X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=errorchecking.cpp;h=e77c1663f25d41ba9a20cd22152c7f946a207b95;hb=f15f7092c97277337d4fdd9ef674015c15a13220;hp=dfe96072e3e8ae8799856982f56b85fff15b0289;hpb=526a868606faa50caf86e7399f7554c0335b39e5;p=mothur.git diff --git a/errorchecking.cpp b/errorchecking.cpp index dfe9607..e77c166 100644 --- a/errorchecking.cpp +++ b/errorchecking.cpp @@ -95,8 +95,6 @@ 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; } @@ -116,9 +114,10 @@ bool ErrorCheck::checkInput(string input) { if (parameter == "soft" ) { soft = value; } if (parameter == "filter" ) { filter = value; } if (parameter == "scale" ) { scale = value; } - if (parameter == "ends" ) { ends = value; } + if (parameter == "countends" ) { countends = value; } if (parameter == "processors" ) { processors = value; } - if (parameter == "template") { templatefile = 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; } @@ -146,8 +145,6 @@ 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; } @@ -165,9 +162,10 @@ bool ErrorCheck::checkInput(string input) { if (parameter == "soft" ) { soft = value; } if (parameter == "filter" ) { filter = value; } if (parameter == "scale" ) { scale = value; } - if (parameter == "ends" ) { ends = value; } + if (parameter == "countends" ) { countends = value; } if (parameter == "processors" ) { processors = value; } - if (parameter == "template") { templatefile = 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; } @@ -175,7 +173,7 @@ bool ErrorCheck::checkInput(string input) { if (parameter == "mismatch") { mismatch = value; } if (parameter == "gapopen") { gapopen = value; } if (parameter == "gapextend" ) { gapextend = value; } - + } } @@ -203,8 +201,8 @@ bool ErrorCheck::checkInput(string input) { } }else if (commandName == "read.tree") { validateTreeFiles(); //checks the treefile and groupfile parameters - }else if (commandName == "deconvolute") { - if (fastafile == "") { cout << "You must enter a fastafile with the deconvolute() command." << endl; return false; } + }else if (commandName == "unique.seqs") { + if (fastafile == "") { cout << "You must enter a fastafile with the unique.seqs() command." << endl; return false; } validateReadFiles(); } @@ -234,7 +232,7 @@ bool ErrorCheck::checkInput(string input) { //check for valid method if(commandName == "get.group") { - if ((globaldata->getGroupFile() == "")) { cout << "You must read a group before you can use the get.group command." << endl; return false; } + 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; } @@ -244,43 +242,85 @@ bool ErrorCheck::checkInput(string input) { else {cout << "Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average." << endl; return false; } } - if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single") ){ + if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")){ 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") || (commandName == "tree.shared") || (commandName == "bootstrap.shared")){ + if (commandName == "get.rabund") { + if (globaldata->getListFile() == "") { cout << "You must read a listfile before you can use the get.rabund command." << endl; return false; } + } + + if (commandName == "get.sabund") { + if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "")) { cout << "You must read a list or rabund before you can use the get.sabund command." << endl; return false; } + } + + 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, summary.shared, tree.shared or bootstrap.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 or bootstrap.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 == "heatmap") || (commandName == "venn")) { + 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.bin") || (commandName == "venn") || (commandName == "heatmap.sim")) { 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; + cout << "You must read a list, or a list and a group, or a shared before you can use the heatmap.bin, heatmap.sim or venn commands." << endl; return false; + } + } + + if (commandName == "filter.seqs") { + if (fastafile == "") { + cout << "You must enter either a fasta file before you can use the filter.seqs command." << endl; return false; } + validateReadFiles(); } - if ((commandName == "filter.seqs") || (commandName == "dist.seqs") || (commandName == "align.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, dist.seqs or align.seqs command." << endl; return false; - }else if ((commandName == "align.seqs") && (templatefile == "")) { - cout << "You must enter a template to use the align.seqs command." << endl; return false; + if (commandName == "dist.seqs") { + if (fastafile == "") { + cout << "You must enter either a fasta file before you can use the dist.seqs command." << endl; return false; + }else { + ifstream filehandle; + int ableToOpen = openInputFile(fastafile, filehandle); + filehandle.close(); + //unable to open + if (ableToOpen == 1) { 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; + } + validateReadFiles(); + + ifstream filehandle; + int ableToOpen = openInputFile(candidatefile, filehandle); + filehandle.close(); + //unable to open + if (ableToOpen == 1) { return false; } } if ((commandName == "bin.seqs")) { - if ((globaldata->getListFile() == "")) { cout << "You must read a list file before you can use the bin.seqs command." << endl; return false; } + 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; } + if (fastafile == "") { cout << "fasta is a required parameter for the get.oturep command." << endl; errorFree = false; } validateBinFiles(); } @@ -346,6 +386,12 @@ 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; } @@ -377,8 +423,8 @@ void ErrorCheck::validateReadDist() { if (ableToOpen == 1) { errorFree = false; } } - 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 ((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 == "") { @@ -427,7 +473,7 @@ void ErrorCheck::validateParseFiles() { ableToOpen = openInputFile(groupfile, filehandle); filehandle.close(); if (ableToOpen == 1) { //unable to open - errorFree = false;; + errorFree = false; } } } @@ -526,77 +572,6 @@ 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 (templatefile != "") { - ableToOpen = openInputFile(templatefile, 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 @@ -606,7 +581,7 @@ void ErrorCheck::validateBinFiles() { int ableToOpen; if (fastafile == "") { - cout << "fasta is a required parameter for bin.seqs and get.oturep commands." << endl; errorFree = false; + 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); @@ -633,9 +608,14 @@ void ErrorCheck::validateBinFiles() { 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"; @@ -663,9 +643,7 @@ void ErrorCheck::clear() { orderfile = ""; sharedfile = ""; fastafile = ""; - nexusfile = ""; - clustalfile = ""; - templatefile = ""; + candidatefile = ""; line = ""; label = ""; method = "furthest";