diff options
Diffstat (limited to 'biology/ssaha/files/patch-testHashTableNoOverlap.cpp')
-rw-r--r-- | biology/ssaha/files/patch-testHashTableNoOverlap.cpp | 178 |
1 files changed, 178 insertions, 0 deletions
diff --git a/biology/ssaha/files/patch-testHashTableNoOverlap.cpp b/biology/ssaha/files/patch-testHashTableNoOverlap.cpp new file mode 100644 index 000000000000..721e03ae9134 --- /dev/null +++ b/biology/ssaha/files/patch-testHashTableNoOverlap.cpp @@ -0,0 +1,178 @@ +--- ./HashTable/testHashTableNoOverlap.cpp.orig 2004-03-01 13:51:29.000000000 -0300 ++++ ./HashTable/testHashTableNoOverlap.cpp 2008-06-12 15:39:31.000000000 -0300 +@@ -70,10 +70,10 @@ + cout << " Test of class HashTable" << endl << endl; + cout << "*******************************************" << endl << endl; + +- int numSeqs = 10; +- int seqSize = 100; +- int wordLength = 10; +- int maxHits = 50; ++ unsigned int numSeqs = 10; ++ unsigned int seqSize = 100; ++ unsigned int wordLength = 10; ++ unsigned int maxHits = 50; + + // Generate a random sequence of (numSeqs*seqSize) base pairs ... + // 1128 is the seed value for the random number generator +@@ -116,7 +116,7 @@ + // so we are checking that all sequence data 'finds itself' in the hash + // table in the correct position + +- for ( int i(1) ; i <= numSeqs ; i++ ) ++ for ( unsigned int i(1) ; i <= numSeqs ; i++ ) + { // for each sequence in testReader ... + testReader.getNextSequence(seq,wordLength); + +@@ -131,7 +131,7 @@ + cout << seq.getNumBasesInLast() << "!!\n"; + // ... go through the Words in the sequence one by one and look + // for matches in the hash table +- for ( int j(0) ; j < (seqSize/wordLength) ; j++ ) ++ for ( unsigned int j(0) ; j < (seqSize/wordLength) ; j++ ) + { + cout << j << " " << printBase(seq[j],wordLength) << endl; + +@@ -146,7 +146,7 @@ + // ... and that the sequence number and offset for the hit are OK + + assert(hits[0].subjectNum == i ); +- assert(hits[0].diff == j*wordLength ); ++ assert((unsigned int)hits[0].diff == j*wordLength ); + assert(hits[0].queryPos == 1); + + hits.clear(); +@@ -157,12 +157,12 @@ + testHash.matchWord(seq,hits); + cout << hits.size() << "!!!!!\n"; + assert( hits.size() == (seqSize/wordLength) ); +- for ( int j(0) ; j < hits.size() ; j ++ ) ++ for ( unsigned int j(0) ; j < hits.size() ; j ++ ) + { + + assert(hits[j].subjectNum == i); + assert(hits[j].diff == 0); +- assert(hits[j].queryPos == 1 + ( j * wordLength ) ); ++ assert((unsigned int)hits[j].queryPos == 1 + ( j * wordLength ) ); + + } // ~for j + +@@ -194,7 +194,7 @@ + assert( testLoad.isInitialized() == true ); + + // and that word length matches original +- assert( testLoad.getWordLength() == wordLength ); ++ assert( (unsigned int)testLoad.getWordLength() == wordLength ); + + testLoad.setMaxNumHits( testHash.getMaxNumHits() ); + +@@ -208,7 +208,7 @@ + // and new hash tables, storing the resulting hits in hitsOrig and + // hitsCopy respectively. + +- for ( int i(0) ; i < numSeqs ; i++ ) ++ for ( unsigned int i(0) ; i < numSeqs ; i++ ) + { + + // ... check that the name strings match +@@ -258,7 +258,7 @@ + HashTable shiftHash(cout); + creator.createHashTable(shiftHash,shiftReader,wordLength,maxHits); + +- for ( int i(0) ; i < wordLength ; i++ ) ++ for ( unsigned int i(0) ; i < wordLength ; i++ ) + { + testSeq = testSeq.substr(1); // delete first character + { // braces ensure a new instance is created each time round loop +@@ -460,7 +460,7 @@ + SequenceEncoderCodon encoder; + encoder.setWordLength(wordLength); + +- for ( int i(1) ; i < hashTrans.getNumSequences() ; i++ ) ++ for ( unsigned int i(1) ; i < hashTrans.getNumSequences() ; i++ ) + { + + hashTrans.getSequenceName( s1, i ); +@@ -477,7 +477,7 @@ + assert(hashTrans.getSequenceSize(i)==hashTrans2.getSequenceSize(i)); + + assert( (((w1.size()-1) * gMaxBasesPerWord ) + w1.getNumBasesInLast()) +- == hashTrans.getSequenceSize(i)); ++ == (unsigned int)hashTrans.getSequenceSize(i)); + + + // Sequence should produce same (nonzero) num hits in fwd direction +@@ -573,19 +573,19 @@ + string s, s1; + Word w; + vector<Word> subs; +- int wl=15; ++ unsigned int wl=15; + + // test substitution for DNA + // + +- for (int i(0); i<wl; i++) s+="A"; ++ for ( unsigned int i(0); i<wl; i++) s+="A"; + + w = makeBase(s); + + generateSubstitutesDNA( w, subs, wl ); + assert(subs.size()==wl); + +- for (int i(0); i<wl ; i++) ++ for (unsigned int i(0); i<wl ; i++) + { + cout << printWord(subs[i],wl) << endl; + s1=s; +@@ -596,14 +596,14 @@ + // + s=""; subs.clear(); + +- for (int i(0); i<wl; i++) s+="C"; ++ for (unsigned int i(0); i<wl; i++) s+="C"; + + w = makeBase(s); + + generateSubstitutesDNA( w, subs, wl ); + assert(subs.size()==wl); + +- for (int i(0); i<wl ; i++) ++ for (unsigned int i(0); i<wl ; i++) + { + cout << printWord(subs[i],wl) << endl; + s1=s; +@@ -614,14 +614,14 @@ + // + s=""; subs.clear(); + +- for (int i(0); i<wl; i++) s+="G"; ++ for (unsigned int i(0); i<wl; i++) s+="G"; + + w = makeBase(s); + + generateSubstitutesDNA( w, subs, wl ); + assert(subs.size()==wl); + +- for (int i(0); i<wl ; i++) ++ for (unsigned int i(0); i<wl ; i++) + { + cout << printWord(subs[i],wl) << endl; + s1=s; +@@ -632,14 +632,14 @@ + // + s=""; subs.clear(); + +- for (int i(0); i<wl; i++) s+="T"; ++ for (unsigned int i(0); i<wl; i++) s+="T"; + + w = makeBase(s); + + generateSubstitutesDNA( w, subs, wl ); + assert(subs.size()==wl); + +- for (int i(0); i<wl ; i++) ++ for (unsigned int i(0); i<wl ; i++) + { + cout << printWord(subs[i],wl) << endl; + s1=s; |