created mothurOut class to handle logfiles

[mothur.git] / clustercommand.cpp

diff --git a/clustercommand.cpp b/clustercommand.cpp
index e4e2d2104e3af44829990b01cef6782147359b98..5d9c7bccfbb250267553997fa3d6b16d7aa560b7 100644 (file)
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -11,9 +11,10 @@
 
 //**********************************************************************************************************************
 //This function checks to make sure the cluster command has no errors and then clusters based on the method chosen.
-ClusterCommand::ClusterCommand(string option){
+ClusterCommand::ClusterCommand(string option)  {
        try{
                globaldata = GlobalData::getInstance();
+               
                abort = false;
                
                //allow user to run help
@@ -41,7 +42,7 @@ ClusterCommand::ClusterCommand(string option){
                        
                        //error checking to make sure they read a distance file
                        if ((globaldata->gSparseMatrix == NULL) || (globaldata->gListVector == NULL)) {
-                               mothurOut("Before you use the cluster command, you first need to read in a distance matrix."); mothurOutEndLine();
+                               m->mothurOut("Before you use the cluster command, you first need to read in a distance matrix."); m->mothurOutEndLine();
                                abort = true;
                        } 
                
@@ -64,7 +65,7 @@ ClusterCommand::ClusterCommand(string option){
                        if (method == "not found") { method = "furthest"; }
                        
                        if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
-                       else { mothurOut("Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average."); mothurOutEndLine(); abort = true; }
+                       else { m->mothurOut("Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average."); m->mothurOutEndLine(); abort = true; }
 
                        showabund = validParameter.validFile(parameters, "showabund", false);
                        if (showabund == "not found") { showabund = "T"; }
@@ -95,11 +96,15 @@ ClusterCommand::ClusterCommand(string option){
                                openOutputFile(fileroot+ tag + ".sabund",       sabundFile);
                                openOutputFile(fileroot+ tag + ".rabund",       rabundFile);
                                openOutputFile(fileroot+ tag + ".list",         listFile);
+                               
+                               outputNames.push_back(fileroot+ tag + ".sabund");
+                               outputNames.push_back(fileroot+ tag + ".rabund");
+                               outputNames.push_back(fileroot+ tag + ".list");
                        }
                }
        }
        catch(exception& e) {
-               errorOut(e, "ClusterCommand", "ClusterCommand");
+               m->errorOut(e, "ClusterCommand", "ClusterCommand");
                exit(1);
        }
 }
@@ -108,14 +113,14 @@ ClusterCommand::ClusterCommand(string option){
 
 void ClusterCommand::help(){
        try {
-               mothurOut("The cluster command can only be executed after a successful read.dist command.\n");
-               mothurOut("The cluster command parameter options are method, cuttoff, precision, showabund and timing. No parameters are required.\n");
-               mothurOut("The cluster command should be in the following format: \n");
-               mothurOut("cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
-               mothurOut("The acceptable cluster methods are furthest, nearest and average.  If no method is provided then furthest is assumed.\n\n"); 
+               m->mothurOut("The cluster command can only be executed after a successful read.dist command.\n");
+               m->mothurOut("The cluster command parameter options are method, cuttoff, precision, showabund and timing. No parameters are required.\n");
+               m->mothurOut("The cluster command should be in the following format: \n");
+               m->mothurOut("cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
+               m->mothurOut("The acceptable cluster methods are furthest, nearest and average.  If no method is provided then furthest is assumed.\n\n");      
        }
        catch(exception& e) {
-               errorOut(e, "ClusterCommand", "help");
+               m->errorOut(e, "ClusterCommand", "help");
                exit(1);
        }
 }
@@ -150,7 +155,7 @@ int ClusterCommand::execute(){
                
                while (matrix->getSmallDist() < cutoff && matrix->getNNodes() > 0){
                        if (print_start && isTrue(timing)) {
-                               mothurOut("Clustering (" + tag + ") dist " + toString(matrix->getSmallDist()) + "/" 
+                               m->mothurOut("Clustering (" + tag + ") dist " + toString(matrix->getSmallDist()) + "/" 
                                        + toString(roundDist(matrix->getSmallDist(), precision)) 
                                        + "\t(precision: " + toString(precision) + ", Nodes: " + toString(matrix->getNNodes()) + ")");
                                cout.flush();
@@ -177,7 +182,7 @@ int ClusterCommand::execute(){
                }
 
                if (print_start && isTrue(timing)) {
-                       mothurOut("Clustering (" + tag + ") for distance " + toString(previousDist) + "/" + toString(rndPreviousDist) 
+                       m->mothurOut("Clustering (" + tag + ") for distance " + toString(previousDist) + "/" + toString(rndPreviousDist) 
                                         + "\t(precision: " + toString(precision) + ", Nodes: " + toString(matrix->getNNodes()) + ")");
                        cout.flush();
                        print_start = false;
@@ -206,17 +211,23 @@ int ClusterCommand::execute(){
                rabundFile.close();
                listFile.close();
                
-               if (saveCutoff != cutoff) { mothurOut("changed cutoff to " + toString(cutoff)); mothurOutEndLine();  }
+               if (saveCutoff != cutoff) { m->mothurOut("changed cutoff to " + toString(cutoff)); m->mothurOutEndLine();  }
+               
+               m->mothurOutEndLine();
+               m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+               for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
+               m->mothurOutEndLine();
+
                
                //if (isTrue(timing)) {
-                       mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster"); mothurOutEndLine();
+                       m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster"); m->mothurOutEndLine();
                //}
                
                
                return 0;
        }
        catch(exception& e) {
-               errorOut(e, "ClusterCommand", "execute");
+               m->errorOut(e, "ClusterCommand", "execute");
                exit(1);
        }
 }
@@ -226,8 +237,8 @@ int ClusterCommand::execute(){
 void ClusterCommand::printData(string label){
        try {
                if (isTrue(timing)) {
-                       mothurOut("\tTime: " + toString(time(NULL) - start) + "\tsecs for " + toString(oldRAbund.getNumBins()) 
-                    + "\tclusters. Updates: " + toString(loops)); mothurOutEndLine();
+                       m->mothurOut("\tTime: " + toString(time(NULL) - start) + "\tsecs for " + toString(oldRAbund.getNumBins()) 
+                    + "\tclusters. Updates: " + toString(loops)); m->mothurOutEndLine();
                }
                print_start = true;
                loops = 0;
@@ -244,7 +255,7 @@ void ClusterCommand::printData(string label){
                oldList.print(listFile);
        }
        catch(exception& e) {
-               errorOut(e, "ClusterCommand", "printData");
+               m->errorOut(e, "ClusterCommand", "printData");
                exit(1);
        }