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;