X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbinding%2FJSeq.java;h=cabf5c85e6f8d39eb88e4594bfeea8da581166ee;hb=588042b69abf8e60bcc950b24c283933c7dd422f;hp=9e02e6008c9183217837086591caa688f53ac03f;hpb=5cd8e373c75fb348ecda4d94d8a46468fb92756d;p=jalview.git

diff --git a/src/jalview/binding/JSeq.java b/src/jalview/binding/JSeq.java
index 9e02e60..cabf5c8 100755
--- a/src/jalview/binding/JSeq.java
+++ b/src/jalview/binding/JSeq.java
@@ -4,7 +4,6 @@
  * Schema.
  * $Id$
  */
-
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -23,33 +22,32 @@
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
 import org.exolab.castor.xml.MarshalException;
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
 import org.exolab.castor.xml.ValidationException;
+
 import org.xml.sax.ContentHandler;
 
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+
+
 /**
  * Class JSeq.
  *
  * @version $Revision$ $Date$
  */
 public class JSeq implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -92,55 +90,46 @@ public class JSeq implements java.io.Serializable {
      */
     private boolean _has_id;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
+    //- Constructors -/
+    //----------------/
     public JSeq() {
         super();
-    } //-- jalview.binding.JSeq()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
+    }
+     //-- jalview.binding.JSeq()
+ //-----------/
 
-    /**
-     * Method deleteColour
-     *
-     */
-    public void deleteColour()
-    {
-        this._has_colour= false;
-    } //-- void deleteColour()
+    public void deleteColour() {
+        this._has_colour = false;
+    }
+     //-- void deleteColour()
 
     /**
      * Method deleteEnd
      *
      */
-    public void deleteEnd()
-    {
-        this._has_end= false;
-    } //-- void deleteEnd()
+    public void deleteEnd() {
+        this._has_end = false;
+    }
+     //-- void deleteEnd()
 
     /**
      * Method deleteId
      *
      */
-    public void deleteId()
-    {
-        this._has_id= false;
-    } //-- void deleteId()
+    public void deleteId() {
+        this._has_id = false;
+    }
+     //-- void deleteId()
 
     /**
      * Method deleteStart
      *
      */
-    public void deleteStart()
-    {
-        this._has_start= false;
-    } //-- void deleteStart()
+    public void deleteStart() {
+        this._has_start = false;
+    }
+     //-- void deleteStart()
 
     /**
      * Returns the value of field 'colour'.
@@ -148,10 +137,10 @@ public class JSeq implements java.io.Serializable {
      * @return int
      * @return the value of field 'colour'.
      */
-    public int getColour()
-    {
+    public int getColour() {
         return this._colour;
-    } //-- int getColour()
+    }
+     //-- int getColour()
 
     /**
      * Returns the value of field 'end'.
@@ -159,10 +148,10 @@ public class JSeq implements java.io.Serializable {
      * @return int
      * @return the value of field 'end'.
      */
-    public int getEnd()
-    {
+    public int getEnd() {
         return this._end;
-    } //-- int getEnd()
+    }
+     //-- int getEnd()
 
     /**
      * Returns the value of field 'id'.
@@ -170,10 +159,10 @@ public class JSeq implements java.io.Serializable {
      * @return int
      * @return the value of field 'id'.
      */
-    public int getId()
-    {
+    public int getId() {
         return this._id;
-    } //-- int getId()
+    }
+     //-- int getId()
 
     /**
      * Returns the value of field 'start'.
@@ -181,10 +170,10 @@ public class JSeq implements java.io.Serializable {
      * @return int
      * @return the value of field 'start'.
      */
-    public int getStart()
-    {
+    public int getStart() {
         return this._start;
-    } //-- int getStart()
+    }
+     //-- int getStart()
 
     /**
      * Method hasColour
@@ -193,10 +182,10 @@ public class JSeq implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasColour()
-    {
+    public boolean hasColour() {
         return this._has_colour;
-    } //-- boolean hasColour()
+    }
+     //-- boolean hasColour()
 
     /**
      * Method hasEnd
@@ -205,10 +194,10 @@ public class JSeq implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasEnd()
-    {
+    public boolean hasEnd() {
         return this._has_end;
-    } //-- boolean hasEnd()
+    }
+     //-- boolean hasEnd()
 
     /**
      * Method hasId
@@ -217,10 +206,10 @@ public class JSeq implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasId()
-    {
+    public boolean hasId() {
         return this._has_id;
-    } //-- boolean hasId()
+    }
+     //-- boolean hasId()
 
     /**
      * Method hasStart
@@ -229,10 +218,10 @@ public class JSeq implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasStart()
-    {
+    public boolean hasStart() {
         return this._has_start;
-    } //-- boolean hasStart()
+    }
+     //-- boolean hasStart()
 
     /**
      * Method isValid
@@ -241,16 +230,16 @@ public class JSeq implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean isValid()
-    {
+    public boolean isValid() {
         try {
             validate();
-        }
-        catch (org.exolab.castor.xml.ValidationException vex) {
+        } catch (org.exolab.castor.xml.ValidationException vex) {
             return false;
         }
+
         return true;
-    } //-- boolean isValid()
+    }
+     //-- boolean isValid()
 
     /**
      * Method marshal
@@ -260,11 +249,11 @@ public class JSeq implements java.io.Serializable {
      * @param out
      */
     public void marshal(java.io.Writer out)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-
+        throws org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException {
         Marshaller.marshal(this, out);
-    } //-- void marshal(java.io.Writer)
+    }
+     //-- void marshal(java.io.Writer)
 
     /**
      * Method marshal
@@ -274,55 +263,55 @@ public class JSeq implements java.io.Serializable {
      * @param handler
      */
     public void marshal(org.xml.sax.ContentHandler handler)
-        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException {
         Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler)
+    }
+     //-- void marshal(org.xml.sax.ContentHandler)
 
     /**
      * Sets the value of field 'colour'.
      *
      * @param colour the value of field 'colour'.
      */
-    public void setColour(int colour)
-    {
+    public void setColour(int colour) {
         this._colour = colour;
         this._has_colour = true;
-    } //-- void setColour(int)
+    }
+     //-- void setColour(int)
 
     /**
      * Sets the value of field 'end'.
      *
      * @param end the value of field 'end'.
      */
-    public void setEnd(int end)
-    {
+    public void setEnd(int end) {
         this._end = end;
         this._has_end = true;
-    } //-- void setEnd(int)
+    }
+     //-- void setEnd(int)
 
     /**
      * Sets the value of field 'id'.
      *
      * @param id the value of field 'id'.
      */
-    public void setId(int id)
-    {
+    public void setId(int id) {
         this._id = id;
         this._has_id = true;
-    } //-- void setId(int)
+    }
+     //-- void setId(int)
 
     /**
      * Sets the value of field 'start'.
      *
      * @param start the value of field 'start'.
      */
-    public void setStart(int start)
-    {
+    public void setStart(int start) {
         this._start = start;
         this._has_start = true;
-    } //-- void setStart(int)
+    }
+     //-- void setStart(int)
 
     /**
      * Method unmarshal
@@ -333,20 +322,20 @@ public class JSeq implements java.io.Serializable {
      * @return Object
      */
     public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        return (jalview.binding.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader)
+        throws org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException {
+        return (jalview.binding.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.class,
+            reader);
+    }
+     //-- java.lang.Object unmarshal(java.io.Reader)
 
     /**
      * Method validate
      *
      */
-    public void validate()
-        throws org.exolab.castor.xml.ValidationException
-    {
+    public void validate() throws org.exolab.castor.xml.ValidationException {
         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
         validator.validate(this);
-    } //-- void validate()
-
+    }
+     //-- void validate()
 }