--- ./SequenceReader/testSequenceReaderFasta.cpp.orig 2004-08-25 11:31:17.000000000 -0300 +++ ./SequenceReader/testSequenceReaderFasta.cpp 2008-06-12 15:39:31.000000000 -0300 @@ -49,12 +49,12 @@ // ### Function Definitions ### void capitalise( string& s ) { - for ( int i(0) ; i < s.size() ; ++i ) s[i] = toupper(s[i]); + for ( unsigned int i(0) ; i < s.size() ; ++i ) s[i] = toupper(s[i]); } void reverseString( string& seq ) { string rc; - for ( int i(0) ; i < seq.size() ; i++ ) + for ( unsigned int i(0) ; i < seq.size() ; i++ ) { if ( ( seq[i] == 'A' ) || (seq[i] == 'a') ) rc = 'T' + rc; else if ( ( seq[i] == 'T' ) || (seq[i] == 't') ) rc = 'A' + rc; @@ -91,7 +91,7 @@ cout << "Test " << ++numTests <<": test of function getNextSequence" << endl << endl; - int numSeqs = 10; + unsigned int numSeqs = 10; int seqSize = 57; // Generate a random sequence of (numSeqs*seqSize) base pairs ... @@ -118,7 +118,7 @@ - for ( int i(0) ; i < numSeqs ; i++ ) + for ( unsigned int i(0) ; i < numSeqs ; i++ ) { testReader.getNextSequence(w,wordLength); @@ -188,7 +188,7 @@ cout << "Test " << ++numTests <<": test of getSequence" << endl << endl; - int toRead = 5; + unsigned int toRead = 5; w.clear(); testReader.getSequence(w,toRead,wordLength); @@ -242,7 +242,7 @@ cout << "Test " << ++numTests <<": test of random access output functions" << endl << endl; - for ( int i(1) ; i <= numSeqs; i++ ) + for ( unsigned int i(1) ; i <= numSeqs; i++ ) { cout << testReader.getName(i) << endl; cout << testReader.getSideInfo(i) << endl; @@ -275,7 +275,7 @@ // add on the end of the expected sequence string for it to match actual. // const string spareBases( wordLength - ( seqSize % wordLength ), 'A'); - for ( int i(0) ; i < numSeqs ; i++ ) + for ( unsigned int i(0) ; i < numSeqs ; i++ ) { testReaderFastq.getNextSequence(w,wordLength); @@ -403,7 +403,7 @@ cout << "Test " << ++numTests <<": test of random access output functions" << endl << endl; - for ( int i(1) ; i <= numSeqs; i++ ) + for ( unsigned int i(1) ; i <= numSeqs; i++ ) { cout << testReaderFastq.getName(i) << endl; cout << testReaderFastq.getSideInfo(i) << endl; @@ -466,7 +466,7 @@ { testReader.rewind(); - for ( int j(0) ; j < testReader.getNumSequencesInFile() ; j ++ ) + for ( unsigned int j(0) ; j < testReader.getNumSequencesInFile() ; j ++ ) { cout << i << " " << j << endl; wSingle.clear(); wMulti.clear(); @@ -772,7 +772,7 @@ for (int wordLength(9); wordLength <= 12; wordLength++) { - for (int i(0) ; i < fiftyAs.size(); i++) + for (unsigned int i(0) ; i < fiftyAs.size(); i++) { thisString=fiftyAs; thisString[i]='X'; @@ -793,7 +793,7 @@ stringReader.changeMode(&ignore); w.clear(); numInLast = stringReader.getNextSequence(w,wordLength); - assert(numInLast==(fiftyAs.size()-1)%wordLength); + assert(numInLast==(int)(fiftyAs.size()-1)%wordLength); assert((w.size()-1)*wordLength+numInLast==fiftyAs.size()-1); for (WordSequence::iterator j(w.begin()); j!=w.end();j++) @@ -810,7 +810,7 @@ numInLast = stringReader.getNextSequence(w,wordLength); cout << "blegh " << wordLength << " " << i << " " << fiftyAs.size() << " " << numInLast << " " << w.size() << endl; - assert(numInLast==fiftyAs.size()%wordLength); + assert(numInLast==(int)fiftyAs.size()%wordLength); assert((w.size()-1)*wordLength+numInLast==fiftyAs.size()); for (WordSequence::iterator j(w.begin()); j!=w.end();j++) @@ -828,7 +828,7 @@ stringReader.changeMode(&tag); w.clear(); numInLast = stringReader.getNextSequence(w,wordLength); - assert(numInLast==fiftyAs.size()%wordLength); + assert(numInLast==(int)fiftyAs.size()%wordLength); assert((w.size()-1)*wordLength+numInLast==fiftyAs.size()); for (WordSequence::iterator j(w.begin()); j!=w.end();j++) @@ -915,7 +915,7 @@ cout << "actual: " << printResidue(W,wordLength) << endl; - for ( int i(0),j(0); i < protString.size() ; i+=wordLength,j++ ) + for ( unsigned int i(0),j(0); i < protString.size() ; i+=wordLength,j++ ) { wordString = protString.substr(i, wordLength); cout << wordString << " " << printResidue(W[j],wordLength) << endl; @@ -1163,7 +1163,7 @@ assert ( localReader.getNumSequencesInFile() == testReader.getNumSequencesInFile() ); - for ( int j(0) ; j < testReader.getNumSequencesInFile() ; j ++ ) + for ( unsigned int j(0) ; j < testReader.getNumSequencesInFile() ; j ++ ) { wSingle.clear(); wMulti.clear(); @@ -1244,7 +1244,7 @@ WordSequence seq; string name; - for ( int i(1) ; i <= filterer.getNumSequencesInFile() ; i++ ) + for ( unsigned int i(1) ; i <= filterer.getNumSequencesInFile() ; i++ ) { filterer.getSequence(seq, i, 16); filterer.getLastSequenceName(name); @@ -1330,12 +1330,12 @@ // assert(v1==v1i); // assert(v2==v2i); - for ( int (i(j)) ; i <=seqSize ; i++ ) assert(v1[i-j]==data[i-1]); - for ( int (i(j)) ; i <=seqSize ; i++ ) assert(v2[i-j]==data[i-1]); - for ( int (i(j)) ; i <=seqSize ; i++ ) assert(v1m[i-j]==data[i-1]); - for ( int (i(j)) ; i <=seqSize ; i++ ) assert(v2m[i-j]==data[i-1]); - for ( int (i(j)) ; i <=seqSize ; i++ ) assert(v1i[i-j]==data[i-1]); - for ( int (i(j)) ; i <=seqSize ; i++ ) assert(v2i[i-j]==data[i-1]); + for ( int i(j) ; i <=seqSize ; i++ ) assert(v1[i-j]==data[i-1]); + for ( int i(j) ; i <=seqSize ; i++ ) assert(v2[i-j]==data[i-1]); + for ( int i(j) ; i <=seqSize ; i++ ) assert(v1m[i-j]==data[i-1]); + for ( int i(j) ; i <=seqSize ; i++ ) assert(v2m[i-j]==data[i-1]); + for ( int i(j) ; i <=seqSize ; i++ ) assert(v1i[i-j]==data[i-1]); + for ( int i(j) ; i <=seqSize ; i++ ) assert(v2i[i-j]==data[i-1]); } cout << "got through first bit" << endl; @@ -1402,7 +1402,7 @@ string n1,n2; - for (int i(0);i