X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Fcore%2FScore.java;h=bf0ce88d4cf6fd2b88ea9b6335064bf13557f428;hb=844ccad5a3fcbedec17b2af66d460f31abc7cff1;hp=8448198457ffb2cf7581d849bd74e25db52e206a;hpb=ac12127b5cf22bb34b6042e543d506894164a94c;p=vamsas.git

diff --git a/src/uk/ac/vamsas/objects/core/Score.java b/src/uk/ac/vamsas/objects/core/Score.java
index 8448198..bf0ce88 100644
--- a/src/uk/ac/vamsas/objects/core/Score.java
+++ b/src/uk/ac/vamsas/objects/core/Score.java
@@ -1,252 +1,282 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * This file is part of the Vamsas Client version 0.1. 
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite, 
+ *  Andrew Waterhouse and Dominik Lindner.
+ * 
+ * Earlier versions have also been incorporated into Jalview version 2.4 
+ * since 2008, and TOPALi version 2 since 2007.
+ * 
+ * The Vamsas Client is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *  
+ * The Vamsas Client 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 Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the Vamsas Client.  If not, see <http://www.gnu.org/licenses/>.
  */
-
 package uk.ac.vamsas.objects.core;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
 
 /**
- * Ordered set of optionally named float values for the
- *  whole annotation 
+ * Ordered set of optionally named float values for the whole annotation
  * 
  * @version $Revision$ $Date$
  */
-public class Score extends uk.ac.vamsas.client.Vobject 
-implements java.io.Serializable
-{
+public class Score extends uk.ac.vamsas.client.Vobject implements
+    java.io.Serializable {
 
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
 
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
+  /**
+   * internal content storage
+   */
+  private float _content;
 
-    /**
-     * internal content storage
-     */
-    private float _content;
+  /**
+   * keeps track of state for field: _content
+   */
+  private boolean _has_content;
 
-    /**
-     * keeps track of state for field: _content
-     */
-    private boolean _has_content;
+  /**
+   * Field _name.
+   */
+  private java.lang.String _name = "score";
 
-    /**
-     * Field _name.
-     */
-    private java.lang.String _name = "score";
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
+  public Score() {
+    super();
+    setName("score");
+  }
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    public Score() {
-        super();
-        setName("score");
-    }
+  /**
+     */
+  public void deleteContent() {
+    this._has_content = false;
+  }
 
+  /**
+   * Overrides the java.lang.Object.equals method.
+   * 
+   * @param obj
+   * @return true if the objects are equal.
+   */
+  public boolean equals(final java.lang.Object obj) {
+    if (this == obj)
+      return true;
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+    if (super.equals(obj) == false)
+      return false;
 
-    /**
-     */
-    public void deleteContent(
-    ) {
-        this._has_content= false;
-    }
+    if (obj instanceof Score) {
 
-    /**
-     * Overrides the java.lang.Object.equals method.
-     * 
-     * @param obj
-     * @return true if the objects are equal.
-     */
-    public boolean equals(
-            final java.lang.Object obj) {
-        if ( this == obj )
-            return true;
-        
-        if (super.equals(obj)==false)
+      Score temp = (Score) obj;
+      boolean thcycle;
+      boolean tmcycle;
+      if (this._content != temp._content)
+        return false;
+      if (this._has_content != temp._has_content)
+        return false;
+      if (this._name != null) {
+        if (temp._name == null)
+          return false;
+        if (this._name != temp._name) {
+          thcycle = org.castor.util.CycleBreaker.startingToCycle(this._name);
+          tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._name);
+          if (thcycle != tmcycle) {
+            if (!thcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._name);
+            }
+            ;
+            if (!tmcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._name);
+            }
+            ;
             return false;
-        
-        if (obj instanceof Score) {
-        
-            Score temp = (Score)obj;
-            if (this._content != temp._content)
-                return false;
-            if (this._has_content != temp._has_content)
-                return false;
-            if (this._name != null) {
-                if (temp._name == null) return false;
-                else if (!(this._name.equals(temp._name))) 
-                    return false;
+          }
+          if (!thcycle) {
+            if (!this._name.equals(temp._name)) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._name);
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._name);
+              return false;
             }
-            else if (temp._name != null)
-                return false;
-            return true;
+            org.castor.util.CycleBreaker.releaseCycleHandle(this._name);
+            org.castor.util.CycleBreaker.releaseCycleHandle(temp._name);
+          }
         }
+      } else if (temp._name != null)
         return false;
+      return true;
     }
+    return false;
+  }
 
-    /**
-     * Returns the value of field 'content'. The field 'content'
-     * has the following description: internal content storage
-     * 
-     * @return the value of field 'Content'.
-     */
-    public float getContent(
-    ) {
-        return this._content;
-    }
+  /**
+   * Returns the value of field 'content'. The field 'content' has the following
+   * description: internal content storage
+   * 
+   * @return the value of field 'Content'.
+   */
+  public float getContent() {
+    return this._content;
+  }
 
-    /**
-     * Returns the value of field 'name'.
-     * 
-     * @return the value of field 'Name'.
-     */
-    public java.lang.String getName(
-    ) {
-        return this._name;
-    }
+  /**
+   * Returns the value of field 'name'.
+   * 
+   * @return the value of field 'Name'.
+   */
+  public java.lang.String getName() {
+    return this._name;
+  }
 
-    /**
-     * Method hasContent.
-     * 
-     * @return true if at least one Content has been added
-     */
-    public boolean hasContent(
-    ) {
-        return this._has_content;
-    }
+  /**
+   * Method hasContent.
+   * 
+   * @return true if at least one Content has been added
+   */
+  public boolean hasContent() {
+    return this._has_content;
+  }
 
-    /**
-     * Overrides the java.lang.Object.hashCode method.
-     * <p>
-     * The following steps came from <b>Effective Java Programming
-     * Language Guide</b> by Joshua Bloch, Chapter 3
-     * 
-     * @return a hash code value for the object.
-     */
-    public int hashCode(
-    ) {
-        int result = super.hashCode();
-        
-        long tmp;
-        result = 37 * result + java.lang.Float.floatToIntBits(_content);
-        if (_name != null) {
-           result = 37 * result + _name.hashCode();
-        }
-        
-        return result;
-    }
+  /**
+   * Overrides the java.lang.Object.hashCode method.
+   * <p>
+   * The following steps came from <b>Effective Java Programming Language
+   * Guide</b> by Joshua Bloch, Chapter 3
+   * 
+   * @return a hash code value for the object.
+   */
+  public int hashCode() {
+    int result = super.hashCode();
 
-    /**
-     * 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;
+    long tmp;
+    result = 37 * result + java.lang.Float.floatToIntBits(_content);
+    if (_name != null && !org.castor.util.CycleBreaker.startingToCycle(_name)) {
+      result = 37 * result + _name.hashCode();
+      org.castor.util.CycleBreaker.releaseCycleHandle(_name);
     }
 
-    /**
-     * 
-     * 
-     * @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);
-    }
+    return result;
+  }
 
-    /**
-     * 
-     * 
-     * @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);
+  /**
+   * 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;
+  }
 
-    /**
-     * Sets the value of field 'content'. The field 'content' has
-     * the following description: internal content storage
-     * 
-     * @param content the value of field 'content'.
-     */
-    public void setContent(
-            final float content) {
-        this._content = content;
-        this._has_content = 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);
+  }
 
-    /**
-     * Sets the value of field 'name'.
-     * 
-     * @param name the value of field 'name'.
-     */
-    public void setName(
-            final java.lang.String name) {
-        this._name = name;
-    }
+  /**
+   * 
+   * 
+   * @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);
+  }
 
-    /**
-     * 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 uk.ac.vamsas.objects.core.Score
-     */
-    public static uk.ac.vamsas.objects.core.Score unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (uk.ac.vamsas.objects.core.Score) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Score.class, reader);
-    }
+  /**
+   * Sets the value of field 'content'. The field 'content' has the following
+   * description: internal content storage
+   * 
+   * @param content
+   *          the value of field 'content'.
+   */
+  public void setContent(final float content) {
+    this._content = content;
+    this._has_content = true;
+  }
 
-    /**
-     * 
-     * 
-     * @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);
-    }
+  /**
+   * Sets the value of field 'name'.
+   * 
+   * @param name
+   *          the value of field 'name'.
+   */
+  public void setName(final java.lang.String name) {
+    this._name = name;
+  }
+
+  /**
+   * 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 uk.ac.vamsas.objects.core.Score
+   */
+  public static uk.ac.vamsas.objects.core.Score unmarshal(
+      final java.io.Reader reader)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException {
+    return (uk.ac.vamsas.objects.core.Score) Unmarshaller.unmarshal(
+        uk.ac.vamsas.objects.core.Score.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);
+  }
 
 }