diff --git a/src/include/ZMap/zmapProtocol.h b/src/include/ZMap/zmapProtocol.h
deleted file mode 100755
index 97b5c6d2496930b08ff63c7dc21038b40e5b7d88..0000000000000000000000000000000000000000
--- a/src/include/ZMap/zmapProtocol.h
+++ /dev/null
@@ -1,114 +0,0 @@
-/*  File: zmapProtocol.h
- *  Author: Ed Griffiths (edgrif@sanger.ac.uk)
- *  Copyright (c) Sanger Institute, 2004
- *-------------------------------------------------------------------
- * ZMap is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- * 
- * This program 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 General Public License for more details.
- * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
- * or see the on-line version at http://www.gnu.org/copyleft/gpl.txt
- *-------------------------------------------------------------------
- * This file is part of the ZMap genome database package
- * originated by
- * 	Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
- *      Rob Clack (Sanger Institute, UK) rnc@sanger.ac.uk
- *
- * Description: 
- * HISTORY:
- * Last edited: Dec 14 09:17 2004 (edgrif)
- * Created: Wed Sep 15 11:46:18 2004 (edgrif)
- * CVS info:   $Id: zmapProtocol.h,v 1.5 2004-12-15 14:10:22 edgrif Exp $
- *-------------------------------------------------------------------
- */
-#ifndef ZMAP_PROTOCOL_H
-#define ZMAP_PROTOCOL_H
-
-#include <glib.h>
-#include <ZMap/zmapFeature.h>
-
-
-
-/* Requests can be of different types with different input parameters and returning
- * different types of results. */
-
-typedef enum
-  {
-    ZMAP_PROTOCOLREQUEST_INVALID = 0,
-
-    ZMAP_PROTOCOLREQUEST_TYPES,				    /* Get the feature types. */
-
-    ZMAP_PROTOCOLREQUEST_FEATURES,			    /* Get the features. */
-
-    ZMAP_PROTOCOLREQUEST_SEQUENCE,			    /* Get the sequence. */
-
-    ZMAP_PROTOCOLREQUEST_FEATURE_SEQUENCE,		    /* Get the features + sequence. */
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-  /* these are things I would like to do but have not implemented yet.... */
-
-    ZMAP_PROTOCOLREQUEST_NEWCONTEXT,			    /* Set a new sequence name/start/end. */
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
-  } ZMapProtocolRequestType ;
-
-
-
-
-
-
-/* ALL request/response structs must include the fields from ZMapProtocolAnyStruct
- * as their first fields in the struct so that code can look in all such structs to decode them. */
-typedef struct
-{
-  ZMapProtocolRequestType request ;
-} ZMapProtocolAnyStruct, *ZMapProtocolAny ;
-
-
-typedef struct
-{
-  ZMapProtocolRequestType request ;
-
-  char *sequence ;
-  int start, end ;
-} ZMapProtocolNewContextStruct, *ZMapProtocolNewContext ;
-
-
-typedef struct
-{
-  ZMapProtocolRequestType request ;
-
-  GData *types_out ;					    /* Returned list of available feature types. */
-} ZMapProtocolGetTypesStruct, *ZMapProtocolGetTypes ;
-
-
-typedef struct
-{
-  ZMapProtocolRequestType request ;
-
-  GData *types ;					    /* lists types of features required,
-							       NULL means "all". */
-  ZMapFeatureContext feature_context_out ;		    /* Returned feature sets. */
-} ZMapProtocolGetFeaturesStruct, *ZMapProtocolGetFeatures ;
-
-
-typedef union
-{
-  ZMapProtocolAny any ;
-  ZMapProtocolGetTypes get_types ;
-  ZMapProtocolGetFeatures get_features ;
-  ZMapProtocolNewContext new_context ;
-} ZMapProtocol ;
-
-
-
-#endif /* !ZMAP_PROTOCOL_H */