applied LGPLv3 and source code formatting.
[vamsas.git] / src / uk / ac / vamsas / objects / core / AppData.java
index d54bca7..221aadd 100644 (file)
@@ -1,14 +1,28 @@
 /*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
- * Schema.\r
- * $Id$\r
+ * This file is part of the Vamsas Client version 0.1. \r
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite, \r
+ *  Andrew Waterhouse and Dominik Lindner.\r
+ * \r
+ * Earlier versions have also been incorporated into Jalview version 2.4 \r
+ * since 2008, and TOPALi version 2 since 2007.\r
+ * \r
+ * The Vamsas Client is free software: you can redistribute it and/or modify\r
+ * it under the terms of the GNU Lesser General Public License as published by\r
+ * the Free Software Foundation, either version 3 of the License, or\r
+ * (at your option) any later version.\r
+ *  \r
+ * The Vamsas Client is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+ * GNU Lesser General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU Lesser General Public License\r
+ * along with the Vamsas Client.  If not, see <http://www.gnu.org/licenses/>.\r
  */\r
-\r
 package uk.ac.vamsas.objects.core;\r
 \r
-  //---------------------------------/\r
- //- Imported classes and packages -/\r
+//---------------------------------/\r
+//- Imported classes and packages -/\r
 //---------------------------------/\r
 \r
 import org.exolab.castor.xml.Marshaller;\r
@@ -19,294 +33,320 @@ import org.exolab.castor.xml.Unmarshaller;
  * \r
  * @version $Revision$ $Date$\r
  */\r
-public class AppData extends uk.ac.vamsas.client.Vobject \r
-implements java.io.Serializable\r
-{\r
+public class AppData extends uk.ac.vamsas.client.Vobject implements\r
+    java.io.Serializable {\r
 \r
+  // --------------------------/\r
+  // - Class/Member Variables -/\r
+  // --------------------------/\r
 \r
-      //--------------------------/\r
-     //- Class/Member Variables -/\r
-    //--------------------------/\r
+  /**\r
+   * Internal choice value storage\r
+   */\r
+  private java.lang.Object _choiceValue;\r
 \r
-    /**\r
-     * Internal choice value storage\r
-     */\r
-    private java.lang.Object _choiceValue;\r
+  /**\r
+   * Field _data.\r
+   */\r
+  private byte[] _data;\r
 \r
-    /**\r
-     * Field _data.\r
-     */\r
-    private byte[] _data;\r
+  /**\r
+   * Field _dataReference.\r
+   */\r
+  private java.lang.String _dataReference;\r
 \r
-    /**\r
-     * Field _dataReference.\r
-     */\r
-    private java.lang.String _dataReference;\r
+  // ----------------/\r
+  // - Constructors -/\r
+  // ----------------/\r
 \r
+  public AppData() {\r
+    super();\r
+  }\r
 \r
-      //----------------/\r
-     //- Constructors -/\r
-    //----------------/\r
+  // -----------/\r
+  // - Methods -/\r
+  // -----------/\r
 \r
-    public AppData() {\r
-        super();\r
-    }\r
+  /**\r
+   * Overrides the java.lang.Object.equals method.\r
+   * \r
+   * @param obj\r
+   * @return true if the objects are equal.\r
+   */\r
+  public boolean equals(final java.lang.Object obj) {\r
+    if (this == obj)\r
+      return true;\r
 \r
+    if (super.equals(obj) == false)\r
+      return false;\r
 \r
-      //-----------/\r
-     //- Methods -/\r
-    //-----------/\r
+    if (obj instanceof AppData) {\r
 \r
-    /**\r
-     * Overrides the java.lang.Object.equals method.\r
-     * \r
-     * @param obj\r
-     * @return true if the objects are equal.\r
-     */\r
-    public boolean equals(\r
-            final java.lang.Object obj) {\r
-        if ( this == obj )\r
-            return true;\r
-        \r
-        if (super.equals(obj)==false)\r
+      AppData temp = (AppData) obj;\r
+      boolean thcycle;\r
+      boolean tmcycle;\r
+      if (this._choiceValue != null) {\r
+        if (temp._choiceValue == null)\r
+          return false;\r
+        if (this._choiceValue != temp._choiceValue) {\r
+          thcycle = org.castor.util.CycleBreaker\r
+              .startingToCycle(this._choiceValue);\r
+          tmcycle = org.castor.util.CycleBreaker\r
+              .startingToCycle(temp._choiceValue);\r
+          if (thcycle != tmcycle) {\r
+            if (!thcycle) {\r
+              org.castor.util.CycleBreaker\r
+                  .releaseCycleHandle(this._choiceValue);\r
+            }\r
+            ;\r
+            if (!tmcycle) {\r
+              org.castor.util.CycleBreaker\r
+                  .releaseCycleHandle(temp._choiceValue);\r
+            }\r
+            ;\r
             return false;\r
-        \r
-        if (obj instanceof AppData) {\r
-        \r
-            AppData temp = (AppData)obj;\r
-            boolean thcycle;\r
-            boolean tmcycle;\r
-            if (this._choiceValue != null) {\r
-                if (temp._choiceValue == null) return false;\r
-                if (this._choiceValue != temp._choiceValue) {\r
-                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._choiceValue);\r
-                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._choiceValue);\r
-                    if (thcycle!=tmcycle) {\r
-                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._choiceValue); };\r
-                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._choiceValue); };\r
-                        return false;\r
-                    }\r
-                    if (!thcycle) {\r
-                        if (!this._choiceValue.equals(temp._choiceValue)) {\r
-                            org.castor.util.CycleBreaker.releaseCycleHandle(this._choiceValue);\r
-                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._choiceValue);\r
-                            return false;\r
-                        }\r
-                        org.castor.util.CycleBreaker.releaseCycleHandle(this._choiceValue);\r
-                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._choiceValue);\r
-                    }\r
-                }\r
-            } else if (temp._choiceValue != null)\r
-                return false;\r
-            if (this._data != null) {\r
-                if (temp._data == null) return false;\r
-                if (this._data != temp._data) {\r
-                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._data);\r
-                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._data);\r
-                    if (thcycle!=tmcycle) {\r
-                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._data); };\r
-                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._data); };\r
-                        return false;\r
-                    }\r
-                    if (!thcycle) {\r
-                        if (!java.util.Arrays.equals(this._data, temp._data)) {\r
-                            org.castor.util.CycleBreaker.releaseCycleHandle(this._data);\r
-                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._data);\r
-                            return false;\r
-                        }\r
-                        org.castor.util.CycleBreaker.releaseCycleHandle(this._data);\r
-                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._data);\r
-                    }\r
-                }\r
-            } else if (temp._data != null)\r
-                return false;\r
-            if (this._dataReference != null) {\r
-                if (temp._dataReference == null) return false;\r
-                if (this._dataReference != temp._dataReference) {\r
-                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._dataReference);\r
-                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._dataReference);\r
-                    if (thcycle!=tmcycle) {\r
-                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._dataReference); };\r
-                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._dataReference); };\r
-                        return false;\r
-                    }\r
-                    if (!thcycle) {\r
-                        if (!this._dataReference.equals(temp._dataReference)) {\r
-                            org.castor.util.CycleBreaker.releaseCycleHandle(this._dataReference);\r
-                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._dataReference);\r
-                            return false;\r
-                        }\r
-                        org.castor.util.CycleBreaker.releaseCycleHandle(this._dataReference);\r
-                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._dataReference);\r
-                    }\r
-                }\r
-            } else if (temp._dataReference != null)\r
-                return false;\r
-            return true;\r
+          }\r
+          if (!thcycle) {\r
+            if (!this._choiceValue.equals(temp._choiceValue)) {\r
+              org.castor.util.CycleBreaker\r
+                  .releaseCycleHandle(this._choiceValue);\r
+              org.castor.util.CycleBreaker\r
+                  .releaseCycleHandle(temp._choiceValue);\r
+              return false;\r
+            }\r
+            org.castor.util.CycleBreaker.releaseCycleHandle(this._choiceValue);\r
+            org.castor.util.CycleBreaker.releaseCycleHandle(temp._choiceValue);\r
+          }\r
         }\r
+      } else if (temp._choiceValue != null)\r
         return false;\r
+      if (this._data != null) {\r
+        if (temp._data == null)\r
+          return false;\r
+        if (this._data != temp._data) {\r
+          thcycle = org.castor.util.CycleBreaker.startingToCycle(this._data);\r
+          tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._data);\r
+          if (thcycle != tmcycle) {\r
+            if (!thcycle) {\r
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._data);\r
+            }\r
+            ;\r
+            if (!tmcycle) {\r
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._data);\r
+            }\r
+            ;\r
+            return false;\r
+          }\r
+          if (!thcycle) {\r
+            if (!java.util.Arrays.equals(this._data, temp._data)) {\r
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._data);\r
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._data);\r
+              return false;\r
+            }\r
+            org.castor.util.CycleBreaker.releaseCycleHandle(this._data);\r
+            org.castor.util.CycleBreaker.releaseCycleHandle(temp._data);\r
+          }\r
+        }\r
+      } else if (temp._data != null)\r
+        return false;\r
+      if (this._dataReference != null) {\r
+        if (temp._dataReference == null)\r
+          return false;\r
+        if (this._dataReference != temp._dataReference) {\r
+          thcycle = org.castor.util.CycleBreaker\r
+              .startingToCycle(this._dataReference);\r
+          tmcycle = org.castor.util.CycleBreaker\r
+              .startingToCycle(temp._dataReference);\r
+          if (thcycle != tmcycle) {\r
+            if (!thcycle) {\r
+              org.castor.util.CycleBreaker\r
+                  .releaseCycleHandle(this._dataReference);\r
+            }\r
+            ;\r
+            if (!tmcycle) {\r
+              org.castor.util.CycleBreaker\r
+                  .releaseCycleHandle(temp._dataReference);\r
+            }\r
+            ;\r
+            return false;\r
+          }\r
+          if (!thcycle) {\r
+            if (!this._dataReference.equals(temp._dataReference)) {\r
+              org.castor.util.CycleBreaker\r
+                  .releaseCycleHandle(this._dataReference);\r
+              org.castor.util.CycleBreaker\r
+                  .releaseCycleHandle(temp._dataReference);\r
+              return false;\r
+            }\r
+            org.castor.util.CycleBreaker\r
+                .releaseCycleHandle(this._dataReference);\r
+            org.castor.util.CycleBreaker\r
+                .releaseCycleHandle(temp._dataReference);\r
+          }\r
+        }\r
+      } else if (temp._dataReference != null)\r
+        return false;\r
+      return true;\r
     }\r
+    return false;\r
+  }\r
 \r
-    /**\r
-     * Returns the value of field 'choiceValue'. The field\r
-     * 'choiceValue' has the following description: Internal choice\r
-     * value storage\r
-     * \r
-     * @return the value of field 'ChoiceValue'.\r
-     */\r
-    public java.lang.Object getChoiceValue(\r
-    ) {\r
-        return this._choiceValue;\r
-    }\r
+  /**\r
+   * Returns the value of field 'choiceValue'. The field 'choiceValue' has the\r
+   * following description: Internal choice value storage\r
+   * \r
+   * @return the value of field 'ChoiceValue'.\r
+   */\r
+  public java.lang.Object getChoiceValue() {\r
+    return this._choiceValue;\r
+  }\r
 \r
-    /**\r
-     * Returns the value of field 'data'.\r
-     * \r
-     * @return the value of field 'Data'.\r
-     */\r
-    public byte[] getData(\r
-    ) {\r
-        return this._data;\r
-    }\r
+  /**\r
+   * Returns the value of field 'data'.\r
+   * \r
+   * @return the value of field 'Data'.\r
+   */\r
+  public byte[] getData() {\r
+    return this._data;\r
+  }\r
 \r
-    /**\r
-     * Returns the value of field 'dataReference'.\r
-     * \r
-     * @return the value of field 'DataReference'.\r
-     */\r
-    public java.lang.String getDataReference(\r
-    ) {\r
-        return this._dataReference;\r
-    }\r
+  /**\r
+   * Returns the value of field 'dataReference'.\r
+   * \r
+   * @return the value of field 'DataReference'.\r
+   */\r
+  public java.lang.String getDataReference() {\r
+    return this._dataReference;\r
+  }\r
 \r
-    /**\r
-     * Overrides the java.lang.Object.hashCode method.\r
-     * <p>\r
-     * The following steps came from <b>Effective Java Programming\r
-     * Language Guide</b> by Joshua Bloch, Chapter 3\r
-     * \r
-     * @return a hash code value for the object.\r
-     */\r
-    public int hashCode(\r
-    ) {\r
-        int result = super.hashCode();\r
-        \r
-        long tmp;\r
-        if (_choiceValue != null\r
-            && !org.castor.util.CycleBreaker.startingToCycle(_choiceValue)) {\r
-           result = 37 * result + _choiceValue.hashCode();\r
-           org.castor.util.CycleBreaker.releaseCycleHandle(_choiceValue);\r
-        }\r
-        if (_data != null\r
-            && !org.castor.util.CycleBreaker.startingToCycle(_data)) {\r
-           result = 37 * result + _data.hashCode();\r
-           org.castor.util.CycleBreaker.releaseCycleHandle(_data);\r
-        }\r
-        if (_dataReference != null\r
-            && !org.castor.util.CycleBreaker.startingToCycle(_dataReference)) {\r
-           result = 37 * result + _dataReference.hashCode();\r
-           org.castor.util.CycleBreaker.releaseCycleHandle(_dataReference);\r
-        }\r
-        \r
-        return result;\r
-    }\r
+  /**\r
+   * Overrides the java.lang.Object.hashCode method.\r
+   * <p>\r
+   * The following steps came from <b>Effective Java Programming Language\r
+   * Guide</b> by Joshua Bloch, Chapter 3\r
+   * \r
+   * @return a hash code value for the object.\r
+   */\r
+  public int hashCode() {\r
+    int result = super.hashCode();\r
 \r
-    /**\r
-     * Method isValid.\r
-     * \r
-     * @return true if this object is valid according to the schema\r
-     */\r
-    public boolean isValid(\r
-    ) {\r
-        try {\r
-            validate();\r
-        } catch (org.exolab.castor.xml.ValidationException vex) {\r
-            return false;\r
-        }\r
-        return true;\r
+    long tmp;\r
+    if (_choiceValue != null\r
+        && !org.castor.util.CycleBreaker.startingToCycle(_choiceValue)) {\r
+      result = 37 * result + _choiceValue.hashCode();\r
+      org.castor.util.CycleBreaker.releaseCycleHandle(_choiceValue);\r
     }\r
-\r
-    /**\r
-     * \r
-     * \r
-     * @param out\r
-     * @throws org.exolab.castor.xml.MarshalException if object is\r
-     * null or if any SAXException is thrown during marshaling\r
-     * @throws org.exolab.castor.xml.ValidationException if this\r
-     * object is an invalid instance according to the schema\r
-     */\r
-    public void marshal(\r
-            final java.io.Writer out)\r
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
-        Marshaller.marshal(this, out);\r
+    if (_data != null && !org.castor.util.CycleBreaker.startingToCycle(_data)) {\r
+      result = 37 * result + _data.hashCode();\r
+      org.castor.util.CycleBreaker.releaseCycleHandle(_data);\r
     }\r
-\r
-    /**\r
-     * \r
-     * \r
-     * @param handler\r
-     * @throws java.io.IOException if an IOException occurs during\r
-     * marshaling\r
-     * @throws org.exolab.castor.xml.ValidationException if this\r
-     * object is an invalid instance according to the schema\r
-     * @throws org.exolab.castor.xml.MarshalException if object is\r
-     * null or if any SAXException is thrown during marshaling\r
-     */\r
-    public void marshal(\r
-            final org.xml.sax.ContentHandler handler)\r
-    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
-        Marshaller.marshal(this, handler);\r
+    if (_dataReference != null\r
+        && !org.castor.util.CycleBreaker.startingToCycle(_dataReference)) {\r
+      result = 37 * result + _dataReference.hashCode();\r
+      org.castor.util.CycleBreaker.releaseCycleHandle(_dataReference);\r
     }\r
 \r
-    /**\r
-     * Sets the value of field 'data'.\r
-     * \r
-     * @param data the value of field 'data'.\r
-     */\r
-    public void setData(\r
-            final byte[] data) {\r
-        this._data = data;\r
-        this._choiceValue = data;\r
-    }\r
+    return result;\r
+  }\r
 \r
-    /**\r
-     * Sets the value of field 'dataReference'.\r
-     * \r
-     * @param dataReference the value of field 'dataReference'.\r
-     */\r
-    public void setDataReference(\r
-            final java.lang.String dataReference) {\r
-        this._dataReference = dataReference;\r
-        this._choiceValue = dataReference;\r
+  /**\r
+   * Method isValid.\r
+   * \r
+   * @return true if this object is valid according to the schema\r
+   */\r
+  public boolean isValid() {\r
+    try {\r
+      validate();\r
+    } catch (org.exolab.castor.xml.ValidationException vex) {\r
+      return false;\r
     }\r
+    return true;\r
+  }\r
 \r
-    /**\r
-     * Method unmarshal.\r
-     * \r
-     * @param reader\r
-     * @throws org.exolab.castor.xml.MarshalException if object is\r
-     * null or if any SAXException is thrown during marshaling\r
-     * @throws org.exolab.castor.xml.ValidationException if this\r
-     * object is an invalid instance according to the schema\r
-     * @return the unmarshaled uk.ac.vamsas.objects.core.AppData\r
-     */\r
-    public static uk.ac.vamsas.objects.core.AppData unmarshal(\r
-            final java.io.Reader reader)\r
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
-        return (uk.ac.vamsas.objects.core.AppData) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.AppData.class, reader);\r
-    }\r
+  /**\r
+   * \r
+   * \r
+   * @param out\r
+   * @throws org.exolab.castor.xml.MarshalException\r
+   *           if object is null or if any SAXException is thrown during\r
+   *           marshaling\r
+   * @throws org.exolab.castor.xml.ValidationException\r
+   *           if this object is an invalid instance according to the schema\r
+   */\r
+  public void marshal(final java.io.Writer out)\r
+      throws org.exolab.castor.xml.MarshalException,\r
+      org.exolab.castor.xml.ValidationException {\r
+    Marshaller.marshal(this, out);\r
+  }\r
 \r
-    /**\r
-     * \r
-     * \r
-     * @throws org.exolab.castor.xml.ValidationException if this\r
-     * object is an invalid instance according to the schema\r
-     */\r
-    public void validate(\r
-    )\r
-    throws org.exolab.castor.xml.ValidationException {\r
-        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
-        validator.validate(this);\r
-    }\r
+  /**\r
+   * \r
+   * \r
+   * @param handler\r
+   * @throws java.io.IOException\r
+   *           if an IOException occurs during marshaling\r
+   * @throws org.exolab.castor.xml.ValidationException\r
+   *           if this object is an invalid instance according to the schema\r
+   * @throws org.exolab.castor.xml.MarshalException\r
+   *           if object is null or if any SAXException is thrown during\r
+   *           marshaling\r
+   */\r
+  public void marshal(final org.xml.sax.ContentHandler handler)\r
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
+      org.exolab.castor.xml.ValidationException {\r
+    Marshaller.marshal(this, handler);\r
+  }\r
+\r
+  /**\r
+   * Sets the value of field 'data'.\r
+   * \r
+   * @param data\r
+   *          the value of field 'data'.\r
+   */\r
+  public void setData(final byte[] data) {\r
+    this._data = data;\r
+    this._choiceValue = data;\r
+  }\r
+\r
+  /**\r
+   * Sets the value of field 'dataReference'.\r
+   * \r
+   * @param dataReference\r
+   *          the value of field 'dataReference'.\r
+   */\r
+  public void setDataReference(final java.lang.String dataReference) {\r
+    this._dataReference = dataReference;\r
+    this._choiceValue = dataReference;\r
+  }\r
+\r
+  /**\r
+   * Method unmarshal.\r
+   * \r
+   * @param reader\r
+   * @throws org.exolab.castor.xml.MarshalException\r
+   *           if object is null or if any SAXException is thrown during\r
+   *           marshaling\r
+   * @throws org.exolab.castor.xml.ValidationException\r
+   *           if this object is an invalid instance according to the schema\r
+   * @return the unmarshaled uk.ac.vamsas.objects.core.AppData\r
+   */\r
+  public static uk.ac.vamsas.objects.core.AppData unmarshal(\r
+      final java.io.Reader reader)\r
+      throws org.exolab.castor.xml.MarshalException,\r
+      org.exolab.castor.xml.ValidationException {\r
+    return (uk.ac.vamsas.objects.core.AppData) Unmarshaller.unmarshal(\r
+        uk.ac.vamsas.objects.core.AppData.class, reader);\r
+  }\r
+\r
+  /**\r
+   * \r
+   * \r
+   * @throws org.exolab.castor.xml.ValidationException\r
+   *           if this object is an invalid instance according to the schema\r
+   */\r
+  public void validate() throws org.exolab.castor.xml.ValidationException {\r
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+    validator.validate(this);\r
+  }\r
 \r
 }\r