added oldfasta and column parameter to dist.seqs so you can append distances to an...

[mothur.git] / rarefactcommand.cpp

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index 566561e9e695c3f74f7ffb1ce0b1d56ee0e3bc20..217a1520bd11c3ef36e1cd48a7ed0e47326e32e8 100644 (file)
--- 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();