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 delete validParameter;
52 /*******************************************************/
54 /******************************************************/
56 bool ErrorCheck::checkInput(string input) {
63 //get command name and parameters
64 int openParen = input.find_first_of('(');
65 int closeParen = input.find_last_of(')');
67 if(openParen != -1 && closeParen != -1){
68 commandName = input.substr(0, openParen); //commandName contains everything before "("
69 optionText = input.substr(openParen+1, closeParen-openParen-1); //optionString contains everything between "(" and ")".
70 }else if (openParen == -1) { //there is no parenthesis
71 cout << input << " is not a valid command. You are missing the ()." << endl;
75 //is it a valid command
76 if (validCommand->isValidCommand(commandName) != true) { return false; }
78 string parameter, value;
80 //reads in parameters and values
81 if((optionText != "") && (commandName != "help")){
82 while((optionText.find_first_of(',') != -1) && (errorFree)) { //while there are parameters
83 splitAtComma(value, optionText);
84 splitAtEquals(parameter, value);
86 //is it a valid parameter
87 if (validParameter->isValidParameter(parameter, commandName, value) != true) { return false; }
91 if (parameter == "phylip" ) { phylipfile = value; }
92 if (parameter == "column" ) { columnfile = value; }
93 if (parameter == "list" ) { listfile = value; }
94 if (parameter == "rabund" ) { rabundfile = value; }
95 if (parameter == "sabund" ) { sabundfile = value; }
96 if (parameter == "name" ) { namefile = value; }
97 if (parameter == "order" ) { orderfile = value; }
98 if (parameter == "fasta" ) { fastafile = value; }
99 if (parameter == "tree" ) { treefile = value; }
100 if (parameter == "group" ) { groupfile = value; }
101 if (parameter == "shared" ) { sharedfile = value; }
102 if (parameter == "cutoff" ) { cutoff = value; }
103 if (parameter == "precision" ) { precision = value; }
104 if (parameter == "iters" ) { iters = value; }
105 if (parameter == "jumble" ) { jumble = value; }
106 if (parameter == "freq" ) { freq = value; }
107 if (parameter == "method" ) { method = value; }
108 if (parameter == "fileroot" ) { fileroot = value; }
109 if (parameter == "line" ) { line = value; }
110 if (parameter == "label" ) { label = value; }
111 if (parameter == "abund" ) { abund = value; }
112 if (parameter == "random" ) { randomtree = value; }
113 if (parameter == "sorted" ) { sorted = value; }
116 //gets the last parameter and value
117 if (errorFree) { //gets the last parameter and value
119 splitAtEquals(parameter, value);
120 //is it a valid parameter
121 if (validParameter->isValidParameter(parameter, commandName, value) != true) { return false; }
124 if (parameter == "phylip" ) { phylipfile = value; }
125 if (parameter == "column" ) { columnfile = value; }
126 if (parameter == "list" ) { listfile = value; }
127 if (parameter == "rabund" ) { rabundfile = value; }
128 if (parameter == "sabund" ) { sabundfile = value; }
129 if (parameter == "name" ) { namefile = value; }
130 if (parameter == "order" ) { orderfile = value; }
131 if (parameter == "group" ) { groupfile = value; }
132 if (parameter == "shared" ) { sharedfile = value; }
133 if (parameter == "fasta" ) { fastafile = value; }
134 if (parameter == "tree" ) { treefile = value; }
135 if (parameter == "cutoff" ) { cutoff = value; }
136 if (parameter == "precision" ) { precision = value; }
137 if (parameter == "iters" ) { iters = value; }
138 if (parameter == "jumble" ) { jumble = value; }
139 if (parameter == "freq" ) { freq = value; }
140 if (parameter == "method" ) { method = value; }
141 if (parameter == "fileroot" ) { fileroot = value; }
142 if (parameter == "line" ) { line = value; }
143 if (parameter == "label" ) { label = value; }
144 if (parameter == "random" ) { randomtree = value; }
145 if (parameter == "abund" ) { abund = value; }
146 if (parameter == "sorted" ) { sorted = value; }
150 //make sure the user does not use both the line and label parameters
151 if ((line != "") && (label != "")) { cout << "You may use either the line or label parameters, but not both." << endl; return false; }
153 //check for valid files
154 if (commandName == "read.dist") {
157 }else if (commandName == "read.otu") {
158 //you want to do shared commands
159 if ((listfile != "") && (groupfile != "")) {
160 validateParseFiles(); //checks the listfile and groupfile parameters
161 //you want to do single commands
162 }else if ((listfile != "") || (rabundfile != "") || (sabundfile != "")){
165 //you have not given a file
166 }else if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "")) {
167 cout << "You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. " << endl; return false;
168 //you want to do shared commands with a shared file
169 }else if (sharedfile != "") {//you are reading a shared file
172 }else if (commandName == "read.tree") {
173 validateTreeFiles(); //checks the treefile and groupfile parameters
174 }else if (commandName == "deconvolute") {
175 if (fastafile == "") { cout << "You must enter a fastafile with the deconvolute() command." << endl; return false; }
179 //are you trying to cluster before you have read something
180 if (((commandName == "cluster") && (globaldata->gSparseMatrix == NULL)) ||
181 ((commandName == "cluster") && (globaldata->gListVector == NULL))) {
182 cout << "Before you use the cluster command, you first need to read in a distance matrix." << endl;
186 if ((commandName == "libshuff") && ((globaldata->gMatrix == NULL) || (globaldata->gGroupmap == NULL))) {
187 cout << "You must read in a matrix and groupfile using the read.dist command, before you use the libshuff command. " << endl; return false;
190 if (commandName == "parsimony") {
191 //are you trying to use parsimony without reading a tree or saying you want random distribution
192 if (randomtree == "") {
193 if (globaldata->gTree.size() == 0) {
194 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; }
198 if ((commandName == "unifrac.weighted") || (commandName == "unifrac.unweighted")) {
199 if (globaldata->gTree.size() == 0) {//no trees were read
200 cout << "You must execute the read.tree command, before you may execute the unifrac.weighted or unifrac.unweighted command." << endl; return false; }
203 //check for valid method
204 if(commandName == "get.group") {
205 if ((globaldata->getGroupFile() == "")) { cout << "You must read a group before you can use the get.group command." << endl; return false; }
207 if (commandName == "get.label" || commandName == "get.line") {
208 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; }
210 if (commandName == "cluster") {
211 if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
212 else {cout << "Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average." << endl; return false; }
215 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single") ){
216 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; }
219 if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") ){
220 if (globaldata->getSharedFile() == "") {
221 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; }
222 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; }
226 if ((commandName == "heatmap") || (commandName == "venn")) {
227 if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
228 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;
232 if ((commandName == "bin.seqs")) {
233 if ((globaldata->getListFile() == "")) { cout << "You must read a list file before you can use the bin.seqs command." << endl; return false; }
237 if ((commandName == "get.oturep")) {
238 if ((globaldata->gSparseMatrix == NULL) || (globaldata->gListVector == NULL)) {
239 cout << "Before you use the get.oturep command, you first need to read in a distance matrix." << endl;
242 if (listfile == "") { cout << "list is a required parameter for the get.oturep command." << endl; errorFree = false; }
250 /*******************************************************/
252 /******************************************************/
253 //This function checks to make sure the user entered a file to
254 // read and that the file exists and can be opened.
255 void ErrorCheck::validateReadFiles() {
257 //Validating files for read
261 //are we reading a phylipfile
262 if (phylipfile != "") {
263 ableToOpen = openInputFile(phylipfile, filehandle);
266 if (ableToOpen == 1) { errorFree = false; }
267 else { globaldata->inputFileName = phylipfile; }
268 //are we reading a columnfile
269 }else if (columnfile != "") {
270 ableToOpen = openInputFile(columnfile, filehandle);
273 if (ableToOpen == 1) { errorFree = false; }
274 else { globaldata->inputFileName = columnfile; }
275 //are we reading a listfile
276 }else if (listfile!= "") {
277 ableToOpen = openInputFile(listfile, filehandle);
280 if (ableToOpen == 1) { errorFree = false; }
281 else { globaldata->inputFileName = listfile; }
282 //are we reading a rabundfile
283 }else if (rabundfile != "") {
284 ableToOpen = openInputFile(rabundfile, filehandle);
287 if (ableToOpen == 1) { errorFree = false; }
288 else { globaldata->inputFileName = rabundfile; }
289 //are we reading a sabundfile
290 }else if (sabundfile != "") {
291 ableToOpen = openInputFile(sabundfile, filehandle);
294 if (ableToOpen == 1) { errorFree = false; }
295 else { globaldata->inputFileName = sabundfile; }
296 }else if (fastafile != "") {
297 ableToOpen = openInputFile(fastafile, filehandle);
300 if (ableToOpen == 1) { errorFree = false; }
301 else { globaldata->inputFileName = fastafile; }
302 }else if (sharedfile != "") {
303 ableToOpen = openInputFile(sharedfile, filehandle);
306 if (ableToOpen == 1) { errorFree = false; }
307 else { globaldata->inputFileName = sharedfile; }
308 }else{ //no file given
312 catch(exception& e) {
313 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
317 cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
322 /*******************************************************/
324 /******************************************************/
325 //This function checks to make sure the user entered appropriate
326 // format parameters on a distfile read
327 void ErrorCheck::validateReadDist() {
332 if (groupfile != "") {
333 ableToOpen = openInputFile(groupfile, filehandle);
336 if (ableToOpen == 1) { errorFree = false; }
339 if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist you must enter a phylip or a column." << endl; errorFree = false; }
340 else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist you must enter ONLY ONE of the following: phylip or column." << endl; errorFree = false; }
342 if (columnfile != "") {
343 if (namefile == "") {
344 cout << "You need to provide a namefile if you are going to use the column format." << endl;
347 ableToOpen = openInputFile(namefile, filehandle);
350 if (ableToOpen == 1) { errorFree = false; }
354 catch(exception& e) {
355 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
359 cout << "An unknown error has occurred in the ErrorCheck class function validateReadDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
363 /*******************************************************/
365 /******************************************************/
366 //This function checks to make sure the user entered appropriate
367 // format parameters on a parselistcommand
368 void ErrorCheck::validateParseFiles() {
373 //checks for valid files
375 if (listfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
376 else if (groupfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
378 //checks parameters on the read command
379 if (listfile != "") {
380 ableToOpen = openInputFile(listfile, filehandle);
382 if (ableToOpen == 1) { //unable to open
385 if (groupfile != "") {
386 ableToOpen = openInputFile(groupfile, filehandle);
388 if (ableToOpen == 1) { //unable to open
394 catch(exception& e) {
395 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
399 cout << "An unknown error has occurred in the ErrorCheck class function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
403 /*******************************************************/
405 /******************************************************/
406 //This function checks to make sure the user entered appropriate
407 // format parameters on a parselistcommand
408 void ErrorCheck::validateTreeFiles() {
413 //checks for valid files
415 if (treefile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
416 else if (groupfile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
418 //checks parameters on the read command
419 if (treefile != "") {
420 ableToOpen = openInputFile(treefile, filehandle);
422 if (ableToOpen == 1) { //unable to open
425 if (groupfile != "") {
426 ableToOpen = openInputFile(groupfile, filehandle);
428 if (ableToOpen == 1) { //unable to open
434 catch(exception& e) {
435 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
439 cout << "An unknown error has occurred in the ErrorCheck class function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
444 /*******************************************************/
446 /******************************************************/
447 //This function checks to make sure the user entered appropriate
448 // format parameters on a distfile read
449 void ErrorCheck::validateReadPhil() {
454 //checks to make sure only one file type is given
455 if (listfile != "") {
456 if ((rabundfile != "") || (sabundfile != "")) {
457 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
458 }else if (rabundfile != "") {
459 if ((listfile != "") || (sabundfile != "")) {
460 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
461 }else if (sabundfile != "") {
462 if ((listfile != "") || (rabundfile != "")) {
463 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
464 }else if ((listfile == "") && (rabundfile == "") && (sabundfile == "") && (sharedfile == "")) {
465 cout << "When executing a read.otu you must enter one of the following: list, rabund or sabund." << endl; errorFree = false;
468 //checks parameters on the read command
469 if (orderfile != "") {
470 ableToOpen = openInputFile(orderfile, filehandle);
472 if (ableToOpen == 1) { //unable to open
477 catch(exception& e) {
478 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
482 cout << "An unknown error has occurred in the ErrorCheck class function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
486 /*******************************************************/
488 /******************************************************/
489 //This function checks to make sure the user entered appropriate
490 // format parameters on a bin.seq command
491 void ErrorCheck::validateBinFiles() {
496 if (fastafile == "") {
497 cout << "fasta is a required parameter for bin.seqs and get.oturep commands." << endl; errorFree = false;
498 }else if (fastafile != "") {
499 //is it a valid filename'
500 ableToOpen = openInputFile(fastafile, filehandle);
503 if (ableToOpen == 1) { errorFree = false; }
504 }else if (listfile != "") {
505 //is it a valid filename'
506 ableToOpen = openInputFile(listfile, filehandle);
509 if (ableToOpen == 1) { errorFree = false; }
510 }else if (globaldata->getNameFile() != "") {
511 //is it a valid filename'
513 int ableToOpen = openInputFile(globaldata->getNameFile(), filehandle);
516 if (ableToOpen == 1) { errorFree = false; }
517 }else if (namefile != "") {
518 //is it a valid filename'
520 int ableToOpen = openInputFile(namefile, filehandle);
523 if (ableToOpen == 1) { errorFree = false; }
528 catch(exception& e) {
529 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateBinFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
533 cout << "An unknown error has occurred in the ErrorCheck class function validateBinFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
538 /*******************************************************/
540 /******************************************************/
542 void ErrorCheck::clear() {
543 //option definitions should go here...
557 /*******************************************************/
559 /******************************************************/