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- 379294890F2E258500B9034A /* parsimony.cpp */,
37D928020F21331F001D4494 /* rarecalc.h */,
37D928010F21331F001D4494 /* rarecalc.cpp */,
37D9281F0F21331F001D4494 /* shannon.h */,
37D9282C0F21331F001D4494 /* sharedjest.cpp */,
37D928350F21331F001D4494 /* sharedsobs.h */,
37D928340F21331F001D4494 /* sharedsobs.cpp */,
- 37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */,
- 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */,
37D928370F21331F001D4494 /* sharedsorabund.h */,
37D928360F21331F001D4494 /* sharedsorabund.cpp */,
37D928390F21331F001D4494 /* sharedsorclass.h */,
37D928410F21331F001D4494 /* simpson.h */,
37D928400F21331F001D4494 /* simpson.cpp */,
37D928430F21331F001D4494 /* sobs.h */,
- 374610810F40652400460C57 /* unweighted.h */,
- 374610820F40652400460C57 /* unweighted.cpp */,
37D9284E0F21331F001D4494 /* uvest.h */,
37D9284D0F21331F001D4494 /* uvest.cpp */,
- 3746107C0F4064D100460C57 /* weighted.h */,
- 3746107D0F4064D100460C57 /* weighted.cpp */,
);
name = calculators;
- sourceTree = "<group>";
+ sourceTree = SOURCE_ROOT;
};
37D928A90F2133E5001D4494 /* commands */ = {
isa = PBXGroup;
37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */,
37B28F660F27590100808A62 /* deconvolutecommand.h */,
37B28F670F27590100808A62 /* deconvolutecommand.cpp */,
+ EBA52D2A0F378B0F00122C15 /* getgroupcommand.h */,
+ EBA52D2B0F378B0F00122C15 /* getgroupcommand.cpp */,
+ EBFD67820F33876C00883537 /* getlabelcommand.h */,
+ EBFD67830F33876C00883537 /* getlabelcommand.cpp */,
+ EBFD67E60F339AAA00883537 /* getlinecommand.h */,
+ EBFD67E70F339AAA00883537 /* getlinecommand.cpp */,
37D927E40F21331F001D4494 /* helpcommand.h */,
37D927E30F21331F001D4494 /* helpcommand.cpp */,
37D927F20F21331F001D4494 /* nocommand.cpp */,
37D927F30F21331F001D4494 /* nocommand.h */,
37D927FA0F21331F001D4494 /* parselistcommand.h */,
37D927F90F21331F001D4494 /* parselistcommand.cpp */,
- 3792946E0F2E191800B9034A /* parsimonycommand.h */,
- 3792946F0F2E191800B9034A /* parsimonycommand.cpp */,
- 37D927FE0F21331F001D4494 /* quitcommand.h */,
- 37D927FD0F21331F001D4494 /* quitcommand.cpp */,
37D928080F21331F001D4494 /* rarefactcommand.h */,
37D928070F21331F001D4494 /* rarefactcommand.cpp */,
37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */,
372E12950F263D5A0095CF7E /* readdistcommand.cpp */,
372E126E0F26365B0095CF7E /* readotucommand.h */,
372E126F0F26365B0095CF7E /* readotucommand.cpp */,
- 37AFC7A10F44703E005F492D /* readsharedcommand.h */,
- 37AFC7A20F44703E005F492D /* readsharedcommand.cpp */,
37E5F4900F2A3DA800F8D827 /* readtreecommand.h */,
37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */,
37D928270F21331F001D4494 /* sharedcommand.h */,
37D928460F21331F001D4494 /* summarycommand.cpp */,
37D9284B0F21331F001D4494 /* summarysharedcommand.h */,
37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */,
- 3746109B0F40657600460C57 /* unifracunweightedcommand.h */,
- 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */,
- 374610760F40645300460C57 /* unifracweightedcommand.h */,
- 374610770F40645300460C57 /* unifracweightedcommand.cpp */,
+ 37D927FE0F21331F001D4494 /* quitcommand.h */,
+ 37D927FD0F21331F001D4494 /* quitcommand.cpp */,
);
name = commands;
- sourceTree = "<group>";
+ sourceTree = SOURCE_ROOT;
};
37D928AC0F213420001D4494 /* containers */ = {
isa = PBXGroup;
37E5F3E20F29FD4200F8D827 /* treenode.cpp */,
);
name = containers;
- sourceTree = "<group>";
+ sourceTree = SOURCE_ROOT;
};
37D928B10F213472001D4494 /* errorcheckor */ = {
isa = PBXGroup;
37D928530F21331F001D4494 /* validparameter.cpp */,
);
name = errorcheckor;
- sourceTree = "<group>";
+ sourceTree = SOURCE_ROOT;
};
C6859E8C029090F304C91782 /* Documentation */ = {
isa = PBXGroup;
37E5F3E30F29FD4200F8D827 /* treenode.cpp in Sources */,
37E5F4920F2A3DA800F8D827 /* readtreecommand.cpp in Sources */,
379293C30F2DE73400B9034A /* treemap.cpp in Sources */,
- 379294700F2E191800B9034A /* parsimonycommand.cpp in Sources */,
- 3792948A0F2E258500B9034A /* parsimony.cpp in Sources */,
- 374610780F40645300460C57 /* unifracweightedcommand.cpp in Sources */,
- 3746107E0F4064D100460C57 /* weighted.cpp in Sources */,
- 374610830F40652400460C57 /* unweighted.cpp in Sources */,
- 3746109D0F40657600460C57 /* unifracunweightedcommand.cpp in Sources */,
- 37AFC71F0F445386005F492D /* sharedsobscollectsummary.cpp in Sources */,
- 37AFC7A30F44703E005F492D /* readsharedcommand.cpp in Sources */,
+ 7E44EBD10F3235D900B0D45D /* makefile in Sources */,
+ EBFD67840F33876C00883537 /* getlabelcommand.cpp in Sources */,
+ EBFD67E80F339AAA00883537 /* getlinecommand.cpp in Sources */,
+ EBA52D2C0F378B0F00122C15 /* getgroupcommand.cpp in Sources */,
);
runOnlyForDeploymentPostprocessing = 0;
};
GCC_DYNAMIC_NO_PIC = NO;
GCC_ENABLE_FIX_AND_CONTINUE = YES;
GCC_MODEL_TUNING = G5;
- GCC_OPTIMIZATION_LEVEL = 3;
+ GCC_OPTIMIZATION_LEVEL = 0;
GCC_PREPROCESSOR_DEFINITIONS = (
"_GLIBCXX_DEBUG=1",
"_GLIBCXX_DEBUG_PEDANTIC=1",
buildSettings = {
DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
GCC_MODEL_TUNING = G5;
- GCC_OPTIMIZATION_LEVEL = 3;
INSTALL_PATH = /usr/local/bin;
PRODUCT_NAME = mothur;
};
ppc,
i386,
);
- GCC_OPTIMIZATION_LEVEL = 0;
+ GCC_OPTIMIZATION_LEVEL = 3;
GCC_WARN_ABOUT_RETURN_TYPE = YES;
GCC_WARN_UNUSED_VARIABLE = YES;
PREBINDING = NO;
*/
#include "errorchecking.h"
+#include <math.h>
/*******************************************************/
cutoff = globaldata->getCutOff();
format = globaldata->getFormat();
method = globaldata->getMethod();
+
+
+ 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
+ "comparegroups", //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;
+
randomtree = globaldata->getRandomTree();
sharedfile = globaldata->getSharedFile();
}
if (validCommand->isValidCommand(commandName) != true) { return false; }
string parameter, value;
+
//reads in parameters and values
if((optionText != "") && (commandName != "help")){
while((optionText.find_first_of(',') != -1) && (errorFree)) { //while there are parameters
//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 (parameter == "phylip" ) { phylipfile = value; }
if (parameter == "column" ) { columnfile = value; }
if (parameter == "list" ) { listfile = value; }
if (parameter == "fileroot" ) { fileroot = value; }
if (parameter == "line" ) { line = value; }
if (parameter == "label" ) { label = value; }
+ if (parameter == "abund" ) { abund = value; }
if (parameter == "random" ) { randomtree = value; }
+ if (parameter == "comparegroups") { //stores groups to be compared
+ sharedGroups.clear(); //clears out old values
+ globaldata->splitAtDash(value, sharedGroups);
+ }
+
}
//gets the last parameter and value
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 (parameter == "phylip" ) { phylipfile = value; }
if (parameter == "column" ) { columnfile = value; }
if (parameter == "list" ) { listfile = value; }
if (parameter == "line" ) { line = value; }
if (parameter == "label" ) { label = value; }
if (parameter == "random" ) { randomtree = value; }
+ if (parameter == "abund" ) { abund = value; }
+ if (parameter == "comparegroups") { //stores groups to be compared
+ sharedGroups.clear(); //clears out old values
+ globaldata->splitAtDash(value, sharedGroups);
+ }
}
}
}
//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 (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 (commandName == "cluster") {
if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
else {cout << "Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average." << 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 or summary.shared commands." << endl; return false; }
}
}
-
+
+ globaldata->clearAbund();
+
return errorFree;
}
}
/*******************************************************/
+/******************************************************/
+//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
projects / mothur.git / commitdiff