X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactcommand.cpp;h=217a1520bd11c3ef36e1cd48a7ed0e47326e32e8;hb=2431fce75705f16d6d7cab7a6f5fe02051d82ca5;hp=566561e9e695c3f74f7ffb1ce0b1d56ee0e3bc20;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index 566561e..217a152 100644
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -103,6 +103,7 @@ void RareFactCommand::help(){
 		m->mothurOut("The rarefaction.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n");
 		m->mothurOut("The rarefaction.single command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster.\n");
 		m->mothurOut("The rarefaction.single command parameters are label, iters, freq, calc and abund.  No parameters are required. \n");
+		m->mothurOut("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");
 		m->mothurOut("The rarefaction.single command should be in the following format: \n");
 		m->mothurOut("rarefaction.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n");
 		m->mothurOut("Example rarefaction.single(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).\n");
@@ -130,17 +131,18 @@ int RareFactCommand::execute(){
 		
 		vector<string> outputNames;
 		
+		string hadShared = "";
 		if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName);  }
-		else {  inputFileNames = parseSharedFile(globaldata->getSharedFile());  globaldata->setFormat("rabund");  }
-		
-		if (m->control_pressed) { return 0; }
+		else { hadShared = globaldata->getSharedFile(); inputFileNames = parseSharedFile(globaldata->getSharedFile());  globaldata->setFormat("rabund");  }
+				
+		if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } return 0; }
 		
 		for (int p = 0; p < inputFileNames.size(); p++) {
 			
 			string fileNameRoot = outputDir + getRootName(getSimpleName(inputFileNames[p]));
 			globaldata->inputFileName = inputFileNames[p];
 			
-			if (m->control_pressed) { return 0; }
+			if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } return 0; }
 			
 			if (inputFileNames.size() > 1) {
 				m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
@@ -202,12 +204,12 @@ int RareFactCommand::execute(){
 			set<string> processedLabels;
 			set<string> userLabels = labels;
 			
-			if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	} delete validCalculator; delete read; delete input; globaldata->ginput = NULL; delete order; globaldata->gorder = NULL; for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
+			if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	} delete validCalculator; delete read; delete input; globaldata->ginput = NULL; delete order; globaldata->gorder = NULL; for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
 			
 			//as long as you are not at the end of the file or done wih the lines you want
 			while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 				
-				if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	} delete validCalculator; delete read; delete input; globaldata->ginput = NULL; delete order; globaldata->gorder = NULL; for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
+				if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	} delete validCalculator; delete read; delete input; globaldata->ginput = NULL; delete order; globaldata->gorder = NULL; for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
 
 				
 				if(allLines == 1 || labels.count(order->getLabel()) == 1){
@@ -245,7 +247,7 @@ int RareFactCommand::execute(){
 				order = (input->getOrderVector());
 			}
 			
-			if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	} delete validCalculator; delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); }  return 0; }
+			if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	} delete validCalculator; delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); }  return 0; }
 
 			//output error messages about any remaining user labels
 			set<string>::iterator it;
@@ -260,7 +262,7 @@ int RareFactCommand::execute(){
 				}
 			}
 			
-			if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	} delete validCalculator; delete read; delete input; globaldata->ginput = NULL;  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
+			if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	} delete validCalculator; delete read; delete input; globaldata->ginput = NULL;  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
 
 			//run last label if you need to
 			if (needToRun == true)  {
@@ -285,6 +287,8 @@ int RareFactCommand::execute(){
 			
 		}
 		
+		if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  }
+		
 		if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } return 0; }
 
 		m->mothurOutEndLine();