extern void ExportBadgesDialog (
DialoG d,
ValNodePtr PNTR head
)
{
Char buf [128], tmp [32];
DoC doc;
IntBadgPtr ibp;
Int2 k, numItems;
SscBadgPtr sbp;
sbp = (SscBadgPtr) GetObjectExtra (d);
if (sbp == NULL || head == NULL) return;
doc = sbp->badglog;
GetDocParams (doc, &numItems, NULL);
for (k = 1; k <= numItems; k++) {
ibp = GetBadgInfo (sbp, k);
if (ibp == NULL) continue;
if (StringHasNoText (ibp->name)) continue;
buf [0] = '\0';
ExportDocCell (doc, k, 1, buf);
TabToCol (buf, 22);
ExportDocCell (doc, k, 3, tmp);
StringCat (buf, tmp);
ValNodeCopyStr (head, k + 100, buf);
}
}
static void AnnotateBestOrf (
BioseqPtr bsp,
Int2 genCode,
Boolean altstart
)
{
CdRegionPtr crp;
Int2 i, best, idx;
OrfData od;
ProtRefPtr prp;
SeqFeatPtr sfp;
SeqInt sint;
TransTablePtr tbl;
ValNode vn;
SeqFeatXrefPtr xref;
if (bsp == NULL) return;
for (i = 0; i < 6; i++) {
od.curlen [i] = INT4_MIN;
od.bestlen [i] = 0;
od.currstart [i] = 0;
od.beststart [i] = 0;
od.sublen [i] = INT4_MIN;
od.inorf [i] = FALSE;
}
od.altstart = altstart;
/* use simultaneous 6-frame translation finite state machine */
tbl = TransTableNew (genCode);
if (tbl != NULL) {
TransTableProcessBioseq (tbl, LookForOrfs, (Pointer) &od, bsp);
}
TransTableFree (tbl);
best = -1;
idx = -1;
for (i = 0; i < 6; i++) {
if (od.bestlen [i] > best) {
best = od.bestlen [i];
idx = i;
}
}
if (idx == -1) return;
/* make feature location on largest ORF */
if (idx < 3) {
MemSet ((Pointer) &sint, 0, sizeof (SeqInt));
sint.from = od.beststart [idx] + idx;
sint.to = sint.from + (od.bestlen [idx]) * 3 + 2;
sint.id = SeqIdFindBest (bsp->id, 0);
sint.strand = Seq_strand_plus;
vn.choice = SEQLOC_INT;
vn.extended = 0;
vn.data.ptrvalue = (Pointer) &sint;
vn.next = NULL;
} else {
MemSet ((Pointer) &sint, 0, sizeof (SeqInt));
sint.from = od.beststart [idx] + idx - 3;
sint.to = sint.from + (od.bestlen [idx]) * 3 + 2;
sint.id = SeqIdFindBest (bsp->id, 0);
sint.strand = Seq_strand_minus;
vn.choice = SEQLOC_INT;
vn.extended = 0;
vn.data.ptrvalue = (Pointer) &sint;
vn.next = NULL;
}
/* make CDS feature with unknown product */
sfp = CreateNewFeatureOnBioseq (bsp, SEQFEAT_CDREGION, &vn);
if (sfp == NULL) return;
crp = CreateNewCdRgn (1, FALSE, genCode);
if (crp == NULL) return;
crp->frame = 1;
sfp->data.value.ptrvalue = (Pointer) crp;
prp = ProtRefNew ();
if (prp == NULL) return;
xref = SeqFeatXrefNew ();
if (xref == NULL) return;
xref->data.choice = SEQFEAT_PROT;
xref->data.value.ptrvalue = (Pointer) prp;
xref->next = sfp->xref;
sfp->xref = xref;
prp->name = ValNodeCopyStr (NULL, 0, "unknown");
}
NLM_EXTERN ValNodePtr LIBCALL Nlm_DirCatalog (Nlm_CharPtr pathname)
{
#ifdef OS_MAC
long dirID;
OSErr err;
short index;
unsigned short num;
Nlm_Char path[PATH_MAX];
CInfoPBRec pbc;
HParamBlockRec pbh;
short vRefNum;
#endif
#ifdef OS_UNIX
Nlm_Uint1 choice;
#ifdef OS_UNIX_DARWIN
DIR *dirp;
struct dirent *dep;
#else
Nlm_Char buf [256];
Nlm_Char ch;
Nlm_Char cmmd [PATH_MAX + 20];
FILE *fp;
Nlm_CharPtr ptr;
#endif
#endif
ValNodePtr vnp = NULL;
if (pathname != NULL && pathname [0] != '\0') {
#ifdef OS_MAC
Nlm_StringNCpy_0 (path, pathname, sizeof (path));
Nlm_CtoPstr ((Nlm_CharPtr) path);
Nlm_MemSet ((Nlm_VoidPtr) (&pbh), 0, sizeof (HParamBlockRec));
pbh.volumeParam.ioNamePtr = (StringPtr) path;
pbh.volumeParam.ioVolIndex = -1;
err = PBHGetVInfo (&pbh, FALSE);
if (err != noErr) return NULL;
vRefNum = pbh.volumeParam.ioVRefNum;
Nlm_StringNCpy_0 (path, pathname, sizeof (path));
Nlm_CtoPstr ((Nlm_CharPtr) path);
Nlm_MemSet ((Nlm_VoidPtr) (&pbc), 0, sizeof (CInfoPBRec));
pbc.dirInfo.ioNamePtr = (StringPtr) path;
pbc.dirInfo.ioVRefNum = vRefNum;
err = PBGetCatInfo (&pbc, FALSE);
if (err != noErr) return NULL;
if (pbc.dirInfo.ioFlAttrib & 16) {
num = pbc.dirInfo.ioDrNmFls;
dirID = pbc.dirInfo.ioDrDirID;
for (index = 1; index <= num; index++) {
Nlm_MemSet ((Nlm_VoidPtr) (&pbc), 0, sizeof (CInfoPBRec));
pbc.dirInfo.ioNamePtr = (StringPtr) path;
pbc.dirInfo.ioVRefNum = vRefNum;
pbc.dirInfo.ioFDirIndex = index;
pbc.dirInfo.ioDrDirID = dirID;
pbc.dirInfo.ioACUser = 0;
err = PBGetCatInfo (&pbc, FALSE);
if (err == noErr) {
Nlm_PtoCstr ((Nlm_CharPtr) path);
if (pbc.dirInfo.ioFlAttrib & 16) {
ValNodeCopyStr (&vnp, 1, path);
} else {
ValNodeCopyStr (&vnp, 0, path);
}
}
}
}
#endif
#if defined(WIN32)
{{
Nlm_Char x_path[PATH_MAX];
WIN32_FIND_DATA fData;
HANDLE hFindFile;
Nlm_StringNCpy_0(x_path, pathname, sizeof(x_path) - 5);
Nlm_StringCat(x_path, "\\*.*");
hFindFile = FindFirstFile(x_path, &fData);
if (hFindFile == INVALID_HANDLE_VALUE)
return 0;
do {
if (fData.cFileName[0] != '.' ||
(fData.cFileName[1] != '.' && fData.cFileName[1] != '\0'))
ValNodeCopyStr
(&vnp, (fData.dwFileAttributes & FILE_ATTRIBUTE_DIRECTORY) ? 1 : 0,
fData.cFileName);
} while ( FindNextFile(hFindFile, &fData) );
FindClose(hFindFile);
}}
#endif
#ifdef OS_UNIX
#ifdef OS_UNIX_DARWIN
dirp = opendir(pathname);
if (dirp == NULL) return NULL;
while ((dep = readdir(dirp)) != NULL) {
/* ignore 'invisible' files. */
if (dep->d_namlen < 1 || dep->d_name[0] == '.')
continue;
if (dep->d_type == DT_DIR) /* directory */
choice = 1;
else /* all other file types. */
choice = 0;
ValNodeCopyStr (&vnp, choice, dep->d_name);
}
closedir(dirp);
#else
sprintf (cmmd, "ls -1p %s 2>/dev/null", pathname);
fp = popen (cmmd, "r");
if (fp == NULL) return NULL;
while (Nlm_FileGets (buf, sizeof (buf), fp) != NULL) {
ptr = buf;
ch = *ptr;
while (ch != '\0' && ch != '\n' && ch != '\r') {
ptr++;
ch = *ptr;
}
*ptr = '\0';
choice = 0;
ptr = Nlm_StringChr (buf, '/');
if (ptr != NULL) {
*ptr = '\0';
choice = 1;
}
ValNodeCopyStr (&vnp, choice, buf);
}
pclose (fp);
#endif
#endif
#ifdef OS_VMS
#endif
}
return vnp;
}