fixed project

[mothur.git] / phylodiversitycommand.cpp

diff --git a/phylodiversitycommand.cpp b/phylodiversitycommand.cpp
index 978b18874923c2273d71b02ca2fcda3aba2e7151..0c2f72d0ad6fd57f628ec01d16ba6c8c31a00d8c 100644 (file)
--- a/phylodiversitycommand.cpp
+++ b/phylodiversitycommand.cpp
@@ -69,7 +69,16 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
 
 void PhyloDiversityCommand::help(){
        try {
-
+               m->mothurOut("The phylo.diversity command can only be executed after a successful read.tree command.\n");
+               m->mothurOut("The phylo.diversity command parameters are groups, iters, freq and rarefy.  No parameters are required.\n");
+               m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. The group names are separated by dashes. By default all groups are used.\n");
+               m->mothurOut("The iters parameter allows you to specify the number of randomizations to preform, by default iters=1000, if you set rarefy to true.\n");
+               m->mothurOut("The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n");
+               m->mothurOut("The rarefy parameter allows you to create a rarefaction curve. The default is false.\n");
+               m->mothurOut("The phylo.diversity command should be in the following format: phylo.diversity(groups=yourGroups, rarefy=yourRarefy, iters=yourIters).\n");
+               m->mothurOut("Example phylo.diversity(groups=A-B-C, rarefy=T, iters=500).\n");
+               m->mothurOut("The phylo.diversity command output two files: .phylo.diversity and if rarefy=T, .rarefaction.\n");
+               m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 
        }
        catch(exception& e) {
@@ -104,7 +113,7 @@ int PhyloDiversityCommand::execute(){
                
                        if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());         } return 0; }
                        
-                       phylo.setTotalGroupBranchLengths(trees[i]);
+                       //phylo.setTotalGroupBranchLengths(trees[i]);
                        
                        string outFile = outputDir + getRootName(getSimpleName(globaldata->getTreeFile()))  + toString(i+1) + ".phylo.diversity";
                        if (rarefy) { outFile += ".rarefaction"; }
@@ -122,14 +131,19 @@ int PhyloDiversityCommand::execute(){
                        
                        numLeafNodes = randomLeaf.size();  //reset the number of leaf nodes you are using 
                        
+                       //convert freq percentage to number
+                       int increment = 100;
+                       if (freq < 1.0) {  increment = numLeafNodes * freq;  }
+                       else { increment = freq;  }
+                       
                        //each group, each sampling, if no rarefy iters = 1;
                        vector< vector<float> > diversity;
                        diversity.resize(globaldata->Groups.size());
                        
                        //initialize sampling spots
                        vector<int> numSampledList;
-                       for(int k = 0; k < numLeafNodes; k++){  if((k == 0) || (k+1) % freq == 0){  numSampledList.push_back(k); }   }
-                       if(numLeafNodes % freq != 0){   numSampledList.push_back(numLeafNodes);   }
+                       for(int k = 0; k < numLeafNodes; k++){  if((k == 0) || (k+1) % increment == 0){  numSampledList.push_back(k); }   }
+                       if(numLeafNodes % increment != 0){      numSampledList.push_back(numLeafNodes);   }
                        
                        //initialize diversity
                        for (int j = 0; j < diversity.size(); j++) {   diversity[j].resize(numSampledList.size(), 0.0);  }  //                  10sampled       20 sampled ...
@@ -147,7 +161,7 @@ int PhyloDiversityCommand::execute(){
                                        
                                        leavesSampled.push_back(randomLeaf[k]);
                                                
-                                       if((k == 0) || (k+1) % freq == 0){ //ready to calc?
+                                       if((k == 0) || (k+1) % increment == 0){ //ready to calc?
                                                
                                                data = phylo.getValues(trees[i], leavesSampled);
                                                
@@ -158,7 +172,7 @@ int PhyloDiversityCommand::execute(){
                                        }
                                }
                
-                               if(numLeafNodes % freq != 0){   
+                               if(numLeafNodes % increment != 0){      
                                        
                                        data = phylo.getValues(trees[i], leavesSampled);