/******************************************************/
void ErrorCheck::refresh() {
+
//columnfile = globaldata->getColumnFile();
//phylipfile = globaldata->getPhylipFile();
//listfile = globaldata->getListFile();
//method = globaldata->getMethod();
//randomtree = globaldata->getRandomTree();
//sharedfile = globaldata->getSharedFile();
+
}
/*******************************************************/
//is it a valid command
if (validCommand->isValidCommand(commandName) != true) { return false; }
-
string parameter, value;
//reads in parameters and values
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; }
if (parameter == "line" ) { line = value; }
if (parameter == "label" ) { label = value; }
if (parameter == "abund" ) { abund = value; }
- if (parameter == "random" ) { randomtree = value; }
- if (parameter == "sorted" ) { sorted = 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 == "ends" ) { ends = value; }
+ if (parameter == "processors" ) { processors = value; }
+ if (parameter == "size" ) { size = value; }
+
+ if (parameter == "template") { templatefile = 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
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; }
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 == "ends" ) { ends = value; }
+ if (parameter == "processors" ) { processors = value; }
+ if (parameter == "size" ) { size = value; }
+ if (parameter == "template") { templatefile = 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; }
+
}
}
validateReadFiles();
}
- //are you trying to cluster before you have read something
+ //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;
}
}
- 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 == "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;
+ }
+ validateSeqsFiles();
+ }
+
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; }
validateBinFiles();
}
/*******************************************************/
+/******************************************************/
+//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
groupfile = "";
orderfile = "";
sharedfile = "";
+ fastafile = "";
+ nexusfile = "";
+ clustalfile = "";
+ templatefile = "";
line = "";
label = "";
method = "furthest";
projects / mothur.git / blobdiff