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added topdown parameter to pre.cluster. added more debugging output to bayesian...
[mothur.git] / treegroupscommand.cpp
diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index bba6289ada54856c25d683126b0d181badab4c15..0d014599fa794217233694f8a28ed707b99c86eb 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -14,23 +14,23 @@
 //**********************************************************************************************************************
 vector<string> TreeGroupCommand::setParameters(){      
        try {
-               CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pshared);
-               CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pphylip);
-               CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName",false,false); parameters.push_back(pname);
-               CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "countcolumn",false,false); parameters.push_back(pcount);
-        CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName-countcolumn",false,false); parameters.push_back(pcolumn);             
-        CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
-        CommandParameter psubsample("subsample", "String", "", "", "", "", "",false,false); parameters.push_back(psubsample);
-        CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
-               CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);                
-               CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-               CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-               CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
+               CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none","tree",false,false,true); parameters.push_back(pshared);
+               CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none","tree",false,false); parameters.push_back(pphylip);
+               CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName","",false,false); parameters.push_back(pname);
+               CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "countcolumn","",false,false); parameters.push_back(pcount);
+        CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName-countcolumn","tree",false,false); parameters.push_back(pcolumn);              
+        CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+        CommandParameter psubsample("subsample", "String", "", "", "", "", "","",false,false); parameters.push_back(psubsample);
+        CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pcutoff);
+               CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);             
+               CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+               CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+               CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "","",true,false,true); parameters.push_back(pcalc);
                
-        CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+        CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
 //CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -71,24 +71,19 @@ string TreeGroupCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string TreeGroupCommand::getOutputFileNameTag(string type, string inputName=""){       
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string TreeGroupCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
         
-        //is this a type this command creates
-        it = outputTypes.find(type);
-        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
-        else {
-            if (type == "tree")            {   outputFileName =  "tre";   }
-            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
-        }
-        return outputFileName;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "TreeGroupCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        if (type == "tree") {  pattern = "[filename],[calc],[distance],[tag],tre-[filename],tre"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "TreeGroupCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 TreeGroupCommand::TreeGroupCommand(){  
@@ -434,7 +429,10 @@ int TreeGroupCommand::execute(){
                        m->Treenames.clear();
                        
                        //fills globaldatas tree names
-                       m->Treenames = m->getGroups();
+                       //m->Treenames = m->getGroups();
+            for (int k = 0; k < lookup.size(); k++) {
+                m->Treenames.push_back(lookup[k]->getGroup());
+            }
                
                        if (m->control_pressed) { return 0; }
                        
@@ -453,6 +451,7 @@ int TreeGroupCommand::execute(){
                        readMatrix->setCutoff(cutoff);
        
             ct = NULL;
+            nameMap = NULL;
             if(namefile != ""){        
                 nameMap = new NameAssignment(namefile);
                 nameMap->readMap();
@@ -461,11 +460,16 @@ int TreeGroupCommand::execute(){
                 ct = new CountTable();
                 ct->readTable(countfile);
                 readMatrix->read(ct);
+            }else {
+                readMatrix->read(nameMap);
             }
 
                        list = readMatrix->getListVector();
                        SparseDistanceMatrix* dMatrix = readMatrix->getDMatrix();
-
+            
+            //clear globaldatas old tree names if any
+                       m->Treenames.clear();
+            
                        //make treemap
             if (ct != NULL) { delete ct; }
                        ct = new CountTable();
@@ -477,17 +481,12 @@ int TreeGroupCommand::execute(){
                 nameMap.insert(bin); 
                 gps.insert(bin); 
                 groupMap[bin] = bin;
+                m->Treenames.push_back(bin);
             }
             ct->createTable(nameMap, groupMap, gps);
                        
                        vector<string> namesGroups = ct->getNamesOfGroups();
                        m->setGroups(namesGroups);
-               
-                       //clear globaldatas old tree names if any
-                       m->Treenames.clear();
-            
-                       //fills globaldatas tree names
-                       m->Treenames = m->getGroups();
                        
                        //used in tree constructor 
                        m->runParse = false;
@@ -501,7 +500,9 @@ int TreeGroupCommand::execute(){
                        if (m->control_pressed) { return 0; }
 
                        //create a new filename
-                       string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + getOutputFileNameTag("tree");     
+            map<string, string> variables; 
+            variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
+                       string outputFile = getOutputFileName("tree",variables);        
                        outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
                                
                        Tree* newTree = createTree(matrix);
@@ -958,7 +959,12 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                 }
                 
                 //create a new filename
-                string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".ave." + getOutputFileNameTag("tree");                                
+                map<string, string> variables; 
+                variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
+                variables["[calc]"] = treeCalculators[i]->getName();
+                variables["[distance]"] = thisLookup[0]->getLabel();
+                variables["[tag]"] = "ave";
+                string outputFile = getOutputFileName("tree",variables);                               
                 outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile); 
                 
                 //creates tree from similarity matrix and write out file
@@ -971,7 +977,13 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                 if (m->control_pressed) { break; }
                 
                 //create a new filename
-                string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".all." + getOutputFileNameTag("tree");                                
+                //create a new filename
+                map<string, string> variables; 
+                variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
+                variables["[calc]"] = treeCalculators[i]->getName();
+                variables["[distance]"] = thisLookup[0]->getLabel();
+                variables["[tag]"] = "all";
+                string outputFile = getOutputFileName("tree",variables);                               
                 outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile); 
                 
                 ofstream outAll;
@@ -1012,7 +1024,8 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                 Tree* conTree = consensus.getTree(trees);
                 
                 //create a new filename
-                string conFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".cons." + getOutputFileNameTag("tree");                          
+                variables["[tag]"] = "cons";
+                string conFile = getOutputFileName("tree",variables);                          
                 outputNames.push_back(conFile); outputTypes["tree"].push_back(conFile); 
                 ofstream outTree;
                 m->openOutputFile(conFile, outTree);
@@ -1040,7 +1053,12 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                 }
                 
                 //create a new filename
-                string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + getOutputFileNameTag("tree");                            
+                map<string, string> variables; 
+                variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
+                variables["[calc]"] = treeCalculators[i]->getName();
+                variables["[distance]"] = thisLookup[0]->getLabel();
+                variables["[tag]"] = "";
+                string outputFile = getOutputFileName("tree",variables);                                       
                 outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile); 
                 
                 //creates tree from similarity matrix and write out file
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