X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FFeature.java;h=a5a4944d418aaf5005d56b5f178f8781648173a8;hb=46ca91c8b2a49f1d2f80b6823ade9f1c29c4121c;hp=2f7f2fae7ec8ebea17fdd96f70135a85bef29323;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/Feature.java b/src/jalview/schemabinding/version2/Feature.java
index 2f7f2fa..a5a4944 100755
--- a/src/jalview/schemabinding/version2/Feature.java
+++ b/src/jalview/schemabinding/version2/Feature.java
@@ -1,35 +1,43 @@
 /*
- * 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 Feature.
- *
+ * 
  * @version $Revision$ $Date$
  */
-public class Feature
-    implements java.io.Serializable
+public class Feature implements java.io.Serializable
 {
 
-  //--------------------------/
-  //- Class/Member Variables -/
-  //--------------------------/
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
 
   /**
-   * Field _begin
+   * Field _begin.
    */
   private int _begin;
 
@@ -39,7 +47,7 @@ public class Feature
   private boolean _has_begin;
 
   /**
-   * Field _end
+   * Field _end.
    */
   private int _end;
 
@@ -49,27 +57,27 @@ public class Feature
   private boolean _has_end;
 
   /**
-   * Field _type
+   * Field _type.
    */
   private java.lang.String _type;
 
   /**
-   * Field _description
+   * Field _description.
    */
   private java.lang.String _description;
 
   /**
-   * Field _status
+   * Field _status.
    */
   private java.lang.String _status;
 
   /**
-   * Field _featureGroup
+   * Field _featureGroup.
    */
   private java.lang.String _featureGroup;
 
   /**
-   * Field _score
+   * Field _score.
    */
   private float _score;
 
@@ -79,468 +87,472 @@ public class Feature
   private boolean _has_score;
 
   /**
-   * Field _otherDataList
+   * Field _otherDataList.
    */
   private java.util.Vector _otherDataList;
 
-  //----------------/
-  //- Constructors -/
-  //----------------/
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
   public Feature()
   {
     super();
-    _otherDataList = new Vector();
-  } //-- jalview.schemabinding.version2.Feature()
+    this._otherDataList = new java.util.Vector();
+  }
 
-  //-----------/
-  //- Methods -/
-  //-----------/
+  // -----------/
+  // - Methods -/
+  // -----------/
 
   /**
-   * Method addOtherData
-   *
-   *
-   *
+   * 
+   * 
    * @param vOtherData
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
    */
-  public void addOtherData(jalview.schemabinding.version2.OtherData vOtherData)
-      throws java.lang.IndexOutOfBoundsException
+  public void addOtherData(
+          final jalview.schemabinding.version2.OtherData vOtherData)
+          throws java.lang.IndexOutOfBoundsException
   {
-    _otherDataList.addElement(vOtherData);
-  } //-- void addOtherData(jalview.schemabinding.version2.OtherData)
+    this._otherDataList.addElement(vOtherData);
+  }
 
   /**
-   * Method addOtherData
-   *
-   *
-   *
+   * 
+   * 
    * @param index
    * @param vOtherData
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
    */
-  public void addOtherData(int index,
-                           jalview.schemabinding.version2.OtherData vOtherData)
-      throws java.lang.IndexOutOfBoundsException
+  public void addOtherData(final int index,
+          final jalview.schemabinding.version2.OtherData vOtherData)
+          throws java.lang.IndexOutOfBoundsException
   {
-    _otherDataList.insertElementAt(vOtherData, index);
-  } //-- void addOtherData(int, jalview.schemabinding.version2.OtherData)
+    this._otherDataList.add(index, vOtherData);
+  }
 
   /**
-   * Method deleteBegin
-   *
-   */
+     */
   public void deleteBegin()
   {
     this._has_begin = false;
-  } //-- void deleteBegin()
+  }
 
   /**
-   * Method deleteEnd
-   *
-   */
+     */
   public void deleteEnd()
   {
     this._has_end = false;
-  } //-- void deleteEnd()
+  }
 
   /**
-   * Method deleteScore
-   *
-   */
+     */
   public void deleteScore()
   {
     this._has_score = false;
-  } //-- void deleteScore()
+  }
 
   /**
-   * Method enumerateOtherData
-   *
-   *
-   *
-   * @return Enumeration
+   * Method enumerateOtherData.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.OtherData
+   *         elements
    */
   public java.util.Enumeration enumerateOtherData()
   {
-    return _otherDataList.elements();
-  } //-- java.util.Enumeration enumerateOtherData()
+    return this._otherDataList.elements();
+  }
 
   /**
    * Returns the value of field 'begin'.
-   *
-   * @return int
-   * @return the value of field 'begin'.
+   * 
+   * @return the value of field 'Begin'.
    */
   public int getBegin()
   {
     return this._begin;
-  } //-- int getBegin()
+  }
 
   /**
    * Returns the value of field 'description'.
-   *
-   * @return String
-   * @return the value of field 'description'.
+   * 
+   * @return the value of field 'Description'.
    */
   public java.lang.String getDescription()
   {
     return this._description;
-  } //-- java.lang.String getDescription()
+  }
 
   /**
    * Returns the value of field 'end'.
-   *
-   * @return int
-   * @return the value of field 'end'.
+   * 
+   * @return the value of field 'End'.
    */
   public int getEnd()
   {
     return this._end;
-  } //-- int getEnd()
+  }
 
   /**
    * Returns the value of field 'featureGroup'.
-   *
-   * @return String
-   * @return the value of field 'featureGroup'.
+   * 
+   * @return the value of field 'FeatureGroup'.
    */
   public java.lang.String getFeatureGroup()
   {
     return this._featureGroup;
-  } //-- java.lang.String getFeatureGroup()
+  }
 
   /**
-   * Method getOtherData
-   *
-   *
-   *
+   * Method getOtherData.
+   * 
    * @param index
-   * @return OtherData
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.OtherData at the
+   *         given index
    */
-  public jalview.schemabinding.version2.OtherData getOtherData(int index)
-      throws java.lang.IndexOutOfBoundsException
+  public jalview.schemabinding.version2.OtherData getOtherData(
+          final int index) throws java.lang.IndexOutOfBoundsException
   {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _otherDataList.size()))
+    // check bounds for index
+    if (index < 0 || index >= this._otherDataList.size())
     {
-      throw new IndexOutOfBoundsException();
+      throw new IndexOutOfBoundsException("getOtherData: Index value '"
+              + index + "' not in range [0.."
+              + (this._otherDataList.size() - 1) + "]");
     }
 
-    return (jalview.schemabinding.version2.OtherData) _otherDataList.elementAt(
-        index);
-  } //-- jalview.schemabinding.version2.OtherData getOtherData(int)
+    return (jalview.schemabinding.version2.OtherData) _otherDataList
+            .get(index);
+  }
 
   /**
-   * Method getOtherData
-   *
-   *
-   *
-   * @return OtherData
+   * Method getOtherData.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.OtherData[] getOtherData()
   {
-    int size = _otherDataList.size();
-    jalview.schemabinding.version2.OtherData[] mArray = new jalview.
-        schemabinding.version2.OtherData[size];
-    for (int index = 0; index < size; index++)
-    {
-      mArray[index] = (jalview.schemabinding.version2.OtherData) _otherDataList.
-          elementAt(index);
-    }
-    return mArray;
-  } //-- jalview.schemabinding.version2.OtherData[] getOtherData()
+    jalview.schemabinding.version2.OtherData[] array = new jalview.schemabinding.version2.OtherData[0];
+    return (jalview.schemabinding.version2.OtherData[]) this._otherDataList
+            .toArray(array);
+  }
 
   /**
-   * Method getOtherDataCount
-   *
-   *
-   *
-   * @return int
+   * Method getOtherDataCount.
+   * 
+   * @return the size of this collection
    */
   public int getOtherDataCount()
   {
-    return _otherDataList.size();
-  } //-- int getOtherDataCount()
+    return this._otherDataList.size();
+  }
 
   /**
    * Returns the value of field 'score'.
-   *
-   * @return float
-   * @return the value of field 'score'.
+   * 
+   * @return the value of field 'Score'.
    */
   public float getScore()
   {
     return this._score;
-  } //-- float getScore()
+  }
 
   /**
    * Returns the value of field 'status'.
-   *
-   * @return String
-   * @return the value of field 'status'.
+   * 
+   * @return the value of field 'Status'.
    */
   public java.lang.String getStatus()
   {
     return this._status;
-  } //-- java.lang.String getStatus()
+  }
 
   /**
    * Returns the value of field 'type'.
-   *
-   * @return String
-   * @return the value of field 'type'.
+   * 
+   * @return the value of field 'Type'.
    */
   public java.lang.String getType()
   {
     return this._type;
-  } //-- java.lang.String getType()
+  }
 
   /**
-   * Method hasBegin
-   *
-   *
-   *
-   * @return boolean
+   * Method hasBegin.
+   * 
+   * @return true if at least one Begin has been added
    */
   public boolean hasBegin()
   {
     return this._has_begin;
-  } //-- boolean hasBegin()
+  }
 
   /**
-   * Method hasEnd
-   *
-   *
-   *
-   * @return boolean
+   * Method hasEnd.
+   * 
+   * @return true if at least one End has been added
    */
   public boolean hasEnd()
   {
     return this._has_end;
-  } //-- boolean hasEnd()
+  }
 
   /**
-   * Method hasScore
-   *
-   *
-   *
-   * @return boolean
+   * Method hasScore.
+   * 
+   * @return true if at least one Score has been added
    */
   public boolean hasScore()
   {
     return this._has_score;
-  } //-- boolean hasScore()
+  }
 
   /**
-   * Method isValid
-   *
-   *
-   *
-   * @return boolean
+   * 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
-   */
-  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
+   *           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(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 removeAllOtherData
-   *
-   */
+     */
   public void removeAllOtherData()
   {
-    _otherDataList.removeAllElements();
-  } //-- void removeAllOtherData()
+    this._otherDataList.clear();
+  }
+
+  /**
+   * Method removeOtherData.
+   * 
+   * @param vOtherData
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeOtherData(
+          final jalview.schemabinding.version2.OtherData vOtherData)
+  {
+    boolean removed = _otherDataList.remove(vOtherData);
+    return removed;
+  }
 
   /**
-   * Method removeOtherData
-   *
-   *
-   *
+   * Method removeOtherDataAt.
+   * 
    * @param index
-   * @return OtherData
+   * @return the element removed from the collection
    */
-  public jalview.schemabinding.version2.OtherData removeOtherData(int index)
+  public jalview.schemabinding.version2.OtherData removeOtherDataAt(
+          final int index)
   {
-    java.lang.Object obj = _otherDataList.elementAt(index);
-    _otherDataList.removeElementAt(index);
+    java.lang.Object obj = this._otherDataList.remove(index);
     return (jalview.schemabinding.version2.OtherData) obj;
-  } //-- jalview.schemabinding.version2.OtherData removeOtherData(int)
+  }
 
   /**
    * Sets the value of field 'begin'.
-   *
-   * @param begin the value of field 'begin'.
+   * 
+   * @param begin
+   *          the value of field 'begin'.
    */
-  public void setBegin(int begin)
+  public void setBegin(final int begin)
   {
     this._begin = begin;
     this._has_begin = true;
-  } //-- void setBegin(int)
+  }
 
   /**
    * Sets the value of field 'description'.
-   *
-   * @param description the value of field 'description'.
+   * 
+   * @param description
+   *          the value of field 'description'.
    */
-  public void setDescription(java.lang.String description)
+  public void setDescription(final java.lang.String description)
   {
     this._description = description;
-  } //-- void setDescription(java.lang.String)
+  }
 
   /**
    * Sets the value of field 'end'.
-   *
-   * @param end the value of field 'end'.
+   * 
+   * @param end
+   *          the value of field 'end'.
    */
-  public void setEnd(int end)
+  public void setEnd(final int end)
   {
     this._end = end;
     this._has_end = true;
-  } //-- void setEnd(int)
+  }
 
   /**
    * Sets the value of field 'featureGroup'.
-   *
-   * @param featureGroup the value of field 'featureGroup'.
+   * 
+   * @param featureGroup
+   *          the value of field 'featureGroup'.
    */
-  public void setFeatureGroup(java.lang.String featureGroup)
+  public void setFeatureGroup(final java.lang.String featureGroup)
   {
     this._featureGroup = featureGroup;
-  } //-- void setFeatureGroup(java.lang.String)
+  }
 
   /**
-   * Method setOtherData
-   *
-   *
-   *
+   * 
+   * 
    * @param index
    * @param vOtherData
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
    */
-  public void setOtherData(int index,
-                           jalview.schemabinding.version2.OtherData vOtherData)
-      throws java.lang.IndexOutOfBoundsException
+  public void setOtherData(final int index,
+          final jalview.schemabinding.version2.OtherData vOtherData)
+          throws java.lang.IndexOutOfBoundsException
   {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _otherDataList.size()))
+    // check bounds for index
+    if (index < 0 || index >= this._otherDataList.size())
     {
-      throw new IndexOutOfBoundsException();
+      throw new IndexOutOfBoundsException("setOtherData: Index value '"
+              + index + "' not in range [0.."
+              + (this._otherDataList.size() - 1) + "]");
     }
-    _otherDataList.setElementAt(vOtherData, index);
-  } //-- void setOtherData(int, jalview.schemabinding.version2.OtherData)
+
+    this._otherDataList.set(index, vOtherData);
+  }
 
   /**
-   * Method setOtherData
-   *
-   *
-   *
-   * @param otherDataArray
+   * 
+   * 
+   * @param vOtherDataArray
    */
-  public void setOtherData(jalview.schemabinding.version2.OtherData[]
-                           otherDataArray)
+  public void setOtherData(
+          final jalview.schemabinding.version2.OtherData[] vOtherDataArray)
   {
-    //-- copy array
-    _otherDataList.removeAllElements();
-    for (int i = 0; i < otherDataArray.length; i++)
+    // -- copy array
+    _otherDataList.clear();
+
+    for (int i = 0; i < vOtherDataArray.length; i++)
     {
-      _otherDataList.addElement(otherDataArray[i]);
+      this._otherDataList.add(vOtherDataArray[i]);
     }
-  } //-- void setOtherData(jalview.schemabinding.version2.OtherData)
+  }
 
   /**
    * Sets the value of field 'score'.
-   *
-   * @param score the value of field 'score'.
+   * 
+   * @param score
+   *          the value of field 'score'.
    */
-  public void setScore(float score)
+  public void setScore(final float score)
   {
     this._score = score;
     this._has_score = true;
-  } //-- void setScore(float)
+  }
 
   /**
    * Sets the value of field 'status'.
-   *
-   * @param status the value of field 'status'.
+   * 
+   * @param status
+   *          the value of field 'status'.
    */
-  public void setStatus(java.lang.String status)
+  public void setStatus(final java.lang.String status)
   {
     this._status = status;
-  } //-- void setStatus(java.lang.String)
+  }
 
   /**
    * Sets the value of field 'type'.
-   *
-   * @param type the value of field 'type'.
+   * 
+   * @param type
+   *          the value of field 'type'.
    */
-  public void setType(java.lang.String type)
+  public void setType(final java.lang.String type)
   {
     this._type = type;
-  } //-- void setType(java.lang.String)
+  }
 
   /**
-   * Method unmarshal
-   *
-   *
-   *
+   * 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
+   *           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.Featur
+   */
+  public static jalview.schemabinding.version2.Feature unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
   {
     return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(
-        jalview.schemabinding.version2.Feature.class, reader);
-  } //-- java.lang.Object unmarshal(java.io.Reader)
+            jalview.schemabinding.version2.Feature.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()
+  }
 
 }