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
-\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
-\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
+\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
-\r
-      //--------------------------/\r
-     //- Class/Member Variables -/\r
+    //--------------------------/\r
+    //- Class/Member Variables -/\r
     //--------------------------/\r
 \r
     /**\r
@@ -92,55 +90,46 @@ public class JSeq implements java.io.Serializable {
      */\r
     private boolean _has_id;\r
 \r
-\r
-      //----------------/\r
-     //- Constructors -/\r
     //----------------/\r
-\r
+    //- Constructors -/\r
+    //----------------/\r
     public JSeq() {\r
         super();\r
-    } //-- jalview.binding.JSeq()\r
-\r
-\r
-      //-----------/\r
-     //- Methods -/\r
-    //-----------/\r
+    }\r
+     //-- jalview.binding.JSeq()\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
-    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
-    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
-    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
@@ -148,10 +137,10 @@ public class JSeq implements java.io.Serializable {
      * @return int\r
      * @return the value of field 'colour'.\r
      */\r
-    public int getColour()\r
-    {\r
+    public int getColour() {\r
         return this._colour;\r
-    } //-- int getColour()\r
+    }\r
+     //-- int getColour()\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
-    public int getEnd()\r
-    {\r
+    public int getEnd() {\r
         return this._end;\r
-    } //-- int getEnd()\r
+    }\r
+     //-- int getEnd()\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
-    public int getId()\r
-    {\r
+    public int getId() {\r
         return this._id;\r
-    } //-- int getId()\r
+    }\r
+     //-- int getId()\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
-    public int getStart()\r
-    {\r
+    public int getStart() {\r
         return this._start;\r
-    } //-- int getStart()\r
+    }\r
+     //-- int getStart()\r
 \r
     /**\r
      * Method hasColour\r
@@ -193,10 +182,10 @@ public class JSeq implements java.io.Serializable {
      *\r
      * @return boolean\r
      */\r
-    public boolean hasColour()\r
-    {\r
+    public boolean hasColour() {\r
         return this._has_colour;\r
-    } //-- boolean hasColour()\r
+    }\r
+     //-- boolean hasColour()\r
 \r
     /**\r
      * Method hasEnd\r
@@ -205,10 +194,10 @@ public class JSeq implements java.io.Serializable {
      *\r
      * @return boolean\r
      */\r
-    public boolean hasEnd()\r
-    {\r
+    public boolean hasEnd() {\r
         return this._has_end;\r
-    } //-- boolean hasEnd()\r
+    }\r
+     //-- boolean hasEnd()\r
 \r
     /**\r
      * Method hasId\r
@@ -217,10 +206,10 @@ public class JSeq implements java.io.Serializable {
      *\r
      * @return boolean\r
      */\r
-    public boolean hasId()\r
-    {\r
+    public boolean hasId() {\r
         return this._has_id;\r
-    } //-- boolean hasId()\r
+    }\r
+     //-- boolean hasId()\r
 \r
     /**\r
      * Method hasStart\r
@@ -229,10 +218,10 @@ public class JSeq implements java.io.Serializable {
      *\r
      * @return boolean\r
      */\r
-    public boolean hasStart()\r
-    {\r
+    public boolean hasStart() {\r
         return this._has_start;\r
-    } //-- boolean hasStart()\r
+    }\r
+     //-- boolean hasStart()\r
 \r
     /**\r
      * Method isValid\r
@@ -241,16 +230,16 @@ public class JSeq implements java.io.Serializable {
      *\r
      * @return boolean\r
      */\r
-    public boolean isValid()\r
-    {\r
+    public boolean isValid() {\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
+\r
         return true;\r
-    } //-- boolean isValid()\r
+    }\r
+     //-- boolean isValid()\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
-        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
-    } //-- void marshal(java.io.Writer)\r
+    }\r
+     //-- void marshal(java.io.Writer)\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
-        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
-    } //-- 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
-    public void setColour(int colour)\r
-    {\r
+    public void setColour(int colour) {\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
-    public void setEnd(int end)\r
-    {\r
+    public void setEnd(int end) {\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
-    public void setId(int id)\r
-    {\r
+    public void setId(int id) {\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
-    public void setStart(int start)\r
-    {\r
+    public void setStart(int start) {\r
         this._start = start;\r
         this._has_start = true;\r
-    } //-- void setStart(int)\r
+    }\r
+     //-- void setStart(int)\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
-        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
-    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
-    } //-- void validate()\r
-\r
+    }\r
+     //-- void validate()\r
 }\r