/**
* Top module to extract the whole string into final OpCode
*
* Input:
* String instructions,with appropriate arguments
*
* Return OpCode in int type
*/
unsigned int interpret(String *instruction){
stringTrimLeft(instruction);
String *instString = stringRemoveWordNotContaining(instruction," ");
char *instChar = stringSubstringInChar(instString,0,instString->length);
instructionTable inst = getInstruction(instChar);
if(inst.type == FDA_TYPE)
return inst.opCode | FDA(instruction);
else if(inst.type == FBA_TYPE)
return inst.opCode | FBA(instruction);
else if(inst.type == FA_TYPE)
return inst.opCode | FA(instruction);
else if(inst.type == FSFD_TYPE)
return inst.opCode | FSFD(instruction);
else if(inst.type == N_TYPE)
return inst.opCode | N(instruction);
else if(inst.type == NS_TYPE)
return inst.opCode | NS(instruction);
else if(inst.type == S_TYPE)
return inst.opCode | S(instruction);
else if(inst.type == K_TYPE)
return inst.opCode | K(instruction);
else if(inst.type == FK_TYPE)
return inst.opCode | FK(instruction);
else
Throw(ERR_ILLEGAL_ARGUMENT);
}
int dirfind (
int curfile,
int forward,
DCLARG *find_spec,
void (*each)(int, int *),
int must_find,
int unfind)
{
#define FIND_FNB find_spec->dcl$l_fnb
#define FIND_TEXT find_spec->dcl_text
PATHNT pz;
FILENT fz;
int flag = TRUE, /* continue-loop unless 'each' quits */
found_any = 0;
int j, k, tst;
char Fpath[MAX_PATH], Fname[MAX_NAME+1], Ftype[MAX_TYPE+1];
dirfind_chop (find_spec, &fz, &pz, Fpath, Fname, Ftype);
/*
* If 'forward' is negative, obtain the proper value from the
* command decoder:
*/
if (forward < 0)
{
forward = dircmd_dirflg(-1);
curfile = dirfind_nxt (curfile, !forward);
}
#define XOR(a,b) ((a && !b) || (!a && b))
#define if_T tst = dirfind_tst(FK_(j), &fz, TRUE);\
if (XOR(tst,unfind))
#define LOOP for (j = dirfind_nxt(curfile,forward), k = numfiles; k > 0;\
j = dirfind_nxt(j,forward), k--)
#define BIT_1 1 /* Use this bit via 'dirent_misc' */
if (each) /* Multiple action ? */
{
dirent_misc (-1, BIT_1); /* Reset all '.fmisc' */
if (strchr(FIND_TEXT,'*') || strchr(FIND_TEXT,'%')
|| strchr(Fpath, '*'))
dds_while (nullC);
for (j = 0; j < numfiles; j++)
{
if_T
dirent_misc (j, BIT_1);
}
LOOP
{
if (DELETED(j)) continue;
dds_while(nullC);
if (FK(j).fmisc & BIT_1)
{
(*each)(j, &flag);
found_any++;
if (!flag) break;
}
}
dirent_misc (-1, BIT_1); /* cleanup after use */
}
else
{
const QVector<GBFeatureKeyInfo>& GBFeatureUtils::allKeys() {
QMutexLocker locker(&allKeys_mutex);
static QVector<GBFeatureKeyInfo> features(GBFeatureKey_NUM_KEYS);
static bool inited = false;
if (inited) {
return features;
}
inited = true;
FK(GBFeatureKey_assembly_gap, U2FeatureTypes::AssemblyGap, "assemlby_gap", cl("000000"), false, QObject::tr("Gap between two components of a genome or transcriptome assembly"));
FK(GBFeatureKey_attenuator, U2FeatureTypes::Attenuator, "attenuator", cl("000000"), false, QObject::tr("Sequence related to transcription termination"));
FK(GBFeatureKey_bond, U2FeatureTypes::Disulfide, "Bond", cl("000000"), false, QObject::tr("Describes disulfide bonds (for protein files)"));
FK(GBFeatureKey_C_region, U2FeatureTypes::CRegion, "C_region", cl("000000"), false, QObject::tr("Span of the C immunological feature"));
FK(GBFeatureKey_CAAT_signal, U2FeatureTypes::CaatSignal, "CAAT_signal", cl("000000"), false, QObject::tr("`CAAT box' in eukaryotic promoters"));
FKE(GBFeatureKey_CDS, U2FeatureTypes::Cds, "CDS", cl("9bffff"), true, QObject::tr("Sequence coding for amino acids in protein (includes stop codon)"),
"label,protein_id,locus_tag,gene,function,product");
FK(GBFeatureKey_conflict, U2FeatureTypes::Conflict, "conflict", cl("000000"), false, QObject::tr("Independent sequence determinations differ"));
FK(GBFeatureKey_centromere, U2FeatureTypes::Centromere, "centromere", cl("000000"), false, QObject::tr("Region of biological interest identified as a centromere and which has been experimentally characterized"));
FK(GBFeatureKey_D_loop, U2FeatureTypes::DLoop, "D-loop", cl("000000"), false, QObject::tr("Displacement loop"));
FK(GBFeatureKey_D_segment, U2FeatureTypes::DSegment, "D_segment", cl("000000"), false, QObject::tr("Span of the D immunological feature"));
FK(GBFeatureKey_enhancer, U2FeatureTypes::Enhancer, "enhancer", cl("000000"), false, QObject::tr("Cis-acting enhancer of promoter function"));
FK(GBFeatureKey_exon, U2FeatureTypes::Exon, "exon", cl("000000"), false, QObject::tr("Region that codes for part of spliced mRNA"));
FK(GBFeatureKey_gap, U2FeatureTypes::Gap, "gap", cl("000000"), false, QObject::tr("Gap in the sequence"));
FKE(GBFeatureKey_gene, U2FeatureTypes::Gene, "gene", cl("00ffc8"), false, QObject::tr("Region that defines a functional gene, possibly including upstream (promotor, enhancer, etc) and downstream control elements, and for which a name has been assigned."),
"label,gene,locus_tag,product,function");
FK(GBFeatureKey_GC_signal, U2FeatureTypes::GcSignal, "GC_signal", cl("000000"), false, QObject::tr("`GC box' in eukaryotic promoters"));
FK(GBFeatureKey_iDNA, U2FeatureTypes::IDna, "iDNA", cl("000000"), false, QObject::tr("Intervening DNA eliminated by recombination"));
FK(GBFeatureKey_intron, U2FeatureTypes::Intron, "intron", cl("000000"), false, QObject::tr("Transcribed region excised by mRNA splicing"));
FK(GBFeatureKey_J_region, U2FeatureTypes::JRegion, "J_region", cl("000000"), false, QObject::tr("Span of the J immunological feature"));
FK(GBFeatureKey_J_segment, U2FeatureTypes::JSegment, "J_segment", cl("000000"), false, QObject::tr("Joining segment of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains"));
FK(GBFeatureKey_LTR, U2FeatureTypes::Ltr, "LTR", cl("000000"), false, QObject::tr("Long terminal repeat"));
FK(GBFeatureKey_mat_peptide, U2FeatureTypes::MaturePeptide, "mat_peptide", cl("000000"), true, QObject::tr("Mature peptide coding region (does not include stop codon)"));
FK(GBFeatureKey_misc_binding, U2FeatureTypes::MiscBindingSite, "misc_binding", cl("000000"), false, QObject::tr("Miscellaneous binding site"));
FK(GBFeatureKey_misc_difference, U2FeatureTypes::MiscDifference, "misc_difference", cl("000000"), false, QObject::tr("Miscellaneous difference feature"));
FKE(GBFeatureKey_misc_feature, U2FeatureTypes::MiscFeature, "misc_feature", cl("000000"), false, QObject::tr("Region of biological significance that cannot be described by any other feature")
, "label,note");
FK(GBFeatureKey_misc_recomb, U2FeatureTypes::MiscRecombination, "misc_recomb", cl("000000"), false, QObject::tr("Miscellaneous, recombination feature"));
FK(GBFeatureKey_misc_RNA, U2FeatureTypes::MiscRna, "misc_RNA", cl("000000"), false, QObject::tr("Miscellaneous transcript feature not defined by other RNA keys"));
FK(GBFeatureKey_misc_signal, U2FeatureTypes::MiscSignal, "misc_signal", cl("000000"), false, QObject::tr("Miscellaneous signal"));
FK(GBFeatureKey_misc_structure, U2FeatureTypes::MiscStructure, "misc_structure", cl("000000"), false, QObject::tr("Miscellaneous DNA or RNA structure"));
FK(GBFeatureKey_mobile_element, U2FeatureTypes::MobileElement, "mobile_element", cl("000000"), false, QObject::tr("Region of genome containing mobile elements"));
FK(GBFeatureKey_modified_base, U2FeatureTypes::ModifiedBase, "modified_base", cl("000000"), false, QObject::tr("The indicated base is a modified nucleotide"));
FK(GBFeatureKey_mRNA, U2FeatureTypes::MRna, "mRNA", cl("000000"), false, QObject::tr("Messenger RNA"));
FK(GBFeatureKey_ncRNA, U2FeatureTypes::NcRna, "ncRNA", cl("000000"), false, QObject::tr("A non-protein-coding gene, other than ribosomal RNA and transfer RNA, the functional molecule of which is the RNA transcrip"))
FK(GBFeatureKey_N_region, U2FeatureTypes::NRegion, "N_region", cl("000000"), false, QObject::tr("Span of the N immunological feature"));
FK(GBFeatureKey_old_sequence, U2FeatureTypes::OldSequence, "old_sequence", cl("000000"), false, QObject::tr("Presented sequence revises a previous version"));
FK(GBFeatureKey_operon, U2FeatureTypes::Operon, "operon", cl("000000"), false, QObject::tr("Region containing polycistronic transcript including a cluster of genes that are under the control of the same regulatory sequences/promotor and in the same biological pathway"));
FK(GBFeatureKey_oriT, U2FeatureTypes::OriT, "oriT", cl("000000"), false, QObject::tr("Origin of transfer; region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization"));
FK(GBFeatureKey_polyA_signal, U2FeatureTypes::PolyASignal, "polyA_signal", cl("000000"), false, QObject::tr("Signal for cleavage & polyadenylation"));
FK(GBFeatureKey_polyA_site, U2FeatureTypes::PolyASite, "polyA_site", cl("000000"), false, QObject::tr("Site at which polyadenine is added to mRNA"));
FK(GBFeatureKey_precursor_RNA, U2FeatureTypes::PrecursorRna, "precursor_RNA", cl("000000"), false, QObject::tr("Any RNA species that is not yet the mature RNA product"));
FK(GBFeatureKey_prim_transcript, U2FeatureTypes::PrimaryTranscript, "prim_transcript", cl("000000"), false, QObject::tr("Primary (unprocessed) transcript"));
FK(GBFeatureKey_primer, U2FeatureTypes::Primer, "primer", cl("000000"), false, QObject::tr("Primer binding region used with PCR"));
FK(GBFeatureKey_primer_bind, U2FeatureTypes::PrimerBindingSite, "primer_bind", cl("000000"), false, QObject::tr("Non-covalent primer binding site"));
FK(GBFeatureKey_promoter, U2FeatureTypes::Promoter, "promoter", cl("000000"), false, QObject::tr("A region involved in transcription initiation"));
FK(GBFeatureKey_protein_bind, U2FeatureTypes::ProteinBindingSite, "protein_bind", cl("000000"), false, QObject::tr("Non-covalent protein binding site on DNA or RNA"));
FK(GBFeatureKey_RBS, U2FeatureTypes::Rbs, "RBS", cl("000000"), false, QObject::tr("Ribosome binding site"));
FK(GBFeatureKey_rep_origin, U2FeatureTypes::ReplicationOrigin, "rep_origin", cl("000000"), false, QObject::tr("Replication origin for duplex DNA"));
FK(GBFeatureKey_repeat_region, U2FeatureTypes::RepeatRegion, "repeat_region", cl("ccccff"), false, QObject::tr("Sequence containing repeated subsequences"));
FK(GBFeatureKey_repeat_unit, U2FeatureTypes::RepeatUnit, "repeat_unit", cl("ccccff"), false, QObject::tr("One repeated unit of a repeat_region"));
FK(GBFeatureKey_rRNA, U2FeatureTypes::RRna, "rRNA", cl("000000"), false, QObject::tr("Ribosomal RNA"));
FK(GBFeatureKey_S_region, U2FeatureTypes::SRegion, "S_region", cl("000000"), false, QObject::tr("Span of the S immunological feature"));
FK(GBFeatureKey_satellite, U2FeatureTypes::Satellite, "satellite", cl("000000"), false, QObject::tr("Satellite repeated sequence"));
FK(GBFeatureKey_scRNA, U2FeatureTypes::ScRna, "scRNA", cl("000000"), false, QObject::tr("Small cytoplasmic RNA"));
FK(GBFeatureKey_sig_peptide, U2FeatureTypes::SignalPeptide, "sig_peptide", cl("000000"), false, QObject::tr("Signal peptide coding region"));
FK(GBFeatureKey_snRNA, U2FeatureTypes::SnRna, "snRNA", cl("000000"), false, QObject::tr("Small nuclear RNA"));
FK(GBFeatureKey_source, U2FeatureTypes::Source, "source", cl("cccccc"), false, QObject::tr("Identifies the biological source of the specified span of the sequence"));
FK(GBFeatureKey_stem_loop, U2FeatureTypes::StemLoop, "stem_loop", cl("000000"), false, QObject::tr("Hair-pin loop structure in DNA or RNA"));
FK(GBFeatureKey_STS, U2FeatureTypes::Sts, "STS", cl("00dcdc"), false, QObject::tr("Sequence Tagged Site; operationally unique sequence that identifies the combination of primer spans used in a PCR assay"));
FK(GBFeatureKey_TATA_signal, U2FeatureTypes::TataSignal, "TATA_signal", cl("000000"), false, QObject::tr("`TATA box' in eukaryotic promoters"));
FK(GBFeatureKey_telomere, U2FeatureTypes::Telomere, "telomere", cl("000000"), false, QObject::tr("Region of biological interest identified as a telomere and which has been experimentally characterized"));
FK(GBFeatureKey_terminator, U2FeatureTypes::Terminator, "terminator", cl("000000"), false, QObject::tr("Sequence causing transcription termination"));
FK(GBFeatureKey_tmRNA, U2FeatureTypes::TmRna, "tmRNA", cl("000000"), false, QObject::tr("Transfer messenger RNA; tmRNA acts as a tRNA first, and then as an mRNA that encodes a peptide tag; the ribosome translates this mRNA region of tmRNA and attaches the encoded peptide tag to the C-terminus of the unfinished protein; this attached tag targets the protein for destruction or proteolysis"));
FK(GBFeatureKey_transit_peptide, U2FeatureTypes::TransitPeptide, "transit_peptide", cl("000000"), false, QObject::tr("Transit peptide coding region"));
FK(GBFeatureKey_transposon, U2FeatureTypes::Transposon, "transposon", cl("000000"), false, QObject::tr("Transposable element (TN)"));
FK(GBFeatureKey_tRNA, U2FeatureTypes::TRna, "tRNA", cl("c8fac8"), false, QObject::tr("Transfer RNA"));
FK(GBFeatureKey_unsure, U2FeatureTypes::Unsure, "unsure", cl("000000"), false, QObject::tr("Authors are unsure about the sequence in this region"));
FK(GBFeatureKey_V_region, U2FeatureTypes::VRegion, "V_region", cl("000000"), false, QObject::tr("Span of the V immunological feature"));
FK(GBFeatureKey_V_segment, U2FeatureTypes::VSegment, "V_segment", cl("000000"), false, QObject::tr("Variable segment of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains; codes for most of the variable region (V_region) and the last few amino acids of the leader peptide"));
FK(GBFeatureKey_variation, U2FeatureTypes::Variation, "variation", cl("ffff9b"), false, QObject::tr("A related population contains stable mutation"));
FK(GBFeatureKey__10_signal, U2FeatureTypes::Minus10Signal, "-10_signal", cl("000000"), false, QObject::tr("`Pribnow box' in prokaryotic promoters"));
FK(GBFeatureKey__35_signal, U2FeatureTypes::Minus35Signal, "-35_signal", cl("000000"), false, QObject::tr("`-35 box' in prokaryotic promoters"));
FK(GBFeatureKey_3_clip, U2FeatureTypes::ThreePrimeClip, "3'clip", cl("000000"), false, QObject::tr("3'-most region of a precursor transcript removed in processing"));
FK(GBFeatureKey_3_UTR, U2FeatureTypes::ThreePrimeUtr, "3'UTR", cl("ffcde6"), false, QObject::tr("3' untranslated region (trailer)"));
FK(GBFeatureKey_5_clip, U2FeatureTypes::FivePrimeClip, "5'clip", cl("000000"), false, QObject::tr("5'-most region of a precursor transcript removed in processing"));
FK(GBFeatureKey_5_UTR, U2FeatureTypes::FivePrimeUtr, "5'UTR", cl("ffc8c8"), false, QObject::tr("5' untranslated region (leader)"));
FK(GBFeatureKey_Protein, U2FeatureTypes::Protein, "Protein", cl("000000"), false, QObject::tr("'Protein' feature key"));
FK(GBFeatureKey_Region, U2FeatureTypes::Region, "Region", cl("000000"), false, QObject::tr("'Region' feature key"));
FK(GBFeatureKey_Site, U2FeatureTypes::Site, "Site", cl("000000"), false, QObject::tr("'Site' feature key"));
FK(GBFeatureKey_regulatory, U2FeatureTypes::Regulatory, "regulatory", cl("000000"), false, QObject::tr("Any region of sequence that functions in the regulation of transcription or translation"));
#ifdef _DEBUG
for (int i=0; i<features.size(); i++) {
assert(features[i].id != GBFeatureKey_UNKNOWN && features[i].id == i);
assert(!features[i].text.isEmpty());
assert(!features[i].desc.isEmpty());
}
#endif
return features;
}
