paralellized parsimony, unifrac.unweighted, phylo.diversity, indicator commands for...

[mothur.git] / splitmatrix.cpp

diff --git a/splitmatrix.cpp b/splitmatrix.cpp
index aea99ef2cccc3dbc070b251d4691209efacd2cbc..2e8b9055eb117f02596864cd35289d92ea3a4a87 100644 (file)
--- a/splitmatrix.cpp
+++ b/splitmatrix.cpp
@@ -191,8 +191,12 @@ int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numG
             else { options = "fasta=" + (fastafile + "." + toString(i) + ".temp") + ", processors=" + toString(processors) + ", cutoff=" + toString(distCutoff); }
                        if (outputDir != "") { options += ", outputdir=" + outputDir; }
                        
+            m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
+            
                        Command* command = new DistanceCommand(options);
                        
+            m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
+            
                        command->execute();
                        delete command;
                        
@@ -328,7 +332,7 @@ int SplitMatrix::splitDistanceLarge(){
                
                int numGroups = 0;
 
-               ofstream outFile;
+               //ofstream outFile;
                ifstream dFile;
                m->openInputFile(distFile, dFile);
        
@@ -404,6 +408,7 @@ int SplitMatrix::splitDistanceLarge(){
                                                                                        
                                        //have we reached the max buffer size
                                        if (numOutputs[groupID] > 60) { //write out sequence
+                        ofstream outFile;
                                                outFile.open(fileName.c_str(), ios::app);
                                                outFile << outputs[groupID] << seqA << '\t' << seqB << '\t' << dist << endl;
                                                outFile.close();
@@ -430,7 +435,7 @@ int SplitMatrix::splitDistanceLarge(){
                                                        //if groupB is written to file it is above buffer size so read and write to new merged file
                                                        if (wroteOutPut[groupIDB]) {
                                                                string fileName2 = distFile + "." + toString(groupIDB) + ".temp";
-                                                               ifstream fileB(fileName2.c_str(), ios::ate);
+                                                               /*ifstream fileB(fileName2.c_str(), ios::ate);
                                                                
                                                                outFile.open(fileName.c_str(), ios::app);
                                                                
@@ -465,17 +470,22 @@ int SplitMatrix::splitDistanceLarge(){
                                                                outFile << temp.substr(0, lastRead);
                                                                delete memblock;
                                                                
-                                                               fileB.close();
+                                                               fileB.close();*/
+                                m->appendFiles(fileName2, fileName);
                                                                m->mothurRemove(fileName2);
+                        
                                                                
                                                                //write out the merged memory
                                                                if (numOutputs[groupID] > 60) {
-                                                                       outFile << outputs[groupID];
+                                    ofstream tempOut;
+                                    m->openOutputFile(fileName, tempOut);
+                                                                       tempOut << outputs[groupID];
                                                                        outputs[groupID] = "";
                                                                        numOutputs[groupID] = 0;
+                                    tempOut.close();
                                                                }
                                                                
-                                                               outFile.close();
+                                                               //outFile.close();
                                                                
                                                                wroteOutPut[groupID] = true;
                                                                wroteOutPut[groupIDB] = false;
@@ -490,7 +500,7 @@ int SplitMatrix::splitDistanceLarge(){
                                                        
                                                        if (wroteOutPut[groupIDA]) {
                                                                string fileName2 = distFile + "." + toString(groupIDA) + ".temp";
-                                                               ifstream fileB(fileName2.c_str(), ios::ate);
+                                                               /*ifstream fileB(fileName2.c_str(), ios::ate);
                                                                
                                                                outFile.open(fileName.c_str(), ios::app);
                                                                
@@ -525,17 +535,21 @@ int SplitMatrix::splitDistanceLarge(){
                                                                        
                                                                delete memblock;
                                                                
-                                                               fileB.close();
+                                                               fileB.close();*/
+                                m->appendFiles(fileName2, fileName);
                                                                m->mothurRemove(fileName2);
                                                                
                                                                //write out the merged memory
                                                                if (numOutputs[groupID] > 60) {
-                                                                       outFile << outputs[groupID];
+                                    ofstream tempOut;
+                                    m->openOutputFile(fileName, tempOut);
+                                                                       tempOut << outputs[groupID];
                                                                        outputs[groupID] = "";
                                                                        numOutputs[groupID] = 0;
+                                    tempOut.close();
                                                                }
                                                                
-                                                               outFile.close();
+                                                               //outFile.close();
                                                                
                                                                wroteOutPut[groupID] = true;
                                                                wroteOutPut[groupIDA] = false;
@@ -555,6 +569,7 @@ int SplitMatrix::splitDistanceLarge(){
             //remove old names files just in case
                        
                        if (numOutputs[i] > 0) {
+                ofstream outFile;
                                outFile.open(fileName.c_str(), ios::app);
                                outFile << outputs[i];
                                outFile.close();