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; }
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; }
if (parameter == "mismatch") { mismatch = value; }
if (parameter == "gapopen") { gapopen = value; }
if (parameter == "gapextend" ) { gapextend = value; }
-
+
}
}
//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; }
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 == "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 == "filter.seqs") || (commandName == "dist.seqs") || (commandName == "align.seqs")) {
+ 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, 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;
+ 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 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();
}
//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;
}
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 == "") {
ableToOpen = openInputFile(groupfile, filehandle);
filehandle.close();
if (ableToOpen == 1) { //unable to open
- errorFree = false;;
+ errorFree = false;
}
}
}
errorFree = false;
}
}
- }else if (templatefile != "") {
- ableToOpen = openInputFile(templatefile, filehandle);
+ }else if (candidatefile != "") {
+ ableToOpen = openInputFile(candidatefile, filehandle);
filehandle.close();
if (ableToOpen == 1) { //unable to open
errorFree = false;
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);
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";
fastafile = "";
nexusfile = "";
clustalfile = "";
- templatefile = "";
+ candidatefile = "";
line = "";
label = "";
method = "furthest";