X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FSequenceSet.java;h=7ed3b52db875f6661879979da2d5b2864cc3912c;hb=03c446f178b6a0b61ad33cb219398132d640fbef;hp=4300c3951138022ebea8373e76a81051127bcae9;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/binding/SequenceSet.java b/src/jalview/binding/SequenceSet.java
index 4300c39..7ed3b52 100755
--- a/src/jalview/binding/SequenceSet.java
+++ b/src/jalview/binding/SequenceSet.java
@@ -1,56 +1,38 @@
 /*
- * 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.
  * $Id$
  */
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* 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;
-
-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;
+package jalview.binding;
 
+  //---------------------------------/
+ //- Imported classes and packages -/
 //---------------------------------/
-//- 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 -/
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -78,443 +60,445 @@ 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
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @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
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @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
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @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
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @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
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @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'.
-     *
+     * 
      * @return boolean
      * @return the value of field 'aligned'.
      */
-    public boolean getAligned() {
+    public boolean getAligned()
+    {
         return this._aligned;
-    }
-     //-- boolean getAligned()
+    } //-- boolean getAligned() 
 
     /**
      * Method getAnnotation
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @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
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @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
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return int
      */
-    public int getAnnotationCount() {
+    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() {
+    public java.lang.String getGapChar()
+    {
         return this._gapChar;
-    }
-     //-- java.lang.String getGapChar()
+    } //-- java.lang.String getGapChar() 
 
     /**
      * Method getSequence
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @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
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @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
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return int
      */
-    public int getSequenceCount() {
+    public int getSequenceCount()
+    {
         return _sequenceList.size();
-    }
-     //-- int getSequenceCount()
+    } //-- int getSequenceCount() 
 
     /**
      * Method hasAligned
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return boolean
      */
-    public boolean hasAligned() {
+    public boolean hasAligned()
+    {
         return this._has_aligned;
-    }
-     //-- boolean hasAligned()
+    } //-- boolean hasAligned() 
 
     /**
      * Method isValid
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @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
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @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() {
+    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
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @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
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @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
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @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
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @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
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @param index
      * @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
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @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
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @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 {
-        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() 
+
 }