added topdown parameter to pre.cluster. added more debugging output to bayesian...

[mothur.git] / preclustercommand.cpp

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index 0c7895cfd3c4b5c1988977f102d5523bfe20f9e0..19616d8b0e4ce5d46e6753bbc58b776d1b5dd656 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -19,6 +19,8 @@ vector<string> PreClusterCommand::setParameters(){
                CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
                CommandParameter pdiffs("diffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(pdiffs);
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+        CommandParameter ptopdown("topdown", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(ptopdown);
+
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
@@ -37,11 +39,12 @@ string PreClusterCommand::getHelpString(){
                string helpString = "";
                helpString += "The pre.cluster command groups sequences that are within a given number of base mismatches.\n";
                helpString += "The pre.cluster command outputs a new fasta and name file.\n";
-               helpString += "The pre.cluster command parameters are fasta, name, group, count, processors and diffs. The fasta parameter is required. \n";
+               helpString += "The pre.cluster command parameters are fasta, name, group, count, topdown, processors and diffs. The fasta parameter is required. \n";
                helpString += "The name parameter allows you to give a list of seqs that are identical. This file is 2 columns, first column is name or representative sequence, second column is a list of its identical sequences separated by commas.\n";
                helpString += "The group parameter allows you to provide a group file so you can cluster by group. \n";
         helpString += "The count parameter allows you to provide a count file so you can cluster by group. \n";
                helpString += "The diffs parameter allows you to specify maximum number of mismatched bases allowed between sequences in a grouping. The default is 1.\n";
+        helpString += "The topdown parameter allows you to specify whether to cluster from largest abundance to smallest or smallest to largest.  Default=T, meanging largest to smallest.\n";
                helpString += "The pre.cluster command should be in the following format: \n";
                helpString += "pre.cluster(fasta=yourFastaFile, names=yourNamesFile, diffs=yourMaxDiffs) \n";
                helpString += "Example pre.cluster(fasta=amazon.fasta, diffs=2).\n";
@@ -210,6 +213,9 @@ PreClusterCommand::PreClusterCommand(string option) {
                        m->setProcessors(temp);
                        m->mothurConvert(temp, processors);
                        
+            temp = validParameter.validFile(parameters, "topdown", false);             if(temp == "not found"){  temp = "T"; }
+                       topdown = m->isTrue(temp);
+            
             if (countfile == "") {
                 if (namefile == "") {
                     vector<string> files; files.push_back(fastafile);
@@ -440,7 +446,7 @@ int PreClusterCommand::createProcessesGroups(string newFName, string newNName, s
                        // Allocate memory for thread data.
                        string extension = toString(i) + ".temp";
                        
-                       preClusterData* tempPreCluster = new preClusterData(fastafile, namefile, groupfile, countfile, (newFName+extension), (newNName+extension), newMFile, groups, m, lines[i].start, lines[i].end, diffs, i);
+                       preClusterData* tempPreCluster = new preClusterData(fastafile, namefile, groupfile, countfile, (newFName+extension), (newNName+extension), newMFile, groups, m, lines[i].start, lines[i].end, diffs, topdown, i);
                        pDataArray.push_back(tempPreCluster);
                        processIDS.push_back(i);
                        
@@ -545,7 +551,8 @@ int PreClusterCommand::process(string newMapFile){
                m->openOutputFile(newMapFile, out);
                
                //sort seqs by number of identical seqs
-               sort(alignSeqs.begin(), alignSeqs.end(), comparePriority);
+        if (topdown) { sort(alignSeqs.begin(), alignSeqs.end(), comparePriorityTopDown);  }
+        else {  sort(alignSeqs.begin(), alignSeqs.end(), comparePriorityDownTop);  }
                
                int count = 0;
                int numSeqs = alignSeqs.size();