From 58c0233d131e09ec75eaf9e25d140432fd394376 Mon Sep 17 00:00:00 2001
From: rnc <rnc>
Date: Thu, 20 Nov 2003 14:32:31 +0000
Subject: [PATCH] removed KEY from methodStruct - using name instead
---
src/zmapWindow/seqregion.h | 2 +-
src/zmapWindow/seqregionconvert.c | 46 +++++++++++++++++--------------
2 files changed, 26 insertions(+), 22 deletions(-)
diff --git a/src/zmapWindow/seqregion.h b/src/zmapWindow/seqregion.h
index 987da76ca..51cc02081 100755
--- a/src/zmapWindow/seqregion.h
+++ b/src/zmapWindow/seqregion.h
@@ -1,3 +1,4 @@
+/* Last edited: Nov 20 13:47 2003 (rnc) */
/* file: seqregion.h
* Author: Richard Durbin (rd@mrc-lmb.cam.ac.uk)
* Copyright (C) J Thierry-Mieg and R Durbin, 1992
@@ -139,7 +140,6 @@ typedef struct segStruct SEG;
typedef struct methodStruct
{
methodID id;
- KEY key; /* private */
char *name, *remark;
unsigned int flags;
int colour, CDS_colour, upStrandColour;
diff --git a/src/zmapWindow/seqregionconvert.c b/src/zmapWindow/seqregionconvert.c
index 89b71df7c..3bf0cfc73 100755
--- a/src/zmapWindow/seqregionconvert.c
+++ b/src/zmapWindow/seqregionconvert.c
@@ -1,3 +1,4 @@
+/* Last edited: Nov 20 14:12 2003 (rnc) */
/* file: seqregionconvert.c
* Author: Simon Kelley (srk@sanger.ac.uk)
* Copyright (c) Sanger Institute, 2003
@@ -35,9 +36,9 @@
#include <whooks/systags.h>
#include <whooks/classes.h>
-static methodID srMethCreate(SeqRegion *region, KEY methodKey);
-static srMeth *methodFromKey(Array methods, KEY key);
-static methodID srMethodMake(SeqRegion *region, KEY key);
+static methodID srMethCreate (SeqRegion *region, char *methodName);
+static srMeth *methodFromName(Array methods , char *methodName);
+static methodID srMethodMake (SeqRegion *region, char *methodName);
/* exported functi
on */
@@ -55,54 +56,52 @@ srMeth *srMethodFromID(SeqRegion *region, methodID id)
return NULL;
}
-static srMeth *methodFromKey(Array methods, KEY key)
+static srMeth *methodFromName(Array methods, char *methodName)
{
int i;
- key = lexAliasOf(key); /* use canonical key */
-
if (methods)
for (i=0; i<arrayMax(methods); i++)
{
srMeth *meth = arrp(methods, i, srMeth);
- if (meth->key == key)
+ if (meth->name == methodName)
return meth;
}
return NULL;
}
-static methodID srMethodMake(SeqRegion *region, KEY key)
+static methodID srMethodMake(SeqRegion *region, char *methodName)
{
srMeth *meth;
- if ((meth = methodFromKey(region->methods, key)))
+ if ((meth = methodFromName(region->methods, methodName)))
return meth->id;
- else if ((meth = methodFromKey(region->oldMethods, key)))
+ else if ((meth = methodFromName(region->oldMethods, methodName)))
{
srMeth *new = arrayp(region->methods, arrayMax(region->methods), srMeth);
*new = *meth;
return new->id;
}
else
- return srMethCreate(region, key);
+ return srMethCreate(region, methodName);
}
-static methodID srMethCreate(SeqRegion *region, KEY methodKey)
+static methodID srMethCreate(SeqRegion *region, char *methodName)
{
srMeth *meth;
OBJ obj ;
int k;
char *text;
+ KEY methodKey;
- if (class(methodKey) != _VMethod)
- messcrash ("methodAdd() - methodKey not in class 'Method'");
+ if (!lexword2key(methodName, &methodKey, _VMethod))
+ messcrash ("srMethodCreate() - methodKey not found in lex.");
if (!(obj = bsCreate (methodKey)))
return 0;
meth = arrayp(region->methods, arrayMax(region->methods), srMeth);
meth->id = region->idc++;
- meth->key = methodKey;
meth->name = str2p(name(methodKey), region->bucket);
meth->flags &= ~METHOD_CALCULATED ;/* unset flag */
meth->flags |= METHOD_DONE ; /* set flag */
@@ -204,14 +203,15 @@ void seqRegionConvert(SeqRegion *region)
for (i = 0 ; i < keySetMax(allKeys) ; i++)
{
- KEY method, key = keySet(allKeys, i);
+ KEY methodKey, key = keySet(allKeys, i);
SMapKeyInfo *info = sMapKeyInfo(region->smap, key);
int x1, x2;
SMapStatus status ;
SEG *seg;
OBJ obj;
-
- if ((obj = bsCreate(key)) && bsGetKey(obj, str2tag("Method"), &method))
+ char *methodName;
+
+ if ((obj = bsCreate(key)) && bsGetKey(obj, str2tag("Method"), &methodKey))
{
Coord cdsStart, cdsEnd;
srType type = SR_SEQUENCE; /* default */
@@ -220,6 +220,9 @@ void seqRegionConvert(SeqRegion *region)
BOOL isCDS = FALSE;
Array exons = NULL;
+ methodName = messalloc(strlen(name(methodKey))); /* need to remember to free this? */
+ methodName = str2p(name(methodKey), region->bucket);
+
if (bsFindTag(obj, str2tag("Start_not_Found")))
{
isStartNotFound = TRUE;
@@ -274,9 +277,9 @@ void seqRegionConvert(SeqRegion *region)
seg->x1 = x1;
seg->x2 = x2;
seg->phase = phase;
- seg->method = srMethodMake(region, method);if (type == SR_TRANSCRIPT);
+ seg->method = srMethodMake(region, methodName);
- if (type = SR_TRANSCRIPT)
+ if (type == SR_TRANSCRIPT)
{
if (!isCDS)
sMapMap(info, 1, 0, &cdsStart, &cdsEnd, NULL, NULL);
@@ -313,7 +316,7 @@ void seqRegionConvert(SeqRegion *region)
seg->x1 = x1;
seg->x2 = x2;
seg->score = u[3].f;
- seg->method = srMethodMake(region, u[0].k);
+ seg->method = srMethodMake(region, str2p(name(u[0].k), region->bucket));
}
}
if (bsFindTag(obj, str2tag("Homol")))
@@ -323,6 +326,7 @@ void seqRegionConvert(SeqRegion *region)
}
}
+
bsDestroy(obj);
--
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