X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FFeature.java;h=109ec6e49102a5e0c7edf36a375fa1af07d41e5c;hb=22d4d2237b099daf76bd1a2ed324763972ed91aa;hp=305e28750fbeeb2eb8454bcee6d4acb13d33d249;hpb=48df59aa393e03aa7269b2df662ac1b8d58cbb25;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/Feature.java b/src/jalview/schemabinding/version2/Feature.java
index 305e287..109ec6e 100755
--- a/src/jalview/schemabinding/version2/Feature.java
+++ b/src/jalview/schemabinding/version2/Feature.java
@@ -1,6 +1,6 @@
 /*
  * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
  * Schema.
  * $Id$
  */
@@ -11,17 +11,8 @@ package jalview.schemabinding.version2;
  //- 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 Feature.
@@ -36,7 +27,7 @@ public class Feature implements java.io.Serializable {
     //--------------------------/
 
     /**
-     * Field _begin
+     * Field _begin.
      */
     private int _begin;
 
@@ -46,7 +37,7 @@ public class Feature implements java.io.Serializable {
     private boolean _has_begin;
 
     /**
-     * Field _end
+     * Field _end.
      */
     private int _end;
 
@@ -56,27 +47,27 @@ public class Feature implements java.io.Serializable {
     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;
 
@@ -86,7 +77,7 @@ public class Feature implements java.io.Serializable {
     private boolean _has_score;
 
     /**
-     * Field _otherDataList
+     * Field _otherDataList.
      */
     private java.util.Vector _otherDataList;
 
@@ -97,8 +88,8 @@ public class Feature implements java.io.Serializable {
 
     public Feature() {
         super();
-        _otherDataList = new Vector();
-    } //-- jalview.schemabinding.version2.Feature()
+        this._otherDataList = new java.util.Vector();
+    }
 
 
       //-----------/
@@ -106,432 +97,423 @@ public class Feature implements java.io.Serializable {
     //-----------/
 
     /**
-     * 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
-    {
-        _otherDataList.addElement(vOtherData);
-    } //-- void addOtherData(jalview.schemabinding.version2.OtherData) 
+    public void addOtherData(
+            final jalview.schemabinding.version2.OtherData vOtherData)
+    throws java.lang.IndexOutOfBoundsException {
+        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
-    {
-        _otherDataList.insertElementAt(vOtherData, index);
-    } //-- void addOtherData(int, jalview.schemabinding.version2.OtherData) 
+    public void addOtherData(
+            final int index,
+            final jalview.schemabinding.version2.OtherData vOtherData)
+    throws java.lang.IndexOutOfBoundsException {
+        this._otherDataList.add(index, vOtherData);
+    }
 
     /**
-     * Method deleteBegin
-     * 
      */
-    public void deleteBegin()
-    {
+    public void deleteBegin(
+    ) {
         this._has_begin= false;
-    } //-- void deleteBegin() 
+    }
 
     /**
-     * Method deleteEnd
-     * 
      */
-    public void deleteEnd()
-    {
+    public void deleteEnd(
+    ) {
         this._has_end= false;
-    } //-- void deleteEnd() 
+    }
 
     /**
-     * Method deleteScore
-     * 
      */
-    public void deleteScore()
-    {
+    public void deleteScore(
+    ) {
         this._has_score= false;
-    } //-- void deleteScore() 
+    }
 
     /**
-     * Method enumerateOtherData
-     * 
+     * Method enumerateOtherData.
      * 
-     * 
-     * @return Enumeration
+     * @return an Enumeration over all
+     * jalview.schemabinding.version2.OtherData elements
      */
-    public java.util.Enumeration enumerateOtherData()
-    {
-        return _otherDataList.elements();
-    } //-- java.util.Enumeration enumerateOtherData() 
+    public 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()
-    {
+    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()
-    {
+    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()
-    {
+    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()
-    {
+    public java.lang.String getFeatureGroup(
+    ) {
         return this._featureGroup;
-    } //-- java.lang.String getFeatureGroup() 
+    }
 
     /**
-     * Method getOtherData
-     * 
-     * 
+     * Method getOtherData.
      * 
      * @param index
-     * @return OtherData
-     */
-    public jalview.schemabinding.version2.OtherData getOtherData(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _otherDataList.size())) {
-            throw new IndexOutOfBoundsException();
+     * @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(
+            final int index)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._otherDataList.size()) {
+            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
-     * 
-     * 
+     * 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 OtherData
+     * @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() 
+    public 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
-     * 
-     * 
+     * Method getOtherDataCount.
      * 
-     * @return int
+     * @return the size of this collection
      */
-    public int getOtherDataCount()
-    {
-        return _otherDataList.size();
-    } //-- int getOtherDataCount() 
+    public 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()
-    {
+    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()
-    {
+    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()
-    {
+    public java.lang.String getType(
+    ) {
         return this._type;
-    } //-- java.lang.String getType() 
+    }
 
     /**
-     * Method hasBegin
+     * Method hasBegin.
      * 
-     * 
-     * 
-     * @return boolean
+     * @return true if at least one Begin has been added
      */
-    public boolean hasBegin()
-    {
+    public boolean hasBegin(
+    ) {
         return this._has_begin;
-    } //-- boolean hasBegin() 
+    }
 
     /**
-     * Method hasEnd
-     * 
+     * Method hasEnd.
      * 
-     * 
-     * @return boolean
+     * @return true if at least one End has been added
      */
-    public boolean hasEnd()
-    {
+    public boolean hasEnd(
+    ) {
         return this._has_end;
-    } //-- boolean hasEnd() 
+    }
 
     /**
-     * Method hasScore
-     * 
-     * 
+     * Method hasScore.
      * 
-     * @return boolean
+     * @return true if at least one Score has been added
      */
-    public boolean hasScore()
-    {
+    public boolean hasScore(
+    ) {
         return this._has_score;
-    } //-- boolean hasScore() 
+    }
 
     /**
-     * Method isValid
-     * 
-     * 
+     * Method isValid.
      * 
-     * @return boolean
+     * @return true if this object is valid according to the schema
      */
-    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() 
+    }
 
     /**
-     * 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 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(
+            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() 
+    public void removeAllOtherData(
+    ) {
+        this._otherDataList.clear();
+    }
 
     /**
-     * Method removeOtherData
-     * 
+     * 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 removeOtherDataAt.
      * 
      * @param index
-     * @return OtherData
+     * @return the element removed from the collection
      */
-    public jalview.schemabinding.version2.OtherData removeOtherData(int index)
-    {
-        java.lang.Object obj = _otherDataList.elementAt(index);
-        _otherDataList.removeElementAt(index);
+    public jalview.schemabinding.version2.OtherData removeOtherDataAt(
+            final int 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'.
      */
-    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'.
      */
-    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'.
      */
-    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'.
      */
-    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
-     */
-    public void setOtherData(int index, jalview.schemabinding.version2.OtherData vOtherData)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _otherDataList.size())) {
-            throw new IndexOutOfBoundsException();
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void setOtherData(
+            final int index,
+            final jalview.schemabinding.version2.OtherData vOtherData)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._otherDataList.size()) {
+            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++) {
-            _otherDataList.addElement(otherDataArray[i]);
+        _otherDataList.clear();
+        
+        for (int i = 0; i < vOtherDataArray.length; 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'.
      */
-    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'.
      */
-    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'.
      */
-    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) 
+    }
 
     /**
-     * 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();
         validator.validate(this);
-    } //-- void validate() 
+    }
 
 }