X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Forg%2Fvamsas%2Fobjects%2Fcore%2FSequenceType.java;h=1adc80a3dd9ade2e83c4ddb59d2fc2aa4b9ed39a;hb=2e92d5449226c6b2423129d779977df26fe74ec6;hp=e6204d6c873ffa58b6ad7a70740eb7be66bc70ff;hpb=c062fe4c183d567877484f0229631dc555ddc9f5;p=vamsas.git

diff --git a/src/org/vamsas/objects/core/SequenceType.java b/src/org/vamsas/objects/core/SequenceType.java
index e6204d6..1adc80a 100644
--- a/src/org/vamsas/objects/core/SequenceType.java
+++ b/src/org/vamsas/objects/core/SequenceType.java
@@ -15,8 +15,6 @@ 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;
@@ -58,11 +56,6 @@ implements java.io.Serializable
     private boolean _has_end;
 
     /**
-     * Field _id
-     */
-    private java.lang.String _id;
-
-    /**
      * Field _sequence
      */
     private java.lang.String _sequence;
@@ -72,11 +65,6 @@ implements java.io.Serializable
      */
     private java.lang.String _name;
 
-    /**
-     * Field _dbRefList
-     */
-    private java.util.Vector _dbRefList;
-
 
       //----------------/
      //- Constructors -/
@@ -85,7 +73,6 @@ implements java.io.Serializable
     public SequenceType() 
      {
         super();
-        _dbRefList = new Vector();
     } //-- org.vamsas.objects.core.SequenceType()
 
 
@@ -94,33 +81,6 @@ implements java.io.Serializable
     //-----------/
 
     /**
-     * Method addDbRef
-     * 
-     * 
-     * 
-     * @param vDbRef
-     */
-    public void addDbRef(org.vamsas.objects.core.DbRef vDbRef)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _dbRefList.addElement(vDbRef);
-    } //-- void addDbRef(org.vamsas.objects.core.DbRef) 
-
-    /**
-     * Method addDbRef
-     * 
-     * 
-     * 
-     * @param index
-     * @param vDbRef
-     */
-    public void addDbRef(int index, org.vamsas.objects.core.DbRef vDbRef)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _dbRefList.insertElementAt(vDbRef, index);
-    } //-- void addDbRef(int, org.vamsas.objects.core.DbRef) 
-
-    /**
      * Method deleteEnd
      * 
      */
@@ -139,18 +99,6 @@ implements java.io.Serializable
     } //-- void deleteStart() 
 
     /**
-     * Method enumerateDbRef
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateDbRef()
-    {
-        return _dbRefList.elements();
-    } //-- java.util.Enumeration enumerateDbRef() 
-
-    /**
      * Note: hashCode() has not been overriden
      * 
      * @param obj
@@ -175,13 +123,6 @@ implements java.io.Serializable
                 return false;
             if (this._has_end != temp._has_end)
                 return false;
-            if (this._id != null) {
-                if (temp._id == null) return false;
-                else if (!(this._id.equals(temp._id))) 
-                    return false;
-            }
-            else if (temp._id != null)
-                return false;
             if (this._sequence != null) {
                 if (temp._sequence == null) return false;
                 else if (!(this._sequence.equals(temp._sequence))) 
@@ -196,67 +137,12 @@ implements java.io.Serializable
             }
             else if (temp._name != null)
                 return false;
-            if (this._dbRefList != null) {
-                if (temp._dbRefList == null) return false;
-                else if (!(this._dbRefList.equals(temp._dbRefList))) 
-                    return false;
-            }
-            else if (temp._dbRefList != null)
-                return false;
             return true;
         }
         return false;
     } //-- boolean equals(java.lang.Object) 
 
     /**
-     * Method getDbRef
-     * 
-     * 
-     * 
-     * @param index
-     * @return DbRef
-     */
-    public org.vamsas.objects.core.DbRef getDbRef(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _dbRefList.size())) {
-            throw new IndexOutOfBoundsException("getDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]");
-        }
-        
-        return (org.vamsas.objects.core.DbRef) _dbRefList.elementAt(index);
-    } //-- org.vamsas.objects.core.DbRef getDbRef(int) 
-
-    /**
-     * Method getDbRef
-     * 
-     * 
-     * 
-     * @return DbRef
-     */
-    public org.vamsas.objects.core.DbRef[] getDbRef()
-    {
-        int size = _dbRefList.size();
-        org.vamsas.objects.core.DbRef[] mArray = new org.vamsas.objects.core.DbRef[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (org.vamsas.objects.core.DbRef) _dbRefList.elementAt(index);
-        }
-        return mArray;
-    } //-- org.vamsas.objects.core.DbRef[] getDbRef() 
-
-    /**
-     * Method getDbRefCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getDbRefCount()
-    {
-        return _dbRefList.size();
-    } //-- int getDbRefCount() 
-
-    /**
      * Returns the value of field 'end'.
      * 
      * @return int
@@ -268,17 +154,6 @@ implements java.io.Serializable
     } //-- int getEnd() 
 
     /**
-     * Returns the value of field 'id'.
-     * 
-     * @return String
-     * @return the value of field 'id'.
-     */
-    public java.lang.String getId()
-    {
-        return this._id;
-    } //-- java.lang.String getId() 
-
-    /**
      * Returns the value of field 'name'.
      * 
      * @return String
@@ -382,64 +257,6 @@ implements java.io.Serializable
     } //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
-     * Method removeAllDbRef
-     * 
-     */
-    public void removeAllDbRef()
-    {
-        _dbRefList.removeAllElements();
-    } //-- void removeAllDbRef() 
-
-    /**
-     * Method removeDbRef
-     * 
-     * 
-     * 
-     * @param index
-     * @return DbRef
-     */
-    public org.vamsas.objects.core.DbRef removeDbRef(int index)
-    {
-        java.lang.Object obj = _dbRefList.elementAt(index);
-        _dbRefList.removeElementAt(index);
-        return (org.vamsas.objects.core.DbRef) obj;
-    } //-- org.vamsas.objects.core.DbRef removeDbRef(int) 
-
-    /**
-     * Method setDbRef
-     * 
-     * 
-     * 
-     * @param index
-     * @param vDbRef
-     */
-    public void setDbRef(int index, org.vamsas.objects.core.DbRef vDbRef)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _dbRefList.size())) {
-            throw new IndexOutOfBoundsException("setDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]");
-        }
-        _dbRefList.setElementAt(vDbRef, index);
-    } //-- void setDbRef(int, org.vamsas.objects.core.DbRef) 
-
-    /**
-     * Method setDbRef
-     * 
-     * 
-     * 
-     * @param dbRefArray
-     */
-    public void setDbRef(org.vamsas.objects.core.DbRef[] dbRefArray)
-    {
-        //-- copy array
-        _dbRefList.removeAllElements();
-        for (int i = 0; i < dbRefArray.length; i++) {
-            _dbRefList.addElement(dbRefArray[i]);
-        }
-    } //-- void setDbRef(org.vamsas.objects.core.DbRef) 
-
-    /**
      * Sets the value of field 'end'.
      * 
      * @param end the value of field 'end'.
@@ -451,16 +268,6 @@ implements java.io.Serializable
     } //-- void setEnd(int) 
 
     /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(java.lang.String id)
-    {
-        this._id = id;
-    } //-- void setId(java.lang.String) 
-
-    /**
      * Sets the value of field 'name'.
      * 
      * @param name the value of field 'name'.