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Commit 97184411 authored by rds's avatar rds
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remove saxparse

parent 6af0d0c2
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src/lib/Makefile.am
+ 0
− 3
View file @ 97184411
......@@ -100,9 +100,6 @@ libZMapThr_a_SOURCES = $(top_srcdir)/zmapServer/zmapServer.c \
$(top_srcdir)/zmapServer/acedb/acedbServer_P.h \
$(top_srcdir)/zmapServer/das/dasServer.c \
$(top_srcdir)/zmapServer/das/dasServer_P.h \
$(top_srcdir)/zmapServer/das/saxparse.c \
$(top_srcdir)/zmapServer/das/saxparse.h \
$(top_srcdir)/zmapServer/das/saxparse_P.h \
$(top_srcdir)/zmapServer/das/das1schema.h \
$(top_srcdir)/zmapServer/das/das1meta.c \
$(top_srcdir)/zmapServer/das/das1features.c \
......
src/zmapServer/das/saxparse.c deleted 100755 → 0
+ 0
− 296
View file @ 6af0d0c2
/* File: saxparse.c
* 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: Uses expat xml parser to parse DAS2 input using the
* SAX processing model.
*
* Exported functions: See saxparse.h
* HISTORY:
* Last edited: Jul 16 09:39 2004 (edgrif)
* Created: Thu Mar 18 15:45:59 2004 (edgrif)
* CVS info: $Id: saxparse.c,v 1.3 2005-08-11 13:13:50 rds Exp $
*-------------------------------------------------------------------
*/
#include <config.h>
#include <stdio.h>
#include <expat.h>
#include <glib.h>
#include <ZMap/zmapUtils.h>
#include <saxparse_P.h>
static void start_tag(void *userData, const char *el, const char **attr) ;
static void end_tag(void *userData, const char *el) ;
static void charhndl(void *userData, const XML_Char *s, int len) ;
static void tagFree(gpointer data, gpointer user_data) ;
#if defined DARWIN
/* total hack to get round problem on mac... See note in runconfig!!!!! */
XML_Bool XML_ParserReset(XML_Parser parser, const XML_Char *encoding)
{
return FALSE ;
}
#endif
SaxParser saxCreateParser(void *user_data)
{
SaxParser parser ;
parser = (SaxParser)g_new0(SaxParserStruct, 1) ;
parser->debug = TRUE ;
if (!(parser->p = XML_ParserCreate(NULL)))
{
zMapLogFatal("%s", "XML_ParserCreate() failed.") ;
}
parser->Depth = 0 ;
parser->tag_stack = g_queue_new() ;
parser->content = g_string_sized_new(20000) ; /* wild guess at size... */
parser->last_errmsg = NULL ;
return parser ;
}
gboolean saxParseData(SaxParser parser, void *data, int size)
{
gboolean result = TRUE ;
int final ;
if (size)
final = 0 ;
else
final = 1 ;
/* try resetting parser..... */
if (XML_ParserReset(parser->p, NULL) != XML_TRUE)
{
zMapLogFatal("%s", "XML_ParserReset() call failed.") ;
}
else
{
/* When the parser is reset it loses just about everything so reset the lot. */
XML_SetElementHandler(parser->p, start_tag, end_tag);
XML_SetCharacterDataHandler(parser->p, charhndl) ;
XML_SetUserData(parser->p, (void *)parser) ;
if (!XML_Parse(parser->p, data, size, final))
{
if (parser->last_errmsg)
g_free(parser->last_errmsg) ;
parser->last_errmsg = g_strdup_printf("saxparse - Parse error (line %d): %s\n",
XML_GetCurrentLineNumber(parser->p),
XML_ErrorString(XML_GetErrorCode(parser->p))) ;
result = FALSE ;
}
}
return result ;
}
void saxDestroyParser(SaxParser parser)
{
XML_ParserFree(parser->p) ;
/* Deallocate tag data and then free the queue. */
if (!g_queue_is_empty(parser->tag_stack))
{
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
/* alpha version of gtk does not have this....so do it by steam...sigh.... */
g_queue_foreach(parser->tag_stack, tagFree, parser) ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
gpointer dummy ;
while ((dummy = g_queue_pop_head(parser->tag_stack)))
{
g_free(dummy) ;
}
}
g_queue_free(parser->tag_stack) ;
g_string_free(parser->content, TRUE) ; /* TRUE => free string data as well. */
if (parser->last_errmsg)
g_free(parser->last_errmsg) ;
g_free(parser) ;
return ;
}
static void tagFree(gpointer data, gpointer user_data_unused)
{
SaxParser parser = (SaxParser)user_data_unused ;
g_free(data) ;
return ;
}
/* Set handlers for start and end tags. Attributes are passed to the start handler
* as a pointer to a vector of char pointers. Each attribute seen in a start (or empty)
* tag occupies 2 consecutive places in this vector: the attribute name followed by the
* attribute value. These pairs are terminated by a null pointer. */
static void start_tag(void *userData, const char *el, const char **attr)
{
SaxParser parser = (SaxParser)userData ;
SaxTag current_tag ;
int i;
if (parser->debug)
{
for (i = 0; i < parser->Depth; i++)
printf(" ");
printf("<%s>", el) ;
if (attr[0])
{
printf(" - ") ;
for (i = 0; attr[i]; i += 2)
{
printf(" %s='%s'", attr[i], attr[i + 1]);
}
}
printf("\n");
}
/* Push the current tag on to our stack of tags. */
current_tag = g_new0(SaxTagStruct, 1) ;
current_tag->element_name = (char *)el ;
current_tag->attributes = (char **)attr ;
g_queue_push_head(parser->tag_stack, current_tag) ;
parser->Depth++;
return ;
}
static void end_tag(void *userData, const char *el)
{
SaxParser parser = (SaxParser)userData ;
int i ;
gpointer dummy ;
SaxTag current_tag ;
parser->Depth-- ;
dummy = g_queue_pop_head(parser->tag_stack) ; /* Now get rid of head element. */
current_tag = (SaxTag)dummy ;
/* If there is content between the start/end tags process it. */
if (parser->content->len)
{
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
gchar *tag = (gchar *)g_queue_peek_head(parser->tag_stack) ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
if (parser->debug)
{
for (i = 0; i < parser->Depth; i++)
printf(" ");
printf("%s content - %s\n", current_tag->element_name, parser->content->str) ;
}
/* Here is where we need to do some of the (most of the ?) gff processing.... */
/* reset once processed..... */
parser->content = g_string_set_size(parser->content, 0) ;
}
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
dummy = g_queue_pop_head(parser->tag_stack) ; /* Now get rid of head element. */
current_tag = (SaxTag)dummy ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
g_free(dummy) ;
if (parser->debug)
{
for (i = 0; i < parser->Depth; i++)
printf(" ") ;
printf("</%s>\n", el) ;
}
return ;
}
/* Set a text handler. The string your handler receives is NOT zero terminated.
* You have to use the length argument to deal with the end of the string.
* A single block of contiguous text free of markup may still result in a
* sequence of calls to this handler. In other words, if you're searching for a pattern
* in the text, it may be split across calls to this handler.
*/
static void charhndl(void *userData, const XML_Char *s, int len)
{
int i ;
SaxParser parser = (SaxParser)userData ;
/* N.B. we _only_ get away with this because XML_Char == char at the moment, this will need
* to be fixed in the future..... */
parser->content = g_string_append_len(parser->content, s, len) ;
return ;
}
src/zmapServer/das/saxparse.h deleted 100755 → 0
+ 0
− 45
View file @ 6af0d0c2
/* File: saxparse.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: Jul 2 09:32 2004 (edgrif)
* Created: Wed Jan 28 16:17:58 2004 (edgrif)
* CVS info: $Id: saxparse.h,v 1.2 2004-07-19 10:13:36 edgrif Exp $
*-------------------------------------------------------------------
*/
#ifndef SAXPARSE_H
#define SAXPARSE_H
#include <glib.h>
typedef struct SaxParserStructName *SaxParser ;
SaxParser saxCreateParser(void *user_data) ;
gboolean saxParseData(SaxParser parser, void *data, int size) ;
void saxDestroyParser(SaxParser parser) ;
#endif /* !SAXPARSE_H */
src/zmapServer/das/saxparse_P.h deleted 100755 → 0
+ 0
− 67
View file @ 6af0d0c2
/* File: saxparse.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: Jul 2 14:55 2004 (edgrif)
* Created: Wed Jan 28 16:17:58 2004 (edgrif)
* CVS info: $Id: saxparse_P.h,v 1.2 2004-07-19 10:13:36 edgrif Exp $
*-------------------------------------------------------------------
*/
#ifndef SAXPARSE_P_H
#define SAXPARSE_P_H
#include <saxparse.h>
typedef enum {SAXPARSE_NOWHERE, SAXPARSE_STARTDOC,
SAXPARSE_START, SAXPARSE_INSIDE, SAXPARSE_END, SAXPARSE_ENDDOC} SaxParseState ;
/* For an XML tag holds the element name and attributes, i.e. <element_name attributes>
* Used to track which tag we are processing. */
typedef struct SaxTagStructName
{
char *element_name ;
char **attributes ;
} SaxTagStruct, *SaxTag ;
typedef struct SaxParserStructName
{
XML_Parser p ;
gboolean debug ;
GQueue *tag_stack ; /* Stack of SaxTagStruct */
int Depth ;
GString *content ;
char *last_errmsg ;
void *user_data ; /* Caller stores any data they need here. */
} SaxParserStruct ;
#endif /* !SAXPARSE_P_H */
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