fixed project

[mothur.git] / clustersplitcommand.cpp

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 9545083f555383d5b48fa4f8e167a93ccd242558..e9ab530936af07faf4375b263d82d79e6d30846a 100644 (file)
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -27,7 +27,7 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"phylip","column","name","cutoff","precision","method","showabund","timing","hard","processors","splitcutoff","outputdir","inputdir"};
+                       string Array[] =  {"phylip","column","name","cutoff","precision","method","showabund","timing","hard","processors","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -93,8 +93,8 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
                        if (namefile == "not open") { abort = true; }   
                        else if (namefile == "not found") { namefile = ""; }
                        
-                       if ((phylipfile == "") && (columnfile == "")) { m->mothurOut("When executing a hcluster command you must enter a phylip or a column."); m->mothurOutEndLine(); abort = true; }
-                       else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When executing a hcluster command you must enter ONLY ONE of the following: phylip or column."); m->mothurOutEndLine(); abort = true; }
+                       if ((phylipfile == "") && (columnfile == "")) { m->mothurOut("When executing a cluster.split command you must enter a phylip or a column."); m->mothurOutEndLine(); abort = true; }
+                       else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When executing a cluster.split command you must enter ONLY ONE of the following: phylip or column."); m->mothurOutEndLine(); abort = true; }
                
                        if (columnfile != "") {
                                if (namefile == "") {  cout << "You need to provide a namefile if you are going to use the column format." << endl; abort = true; }
@@ -121,11 +121,6 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
                        convert(temp, cutoff); 
                        if (!hard) {    cutoff += (5 / (precision * 10.0));  }
                        
-                       temp = validParameter.validFile(parameters, "splitcutoff", false);
-                       if (temp == "not found") { temp = "0.10"; }
-                       convert(temp, splitcutoff); 
-                       if (!hard) {    splitcutoff += (5 / (precision * 10.0));  }
-                       
                        method = validParameter.validFile(parameters, "method", false);
                        if (method == "not found") { method = "furthest"; }
                        
@@ -208,7 +203,7 @@ int ClusterSplitCommand::execute(){
                time_t estart = time(NULL);
                
                //split matrix into non-overlapping groups
-               SplitMatrix* split = new SplitMatrix(distfile, namefile, splitcutoff);
+               SplitMatrix* split = new SplitMatrix(distfile, namefile, cutoff);
                split->split();
                
                if (m->control_pressed) { delete split; return 0; }
@@ -242,6 +237,12 @@ int ClusterSplitCommand::execute(){
                                                dividedNames[(processToAssign-1)].push_back(distName[i]);
                                        }
                                        
+                                       //not lets reverse the order of ever other process, so we balance big files running with little ones
+                                       for (int i = 0; i < processors; i++) {
+                                               int remainder = ((i+1) % processors);
+                                               if (remainder) {  reverse(dividedNames[i].begin(), dividedNames[i].end());  }
+                                       }
+                                       
                                        createProcesses(dividedNames);
                                                        
                                        if (m->control_pressed) { return 0; }