static void DoFastaTrans (
SeqFeatPtr sfp,
Pointer userdata
)
{
ByteStorePtr bs;
CSpeedFlagPtr cfp;
CharPtr seq, str;
if (sfp == NULL) return;
cfp = (CSpeedFlagPtr) userdata;
if (cfp == NULL) return;
if (sfp->data.choice != SEQFEAT_CDREGION) return;
bs = ProteinFromCdRegion (sfp, FALSE);
if (bs == NULL) return;
seq = (CharPtr) BSMerge (bs, NULL);
BSFree (bs);
if (seq == NULL) return;
if (cfp->ofp != NULL) {
str = SeqLocPrint (sfp->location);
if (str != NULL) {
fprintf (cfp->ofp, "> (%s)\n", str);
MemFree (str);
}
fprintf (cfp->ofp, "%s\n", seq);
}
MemFree (seq);
}
/*****************************************************************************
*
* StdAuthListNamesPrint(dvp)
* prints just Auth-list.names to a string
*
*****************************************************************************/
NLM_EXTERN CharPtr StdAuthListNamesPrint(DataValPtr dvp)
{
AuthListPtr alp;
Boolean first = TRUE;
ValNodePtr vnp;
PersonIdPtr pip;
AuthorPtr ap;
ByteStorePtr bsp;
CharPtr str;
Char buf[60];
if (dvp == NULL) return NULL;
alp = (AuthListPtr)(dvp->ptrvalue);
if (alp == NULL) return NULL;
bsp = BSNew(80);
for (vnp = alp->names; vnp != NULL; vnp = vnp->next)
{
if (! first) /* separators for names after first one */
{
if (vnp->next != NULL)
BSPutByte(bsp, (Int2)',');
else
{
BSPutByte(bsp, (Int2)' ');
BSPutByte(bsp, (Int2)'&');
}
BSPutByte(bsp, (Int2)' ');
}
first = FALSE;
if (alp->choice == 3 || alp->choice == 2) /* ml or str */
{
BSWrite(bsp, vnp->data.ptrvalue, (Int4)(StringLen((CharPtr)(vnp->data.ptrvalue))));
}
else if (alp->choice == 1) /* std */
{
ap = (AuthorPtr) (vnp->data.ptrvalue);
if (ap != NULL)
{
pip = ap->name;
PersonIdPrint(pip, buf);
BSWrite(bsp, buf, (Int4)StringLen(buf));
}
else
BSPutByte(bsp, (Int2)'?');
}
}
str = BSMerge(bsp, NULL);
BSFree(bsp);
return str;
}
static Pointer AsnLexReadStringEx (AsnIoPtr aip, AsnTypePtr atp, Uint1 fix_non_print)
{
Int2 token;
ByteStorePtr ssp;
CharPtr result=NULL;
Int4 bytes;
token = AsnLexWordEx (aip, fix_non_print); /* read the start */
if (token != START_STRING)
{
AsnIoErrorMsg(aip, 43, AsnErrGetTypeName(atp->name), aip->linenumber);
return NULL;
}
ssp = BSNew(0);
if (ssp == NULL) return result;
token = AsnLexWordEx (aip, fix_non_print); /* read the string(s) */
while (token == IN_STRING)
{
bytes = BSWrite(ssp, aip->word, (Int4)aip->wordlen);
if (bytes != (Int4)(aip->wordlen))
{
BSFree(ssp);
return result;
}
token = AsnLexWord(aip);
}
if (token == ERROR_TOKEN) return NULL;
if (token != END_STRING)
{
AsnIoErrorMsg(aip, 44, AsnErrGetTypeName(atp->name), aip->linenumber);
return NULL;
}
if (AsnFindBaseIsa(atp) == STRSTORE_TYPE) /* string store */
return ssp;
result = (CharPtr) BSMerge(ssp, NULL);
BSFree(ssp);
return result;
}
/*****************************************************************************
*
* StdFormatPrint(data, func, templatename, options)
*
*****************************************************************************/
NLM_EXTERN Boolean StdFormatPrint (Pointer data, AsnWriteFunc func, CharPtr templatename, StdPrintOptionsPtr options)
{
PrintStackPtr psp;
CharPtr ptr = NULL;
PrintFormatListPtr pflp;
if ((data == NULL) || (func == NULL) || (templatename == NULL) || (options == NULL))
return FALSE;
pflp = PrintFormatListGet(templatename);
if (pflp == NULL) return FALSE;
if (options->fp == NULL)
{
options->bstp = BSNew(80);
options->ptr = NULL;
}
psp = PrintStackBuild(data, func, pflp);
/***
printf("Before sort\n");
PrintStackDump(psp, stdout, 0);
***/
PrintStackSort(psp);
/***
printf("After sort\n");
PrintStackDump(psp, stdout, 0);
printf("\n\n");
***/
PrintStackPrint(psp, options);
PrintStackFree(psp);
if (options->fp == NULL)
{
if (BSLen(options->bstp))
options->ptr = BSMerge(options->bstp, NULL);
BSFree(options->bstp);
}
return TRUE;
}
static void Get_Sequence (FILE *f, SeqRecPtr seqrp)
{
Char ch;
CharPtr chptr;
Boolean goOn;
IdRecPtr last;
Int4 len;
Char str [256];
IdRecPtr this;
Int4 total;
if (f != NULL && seqrp != NULL) {
if (seqrp->rawSeq == NULL) {
seqrp->rawSeq = BSNew (1000);
}
if (seqrp->segLens == NULL) {
seqrp->segLens = BSNew (10);
}
len = 0;
total = 0;
goOn = TRUE;
while (goOn && ReadNextLine (f, str, sizeof (str))) {
if (str [0] == '&') {
goOn = FALSE;
} else if (str [0] == '!') {
goOn = FALSE;
} else if (str [0] == '>') {
if (len > 0) {
if (seqrp->lookForStop) {
BSPutByte (seqrp->rawSeq, (Int2) '*');
len++;
}
BSWrite (seqrp->segLens, &len, sizeof (Int4));
total += len;
len = 0;
}
chptr = StringChr (str, ' ');
if (chptr != NULL) {
*chptr = '\0';
}
if (seqrp->ids != NULL) {
last = seqrp->ids;
while (last->next != NULL) {
last = last->next;
}
this = MemNew (sizeof (IdRec));
if (this != NULL) {
this->id.accn = StringSave (str + 1);
}
last->next = this;
} else {
last = MemNew (sizeof (IdRec));
if (last != NULL) {
last->id.accn = StringSave (str + 1);
}
seqrp->ids = last;
}
} else if (str [0] != '\0') {
chptr = str;
while (*chptr != '\0') {
ch = TO_UPPER (*chptr);
if (ch >= 'A' && ch <= 'Z') {
if (seqrp->nuc) {
if (ch == 'U') {
ch = 'T';
}
if (StringChr ("BDEFHIJKLMOPQRSUVWXYZ", ch) == NULL) {
BSPutByte (seqrp->rawSeq, (Int2) ch);
len++;
}
} else {
if (StringChr ("JOU", ch) == NULL) {
BSPutByte (seqrp->rawSeq, (Int2) ch);
len++;
}
}
}
chptr++;
}
}
}
if (seqrp->nuc) {
BSPutByte (seqrp->rawSeq, (Int2) 'N');
BSPutByte (seqrp->rawSeq, (Int2) 'N');
BSPutByte (seqrp->rawSeq, (Int2) 'N');
len += 3;
}
if (len > 0) {
if (seqrp->lookForStop) {
BSPutByte (seqrp->rawSeq, (Int2) '*');
len++;
}
BSWrite (seqrp->segLens, &len, sizeof (Int4));
total += len;
len = 0;
}
if (total > 0) {
seqrp->sequence = BSMerge (seqrp->rawSeq, NULL);
seqrp->length = total;
} else {
seqrp->sequence = NULL;
seqrp->length = 0;
}
}
}
