-void FilterSeqsCommand::doSoft() {
- //soft = atoi(globaldata->getSoft().c_str());
-// vector<vector<int> > columnSymbolSums;
-// vector<vector<string> > columnSymbols;
-// for(int i = 0; i < db->get(0).getLength(); i++) {
-// vector<string> symbols;
-// vector<int> sums;
-// columnSymbols[i] = symbols;
-// columnSymbolSums[i] = sums;
-// }
-//
-// for(int i = 0; i < db->size(); i++) {
-// Sequence cur = db->get(i);
-// string curAligned = cur.getAligned();
-//
-// for(int j = 0; j < curAligned.length-1; j++) {
-// string curChar = curAligned.substr(j, j+1);
-// vector<string> curColumnSymbols = columnSymbols[j];
-//
-// bool newSymbol = true;
-//
-// for(int k = 0; j < curColumnSymbols.size(); j++)
-// if(curChar.compare(curColumnSymbols[k]) == 0) {
-// newSymbol = false;
-// columnSymbolSums[j][k]++;
-// }
-//
-// if(newSymbol) {
-// columnSymbols.push_back(curChar);
-// columnSymbolSums[j].push_back(1);
-// }
-// }
-// }
-//
-// for(int i = 0; i < columnSymbolSums.size(); i++) {
-// int totalSum = 0;
-// int max = 0;
-// vector<int> curColumn = columnSymbolSums[i];
-//
-// for(int j = 0; j < curColumn.size(); j++) {
-// int curSum = curColumn[j];
-// if(curSum > max)
-// max = curSum;
-// totalSum += curSum;
-// }
-//
-// if((double)max/(double)totalSum * 100 < soft)
-// columnsToRemove[i] = true;
-// }
+FilterSeqsCommand::FilterSeqsCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+ filterFileName = "";
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter("filter.seqs");
+ map<string,string>::iterator it;
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["filter"] = tempOutNames;
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("fasta");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["fasta"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("hard");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["hard"] = inputDir + it->second; }
+ }
+ }
+
+ //check for required parameters
+ fasta = validParameter.validFile(parameters, "fasta", false);
+ if (fasta == "not found") {
+ fasta = m->getFastaFile();
+ if (fasta != "") { fastafileNames.push_back(fasta); m->mothurOut("Using " + fasta + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
+ else {
+ m->splitAtDash(fasta, fastafileNames);
+
+ //go through files and make sure they are good, if not, then disregard them
+ for (int i = 0; i < fastafileNames.size(); i++) {
+
+ bool ignore = false;
+ if (fastafileNames[i] == "current") {
+ fastafileNames[i] = m->getFastaFile();
+ if (fastafileNames[i] != "") { m->mothurOut("Using " + fastafileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
+ //erase from file list
+ fastafileNames.erase(fastafileNames.begin()+i);
+ i--;
+ }
+ }
+
+ if (!ignore) {
+ if (inputDir != "") {
+ string path = m->hasPath(fastafileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { fastafileNames[i] = inputDir + fastafileNames[i]; }
+ }
+
+ ifstream in;
+ int ableToOpen = m->openInputFile(fastafileNames[i], in, "noerror");
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(fastafileNames[i]);
+ m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ fastafileNames[i] = tryPath;
+ }
+ }
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(fastafileNames[i]);
+ m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ fastafileNames[i] = tryPath;
+ }
+ }
+
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + fastafileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ fastafileNames.erase(fastafileNames.begin()+i);
+ i--;
+ }else{
+ string simpleName = m->getSimpleName(fastafileNames[i]);
+ filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
+ m->setFastaFile(fastafileNames[i]);
+ }
+ in.close();
+ }
+ }
+
+ //make sure there is at least one valid file left
+ if (fastafileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
+ }
+
+ if (!abort) {
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
+ outputDir = "";
+ outputDir += m->hasPath(fastafileNames[0]); //if user entered a file with a path then preserve it
+ }
+ }
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+
+ string temp;
+ hard = validParameter.validFile(parameters, "hard", true); if (hard == "not found") { hard = ""; }
+ else if (hard == "not open") { hard = ""; abort = true; }
+
+ temp = validParameter.validFile(parameters, "trump", false); if (temp == "not found") { temp = "*"; }
+ trump = temp[0];
+
+ temp = validParameter.validFile(parameters, "soft", false); if (temp == "not found") { soft = 0; }
+ else { soft = (float)atoi(temp.c_str()) / 100.0; }
+
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ m->mothurConvert(temp, processors);
+
+ vertical = validParameter.validFile(parameters, "vertical", false);
+ if (vertical == "not found") {
+ if ((hard == "") && (trump == '*') && (soft == 0)) { vertical = "T"; } //you have not given a hard file or set the trump char.
+ else { vertical = "F"; }
+ }
+
+ numSeqs = 0;
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
+ exit(1);
+ }