//**********************************************************************************************************************
vector<string> LoadLogfileCommand::setParameters(){
try {
- CommandParameter plogfile("logfile", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plogfile);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter plogfile("logfile", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(plogfile);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
//look for "mothur >"
int pos = line.find("mothur > "); //command line
int pos2 = line.find("Output File "); //indicates command completed and we can update the current file
- int pos3 = line.find("*****************");
+ int pos3 = line.find("/*****************");
//skipping over parts where a command runs another command
if (pos3 != string::npos) {
while (!in.eof()) {
if (m->control_pressed) { break; }
line = m->getline(in); m->gobble(in);
- int posTemp = line.find("*****************");
+ int posTemp = line.find("/*****************");
if (posTemp != string::npos) { break; }
}
}
Command* command = cFactory->getCommand(commandName);
map<string, vector<string> > thisOutputTypes = command->getOutputFiles();
+
for (map<string, vector<string> >::iterator it = thisOutputTypes.begin(); it != thisOutputTypes.end(); it++) {
if (currentTypes.count((it->first)) != 0) { //do we save this type
//if yes whats its tag
string thisTypesCurrentFile = "";
if (itCurrentFiles != currentFiles.end()) { thisTypesCurrentFile = itCurrentFiles->second; }
- string tag = command->getOutputFileNameTag(it->first, thisTypesCurrentFile); //pass it "fasta" and the current fasta file name. some commands use the current name to get the extension, the others wont care.
- //search for the tag in the list of output files
- for (int h = 0; h < theseOutputNames.size(); h++) {
- string ending = theseOutputNames[h].substr(theseOutputNames[h].length()-tag.length(), tag.length());
- if (ending == tag) { //if it's there and this is a type we save a current version of, save it
- if ((it->first == "column") || (it->first == "phylip")) { //check for format
- string RippedName = "";
- bool foundDot = false;
- for (int i = theseOutputNames[h].length()-1; i >= 0; i--) {
- if (foundDot && (theseOutputNames[h][i] != '.')) { RippedName = theseOutputNames[h][i] + RippedName; }
- else if (foundDot && (theseOutputNames[h][i] == '.')) { break; }
- else if (!foundDot && (theseOutputNames[h][i] == '.')) { foundDot = true; }
- }
- if ((RippedName == "phylip") || (RippedName == "lt") || (RippedName == "square")) { currentFiles["phylip"] = theseOutputNames[h]; }
- else { currentFiles["column"] = theseOutputNames[h]; }
- }else { currentFiles[it->first] = theseOutputNames[h]; }
- break;
- }
- }
+ //outputfilename pattern for this input type
+ string pattern = command->getOutputPattern(it->first);
+ updateCurrent(pattern, it->first, thisTypesCurrentFile, theseOutputNames, currentFiles);
+
+ //cout << "current=\n\n";
+ //for (map<string, string>::iterator itcc = currentFiles.begin(); itcc != currentFiles.end(); itcc++) {
+ // cout << itcc->first << '\t' << itcc->second << endl;
+ // }
}
}
}
}
//**********************************************************************************************************************
+int LoadLogfileCommand::updateCurrent(string pattern, string type, string thisTypesCurrentFile, vector<string> filenames, map<string, string>& currentFiles){
+ try {
+
+ vector<string> patterns; m->splitAtChar(pattern, patterns, '-');
+
+ for (int i = 0; i < patterns.size(); i++) {
+
+ vector<string> peices; m->splitAtChar(patterns[i], peices, ',');
+ //cout << "patterns i = " << patterns[i] << endl;
+ if (peices.size() != 0) {
+ string tag = peices[peices.size()-1];
+ //cout << "tag = " << tag << endl;
+ if (peices[peices.size()-1] == "[extension]") { tag = m->getExtension(thisTypesCurrentFile); }
+
+ //search for the tag in the list of output files
+ for (int h = 0; h < filenames.size(); h++) {
+
+ if (m->control_pressed) { return 0; }
+ //cout << "filename h = " << filenames[h]<< endl;
+ string ending = filenames[h].substr(filenames[h].length()-tag.length(), tag.length());
+ if (ending == tag) { //if it's there and this is a type we save a current version of, save it
+ if ((type == "column") || (type == "phylip")) { //check for format
+ string RippedName = "";
+ bool foundDot = false;
+ for (int i = filenames[h].length()-1; i >= 0; i--) {
+ if (foundDot && (filenames[h][i] != '.')) { RippedName = filenames[h][i] + RippedName; }
+ else if (foundDot && (filenames[h][i] == '.')) { break; }
+ else if (!foundDot && (filenames[h][i] == '.')) { foundDot = true; }
+ }
+ if ((RippedName == "phylip") || (RippedName == "lt") || (RippedName == "square")) { currentFiles["phylip"] = filenames[h]; }
+ else { currentFiles["column"] = filenames[h]; }
+ }else { currentFiles[type] = filenames[h]; }
+ break;
+ }
+ }
+ }
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LoadLogfileCommand", "updateCurrent");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
projects / mothur.git / blobdiff