working on pam

[mothur.git] / readblast.cpp

diff --git a/readblast.cpp b/readblast.cpp
index e98b69c68bfdb8f90fa841429cf4d607ba6fe1c3..84fddcf263cfdeb572f72ff3bd658325f31271e0 100644 (file)
--- a/readblast.cpp
+++ b/readblast.cpp
@@ -110,9 +110,8 @@ int ReadBlast::read(NameAssignment* nameMap) {
                                }
                        }
                }else { m->mothurOut("Error in your blast file, cannot read."); m->mothurOutEndLine(); exit(1); }
-string outDistFilem = "../kathryn/blastDist.dist";
-        ofstream outMDist;
-        m->openOutputFile(outDistFilem, outMDist);
+
+       
                //read file
                while(!fileHandle.eof()){  
                
@@ -194,8 +193,7 @@ string outDistFilem = "../kathryn/blastDist.dist";
                                         PDistCell value(itA->second, distance);
                                         matrix->addCell(it->first, value);
                                     }
-                                    outMDist << itA->first << '\t' << nameMap->get(it->first) << '\t' << distance << endl;
-                                                               }else{
+                                }else{
                                                                        outDist << itA->first << '\t' << nameMap->get(it->first) << '\t' << distance << endl;
                                                                }
                                                        }
@@ -326,8 +324,8 @@ int ReadBlast::readNames(NameAssignment* nameMap) {
                ifstream in;
                m->openInputFile(blastfile, in);
                
-               ofstream outName;
-               m->openOutputFile((blastfile + ".tempOutNames"), outName);
+               //ofstream outName;
+               //m->openOutputFile((blastfile + ".tempOutNames"), outName);
                
                //read first line
                in >> prevName;
@@ -350,8 +348,12 @@ int ReadBlast::readNames(NameAssignment* nameMap) {
                        //is this a new name?
                        if (name != prevName) {
                                prevName = name;
-                               nameMap->push_back(name);
-                outName << name << '\t' << name << endl;
+                
+                if (nameMap->get(name) != -1) { m->mothurOut("[ERROR]: trying to exact names from blast file, and I found dups.  Are you sequence names unique? quitting.\n"); m->control_pressed = true; }
+                else {
+                    nameMap->push_back(name);
+                }
+                //outName << name << '\t' << name << endl;
                                num++;
                        }
                }