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; }
124 //gets the last parameter and value
125 if (errorFree) { //gets the last parameter and value
127 splitAtEquals(parameter, value);
128 //is it a valid parameter
129 if (validParameter->isValidParameter(parameter, commandName, value) != true) { return false; }
132 if (parameter == "phylip" ) { phylipfile = value; }
133 if (parameter == "column" ) { columnfile = value; }
134 if (parameter == "list" ) { listfile = value; }
135 if (parameter == "rabund" ) { rabundfile = value; }
136 if (parameter == "sabund" ) { sabundfile = value; }
137 if (parameter == "name" ) { namefile = value; }
138 if (parameter == "order" ) { orderfile = value; }
139 if (parameter == "group" ) { groupfile = value; }
140 if (parameter == "shared" ) { sharedfile = value; }
141 if (parameter == "fasta" ) { fastafile = value; }
142 if (parameter == "nexus" ) { nexusfile = value; }
143 if (parameter == "clustal" ) { clustalfile = value; }
144 if (parameter == "tree" ) { treefile = value; }
145 if (parameter == "cutoff" ) { cutoff = value; }
146 if (parameter == "precision" ) { precision = value; }
147 if (parameter == "iters" ) { iters = value; }
148 if (parameter == "jumble" ) { jumble = value; }
149 if (parameter == "freq" ) { freq = value; }
150 if (parameter == "method" ) { method = value; }
151 if (parameter == "fileroot" ) { fileroot = value; }
152 if (parameter == "line" ) { line = value; }
153 if (parameter == "label" ) { label = value; }
154 if (parameter == "random" ) { randomtree = value; }
155 if (parameter == "abund" ) { abund = value; }
156 if (parameter == "sorted" ) { sorted = value; }
157 if (parameter == "trump" ) { trump = value; }
158 if (parameter == "soft" ) { soft = value; }
159 if (parameter == "filter" ) { filter = value; }
160 if (parameter == "scale" ) { scale = value; }
161 if (parameter == "ends" ) { ends = value; }
162 if (parameter == "processors" ) { processors = value; }
167 //make sure the user does not use both the line and label parameters
168 if ((line != "") && (label != "")) { cout << "You may use either the line or label parameters, but not both." << endl; return false; }
170 //check for valid files
171 if (commandName == "read.dist") {
174 }else if (commandName == "read.otu") {
175 //you want to do shared commands
176 if ((listfile != "") && (groupfile != "")) {
177 validateParseFiles(); //checks the listfile and groupfile parameters
178 //you want to do single commands
179 }else if ((listfile != "") || (rabundfile != "") || (sabundfile != "")){
182 //you have not given a file
183 }else if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "")) {
184 cout << "You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. " << endl; return false;
185 //you want to do shared commands with a shared file
186 }else if (sharedfile != "") {//you are reading a shared file
189 }else if (commandName == "read.tree") {
190 validateTreeFiles(); //checks the treefile and groupfile parameters
191 }else if (commandName == "deconvolute") {
192 if (fastafile == "") { cout << "You must enter a fastafile with the deconvolute() command." << endl; return false; }
196 //are you trying to cluster before you have read something
197 if (((commandName == "cluster") && (globaldata->gSparseMatrix == NULL)) ||
198 ((commandName == "cluster") && (globaldata->gListVector == NULL))) {
199 cout << "Before you use the cluster command, you first need to read in a distance matrix." << endl;
203 if ((commandName == "libshuff") && ((globaldata->gMatrix == NULL) || (globaldata->gGroupmap == NULL))) {
204 cout << "You must read in a matrix and groupfile using the read.dist command, before you use the libshuff command. " << endl; return false;
207 if (commandName == "parsimony") {
208 //are you trying to use parsimony without reading a tree or saying you want random distribution
209 if (randomtree == "") {
210 if (globaldata->gTree.size() == 0) {
211 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; }
215 if ((commandName == "unifrac.weighted") || (commandName == "unifrac.unweighted") || (commandName == "concensus")) {
216 if (globaldata->gTree.size() == 0) {//no trees were read
217 cout << "You must execute the read.tree command, before you may execute the unifrac.weighted, unifrac.unweighted or concensus command." << endl; return false; }
220 //check for valid method
221 if(commandName == "get.group") {
222 if ((globaldata->getGroupFile() == "")) { cout << "You must read a group before you can use the get.group command." << endl; return false; }
224 if (commandName == "get.label" || commandName == "get.line") {
225 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; }
227 if (commandName == "cluster") {
228 if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
229 else {cout << "Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average." << endl; return false; }
232 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single") ){
233 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; }
236 if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") || (commandName == "tree.shared") || (commandName == "bootstrap.shared")){
237 if (globaldata->getSharedFile() == "") {
238 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; }
239 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; }
243 if ((commandName == "heatmap") || (commandName == "venn")) {
244 if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
245 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;
249 if ((commandName == "filter.seqs") || (commandName == "dist.seqs")) {
250 if ((fastafile == "") && (nexusfile == "") && (clustalfile == "") && (phylipfile == "")) {
251 cout << "You must read either a fasta, nexus, clustal, or phylip file before you can use the filter.seqs command." << endl; return false;
256 if ((commandName == "bin.seqs")) {
257 if ((globaldata->getListFile() == "")) { cout << "You must read a list file before you can use the bin.seqs command." << endl; return false; }
261 if ((commandName == "get.oturep")) {
262 if ((globaldata->gSparseMatrix == NULL) || (globaldata->gListVector == NULL)) {
263 cout << "Before you use the get.oturep command, you first need to read in a distance matrix." << endl;
266 if (listfile == "") { cout << "list is a required parameter for the get.oturep command." << endl; errorFree = false; }
274 /*******************************************************/
276 /******************************************************/
277 //This function checks to make sure the user entered a file to
278 // read and that the file exists and can be opened.
279 void ErrorCheck::validateReadFiles() {
281 //Validating files for read
285 //are we reading a phylipfile
286 if (phylipfile != "") {
287 ableToOpen = openInputFile(phylipfile, filehandle);
290 if (ableToOpen == 1) { errorFree = false; }
291 else { globaldata->inputFileName = phylipfile; }
292 //are we reading a columnfile
293 }else if (columnfile != "") {
294 ableToOpen = openInputFile(columnfile, filehandle);
297 if (ableToOpen == 1) { errorFree = false; }
298 else { globaldata->inputFileName = columnfile; }
299 //are we reading a listfile
300 }else if (listfile!= "") {
301 ableToOpen = openInputFile(listfile, filehandle);
304 if (ableToOpen == 1) { errorFree = false; }
305 else { globaldata->inputFileName = listfile; }
306 //are we reading a rabundfile
307 }else if (rabundfile != "") {
308 ableToOpen = openInputFile(rabundfile, filehandle);
311 if (ableToOpen == 1) { errorFree = false; }
312 else { globaldata->inputFileName = rabundfile; }
313 //are we reading a sabundfile
314 }else if (sabundfile != "") {
315 ableToOpen = openInputFile(sabundfile, filehandle);
318 if (ableToOpen == 1) { errorFree = false; }
319 else { globaldata->inputFileName = sabundfile; }
320 }else if (fastafile != "") {
321 ableToOpen = openInputFile(fastafile, filehandle);
324 if (ableToOpen == 1) { errorFree = false; }
325 else { globaldata->inputFileName = fastafile; }
326 }else if (sharedfile != "") {
327 ableToOpen = openInputFile(sharedfile, filehandle);
330 if (ableToOpen == 1) { errorFree = false; }
331 else { globaldata->inputFileName = sharedfile; }
332 }else{ //no file given
336 catch(exception& e) {
337 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
341 cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
346 /*******************************************************/
348 /******************************************************/
349 //This function checks to make sure the user entered appropriate
350 // format parameters on a distfile read
351 void ErrorCheck::validateReadDist() {
356 if (groupfile != "") {
357 ableToOpen = openInputFile(groupfile, filehandle);
360 if (ableToOpen == 1) { errorFree = false; }
363 if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist you must enter a phylip or a column." << endl; errorFree = false; }
364 else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist you must enter ONLY ONE of the following: phylip or column." << endl; errorFree = false; }
366 if (columnfile != "") {
367 if (namefile == "") {
368 cout << "You need to provide a namefile if you are going to use the column format." << endl;
371 ableToOpen = openInputFile(namefile, filehandle);
374 if (ableToOpen == 1) { errorFree = false; }
378 catch(exception& e) {
379 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
383 cout << "An unknown error has occurred in the ErrorCheck class function validateReadDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
387 /*******************************************************/
389 /******************************************************/
390 //This function checks to make sure the user entered appropriate
391 // format parameters on a parselistcommand
392 void ErrorCheck::validateParseFiles() {
397 //checks for valid files
399 if (listfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
400 else if (groupfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
402 //checks parameters on the read command
403 if (listfile != "") {
404 ableToOpen = openInputFile(listfile, filehandle);
406 if (ableToOpen == 1) { //unable to open
409 if (groupfile != "") {
410 ableToOpen = openInputFile(groupfile, filehandle);
412 if (ableToOpen == 1) { //unable to open
418 catch(exception& e) {
419 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
423 cout << "An unknown error has occurred in the ErrorCheck class function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
427 /*******************************************************/
429 /******************************************************/
430 //This function checks to make sure the user entered appropriate
431 // format parameters on a parselistcommand
432 void ErrorCheck::validateTreeFiles() {
437 //checks for valid files
439 if (treefile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
440 else if (groupfile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
442 //checks parameters on the read command
443 if (treefile != "") {
444 ableToOpen = openInputFile(treefile, filehandle);
446 if (ableToOpen == 1) { //unable to open
449 if (groupfile != "") {
450 ableToOpen = openInputFile(groupfile, filehandle);
452 if (ableToOpen == 1) { //unable to open
458 catch(exception& e) {
459 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
463 cout << "An unknown error has occurred in the ErrorCheck class function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
468 /*******************************************************/
470 /******************************************************/
471 //This function checks to make sure the user entered appropriate
472 // format parameters on a distfile read
473 void ErrorCheck::validateReadPhil() {
478 //checks to make sure only one file type is given
479 if (listfile != "") {
480 if ((rabundfile != "") || (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 (rabundfile != "") {
483 if ((listfile != "") || (sabundfile != "")) {
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 (sabundfile != "") {
486 if ((listfile != "") || (rabundfile != "")) {
487 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
488 }else if ((listfile == "") && (rabundfile == "") && (sabundfile == "") && (sharedfile == "")) {
489 cout << "When executing a read.otu you must enter one of the following: list, rabund or sabund." << endl; errorFree = false;
492 //checks parameters on the read command
493 if (orderfile != "") {
494 ableToOpen = openInputFile(orderfile, filehandle);
496 if (ableToOpen == 1) { //unable to open
501 catch(exception& e) {
502 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
506 cout << "An unknown error has occurred in the ErrorCheck class function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
510 /*******************************************************/
512 /******************************************************/
513 //This function checks to make sure the user entered appropriate
514 // format parameters on a distfile read
515 void ErrorCheck::validateSeqsFiles() {
520 //checks to make sure only one file type is given
521 if (phylipfile != "") {
522 if ((nexusfile != "") || (fastafile != "") || (clustalfile != "")) {
523 cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; }
525 ableToOpen = openInputFile(phylipfile, filehandle);
527 if (ableToOpen == 1) { //unable to open
531 }else if (nexusfile != "") {
532 if ((phylipfile != "") || (fastafile != "") || (clustalfile != "")) {
533 cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; }
535 ableToOpen = openInputFile(nexusfile, filehandle);
537 if (ableToOpen == 1) { //unable to open
541 }else if (fastafile != "") {
542 if ((phylipfile != "") || (nexusfile != "") || (clustalfile != "")) {
543 cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; }
545 ableToOpen = openInputFile(fastafile, filehandle);
547 if (ableToOpen == 1) { //unable to open
551 }else if (clustalfile != "") {
552 if ((phylipfile != "") || (nexusfile != "") || (fastafile != "")) {
553 cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; }
555 ableToOpen = openInputFile(clustalfile, filehandle);
557 if (ableToOpen == 1) { //unable to open
565 catch(exception& e) {
566 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateSeqsFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
570 cout << "An unknown error has occurred in the ErrorCheck class function validateSeqsFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
575 /*******************************************************/
577 /******************************************************/
578 //This function checks to make sure the user entered appropriate
579 // format parameters on a bin.seq command
580 void ErrorCheck::validateBinFiles() {
585 if (fastafile == "") {
586 cout << "fasta is a required parameter for bin.seqs and get.oturep commands." << endl; errorFree = false;
587 }else if (fastafile != "") {
588 //is it a valid filename'
589 ableToOpen = openInputFile(fastafile, filehandle);
592 if (ableToOpen == 1) { errorFree = false; }
593 }else if (listfile != "") {
594 //is it a valid filename'
595 ableToOpen = openInputFile(listfile, filehandle);
598 if (ableToOpen == 1) { errorFree = false; }
599 }else if (globaldata->getNameFile() != "") {
600 //is it a valid filename'
602 int ableToOpen = openInputFile(globaldata->getNameFile(), filehandle);
605 if (ableToOpen == 1) { errorFree = false; }
606 }else if (namefile != "") {
607 //is it a valid filename'
609 int ableToOpen = openInputFile(namefile, filehandle);
612 if (ableToOpen == 1) { errorFree = false; }
617 catch(exception& e) {
618 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateBinFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
622 cout << "An unknown error has occurred in the ErrorCheck class function validateBinFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
627 /*******************************************************/
629 /******************************************************/
631 void ErrorCheck::clear() {
632 //option definitions should go here...
649 /*******************************************************/
651 /******************************************************/