X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Fcore%2FAttachment.java;h=10b36ecc532bdd85ac8a89055c51cd03692e25e6;hb=844ccad5a3fcbedec17b2af66d460f31abc7cff1;hp=7b6fcc4971a9e79236eb06355b361ce2c3c678fe;hpb=ac12127b5cf22bb34b6042e543d506894164a94c;p=vamsas.git

diff --git a/src/uk/ac/vamsas/objects/core/Attachment.java b/src/uk/ac/vamsas/objects/core/Attachment.java
index 7b6fcc4..10b36ec 100644
--- a/src/uk/ac/vamsas/objects/core/Attachment.java
+++ b/src/uk/ac/vamsas/objects/core/Attachment.java
@@ -1,14 +1,28 @@
 /*
- * 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;
@@ -19,341 +33,394 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Attachment extends uk.ac.vamsas.objects.core.AppData 
-implements java.io.Serializable
-{
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * true implies data will be decompresses with Zip
-     *  before presenting to application 
-     */
-    private boolean _compressed = false;
-
-    /**
-     * keeps track of state for field: _compressed
-     */
-    private boolean _has_compressed;
-
-    /**
-     * Type of arbitrary data - TODO: decide format - use
-     *  (extended) MIME types ? 
-     */
-    private java.lang.String _type;
-
-    /**
-     * Object the arbitrary data is associated with
-     *  
+public class Attachment extends uk.ac.vamsas.objects.core.AppData implements
+    java.io.Serializable {
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * true implies data will be decompresses with Zip before presenting to
+   * application
+   */
+  private boolean _compressed = false;
+
+  /**
+   * keeps track of state for field: _compressed
+   */
+  private boolean _has_compressed;
+
+  /**
+   * Type of arbitrary data - TODO: decide format - use (extended) MIME types ?
+   */
+  private java.lang.String _type;
+
+  /**
+   * Object the arbitrary data is associated with
+   * 
+   */
+  private java.lang.Object _objectref;
+
+  /**
+   * Primary Key for vamsas object referencing
+   * 
+   */
+  private java.lang.String _id;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Attachment() {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
      */
-    private java.lang.Object _objectref;
-
-    /**
-     * Primary Key for vamsas object referencing
-     *  
-     */
-    private java.lang.String _id;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Attachment() {
-        super();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteCompressed(
-    ) {
-        this._has_compressed= 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;
-        
-        if (super.equals(obj)==false)
-            return false;
-        
-        if (obj instanceof Attachment) {
-        
-            Attachment temp = (Attachment)obj;
-            if (this._compressed != temp._compressed)
-                return false;
-            if (this._has_compressed != temp._has_compressed)
-                return false;
-            if (this._type != null) {
-                if (temp._type == null) return false;
-                else if (!(this._type.equals(temp._type))) 
-                    return false;
+  public void deleteCompressed() {
+    this._has_compressed = 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;
+
+    if (super.equals(obj) == false)
+      return false;
+
+    if (obj instanceof Attachment) {
+
+      Attachment temp = (Attachment) obj;
+      boolean thcycle;
+      boolean tmcycle;
+      if (this._compressed != temp._compressed)
+        return false;
+      if (this._has_compressed != temp._has_compressed)
+        return false;
+      if (this._type != null) {
+        if (temp._type == null)
+          return false;
+        if (this._type != temp._type) {
+          thcycle = org.castor.util.CycleBreaker.startingToCycle(this._type);
+          tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._type);
+          if (thcycle != tmcycle) {
+            if (!thcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._type);
             }
-            else if (temp._type != null)
-                return false;
-            if (this._objectref != null) {
-                if (temp._objectref == null) return false;
-                else if (!(this._objectref.equals(temp._objectref))) 
-                    return false;
+            ;
+            if (!tmcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._type);
             }
-            else if (temp._objectref != null)
-                return false;
-            if (this._id != null) {
-                if (temp._id == null) return false;
-                else if (!(this._id.equals(temp._id))) 
-                    return false;
+            ;
+            return false;
+          }
+          if (!thcycle) {
+            if (!this._type.equals(temp._type)) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._type);
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._type);
+              return false;
             }
-            else if (temp._id != null)
-                return false;
-            return true;
+            org.castor.util.CycleBreaker.releaseCycleHandle(this._type);
+            org.castor.util.CycleBreaker.releaseCycleHandle(temp._type);
+          }
         }
+      } else if (temp._type != null)
         return false;
-    }
-
-    /**
-     * Returns the value of field 'compressed'. The field
-     * 'compressed' has the following description: true implies
-     * data will be decompresses with Zip
-     *  before presenting to application 
-     * 
-     * @return the value of field 'Compressed'.
-     */
-    public boolean getCompressed(
-    ) {
-        return this._compressed;
-    }
-
-    /**
-     * Returns the value of field 'id'. The field 'id' has the
-     * following description: Primary Key for vamsas object
-     * referencing
-     *  
-     * 
-     * @return the value of field 'Id'.
-     */
-    public java.lang.String getId(
-    ) {
-        return this._id;
-    }
-
-    /**
-     * Returns the value of field 'objectref'. The field
-     * 'objectref' has the following description: Object the
-     * arbitrary data is associated with
-     *  
-     * 
-     * @return the value of field 'Objectref'.
-     */
-    public java.lang.Object getObjectref(
-    ) {
-        return this._objectref;
-    }
-
-    /**
-     * Returns the value of field 'type'. The field 'type' has the
-     * following description: Type of arbitrary data - TODO: decide
-     * format - use
-     *  (extended) MIME types ? 
-     * 
-     * @return the value of field 'Type'.
-     */
-    public java.lang.String getType(
-    ) {
-        return this._type;
-    }
-
-    /**
-     * Method hasCompressed.
-     * 
-     * @return true if at least one Compressed has been added
-     */
-    public boolean hasCompressed(
-    ) {
-        return this._has_compressed;
-    }
-
-    /**
-     * 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 + (_compressed?0:1);
-        if (_type != null) {
-           result = 37 * result + _type.hashCode();
-        }
-        if (_objectref != null) {
-           result = 37 * result + _objectref.hashCode();
-        }
-        if (_id != null) {
-           result = 37 * result + _id.hashCode();
+      if (this._objectref != null) {
+        if (temp._objectref == null)
+          return false;
+        if (this._objectref != temp._objectref) {
+          thcycle = org.castor.util.CycleBreaker
+              .startingToCycle(this._objectref);
+          tmcycle = org.castor.util.CycleBreaker
+              .startingToCycle(temp._objectref);
+          if (thcycle != tmcycle) {
+            if (!thcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._objectref);
+            }
+            ;
+            if (!tmcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._objectref);
+            }
+            ;
+            return false;
+          }
+          if (!thcycle) {
+            if (!this._objectref.equals(temp._objectref)) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._objectref);
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._objectref);
+              return false;
+            }
+            org.castor.util.CycleBreaker.releaseCycleHandle(this._objectref);
+            org.castor.util.CycleBreaker.releaseCycleHandle(temp._objectref);
+          }
         }
-        
-        return result;
-    }
-
-    /**
-     * Returns the value of field 'compressed'. The field
-     * 'compressed' has the following description: true implies
-     * data will be decompresses with Zip
-     *  before presenting to application 
-     * 
-     * @return the value of field 'Compressed'.
-     */
-    public boolean isCompressed(
-    ) {
-        return this._compressed;
-    }
-
-    /**
-     * 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) {
+      } else if (temp._objectref != null)
+        return false;
+      if (this._id != null) {
+        if (temp._id == null)
+          return false;
+        if (this._id != temp._id) {
+          thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
+          tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
+          if (thcycle != tmcycle) {
+            if (!thcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+            }
+            ;
+            if (!tmcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+            }
+            ;
             return false;
+          }
+          if (!thcycle) {
+            if (!this._id.equals(temp._id)) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+              return false;
+            }
+            org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+            org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+          }
         }
-        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);
-    }
-
-    /**
-     * Sets the value of field 'compressed'. The field 'compressed'
-     * has the following description: true implies data will be
-     * decompresses with Zip
-     *  before presenting to application 
-     * 
-     * @param compressed the value of field 'compressed'.
-     */
-    public void setCompressed(
-            final boolean compressed) {
-        this._compressed = compressed;
-        this._has_compressed = true;
-    }
-
-    /**
-     * Sets the value of field 'id'. The field 'id' has the
-     * following description: Primary Key for vamsas object
-     * referencing
-     *  
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(
-            final java.lang.String id) {
-        this._id = id;
+      } else if (temp._id != null)
+        return false;
+      return true;
     }
-
-    /**
-     * Sets the value of field 'objectref'. The field 'objectref'
-     * has the following description: Object the arbitrary data is
-     * associated with
-     *  
-     * 
-     * @param objectref the value of field 'objectref'.
-     */
-    public void setObjectref(
-            final java.lang.Object objectref) {
-        this._objectref = objectref;
+    return false;
+  }
+
+  /**
+   * Returns the value of field 'compressed'. The field 'compressed' has the
+   * following description: true implies data will be decompresses with Zip
+   * before presenting to application
+   * 
+   * @return the value of field 'Compressed'.
+   */
+  public boolean getCompressed() {
+    return this._compressed;
+  }
+
+  /**
+   * Returns the value of field 'id'. The field 'id' has the following
+   * description: Primary Key for vamsas object referencing
+   * 
+   * 
+   * @return the value of field 'Id'.
+   */
+  public java.lang.String getId() {
+    return this._id;
+  }
+
+  /**
+   * Returns the value of field 'objectref'. The field 'objectref' has the
+   * following description: Object the arbitrary data is associated with
+   * 
+   * 
+   * @return the value of field 'Objectref'.
+   */
+  public java.lang.Object getObjectref() {
+    return this._objectref;
+  }
+
+  /**
+   * Returns the value of field 'type'. The field 'type' has the following
+   * description: Type of arbitrary data - TODO: decide format - use (extended)
+   * MIME types ?
+   * 
+   * @return the value of field 'Type'.
+   */
+  public java.lang.String getType() {
+    return this._type;
+  }
+
+  /**
+   * Method hasCompressed.
+   * 
+   * @return true if at least one Compressed has been added
+   */
+  public boolean hasCompressed() {
+    return this._has_compressed;
+  }
+
+  /**
+   * 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 + (_compressed ? 0 : 1);
+    if (_type != null && !org.castor.util.CycleBreaker.startingToCycle(_type)) {
+      result = 37 * result + _type.hashCode();
+      org.castor.util.CycleBreaker.releaseCycleHandle(_type);
     }
-
-    /**
-     * Sets the value of field 'type'. The field 'type' has the
-     * following description: Type of arbitrary data - TODO: decide
-     * format - use
-     *  (extended) MIME types ? 
-     * 
-     * @param type the value of field 'type'.
-     */
-    public void setType(
-            final java.lang.String type) {
-        this._type = type;
+    if (_objectref != null
+        && !org.castor.util.CycleBreaker.startingToCycle(_objectref)) {
+      result = 37 * result + _objectref.hashCode();
+      org.castor.util.CycleBreaker.releaseCycleHandle(_objectref);
     }
-
-    /**
-     * 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.AppData
-     */
-    public static uk.ac.vamsas.objects.core.AppData unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (uk.ac.vamsas.objects.core.AppData) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Attachment.class, reader);
+    if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
+      result = 37 * result + _id.hashCode();
+      org.castor.util.CycleBreaker.releaseCycleHandle(_id);
     }
 
-    /**
-     * 
-     * 
-     * @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);
+    return result;
+  }
+
+  /**
+   * Returns the value of field 'compressed'. The field 'compressed' has the
+   * following description: true implies data will be decompresses with Zip
+   * before presenting to application
+   * 
+   * @return the value of field 'Compressed'.
+   */
+  public boolean isCompressed() {
+    return this._compressed;
+  }
+
+  /**
+   * 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);
+  }
+
+  /**
+   * Sets the value of field 'compressed'. The field 'compressed' has the
+   * following description: true implies data will be decompresses with Zip
+   * before presenting to application
+   * 
+   * @param compressed
+   *          the value of field 'compressed'.
+   */
+  public void setCompressed(final boolean compressed) {
+    this._compressed = compressed;
+    this._has_compressed = true;
+  }
+
+  /**
+   * Sets the value of field 'id'. The field 'id' has the following description:
+   * Primary Key for vamsas object referencing
+   * 
+   * 
+   * @param id
+   *          the value of field 'id'.
+   */
+  public void setId(final java.lang.String id) {
+    this._id = id;
+  }
+
+  /**
+   * Sets the value of field 'objectref'. The field 'objectref' has the
+   * following description: Object the arbitrary data is associated with
+   * 
+   * 
+   * @param objectref
+   *          the value of field 'objectref'.
+   */
+  public void setObjectref(final java.lang.Object objectref) {
+    this._objectref = objectref;
+  }
+
+  /**
+   * Sets the value of field 'type'. The field 'type' has the following
+   * description: Type of arbitrary data - TODO: decide format - use (extended)
+   * MIME types ?
+   * 
+   * @param type
+   *          the value of field 'type'.
+   */
+  public void setType(final java.lang.String type) {
+    this._type = type;
+  }
+
+  /**
+   * 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.AppData
+   */
+  public static uk.ac.vamsas.objects.core.AppData unmarshal(
+      final java.io.Reader reader)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException {
+    return (uk.ac.vamsas.objects.core.AppData) Unmarshaller.unmarshal(
+        uk.ac.vamsas.objects.core.Attachment.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);
+  }
 
 }