adding labels to list file.

[mothur.git] / otuassociationcommand.cpp

diff --git a/otuassociationcommand.cpp b/otuassociationcommand.cpp
index 968d76744be5b296a9b9f98a5294356366783bce..705540c3a62564a14da7a7ed00262c4adb5f220b 100644 (file)
--- a/otuassociationcommand.cpp
+++ b/otuassociationcommand.cpp
@@ -13,15 +13,15 @@
 //**********************************************************************************************************************
 vector<string> OTUAssociationCommand::setParameters(){ 
        try {
-               CommandParameter pshared("shared", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(pshared);
-               CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(prelabund);
-        CommandParameter pmetadata("metadata", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(pmetadata);
-        CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
-               CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-               CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-               CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "",false,false); parameters.push_back(pmethod);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pshared("shared", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","otucorr",false,false,true); parameters.push_back(pshared);
+               CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","otucorr",false,false); parameters.push_back(prelabund);
+        CommandParameter pmetadata("metadata", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pmetadata);
+        CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false,true); parameters.push_back(pcutoff);
+               CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+               CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+               CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "","",false,false,true); parameters.push_back(pmethod);
+               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);          }
@@ -55,24 +55,19 @@ string OTUAssociationCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string OTUAssociationCommand::getOutputFileNameTag(string type, string inputName=""){  
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string OTUAssociationCommand::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 == "otucorr") {  outputFileName =  "otu.corr"; }
-            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, "OTUAssociationCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        if (type == "otucorr") {  pattern = "[filename],[distance],[tag],otu.corr"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "OTUAssociationCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 OTUAssociationCommand::OTUAssociationCommand(){        
@@ -331,8 +326,11 @@ int OTUAssociationCommand::processShared(){
 //**********************************************************************************************************************
 int OTUAssociationCommand::process(vector<SharedRAbundVector*>& lookup){
        try {
-               
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + "." + method + "." + getOutputFileNameTag("otucorr");
+               map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
+        variables["[distance]"] = lookup[0]->getLabel();
+        variables["[tag]"] = method;
+               string outputFileName = getOutputFileName("otucorr",variables);
                outputNames.push_back(outputFileName); outputTypes["otucorr"].push_back(outputFileName);
                
                ofstream out;
@@ -362,7 +360,7 @@ int OTUAssociationCommand::process(vector<SharedRAbundVector*>& lookup){
                     else if (method == "kendall")      {       coef = linear.calcKendall(xy[i], xy[k], sig);   }                   
                     else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall."); m->mothurOutEndLine(); m->control_pressed = true; }
                     
-                    if (sig < cutoff) { out << m->binLabelsInFile[i] << '\t' << m->binLabelsInFile[k] << '\t' << coef << '\t' << sig << endl; }
+                    if (sig < cutoff) { out << m->currentSharedBinLabels[i] << '\t' << m->currentSharedBinLabels[k] << '\t' << coef << '\t' << sig << endl; }
                 }
             }
                }else { //compare otus to metadata
@@ -379,7 +377,7 @@ int OTUAssociationCommand::process(vector<SharedRAbundVector*>& lookup){
                     else if (method == "kendall")      {       coef = linear.calcKendall(xy[i], metadata[k], sig);     }                   
                     else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall."); m->mothurOutEndLine(); m->control_pressed = true; }
                     
-                    if (sig < cutoff) { out << m->binLabelsInFile[i] << '\t' << metadataLabels[k] << '\t' << coef << '\t' << sig << endl; }
+                    if (sig < cutoff) { out << m->currentSharedBinLabels[i] << '\t' << metadataLabels[k] << '\t' << coef << '\t' << sig << endl; }
                 }
             }
 
@@ -492,7 +490,11 @@ int OTUAssociationCommand::processRelabund(){
 int OTUAssociationCommand::process(vector<SharedRAbundFloatVector*>& lookup){
        try {
                
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + "." + method + "." + getOutputFileNameTag("otucorr");
+               map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
+        variables["[distance]"] = lookup[0]->getLabel();
+        variables["[tag]"] = method;
+        string outputFileName = getOutputFileName("otucorr",variables);
                outputNames.push_back(outputFileName); outputTypes["otucorr"].push_back(outputFileName);
                
                ofstream out;
@@ -521,7 +523,7 @@ int OTUAssociationCommand::process(vector<SharedRAbundFloatVector*>& lookup){
                     else if (method == "kendall")      {       coef = linear.calcKendall(xy[i], xy[k], sig);   }                   
                     else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall."); m->mothurOutEndLine(); m->control_pressed = true; }
                     
-                    if (sig < cutoff) { out << m->binLabelsInFile[i] << '\t' << m->binLabelsInFile[k] << '\t' << coef << '\t' << sig << endl; }
+                    if (sig < cutoff) { out << m->currentSharedBinLabels[i] << '\t' << m->currentSharedBinLabels[k] << '\t' << coef << '\t' << sig << endl; }
                 }
             }
                }else { //compare otus to metadata
@@ -538,7 +540,7 @@ int OTUAssociationCommand::process(vector<SharedRAbundFloatVector*>& lookup){
                     else if (method == "kendall")      {       coef = linear.calcKendall(xy[i], metadata[k], sig);     }                   
                     else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall."); m->mothurOutEndLine(); m->control_pressed = true; }
                     
-                    if (sig < cutoff) { out << m->binLabelsInFile[i] << '\t' << metadataLabels[k] << '\t' << coef << '\t' << sig << endl; }
+                    if (sig < cutoff) { out << m->currentSharedBinLabels[i] << '\t' << metadataLabels[k] << '\t' << coef << '\t' << sig << endl; }
                 }
             }
             
@@ -570,6 +572,7 @@ int OTUAssociationCommand::readMetadata(){
                //save names of columns you are reading
                while (!iss.eof()) {
                        iss >> columnLabel; m->gobble(iss);
+            if (m->debug) { m->mothurOut("[DEBUG]: metadata column Label = " + columnLabel + "\n"); }
                        metadataLabels.push_back(columnLabel);
                }
                int count = metadataLabels.size();
@@ -581,6 +584,7 @@ int OTUAssociationCommand::readMetadata(){
                        
                        string group = "";
                        in >> group; m->gobble(in);
+            if (m->debug) { m->mothurOut("[DEBUG]: metadata group = " + group + "\n"); }
             
                        SharedRAbundFloatVector* tempLookup = new SharedRAbundFloatVector();
                        tempLookup->setGroup(group);
@@ -588,7 +592,8 @@ int OTUAssociationCommand::readMetadata(){
                        
                        for (int i = 0; i < count; i++) {
                                float temp = 0.0;
-                               in >> temp; 
+                               in >> temp;
+                if (m->debug) { m->mothurOut("[DEBUG]: metadata value = " + toString(temp) + "\n"); }
                                tempLookup->push_back(temp, group);
                        }