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

[mothur.git] / heatmapsimcommand.cpp

diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp
index dc67a8d4374ae90aebf182ce80d5474b17431f95..61e29390c21ae0a851a3acaede4c9da681d4d7d4 100644 (file)
--- a/heatmapsimcommand.cpp
+++ b/heatmapsimcommand.cpp
@@ -62,7 +62,7 @@ HeatMapSimCommand::HeatMapSimCommand(string option)  {
                                it = parameters.find("phylip");
                                //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["phylip"] = inputDir + it->second;           }
                                }
@@ -70,7 +70,7 @@ HeatMapSimCommand::HeatMapSimCommand(string option)  {
                                it = parameters.find("column");
                                //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["column"] = inputDir + it->second;           }
                                }
@@ -78,7 +78,7 @@ HeatMapSimCommand::HeatMapSimCommand(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;             }
                                }
@@ -88,12 +88,12 @@ HeatMapSimCommand::HeatMapSimCommand(string option)  {
                        phylipfile = validParameter.validFile(parameters, "phylip", true);
                        if (phylipfile == "not open") { abort = true; }
                        else if (phylipfile == "not found") { phylipfile = ""; }        
-                       else {  format = "phylip";      if (outputDir == "") { outputDir += hasPath(phylipfile); }  }
+                       else {  format = "phylip";      if (outputDir == "") { outputDir += m->hasPath(phylipfile); }  }
                        
                        columnfile = validParameter.validFile(parameters, "column", true);
                        if (columnfile == "not open") { abort = true; } 
                        else if (columnfile == "not found") { columnfile = ""; }
-                       else {  format = "column";      if (outputDir == "") { outputDir += hasPath(columnfile); } }
+                       else {  format = "column";      if (outputDir == "") { outputDir += m->hasPath(columnfile); } }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }   
@@ -113,12 +113,12 @@ HeatMapSimCommand::HeatMapSimCommand(string option)  {
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
                        if (format == "shared") {
-                               if (outputDir == "") { outputDir += hasPath(globaldata->getSharedFile()); }
+                               if (outputDir == "") { outputDir += m->hasPath(globaldata->getSharedFile()); }
                                
                                label = validParameter.validFile(parameters, "label", false);                   
                                if (label == "not found") { label = ""; }
                                else { 
-                                       if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
+                                       if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
                                        else { allLines = 1;  }
                                }
                                
@@ -133,12 +133,12 @@ HeatMapSimCommand::HeatMapSimCommand(string option)  {
                                else { 
                                        if (calc == "default")  {  calc = "jest-thetayc";  }
                                }
-                               splitAtDash(calc, Estimators);
+                               m->splitAtDash(calc, Estimators);
                                
                                groups = validParameter.validFile(parameters, "groups", false);                 
                                if (groups == "not found") { groups = ""; }
                                else { 
-                                       splitAtDash(groups, Groups);
+                                       m->splitAtDash(groups, Groups);
                                        globaldata->Groups = Groups;
                                }
                        }
@@ -292,7 +292,7 @@ int HeatMapSimCommand::runCommandShared() {
                                userLabels.erase(lookup[0]->getLabel());
                        }
                                
-                       if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                       if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
                                string saveLabel = lookup[0]->getLabel();
                        
                                for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
@@ -374,7 +374,7 @@ int HeatMapSimCommand::runCommandDist() {
                //read distance file and create distance vector and names vector
                if (format == "phylip") {
                        //read phylip file
-                       openInputFile(phylipfile, in);
+                       m->openInputFile(phylipfile, in);
                        
                        string name;
                        int numSeqs;
@@ -422,7 +422,7 @@ int HeatMapSimCommand::runCommandDist() {
                                        if (m->control_pressed) { return 0; }
                                        
                                        for(int j=0;j<numSeqs;j++) { in >> matrix[i][j];  }
-                                       gobble(in);
+                                       m->gobble(in);
                                }
                        }else { 
                                double dist;
@@ -436,7 +436,7 @@ int HeatMapSimCommand::runCommandDist() {
                                                in >> dist;
                                                matrix[i][j] = dist;  matrix[j][i] = dist;
                                        }
-                                       gobble(in);
+                                       m->gobble(in);
                                }
                        }
                        in.close();
@@ -459,10 +459,10 @@ int HeatMapSimCommand::runCommandDist() {
                        //read column file
                        string first, second;
                        double dist;
-                       openInputFile(columnfile, in);
+                       m->openInputFile(columnfile, in);
                        
                        while (!in.eof()) {
-                               in >> first >> second >> dist; gobble(in);
+                               in >> first >> second >> dist; m->gobble(in);
                                
                                if (m->control_pressed) { return 0; }