/******************************************************/
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();
+
}
/*******************************************************/
//is it a valid command
if (validCommand->isValidCommand(commandName) != true) { return false; }
-
string parameter, value;
//reads in parameters and values
//is it a valid parameter
if (validParameter->isValidParameter(parameter, commandName, value) != true) { return false; }
-
-
if (parameter == "phylip" ) { phylipfile = value; }
if (parameter == "column" ) { columnfile = value; }
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 == "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
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 == "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; }
+
}
}
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 == "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; }
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 == "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")) {
+ 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 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;
}
}
}
}
/*******************************************************/
+/******************************************************/
+//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
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";
groupfile = "";
orderfile = "";
sharedfile = "";
+ fastafile = "";
+ nexusfile = "";
+ clustalfile = "";
+ candidatefile = "";
line = "";
label = "";
method = "furthest";
projects / mothur.git / blobdiff