JAL-2843 missed Castor class

diff --git a/src/jalview/schemabinding/version2/Colour.java b/src/jalview/schemabinding/version2/Colour.java
index 9d5a916..8f709d7 100644 (file)
--- a/src/jalview/schemabinding/version2/Colour.java
+++ b/src/jalview/schemabinding/version2/Colour.java
@@ -27,7 +27,8 @@ public class Colour implements java.io.Serializable
   // --------------------------/
 
   /**
-   * Field _name.
+   * Single letter residue code for an alignment colour scheme, or feature type
+   * for a feature colour scheme
    */
   private java.lang.String _name;
 
@@ -42,9 +43,15 @@ public class Colour implements java.io.Serializable
   private java.lang.String _minRGB;
 
   /**
-   * loosely specified enumeration: NONE,ABOVE, or BELOW
+   * Colour if no attribute or score value
    */
-  private java.lang.String _threshType;
+  private jalview.schemabinding.version2.types.ColourNoValueColourType _noValueColour = jalview.schemabinding.version2.types.ColourNoValueColourType
+          .valueOf("Min");
+
+  /**
+   * Field _threshType.
+   */
+  private jalview.schemabinding.version2.types.ColourThreshTypeType _threshType;
 
   /**
    * Field _threshold.
@@ -96,6 +103,11 @@ public class Colour implements java.io.Serializable
    */
   private boolean _has_autoScale;
 
+  /**
+   * name of feature attribute to colour by, or attribute and sub-attribute
+   */
+  private java.util.Vector _attributeNameList;
+
   // ----------------/
   // - Constructors -/
   // ----------------/
@@ -103,6 +115,10 @@ public class Colour implements java.io.Serializable
   public Colour()
   {
     super();
+    setNoValueColour(
+            jalview.schemabinding.version2.types.ColourNoValueColourType
+                    .valueOf("Min"));
+    this._attributeNameList = new java.util.Vector();
   }
 
   // -----------/
@@ -110,41 +126,140 @@ public class Colour implements java.io.Serializable
   // -----------/
 
   /**
-     */
+   * 
+   * 
+   * @param vAttributeName
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAttributeName(final java.lang.String vAttributeName)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check for the maximum size
+    if (this._attributeNameList.size() >= 2)
+    {
+      throw new IndexOutOfBoundsException(
+              "addAttributeName has a maximum of 2");
+    }
+
+    this._attributeNameList.addElement(vAttributeName);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAttributeName
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addAttributeName(final int index,
+          final java.lang.String vAttributeName)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check for the maximum size
+    if (this._attributeNameList.size() >= 2)
+    {
+      throw new IndexOutOfBoundsException(
+              "addAttributeName has a maximum of 2");
+    }
+
+    this._attributeNameList.add(index, vAttributeName);
+  }
+
+  /**
+   */
   public void deleteAutoScale()
   {
     this._has_autoScale = false;
   }
 
   /**
-     */
+   */
   public void deleteColourByLabel()
   {
     this._has_colourByLabel = false;
   }
 
   /**
-     */
+   */
   public void deleteMax()
   {
     this._has_max = false;
   }
 
   /**
-     */
+   */
   public void deleteMin()
   {
     this._has_min = false;
   }
 
   /**
-     */
+   */
   public void deleteThreshold()
   {
     this._has_threshold = false;
   }
 
   /**
+   * Method enumerateAttributeName.
+   * 
+   * @return an Enumeration over all java.lang.String elements
+   */
+  public java.util.Enumeration enumerateAttributeName()
+  {
+    return this._attributeNameList.elements();
+  }
+
+  /**
+   * Method getAttributeName.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the java.lang.String at the given index
+   */
+  public java.lang.String getAttributeName(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._attributeNameList.size())
+    {
+      throw new IndexOutOfBoundsException("getAttributeName: Index value '"
+              + index + "' not in range [0.."
+              + (this._attributeNameList.size() - 1) + "]");
+    }
+
+    return (java.lang.String) _attributeNameList.get(index);
+  }
+
+  /**
+   * Method getAttributeName.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 java.lang.String[] getAttributeName()
+  {
+    java.lang.String[] array = new java.lang.String[0];
+    return (java.lang.String[]) this._attributeNameList.toArray(array);
+  }
+
+  /**
+   * Method getAttributeNameCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getAttributeNameCount()
+  {
+    return this._attributeNameList.size();
+  }
+
+  /**
    * Returns the value of field 'autoScale'.
    * 
    * @return the value of field 'AutoScale'.
@@ -195,7 +310,9 @@ public class Colour implements java.io.Serializable
   }
 
   /**
-   * Returns the value of field 'name'.
+   * Returns the value of field 'name'. The field 'name' has the following
+   * description: Single letter residue code for an alignment colour scheme, or
+   * feature type for a feature colour scheme
    * 
    * @return the value of field 'Name'.
    */
@@ -205,6 +322,17 @@ public class Colour implements java.io.Serializable
   }
 
   /**
+   * Returns the value of field 'noValueColour'. The field 'noValueColour' has
+   * the following description: Colour if no attribute or score value
+   * 
+   * @return the value of field 'NoValueColour'.
+   */
+  public jalview.schemabinding.version2.types.ColourNoValueColourType getNoValueColour()
+  {
+    return this._noValueColour;
+  }
+
+  /**
    * Returns the value of field 'RGB'.
    * 
    * @return the value of field 'RGB'.
@@ -215,12 +343,11 @@ public class Colour implements java.io.Serializable
   }
 
   /**
-   * Returns the value of field 'threshType'. The field 'threshType' has the
-   * following description: loosely specified enumeration: NONE,ABOVE, or BELOW
+   * Returns the value of field 'threshType'.
    * 
    * @return the value of field 'ThreshType'.
    */
-  public java.lang.String getThreshType()
+  public jalview.schemabinding.version2.types.ColourThreshTypeType getThreshType()
   {
     return this._threshType;
   }
@@ -360,6 +487,76 @@ public class Colour implements java.io.Serializable
   }
 
   /**
+   */
+  public void removeAllAttributeName()
+  {
+    this._attributeNameList.clear();
+  }
+
+  /**
+   * Method removeAttributeName.
+   * 
+   * @param vAttributeName
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeAttributeName(final java.lang.String vAttributeName)
+  {
+    boolean removed = _attributeNameList.remove(vAttributeName);
+    return removed;
+  }
+
+  /**
+   * Method removeAttributeNameAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public java.lang.String removeAttributeNameAt(final int index)
+  {
+    java.lang.Object obj = this._attributeNameList.remove(index);
+    return (java.lang.String) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vAttributeName
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setAttributeName(final int index,
+          final java.lang.String vAttributeName)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._attributeNameList.size())
+    {
+      throw new IndexOutOfBoundsException("setAttributeName: Index value '"
+              + index + "' not in range [0.."
+              + (this._attributeNameList.size() - 1) + "]");
+    }
+
+    this._attributeNameList.set(index, vAttributeName);
+  }
+
+  /**
+   * 
+   * 
+   * @param vAttributeNameArray
+   */
+  public void setAttributeName(final java.lang.String[] vAttributeNameArray)
+  {
+    // -- copy array
+    _attributeNameList.clear();
+
+    for (int i = 0; i < vAttributeNameArray.length; i++)
+    {
+      this._attributeNameList.add(vAttributeNameArray[i]);
+    }
+  }
+
+  /**
    * Sets the value of field 'autoScale'.
    * 
    * @param autoScale
@@ -419,7 +616,9 @@ public class Colour implements java.io.Serializable
   }
 
   /**
-   * Sets the value of field 'name'.
+   * Sets the value of field 'name'. The field 'name' has the following
+   * description: Single letter residue code for an alignment colour scheme, or
+   * feature type for a feature colour scheme
    * 
    * @param name
    *          the value of field 'name'.
@@ -430,6 +629,19 @@ public class Colour implements java.io.Serializable
   }
 
   /**
+   * Sets the value of field 'noValueColour'. The field 'noValueColour' has the
+   * following description: Colour if no attribute or score value
+   * 
+   * @param noValueColour
+   *          the value of field 'noValueColour'.
+   */
+  public void setNoValueColour(
+          final jalview.schemabinding.version2.types.ColourNoValueColourType noValueColour)
+  {
+    this._noValueColour = noValueColour;
+  }
+
+  /**
    * Sets the value of field 'RGB'.
    * 
    * @param RGB
@@ -441,13 +653,13 @@ public class Colour implements java.io.Serializable
   }
 
   /**
-   * Sets the value of field 'threshType'. The field 'threshType' has the
-   * following description: loosely specified enumeration: NONE,ABOVE, or BELOW
+   * Sets the value of field 'threshType'.
    * 
    * @param threshType
    *          the value of field 'threshType'.
    */
-  public void setThreshType(final java.lang.String threshType)
+  public void setThreshType(
+          final jalview.schemabinding.version2.types.ColourThreshTypeType threshType)
   {
     this._threshType = threshType;
   }
@@ -480,8 +692,8 @@ public class Colour implements java.io.Serializable
           throws org.exolab.castor.xml.MarshalException,
           org.exolab.castor.xml.ValidationException
   {
-    return (jalview.schemabinding.version2.Colour) Unmarshaller.unmarshal(
-            jalview.schemabinding.version2.Colour.class, reader);
+    return (jalview.schemabinding.version2.Colour) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.Colour.class, reader);
   }
 
   /**