SetPartition CCPivot::_Run(const SetPartitionVector &SPV)
{
unsigned int k = SPV.size();
unsigned int n = SPV[0].GetN();
SetPartition consensus(n);
consensus.MakeLast();
Matrix<double> mat(n + 1, n + 1);
mat.FillWithValue(0.0);
for (int p = 0; p < SPV.size(); ++p)
{
for (int i = 1; i <= n; ++i)
{
for (int j = 1; j <= n; ++j)
{
if (SPV[p].CoClustered(i, j))
mat(i, j) += 1.0 / (double)k;
}
}
}
set<int> isClustered;
for (int i = 1; i <= n; ++i)
isClustered.insert(i);
while (true)
{
int which = ChooseRandom(isClustered, SPV[0]);
if (which == -1)
break;
isClustered.erase(which);
// cluster everyone with which
for (int i = 1; i <= n; ++i)
{
if (isClustered.find(i) == isClustered.end())
continue;
if (mat(which, i) > cutoff)
{
isClustered.erase(i);
consensus.MergeBlocks(consensus.WhichBlock(i), consensus.WhichBlock(which));
}
}
}
return consensus;
}
int main(int argc, char** argv)
{
if(argc > 3)
{
image_height=atoi(argv[1]);
image_width=atoi(argv[1]);
if(atoi(argv[2]) == 1)
create_image();
image = (char*)malloc(sizeof(char)*image_height*image_width);
meet=(ConsensusGrid*)malloc(sizeof(ConsensusGrid)*image_height*image_width);
basis = (int*)malloc(sizeof(int)*image_height*image_width);
read_raw_image("image.raw",image,image_height,image_width);
for(int i=0; i<image_height; i++)
{
for(int j = 0; j<image_width; j++)
{
if(atoi(argv[3]) == 1)
meet[i*image_width+j]=consensus_parallel(i, j, image,image_height,image_width);
else
meet[i*image_width+j]=consensus(i, j, image,image_height,image_width);
}
}
printf("Calculating list\n");
if(atoi(argv[3]) == 1)
calculate_list_parallel();
else
calculate_list();
printf("Calculating basis\n");
if(atoi(argv[3]) == 1)
calculate_basis_parallel();
else
calculate_basis();
cout << "Basis count = " << basis_count << endl;
}
else
{
cout << "Insufficient arguments\n" << endl;
cout << "First argument = Image Size" << endl;
cout << "Second argument = 1 to create image, 0 not to create image" << endl;
cout << "Third argument = 1 for parallel, 0 for not parallel\n" << endl;
}
}
int main_consensus(int argc, char *argv[])
{
args_t *args = (args_t*) calloc(1,sizeof(args_t));
args->argc = argc; args->argv = argv;
static struct option loptions[] =
{
{"sample",1,0,'s'},
{"iupac-codes",0,0,'i'},
{"haplotype",1,0,'H'},
{"output",1,0,'o'},
{"fasta-ref",1,0,'f'},
{"mask",1,0,'m'},
{"chain",1,0,'c'},
{0,0,0,0}
};
char c;
while ((c = getopt_long(argc, argv, "h?s:1iH:f:o:m:c:",loptions,NULL)) >= 0)
{
switch (c)
{
case 's': args->sample = optarg; break;
case 'o': args->output_fname = optarg; break;
case 'i': args->output_iupac = 1; break;
case 'f': args->ref_fname = optarg; break;
case 'm': args->mask_fname = optarg; break;
case 'c': args->chain_fname = optarg; break;
case 'H':
args->haplotype = optarg[0] - '0';
if ( args->haplotype <=0 ) error("Expected positive integer with --haplotype\n");
break;
default: usage(args); break;
}
}
if ( optind>=argc ) usage(args);
args->fname = argv[optind];
if ( !args->ref_fname && !isatty(fileno((FILE *)stdin)) ) args->ref_fname = "-";
if ( !args->ref_fname ) usage(args);
init_data(args);
consensus(args);
destroy_data(args);
free(args);
return 0;
}
void AgentCore::algorithmCallback(const ros::TimerEvent &timer_event) {
consensus(); // also clears the received statistics container
control(); // also publishes virtual agent pose and path
guidance();
dynamics(); // also publishes agent pose and path
waitForSlotTDMA(slot_tdma_*agent_id_); // sync to the next transmission TDMA slot (agent dependent)
// publishes the last estimated statistics in the proper TDMA slot
formation_control::FormationStatisticsStamped msg;
msg.header.frame_id = agent_virtual_frame_;
msg.header.stamp = ros::Time::now();
msg.agent_id = agent_id_;
msg.stats = estimated_statistics_;
stats_publisher_.publish(msg);
std::stringstream s;
s << "Estimated statistics published.";
console(__func__, s, DEBUG);
}
template<class T> cv::Mat filter::trends(const cv::Mat &data, size_t w, const T &fallback) {
cv::Mat trend = cv::Mat_<T>(data.size());
size_t m = data.rows;
size_t n = data.cols;
size_t u = w / 2;
for (size_t i = 0; i < m; i++) {
T *cell = trend.ptr<T>(i);
for (size_t j = 0; j < n; j++, cell++) {
size_t x = (j < u ? j : j - u);
size_t y = (i < u ? i : i - u);
size_t width = (x + w > n ? n - x : w);
size_t height = (y + w > m ? m - y : w);
cv::Rect roi(x, y, width, height);
cv::Mat patch(data, roi);
*cell = consensus(patch, fallback);
}
}
return trend;
}
template<class T> cv::Mat filter::trends(const cv::Mat &data, size_t w) {
cv::Mat c = cv::Mat_<T>(data.size());
size_t m = data.rows;
size_t n = data.cols;
size_t u = w / 2;
for (size_t i = 0; i < m; i++) {
for (size_t j = 0; j < n; j++) {
size_t x = (j < u ? j : j - u);
size_t y = (i < u ? i : i - u);
size_t width = (x + w > n ? n - x : w);
size_t height = (y + w > m ? m - y : w);
cv::Rect roi(x, y, width, height);
cv::Mat patch(data, roi);
const T &t = data.at<T>(i, j);
c.at<T>(i, j) = consensus(patch, t);
}
}
return c;
}
PRIVATE void
set_fold_compound(vrna_fold_compound_t *vc,
vrna_md_t *md_p,
unsigned int options,
unsigned int aux){
char *sequence, **sequences;
unsigned int length, s;
int cp; /* cut point for cofold */
char *seq, *seq2;
sequence = NULL;
sequences = NULL;
cp = -1;
/* some default init values */
vc->params = NULL;
vc->exp_params = NULL;
vc->matrices = NULL;
vc->exp_matrices = NULL;
vc->hc = NULL;
vc->auxdata = NULL;
vc->free_auxdata = NULL;
switch(vc->type){
case VRNA_VC_TYPE_SINGLE: sequence = vc->sequence;
seq2 = strdup(sequence);
seq = vrna_cut_point_remove(seq2, &cp); /* splice out the '&' if concatenated sequences and
reset cp... this should also be safe for
single sequences */
vc->cutpoint = cp;
if((cp > 0) && (md_p->min_loop_size == TURN))
md_p->min_loop_size = 0; /* is it safe to set this here? */
free(vc->sequence);
vc->sequence = seq;
vc->length = length = strlen(seq);
vc->sequence_encoding = vrna_seq_encode(seq, md_p);
vc->sequence_encoding2 = vrna_seq_encode_simple(seq, md_p);
if(!(options & VRNA_OPTION_EVAL_ONLY)){
vc->ptype = (aux & WITH_PTYPE) ? vrna_ptypes(vc->sequence_encoding2, md_p) : NULL;
/* backward compatibility ptypes */
vc->ptype_pf_compat = (aux & WITH_PTYPE_COMPAT) ? get_ptypes(vc->sequence_encoding2, md_p, 1) : NULL;
} else {
vc->ptype = NULL;
vc->ptype_pf_compat = NULL;
}
vc->sc = NULL;
free(seq2);
break;
case VRNA_VC_TYPE_ALIGNMENT: sequences = vc->sequences;
vc->length = length = vc->length;
vc->cons_seq = consensus((const char **)sequences);
vc->S_cons = vrna_seq_encode_simple(vc->cons_seq, md_p);
vc->pscore = vrna_alloc(sizeof(int)*((length*(length+1))/2+2));
/* backward compatibility ptypes */
vc->pscore_pf_compat = (aux & WITH_PTYPE_COMPAT) ? vrna_alloc(sizeof(int)*((length*(length+1))/2+2)) : NULL;
oldAliEn = vc->oldAliEn = md_p->oldAliEn;
vc->S = vrna_alloc((vc->n_seq+1) * sizeof(short *));
vc->S5 = vrna_alloc((vc->n_seq+1) * sizeof(short *));
vc->S3 = vrna_alloc((vc->n_seq+1) * sizeof(short *));
vc->a2s = vrna_alloc((vc->n_seq+1) * sizeof(unsigned short *));
vc->Ss = vrna_alloc((vc->n_seq+1) * sizeof(char *));
for (s = 0; s < vc->n_seq; s++) {
vrna_aln_encode(vc->sequences[s],
&(vc->S[s]),
&(vc->S5[s]),
&(vc->S3[s]),
&(vc->Ss[s]),
&(vc->a2s[s]),
md_p);
}
vc->S5[vc->n_seq] = NULL;
vc->S3[vc->n_seq] = NULL;
vc->a2s[vc->n_seq] = NULL;
vc->Ss[vc->n_seq] = NULL;
vc->S[vc->n_seq] = NULL;
vc->scs = NULL;
break;
default: /* do nothing ? */
break;
}
vc->iindx = vrna_idx_row_wise(vc->length);
vc->jindx = vrna_idx_col_wise(vc->length);
/* now come the energy parameters */
add_params(vc, md_p, options);
}
int PS_color_aln(const char *structure, const char *filename,
const char *seqs[], const char *names[]) {
/* produce PS sequence alignment color-annotated by consensus structure */
int N,i,j,k,x,y,tmp,columnWidth;
char *tmpBuffer,*ssEscaped,*ruler, *cons;
char c;
float fontWidth, fontHeight, imageHeight, imageWidth,tmpColumns;
int length, maxName, maxNum, currPos;
float lineStep,blockStep,consStep,ssStep,rulerStep,nameStep,numberStep;
float maxConsBar,startY,namesX,seqsX, currY;
float score,barHeight,xx,yy;
int match,block;
FILE *outfile;
short *pair_table;
char * colorMatrix[6][3] = {
{"0.0 1", "0.0 0.6", "0.0 0.2"}, /* red */
{"0.16 1","0.16 0.6", "0.16 0.2"}, /* ochre */
{"0.32 1","0.32 0.6", "0.32 0.2"}, /* turquoise */
{"0.48 1","0.48 0.6", "0.48 0.2"}, /* green */
{"0.65 1","0.65 0.6", "0.65 0.2"}, /* blue */
{"0.81 1","0.81 0.6", "0.81 0.2"} /* violet */
};
const char *alnPlotHeader =
"%%!PS-Adobe-3.0 EPSF-3.0\n"
"%%%%BoundingBox: %i %i %i %i\n"
"%%%%EndComments\n"
"%% draws Vienna RNA like colored boxes\n"
"/box { %% x1 y1 x2 y2 hue saturation\n"
" gsave\n"
" dup 0.3 mul 1 exch sub sethsbcolor\n"
" exch 3 index sub exch 2 index sub rectfill\n"
" grestore\n"
"} def\n"
"%% draws a box in current color\n"
"/box2 { %% x1 y1 x2 y2\n"
" exch 3 index sub exch 2 index sub rectfill\n"
"} def\n"
"/string { %% (Text) x y\n"
" 6 add\n"
" moveto\n"
" show\n"
"} def\n"
"0 %i translate\n"
"1 -1 scale\n"
"/Courier findfont\n"
"[10 0 0 -10 0 0] makefont setfont\n";
outfile = fopen(filename, "w");
if (outfile == NULL) {
fprintf(stderr, "can't open file %s - not doing alignment plot\n",
filename);
return 0;
}
columnWidth=60; /* Display long alignments in blocks of this size */
fontWidth=6; /* Font metrics */
fontHeight=6.5;
lineStep=fontHeight+2; /* distance between lines */
blockStep=3.5*fontHeight; /* distance between blocks */
consStep=fontHeight*0.5; /* distance between alignment and conservation curve */
ssStep=2; /* distance between secondary structure line and sequences */
rulerStep=2; /* distance between sequences and ruler */
nameStep=3*fontWidth; /* distance between names and sequences */
numberStep=fontWidth; /* distance between sequeces and numbers */
maxConsBar=2.5*fontHeight; /* Height of conservation curve */
startY=2; /* "y origin" */
namesX=fontWidth; /* "x origin" */
/* Number of columns of the alignment */
length=strlen(seqs[0]);
/* Allocate memory for various strings, length*2 is (more than)
enough for all of them */
tmpBuffer = (char *) space((unsigned) length*2);
ssEscaped=(char *) space((unsigned) length*2);
ruler=(char *) space((unsigned) length*2);
pair_table=make_pair_table(structure);
/* Get length of longest name and count sequences in alignment*/
for (i=maxName=N=0; names[i] != NULL; i++) {
N++;
tmp=strlen(names[i]);
if (tmp>maxName) maxName=tmp;
}
/* x-coord. where sequences start */
seqsX=namesX+maxName*fontWidth+nameStep;
/* calculate number of digits of the alignment length */
snprintf(tmpBuffer,length, "%i",length);
maxNum=strlen(tmpBuffer);
/* Calculate bounding box */
tmpColumns=columnWidth;
if (length<columnWidth){
tmpColumns=length;
}
imageWidth=ceil(namesX+(maxName+tmpColumns+maxNum)*fontWidth+2*nameStep+fontWidth+numberStep);
imageHeight=startY+ceil((float)length/columnWidth)*((N+2)*lineStep+blockStep+consStep+ssStep+rulerStep);
/* Write postscript header including correct bounding box */
fprintf(outfile,alnPlotHeader,0,0,(int)imageWidth,(int)imageHeight,(int)imageHeight);
/* Create ruler and secondary structure lines */
i=0;
/* Init all with dots */
for (i=0;i<(length);i++){
ruler[i]='.';
}
i=0;
for (i=0;i<length;i++){
/* Write number every 10th position, leave out block breaks */
if ((i+1)%10==0 && (i+1)%columnWidth!=0){
snprintf(tmpBuffer,length,"%i",i+1);
strncpy(ruler+i,tmpBuffer,strlen(tmpBuffer));
}
}
ruler[length]='\0';
/* Draw color annotation first */
/* Repeat for all pairs */
for (i=1; i<=length; i++) {
if ((j=pair_table[i])>i) {
/* Repeat for open and closing position */
for (k=0;k<2;k++){
int pairings, nonpair, s, col;
int ptype[8] = {0,0,0,0,0,0,0,0};
char *color;
col = (k==0)?i-1:j-1;
block=ceil((float)(col+1)/columnWidth);
xx=seqsX+(col-(block-1)*columnWidth)*fontWidth;
/* Repeat for each sequence */
for (s=pairings=nonpair=0; s<N; s++) {
ptype[BP_pair[ENCODE(seqs[s][i-1])][ENCODE(seqs[s][j-1])]]++;
}
for (pairings=0,s=1; s<=7; s++) {
if (ptype[s]) pairings++;
}
nonpair=ptype[0];
if (nonpair <=2) {
color = colorMatrix[pairings-1][nonpair];
for (s=0; s<N; s++) {
yy=startY+(block-1)*(lineStep*(N+2)+blockStep+consStep+rulerStep)+ssStep*(block)+(s+1)*lineStep;
/* Color according due color information in pi-array, only if base pair is possible */
if (BP_pair[ENCODE(seqs[s][i-1])][ENCODE(seqs[s][j-1])]) {
fprintf(outfile, "%.1f %.1f %.1f %.1f %s box\n",
xx,yy-1,xx+fontWidth,yy+fontHeight+1,color);
}
}
}
}
}
}
free(pair_table);
/* Process rest of the output in blocks of columnWidth */
currY=startY;
currPos=0;
cons = consensus(seqs);
while (currPos<length) {
/* Display secondary structure line */
fprintf(outfile,"0 setgray\n");
strncpy(tmpBuffer,structure+currPos,columnWidth);
tmpBuffer[columnWidth]='\0';
x=0;y=0;
while ((c=tmpBuffer[x])){
if (c=='.'){
ssEscaped[y++]='.';
} else {
ssEscaped[y++]='\\';
ssEscaped[y++]=c;
}
x++;
}
ssEscaped[y]='\0';
fprintf(outfile, "(%s) %.1f %.1f string\n", ssEscaped,seqsX,currY);
currY+=ssStep+lineStep;
/* Display names, sequences and numbers */
for (i=0; i<N; i++) {
strncpy(tmpBuffer,seqs[i]+currPos,columnWidth);
tmpBuffer[columnWidth]='\0';
match=0;
for (j=0;j<(currPos+strlen(tmpBuffer));j++){
if (seqs[i][j] != '-') match++;
}
fprintf(outfile, "(%s) %.1f %.1f string\n", names[i],namesX,currY);
fprintf(outfile, "(%s) %.1f %.1f string\n", tmpBuffer,seqsX,currY);
fprintf(outfile, "(%i) %.1f %.1f string\n", match,seqsX+fontWidth*(strlen(tmpBuffer))+numberStep,currY);
currY+=lineStep;
}
currY+=rulerStep;
strncpy(tmpBuffer,ruler+currPos,columnWidth);
tmpBuffer[columnWidth]='\0';
fprintf(outfile, "(%s) %.1f %.1f string\n", tmpBuffer,seqsX,currY);
currY+=lineStep;
currY+=consStep;
/*Display conservation bar*/
fprintf(outfile,"0.6 setgray\n");
for (i=currPos;(i<currPos+columnWidth && i<length);i++){
match=0;
for (j=0;j<N;j++){
if (cons[i] == seqs[j][i]) match++;
if (cons[i]=='U' && seqs[j][i]=='T') match++;
if (cons[i]=='T' && seqs[j][i]=='U') match++;
}
score=(float)(match-1)/(N-1);
if (cons[i] == '-' ||
cons[i] == '_' ||
cons[i] == '.'){
score=0;
}
barHeight=maxConsBar*score;
if (barHeight==0){
barHeight=1;
}
xx=seqsX+(i-(columnWidth*currPos/columnWidth))*fontWidth;
fprintf(outfile,"%.1f %.1f %.1f %.1f box2\n",
xx,
currY+maxConsBar-barHeight,
xx+fontWidth,
currY+maxConsBar);
}
currY+=blockStep;
currPos+=columnWidth;
}
free(cons);
fprintf(outfile,"showpage\n");
fclose(outfile);
free(tmpBuffer);
free(ssEscaped);free(ruler);
return 0;
}
int main(int argc, char *argv[])
{
char *modelDir=NULL; /* Directory with model files */
struct svm_model* decision_model; /* SVM classification model */
/* Command line options */
int reverse=0; /* Scan reverse complement */
int showVersion=0; /* Shows version and exits */
int showHelp=0; /* Show short help and exits */
int from=-1; /* Scan slice from-to */
int to=-1;
FILE *clust_file=stdin; /* Input file */
FILE *out=stdout; /* Output file */
struct aln *AS[MAX_NUM_NAMES];
struct aln *window[MAX_NUM_NAMES];
char *tmpAln[MAX_NUM_NAMES];
int n_seq; /* number of input sequences */
int length; /* length of alignment/window */
int z_score_type;
int decision_model_type;
char *structure=NULL;
char *singleStruc,*gapStruc, *output,*woGapsSeq;
char strand[8];
char warningString[2000];
char warningString_regression[2000];
char *string=NULL;
double singleMFE,sumMFE,singleZ,sumZ,z,sci,id,decValue,prob,comb,entropy,GC;
double min_en, real_en;
int i,j,k,l,ll,r,countAln,nonGaps,singleGC;
int (*readFunction)(FILE *clust,struct aln *alignedSeqs[]);
char** lines=NULL;
int directions[3]={FORWARD,0,0};
int currDirection;
struct gengetopt_args_info args;
double meanMFE_fwd=0;
double consensusMFE_fwd=0;
double sci_fwd=0;
double z_fwd=0;
int strandGuess;
int avoid_shuffle=0;
double strandProb,strandDec;
if (cmdline_parser (argc, argv, &args) != 0){
usage();
exit(EXIT_FAILURE);
}
if (args.help_given){
help();
exit(EXIT_SUCCESS);
}
if (args.version_given){
version();
exit(EXIT_SUCCESS);
}
if (args.outfile_given){
out = fopen(args.outfile_arg, "w");
if (out == NULL){
fprintf(stderr, "ERROR: Can't open output file %s\n", args.outfile_arg);
exit(1);
}
}
/* Strand prediction implies both strands scored */
if (args.predict_strand_flag){
args.both_strands_flag=1;
}
if (args.forward_flag && !args.reverse_flag){
directions[0]=FORWARD;
directions[1]=directions[2]=0;
}
if (!args.forward_flag && args.reverse_flag){
directions[0]=REVERSE;
directions[1]=directions[2]=0;
}
if ((args.forward_flag && args.reverse_flag) || args.both_strands_flag){
directions[0]=FORWARD;
directions[1]=REVERSE;
}
if (args.window_given){
if (sscanf(args.window_arg,"%d-%d",&from,&to)!=2){
nrerror("ERROR: Invalid --window/-w command. "
"Use it like '--window 100-200'\n");
}
printf("from:%d,to:%d\n",from,to);
}
if (args.inputs_num>=1){
clust_file = fopen(args.inputs[0], "r");
if (clust_file == NULL){
fprintf(stderr, "ERROR: Can't open input file %s\n", args.inputs[0]);
exit(1);
}
}
/* Global RNA package variables */
do_backtrack = 1;
dangles=2;
switch(checkFormat(clust_file)){
case CLUSTAL:
readFunction=&read_clustal;
break;
case MAF:
readFunction=&read_maf;
break;
case 0:
nrerror("ERROR: Unknown alignment file format. Use Clustal W or MAF format.\n");
}
/* Set z-score type (mono/dinucleotide) here */
z_score_type = 2;
if (args.mononucleotide_given) z_score_type = 0;
/* now let's decide which decision model to take */
/* decision_model_type = 1 for normal model used in RNAz 1.0 */
/* decision_model_type = 2 for normal model using dinucelotide background */
/* decision_model_type = 3 for structural model using dinucelotide background */
decision_model_type = 2;
if (args.mononucleotide_given) decision_model_type = 1;
if (args.locarnate_given) decision_model_type = 3;
if ((args.mononucleotide_given) && args.locarnate_given){
z_score_type=2;
nrerror("ERROR: Structural decision model only trained with dinucleotide background model.\n");
}
if (args.no_shuffle_given) avoid_shuffle = 1;
decision_model=get_decision_model(NULL, decision_model_type);
/* Initialize Regression Models for mononucleotide */
/* Not needed if we score with dinucleotides */
if (z_score_type == 0) regression_svm_init();
countAln=0;
while ((n_seq=readFunction(clust_file, AS))!=0){
if (n_seq ==1){
nrerror("ERROR: You need at least two sequences in the alignment.\n");
}
countAln++;
length = (int) strlen(AS[0]->seq);
/* if a slice is specified by the user */
if ((from!=-1 || to!=-1) && (countAln==1)){
if ((from>=to)||(from<=0)||(to>length)){
nrerror("ERROR: Invalid window range given.\n");
}
sliceAln((const struct aln**)AS, (struct aln **)window, from, to);
length=to-from+1;
} else { /* take complete alignment */
/* window=AS does not work..., deep copy seems not necessary here*/
from=1;
to=length;
sliceAln((const struct aln **)AS, (struct aln **)window, 1, length);
}
/* Convert all Us to Ts for RNAalifold. There is a slight
difference in the results. During training we used alignments
with Ts, so we use Ts here as well. */
for (i=0;i<n_seq;i++){
j=0;
while (window[i]->seq[j]){
window[i]->seq[j]=toupper(window[i]->seq[j]);
if (window[i]->seq[j]=='U') window[i]->seq[j]='T';
++j;
}
}
k=0;
while ((currDirection=directions[k++])!=0){
if (currDirection==REVERSE){
revAln((struct aln **)window);
strcpy(strand,"reverse");
} else {
strcpy(strand,"forward");
}
structure = (char *) space((unsigned) length+1);
for (i=0;window[i]!=NULL;i++){
tmpAln[i]=window[i]->seq;
}
tmpAln[i]=NULL;
min_en = alifold(tmpAln, structure);
free_alifold_arrays();
comb=combPerPair(window,structure);
sumZ=0.0;
sumMFE=0.0;
GC=0.0;
output=(char *)space(sizeof(char)*(length+160)*(n_seq+1)*3);
strcpy(warningString,"");
strcpy(warningString_regression,"");
for (i=0;i<n_seq;i++){
singleStruc = space(strlen(window[i]->seq)+1);
woGapsSeq = space(strlen(window[i]->seq)+1);
j=0;
nonGaps=0;
singleGC=0;
while (window[i]->seq[j]){
/* Convert all Ts to Us for RNAfold. There is a difference
between the results. With U in the function call, we get
the results as RNAfold gives on the command line. Since
this variant was also used during training, we use it here
as well. */
if (window[i]->seq[j]=='T') window[i]->seq[j]='U';
if (window[i]->seq[j]=='C') singleGC++;
if (window[i]->seq[j]=='G') singleGC++;
if (window[i]->seq[j]!='-'){
nonGaps++;
woGapsSeq[strlen(woGapsSeq)]=window[i]->seq[j];
woGapsSeq[strlen(woGapsSeq)]='\0';
}
++j;
}
/* z-score is calculated here! */
singleMFE = fold(woGapsSeq, singleStruc);
free_arrays();
/* z-score type may be overwritten. If it is out of training
bounds, we switch to shuffling if allowed (avoid_shuffle). */
int z_score_type_orig = z_score_type;
singleZ=mfe_zscore(woGapsSeq,singleMFE, &z_score_type, avoid_shuffle, warningString_regression);
GC+=(double) singleGC/nonGaps;
sumZ+=singleZ;
sumMFE+=singleMFE;
if (window[1]->strand!='?' && !args.window_given){
sprintf(output+strlen(output),
">%s %d %d %c %d\n",
window[i]->name,window[i]->start,
window[i]->length,window[i]->strand,
window[i]->fullLength);
} else {
sprintf(output+strlen(output),">%s\n",window[i]->name);
}
gapStruc= (char *) space(sizeof(char)*(strlen(window[i]->seq)+1));
l=ll=0;
while (window[i]->seq[l]!='\0'){
if (window[i]->seq[l]!='-'){
gapStruc[l]=singleStruc[ll];
l++;
ll++;
} else {
gapStruc[l]='-';
l++;
}
}
char ch;
ch = 'R';
if (z_score_type == 1 || z_score_type == 3) ch = 'S';
sprintf(output+strlen(output),"%s\n%s ( %6.2f, z-score = %6.2f, %c)\n",
window[i]->seq,gapStruc,singleMFE,singleZ,ch);
z_score_type = z_score_type_orig;
free(woGapsSeq);
free(singleStruc);
}
{
int i; double s=0;
extern int eos_debug;
eos_debug=-1; /* shut off warnings about nonstandard pairs */
for (i=0; window[i]!=NULL; i++)
s += energy_of_struct(window[i]->seq, structure);
real_en = s/i;
}
string = consensus((const struct aln**) window);
sprintf(output+strlen(output),
">consensus\n%s\n%s (%6.2f = %6.2f + %6.2f) \n",
string, structure, min_en, real_en, min_en-real_en );
free(string);
id=meanPairID((const struct aln**)window);
entropy=NormShannonEntropy((const struct aln**)window);
z=sumZ/n_seq;
GC=(double)GC/n_seq;
if (sumMFE==0){
/*Set SCI to 0 in the weird case of no structure in single
sequences*/
sci=0;
} else {
sci=min_en/(sumMFE/n_seq);
}
decValue=999;
prob=0;
classify(&prob,&decValue,decision_model,id,n_seq,z,sci,entropy,decision_model_type);
if (args.cutoff_given){
if (prob<args.cutoff_arg){
continue;
}
}
warning(warningString,id,n_seq,z,sci,entropy,(struct aln **)window,decision_model_type);
fprintf(out,"\n############################ RNAz "PACKAGE_VERSION" ##############################\n\n");
fprintf(out," Sequences: %u\n", n_seq);
if (args.window_given){
fprintf(out," Slice: %u to %u\n",from,to);
}
fprintf(out," Columns: %u\n",length);
fprintf(out," Reading direction: %s\n",strand);
fprintf(out," Mean pairwise identity: %6.2f\n", id);
fprintf(out," Shannon entropy: %2.5f\n", entropy);
fprintf(out," G+C content: %2.5f\n", GC);
fprintf(out," Mean single sequence MFE: %6.2f\n", sumMFE/n_seq);
fprintf(out," Consensus MFE: %6.2f\n",min_en);
fprintf(out," Energy contribution: %6.2f\n",real_en);
fprintf(out," Covariance contribution: %6.2f\n",min_en-real_en);
fprintf(out," Combinations/Pair: %6.2f\n",comb);
fprintf(out," Mean z-score: %6.2f\n",z);
fprintf(out," Structure conservation index: %6.2f\n",sci);
if (decision_model_type == 1) {
fprintf(out," Background model: mononucleotide\n");
fprintf(out," Decision model: sequence based alignment quality\n");
}
if (decision_model_type == 2) {
fprintf(out," Background model: dinucleotide\n");
fprintf(out," Decision model: sequence based alignment quality\n");
}
if (decision_model_type == 3) {
fprintf(out," Background model: dinucleotide\n");
fprintf(out," Decision model: structural RNA alignment quality\n");
}
fprintf(out," SVM decision value: %6.2f\n",decValue);
fprintf(out," SVM RNA-class probability: %6f\n",prob);
if (prob>0.5){
fprintf(out," Prediction: RNA\n");
}
else {
fprintf(out," Prediction: OTHER\n");
}
fprintf(out,"%s",warningString_regression);
fprintf(out,"%s",warningString);
fprintf(out,"\n######################################################################\n\n");
fprintf(out,"%s",output);
fflush(out);
free(structure);
free(output);
if (currDirection==FORWARD && args.predict_strand_flag){
meanMFE_fwd=sumMFE/n_seq;
consensusMFE_fwd=min_en;
sci_fwd=sci;
z_fwd=z;
}
if (currDirection==REVERSE && args.predict_strand_flag){
if (predict_strand(sci_fwd-sci, meanMFE_fwd-(sumMFE/n_seq),
consensusMFE_fwd-min_en, z_fwd-z, n_seq, id,
&strandGuess, &strandProb, &strandDec, NULL)){
if (strandGuess==1){
fprintf(out, "\n# Strand winner: forward (%.2f)\n",strandProb);
} else {
fprintf(out, "\n# Strand winner: reverse (%.2f)\n",1-strandProb);
}
} else {
fprintf(out, "\n# WARNING: No strand prediction (values out of range)\n");
}
}
}
freeAln((struct aln **)AS);
freeAln((struct aln **)window);
}
if (args.inputs_num>=1){
fclose(clust_file);
}
cmdline_parser_free (&args);
if (countAln==0){
nrerror("ERROR: Empty alignment file\n");
}
svm_destroy_model(decision_model);
regression_svm_free();
return 0;
}
int main(int argc, char *argv[]){
struct RNALalifold_args_info args_info;
char *string, *structure, *ParamFile, *ns_bases, *c;
char ffname[80], gfname[80], fname[80];
int n_seq, i, length, sym, r, maxdist;
int mis, pf, istty;
float cutoff;
double min_en, real_en, sfact;
char *AS[MAX_NUM_NAMES]; /* aligned sequences */
char *names[MAX_NUM_NAMES]; /* sequence names */
FILE *clust_file = stdin;
string = structure = ParamFile = ns_bases = NULL;
mis = pf = 0;
maxdist = 70;
do_backtrack = 1;
dangles = 2;
sfact = 1.07;
cutoff = 0.0005;
/*
#############################################
# check the command line parameters
#############################################
*/
if(RNALalifold_cmdline_parser (argc, argv, &args_info) != 0) exit(1);
/* temperature */
if(args_info.temp_given) temperature = args_info.temp_arg;
/* structure constraint */
if(args_info.noTetra_given) tetra_loop=0;
/* set dangle model */
if(args_info.dangles_given) dangles = args_info.dangles_arg;
/* do not allow weak pairs */
if(args_info.noLP_given) noLonelyPairs = 1;
/* do not allow wobble pairs (GU) */
if(args_info.noGU_given) noGU = 1;
/* do not allow weak closing pairs (AU,GU) */
if(args_info.noClosingGU_given) no_closingGU = 1;
/* set energy model */
if(args_info.energyModel_given) energy_set = args_info.energyModel_arg;
/* take another energy parameter set */
if(args_info.paramFile_given) ParamFile = strdup(args_info.paramFile_arg);
/* Allow other pairs in addition to the usual AU,GC,and GU pairs */
if(args_info.nsp_given) ns_bases = strdup(args_info.nsp_arg);
/* set pf scaling factor */
if(args_info.pfScale_given) sfact = args_info.pfScale_arg;
/* partition function settings */
if(args_info.partfunc_given){
pf = 1;
if(args_info.partfunc_arg != -1)
do_backtrack = args_info.partfunc_arg;
}
/* set cfactor */
if(args_info.cfactor_given) cv_fact = args_info.cfactor_arg;
/* set nfactor */
if(args_info.nfactor_given) nc_fact = args_info.nfactor_arg;
/* set the maximum base pair span */
if(args_info.span_given) maxdist = args_info.span_arg;
/* set the pair probability cutoff */
if(args_info.cutoff_given) cutoff = args_info.cutoff_arg;
/* calculate most informative sequence */
if(args_info.mis_given) mis = 1;
/* check unnamed options a.k.a. filename of input alignment */
if(args_info.inputs_num == 1){
clust_file = fopen(args_info.inputs[0], "r");
if(clust_file == NULL){
fprintf(stderr, "can't open %s\n", args_info.inputs[0]);
}
}
else{
RNALalifold_cmdline_parser_print_help();
exit(1);
}
/* free allocated memory of command line data structure */
RNALalifold_cmdline_parser_free (&args_info);
/*
#############################################
# begin initializing
#############################################
*/
if (ParamFile != NULL)
read_parameter_file(ParamFile);
if (ns_bases != NULL) {
nonstandards = space(33);
c=ns_bases;
i=sym=0;
if (*c=='-') {
sym=1; c++;
}
while (*c!='\0') {
if (*c!=',') {
nonstandards[i++]=*c++;
nonstandards[i++]=*c;
if ((sym)&&(*c!=*(c-1))) {
nonstandards[i++]=*c;
nonstandards[i++]=*(c-1);
}
}
c++;
}
}
istty = isatty(fileno(stdout))&&isatty(fileno(stdin));
if (istty && (clust_file == stdin)) {
print_tty_input_seq_str("Input aligned sequences in clustalw format");
}
n_seq = read_clustal(clust_file, AS, names);
if (clust_file != stdin) fclose(clust_file);
if (n_seq==0)
nrerror("no sequences found");
length = (int) strlen(AS[0]);
if (length<maxdist) {
fprintf(stderr, "Alignment length < window size: setting L=%d\n",length);
maxdist=length;
}
structure = (char *) space((unsigned) length+1);
/*
#############################################
# begin calculations
#############################################
*/
update_fold_params();
if(!pf)
min_en = aliLfold(AS, structure, maxdist);
{
eos_debug=-1; /* shut off warnings about nonstandard pairs */
/* for (i=0; AS[i]!=NULL; i++)
s += energy_of_struct(AS[i], structure);
real_en = s/i;*/
}
string = (mis) ? consens_mis((const char **) AS) : consensus((const char **) AS);
printf("%s\n%s\n", string, structure);
/* if (istty)
printf("\n minimum free energy = %6.2f kcal/mol (%6.2f + %6.2f)\n",
min_en, real_en, min_en - real_en);
else
printf(" (%6.2f = %6.2f + %6.2f) \n", min_en, real_en, min_en-real_en );
*/
strcpy(ffname, "alirna.ps");
strcpy(gfname, "alirna.g");
/* if (length<=2500) {
char *A;
A = annote(structure, (const char**) AS);
(void) PS_rna_plot_a(string, structure, ffname, NULL, A);
free(A);
} else
fprintf(stderr,"INFO: structure too long, not doing xy_plot\n");
*/
/* {*/ /* free mfe arrays but preserve base_pair for PS_dot_plot */
/* struct bond *bp;
bp = base_pair; base_pair = space(16);
free_alifold_arrays(); / * frees base_pair * /
base_pair = bp;
}*/
if (pf) {
double energy, kT;
plist *pl;
char * mfe_struc;
mfe_struc = strdup(structure);
kT = (temperature+273.15)*1.98717/1000.; /* in Kcal */
pf_scale = -1;/*exp(-(sfact*min_en)/kT/length);*/
if (length>2000) fprintf(stderr, "scaling factor %f\n", pf_scale);
fflush(stdout);
/* init_alipf_fold(length); */
/* energy = alipfW_fold(AS, structure, &pl, maxdist, cutoff); */
if (do_backtrack) {
printf("%s", structure);
/*if (!istty) printf(" [%6.2f]\n", energy);
else */
printf("\n");
}
/*if ((istty)||(!do_backtrack))
printf(" free energy of ensemble = %6.2f kcal/mol\n", energy);
useless!!*/
/* printf(" frequency of mfe structure in ensemble %g\n",
exp((energy-min_en)/kT));*/
if (do_backtrack) {
FILE *aliout;
cpair *cp;
strcpy(ffname, "alifold.out");
aliout = fopen(ffname, "w");
if (!aliout) {
fprintf(stderr, "can't open %s skipping output\n", ffname);
} else {
fprintf(aliout, "%d sequence; length of alignment %d\n",
n_seq, length);
fprintf(aliout, "alifold output\n");
fprintf(aliout, "%s\n", structure);
}
strcpy(ffname, "alidotL.ps");
cp = make_color_pinfo2(AS,pl,n_seq);
(void) PS_color_dot_plot_turn(string, cp, ffname, maxdist);
free(cp);
}
free(mfe_struc);
free(pl);
}
free(base_pair);
(void) fflush(stdout);
free(string);
free(structure);
for (i=0; AS[i]; i++) {
free(AS[i]); free(names[i]);
}
return 0;
}
/*--------------------------------------------------------------------------*/
int main(int argc, char *argv[]){
struct RNAalifold_args_info args_info;
unsigned int input_type;
char ffname[FILENAME_MAX_LENGTH], gfname[FILENAME_MAX_LENGTH], fname[FILENAME_MAX_LENGTH];
char *input_string, *string, *structure, *cstruc, *ParamFile, *ns_bases, *c;
int n_seq, i, length, sym, r, noPS, with_sci;
int endgaps, mis, circular, doAlnPS, doColor, doMEA, n_back, eval_energy, pf, istty;
double min_en, real_en, sfact, MEAgamma, bppmThreshold, betaScale;
char *AS[MAX_NUM_NAMES]; /* aligned sequences */
char *names[MAX_NUM_NAMES]; /* sequence names */
FILE *clust_file = stdin;
pf_paramT *pf_parameters;
model_detailsT md;
fname[0] = ffname[0] = gfname[0] = '\0';
string = structure = cstruc = ParamFile = ns_bases = NULL;
pf_parameters = NULL;
endgaps = mis = pf = circular = doAlnPS = doColor = n_back = eval_energy = oldAliEn = doMEA = ribo = noPS = 0;
do_backtrack = 1;
dangles = 2;
gquad = 0;
sfact = 1.07;
bppmThreshold = 1e-6;
MEAgamma = 1.0;
betaScale = 1.;
with_sci = 0;
set_model_details(&md);
/*
#############################################
# check the command line prameters
#############################################
*/
if(RNAalifold_cmdline_parser (argc, argv, &args_info) != 0) exit(1);
/* temperature */
if(args_info.temp_given) temperature = args_info.temp_arg;
/* structure constraint */
if(args_info.constraint_given) fold_constrained=1;
/* do not take special tetra loop energies into account */
if(args_info.noTetra_given) md.special_hp = tetra_loop=0;
/* set dangle model */
if(args_info.dangles_given){
if((args_info.dangles_arg != 0) && (args_info.dangles_arg != 2))
warn_user("required dangle model not implemented, falling back to default dangles=2");
else
md.dangles = dangles=args_info.dangles_arg;
}
/* do not allow weak pairs */
if(args_info.noLP_given) md.noLP = noLonelyPairs = 1;
/* do not allow wobble pairs (GU) */
if(args_info.noGU_given) md.noGU = noGU = 1;
/* do not allow weak closing pairs (AU,GU) */
if(args_info.noClosingGU_given) md.noGUclosure = no_closingGU = 1;
/* gquadruplex support */
if(args_info.gquad_given) md.gquad = gquad = 1;
/* sci computation */
if(args_info.sci_given) with_sci = 1;
/* do not convert DNA nucleotide "T" to appropriate RNA "U" */
/* set energy model */
if(args_info.energyModel_given) energy_set = args_info.energyModel_arg;
/* take another energy parameter set */
if(args_info.paramFile_given) ParamFile = strdup(args_info.paramFile_arg);
/* Allow other pairs in addition to the usual AU,GC,and GU pairs */
if(args_info.nsp_given) ns_bases = strdup(args_info.nsp_arg);
/* set pf scaling factor */
if(args_info.pfScale_given) sfact = args_info.pfScale_arg;
/* assume RNA sequence to be circular */
if(args_info.circ_given) circular=1;
/* do not produce postscript output */
if(args_info.noPS_given) noPS = 1;
/* partition function settings */
if(args_info.partfunc_given){
pf = 1;
if(args_info.partfunc_arg != -1)
do_backtrack = args_info.partfunc_arg;
}
/* MEA (maximum expected accuracy) settings */
if(args_info.MEA_given){
pf = doMEA = 1;
if(args_info.MEA_arg != -1)
MEAgamma = args_info.MEA_arg;
}
if(args_info.betaScale_given) betaScale = args_info.betaScale_arg;
/* set the bppm threshold for the dotplot */
if(args_info.bppmThreshold_given)
bppmThreshold = MIN2(1., MAX2(0.,args_info.bppmThreshold_arg));
/* set cfactor */
if(args_info.cfactor_given) cv_fact = args_info.cfactor_arg;
/* set nfactor */
if(args_info.nfactor_given) nc_fact = args_info.nfactor_arg;
if(args_info.endgaps_given) endgaps = 1;
if(args_info.mis_given) mis = 1;
if(args_info.color_given) doColor=1;
if(args_info.aln_given) doAlnPS=1;
if(args_info.old_given) oldAliEn = 1;
if(args_info.stochBT_given){
n_back = args_info.stochBT_arg;
do_backtrack = 0;
pf = 1;
init_rand();
}
if(args_info.stochBT_en_given){
n_back = args_info.stochBT_en_arg;
do_backtrack = 0;
pf = 1;
eval_energy = 1;
init_rand();
}
if(args_info.ribosum_file_given){
RibosumFile = strdup(args_info.ribosum_file_arg);
ribo = 1;
}
if(args_info.ribosum_scoring_given){
RibosumFile = NULL;
ribo = 1;
}
if(args_info.layout_type_given)
rna_plot_type = args_info.layout_type_arg;
/* alignment file name given as unnamed option? */
if(args_info.inputs_num == 1){
clust_file = fopen(args_info.inputs[0], "r");
if (clust_file == NULL) {
fprintf(stderr, "can't open %s\n", args_info.inputs[0]);
}
}
/* free allocated memory of command line data structure */
RNAalifold_cmdline_parser_free (&args_info);
/*
#############################################
# begin initializing
#############################################
*/
if(circular && gquad){
nrerror("G-Quadruplex support is currently not available for circular RNA structures");
}
make_pair_matrix();
if (circular && noLonelyPairs)
warn_user("depending on the origin of the circular sequence, "
"some structures may be missed when using --noLP\n"
"Try rotating your sequence a few times\n");
if (ParamFile != NULL) read_parameter_file(ParamFile);
if (ns_bases != NULL) {
nonstandards = space(33);
c=ns_bases;
i=sym=0;
if (*c=='-') {
sym=1; c++;
}
while (*c!='\0') {
if (*c!=',') {
nonstandards[i++]=*c++;
nonstandards[i++]=*c;
if ((sym)&&(*c!=*(c-1))) {
nonstandards[i++]=*c;
nonstandards[i++]=*(c-1);
}
}
c++;
}
}
istty = isatty(fileno(stdout))&&isatty(fileno(stdin));
/*
########################################################
# handle user input from 'stdin' if necessary
########################################################
*/
if(fold_constrained){
if(istty){
print_tty_constraint_full();
print_tty_input_seq_str("");
}
input_type = get_input_line(&input_string, VRNA_INPUT_NOSKIP_COMMENTS);
if(input_type & VRNA_INPUT_QUIT){ return 0;}
else if((input_type & VRNA_INPUT_MISC) && (strlen(input_string) > 0)){
cstruc = strdup(input_string);
free(input_string);
}
else warn_user("constraints missing");
}
if (istty && (clust_file == stdin))
print_tty_input_seq_str("Input aligned sequences in clustalw or stockholm format\n(enter a line starting with \"//\" to indicate the end of your input)");
n_seq = read_clustal(clust_file, AS, names);
if (n_seq==0) nrerror("no sequences found");
if (clust_file != stdin) fclose(clust_file);
/*
########################################################
# done with 'stdin' handling, now init everything properly
########################################################
*/
length = (int) strlen(AS[0]);
structure = (char *)space((unsigned) length+1);
if(fold_constrained && cstruc != NULL)
strncpy(structure, cstruc, length);
if (endgaps)
for (i=0; i<n_seq; i++) mark_endgaps(AS[i], '~');
/*
########################################################
# begin actual calculations
########################################################
*/
if (circular) {
int i;
double s = 0;
min_en = circalifold((const char **)AS, structure);
for (i=0; AS[i]!=NULL; i++)
s += energy_of_circ_structure(AS[i], structure, -1);
real_en = s/i;
} else {
float *ens = (float *)space(2*sizeof(float));
min_en = alifold((const char **)AS, structure);
if(md.gquad)
energy_of_ali_gquad_structure((const char **)AS, structure, n_seq, ens);
else
energy_of_alistruct((const char **)AS, structure, n_seq, ens);
real_en = ens[0];
free(ens);
}
string = (mis) ? consens_mis((const char **) AS) : consensus((const char **) AS);
printf("%s\n%s", string, structure);
if(istty){
if(with_sci){
float sci = min_en;
float e_mean = 0;
for (i=0; AS[i]!=NULL; i++){
char *seq = get_ungapped_sequence(AS[i]);
char *str = (char *)space(sizeof(char) * (strlen(seq) + 1));
e_mean += fold(seq, str);
free(seq);
free(str);
}
e_mean /= i;
sci /= e_mean;
printf( "\n minimum free energy = %6.2f kcal/mol (%6.2f + %6.2f)"
"\n SCI = %2.4f\n",
min_en, real_en, min_en-real_en, sci);
} else
printf("\n minimum free energy = %6.2f kcal/mol (%6.2f + %6.2f)\n",
min_en, real_en, min_en - real_en);
} else {
if(with_sci){
float sci = min_en;
float e_mean = 0;
for (i=0; AS[i]!=NULL; i++){
char *seq = get_ungapped_sequence(AS[i]);
char *str = (char *)space(sizeof(char) * (strlen(seq) + 1));
e_mean += fold(seq, str);
free(seq);
free(str);
}
e_mean /= i;
sci /= e_mean;
printf(" (%6.2f = %6.2f + %6.2f) [%2.4f]\n", min_en, real_en, min_en-real_en, sci);
}
else
printf(" (%6.2f = %6.2f + %6.2f) \n", min_en, real_en, min_en-real_en );
}
strcpy(ffname, "alirna.ps");
strcpy(gfname, "alirna.g");
if (!noPS) {
char **A;
A = annote(structure, (const char**) AS);
if(md.gquad){
if (doColor)
(void) PS_rna_plot_a_gquad(string, structure, ffname, A[0], A[1]);
else
(void) PS_rna_plot_a_gquad(string, structure, ffname, NULL, A[1]);
} else {
if (doColor)
(void) PS_rna_plot_a(string, structure, ffname, A[0], A[1]);
else
(void) PS_rna_plot_a(string, structure, ffname, NULL, A[1]);
}
free(A[0]); free(A[1]); free(A);
}
if (doAlnPS)
PS_color_aln(structure, "aln.ps", (const char const **) AS, (const char const **) names);
/* free mfe arrays */
free_alifold_arrays();
if (pf) {
float energy, kT;
char * mfe_struc;
mfe_struc = strdup(structure);
kT = (betaScale*((temperature+K0)*GASCONST))/1000.; /* in Kcal */
pf_scale = exp(-(sfact*min_en)/kT/length);
if (length>2000) fprintf(stderr, "scaling factor %f\n", pf_scale);
fflush(stdout);
if (cstruc!=NULL) strncpy(structure, cstruc, length+1);
pf_parameters = get_boltzmann_factors_ali(n_seq, temperature, betaScale, md, pf_scale);
energy = alipf_fold_par((const char **)AS, structure, NULL, pf_parameters, do_backtrack, fold_constrained, circular);
if (n_back>0) {
/*stochastic sampling*/
for (i=0; i<n_back; i++) {
char *s;
double prob=1.;
s = alipbacktrack(&prob);
printf("%s ", s);
if (eval_energy ) printf("%6g %.2f ",prob, -1*(kT*log(prob)-energy));
printf("\n");
free(s);
}
}
if (do_backtrack) {
printf("%s", structure);
if (!istty) printf(" [%6.2f]\n", energy);
else printf("\n");
}
if ((istty)||(!do_backtrack))
printf(" free energy of ensemble = %6.2f kcal/mol\n", energy);
printf(" frequency of mfe structure in ensemble %g\n",
exp((energy-min_en)/kT));
if (do_backtrack) {
FILE *aliout;
cpair *cp;
char *cent;
double dist;
FLT_OR_DBL *probs = export_ali_bppm();
plist *pl, *mfel;
assign_plist_from_pr(&pl, probs, length, bppmThreshold);
assign_plist_from_db(&mfel, mfe_struc, 0.95*0.95);
if (!circular){
float *ens;
cent = get_centroid_struct_pr(length, &dist, probs);
ens=(float *)space(2*sizeof(float));
energy_of_alistruct((const char **)AS, cent, n_seq, ens);
/*cent_en = energy_of_struct(string, cent);*/ /*ali*/
printf("%s %6.2f {%6.2f + %6.2f}\n",cent,ens[0]-ens[1],ens[0],(-1)*ens[1]);
free(cent);
free(ens);
}
if(doMEA){
float mea, *ens;
plist *pl2;
assign_plist_from_pr(&pl2, probs, length, 1e-4/(1+MEAgamma));
mea = MEA(pl2, structure, MEAgamma);
ens = (float *)space(2*sizeof(float));
if(circular)
energy_of_alistruct((const char **)AS, structure, n_seq, ens);
else
ens[0] = energy_of_structure(string, structure, 0);
printf("%s {%6.2f MEA=%.2f}\n", structure, ens[0], mea);
free(ens);
free(pl2);
}
if (fname[0]!='\0') {
strcpy(ffname, fname);
strcat(ffname, "_ali.out");
} else strcpy(ffname, "alifold.out");
aliout = fopen(ffname, "w");
if (!aliout) {
fprintf(stderr, "can't open %s skipping output\n", ffname);
} else {
print_aliout(AS, pl, bppmThreshold, n_seq, mfe_struc, aliout);
}
fclose(aliout);
if (fname[0]!='\0') {
strcpy(ffname, fname);
strcat(ffname, "_dp.ps");
} else strcpy(ffname, "alidot.ps");
cp = make_color_pinfo(AS,pl, bppmThreshold, n_seq, mfel);
(void) PS_color_dot_plot(string, cp, ffname);
free(cp);
free(pl);
free(mfel);
}
free(mfe_struc);
free_alipf_arrays();
free(pf_parameters);
}
if (cstruc!=NULL) free(cstruc);
(void) fflush(stdout);
free(string);
free(structure);
for (i=0; AS[i]; i++) {
free(AS[i]); free(names[i]);
}
return 0;
}
int
main (int argc, char** argv)
{
Sint optindex, c;
unsigned char depictsw=0;
unsigned char wurst=1;
unsigned char gnuplot=0;
Uint i, j, noofseqs=0, nooffreqs=0, noofqueries=0;
Uint noofhits=100;
Uint substrlen = 10;
Uint minseeds = 5;
Uint maxmatches = 10000;
char *seq, *vec, *bin;
imbissinfo *imbiss;
void *space = NULL;
double *scores = NULL;
int swscores[2]={3,-2};
char *pveclistfile=NULL;
char *alphabetfile=NULL;
char *inputfile=NULL;
char *batchfile = NULL;
char *subfile=NULL;
char *reportfile = NULL;
int (*handler)
(void *, Matchtype *, IntSequence **, Uint,
Uint, void *) = allscores;
double (*filter)
(void *, Matchtype *, IntSequence *, IntSequence *,
Uint *, Uint, Uint, void *) = swconstfilter;
Matchtype* (*select)
(void *, Matchtype *, Uint k,
IntSequence *, IntSequence **, void *) = selectSW;
stringset_t **fn, **freq, *queryurl, **queries=NULL;
Suffixarray *arr = NULL;
IntSequence **sequences = NULL;
IntSequence *input = NULL;
FAlphabet *alphabet = NULL;
PairSint *matches=NULL;
Uint percent=0;
time_t startsuf, endsuf;
double difsuf, difmatch, difrank;
#ifdef MEMMAN_H
Spacetable spacetab;
initmemoryblocks(&spacetab, 100000);
space = &spacetab;
#endif
while(1)
{
c=getopt_long(argc, argv, "SAghFGBLM:D:r:m:x:n:p:b:s:a:q:l:c:dvw",
long_options, &optindex);
if (c==-1) break;
switch(c) {
case 'r':
reportfile=optarg;
break;
case 'v':
verbose_flag=1;
break;
case 'd':
depictsw = 1;
break;
case 's':
pveclistfile = optarg;
break;
case 'a':
alphabetfile = optarg;
break;
case 'q':
inputfile = optarg;
noofqueries = 1;
break;
case 'l':
substrlen = atoi(optarg);
break;
case 'c':
minseeds = atoi(optarg);
break;
case 'b':
batchfile = optarg;
break;
case 'p':
percent = atoi(optarg);
break;
case 'x':
subfile = optarg;
break;
case 'n':
noofhits = atoi(optarg);
break;
case 'w':
wurst = 0;
break;
case 'B':
filter = scorefilter;
select = selectBlastScore;
break;
case 'S':
filter = scorefilter;
select = selectScore;
break;
case 'A':
filter = swconstfilter;
select = selectSW;
break;
case 'F':
filter = scorefilter;
select = selectScoreSWconst;
break;
case 'G':
filter = scorefilter;
select = selectBlastScoreSWconst;
break;
case 'M':
swscores[0]=atoi(optarg);
break;
case 'L':
handler = latexscores;
break;
case 'D':
swscores[1]=atoi(optarg);
break;
case 'g':
gnuplot = 1;
break;
case 'm':
maxmatches=atoi(optarg);
break;
case 'h':
default:
usage(argv[0]);
exit (EXIT_FAILURE);
}
}
if (pveclistfile==NULL || (inputfile == NULL && batchfile==NULL)
|| alphabetfile == NULL) {
usage(argv[0]);
exit (EXIT_FAILURE);
}
imbiss = ALLOCMEMORY(space, NULL, imbissinfo, 1);
imbiss->reportfile = reportfile;
imbiss->swscores = swscores;
imbiss->noofhits = noofhits;
imbiss->minseeds = minseeds;
imbiss->wurst = wurst;
/*read batch file*/
if (batchfile) {
queries = readcsv(space, batchfile, "", &noofqueries);
}
/*read substitution matrix*/
if (subfile) {
freq=readcsv(space, subfile,",", &nooffreqs);
scores = ALLOCMEMORY(space, NULL, double, ((nooffreqs-1)*(nooffreqs-1)) );
for(i=1; i < nooffreqs; i++) {
for(j=1; j < nooffreqs; j++) {
if(strcmp(SETSTR(freq[i],j),"inf")==0){
MATRIX2D(scores, nooffreqs-1, i, j)=0;
}else{
MATRIX2D(scores, nooffreqs-1, i, j)=atof(SETSTR(freq[i],j));
}
}
}
}
/*read alphabet*/
if (alphabetfile != NULL) {
alphabet = loadCSValphabet(space, alphabetfile);
sortMapdomain(space, alphabet);
}
/*load sequence database*/
fn=readcsv(space, pveclistfile, "", &noofseqs);
sequences = ALLOCMEMORY(space, NULL, IntSequence *, noofseqs);
for(i=0; i < noofseqs; i++)
{
sequences[i] = loadSequence(space, SETSTR(fn[i],0));
}
for (i=0; i < noofseqs; i++) {
destructStringset(space, fn[i]);
}
FREEMEMORY(space, fn);
/*construct the suffix array*/
time (&startsuf);
arr = constructSufArr(space, sequences, noofseqs, NULL);
constructLcp(space, arr);
time (&endsuf);
difsuf = difftime (endsuf, startsuf);
/*do search*/
for (i=0; i < noofqueries; i++) {
/*get query form batchfile*/
if (queries) {
inputfile = SETSTR(queries[i],0);
}
/*typically only used with batchfile*/
if (percent != 0) {
substrlen =
((double)((double)input->length/100)*(double) percent);
}
input = loadSequence(space, inputfile);
//seq = printSequence (space, input, 60);
printf(">IMBISS order delivered\n");
//printf("%s\n",seq);
printf("%s\n", input->url);
//FREEMEMORY(space, seq);
time (&startsuf);
matches=sufSubstring(space, arr, input->sequence, input->length, substrlen);
time (&endsuf);
difmatch = difftime (endsuf, startsuf);
/*get prob vector url for salami/wurst*/
//printf("%.*s\n", 5, input->url + 58);
vec = malloc(sizeof(char)*66);
sprintf(vec, "/smallfiles/public/no_backup/bm/pdb_all_vec_6mer_struct/%5s.vec\0", input->url+56);
bin = malloc(sizeof(char)*54);
sprintf(bin, "/smallfiles/public/no_backup/bm/pdb_all_bin/%5s.bin\0", input->url+56);
queryurl = initStringset(space);
addString(space, queryurl, bin, strlen(bin));
addString(space, queryurl, vec, strlen(vec));
getimbissblast(space, input, sequences, noofseqs, alphabet, imbiss);
imbiss->query = queryurl;
imbiss->substrlen = substrlen;
imbiss->alphabet = alphabet;
/*if a substition file was given ...*/
if (subfile) {
imbiss->sub = createsubmatrix(scores, imbiss->score, nooffreqs-1);
}
/*match 'n' report*/
time (&startsuf);
imbiss->consensus = ALLOCMEMORY(space, NULL, Uint, (input->length-substrlen));
memset(imbiss->consensus, 0, (sizeof(Uint)*(input->length-substrlen)));
rankSufmatch(space, arr, matches, input->length-substrlen,
maxmatches, substrlen,
sequences, noofseqs, filter, select, handler,
input, imbiss, scores, depictsw);
if (gnuplot) {
consensus (space, imbiss->consensus, input->length-substrlen,
input, substrlen, imbiss);
}
time (&endsuf);
difrank = difftime (endsuf, startsuf);
printf ("Building the suffixtree has taken %f seconds.\n", difsuf);
printf ("Match the suffixtree has taken %f seconds.\n", difmatch);
printf ("Rank the suffixtree has taken %f seconds.\n", difrank);
/*partial cleanup*/
//destructStringset(space, queryurl);
destructSequence(space, input);
if(subfile) {
FREEMEMORY(space, imbiss->sub);
}
FREEMEMORY(space, imbiss->consensus);
FREEMEMORY(space, imbiss->score);
FREEMEMORY(space, matches);
free(bin);
free(vec);
}
/*final cleanup*/
for (i=0; i < noofseqs; i++) {
destructSequence(space, sequences[i]);
}
FREEMEMORY(space, sequences);
destructSufArr(space, arr);
#ifdef MEMMAN_H
activeblocks(space);
#endif
printf("Goodbye.\n");
return EXIT_SUCCESS;
}
int main(int argc, char *argv[])
{
char *string;
char *structure=NULL;
char *cstruc=NULL;
char *ns_bases=NULL;
char *c;
int n_seq;
int i;
int length;
int sym;
int endgaps = 0;
int mis = 0;
double min_en;
double real_en;
double sfact = 1.07;
int pf = 0;
int istty;
char *AS[MAX_NUM_NAMES]; /* aligned sequences */
char *names[MAX_NUM_NAMES]; /* sequence names */
AjPSeqset seq = NULL;
AjPFile confile = NULL;
AjPFile alifile = NULL;
AjPFile paramfile = NULL;
AjPFile outf = NULL;
AjPFile essfile = NULL;
AjPFile dotfile = NULL;
AjPStr constring = NULL;
float eT = 0.;
AjBool eGU;
AjBool eclose;
AjBool lonely;
AjPStr ensbases = NULL;
AjBool etloop;
AjPStr eenergy = NULL;
char ewt = '\0';
float escale = 0.;
AjPStr edangles = NULL;
char edangle = '\0';
ajint len;
AjPSeq tseq = NULL;
AjPStr tname = NULL;
int circ = 0;
int doAlnPS = 0;
int doColor = 0;
embInitPV("vrnaalifoldpf",argc,argv,"VIENNA",VERSION);
constring = ajStrNew();
seq = ajAcdGetSeqset("sequence");
confile = ajAcdGetInfile("constraintfile");
paramfile = ajAcdGetInfile("paramfile");
eT = ajAcdGetFloat("temperature");
eGU = ajAcdGetBoolean("gu");
eclose = ajAcdGetBoolean("closegu");
lonely = ajAcdGetBoolean("lp");
ensbases = ajAcdGetString("nsbases");
etloop = ajAcdGetBoolean("tetraloop");
eenergy = ajAcdGetListSingle("energy");
escale = ajAcdGetFloat("scale");
edangles = ajAcdGetListSingle("dangles");
mis = !!ajAcdGetBoolean("most");
endgaps = !!ajAcdGetBoolean("endgaps");
nc_fact = (double) ajAcdGetFloat("nspenalty");
cv_fact = (double) ajAcdGetFloat("covariance");
outf = ajAcdGetOutfile("outfile");
essfile = ajAcdGetOutfile("ssoutfile");
alifile = ajAcdGetOutfile("alignoutfile");
circ = !!ajAcdGetBoolean("circular");
doColor = !!ajAcdGetBoolean("colour");
dotfile = ajAcdGetOutfile("dotoutfile");
do_backtrack = 1;
pf = 1;
string = NULL;
istty = 0;
dangles = 2;
temperature = (double) eT;
noGU = (eGU) ? 0 : 1;
no_closingGU = (eclose) ? 0 : 1;
noLonelyPairs = (lonely) ? 0 : 1;
ns_bases = (ajStrGetLen(ensbases)) ? MAJSTRGETPTR(ensbases) : NULL;
tetra_loop = !!etloop;
ewt = *ajStrGetPtr(eenergy);
if(ewt == '0')
energy_set = 0;
else if(ewt == '1')
energy_set = 1;
else if(ewt == '2')
energy_set = 2;
sfact = (double) escale;
edangle = *ajStrGetPtr(edangles);
if(edangle == '0')
dangles = 0;
else if(edangle == '1')
dangles = 1;
else if(edangle == '2')
dangles = 2;
else if(edangle == '3')
dangles = 3;
if(paramfile)
read_parameter_file(paramfile);
if (ns_bases != NULL)
{
nonstandards = space(33);
c=ns_bases;
i=sym=0;
if (*c=='-')
{
sym=1;
c++;
}
while (*c!='\0')
{
if (*c!=',')
{
nonstandards[i++]=*c++;
nonstandards[i++]=*c;
if ((sym)&&(*c!=*(c-1)))
{
nonstandards[i++]=*c;
nonstandards[i++]=*(c-1);
}
}
c++;
}
}
if(alifile)
doAlnPS = 1;
if(confile)
vienna_GetConstraints(confile,&constring);
n_seq = ajSeqsetGetSize(seq);
if(n_seq > MAX_NUM_NAMES - 1)
ajFatal("[e]RNAalifold is restricted to %d sequences\n",
MAX_NUM_NAMES - 1);
if (n_seq==0)
ajFatal("No sequences found");
for(i=0;i<n_seq;++i)
{
tseq = (AjPSeq) ajSeqsetGetseqSeq(seq,i);
ajSeqGapStandard(tseq, '-');
tname = (AjPStr) ajSeqsetGetseqNameS(seq,i);
len = ajSeqGetLen(tseq);
AS[i] = (char *) space(len+1);
names[i] = (char *) space(ajStrGetLen(tname)+1);
strcpy(AS[i],ajSeqGetSeqC(tseq));
strcpy(names[i],ajStrGetPtr(tname));
}
AS[n_seq] = NULL;
names[n_seq] = NULL;
if (endgaps)
for (i=0; i<n_seq; i++)
mark_endgaps(AS[i], '~');
length = (int) strlen(AS[0]);
structure = (char *) space((unsigned) length+1);
if(confile)
{
fold_constrained = 1;
strcpy(structure,ajStrGetPtr(constring));
}
if (circ && noLonelyPairs)
ajWarn(
"warning, depending on the origin of the circular sequence, "
"some structures may be missed when using -noLP\n"
"Try rotating your sequence a few times\n");
if (circ)
min_en = circalifold((const char **)AS, structure);
else
min_en = alifold(AS, structure);
{
int i;
double s=0;
extern int eos_debug;
eos_debug=-1; /* shut off warnings about nonstandard pairs */
for (i=0; AS[i]!=NULL; i++)
if (circ)
s += energy_of_circ_struct(AS[i], structure);
else
s += energy_of_struct(AS[i], structure);
real_en = s/i;
}
string = (mis) ?
consens_mis((const char **) AS) : consensus((const char **) AS);
ajFmtPrintF(outf,"%s\n%s", string, structure);
ajFmtPrintF(outf," (%6.2f = %6.2f + %6.2f) \n", min_en, real_en,
min_en-real_en );
if (length<=2500) {
char **A;
A = annote(structure, (const char**) AS);
if (doColor)
(void) PS_rna_plot_a(string, structure, essfile, A[0], A[1]);
else
(void) PS_rna_plot_a(string, structure, essfile, NULL, A[1]);
free(A[0]); free(A[1]);free(A);
} else
ajWarn("INFO: structure too long, not doing xy_plot\n");
if (doAlnPS)
PS_color_aln(structure, alifile, AS, names);
{ /* free mfe arrays but preserve base_pair for PS_dot_plot */
struct bond *bp;
bp = base_pair; base_pair = space(16);
free_alifold_arrays(); /* free's base_pair */
free_alipf_arrays();
base_pair = bp;
}
if (pf) {
double energy, kT;
pair_info *pi;
char * mfe_struc;
mfe_struc = strdup(structure);
kT = (temperature+273.15)*1.98717/1000.; /* in Kcal */
pf_scale = exp(-(sfact*min_en)/kT/length);
if (length>2000)
ajWarn("scaling factor %f\n", pf_scale);
/* init_alipf_fold(length); */
if (confile)
strncpy(structure, ajStrGetPtr(constring), length+1);
energy = (circ) ? alipf_circ_fold(AS, structure, &pi) : alipf_fold(AS, structure, &pi);
if (do_backtrack) {
ajFmtPrintF(outf,"%s", structure);
ajFmtPrintF(outf," [%6.2f]\n", energy);
}
if ((istty)||(!do_backtrack))
ajFmtPrintF(outf," free energy of ensemble = %6.2f kcal/mol\n", energy);
ajFmtPrintF(outf," frequency of mfe structure in ensemble %g\n",
exp((energy-min_en)/kT));
if (do_backtrack) {
FILE *aliout;
cpair *cp;
short *ptable; int k;
ptable = make_pair_table(mfe_struc);
ajFmtPrintF(outf,"\n# Alignment section\n\n");
aliout = ajFileGetFileptr(outf);
fprintf(aliout, "%d sequences; length of alignment %d\n",
n_seq, length);
fprintf(aliout, "alifold output\n");
for (k=0; pi[k].i>0; k++) {
pi[k].comp = (ptable[pi[k].i] == pi[k].j) ? 1:0;
print_pi(pi[k], aliout);
}
fprintf(aliout, "%s\n", structure);
free(ptable);
cp = make_color_pinfo(pi);
(void) PS_color_dot_plot(string, cp, dotfile);
free(cp);
free(mfe_struc);
free(pi);
}
}
if (cstruc!=NULL) free(cstruc);
free(base_pair);
(void) fflush(stdout);
free(string);
free(structure);
for (i=0; AS[i]; i++) {
free(AS[i]); free(names[i]);
}
ajSeqsetDel(&seq);
ajStrDel(&constring);
ajStrDel(&eenergy);
ajStrDel(&edangles);
ajStrDel(&ensbases);
ajFileClose(&confile);
ajFileClose(¶mfile);
ajFileClose(&outf);
ajFileClose(&essfile);
ajFileClose(&alifile);
ajFileClose(&dotfile);
embExit();
return 0;
}
int main(int argc, char** argv)
{
if(argc > 3)
{
double t1, t2, t3;
struct timeval t_s1, t_e1, t_s2, t_e2, t_s3, t_e3;
image_height=atoi(argv[1]);
image_width=atoi(argv[1]);
if(atoi(argv[2]) == 1)
create_image();
image = (char*)malloc(sizeof(char)*image_height*image_width);
meet=(ConsensusGrid*)malloc(sizeof(ConsensusGrid)*image_height*image_width);
basis = (int*)malloc(sizeof(int)*image_height*image_width);
read_raw_image("image.raw",image,image_height,image_width);
cout << "Calculating consensus..." << endl << endl;
for(int i=0; i<image_height; i++)
{
for(int j = 0; j<image_width; j++)
{
if(atoi(argv[3]) == 1)
{
gettimeofday(&t_s1, NULL);
meet[i*image_width+j]=consensus_parallel(i, j, image,image_height,image_width);
gettimeofday(&t_e1, NULL);
t1 = (((double)t_e1.tv_sec-(double)t_s1.tv_sec)*1000) + ((double)t_e1.tv_usec - (double)t_s1.tv_usec)/1000;
}
else
{
gettimeofday(&t_s1, NULL);
meet[i*image_width+j]=consensus(i, j, image,image_height,image_width);
gettimeofday(&t_e1, NULL);
t1 = (((double)t_e1.tv_sec-(double)t_s1.tv_sec)*1000) + ((double)t_e1.tv_usec - (double)t_s1.tv_usec)/1000;
}
}
}
cout << "Calculating list..." << endl << endl;
if(atoi(argv[3]) == 1)
{
gettimeofday(&t_s2, NULL);
calculate_list_parallel();
gettimeofday(&t_e2, NULL);
t2 = (((double)t_e2.tv_sec-(double)t_s2.tv_sec)*1000) + ((double)t_e2.tv_usec - (double)t_s2.tv_usec)/1000;
}
else
{
gettimeofday(&t_s2, NULL);
calculate_list();
gettimeofday(&t_e2, NULL);
t2 = (((double)t_e2.tv_sec-(double)t_s2.tv_sec)*1000) + ((double)t_e2.tv_usec - (double)t_s2.tv_usec)/1000;
}
cout << "Calculating basis..." << endl << endl;
if(atoi(argv[3]) == 1)
{
gettimeofday(&t_s3, NULL);
calculate_basis();
gettimeofday(&t_e3, NULL);
t3 = (((double)t_e3.tv_sec-(double)t_s3.tv_sec)*1000) + ((double)t_e3.tv_usec - (double)t_s3.tv_usec)/1000;
}
else
{
gettimeofday(&t_s3, NULL);
calculate_basis();
gettimeofday(&t_e3, NULL);
t3 = (((double)t_e3.tv_sec-(double)t_s3.tv_sec)*1000) + ((double)t_e3.tv_usec - (double)t_s3.tv_usec)/1000;
}
cout << "Basis count = " << basis_count << endl;
cout << endl << "Time for Parallel Consensus Calculation = " << t1 << " msec" << endl;
cout << "Time for Parallel List Calculation = " << t2 << " msec" << endl;
cout << "Time for Basis Calculation = " << t3 << " msec" << endl;
}
else
{
cout << "Insufficient arguments\n" << endl;
cout << "First argument = Image Size" << endl;
cout << "Second argument = 1 to create image, 0 not to create image" << endl;
cout << "Third argument = 1 for parallel, 0 for not parallel\n" << endl;
}
}
int main(int argc, char** argv)
{
if(argc > 1)
{
int* basis_serial;
int* basis_parallel;
int basis_count1, basis_count2;
image_height=atoi(argv[1]);
image_width=atoi(argv[1]);
create_image();
image = (char*)malloc(sizeof(char)*image_height*image_width);
meet=(ConsensusGrid*)malloc(sizeof(ConsensusGrid)*image_height*image_width);
basis = (int*)malloc(sizeof(int)*image_height*image_width);
read_raw_image("image.raw",image,image_height,image_width);
struct timeval t_s, t_e;
gettimeofday(&t_s, NULL);
/// For serial implementation
for(int i=0; i<image_height; i++)
{
for(int j = 0; j<image_width; j++)
{
meet[i*image_width+j]=consensus(i, j, image,image_height,image_width);
}
}
printf("Calculating list for serial\n");
calculate_list();
printf("Calculating basis for serial\n");
calculate_basis();
gettimeofday(&t_e, NULL);
double t1 = (((double)t_e.tv_sec-(double)t_s.tv_sec)*1000) + ((double)t_e.tv_usec - (double)t_s.tv_usec)/1000;
basis_serial = basis;
basis_count1 = basis_count;
cout << "Serial Basis count = " << basis_count << endl << endl;;
reset_values();
/// For parallel implementation
struct timeval t_s2, t_e2;
gettimeofday(&t_s2, NULL);
for(int i=0; i<image_height; i++)
{
for(int j = 0; j<image_width; j++)
{
meet[i*image_width+j]=consensus_parallel(i, j, image,image_height,image_width);
}
}
printf("Calculating list for parallel\n");
calculate_list();
printf("Calculating basis for parallel\n");
calculate_basis();
gettimeofday(&t_e2, NULL);
double t2 = (((double)t_e2.tv_sec-(double)t_s2.tv_sec)*1000) + ((double)t_e2.tv_usec - (double)t_s2.tv_usec)/1000;
basis_parallel = basis;
basis_count2 = basis_count;
cout << "Parallel Basis count = " << basis_count << endl << endl;
Assert_Output(basis_serial, basis_parallel, basis_count1, basis_count2);
}
else
{
cout << "Insufficient arguments\n" << endl;
cout << "First argument = Image Size" << endl;
}
}