fixed subsample name file name issue. added count parameter to cluster command....

[mothur.git] / splitmatrix.cpp

diff --git a/splitmatrix.cpp b/splitmatrix.cpp
index dabcd0469461f25a79ac707cf0e785c19974cc1e..384b09af1bb94be09c5607c8b863b28b16215731 100644 (file)
--- a/splitmatrix.cpp
+++ b/splitmatrix.cpp
@@ -25,7 +25,7 @@ SplitMatrix::SplitMatrix(string distfile, string name, string tax, float c, stri
 }
 /***********************************************************************/
 
-SplitMatrix::SplitMatrix(string ffile, string name, string tax, float c, float cu, string t, int p, string output){
+SplitMatrix::SplitMatrix(string ffile, string name, string tax, float c, float cu, string t, int p, bool cl, string output){
        m = MothurOut::getInstance();
        fastafile = ffile;
        namefile = name;
@@ -34,6 +34,7 @@ SplitMatrix::SplitMatrix(string ffile, string name, string tax, float c, float c
        distCutoff = cu; //for fasta method if you are creating distance matrix you need a cutoff for that
        method = t;
        processors = p;
+    classic = cl;
        outputDir = output;
 }
 
@@ -90,16 +91,13 @@ int SplitMatrix::splitClassify(){
                //build tree from users taxonomy file
                PhyloTree* phylo = new PhyloTree();
                
-               ifstream in;
-               m->openInputFile(taxFile, in);
-                       
-               //read in users taxonomy file and add sequences to tree
-               string seqname, tax;
-               while(!in.eof()){
-                       in >> seqname >> tax; m->gobble(in);
-                       phylo->addSeqToTree(seqname, tax);
-               }
-               in.close();
+        map<string, string> temp;
+        m->readTax(taxFile, temp);
+        
+        for (map<string, string>::iterator itTemp = temp.begin(); itTemp != temp.end();) {
+            phylo->addSeqToTree(itTemp->first, itTemp->second);
+            temp.erase(itTemp++);
+        }
                
                phylo->assignHeirarchyIDs(0);
 
@@ -185,7 +183,9 @@ 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) + ", cutoff=" + toString(distCutoff);
+                       string options = "";
+            if (classic) { options = "fasta=" + (fastafile + "." + toString(i) + ".temp") + ", processors=" + toString(processors) + ", output=lt"; }
+            else { options = "fasta=" + (fastafile + "." + toString(i) + ".temp") + ", processors=" + toString(processors) + ", cutoff=" + toString(distCutoff); }
                        if (outputDir != "") { options += ", outputdir=" + outputDir; }
                        
                        Command* command = new DistanceCommand(options);
@@ -229,7 +229,9 @@ int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numG
                for(int i=0;i<numGroups;i++){
                        string tempNameFile = namefile + "." + toString(i) + ".temp";
                        if (outputDir == "") { outputDir = m->hasPath(fastafile); }
-                       string tempDistFile = outputDir + m->getRootName(m->getSimpleName((fastafile + "." + toString(i) + ".temp"))) + "dist";
+                       string tempDistFile = "";
+            if (classic) { tempDistFile =  outputDir + m->getRootName(m->getSimpleName((fastafile + "." + toString(i) + ".temp"))) + "phylip.dist";}
+            else { tempDistFile = outputDir + m->getRootName(m->getSimpleName((fastafile + "." + toString(i) + ".temp"))) + "dist"; }
 
                        //if there are valid distances
                        ifstream fileHandle;