void VideoWriter_ufmf::setupOutputFile(StampedImage stampedImg)
{
// Set error control state, set exceptions mask
file_.clear();
file_.exceptions(std::ifstream::failbit | std::ifstream::badbit);
// Get unique name for file and open for reading
QString incrFileName = getUniqueFileName();
try
{
file_.open(incrFileName.toStdString(), std::ios::binary | std::ios::out);
}
catch (std::ifstream::failure &exc)
{
unsigned int errorId = ERROR_VIDEO_WRITER_INITIALIZE;
std::string errorMsg("video writer unable to open file:\n\n");
errorMsg += exc.what();
throw RuntimeError(errorId, errorMsg);
}
if (!file_.is_open())
{
unsigned int errorId = ERROR_VIDEO_WRITER_INITIALIZE;
std::string errorMsg("video writer unable to open file:\n\n");
errorMsg += "no exception thrown";
throw RuntimeError(errorId, errorMsg);
}
setSize(stampedImg.image.size());
}
int main(int argc, char **argv) {
embInitPV("kdnapenny", argc, argv, "KBWS", "1.0.8");
struct soap soap;
char* jobid;
char* result;
AjPSeqall seqall;
AjPSeq seq;
AjPFile outf;
AjPStr substr;
AjPStr inseq = NULL;
seqall = ajAcdGetSeqall("seqall");
outf = ajAcdGetOutfile("outfile");
AjPStr tmp = NULL;
AjPStr tmpFileName = NULL;
AjPSeqout fil_file;
AjPStr line = NULL;
AjPStr sizestr = NULL;
ajint thissize = 0;
ajint nb = 0;
AjBool are_prot = ajFalse;
ajint size = 0;
AjPFile infile;
tmp = ajStrNewC("fasta");
fil_file = ajSeqoutNew();
tmpFileName = getUniqueFileName();
if( !ajSeqoutOpenFilename(fil_file, tmpFileName) ) {
embExitBad();
}
ajSeqoutSetFormatS(fil_file, tmp);
while (ajSeqallNext(seqall, &seq)) {
if (!nb) {
are_prot = ajSeqIsProt(seq);
}
ajSeqoutWriteSeq(fil_file, seq);
++nb;
}
ajSeqoutClose(fil_file);
ajSeqoutDel(&fil_file);
if (nb < 2) {
ajFatal("Multiple alignments need at least two sequences");
}
infile = ajFileNewInNameS(tmpFileName);
while (ajReadline(infile, &line)) {
ajStrAppendS(&inseq,line);
ajStrAppendC(&inseq,"\n");
}
soap_init(&soap);
char* in0;
in0 = ajCharNewS(inseq);
if ( soap_call_ns1__runDnapenny( &soap, NULL, NULL, in0, &jobid ) == SOAP_OK ) {
fprintf(stderr,"Jobid: %s\n",jobid);
} else {
soap_print_fault(&soap, stderr);
}
int check = 0;
while ( check == 0 ) {
if ( soap_call_ns1__checkStatus( &soap, NULL, NULL, jobid, &check ) == SOAP_OK ) {
fprintf(stderr,"*");
} else {
soap_print_fault(&soap, stderr);
}
sleep(3);
}
fprintf(stderr, "\n");
if ( soap_call_ns1__getResult( &soap, NULL, NULL, jobid, &result ) == SOAP_OK ) {
substr = ajStrNewC(result);
ajFmtPrintF(outf,"%S\n",substr);
} else {
soap_print_fault(&soap, stderr);
}
ajSysFileUnlinkS(tmpFileName);
soap_destroy(&soap);
soap_end(&soap);
soap_done(&soap);
ajFileClose(&outf);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&substr);
embExit();
return 0;
}
int main(int argc, char **argv) {
// initialize EMBASSY info
embInitPV("kweblogo", argc, argv, "KBWS", "1.0.9");
// soap driver and parameter object
struct soap soap;
struct ns1__weblogoInputParams params;
char* jobid;
AjPSeqall seqall;
AjPSeq seq;
AjPStr substr;
AjPStr inseq = NULL;
// get input sequence
seqall= ajAcdGetSeqall("seqall");
// get/set parameters
params.format = ajCharNewS(ajAcdGetString("format"));
AjPStr tmp= NULL;
AjPStr tmpFileName= NULL;
AjPSeqout fil_file;
AjPStr line= NULL; /* if "AjPStr line; -> ajReadline is not success!" */
AjPStr sizestr= NULL;
ajint thissize;
ajint nb= 0;
AjBool are_prot= ajFalse;
ajint size= 0;
AjPFile infile;
AjPFile goutf;
AjPStr goutfile;
goutfile= ajAcdGetString("goutfile");
tmp= ajStrNewC("fasta");
fil_file= ajSeqoutNew();
tmpFileName= getUniqueFileName();
if(!ajSeqoutOpenFilename(fil_file, tmpFileName)) {
embExitBad();
}
ajSeqoutSetFormatS(fil_file, tmp);
while (ajSeqallNext(seqall, &seq)) {
if (!nb) {
are_prot = ajSeqIsProt(seq);
}
ajSeqoutWriteSeq(fil_file, seq);
++nb;
}
ajSeqoutClose(fil_file);
ajSeqoutDel(&fil_file);
if (nb < 2) {
ajFatal("Multiple alignments need at least two sequences");
}
infile = ajFileNewInNameS(tmpFileName);
while (ajReadline(infile, &line)) {
ajStrAppendS(&inseq,line);
ajStrAppendC(&inseq,"\n");
}
soap_init(&soap);
char* in0;
in0= ajCharNewS(inseq);
if (soap_call_ns1__runWeblogo( &soap, NULL, NULL, in0, ¶ms, &jobid) == SOAP_OK) {
} else {
soap_print_fault(&soap, stderr);
}
int check= 0;
while (check == 0 ) {
if (soap_call_ns1__checkStatus(&soap, NULL, NULL, jobid, &check) == SOAP_OK) {
} else {
soap_print_fault(&soap, stderr);
}
sleep(3);
}
char* image_url;
if (soap_call_ns1__getResult(&soap, NULL, NULL, jobid, &image_url) == SOAP_OK) {
goutf= ajFileNewOutNameS(goutfile);
if (!goutf) {
// can not open image output file
ajFmtError("Problem writing out image file");
embExitBad();
}
if (!gHttpGetBinC(image_url, &goutf)) {
// can not download image file
ajFmtError("Problem downloading image file");
embExitBad();
}
} else {
soap_print_fault(&soap, stderr);
}
// delete temporary multi-fasta sequence file
ajSysFileUnlinkS(tmpFileName);
// destruct SOAP driver
soap_destroy(&soap);
soap_end(&soap);
soap_done(&soap);
// destruct EMBOSS object
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&substr);
// exit
embExit();
return 0;
}
int main(int argc, char **argv) {
embInitPV("kmafft", argc, argv, "KBWS", "1.0.8");
struct soap soap;
struct ns1__mafftInputParams params;
char* jobid;
char* result;
AjPSeqall seqall;
AjPSeq seq;
AjPFile outf;
AjPStr substr;
AjPStr inseq = NULL;
AjPStr strategy;
AjPStr outorder;
float op;
float ep;
AjPStr scorematrix;
AjBool homologs;
AjBool showhomologs;
float threshold;
AjPStr referenceseq;
AjPStr harrplot;
strategy = ajAcdGetString("strategy");
outorder = ajAcdGetString("outorder");
op = ajAcdGetFloat("op");
ep = ajAcdGetFloat("ep");
scorematrix = ajAcdGetString("scorematrix");
homologs = ajAcdGetBoolean("homologs");
showhomologs = ajAcdGetBoolean("showhomologs");
threshold = ajAcdGetFloat("threshold");
referenceseq = ajAcdGetString("referenceseq");
harrplot = ajAcdGetString("harrplot");
seqall = ajAcdGetSeqall("seqall");
outf = ajAcdGetOutfile("outfile");
params.strategy = ajCharNewS(strategy);
params.outorder = ajCharNewS(outorder);
params.op = op;
params.ep = ep;
params.scorematrix = ajCharNewS(scorematrix);
if (homologs) {
params.homologs = xsd__boolean__true_;
} else {
params.homologs = xsd__boolean__false_;
}
if (showhomologs) {
params.showhomologs = xsd__boolean__true_;
} else {
params.showhomologs = xsd__boolean__false_;
}
params.threshold = threshold;
params.referenceseq = ajCharNewS(referenceseq);
params.harrplot = ajCharNewS(harrplot);
AjPStr tmp = NULL;
AjPStr tmpFileName = NULL;
AjPSeqout fil_file;
AjPStr line = NULL; /* if "AjPStr line; -> ajReadline is not success!" */
AjPStr sizestr = NULL;
ajint thissize;
ajint nb = 0;
AjBool are_prot = ajFalse;
ajint size = 0;
AjPFile infile;
tmp = ajStrNewC("fasta");
fil_file = ajSeqoutNew();
tmpFileName = getUniqueFileName();
if( !ajSeqoutOpenFilename(fil_file, tmpFileName) ) {
embExitBad();
}
ajSeqoutSetFormatS(fil_file, tmp);
while (ajSeqallNext(seqall, &seq)) {
if (!nb) {
are_prot = ajSeqIsProt(seq);
}
ajSeqoutWriteSeq(fil_file, seq);
++nb;
}
ajSeqoutClose(fil_file);
ajSeqoutDel(&fil_file);
if (nb < 2) {
ajFatal("Multiple alignments need at least two sequences");
}
infile = ajFileNewInNameS(tmpFileName);
while (ajReadline(infile, &line)) {
ajStrAppendS(&inseq,line);
ajStrAppendC(&inseq,"\n");
}
soap_init(&soap);
char* in0;
in0 = ajCharNewS(inseq);
if ( soap_call_ns1__runMafft( &soap, NULL, NULL, in0, ¶ms, &jobid ) == SOAP_OK ) {
fprintf(stderr,"Jobid: %s\n",jobid);
} else {
soap_print_fault(&soap, stderr);
}
int check = 0;
while ( check == 0 ) {
if ( soap_call_ns1__checkStatus( &soap, NULL, NULL, jobid, &check ) == SOAP_OK ) {
fprintf(stderr,"*");
} else {
soap_print_fault(&soap, stderr);
}
sleep(3);
}
fprintf(stderr,"\n");
if ( soap_call_ns1__getResult( &soap, NULL, NULL, jobid, &result ) == SOAP_OK ) {
substr = ajStrNewC(result);
ajFmtPrintF(outf,"%S\n",substr);
} else {
soap_print_fault(&soap, stderr);
}
ajSysFileUnlinkS(tmpFileName);
soap_destroy(&soap);
soap_end(&soap);
soap_done(&soap);
ajFileClose(&outf);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&substr);
embExit();
return 0;
}
int main(int argc, char **argv) {
embInitPV("kclustalw", argc, argv, "KBWS", "1.0.8");
struct soap soap;
struct ns1__clustalwInputParams params;
char* jobid;
char* result;
AjPSeqall seqall;
AjPSeq seq;
AjPFile outf;
AjPFile outf_dnd;
AjPStr substr;
AjPStr inseq = NULL;
AjPStr alignment;
AjPStr output;
AjPStr matrix;
AjPStr outorder;
ajint ktup;
ajint window;
ajint gapopen;
float gapext;
ajint gapdist;
AjBool endgaps;
ajint pairgap;
ajint topdiags;
AjPStr score;
AjBool tossgaps;
AjBool kimura;
AjPStr outputtree;
AjBool tree;
AjBool quicktree;
AjBool align;
AjPStr clustering;
ajint numiter;
AjPStr iteration;
alignment = ajAcdGetString("alignment");
output = ajAcdGetString("output");
matrix = ajAcdGetString("matrix");
outorder = ajAcdGetString("outorder");
ktup = ajAcdGetInt("ktup");
window = ajAcdGetInt("window");
gapopen = ajAcdGetInt("gapopen");
gapext = ajAcdGetFloat("gapext");
gapdist = ajAcdGetInt("gapdist");
endgaps = ajAcdGetBoolean("endgaps");
pairgap = ajAcdGetInt("pairgap");
topdiags = ajAcdGetInt("topdiags");
score = ajAcdGetString("score");
tossgaps = ajAcdGetBoolean("tossgaps");
kimura = ajAcdGetBoolean("kimura");
outputtree = ajAcdGetString("outputtree");
tree = ajAcdGetBoolean("tree");
quicktree = ajAcdGetBoolean("quicktree");
align = ajAcdGetBoolean("align");
clustering = ajAcdGetString("clustering");
numiter = ajAcdGetInt("numiter");
iteration = ajAcdGetString("iteration");
seqall = ajAcdGetSeqall("seqall");
outf = ajAcdGetOutfile("outfile");
outf_dnd = ajAcdGetOutfile("dndoutfile");
params.alignment = ajCharNewS(alignment);
params.output = ajCharNewS(output);
params.matrix = ajCharNewS(matrix);
params.outorder = ajCharNewS(outorder);
params.ktup = ktup;
params.window = window;
params.gapopen = gapopen;
params.gapext = gapext;
params.gapdist = gapdist;
if (endgaps) {
params.endgaps = xsd__boolean__true_;
} else {
params.endgaps = xsd__boolean__false_;
}
params.pairgap = pairgap;
params.topdiags = topdiags;
params.score = ajCharNewS(score);
if (tossgaps) {
params.tossgaps = xsd__boolean__true_;
} else {
params.tossgaps = xsd__boolean__false_;
}
if (kimura) {
params.kimura = xsd__boolean__true_;
} else {
params.kimura = xsd__boolean__false_;
}
params.outputtree = ajCharNewS(outputtree);
if (tree) {
params.tree = xsd__boolean__true_;
} else {
params.tree = xsd__boolean__false_;
}
if (quicktree) {
params.quicktree = xsd__boolean__true_;
} else {
params.quicktree = xsd__boolean__false_;
}
if (align) {
params.align = xsd__boolean__true_;
} else {
params.align = xsd__boolean__false_;
}
params.clustering = ajCharNewS(clustering);
params.numiter = numiter;
params.iteration = ajCharNewS(iteration);
AjPStr tmp = NULL;
AjPStr tmpFileName = NULL;
AjPSeqout fil_file;
AjPStr line = NULL; /* if "AjPStr line; -> ajReadline is not success!" */
AjPStr sizestr = NULL;
ajint thissize;
ajint nb = 0;
AjBool are_prot = ajFalse;
ajint size = 0;
AjPFile infile;
tmp = ajStrNewC("fasta");
fil_file = ajSeqoutNew();
tmpFileName = getUniqueFileName();
if( !ajSeqoutOpenFilename(fil_file, tmpFileName) ) {
embExitBad();
}
ajSeqoutSetFormatS(fil_file, tmp);
while (ajSeqallNext(seqall, &seq)) {
if (!nb) {
are_prot = ajSeqIsProt(seq);
}
ajSeqoutWriteSeq(fil_file, seq);
++nb;
}
ajSeqoutClose(fil_file);
ajSeqoutDel(&fil_file);
if (nb < 2) {
ajFatal("Multiple alignments need at least two sequences");
}
infile = ajFileNewInNameS(tmpFileName);
while (ajReadline(infile, &line)) {
ajStrAppendS(&inseq,line);
ajStrAppendC(&inseq,"\n");
}
soap_init(&soap);
char* in0;
in0 = ajCharNewS(inseq);
if ( soap_call_ns1__runClustalw( &soap, NULL, NULL, in0, ¶ms, &jobid ) == SOAP_OK ) {
fprintf(stderr,"Jobid: %s\n",jobid);
} else {
soap_print_fault(&soap, stderr);
}
int check = 0;
while ( check == 0 ) {
if ( soap_call_ns1__checkStatus( &soap, NULL, NULL, jobid, &check ) == SOAP_OK ) {
fprintf(stderr,"*");
} else {
soap_print_fault(&soap, stderr);
}
sleep(3);
}
fprintf(stderr,"\n");
char* type;
type = "out";
if(soap_call_ns1__getMultiResult( &soap, NULL, NULL, jobid, type, &result )== SOAP_OK) {
substr = ajStrNewC(result);
fprintf(stdout, "%s\n", ajStrGetPtr(substr));
} else {
soap_print_fault(&soap, stderr);
}
type = "aln";
if(soap_call_ns1__getMultiResult( &soap, NULL, NULL, jobid, type, &result )== SOAP_OK) {
substr = ajStrNewC(result);
ajFmtPrintF(outf,"%S\n",substr);
} else {
soap_print_fault(&soap, stderr);
}
type = "dnd";
if(soap_call_ns1__getMultiResult( &soap, NULL, NULL, jobid, type, &result )== SOAP_OK) {
substr = ajStrNewC(result);
ajFmtPrintF(outf_dnd,"%S\n",substr);
} else {
soap_print_fault(&soap, stderr);
}
ajSysFileUnlinkS(tmpFileName);
soap_destroy(&soap);
soap_end(&soap);
soap_done(&soap);
ajFileClose(&outf_dnd);
ajFileClose(&outf);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&substr);
embExit();
return 0;
}
