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/*****************************************************************************
*
* makeset.c
* build a Bioseq-set from a bunch of Seq-entry files
* expects a file of file names in stdin
* prints the Bioseq-set out stdout in binary
*
*****************************************************************************/
#include <all.h>
#define NUMARGS 6
Args myargs[NUMARGS] = {
{ "Input File Names", "stdin", NULL, NULL, FALSE, 'i', ARG_FILE_IN, 0.0,0,NULL},
{ "Input data is binary", "F", NULL, NULL, TRUE , 'd', ARG_BOOLEAN, 0.0,0,NULL},
{ "Output data as binary", "T", NULL, NULL, TRUE , 'b', ARG_BOOLEAN, 0.0,0,NULL},
{ "Output Bioseq-set", "stdout", "Bioseq-set", NULL, FALSE, 'o', ARG_DATA_OUT, 0.0,0,NULL},
{ "Bioseq-set.class", "255", NULL, NULL, FALSE , 'c', ARG_INT, 0.0,0,NULL},
{ "Bioseq-set.release", NULL, NULL, NULL, TRUE , 'r', ARG_STRING, 0.0,0,NULL}};
Int2 Main(void)
{
AsnIoPtr aipin, aip;
AsnTypePtr atp;
DataVal value;
Int4 seekptr, tempseek, uid;
static CharPtr outtypes[2] = { "w", "wb" };
static CharPtr intypes[2] = { "r", "rb" };
Int2 outtype, intype;
FILE *fp;
Char fname[80];
CharPtr tmp;
if (! AsnLoad())
Message(MSG_FATAL, "Unable to load all parse tree.");
if (! GetArgs("MakeSet 1.0", NUMARGS, myargs))
return 1;
if (myargs[1].intvalue) /* binary input is TRUE */
intype = 1;
else
intype = 0;
if (myargs[2].intvalue) /* binary output is TRUE */
outtype = 1;
else
outtype = 0;
if ((aip = AsnIoOpen(myargs[3].strvalue, outtypes[outtype])) == NULL)
{
Message(MSG_ERROR, "Couldn't open %s for output", myargs[3].strvalue);
return 1;
}
if ((fp = FileOpen(myargs[0].strvalue, "r")) == NULL)
{
Message(MSG_ERROR, "Couldn't open %s for input", myargs[0].strvalue);
return 1;
}
AsnOpenStruct(aip, BIOSEQ_SET, NULL);
value.intvalue = myargs[4].intvalue;
AsnWrite(aip, BIOSEQ_SET_class, &value);
if (myargs[5].strvalue != NULL)
{
value.ptrvalue = myargs[5].strvalue;
AsnWrite(aip, BIOSEQ_SET_release, &value);
}
AsnOpenStruct(aip, BIOSEQ_SET_seq_set, NULL);
while (FileGets(fname, (size_t)78, fp) != NULL)
{
tmp = fname;
if (*tmp <= ' ') break;
while (*tmp >= ' ') tmp++;
*tmp = '\0';
aipin = AsnIoOpen(fname, intypes[intype]);
if (aipin == NULL)
{
Message(MSG_ERROR, "Couldn't open %s for input", fname);
return 1;
}
atp = SEQ_ENTRY;
atp = AsnReadId(aipin, amp, atp);
AsnReadVal(aipin, atp, &value);
AsnWrite(aip, BIOSEQ_SET_seq_set_E, &value);
while (AsnGetLevel(aipin) > 0)
{
atp = AsnReadId(aipin, amp, atp);
AsnReadVal(aipin, atp, &value);
AsnWrite(aip, atp, &value);
AsnKillValue(atp, &value);
}
aipin = AsnIoClose(aipin);
}
AsnCloseStruct(aip, BIOSEQ_SET_seq_set, NULL);
AsnCloseStruct(aip, BIOSEQ_SET, NULL);
aip = AsnIoClose(aip);
FileClose(fp);
return 0;
}
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