5 * Created by Sarah Westcott on 1/2/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "errorchecking.h"
12 /*******************************************************/
14 /******************************************************/
16 ErrorCheck::ErrorCheck() {
17 globaldata = GlobalData::getInstance();
18 validCommand = new ValidCommands();
19 validParameter = new ValidParameters();
21 /*******************************************************/
23 /******************************************************/
25 void ErrorCheck::refresh() {
26 columnfile = globaldata->getColumnFile();
27 phylipfile = globaldata->getPhylipFile();
28 listfile = globaldata->getListFile();
29 rabundfile = globaldata->getRabundFile();
30 sabundfile = globaldata->getSabundFile();
31 namefile = globaldata->getNameFile();
32 groupfile = globaldata->getGroupFile();
33 orderfile = globaldata->getOrderFile();
34 fastafile = globaldata->getFastaFile();
35 treefile = globaldata->getTreeFile();
36 cutoff = globaldata->getCutOff();
37 format = globaldata->getFormat();
38 method = globaldata->getMethod();
39 randomtree = globaldata->getRandomTree();
40 sharedfile = globaldata->getSharedFile();
43 /*******************************************************/
45 /******************************************************/
47 ErrorCheck::~ErrorCheck() {}
49 /*******************************************************/
51 /******************************************************/
53 bool ErrorCheck::checkInput(string input) {
60 //get command name and parameters
61 int openParen = input.find_first_of('(');
62 int closeParen = input.find_last_of(')');
64 if(openParen != -1 && closeParen != -1){
65 commandName = input.substr(0, openParen); //commandName contains everything before "("
66 optionText = input.substr(openParen+1, closeParen-openParen-1); //optionString contains everything between "(" and ")".
67 }else if (openParen == -1) { //there is no parenthesis
68 cout << input << " is not a valid command. You are missing the ()." << endl;
72 //is it a valid command
73 if (validCommand->isValidCommand(commandName) != true) { return false; }
75 string parameter, value;
76 //reads in parameters and values
77 if((optionText != "") && (commandName != "help")){
78 while((optionText.find_first_of(',') != -1) && (errorFree)) { //while there are parameters
79 splitAtComma(value, optionText);
80 splitAtEquals(parameter, value);
82 //is it a valid parameter
83 if (validParameter->isValidParameter(parameter) != true) { return false; }
85 if (parameter == "phylip" ) { phylipfile = value; }
86 if (parameter == "column" ) { columnfile = value; }
87 if (parameter == "list" ) { listfile = value; }
88 if (parameter == "rabund" ) { rabundfile = value; }
89 if (parameter == "sabund" ) { sabundfile = value; }
90 if (parameter == "name" ) { namefile = value; }
91 if (parameter == "order" ) { orderfile = value; }
92 if (parameter == "fasta" ) { fastafile = value; }
93 if (parameter == "tree" ) { treefile = value; }
94 if (parameter == "group" ) { groupfile = value; }
95 if (parameter == "shared" ) { sharedfile = value; }
96 if (parameter == "cutoff" ) { cutoff = value; }
97 if (parameter == "precision" ) { precision = value; }
98 if (parameter == "iters" ) { iters = value; }
99 if (parameter == "jumble" ) { jumble = value; }
100 if (parameter == "freq" ) { freq = value; }
101 if (parameter == "method" ) { method = value; }
102 if (parameter == "fileroot" ) { fileroot = value; }
103 if (parameter == "line" ) { line = value; }
104 if (parameter == "label" ) { label = value; }
105 if (parameter == "random" ) { randomtree = value; }
109 //gets the last parameter and value
110 if (errorFree) { //gets the last parameter and value
112 splitAtEquals(parameter, value);
113 //is it a valid parameter
114 if (validParameter->isValidParameter(parameter) != true) { return false; }
116 if (parameter == "phylip" ) { phylipfile = value; }
117 if (parameter == "column" ) { columnfile = value; }
118 if (parameter == "list" ) { listfile = value; }
119 if (parameter == "rabund" ) { rabundfile = value; }
120 if (parameter == "sabund" ) { sabundfile = value; }
121 if (parameter == "name" ) { namefile = value; }
122 if (parameter == "order" ) { orderfile = value; }
123 if (parameter == "group" ) { groupfile = value; }
124 if (parameter == "shared" ) { sharedfile = value; }
125 if (parameter == "fasta" ) { fastafile = value; }
126 if (parameter == "tree" ) { treefile = value; }
127 if (parameter == "cutoff" ) { cutoff = value; }
128 if (parameter == "precision" ) { precision = value; }
129 if (parameter == "iters" ) { iters = value; }
130 if (parameter == "jumble" ) { jumble = value; }
131 if (parameter == "freq" ) { freq = value; }
132 if (parameter == "method" ) { method = value; }
133 if (parameter == "fileroot" ) { fileroot = value; }
134 if (parameter == "line" ) { line = value; }
135 if (parameter == "label" ) { label = value; }
136 if (parameter == "random" ) { randomtree = value; }
141 //make sure the user does not use both the line and label parameters
142 if ((line != "") && (label != "")) { cout << "You may use either the line or label parameters, but not both." << endl; return false; }
144 if (commandName == "read.dist") {
147 }else if (commandName == "read.otu") {
148 //you want to do shared commands
149 if ((listfile != "") && (groupfile != "")) {
150 validateParseFiles(); //checks the listfile and groupfile parameters
151 }else { //you want to do single commands
155 }else if (commandName == "read.shared") {
156 //you want to do shared commands with just the shared file
158 }else if (commandName == "read.tree") {
159 validateTreeFiles(); //checks the treefile and groupfile parameters
160 }else if (commandName == "deconvolute") {
161 if (fastafile == "") { cout << "You must enter a fastafile with the deconvolute() command." << endl; return false; }
165 //are you trying to cluster before you have read something
166 if ((commandName == "cluster") && (globaldata->getSparseMatrix() == NULL) ||
167 (commandName == "cluster") && (globaldata->getListVector() == NULL)) {
168 cout << "Before you use the cluster command, you first need to read in a distance matrix." << endl;
172 if (commandName == "parsimony") {
173 //are you trying to use parsimony without reading a tree or saying you want random distribution
174 if (randomtree == "") {
175 if (globaldata->gTree.size() == 0) {
176 cout << "You must read a treefile and a groupfile or set the randomtree parameter to the output filename you wish, before you may execute the parsimony command." << endl; return false; }
180 if ((commandName == "unifrac.weighted") || (commandName == "unifrac.unweighted")) {
181 if (globaldata->gTree.size() == 0) {//no trees were read
182 cout << "You must execute the read.tree command, before you may execute the unifrac.weighted or unifrac.unweighted command." << endl; return false; }
185 //check for valid method
186 if (commandName == "cluster") {
187 if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
188 else {cout << "Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average." << endl; return false; }
191 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single") ){
192 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; }
195 if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") ){
196 if (globaldata->getSharedFile() == "") {
197 if (globaldata->getListFile() == "") { 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; }
198 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; }
205 /*******************************************************/
207 /******************************************************/
208 //This function checks to make sure the user entered a file to
209 // read and that the file exists and can be opened.
210 void ErrorCheck::validateReadFiles() {
212 //Validating files for read
216 //are we reading a phylipfile
217 if (phylipfile != "") {
218 ableToOpen = openInputFile(phylipfile, filehandle);
221 if (ableToOpen == 1) { errorFree = false; }
222 else { globaldata->inputFileName = phylipfile; }
223 //are we reading a phylipfile
224 }else if (columnfile != "") {
225 ableToOpen = openInputFile(columnfile, filehandle);
228 if (ableToOpen == 1) { errorFree = false; }
229 else { globaldata->inputFileName = columnfile; }
230 //are we reading a listfile
231 }else if (listfile!= "") {
232 ableToOpen = openInputFile(listfile, filehandle);
235 if (ableToOpen == 1) { errorFree = false; }
236 else { globaldata->inputFileName = listfile; }
237 //are we reading a rabundfile
238 }else if (rabundfile != "") {
239 ableToOpen = openInputFile(rabundfile, filehandle);
242 if (ableToOpen == 1) { errorFree = false; }
243 else { globaldata->inputFileName = rabundfile; }
244 //are we reading a sabundfile
245 }else if (sabundfile != "") {
246 ableToOpen = openInputFile(sabundfile, filehandle);
249 if (ableToOpen == 1) { errorFree = false; }
250 else { globaldata->inputFileName = sabundfile; }
251 }else if (fastafile != "") {
252 ableToOpen = openInputFile(fastafile, filehandle);
255 if (ableToOpen == 1) { errorFree = false; }
256 else { globaldata->inputFileName = fastafile; }
257 }else if (sharedfile != "") {
258 ableToOpen = openInputFile(sharedfile, filehandle);
261 if (ableToOpen == 1) { errorFree = false; }
262 else { globaldata->inputFileName = sharedfile; }
263 }else{ //no file given
267 catch(exception& e) {
268 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
272 cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
277 /*******************************************************/
279 /******************************************************/
280 //This function checks to make sure the user entered appropriate
281 // format parameters on a distfile read
282 void ErrorCheck::validateReadDist() {
287 if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist you must enter a phylip or a column." << endl; errorFree = false; }
288 else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist you must enter ONLY ONE of the following: phylip or column." << endl; errorFree = false; }
290 if (columnfile != "") {
291 if (namefile == "") {
292 cout << "You need to provide a namefile if you are going to use the column format." << endl;
295 ableToOpen = openInputFile(namefile, filehandle);
298 if (ableToOpen == 1) { errorFree = false; }
302 catch(exception& e) {
303 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
307 cout << "An unknown error has occurred in the ErrorCheck class function validateReadDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
311 /*******************************************************/
313 /******************************************************/
314 //This function checks to make sure the user entered appropriate
315 // format parameters on a parselistcommand
316 void ErrorCheck::validateParseFiles() {
321 //checks for valid files
323 if (listfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
324 else if (groupfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
326 //checks parameters on the read command
327 if (listfile != "") {
328 ableToOpen = openInputFile(listfile, filehandle);
330 if (ableToOpen == 1) { //unable to open
333 if (groupfile != "") {
334 ableToOpen = openInputFile(groupfile, filehandle);
336 if (ableToOpen == 1) { //unable to open
342 catch(exception& e) {
343 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
347 cout << "An unknown error has occurred in the ErrorCheck class function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
351 /*******************************************************/
353 /******************************************************/
354 //This function checks to make sure the user entered appropriate
355 // format parameters on a parselistcommand
356 void ErrorCheck::validateTreeFiles() {
361 //checks for valid files
363 if (treefile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
364 else if (groupfile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
366 //checks parameters on the read command
367 if (treefile != "") {
368 ableToOpen = openInputFile(treefile, filehandle);
370 if (ableToOpen == 1) { //unable to open
373 if (groupfile != "") {
374 ableToOpen = openInputFile(groupfile, filehandle);
376 if (ableToOpen == 1) { //unable to open
382 catch(exception& e) {
383 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
387 cout << "An unknown error has occurred in the ErrorCheck class function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
392 /*******************************************************/
394 /******************************************************/
395 //This function checks to make sure the user entered appropriate
396 // format parameters on a distfile read
397 void ErrorCheck::validateReadPhil() {
402 //checks to make sure only one file type is given
403 if (listfile != "") {
404 if ((rabundfile != "") || (sabundfile != "")) {
405 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
406 }else if (rabundfile != "") {
407 if ((listfile != "") || (sabundfile != "")) {
408 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
409 }else if (sabundfile != "") {
410 if ((listfile != "") || (rabundfile != "")) {
411 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
412 }else if ((listfile == "") && (rabundfile == "") && (sabundfile == "")) {
413 cout << "When executing a read.otu you must enter one of the following: list, rabund or sabund." << endl; errorFree = false;
416 //checks parameters on the read command
417 if (orderfile != "") {
418 ableToOpen = openInputFile(orderfile, filehandle);
420 if (ableToOpen == 1) { //unable to open
425 catch(exception& e) {
426 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
430 cout << "An unknown error has occurred in the ErrorCheck class function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
434 /*******************************************************/
436 /******************************************************/
438 void ErrorCheck::clear() {
439 //option definitions should go here...
453 /*******************************************************/
455 /******************************************************/