quick commit before refactoring

[vamsas.git] / src / org / vamsas / objects / core / Alignment.java

diff --git a/src/org/vamsas/objects/core/Alignment.java b/src/org/vamsas/objects/core/Alignment.java
index ef58ddc..bf70f4e 100644 (file)
--- a/src/org/vamsas/objects/core/Alignment.java
+++ b/src/org/vamsas/objects/core/Alignment.java
@@ -53,29 +53,19 @@ implements java.io.Serializable
     private boolean _has_aligned;
 
     /**
-     * Primary Key for vamsas object
-     *  referencing
+     * Primary Key for vamsas object referencing
      *  
      */
     private java.lang.String _id;
 
     /**
-     * objects with modifiable=false will
-     *  not be modified by a vamsas client
-     *  update
-     *  
-     */
-    private boolean _modifiable = true;
-
-    /**
-     * keeps track of state for field: _modifiable
+     * Field _modifiable
      */
-    private boolean _has_modifiable;
+    private java.lang.String _modifiable;
 
     /**
-     * This is annotation over the
-     *  coordinate frame defined by all
-     *  the columns in the alignment.
+     * This is annotation over the coordinate frame
+     *  defined by all the columns in the alignment.
      *  
      */
     private java.util.Vector _alignmentAnnotationList;
@@ -91,10 +81,8 @@ implements java.io.Serializable
     private java.util.Vector _alignmentSequenceList;
 
     /**
-     * typical properties may be
-     *  additional alignment score
-     *  objects
-     *  
+     * typical properties may be additional
+     *  alignment score objects 
      */
     private java.util.Vector _propertyList;
 
@@ -240,15 +228,6 @@ implements java.io.Serializable
     } //-- void deleteAligned() 
 
     /**
-     * Method deleteModifiable
-     * 
-     */
-    public void deleteModifiable()
-    {
-        this._has_modifiable= false;
-    } //-- void deleteModifiable() 
-
-    /**
      * Method enumerateAlignmentAnnotation
      * 
      * 
@@ -331,9 +310,12 @@ implements java.io.Serializable
             }
             else if (temp._id != null)
                 return false;
-            if (this._modifiable != temp._modifiable)
-                return false;
-            if (this._has_modifiable != temp._has_modifiable)
+            if (this._modifiable != null) {
+                if (temp._modifiable == null) return false;
+                else if (!(this._modifiable.equals(temp._modifiable))) 
+                    return false;
+            }
+            else if (temp._modifiable != null)
                 return false;
             if (this._alignmentAnnotationList != null) {
                 if (temp._alignmentAnnotationList == null) return false;
@@ -496,7 +478,7 @@ implements java.io.Serializable
     /**
      * Returns the value of field 'id'. The field 'id' has the
      * following description: Primary Key for vamsas object
-     *  referencing
+     * referencing
      *  
      * 
      * @return String
@@ -508,20 +490,15 @@ implements java.io.Serializable
     } //-- java.lang.String getId() 
 
     /**
-     * Returns the value of field 'modifiable'. The field
-     * 'modifiable' has the following description: objects with
-     * modifiable=false will
-     *  not be modified by a vamsas client
-     *  update
-     *  
+     * Returns the value of field 'modifiable'.
      * 
-     * @return boolean
+     * @return String
      * @return the value of field 'modifiable'.
      */
-    public boolean getModifiable()
+    public java.lang.String getModifiable()
     {
         return this._modifiable;
-    } //-- boolean getModifiable() 
+    } //-- java.lang.String getModifiable() 
 
     /**
      * Method getProperty
@@ -643,18 +620,6 @@ implements java.io.Serializable
     } //-- boolean hasAligned() 
 
     /**
-     * Method hasModifiable
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasModifiable()
-    {
-        return this._has_modifiable;
-    } //-- boolean hasModifiable() 
-
-    /**
      * Method isValid
      * 
      * 
@@ -888,7 +853,7 @@ implements java.io.Serializable
     /**
      * Sets the value of field 'id'. The field 'id' has the
      * following description: Primary Key for vamsas object
-     *  referencing
+     * referencing
      *  
      * 
      * @param id the value of field 'id'.
@@ -899,20 +864,14 @@ implements java.io.Serializable
     } //-- void setId(java.lang.String) 
 
     /**
-     * Sets the value of field 'modifiable'. The field 'modifiable'
-     * has the following description: objects with modifiable=false
-     * will
-     *  not be modified by a vamsas client
-     *  update
-     *  
+     * Sets the value of field 'modifiable'.
      * 
      * @param modifiable the value of field 'modifiable'.
      */
-    public void setModifiable(boolean modifiable)
+    public void setModifiable(java.lang.String modifiable)
     {
         this._modifiable = modifiable;
-        this._has_modifiable = true;
-    } //-- void setModifiable(boolean) 
+    } //-- void setModifiable(java.lang.String) 
 
     /**
      * Method setProperty