finished cluster.split adding classify method.

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 4b3c27b14641059d8a61a8dc6d8c7a858ed41f7e..ed995fcd9586d5f2e5f86b1c5b733f247925a9f1 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","splitmethod","taxonomy","showabund","timing","hard","processors","outputdir","inputdir"};
+                       string Array[] =  {"phylip","column","name","cutoff","precision","method","splitmethod","taxonomy","taxlevel","showabund","timing","hard","processors","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -128,14 +128,16 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
                        convert(temp, processors); 
                        
-                       temp = validParameter.validFile(parameters, "cutoff", false);
-                       if (temp == "not found") { temp = "10"; }
+                       splitmethod = validParameter.validFile(parameters, "splitmethod", false);               if (splitmethod == "not found") { splitmethod = "distance"; }
+                       
+                       temp = validParameter.validFile(parameters, "cutoff", false);           if (temp == "not found")  { temp = "10"; }
                        convert(temp, cutoff); 
                        cutoff += (5 / (precision * 10.0));  
                        
-                       method = validParameter.validFile(parameters, "method", false);         if (method == "not found") { method = "furthest"; }
+                       temp = validParameter.validFile(parameters, "taxlevel", false);         if (temp == "not found")  { temp = "1"; }
+                       convert(temp, taxLevelCutoff); 
                        
-                       splitmethod = validParameter.validFile(parameters, "splitmethod", false);               if (splitmethod == "not found") { method = "distance"; }
+                       method = validParameter.validFile(parameters, "method", false);         if (method == "not found") { method = "furthest"; }
                        
                        if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
                        else { m->mothurOut("Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average."); m->mothurOutEndLine(); abort = true; }
@@ -163,12 +165,18 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
 
 void ClusterSplitCommand::help(){
        try {
-               m->mothurOut("The cluster.split command parameter options are cutoff, splitcutoff, precision, method, splitmethod, phylip, column, name, showabund, timing. Phylip or column and name are required.\n");
+               m->mothurOut("The cluster.split command parameter options are phylip, column, name, cutoff, precision, method, splitmethod, taxonomy, taxlevel, showabund, timing, hard, processors. Phylip or column and name are required.\n");
                m->mothurOut("The phylip and column parameter allow you to enter your distance file. \n");
                m->mothurOut("The name parameter allows you to enter your name file and is required if your distance file is in column format. \n");
+               m->mothurOut("The cutoff parameter allow you to set the distance you want to cluster to, default is 10.0. \n");
+               m->mothurOut("The precision parameter allows you specify the precision of the precision of the distances outputted, default=100, meaning 2 decimal places. \n");
+               m->mothurOut("The method allows you to specify what clustering algorythm you want to use, default=furthest, option furthest, nearest, or average. \n");
+               m->mothurOut("The splitmethod parameter allows you to specify how you want to split your distance file before you cluster, default=distance, options distance or classify. \n");
+               m->mothurOut("The taxonomy parameter allows you to enter the taxonomy file for your sequences, this is only valid if you are using splitmethod=classify. Be sure your taxonomy file does not include the probability scores. \n");
+               m->mothurOut("The taxlevel parameter allows you to specify the taxonomy level you want to use to split the distance file, default=1. \n");
                m->mothurOut("The cluster.split command should be in the following format: \n");
-               m->mothurOut("cluster.split(column=youDistanceFile, name=yourNameFile, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
-               m->mothurOut("Example: cluster.split(column=abrecovery.dist, name=abrecovery.names, method=furthest, cutoff=0.10, precision=1000, splitmethod=classify) \n");   
+               m->mothurOut("cluster.split(column=youDistanceFile, name=yourNameFile, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision, splitmethod=yourSplitmethod, taxonomy=yourTaxonomyfile, taxlevel=yourtaxlevel) \n");
+               m->mothurOut("Example: cluster.split(column=abrecovery.dist, name=abrecovery.names, method=furthest, cutoff=0.10, precision=1000, splitmethod=classify, taxonomy=abrecovery.silva.slv.taxonomy, taxlevel=5) \n");       
 
        }
        catch(exception& e) {
@@ -223,7 +231,10 @@ int ClusterSplitCommand::execute(){
                time_t estart = time(NULL);
                
                //split matrix into non-overlapping groups
-               SplitMatrix* split = new SplitMatrix(distfile, namefile, taxFile, cutoff, splitmethod);
+               SplitMatrix* split;
+               if (splitmethod == "distance")  {       split = new SplitMatrix(distfile, namefile, taxFile, cutoff, splitmethod);                      }
+               else                                                    {       split = new SplitMatrix(distfile, namefile, taxFile, taxLevelCutoff, splitmethod);  }
+               
                split->split();
                
                if (m->control_pressed) { delete split; return 0; }
@@ -334,7 +345,7 @@ int ClusterSplitCommand::mergeLists(vector<string> listNames, string singleton,
                outputNames.push_back(fileroot+ tag + ".sabund");
                outputNames.push_back(fileroot+ tag + ".rabund");
                outputNames.push_back(fileroot+ tag + ".list");
-                       
+               
                //read in singletons
                ListVector* listSingle = NULL;
                if (singleton != "none") {
@@ -365,7 +376,7 @@ int ClusterSplitCommand::mergeLists(vector<string> listNames, string singleton,
                                it--;
                        }
                }
-               
+       
                //sort order
                sort(orderFloat.begin(), orderFloat.end());
 
@@ -381,7 +392,7 @@ int ClusterSplitCommand::mergeLists(vector<string> listNames, string singleton,
                        lastLabels.push_back(tempList.getLabel());
                        in.close();
                }
-               
+       
                ListVector* merged = NULL;
                                
                //for each label needed
@@ -429,10 +440,12 @@ int ClusterSplitCommand::mergeLists(vector<string> listNames, string singleton,
                        }
                        
                        //add in singletons
-                       for (int j = 0; j < listSingle->getNumBins(); j++) {
-                               merged->push_back(listSingle->get(j));
+                       if (listSingle != NULL) {
+                               for (int j = 0; j < listSingle->getNumBins(); j++) {
+                                       merged->push_back(listSingle->get(j));
+                               }
                        }
-
+                       
                        //print to files
                        printData(merged);
                        
@@ -640,7 +653,7 @@ vector<string> ClusterSplitCommand::cluster(vector< map<string, string> > distNa
                                oldList.print(listFile);
                                if (labels.count(toString(rndPreviousDist,  length-1)) == 0) { labels.insert(toString(rndPreviousDist,  length-1)); }
                        }
-               
+       
                        delete matrix; delete list;     delete cluster; delete rabund; 
                        listFile.close();
                        
@@ -653,7 +666,7 @@ vector<string> ClusterSplitCommand::cluster(vector< map<string, string> > distNa
                        remove(thisNamefile.c_str());
                }
                
-                               
+                                       
                return listFileNames;
        
        }

diff --git a/clustersplitcommand.h b/clustersplitcommand.h
index 631a8b6c8b95bfa87c52035cdb91d53bc7b378aa..e838bc41ee1b3616d3f0f95e6a512c5bde136d33 100644 (file)
--- a/clustersplitcommand.h
+++ b/clustersplitcommand.h
@@ -34,7 +34,7 @@ private:
 
        string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, distfile, format, showabund, timing, splitmethod, taxFile;
        double cutoff, splitcutoff;
-       int precision, length, processors;
+       int precision, length, processors, taxLevelCutoff;
        bool print_start, abort, hard;
        time_t start;
        ofstream outList, outRabund, outSabund;

diff --git a/splitmatrix.cpp b/splitmatrix.cpp
index 0b59fa2e2548ac14c5baa8923510409ad56274b3..1c61f31775d55d5a6baae57c1e54301faac42002 100644 (file)
--- a/splitmatrix.cpp
+++ b/splitmatrix.cpp
@@ -241,6 +241,8 @@ int SplitMatrix::splitDistance(){
 /***********************************************************************/
 int SplitMatrix::splitClassify(){
        try {
+               cutoff = int(cutoff);
+               
                map<string, int> seqGroup;
                map<string, int>::iterator it;
                map<string, int>::iterator it2;
@@ -272,11 +274,11 @@ int SplitMatrix::splitClassify(){
                
                        //is this node within the cutoff
                        TaxNode taxon = phylo->get(i);
-                       
+               
                        if (taxon.level == cutoff) {//if yes, then create group containing this nodes sequences
-                               if (taxon.children.size() > 1) { //if this taxon just has one seq its a singleton
-                                       for (it = taxon.children.begin(); it != taxon.children.end(); it++) {
-                                               seqGroup[it->first] = numGroups;
+                               if (taxon.accessions.size() > 1) { //if this taxon just has one seq its a singleton
+                                       for (int j = 0; j < taxon.accessions.size(); j++) {
+                                               seqGroup[taxon.accessions[j]] = numGroups;
                                        }
                                        numGroups++;
                                }