X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=splitmatrix.cpp;h=80f311dc61cbd8d52342ee55d39c2284b161761d;hb=fca3f55d5ded10c3dc77856f3cc4a1c53b02bb6f;hp=a4e1f98581b9ce947dd53ad016dc347c71c99ffe;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;p=mothur.git

diff --git a/splitmatrix.cpp b/splitmatrix.cpp
index a4e1f98..80f311d 100644
--- a/splitmatrix.cpp
+++ b/splitmatrix.cpp
@@ -10,6 +10,7 @@
 #include "splitmatrix.h"
 #include "phylotree.h"
 #include "distancecommand.h"
+#include "seqsummarycommand.h"
 
 /***********************************************************************/
 
@@ -24,12 +25,13 @@ 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, string output){
+SplitMatrix::SplitMatrix(string ffile, string name, string tax, float c, float cu, string t, int p, string output){
 	m = MothurOut::getInstance();
 	fastafile = ffile;
 	namefile = name;
 	taxFile = tax;
-	cutoff = c;
+	cutoff = c;  //tax level cutoff
+	distCutoff = cu; //for fasta method if you are creating distance matrix you need a cutoff for that
 	method = t;
 	processors = p;
 	outputDir = output;
@@ -64,6 +66,8 @@ int SplitMatrix::splitDistance(){
         
 		if (large)	{ splitDistanceLarge(); }
 		else		{ splitDistanceRAM();	}
+		
+		return 0;
 			
 	}
 	catch(exception& e) {
@@ -76,7 +80,7 @@ int SplitMatrix::splitDistance(){
 int SplitMatrix::splitClassify(){
 	try {
 		cutoff = int(cutoff);
-		
+				
 		map<string, int> seqGroup;
 		map<string, int>::iterator it;
 		map<string, int>::iterator it2;
@@ -181,9 +185,10 @@ 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(cutoff);
+			string options = "fasta=" + (fastafile + "." + toString(i) + ".temp") + ", processors=" + toString(processors) + ", cutoff=" + toString(distCutoff);
 			
 			Command* command = new DistanceCommand(options);
+			
 			command->execute();
 			delete command;
 			
@@ -192,7 +197,7 @@ int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numG
 			//remove old names files just in case
 			remove((namefile + "." + toString(i) + ".temp").c_str());
 		}
-		
+			
 		singleton = namefile + ".extra.temp";
 		ofstream remainingNames;
 		m->openOutputFile(singleton, remainingNames);
@@ -222,6 +227,7 @@ 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";
 
 			//if there are valid distances