added *.count.summary file to count.groups command. added deltaq and insert parameter...

[mothur.git] / command.hpp

diff --git a/command.hpp b/command.hpp
index f5e09042234f1c39ac8010f859e6f69708871dc3..48dcf283c8874c8168ac6cf48748bf80851caef3 100644 (file)
--- a/command.hpp
+++ b/command.hpp
@@ -33,7 +33,82 @@ class Command {
                virtual string getDescription() = 0;
                
                virtual map<string, vector<string> > getOutputFiles() { return outputTypes; }
-        virtual string getOutputFileNameTag(string, string) = 0;  //we may not know the complete filename, because some commands use info from the file to create the output file name (ie label). but we do the ending tag which should be enough to find the output file name from a list. Allows for optional passing of the inputFileName for the commands that require its extension.
+        string getOutputFileName(string type, map<string, string> variableParts) {  //uses the pattern to create an output filename for a given type and input file name.  
+               try {
+                    string filename = "";
+                    map<string, vector<string> >::iterator it;
+                    
+                    //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 {
+                        
+                        string patternTemp = getOutputPattern(type);
+                        vector<string> patterns;
+                        m->splitAtDash(patternTemp, patterns);
+                        
+                        //find pattern to use based on number of variables passed in
+                        string pattern = "";
+                        bool foundPattern = false;
+                        vector<int> numVariablesPerPattern;
+                        for (int i = 0; i < patterns.size(); i++) {
+                            int numVariables = 0;
+                            for (int j = 0; j < patterns[i].length(); j++) { if (patterns[i][j] == '[') { numVariables++; } }
+                            numVariablesPerPattern.push_back(numVariables);
+                            
+                            if (numVariables == variableParts.size()) { pattern = patterns[i]; foundPattern = true; break; }
+                        }
+                        
+                        //if you didn't find an exact match do we have something that might work
+                        if (!foundPattern) {  
+                            for (int i = 0; i < numVariablesPerPattern.size(); i++) {
+                                if (numVariablesPerPattern[i] < variableParts.size()) { pattern = patterns[i]; foundPattern = true; break; }
+                            }
+                            if (!foundPattern) {  m->mothurOut("[ERROR]: Not enough variable pieces for " + type + ".\n"); m->control_pressed = true; }
+                        }
+                        
+                        if (pattern != "") {
+                            int numVariables = 0;
+                            for (int i = 0; i < pattern.length(); i++) { if (pattern[i] == '[') { numVariables++; } }
+                            
+                            vector<string> pieces;
+                            m->splitAtComma(pattern, pieces);
+                            
+                        
+                            for (int i = 0; i < pieces.size(); i++) {
+                                if (pieces[i][0] == '[') {
+                                    map<string, string>::iterator it = variableParts.find(pieces[i]);
+                                    if (it == variableParts.end()) {
+                                        m->mothurOut("[ERROR]: Did not provide variable for " + pieces[i] + ".\n"); m->control_pressed = true;
+                                    }else {
+                                        if (it->second != "") {
+                                            if (it->first == "[filename]") { filename += it->second; }
+                                            else if (it->first == "[extension]") { 
+                                                if (filename.length() > 0) { //rip off last "."
+                                                    filename = filename.substr(0, filename.length()-1);
+                                                }
+                                                filename += it->second + "."; 
+                                            }else { filename += it->second + "."; }
+                                        }
+                                    }
+                                }else {
+                                    filename += pieces[i] + ".";
+                                }
+                            }
+                            if (filename.length() > 0) { //rip off last "."
+                                filename = filename.substr(0, filename.length()-1);
+                            }
+                        }
+                    }
+                    return filename;
+                }
+                catch(exception& e) {
+                    m->errorOut(e, "command", "getOutputFileName");
+                    exit(1);
+                }
+        }
+        
+        virtual string getOutputPattern(string) = 0; //pass in type, returns something like: [filename],align or [filename],[distance],subsample.shared  strings in [] means its a variable.  This is used by the gui to predict output file names.  use variable keywords: [filename], [distance], [group], [extension], [tag]
                virtual vector<string> setParameters() = 0; //to fill parameters
                virtual vector<CommandParameter> getParameters() { return parameters; }