Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / probcons / ProjectPairwise.cc

diff --git a/website/archive/binaries/mac/src/probcons/ProjectPairwise.cc b/website/archive/binaries/mac/src/probcons/ProjectPairwise.cc
deleted file mode 100644 (file)
index 4696ba1..0000000
--- a/website/archive/binaries/mac/src/probcons/ProjectPairwise.cc
+++ /dev/null
@@ -1,71 +0,0 @@
-/////////////////////////////////////////////////////////////////
-// ProjectPairwise
-//
-// Program for projecting multiple alignments to all pairwise
-// alignments.
-/////////////////////////////////////////////////////////////////
-
-#include "SafeVector.h"
-#include "MultiSequence.h"
-#include <string>
-#include <sstream>
-#include <iomanip>
-#include <iostream>
-#include <list>
-#include <set>
-#include <limits>
-#include <cstdio>
-#include <cstdlib>
-#include <cerrno>
-#include <iomanip>
-
-bool compressGaps = true;
-
-/////////////////////////////////////////////////////////////////
-// main()
-//
-// Main program.
-/////////////////////////////////////////////////////////////////
-
-int main (int argc, char **argv){
-
-  // check arguments
-  if (argc < 2){
-    cerr << "Usage: project ALIGNMENT [-nocompressgaps]" << endl;
-    exit (1);
-  }
-
-  for (int i = 2; i < argc; i++){
-    if (strcmp (argv[i], "-nocompressgaps") == 0)
-      compressGaps = false;
-    else {
-      cerr << "Unrecognized option: " << argv[i] << endl;
-      exit (1);
-    }
-  }
-
-  MultiSequence *align = new MultiSequence (string (argv[1])); assert (align);
-
-  int N = align->GetNumSequences();
-  for (int i = 0; i < N; i++){
-    for (int j = i+1; j < N; j++){
-      string name = align->GetSequence(i)->GetHeader() + "-" + align->GetSequence(j)->GetHeader() + ".fasta";
-      ofstream outfile (name.c_str());
-
-      if (compressGaps){
-       set<int> s;
-       s.insert (i); s.insert (j);
-       MultiSequence *proj = align->Project (s);
-       proj->WriteMFA (outfile);
-       delete proj;
-      }
-      else {
-       align->GetSequence(i)->WriteMFA (outfile, 60);
-       align->GetSequence(j)->WriteMFA (outfile, 60);
-      }
-      outfile.close();
-    }
-  }
-
-  delete align;
-}