pat's ../ bug fix

[mothur.git] / readcluster.cpp

diff --git a/readcluster.cpp b/readcluster.cpp
index 50787e984bd2a3c45cbce0af354fea178771a6b0..11b8d012a22e592d99bb71e3063c0c89a710252a 100644 (file)
--- a/readcluster.cpp
+++ b/readcluster.cpp
@@ -12,6 +12,7 @@
 /***********************************************************************/
 
 ReadCluster::ReadCluster(string distfile, float c){
+               globaldata = GlobalData::getInstance();
         distFile = distfile;
                cutoff = c;
 }
@@ -24,7 +25,7 @@ void ReadCluster::read(NameAssignment* nameMap){
                if (format == "phylip") { convertPhylip2Column(nameMap); }
                else { list = new ListVector(nameMap->getListVector());  }
                
-               createHClusterFile();
+               OutPutFile = sortFile(distFile);
                        
        }
        catch(exception& e) {
@@ -34,71 +35,6 @@ void ReadCluster::read(NameAssignment* nameMap){
 }
 /***********************************************************************/
 
-void ReadCluster::createHClusterFile(){
-       try {   
-               string outfile = getRootName(distFile) + "sorted.dist";
-               
-               //if you can, use the unix sort since its been optimized for years
-               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-                       string command = "sort -n -k +3 " + distFile + " -o " + outfile;
-                       system(command.c_str());
-               #else //you are stuck with my best attempt...
-                       //windows sort does not have a way to specify a column, only a character in the line
-                       //since we cannot assume that the distance will always be at the the same character location on each line
-                       //due to variable sequence name lengths, I chose to force the distance into first position, then sort and then put it back.
-               
-                       //read in file line by file and put distance first
-                       string tempDistFile = distFile + ".temp";
-                       ifstream input;
-                       ofstream output;
-                       openInputFile(distFile, input);
-                       openOutputFile(tempDistFile, output);
-
-                       string firstName, secondName;
-                       float dist;
-                       while (input) {
-                               input >> firstName >> secondName >> dist;
-                               output << dist << '\t' << firstName << '\t' << secondName << endl;
-                               gobble(input);
-                       }
-                       input.close();
-                       output.close();
-               
-       
-                       //sort using windows sort
-                       string tempOutfile = outfile + ".temp";
-                       string command = "sort " + tempDistFile + " /O " + tempOutfile;
-                       system(command.c_str());
-               
-                       //read in sorted file and put distance at end again
-                       ifstream input2;
-                       openInputFile(tempOutfile, input2);
-                       openOutputFile(outfile, output);
-               
-                       while (input2) {
-                               input2 >> dist >> firstName >> secondName;
-                               output << firstName << '\t' << secondName << '\t' << dist << endl;
-                               gobble(input2);
-                       }
-                       input2.close();
-                       output.close();
-               
-                       //remove temp files
-                       remove(tempDistFile.c_str());
-                       remove(tempOutfile.c_str());
-               #endif
-               
-               OutPutFile = outfile;
-       }
-       catch(exception& e) {
-               errorOut(e, "ReadCluster", "createHClusterFile");
-               exit(1);
-       }
-}
-
-
-/***********************************************************************/
-
 void ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
        try {   
                //convert phylip file to column file
@@ -185,24 +121,22 @@ void ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
                        }
                }
                else{
-                       
                        for(int i=1;i<nseqs;i++){
                                in >> name;                
                                rowToName[i] = name;
                                matrixNames.push_back(name);
-                               
+               
                                if(nameMap == NULL){
                                        list->set(i, name);
                                        for(int j=0;j<nseqs;j++){
                                                in >> distance;
-                                               
+                                       
                                                if (distance == -1) { distance = 1000000; }
                                                
                                                if(distance < cutoff && j < i){
                                                        out << i << '\t' << j << '\t' << distance << endl;
                                                }
                                        }
-                                       
                                }
                                else{
                                        if(nameMap->count(name)==0){        mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); mothurOutEndLine(); }
@@ -226,11 +160,14 @@ void ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
                out.close();
                
                if(nameMap == NULL){
+                       nameMap = new NameAssignment();
                        for(int i=0;i<matrixNames.size();i++){
                                nameMap->push_back(matrixNames[i]);
                        }
+                       globaldata->nameMap = nameMap;
                }
                
+       
                ifstream in2;
                ofstream out2;