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Formatted source
[jalview.git]
/
src
/
jalview
/
binding
/
JSeq.java
diff --git
a/src/jalview/binding/JSeq.java
b/src/jalview/binding/JSeq.java
index
9e02e60
..
cabf5c8
100755
(executable)
--- a/
src/jalview/binding/JSeq.java
+++ b/
src/jalview/binding/JSeq.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 JSeq.
\r
*
\r
* @version $Revision$ $Date$
\r
*/
\r
public class JSeq implements java.io.Serializable {
\r
/**
\r
* Class JSeq.
\r
*
\r
* @version $Revision$ $Date$
\r
*/
\r
public class JSeq implements java.io.Serializable {
\r
-
\r
-
\r
- //--------------------------/
\r
- //- Class/Member Variables -/
\r
+ //--------------------------/
\r
+ //- Class/Member Variables -/
\r
//--------------------------/
\r
\r
/**
\r
//--------------------------/
\r
\r
/**
\r
@@
-92,55
+90,46
@@
public class JSeq implements java.io.Serializable {
*/
\r
private boolean _has_id;
\r
\r
*/
\r
private boolean _has_id;
\r
\r
-
\r
- //----------------/
\r
- //- Constructors -/
\r
//----------------/
\r
//----------------/
\r
-
\r
+ //- Constructors -/
\r
+ //----------------/
\r
public JSeq() {
\r
super();
\r
public JSeq() {
\r
super();
\r
- } //-- jalview.binding.JSeq()
\r
-
\r
-
\r
- //-----------/
\r
- //- Methods -/
\r
- //-----------/
\r
+ }
\r
+ //-- jalview.binding.JSeq()
\r
+ //-----------/
\r
\r
\r
- /**
\r
- * Method deleteColour
\r
- *
\r
- */
\r
- public void deleteColour()
\r
- {
\r
- this._has_colour= false;
\r
- } //-- void deleteColour()
\r
+ public void deleteColour() {
\r
+ this._has_colour = false;
\r
+ }
\r
+ //-- void deleteColour()
\r
\r
/**
\r
* Method deleteEnd
\r
*
\r
*/
\r
\r
/**
\r
* Method deleteEnd
\r
*
\r
*/
\r
- public void deleteEnd()
\r
- {
\r
- this._has_end= false;
\r
- } //-- void deleteEnd()
\r
+ public void deleteEnd() {
\r
+ this._has_end = false;
\r
+ }
\r
+ //-- void deleteEnd()
\r
\r
/**
\r
* Method deleteId
\r
*
\r
*/
\r
\r
/**
\r
* Method deleteId
\r
*
\r
*/
\r
- public void deleteId()
\r
- {
\r
- this._has_id= false;
\r
- } //-- void deleteId()
\r
+ public void deleteId() {
\r
+ this._has_id = false;
\r
+ }
\r
+ //-- void deleteId()
\r
\r
/**
\r
* Method deleteStart
\r
*
\r
*/
\r
\r
/**
\r
* Method deleteStart
\r
*
\r
*/
\r
- public void deleteStart()
\r
- {
\r
- this._has_start= false;
\r
- } //-- void deleteStart()
\r
+ public void deleteStart() {
\r
+ this._has_start = false;
\r
+ }
\r
+ //-- void deleteStart()
\r
\r
/**
\r
* Returns the value of field 'colour'.
\r
\r
/**
\r
* Returns the value of field 'colour'.
\r
@@
-148,10
+137,10
@@
public class JSeq implements java.io.Serializable {
* @return int
\r
* @return the value of field 'colour'.
\r
*/
\r
* @return int
\r
* @return the value of field 'colour'.
\r
*/
\r
- public int getColour()
\r
- {
\r
+ public int getColour() {
\r
return this._colour;
\r
return this._colour;
\r
- } //-- int getColour()
\r
+ }
\r
+ //-- int getColour()
\r
\r
/**
\r
* Returns the value of field 'end'.
\r
\r
/**
\r
* Returns the value of field 'end'.
\r
@@
-159,10
+148,10
@@
public class JSeq implements java.io.Serializable {
* @return int
\r
* @return the value of field 'end'.
\r
*/
\r
* @return int
\r
* @return the value of field 'end'.
\r
*/
\r
- public int getEnd()
\r
- {
\r
+ public int getEnd() {
\r
return this._end;
\r
return this._end;
\r
- } //-- int getEnd()
\r
+ }
\r
+ //-- int getEnd()
\r
\r
/**
\r
* Returns the value of field 'id'.
\r
\r
/**
\r
* Returns the value of field 'id'.
\r
@@
-170,10
+159,10
@@
public class JSeq implements java.io.Serializable {
* @return int
\r
* @return the value of field 'id'.
\r
*/
\r
* @return int
\r
* @return the value of field 'id'.
\r
*/
\r
- public int getId()
\r
- {
\r
+ public int getId() {
\r
return this._id;
\r
return this._id;
\r
- } //-- int getId()
\r
+ }
\r
+ //-- int getId()
\r
\r
/**
\r
* Returns the value of field 'start'.
\r
\r
/**
\r
* Returns the value of field 'start'.
\r
@@
-181,10
+170,10
@@
public class JSeq implements java.io.Serializable {
* @return int
\r
* @return the value of field 'start'.
\r
*/
\r
* @return int
\r
* @return the value of field 'start'.
\r
*/
\r
- public int getStart()
\r
- {
\r
+ public int getStart() {
\r
return this._start;
\r
return this._start;
\r
- } //-- int getStart()
\r
+ }
\r
+ //-- int getStart()
\r
\r
/**
\r
* Method hasColour
\r
\r
/**
\r
* Method hasColour
\r
@@
-193,10
+182,10
@@
public class JSeq implements java.io.Serializable {
*
\r
* @return boolean
\r
*/
\r
*
\r
* @return boolean
\r
*/
\r
- public boolean hasColour()
\r
- {
\r
+ public boolean hasColour() {
\r
return this._has_colour;
\r
return this._has_colour;
\r
- } //-- boolean hasColour()
\r
+ }
\r
+ //-- boolean hasColour()
\r
\r
/**
\r
* Method hasEnd
\r
\r
/**
\r
* Method hasEnd
\r
@@
-205,10
+194,10
@@
public class JSeq implements java.io.Serializable {
*
\r
* @return boolean
\r
*/
\r
*
\r
* @return boolean
\r
*/
\r
- public boolean hasEnd()
\r
- {
\r
+ public boolean hasEnd() {
\r
return this._has_end;
\r
return this._has_end;
\r
- } //-- boolean hasEnd()
\r
+ }
\r
+ //-- boolean hasEnd()
\r
\r
/**
\r
* Method hasId
\r
\r
/**
\r
* Method hasId
\r
@@
-217,10
+206,10
@@
public class JSeq implements java.io.Serializable {
*
\r
* @return boolean
\r
*/
\r
*
\r
* @return boolean
\r
*/
\r
- public boolean hasId()
\r
- {
\r
+ public boolean hasId() {
\r
return this._has_id;
\r
return this._has_id;
\r
- } //-- boolean hasId()
\r
+ }
\r
+ //-- boolean hasId()
\r
\r
/**
\r
* Method hasStart
\r
\r
/**
\r
* Method hasStart
\r
@@
-229,10
+218,10
@@
public class JSeq implements java.io.Serializable {
*
\r
* @return boolean
\r
*/
\r
*
\r
* @return boolean
\r
*/
\r
- public boolean hasStart()
\r
- {
\r
+ public boolean hasStart() {
\r
return this._has_start;
\r
return this._has_start;
\r
- } //-- boolean hasStart()
\r
+ }
\r
+ //-- boolean hasStart()
\r
\r
/**
\r
* Method isValid
\r
\r
/**
\r
* Method isValid
\r
@@
-241,16
+230,16
@@
public class JSeq 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
@@
-260,11
+249,11
@@
public class JSeq 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
@@
-274,55
+263,55
@@
public class JSeq 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 'colour'.
\r
*
\r
* @param colour the value of field 'colour'.
\r
*/
\r
\r
/**
\r
* Sets the value of field 'colour'.
\r
*
\r
* @param colour the value of field 'colour'.
\r
*/
\r
- public void setColour(int colour)
\r
- {
\r
+ public void setColour(int colour) {
\r
this._colour = colour;
\r
this._has_colour = true;
\r
this._colour = colour;
\r
this._has_colour = true;
\r
- } //-- void setColour(int)
\r
+ }
\r
+ //-- void setColour(int)
\r
\r
/**
\r
* Sets the value of field 'end'.
\r
*
\r
* @param end the value of field 'end'.
\r
*/
\r
\r
/**
\r
* Sets the value of field 'end'.
\r
*
\r
* @param end the value of field 'end'.
\r
*/
\r
- public void setEnd(int end)
\r
- {
\r
+ public void setEnd(int end) {
\r
this._end = end;
\r
this._has_end = true;
\r
this._end = end;
\r
this._has_end = true;
\r
- } //-- void setEnd(int)
\r
+ }
\r
+ //-- void setEnd(int)
\r
\r
/**
\r
* Sets the value of field 'id'.
\r
*
\r
* @param id the value of field 'id'.
\r
*/
\r
\r
/**
\r
* Sets the value of field 'id'.
\r
*
\r
* @param id the value of field 'id'.
\r
*/
\r
- public void setId(int id)
\r
- {
\r
+ public void setId(int id) {
\r
this._id = id;
\r
this._has_id = true;
\r
this._id = id;
\r
this._has_id = true;
\r
- } //-- void setId(int)
\r
+ }
\r
+ //-- void setId(int)
\r
\r
/**
\r
* Sets the value of field 'start'.
\r
*
\r
* @param start the value of field 'start'.
\r
*/
\r
\r
/**
\r
* Sets the value of field 'start'.
\r
*
\r
* @param start the value of field 'start'.
\r
*/
\r
- public void setStart(int start)
\r
- {
\r
+ public void setStart(int start) {
\r
this._start = start;
\r
this._has_start = true;
\r
this._start = start;
\r
this._has_start = true;
\r
- } //-- void setStart(int)
\r
+ }
\r
+ //-- void setStart(int)
\r
\r
/**
\r
* Method unmarshal
\r
\r
/**
\r
* Method unmarshal
\r
@@
-333,20
+322,20
@@
public class JSeq 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.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.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.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.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