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; }
89 if (parameter == "phylip" ) { phylipfile = value; }
90 if (parameter == "column" ) { columnfile = value; }
91 if (parameter == "list" ) { listfile = value; }
92 if (parameter == "rabund" ) { rabundfile = value; }
93 if (parameter == "sabund" ) { sabundfile = value; }
94 if (parameter == "name" ) { namefile = value; }
95 if (parameter == "order" ) { orderfile = value; }
96 if (parameter == "fasta" ) { fastafile = value; }
97 if (parameter == "tree" ) { treefile = value; }
98 if (parameter == "group" ) { groupfile = value; }
99 if (parameter == "shared" ) { sharedfile = value; }
100 if (parameter == "cutoff" ) { cutoff = value; }
101 if (parameter == "precision" ) { precision = value; }
102 if (parameter == "iters" ) { iters = value; }
103 if (parameter == "jumble" ) { jumble = value; }
104 if (parameter == "freq" ) { freq = value; }
105 if (parameter == "method" ) { method = value; }
106 if (parameter == "fileroot" ) { fileroot = value; }
107 if (parameter == "line" ) { line = value; }
108 if (parameter == "label" ) { label = value; }
109 if (parameter == "abund" ) { abund = value; }
110 if (parameter == "random" ) { randomtree = value; }
111 if (parameter == "sorted" ) { sorted = value; }
112 if (parameter == "scale" ) { scale = 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; }
147 if (parameter == "scale" ) { scale = value; }
151 //make sure the user does not use both the line and label parameters
152 if ((line != "") && (label != "")) { cout << "You may use either the line or label parameters, but not both." << endl; return false; }
154 //check for valid files
155 if (commandName == "read.dist") {
158 }else if (commandName == "read.otu") {
159 //you want to do shared commands
160 if ((listfile != "") && (groupfile != "")) {
161 validateParseFiles(); //checks the listfile and groupfile parameters
162 //you want to do single commands
163 }else if ((listfile != "") || (rabundfile != "") || (sabundfile != "")){
166 //you have not given a file
167 }else if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "")) {
168 cout << "You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. " << endl; return false;
169 //you want to do shared commands with a shared file
170 }else if (sharedfile != "") {//you are reading a shared file
173 }else if (commandName == "read.tree") {
174 validateTreeFiles(); //checks the treefile and groupfile parameters
175 }else if (commandName == "deconvolute") {
176 if (fastafile == "") { cout << "You must enter a fastafile with the deconvolute() command." << endl; return false; }
180 //are you trying to cluster before you have read something
181 if (((commandName == "cluster") && (globaldata->gSparseMatrix == NULL)) ||
182 ((commandName == "cluster") && (globaldata->gListVector == NULL))) {
183 cout << "Before you use the cluster command, you first need to read in a distance matrix." << endl;
187 if ((commandName == "libshuff") && ((globaldata->gMatrix == NULL) || (globaldata->gGroupmap == NULL))) {
188 cout << "You must read in a matrix and groupfile using the read.dist command, before you use the libshuff command. " << endl; return false;
191 if (commandName == "parsimony") {
192 //are you trying to use parsimony without reading a tree or saying you want random distribution
193 if (randomtree == "") {
194 if (globaldata->gTree.size() == 0) {
195 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; }
199 if ((commandName == "unifrac.weighted") || (commandName == "unifrac.unweighted") || (commandName == "concensus")) {
200 if (globaldata->gTree.size() == 0) {//no trees were read
201 cout << "You must execute the read.tree command, before you may execute the unifrac.weighted, unifrac.unweighted or concensus command." << endl; return false; }
204 //check for valid method
205 if(commandName == "get.group") {
206 if ((globaldata->getGroupFile() == "")) { cout << "You must read a group before you can use the get.group command." << endl; return false; }
208 if (commandName == "get.label" || commandName == "get.line") {
209 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; }
211 if (commandName == "cluster") {
212 if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
213 else {cout << "Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average." << endl; return false; }
216 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single") ){
217 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; }
220 if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") || (commandName == "tree.shared") || (commandName == "bootstrap.shared")){
221 if (globaldata->getSharedFile() == "") {
222 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; }
223 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; }
227 if ((commandName == "heatmap") || (commandName == "venn")) {
228 if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
229 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;
233 if ((commandName == "bin.seqs")) {
234 if ((globaldata->getListFile() == "")) { cout << "You must read a list file before you can use the bin.seqs command." << endl; return false; }
238 if ((commandName == "get.oturep")) {
239 if ((globaldata->gSparseMatrix == NULL) || (globaldata->gListVector == NULL)) {
240 cout << "Before you use the get.oturep command, you first need to read in a distance matrix." << endl;
243 if (listfile == "") { cout << "list is a required parameter for the get.oturep command." << endl; errorFree = false; }
251 /*******************************************************/
253 /******************************************************/
254 //This function checks to make sure the user entered a file to
255 // read and that the file exists and can be opened.
256 void ErrorCheck::validateReadFiles() {
258 //Validating files for read
262 //are we reading a phylipfile
263 if (phylipfile != "") {
264 ableToOpen = openInputFile(phylipfile, filehandle);
267 if (ableToOpen == 1) { errorFree = false; }
268 else { globaldata->inputFileName = phylipfile; }
269 //are we reading a columnfile
270 }else if (columnfile != "") {
271 ableToOpen = openInputFile(columnfile, filehandle);
274 if (ableToOpen == 1) { errorFree = false; }
275 else { globaldata->inputFileName = columnfile; }
276 //are we reading a listfile
277 }else if (listfile!= "") {
278 ableToOpen = openInputFile(listfile, filehandle);
281 if (ableToOpen == 1) { errorFree = false; }
282 else { globaldata->inputFileName = listfile; }
283 //are we reading a rabundfile
284 }else if (rabundfile != "") {
285 ableToOpen = openInputFile(rabundfile, filehandle);
288 if (ableToOpen == 1) { errorFree = false; }
289 else { globaldata->inputFileName = rabundfile; }
290 //are we reading a sabundfile
291 }else if (sabundfile != "") {
292 ableToOpen = openInputFile(sabundfile, filehandle);
295 if (ableToOpen == 1) { errorFree = false; }
296 else { globaldata->inputFileName = sabundfile; }
297 }else if (fastafile != "") {
298 ableToOpen = openInputFile(fastafile, filehandle);
301 if (ableToOpen == 1) { errorFree = false; }
302 else { globaldata->inputFileName = fastafile; }
303 }else if (sharedfile != "") {
304 ableToOpen = openInputFile(sharedfile, filehandle);
307 if (ableToOpen == 1) { errorFree = false; }
308 else { globaldata->inputFileName = sharedfile; }
309 }else{ //no file given
313 catch(exception& e) {
314 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
318 cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
323 /*******************************************************/
325 /******************************************************/
326 //This function checks to make sure the user entered appropriate
327 // format parameters on a distfile read
328 void ErrorCheck::validateReadDist() {
333 if (groupfile != "") {
334 ableToOpen = openInputFile(groupfile, filehandle);
337 if (ableToOpen == 1) { errorFree = false; }
340 if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist you must enter a phylip or a column." << endl; errorFree = false; }
341 else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist you must enter ONLY ONE of the following: phylip or column." << endl; errorFree = false; }
343 if (columnfile != "") {
344 if (namefile == "") {
345 cout << "You need to provide a namefile if you are going to use the column format." << endl;
348 ableToOpen = openInputFile(namefile, filehandle);
351 if (ableToOpen == 1) { errorFree = false; }
355 catch(exception& e) {
356 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
360 cout << "An unknown error has occurred in the ErrorCheck class function validateReadDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
364 /*******************************************************/
366 /******************************************************/
367 //This function checks to make sure the user entered appropriate
368 // format parameters on a parselistcommand
369 void ErrorCheck::validateParseFiles() {
374 //checks for valid files
376 if (listfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
377 else if (groupfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
379 //checks parameters on the read command
380 if (listfile != "") {
381 ableToOpen = openInputFile(listfile, filehandle);
383 if (ableToOpen == 1) { //unable to open
386 if (groupfile != "") {
387 ableToOpen = openInputFile(groupfile, filehandle);
389 if (ableToOpen == 1) { //unable to open
395 catch(exception& e) {
396 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
400 cout << "An unknown error has occurred in the ErrorCheck class function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
404 /*******************************************************/
406 /******************************************************/
407 //This function checks to make sure the user entered appropriate
408 // format parameters on a parselistcommand
409 void ErrorCheck::validateTreeFiles() {
414 //checks for valid files
416 if (treefile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
417 else if (groupfile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
419 //checks parameters on the read command
420 if (treefile != "") {
421 ableToOpen = openInputFile(treefile, filehandle);
423 if (ableToOpen == 1) { //unable to open
426 if (groupfile != "") {
427 ableToOpen = openInputFile(groupfile, filehandle);
429 if (ableToOpen == 1) { //unable to open
435 catch(exception& e) {
436 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
440 cout << "An unknown error has occurred in the ErrorCheck class function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
445 /*******************************************************/
447 /******************************************************/
448 //This function checks to make sure the user entered appropriate
449 // format parameters on a distfile read
450 void ErrorCheck::validateReadPhil() {
455 //checks to make sure only one file type is given
456 if (listfile != "") {
457 if ((rabundfile != "") || (sabundfile != "")) {
458 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
459 }else if (rabundfile != "") {
460 if ((listfile != "") || (sabundfile != "")) {
461 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
462 }else if (sabundfile != "") {
463 if ((listfile != "") || (rabundfile != "")) {
464 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
465 }else if ((listfile == "") && (rabundfile == "") && (sabundfile == "") && (sharedfile == "")) {
466 cout << "When executing a read.otu you must enter one of the following: list, rabund or sabund." << endl; errorFree = false;
469 //checks parameters on the read command
470 if (orderfile != "") {
471 ableToOpen = openInputFile(orderfile, filehandle);
473 if (ableToOpen == 1) { //unable to open
478 catch(exception& e) {
479 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
483 cout << "An unknown error has occurred in the ErrorCheck class function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
487 /*******************************************************/
489 /******************************************************/
490 //This function checks to make sure the user entered appropriate
491 // format parameters on a bin.seq command
492 void ErrorCheck::validateBinFiles() {
497 if (fastafile == "") {
498 cout << "fasta is a required parameter for bin.seqs and get.oturep commands." << endl; errorFree = false;
499 }else if (fastafile != "") {
500 //is it a valid filename'
501 ableToOpen = openInputFile(fastafile, filehandle);
504 if (ableToOpen == 1) { errorFree = false; }
505 }else if (listfile != "") {
506 //is it a valid filename'
507 ableToOpen = openInputFile(listfile, filehandle);
510 if (ableToOpen == 1) { errorFree = false; }
511 }else if (globaldata->getNameFile() != "") {
512 //is it a valid filename'
514 int ableToOpen = openInputFile(globaldata->getNameFile(), filehandle);
517 if (ableToOpen == 1) { errorFree = false; }
518 }else if (namefile != "") {
519 //is it a valid filename'
521 int ableToOpen = openInputFile(namefile, filehandle);
524 if (ableToOpen == 1) { errorFree = false; }
529 catch(exception& e) {
530 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateBinFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
534 cout << "An unknown error has occurred in the ErrorCheck class function validateBinFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
539 /*******************************************************/
541 /******************************************************/
543 void ErrorCheck::clear() {
544 //option definitions should go here...
558 /*******************************************************/
560 /******************************************************/