X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactcommand.cpp;h=1775944ad1b53c6e9677fe5c2b1280a9171432da;hb=60928795782d8f8648ec373d6a96b53032a77429;hp=0fdd0798e2cdda014a6cc568d3a1c895362c3158;hpb=050e1297eaf24fabbbe0e9b76c3a5acfb90eed7d;p=mothur.git

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index 0fdd079..1775944 100644
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -23,24 +23,26 @@
 #include "shannon.h"
 #include "jackknife.h"
 #include "coverage.h"
+#include "shannonrange.h"
 
 
 //**********************************************************************************************************************
 vector<string> RareFactCommand::setParameters(){	
 	try {
-		CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
-		CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
-		CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
-		CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
-		CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-		CommandParameter pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq);
-		CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
-		CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap", "sobs", "", "", "",true,false); parameters.push_back(pcalc);
-		CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
-		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-		CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pgroupmode);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(plist);
+		CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false); parameters.push_back(prabund);
+		CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false); parameters.push_back(psabund);
+		CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(pshared);
+		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+		CommandParameter pfreq("freq", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pfreq);
+		CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+		CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-shannonrange", "sobs", "", "", "","",true,false,true); parameters.push_back(pcalc);
+		CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund);
+        CommandParameter palpha("alpha", "Multiple", "0-1-2", "1", "", "", "","",false,false,true); parameters.push_back(palpha);
+		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+		CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pgroupmode);
+		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);		}
@@ -56,13 +58,14 @@ string RareFactCommand::getHelpString(){
 	try {
 		ValidCalculators validCalculator;
 		string helpString = "";
-		helpString += "The rarefaction.single command parameters are list, sabund, rabund, shared, label, iters, freq, calc, processors and abund.  list, sabund, rabund or shared is required unless you have a valid current file. \n";
+		helpString += "The rarefaction.single command parameters are list, sabund, rabund, shared, label, iters, freq, calc, processors, groupmode and abund.  list, sabund, rabund or shared is required unless you have a valid current file. \n";
 		helpString += "The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n";
 		helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
 		helpString += "The rarefaction.single command should be in the following format: \n";
 		helpString += "rarefaction.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n";
 		helpString += "Example rarefaction.single(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).\n";
 		helpString += "The default values for iters is 1000, freq is 100, and calc is rarefaction which calculates the rarefaction curve for the observed richness.\n";
+        helpString += "The alpha parameter is used to set the alpha value for the shannonrange calculator.\n";
 		validCalculator.printCalc("rarefaction");
 		helpString += "If you are running rarefaction.single with a shared file and would like your results collated in one file, set groupmode=t. (Default=true).\n";
 		helpString += "The label parameter is used to analyze specific labels in your input.\n";
@@ -74,7 +77,35 @@ string RareFactCommand::getHelpString(){
 		exit(1);
 	}
 }
-
+//**********************************************************************************************************************
+string RareFactCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        if (type == "rarefaction") {  pattern =  "[filename],rarefaction"; }
+        else if (type == "r_chao") {  pattern =  "[filename],r_chao"; }
+        else if (type == "r_ace") {  pattern =  "[filename],r_ace"; }
+        else if (type == "r_jack") {  pattern =  "[filename],r_jack"; }
+        else if (type == "r_shannon") {  pattern =  "[filename],r_shannon"; }
+        else if (type == "r_shannoneven") {  pattern =  "[filename],r_shannoneven"; }
+        else if (type == "r_smithwilson") {  pattern =  "[filename],r_smithwilson"; }
+        else if (type == "r_npshannon") {  pattern =  "[filename],r_npshannon"; }
+        else if (type == "r_shannonrange"){  pattern =  "[filename],r_shannonrange";    }
+        else if (type == "r_simpson") {  pattern =  "[filename],r_simpson"; }
+        else if (type == "r_simpsoneven") {  pattern =  "[filename],r_simpsoneven"; }
+        else if (type == "r_invsimpson") {  pattern =  "[filename],r_invsimpson"; }
+        else if (type == "r_bootstrap") {  pattern =  "[filename],r_bootstrap"; }
+        else if (type == "r_coverage") {  pattern =  "[filename],r_coverage"; }
+        else if (type == "r_nseqs") {  pattern =  "[filename],r_nseqs"; }
+        else if (type == "r_heip") {  pattern =  "[filename],r_heip"; }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "RareFactCommand", "getOutputPattern");
+        exit(1);
+    }
+}
 //**********************************************************************************************************************
 RareFactCommand::RareFactCommand(){	
 	try {
@@ -87,6 +118,7 @@ RareFactCommand::RareFactCommand(){
 		outputTypes["r_jack"] = tempOutNames;
 		outputTypes["r_shannon"] = tempOutNames;
 		outputTypes["r_shannoneven"] = tempOutNames;
+        outputTypes["r_shannonrange"] = tempOutNames;
 		outputTypes["r_heip"] = tempOutNames;
 		outputTypes["r_smithwilson"] = tempOutNames;
 		outputTypes["r_npshannon"] = tempOutNames;
@@ -134,6 +166,7 @@ RareFactCommand::RareFactCommand(string option)  {
 			outputTypes["r_jack"] = tempOutNames;
 			outputTypes["r_shannon"] = tempOutNames;
 			outputTypes["r_shannoneven"] = tempOutNames;
+            outputTypes["r_shannonrange"] = tempOutNames;
 			outputTypes["r_heip"] = tempOutNames;
 			outputTypes["r_smithwilson"] = tempOutNames;
 			outputTypes["r_npshannon"] = tempOutNames;
@@ -264,6 +297,11 @@ RareFactCommand::RareFactCommand(string option)  {
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
 			m->mothurConvert(temp, processors);
+            
+            temp = validParameter.validFile(parameters, "alpha", false);		if (temp == "not found") { temp = "1"; }
+			m->mothurConvert(temp, alpha);
+            
+            if ((alpha != 0) && (alpha != 1) && (alpha != 2)) { m->mothurOut("[ERROR]: Not a valid alpha value. Valid values are 0, 1 and 2."); m->mothurOutEndLine(); abort=true; }
 			
 			temp = validParameter.validFile(parameters, "groupmode", false);		if (temp == "not found") { temp = "T"; }
 			groupMode = m->isTrue(temp);
@@ -301,56 +339,61 @@ int RareFactCommand::execute(){
 			int i;
 			ValidCalculators validCalculator;
 			
+            map<string, string> variables; 
+            variables["[filename]"] = fileNameRoot;
 			  
 			for (i=0; i<Estimators.size(); i++) {
 				if (validCalculator.isValidCalculator("rarefaction", Estimators[i]) == true) { 
 					if (Estimators[i] == "sobs") { 
-						rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+"rarefaction")));
-						outputNames.push_back(fileNameRoot+"rarefaction"); outputTypes["rarefaction"].push_back(fileNameRoot+"rarefaction");
+						rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(getOutputFileName("rarefaction",variables))));
+						outputNames.push_back(getOutputFileName("rarefaction",variables)); outputTypes["rarefaction"].push_back(getOutputFileName("rarefaction",variables));
 					}else if (Estimators[i] == "chao") { 
-						rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao")));
-						outputNames.push_back(fileNameRoot+"r_chao"); outputTypes["r_chao"].push_back(fileNameRoot+"r_chao");
+						rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(getOutputFileName("r_chao",variables))));
+						outputNames.push_back(getOutputFileName("r_chao",variables)); outputTypes["r_chao"].push_back(getOutputFileName("r_chao",variables));
 					}else if (Estimators[i] == "ace") { 
 						if(abund < 5)
 							abund = 10;
-						rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"r_ace")));
-						outputNames.push_back(fileNameRoot+"r_ace"); outputTypes["r_ace"].push_back(fileNameRoot+"r_ace");
+						rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(getOutputFileName("r_ace",variables))));
+						outputNames.push_back(getOutputFileName("r_ace",variables)); outputTypes["r_ace"].push_back(getOutputFileName("r_ace",variables));
 					}else if (Estimators[i] == "jack") { 
-						rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack")));
-						outputNames.push_back(fileNameRoot+"r_jack"); outputTypes["r_jack"].push_back(fileNameRoot+"r_jack");
+						rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(getOutputFileName("r_jack",variables))));
+						outputNames.push_back(getOutputFileName("r_jack",variables)); outputTypes["r_jack"].push_back(getOutputFileName("r_jack",variables));
 					}else if (Estimators[i] == "shannon") { 
-						rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon")));
-						outputNames.push_back(fileNameRoot+"r_shannon"); outputTypes["r_shannon"].push_back(fileNameRoot+"r_shannon");
+						rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(getOutputFileName("r_shannon",variables))));
+						outputNames.push_back(getOutputFileName("r_shannon",variables)); outputTypes["r_shannon"].push_back(getOutputFileName("r_shannon",variables));
 					}else if (Estimators[i] == "shannoneven") { 
-						rDisplays.push_back(new RareDisplay(new ShannonEven(), new ThreeColumnFile(fileNameRoot+"r_shannoneven")));
-						outputNames.push_back(fileNameRoot+"r_shannoneven"); outputTypes["r_shannoneven"].push_back(fileNameRoot+"r_shannoneven");
+						rDisplays.push_back(new RareDisplay(new ShannonEven(), new ThreeColumnFile(getOutputFileName("r_shannoneven",variables))));
+						outputNames.push_back(getOutputFileName("r_shannoneven",variables)); outputTypes["r_shannoneven"].push_back(getOutputFileName("r_shannoneven",variables));
 					}else if (Estimators[i] == "heip") { 
-						rDisplays.push_back(new RareDisplay(new Heip(), new ThreeColumnFile(fileNameRoot+"r_heip")));
-						outputNames.push_back(fileNameRoot+"r_heip"); outputTypes["r_heip"].push_back(fileNameRoot+"r_heip");
-					}else if (Estimators[i] == "smithwilson") { 
-						rDisplays.push_back(new RareDisplay(new SmithWilson(), new ThreeColumnFile(fileNameRoot+"r_smithwilson")));
-						outputNames.push_back(fileNameRoot+"r_smithwilson"); outputTypes["r_smithwilson"].push_back(fileNameRoot+"r_smithwilson");
+						rDisplays.push_back(new RareDisplay(new Heip(), new ThreeColumnFile(getOutputFileName("r_heip",variables))));
+						outputNames.push_back(getOutputFileName("r_heip",variables)); outputTypes["r_heip"].push_back(getOutputFileName("r_heip",variables));
+                    }else if (Estimators[i] == "r_shannonrange") {
+                        rDisplays.push_back(new RareDisplay(new RangeShannon(alpha), new ThreeColumnFile(getOutputFileName("r_shannonrange", variables))));
+                        outputNames.push_back(getOutputFileName("r_shannonrange", variables)); outputTypes["r_shannoneven"].push_back(getOutputFileName("r_shannonrange", variables));
+					}else if (Estimators[i] == "smithwilson") {
+						rDisplays.push_back(new RareDisplay(new SmithWilson(), new ThreeColumnFile(getOutputFileName("r_smithwilson",variables))));
+						outputNames.push_back(getOutputFileName("r_smithwilson",variables)); outputTypes["r_smithwilson"].push_back(getOutputFileName("r_smithwilson",variables));
 					}else if (Estimators[i] == "npshannon") { 
-						rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon")));
-						outputNames.push_back(fileNameRoot+"r_npshannon"); outputTypes["r_npshannon"].push_back(fileNameRoot+"r_npshannon");
+						rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(getOutputFileName("r_npshannon",variables))));
+						outputNames.push_back(getOutputFileName("r_npshannon",variables)); outputTypes["r_npshannon"].push_back(getOutputFileName("r_npshannon",variables));
 					}else if (Estimators[i] == "simpson") { 
-						rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson")));
-						outputNames.push_back(fileNameRoot+"r_simpson"); outputTypes["r_simpson"].push_back(fileNameRoot+"r_simpson");
+						rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(getOutputFileName("r_simpson",variables))));
+						outputNames.push_back(getOutputFileName("r_simpson",variables)); outputTypes["r_simpson"].push_back(getOutputFileName("r_simpson",variables));
 					}else if (Estimators[i] == "simpsoneven") { 
-						rDisplays.push_back(new RareDisplay(new SimpsonEven(), new ThreeColumnFile(fileNameRoot+"r_simpsoneven")));
-						outputNames.push_back(fileNameRoot+"r_simpsoneven"); outputTypes["r_simpsoneven"].push_back(fileNameRoot+"r_simpsoneven");
+						rDisplays.push_back(new RareDisplay(new SimpsonEven(), new ThreeColumnFile(getOutputFileName("r_simpsoneven",variables))));
+						outputNames.push_back(getOutputFileName("r_simpsoneven",variables)); outputTypes["r_simpsoneven"].push_back(getOutputFileName("r_simpsoneven",variables));
 					}else if (Estimators[i] == "invsimpson") { 
-						rDisplays.push_back(new RareDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+"r_invsimpson")));
-						outputNames.push_back(fileNameRoot+"r_invsimpson"); outputTypes["r_invsimpson"].push_back(fileNameRoot+"r_invsimpson");
+						rDisplays.push_back(new RareDisplay(new InvSimpson(), new ThreeColumnFile(getOutputFileName("r_invsimpson",variables))));
+						outputNames.push_back(getOutputFileName("r_invsimpson",variables)); outputTypes["r_invsimpson"].push_back(getOutputFileName("r_invsimpson",variables));
 					}else if (Estimators[i] == "bootstrap") { 
-						rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap")));
-						outputNames.push_back(fileNameRoot+"r_bootstrap"); outputTypes["r_bootstrap"].push_back(fileNameRoot+"r_bootstrap");
+						rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(getOutputFileName("r_bootstrap",variables))));
+						outputNames.push_back(getOutputFileName("r_bootstrap",variables)); outputTypes["r_bootstrap"].push_back(getOutputFileName("r_bootstrap",variables));
 					}else if (Estimators[i] == "coverage") { 
-						rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(fileNameRoot+"r_coverage")));
-						outputNames.push_back(fileNameRoot+"r_coverage"); outputTypes["r_coverage"].push_back(fileNameRoot+"r_coverage");
+						rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(getOutputFileName("r_coverage",variables))));
+						outputNames.push_back(getOutputFileName("r_coverage",variables)); outputTypes["r_coverage"].push_back(getOutputFileName("r_coverage",variables));
 					}else if (Estimators[i] == "nseqs") { 
-						rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+"r_nseqs")));
-						outputNames.push_back(fileNameRoot+"r_nseqs"); outputTypes["r_nseqs"].push_back(fileNameRoot+"r_nseqs");
+						rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(getOutputFileName("r_nseqs",variables))));
+						outputNames.push_back(getOutputFileName("r_nseqs",variables)); outputTypes["r_nseqs"].push_back(getOutputFileName("r_nseqs",variables));
 					}
                     if (inputFileNames.size() > 1) { file2Group[outputNames.size()-1] = groups[p]; }
 				}
@@ -527,6 +570,7 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
                 typesFiles[extension] = temp;
             }
             if (!(m->inUsersGroups(file2Group[i], groupNames))) {  groupNames.push_back(file2Group[i]); }
+            
 		}
 		
 		//for each type create a combo file
@@ -605,9 +649,8 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
                 
                 for (int k = 1; k < fileLabels[combineFileName].size(); k++) { //each chunk
 				    //grab data for each group
-                    for (map<string, map<int, vector< vector<string> > > >::iterator itFileNameGroup = files.begin(); itFileNameGroup != files.end(); itFileNameGroup++) {
-                        
-                        string group = itFileNameGroup->first;
+                    for (int n = 0; n < groupNames.size(); n++) {
+                        string group = groupNames[n];
                        
                         map<int, vector< vector<string> > >::iterator itLine = files[group].find(*itNumSampled);
                         if (itLine != files[group].end()) {