/**
* @brief Main program.
* @param None
* @retval None
*/
int main(void)
{
/*!< At this stage the microcontroller clock setting is already configured,
this is done through SystemInit() function which is called from startup
file (startup_stm32f072xb.s) before to branch to application main.
To reconfigure the default setting of SystemInit() function, refer to
system_stm32f0xx.c file
*/
Configure_GPIO_LED();
CheckId();
/* Infinite loop */
while (1)
{
}
}
Boolean LIBCALL VastToCn3D(WWWInfoPtr www_info)
{
FILE *pFile = NULL;
FILE *pIn = NULL;
Char pcBuf[100], pcLine[256], giBuf[20], URL[200];
CharPtr pcTest, pcL1 = NULL, Name, www_arg;
Int4 GetGi, Fid, Fsid, iFileExists = 0, indx;
BiostrucAnnotSetPtr pbsa = NULL;
BiostrucAnnotSetPtr pbsaShort = NULL;
BiostrucFeatureSetPtr pbsfs = NULL;
BiostrucFeaturePtr pbsf = NULL;
BiostrucResidueGraphSetPtr stdDictionary;
ValNodePtr pvnFids = NULL, pvnFid = NULL;
Int2 iTest = 0, iPDB = 0, iColor;
AsnIoPtr aip = NULL;
Byte bRender;
Char *IPAddress = getenv("REMOTE_HOST");
Int4 NumLabels, iMMDBId;
ValNode * pbsidThis;
BiostrucPtr pbsMaster, pbsSlave, pbsSlaveHead = NULL, pbsSlaveTail, pbsTemp;
Char szName[5], chain[2];
Char * szTemp;
SeqAnnotPtr psaAlignHead = NULL, psaAlignTail;
SeqAlignPtr salpHead, salpTail;
SeqIdPtr sip;
DenseSegPtr dsp;
BioseqPtr bsp;
SeqEntryPtr sep;
char str [52];
NcbiMimeAsn1Ptr pvnNcbi;
BiostrucAlignPtr pbsaStruct;
AsnIoPtr paiFile, aipr;
Boolean is_network;
Int4 uid, uidmaster = 0;
Int2 retcode = 3;
CharPtr JobID = NULL, pcPass;
Char AsnPath[PATH_MAX];
Char AsnName[10];
Int2 ret, complexity;
Int4 iFidCount = 0;
Boolean Chain;
/* SeqAsnLoad();
objmmdb1AsnLoad();
objmmdb2AsnLoad();
objmmdb3AsnLoad();
SeqAlignAsnLoad();
objmimeAsnLoad();
*/
if ((indx = WWWFindName(www_info, "uid")) < 0) {
printf("Content-type: text/html\n\n");
printf("<h3>No accession (PDB ID) was input - nothing to report.</h3>\n");
return 0;
}
www_arg = WWWGetValueByIndex(www_info, indx);
if (isdigit(www_arg[0]))
GetGi = (Int4) atoi(www_arg);
else {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>Non-numeric MMDB-id input - no results.</h3>\n");
return 0;
}
/* vsid and pass are to look at alignments from VAST Search */
if ((indx = WWWFindName(www_info, "vsid")) >= 0) {
www_arg = WWWGetValueByIndex(www_info, indx);
JobID = StringSave(www_arg);
if ((indx = WWWFindName(www_info, "pass")) < 0) {
printf("Content-type: text/html\n\n");
printf("<body bgcolor = \"#f0f0f0\">\n");
printf("<h2>VAST SEARCH</h2>\n");
printf("<h3>Password required.</h3>\n");
return 0;
}
else {
www_arg = WWWGetValueByIndex(www_info, indx);
pcPass = StringSave(www_arg);
if ((ret = Check_VastSearch_Password(pcPass, JobID)) != 1) {
if (ret == 2) return 0;
printf("Content-type: text/html\n\n");
printf("<body bgcolor = \"#f0f0f0\">\n");
printf("<h2>VAST SEARCH</h2>\n");
printf("<h3>Incorrect password.</h3>\n");
return 0;
}
}
}
if ((indx = WWWFindName(www_info, "hit")) < 0) {
printf("Content-type: text/html\n\n");
printf("<body bgcolor = \"#f0f0f0\">\n");
printf("<br>\n<h2>No alignment was selected!</h2>\n");
printf("<h3>Please click on up to 5 boxes in the leftmost column of the table.</h3>\n");
return 0;
}
/* loop over all the "hit" values in the list */
NumLabels = WWWGetNumEntries(www_info);
for (indx = 0; indx < NumLabels; indx++) {
Name = WWWGetNameByIndex(www_info, indx);
if (StrICmp(Name, "hit") == 0) {
www_arg = WWWGetValueByIndex(www_info, indx);
if (isdigit(www_arg[0]))
Fid = (Int4) atol(www_arg);
else {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>Non-numeric slave alignment code - no results.</h3>\n");
return 0;
}
if (++iFidCount > 5) break;
pvnFid = ValNodeAddInt(&pvnFids, 0, Fid);
}
}
if ((indx = WWWFindName(www_info, "chaindom")) < 0) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>No feature set ID (master alignment code) - nothing to report.</h3>\n");
return 0;
}
www_arg = WWWGetValueByIndex(www_info, indx);
if (isdigit(www_arg[0]))
Fsid = (Int4) atoi(www_arg);
else {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>Non-numeric master alignment code - no results.</h3>\n");
return 0;
}
if ((indx = WWWFindName(www_info, "chn_complexity")) < 0)
Chain = TRUE;
else
{
www_arg = WWWGetValueByIndex(www_info, indx);
complexity =(Int2)atoi(www_arg);
if (complexity) Chain = TRUE;
else Chain = FALSE;
}
if ((indx = WWWFindName(www_info, "atm_complexity")) < 0)
/* select alpha Carbons only by default */
complexity = ONECOORDRES;
else {
www_arg = WWWGetValueByIndex(www_info, indx);
if (isdigit(www_arg[0]))
complexity = (Int2) atoi(www_arg);
else
complexity = ONECOORDRES;
}
if ((complexity != ONECOORDRES) && (complexity != ONECOORDATOM))
/* bizarre value, but default to alpha-Carbons only */
complexity = ONECOORDRES;
/* action == 0 indicates MIME; action == 1 is text; action == 2 is save */
if ((indx = WWWFindName(www_info, "action")) < 0)
iPDB = 0;
else {
www_arg = WWWGetValueByIndex(www_info, indx);
if (isdigit(www_arg[0]))
iPDB = (Int4) atoi(www_arg);
else
iPDB = 0;
}
if (VASTInit() != TRUE) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>Can't find VAST data on server.\n");
printf("Contact [email protected]</h3>\n");
return 0;
}
OpenMMDBAPI((POWER_VIEW /* ^ FETCH_ENTREZ */), NULL);
pbsa = LocalGetFeatureSet(GetGi, Fsid, JobID);
if (pbsa == NULL) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>No master alignment record exists for %ld.</h3>\n", (long) GetGi);
return 0;
}
if (iFidCount == 1)
pbsaShort = BiostrucAnnotSetGetByFid(pbsa, Fid, Fsid);
else
pbsaShort = PruneBiostrucAnnotHits(pbsa, Fsid, pvnFids);
if (pbsaShort == NULL) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>Can't find alignment record.</h3>\n");
return 0;
}
if (MMDBInit() == FALSE) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>MMDBInit failed.</h3>\n");
return 0;
}
pbsfs = pbsaShort->features;
pbsaStruct = BiostrucAlignNew();
if (pbsfs)
{
pbsf = pbsfs->features;
szTemp = pbsf->name;
szName[0] = szTemp[0];
szName[1] = szTemp[1];
szName[2] = szTemp[2];
szName[3] = szTemp[3];
szName[4] = '\0';
}
if (JobID == NULL)
pbsMaster = FetchBiostrucPDB(szName, complexity, 1);
else
{
AsnName[0]='\0';
StringCpy(AsnName, "/b");
StringCat(AsnName, szName);
AsnPath[0]='\0';
StringCpy(AsnPath, VSPATH);
StringCat(AsnPath, JobID);
StringCat(AsnPath, AsnName);
pbsMaster = FetchBS(AsnPath, 0, complexity, 1, POWER_VIEW);
}
if (pbsMaster == NULL)
{
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3> Unable to load master structure.</h3>\n");
return 0;
}
/* Load in Standard Dictionary to make sequences - Ken */
aipr = NULL;
aipr = AsnIoOpen("bstdt", "rb");
if (aipr == NULL)
{
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3>Can't find standard dictionary.</h3>\n");
return 0;
}
stdDictionary = BiostrucResidueGraphSetAsnRead(aipr, NULL);
AsnIoFlush(aipr);
aipr = AsnIoClose(aipr);
/* retrieve the bioseq for master and put in ValNode */
sep = (SeqEntryPtr) MakeBioseqs(pbsMaster, stdDictionary);
if ( sep == NULL )
{
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3d)</h2>\n");
printf("<h3>Unable to get SeqEntry.</h3>\n");
return 0;
}
ValNodeLink(&(pbsaStruct->sequences), sep);
/* PruneBiostruc if Aligned Chain Options has been chosen */
if (Chain)
{
if (szTemp[4] != ' ')
{
chain[0] = szTemp[4];
chain[1] = '\0';
pbsTemp = (BiostrucPtr)PruneBiostruc(pbsMaster, chain);
pbsMaster = NULL;
pbsMaster = pbsTemp;
}
}
/* Make a linked list of Biostrucs of the slave structures*/
while (pbsf)
{
szTemp = pbsf->name;
szName[0] = szTemp[7];
szName[1] = szTemp[8];
szName[2] = szTemp[9];
szName[3] = szTemp[10];
szName[4] = '\0';
if (!pbsSlaveHead)
{
pbsSlaveHead = FetchBiostrucPDB(szName, complexity, 1);
if (!pbsSlaveHead)
{
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3> Unable to load slave structure.</h3>\n");
return 0;
}
/* Make Bioseq for Slaves */
sep = (SeqEntryPtr) MakeBioseqs(pbsSlaveHead, stdDictionary);
if ( sep == NULL )
{
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3d)</h2>\n");
printf("<h3>Unable to get SeqEntry.</h3>\n");
return 0;
}
ValNodeLink(&(pbsaStruct->sequences), sep);
/* PruneBiostruc if Aligned Chain Options has been chosen */
if (Chain)
{
if (szTemp[11] != ' ')
{
chain[0] = szTemp[11];
chain[1] = '\0';
pbsTemp = (BiostrucPtr)PruneBiostruc(pbsSlaveHead, chain);
pbsSlaveHead = NULL;
pbsSlaveHead = pbsTemp;
}
}
pbsSlaveTail = pbsSlaveHead;
}
else
{
pbsSlave = FetchBiostrucPDB(szName, complexity, 1);
if (!pbsSlave)
{
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3D)</h2>\n");
printf("<h3> Unable to load slave structure.</h3>\n");
return 0;
}
/* Make Bioseq for Slaves */
sep = (SeqEntryPtr) MakeBioseqs(pbsSlave, stdDictionary);
if ( sep == NULL )
{
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3d)</h2>\n");
printf("<h3>Unable to get SeqEntry.</h3>\n");
return 0;
}
ValNodeLink(&(pbsaStruct->sequences), sep);
/* PruneBiostruc if Aligned Chain Options has been chosen */
if (Chain)
{
if (szTemp[11] != ' ')
{
chain[0] = szTemp[11];
chain[1] = '\0';
pbsTemp = (BiostrucPtr)PruneBiostruc(pbsSlave, chain);
pbsSlave = NULL;
pbsSlave = pbsTemp;
}
}
pbsSlaveTail->next = pbsSlave;
pbsSlaveTail = pbsSlaveTail->next;
pbsSlaveTail->next = NULL;
}
pbsf = pbsf->next;
}
/* Make a linked list of sequence alignments of master and slaves */
pbsf=pbsfs->features;
while (pbsf) {
if (!psaAlignHead) {
psaAlignHead = fnPBSFtoPSA (pbsf); /* get the sequence alignments */
if (psaAlignHead == NULL || psaAlignHead->data == NULL) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3d)</h2>\n");
printf("<h3>Unable to create SeqAnnot.</h3>\n");
return 0;
}
salpHead = (SeqAlignPtr)(psaAlignHead->data);
salpTail = salpHead;
}
else {
psaAlignTail = fnPBSFtoPSA (pbsf);
salpTail->next = (SeqAlignPtr)(psaAlignTail->data);
if (psaAlignTail == NULL || psaAlignTail->data == NULL) {
printf("Content-type: text/html\n\n");
printf("<h2>VASTSERV Error (VastToCn3d)</h2>\n");
printf("<h3>Unable to create SeqAnnot.</h3>\n");
return 0;
}
salpTail = salpTail->next;
salpTail->next = NULL;
}
pbsf = pbsf->next;
}
pbsaStruct->master = pbsMaster;
pbsaStruct->slaves = pbsSlaveHead;
pbsaStruct->alignments = pbsaShort;
pbsaStruct->seqalign = psaAlignHead;
pvnNcbi = ValNodeNew(NULL);
pvnNcbi->choice = NcbiMimeAsn1_alignstruc;
pvnNcbi->data.ptrvalue = pbsaStruct;
pvnNcbi = (NcbiMimeAsn1Ptr) CheckId(pvnNcbi, JobID); /* to check identity, yanli */
OutputFile = stdout;
if (iPDB == 0) /* cn3d MIME */
printf ("Content-type: chemical/ncbi-asn1-binary\n\n");
else if (iPDB == 1) { /* "See File" */
printf ("Content-type: text/html\n\n");
printf ("<HTML><body><pre>\n");
}
else /* "Save File" */
printf ("Content-type: application/octet-stream\n\n");
if (iPDB != 1)
paiFile = AsnIoNew(ASNIO_BIN_OUT, stdout, NULL, NULL, NULL);
else
paiFile = AsnIoNew(ASNIO_TEXT_OUT, stdout, NULL, NULL, NULL);
NcbiMimeAsn1AsnWrite(pvnNcbi, paiFile, NULL);
AsnIoFlush(paiFile);
AsnIoClose(paiFile);
CloseMMDBAPI();
MMDBFini();
VASTFini();
return 0;
} /* end of VastToCn3D */