X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FJSeq.java;h=ee559455cd465b7c4dbb275e78380841a7f9c497;hb=608832fec5a504b4c56e5837b2b3dfc1993fe734;hp=9b8ddcb54574ee491f1a34afffe8e53942c6a59b;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/binding/JSeq.java b/src/jalview/binding/JSeq.java
index 9b8ddcb..ee55945 100755
--- a/src/jalview/binding/JSeq.java
+++ b/src/jalview/binding/JSeq.java
@@ -1,36 +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.
  * $Id$
  */
-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 JSeq.
- *
+ * 
  * @version $Revision$ $Date$
  */
-public class JSeq implements java.io.Serializable
-{
-    //--------------------------/
-    //- Class/Member Variables -/
+public class JSeq implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
     //--------------------------/
 
     /**
@@ -73,302 +75,563 @@ public class JSeq implements java.io.Serializable
      */
     private boolean _has_id;
 
+    /**
+     * Field _featuresList
+     */
+    private java.util.Vector _featuresList;
+
+    /**
+     * Field _pdbidsList
+     */
+    private java.util.Vector _pdbidsList;
+
+
+      //----------------/
+     //- Constructors -/
     //----------------/
-    //- Constructors -/
-    //----------------/
-    public JSeq()
-    {
+
+    public JSeq() {
         super();
-    }
+        _featuresList = new Vector();
+        _pdbidsList = new Vector();
+    } //-- jalview.binding.JSeq()
 
-    //-- jalview.binding.JSeq()
+
+      //-----------/
+     //- Methods -/
     //-----------/
 
     /**
-     * DOCUMENT ME!
+     * Method addFeatures
+     * 
+     * 
+     * 
+     * @param vFeatures
      */
-    public void deleteColour()
+    public void addFeatures(jalview.binding.Features vFeatures)
+        throws java.lang.IndexOutOfBoundsException
     {
-        this._has_colour = false;
-    }
+        _featuresList.addElement(vFeatures);
+    } //-- void addFeatures(jalview.binding.Features) 
 
-    //-- void deleteColour() 
+    /**
+     * Method addFeatures
+     * 
+     * 
+     * 
+     * @param index
+     * @param vFeatures
+     */
+    public void addFeatures(int index, jalview.binding.Features vFeatures)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _featuresList.insertElementAt(vFeatures, index);
+    } //-- void addFeatures(int, jalview.binding.Features) 
+
+    /**
+     * Method addPdbids
+     * 
+     * 
+     * 
+     * @param vPdbids
+     */
+    public void addPdbids(jalview.binding.Pdbids vPdbids)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _pdbidsList.addElement(vPdbids);
+    } //-- void addPdbids(jalview.binding.Pdbids) 
+
+    /**
+     * Method addPdbids
+     * 
+     * 
+     * 
+     * @param index
+     * @param vPdbids
+     */
+    public void addPdbids(int index, jalview.binding.Pdbids vPdbids)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _pdbidsList.insertElementAt(vPdbids, index);
+    } //-- void addPdbids(int, jalview.binding.Pdbids) 
+
+    /**
+     * Method deleteColour
+     * 
+     */
+    public void deleteColour()
+    {
+        this._has_colour= false;
+    } //-- void deleteColour() 
 
     /**
      * Method deleteEnd
-     *
+     * 
      */
     public void deleteEnd()
     {
-        this._has_end = false;
-    }
-
-    //-- void deleteEnd() 
+        this._has_end= false;
+    } //-- void deleteEnd() 
 
     /**
      * Method deleteId
-     *
+     * 
      */
     public void deleteId()
     {
-        this._has_id = false;
-    }
-
-    //-- void deleteId() 
+        this._has_id= false;
+    } //-- void deleteId() 
 
     /**
      * Method deleteStart
-     *
+     * 
      */
     public void deleteStart()
     {
-        this._has_start = false;
-    }
+        this._has_start= false;
+    } //-- void deleteStart() 
 
-    //-- void deleteStart() 
+    /**
+     * Method enumerateFeatures
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateFeatures()
+    {
+        return _featuresList.elements();
+    } //-- java.util.Enumeration enumerateFeatures() 
+
+    /**
+     * Method enumeratePdbids
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumeratePdbids()
+    {
+        return _pdbidsList.elements();
+    } //-- java.util.Enumeration enumeratePdbids() 
 
     /**
      * Returns the value of field 'colour'.
-     *
+     * 
      * @return int
      * @return the value of field 'colour'.
      */
     public int getColour()
     {
         return this._colour;
-    }
-
-    //-- int getColour() 
+    } //-- int getColour() 
 
     /**
      * Returns the value of field 'end'.
-     *
+     * 
      * @return int
      * @return the value of field 'end'.
      */
     public int getEnd()
     {
         return this._end;
-    }
+    } //-- int getEnd() 
 
-    //-- int getEnd() 
+    /**
+     * Method getFeatures
+     * 
+     * 
+     * 
+     * @param index
+     * @return Features
+     */
+    public jalview.binding.Features getFeatures(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _featuresList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.binding.Features) _featuresList.elementAt(index);
+    } //-- jalview.binding.Features getFeatures(int) 
+
+    /**
+     * Method getFeatures
+     * 
+     * 
+     * 
+     * @return Features
+     */
+    public jalview.binding.Features[] getFeatures()
+    {
+        int size = _featuresList.size();
+        jalview.binding.Features[] mArray = new jalview.binding.Features[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.binding.Features) _featuresList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.binding.Features[] getFeatures() 
+
+    /**
+     * Method getFeaturesCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getFeaturesCount()
+    {
+        return _featuresList.size();
+    } //-- int getFeaturesCount() 
 
     /**
      * Returns the value of field 'id'.
-     *
+     * 
      * @return int
      * @return the value of field 'id'.
      */
     public int getId()
     {
         return this._id;
-    }
+    } //-- int getId() 
+
+    /**
+     * Method getPdbids
+     * 
+     * 
+     * 
+     * @param index
+     * @return Pdbids
+     */
+    public jalview.binding.Pdbids getPdbids(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _pdbidsList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.binding.Pdbids) _pdbidsList.elementAt(index);
+    } //-- jalview.binding.Pdbids getPdbids(int) 
+
+    /**
+     * Method getPdbids
+     * 
+     * 
+     * 
+     * @return Pdbids
+     */
+    public jalview.binding.Pdbids[] getPdbids()
+    {
+        int size = _pdbidsList.size();
+        jalview.binding.Pdbids[] mArray = new jalview.binding.Pdbids[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.binding.Pdbids) _pdbidsList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.binding.Pdbids[] getPdbids() 
 
-    //-- int getId() 
+    /**
+     * Method getPdbidsCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getPdbidsCount()
+    {
+        return _pdbidsList.size();
+    } //-- int getPdbidsCount() 
 
     /**
      * Returns the value of field 'start'.
-     *
+     * 
      * @return int
      * @return the value of field 'start'.
      */
     public int getStart()
     {
         return this._start;
-    }
-
-    //-- int getStart() 
+    } //-- int getStart() 
 
     /**
      * Method hasColour
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return boolean
      */
     public boolean hasColour()
     {
         return this._has_colour;
-    }
-
-    //-- boolean hasColour() 
+    } //-- boolean hasColour() 
 
     /**
      * Method hasEnd
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return boolean
      */
     public boolean hasEnd()
     {
         return this._has_end;
-    }
-
-    //-- boolean hasEnd() 
+    } //-- boolean hasEnd() 
 
     /**
      * Method hasId
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return boolean
      */
     public boolean hasId()
     {
         return this._has_id;
-    }
-
-    //-- boolean hasId() 
+    } //-- boolean hasId() 
 
     /**
      * Method hasStart
-     *
-     *
-     *
+     * 
+     * 
+     * 
      * @return boolean
      */
     public boolean hasStart()
     {
         return this._has_start;
-    }
-
-    //-- boolean hasStart() 
+    } //-- boolean hasStart() 
 
     /**
      * 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) 
+
+    /**
+     * Method removeAllFeatures
+     * 
+     */
+    public void removeAllFeatures()
+    {
+        _featuresList.removeAllElements();
+    } //-- void removeAllFeatures() 
 
-    //-- void marshal(org.xml.sax.ContentHandler) 
+    /**
+     * Method removeAllPdbids
+     * 
+     */
+    public void removeAllPdbids()
+    {
+        _pdbidsList.removeAllElements();
+    } //-- void removeAllPdbids() 
+
+    /**
+     * Method removeFeatures
+     * 
+     * 
+     * 
+     * @param index
+     * @return Features
+     */
+    public jalview.binding.Features removeFeatures(int index)
+    {
+        java.lang.Object obj = _featuresList.elementAt(index);
+        _featuresList.removeElementAt(index);
+        return (jalview.binding.Features) obj;
+    } //-- jalview.binding.Features removeFeatures(int) 
+
+    /**
+     * Method removePdbids
+     * 
+     * 
+     * 
+     * @param index
+     * @return Pdbids
+     */
+    public jalview.binding.Pdbids removePdbids(int index)
+    {
+        java.lang.Object obj = _pdbidsList.elementAt(index);
+        _pdbidsList.removeElementAt(index);
+        return (jalview.binding.Pdbids) obj;
+    } //-- jalview.binding.Pdbids removePdbids(int) 
 
     /**
      * Sets the value of field 'colour'.
-     *
+     * 
      * @param colour the value of field '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)
     {
         this._end = end;
         this._has_end = true;
-    }
+    } //-- void setEnd(int) 
+
+    /**
+     * Method setFeatures
+     * 
+     * 
+     * 
+     * @param index
+     * @param vFeatures
+     */
+    public void setFeatures(int index, jalview.binding.Features vFeatures)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _featuresList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _featuresList.setElementAt(vFeatures, index);
+    } //-- void setFeatures(int, jalview.binding.Features) 
 
-    //-- void setEnd(int) 
+    /**
+     * Method setFeatures
+     * 
+     * 
+     * 
+     * @param featuresArray
+     */
+    public void setFeatures(jalview.binding.Features[] featuresArray)
+    {
+        //-- copy array
+        _featuresList.removeAllElements();
+        for (int i = 0; i < featuresArray.length; i++) {
+            _featuresList.addElement(featuresArray[i]);
+        }
+    } //-- void setFeatures(jalview.binding.Features) 
 
     /**
      * Sets the value of field 'id'.
-     *
+     * 
      * @param id the value of field 'id'.
      */
     public void setId(int id)
     {
         this._id = id;
         this._has_id = true;
-    }
+    } //-- void setId(int) 
+
+    /**
+     * Method setPdbids
+     * 
+     * 
+     * 
+     * @param index
+     * @param vPdbids
+     */
+    public void setPdbids(int index, jalview.binding.Pdbids vPdbids)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _pdbidsList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _pdbidsList.setElementAt(vPdbids, index);
+    } //-- void setPdbids(int, jalview.binding.Pdbids) 
 
-    //-- void setId(int) 
+    /**
+     * Method setPdbids
+     * 
+     * 
+     * 
+     * @param pdbidsArray
+     */
+    public void setPdbids(jalview.binding.Pdbids[] pdbidsArray)
+    {
+        //-- copy array
+        _pdbidsList.removeAllElements();
+        for (int i = 0; i < pdbidsArray.length; i++) {
+            _pdbidsList.addElement(pdbidsArray[i]);
+        }
+    } //-- void setPdbids(jalview.binding.Pdbids) 
 
     /**
      * Sets the value of field 'start'.
-     *
+     * 
      * @param start the value of field 'start'.
      */
     public void setStart(int start)
     {
         this._start = start;
         this._has_start = true;
-    }
-
-    //-- void setStart(int) 
+    } //-- void setStart(int) 
 
     /**
      * 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.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.class,
-            reader);
-    }
-
-    //-- java.lang.Object unmarshal(java.io.Reader) 
+        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() 
 }