moved utilities out of mothur.h and into mothurOut class.

[mothur.git] / splitmatrix.cpp

diff --git a/splitmatrix.cpp b/splitmatrix.cpp
index 6e40e97a10b0fd2af75b09c97ae43a26095016b8..a4e1f98581b9ce947dd53ad016dc347c71c99ffe 100644 (file)
--- a/splitmatrix.cpp
+++ b/splitmatrix.cpp
@@ -87,12 +87,12 @@ int SplitMatrix::splitClassify(){
                PhyloTree* phylo = new PhyloTree();
                
                ifstream in;
-               openInputFile(taxFile, in);
+               m->openInputFile(taxFile, in);
                        
                //read in users taxonomy file and add sequences to tree
                string seqname, tax;
                while(!in.eof()){
-                       in >> seqname >> tax; gobble(in);
+                       in >> seqname >> tax; m->gobble(in);
                        phylo->addSeqToTree(seqname, tax);
                }
                in.close();
@@ -146,12 +146,12 @@ int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numG
                }
                        
                ifstream in;
-               openInputFile(fastafile, in);
+               m->openInputFile(fastafile, in);
        
                //parse fastafile
                ofstream outFile;
                while (!in.eof()) {
-                       Sequence query(in); gobble(in);
+                       Sequence query(in); m->gobble(in);
                        if (query.getName() != "") {
                
                                it = seqGroup.find(query.getName());
@@ -160,7 +160,7 @@ int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numG
                                if (namefile == "") {  names.insert(query.getName()); }
                        
                                if (it != seqGroup.end()) { //not singleton 
-                                       openOutputFileAppend((fastafile + "." + toString(it->second) + ".temp"), outFile);
+                                       m->openOutputFileAppend((fastafile + "." + toString(it->second) + ".temp"), outFile);
                                        query.printSequence(outFile); 
                                        outFile.close();
                                        
@@ -195,22 +195,22 @@ int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numG
                
                singleton = namefile + ".extra.temp";
                ofstream remainingNames;
-               openOutputFile(singleton, remainingNames);
+               m->openOutputFile(singleton, remainingNames);
                
                bool wroteExtra = false;
 
                ifstream bigNameFile;
-               openInputFile(namefile, bigNameFile);
+               m->openInputFile(namefile, bigNameFile);
                
                string name, nameList;
                while(!bigNameFile.eof()){
-                       bigNameFile >> name >> nameList;  gobble(bigNameFile);
+                       bigNameFile >> name >> nameList;  m->gobble(bigNameFile);
                        
                        //did this sequence get assigned a group
                        it = seqGroup.find(name);
                        
                        if (it != seqGroup.end()) {  
-                               openOutputFileAppend((namefile + "." + toString(it->second) + ".temp"), outFile);
+                               m->openOutputFileAppend((namefile + "." + toString(it->second) + ".temp"), outFile);
                                outFile << name << '\t' << nameList << endl;
                                outFile.close();
                        }else{
@@ -222,23 +222,23 @@ int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numG
                
                for(int i=0;i<numGroups;i++){
                        string tempNameFile = namefile + "." + toString(i) + ".temp";
-                       string tempDistFile = outputDir + getRootName(getSimpleName((fastafile + "." + toString(i) + ".temp"))) + "dist";
+                       string tempDistFile = outputDir + m->getRootName(m->getSimpleName((fastafile + "." + toString(i) + ".temp"))) + "dist";
 
                        //if there are valid distances
                        ifstream fileHandle;
                        fileHandle.open(tempDistFile.c_str());
                        if(fileHandle)  {       
-                               gobble(fileHandle);
+                               m->gobble(fileHandle);
                                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);
+                                       m->openInputFile(tempNameFile, in);
                                
                                        while(!in.eof()) { 
-                                               in >> name >> nameList;  gobble(in);
+                                               in >> name >> nameList;  m->gobble(in);
                                                wroteExtra = true;
                                                remainingNames << name << '\t' << nameList << endl;
                                        }
@@ -271,7 +271,7 @@ int SplitMatrix::splitDistanceFileByTax(map<string, int>& seqGroup, int numGroup
                map<string, int>::iterator it2;
                
                ifstream dFile;
-               openInputFile(distFile, dFile);
+               m->openInputFile(distFile, dFile);
                ofstream outFile;
                
                for (int i = 0; i < numGroups; i++) { //remove old temp files, just in case
@@ -294,7 +294,7 @@ int SplitMatrix::splitDistanceFileByTax(map<string, int>& seqGroup, int numGroup
                        
                        if (m->control_pressed) { dFile.close(); for (int i = 0; i < numGroups; i++) { remove((distFile + "." + toString(i) + ".temp").c_str());        } }
                        
-                       dFile >> seqA >> seqB >> dist;  gobble(dFile);
+                       dFile >> seqA >> seqB >> dist;  m->gobble(dFile);
                        
                        //if both sequences are in the same group then they are within the cutoff
                        it = seqGroup.find(seqA);
@@ -303,7 +303,7 @@ int SplitMatrix::splitDistanceFileByTax(map<string, int>& seqGroup, int numGroup
                        if ((it != seqGroup.end()) && (it2 != seqGroup.end())) { //they are both not singletons 
                                if (it->second == it2->second) { //they are from the same group so add the distance
                                        if (numOutputs[it->second] > 30) {
-                                               openOutputFileAppend((distFile + "." + toString(it->second) + ".temp"), outFile);
+                                               m->openOutputFileAppend((distFile + "." + toString(it->second) + ".temp"), outFile);
                                                outFile << outputs[it->second] << seqA << '\t' << seqB << '\t' << dist << endl;
                                                outFile.close();
                                                outputs[it->second] = "";
@@ -323,7 +323,7 @@ int SplitMatrix::splitDistanceFileByTax(map<string, int>& seqGroup, int numGroup
                        
                        //write out any remaining buffers
                        if (numOutputs[i] > 0) {
-                               openOutputFileAppend((distFile + "." + toString(i) + ".temp"), outFile);
+                               m->openOutputFileAppend((distFile + "." + toString(i) + ".temp"), outFile);
                                outFile << outputs[i];
                                outFile.close();
                                outputs[i] = "";
@@ -333,23 +333,23 @@ int SplitMatrix::splitDistanceFileByTax(map<string, int>& seqGroup, int numGroup
                }
                
                ifstream bigNameFile;
-               openInputFile(namefile, bigNameFile);
+               m->openInputFile(namefile, bigNameFile);
                
                singleton = namefile + ".extra.temp";
                ofstream remainingNames;
-               openOutputFile(singleton, remainingNames);
+               m->openOutputFile(singleton, remainingNames);
                
                bool wroteExtra = false;
                                                
                string name, nameList;
                while(!bigNameFile.eof()){
-                       bigNameFile >> name >> nameList;  gobble(bigNameFile);
+                       bigNameFile >> name >> nameList;  m->gobble(bigNameFile);
                        
                        //did this sequence get assigned a group
                        it = seqGroup.find(name);
                        
                        if (it != seqGroup.end()) {  
-                               openOutputFileAppend((namefile + "." + toString(it->second) + ".temp"), outFile);
+                               m->openOutputFileAppend((namefile + "." + toString(it->second) + ".temp"), outFile);
                                outFile << name << '\t' << nameList << endl;
                                outFile.close();
                        }else{
@@ -370,10 +370,10 @@ int SplitMatrix::splitDistanceFileByTax(map<string, int>& seqGroup, int numGroup
                                dists.push_back(temp);
                        }else{
                                ifstream in;
-                               openInputFile(tempNameFile, in);
+                               m->openInputFile(tempNameFile, in);
                                
                                while(!in.eof()) { 
-                                       in >> name >> nameList;  gobble(in);
+                                       in >> name >> nameList;  m->gobble(in);
                                        wroteExtra = true;
                                        remainingNames << name << '\t' << nameList << endl;
                                }
@@ -419,7 +419,7 @@ int SplitMatrix::splitDistanceLarge(){
 
                ofstream outFile;
                ifstream dFile;
-               openInputFile(distFile, dFile);
+               m->openInputFile(distFile, dFile);
        
                while(dFile){
                        string seqA, seqB;
@@ -633,7 +633,7 @@ int SplitMatrix::splitDistanceLarge(){
                                        }
                                }
                        }
-                       gobble(dFile);
+                       m->gobble(dFile);
                }
                dFile.close();
                
@@ -671,7 +671,7 @@ int SplitMatrix::splitNames(vector<set<string> >& groups){
                while(bigNameFile){
                        bigNameFile >> name >> nameList;
                        nameMap[name] = nameList;
-                       gobble(bigNameFile);
+                       m->gobble(bigNameFile);
                }
                bigNameFile.close();
                        
@@ -740,7 +740,7 @@ int SplitMatrix::splitDistanceRAM(){
                int numGroups = 0;
 
                ifstream dFile;
-               openInputFile(distFile, dFile);
+               m->openInputFile(distFile, dFile);
 
                while(dFile){
                        string seqA, seqB;
@@ -823,7 +823,7 @@ int SplitMatrix::splitDistanceRAM(){
                                        }
                                }
                        }
-                       gobble(dFile);
+                       m->gobble(dFile);
                }
                dFile.close();