X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJalviewUserColours.java;h=f1217e78b4f29f59f53e23c2af5b44e9908aaac4;hb=46ca91c8b2a49f1d2f80b6823ade9f1c29c4121c;hp=5b4fb76d74c6069e982862b64f1149d74539dae7;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/JalviewUserColours.java b/src/jalview/schemabinding/version2/JalviewUserColours.java
index 5b4fb76..f1217e7 100755
--- a/src/jalview/schemabinding/version2/JalviewUserColours.java
+++ b/src/jalview/schemabinding/version2/JalviewUserColours.java
@@ -1,308 +1,356 @@
 /*
- * 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 (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
-
 package jalview.schemabinding.version2;
 
 //---------------------------------/
 //- Imported classes and packages -/
 //---------------------------------/
 
-import java.util.*;
-
-import org.exolab.castor.xml.*;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
 
 /**
  * Class JalviewUserColours.
- *
+ * 
  * @version $Revision$ $Date$
  */
-public class JalviewUserColours
-    implements java.io.Serializable
+public class JalviewUserColours implements java.io.Serializable
 {
 
-  //--------------------------/
-  //- Class/Member Variables -/
-  //--------------------------/
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
 
   /**
-   * Field _schemeName
+   * Field _schemeName.
    */
   private java.lang.String _schemeName;
 
   /**
-   * Field _colourList
+   * Jalview colour scheme document version.
+   * 
+   */
+  private java.lang.String _version;
+
+  /**
+   * Field _colourList.
    */
   private java.util.Vector _colourList;
 
-  //----------------/
-  //- Constructors -/
-  //----------------/
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
   public JalviewUserColours()
   {
     super();
-    _colourList = new Vector();
-  } //-- jalview.schemabinding.version2.JalviewUserColours()
+    this._colourList = new java.util.Vector();
+  }
 
-  //-----------/
-  //- Methods -/
-  //-----------/
+  // -----------/
+  // - Methods -/
+  // -----------/
 
   /**
-   * Method addColour
-   *
-   *
-   *
+   * 
+   * 
    * @param vColour
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
    */
-  public void addColour(jalview.schemabinding.version2.Colour vColour)
-      throws java.lang.IndexOutOfBoundsException
+  public void addColour(final Colour vColour)
+          throws java.lang.IndexOutOfBoundsException
   {
-    _colourList.addElement(vColour);
-  } //-- void addColour(jalview.schemabinding.version2.Colour)
+    this._colourList.addElement(vColour);
+  }
 
   /**
-   * Method addColour
-   *
-   *
-   *
+   * 
+   * 
    * @param index
    * @param vColour
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
    */
-  public void addColour(int index,
-                        jalview.schemabinding.version2.Colour vColour)
-      throws java.lang.IndexOutOfBoundsException
+  public void addColour(final int index, final Colour vColour)
+          throws java.lang.IndexOutOfBoundsException
   {
-    _colourList.insertElementAt(vColour, index);
-  } //-- void addColour(int, jalview.schemabinding.version2.Colour)
+    this._colourList.add(index, vColour);
+  }
 
   /**
-   * Method enumerateColour
-   *
-   *
-   *
-   * @return Enumeration
+   * Method enumerateColour.
+   * 
+   * @return an Enumeration over all Colour elements
    */
   public java.util.Enumeration enumerateColour()
   {
-    return _colourList.elements();
-  } //-- java.util.Enumeration enumerateColour()
+    return this._colourList.elements();
+  }
 
   /**
-   * Method getColour
-   *
-   *
-   *
+   * Method getColour.
+   * 
    * @param index
-   * @return Colour
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the Colour at the given index
    */
-  public jalview.schemabinding.version2.Colour getColour(int index)
-      throws java.lang.IndexOutOfBoundsException
+  public Colour getColour(final int index)
+          throws java.lang.IndexOutOfBoundsException
   {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _colourList.size()))
+    // check bounds for index
+    if (index < 0 || index >= this._colourList.size())
     {
-      throw new IndexOutOfBoundsException();
+      throw new IndexOutOfBoundsException("getColour: Index value '"
+              + index + "' not in range [0.."
+              + (this._colourList.size() - 1) + "]");
     }
 
-    return (jalview.schemabinding.version2.Colour) _colourList.elementAt(index);
-  } //-- jalview.schemabinding.version2.Colour getColour(int)
+    return (Colour) _colourList.get(index);
+  }
 
   /**
-   * Method getColour
-   *
-   *
-   *
-   * @return Colour
+   * Method getColour.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
    */
-  public jalview.schemabinding.version2.Colour[] getColour()
+  public Colour[] getColour()
   {
-    int size = _colourList.size();
-    jalview.schemabinding.version2.Colour[] mArray = new jalview.schemabinding.
-        version2.Colour[size];
-    for (int index = 0; index < size; index++)
-    {
-      mArray[index] = (jalview.schemabinding.version2.Colour) _colourList.
-          elementAt(index);
-    }
-    return mArray;
-  } //-- jalview.schemabinding.version2.Colour[] getColour()
+    Colour[] array = new Colour[0];
+    return (Colour[]) this._colourList.toArray(array);
+  }
 
   /**
-   * Method getColourCount
-   *
-   *
-   *
-   * @return int
+   * Method getColourCount.
+   * 
+   * @return the size of this collection
    */
   public int getColourCount()
   {
-    return _colourList.size();
-  } //-- int getColourCount()
+    return this._colourList.size();
+  }
 
   /**
    * Returns the value of field 'schemeName'.
-   *
-   * @return String
-   * @return the value of field 'schemeName'.
+   * 
+   * @return the value of field 'SchemeName'.
    */
   public java.lang.String getSchemeName()
   {
     return this._schemeName;
-  } //-- java.lang.String getSchemeName()
+  }
 
   /**
-   * Method isValid
-   *
-   *
-   *
-   * @return boolean
+   * Returns the value of field 'version'. The field 'version' has the following
+   * description: Jalview colour scheme document version.
+   * 
+   * 
+   * @return the value of field 'Version'.
+   */
+  public java.lang.String getVersion()
+  {
+    return this._version;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
    */
   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()
+  }
 
   /**
-   * Method marshal
-   *
-   *
-   *
+   * 
+   * 
    * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
    */
-  public void marshal(java.io.Writer out)
-      throws org.exolab.castor.xml.MarshalException,
-      org.exolab.castor.xml.ValidationException
+  public void marshal(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
   {
-
     Marshaller.marshal(this, out);
-  } //-- void marshal(java.io.Writer)
+  }
 
   /**
-   * Method marshal
-   *
-   *
-   *
+   * 
+   * 
    * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
    */
-  public void marshal(org.xml.sax.ContentHandler handler)
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
-      org.exolab.castor.xml.ValidationException
+  public void marshal(final org.xml.sax.ContentHandler handler)
+          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 removeAllColour
-   *
-   */
+     */
   public void removeAllColour()
   {
-    _colourList.removeAllElements();
-  } //-- void removeAllColour()
+    this._colourList.clear();
+  }
+
+  /**
+   * Method removeColour.
+   * 
+   * @param vColour
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeColour(final Colour vColour)
+  {
+    boolean removed = _colourList.remove(vColour);
+    return removed;
+  }
 
   /**
-   * Method removeColour
-   *
-   *
-   *
+   * Method removeColourAt.
+   * 
    * @param index
-   * @return Colour
+   * @return the element removed from the collection
    */
-  public jalview.schemabinding.version2.Colour removeColour(int index)
+  public Colour removeColourAt(final int index)
   {
-    java.lang.Object obj = _colourList.elementAt(index);
-    _colourList.removeElementAt(index);
-    return (jalview.schemabinding.version2.Colour) obj;
-  } //-- jalview.schemabinding.version2.Colour removeColour(int)
+    java.lang.Object obj = this._colourList.remove(index);
+    return (Colour) obj;
+  }
 
   /**
-   * Method setColour
-   *
-   *
-   *
+   * 
+   * 
    * @param index
    * @param vColour
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
    */
-  public void setColour(int index,
-                        jalview.schemabinding.version2.Colour vColour)
-      throws java.lang.IndexOutOfBoundsException
+  public void setColour(final int index, final Colour vColour)
+          throws java.lang.IndexOutOfBoundsException
   {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _colourList.size()))
+    // check bounds for index
+    if (index < 0 || index >= this._colourList.size())
     {
-      throw new IndexOutOfBoundsException();
+      throw new IndexOutOfBoundsException("setColour: Index value '"
+              + index + "' not in range [0.."
+              + (this._colourList.size() - 1) + "]");
     }
-    _colourList.setElementAt(vColour, index);
-  } //-- void setColour(int, jalview.schemabinding.version2.Colour)
+
+    this._colourList.set(index, vColour);
+  }
 
   /**
-   * Method setColour
-   *
-   *
-   *
-   * @param colourArray
+   * 
+   * 
+   * @param vColourArray
    */
-  public void setColour(jalview.schemabinding.version2.Colour[] colourArray)
+  public void setColour(final Colour[] vColourArray)
   {
-    //-- copy array
-    _colourList.removeAllElements();
-    for (int i = 0; i < colourArray.length; i++)
+    // -- copy array
+    _colourList.clear();
+
+    for (int i = 0; i < vColourArray.length; i++)
     {
-      _colourList.addElement(colourArray[i]);
+      this._colourList.add(vColourArray[i]);
     }
-  } //-- void setColour(jalview.schemabinding.version2.Colour)
+  }
 
   /**
    * Sets the value of field 'schemeName'.
-   *
-   * @param schemeName the value of field 'schemeName'.
+   * 
+   * @param schemeName
+   *          the value of field 'schemeName'.
    */
-  public void setSchemeName(java.lang.String schemeName)
+  public void setSchemeName(final java.lang.String schemeName)
   {
     this._schemeName = schemeName;
-  } //-- void setSchemeName(java.lang.String)
+  }
+
+  /**
+   * Sets the value of field 'version'. The field 'version' has the following
+   * description: Jalview colour scheme document version.
+   * 
+   * 
+   * @param version
+   *          the value of field 'version'.
+   */
+  public void setVersion(final java.lang.String version)
+  {
+    this._version = version;
+  }
 
   /**
-   * Method unmarshal
-   *
-   *
-   *
+   * Method unmarshal.
+   * 
    * @param reader
-   * @return Object
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled jalview.schemabinding.version2.JalviewUserColours
    */
-  public static java.lang.Object unmarshal(java.io.Reader reader)
-      throws org.exolab.castor.xml.MarshalException,
-      org.exolab.castor.xml.ValidationException
+  public static jalview.schemabinding.version2.JalviewUserColours unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
   {
-    return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller.
-        unmarshal(jalview.schemabinding.version2.JalviewUserColours.class,
-                  reader);
-  } //-- java.lang.Object unmarshal(java.io.Reader)
+    return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller
+            .unmarshal(
+                    jalview.schemabinding.version2.JalviewUserColours.class,
+                    reader);
+  }
 
   /**
-   * Method validate
-   *
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
    */
-  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();
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
     validator.validate(this);
-  } //-- void validate()
+  }
 
 }