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--- ./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<numSeqs; i++)
+ for (unsigned int i(0);i<(unsigned int)numSeqs; i++)
{
cout << "i: " << i << endl;
w1.clear(); w2.clear();
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