X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=errorchecking.cpp;h=e4c1877907e272c89a0be023ec21ad6bf2947f50;hb=825512fb96e5bb00e08665396d9fa6a8c4da5a68;hp=7f581d9e91fd4ef1352e866180f36a4aefccc69f;hpb=1b2517db06f3c6cd5f5c67198261361ce8dad611;p=mothur.git diff --git a/errorchecking.cpp b/errorchecking.cpp index 7f581d9..e4c1877 100644 --- a/errorchecking.cpp +++ b/errorchecking.cpp @@ -23,28 +23,33 @@ ErrorCheck::ErrorCheck() { /******************************************************/ void ErrorCheck::refresh() { - columnfile = globaldata->getColumnFile(); - phylipfile = globaldata->getPhylipFile(); - listfile = globaldata->getListFile(); - rabundfile = globaldata->getRabundFile(); - sabundfile = globaldata->getSabundFile(); - namefile = globaldata->getNameFile(); - groupfile = globaldata->getGroupFile(); - orderfile = globaldata->getOrderFile(); - fastafile = globaldata->getFastaFile(); - treefile = globaldata->getTreeFile(); - cutoff = globaldata->getCutOff(); - format = globaldata->getFormat(); - method = globaldata->getMethod(); - randomtree = globaldata->getRandomTree(); - sharedfile = globaldata->getSharedFile(); + + //columnfile = globaldata->getColumnFile(); + //phylipfile = globaldata->getPhylipFile(); + //listfile = globaldata->getListFile(); + //rabundfile = globaldata->getRabundFile(); + //sabundfile = globaldata->getSabundFile(); + //namefile = globaldata->getNameFile(); + //groupfile = globaldata->getGroupFile(); + //orderfile = globaldata->getOrderFile(); + //fastafile = globaldata->getFastaFile(); + //treefile = globaldata->getTreeFile(); + //cutoff = globaldata->getCutOff(); + //format = globaldata->getFormat(); + //method = globaldata->getMethod(); + //randomtree = globaldata->getRandomTree(); + //sharedfile = globaldata->getSharedFile(); + } /*******************************************************/ /******************************************************/ -ErrorCheck::~ErrorCheck() {} +ErrorCheck::~ErrorCheck() { + delete validCommand; + delete validParameter; +} /*******************************************************/ @@ -71,8 +76,8 @@ bool ErrorCheck::checkInput(string input) { //is it a valid command if (validCommand->isValidCommand(commandName) != true) { return false; } - string parameter, value; + //reads in parameters and values if((optionText != "") && (commandName != "help")){ while((optionText.find_first_of(',') != -1) && (errorFree)) { //while there are parameters @@ -80,7 +85,7 @@ bool ErrorCheck::checkInput(string input) { splitAtEquals(parameter, value); //is it a valid parameter - if (validParameter->isValidParameter(parameter) != true) { return false; } + if (validParameter->isValidParameter(parameter, commandName, value) != true) { return false; } if (parameter == "phylip" ) { phylipfile = value; } if (parameter == "column" ) { columnfile = value; } @@ -90,9 +95,11 @@ bool ErrorCheck::checkInput(string input) { if (parameter == "name" ) { namefile = value; } if (parameter == "order" ) { orderfile = value; } if (parameter == "fasta" ) { fastafile = value; } + if (parameter == "nexus" ) { nexusfile = value; } + if (parameter == "clustal" ) { clustalfile = value; } if (parameter == "tree" ) { treefile = value; } - if (parameter == "group" ) { groupfile = value; } - if (parameter == "shared" ) { sharedfile = value; } + if (parameter == "group" ) { groupfile = value; } + if (parameter == "shared" ) { sharedfile = value; } if (parameter == "cutoff" ) { cutoff = value; } if (parameter == "precision" ) { precision = value; } if (parameter == "iters" ) { iters = value; } @@ -102,8 +109,24 @@ bool ErrorCheck::checkInput(string input) { if (parameter == "fileroot" ) { fileroot = value; } if (parameter == "line" ) { line = value; } if (parameter == "label" ) { label = value; } - if (parameter == "randomtree" ) { randomtree = value; } - + if (parameter == "abund" ) { abund = value; } + if (parameter == "random" ) { randomtree = value; } + if (parameter == "sorted" ) { sorted = value; } + if (parameter == "trump" ) { trump = value; } + if (parameter == "soft" ) { soft = value; } + if (parameter == "filter" ) { filter = value; } + if (parameter == "scale" ) { scale = value; } + if (parameter == "countends" ) { countends = value; } + if (parameter == "processors" ) { processors = value; } + if (parameter == "size" ) { size = value; } + if (parameter == "candidate") { candidatefile = value; } + if (parameter == "search") { search = value; } + if (parameter == "ksize") { ksize = value; } + if (parameter == "align") { align = value; } + if (parameter == "match") { match = value; } + if (parameter == "mismatch") { mismatch = value; } + if (parameter == "gapopen") { gapopen = value; } + if (parameter == "gapextend" ) { gapextend = value; } } //gets the last parameter and value @@ -111,7 +134,8 @@ bool ErrorCheck::checkInput(string input) { value = optionText; splitAtEquals(parameter, value); //is it a valid parameter - if (validParameter->isValidParameter(parameter) != true) { return false; } + if (validParameter->isValidParameter(parameter, commandName, value) != true) { return false; } + if (parameter == "phylip" ) { phylipfile = value; } if (parameter == "column" ) { columnfile = value; } @@ -123,6 +147,8 @@ bool ErrorCheck::checkInput(string input) { if (parameter == "group" ) { groupfile = value; } if (parameter == "shared" ) { sharedfile = value; } if (parameter == "fasta" ) { fastafile = value; } + if (parameter == "nexus" ) { nexusfile = value; } + if (parameter == "clustal" ) { clustalfile = value; } if (parameter == "tree" ) { treefile = value; } if (parameter == "cutoff" ) { cutoff = value; } if (parameter == "precision" ) { precision = value; } @@ -133,17 +159,32 @@ bool ErrorCheck::checkInput(string input) { if (parameter == "fileroot" ) { fileroot = value; } if (parameter == "line" ) { line = value; } if (parameter == "label" ) { label = value; } - if (parameter == "randomtree" ) { randomtree = value; } - + if (parameter == "random" ) { randomtree = value; } + if (parameter == "abund" ) { abund = value; } + if (parameter == "sorted" ) { sorted = value; } + if (parameter == "trump" ) { trump = value; } + if (parameter == "soft" ) { soft = value; } + if (parameter == "filter" ) { filter = value; } + if (parameter == "scale" ) { scale = value; } + if (parameter == "countends" ) { countends = value; } + if (parameter == "processors" ) { processors = value; } + if (parameter == "size" ) { size = value; } + if (parameter == "candidate") { candidatefile = value; } + if (parameter == "search") { search = value; } + if (parameter == "ksize") { ksize = value; } + if (parameter == "align") { align = value; } + if (parameter == "match") { match = value; } + if (parameter == "mismatch") { mismatch = value; } + if (parameter == "gapopen") { gapopen = value; } + if (parameter == "gapextend" ) { gapextend = value; } + } } //make sure the user does not use both the line and label parameters if ((line != "") && (label != "")) { cout << "You may use either the line or label parameters, but not both." << endl; return false; } - //make sure you have a valid random tree value - if ((randomtree != "0") && (randomtree != "1")) { cout << randomtree << " is not a valid randomtree value. Valid values for randomtree are 0, (meaning you have read your own trees) or 1 (meaning you want to random distribution of trees)." << endl; return false; } - + //check for valid files if (commandName == "read.dist") { validateReadFiles(); validateReadDist(); @@ -151,13 +192,17 @@ bool ErrorCheck::checkInput(string input) { //you want to do shared commands if ((listfile != "") && (groupfile != "")) { validateParseFiles(); //checks the listfile and groupfile parameters - }else { //you want to do single commands + //you want to do single commands + }else if ((listfile != "") || (rabundfile != "") || (sabundfile != "")){ validateReadFiles(); validateReadPhil(); + //you have not given a file + }else if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "")) { + cout << "You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. " << endl; return false; + //you want to do shared commands with a shared file + }else if (sharedfile != "") {//you are reading a shared file + validateReadFiles(); } - }else if (commandName == "read.shared") { - //you want to do shared commands with just the shared file - validateReadFiles(); }else if (commandName == "read.tree") { validateTreeFiles(); //checks the treefile and groupfile parameters }else if (commandName == "deconvolute") { @@ -165,27 +210,37 @@ bool ErrorCheck::checkInput(string input) { validateReadFiles(); } - //are you trying to cluster before you have read something - if ((commandName == "cluster") && (globaldata->getSparseMatrix() == NULL) || - (commandName == "cluster") && (globaldata->getListVector() == NULL)) { + //are you trying to cluster before you have read something + if (((commandName == "cluster") && (globaldata->gSparseMatrix == NULL)) || + ((commandName == "cluster") && (globaldata->gListVector == NULL))) { cout << "Before you use the cluster command, you first need to read in a distance matrix." << endl; errorFree = false; } + if ((commandName == "libshuff") && ((globaldata->gMatrix == NULL) || (globaldata->gGroupmap == NULL))) { + cout << "You must read in a matrix and groupfile using the read.dist command, before you use the libshuff command. " << endl; return false; + } + if (commandName == "parsimony") { //are you trying to use parsimony without reading a tree or saying you want random distribution - if (randomtree == "0") { + if (randomtree == "") { if (globaldata->gTree.size() == 0) { - cout << "You must read a treefile and a groupfile or set the randomtree parameter to 1, before you may execute the parsimony command." << endl; return false; } + cout << "You must read a treefile and a groupfile or set the randomtree parameter to the output filename you wish, before you may execute the parsimony command." << endl; return false; } } } - if ((commandName == "unifrac.weighted") || (commandName == "unifrac.unweighted")) { + if ((commandName == "unifrac.weighted") || (commandName == "unifrac.unweighted") || (commandName == "concensus")) { if (globaldata->gTree.size() == 0) {//no trees were read - cout << "You must execute the read.tree command, before you may execute the unifrac.weighted or unifrac.unweighted command." << endl; return false; } + cout << "You must execute the read.tree command, before you may execute the unifrac.weighted, unifrac.unweighted or concensus command." << endl; return false; } } //check for valid method + if(commandName == "get.group") { + if ((globaldata->getSharedFile() == "")) { cout << "You must read a groupfile or a sharedfile before you can use the get.group command." << endl; return false; } + } + if (commandName == "get.label" || commandName == "get.line") { + if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a list, sabund or rabund before you can use the get.label or get.line command." << endl; return false; } + } if (commandName == "cluster") { if ((method == "furthest") || (method == "nearest") || (method == "average")) { } else {cout << "Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average." << endl; return false; } @@ -195,13 +250,58 @@ bool ErrorCheck::checkInput(string input) { if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a list, sabund or rabund before you can use the collect.single, rarefaction.single or summary.single commands." << endl; return false; } } - if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") ){ + if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") || (commandName == "bootstrap.shared") || (commandName == "dist.shared")){ if (globaldata->getSharedFile() == "") { - if (globaldata->getListFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; } - else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; } + if (globaldata->getListFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared, rarefaction.shared, summary.shared, tree.shared, bootstrap.shared or dist.shared commands." << endl; return false; } + else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared, rarefaction.shared, summary.shared, tree.shared, bootstrap.shared or dist.shared commands." << endl; return false; } + } + } + + if (commandName == "tree.shared") { + //given no files + if ((globaldata->getSharedFile() == "") && ((phylipfile == "") && (columnfile == ""))) { cout << "You must run the read.otu command or provide a distance file before running the tree.shared command." << endl; return false; } + //you want to do single commands + else if ((globaldata->getSharedFile() == "") && ((phylipfile != "") || (columnfile != ""))) { + validateReadDist(); + } + } + + if ((commandName == "heatmap") || (commandName == "venn")) { + if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) { + cout << "You must read a list, or a list and a group, or a shared before you can use the heatmap or venn commands." << endl; return false; + } + } + + if ((commandName == "filter.seqs") || (commandName == "dist.seqs")) { + if ((fastafile == "") && (nexusfile == "") && (clustalfile == "") && (phylipfile == "")) { + cout << "You must enter either a fasta, nexus, clustal, or phylip file before you can use the filter.seqs or dist.seqs command." << endl; return false; + } + validateSeqsFiles(); + } + + if (commandName == "align.seqs") { + if ((fastafile == "") || (candidatefile == "")) { + cout << "You must enter fasta and a candidate file to use the align.seqs command." << endl; return false; } + validateSeqsFiles(); + } + + if ((commandName == "bin.seqs")) { + if ((globaldata->getListFile() == "")) { cout << "You must read a list file before you can use the bin.seqs commands." << endl; return false; } + validateBinFiles(); } - + + + if ((commandName == "get.oturep")) { + if ((globaldata->gSparseMatrix == NULL) || (globaldata->gListVector == NULL)) { + cout << "Before you use the get.oturep command, you first need to read in a distance matrix." << endl; + errorFree = false; + } + if (listfile == "") { cout << "list is a required parameter for the get.oturep command." << endl; errorFree = false; } + validateBinFiles(); + } + + return errorFree; } @@ -223,7 +323,7 @@ void ErrorCheck::validateReadFiles() { //unable to open if (ableToOpen == 1) { errorFree = false; } else { globaldata->inputFileName = phylipfile; } - //are we reading a phylipfile + //are we reading a columnfile }else if (columnfile != "") { ableToOpen = openInputFile(columnfile, filehandle); filehandle.close(); @@ -263,6 +363,12 @@ void ErrorCheck::validateReadFiles() { //unable to open if (ableToOpen == 1) { errorFree = false; } else { globaldata->inputFileName = sharedfile; } + }else if (groupfile != "") { + ableToOpen = openInputFile(groupfile, filehandle); + filehandle.close(); + if (ableToOpen == 1) { //unable to open + errorFree = false; + } }else{ //no file given errorFree = false; } @@ -287,8 +393,15 @@ void ErrorCheck::validateReadDist() { ifstream filehandle; int ableToOpen; - if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist you must enter a phylip or a column." << endl; errorFree = false; } - else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist you must enter ONLY ONE of the following: phylip or column." << endl; errorFree = false; } + if (groupfile != "") { + ableToOpen = openInputFile(groupfile, filehandle); + filehandle.close(); + //unable to open + if (ableToOpen == 1) { errorFree = false; } + } + + if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist or a tree.shared command with a distance file you must enter a phylip or a column." << endl; errorFree = false; } + else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist or a tree.shared command with a distance file you must enter ONLY ONE of the following: phylip or column." << endl; errorFree = false; } if (columnfile != "") { if (namefile == "") { @@ -337,7 +450,7 @@ void ErrorCheck::validateParseFiles() { ableToOpen = openInputFile(groupfile, filehandle); filehandle.close(); if (ableToOpen == 1) { //unable to open - errorFree = false;; + errorFree = false; } } } @@ -412,7 +525,7 @@ void ErrorCheck::validateReadPhil() { }else if (sabundfile != "") { if ((listfile != "") || (rabundfile != "")) { cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; } - }else if ((listfile == "") && (rabundfile == "") && (sabundfile == "")) { + }else if ((listfile == "") && (rabundfile == "") && (sabundfile == "") && (sharedfile == "")) { cout << "When executing a read.otu you must enter one of the following: list, rabund or sabund." << endl; errorFree = false; } @@ -436,6 +549,137 @@ void ErrorCheck::validateReadPhil() { } /*******************************************************/ +/******************************************************/ +//This function checks to make sure the user entered appropriate +// format parameters on a distfile read +void ErrorCheck::validateSeqsFiles() { + try { + ifstream filehandle; + int ableToOpen; + + //checks to make sure only one file type is given + if (phylipfile != "") { + if ((nexusfile != "") || (fastafile != "") || (clustalfile != "")) { + cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; } + else { + ableToOpen = openInputFile(phylipfile, filehandle); + filehandle.close(); + if (ableToOpen == 1) { //unable to open + errorFree = false; + } + } + }else if (nexusfile != "") { + if ((phylipfile != "") || (fastafile != "") || (clustalfile != "")) { + cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; } + else { + ableToOpen = openInputFile(nexusfile, filehandle); + filehandle.close(); + if (ableToOpen == 1) { //unable to open + errorFree = false; + } + } + }else if (fastafile != "") { + if ((phylipfile != "") || (nexusfile != "") || (clustalfile != "")) { + cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; } + else { + ableToOpen = openInputFile(fastafile, filehandle); + filehandle.close(); + if (ableToOpen == 1) { //unable to open + errorFree = false; + } + } + }else if (clustalfile != "") { + if ((phylipfile != "") || (nexusfile != "") || (fastafile != "")) { + cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; } + else { + ableToOpen = openInputFile(clustalfile, filehandle); + filehandle.close(); + if (ableToOpen == 1) { //unable to open + errorFree = false; + } + } + }else if (candidatefile != "") { + ableToOpen = openInputFile(candidatefile, filehandle); + filehandle.close(); + if (ableToOpen == 1) { //unable to open + errorFree = false; + } + } + + + } + catch(exception& e) { + cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateSeqsFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } + catch(...) { + cout << "An unknown error has occurred in the ErrorCheck class function validateSeqsFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } +} + +/*******************************************************/ + +/******************************************************/ +//This function checks to make sure the user entered appropriate +// format parameters on a bin.seq command +void ErrorCheck::validateBinFiles() { + try { + ifstream filehandle; + int ableToOpen; + + if (fastafile == "") { + cout << "fasta is a required parameter for bin.seqs, get.oturep and get.repseqs commands." << endl; errorFree = false; + }else if (fastafile != "") { + //is it a valid filename' + ableToOpen = openInputFile(fastafile, filehandle); + filehandle.close(); + //unable to open + if (ableToOpen == 1) { errorFree = false; } + }else if (listfile != "") { + //is it a valid filename' + ableToOpen = openInputFile(listfile, filehandle); + filehandle.close(); + //unable to open + if (ableToOpen == 1) { errorFree = false; } + }else if (globaldata->getNameFile() != "") { + //is it a valid filename' + ifstream filehandle; + int ableToOpen = openInputFile(globaldata->getNameFile(), filehandle); + filehandle.close(); + //unable to open + if (ableToOpen == 1) { errorFree = false; } + }else if (namefile != "") { + //is it a valid filename' + ifstream filehandle; + int ableToOpen = openInputFile(namefile, filehandle); + filehandle.close(); + //unable to open + if (ableToOpen == 1) { errorFree = false; } + }else if (groupfile != "") { + //is it a valid filename' + ifstream filehandle; + int ableToOpen = openInputFile(groupfile, filehandle); + filehandle.close(); + //unable to open + if (ableToOpen == 1) { errorFree = false; } + } + + + + } + catch(exception& e) { + cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateBinFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } + catch(...) { + cout << "An unknown error has occurred in the ErrorCheck class function validateBinFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } +} + +/*******************************************************/ + /******************************************************/ void ErrorCheck::clear() { @@ -449,6 +693,10 @@ void ErrorCheck::clear() { groupfile = ""; orderfile = ""; sharedfile = ""; + fastafile = ""; + nexusfile = ""; + clustalfile = ""; + candidatefile = ""; line = ""; label = ""; method = "furthest";