]> git.donarmstrong.com Git - mothur.git/blobdiff - summarysharedcommand.cpp
added get.sharedotu command
[mothur.git] / summarysharedcommand.cpp
index 7c1275f3a8ea9977a39e5294fa7ac330de59d857..ef0485c61886e6f14ae3135f908bf8317855130f 100644 (file)
@@ -40,7 +40,6 @@ SummarySharedCommand::SummarySharedCommand(string option){
                globaldata = GlobalData::getInstance();
                abort = false;
                allLines = 1;
-               lines.clear();
                labels.clear();
                Estimators.clear();
                
@@ -49,7 +48,7 @@ SummarySharedCommand::SummarySharedCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"line","label","calc","groups"};
+                       string Array[] =  {"label","calc","groups"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -64,18 +63,11 @@ SummarySharedCommand::SummarySharedCommand(string option){
                        
                        //make sure the user has already run the read.otu command
                        if (globaldata->getSharedFile() == "") {
-                                cout << "You must read a list and a group, or a shared before you can use the summary.shared command." << endl; abort = true; 
+                                mothurOut("You must read a list and a group, or a shared before you can use the summary.shared command."); mothurOutEndLine(); abort = true; 
                        }
                        
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
-                       line = validParameter.validFile(parameters, "line", false);                             
-                       if (line == "not found") { line = "";  }
-                       else { 
-                               if(line != "all") {  splitAtDash(line, lines);  allLines = 0;  }
-                               else { allLines = 1;  }
-                       }
-                       
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; }
                        else { 
@@ -83,13 +75,10 @@ SummarySharedCommand::SummarySharedCommand(string option){
                                else { allLines = 1;  }
                        }
                        
-                       //make sure user did not use both the line and label parameters
-                       if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; }
-                       //if the user has not specified any line or labels use the ones from read.otu
-                       else if((line == "") && (label == "")) {  
+                       //if the user has not specified any labels use the ones from read.otu
+                       if(label == "") {  
                                allLines = globaldata->allLines; 
                                labels = globaldata->labels; 
-                               lines = globaldata->lines;
                        }
                                
                        calc = validParameter.validFile(parameters, "calc", false);                     
@@ -166,46 +155,40 @@ SummarySharedCommand::SummarySharedCommand(string option){
                }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function SummarySharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SummarySharedCommand", "SummarySharedCommand");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SummarySharedCommand class function SummarySharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 //**********************************************************************************************************************
 
 void SummarySharedCommand::help(){
        try {
-               cout << "The summary.shared command can only be executed after a successful read.otu command." << "\n";
-               cout << "The summary.shared command parameters are label, line and calc.  No parameters are required, but you may not use " << "\n";
-               cout << "both the line and label parameters at the same time. The summary.shared command should be in the following format: " << "\n";
-               cout << "summary.shared(label=yourLabel, line=yourLines, calc=yourEstimators, groups=yourGroups)." << "\n";
-               cout << "Example summary.shared(label=unique-.01-.03, line=0,5,10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan)." << "\n";
+               mothurOut("The summary.shared command can only be executed after a successful read.otu command.\n");
+               mothurOut("The summary.shared command parameters are label and calc.  No parameters are required.\n");
+               mothurOut("The summary.shared command should be in the following format: \n");
+               mothurOut("summary.shared(label=yourLabel, calc=yourEstimators, groups=yourGroups).\n");
+               mothurOut("Example summary.shared(label=unique-.01-.03, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n");
                validCalculator->printCalc("sharedsummary", cout);
-               cout << "The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan" << "\n";
-               cout << "The default value for groups is all the groups in your groupfile." << "\n";
-               cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
-               cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 2 valid groups." << "\n";
-               cout << "Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines)." << "\n" << "\n";
+               mothurOut("The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan\n");
+               mothurOut("The default value for groups is all the groups in your groupfile.\n");
+               mothurOut("The label parameter is used to analyze specific labels in your input.\n");
+               mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 2 valid groups.\n");
+               mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n");
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SummarySharedCommand", "help");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SummarySharedCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 //**********************************************************************************************************************
 
 SummarySharedCommand::~SummarySharedCommand(){
-       delete read;
-       delete validCalculator;
+       if (abort == false) {
+               delete read;
+               delete validCalculator;
+       }
 }
 
 //**********************************************************************************************************************
@@ -214,8 +197,6 @@ int SummarySharedCommand::execute(){
        try {
        
                if (abort == true) { return 0; }
-               
-               int count = 1;  
        
                //if the users entered no valid calculators don't execute command
                if (sumCalculators.size() == 0) { return 0; }
@@ -232,7 +213,7 @@ int SummarySharedCommand::execute(){
                        
                input = globaldata->ginput;
                lookup = input->getSharedRAbundVectors();
-               vector<SharedRAbundVector*> lastLookup = lookup;
+               string lastLabel = lookup[0]->getLabel();
                
                //output estimator names as column headers
                outputFileHandle << "label" <<'\t' << "comparison" << '\t'; 
@@ -256,7 +237,7 @@ int SummarySharedCommand::execute(){
                }
                
                if (lookup.size() < 2) { 
-                       cout << "I cannot run the command without at least 2 valid groups."
+                       mothurOut("I cannot run the command without at least 2 valid groups.")
                        for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
                        
                        //close files and clean up
@@ -273,58 +254,62 @@ int SummarySharedCommand::execute(){
                //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
                set<string> processedLabels;
                set<string> userLabels = labels;
-               set<int> userLines = lines;
-               
+                       
                //as long as you are not at the end of the file or done wih the lines you want
-               while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+               while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                
-                       if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){                       
-                               cout << lookup[0]->getLabel() << '\t' << count << endl;
+                       if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
+                               mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
                                process(lookup);
                                
                                processedLabels.insert(lookup[0]->getLabel());
                                userLabels.erase(lookup[0]->getLabel());
-                               userLines.erase(count);
                        }
                        
-                       if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
-                                       cout << lastLookup[0]->getLabel() << '\t' << count << endl;
-                                       process(lastLookup);
+                       if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                                       for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
+                                       lookup = input->getSharedRAbundVectors(lastLabel);
+
+                                       mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+                                       process(lookup);
                                        
-                                       processedLabels.insert(lastLookup[0]->getLabel());
-                                       userLabels.erase(lastLookup[0]->getLabel());
+                                       processedLabels.insert(lookup[0]->getLabel());
+                                       userLabels.erase(lookup[0]->getLabel());
                        }
 
                
-                       //prevent memory leak
-                       if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  } }
-                       lastLookup = lookup;                    
+                       
+                       lastLabel = lookup[0]->getLabel();                      
                                
                        //get next line to process
+                       //prevent memory leak
+                       for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
                        lookup = input->getSharedRAbundVectors();
-                       count++;
                }
                
                //output error messages about any remaining user labels
                set<string>::iterator it;
                bool needToRun = false;
                for (it = userLabels.begin(); it != userLabels.end(); it++) {  
-                       cout << "Your file does not include the label "<< *it
-                       if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
-                               cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
+                       mothurOut("Your file does not include the label " + *it)
+                       if (processedLabels.count(lastLabel) != 1) {
+                               mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
                                needToRun = true;
                        }else {
-                               cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+                               mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
                        }
                }
                
-               //run last line if you need to
+               //run last label if you need to
                if (needToRun == true)  {
-                       cout << lastLookup[0]->getLabel() << '\t' << count << endl;
-                       process(lastLookup);
+                               for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i];       } } 
+                               lookup = input->getSharedRAbundVectors(lastLabel);
+
+                               mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+                               process(lookup);
+                               for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
                }
                
-               for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  }
 
                //reset groups parameter
                globaldata->Groups.clear();  
@@ -335,18 +320,14 @@ int SummarySharedCommand::execute(){
                
                for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
                
-               delete input;
+               delete input;  globaldata->ginput = NULL;
 
                return 0;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SummarySharedCommand", "execute");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SummarySharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
 }
 
 /***********************************************************/
@@ -406,13 +387,9 @@ void SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup) {
 
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SummarySharedCommand", "process");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SummarySharedCommand class function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
 }
 
-/***********************************************************/
\ No newline at end of file
+/***********************************************************/