added run-sequential wrapper script and HIV-1 files

git-svn-id: svn://anubis/gvsu@163 45c1a28c-8058-47b2-ae61-ca45b979098e

cs677/pa2/HIV-1_Polymerase.txt

@@ -0,0 +1,2 @@
+TTTTTTAGGGAAAATTTGGCCTTCCA?CAAGGGGAGGCCAGG?AATTT
+

cs677/pa2/HIV-1_db.fasta

@@ -0,0 +1,186 @@
+GGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAGCTA
+GGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGT
+AGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGAC
+CCTTAAAGTCAGTGTGGAAAAATCTCTAGCAGTGGCGCCCGAACAGGGAC
+GCGAAAGCGAAAGTAGAACCAGAGAAGCTCTCTCGACGCAGGACTCGGCT
+TGCTGAAGCGCGCACAGCAAGAGGCGAGGGGAGGCGACTGGTGAGTACGC
+CAATATTTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGC
+GTCGGTATTAAGCGGGGGAGATTTAGATCGATGGGAAAAAATTCGGTTAA
+GGCCAGGGGGAAAGAAAAAATATATGTTAAAACATATAGTATGGGCAAGC
+AGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACAGCTGA
+AGGCTGTAGACAAATACTAGAACAGCTACAGCCATCCCTTCAGACAGGAT
+CAGAAGAACTTAGATCCTTATATAATACAATAGCAACCCTCTATTGTGTG
+CATCAAAAAATAGAGGTAAAAGACACCAAGGAAGCTTTAGAAAAAATAGA
+GGAAGAGCAAAACAAAAGTAAGAAAAAAGTACAGCAAGCAGCAGCTGCAA
+CTGGCACAGGAAACAGCAGCCAGGTCAGCCAAAATTACCCTATAGTGCAG
+AACCTACAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAA
+TGCATGGGTAAAAGTAATAGAAGAGAAGGCTTTCAGCCCAGAAGTGATAC
+CCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACC
+ATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGA
+GACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCAGG
+CAGGGCTTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATA
+GCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAGTAA
+TCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATTTTGGGCT
+TAAATAAAATAGTAAGAATGTATAGCCCTATCAGCATTCTGGATATAAGA
+CAAGGACCAAAAGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAAC
+TCTAAGAGCCGAGCAAGCTTCACAGGAAGTAAAAAATTGGATGACAGAAA
+CCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCA
+TTAGGACCAGGAGCTACATTAGAAGAAATGATGACAGCATGTCAGGGAGT
+GGGAGGACCCGGCCATAAGGCAAGGGTTTTAGCTGAAGCAATGAGCCAAG
+TAACAAATTCAGCTGCCATAATGATGCAGAGAGGCAATTTTAAAAACCAA
+AGAAAGATGGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCATGTAGCCAG
+AAATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAATGTGGAAAGGAAG
+GACACCAAATGAAAGATTGTATTGAAAGACAGGCTAATTTTTTAGGGAAA
+ATCTGGCCTTCCCACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACC
+AGAGCCAACAGCCCCACCAGAAGAGAGCCTCAGGTCTGGGATAGAGACAA
+CAACTCCCTCTCAGAAGCAGGAGCCAATAGACAAGGAAGTGTATCCTTTA
+ACTTCCCTCAGATCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATA
+GGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGT
+ATTAGAAGAAATGAATTTGCCAGGAAGATGGAAACCAAAAATGATAGGGG
+GAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACCCATAGAA
+ATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGT
+CAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATT
+TTCCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATG
+GATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGC
+ATTAATAGAAATTTGTACAGAAATGGAAAAGGAAGGGAAAATTTCAAAAA
+TTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAA
+GACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAG
+AACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGT
+TAAAAAAGAAAAAATCAGTAACAGTACTAGATGTGGGTGATGCATATTTT
+TCAGTTCCCTTAGATGAAGATTTCAGGAAGTATACTGCATTTACCATACC
+TAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTGC
+CACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAA
+ATCTTAGAGCCTTTTAGAAAACAGAATCCAGACATAGTTATCTATCAATA
+TATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGAGCAGCATAGAA
+CAAAAATAGAGGAACTGAGACAGCATCTGTTGAAGTGGGGATTTACCACA
+CCAGACAAAAAACATCAGAAGGAACCTCCATTCCTCTGGATGGGTTATGA
+ACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAGAAAG
+ACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTAAATTGG
+GCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCT
+TAGGGGAGCCAAAGCACTAACAGATGTAATACCACTAACAGAAGGAGCAG
+AGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGA
+GTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGG
+ACAAGGTCAATGGACATATCAGATTTATCAAGAGCCATTTAAAAATCTGA
+GAACAGGAAAATATGCAAGAACGAGGGGTGCCCACACTAATGATATAAAA
+CAATTAACAGAGGCAGTGCAAAAAATAGCCACAGAAAGCATAGTAATATG
+GGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAA
+CATGGTGGACAGAGTATTGGCAAGCTACCTGGATTCCTGAGTGGGAGTTT
+GTCAATACCCCTCCTTTAGTAAAATTATGGTACCAGTTAGAGAAAGAACC
+CATAGTAGGAGCAGAAACTTTCTATGTAGATGGGGCAGCTAACAGGGAGA
+CTAAATTAGGAAAAGCAGGATATGTTACTAACAGAGGAAGACAAAAGGTA
+GTCCCCCTGACTAACACAACAAATCAGAAGACTGAGTTACAAGCAATTCA
+TCTAGCTTTACAGGATTCAGGATCAGAAGTAAACATAGTAACAGACTCAC
+AATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAG
+TTAGTCAATCAAATAATAGAACAGTTAATAAAAAAGGAAAAGGTCTATCT
+GGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATA
+AATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTCTAGATGGAATAGAT
+AAGGCCCAAGAAGAACATGAGAAATATCATAATAATTGGAGAGCAATGGC
+TAGTGATTTTAACCTGCCACCTGTAGTAGCAAAGGAAATAGTAGCCAGCT
+GTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGT
+AGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTAT
+CCTAGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTC
+CAGCAGAAACAGGGCAGGAAACAGCATACTTTCTCTTAAAATTAGCAGGA
+AGATGGCCAGTAAAAACAATACACACAGATAATGGCAGCAATTTCACCAG
+TGCTGCGGTTAAGGCCGCCTGTTGGTGGGCGGGAGTCAAGCAGGAATTTG
+GAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAA
+GAATTAAAGAAAATTATAGGACAGGTAAGAGATCAAGCTGAACATCTTAA
+GACAGCAGTACAAATGGCAGTATTTGTCCACAATTTTAAAAGAAAAGGGG
+GGATTGGGGGGTACAGTGCAGGGGAAAGAATAATAGACATAATAGCAACA
+GACATACAAACTAGAGAACTACAAAAACAAATTACAAAAATTCAAAATTT
+TCGGGTTTATTACAGGGACAGCAGAGACCCACTTTGGAAAGGACCAGCAA
+AGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGAC
+ATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAA
+ACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGA
+ACATGGACAAGTTTAGTAAAACATCATGTATATGTTTCAAAGAAAGCTAG
+GGGATGGTTTTATAGACATCACTATGAAAGCACTCATCCAAAAATAAGTT
+CAGAAATACACATTCCACTAGGGGATGCTAGATTGGTAGTAACAACATAT
+TGGGGTCTGCATACAGGAGAAAGAGAATGGCATTTGGGTCATGGAGTTTC
+CATAGAATGGAGGAAAAGGAGCTATAGCACACAAGTAGACCCTGAACTAG
+CAGACCAACTAATTCATCTGTATTACTTTGATTGTTTTGCAGACTCTGCT
+ATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGCATATCA
+AGCAGGACATTCCAAGGTAGGATCTCTACAATACTTGGCACTATCAGCCT
+TAATAACACCAAAGAAGATAAAGCCACCTTTGCCTAGTGTTACAAAACTG
+ACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAG
+CCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGACAGAAGC
+TGTTAGACATTTTCCTAGGCCATGGCTCCATAGCTTAGGACAACATATCT
+ATGAAACTTATGGAGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATT
+CTGCAACAATTGCTGTTTATTCATTTCAGAATTGGGTGTCAACATAGCAG
+AATAGGCATTATTCAACAGAGGAGAGCAAGAAGAAATGGAGCCAGTAGAT
+CCTAATCTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTG
+TACCAAATGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCA
+CAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGA
+CGAAGAGCTCCTCAGGGCAGCCAGGCTCATCAAGCTTCTCTATCAGAGCA
+GTAAGTAGTATATGTAATGCAACTTATATTAATAGTAACAATAGTAGCTT
+TAGTAGTAACATTAATAATAGCAATAGTTGTGTGGTCCATAGTACTCATA
+GAATATAGGAAAATATTAAGACAAAGGAAAATAGACAAGTTAATTAATAG
+ACTAGTAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAACTAT
+CAGCACTTGTGGAGATGGGGGTGGAAATGGGGCATCATGCTCCTTGGGAT
+GTTAATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATG
+GGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGAT
+GCTAAAGCATATGAAGAAGAGGTACATAATGTTTGGGCCACACATGCCTG
+TGTACCCACAGACCCCAACCCACAAGAAATAGTATTGGCAAATGTGACAG
+AAGATTTTAACATGTGGAAAAATGAAATGGTAGAACAGATGCATACTGAT
+ATAATCAGTTTATGGGATGAAAGCCTAAAACCATGTGTAAAATTAACCCC
+ACTCTGTGTTACTTTAAATTGCACTGATTTGAAGAATGAAACTAAGACCA
+ATAGTAGTGATGCCAATAGTAATAGCGGGGAAATAATGGGGAACGAAGAG
+ATAAAAAATTGCTCTTTCAATGTCAGCACAGGCGCACCAGGTAAGGTGCA
+GAAAGAATATGCACTTTTTTATGCACTTGATATAGTATCAATAAAGAATG
+AAAATAATAGTACCAGCCATATGTTGACAAGTTGTAACACCTCAGTCAGT
+ACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTG
+TGCCCCGGCTGGTTTTGCAATTCTAAAATGTAATGATAAGAAGTTCAATG
+GAACAGGACCATGTAACAATGTCAGCACAGTACAATGTACACATGGAATT
+AGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGA
+AGAGGTAGTACTTAGATCTGCCAATTTCTCAGACAATGCTAAAACCATAA
+TAGTACAGCTGAACCACTCTGTAGAAATTACTTGTACAAGACCCAACTAC
+AATGAAACAAAAAGAATCCGTATCCACAGAGGATATGGAAGATCATTTGT
+TACAGTAAGAAAATTGGGAGATAGGAAACAAGCACATTGTACCATGAATA
+GAACGAAATGGGACAACGCTTTAAAACAGATAGCTAGCAAATTAAGAGAA
+CAATTTAATAAAACAGCAATAATCTTTAACCGGTCCTCAGGAGGGGACCT
+AGAAATTGAAATGCACAGTTTTAATTGCGGAGGGGAATTGTTCTACTGTA
+ATACAACAAAACTGTTTAATAGTACTTGGAATGAGACTACAGAGTCAAAT
+GGCAAGGGAGAAAATATCACACTCCCATGCAGAATAAGACAATTTGTAAA
+CATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCAGCGATGGAC
+AAATTAGGTGTACATCAAATATTACTGGGCTACTATTAACAAGAGATGGG
+GGTGGTCCTAGTGATAACAAAACCGACAAGACCTTCAGACCAGGAGGAGG
+AGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAATAA
+AAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTG
+CAAAGAGAAAAAAGAGCAGTGGGAATGGTAGGAGCTATGTTCCTTGGGTT
+CTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCATTGACGCTGACGG
+TACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATCTG
+CTGAGAGCTATTGAGGCGCAACAACATCTGTTGCAACTCACAGTCTGGGG
+CATCAAGCAGCTCCAGGCAAGAGTCCTGGCTGTAGAAAGATACCTAAAGG
+ATCAACAGCTCCTGGGGATCTGGGGTTGCTCTGGAAAACTCATTTGCACC
+ACTACTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGATCAGAT
+TTGGAATAACATGACCTGGTTGGAGTGGGACAGAGAAATTGCCAATTACA
+CAAACTTAATACATCACTTAATTGAAGAATCGCAAAACCAGCAAGAAAAG
+AATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAGTTG
+GTTTGACATATCAAACTGGCTGTGGTATATAAAAATATTCATAATGATAG
+TAGCAGGCTTAGTAGGTTTAAGAATAGTTTTTGCTGTGCTTTCTATAGTA
+AATAGAGTTAGGCAGGGATACTCACCATTGTCATTCCAGACCCACTTCCC
+AGCTCCGAGGGGACCCGACAGGCCAGACGGAATCGAAGGAGAAGGTGGAG
+AGAGAGACAGAGACAGATCCGTGCGATTAGTGGATGGATTCTTAGCACTT
+CTCTGGGAAGACCTGCGCAACCTGTGCCTCTTCAGCTACCACCGCTTGAG
+AGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGG
+GGTGGGAAGCCCTCAAATATTGGTGGAGTCTCCTACAGTATTGGAGTCAG
+GAGCTAAAGAATAGTGCTGTCAACTTGTTCAATACCAGAGCTATAGTAGT
+AGCTGAGGGGACAGATAGGATCATAGAAGTAGTACAAAGACTTTGTAGAG
+CTATTCTCCACATACCTAGAAGAATTAGACAGGGCTTGGAAAGATTTTTG
+CTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTATAGTTGGATGGCCTA
+CTATAAGGGAAAGAATGAAACGAGCTGGACCAGCAGCAGATGGGGTGGGA
+GCAGCATCTCGAGACCTAGAAAAACATCGAGCAATCACAAGTAGCAATAC
+AGCAGCTACCAATGCTGATTGTGCCTGGCTAGAAGCACAAGAGGAGGAAG
+AGGTGGGTTTTCCAGTCAGACCTCAGGTACCTTTAAGACCAATGACTTAC
+AAGGCAGGTATAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGA
+AGGGCTAGTTTGGTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCT
+ACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCA
+GGGATCAGATATCCACTGACCTTTGGATGGTGCTTCAAGCTAGTACCAGT
+TGAGCCAGATAAGGTAGAAGAGGCCAATGAAGGAGAGGACAACATCTTGT
+TACACCCTATGTGTCTACATGGAATGGAGGACGCGGAGAAAGAAGTGTTA
+GTGTGGAGATTTGACAGTAAACTAGCCTTCCATCACGTAGCCCGAGAGCT
+GCATCCGGAGTACTACAAAGACTGCTGACATCGAGCTTTCTACAAGGGAC
+TTTCCGCTGGGGACTTTCCAGGGAGGCGTGATCTGGGTGGGACTGGGGAG
+TGGCGTGCCCTCAGATGCTGCATATAAGCAGCTGCTTTTGCCTGTACTGG
+GTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAGCTAG
+GGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCA
+
+

cs677/pa2/run-sequential

@@ -0,0 +1,2 @@
+#!/bin/sh
+time ./sequential HIV-1_db.fasta HIV-1_Polymerase.txt

cs677/pa2/sequential.cc

@@ -36,7 +36,6 @@ bool readFile(char * fileName, vector<char> & v)
     {
         char chr;
         in >> chr;
-        cout << "Read char 0x" << hex << (int) chr << ", '" << chr << "'" << endl;
         v.push_back(chr);
     }
     return true;
@@ -44,4 +43,11 @@ bool readFile(char * fileName, vector<char> & v)
 
 void similarityMatrix(vector<char> & s, vector<char> & t)
 {
+    int s_size = s.size();
+    int t_size = t.size();
+    unsigned int F[s_size][t_size];
+    for (int i = 0; i < t_size; i++)
+        F[0][i] = 0;
+    for (int i = 0; i < s_size; i++)
+        F[i][0] = 0;
 }