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

[mothur.git] / mgclustercommand.cpp

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index 9a1ac215388e09e6477fffa034e0542c38c208b1..eef54ef23b290a930d5560e8dbf444a20da46073 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -42,7 +42,7 @@ MGClusterCommand::MGClusterCommand(string option) {
                                it = parameters.find("blast");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["blast"] = inputDir + it->second;            }
                                }
@@ -50,7 +50,7 @@ MGClusterCommand::MGClusterCommand(string option) {
                                it = parameters.find("name");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["name"] = inputDir + it->second;             }
                                }
@@ -65,7 +65,7 @@ MGClusterCommand::MGClusterCommand(string option) {
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
                                outputDir = ""; 
-                               outputDir += hasPath(blastfile); //if user entered a file with a path then preserve it  
+                               outputDir += m->hasPath(blastfile); //if user entered a file with a path then preserve it       
                        }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
@@ -97,16 +97,16 @@ MGClusterCommand::MGClusterCommand(string option) {
                        convert(temp, penalty); 
                        
                        temp = validParameter.validFile(parameters, "min", false);                              if (temp == "not found") { temp = "true"; }
-                       minWanted = isTrue(temp); 
+                       minWanted = m->isTrue(temp); 
                        
                        temp = validParameter.validFile(parameters, "merge", false);                    if (temp == "not found") { temp = "true"; }
-                       merge = isTrue(temp); 
+                       merge = m->isTrue(temp); 
                        
                        temp = validParameter.validFile(parameters, "hcluster", false);                 if (temp == "not found") { temp = "false"; }
-                       hclusterWanted = isTrue(temp); 
+                       hclusterWanted = m->isTrue(temp); 
                        
                        temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "F"; }
-                       hard = isTrue(temp);
+                       hard = m->isTrue(temp);
                }
 
        }
@@ -153,7 +153,7 @@ int MGClusterCommand::execute(){
                        nameMap->readMap();
                }else{ nameMap= new NameAssignment(); }
                
-               string fileroot = outputDir + getRootName(getSimpleName(blastfile));
+               string fileroot = outputDir + m->getRootName(m->getSimpleName(blastfile));
                string tag = "";
                time_t start;
                float previousDist = 0.00000;
@@ -179,9 +179,9 @@ int MGClusterCommand::execute(){
                else                                                    { tag = "an";  }
                
                //open output files
-               openOutputFile(fileroot+ tag + ".list",  listFile);
-               openOutputFile(fileroot+ tag + ".rabund",  rabundFile);
-               openOutputFile(fileroot+ tag + ".sabund",  sabundFile);
+               m->openOutputFile(fileroot+ tag + ".list",  listFile);
+               m->openOutputFile(fileroot+ tag + ".rabund",  rabundFile);
+               m->openOutputFile(fileroot+ tag + ".sabund",  sabundFile);
                
                if (m->control_pressed) { 
                        delete nameMap; delete read; delete list; delete rabund; 
@@ -223,9 +223,9 @@ int MGClusterCommand::execute(){
                                float dist = distMatrix->getSmallDist();
                                float rndDist;
                                if (hard) {
-                                       rndDist = ceilDist(dist, precision); 
+                                       rndDist = m->ceilDist(dist, precision); 
                                }else{
-                                       rndDist = roundDist(dist, precision); 
+                                       rndDist = m->roundDist(dist, precision); 
                                }
                                
                                if(previousDist <= 0.0000 && dist != previousDist){
@@ -309,7 +309,7 @@ int MGClusterCommand::execute(){
                        
                        vector<seqDist> seqs; seqs.resize(1); // to start loop
                        //ifstream inHcluster;
-                       //openInputFile(distFile, inHcluster);
+                       //m->openInputFile(distFile, inHcluster);
                        
                        if (m->control_pressed) { 
                                delete nameMap;  delete list; delete rabund; delete hcluster;
@@ -345,9 +345,9 @@ int MGClusterCommand::execute(){
        
                                                float rndDist;
                                                if (hard) {
-                                                       rndDist = ceilDist(seqs[i].dist, precision); 
+                                                       rndDist = m->ceilDist(seqs[i].dist, precision); 
                                                }else{
-                                                       rndDist = roundDist(seqs[i].dist, precision); 
+                                                       rndDist = m->roundDist(seqs[i].dist, precision); 
                                                }
                                                                                                
                                                if((previousDist <= 0.0000) && (seqs[i].dist != previousDist)){
@@ -477,7 +477,7 @@ ListVector* MGClusterCommand::mergeOPFs(map<string, int> binInfo, float dist){
                int count = 0;
                
                if (hclusterWanted) {  
-                       openInputFile(overlapFile, inOverlap);  
+                       m->openInputFile(overlapFile, inOverlap);  
                        if (inOverlap.eof()) {  done = true;  }
                }else { if (overlapMatrix.size() == 0)  {  done = true;  } } 
                
@@ -498,7 +498,7 @@ ListVector* MGClusterCommand::mergeOPFs(map<string, int> binInfo, float dist){
                                if (!inOverlap.eof()) {
                                        string firstName, secondName;
                                        float overlapDistance;
-                                       inOverlap >> firstName >> secondName >> overlapDistance; gobble(inOverlap);
+                                       inOverlap >> firstName >> secondName >> overlapDistance; m->gobble(inOverlap);
                                        
                                        //commented out because we check this in readblast already
                                        //map<string,int>::iterator itA = nameMap->find(firstName);
@@ -571,12 +571,12 @@ ListVector* MGClusterCommand::mergeOPFs(map<string, int> binInfo, float dist){
 void MGClusterCommand::sortHclusterFiles(string unsortedDist, string unsortedOverlap) {
        try {
                //sort distFile
-               string sortedDistFile = sortFile(unsortedDist, outputDir);
+               string sortedDistFile = m->sortFile(unsortedDist, outputDir);
                remove(unsortedDist.c_str());  //delete unsorted file
                distFile = sortedDistFile;
                
                //sort overlap file
-               string sortedOverlapFile = sortFile(unsortedOverlap, outputDir);
+               string sortedOverlapFile = m->sortFile(unsortedOverlap, outputDir);
                remove(unsortedOverlap.c_str());  //delete unsorted file
                overlapFile = sortedOverlapFile;
        }