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() {
27 //columnfile = globaldata->getColumnFile();
28 //phylipfile = globaldata->getPhylipFile();
29 //listfile = globaldata->getListFile();
30 //rabundfile = globaldata->getRabundFile();
31 //sabundfile = globaldata->getSabundFile();
32 //namefile = globaldata->getNameFile();
33 //groupfile = globaldata->getGroupFile();
34 //orderfile = globaldata->getOrderFile();
35 //fastafile = globaldata->getFastaFile();
36 //treefile = globaldata->getTreeFile();
37 //cutoff = globaldata->getCutOff();
38 //format = globaldata->getFormat();
39 //method = globaldata->getMethod();
40 //randomtree = globaldata->getRandomTree();
41 //sharedfile = globaldata->getSharedFile();
45 /*******************************************************/
47 /******************************************************/
49 ErrorCheck::~ErrorCheck() {
51 delete validParameter;
54 /*******************************************************/
56 /******************************************************/
58 bool ErrorCheck::checkInput(string input) {
65 //get command name and parameters
66 int openParen = input.find_first_of('(');
67 int closeParen = input.find_last_of(')');
69 if(openParen != -1 && closeParen != -1){
70 commandName = input.substr(0, openParen); //commandName contains everything before "("
71 optionText = input.substr(openParen+1, closeParen-openParen-1); //optionString contains everything between "(" and ")".
72 }else if (openParen == -1) { //there is no parenthesis
73 cout << input << " is not a valid command. You are missing the ()." << endl;
77 //is it a valid command
78 if (validCommand->isValidCommand(commandName) != true) { return false; }
79 string parameter, value;
81 //reads in parameters and values
82 if((optionText != "") && (commandName != "help")){
83 while((optionText.find_first_of(',') != -1) && (errorFree)) { //while there are parameters
84 splitAtComma(value, optionText);
85 splitAtEquals(parameter, value);
87 //is it a valid parameter
88 if (validParameter->isValidParameter(parameter, commandName, value) != true) { return false; }
90 if (parameter == "phylip" ) { phylipfile = value; }
91 if (parameter == "column" ) { columnfile = value; }
92 if (parameter == "list" ) { listfile = value; }
93 if (parameter == "rabund" ) { rabundfile = value; }
94 if (parameter == "sabund" ) { sabundfile = value; }
95 if (parameter == "name" ) { namefile = value; }
96 if (parameter == "order" ) { orderfile = value; }
97 if (parameter == "fasta" ) { fastafile = value; }
98 if (parameter == "nexus" ) { nexusfile = value; }
99 if (parameter == "clustal" ) { clustalfile = value; }
100 if (parameter == "tree" ) { treefile = value; }
101 if (parameter == "group" ) { groupfile = value; }
102 if (parameter == "shared" ) { sharedfile = value; }
103 if (parameter == "cutoff" ) { cutoff = value; }
104 if (parameter == "precision" ) { precision = value; }
105 if (parameter == "iters" ) { iters = value; }
106 if (parameter == "jumble" ) { jumble = value; }
107 if (parameter == "freq" ) { freq = value; }
108 if (parameter == "method" ) { method = value; }
109 if (parameter == "fileroot" ) { fileroot = value; }
110 if (parameter == "line" ) { line = value; }
111 if (parameter == "label" ) { label = value; }
112 if (parameter == "abund" ) { abund = value; }
113 if (parameter == "random" ) { randomtree = value; }
114 if (parameter == "sorted" ) { sorted = value; }
115 if (parameter == "trump" ) { trump = value; }
116 if (parameter == "soft" ) { soft = value; }
117 if (parameter == "filter" ) { filter = value; }
118 if (parameter == "scale" ) { scale = value; }
122 //gets the last parameter and value
123 if (errorFree) { //gets the last parameter and value
125 splitAtEquals(parameter, value);
126 //is it a valid parameter
127 if (validParameter->isValidParameter(parameter, commandName, value) != true) { return false; }
130 if (parameter == "phylip" ) { phylipfile = value; }
131 if (parameter == "column" ) { columnfile = value; }
132 if (parameter == "list" ) { listfile = value; }
133 if (parameter == "rabund" ) { rabundfile = value; }
134 if (parameter == "sabund" ) { sabundfile = value; }
135 if (parameter == "name" ) { namefile = value; }
136 if (parameter == "order" ) { orderfile = value; }
137 if (parameter == "group" ) { groupfile = value; }
138 if (parameter == "shared" ) { sharedfile = value; }
139 if (parameter == "fasta" ) { fastafile = value; }
140 if (parameter == "nexus" ) { nexusfile = value; }
141 if (parameter == "clustal" ) { clustalfile = value; }
142 if (parameter == "tree" ) { treefile = value; }
143 if (parameter == "cutoff" ) { cutoff = value; }
144 if (parameter == "precision" ) { precision = value; }
145 if (parameter == "iters" ) { iters = value; }
146 if (parameter == "jumble" ) { jumble = value; }
147 if (parameter == "freq" ) { freq = value; }
148 if (parameter == "method" ) { method = value; }
149 if (parameter == "fileroot" ) { fileroot = value; }
150 if (parameter == "line" ) { line = value; }
151 if (parameter == "label" ) { label = value; }
152 if (parameter == "random" ) { randomtree = value; }
153 if (parameter == "abund" ) { abund = value; }
154 if (parameter == "sorted" ) { sorted = value; }
155 if (parameter == "trump" ) { trump = value; }
156 if (parameter == "soft" ) { soft = value; }
157 if (parameter == "filter" ) { filter = value; }
158 if (parameter == "scale" ) { scale = value; }
163 //make sure the user does not use both the line and label parameters
164 if ((line != "") && (label != "")) { cout << "You may use either the line or label parameters, but not both." << endl; return false; }
166 //check for valid files
167 if (commandName == "read.dist") {
170 }else if (commandName == "read.otu") {
171 //you want to do shared commands
172 if ((listfile != "") && (groupfile != "")) {
173 validateParseFiles(); //checks the listfile and groupfile parameters
174 //you want to do single commands
175 }else if ((listfile != "") || (rabundfile != "") || (sabundfile != "")){
178 //you have not given a file
179 }else if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "")) {
180 cout << "You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. " << endl; return false;
181 //you want to do shared commands with a shared file
182 }else if (sharedfile != "") {//you are reading a shared file
185 }else if (commandName == "read.tree") {
186 validateTreeFiles(); //checks the treefile and groupfile parameters
187 }else if (commandName == "read.seqs") {
188 if ((fastafile == "") && (nexusfile == "") && (clustalfile == "") && (phylipfile == "")) { cout << "You must enter a fastafile, nexusfile, or clustalfile with the read.seqs() command." << endl; return false; }
189 }else if (commandName == "deconvolute") {
190 if (fastafile == "") { cout << "You must enter a fastafile with the deconvolute() command." << endl; return false; }
194 //are you trying to cluster before you have read something
195 if (((commandName == "cluster") && (globaldata->gSparseMatrix == NULL)) ||
196 ((commandName == "cluster") && (globaldata->gListVector == NULL))) {
197 cout << "Before you use the cluster command, you first need to read in a distance matrix." << endl;
201 if ((commandName == "libshuff") && ((globaldata->gMatrix == NULL) || (globaldata->gGroupmap == NULL))) {
202 cout << "You must read in a matrix and groupfile using the read.dist command, before you use the libshuff command. " << endl; return false;
205 if (commandName == "parsimony") {
206 //are you trying to use parsimony without reading a tree or saying you want random distribution
207 if (randomtree == "") {
208 if (globaldata->gTree.size() == 0) {
209 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; }
213 if ((commandName == "unifrac.weighted") || (commandName == "unifrac.unweighted") || (commandName == "concensus")) {
214 if (globaldata->gTree.size() == 0) {//no trees were read
215 cout << "You must execute the read.tree command, before you may execute the unifrac.weighted, unifrac.unweighted or concensus command." << endl; return false; }
218 //check for valid method
219 if(commandName == "get.group") {
220 if ((globaldata->getGroupFile() == "")) { cout << "You must read a group before you can use the get.group command." << endl; return false; }
222 if (commandName == "get.label" || commandName == "get.line") {
223 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; }
225 if (commandName == "cluster") {
226 if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
227 else {cout << "Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average." << endl; return false; }
230 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single") ){
231 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; }
234 if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") || (commandName == "tree.shared") || (commandName == "bootstrap.shared")){
235 if (globaldata->getSharedFile() == "") {
236 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; }
237 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; }
241 if ((commandName == "heatmap") || (commandName == "venn")) {
242 if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
243 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;
247 if (commandName == "filter.seqs"){
248 if ((globaldata->getFastaFile() == "") && (globaldata->getNexusFile() == "") && (globaldata->getClustalFile() == "") && (globaldata->getPhylipFile() == "")) {
249 cout << "You must read either a fasta, nexus, clustal, or phylip file before you can use the filter.seqs command." << endl; return false;
253 if ((commandName == "bin.seqs")) {
254 if ((globaldata->getListFile() == "")) { cout << "You must read a list file before you can use the bin.seqs command." << endl; return false; }
258 if ((commandName == "get.oturep")) {
259 if ((globaldata->gSparseMatrix == NULL) || (globaldata->gListVector == NULL)) {
260 cout << "Before you use the get.oturep command, you first need to read in a distance matrix." << endl;
263 if (listfile == "") { cout << "list is a required parameter for the get.oturep command." << endl; errorFree = false; }
271 /*******************************************************/
273 /******************************************************/
274 //This function checks to make sure the user entered a file to
275 // read and that the file exists and can be opened.
276 void ErrorCheck::validateReadFiles() {
278 //Validating files for read
282 //are we reading a phylipfile
283 if (phylipfile != "") {
284 ableToOpen = openInputFile(phylipfile, filehandle);
287 if (ableToOpen == 1) { errorFree = false; }
288 else { globaldata->inputFileName = phylipfile; }
289 //are we reading a columnfile
290 }else if (columnfile != "") {
291 ableToOpen = openInputFile(columnfile, filehandle);
294 if (ableToOpen == 1) { errorFree = false; }
295 else { globaldata->inputFileName = columnfile; }
296 //are we reading a listfile
297 }else if (listfile!= "") {
298 ableToOpen = openInputFile(listfile, filehandle);
301 if (ableToOpen == 1) { errorFree = false; }
302 else { globaldata->inputFileName = listfile; }
303 //are we reading a rabundfile
304 }else if (rabundfile != "") {
305 ableToOpen = openInputFile(rabundfile, filehandle);
308 if (ableToOpen == 1) { errorFree = false; }
309 else { globaldata->inputFileName = rabundfile; }
310 //are we reading a sabundfile
311 }else if (sabundfile != "") {
312 ableToOpen = openInputFile(sabundfile, filehandle);
315 if (ableToOpen == 1) { errorFree = false; }
316 else { globaldata->inputFileName = sabundfile; }
317 }else if (fastafile != "") {
318 ableToOpen = openInputFile(fastafile, filehandle);
321 if (ableToOpen == 1) { errorFree = false; }
322 else { globaldata->inputFileName = fastafile; }
323 }else if (sharedfile != "") {
324 ableToOpen = openInputFile(sharedfile, filehandle);
327 if (ableToOpen == 1) { errorFree = false; }
328 else { globaldata->inputFileName = sharedfile; }
329 }else{ //no file given
333 catch(exception& e) {
334 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
338 cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
343 /*******************************************************/
345 /******************************************************/
346 //This function checks to make sure the user entered appropriate
347 // format parameters on a distfile read
348 void ErrorCheck::validateReadDist() {
353 if (groupfile != "") {
354 ableToOpen = openInputFile(groupfile, filehandle);
357 if (ableToOpen == 1) { errorFree = false; }
360 if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist you must enter a phylip or a column." << endl; errorFree = false; }
361 else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist you must enter ONLY ONE of the following: phylip or column." << endl; errorFree = false; }
363 if (columnfile != "") {
364 if (namefile == "") {
365 cout << "You need to provide a namefile if you are going to use the column format." << endl;
368 ableToOpen = openInputFile(namefile, filehandle);
371 if (ableToOpen == 1) { errorFree = false; }
375 catch(exception& e) {
376 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
380 cout << "An unknown error has occurred in the ErrorCheck class function validateReadDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
384 /*******************************************************/
386 /******************************************************/
387 //This function checks to make sure the user entered appropriate
388 // format parameters on a parselistcommand
389 void ErrorCheck::validateParseFiles() {
394 //checks for valid files
396 if (listfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
397 else if (groupfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
399 //checks parameters on the read command
400 if (listfile != "") {
401 ableToOpen = openInputFile(listfile, filehandle);
403 if (ableToOpen == 1) { //unable to open
406 if (groupfile != "") {
407 ableToOpen = openInputFile(groupfile, filehandle);
409 if (ableToOpen == 1) { //unable to open
415 catch(exception& e) {
416 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
420 cout << "An unknown error has occurred in the ErrorCheck class function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
424 /*******************************************************/
426 /******************************************************/
427 //This function checks to make sure the user entered appropriate
428 // format parameters on a parselistcommand
429 void ErrorCheck::validateTreeFiles() {
434 //checks for valid files
436 if (treefile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
437 else if (groupfile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
439 //checks parameters on the read command
440 if (treefile != "") {
441 ableToOpen = openInputFile(treefile, filehandle);
443 if (ableToOpen == 1) { //unable to open
446 if (groupfile != "") {
447 ableToOpen = openInputFile(groupfile, filehandle);
449 if (ableToOpen == 1) { //unable to open
455 catch(exception& e) {
456 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
460 cout << "An unknown error has occurred in the ErrorCheck class function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
465 /*******************************************************/
467 /******************************************************/
468 //This function checks to make sure the user entered appropriate
469 // format parameters on a distfile read
470 void ErrorCheck::validateReadPhil() {
475 //checks to make sure only one file type is given
476 if (listfile != "") {
477 if ((rabundfile != "") || (sabundfile != "")) {
478 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
479 }else if (rabundfile != "") {
480 if ((listfile != "") || (sabundfile != "")) {
481 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
482 }else if (sabundfile != "") {
483 if ((listfile != "") || (rabundfile != "")) {
484 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
485 }else if ((listfile == "") && (rabundfile == "") && (sabundfile == "") && (sharedfile == "")) {
486 cout << "When executing a read.otu you must enter one of the following: list, rabund or sabund." << endl; errorFree = false;
489 //checks parameters on the read command
490 if (orderfile != "") {
491 ableToOpen = openInputFile(orderfile, filehandle);
493 if (ableToOpen == 1) { //unable to open
498 catch(exception& e) {
499 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
503 cout << "An unknown error has occurred in the ErrorCheck class function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
507 /*******************************************************/
509 /******************************************************/
510 //This function checks to make sure the user entered appropriate
511 // format parameters on a bin.seq command
512 void ErrorCheck::validateBinFiles() {
517 if (fastafile == "") {
518 cout << "fasta is a required parameter for bin.seqs and get.oturep commands." << endl; errorFree = false;
519 }else if (fastafile != "") {
520 //is it a valid filename'
521 ableToOpen = openInputFile(fastafile, filehandle);
524 if (ableToOpen == 1) { errorFree = false; }
525 }else if (listfile != "") {
526 //is it a valid filename'
527 ableToOpen = openInputFile(listfile, filehandle);
530 if (ableToOpen == 1) { errorFree = false; }
531 }else if (globaldata->getNameFile() != "") {
532 //is it a valid filename'
534 int ableToOpen = openInputFile(globaldata->getNameFile(), filehandle);
537 if (ableToOpen == 1) { errorFree = false; }
538 }else if (namefile != "") {
539 //is it a valid filename'
541 int ableToOpen = openInputFile(namefile, filehandle);
544 if (ableToOpen == 1) { errorFree = false; }
549 catch(exception& e) {
550 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateBinFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
554 cout << "An unknown error has occurred in the ErrorCheck class function validateBinFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
559 /*******************************************************/
561 /******************************************************/
563 void ErrorCheck::clear() {
564 //option definitions should go here...
581 /*******************************************************/
583 /******************************************************/