d4/de4/_bio_features_8h_source.html

00001
00002 #ifndef BIOFEATURES_H
00003 #define BIOFEATURES_H
00004
00005 using namespace std;
00006 #include <string>
00007 #include <vector>
00008 #include <fstream>
00009 #include <iostream>
00010
00011 #include "BioFTKSingleSource.h"
00012 #include "BioFTKSingleGene.h"
00013 #include "BioFTKSingleCds.h"
00014 #include "BioFTKSingleEnhancer.h"
00015 #include "BioFTKSingleTATASignal.h"
00016 #include "BioFTKSingleCAATSignal.h"
00017 #include "BioFTKSingleLtr.h"
00018 #include "BioFTKSingle3PrimeClip.h"
00019 #include "BioFTKSingle3PrimeUtr.h"
00020 #include "BioFTKSingle5PrimeClip.h"
00021 #include "BioFTKSingle5PrimeUtr.h"
00022 #include "BioFTKSingle_10Signal.h"
00023 #include "BioFTKSingle_35Signal.h"
00024 #include "BioFTKSingleVariation.h"
00025 #include "BioFTKSingleUnsure.h"
00026 #include "BioFTKSingleExon.h"
00027
00028 #include "BioFTKSingle_.h"
00029 #include "BioFTKSingleAttenuator.h"
00030 #include "BioFTKSingleCRegion.h"
00031 #include "BioFTKSingleConflict.h"
00032 #include "BioFTKSingleDLoop.h"
00033
00034
00035 #include "BioFTKSingleDSegment.h"
00036 #include "BioFTKSingleGCSignal.h"
00037 #include "BioFTKSingleIDna.h"
00038 #include "BioFTKSingleIntron.h"
00039 #include "BioFTKSingleJSegment.h"
00040
00041 #include "BioFTKSingleMatPeptide.h"
00042 #include "BioFTKSingleMiscBinding.h"
00043 #include "BioFTKSingleMiscDifference.h"
00044 #include "BioFTKSingleMiscFeature.h"
00045 #include "BioFTKSingleMiscRecomb.h"
00046
00047 #include "BioFTKSingleMiscRna.h"
00048 #include "BioFTKSingleMiscSignal.h"
00049 #include "BioFTKSingleMiscStructure.h"
00050 #include "BioFTKSingleModifiedBase.h"
00051 #include "BioFTKSingleMRna.h"
00052
00053 #include "BioFTKSingleNRegion.h"
00054 #include "BioFTKSingleOldSequence.h"
00055 #include "BioFTKSinglePolyASignal.h"
00056 #include "BioFTKSinglePolyASite.h"
00057 #include "BioFTKSinglePrecursorRna.h"
00058
00059 #include "BioFTKSinglePrimerBind.h"
00060 #include "BioFTKSinglePrimTranscript.h"
00061 #include "BioFTKSinglePromoter.h"
00062 #include "BioFTKSingleProteinBind.h"
00063 #include "BioFTKSingleRbs.h"
00064
00065 #include "BioFTKSingleRepeatRegion.h"
00066 #include "BioFTKSingleRepeatUnit.h"
00067 #include "BioFTKSingleRepOrigin.h"
00068 #include "BioFTKSingleRRna.h"
00069 #include "BioFTKSingleSatellite.h"
00070
00071 #include "BioFTKSingleSCRna.h"
00072 #include "BioFTKSingleSigPeptide.h"
00073 #include "BioFTKSingleSNORna.h"
00074 #include "BioFTKSingleSNRna.h"
00075 #include "BioFTKSingleSRegion.h"
00076 #include "BioFTKSingleStemLoop.h"
00077
00078 #include "BioFTKSingleSts.h"
00079 #include "BioFTKSingleTerminator.h"
00080 #include "BioFTKSingleTransitPeptide.h"
00081 #include "BioFTKSingleTRna.h"
00082 #include "BioFTKSingleVRegion.h"
00083
00084 #include "BioFTKSingleVSegment.h"
00085 #include "BioFTKSingleGap.h"
00086 #include "BioFTKSingleOperon.h"
00087 #include "BioFTKSingleOriT.h"
00088
00089 class BioFeatures
00090 {
00091   vector <BioFTKSingleGap> gap_;
00092   vector <BioFTKSingleOperon> operon_;
00093   vector <BioFTKSingleOriT> orit_;
00094         vector <BioFTKSingleSource> source_;
00095         vector <BioFTKSingleGene> gene_;
00096   vector <BioFTKSingleCds> cds_;
00097   vector <BioFTKSingleEnhancer> enhancer_;
00098   vector <BioFTKSingleTATASignal> tataSignal_;
00099   vector <BioFTKSingleCAATSignal> caatSignal_;
00100   vector <BioFTKSingleLtr> ltr_;
00101   vector <BioFTKSingle_10Signal> _10Signal_;
00102   vector <BioFTKSingle_35Signal> _35Signal_;
00103   vector <BioFTKSingle3PrimeClip> _3PrimeClip_;
00104         vector <BioFTKSingle5PrimeClip> _5PrimeClip_;
00105         vector <BioFTKSingle3PrimeUtr> _3PrimeUtr_;
00106         vector <BioFTKSingle5PrimeUtr> _5PrimeUtr_;
00107   vector <BioFTKSingleVariation> variation_;
00108   vector <BioFTKSingleUnsure> unsure_;
00109   vector <BioFTKSingleExon> exon_;
00110         vector <BioFTKSingle_> single_;
00111   vector <BioFTKSingleAttenuator> attenuator_;
00112   vector <BioFTKSingleConflict> conflict_;
00113   vector <BioFTKSingleCRegion> cregion_;
00114   vector <BioFTKSingleDLoop> dloop_;
00115   vector <BioFTKSingleDSegment> dsegment_;
00116   vector <BioFTKSingleGCSignal> gcsignal_;
00117   vector <BioFTKSingleIDna> idna_;
00118   vector <BioFTKSingleIntron> intron_;
00119   vector <BioFTKSingleJSegment> jsegment_;
00120   vector <BioFTKSingleMatPeptide> matpeptide_;
00121   vector <BioFTKSingleMiscBinding> miscbinding_;
00122   vector <BioFTKSingleMiscDifference> miscdifference_;
00123   vector <BioFTKSingleMiscFeature> miscfeature_;
00124   vector <BioFTKSingleMiscRecomb> miscrecomb_;
00125   vector <BioFTKSingleMiscRna> miscrna_;
00126   vector <BioFTKSingleMiscSignal> miscsignal_;
00127   vector <BioFTKSingleMiscStructure> miscstructure_;
00128   vector <BioFTKSingleModifiedBase> modifiedbase_;
00129   vector <BioFTKSingleMRna> mrna_;
00130   vector <BioFTKSingleNRegion> nregion_;
00131   vector <BioFTKSingleOldSequence> oldsequence_;
00132   vector <BioFTKSinglePolyASignal> polyAsignal_;
00133   vector <BioFTKSinglePolyASite> polyAsite_;
00134   vector <BioFTKSinglePrecursorRna> precursorRna_;
00135   vector <BioFTKSinglePrimerBind> primerbind_;
00136   vector <BioFTKSinglePrimTranscript> primtranscript_;
00137   vector <BioFTKSinglePromoter> promoter_;
00138   vector <BioFTKSingleProteinBind> proteinbind_;
00139   vector <BioFTKSingleRbs> rbs_;
00140   vector <BioFTKSingleRepeatRegion> repeatregion_;
00141   vector <BioFTKSingleRepeatUnit> repeatunit_;
00142   vector <BioFTKSingleRepOrigin> reporigin_;
00143   vector <BioFTKSingleRRna> rrna_;
00144   vector <BioFTKSingleSatellite> satellite_;
00145   vector <BioFTKSingleSCRna>scrna_;
00146   vector <BioFTKSingleSigPeptide> sigpeptide_;
00147   vector <BioFTKSingleSNORna>  snorna_;
00148   vector <BioFTKSingleSNRna>   snrna_;
00149   vector <BioFTKSingleSRegion> sregion_;
00150   vector <BioFTKSingleStemLoop> stemloop_;
00151   vector <BioFTKSingleSts> sts_;
00152   vector <BioFTKSingleTerminator> terminator_;
00153   vector <BioFTKSingleTransitPeptide> transitpeptide_;
00154   vector <BioFTKSingleTRna> trna_;
00155   vector <BioFTKSingleVRegion> vregion_;
00156   vector <BioFTKSingleVSegment> vsegment_;
00157
00158
00159 public:
00160         BioFeatures(){}
00161         ~BioFeatures();
00162
00163         void setFeatures(vector<string>);
00164         //bool find(const string& );
00165
00166         // FTKSource Methods:::::
00167         int getNumberOfSources();
00168   BioFTKSingleSource getSource(int);
00169
00170         // FTKGene Methods:::::
00171         int getNumberOfGenes();
00172   BioFTKSingleGene getGene(int);
00173
00174
00175         //FTKCds Methods:::::
00176         int getNumberOfCdss();
00177   BioFTKSingleCds getCds(int);
00178   void showCds(int, ostream& os = cout);
00179
00180   //FTKEnhancer Methods:::::
00181   int getNumberOfEnhancers();
00182   BioFTKSingleEnhancer getEnhancer(int);
00183
00184   //FTKTATASignal Methods:::::
00185   int getNumberOfTATASignals();
00186   BioFTKSingleTATASignal getTATASignal(int);
00187
00188   //FTKCAATSignal Methods:::::
00189   int getNumberOfCAATSignals();
00190   BioFTKSingleCAATSignal getCAATSignal(int);
00191
00192   //FTKLtr Methods:::::::
00193   int getNumberOfLtrs();
00194   BioFTKSingleLtr getLtr(int);
00195
00196   //FTK5PrimeClip Methods:::::
00197   int getNumberOf5PrimeClips();
00198   BioFTKSingle5PrimeClip get5PrimeClip(int);
00199
00200
00201   //FTK3PrimeClip Methods:::::
00202   int getNumberOf3PrimeClips();
00203   BioFTKSingle3PrimeClip get3PrimeClip(int);
00204
00205   //FTK5PrimeUtr Methods:::::
00206   int getNumberOf5PrimeUtrs();
00207   BioFTKSingle5PrimeUtr get5PrimeUtr(int);
00208
00209   //FTK3PrimeUtr Methods:::::
00210   int getNumberOf3PrimeUtrs();
00211   BioFTKSingle3PrimeUtr get3PrimeUtr(int);
00212
00213   //FTK_10Signal Methods:::::
00214   int getNumberOf_10Signals();
00215   BioFTKSingle_10Signal get_10Signal(int);
00216
00217   //FTK_35Signal Methods:::::
00218   int getNumberOf_35Signals();
00219   BioFTKSingle_35Signal get_35Signal(int);
00220
00221   //FTKVariation Methods:::::
00222   int getNumberOfVariations();
00223   BioFTKSingleVariation getVariation(int);
00224
00225   //FTKUnsure Methods::::::
00226   int getNumberOfUnsures();
00227   BioFTKSingleUnsure getUnsure(int);
00228
00229   //FTKExon Methods::::::
00230   int getNumberOfExons();
00231   BioFTKSingleExon getExon(int );
00232
00233  //FTK- Methods :::::::
00234   int getNumberOf_s();
00235   BioFTKSingle_ get_(int );
00236
00237  //FTKAttenuator Methods :::::::
00238    int getNumberOfAttenuators();
00239   BioFTKSingleAttenuator getAttenuator(int );
00240
00241  //FTKConflict Methods :::::::
00242    int getNumberOfConflicts();
00243   BioFTKSingleConflict getConflict(int );
00244
00245  //FTKCRegion Methods :::::::
00246    int getNumberOfCRegions();
00247   BioFTKSingleCRegion getCRegion(int );
00248
00249  //FTKDLoop Methods :::::::
00250    int getNumberOfDLoops();
00251   BioFTKSingleDLoop getDLoop(int );
00252
00253  //FTKDSegment Methods :::::::
00254    int getNumberOfDSegments();
00255   BioFTKSingleDSegment getDSegment(int );
00256
00257  //FTKGCSignal Methods :::::::
00258    int getNumberOfGCSignals();
00259   BioFTKSingleGCSignal getGCSignal(int );
00260
00261  //FTKIDna Methods :::::::
00262    int getNumberOfIDnas();
00263   BioFTKSingleIDna getIDna(int );
00264
00265  //FTKIntron Methods :::::::
00266    int getNumberOfIntrons();
00267   BioFTKSingleIntron getIntron(int );
00268
00269  //FTKJSegment Methods :::::::
00270    int getNumberOfJSegments();
00271   BioFTKSingleJSegment getJSegment(int );
00272
00273  //FTKMatPeptide Methods :::::::
00274    int getNumberOfMatPeptides();
00275   BioFTKSingleMatPeptide getMatPeptide(int );
00276
00277  //FTKMiscBinding Methods :::::::
00278    int getNumberOfMiscBindings();
00279   BioFTKSingleMiscBinding getMiscBinding(int );
00280
00281  //FTKMiscDifference Methods :::::::
00282    int getNumberOfMiscDifferences();
00283   BioFTKSingleMiscDifference getMiscDifference(int );
00284
00285  //FTKMiscFeature Methods :::::::
00286    int getNumberOfMiscFeatures();
00287   BioFTKSingleMiscFeature getMiscFeature(int );
00288
00289  //FTKMiscRecomb Methods :::::::
00290    int getNumberOfMiscRecombs();
00291   BioFTKSingleMiscRecomb getMiscRecomb(int );
00292
00293  //FTKMiscRna Methods :::::::
00294    int getNumberOfMiscRnas();
00295   BioFTKSingleMiscRna getMiscRna(int );
00296
00297  //FTKMiscSignal Methods :::::::
00298    int getNumberOfMiscSignals();
00299   BioFTKSingleMiscSignal getMiscSignal(int );
00300
00301  //FTKMiscSignal Methods :::::::
00302    int getNumberOfMiscStructures();
00303   BioFTKSingleMiscStructure getMiscStructure(int );
00304
00305  //FTKModifiedBase Methods :::::::
00306    int getNumberOfModifiedBases();
00307   BioFTKSingleModifiedBase getModifiedBase(int );
00308
00309  //FTKMRna Methods :::::::
00310    int getNumberOfMRnas();
00311   BioFTKSingleMRna getMRna(int );
00312
00313  //FTKNRegion Methods :::::::
00314    int getNumberOfNRegions();
00315   BioFTKSingleNRegion getNRegion(int );
00316
00317  //FTKOldSequence Methods :::::::
00318    int getNumberOfOldSequences();
00319   BioFTKSingleOldSequence getOldSequence(int );
00320
00321  //FTKPolyASignal Methods :::::::
00322    int getNumberOfPolyASignals();
00323   BioFTKSinglePolyASignal getPolyASignal(int );
00324
00325  //FTKPolyASite Methods :::::::
00326    int getNumberOfPolyASites();
00327   BioFTKSinglePolyASite getPolyASite(int );
00328
00329  //FTKPrecursorRna Methods :::::::
00330    int getNumberOfPrecursorRnas();
00331   BioFTKSinglePrecursorRna getPrecursorRna(int );
00332
00333  //FTKPrimerBind Methods :::::::
00334    int getNumberOfPrimerBinds();
00335   BioFTKSinglePrimerBind getPrimerBind(int );
00336
00337  //FTKPrimTranscript Methods :::::::
00338    int getNumberOfPrimTranscripts();
00339   BioFTKSinglePrimTranscript getPrimTranscript(int );
00340
00341  //FTKPromoter Methods :::::::
00342    int getNumberOfPromoters();
00343   BioFTKSinglePromoter getPromoter(int );
00344
00345  //FTKProteinBind Methods :::::::
00346    int getNumberOfProteinBinds();
00347   BioFTKSingleProteinBind getProteinBind(int );
00348
00349  //FTKRbs Methods :::::::
00350    int getNumberOfRbs();
00351   BioFTKSingleRbs getRbs(int );
00352
00353  //FTKRepeatRegion Methods :::::::
00354    int getNumberOfRepeatRegions();
00355   BioFTKSingleRepeatRegion getRepeatRegion(int );
00356
00357  //FTKRepeatUnit Methods :::::::
00358    int getNumberOfRepeatUnits();
00359   BioFTKSingleRepeatUnit getRepeatUnit(int );
00360
00361  //FTKRepOrigin Methods :::::::
00362    int getNumberOfRepOrigins();
00363   BioFTKSingleRepOrigin getRepOrigin(int );
00364
00365  //FTKRRna Methods :::::::
00366    int getNumberOfRRnas();
00367   BioFTKSingleRRna getRRna(int );
00368
00369  //FTKSatellite Methods :::::::
00370    int getNumberOfSatellites();
00371   BioFTKSingleSatellite getSatellite(int );
00372
00373  //FTKSCRna Methods :::::::
00374    int getNumberOfSCRnas();
00375   BioFTKSingleSCRna getSCRna(int );
00376
00377  //FTKSigPeptide Methods :::::::
00378    int getNumberOfSigPeptides();
00379   BioFTKSingleSigPeptide getSigPeptide(int );
00380
00381  //FTKSNORna Methods :::::::
00382    int getNumberOfSNORnas();
00383   BioFTKSingleSNORna getSNORna(int );
00384
00385  //FTKSNRna Methods :::::::
00386    int getNumberOfSNRnas();
00387   BioFTKSingleSNRna getSNRna(int );
00388
00389  //FTKSRegion Methods :::::::
00390    int getNumberOfSRegions();
00391   BioFTKSingleSRegion getSRegion(int );
00392
00393  //FTKStemLoop Methods :::::::
00394    int getNumberOfStemLoops();
00395   BioFTKSingleStemLoop getStemLoop(int );
00396
00397  //FTKSts Methods :::::::
00398    int getNumberOfSts();
00399   BioFTKSingleSts getSts(int );
00400
00401  //FTKTerminator Methods :::::::
00402    int getNumberOfTerminators();
00403   BioFTKSingleTerminator getTerminator(int );
00404
00405  //FTKTransitPeptide Methods :::::::
00406    int getNumberOfTransitPeptides();
00407   BioFTKSingleTransitPeptide getTransitPeptide(int );
00408
00409  //FTKTRna Methods :::::::
00410    int getNumberOfTRnas();
00411   BioFTKSingleTRna getTRna(int );
00412
00413  //FTKVRegion Methods :::::::
00414    int getNumberOfVRegions();
00415   BioFTKSingleVRegion getVRegion(int );
00416
00417  //FTKVSegment Methods :::::::
00418    int getNumberOfVSegments();
00419   BioFTKSingleVSegment getVSegment(int );
00420
00421
00422  //FTKGap Methods :::::::
00423    int getNumberOfGaps();
00424   BioFTKSingleGap getGap(int );
00425  //FTKOperon Methods :::::::
00426    int getNumberOfOperons();
00427   BioFTKSingleOperon getOperon(int );
00428  //FTKOriT Methods :::::::
00429    int getNumberOfOriTs();
00430   BioFTKSingleOriT getOriT(int );
00431
00432   void showBioFeatures(ostream & = cout,string st=" ");
00433     void showFeatureKeys(ostream & = cout);
00434 };
00435
00436 #endif