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ensembl-gh-mirror
zmap
Commits
5c08db5f
Commit
5c08db5f
authored
15 years ago
by
edgrif
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TEMP FIX, MORE WORK TO BE DONE: we want align and block tags in xml, it's hacked for now.
parent
c25a5d7e
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1 changed file
src/zmapFeature/zmapFeatureXML.c
+59
-35
59 additions, 35 deletions
src/zmapFeature/zmapFeatureXML.c
with
59 additions
and
35 deletions
src/zmapFeature/zmapFeatureXML.c
+
59
−
35
View file @
5c08db5f
...
...
@@ -27,9 +27,9 @@
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
* Last edited:
Feb
3
1
0:48
2009 (
rds
)
* Last edited:
Sep
1
1
7:24
2009 (
edgrif
)
* Created: Fri Jul 21 14:48:18 2006 (rds)
* CVS info: $Id: zmapFeatureXML.c,v 1.
9
2009-0
2
-0
3
1
0:48:14 rds
Exp $
* CVS info: $Id: zmapFeatureXML.c,v 1.
10
2009-0
9
-0
2
1
3:52:35 edgrif
Exp $
*-------------------------------------------------------------------
*/
...
...
@@ -87,7 +87,12 @@ GArray *zMapFeatureAnyAsXMLEvents(ZMapFeatureAny feature_any,
return
array
;
}
/* don't like this interface of either or with xml_writer and xml_events_out!!! */
/* don't like this interface of either or with xml_writer and xml_events_out!!!
*
* Yes...there's quite a lot that needs changing to make things easier in the
* future....
*
* */
gboolean
zMapFeatureAnyAsXML
(
ZMapFeatureAny
feature_any
,
ZMapXMLWriter
xml_writer
,
GArray
**
xml_events_out
,
...
...
@@ -151,29 +156,29 @@ ZMapFeatureContextExecuteStatus xmlDumpCB(GQuark key,
{
case
ZMAPFEATURE_STRUCT_CONTEXT
:
feature_context
=
(
ZMapFeatureContext
)
feature_any
;
if
(
xml_data
->
doEndTag
.
context
)
generateContextXMLEndEvent
(
xml_data
);
generateContextXMLEvents
(
feature_context
,
xml_data
);
xml_data
->
doEndTag
.
context
=
1
;
xml_data
->
doEndTag
.
align
=
xml_data
->
doEndTag
.
block
=
xml_data
->
doEndTag
.
featureset
=
xml_data
->
doEndTag
.
align
=
xml_data
->
doEndTag
.
block
=
xml_data
->
doEndTag
.
featureset
=
xml_data
->
doEndTag
.
feature
=
0
;
break
;
case
ZMAPFEATURE_STRUCT_ALIGN
:
feature_align
=
(
ZMapFeatureAlignment
)
feature_any
;
if
(
xml_data
->
doEndTag
.
align
)
generateAlignXMLEndEvent
(
xml_data
);
generateAlignXMLEvents
(
feature_align
,
xml_data
);
xml_data
->
doEndTag
.
align
=
1
;
xml_data
->
doEndTag
.
block
=
xml_data
->
doEndTag
.
featureset
=
xml_data
->
doEndTag
.
feature
=
0
;
xml_data
->
doEndTag
.
block
=
xml_data
->
doEndTag
.
featureset
=
xml_data
->
doEndTag
.
feature
=
0
;
break
;
case
ZMAPFEATURE_STRUCT_BLOCK
:
feature_block
=
(
ZMapFeatureBlock
)
feature_any
;
if
(
xml_data
->
doEndTag
.
block
)
...
...
@@ -182,9 +187,9 @@ ZMapFeatureContextExecuteStatus xmlDumpCB(GQuark key,
generateBlockXMLEvents
(
feature_block
,
xml_data
);
xml_data
->
doEndTag
.
block
=
1
;
xml_data
->
doEndTag
.
featureset
=
xml_data
->
doEndTag
.
feature
=
0
;
xml_data
->
doEndTag
.
featureset
=
xml_data
->
doEndTag
.
feature
=
0
;
break
;
case
ZMAPFEATURE_STRUCT_FEATURESET
:
feature_set
=
(
ZMapFeatureSet
)
feature_any
;
if
(
xml_data
->
doEndTag
.
featureset
)
...
...
@@ -192,9 +197,10 @@ ZMapFeatureContextExecuteStatus xmlDumpCB(GQuark key,
generateFeatureSetXMLEvents
(
feature_set
,
xml_data
);
xml_data
->
doEndTag
.
featureset
=
1
;
xml_data
->
doEndTag
.
align
=
xml_data
->
doEndTag
.
block
=
xml_data
->
doEndTag
.
featureset
=
1
;
xml_data
->
doEndTag
.
feature
=
0
;
break
;
case
ZMAPFEATURE_STRUCT_FEATURE
:
feature_ft
=
(
ZMapFeature
)
feature_any
;
if
(
xml_data
->
doEndTag
.
feature
)
...
...
@@ -204,6 +210,7 @@ ZMapFeatureContextExecuteStatus xmlDumpCB(GQuark key,
xml_data
->
doEndTag
.
feature
=
1
;
break
;
case
ZMAPFEATURE_STRUCT_INVALID
:
default:
zMapAssertNotReached
();
...
...
@@ -229,9 +236,13 @@ void generateClosingEvents(ZMapFeatureAny feature_any,
end_point
=
ZMAPFEATURE_STRUCT_CONTEXT
;
int
i
=
0
;
end_point
=
feature_any
->
struct_type
;
/* HACK.....SEE COMMENTS IN CALLER OF THIS FUNC.... */
if
(
feature_any
->
struct_type
==
ZMAPFEATURE_STRUCT_FEATURESET
)
end_point
=
ZMAPFEATURE_STRUCT_ALIGN
;
else
end_point
=
feature_any
->
struct_type
;
if
(
start_point
>=
end_point
)
if
(
start_point
>=
end_point
)
{
for
(
i
=
start_point
;
i
>=
end_point
;
i
--
)
{
...
...
@@ -342,33 +353,42 @@ void generateFeatureSetXMLEvents(ZMapFeatureSet feature_set,
{
case
ZMAPFEATURE_XML_XREMOTE
:
{
ZMapFeatureAny
feature_any
=
NULL
;
ZMapFeatureAlignment
align
;
ZMapFeatureBlock
block
;
block
=
zMapFeatureGetParentGroup
((
ZMapFeatureAny
)
feature_set
,
ZMAPFEATURE_STRUCT_BLOCK
)
;
align
=
zMapFeatureGetParentGroup
((
ZMapFeatureAny
)
block
,
ZMAPFEATURE_STRUCT_ALIGN
)
;
event
.
type
=
ZMAPXML_START_ELEMENT_EVENT
;
event
.
data
.
name
=
g_quark_from_string
(
"align"
)
;
xml_data
->
xml_events_out
=
g_array_append_val
(
xml_data
->
xml_events_out
,
event
)
;
event
.
type
=
ZMAPXML_ATTRIBUTE_EVENT
;
event
.
data
.
comp
.
name
=
g_quark_from_string
(
"name"
);
event
.
data
.
comp
.
data
=
ZMAPXML_EVENT_DATA_QUARK
;
event
.
data
.
comp
.
value
.
quark
=
align
->
unique_id
;
xml_data
->
xml_events_out
=
g_array_append_val
(
xml_data
->
xml_events_out
,
event
);
event
.
type
=
ZMAPXML_START_ELEMENT_EVENT
;
event
.
data
.
name
=
g_quark_from_string
(
"block"
)
;
xml_data
->
xml_events_out
=
g_array_append_val
(
xml_data
->
xml_events_out
,
event
)
;
event
.
type
=
ZMAPXML_ATTRIBUTE_EVENT
;
event
.
data
.
comp
.
name
=
g_quark_from_string
(
"name"
);
event
.
data
.
comp
.
data
=
ZMAPXML_EVENT_DATA_QUARK
;
event
.
data
.
comp
.
value
.
quark
=
block
->
unique_id
;
xml_data
->
xml_events_out
=
g_array_append_val
(
xml_data
->
xml_events_out
,
event
);
event
.
type
=
ZMAPXML_START_ELEMENT_EVENT
;
event
.
data
.
name
=
g_quark_from_string
(
"featureset"
);
xml_data
->
xml_events_out
=
g_array_append_val
(
xml_data
->
xml_events_out
,
event
);
if
((
feature_any
=
zMapFeatureGetParentGroup
((
ZMapFeatureAny
)
feature_set
,
ZMAPFEATURE_STRUCT_BLOCK
)))
{
event
.
type
=
ZMAPXML_ATTRIBUTE_EVENT
;
event
.
data
.
comp
.
name
=
g_quark_from_string
(
"block"
);
event
.
data
.
comp
.
data
=
ZMAPXML_EVENT_DATA_QUARK
;
event
.
data
.
comp
.
value
.
quark
=
feature_any
->
unique_id
;
xml_data
->
xml_events_out
=
g_array_append_val
(
xml_data
->
xml_events_out
,
event
);
}
if
(
feature_any
&&
(
feature_any
=
zMapFeatureGetParentGroup
(
feature_any
,
ZMAPFEATURE_STRUCT_ALIGN
)))
{
event
.
type
=
ZMAPXML_ATTRIBUTE_EVENT
;
event
.
data
.
comp
.
name
=
g_quark_from_string
(
"align"
);
event
.
data
.
comp
.
data
=
ZMAPXML_EVENT_DATA_QUARK
;
event
.
data
.
comp
.
value
.
quark
=
feature_any
->
unique_id
;
xml_data
->
xml_events_out
=
g_array_append_val
(
xml_data
->
xml_events_out
,
event
);
}
break
;
}
break
;
default:
zMapLogWarning
(
"%s"
,
"What type of xml did you want?"
);
break
;
...
...
@@ -539,6 +559,8 @@ void generateAlignXMLEndEvent(XMLContextDump xml_data)
switch
(
xml_data
->
xml_type
)
{
case
ZMAPFEATURE_XML_XREMOTE
:
event
.
data
.
name
=
g_quark_from_string
(
"align"
);
xml_data
->
xml_events_out
=
g_array_append_val
(
xml_data
->
xml_events_out
,
event
);
break
;
default:
zMapLogWarning
(
"%s"
,
"What type of xml did you want?"
);
...
...
@@ -557,6 +579,8 @@ void generateBlockXMLEndEvent(XMLContextDump xml_data)
switch
(
xml_data
->
xml_type
)
{
case
ZMAPFEATURE_XML_XREMOTE
:
event
.
data
.
name
=
g_quark_from_string
(
"block"
);
xml_data
->
xml_events_out
=
g_array_append_val
(
xml_data
->
xml_events_out
,
event
);
break
;
default:
zMapLogWarning
(
"%s"
,
"What type of xml did you want?"
);
...
...
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