281,21
+270,21
@@
public class AnnotationElement implements java.io.Serializable {
* @param secondaryStructure the value of field
\r
* 'secondaryStructure'.
\r
*/
\r
* @param secondaryStructure the value of field
\r
* 'secondaryStructure'.
\r
*/
\r
- public void setSecondaryStructure(java.lang.String secondaryStructure)
\r
- {
\r
+ public void setSecondaryStructure(java.lang.String secondaryStructure) {
\r
this._secondaryStructure = secondaryStructure;
\r
this._secondaryStructure = secondaryStructure;
\r
- } //-- void setSecondaryStructure(java.lang.String)
\r
+ }
\r
+ //-- void setSecondaryStructure(java.lang.String)
\r
\r
/**
\r
* Sets the value of field 'value'.
\r
*
\r
* @param value the value of field 'value'.
\r
*/
\r
\r
/**
\r
* Sets the value of field 'value'.
\r
*
\r
* @param value the value of field 'value'.
\r
*/
\r
- public void setValue(float value)
\r
- {
\r
+ public void setValue(float value) {
\r
this._value = value;
\r
this._has_value = true;
\r
this._value = value;
\r
this._has_value = true;
\r
- } //-- void setValue(float)
\r
+ }
\r
+ //-- void setValue(float)
\r
\r
/**
\r
* Method unmarshal
\r
\r
/**
\r
* Method unmarshal
\r
@@
-306,20
+295,20
@@
public class AnnotationElement 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.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.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.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.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