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 for the command
87 if (validParameter->isValidParameter(parameter, commandName) != true) { return false; }
89 if (parameter == "phylip" ) { phylipfile = value; }
90 if (parameter == "column" ) { columnfile = value; }
91 if (parameter == "list" ) { listfile = value; }
92 if (parameter == "rabund" ) { rabundfile = value; }
93 if (parameter == "sabund" ) { sabundfile = value; }
94 if (parameter == "name" ) { namefile = value; }
95 if (parameter == "order" ) { orderfile = value; }
96 if (parameter == "fasta" ) { fastafile = value; }
97 if (parameter == "tree" ) { treefile = value; }
98 if (parameter == "group" ) { groupfile = value; }
99 if (parameter == "shared" ) { sharedfile = value; }
100 if (parameter == "cutoff" ) { cutoff = value; }
101 if (parameter == "precision" ) { precision = value; }
102 if (parameter == "iters" ) { iters = value; }
103 if (parameter == "jumble" ) { jumble = value; }
104 if (parameter == "freq" ) { freq = value; }
105 if (parameter == "method" ) { method = value; }
106 if (parameter == "fileroot" ) { fileroot = value; }
107 if (parameter == "line" ) { line = value; }
108 if (parameter == "label" ) { label = value; }
109 if (parameter == "abund" ) { abund = value; }
110 if (parameter == "random" ) { randomtree = value; }
113 //gets the last parameter and value
114 if (errorFree) { //gets the last parameter and value
116 splitAtEquals(parameter, value);
118 //is it a valid parameter for the command
119 if (validParameter->isValidParameter(parameter, commandName) != true) { return false; }
121 if (parameter == "phylip" ) { phylipfile = value; }
122 if (parameter == "column" ) { columnfile = value; }
123 if (parameter == "list" ) { listfile = value; }
124 if (parameter == "rabund" ) { rabundfile = value; }
125 if (parameter == "sabund" ) { sabundfile = value; }
126 if (parameter == "name" ) { namefile = value; }
127 if (parameter == "order" ) { orderfile = value; }
128 if (parameter == "group" ) { groupfile = value; }
129 if (parameter == "shared" ) { sharedfile = value; }
130 if (parameter == "fasta" ) { fastafile = value; }
131 if (parameter == "tree" ) { treefile = value; }
132 if (parameter == "cutoff" ) { cutoff = value; }
133 if (parameter == "precision" ) { precision = value; }
134 if (parameter == "iters" ) { iters = value; }
135 if (parameter == "jumble" ) { jumble = value; }
136 if (parameter == "freq" ) { freq = value; }
137 if (parameter == "method" ) { method = value; }
138 if (parameter == "fileroot" ) { fileroot = value; }
139 if (parameter == "line" ) { line = value; }
140 if (parameter == "label" ) { label = value; }
141 if (parameter == "random" ) { randomtree = value; }
142 if (parameter == "abund" ) { abund = value; }
146 //make sure the user does not use both the line and label parameters
147 if ((line != "") && (label != "")) { cout << "You may use either the line or label parameters, but not both." << endl; return false; }
149 //check for valid files
150 if (commandName == "read.dist") {
153 }else if (commandName == "read.otu") {
154 //you want to do shared commands
155 if ((listfile != "") && (groupfile != "")) {
156 validateParseFiles(); //checks the listfile and groupfile parameters
157 //you want to do single commands
158 }else if ((listfile != "") || (rabundfile != "") || (sabundfile != "")){
161 //you have not given a file
162 }else if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "")) {
163 cout << "You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. " << endl; return false;
164 //you want to do shared commands with a shared file
165 }else if (sharedfile != "") {//you are reading a shared file
168 }else if (commandName == "read.tree") {
169 validateTreeFiles(); //checks the treefile and groupfile parameters
170 }else if (commandName == "deconvolute") {
171 if (fastafile == "") { cout << "You must enter a fastafile with the deconvolute() command." << endl; return false; }
175 //are you trying to cluster before you have read something
176 if (((commandName == "cluster") && (globaldata->gSparseMatrix == NULL)) ||
177 ((commandName == "cluster") && (globaldata->gListVector == NULL))) {
178 cout << "Before you use the cluster command, you first need to read in a distance matrix." << endl;
182 if ((commandName == "libshuff") && ((globaldata->gMatrix == NULL) || (globaldata->gGroupmap == NULL))) {
183 cout << "You must read in a matrix and groupfile using the read.dist command, before you use the libshuff command. " << endl; return false;
186 if (commandName == "parsimony") {
187 //are you trying to use parsimony without reading a tree or saying you want random distribution
188 if (randomtree == "") {
189 if (globaldata->gTree.size() == 0) {
190 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; }
194 if ((commandName == "unifrac.weighted") || (commandName == "unifrac.unweighted")) {
195 if (globaldata->gTree.size() == 0) {//no trees were read
196 cout << "You must execute the read.tree command, before you may execute the unifrac.weighted or unifrac.unweighted command." << endl; return false; }
199 //check for valid method
200 if(commandName == "get.group") {
201 if ((globaldata->getGroupFile() == "")) { cout << "You must read a group before you can use the get.group command." << endl; return false; }
203 if (commandName == "get.label" || commandName == "get.line") {
204 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; }
206 if (commandName == "cluster") {
207 if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
208 else {cout << "Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average." << endl; return false; }
211 if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single") ){
212 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; }
215 if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") ){
216 if (globaldata->getSharedFile() == "") {
217 if (globaldata->getListFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; }
218 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 or summary.shared commands." << endl; return false; }
225 /*******************************************************/
227 /******************************************************/
228 //This function checks to make sure the user entered a file to
229 // read and that the file exists and can be opened.
230 void ErrorCheck::validateReadFiles() {
232 //Validating files for read
236 //are we reading a phylipfile
237 if (phylipfile != "") {
238 ableToOpen = openInputFile(phylipfile, filehandle);
241 if (ableToOpen == 1) { errorFree = false; }
242 else { globaldata->inputFileName = phylipfile; }
243 //are we reading a columnfile
244 }else if (columnfile != "") {
245 ableToOpen = openInputFile(columnfile, filehandle);
248 if (ableToOpen == 1) { errorFree = false; }
249 else { globaldata->inputFileName = columnfile; }
250 //are we reading a listfile
251 }else if (listfile!= "") {
252 ableToOpen = openInputFile(listfile, filehandle);
255 if (ableToOpen == 1) { errorFree = false; }
256 else { globaldata->inputFileName = listfile; }
257 //are we reading a rabundfile
258 }else if (rabundfile != "") {
259 ableToOpen = openInputFile(rabundfile, filehandle);
262 if (ableToOpen == 1) { errorFree = false; }
263 else { globaldata->inputFileName = rabundfile; }
264 //are we reading a sabundfile
265 }else if (sabundfile != "") {
266 ableToOpen = openInputFile(sabundfile, filehandle);
269 if (ableToOpen == 1) { errorFree = false; }
270 else { globaldata->inputFileName = sabundfile; }
271 }else if (fastafile != "") {
272 ableToOpen = openInputFile(fastafile, filehandle);
275 if (ableToOpen == 1) { errorFree = false; }
276 else { globaldata->inputFileName = fastafile; }
277 }else if (sharedfile != "") {
278 ableToOpen = openInputFile(sharedfile, filehandle);
281 if (ableToOpen == 1) { errorFree = false; }
282 else { globaldata->inputFileName = sharedfile; }
283 }else{ //no file given
287 catch(exception& e) {
288 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
292 cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
297 /*******************************************************/
299 /******************************************************/
300 //This function checks to make sure the user entered appropriate
301 // format parameters on a distfile read
302 void ErrorCheck::validateReadDist() {
307 if (groupfile != "") {
308 ableToOpen = openInputFile(groupfile, filehandle);
311 if (ableToOpen == 1) { errorFree = false; }
314 if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist you must enter a phylip or a column." << endl; errorFree = false; }
315 else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist you must enter ONLY ONE of the following: phylip or column." << endl; errorFree = false; }
317 if (columnfile != "") {
318 if (namefile == "") {
319 cout << "You need to provide a namefile if you are going to use the column format." << endl;
322 ableToOpen = openInputFile(namefile, filehandle);
325 if (ableToOpen == 1) { errorFree = false; }
329 catch(exception& e) {
330 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
334 cout << "An unknown error has occurred in the ErrorCheck class function validateReadDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
338 /*******************************************************/
340 /******************************************************/
341 //This function checks to make sure the user entered appropriate
342 // format parameters on a parselistcommand
343 void ErrorCheck::validateParseFiles() {
348 //checks for valid files
350 if (listfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
351 else if (groupfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
353 //checks parameters on the read command
354 if (listfile != "") {
355 ableToOpen = openInputFile(listfile, filehandle);
357 if (ableToOpen == 1) { //unable to open
360 if (groupfile != "") {
361 ableToOpen = openInputFile(groupfile, filehandle);
363 if (ableToOpen == 1) { //unable to open
369 catch(exception& e) {
370 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
374 cout << "An unknown error has occurred in the ErrorCheck class function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
378 /*******************************************************/
380 /******************************************************/
381 //This function checks to make sure the user entered appropriate
382 // format parameters on a parselistcommand
383 void ErrorCheck::validateTreeFiles() {
388 //checks for valid files
390 if (treefile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
391 else if (groupfile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
393 //checks parameters on the read command
394 if (treefile != "") {
395 ableToOpen = openInputFile(treefile, filehandle);
397 if (ableToOpen == 1) { //unable to open
400 if (groupfile != "") {
401 ableToOpen = openInputFile(groupfile, filehandle);
403 if (ableToOpen == 1) { //unable to open
409 catch(exception& e) {
410 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
414 cout << "An unknown error has occurred in the ErrorCheck class function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
419 /*******************************************************/
421 /******************************************************/
422 //This function checks to make sure the user entered appropriate
423 // format parameters on a distfile read
424 void ErrorCheck::validateReadPhil() {
429 //checks to make sure only one file type is given
430 if (listfile != "") {
431 if ((rabundfile != "") || (sabundfile != "")) {
432 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
433 }else if (rabundfile != "") {
434 if ((listfile != "") || (sabundfile != "")) {
435 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
436 }else if (sabundfile != "") {
437 if ((listfile != "") || (rabundfile != "")) {
438 cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
439 }else if ((listfile == "") && (rabundfile == "") && (sabundfile == "")) {
440 cout << "When executing a read.otu you must enter one of the following: list, rabund or sabund." << endl; errorFree = false;
443 //checks parameters on the read command
444 if (orderfile != "") {
445 ableToOpen = openInputFile(orderfile, filehandle);
447 if (ableToOpen == 1) { //unable to open
452 catch(exception& e) {
453 cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
457 cout << "An unknown error has occurred in the ErrorCheck class function validateReadPhil. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
461 /*******************************************************/
463 /******************************************************/
465 void ErrorCheck::clear() {
466 //option definitions should go here...
480 /*******************************************************/
482 /******************************************************/