X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FSequenceSet.java;h=a0d116e92762320ace5bf395c09d610a732550b4;hb=b8d09897dacc7b0ad203982b4578e2c1d8929142;hp=7ed3b52db875f6661879979da2d5b2864cc3912c;hpb=c68ce4c63bd79f23b87aac3eb0afa7f6b42a3098;p=jalview.git

diff --git a/src/jalview/binding/SequenceSet.java b/src/jalview/binding/SequenceSet.java
index 7ed3b52..a0d116e 100755
--- a/src/jalview/binding/SequenceSet.java
+++ b/src/jalview/binding/SequenceSet.java
@@ -1,38 +1,39 @@
 /*
- * This class was automatically generated with 
+ * This class was automatically generated with
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
  */
-
 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.
- * 
+ *
  * @version $Revision$ $Date$
  */
-public class SequenceSet implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
+public class SequenceSet implements java.io.Serializable
+{
+    //--------------------------/
+    //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -60,40 +61,39 @@ public class SequenceSet implements java.io.Serializable {
      */
     private java.util.Vector _annotationList;
 
-
-      //----------------/
-     //- Constructors -/
     //----------------/
-
-    public SequenceSet() {
+    //- Constructors -/
+    //----------------/
+    public SequenceSet()
+    {
         super();
         _sequenceList = new Vector();
         _annotationList = new Vector();
-    } //-- jalview.binding.SequenceSet()
-
+    }
 
-      //-----------/
-     //- Methods -/
+    //-- jalview.binding.SequenceSet()
     //-----------/
 
     /**
-     * Method addAnnotation
-     * 
-     * 
-     * 
-     * @param vAnnotation
+     * DOCUMENT ME!
+     *
+     * @param vAnnotation DOCUMENT ME!
+     *
+     * @throws java.lang.IndexOutOfBoundsException DOCUMENT ME!
      */
     public void addAnnotation(jalview.binding.Annotation vAnnotation)
         throws java.lang.IndexOutOfBoundsException
     {
         _annotationList.addElement(vAnnotation);
-    } //-- void addAnnotation(jalview.binding.Annotation) 
+    }
+
+    //-- void addAnnotation(jalview.binding.Annotation) 
 
     /**
      * Method addAnnotation
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @param vAnnotation
      */
@@ -101,26 +101,30 @@ public class SequenceSet implements java.io.Serializable {
         throws java.lang.IndexOutOfBoundsException
     {
         _annotationList.insertElementAt(vAnnotation, index);
-    } //-- void addAnnotation(int, jalview.binding.Annotation) 
+    }
+
+    //-- void addAnnotation(int, jalview.binding.Annotation) 
 
     /**
      * Method addSequence
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param vSequence
      */
     public void addSequence(jalview.binding.Sequence vSequence)
         throws java.lang.IndexOutOfBoundsException
     {
         _sequenceList.addElement(vSequence);
-    } //-- void addSequence(jalview.binding.Sequence) 
+    }
+
+    //-- void addSequence(jalview.binding.Sequence) 
 
     /**
      * Method addSequence
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @param vSequence
      */
@@ -128,57 +132,67 @@ public class SequenceSet implements java.io.Serializable {
         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() 
+        this._has_aligned = false;
+    }
+
+    //-- void deleteAligned() 
 
     /**
      * Method enumerateAnnotation
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return Enumeration
      */
     public java.util.Enumeration enumerateAnnotation()
     {
         return _annotationList.elements();
-    } //-- java.util.Enumeration enumerateAnnotation() 
+    }
+
+    //-- java.util.Enumeration enumerateAnnotation() 
 
     /**
      * Method enumerateSequence
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return Enumeration
      */
     public java.util.Enumeration enumerateSequence()
     {
         return _sequenceList.elements();
-    } //-- java.util.Enumeration enumerateSequence() 
+    }
+
+    //-- java.util.Enumeration enumerateSequence() 
 
     /**
      * Returns the value of field 'aligned'.
-     * 
+     *
      * @return boolean
      * @return the value of field 'aligned'.
      */
     public boolean getAligned()
     {
         return this._aligned;
-    } //-- boolean getAligned() 
+    }
+
+    //-- boolean getAligned() 
 
     /**
      * Method getAnnotation
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @return Annotation
      */
@@ -186,58 +200,70 @@ public class SequenceSet implements java.io.Serializable {
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _annotationList.size())) {
+        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
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return Annotation
      */
     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++) {
+
+        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
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return int
      */
     public int getAnnotationCount()
     {
         return _annotationList.size();
-    } //-- int getAnnotationCount() 
+    }
+
+    //-- int getAnnotationCount() 
 
     /**
      * Returns the value of field 'gapChar'.
-     * 
+     *
      * @return String
      * @return the value of field 'gapChar'.
      */
     public java.lang.String getGapChar()
     {
         return this._gapChar;
-    } //-- java.lang.String getGapChar() 
+    }
+
+    //-- java.lang.String getGapChar() 
 
     /**
      * Method getSequence
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @return Sequence
      */
@@ -245,123 +271,148 @@ public class SequenceSet implements java.io.Serializable {
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _sequenceList.size())) {
+        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
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return Sequence
      */
     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++) {
+
+        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
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return int
      */
     public int getSequenceCount()
     {
         return _sequenceList.size();
-    } //-- int getSequenceCount() 
+    }
+
+    //-- int getSequenceCount() 
 
     /**
      * Method hasAligned
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean hasAligned()
     {
         return this._has_aligned;
-    } //-- boolean hasAligned() 
+    }
+
+    //-- boolean hasAligned() 
 
     /**
      * Method isValid
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @return boolean
      */
     public boolean isValid()
     {
-        try {
+        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
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @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
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @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()
     {
         _annotationList.removeAllElements();
-    } //-- void removeAllAnnotation() 
+    }
+
+    //-- void removeAllAnnotation() 
 
     /**
      * Method removeAllSequence
-     * 
+     *
      */
     public void removeAllSequence()
     {
         _sequenceList.removeAllElements();
-    } //-- void removeAllSequence() 
+    }
+
+    //-- void removeAllSequence() 
 
     /**
      * Method removeAnnotation
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @return Annotation
      */
@@ -369,14 +420,17 @@ public class SequenceSet implements java.io.Serializable {
     {
         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
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @return Sequence
      */
@@ -384,25 +438,30 @@ public class SequenceSet implements java.io.Serializable {
     {
         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)
     {
         this._aligned = aligned;
         this._has_aligned = true;
-    } //-- void setAligned(boolean) 
+    }
+
+    //-- void setAligned(boolean) 
 
     /**
      * Method setAnnotation
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @param vAnnotation
      */
@@ -410,43 +469,53 @@ public class SequenceSet implements java.io.Serializable {
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _annotationList.size())) {
+        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
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param annotationArray
      */
     public void setAnnotation(jalview.binding.Annotation[] annotationArray)
     {
         //-- copy array
         _annotationList.removeAllElements();
-        for (int i = 0; i < annotationArray.length; i++) {
+
+        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)
     {
         this._gapChar = gapChar;
-    } //-- void setGapChar(java.lang.String) 
+    }
+
+    //-- void setGapChar(java.lang.String) 
 
     /**
      * Method setSequence
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param index
      * @param vSequence
      */
@@ -454,51 +523,63 @@ public class SequenceSet implements java.io.Serializable {
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _sequenceList.size())) {
+        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
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param sequenceArray
      */
     public void setSequence(jalview.binding.Sequence[] sequenceArray)
     {
         //-- copy array
         _sequenceList.removeAllElements();
-        for (int i = 0; i < sequenceArray.length; i++) {
+
+        for (int i = 0; i < sequenceArray.length; i++)
+        {
             _sequenceList.addElement(sequenceArray[i]);
         }
-    } //-- void setSequence(jalview.binding.Sequence) 
+    }
+
+    //-- void setSequence(jalview.binding.Sequence) 
 
     /**
      * Method unmarshal
-     * 
-     * 
-     * 
+     *
+     *
+     *
      * @param reader
      * @return Object
      */
     public static java.lang.Object unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+        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) 
+        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() 
 }