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 == "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; }
}
}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();
}
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 == "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, bootstrap.shared or dist.shared 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;
+ 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 == "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;
}
- validateSeqsFiles();
+ validateReadFiles();
+
+ ifstream filehandle;
+ int ableToOpen = openInputFile(candidatefile, filehandle);
+ filehandle.close();
+ //unable to open
+ if (ableToOpen == 1) { return false; }
}
if ((commandName == "bin.seqs")) {
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();
}
}
/*******************************************************/
-/******************************************************/
-//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
//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";
orderfile = "";
sharedfile = "";
fastafile = "";
- nexusfile = "";
- clustalfile = "";
candidatefile = "";
line = "";
label = "";
projects / mothur.git / blobdiff