X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FSequenceSet.java;h=4300c3951138022ebea8373e76a81051127bcae9;hb=588042b69abf8e60bcc950b24c283933c7dd422f;hp=7ef5fe75336f8a0b49ce0163d4f57d6c40212849;hpb=5cd8e373c75fb348ecda4d94d8a46468fb92756d;p=jalview.git

diff --git a/src/jalview/binding/SequenceSet.java b/src/jalview/binding/SequenceSet.java
index 7ef5fe7..4300c39 100755
--- a/src/jalview/binding/SequenceSet.java
+++ b/src/jalview/binding/SequenceSet.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
@@ -23,24 +22,26 @@
 * 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 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;
+
 import java.util.Enumeration;
 import java.util.Vector;
-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;
+
 
 /**
  * Class SequenceSet.
@@ -48,10 +49,8 @@ import org.xml.sax.ContentHandler;
  * @version $Revision$ $Date$
  */
 public class SequenceSet implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -79,34 +78,22 @@ public class SequenceSet implements java.io.Serializable {
      */
     private java.util.Vector _annotationList;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
+    //- Constructors -/
+    //----------------/
     public SequenceSet() {
         super();
         _sequenceList = new Vector();
         _annotationList = new Vector();
-    } //-- jalview.binding.SequenceSet()
+    }
+     //-- jalview.binding.SequenceSet()
+ //-----------/
 
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addAnnotation
-     *
-     *
-     *
-     * @param vAnnotation
-     */
     public void addAnnotation(jalview.binding.Annotation vAnnotation)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         _annotationList.addElement(vAnnotation);
-    } //-- void addAnnotation(jalview.binding.Annotation)
+    }
+     //-- void addAnnotation(jalview.binding.Annotation)
 
     /**
      * Method addAnnotation
@@ -117,10 +104,10 @@ public class SequenceSet implements java.io.Serializable {
      * @param vAnnotation
      */
     public void addAnnotation(int index, jalview.binding.Annotation vAnnotation)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         _annotationList.insertElementAt(vAnnotation, index);
-    } //-- void addAnnotation(int, jalview.binding.Annotation)
+    }
+     //-- void addAnnotation(int, jalview.binding.Annotation)
 
     /**
      * Method addSequence
@@ -130,10 +117,10 @@ public class SequenceSet implements java.io.Serializable {
      * @param vSequence
      */
     public void addSequence(jalview.binding.Sequence vSequence)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         _sequenceList.addElement(vSequence);
-    } //-- void addSequence(jalview.binding.Sequence)
+    }
+     //-- void addSequence(jalview.binding.Sequence)
 
     /**
      * Method addSequence
@@ -144,19 +131,19 @@ public class SequenceSet implements java.io.Serializable {
      * @param vSequence
      */
     public void addSequence(int index, jalview.binding.Sequence vSequence)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         _sequenceList.insertElementAt(vSequence, index);
-    } //-- void addSequence(int, jalview.binding.Sequence)
+    }
+     //-- void addSequence(int, jalview.binding.Sequence)
 
     /**
      * Method deleteAligned
      *
      */
-    public void deleteAligned()
-    {
-        this._has_aligned= false;
-    } //-- void deleteAligned()
+    public void deleteAligned() {
+        this._has_aligned = false;
+    }
+     //-- void deleteAligned()
 
     /**
      * Method enumerateAnnotation
@@ -165,10 +152,10 @@ public class SequenceSet implements java.io.Serializable {
      *
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateAnnotation()
-    {
+    public java.util.Enumeration enumerateAnnotation() {
         return _annotationList.elements();
-    } //-- java.util.Enumeration enumerateAnnotation()
+    }
+     //-- java.util.Enumeration enumerateAnnotation()
 
     /**
      * Method enumerateSequence
@@ -177,10 +164,10 @@ public class SequenceSet implements java.io.Serializable {
      *
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateSequence()
-    {
+    public java.util.Enumeration enumerateSequence() {
         return _sequenceList.elements();
-    } //-- java.util.Enumeration enumerateSequence()
+    }
+     //-- java.util.Enumeration enumerateSequence()
 
     /**
      * Returns the value of field 'aligned'.
@@ -188,10 +175,10 @@ public class SequenceSet implements java.io.Serializable {
      * @return boolean
      * @return the value of field 'aligned'.
      */
-    public boolean getAligned()
-    {
+    public boolean getAligned() {
         return this._aligned;
-    } //-- boolean getAligned()
+    }
+     //-- boolean getAligned()
 
     /**
      * Method getAnnotation
@@ -202,15 +189,15 @@ public class SequenceSet implements java.io.Serializable {
      * @return Annotation
      */
     public jalview.binding.Annotation getAnnotation(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         //-- check bounds for index
         if ((index < 0) || (index > _annotationList.size())) {
             throw new IndexOutOfBoundsException();
         }
 
         return (jalview.binding.Annotation) _annotationList.elementAt(index);
-    } //-- jalview.binding.Annotation getAnnotation(int)
+    }
+     //-- jalview.binding.Annotation getAnnotation(int)
 
     /**
      * Method getAnnotation
@@ -219,15 +206,17 @@ public class SequenceSet implements java.io.Serializable {
      *
      * @return Annotation
      */
-    public jalview.binding.Annotation[] getAnnotation()
-    {
+    public jalview.binding.Annotation[] getAnnotation() {
         int size = _annotationList.size();
         jalview.binding.Annotation[] mArray = new jalview.binding.Annotation[size];
+
         for (int index = 0; index < size; index++) {
             mArray[index] = (jalview.binding.Annotation) _annotationList.elementAt(index);
         }
+
         return mArray;
-    } //-- jalview.binding.Annotation[] getAnnotation()
+    }
+     //-- jalview.binding.Annotation[] getAnnotation()
 
     /**
      * Method getAnnotationCount
@@ -236,10 +225,10 @@ public class SequenceSet implements java.io.Serializable {
      *
      * @return int
      */
-    public int getAnnotationCount()
-    {
+    public int getAnnotationCount() {
         return _annotationList.size();
-    } //-- int getAnnotationCount()
+    }
+     //-- int getAnnotationCount()
 
     /**
      * Returns the value of field 'gapChar'.
@@ -247,10 +236,10 @@ public class SequenceSet implements java.io.Serializable {
      * @return String
      * @return the value of field 'gapChar'.
      */
-    public java.lang.String getGapChar()
-    {
+    public java.lang.String getGapChar() {
         return this._gapChar;
-    } //-- java.lang.String getGapChar()
+    }
+     //-- java.lang.String getGapChar()
 
     /**
      * Method getSequence
@@ -261,15 +250,15 @@ public class SequenceSet implements java.io.Serializable {
      * @return Sequence
      */
     public jalview.binding.Sequence getSequence(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         //-- check bounds for index
         if ((index < 0) || (index > _sequenceList.size())) {
             throw new IndexOutOfBoundsException();
         }
 
         return (jalview.binding.Sequence) _sequenceList.elementAt(index);
-    } //-- jalview.binding.Sequence getSequence(int)
+    }
+     //-- jalview.binding.Sequence getSequence(int)
 
     /**
      * Method getSequence
@@ -278,15 +267,17 @@ public class SequenceSet implements java.io.Serializable {
      *
      * @return Sequence
      */
-    public jalview.binding.Sequence[] getSequence()
-    {
+    public jalview.binding.Sequence[] getSequence() {
         int size = _sequenceList.size();
         jalview.binding.Sequence[] mArray = new jalview.binding.Sequence[size];
+
         for (int index = 0; index < size; index++) {
             mArray[index] = (jalview.binding.Sequence) _sequenceList.elementAt(index);
         }
+
         return mArray;
-    } //-- jalview.binding.Sequence[] getSequence()
+    }
+     //-- jalview.binding.Sequence[] getSequence()
 
     /**
      * Method getSequenceCount
@@ -295,10 +286,10 @@ public class SequenceSet implements java.io.Serializable {
      *
      * @return int
      */
-    public int getSequenceCount()
-    {
+    public int getSequenceCount() {
         return _sequenceList.size();
-    } //-- int getSequenceCount()
+    }
+     //-- int getSequenceCount()
 
     /**
      * Method hasAligned
@@ -307,10 +298,10 @@ public class SequenceSet implements java.io.Serializable {
      *
      * @return boolean
      */
-    public boolean hasAligned()
-    {
+    public boolean hasAligned() {
         return this._has_aligned;
-    } //-- boolean hasAligned()
+    }
+     //-- boolean hasAligned()
 
     /**
      * Method isValid
@@ -319,16 +310,16 @@ public class SequenceSet 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
@@ -338,11 +329,11 @@ public class SequenceSet 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
@@ -352,29 +343,29 @@ public class SequenceSet 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)
 
     /**
      * Method removeAllAnnotation
      *
      */
-    public void removeAllAnnotation()
-    {
+    public void removeAllAnnotation() {
         _annotationList.removeAllElements();
-    } //-- void removeAllAnnotation()
+    }
+     //-- void removeAllAnnotation()
 
     /**
      * Method removeAllSequence
      *
      */
-    public void removeAllSequence()
-    {
+    public void removeAllSequence() {
         _sequenceList.removeAllElements();
-    } //-- void removeAllSequence()
+    }
+     //-- void removeAllSequence()
 
     /**
      * Method removeAnnotation
@@ -384,12 +375,13 @@ public class SequenceSet implements java.io.Serializable {
      * @param index
      * @return Annotation
      */
-    public jalview.binding.Annotation removeAnnotation(int index)
-    {
+    public jalview.binding.Annotation removeAnnotation(int index) {
         java.lang.Object obj = _annotationList.elementAt(index);
         _annotationList.removeElementAt(index);
+
         return (jalview.binding.Annotation) obj;
-    } //-- jalview.binding.Annotation removeAnnotation(int)
+    }
+     //-- jalview.binding.Annotation removeAnnotation(int)
 
     /**
      * Method removeSequence
@@ -399,23 +391,24 @@ public class SequenceSet implements java.io.Serializable {
      * @param index
      * @return Sequence
      */
-    public jalview.binding.Sequence removeSequence(int index)
-    {
+    public jalview.binding.Sequence removeSequence(int index) {
         java.lang.Object obj = _sequenceList.elementAt(index);
         _sequenceList.removeElementAt(index);
+
         return (jalview.binding.Sequence) obj;
-    } //-- jalview.binding.Sequence removeSequence(int)
+    }
+     //-- jalview.binding.Sequence removeSequence(int)
 
     /**
      * Sets the value of field 'aligned'.
      *
      * @param aligned the value of field 'aligned'.
      */
-    public void setAligned(boolean aligned)
-    {
+    public void setAligned(boolean aligned) {
         this._aligned = aligned;
         this._has_aligned = true;
-    } //-- void setAligned(boolean)
+    }
+     //-- void setAligned(boolean)
 
     /**
      * Method setAnnotation
@@ -426,14 +419,15 @@ public class SequenceSet implements java.io.Serializable {
      * @param vAnnotation
      */
     public void setAnnotation(int index, jalview.binding.Annotation vAnnotation)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         //-- check bounds for index
         if ((index < 0) || (index > _annotationList.size())) {
             throw new IndexOutOfBoundsException();
         }
+
         _annotationList.setElementAt(vAnnotation, index);
-    } //-- void setAnnotation(int, jalview.binding.Annotation)
+    }
+     //-- void setAnnotation(int, jalview.binding.Annotation)
 
     /**
      * Method setAnnotation
@@ -442,24 +436,25 @@ public class SequenceSet implements java.io.Serializable {
      *
      * @param annotationArray
      */
-    public void setAnnotation(jalview.binding.Annotation[] annotationArray)
-    {
+    public void setAnnotation(jalview.binding.Annotation[] annotationArray) {
         //-- copy array
         _annotationList.removeAllElements();
+
         for (int i = 0; i < annotationArray.length; i++) {
             _annotationList.addElement(annotationArray[i]);
         }
-    } //-- void setAnnotation(jalview.binding.Annotation)
+    }
+     //-- void setAnnotation(jalview.binding.Annotation)
 
     /**
      * Sets the value of field 'gapChar'.
      *
      * @param gapChar the value of field 'gapChar'.
      */
-    public void setGapChar(java.lang.String gapChar)
-    {
+    public void setGapChar(java.lang.String gapChar) {
         this._gapChar = gapChar;
-    } //-- void setGapChar(java.lang.String)
+    }
+     //-- void setGapChar(java.lang.String)
 
     /**
      * Method setSequence
@@ -470,14 +465,15 @@ public class SequenceSet implements java.io.Serializable {
      * @param vSequence
      */
     public void setSequence(int index, jalview.binding.Sequence vSequence)
-        throws java.lang.IndexOutOfBoundsException
-    {
+        throws java.lang.IndexOutOfBoundsException {
         //-- check bounds for index
         if ((index < 0) || (index > _sequenceList.size())) {
             throw new IndexOutOfBoundsException();
         }
+
         _sequenceList.setElementAt(vSequence, index);
-    } //-- void setSequence(int, jalview.binding.Sequence)
+    }
+     //-- void setSequence(int, jalview.binding.Sequence)
 
     /**
      * Method setSequence
@@ -486,14 +482,15 @@ public class SequenceSet implements java.io.Serializable {
      *
      * @param sequenceArray
      */
-    public void setSequence(jalview.binding.Sequence[] sequenceArray)
-    {
+    public void setSequence(jalview.binding.Sequence[] sequenceArray) {
         //-- copy array
         _sequenceList.removeAllElements();
+
         for (int i = 0; i < sequenceArray.length; i++) {
             _sequenceList.addElement(sequenceArray[i]);
         }
-    } //-- void setSequence(jalview.binding.Sequence)
+    }
+     //-- void setSequence(jalview.binding.Sequence)
 
     /**
      * Method unmarshal
@@ -504,20 +501,20 @@ public class SequenceSet 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.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader)
+        throws org.exolab.castor.xml.MarshalException, 
+            org.exolab.castor.xml.ValidationException {
+        return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.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()
 }