method = globaldata->getMethod();
randomtree = globaldata->getRandomTree();
sharedfile = globaldata->getSharedFile();
-
-
-
-/* string p[] = {
- "phylip", //0
- "column", //1
- "list", //2
- "rabund", //3
- "sabund", //4
- "name", //5
- "order", //6
- "group", //7
- "fasta", //8
- "treefile", //9
- "cutoff", //10
- "precision", //11
- "iters", //12
- "jumble", //13
- "freq", //14
- "method", //15
- "fileroot", //16
- "line", //17
- "label", //18
- "single", //19
- "rarefaction", //20
- "shared", //21
- "summary", //22
- "sharedrarefaction", //23
- "sharedsummary", //24
- "groups", //25
- "abund", //26
- };
-
- string c0[] = {p[0],p[5],p[10],p[11]};
- string c1[] = {p[2],p[6],p[7]};
- string c2[] = {p[10],p[11],p[15]};
- string c3[] = {p[8]};
- string c4[] = {p[14],p[17],p[18],p[19],p[26]};
- string c5[] = {p[13],p[14],p[17],p[18],p[21],p[25]};
- string c6[] = {""};
- string c7[] = {""};
- string c8[] = {""};
- string c9[] = {p[12],p[14],p[17],p[18],p[20],p[26]};
- string c10[] = {p[12],p[13],p[17],p[18],p[23]};
- string c11[] = {p[17],p[18],p[22],p[26]};
- string c12[] = {p[13],p[17],p[18],p[24]};
- string c13[] = {""};
-
- vector<string> v0 (c0, c0+sizeof(c0)/sizeof(string));
- vector<string> v1 (c1, c1+sizeof(c1)/sizeof(string));
- vector<string> v2 (c2, c2+sizeof(c2)/sizeof(string));
- vector<string> v3 (c3, c3+sizeof(c3)/sizeof(string));
- vector<string> v4 (c4, c4+sizeof(c4)/sizeof(string));
- vector<string> v5 (c5, c5+sizeof(c5)/sizeof(string));
- vector<string> v6 (c6, c6+sizeof(c6)/sizeof(string));
- vector<string> v7 (c7, c7+sizeof(c7)/sizeof(string));
- vector<string> v8 (c8, c8+sizeof(c8)/sizeof(string));
- vector<string> v9 (c9, c9+sizeof(c9)/sizeof(string));
- vector<string> v10 (c10, c10+sizeof(c10)/sizeof(string));
- vector<string> v11 (c11, c11+sizeof(c11)/sizeof(string));
- vector<string> v12 (c12, c12+sizeof(c12)/sizeof(string));
- vector<string> v13 (c13, c13+sizeof(c13)/sizeof(string));
-
- vector<vector<string> > allCommands;
- allCommands.push_back(v0);
- allCommands.push_back(v1);
- allCommands.push_back(v2);
- allCommands.push_back(v3);
- allCommands.push_back(v4);
- allCommands.push_back(v5);
- allCommands.push_back(v6);
- allCommands.push_back(v7);
- allCommands.push_back(v8);
- allCommands.push_back(v9);
- allCommands.push_back(v10);
- allCommands.push_back(v11);
- allCommands.push_back(v12);
- allCommands.push_back(v13);
-
- string commands[] = {
- "read.dist", //0
- "read.otu", //1
- "cluster", //2
- "deconvolute", //3
- "collect.single", //4
- "collect.shared", //5
- "get.group", //6
- "get.label", //7
- "get.line", //8
- "rarefaction.single", //9
- "rarefaction.shared", //10
- "summary.single", //11
- "summary.shared", //12
- "quit" //13
- };
-
- for(int i = 0; i < allCommands.size(); i++)
- commandParameters[commands[i]] = allCommands.at(i);
-
- //{Lowerbound(piSent if no lowerbound), Upperbound(piSent if no upperbound), 1 if only the first 2 values, 0 if greater than, 0 if less than};
- piSent = 3.14159;
- double ip0[] = {10, piSent, 0, 1, 0};
- double ip1[] = {10, piSent, 0, 1, 0};
- double ip2[] = {0, 1, 1, 0, 0};
- double ip3[] = {1, piSent, 0, 0, 0};
- double ip4[] = {1, piSent, 0, 1, 0};
- double ip5[] = {5, piSent, 0, 1, 0};
-
- vector<double> ipv0 (ip0, ip0+sizeof(ip0)/sizeof(double));
- vector<double> ipv1 (ip1, ip1+sizeof(ip1)/sizeof(double));
- vector<double> ipv2 (ip2, ip2+sizeof(ip2)/sizeof(double));
- vector<double> ipv3 (ip3, ip3+sizeof(ip3)/sizeof(double));
- vector<double> ipv4 (ip4, ip4+sizeof(ip4)/sizeof(double));
- vector<double> ipv5 (ip5, ip5+sizeof(ip5)/sizeof(double));
-
- intParams[p[11]] = ipv0;
- intParams[p[12]] = ipv1;
- intParams[p[13]] = ipv2;
- intParams[p[14]] = ipv3;
- intParams[p[17]] = ipv4;
- intParams[p[26]] = ipv5; */
-
}
/*******************************************************/
/******************************************************/
-ErrorCheck::~ErrorCheck() {}
+ErrorCheck::~ErrorCheck() {
+ delete validCommand;
+ delete validParameter;
+}
/*******************************************************/
splitAtEquals(parameter, value);
//is it a valid parameter
- if (validParameter->isValidParameter(parameter) != true) { return false; }
- //if(!validCommandParameter(parameter,commandName)) {
- // cout << "'" << parameter << "' is not a valid parameter for the " << commandName << " command.\n";
- // return false;
- //}
- //if(!validParameterValue(value, parameter)) {
- // if(parameter.compare("precision") == 0)
- // cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n";
- // else {
- /* vector<double> bounds = intParams[parameter];
- double a = bounds.at(0);
- double b = bounds.at(1);
- double c = bounds.at(2);
- double d = bounds.at(3);
- double e = bounds.at(4);
- cout << "The '" << parameter << "' parameter needs to be ";
- if(c == 1)
- cout << "either '" << a << "' or '" << b << "'.\n";
- else
- {
- if(a != piSent)
- {
- cout << ">";
- if(d != 0)
- cout << "=";
- cout << " '" << a << "'";
- }
- if(b == piSent)
- cout << ".\n";
- else if(a != piSent)
- cout << " and ";
- if(b != piSent)
- {
- cout << "<";
- if(e != 0)
- cout << "=";
- cout << " '" << b << ".\n";
- }
- }
- }
- return false;
- } */
+ if (validParameter->isValidParameter(parameter, commandName, value) != true) { return false; }
+
+
if (parameter == "phylip" ) { phylipfile = value; }
if (parameter == "column" ) { columnfile = value; }
if (parameter == "list" ) { listfile = value; }
if (parameter == "label" ) { label = value; }
if (parameter == "abund" ) { abund = value; }
if (parameter == "random" ) { randomtree = value; }
+ if (parameter == "sorted" ) { sorted = value; }
}
//gets the last parameter and value
value = optionText;
splitAtEquals(parameter, value);
//is it a valid parameter
- if (validParameter->isValidParameter(parameter) != true) { return false; }
- // if(!validCommandParameter(parameter,commandName)) {
- // cout << "'" << parameter << "' is not a valid parameter for the " << commandName << " command.\n";
- // return false;
- // }
- /* if(!validParameterValue(value, parameter)) {
- if(parameter.compare("precision") == 0)
- cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n";
- else {
- vector<double> bounds = intParams[parameter];
- double a = bounds.at(0);
- double b = bounds.at(1);
- double c = bounds.at(2);
- double d = bounds.at(3);
- double e = bounds.at(4);
- cout << "The '" << parameter << "' parameter needs to be ";
- if(c == 1)
- cout << "either '" << a << "' or '" << b << "'.\n";
- else
- {
- if(a != piSent)
- {
- cout << ">";
- if(d != 0)
- cout << "=";
- cout << " '" << a << "'";
- }
- if(b == piSent)
- cout << ".\n";
- else if(a != piSent)
- cout << " and ";
- if(b != piSent)
- {
- cout << "<";
- if(e != 0)
- cout << "=";
- cout << " '" << b << ".\n";
- }
- }
- }
- return false;
- }*/
+ if (validParameter->isValidParameter(parameter, commandName, value) != true) { return false; }
+
+
if (parameter == "phylip" ) { phylipfile = value; }
if (parameter == "column" ) { columnfile = value; }
if (parameter == "list" ) { listfile = value; }
if (parameter == "label" ) { label = value; }
if (parameter == "random" ) { randomtree = value; }
if (parameter == "abund" ) { abund = value; }
+ if (parameter == "sorted" ) { sorted = value; }
}
}
//make sure the user does not use both the line and label parameters
if ((line != "") && (label != "")) { cout << "You may use either the line or label parameters, but not both." << endl; return false; }
+ //check for valid files
if (commandName == "read.dist") {
validateReadFiles();
validateReadDist();
//you want to do shared commands
if ((listfile != "") && (groupfile != "")) {
validateParseFiles(); //checks the listfile and groupfile parameters
- }else { //you want to do single commands
+ //you want to do single commands
+ }else if ((listfile != "") || (rabundfile != "") || (sabundfile != "")){
validateReadFiles();
validateReadPhil();
+ //you have not given a file
+ }else if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "")) {
+ cout << "You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. " << endl; return false;
+ //you want to do shared commands with a shared file
+ }else if (sharedfile != "") {//you are reading a shared file
+ validateReadFiles();
}
- }else if (commandName == "read.shared") {
- //you want to do shared commands with just the shared file
- validateReadFiles();
}else if (commandName == "read.tree") {
validateTreeFiles(); //checks the treefile and groupfile parameters
}else if (commandName == "deconvolute") {
}
//are you trying to cluster before you have read something
- if ((commandName == "cluster") && (globaldata->getSparseMatrix() == NULL) ||
- (commandName == "cluster") && (globaldata->getListVector() == NULL)) {
+ 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;
errorFree = false;
}
+ if ((commandName == "libshuff") && ((globaldata->gMatrix == NULL) || (globaldata->gGroupmap == NULL))) {
+ cout << "You must read in a matrix and groupfile using the read.dist command, before you use the libshuff command. " << endl; return false;
+ }
+
if (commandName == "parsimony") {
//are you trying to use parsimony without reading a tree or saying you want random distribution
if (randomtree == "") {
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 or summary.shared commands." << endl; return false; }
}
}
+
+ if ((commandName == "heatmap") || (commandName == "venn")) {
+ 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;
+ }
+ }
+
+ 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();
+ }
+
+ 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; }
+ validateBinFiles();
+ }
+
return errorFree;
}
//unable to open
if (ableToOpen == 1) { errorFree = false; }
else { globaldata->inputFileName = phylipfile; }
- //are we reading a phylipfile
+ //are we reading a columnfile
}else if (columnfile != "") {
ableToOpen = openInputFile(columnfile, filehandle);
filehandle.close();
}
/*******************************************************/
-/******************************************************
-//This function checks to see if the given paramter
-//is a valid paramter for the given command.
-bool ErrorCheck::validCommandParameter(string parameter, string commandName) {
- try {
- for(int i = 0; i < commandParameters[commandName].size(); i++)
- if(parameter.compare(commandParameters[commandName][i]) == 0)
- return true;
- return false;
- }
-
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-/*******************************************************/
-
-/******************************************************
-//This function checks to see if the given paramter value
-//is convertable into an int if that parameter requires it.
-bool ErrorCheck::validParameterValue(string value, string parameter) {
- try {
- int pVal;
- if(intParams.count(parameter) == 1)
- {
- vector<double> bounds = intParams[parameter];
- bool valid = convertTest(value, pVal);
- if(!valid)
- return false;
- if(parameter.compare("precision") == 0)
- {
- double logNum = log10((double)pVal);
- double diff = (double)((int)logNum - logNum);
- if(diff != 0)
- return false;
- }
- double a = bounds.at(0);
- double b = bounds.at(1);
- double c = bounds.at(2);
- double d = bounds.at(3);
- double e = bounds.at(4);
- bool a0 = pVal > a;
- bool a1 = pVal >= a;
- bool b0 = pVal < b;
- bool b1 = pVal <= b;
-
- if(c != 1)
- {
- if(a == piSent && b == piSent)
- return true;
- if(a != piSent && b == piSent)
- {
- if(d == 0)
- return a0;
- else
- return a1;
- }
- else if(a == piSent && b != piSent)
- {
- if(e == 0)
- return b0;
- else
- return b1;
- }
- else
- {
- if(d == 0 && e == 0)
- return (a0 && b0);
- else if(d == 0 && e == 1)
- return (a0 && b1);
- else if(d == 1 && e == 0)
- return (a1 && b0);
- else
- return (a1 && b1);
- }
- }
- else
- {
- if(a == piSent && b == piSent)
- return true;
- if(a != piSent && b == piSent)
- return (pVal == a);
- else if(a == piSent && b != piSent)
- return (pVal == b);
- else
- return (pVal == a || pVal == b);
- }
- }
- return true;
- }
-
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. 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 distfile read
ifstream filehandle;
int ableToOpen;
+ if (groupfile != "") {
+ ableToOpen = openInputFile(groupfile, filehandle);
+ filehandle.close();
+ //unable to open
+ 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; }
}else if (sabundfile != "") {
if ((listfile != "") || (rabundfile != "")) {
cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
- }else if ((listfile == "") && (rabundfile == "") && (sabundfile == "")) {
+ }else if ((listfile == "") && (rabundfile == "") && (sabundfile == "") && (sharedfile == "")) {
cout << "When executing a read.otu you must enter one of the following: list, rabund or sabund." << endl; errorFree = false;
}
}
/*******************************************************/
+/******************************************************/
+//This function checks to make sure the user entered appropriate
+// format parameters on a bin.seq command
+void ErrorCheck::validateBinFiles() {
+ try {
+ ifstream filehandle;
+ int ableToOpen;
+
+ if (fastafile == "") {
+ cout << "fasta is a required parameter for bin.seqs and get.oturep 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 (listfile != "") {
+ //is it a valid filename'
+ ableToOpen = openInputFile(listfile, filehandle);
+ filehandle.close();
+ //unable to open
+ if (ableToOpen == 1) { errorFree = false; }
+ }else if (globaldata->getNameFile() != "") {
+ //is it a valid filename'
+ ifstream filehandle;
+ int ableToOpen = openInputFile(globaldata->getNameFile(), filehandle);
+ filehandle.close();
+ //unable to open
+ if (ableToOpen == 1) { errorFree = false; }
+ }else if (namefile != "") {
+ //is it a valid filename'
+ ifstream filehandle;
+ int ableToOpen = openInputFile(namefile, 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";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ErrorCheck class function validateBinFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/*******************************************************/
+
/******************************************************/
void ErrorCheck::clear() {
projects / mothur.git / blobdiff