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 == "countends" ) { countends = 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 == "countends" ) { countends = 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 == "unique.seqs") {
209 if (fastafile == "") { cout << "You must enter a fastafile with the unique.seqs() 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->getSharedFile() == "")) { cout << "You must read a groupfile or a sharedfile 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 == "get.rabund") {
254 if (globaldata->getListFile() == "") { cout << "You must read a listfile before you can use the get.rabund command." << endl; return false; }
257 if (commandName == "get.sabund") {
258 if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "")) { cout << "You must read a list or rabund before you can use the get.sabund command." << endl; return false; }
261 if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") || (commandName == "bootstrap.shared") || (commandName == "dist.shared")){
262 if (globaldata->getSharedFile() == "") {
263 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; }
264 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; }
268 if (commandName == "tree.shared") {
270 if ((globaldata->getSharedFile() == "") && ((phylipfile == "") && (columnfile == ""))) { cout << "You must run the read.otu command or provide a distance file before running the tree.shared command." << endl; return false; }
271 //you want to do single commands
272 else if ((globaldata->getSharedFile() == "") && ((phylipfile != "") || (columnfile != ""))) {
277 if ((commandName == "heatmap") || (commandName == "venn")) {
278 if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
279 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;
283 if ((commandName == "filter.seqs") || (commandName == "dist.seqs")) {
284 if (fastafile == "") {
285 cout << "You must enter either a fasta file before you can use the filter.seqs or dist.seqs command." << endl; return false;
290 if (commandName == "align.seqs") {
291 if ((fastafile == "") || (candidatefile == "")) {
292 cout << "You must enter fasta and a candidate file to use the align.seqs command." << endl; return false;
297 if ((commandName == "bin.seqs")) {
298 if ((globaldata->getListFile() == "")) { cout << "You must read a list file before you can use the bin.seqs commands." << endl; return false; }
303 if ((commandName == "get.oturep")) {
304 if ((globaldata->gSparseMatrix == NULL) || (globaldata->gListVector == NULL)) {
305 cout << "Before you use the get.oturep command, you first need to read in a distance matrix." << endl;
308 if (listfile == "") { cout << "list is a required parameter for the get.oturep command." << endl; errorFree = false; }
309 if (fastafile == "") { cout << "fasta is a required parameter for the get.oturep command." << endl; errorFree = false; }
317 /*******************************************************/
319 /******************************************************/
320 //This function checks to make sure the user entered a file to
321 // read and that the file exists and can be opened.
322 void ErrorCheck::validateReadFiles() {
324 //Validating files for read
328 //are we reading a phylipfile
329 if (phylipfile != "") {
330 ableToOpen = openInputFile(phylipfile, filehandle);
333 if (ableToOpen == 1) { errorFree = false; }
334 else { globaldata->inputFileName = phylipfile; }
335 //are we reading a columnfile
336 }else if (columnfile != "") {
337 ableToOpen = openInputFile(columnfile, filehandle);
340 if (ableToOpen == 1) { errorFree = false; }
341 else { globaldata->inputFileName = columnfile; }
342 //are we reading a listfile
343 }else if (listfile!= "") {
344 ableToOpen = openInputFile(listfile, filehandle);
347 if (ableToOpen == 1) { errorFree = false; }
348 else { globaldata->inputFileName = listfile; }
349 //are we reading a rabundfile
350 }else if (rabundfile != "") {
351 ableToOpen = openInputFile(rabundfile, filehandle);
354 if (ableToOpen == 1) { errorFree = false; }
355 else { globaldata->inputFileName = rabundfile; }
356 //are we reading a sabundfile
357 }else if (sabundfile != "") {
358 ableToOpen = openInputFile(sabundfile, filehandle);
361 if (ableToOpen == 1) { errorFree = false; }
362 else { globaldata->inputFileName = sabundfile; }
363 }else if (fastafile != "") {
364 ableToOpen = openInputFile(fastafile, filehandle);
367 if (ableToOpen == 1) { errorFree = false; }
368 else { globaldata->inputFileName = fastafile; }
369 }else if (sharedfile != "") {
370 ableToOpen = openInputFile(sharedfile, filehandle);
373 if (ableToOpen == 1) { errorFree = false; }
374 else { globaldata->inputFileName = sharedfile; }
375 }else if (groupfile != "") {
376 ableToOpen = openInputFile(groupfile, filehandle);
378 if (ableToOpen == 1) { //unable to open
381 }else{ //no file given
385 catch(exception& e) {
386 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
390 cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
395 /*******************************************************/
397 /******************************************************/
398 //This function checks to make sure the user entered appropriate
399 // format parameters on a distfile read
400 void ErrorCheck::validateReadDist() {
405 if (groupfile != "") {
406 ableToOpen = openInputFile(groupfile, filehandle);
409 if (ableToOpen == 1) { errorFree = false; }
412 if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist or a tree.shared command with a distance file you must enter a phylip or a column." << endl; errorFree = false; }
413 else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist or a tree.shared command with a distance file you must enter ONLY ONE of the following: phylip or column." << endl; errorFree = false; }
415 if (columnfile != "") {
416 if (namefile == "") {
417 cout << "You need to provide a namefile if you are going to use the column format." << endl;
420 ableToOpen = openInputFile(namefile, filehandle);
423 if (ableToOpen == 1) { errorFree = false; }
427 catch(exception& e) {
428 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
432 cout << "An unknown error has occurred in the ErrorCheck class function validateReadDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
436 /*******************************************************/
438 /******************************************************/
439 //This function checks to make sure the user entered appropriate
440 // format parameters on a parselistcommand
441 void ErrorCheck::validateParseFiles() {
446 //checks for valid files
448 if (listfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
449 else if (groupfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
451 //checks parameters on the read command
452 if (listfile != "") {
453 ableToOpen = openInputFile(listfile, filehandle);
455 if (ableToOpen == 1) { //unable to open
458 if (groupfile != "") {
459 ableToOpen = openInputFile(groupfile, filehandle);
461 if (ableToOpen == 1) { //unable to open
467 catch(exception& e) {
468 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
472 cout << "An unknown error has occurred in the ErrorCheck class function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
476 /*******************************************************/
478 /******************************************************/
479 //This function checks to make sure the user entered appropriate
480 // format parameters on a parselistcommand
481 void ErrorCheck::validateTreeFiles() {
486 //checks for valid files
488 if (treefile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
489 else if (groupfile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
491 //checks parameters on the read command
492 if (treefile != "") {
493 ableToOpen = openInputFile(treefile, filehandle);
495 if (ableToOpen == 1) { //unable to open
498 if (groupfile != "") {
499 ableToOpen = openInputFile(groupfile, filehandle);
501 if (ableToOpen == 1) { //unable to open
507 catch(exception& e) {
508 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
512 cout << "An unknown error has occurred in the ErrorCheck class function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
517 /*******************************************************/
519 /******************************************************/
520 //This function checks to make sure the user entered appropriate
521 // format parameters on a distfile read
522 void ErrorCheck::validateReadPhil() {
527 //checks to make sure only one file type is given
528 if (listfile != "") {
529 if ((rabundfile != "") || (sabundfile != "")) {
530 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
531 }else if (rabundfile != "") {
532 if ((listfile != "") || (sabundfile != "")) {
533 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
534 }else if (sabundfile != "") {
535 if ((listfile != "") || (rabundfile != "")) {
536 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
537 }else if ((listfile == "") && (rabundfile == "") && (sabundfile == "") && (sharedfile == "")) {
538 cout << "When executing a read.otu you must enter one of the following: list, rabund or sabund." << endl; errorFree = false;
541 //checks parameters on the read command
542 if (orderfile != "") {
543 ableToOpen = openInputFile(orderfile, filehandle);
545 if (ableToOpen == 1) { //unable to open
550 catch(exception& e) {
551 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
555 cout << "An unknown error has occurred in the ErrorCheck class function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
559 /*******************************************************/
561 /******************************************************/
562 //This function checks to make sure the user entered appropriate
563 // format parameters on a distfile read
564 void ErrorCheck::validateSeqsFiles() {
569 //checks to make sure only one file type is given
570 if (phylipfile != "") {
571 if ((nexusfile != "") || (fastafile != "") || (clustalfile != "")) {
572 cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; }
574 ableToOpen = openInputFile(phylipfile, filehandle);
576 if (ableToOpen == 1) { //unable to open
580 }else if (nexusfile != "") {
581 if ((phylipfile != "") || (fastafile != "") || (clustalfile != "")) {
582 cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; }
584 ableToOpen = openInputFile(nexusfile, filehandle);
586 if (ableToOpen == 1) { //unable to open
590 }else if (fastafile != "") {
591 if ((phylipfile != "") || (nexusfile != "") || (clustalfile != "")) {
592 cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; }
594 ableToOpen = openInputFile(fastafile, filehandle);
596 if (ableToOpen == 1) { //unable to open
600 }else if (clustalfile != "") {
601 if ((phylipfile != "") || (nexusfile != "") || (fastafile != "")) {
602 cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; }
604 ableToOpen = openInputFile(clustalfile, filehandle);
606 if (ableToOpen == 1) { //unable to open
610 }else if (candidatefile != "") {
611 ableToOpen = openInputFile(candidatefile, filehandle);
613 if (ableToOpen == 1) { //unable to open
620 catch(exception& e) {
621 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateSeqsFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
625 cout << "An unknown error has occurred in the ErrorCheck class function validateSeqsFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
630 /*******************************************************/
632 /******************************************************/
633 //This function checks to make sure the user entered appropriate
634 // format parameters on a bin.seq command
635 void ErrorCheck::validateBinFiles() {
640 if (fastafile == "") {
641 cout << "fasta is a required parameter for bin.seqs, get.oturep and get.repseqs commands." << endl; errorFree = false;
642 }else if (fastafile != "") {
643 //is it a valid filename'
644 ableToOpen = openInputFile(fastafile, filehandle);
647 if (ableToOpen == 1) { errorFree = false; }
648 }else if (listfile != "") {
649 //is it a valid filename'
650 ableToOpen = openInputFile(listfile, filehandle);
653 if (ableToOpen == 1) { errorFree = false; }
654 }else if (globaldata->getNameFile() != "") {
655 //is it a valid filename'
657 int ableToOpen = openInputFile(globaldata->getNameFile(), filehandle);
660 if (ableToOpen == 1) { errorFree = false; }
661 }else if (namefile != "") {
662 //is it a valid filename'
664 int ableToOpen = openInputFile(namefile, filehandle);
667 if (ableToOpen == 1) { errorFree = false; }
668 }else if (groupfile != "") {
669 //is it a valid filename'
671 int ableToOpen = openInputFile(groupfile, filehandle);
674 if (ableToOpen == 1) { errorFree = false; }
680 catch(exception& e) {
681 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateBinFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
685 cout << "An unknown error has occurred in the ErrorCheck class function validateBinFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
690 /*******************************************************/
692 /******************************************************/
694 void ErrorCheck::clear() {
695 //option definitions should go here...
713 /*******************************************************/
715 /******************************************************/