Merge remote-tracking branch 'origin'

[mothur.git] / makebiomcommand.cpp

diff --git a/makebiomcommand.cpp b/makebiomcommand.cpp
index 6385adef0fd1c36f73e509604f10b082a75e54a5..a1018833e6268b6d0fe04aa25d4598f37df9cb4d 100644 (file)
--- a/makebiomcommand.cpp
+++ b/makebiomcommand.cpp
@@ -92,14 +92,14 @@
 //**********************************************************************************************************************
 vector<string> MakeBiomCommand::setParameters(){       
        try {
-               CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
-        CommandParameter pcontaxonomy("contaxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pcontaxonomy);
-        CommandParameter pmetadata("metadata", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pmetadata);
-               CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-               CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
-        CommandParameter pmatrixtype("matrixtype", "Multiple", "sparse-dense", "sparse", "", "", "",false,false); parameters.push_back(pmatrixtype);
+               CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","biom",false,true,true); parameters.push_back(pshared);
+        CommandParameter pcontaxonomy("contaxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcontaxonomy);
+        CommandParameter pmetadata("metadata", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pmetadata);
+               CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+               CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+        CommandParameter pmatrixtype("matrixtype", "Multiple", "sparse-dense", "sparse", "", "", "","",false,false); parameters.push_back(pmatrixtype);
 
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -133,24 +133,19 @@ string MakeBiomCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string MakeBiomCommand::getOutputFileNameTag(string type, string inputName=""){        
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string MakeBiomCommand::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 == "biom")             {   outputFileName =  "biom";       }
-            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, "MakeBiomCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        if (type == "biom") {  pattern = "[filename],[distance],biom"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "MakeBiomCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 
 //**********************************************************************************************************************
@@ -388,8 +383,10 @@ int MakeBiomCommand::execute(){
 //**********************************************************************************************************************
 int MakeBiomCommand::getBiom(vector<SharedRAbundVector*>& lookup){
        try {
-        
-        string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + "." + getOutputFileNameTag("biom");
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+        variables["[distance]"] = lookup[0]->getLabel();
+        string outputFileName = getOutputFileName("biom",variables);
                ofstream out;
                m->openOutputFile(outputFileName, out);
                outputNames.push_back(outputFileName); outputTypes["biom"].push_back(outputFileName);
@@ -408,6 +405,7 @@ int MakeBiomCommand::getBiom(vector<SharedRAbundVector*>& lookup){
         out << "{\n" + spaces + "\"id\":\"" + sharedfile + "-" + lookup[0]->getLabel() + "\",\n" + spaces + "\"format\": \"Biological Observation Matrix 0.9.1\",\n" + spaces + "\"format_url\": \"http://biom-format.org\",\n";
         out << spaces + "\"type\": \"OTU table\",\n" + spaces + "\"generated_by\": \"" << mothurString << "\",\n" + spaces + "\"date\": \"" << dateString << "\",\n";
         
+        int numBins = lookup[0]->getNumBins();
         vector<string> metadata = getMetaData(lookup);  
         
         if (m->control_pressed) {  out.close(); return 0; }
@@ -423,11 +421,11 @@ int MakeBiomCommand::getBiom(vector<SharedRAbundVector*>& lookup){
         out << spaces + "\"rows\":[\n";
         string rowFront = spaces + spaces + "{\"id\":\"";
         string rowBack = "\", \"metadata\":";
-        for (int i = 0; i < m->currentBinLabels.size()-1; i++) {
+        for (int i = 0; i < numBins-1; i++) {
             if (m->control_pressed) {  out.close(); return 0; }
             out << rowFront << m->currentBinLabels[i] << rowBack << metadata[i] << "},\n";
         }
-        out << rowFront << m->currentBinLabels[(m->currentBinLabels.size()-1)] << rowBack << metadata[(m->currentBinLabels.size()-1)] << "}\n" + spaces + "],\n";
+        out << rowFront << m->currentBinLabels[(numBins-1)] << rowBack << metadata[(numBins-1)] << "}\n" + spaces + "],\n";
         
         //get column info
         /*"columns": [
@@ -627,8 +625,8 @@ vector<string> MakeBiomCommand::getMetaData(vector<SharedRAbundVector*>& lookup)
 //**********************************************************************************************************************
 int MakeBiomCommand::getSampleMetaData(vector<SharedRAbundVector*>& lookup){
        try {
-        
-        if (metadatafile == "") { for (int i = 0; i < lookup.size(); i++) {  sampleMetadata.push_back("null");  } }
+        sampleMetadata.clear();
+        if (metadatafile == "") {  for (int i = 0; i < lookup.size(); i++) {  sampleMetadata.push_back("null");  } }
         else {
             ifstream in;
             m->openInputFile(metadatafile, in);