tests: removed unused old file

algo/tests/tools.cpp

-#include <core/tools.h>
-#include <iostream>
-#include <cassert>
-#include <core/fasta.h>
-#include <core/kmerstore.h>
-#include <core/kmeraffect.h>
-#include <core/affectanalyser.h>
-#include <core/segment.h>
-#include "tests.h"
-
-using namespace std;
-
-const string seq[] = {"CCCCCCCCCCCCCCCCCCCC", "C lots of",
-                      "GGGGGGGGGGGGGGGGGGGG", "G lots of",
-                      "AAAAAAAAAAAAAAAAAAAA", "A lots of",
-                      "TTTTTTTTTTTTTTTTTTTT", "T lots of",
-                      "TTTTATTTTATTTTATTTTA", "U : TTTA lots of",
-                      "AAAACAAAACAAAACAAAAC", "V : AAAC lots of"};
-const int nb_seq = 6;
-
-template<typename Index>
-Index *createIndex(int k, bool revcomp) {
-  Index *index = new Index(k, revcomp);
-  for (int i=0; i < nb_seq; i++)
-    index->insert(seq[2*i], seq[2*i+1]);
-  return index;
-}
-
-void testFasta1() {
-  Fasta fa("data/test1.fa");
-  Fasta fq("data/test1.fq");
-
-  TAP_TEST(fa.size() == fq.size(), TEST_FASTA_SIZE, "");
-  for (int i=0; i < fa.size(); i++) {
-    TAP_TEST(fa.label(i) == fq.label(i), TEST_FASTA_LABEL, "");
-    TAP_TEST(fa.label_full(i) == fq.label_full(i), TEST_FASTA_LABEL_FULL, "");
-    TAP_TEST(fa.sequence(i) == fq.sequence(i), TEST_FASTA_SEQUENCE, "");
-  }
-}
-
-template<template <class> class T>
-void testKmerStoreWithKmer(int k, bool revcomp, int test_id ) {
-  T<Kmer> *index = createIndex<T<Kmer> >(k, revcomp);
-  
-  for (int i = 0; i < nb_seq-2; i++) {
-    string tmp = seq[2*i].substr(0, k);
-    if (revcomp) {
-      TAP_TEST((*index)[tmp].count == (seq[2*i].length()-k+1)*2, test_id, "");
-    } else {
-      TAP_TEST((*index)[tmp].count == (seq[2*i].length()-k+1), test_id, "");
-    }
-  }
-  delete index;
-}
-
-template<template <class> class T, class KAffect>
-void testAffectAnalyser1() {
-  const int k = 4;
-  const bool revcomp = false;
-  T<KAffect> *index = createIndex<T<KAffect> >(k, revcomp);
-  
-  KmerAffectAnalyser<KAffect> kaa(*index, "AAAACCCCCGGGGG");
-
-  for (int i = 2; i < nb_seq-1; i++) {
-    KAffect current_affect("", seq[2*i+1], 1);
-    TAP_TEST(kaa.count(current_affect) == 0, TEST_AA_COUNT, "");
-    TAP_TEST(kaa.first(current_affect) == (int)string::npos, TEST_AA_FIRST, "");
-    TAP_TEST(kaa.last(current_affect) == (int)string::npos, TEST_AA_LAST, "");
-  }
-  for (int i = 0; i < 2; i++) {
-    KAffect current_affect("", seq[2*i+1], 1);
-    TAP_TEST(kaa.count(current_affect) == 2, TEST_AA_COUNT, "");
-    TAP_TEST(kaa.getAffectation(kaa.first(current_affect)) == current_affect, TEST_AA_GET_AFFECT, "");
-    TAP_TEST(kaa.getAffectation(kaa.last(current_affect)) == current_affect, TEST_AA_GET_AFFECT, "");
-  }
-  TAP_TEST(kaa.count(KAffect("", seq[2*(nb_seq-1)+1], 1)) == 1, TEST_AA_COUNT, "");
-  TAP_TEST((kaa.first(KAffect("", seq[2*(nb_seq-1)+1], 1)) 
-          == kaa.last(KAffect("", seq[2*(nb_seq-1)+1], 1)))
-           == 1, TEST_AA_FIRST, "");
-  TAP_TEST(kaa.getAffectation(3).isUnknown(), TEST_AA_PREDICATES, "");
-  TAP_TEST(kaa.getAffectation(8).isUnknown(), TEST_AA_PREDICATES, "");
-  TAP_TEST(kaa.getAffectation(0).isAmbiguous(), TEST_AA_PREDICATES, "");
-  
-  TAP_TEST(kaa.getDistinctAffectations().size() == 5, TEST_AA_GET_DISTINCT_AFFECT, "");
-
-  delete index;
-}
-
-template<template <class> class T, class KAffect>
-void testAffectAnalyser2() {
-  const int k = 5;
-  const bool revcomp = true;
-  T<KAffect> *index = createIndex<T<KAffect> >(k, revcomp);
-  
-  KmerAffectAnalyser<KAffect> kaa(*index, "TTTTTGGGGG");
-  
-  TAP_TEST(kaa.getAffectation(1) == KAffect("", seq[2*(nb_seq-1)+1], -1), TEST_AA_GET_AFFECT, "");
-  TAP_TEST(kaa.count(kaa.getAffectation(1)) == 1, TEST_AA_GET_AFFECT, "");
-  TAP_TEST(kaa.getAffectation(0) == kaa.getAffectation(10 - k), TEST_AA_GET_AFFECT, "");
-  for (int i = 2; i < 10 - k; i++)
-    TAP_TEST(kaa.getAffectation(i).isUnknown(), TEST_AA_PREDICATES, "");
-
-  TAP_TEST(kaa.getDistinctAffectations().size() == 3, TEST_AA_GET_DISTINCT_AFFECT, "");
-
-  delete index;
-}
-
-void testSegmentationBug1(int delta_min, int delta_max) {
-  string buggy_sequences = "bugs/kmersegment.fa";
-  int k = 14;
-  bool rc = true;
-  Fasta seqV("data/Repertoire/TRGV.fa");
-  Fasta seqJ("data/Repertoire/TRGJ.fa");
-
-  IKmerStore<KmerAffect>  *index = new ArrayKmerStore<KmerAffect>(k, rc);
-  index->insert(seqV, "V");
-  index->insert(seqJ, "J");
-
-  OnlineFasta input(buggy_sequences);
-
-  while (input.hasNext()) {
-    input.next();
-    KmerAffectAnalyser<KmerAffect> *kaa = new KmerAffectAnalyser<KmerAffect>(*index, input.getSequence().sequence);
-
-    set<KmerAffect> distinct_a = kaa->getDistinctAffectations();
-    int strand = 0;
-    for (set<KmerAffect>::iterator it = distinct_a.begin(); 
-         it != distinct_a.end() && strand != 2; it++) {
-      if (! it->isAmbiguous() && ! it->isUnknown()) {
-        if (strand == 0)
-          strand = affect_strand(it->affect);
-        else if ((strand == 1 && affect_strand(it->affect) == -1)
-                 || (strand == -1 && affect_strand(it->affect) == 1))
-          strand = 2;
-      }
-    }
-
-    int stats[STATS_SIZE];
-    Segmenter *segment = new KmerSegmenter(input.getSequence(), index, 
-                                           delta_min, delta_max, stats);
-
-    if (strand == 2 
-        || (strand == 1
-            && (kaa->last(AFFECT_V) == (int)string::npos
-                || kaa->first(AFFECT_J) == (int) string::npos))
-        || (strand == -1
-            && (kaa->first(AFFECT_V) == (int)string::npos
-                || kaa->last(AFFECT_J) == (int) string::npos)))
-      TAP_TEST(! segment->isSegmented(), TEST_BUG_SEGMENTATION, "");
-      
-    delete segment;
-    delete kaa;
-  }
-  delete index;
-}
-
-int main(void) {
-  TAP_START(NB_TESTS);
-  declare_tests();
-
-  TAP_TEST(complement("AATCAGactgactagATCGAn") == "TTAGTCTGACTGATCTAGCTN", TEST_REVCOMP, "");
-  TAP_TEST(revcomp("AATCAGactgactagATCGAn") == "NTCGATCTAGTCAGTCTGATT", TEST_REVCOMP, "");
-  TAP_TEST(revcomp("") == "", TEST_REVCOMP, "");
-  TAP_TEST(revcomp("aaaaaa") == "TTTTTT", TEST_REVCOMP, "");
-
-  testFasta1();
-
-  testKmerStoreWithKmer<ArrayKmerStore>(5, false, TEST_ARRAY_KMERSTORE);
-  testKmerStoreWithKmer<ArrayKmerStore>(5, true, TEST_ARRAY_KMERSTORE_RC);
-
-  testKmerStoreWithKmer<MapKmerStore>(5, false, TEST_MAP_KMERSTORE);
-  testKmerStoreWithKmer<MapKmerStore>(5, true, TEST_MAP_KMERSTORE_RC);
-
-  testAffectAnalyser1<ArrayKmerStore,KmerAffect>();
-  testAffectAnalyser2<ArrayKmerStore,KmerAffect>();
-  testAffectAnalyser1<ArrayKmerStore,KmerStringAffect>();
-  testAffectAnalyser2<ArrayKmerStore,KmerStringAffect>();
-
-  // Bug with one sequence on segmentation
-  testSegmentationBug1(-10, 15);
-  
-  TAP_END_TEST_EXIT
-}