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/*****************************************************************************
*
* testprt.c
* test program for print functions
*
*****************************************************************************/
#include <prtutil.h>
#include <seqport.h>
void BuildList (SeqEntryPtr sep, Pointer data, Int4 index, Int2 indent);
Int2 Main(void)
{
AsnIoPtr aip;
SeqEntryPtr sep;
SeqEntryPtr PNTR seqlist;
Int4 seqnum, i;
FILE* fp;
BioseqPtr bsp;
BioseqSetPtr bssp;
SeqAnnotPtr sap;
SeqFeatPtr sfp;
StdPrintOptionsPtr spop;
/*
** Load SeqEntry object loader and sequence alphabets
*/
if (! SeqEntryLoad()) {
Message(MSG_ERROR, "SeqEntryLoad failed");
return 1;
}
if (! PrintTemplateSetLoad("objprt.prt")) {
Message(MSG_ERROR, "PrintTemplateSetLoad failed");
return 1;
}
spop = StdPrintOptionsNew(NULL); /* open for generating strings */
/****
spop->newline = "\r";
*****/
/*
** Use the file "example.prt" as the ASN I/O stream. This file
** can be found in the ncbi/demo. It is in ASN.1 Print Value format.
*/
if ((aip = AsnIoOpen("example.prt", "r")) == NULL)
return 1;
/*
** Write the output to "testprt.out".
*/
fp = FileOpen("stdout", "w");
spop->fp = fp;
spop->linelength = 80;
fprintf(fp, "Sequence summary:\n\n");
/*
** Read in the whole entry into the Sequence Entry Pointer, sep.
** Close the ASN stream, which in turn closes the input file.
*/
sep = SeqEntryAsnRead(aip, NULL);
aip = AsnIoClose(aip);
/*
** Determine how many Bioseqs are in this SeqEntry. Allocate
** enough memory to hold a list of pointer to all of these
** Bioseqs. Invoke an Explore function to "visit"each Bioseq.
** We are allowed to pass one pointer for use by the exploring
** function, in this case, "BuildList".
*/
seqnum = SeqEntryCount(sep);
seqlist = MemNew((size_t)(seqnum * sizeof(SeqEntryPtr)));
SeqEntryExplore(sep, (Pointer) seqlist, BuildList);
/*
** For each Bioseq in the SeqEntry write out it's title
** len, number of gaps, and number of segments. Write out
** the length of each segment, up to 10.
*/
for(i = 0; i < seqnum; i++) {
fprintf(fp, "\n[%d]========================\n", (int)i);
if (IS_Bioseq(seqlist[i]))
{
bsp = (BioseqPtr)(seqlist[i]->data.ptrvalue);
sap = bsp->annot;
}
else
{
bssp = (BioseqSetPtr)(seqlist[i]->data.ptrvalue);
sap = bssp->annot;
}
for (sap; sap != NULL; sap = sap->next)
{
if (sap->type == 1) /* feature table */
{
for (sfp = (SeqFeatPtr)(sap->data); sfp != NULL; sfp = sfp->next)
{
if (! StdFormatPrint((Pointer)sfp, (AsnWriteFunc)SeqFeatAsnWrite, "StdSeqFeat", spop))
Message(MSG_ERROR, "StdFormatPrint failed");
/********
if (! StdFormatPrint((Pointer)sfp, (AsnWriteFunc)SeqFeatAsnWrite, "EntrySeqFeatData", spop))
Message(MSG_ERROR, "StdFormatPrint failed");
else if (spop->ptr != NULL)
{
fprintf(fp, "%s\n", spop->ptr);
MemFree(spop->ptr);
}
if (! StdFormatPrint((Pointer)sfp, (AsnWriteFunc)SeqFeatAsnWrite, "StdSeqFeatCommon", spop))
Message(MSG_ERROR, "StdFormatPrint failed");
else if (spop->ptr != NULL)
{
fprintf(fp, "%s\n", spop->ptr);
MemFree(spop->ptr);
}
if (! StdFormatPrint((Pointer)sfp, (AsnWriteFunc)SeqFeatAsnWrite, "StdSeqFeatProduct", spop))
Message(MSG_ERROR, "StdFormatPrint failed");
else if (spop->ptr != NULL)
{
fprintf(fp, "%s\n", spop->ptr);
MemFree(spop->ptr);
}
if (! StdFormatPrint((Pointer)sfp, (AsnWriteFunc)SeqFeatAsnWrite, "StdSeqFeatLocation", spop))
Message(MSG_ERROR, "StdFormatPrint failed");
else if (spop->ptr != NULL)
{
fprintf(fp, "%s\n", spop->ptr);
MemFree(spop->ptr);
}
********/
}
}
}
fprintf(fp, "++++++++++++++\n");
}
FileClose(fp);
MemFree(seqlist);
SeqEntryFree(sep);
StdPrintOptionsFree(spop);
PrintFormatListFreeAll(TRUE); /* free all formats and templates */
return 0;
}
/*
** This SeqEntry exploration function copy the current pointer position inthe
** the Bioseq entry to a list of Bioseq pointers
*/
void BuildList(SeqEntryPtr sep, Pointer data, Int4 index, Int2 indent)
{
((SeqEntryPtr PNTR) data)[index] = sep;
return;
}
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