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/*****************************************************************************
*
* asn2asn.c
* This is a framework for reading an ASN.1 Seq-entry or Bioseq-set,
* doing some processing on it, and outputting it again. seqport.h
* is included since it covers most necessary utilities that you might
* need. You may need to add others for specialized reports and so on.
*
* The check for aipout == NULL is to show how to change the code if
* no output is desired. Change the default in myargs from "stdout" to
* NULL to make output command line optional.
*
* This program can be used "as is" to convert between binary and text
* ASN.1 through the object loaders.
*
*****************************************************************************/
#include <seqport.h>
#define NUMARG 7
Args myargs[NUMARG] = {
{"Filename for asn.1 input","stdin",NULL,NULL,FALSE,'i',ARG_FILE_IN,0.0,0,NULL},
{"Input is a Seq-entry","F", NULL ,NULL ,TRUE,'e',ARG_BOOLEAN,0.0,0,NULL},
{"Input asnfile in binary mode","F",NULL,NULL,TRUE,'b',ARG_BOOLEAN,0.0,0,NULL},
{"Filename for asn.1 output","stdout", NULL,NULL,TRUE,'o',ARG_FILE_OUT,0.0,0,NULL},
{"Output asnfile in binary mode?","F", NULL ,NULL ,TRUE,'s',ARG_BOOLEAN,0.0,0,NULL},
{"Log errors to file named:",NULL,NULL,NULL,TRUE,'l',ARG_FILE_OUT, 0.0,0,NULL},
{"Output asnfile in XML?","F", NULL ,NULL ,TRUE,'x',ARG_BOOLEAN,0.0,0,NULL}};
/*****************************************************************************
*
* Put any internal prototypes here
* NB: the function must match the prototype exactly, including "static" or
* not.
*
*****************************************************************************/
static void SeqEntryProcess PROTO((SeqEntryPtr sep)); /* dummy function */
/*****************************************************************************
*
* Main program loop to read, process, write SeqEntrys
*
*****************************************************************************/
Int2 Main(void)
{
AsnIoPtr aipout=NULL, aipin;
SeqEntryPtr sep;
AsnTypePtr atp, atp2;
AsnModulePtr amp;
DataVal dv;
CharPtr ftype;
/* check command line arguments */
if ( ! GetArgs("asn2asn",NUMARG, myargs))
return 1;
/* load the sequence alphabets */
/* (and sequence parse trees) */
if (! SeqEntryLoad())
ErrShow();
/* get pointer to all loaded ASN.1 modules */
amp = AsnAllModPtr();
if (amp == NULL)
{
ErrShow();
return 1;
}
atp = AsnFind("Bioseq-set"); /* get the initial type pointers */
if (atp == NULL)
{
ErrShow();
return 1;
}
atp2 = AsnFind("Bioseq-set.seq-set.E");
if (atp2 == NULL)
{
ErrShow();
return 1;
}
/* open the ASN.1 input file in the right mode */
if ((aipin = AsnIoOpen (myargs[0].strvalue, myargs[2].intvalue?"rb":"r"))
== NULL)
{
ErrPostEx(SEV_ERROR,0,0, "Can't open %s", myargs[0].strvalue);
ErrShow();
return 1;
}
/* open the ASN.1 output file in the right mode */
if (myargs[3].strvalue != NULL) /* output desired? */
{
ftype = "w";
if (myargs[4].intvalue)
ftype = "wb";
if (myargs[6].intvalue)
ftype = "wx";
if ((aipout = AsnIoOpen (myargs[3].strvalue, ftype)) == NULL)
{
ErrPostEx(SEV_ERROR,0,0, "Can't open %s", myargs[3].strvalue);
ErrShow();
return 1;
}
}
/* log errors instead of die */
if (myargs[5].strvalue != NULL)
{
if (! ErrSetLog (myargs[5].strvalue))
{
ErrShow();
return 1;
}
else
ErrSetOpts (ERR_CONTINUE, ERR_LOG_ON);
}
if ( myargs[1].intvalue) /* read one Seq-entry */
{
sep = SeqEntryAsnRead(aipin, NULL);
SeqEntryProcess(sep); /* do any processing */
if (aipout != NULL)
SeqEntryAsnWrite(sep, aipout, NULL);
SeqEntryFree(sep);
}
else /* read Seq-entry's from a Bioseq-set */
{
while ((atp = AsnReadId(aipin, amp, atp)) != NULL)
{
if (atp == atp2) /* top level Seq-entry */
{
sep = SeqEntryAsnRead(aipin, atp);
SeqEntryProcess(sep); /* do any processing */
if (aipout != NULL)
SeqEntryAsnWrite(sep, aipout, atp);
SeqEntryFree(sep);
}
else
{
if (aipout == NULL) /* don't need to read the data */
AsnReadVal(aipin, atp, NULL);
else
{
AsnReadVal(aipin, atp, &dv); /* read it */
AsnWrite(aipout, atp, &dv); /* write it */
AsnKillValue(atp, &dv); /* free it */
}
}
}
}
AsnIoClose(aipin);
AsnIoClose(aipout);
return(0);
}
/*****************************************************************************
*
* void SeqEntryProcess (sep)
* just a dummy routine that does nothing
*
*****************************************************************************/
static void SeqEntryProcess (SeqEntryPtr sep)
{
if (sep == NULL)
return;
return;
}
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