added fasta method to cluster.split

[mothur.git] / splitmatrix.cpp

diff --git a/splitmatrix.cpp b/splitmatrix.cpp
index 9e53c51a8f1b6fbba8e755279e68993fb7f03fa5..6e40e97a10b0fd2af75b09c97ae43a26095016b8 100644 (file)
--- a/splitmatrix.cpp
+++ b/splitmatrix.cpp
@@ -24,7 +24,7 @@ SplitMatrix::SplitMatrix(string distfile, string name, string tax, float c, stri
 }
 /***********************************************************************/
 
-SplitMatrix::SplitMatrix(string ffile, string name, string tax, float c, string t, int p){
+SplitMatrix::SplitMatrix(string ffile, string name, string tax, float c, string t, int p, string output){
        m = MothurOut::getInstance();
        fastafile = ffile;
        namefile = name;
@@ -32,6 +32,7 @@ SplitMatrix::SplitMatrix(string ffile, string name, string tax, float c, string
        cutoff = c;
        method = t;
        processors = p;
+       outputDir = output;
 }
 
 /***********************************************************************/
@@ -163,7 +164,7 @@ int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numG
                                        query.printSequence(outFile); 
                                        outFile.close();
                                        
-                                       copyGroups.erase(it);
+                                       copyGroups.erase(query.getName());
                                }
                        }
                }
@@ -180,7 +181,7 @@ int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numG
                //process each distance file
                for (int i = 0; i < numGroups; i++) { 
                        
-                       string options = "fasta=" + (fastafile + "." + toString(i) + ".temp") + ", processors=" + toString(processors);
+                       string options = "fasta=" + (fastafile + "." + toString(i) + ".temp") + ", processors=" + toString(processors) + ", cutoff=" + toString(cutoff);
                        
                        Command* command = new DistanceCommand(options);
                        command->execute();
@@ -219,30 +220,41 @@ int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numG
                }
                bigNameFile.close();
                
-               remainingNames.close();
-               if (!wroteExtra) { 
-                       remove(singleton.c_str());
-                       singleton = "none";
-               }
-
                for(int i=0;i<numGroups;i++){
                        string tempNameFile = namefile + "." + toString(i) + ".temp";
-                       string tempDistFile = getRootName(getSimpleName((fastafile + "." + toString(i) + ".temp"))) + "dist";
+                       string tempDistFile = outputDir + getRootName(getSimpleName((fastafile + "." + toString(i) + ".temp"))) + "dist";
 
                        //if there are valid distances
                        ifstream fileHandle;
                        fileHandle.open(tempDistFile.c_str());
                        if(fileHandle)  {       
                                gobble(fileHandle);
-                               if (!fileHandle.eof()) {  //check for blank file
+                               if (!fileHandle.eof()) {  //check for blank file - this could occur if all dists in group are above cutoff
                                        map<string, string> temp;
                                        temp[tempDistFile] = tempNameFile;
                                        dists.push_back(temp);
+                               }else {
+                                       ifstream in;
+                                       openInputFile(tempNameFile, in);
+                               
+                                       while(!in.eof()) { 
+                                               in >> name >> nameList;  gobble(in);
+                                               wroteExtra = true;
+                                               remainingNames << name << '\t' << nameList << endl;
+                                       }
+                                       in.close();
+                                       remove(tempNameFile.c_str());
                                }
                        }
                        fileHandle.close();
                }
                
+               remainingNames.close();
+               if (!wroteExtra) { 
+                       remove(singleton.c_str());
+                       singleton = "none";
+               }
+
                if (m->control_pressed)  {  for (int i = 0; i < dists.size(); i++) { remove((dists[i].begin()->first).c_str()); remove((dists[i].begin()->second).c_str()); } dists.clear(); }
                
                return 0;