5 * Created by Sarah Westcott on 1/2/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "errorchecking.h"
12 /*******************************************************/
14 /******************************************************/
16 ErrorCheck::ErrorCheck() {
17 globaldata = GlobalData::getInstance();
18 validCommand = new ValidCommands();
19 validParameter = new ValidParameters();
21 /*******************************************************/
23 /******************************************************/
25 void ErrorCheck::refresh() {
26 columnfile = globaldata->getColumnFile();
27 phylipfile = globaldata->getPhylipFile();
28 listfile = globaldata->getListFile();
29 rabundfile = globaldata->getRabundFile();
30 sabundfile = globaldata->getSabundFile();
31 namefile = globaldata->getNameFile();
32 groupfile = globaldata->getGroupFile();
33 orderfile = globaldata->getOrderFile();
34 fastafile = globaldata->getFastaFile();
35 treefile = globaldata->getTreeFile();
36 cutoff = globaldata->getCutOff();
37 format = globaldata->getFormat();
38 method = globaldata->getMethod();
39 randomtree = globaldata->getRandomTree();
40 sharedfile = globaldata->getSharedFile();
43 /*******************************************************/
45 /******************************************************/
47 ErrorCheck::~ErrorCheck() {
49 delete validParameter;
52 /*******************************************************/
54 /******************************************************/
56 bool ErrorCheck::checkInput(string input) {
63 //get command name and parameters
64 int openParen = input.find_first_of('(');
65 int closeParen = input.find_last_of(')');
67 if(openParen != -1 && closeParen != -1){
68 commandName = input.substr(0, openParen); //commandName contains everything before "("
69 optionText = input.substr(openParen+1, closeParen-openParen-1); //optionString contains everything between "(" and ")".
70 }else if (openParen == -1) { //there is no parenthesis
71 cout << input << " is not a valid command. You are missing the ()." << endl;
75 //is it a valid command
76 if (validCommand->isValidCommand(commandName) != true) { return false; }
78 string parameter, value;
80 //reads in parameters and values
81 if((optionText != "") && (commandName != "help")){
82 while((optionText.find_first_of(',') != -1) && (errorFree)) { //while there are parameters
83 splitAtComma(value, optionText);
84 splitAtEquals(parameter, value);
86 //is it a valid parameter
87 if (validParameter->isValidParameter(parameter, commandName, value) != true) { return false; }
91 if (parameter == "phylip" ) { phylipfile = value; }
92 if (parameter == "column" ) { columnfile = value; }
93 if (parameter == "list" ) { listfile = value; }
94 if (parameter == "rabund" ) { rabundfile = value; }
95 if (parameter == "sabund" ) { sabundfile = value; }
96 if (parameter == "name" ) { namefile = value; }
97 if (parameter == "order" ) { orderfile = value; }
98 if (parameter == "fasta" ) { fastafile = value; }
99 if (parameter == "tree" ) { treefile = value; }
100 if (parameter == "group" ) { groupfile = value; }
101 if (parameter == "shared" ) { sharedfile = value; }
102 if (parameter == "cutoff" ) { cutoff = value; }
103 if (parameter == "precision" ) { precision = value; }
104 if (parameter == "iters" ) { iters = value; }
105 if (parameter == "jumble" ) { jumble = value; }
106 if (parameter == "freq" ) { freq = value; }
107 if (parameter == "method" ) { method = value; }
108 if (parameter == "fileroot" ) { fileroot = value; }
109 if (parameter == "line" ) { line = value; }
110 if (parameter == "label" ) { label = value; }
111 if (parameter == "abund" ) { abund = value; }
112 if (parameter == "random" ) { randomtree = value; }
113 if (parameter == "sorted" ) { sorted = value; }
114 if (parameter == "scale" ) { scale = value; }
118 //gets the last parameter and value
119 if (errorFree) { //gets the last parameter and value
121 splitAtEquals(parameter, value);
122 //is it a valid parameter
123 if (validParameter->isValidParameter(parameter, commandName, value) != true) { return false; }
126 if (parameter == "phylip" ) { phylipfile = value; }
127 if (parameter == "column" ) { columnfile = value; }
128 if (parameter == "list" ) { listfile = value; }
129 if (parameter == "rabund" ) { rabundfile = value; }
130 if (parameter == "sabund" ) { sabundfile = value; }
131 if (parameter == "name" ) { namefile = value; }
132 if (parameter == "order" ) { orderfile = value; }
133 if (parameter == "group" ) { groupfile = value; }
134 if (parameter == "shared" ) { sharedfile = value; }
135 if (parameter == "fasta" ) { fastafile = value; }
136 if (parameter == "tree" ) { treefile = value; }
137 if (parameter == "cutoff" ) { cutoff = value; }
138 if (parameter == "precision" ) { precision = value; }
139 if (parameter == "iters" ) { iters = value; }
140 if (parameter == "jumble" ) { jumble = value; }
141 if (parameter == "freq" ) { freq = value; }
142 if (parameter == "method" ) { method = value; }
143 if (parameter == "fileroot" ) { fileroot = value; }
144 if (parameter == "line" ) { line = value; }
145 if (parameter == "label" ) { label = value; }
146 if (parameter == "random" ) { randomtree = value; }
147 if (parameter == "abund" ) { abund = value; }
148 if (parameter == "sorted" ) { sorted = value; }
149 if (parameter == "scale" ) { scale = value; }
153 //make sure the user does not use both the line and label parameters
154 if ((line != "") && (label != "")) { cout << "You may use either the line or label parameters, but not both." << endl; return false; }
156 //check for valid files
157 if (commandName == "read.dist") {
160 }else if (commandName == "read.otu") {
161 //you want to do shared commands
162 if ((listfile != "") && (groupfile != "")) {
163 validateParseFiles(); //checks the listfile and groupfile parameters
164 //you want to do single commands
165 }else if ((listfile != "") || (rabundfile != "") || (sabundfile != "")){
168 //you have not given a file
169 }else if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "")) {
170 cout << "You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. " << endl; return false;
171 //you want to do shared commands with a shared file
172 }else if (sharedfile != "") {//you are reading a shared file
175 }else if (commandName == "read.tree") {
176 validateTreeFiles(); //checks the treefile and groupfile parameters
177 }else if (commandName == "deconvolute") {
178 if (fastafile == "") { cout << "You must enter a fastafile with the deconvolute() command." << endl; return false; }
182 //are you trying to cluster before you have read something
183 if (((commandName == "cluster") && (globaldata->gSparseMatrix == NULL)) ||
184 ((commandName == "cluster") && (globaldata->gListVector == NULL))) {
185 cout << "Before you use the cluster command, you first need to read in a distance matrix." << endl;
189 if ((commandName == "libshuff") && ((globaldata->gMatrix == NULL) || (globaldata->gGroupmap == NULL))) {
190 cout << "You must read in a matrix and groupfile using the read.dist command, before you use the libshuff command. " << endl; return false;
193 if (commandName == "parsimony") {
194 //are you trying to use parsimony without reading a tree or saying you want random distribution
195 if (randomtree == "") {
196 if (globaldata->gTree.size() == 0) {
197 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; }
201 if ((commandName == "unifrac.weighted") || (commandName == "unifrac.unweighted")) {
202 if (globaldata->gTree.size() == 0) {//no trees were read
203 cout << "You must execute the read.tree command, before you may execute the unifrac.weighted or unifrac.unweighted command." << endl; return false; }
206 //check for valid method
207 if(commandName == "get.group") {
208 if ((globaldata->getGroupFile() == "")) { cout << "You must read a group before you can use the get.group command." << endl; return false; }
210 if (commandName == "get.label" || commandName == "get.line") {
211 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; }
213 if (commandName == "cluster") {
214 if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
215 else {cout << "Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average." << endl; return false; }
218 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single") ){
219 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; }
222 if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") || (commandName == "tree.shared") || (commandName == "bootstrap.shared")){
223 if (globaldata->getSharedFile() == "") {
224 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; }
225 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; }
229 if ((commandName == "heatmap") || (commandName == "venn")) {
230 if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
231 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;
235 if ((commandName == "bin.seqs")) {
236 if ((globaldata->getListFile() == "")) { cout << "You must read a list file before you can use the bin.seqs command." << endl; return false; }
240 if ((commandName == "get.oturep")) {
241 if ((globaldata->gSparseMatrix == NULL) || (globaldata->gListVector == NULL)) {
242 cout << "Before you use the get.oturep command, you first need to read in a distance matrix." << endl;
245 if (listfile == "") { cout << "list is a required parameter for the get.oturep command." << endl; errorFree = false; }
253 /*******************************************************/
255 /******************************************************/
256 //This function checks to make sure the user entered a file to
257 // read and that the file exists and can be opened.
258 void ErrorCheck::validateReadFiles() {
260 //Validating files for read
264 //are we reading a phylipfile
265 if (phylipfile != "") {
266 ableToOpen = openInputFile(phylipfile, filehandle);
269 if (ableToOpen == 1) { errorFree = false; }
270 else { globaldata->inputFileName = phylipfile; }
271 //are we reading a columnfile
272 }else if (columnfile != "") {
273 ableToOpen = openInputFile(columnfile, filehandle);
276 if (ableToOpen == 1) { errorFree = false; }
277 else { globaldata->inputFileName = columnfile; }
278 //are we reading a listfile
279 }else if (listfile!= "") {
280 ableToOpen = openInputFile(listfile, filehandle);
283 if (ableToOpen == 1) { errorFree = false; }
284 else { globaldata->inputFileName = listfile; }
285 //are we reading a rabundfile
286 }else if (rabundfile != "") {
287 ableToOpen = openInputFile(rabundfile, filehandle);
290 if (ableToOpen == 1) { errorFree = false; }
291 else { globaldata->inputFileName = rabundfile; }
292 //are we reading a sabundfile
293 }else if (sabundfile != "") {
294 ableToOpen = openInputFile(sabundfile, filehandle);
297 if (ableToOpen == 1) { errorFree = false; }
298 else { globaldata->inputFileName = sabundfile; }
299 }else if (fastafile != "") {
300 ableToOpen = openInputFile(fastafile, filehandle);
303 if (ableToOpen == 1) { errorFree = false; }
304 else { globaldata->inputFileName = fastafile; }
305 }else if (sharedfile != "") {
306 ableToOpen = openInputFile(sharedfile, filehandle);
309 if (ableToOpen == 1) { errorFree = false; }
310 else { globaldata->inputFileName = sharedfile; }
311 }else{ //no file given
315 catch(exception& e) {
316 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
320 cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
325 /*******************************************************/
327 /******************************************************/
328 //This function checks to make sure the user entered appropriate
329 // format parameters on a distfile read
330 void ErrorCheck::validateReadDist() {
335 if (groupfile != "") {
336 ableToOpen = openInputFile(groupfile, filehandle);
339 if (ableToOpen == 1) { errorFree = false; }
342 if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist you must enter a phylip or a column." << endl; errorFree = false; }
343 else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist you must enter ONLY ONE of the following: phylip or column." << endl; errorFree = false; }
345 if (columnfile != "") {
346 if (namefile == "") {
347 cout << "You need to provide a namefile if you are going to use the column format." << endl;
350 ableToOpen = openInputFile(namefile, filehandle);
353 if (ableToOpen == 1) { errorFree = false; }
357 catch(exception& e) {
358 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
362 cout << "An unknown error has occurred in the ErrorCheck class function validateReadDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
366 /*******************************************************/
368 /******************************************************/
369 //This function checks to make sure the user entered appropriate
370 // format parameters on a parselistcommand
371 void ErrorCheck::validateParseFiles() {
376 //checks for valid files
378 if (listfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
379 else if (groupfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
381 //checks parameters on the read command
382 if (listfile != "") {
383 ableToOpen = openInputFile(listfile, filehandle);
385 if (ableToOpen == 1) { //unable to open
388 if (groupfile != "") {
389 ableToOpen = openInputFile(groupfile, filehandle);
391 if (ableToOpen == 1) { //unable to open
397 catch(exception& e) {
398 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
402 cout << "An unknown error has occurred in the ErrorCheck class function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
406 /*******************************************************/
408 /******************************************************/
409 //This function checks to make sure the user entered appropriate
410 // format parameters on a parselistcommand
411 void ErrorCheck::validateTreeFiles() {
416 //checks for valid files
418 if (treefile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
419 else if (groupfile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
421 //checks parameters on the read command
422 if (treefile != "") {
423 ableToOpen = openInputFile(treefile, filehandle);
425 if (ableToOpen == 1) { //unable to open
428 if (groupfile != "") {
429 ableToOpen = openInputFile(groupfile, filehandle);
431 if (ableToOpen == 1) { //unable to open
437 catch(exception& e) {
438 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
442 cout << "An unknown error has occurred in the ErrorCheck class function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
447 /*******************************************************/
449 /******************************************************/
450 //This function checks to make sure the user entered appropriate
451 // format parameters on a distfile read
452 void ErrorCheck::validateReadPhil() {
457 //checks to make sure only one file type is given
458 if (listfile != "") {
459 if ((rabundfile != "") || (sabundfile != "")) {
460 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
461 }else if (rabundfile != "") {
462 if ((listfile != "") || (sabundfile != "")) {
463 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
464 }else if (sabundfile != "") {
465 if ((listfile != "") || (rabundfile != "")) {
466 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
467 }else if ((listfile == "") && (rabundfile == "") && (sabundfile == "") && (sharedfile == "")) {
468 cout << "When executing a read.otu you must enter one of the following: list, rabund or sabund." << endl; errorFree = false;
471 //checks parameters on the read command
472 if (orderfile != "") {
473 ableToOpen = openInputFile(orderfile, filehandle);
475 if (ableToOpen == 1) { //unable to open
480 catch(exception& e) {
481 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
485 cout << "An unknown error has occurred in the ErrorCheck class function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
489 /*******************************************************/
491 /******************************************************/
492 //This function checks to make sure the user entered appropriate
493 // format parameters on a bin.seq command
494 void ErrorCheck::validateBinFiles() {
499 if (fastafile == "") {
500 cout << "fasta is a required parameter for bin.seqs and get.oturep commands." << endl; errorFree = false;
501 }else if (fastafile != "") {
502 //is it a valid filename'
503 ableToOpen = openInputFile(fastafile, filehandle);
506 if (ableToOpen == 1) { errorFree = false; }
507 }else if (listfile != "") {
508 //is it a valid filename'
509 ableToOpen = openInputFile(listfile, filehandle);
512 if (ableToOpen == 1) { errorFree = false; }
513 }else if (globaldata->getNameFile() != "") {
514 //is it a valid filename'
516 int ableToOpen = openInputFile(globaldata->getNameFile(), filehandle);
519 if (ableToOpen == 1) { errorFree = false; }
520 }else if (namefile != "") {
521 //is it a valid filename'
523 int ableToOpen = openInputFile(namefile, filehandle);
526 if (ableToOpen == 1) { errorFree = false; }
531 catch(exception& e) {
532 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateBinFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
536 cout << "An unknown error has occurred in the ErrorCheck class function validateBinFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
541 /*******************************************************/
543 /******************************************************/
545 void ErrorCheck::clear() {
546 //option definitions should go here...
560 /*******************************************************/
562 /******************************************************/