diff --git a/src/zmapServer/file/fileServer.c b/src/zmapServer/file/fileServer.c
index b6357973558791bd3ccd9fca9dde5657c5755575..a3736aa73719baa0fa2008087cb6415ca0c68f04 100755
--- a/src/zmapServer/file/fileServer.c
+++ b/src/zmapServer/file/fileServer.c
@@ -20,28 +20,33 @@
* 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
+ * Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
* Description: These functions provide code to read a file as though
* it were a server according to the interface defined
* for accessing servers. It's crude at the moment but
* the aim is to allow zmap to be run from just files
- * if required.
+ * if required. Read the caveats below though...
*
* Exported functions: See ZMap/zmapServerPrototype.h
+ *
* HISTORY:
- * Last edited: Oct 2 08:12 2009 (edgrif)
+ * Last edited: Nov 27 15:41 2009 (edgrif)
* Created: Fri Sep 10 18:29:18 2004 (edgrif)
- * CVS info: $Id: fileServer.c,v 1.41 2009-10-02 09:21:53 edgrif Exp $
+ * CVS info: $Id: fileServer.c,v 1.42 2009-11-30 10:51:45 edgrif Exp $
*-------------------------------------------------------------------
*/
-/* WARNING, THIS DOES NOT COPE WITH MULTIPLE ALIGNS/BLOCKS AS IT STANDS, TO DO THAT REQUIRES
- * WORK BOTH ON THE GFF PARSER CODE (TO ACCEPT ALIGN/BLOCK ID/COORDS AND ON THIS CODE TO
- * GENERALISE IT MORE TO DEAL WITH BLOCKS...I'LL DO THAT NEXT....EG */
-
-
+/* GFF files have a prescribed format which specifically does not include anything
+ * about how the features are displayed so the zmap styles must be provided separatly.
+ *
+ * In addition the code assumes that the gff file describes just one block of features.
+ * In theory the file could contain multiple blocks but that is not straight forward
+ * as gff provides for multiple sequences with their features in a single file but _not_
+ * multiple sub-parts of a single sequence. Hence we do not support that currently.
+ *
+ * */
#include <glib.h>
#include <ZMap/zmapUtils.h>
@@ -57,7 +62,9 @@ typedef struct
ZMapServerResponseType result ;
FileServer server ;
ZMapGFFParser parser ;
- GString* gff_line ;
+ GString *gff_line ;
+
+ gboolean sequence_finished ;
} GetFeaturesStruct, *GetFeatures ;
@@ -85,15 +92,22 @@ static char *lastErrorMsg(void *server) ;
static ZMapServerResponseType closeConnection(void *server_in) ;
static ZMapServerResponseType destroyConnection(void *server) ;
+static gboolean getSequenceMapping(FileServer server, ZMapFeatureContext feature_context) ;
static void addMapping(ZMapFeatureContext feature_context, ZMapGFFHeader header) ;
+
static void eachAlignment(gpointer key, gpointer data, gpointer user_data) ;
static void eachBlock(gpointer key, gpointer data, gpointer user_data) ;
-static gboolean sequenceRequest(FileServer server, ZMapGFFParser parser, GString* gff_line,
+static gboolean featuresRequest(FileServer server, ZMapGFFParser parser, GString *gff_line,
ZMapFeatureBlock feature_block) ;
-static void setLastErrorMsg(FileServer server, GError **gff_file_err_inout) ;
+
+static void eachAlignmentSequence(gpointer key, gpointer data, gpointer user_data) ;
+static void eachBlockSequence(gpointer key, gpointer data, gpointer user_data) ;
static gboolean getServerInfo(FileServer server, ZMapServerInfo info) ;
+
+static void setLastErrorMsg(FileServer server, GError **gff_file_err_inout) ;
static void setErrMsg(FileServer server, char *new_msg) ;
+static gboolean resetToStart(FileServer server) ;
@@ -182,6 +196,10 @@ static gboolean createConnection(void **server_out,
}
+/* The model we use for processing the GFF file is that we open it just once
+ * and then close it when the closeConnection is called. If we need to start
+ * at the beginning of the file again we just reset the file pointer to the
+ * start. */
static ZMapServerResponseType openConnection(void *server_in)
{
ZMapServerResponseType result = ZMAP_SERVERRESPONSE_REQFAIL ;
@@ -255,8 +273,10 @@ static ZMapServerResponseType getFeatureSetNames(void *server_in,
ZMAPSERVER_LOG(Warning, FILE_PROTOCOL_STR, server->file_path,
"%s", server->last_err_msg) ;
+
result = ZMAP_SERVERRESPONSE_UNSUPPORTED ;
+
return result ;
}
@@ -298,9 +318,12 @@ static ZMapServerResponseType haveModes(void *server_in, gboolean *have_mode)
}
+/* Currently we don't support this even though we could in theory as gff files can
+ * contains arbitrary sequences. */
static ZMapServerResponseType getSequences(void *server_in, GList *sequences_inout)
{
- ZMapServerResponseType result = ZMAP_SERVERRESPONSE_OK ;
+ ZMapServerResponseType result = ZMAP_SERVERRESPONSE_UNSUPPORTED ;
+
return result ;
}
@@ -314,13 +337,27 @@ static ZMapServerResponseType setContext(void *server_in, ZMapFeatureContext fea
{
ZMapServerResponseType result = ZMAP_SERVERRESPONSE_OK ;
FileServer server = (FileServer)server_in ;
+ gboolean status ;
server->req_context = feature_context ;
-
- /* Like the acedb server we should be getting the mapping from the gff file here....
- * then we could set up the block/etc stuff...this is where add mapping should be called from... */
-
+ if (!(status = getSequenceMapping(server, feature_context)))
+ {
+ result = ZMAP_SERVERRESPONSE_REQFAIL ;
+ ZMAPSERVER_LOG(Warning, FILE_PROTOCOL_STR, server->file_path,
+ "Could not map %s because: %s",
+ g_quark_to_string(server->req_context->sequence_name), server->last_err_msg) ;
+ }
+ else
+ {
+ if (!resetToStart(server))
+ {
+ result = ZMAP_SERVERRESPONSE_REQFAIL ;
+ ZMAPSERVER_LOG(Warning, FILE_PROTOCOL_STR, server->file_path,
+ "Could not reset to file start %s because: %s",
+ g_quark_to_string(server->req_context->sequence_name), server->last_err_msg) ;
+ }
+ }
return result ;
@@ -331,7 +368,7 @@ static ZMapServerResponseType setContext(void *server_in, ZMapFeatureContext fea
static ZMapServerResponseType getFeatures(void *server_in, GData *styles, ZMapFeatureContext feature_context)
{
FileServer server = (FileServer)server_in ;
- GetFeaturesStruct get_features ;
+ GetFeaturesStruct get_features = {0} ;
GIOStatus status ;
gsize terminator_pos = 0 ;
GError *gff_file_err = NULL ;
@@ -355,9 +392,8 @@ static ZMapServerResponseType getFeatures(void *server_in, GData *styles, ZMapFe
get_features.result = ZMAP_SERVERRESPONSE_OK ;
get_features.server = (FileServer)server_in ;
- get_features.parser = zMapGFFCreateParser(styles, FALSE) ;
- /* FALSE => do the real parse. */
-
+ get_features.parser = zMapGFFCreateParser() ;
+ zMapGFFParserInitForFeatures(get_features.parser, styles, FALSE) ;
get_features.gff_line = g_string_sized_new(2000) ; /* Probably not many lines will be >
2k chars. */
@@ -422,13 +458,6 @@ static ZMapServerResponseType getFeatures(void *server_in, GData *styles, ZMapFe
if (get_features.result == ZMAP_SERVERRESPONSE_OK)
{
- header = zMapGFFGetHeader(get_features.parser) ;
-
- addMapping(feature_context, header) ;
-
- zMapGFFFreeHeader(header) ;
-
-
/* Fetch all the alignment blocks for all the sequences, this all hacky right now as really.
* we would have to parse and reparse the file....can be done but not needed this second. */
g_hash_table_foreach(feature_context->alignments, eachAlignment, (gpointer)&get_features) ;
@@ -456,173 +485,106 @@ static ZMapServerResponseType getFeatures(void *server_in, GData *styles, ZMapFe
}
-static void eachBlockSequence(gpointer key, gpointer data, gpointer user_data)
-{
- ZMapFeatureBlock feature_block = (ZMapFeatureBlock)data ;
- GetFeatures get_features = (GetFeatures)user_data ;
-
- if (get_features->result == ZMAP_SERVERRESPONSE_OK)
- {
- ZMapSequence sequence;
- if(!(sequence = zMapGFFGetSequence(get_features->parser)))
- {
- GError *error;
- error = zMapGFFGetError(get_features->parser);
- setErrMsg(get_features->server,
- g_strdup_printf("zMapGFFGetSequence() failed, error=%s",
- error->message));
- ZMAPSERVER_LOG(Warning, FILE_PROTOCOL_STR,
- get_features->server->file_path,
- "%s", get_features->server->last_err_msg);
- }
- else
- {
- ZMapFeatureContext context;
- ZMapFeatureSet feature_set;
-
- if(zMapFeatureDNACreateFeatureSet(feature_block, &feature_set))
- {
- ZMapFeatureTypeStyle dna_style = NULL;
- ZMapFeature feature;
-
- /* This temp style creation feels wrong, and probably is,
- * but we don't have the merged in default styles in here,
- * or so it seems... */
- dna_style = zMapStyleCreate(ZMAP_FIXED_STYLE_DNA_NAME,
- ZMAP_FIXED_STYLE_DNA_NAME_TEXT);
-
- feature = zMapFeatureDNACreateFeature(feature_block, dna_style,
- sequence->sequence, sequence->length);
-
- zMapStyleDestroy(dna_style);
- }
-
- context = (ZMapFeatureContext)zMapFeatureGetParentGroup((ZMapFeatureAny)feature_block,
- ZMAPFEATURE_STRUCT_CONTEXT) ;
-
- /* I'm going to create the three frame translation up front! */
- if (zMap_g_list_find_quark(context->feature_set_names, zMapStyleCreateID(ZMAP_FIXED_STYLE_3FT_NAME)))
- {
- if ((zMapFeature3FrameTranslationCreateSet(feature_block, &feature_set)))
- {
- ZMapFeatureTypeStyle frame_style = NULL;
-
- frame_style = zMapStyleCreate(ZMAP_FIXED_STYLE_DNA_NAME,
- ZMAP_FIXED_STYLE_DNA_NAME_TEXT);
-
- zMapFeature3FrameTranslationSetCreateFeatures(feature_set, frame_style);
-
- zMapStyleDestroy(frame_style);
- }
- }
-
- g_free(sequence);
- }
- }
-
- return ;
-}
-
-/* Process all the alignments in a context. */
-static void eachAlignmentSequence(gpointer key, gpointer data, gpointer user_data)
-{
- ZMapFeatureAlignment alignment = (ZMapFeatureAlignment)data ;
- GetFeatures get_features = (GetFeatures)user_data ;
-
- if (get_features->result == ZMAP_SERVERRESPONSE_OK)
- g_hash_table_foreach(alignment->blocks, eachBlockSequence, (gpointer)get_features) ;
- return ;
-}
-/* We don't support this for now... */
-static ZMapServerResponseType getContextSequence(void *server_in, GData *styles, ZMapFeatureContext feature_context_out)
+static ZMapServerResponseType getContextSequence(void *server_in, GData *styles,
+ ZMapFeatureContext feature_context_out)
{
FileServer server = (FileServer)server_in ;
- GetFeaturesStruct get_features ;
+ GetFeaturesStruct get_features = {0} ;
GIOStatus status ;
gsize terminator_pos = 0 ;
GError *gff_file_err = NULL ;
GError *error = NULL ;
+
+
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
+ return ZMAP_SERVERRESPONSE_UNSUPPORTED ;
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+
+
+
get_features.result = ZMAP_SERVERRESPONSE_OK ;
get_features.server = (FileServer)server_in ;
- get_features.parser = zMapGFFCreateParser(styles, FALSE) ;
- /* FALSE => do the real parse. */
-
+ get_features.parser = zMapGFFCreateParser() ;
zMapGFFParserSetSequenceFlag(get_features.parser);
+
get_features.gff_line = g_string_sized_new(2000) ; /* Probably not many lines will be >
2k chars. */
- g_io_channel_seek_position(server->gff_file, 0, G_SEEK_SET, &gff_file_err);
-
- /* Read the header, needed for feature coord range. */
- while ((status = g_io_channel_read_line_string(server->gff_file, get_features.gff_line,
- &terminator_pos,
- &gff_file_err)) == G_IO_STATUS_NORMAL)
+ if (resetToStart(server))
{
gboolean done_header = FALSE ;
- *(get_features.gff_line->str + terminator_pos) = '\0' ; /* Remove terminating newline. */
-
- if (zMapGFFParseHeader(get_features.parser, get_features.gff_line->str, &done_header))
- {
- if (done_header)
- break ;
- else
- get_features.gff_line = g_string_truncate(get_features.gff_line, 0) ;
- /* Reset line to empty. */
- }
- else
+ /* Read the header, needed for feature coord range. */
+ while ((status = g_io_channel_read_line_string(server->gff_file, get_features.gff_line,
+ &terminator_pos,
+ &gff_file_err)) == G_IO_STATUS_NORMAL)
{
+ *(get_features.gff_line->str + terminator_pos) = '\0' ; /* Remove terminating newline. */
+
if (!done_header)
{
- error = zMapGFFGetError(get_features.parser) ;
-
- if (!error)
+ if (zMapGFFParseHeader(get_features.parser, get_features.gff_line->str, &done_header))
{
- /* SHOULD ABORT HERE.... */
- setErrMsg(server,
- g_strdup_printf("zMapGFFParseLine() failed with no GError for line %d: %s",
- zMapGFFGetLineNumber(get_features.parser), get_features.gff_line->str)) ;
- ZMAPSERVER_LOG(Critical, FILE_PROTOCOL_STR, server->file_path,
- "%s", server->last_err_msg) ;
+ if (!done_header)
+ get_features.gff_line = g_string_truncate(get_features.gff_line, 0) ;
+ /* Reset line to empty. */
}
else
{
- /* If the error was serious we stop processing and return the error,
- * otherwise we just log the error. */
- if (zMapGFFTerminated(get_features.parser))
+ if (!done_header)
{
+ error = zMapGFFGetError(get_features.parser) ;
+
+ if (!error)
+ {
+ /* SHOULD ABORT HERE.... */
+ setErrMsg(server,
+ g_strdup_printf("zMapGFFParseLine() failed with no GError for line %d: %s",
+ zMapGFFGetLineNumber(get_features.parser), get_features.gff_line->str)) ;
+ ZMAPSERVER_LOG(Critical, FILE_PROTOCOL_STR, server->file_path,
+ "%s", server->last_err_msg) ;
+ }
+ else
+ {
+ /* If the error was serious we stop processing and return the error,
+ * otherwise we just log the error. */
+ if (zMapGFFTerminated(get_features.parser))
+ {
+ get_features.result = ZMAP_SERVERRESPONSE_REQFAIL ;
+ setErrMsg(server, g_strdup_printf("GFFTerminated! %s", error->message)) ;
+ ZMAPSERVER_LOG(Critical, FILE_PROTOCOL_STR, server->file_path,
+ "%s", server->last_err_msg) ; }
+ else
+ {
+ setErrMsg(server,
+ g_strdup_printf("zMapGFFParseHeader() failed for line %d: %s",
+ zMapGFFGetLineNumber(get_features.parser),
+ get_features.gff_line->str)) ;
+ ZMAPSERVER_LOG(Critical, FILE_PROTOCOL_STR, server->file_path,
+ "%s", server->last_err_msg) ;
+ }
+ }
get_features.result = ZMAP_SERVERRESPONSE_REQFAIL ;
- setErrMsg(server, g_strdup_printf("GFFTerminated! %s", error->message)) ;
- ZMAPSERVER_LOG(Critical, FILE_PROTOCOL_STR, server->file_path,
- "%s", server->last_err_msg) ; }
- else
- {
- setErrMsg(server,
- g_strdup_printf("zMapGFFParseHeader() failed for line %d: %s",
- zMapGFFGetLineNumber(get_features.parser),
- get_features.gff_line->str)) ;
- ZMAPSERVER_LOG(Critical, FILE_PROTOCOL_STR, server->file_path,
- "%s", server->last_err_msg) ;
}
+
+ break ;
}
- get_features.result = ZMAP_SERVERRESPONSE_REQFAIL ;
}
+ else
+ {
+ /* Fetch all the alignment blocks for all the sequences, this all hacky right now as really.
+ * we would have to parse and reparse the file....can be done but not needed this second. */
+ g_hash_table_foreach(feature_context_out->alignments, eachAlignmentSequence, (gpointer)&get_features) ;
- break ;
+ if (get_features.sequence_finished)
+ break ;
+ }
}
}
- if (get_features.result == ZMAP_SERVERRESPONSE_OK)
- {
- /* Fetch all the alignment blocks for all the sequences, this all hacky right now as really.
- * we would have to parse and reparse the file....can be done but not needed this second. */
- g_hash_table_foreach(feature_context_out->alignments, eachAlignmentSequence, (gpointer)&get_features) ;
-
- }
-
/* Clear up. */
zMapGFFDestroyParser(get_features.parser) ;
@@ -633,6 +595,7 @@ static ZMapServerResponseType getContextSequence(void *server_in, GData *styles,
}
+/* THIS ISN'T RIGHT..... */
/* Return the last error message. */
static char *lastErrorMsg(void *server_in)
{
@@ -697,40 +660,6 @@ static ZMapServerResponseType destroyConnection(void *server_in)
*/
-/* A bit of a lash up for now, we need the parent->child mapping for a sequence and since
- * the code in this file so far simply reads a GFF file for now, we just fake it by setting
- * everything to be the same for child/parent... */
-static void addMapping(ZMapFeatureContext feature_context, ZMapGFFHeader header)
-{
- ZMapFeatureBlock feature_block = NULL;//feature_context->master_align->blocks->data ;
-
- feature_block = (ZMapFeatureBlock)(zMap_g_hash_table_nth(feature_context->master_align->blocks, 0)) ;
-
- /* We just override whatever is already there...this may not be the thing to do if there
- * are several files.... */
- feature_context->parent_name = feature_context->sequence_name ;
-
- feature_context->parent_span.x1 = header->features_start ;
- feature_context->parent_span.x2 = header->features_end ;
-
- /* I don't like having to do this right down here but user is allowed to specify "0" for
- * end coord meaning "to the end of the sequence" and this is where we know the end... */
- if (feature_block->block_to_sequence.t2 == 0)
- feature_block->block_to_sequence.t2 = header->features_end ;
-
- feature_context->sequence_to_parent.p1 = feature_context->sequence_to_parent.c1
- = feature_block->block_to_sequence.q1 = feature_block->block_to_sequence.t1 ;
-
- feature_context->sequence_to_parent.p2 = feature_context->sequence_to_parent.c2
- = feature_block->block_to_sequence.q2 = feature_block->block_to_sequence.t2 ;
-
- feature_context->length = feature_context->sequence_to_parent.c2 - feature_context->sequence_to_parent.c1 + 1;
-
- return ;
-}
-
-
-
/* Small utility to deal with error messages from the GIOchannel package.
* Note that we set gff_file_err_inout to NULL */
static void setLastErrorMsg(FileServer server, GError **gff_file_err_inout)
@@ -773,7 +702,7 @@ static void eachBlock(gpointer key, gpointer data, gpointer user_data)
if (get_features->result == ZMAP_SERVERRESPONSE_OK)
{
- if (!sequenceRequest(get_features->server, get_features->parser,
+ if (!featuresRequest(get_features->server, get_features->parser,
get_features->gff_line, feature_block))
{
ZMAPSERVER_LOG(Warning, FILE_PROTOCOL_STR, get_features->server->file_path,
@@ -787,7 +716,7 @@ static void eachBlock(gpointer key, gpointer data, gpointer user_data)
}
-static gboolean sequenceRequest(FileServer server, ZMapGFFParser parser, GString* gff_line,
+static gboolean featuresRequest(FileServer server, ZMapGFFParser parser, GString* gff_line,
ZMapFeatureBlock feature_block)
{
gboolean result = FALSE ;
@@ -880,6 +809,103 @@ static gboolean sequenceRequest(FileServer server, ZMapGFFParser parser, GString
}
+
+/* Process all the alignments in a context. */
+static void eachAlignmentSequence(gpointer key, gpointer data, gpointer user_data)
+{
+ ZMapFeatureAlignment alignment = (ZMapFeatureAlignment)data ;
+ GetFeatures get_features = (GetFeatures)user_data ;
+
+ if (get_features->result == ZMAP_SERVERRESPONSE_OK)
+ g_hash_table_foreach(alignment->blocks, eachBlockSequence, (gpointer)get_features) ;
+
+ return ;
+}
+
+
+static void eachBlockSequence(gpointer key, gpointer data, gpointer user_data)
+{
+ ZMapFeatureBlock feature_block = (ZMapFeatureBlock)data ;
+ GetFeatures get_features = (GetFeatures)user_data ;
+
+ if (get_features->result == ZMAP_SERVERRESPONSE_OK)
+ {
+ gboolean sequence_finished ;
+
+
+ if (zMapGFFParseSequence(get_features->parser, get_features->gff_line->str, &sequence_finished)
+ && sequence_finished)
+ {
+ ZMapSequence sequence ;
+
+ if (!(sequence = zMapGFFGetSequence(get_features->parser)))
+ {
+ GError *error = NULL ;
+
+ error = zMapGFFGetError(get_features->parser);
+
+ setErrMsg(get_features->server,
+ g_strdup_printf("zMapGFFGetSequence() failed, error=%s",
+ error->message));
+ ZMAPSERVER_LOG(Warning, FILE_PROTOCOL_STR,
+ get_features->server->file_path,
+ "%s", get_features->server->last_err_msg);
+ }
+ else
+ {
+ ZMapFeatureContext context ;
+ ZMapFeatureSet feature_set ;
+
+ get_features->sequence_finished = TRUE ;
+
+ if (zMapFeatureDNACreateFeatureSet(feature_block, &feature_set))
+ {
+ ZMapFeatureTypeStyle dna_style = NULL;
+ ZMapFeature feature;
+
+ /* This temp style creation feels wrong, and probably is,
+ * but we don't have the merged in default styles in here,
+ * or so it seems... */
+ dna_style = zMapStyleCreate(ZMAP_FIXED_STYLE_DNA_NAME,
+ ZMAP_FIXED_STYLE_DNA_NAME_TEXT);
+
+ feature = zMapFeatureDNACreateFeature(feature_block, dna_style,
+ sequence->sequence, sequence->length);
+
+ zMapStyleDestroy(dna_style);
+ }
+
+ context = (ZMapFeatureContext)zMapFeatureGetParentGroup((ZMapFeatureAny)feature_block,
+ ZMAPFEATURE_STRUCT_CONTEXT) ;
+
+ /* I'm going to create the three frame translation up front! */
+ if (zMap_g_list_find_quark(context->feature_set_names, zMapStyleCreateID(ZMAP_FIXED_STYLE_3FT_NAME)))
+ {
+ if ((zMapFeature3FrameTranslationCreateSet(feature_block, &feature_set)))
+ {
+ ZMapFeatureTypeStyle frame_style = NULL;
+
+ frame_style = zMapStyleCreate(ZMAP_FIXED_STYLE_DNA_NAME,
+ ZMAP_FIXED_STYLE_DNA_NAME_TEXT);
+
+ zMapFeature3FrameTranslationSetCreateFeatures(feature_set, frame_style);
+
+ zMapStyleDestroy(frame_style);
+ }
+ }
+
+ g_free(sequence);
+ }
+ }
+ }
+
+
+ return ;
+}
+
+
+
+
static gboolean getServerInfo(FileServer server, ZMapServerInfo info)
{
gboolean result = FALSE ;
@@ -902,3 +928,166 @@ static void setErrMsg(FileServer server, char *new_msg)
return ;
}
+
+
+
+/* Tries to smap sequence into whatever its parent is, if the call fails then we set all the
+ * mappings in feature_context to be something sensible...we hope....
+ */
+static gboolean getSequenceMapping(FileServer server, ZMapFeatureContext feature_context)
+{
+ gboolean result = TRUE ;
+ ZMapGFFParser parser ;
+ GString *gff_line ;
+ gsize terminator_pos = 0 ;
+ GError *gff_file_err = NULL ;
+ ZMapGFFHeader header ;
+ GError *error = NULL ;
+
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
+ char *parent_name = NULL, *parent_class = NULL ;
+ ZMapMapBlockStruct sequence_to_parent = {0, 0, 0, 0}, parent_to_self = {0, 0, 0, 0} ;
+ int parent_length = 0 ;
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+
+ GIOStatus gio_status ;
+ gboolean status ;
+
+
+ parser = zMapGFFCreateParser() ;
+
+ gff_line = g_string_sized_new(2000) ; /* Probably not many lines will be >
+ 2k chars. */
+
+ /* Read the header, needed for feature coord range. */
+ while ((gio_status = g_io_channel_read_line_string(server->gff_file, gff_line,
+ &terminator_pos,
+ &gff_file_err)) == G_IO_STATUS_NORMAL)
+ {
+ gboolean done_header = FALSE ;
+
+ *(gff_line->str + terminator_pos) = '\0' ; /* Remove terminating newline. */
+
+ if (zMapGFFParseHeader(parser, gff_line->str, &done_header))
+ {
+ if (done_header)
+ break ;
+ else
+ gff_line = g_string_truncate(gff_line, 0) ; /* Reset line to empty. */
+ }
+ else
+ {
+ if (!done_header)
+ {
+ error = zMapGFFGetError(parser) ;
+
+ if (!error)
+ {
+ /* SHOULD ABORT HERE.... */
+ setErrMsg(server,
+ g_strdup_printf("zMapGFFParseLine() failed with no GError for line %d: %s",
+ zMapGFFGetLineNumber(parser), gff_line->str)) ;
+ ZMAPSERVER_LOG(Critical, FILE_PROTOCOL_STR, server->file_path,
+ "%s", server->last_err_msg) ;
+
+ result = FALSE ;
+ }
+ else
+ {
+ /* If the error was serious we stop processing and return the error,
+ * otherwise we just log the error. */
+ if (zMapGFFTerminated(parser))
+ {
+ result = FALSE ;
+ setErrMsg(server, g_strdup_printf("%s", error->message)) ;
+ }
+ else
+ {
+ setErrMsg(server,
+ g_strdup_printf("zMapGFFParseHeader() failed for line %d: %s",
+ zMapGFFGetLineNumber(parser),
+ gff_line->str)) ;
+ ZMAPSERVER_LOG(Critical, FILE_PROTOCOL_STR, server->file_path,
+ "%s", server->last_err_msg) ;
+ }
+ }
+ }
+
+ break ;
+ }
+ }
+
+ if (gio_status == G_IO_STATUS_NORMAL && result)
+ {
+ header = zMapGFFGetHeader(parser) ;
+
+ addMapping(feature_context, header) ;
+
+ zMapGFFFreeHeader(header) ;
+ }
+
+
+ /* Clear up. */
+ zMapGFFDestroyParser(parser) ;
+ g_string_free(gff_line, TRUE) ;
+
+ return result ;
+}
+
+
+/* We insist that the header specifies the range of features required and we just use that
+ * for all the mappings. */
+static void addMapping(ZMapFeatureContext feature_context, ZMapGFFHeader header)
+{
+ ZMapFeatureBlock feature_block = NULL;//feature_context->master_align->blocks->data ;
+
+ feature_block = (ZMapFeatureBlock)(zMap_g_hash_table_nth(feature_context->master_align->blocks, 0)) ;
+
+ /* We just override whatever is already there...this may not be the thing to do if there
+ * are several files.... */
+ feature_context->parent_name = feature_context->sequence_name ;
+
+ /* In theory sequences all start at '1' so we insert that as the start of the parent, best we
+ * can do really. */
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
+ feature_context->parent_span.x1 = header->features_start ;
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+ feature_context->parent_span.x1 = 1 ;
+ feature_context->parent_span.x2 = header->features_end ;
+
+ feature_context->sequence_to_parent.p1 = feature_context->sequence_to_parent.c1
+ = feature_block->block_to_sequence.q1 = feature_block->block_to_sequence.t1 = header->features_start ;
+
+ feature_context->sequence_to_parent.p2 = feature_context->sequence_to_parent.c2
+ = feature_block->block_to_sequence.q2 = feature_block->block_to_sequence.t2 = header->features_end ;
+
+ feature_context->length = feature_context->sequence_to_parent.c2 - feature_context->sequence_to_parent.c1 + 1;
+
+ return ;
+}
+
+
+
+/* For some data we need to go back to the start of the file and reread so this function
+ * simply resets the file pointer. */
+static gboolean resetToStart(FileServer server)
+{
+ gboolean result = FALSE ;
+ GError *error = NULL ;
+
+ if (g_io_channel_seek_position(server->gff_file, 0, G_SEEK_SET, &error) == G_IO_STATUS_NORMAL)
+ {
+ result = TRUE ;
+ }
+ else
+ {
+ setLastErrorMsg(server, &error) ;
+
+ result = FALSE ;
+ }
+
+ return result ;
+}
+
+
+