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; }
119 if (parameter == "ends" ) { ends = value; }
120 if (parameter == "processors" ) { processors = value; }
121 if (parameter == "size" ) { size = value; }
122 if (parameter == "candidate") { candidatefile = value; }
123 if (parameter == "search") { search = value; }
124 if (parameter == "ksize") { ksize = value; }
125 if (parameter == "align") { align = value; }
126 if (parameter == "match") { match = value; }
127 if (parameter == "mismatch") { mismatch = value; }
128 if (parameter == "gapopen") { gapopen = value; }
129 if (parameter == "gapextend" ) { gapextend = value; }
132 //gets the last parameter and value
133 if (errorFree) { //gets the last parameter and value
135 splitAtEquals(parameter, value);
136 //is it a valid parameter
137 if (validParameter->isValidParameter(parameter, commandName, value) != true) { return false; }
140 if (parameter == "phylip" ) { phylipfile = value; }
141 if (parameter == "column" ) { columnfile = value; }
142 if (parameter == "list" ) { listfile = value; }
143 if (parameter == "rabund" ) { rabundfile = value; }
144 if (parameter == "sabund" ) { sabundfile = value; }
145 if (parameter == "name" ) { namefile = value; }
146 if (parameter == "order" ) { orderfile = value; }
147 if (parameter == "group" ) { groupfile = value; }
148 if (parameter == "shared" ) { sharedfile = value; }
149 if (parameter == "fasta" ) { fastafile = value; }
150 if (parameter == "nexus" ) { nexusfile = value; }
151 if (parameter == "clustal" ) { clustalfile = value; }
152 if (parameter == "tree" ) { treefile = value; }
153 if (parameter == "cutoff" ) { cutoff = value; }
154 if (parameter == "precision" ) { precision = value; }
155 if (parameter == "iters" ) { iters = value; }
156 if (parameter == "jumble" ) { jumble = value; }
157 if (parameter == "freq" ) { freq = value; }
158 if (parameter == "method" ) { method = value; }
159 if (parameter == "fileroot" ) { fileroot = value; }
160 if (parameter == "line" ) { line = value; }
161 if (parameter == "label" ) { label = value; }
162 if (parameter == "random" ) { randomtree = value; }
163 if (parameter == "abund" ) { abund = value; }
164 if (parameter == "sorted" ) { sorted = value; }
165 if (parameter == "trump" ) { trump = value; }
166 if (parameter == "soft" ) { soft = value; }
167 if (parameter == "filter" ) { filter = value; }
168 if (parameter == "scale" ) { scale = value; }
169 if (parameter == "ends" ) { ends = value; }
170 if (parameter == "processors" ) { processors = value; }
171 if (parameter == "size" ) { size = value; }
172 if (parameter == "candidate") { candidatefile = value; }
173 if (parameter == "search") { search = value; }
174 if (parameter == "ksize") { ksize = value; }
175 if (parameter == "align") { align = value; }
176 if (parameter == "match") { match = value; }
177 if (parameter == "mismatch") { mismatch = value; }
178 if (parameter == "gapopen") { gapopen = value; }
179 if (parameter == "gapextend" ) { gapextend = value; }
184 //make sure the user does not use both the line and label parameters
185 if ((line != "") && (label != "")) { cout << "You may use either the line or label parameters, but not both." << endl; return false; }
187 //check for valid files
188 if (commandName == "read.dist") {
191 }else if (commandName == "read.otu") {
192 //you want to do shared commands
193 if ((listfile != "") && (groupfile != "")) {
194 validateParseFiles(); //checks the listfile and groupfile parameters
195 //you want to do single commands
196 }else if ((listfile != "") || (rabundfile != "") || (sabundfile != "")){
199 //you have not given a file
200 }else if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "")) {
201 cout << "You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. " << endl; return false;
202 //you want to do shared commands with a shared file
203 }else if (sharedfile != "") {//you are reading a shared file
206 }else if (commandName == "read.tree") {
207 validateTreeFiles(); //checks the treefile and groupfile parameters
208 }else if (commandName == "deconvolute") {
209 if (fastafile == "") { cout << "You must enter a fastafile with the deconvolute() command." << endl; return false; }
213 //are you trying to cluster before you have read something
214 if (((commandName == "cluster") && (globaldata->gSparseMatrix == NULL)) ||
215 ((commandName == "cluster") && (globaldata->gListVector == NULL))) {
216 cout << "Before you use the cluster command, you first need to read in a distance matrix." << endl;
220 if ((commandName == "libshuff") && ((globaldata->gMatrix == NULL) || (globaldata->gGroupmap == NULL))) {
221 cout << "You must read in a matrix and groupfile using the read.dist command, before you use the libshuff command. " << endl; return false;
224 if (commandName == "parsimony") {
225 //are you trying to use parsimony without reading a tree or saying you want random distribution
226 if (randomtree == "") {
227 if (globaldata->gTree.size() == 0) {
228 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; }
232 if ((commandName == "unifrac.weighted") || (commandName == "unifrac.unweighted") || (commandName == "concensus")) {
233 if (globaldata->gTree.size() == 0) {//no trees were read
234 cout << "You must execute the read.tree command, before you may execute the unifrac.weighted, unifrac.unweighted or concensus command." << endl; return false; }
237 //check for valid method
238 if(commandName == "get.group") {
239 if ((globaldata->getGroupFile() == "")) { cout << "You must read a group before you can use the get.group command." << endl; return false; }
241 if (commandName == "get.label" || commandName == "get.line") {
242 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; }
244 if (commandName == "cluster") {
245 if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
246 else {cout << "Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average." << endl; return false; }
249 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single") ){
250 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; }
253 if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") || (commandName == "tree.shared") || (commandName == "bootstrap.shared") || (commandName == "dist.shared")){
254 if (globaldata->getSharedFile() == "") {
255 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, bootstrap.shared or dist.shared commands." << endl; return false; }
256 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, bootstrap.shared or dist.shared commands." << endl; return false; }
260 if ((commandName == "heatmap") || (commandName == "venn")) {
261 if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
262 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;
266 if ((commandName == "filter.seqs") || (commandName == "dist.seqs")) {
267 if ((fastafile == "") && (nexusfile == "") && (clustalfile == "") && (phylipfile == "")) {
268 cout << "You must enter either a fasta, nexus, clustal, or phylip file before you can use the filter.seqs or dist.seqs command." << endl; return false;
273 if (commandName == "align.seqs") {
274 if ((fastafile == "") || (candidatefile == "")) {
275 cout << "You must enter fasta and a candidate file to use the align.seqs command." << endl; return false;
280 if ((commandName == "bin.seqs")) {
281 if ((globaldata->getListFile() == "")) { cout << "You must read a list file before you can use the bin.seqs commands." << endl; return false; }
286 if ((commandName == "get.oturep")) {
287 if ((globaldata->gSparseMatrix == NULL) || (globaldata->gListVector == NULL)) {
288 cout << "Before you use the get.oturep command, you first need to read in a distance matrix." << endl;
291 if (listfile == "") { cout << "list is a required parameter for the get.oturep command." << endl; errorFree = false; }
299 /*******************************************************/
301 /******************************************************/
302 //This function checks to make sure the user entered a file to
303 // read and that the file exists and can be opened.
304 void ErrorCheck::validateReadFiles() {
306 //Validating files for read
310 //are we reading a phylipfile
311 if (phylipfile != "") {
312 ableToOpen = openInputFile(phylipfile, filehandle);
315 if (ableToOpen == 1) { errorFree = false; }
316 else { globaldata->inputFileName = phylipfile; }
317 //are we reading a columnfile
318 }else if (columnfile != "") {
319 ableToOpen = openInputFile(columnfile, filehandle);
322 if (ableToOpen == 1) { errorFree = false; }
323 else { globaldata->inputFileName = columnfile; }
324 //are we reading a listfile
325 }else if (listfile!= "") {
326 ableToOpen = openInputFile(listfile, filehandle);
329 if (ableToOpen == 1) { errorFree = false; }
330 else { globaldata->inputFileName = listfile; }
331 //are we reading a rabundfile
332 }else if (rabundfile != "") {
333 ableToOpen = openInputFile(rabundfile, filehandle);
336 if (ableToOpen == 1) { errorFree = false; }
337 else { globaldata->inputFileName = rabundfile; }
338 //are we reading a sabundfile
339 }else if (sabundfile != "") {
340 ableToOpen = openInputFile(sabundfile, filehandle);
343 if (ableToOpen == 1) { errorFree = false; }
344 else { globaldata->inputFileName = sabundfile; }
345 }else if (fastafile != "") {
346 ableToOpen = openInputFile(fastafile, filehandle);
349 if (ableToOpen == 1) { errorFree = false; }
350 else { globaldata->inputFileName = fastafile; }
351 }else if (sharedfile != "") {
352 ableToOpen = openInputFile(sharedfile, filehandle);
355 if (ableToOpen == 1) { errorFree = false; }
356 else { globaldata->inputFileName = sharedfile; }
357 }else{ //no file given
361 catch(exception& e) {
362 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
366 cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
371 /*******************************************************/
373 /******************************************************/
374 //This function checks to make sure the user entered appropriate
375 // format parameters on a distfile read
376 void ErrorCheck::validateReadDist() {
381 if (groupfile != "") {
382 ableToOpen = openInputFile(groupfile, filehandle);
385 if (ableToOpen == 1) { errorFree = false; }
388 if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist you must enter a phylip or a column." << endl; errorFree = false; }
389 else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist you must enter ONLY ONE of the following: phylip or column." << endl; errorFree = false; }
391 if (columnfile != "") {
392 if (namefile == "") {
393 cout << "You need to provide a namefile if you are going to use the column format." << endl;
396 ableToOpen = openInputFile(namefile, filehandle);
399 if (ableToOpen == 1) { errorFree = false; }
403 catch(exception& e) {
404 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
408 cout << "An unknown error has occurred in the ErrorCheck class function validateReadDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
412 /*******************************************************/
414 /******************************************************/
415 //This function checks to make sure the user entered appropriate
416 // format parameters on a parselistcommand
417 void ErrorCheck::validateParseFiles() {
422 //checks for valid files
424 if (listfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
425 else if (groupfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
427 //checks parameters on the read command
428 if (listfile != "") {
429 ableToOpen = openInputFile(listfile, filehandle);
431 if (ableToOpen == 1) { //unable to open
434 if (groupfile != "") {
435 ableToOpen = openInputFile(groupfile, filehandle);
437 if (ableToOpen == 1) { //unable to open
443 catch(exception& e) {
444 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
448 cout << "An unknown error has occurred in the ErrorCheck class function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
452 /*******************************************************/
454 /******************************************************/
455 //This function checks to make sure the user entered appropriate
456 // format parameters on a parselistcommand
457 void ErrorCheck::validateTreeFiles() {
462 //checks for valid files
464 if (treefile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
465 else if (groupfile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
467 //checks parameters on the read command
468 if (treefile != "") {
469 ableToOpen = openInputFile(treefile, filehandle);
471 if (ableToOpen == 1) { //unable to open
474 if (groupfile != "") {
475 ableToOpen = openInputFile(groupfile, filehandle);
477 if (ableToOpen == 1) { //unable to open
483 catch(exception& e) {
484 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
488 cout << "An unknown error has occurred in the ErrorCheck class function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
493 /*******************************************************/
495 /******************************************************/
496 //This function checks to make sure the user entered appropriate
497 // format parameters on a distfile read
498 void ErrorCheck::validateReadPhil() {
503 //checks to make sure only one file type is given
504 if (listfile != "") {
505 if ((rabundfile != "") || (sabundfile != "")) {
506 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
507 }else if (rabundfile != "") {
508 if ((listfile != "") || (sabundfile != "")) {
509 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
510 }else if (sabundfile != "") {
511 if ((listfile != "") || (rabundfile != "")) {
512 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
513 }else if ((listfile == "") && (rabundfile == "") && (sabundfile == "") && (sharedfile == "")) {
514 cout << "When executing a read.otu you must enter one of the following: list, rabund or sabund." << endl; errorFree = false;
517 //checks parameters on the read command
518 if (orderfile != "") {
519 ableToOpen = openInputFile(orderfile, filehandle);
521 if (ableToOpen == 1) { //unable to open
526 catch(exception& e) {
527 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
531 cout << "An unknown error has occurred in the ErrorCheck class function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
535 /*******************************************************/
537 /******************************************************/
538 //This function checks to make sure the user entered appropriate
539 // format parameters on a distfile read
540 void ErrorCheck::validateSeqsFiles() {
545 //checks to make sure only one file type is given
546 if (phylipfile != "") {
547 if ((nexusfile != "") || (fastafile != "") || (clustalfile != "")) {
548 cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; }
550 ableToOpen = openInputFile(phylipfile, filehandle);
552 if (ableToOpen == 1) { //unable to open
556 }else if (nexusfile != "") {
557 if ((phylipfile != "") || (fastafile != "") || (clustalfile != "")) {
558 cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; }
560 ableToOpen = openInputFile(nexusfile, filehandle);
562 if (ableToOpen == 1) { //unable to open
566 }else if (fastafile != "") {
567 if ((phylipfile != "") || (nexusfile != "") || (clustalfile != "")) {
568 cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; }
570 ableToOpen = openInputFile(fastafile, filehandle);
572 if (ableToOpen == 1) { //unable to open
576 }else if (clustalfile != "") {
577 if ((phylipfile != "") || (nexusfile != "") || (fastafile != "")) {
578 cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; }
580 ableToOpen = openInputFile(clustalfile, filehandle);
582 if (ableToOpen == 1) { //unable to open
586 }else if (candidatefile != "") {
587 ableToOpen = openInputFile(candidatefile, filehandle);
589 if (ableToOpen == 1) { //unable to open
596 catch(exception& e) {
597 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateSeqsFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
601 cout << "An unknown error has occurred in the ErrorCheck class function validateSeqsFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
606 /*******************************************************/
608 /******************************************************/
609 //This function checks to make sure the user entered appropriate
610 // format parameters on a bin.seq command
611 void ErrorCheck::validateBinFiles() {
616 if (fastafile == "") {
617 cout << "fasta is a required parameter for bin.seqs, get.oturep and get.repseqs commands." << endl; errorFree = false;
618 }else if (fastafile != "") {
619 //is it a valid filename'
620 ableToOpen = openInputFile(fastafile, filehandle);
623 if (ableToOpen == 1) { errorFree = false; }
624 }else if (listfile != "") {
625 //is it a valid filename'
626 ableToOpen = openInputFile(listfile, filehandle);
629 if (ableToOpen == 1) { errorFree = false; }
630 }else if (globaldata->getNameFile() != "") {
631 //is it a valid filename'
633 int ableToOpen = openInputFile(globaldata->getNameFile(), filehandle);
636 if (ableToOpen == 1) { errorFree = false; }
637 }else if (namefile != "") {
638 //is it a valid filename'
640 int ableToOpen = openInputFile(namefile, filehandle);
643 if (ableToOpen == 1) { errorFree = false; }
644 }else if (groupfile != "") {
645 //is it a valid filename'
647 int ableToOpen = openInputFile(groupfile, filehandle);
650 if (ableToOpen == 1) { errorFree = false; }
656 catch(exception& e) {
657 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateBinFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
661 cout << "An unknown error has occurred in the ErrorCheck class function validateBinFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
666 /*******************************************************/
668 /******************************************************/
670 void ErrorCheck::clear() {
671 //option definitions should go here...
689 /*******************************************************/
691 /******************************************************/