702ce22305
sequences. It stands for Sequence Search and Alignment by Hashing Algorithm. It achieves its fast search speed by converting sequence information into a `hash table' data structure, which can then be searched very rapidly for matches. WWW: http://www.sanger.ac.uk/Software/analysis/SSAHA/ PR: ports/124525 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Approved by: gabor (mentor, implicit)
171 lines
6.2 KiB
C++
171 lines
6.2 KiB
C++
--- ./SequenceReader/testSequenceReaderFasta.cpp.orig 2004-08-25 11:31:17.000000000 -0300
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+++ ./SequenceReader/testSequenceReaderFasta.cpp 2008-06-12 15:39:31.000000000 -0300
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@@ -49,12 +49,12 @@
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// ### Function Definitions ###
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void capitalise( string& s )
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{
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- for ( int i(0) ; i < s.size() ; ++i ) s[i] = toupper(s[i]);
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+ for ( unsigned int i(0) ; i < s.size() ; ++i ) s[i] = toupper(s[i]);
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}
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void reverseString( string& seq )
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{
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string rc;
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- for ( int i(0) ; i < seq.size() ; i++ )
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+ for ( unsigned int i(0) ; i < seq.size() ; i++ )
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{
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if ( ( seq[i] == 'A' ) || (seq[i] == 'a') ) rc = 'T' + rc;
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else if ( ( seq[i] == 'T' ) || (seq[i] == 't') ) rc = 'A' + rc;
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@@ -91,7 +91,7 @@
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cout << "Test " << ++numTests <<": test of function getNextSequence"
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<< endl << endl;
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- int numSeqs = 10;
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+ unsigned int numSeqs = 10;
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int seqSize = 57;
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// Generate a random sequence of (numSeqs*seqSize) base pairs ...
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@@ -118,7 +118,7 @@
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- for ( int i(0) ; i < numSeqs ; i++ )
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+ for ( unsigned int i(0) ; i < numSeqs ; i++ )
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{
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testReader.getNextSequence(w,wordLength);
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@@ -188,7 +188,7 @@
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cout << "Test " << ++numTests <<": test of getSequence"
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<< endl << endl;
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- int toRead = 5;
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+ unsigned int toRead = 5;
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w.clear();
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testReader.getSequence(w,toRead,wordLength);
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@@ -242,7 +242,7 @@
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cout << "Test " << ++numTests <<": test of random access output functions"
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<< endl << endl;
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- for ( int i(1) ; i <= numSeqs; i++ )
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+ for ( unsigned int i(1) ; i <= numSeqs; i++ )
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{
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cout << testReader.getName(i) << endl;
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cout << testReader.getSideInfo(i) << endl;
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@@ -275,7 +275,7 @@
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// add on the end of the expected sequence string for it to match actual.
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// const string spareBases( wordLength - ( seqSize % wordLength ), 'A');
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- for ( int i(0) ; i < numSeqs ; i++ )
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+ for ( unsigned int i(0) ; i < numSeqs ; i++ )
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{
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testReaderFastq.getNextSequence(w,wordLength);
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@@ -403,7 +403,7 @@
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cout << "Test " << ++numTests <<": test of random access output functions"
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<< endl << endl;
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- for ( int i(1) ; i <= numSeqs; i++ )
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+ for ( unsigned int i(1) ; i <= numSeqs; i++ )
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{
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cout << testReaderFastq.getName(i) << endl;
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cout << testReaderFastq.getSideInfo(i) << endl;
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@@ -466,7 +466,7 @@
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{
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testReader.rewind();
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- for ( int j(0) ; j < testReader.getNumSequencesInFile() ; j ++ )
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+ for ( unsigned int j(0) ; j < testReader.getNumSequencesInFile() ; j ++ )
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{
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cout << i << " " << j << endl;
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wSingle.clear(); wMulti.clear();
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@@ -772,7 +772,7 @@
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for (int wordLength(9); wordLength <= 12; wordLength++)
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{
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- for (int i(0) ; i < fiftyAs.size(); i++)
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+ for (unsigned int i(0) ; i < fiftyAs.size(); i++)
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{
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thisString=fiftyAs;
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thisString[i]='X';
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@@ -793,7 +793,7 @@
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stringReader.changeMode(&ignore);
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w.clear();
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numInLast = stringReader.getNextSequence(w,wordLength);
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- assert(numInLast==(fiftyAs.size()-1)%wordLength);
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+ assert(numInLast==(int)(fiftyAs.size()-1)%wordLength);
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assert((w.size()-1)*wordLength+numInLast==fiftyAs.size()-1);
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for (WordSequence::iterator j(w.begin()); j!=w.end();j++)
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@@ -810,7 +810,7 @@
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numInLast = stringReader.getNextSequence(w,wordLength);
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cout << "blegh " << wordLength << " " << i << " " << fiftyAs.size() << " " << numInLast << " " << w.size() << endl;
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- assert(numInLast==fiftyAs.size()%wordLength);
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+ assert(numInLast==(int)fiftyAs.size()%wordLength);
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assert((w.size()-1)*wordLength+numInLast==fiftyAs.size());
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for (WordSequence::iterator j(w.begin()); j!=w.end();j++)
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@@ -828,7 +828,7 @@
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stringReader.changeMode(&tag);
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w.clear();
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numInLast = stringReader.getNextSequence(w,wordLength);
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- assert(numInLast==fiftyAs.size()%wordLength);
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+ assert(numInLast==(int)fiftyAs.size()%wordLength);
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assert((w.size()-1)*wordLength+numInLast==fiftyAs.size());
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for (WordSequence::iterator j(w.begin()); j!=w.end();j++)
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@@ -915,7 +915,7 @@
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cout << "actual: " << printResidue(W,wordLength) << endl;
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- for ( int i(0),j(0); i < protString.size() ; i+=wordLength,j++ )
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+ for ( unsigned int i(0),j(0); i < protString.size() ; i+=wordLength,j++ )
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{
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wordString = protString.substr(i, wordLength);
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cout << wordString << " " << printResidue(W[j],wordLength) << endl;
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@@ -1163,7 +1163,7 @@
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assert ( localReader.getNumSequencesInFile()
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== testReader.getNumSequencesInFile() );
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- for ( int j(0) ; j < testReader.getNumSequencesInFile() ; j ++ )
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+ for ( unsigned int j(0) ; j < testReader.getNumSequencesInFile() ; j ++ )
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{
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wSingle.clear(); wMulti.clear();
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@@ -1244,7 +1244,7 @@
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WordSequence seq;
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string name;
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- for ( int i(1) ; i <= filterer.getNumSequencesInFile() ; i++ )
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+ for ( unsigned int i(1) ; i <= filterer.getNumSequencesInFile() ; i++ )
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{
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filterer.getSequence(seq, i, 16);
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filterer.getLastSequenceName(name);
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@@ -1330,12 +1330,12 @@
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// assert(v1==v1i);
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// assert(v2==v2i);
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- for ( int (i(j)) ; i <=seqSize ; i++ ) assert(v1[i-j]==data[i-1]);
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- for ( int (i(j)) ; i <=seqSize ; i++ ) assert(v2[i-j]==data[i-1]);
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- for ( int (i(j)) ; i <=seqSize ; i++ ) assert(v1m[i-j]==data[i-1]);
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- for ( int (i(j)) ; i <=seqSize ; i++ ) assert(v2m[i-j]==data[i-1]);
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- for ( int (i(j)) ; i <=seqSize ; i++ ) assert(v1i[i-j]==data[i-1]);
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- for ( int (i(j)) ; i <=seqSize ; i++ ) assert(v2i[i-j]==data[i-1]);
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+ for ( int i(j) ; i <=seqSize ; i++ ) assert(v1[i-j]==data[i-1]);
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+ for ( int i(j) ; i <=seqSize ; i++ ) assert(v2[i-j]==data[i-1]);
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+ for ( int i(j) ; i <=seqSize ; i++ ) assert(v1m[i-j]==data[i-1]);
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+ for ( int i(j) ; i <=seqSize ; i++ ) assert(v2m[i-j]==data[i-1]);
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+ for ( int i(j) ; i <=seqSize ; i++ ) assert(v1i[i-j]==data[i-1]);
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+ for ( int i(j) ; i <=seqSize ; i++ ) assert(v2i[i-j]==data[i-1]);
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}
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cout << "got through first bit" << endl;
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@@ -1402,7 +1402,7 @@
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string n1,n2;
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- for (int i(0);i<numSeqs; i++)
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+ for (unsigned int i(0);i<(unsigned int)numSeqs; i++)
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{
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cout << "i: " << i << endl;
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w1.clear(); w2.clear();
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