X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=command.hpp;h=37186529ab1f75e5747138d74f976c5df3c1bbe9;hp=22f118164eb04e7d22c0438e3e42c56b79ed0f3d;hb=615301e57c25e241356a9c2380648d117709458d;hpb=6f1c0c62e5199454868227e5c3723ea3b4794735

diff --git a/command.hpp b/command.hpp
index 22f1181..3718652 100644
--- a/command.hpp
+++ b/command.hpp
@@ -3,7 +3,7 @@
 //test2
 /*
  *  command.h
- *  
+ *  nast
  *
  *  Created by Pat Schloss on 10/23/08.
  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
@@ -33,6 +33,82 @@ class Command {
 		virtual string getDescription() = 0;
 		
 		virtual map<string, vector<string> > getOutputFiles() { return outputTypes; }
+        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; }