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/*
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* File Name: cnsrt.c
*
* Author(s): John Kuzio
*
* Version Creation Date: 98-01-01
*
* $Revision: 6.4 $
*
* File Description: consort - codon usage
*
* Modifications:
* --------------------------------------------------------------------------
* Date Name Description of modification
* --------------------------------------------------------------------------
* $Log: cnsrt.c,v $
* Revision 6.4 1998/12/18 16:24:53 kuzio
* big GIs
*
* Revision 6.3 1998/09/16 18:19:27 kuzio
* cvs logging
*
* ==========================================================================
*/
#include <ncbi.h>
#include <accentr.h>
#include <gather.h>
#include <urkcnsrt.h>
#define TOP_ERROR 1
static char _this_module[] = "consort";
#undef THIS_MODULE
#define THIS_MODULE _this_module
static char _this_file[] = __FILE__;
#undef THIS_FILE
#define THIS_FILE _this_file
Args myargs[] =
{
{ "nucleotide GI", "0", "0", "9000000", TRUE,
'g', ARG_INT, 0.0, 0, NULL},
{ "ASN.1 SeqEntry", NULL, NULL, NULL, TRUE,
'f', ARG_STRING, 0.0, 0, NULL}
};
Int2 Main (void)
{
Int2 argcount;
Boolean flagHaveNet, flagTakeNext;
Int4 gi;
CharPtr filename;
AsnIoPtr aiop;
SeqEntryPtr sep;
TreeNodePtr ptrNode, ptrNodeFind;
Char nameL[256], nameR[256];
Int4Ptr freq;
argcount = sizeof (myargs) / sizeof (Args);
if (!GetArgs ("consort", argcount, myargs))
return 1;
gi = myargs[0].intvalue;
filename = myargs[1].strvalue;
if (gi > 0)
{
if (!EntrezInit ("consort", FALSE, &flagHaveNet))
{
ErrPostEx (SEV_ERROR, TOP_ERROR, 101,
"Entrez init failed");
ErrShow ();
exit (1);
}
sep = EntrezSeqEntryGet (myargs[0].intvalue, SEQENTRY_READ_BIOSEQ);
EntrezFini ();
}
else if (filename != NULL)
{
if ((aiop = AsnIoOpen (filename, "r")) == NULL)
{
ErrPostEx (SEV_ERROR, TOP_ERROR, 102,
"Failed to open: %s", filename);
ErrShow ();
}
sep = SeqEntryAsnRead (aiop, NULL);
AsnIoClose (aiop);
}
else
{
ErrPostEx (SEV_ERROR, TOP_ERROR, 103,
"No gi or ASN.1 file given :: for help : cnsrt -");
ErrShow ();
exit (1);
}
if (sep == NULL)
{
ErrPostEx (SEV_ERROR, TOP_ERROR, 104,
"No seqentry found");
ErrShow ();
exit (1);
}
if ((freq = ConformSeqEntry (sep)) != NULL)
Conform (freq, stdout);
ptrNode = ConsortSeqEntry (sep);
SeqEntryFree (sep);
SetAllNumberNodes (ptrNode);
printf ("%4s %24s %24s %16s\n", "Node", "Left", "Right", "Score");
ptrNodeFind = NULL;
flagTakeNext = FALSE;
while ((ptrNodeFind = ExploreTree (ptrNode, ptrNodeFind,
&flagTakeNext)) != NULL)
{
if (ptrNodeFind->ptrChildLeft != NULL &&
ptrNodeFind->ptrChildRight != NULL)
{
StrCpy (nameL, ptrNodeFind->ptrChildLeft->name);
if (StrLen (nameL) > 24)
nameL[24] = '\0';
StrCpy (nameR, ptrNodeFind->ptrChildRight->name);
if (StrLen (nameR) > 24)
nameR[24] = '\0';
printf ("%4ld %24s %24s %16.5f\n", ptrNodeFind->nodenumber,
nameL, nameR, ptrNodeFind->score);
}
flagTakeNext = FALSE;
}
return 0;
}
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