X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FSequence.java;h=00b903941854c3bc0d95a082d57f59abe2477bdf;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=993ad23609b227ec32ae07d817e49cd2abed549c;hpb=48df59aa393e03aa7269b2df662ac1b8d58cbb25;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/Sequence.java b/src/jalview/schemabinding/version2/Sequence.java
old mode 100755
new mode 100644
index 993ad23..00b9039
--- a/src/jalview/schemabinding/version2/Sequence.java
+++ b/src/jalview/schemabinding/version2/Sequence.java
@@ -1,276 +1,339 @@
-/*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
- * Schema.
- * $Id$
- */
-
-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 Sequence.
- * 
- * @version $Revision$ $Date$
- */
-public class Sequence extends jalview.schemabinding.version2.SequenceType 
-implements java.io.Serializable
-{
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _DBRefList
-     */
-    private java.util.Vector _DBRefList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Sequence() {
-        super();
-        _DBRefList = new Vector();
-    } //-- jalview.schemabinding.version2.Sequence()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addDBRef
-     * 
-     * 
-     * 
-     * @param vDBRef
-     */
-    public void addDBRef(jalview.schemabinding.version2.DBRef vDBRef)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _DBRefList.addElement(vDBRef);
-    } //-- void addDBRef(jalview.schemabinding.version2.DBRef) 
-
-    /**
-     * Method addDBRef
-     * 
-     * 
-     * 
-     * @param index
-     * @param vDBRef
-     */
-    public void addDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _DBRefList.insertElementAt(vDBRef, index);
-    } //-- void addDBRef(int, jalview.schemabinding.version2.DBRef) 
-
-    /**
-     * Method enumerateDBRef
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateDBRef()
-    {
-        return _DBRefList.elements();
-    } //-- java.util.Enumeration enumerateDBRef() 
-
-    /**
-     * Method getDBRef
-     * 
-     * 
-     * 
-     * @param index
-     * @return DBRef
-     */
-    public jalview.schemabinding.version2.DBRef getDBRef(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _DBRefList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.schemabinding.version2.DBRef) _DBRefList.elementAt(index);
-    } //-- jalview.schemabinding.version2.DBRef getDBRef(int) 
-
-    /**
-     * Method getDBRef
-     * 
-     * 
-     * 
-     * @return DBRef
-     */
-    public jalview.schemabinding.version2.DBRef[] getDBRef()
-    {
-        int size = _DBRefList.size();
-        jalview.schemabinding.version2.DBRef[] mArray = new jalview.schemabinding.version2.DBRef[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.schemabinding.version2.DBRef) _DBRefList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.schemabinding.version2.DBRef[] getDBRef() 
-
-    /**
-     * Method getDBRefCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getDBRefCount()
-    {
-        return _DBRefList.size();
-    } //-- int getDBRefCount() 
-
-    /**
-     * Method isValid
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean isValid()
-    {
-        try {
-            validate();
-        }
-        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
-    {
-        
-        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
-    {
-        
-        Marshaller.marshal(this, handler);
-    } //-- void marshal(org.xml.sax.ContentHandler) 
-
-    /**
-     * Method removeAllDBRef
-     * 
-     */
-    public void removeAllDBRef()
-    {
-        _DBRefList.removeAllElements();
-    } //-- void removeAllDBRef() 
-
-    /**
-     * Method removeDBRef
-     * 
-     * 
-     * 
-     * @param index
-     * @return DBRef
-     */
-    public jalview.schemabinding.version2.DBRef removeDBRef(int index)
-    {
-        java.lang.Object obj = _DBRefList.elementAt(index);
-        _DBRefList.removeElementAt(index);
-        return (jalview.schemabinding.version2.DBRef) obj;
-    } //-- jalview.schemabinding.version2.DBRef removeDBRef(int) 
-
-    /**
-     * Method setDBRef
-     * 
-     * 
-     * 
-     * @param index
-     * @param vDBRef
-     */
-    public void setDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _DBRefList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _DBRefList.setElementAt(vDBRef, index);
-    } //-- void setDBRef(int, jalview.schemabinding.version2.DBRef) 
-
-    /**
-     * Method setDBRef
-     * 
-     * 
-     * 
-     * @param DBRefArray
-     */
-    public void setDBRef(jalview.schemabinding.version2.DBRef[] DBRefArray)
-    {
-        //-- copy array
-        _DBRefList.removeAllElements();
-        for (int i = 0; i < DBRefArray.length; i++) {
-            _DBRefList.addElement(DBRefArray[i]);
-        }
-    } //-- void setDBRef(jalview.schemabinding.version2.DBRef) 
-
-    /**
-     * 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
-    {
-        return (jalview.schemabinding.version2.Sequence) Unmarshaller.unmarshal(jalview.schemabinding.version2.Sequence.class, reader);
-    } //-- java.lang.Object unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
-     */
-    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() 
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class Sequence.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class Sequence extends jalview.schemabinding.version2.SequenceType
+        implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * dataset sequence id for this sequence. Will be created as union of
+   * sequences.
+   * 
+   */
+  private java.lang.String _dsseqid;
+
+  /**
+   * Field _DBRefList.
+   */
+  private java.util.Vector _DBRefList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Sequence()
+  {
+    super();
+    this._DBRefList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vDBRef
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addDBRef(final jalview.schemabinding.version2.DBRef vDBRef)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._DBRefList.addElement(vDBRef);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vDBRef
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addDBRef(final int index,
+          final jalview.schemabinding.version2.DBRef vDBRef)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._DBRefList.add(index, vDBRef);
+  }
+
+  /**
+   * Method enumerateDBRef.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.DBRef
+   *         elements
+   */
+  public java.util.Enumeration enumerateDBRef()
+  {
+    return this._DBRefList.elements();
+  }
+
+  /**
+   * Method getDBRef.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.DBRef at the given
+   *         index
+   */
+  public jalview.schemabinding.version2.DBRef getDBRef(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._DBRefList.size())
+    {
+      throw new IndexOutOfBoundsException("getDBRef: Index value '" + index
+              + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.DBRef) _DBRefList.get(index);
+  }
+
+  /**
+   * Method getDBRef.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.DBRef[] getDBRef()
+  {
+    jalview.schemabinding.version2.DBRef[] array = new jalview.schemabinding.version2.DBRef[0];
+    return (jalview.schemabinding.version2.DBRef[]) this._DBRefList
+            .toArray(array);
+  }
+
+  /**
+   * Method getDBRefCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getDBRefCount()
+  {
+    return this._DBRefList.size();
+  }
+
+  /**
+   * Returns the value of field 'dsseqid'. The field 'dsseqid' has the following
+   * description: dataset sequence id for this sequence. Will be created as
+   * union of sequences.
+   * 
+   * 
+   * @return the value of field 'Dsseqid'.
+   */
+  public java.lang.String getDsseqid()
+  {
+    return this._dsseqid;
+  }
+
+  /**
+   * 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)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @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(final java.io.Writer out)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @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(final org.xml.sax.ContentHandler handler)
+          throws java.io.IOException,
+          org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
+     */
+  public void removeAllDBRef()
+  {
+    this._DBRefList.clear();
+  }
+
+  /**
+   * Method removeDBRef.
+   * 
+   * @param vDBRef
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeDBRef(
+          final jalview.schemabinding.version2.DBRef vDBRef)
+  {
+    boolean removed = _DBRefList.remove(vDBRef);
+    return removed;
+  }
+
+  /**
+   * Method removeDBRefAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.DBRef removeDBRefAt(final int index)
+  {
+    java.lang.Object obj = this._DBRefList.remove(index);
+    return (jalview.schemabinding.version2.DBRef) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vDBRef
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setDBRef(final int index,
+          final jalview.schemabinding.version2.DBRef vDBRef)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._DBRefList.size())
+    {
+      throw new IndexOutOfBoundsException("setDBRef: Index value '" + index
+              + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");
+    }
+
+    this._DBRefList.set(index, vDBRef);
+  }
+
+  /**
+   * 
+   * 
+   * @param vDBRefArray
+   */
+  public void setDBRef(
+          final jalview.schemabinding.version2.DBRef[] vDBRefArray)
+  {
+    // -- copy array
+    _DBRefList.clear();
+
+    for (int i = 0; i < vDBRefArray.length; i++)
+    {
+      this._DBRefList.add(vDBRefArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of field 'dsseqid'. The field 'dsseqid' has the following
+   * description: dataset sequence id for this sequence. Will be created as
+   * union of sequences.
+   * 
+   * 
+   * @param dsseqid
+   *          the value of field 'dsseqid'.
+   */
+  public void setDsseqid(final java.lang.String dsseqid)
+  {
+    this._dsseqid = dsseqid;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @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.SequenceType
+   */
+  public static jalview.schemabinding.version2.SequenceType unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.SequenceType) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.Sequence.class,
+                    reader);
+  }
+
+  /**
+   * 
+   * 
+   * @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
+  {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
+
+}