/** \brief pack bit states in byte buffer
* \param[in] number of pins to read (normally ciaaDriverDio_OutputCount or ciaaDriverDio_InputCount)
* \param[out] buffer user buffer
* \param[in] size user buffer size
* \param[in] readFunction function used to read pins (normally ciaa_lpc4337_readOutput or ciaa_lpc4337_readInput)
* \return number bytes required in buffer to store bits
*/
static int32_t ciaa_lpc4337_readPins(int32_t pinCount, uint8_t * buffer, size_t size, int32_t (*readFunction)(uint32_t))
{
int32_t count, i, j;
/* amount of bytes necessary to store all input states */
count = pinCount >> 3; /* ciaaDriverDio_InputCount / 8 */
if( (pinCount & 0x07) != 0) /* (ciaaDriverDio_InputCount % 8) != 0 */
{
count += 1;
}
/* adjust gpios to read according to provided buffer length */
if(count > size)
{
count = size;
}
/* read and store all inputs in user buffer */
ciaaPOSIX_memset(buffer, 0, count);
for(i = 0, j = 0; (i < pinCount) && (j < count); i++)
{
if((i > 0) && ((i & 0x07)==0))
{
j++;
}
buffer[j] |= readFunction(i) << (i - 8 * j);
}
return count;
}
bool VrmlScene::loadFromFunction( LoadCB cb, const char *url )
{
Doc *doc = url ? new Doc( url, 0 ) : 0;
VrmlNamespace *ns = new VrmlNamespace();
VrmlMFNode *newNodes = readFunction( cb, doc, ns );
if ( newNodes )
{
replaceWorld( *newNodes, ns, doc, 0 );
delete newNodes;
return true;
}
if (doc) delete doc;
return false;
}
void numberToFunction(int number, char* secondary){
if (number == 1){
readFunction(secondary);
}
else if (number == 2){
writeFunction(secondary);
}
else if (number == 3){
deleteFunction(secondary);
}
else if (number == 4){
printFunction();
}
else if (number == 0){
printf("Not a valid command!\n");
}
else if (number == 404){
printf("The file you provided does not exist.\n");
}
}
bool Origin410Parser::parse()
{
unsigned int dataIndex = 0;
#ifndef NO_LOG_FILE
// append progress in log file
logfile = fopen("opjfile.log", "a");
#endif
/////////////////// find column ///////////////////////////////////////////////////////////
skipLine();
unsigned int size;
file >> size;
file.seekg(1 + size + 1 + 5, ios_base::cur);
file >> size;
file.seekg(1, ios_base::cur);
LOG_PRINT(logfile, " [column found = %d/0x%X @ 0x%X]\n", size, size, (unsigned int) file.tellg());
unsigned int colpos = file.tellg();
unsigned int current_col = 1, nr = 0, nbytes = 0;
while(size > 0 && size <= 0x8B){// should be 0x72, 0x73 or 0x83 ?
//////////////////////////////// COLUMN HEADER /////////////////////////////////////////////
short data_type;
char data_type_u;
unsigned int oldpos = (unsigned int)file.tellg();
file.seekg(oldpos + 0x16, ios_base::beg);
file >> data_type;
file.seekg(oldpos + 0x3F, ios_base::beg);
file >> data_type_u;
char valuesize;
file.seekg(oldpos + 0x3D, ios_base::beg);
file >> valuesize;
LOG_PRINT(logfile, " [valuesize = %d @ 0x%X]\n", (int)valuesize, ((unsigned int) file.tellg()-1));
if(valuesize <= 0)
{
LOG_PRINT(logfile, " WARNING : found strange valuesize of %d\n", (int)valuesize);
valuesize = 10;
}
file.seekg(oldpos + 0x58, ios_base::beg);
LOG_PRINT(logfile, " [Spreadsheet @ 0x%X]\n", (unsigned int) file.tellg());
string name(25, 0);
file >> name;
string::size_type pos = name.find_last_of("_");
string columnname;
if(pos != string::npos){
columnname = name.substr(pos + 1);
name.resize(pos);
}
LOG_PRINT(logfile, " NAME: %s\n", name.c_str());
unsigned int spread = 0;
pos = name.find("DPk");//multipeak fits generate these tables
if(columnname.empty() && pos == string::npos){
LOG_PRINT(logfile, "NO COLUMN NAME FOUND! Must be a Matrix or Function.");
////////////////////////////// READ matrices or functions ////////////////////////////////////
LOG_PRINT(logfile, " [position @ 0x%X]\n", (unsigned int) file.tellg());
file.seekg(oldpos + 0x18, ios_base::beg);
short signature;
file >> signature;
LOG_PRINT(logfile, " SIGNATURE : %02X @ 0x%X\n", signature, (unsigned int) file.tellg());
file.seekg(oldpos + size + 1, ios_base::beg);
file >> size;
file.seekg(1, ios_base::cur);
size /= valuesize;
LOG_PRINT(logfile, " SIZE = %d\n", size);
if (size == 1){
functions.push_back(Function(name, dataIndex));
++dataIndex;
readFunction(colpos, valuesize, &oldpos);
} else if (size > 1){
if (signature == 1){
matrices.push_back(Matrix(name));
matrices.back().sheets.push_back(MatrixSheet(name, dataIndex));
++dataIndex;
readMatrixValues(data_type, data_type_u, valuesize, size);
} else {
LOG_PRINT(logfile, "UNKNOWN SIGNATURE, SKIP DATA\n");
file.seekg(valuesize*size, ios_base::cur);
++dataIndex;
if(valuesize != 8 && valuesize <= 16)
file.seekg(2, ios_base::cur);
}
}
}
else
{ // worksheet
if(speadSheets.size() == 0 || findSpreadByName(name) == -1)
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 n, m, a[128][128], aa[128][128], b[128], bb[128], c[128], cc[128];
int tmp;
char minmax[16], buf[32], ch;
freopen("dual.in", "r", stdin);
freopen("dual.out", "w", stdout);
scanf("%d%d", &n, &m);
scanf("%s", minmax);
readFunction(a[0], n);
scanf(" with");
for (int i = 1; i <= n; ++i) {
scanf(" x%d%[^\n]", &tmp, buf);
switch (buf[0]) {
case ' ': c[i] = 0; break;
case '>': c[i] = 1; break;
case '<': c[i] = 2; break;
}
}
scanf(" under");
for (int i = 1; i <= m; ++i) {
readFunction(a[i], n);
ch = getchar();
switch (ch) {
case '=': b[i] = 0; break;
case '>': b[i] = 1; getchar(); break;
case '<': b[i] = 2; getchar(); break;
}
scanf("%d", &a[i][0]);
}
for (int i = 0; i <= m; ++i) {
for (int j = 0; j <= n; ++j) {
aa[j][i] = a[i][j];
}
}
// WA
/* for (int i = 1; i <= m; ++i) {
cc[i] = b[i];
}
for (int i = 1; i <= n; ++i) {
bb[i] = (c[i] == 0 ? 0 : 3 - c[i]);
}
*/ if (strcmp(minmax, "min") == 0) {
for (int i = 1; i <= m; ++i) {
cc[i] = b[i];
}
for (int i = 1; i <= n; ++i) {
bb[i] = (c[i] == 0 ? 0 : 3 - c[i]);
}
} else {
for (int i = 1; i <= m; ++i) {
cc[i] = (b[i] == 0 ? 0 : 3 - b[i]);
}
for (int i = 1; i <= n; ++i) {
bb[i] = c[i];
}
}
printf("%d %d\n", m, n);
if (strcmp(minmax, "min") == 0) {
printf("max ");
} else {
printf("min ");
}
writeFunction(aa[0], m);
printf("\nwith\n");
for (int i = 1; i <= m; ++i) {
printf("y%d%s\n", i, condition[cc[i]]);
}
printf("under\n");
for (int i = 1; i <= n; ++i) {
writeFunction(aa[i], m);
printf("%s%d\n", restriction[bb[i]], aa[i][0]);
}
return 0;
}
void readPackage(FILE *in) {
static uint16_t classNextIndex = 0;
FunctionFunctionPointer *linkingTable;
PrepareClassFunction prepareClass;
uint_fast8_t packageNameLength = fgetc(in);
if (packageNameLength == 0) {
DEBUG_LOG("Package does not have native binary");
linkingTable = sLinkingTable;
prepareClass = sPrepareClass;
}
else {
DEBUG_LOG("Package has native binary");
auto name = new char[packageNameLength];
fread(name, sizeof(char), packageNameLength, in);
uint16_t major = readUInt16(in);
uint16_t minor = readUInt16(in);
DEBUG_LOG("Package is named %s and has version %d.%d.x", name, major, minor);
PackageLoadingState s = packageLoad(name, major, minor, &linkingTable, &prepareClass);
if (s == PACKAGE_INAPPROPRIATE_MAJOR) {
error("Installed version of package \"%s\" is incompatible with required version %d.%d. (How did you made Emojicode load this version of the package?!)", name, major, minor);
}
else if (s == PACKAGE_INAPPROPRIATE_MINOR) {
error("Installed version of package \"%s\" is incompatible with required version %d.%d. Please update to the latest minor version.", name, major, minor);
}
else if (s == PACKAGE_LOADING_FAILED) {
error("Could not load package \"%s\" %s.", name, packageError());
}
delete [] name;
}
for (int classCount = readUInt16(in); classCount > 0; classCount--) {
DEBUG_LOG("➡️ Still %d class(es) to load", classCount);
EmojicodeChar name = readEmojicodeChar(in);
auto *klass = new Class;
classTable[classNextIndex++] = klass;
DEBUG_LOG("Loading class %X into %p", name, klass);
klass->superclass = classTable[readUInt16(in)];
int instanceVariableCount = readUInt16(in);
int methodCount = readUInt16(in);
klass->methodsVtable = new Function*[methodCount];
bool inheritsInitializers = fgetc(in);
int initializerCount = readUInt16(in);
klass->initializersVtable = new Function*[initializerCount];
DEBUG_LOG("Inherting intializers: %s", inheritsInitializers ? "true" : "false");
DEBUG_LOG("%d instance variable(s); %d methods; %d initializer(s)",
instanceVariableCount, initializerCount, methodCount);
uint_fast16_t localMethodCount = readUInt16(in);
uint_fast16_t localInitializerCount = readUInt16(in);
DEBUG_LOG("Reading %d method(s) and %d initializer(s) that are not inherited or overriden",
localMethodCount, localInitializerCount);
if (klass != klass->superclass) {
memcpy(klass->methodsVtable, klass->superclass->methodsVtable, methodCount * sizeof(Function*));
if (inheritsInitializers) {
memcpy(klass->initializersVtable, klass->superclass->initializersVtable,
initializerCount * sizeof(Function*));
}
}
else {
klass->superclass = nullptr;
}
for (uint_fast16_t i = 0; i < localMethodCount; i++) {
DEBUG_LOG("Reading method %d", i);
readFunction(klass->methodsVtable, in, linkingTable);
}
for (uint_fast16_t i = 0; i < localInitializerCount; i++) {
DEBUG_LOG("Reading initializer %d", i);
readFunction(klass->initializersVtable, in, linkingTable);
}
readProtocolTable(klass->protocolTable, klass->methodsVtable, in);
// Allow inheritance from class with value, e.g. list
klass->valueSize = klass->superclass && klass->superclass->valueSize ? klass->superclass->valueSize : 0;
prepareClass(klass, name);
klass->size = alignSize(sizeof(Object) + klass->valueSize + instanceVariableCount * sizeof(Value));
klass->instanceVariableRecordsCount = readUInt16(in);
klass->instanceVariableRecords = new FunctionObjectVariableRecord[klass->instanceVariableRecordsCount];
for (size_t i = 0; i < klass->instanceVariableRecordsCount; i++) {
klass->instanceVariableRecords[i].variableIndex = readUInt16(in);
klass->instanceVariableRecords[i].condition = readUInt16(in);
klass->instanceVariableRecords[i].type = static_cast<ObjectVariableType>(readUInt16(in));
}
DEBUG_LOG("Read %d object variable records", klass->instanceVariableRecordsCount);
}
for (int functionCount = readUInt16(in); functionCount > 0; functionCount--) {
DEBUG_LOG("➡️ Still %d functions to come", functionCount);
readFunction(functionTable, in, linkingTable);
}
}
