| 1 | package PIANOS.io; |
| 2 | import PIANOS.datastructures.*; |
| 3 | import PIANOS.exceptions.*; |
| 4 | |
| 5 | // data structures |
| 6 | import java.util.HashMap; |
| 7 | import java.util.LinkedList; |
| 8 | import java.util.ArrayList; |
| 9 | |
| 10 | // general reading |
| 11 | import java.util.Scanner; |
| 12 | |
| 13 | // reading the data files |
| 14 | import java.util.StringTokenizer; |
| 15 | |
| 16 | // parsing the equations correctly |
| 17 | import java.util.regex.Pattern; |
| 18 | import java.util.regex.Matcher; |
| 19 | |
| 20 | // File, IOException, etc... |
| 21 | import java.io.*; |
| 22 | |
| 23 | /** |
| 24 | * The PIANOS parser |
| 25 | * Reads input files with readModel and returns the corresponding model. |
| 26 | * @author Eemil Lagerspetz |
| 27 | */ |
| 28 | public class ComputationalModelParser{ |
| 29 | |
| 30 | private ComputationalModelParser(){ |
| 31 | } |
| 32 | |
| 33 | private static int line; |
| 34 | /** Public for testing purposes, do not modify. |
| 35 | */ |
| 36 | public static ArrayList<Variable> toBeChecked; |
| 37 | /** Public for testing purposes, do not modify. |
| 38 | */ |
| 39 | public static HashMap<Variable, String> spatAffectedMap; |
| 40 | private static HashMap<String, Entity> belongMap; |
| 41 | |
| 42 | public static ComputationalModel modelTestOnly(String modelFileName, |
| 43 | String proposalFileName, |
| 44 | DistributionFactory factory) |
| 45 | throws IOException, SyntaxException, MissingDistributionException{ |
| 46 | |
| 47 | // we are supposed to create a ComputationalModel, so let's do just that. |
| 48 | // First initialize the files... |
| 49 | if (modelFileName == null) |
| 50 | throw new IOException("Can't read a file with null name as modelFileName"); |
| 51 | if (proposalFileName == null) |
| 52 | throw new IOException("Can't read a file with null name as proposalFileName"); |
| 53 | |
| 54 | File modelFile = new File(modelFileName); |
| 55 | File proposalFile = new File(proposalFileName); |
| 56 | |
| 57 | // build the components... |
| 58 | int iterations = 0; |
| 59 | int burnIn = 0; |
| 60 | int thinning = 0; |
| 61 | int neighbours = 0; |
| 62 | String updateStrategy = ""; |
| 63 | |
| 64 | LinkedList<Variable> variableList = new LinkedList<Variable>(); |
| 65 | LinkedList<Entity> entityList = new LinkedList<Entity>(); |
| 66 | HashMap<String, Entity> entityMapper = new HashMap<String, Entity>(); |
| 67 | HashMap<String, Variable> variableMapper = new HashMap<String, Variable>(); |
| 68 | |
| 69 | // and start setting them: |
| 70 | toBeChecked = new ArrayList<Variable>(); |
| 71 | spatAffectedMap = new HashMap<Variable, String>(); |
| 72 | |
| 73 | readModelFile(modelFile, variableList, entityList, entityMapper, variableMapper, factory); |
| 74 | |
| 75 | // now we might have stuff in toBeChecked and spatAffectedMap. |
| 76 | |
| 77 | /* These operations still need to be done for stuff in them. |
| 78 | toAdd.addDependence(dep); |
| 79 | dep.addAffected(toAdd); |
| 80 | variables.add(dep); |
| 81 | */ |
| 82 | |
| 83 | checkSpats(variableMapper, modelFile); |
| 84 | |
| 85 | // now they should be alright. |
| 86 | |
| 87 | readProposal(proposalFile, variableMapper, factory); |
| 88 | |
| 89 | readEntityData(entityList); |
| 90 | |
| 91 | neighbours = countNeighbours(entityList); |
| 92 | |
| 93 | checkVariablesAreOk(new ArrayList<Variable>(variableMapper.values())); |
| 94 | |
| 95 | ComputationalModel model = new ComputationalModel(iterations, burnIn, thinning, neighbours, |
| 96 | updateStrategy, variableList, entityList, entityMapper, variableMapper, modelFileName, |
| 97 | null, null, null); |
| 98 | return model; |
| 99 | } |
| 100 | |
| 101 | public static ComputationalModel testNoInitialValues(String modelFileName, |
| 102 | String simulationFileName, |
| 103 | String proposalFileName, |
| 104 | String updateFileName, |
| 105 | String toOutputFileName, DistributionFactory factory) |
| 106 | throws IOException, SyntaxException, MissingDistributionException{ |
| 107 | if (modelFileName == null) |
| 108 | throw new IOException("Can't read a file with null name as modelFileName"); |
| 109 | // if (initialValueFileName == null) |
| 110 | // throw new IOException("Can't read a file with null name as initialValueFileName"); |
| 111 | if (simulationFileName == null) |
| 112 | throw new IOException("Can't read a file with null name as simulationFileName"); |
| 113 | if (proposalFileName == null) |
| 114 | throw new IOException("Can't read a file with null name as proposalFileName"); |
| 115 | if (updateFileName == null) |
| 116 | throw new IOException("Can't read a file with null name as updateFileName"); |
| 117 | if (toOutputFileName == null) |
| 118 | throw new IOException("Can't read a file with null name as toOutputFileName"); |
| 119 | |
| 120 | File modelFile = new File(modelFileName); |
| 121 | // File initialValuesFile = new File(initialValueFileName); |
| 122 | File simulationFile = new File(simulationFileName); |
| 123 | File proposalFile = new File(proposalFileName); |
| 124 | File updateFile = new File(updateFileName); |
| 125 | File toOutputFile = new File(toOutputFileName); |
| 126 | |
| 127 | // build the components... |
| 128 | int iterations = 0; |
| 129 | int burnIn = 0; |
| 130 | int thinning = 0; |
| 131 | int neighbours = 0; |
| 132 | String updateStrategy = ""; |
| 133 | |
| 134 | LinkedList<Variable> variableList = new LinkedList<Variable>(); |
| 135 | LinkedList<Entity> entityList = new LinkedList<Entity>(); |
| 136 | HashMap<String, Entity> entityMapper = new HashMap<String, Entity>(); |
| 137 | HashMap<String, Variable> variableMapper = new HashMap<String, Variable>(); |
| 138 | |
| 139 | // and start setting them: |
| 140 | toBeChecked = new ArrayList<Variable>(); |
| 141 | spatAffectedMap = new HashMap<Variable, String>(); |
| 142 | |
| 143 | readModelFile(modelFile, variableList, entityList, entityMapper, variableMapper, factory); |
| 144 | |
| 145 | // now we might have stuff in toBeChecked and spatAffectedMap. |
| 146 | |
| 147 | /* These operations still need to be done for stuff in them. |
| 148 | toAdd.addDependence(dep); |
| 149 | dep.addAffected(toAdd); |
| 150 | variables.add(dep); |
| 151 | */ |
| 152 | |
| 153 | checkSpats(variableMapper, modelFile); |
| 154 | |
| 155 | // now they should be alright. |
| 156 | |
| 157 | int[] temp = readSimulation(simulationFile); |
| 158 | burnIn = temp[0]; |
| 159 | thinning = temp[1]; |
| 160 | |
| 161 | Object[] updateTemp = readUpdate(updateFile, variableMapper , updateStrategy); |
| 162 | updateStrategy = (String)updateTemp[0]; |
| 163 | iterations = (Integer)updateTemp[1]; |
| 164 | |
| 165 | String[] opFiles = readOutput(toOutputFile, variableMapper); |
| 166 | |
| 167 | readProposal(proposalFile, variableMapper, factory); |
| 168 | |
| 169 | readEntityData(entityList); |
| 170 | |
| 171 | neighbours = countNeighbours(entityList); |
| 172 | // readInitialValues(initialValuesFile, variableMapper); |
| 173 | |
| 174 | checkVariablesAreOk(new ArrayList<Variable>(variableMapper.values())); |
| 175 | |
| 176 | ComputationalModel model = new ComputationalModel(iterations, burnIn, thinning, neighbours, |
| 177 | updateStrategy, variableList, entityList, entityMapper, variableMapper, modelFileName, |
| 178 | null, opFiles[0], opFiles[1]); |
| 179 | return model; |
| 180 | } |
| 181 | |
| 182 | |
| 183 | /** |
| 184 | * The main interface for the Parser. All filenames are valid with a relative path. |
| 185 | * @param modelFileName the name of the model file |
| 186 | * @param initialValueFileName the name of the initial |
| 187 | * values file |
| 188 | * @param simulationFileName the name of the model file |
| 189 | * @param proposalFileName the name of the proposal distributions |
| 190 | * file |
| 191 | * @param updateFileName the name of the variables update strategy |
| 192 | * file |
| 193 | * @param toOutputFileName the name of the to_output file |
| 194 | * @param factory the DistributionFactory with the user distributions used |
| 195 | @return the complete model data structure constructed from the files given. |
| 196 | */ |
| 197 | |
| 198 | public static ComputationalModel readModel(String modelFileName, |
| 199 | String initialValueFileName, |
| 200 | String simulationFileName, |
| 201 | String proposalFileName, |
| 202 | String updateFileName, |
| 203 | String toOutputFileName, DistributionFactory factory) |
| 204 | throws IOException, SyntaxException, MissingDistributionException{ |
| 205 | |
| 206 | // we are supposed to create a ComputationalModel, so let's do just that. |
| 207 | // First initialize the files... |
| 208 | if (modelFileName == null) |
| 209 | throw new IOException("Can't read a file with null name as modelFileName"); |
| 210 | if (initialValueFileName == null) |
| 211 | throw new IOException("Can't read a file with null name as initialValueFileName"); |
| 212 | if (simulationFileName == null) |
| 213 | throw new IOException("Can't read a file with null name as simulationFileName"); |
| 214 | if (proposalFileName == null) |
| 215 | throw new IOException("Can't read a file with null name as proposalFileName"); |
| 216 | if (updateFileName == null) |
| 217 | throw new IOException("Can't read a file with null name as updateFileName"); |
| 218 | if (toOutputFileName == null) |
| 219 | throw new IOException("Can't read a file with null name as toOutputFileName"); |
| 220 | |
| 221 | File modelFile = new File(modelFileName); |
| 222 | File initialValuesFile = new File(initialValueFileName); |
| 223 | File simulationFile = new File(simulationFileName); |
| 224 | File proposalFile = new File(proposalFileName); |
| 225 | File updateFile = new File(updateFileName); |
| 226 | File toOutputFile = new File(toOutputFileName); |
| 227 | |
| 228 | // build the components... |
| 229 | int iterations = 0; |
| 230 | int burnIn = 0; |
| 231 | int thinning = 0; |
| 232 | int neighbours = 0; |
| 233 | String updateStrategy = ""; |
| 234 | |
| 235 | LinkedList<Variable> variableList = new LinkedList<Variable>(); |
| 236 | LinkedList<Entity> entityList = new LinkedList<Entity>(); |
| 237 | HashMap<String, Entity> entityMapper = new HashMap<String, Entity>(); |
| 238 | HashMap<String, Variable> variableMapper = new HashMap<String, Variable>(); |
| 239 | |
| 240 | // and start setting them: |
| 241 | toBeChecked = new ArrayList<Variable>(); |
| 242 | spatAffectedMap = new HashMap<Variable, String>(); |
| 243 | |
| 244 | |
| 245 | System.out.print("Reading the model file..."); |
| 246 | readModelFile(modelFile, variableList, entityList, entityMapper, variableMapper, factory); |
| 247 | System.out.println("\t\t\t\t\t[OK]"); |
| 248 | // now we might have stuff in toBeChecked and spatAffectedMap. |
| 249 | |
| 250 | /* These operations still need to be done for stuff in them. |
| 251 | toAdd.addDependence(dep); |
| 252 | dep.addAffected(toAdd); |
| 253 | variables.add(dep); |
| 254 | */ |
| 255 | |
| 256 | checkSpats(variableMapper, modelFile); |
| 257 | |
| 258 | |
| 259 | // now they should be alright. |
| 260 | |
| 261 | System.out.print("Reading simulation parameters..."); |
| 262 | int[] temp = readSimulation(simulationFile); |
| 263 | burnIn = temp[0]; |
| 264 | thinning = temp[1]; |
| 265 | |
| 266 | System.out.println("\t\t\t\t[OK]"); |
| 267 | |
| 268 | System.out.print("Reading update file..."); |
| 269 | Object[] updateTemp = readUpdate(updateFile, variableMapper , updateStrategy); |
| 270 | updateStrategy = (String)updateTemp[0]; |
| 271 | iterations = (Integer)updateTemp[1]; |
| 272 | System.out.println("\t\t\t\t\t\t[OK]"); |
| 273 | |
| 274 | System.out.print("Getting output variable names..."); |
| 275 | String[] opFiles = readOutput(toOutputFile, variableMapper); |
| 276 | |
| 277 | System.out.println("\t\t\t\t[OK]"); |
| 278 | |
| 279 | |
| 280 | System.out.print("Validating proposal distributions..."); |
| 281 | readProposal(proposalFile, variableMapper, factory); |
| 282 | System.out.println("\t\t\t\t[OK]"); |
| 283 | |
| 284 | |
| 285 | System.out.print("Validating data..."); |
| 286 | readEntityData(entityList); |
| 287 | System.out.println("\t\t\t\t\t\t[OK]"); |
| 288 | |
| 289 | System.out.print("Finding maximum number of neighbours..."); |
| 290 | neighbours = countNeighbours(entityList); |
| 291 | System.out.println("\t\t\t\t[OK]"); |
| 292 | |
| 293 | System.out.print("Checking initial values..."); |
| 294 | readInitialValues(initialValuesFile, variableMapper); |
| 295 | System.out.println("\t\t\t\t\t[OK]"); |
| 296 | |
| 297 | System.out.print("Model check..."); |
| 298 | checkVariablesAreOk(new ArrayList<Variable>(variableMapper.values())); |
| 299 | System.out.println("\t\t\t\t\t\t\t[OK]"); |
| 300 | |
| 301 | ComputationalModel model = new ComputationalModel(iterations, burnIn, thinning, neighbours, |
| 302 | updateStrategy, variableList, entityList, entityMapper, variableMapper, modelFileName, |
| 303 | initialValueFileName, opFiles[0], opFiles[1]); |
| 304 | |
| 305 | System.out.println("Model built."); |
| 306 | return model; |
| 307 | } |
| 308 | |
| 309 | private static void checkSpats(HashMap <String, Variable> variableMapper, File modelFile) |
| 310 | throws SyntaxException{ |
| 311 | for (Variable aff : toBeChecked){ |
| 312 | String varname = spatAffectedMap.get(aff); |
| 313 | Variable var = variableMapper.get(varname); |
| 314 | if (aff == null) |
| 315 | throw new SyntaxException("In "+ modelFile + ": Variable "+ varname + |
| 316 | " is used in a COUNT or SUM statement but never defined"); |
| 317 | aff.addDependence(var); |
| 318 | var.addAffected(aff); |
| 319 | // It's good that we defined that SUM and COUNT must appear alone. |
| 320 | // otherwise this would have been VERY troublesome. |
| 321 | aff.getEquation().setParameters(var); |
| 322 | } |
| 323 | } |
| 324 | |
| 325 | /** Reads the model file and puts the information into the maps and lists provided. |
| 326 | * |
| 327 | */ |
| 328 | |
| 329 | private static void readModelFile(File file, LinkedList<Variable> variableList, |
| 330 | LinkedList<Entity> entityList, HashMap<String, Entity> entityMapper, |
| 331 | HashMap<String, Variable> variableMapper, DistributionFactory fact) |
| 332 | throws IOException, SyntaxException, MissingDistributionException{ |
| 333 | // reads the model, creates data structures from it, sets the variables' sizes correctly |
| 334 | // with help from readData(which creates the missing binary matrix and the modified data |
| 335 | // file as a side-product) |
| 336 | |
| 337 | |
| 338 | Scanner reader = new Scanner(file); |
| 339 | String temp = null; |
| 340 | line = 0; |
| 341 | while (reader.hasNextLine()){ |
| 342 | temp = reader.nextLine(); |
| 343 | line++; |
| 344 | temp = temp.trim(); |
| 345 | |
| 346 | if (temp.length() == 0 || temp.charAt(0) == '#') |
| 347 | continue; |
| 348 | |
| 349 | // now we have a non-comment non-zero line. |
| 350 | |
| 351 | // it can either be a global variable starting with |
| 352 | // REAL or INTEGER, |
| 353 | // or it can be an ENTITY definition line starting with ENTITY. |
| 354 | |
| 355 | if (temp.startsWith("REAL")){ |
| 356 | temp = temp.substring(4).trim(); |
| 357 | readglobal(file, false, temp, variableMapper, variableList, fact); |
| 358 | } else if (temp.startsWith("INTEGER")){ |
| 359 | temp = temp.substring(7).trim(); |
| 360 | readglobal(file, true, temp, variableMapper, variableList, fact); |
| 361 | } else if (temp.startsWith("ENTITY")){ |
| 362 | temp = temp.substring(6).trim(); |
| 363 | readEntity(file, entityList, entityMapper, variableMapper, temp, reader, fact); |
| 364 | } else |
| 365 | throw new SyntaxException("No entity or variable on line " + line); |
| 366 | |
| 367 | } |
| 368 | reader.close(); |
| 369 | } |
| 370 | |
| 371 | /** Reads a global variable's information from the line provided and saves it to the variablelist and mapper. |
| 372 | * |
| 373 | */ |
| 374 | |
| 375 | private static void readglobal(File file, boolean isInteger, String toParse, |
| 376 | HashMap<String, Variable> variableMapper, LinkedList<Variable> variableList, |
| 377 | DistributionFactory fact) throws SyntaxException, |
| 378 | MissingDistributionException { |
| 379 | Variable toAdd = parseVariable(file, isInteger, toParse, variableMapper, fact); |
| 380 | toAdd.setEntity(null); // global |
| 381 | variableMapper.put(toAdd.getName(), toAdd); |
| 382 | variableList.add(toAdd); // global variables list |
| 383 | } |
| 384 | |
| 385 | /** Reads a variable definition line and returns a representation of the variable, public for testing purposes. Do not call directly. |
| 386 | * |
| 387 | */ |
| 388 | |
| 389 | public static Variable parseVariable(File file, boolean isInteger, String toParse, |
| 390 | HashMap<String, Variable> variableMapper, DistributionFactory fact) throws |
| 391 | SyntaxException, MissingDistributionException{ |
| 392 | Variable toAdd = new Variable(); |
| 393 | |
| 394 | toAdd.setType(isInteger); |
| 395 | toParse = toParse.replaceAll("\\p{Space}+", ""); |
| 396 | /* |
| 397 | *Now we have either |
| 398 | *nam4e~dist(par,par2,..,par83) |
| 399 | *or |
| 400 | *nam4e=expression |
| 401 | *or |
| 402 | *nam4e(index) |
| 403 | *or |
| 404 | *nam4e(index)~dist(par,...) |
| 405 | *or |
| 406 | *nam4e(index)=expr |
| 407 | */ |
| 408 | |
| 409 | int parenIndex = toParse.indexOf('('); |
| 410 | int eqIndex = toParse.indexOf('='); |
| 411 | int tildeIndex = toParse.indexOf('~'); |
| 412 | if (parenIndex == -1) |
| 413 | parenIndex = toParse.length(); |
| 414 | if (eqIndex == -1) |
| 415 | eqIndex = toParse.length(); |
| 416 | if (tildeIndex == -1) |
| 417 | tildeIndex = toParse.length(); |
| 418 | |
| 419 | String name = toParse.substring(0, Math.min(parenIndex, |
| 420 | Math.min(eqIndex, tildeIndex))); |
| 421 | |
| 422 | |
| 423 | Pattern p = Pattern.compile("[a-z][a-z0-9]*"); |
| 424 | Matcher m = p.matcher(name); |
| 425 | if (!m.matches()) |
| 426 | throw new SyntaxException("In "+ file + ": Invalid variable name " + |
| 427 | "on line " + line); |
| 428 | |
| 429 | toAdd.setName(name); |
| 430 | |
| 431 | toParse = toParse.substring(name.length()); // the char after the last of name |
| 432 | |
| 433 | /* |
| 434 | *Now we have either |
| 435 | *~dist(par,par2,..,par83) |
| 436 | *or |
| 437 | *=expression |
| 438 | *or |
| 439 | *(index) |
| 440 | *or |
| 441 | *(index)~dist(par,...) |
| 442 | *or |
| 443 | *(index)=expr |
| 444 | */ |
| 445 | |
| 446 | if (toParse.length() <= 0) |
| 447 | throw new SyntaxException("In "+ file +": No column definition, expression or distribution " + |
| 448 | "found for variable on line " + line); |
| 449 | |
| 450 | if (toParse.charAt(0) == '('){ |
| 451 | // parse the column definition and parse it out |
| 452 | String col = toParse.substring(1, toParse.indexOf(')')); |
| 453 | toParse = toParse.substring(toParse.indexOf(')') +1); |
| 454 | toAdd.setData(true); |
| 455 | if (col.equals("*")) // *, nothing else |
| 456 | toAdd.setColumn(-1); |
| 457 | else{ |
| 458 | try{ |
| 459 | int temp = Integer.parseInt(col); |
| 460 | if (temp < 1) |
| 461 | throw new SyntaxException("In "+ file +": Invalid column number on line " + line |
| 462 | + " (columns start at 1)"); |
| 463 | toAdd.setColumn(temp); |
| 464 | }catch (NumberFormatException nfe){ |
| 465 | // not *, not an integer, problem |
| 466 | throw new SyntaxException("In "+ file + ": Invalid column number on line " + line); |
| 467 | } |
| 468 | } |
| 469 | } else { // no column def |
| 470 | toAdd.setData(false); |
| 471 | } |
| 472 | |
| 473 | |
| 474 | // name, column, isData are set |
| 475 | |
| 476 | /* |
| 477 | *Now we have either |
| 478 | *~dist(par,par2,..,par83) |
| 479 | *or |
| 480 | *=expression |
| 481 | *or |
| 482 | * |
| 483 | */ |
| 484 | |
| 485 | |
| 486 | if (toParse.length() <= 0) |
| 487 | return toAdd; |
| 488 | |
| 489 | /* |
| 490 | *Now we have either |
| 491 | *~dist(par,par2,..,par83) |
| 492 | *or |
| 493 | *=expression |
| 494 | */ |
| 495 | |
| 496 | if (toParse.charAt(0) == '~') { |
| 497 | toAdd.setFunctional(false); |
| 498 | String distStr = null; |
| 499 | if (toParse.indexOf('(') < 0) |
| 500 | distStr = ""; |
| 501 | else |
| 502 | distStr = toParse.substring(1, toParse.indexOf('(')).trim(); |
| 503 | Distribution dist = fact.getDistribution(distStr); |
| 504 | // this might throw a MissingDistributionException. |
| 505 | toAdd.setDistribution(dist); |
| 506 | |
| 507 | if (toParse.indexOf(')') < 0){ |
| 508 | throw new SyntaxException("In "+ file +": Mismatching parentheses on line "+ line); |
| 509 | } |
| 510 | |
| 511 | |
| 512 | toParse = toParse.substring(toParse.indexOf('(') +1, toParse.lastIndexOf(')')).trim(); |
| 513 | // Now we have "param1, param2, ..., paramn" |
| 514 | |
| 515 | if (toParse.length() == 0) |
| 516 | throw new SyntaxException("In "+ file +": Too few parameters on line "+ line); |
| 517 | |
| 518 | int index = 0; |
| 519 | while (toParse != null) { |
| 520 | int comma = toParse.indexOf(','); |
| 521 | String param = null; |
| 522 | if (comma > 0) { |
| 523 | param = toParse.substring(0, comma).trim(); |
| 524 | // there is a comma, so the next parameter should be before it |
| 525 | // for the next round: |
| 526 | toParse = toParse.substring(comma +1).trim(); |
| 527 | } else { |
| 528 | param = toParse.trim(); |
| 529 | // no comma found, so this is the last parameter |
| 530 | |
| 531 | // to terminate the loop |
| 532 | toParse = null; |
| 533 | |
| 534 | // are there too few parameters in the file? |
| 535 | |
| 536 | } |
| 537 | |
| 538 | // are there too many parameters in the file? |
| 539 | if (dist.getNumberOfParameters() <= index) |
| 540 | throw new SyntaxException("In "+ file +": Too many parameters on line "+ line); |
| 541 | boolean integer = dist.isInteger(index); |
| 542 | if (integer){ |
| 543 | try{ |
| 544 | int paramInt = Integer.parseInt(param); |
| 545 | dist.setParameter(index, paramInt); |
| 546 | // it's a good integer, no need to check for anything else |
| 547 | |
| 548 | } catch(NumberFormatException e){ |
| 549 | // okay, it's not an Integer. |
| 550 | // it may still be a Variable reference |
| 551 | // or something malformed |
| 552 | p = Pattern.compile("[a-z][a-z0-9]*"); |
| 553 | |
| 554 | m = p.matcher(param); |
| 555 | if (!m.matches()){ |
| 556 | //Ok, it's definitely something malformed. |
| 557 | throw new SyntaxException("In "+ file +": Parameter " + (index +1) + |
| 558 | " on line " + line + " is not an integer or a correct variable name"); |
| 559 | } |
| 560 | Variable paramVar = variableMapper.get(param); |
| 561 | if (paramVar == null) // run out of tricks |
| 562 | throw new SyntaxException("In "+ file +": Parameter " + (index +1) + |
| 563 | " on line " + line + " is not defined before it is used"); |
| 564 | else{ |
| 565 | if (!paramVar.isInteger()) |
| 566 | throw new SyntaxException("In "+ file +": Parameter " + (index +1) + |
| 567 | " on line " + line + " is not of type INTEGER"); |
| 568 | dist.setParameter(index, paramVar); |
| 569 | paramVar.addAffected(toAdd); |
| 570 | toAdd.addDependence(paramVar); |
| 571 | } |
| 572 | } |
| 573 | } else{ |
| 574 | // not an integer, so it should be REAL |
| 575 | try { |
| 576 | double paramDouble = Double.parseDouble(param); |
| 577 | dist.setParameter(index, paramDouble); |
| 578 | // it's a good double, continue |
| 579 | |
| 580 | } catch (NumberFormatException nfe){ |
| 581 | // okay, not a good double. |
| 582 | |
| 583 | // is it something malformed? |
| 584 | p = Pattern.compile("[a-z][a-z0-9]*"); |
| 585 | m = p.matcher(param); |
| 586 | |
| 587 | if (!m.matches()){ |
| 588 | //Ok, it's definitely something malformed. |
| 589 | throw new SyntaxException("In "+ file +": Parameter " + (index +1) + |
| 590 | " on line " + line + " is not a decimal number or a correct " + |
| 591 | "variable name"); |
| 592 | } |
| 593 | |
| 594 | // is it a Variable? |
| 595 | |
| 596 | Variable paramVar = variableMapper.get(param); |
| 597 | if (paramVar == null) // run out of tricks |
| 598 | throw new SyntaxException("In "+ file +": Parameter " + (index +1) + |
| 599 | " on line " + line + " is not defined before it is used"); |
| 600 | else{ |
| 601 | // new desireable behaviour: Accept integers on places of REALs, |
| 602 | // consider REAL a more extensive type |
| 603 | /* |
| 604 | if (paramVar.isInteger()) |
| 605 | throw new SyntaxException("In "+ file +": Parameter " + (index +1) + |
| 606 | " on line " + line + " is not of type REAL"); |
| 607 | */ |
| 608 | dist.setParameter(index, paramVar); |
| 609 | paramVar.addAffected(toAdd); |
| 610 | toAdd.addDependence(paramVar); |
| 611 | } |
| 612 | } |
| 613 | |
| 614 | } |
| 615 | if (toParse == null){ // if we are going to terminate after this... |
| 616 | if (index+1 != dist.getNumberOfParameters()) |
| 617 | throw new SyntaxException("In "+ file +": Too few parameters on line "+ line); |
| 618 | } |
| 619 | // if we didn't exit yet, the param is good, let's add the |
| 620 | // String too |
| 621 | dist.setParameterString(index, param); |
| 622 | |
| 623 | index++; |
| 624 | } |
| 625 | |
| 626 | } else if(toParse.charAt(0) == '=') { |
| 627 | toParse = toParse.substring(1).trim(); |
| 628 | toAdd.setFunctional(true); |
| 629 | |
| 630 | String equation = toParse; |
| 631 | equation = equation.replaceAll("\\p{Space}+", ""); |
| 632 | |
| 633 | ArrayList<String> tempString; |
| 634 | ArrayList<Variable> variables; |
| 635 | |
| 636 | |
| 637 | // now we have |
| 638 | // EXP(alpha * 12 / LOG(beta - 1.0 * gamma)) ... |
| 639 | // we are interested in parts alpha, beta, gamma and their starting indices. |
| 640 | // IF I understand correctly, variable names are |
| 641 | // the only part here written in lowercase a-z. |
| 642 | p = Pattern.compile("[a-z][a-z0-9]*"); |
| 643 | m = p.matcher(equation); |
| 644 | int last = 0; |
| 645 | int index = 0; |
| 646 | |
| 647 | Pattern sum = Pattern.compile("SUM\\(\\&[a-z][a-z0-9]*\\)"); |
| 648 | Pattern count = Pattern.compile("COUNT\\(\\&[a-z][a-z0-9]*\\)"); |
| 649 | |
| 650 | Matcher sumM = sum.matcher(equation); |
| 651 | Matcher countM = count.matcher(equation); |
| 652 | |
| 653 | tempString = new ArrayList<String>(); |
| 654 | variables = new ArrayList<Variable>(); |
| 655 | boolean add = true; |
| 656 | |
| 657 | if (!sumM.matches() && equation.contains("SUM(")) |
| 658 | throw new SyntaxException("In " + file + ": 'SUM(&varname)' must be the only " + |
| 659 | "element of an equation if it is used (line " + line +")"); |
| 660 | if (!countM.matches() && equation.contains("COUNT(")) |
| 661 | throw new SyntaxException("In " + file + ": 'COUNT(&varname)' must be the only " + |
| 662 | "element of an equation if it is used (line " + line +")"); |
| 663 | |
| 664 | // toAdd is spatial iff the equation matches |
| 665 | // either one of the spatial statements. |
| 666 | toAdd.setSpatial(sumM.matches() || countM.matches()); |
| 667 | |
| 668 | while (m.find()){ |
| 669 | add = true; |
| 670 | tempString.add(equation.substring(last, m.start())); |
| 671 | last = m.end(); |
| 672 | String newvar = m.group(); |
| 673 | index++; |
| 674 | tempString.add(newvar); |
| 675 | for (Variable var : variables){ |
| 676 | if (var.getName().equals(newvar)) |
| 677 | add = false; |
| 678 | } |
| 679 | if (add){ |
| 680 | if ((equation.indexOf('&') != -1) && equation.indexOf('&') == m.start() -1 ){ |
| 681 | // if the variable is preceded with a '&' |
| 682 | // then it is to be checked later. |
| 683 | toBeChecked.add(toAdd); |
| 684 | spatAffectedMap.put(toAdd, newvar); |
| 685 | } else{ |
| 686 | Variable dep = variableMapper.get(newvar); |
| 687 | if (dep == null) |
| 688 | throw new SyntaxException("In "+ file +": Variable " + index + " on line " + line |
| 689 | + " is not defined before it is used"); |
| 690 | else{ |
| 691 | toAdd.addDependence(dep); |
| 692 | dep.addAffected(toAdd); |
| 693 | variables.add(dep); |
| 694 | } |
| 695 | } |
| 696 | } |
| 697 | } |
| 698 | // note to self: last is the offset AFTER the last match. |
| 699 | if (last != equation.length()) |
| 700 | tempString.add(equation.substring(last)); |
| 701 | |
| 702 | toAdd.setEquation(new Equation(tempString.toArray(new String[tempString.size()]), |
| 703 | variables.toArray(new Variable[variables.size()]))); |
| 704 | |
| 705 | } |
| 706 | |
| 707 | return toAdd; |
| 708 | } |
| 709 | |
| 710 | /** Reads an entity section in the model file and saves the information into the structures provided. |
| 711 | * |
| 712 | * |
| 713 | */ |
| 714 | |
| 715 | private static void readEntity(File file, LinkedList<Entity> entityList, |
| 716 | HashMap<String, Entity> entityMapper, HashMap<String, Variable> variableMapper, |
| 717 | String header, Scanner reader, DistributionFactory fact) |
| 718 | throws SyntaxException, MissingDistributionException{ |
| 719 | Entity toAdd = new Entity(); |
| 720 | |
| 721 | // the line we have is an ENTITY definition line. |
| 722 | //let's parse it first, and then |
| 723 | |
| 724 | /* header is: |
| 725 | square |
| 726 | or |
| 727 | square, "squares.txt" |
| 728 | or |
| 729 | square, "ehkäjotain.txt", "jotain.txt" |
| 730 | or |
| 731 | squarebird, "observations.txt", combines(square, bird) |
| 732 | it can have a { at the line end, or not. let's check that first. |
| 733 | */ |
| 734 | boolean curly = header.indexOf('{') == header.length() -1; |
| 735 | int comma = header.indexOf(','); |
| 736 | |
| 737 | // name , "sth" [, "sth1" || combines(sth2, sth3)] |
| 738 | |
| 739 | String name = null; |
| 740 | |
| 741 | if (comma > 0) |
| 742 | name = header.substring(0, header.indexOf(',')).trim(); |
| 743 | else { |
| 744 | throw new SyntaxException("In " + file + ": name, \"datafile\" expected on line "+ line); |
| 745 | } |
| 746 | |
| 747 | |
| 748 | toAdd.setName(name); |
| 749 | |
| 750 | String dataFile = null; |
| 751 | String spatialFile = null; |
| 752 | String x = null; |
| 753 | String y = null; |
| 754 | |
| 755 | comma = header.indexOf(','); |
| 756 | |
| 757 | header = header.substring(comma +1).trim(); |
| 758 | // "sth" , "sth1" || combines(sth2,sth3) |
| 759 | int caption = header.indexOf('"'); |
| 760 | if (caption < 0) |
| 761 | throw new SyntaxException("In " + file + ": \"datafile\" expected on line " + line); |
| 762 | header = header.substring(caption +1).trim(); |
| 763 | dataFile = header.substring(0, header.indexOf('"')).trim(); |
| 764 | header = header.substring(header.indexOf('"') +1).trim(); |
| 765 | if (dataFile.length() == 0) |
| 766 | dataFile = null; |
| 767 | toAdd.setDataFile(dataFile); |
| 768 | |
| 769 | |
| 770 | |
| 771 | // now dataFile is either null or "something.txt" |
| 772 | |
| 773 | /* |
| 774 | header is: |
| 775 | "" |
| 776 | or |
| 777 | , "sth1" |
| 778 | or |
| 779 | , combines(sth2, sth3) |
| 780 | */ |
| 781 | |
| 782 | comma = header.indexOf(','); |
| 783 | if (comma >= 0 && header.length() > 0){ // something more, so header is |
| 784 | header = header.substring(header.indexOf(',') +1).trim(); |
| 785 | /* |
| 786 | "sth1" |
| 787 | or |
| 788 | combines(sth2, sth3) |
| 789 | */ |
| 790 | if (header.startsWith("combines")){ |
| 791 | toAdd.setMatrix(true); |
| 792 | int lparen = header.indexOf('('); |
| 793 | int rparen = header.indexOf(')'); |
| 794 | if (lparen < 0 || rparen < 0) |
| 795 | throw new SyntaxException("Incorrect parentheses after combines-keyword on line " |
| 796 | + line); |
| 797 | |
| 798 | header = header.substring(lparen +1, rparen).trim(); |
| 799 | comma = header.indexOf(','); |
| 800 | if (comma < 0) |
| 801 | throw new SyntaxException("combines(entity1, entity2) expected on line " + line); |
| 802 | |
| 803 | y = header.substring(0, comma).trim(); |
| 804 | x = header.substring(comma +1).trim(); |
| 805 | Entity yEntity = entityMapper.get(y); |
| 806 | Entity xEntity = entityMapper.get(x); |
| 807 | |
| 808 | if (yEntity == null) |
| 809 | throw new SyntaxException("First entity for combines on line " + line + |
| 810 | " is not defined before it is used"); |
| 811 | if (xEntity == null) |
| 812 | throw new SyntaxException("Second entity for combines on line " + line + |
| 813 | " is not defined before it is used"); |
| 814 | |
| 815 | toAdd.setYCoordinate(yEntity); |
| 816 | toAdd.setXCoordinate(xEntity); |
| 817 | |
| 818 | |
| 819 | |
| 820 | } else{ // not a matrix |
| 821 | toAdd.setMatrix(false); |
| 822 | caption = header.indexOf('"'); |
| 823 | if (caption < 0) |
| 824 | throw new SyntaxException("\"spatialfile\" expected on line " + line); |
| 825 | else{ |
| 826 | header = header.substring(caption +1); |
| 827 | caption = header.indexOf('"'); |
| 828 | if (caption < 0) |
| 829 | throw new SyntaxException("ending \" missing for \"spatialfile\" on line " + line); |
| 830 | spatialFile = header.substring(0, caption); |
| 831 | toAdd.setSpatialMatrixFile(spatialFile); |
| 832 | } |
| 833 | } |
| 834 | } |
| 835 | |
| 836 | // now Entity properties name, dataFile, spatialFile, isMatrix, x and y |
| 837 | // have been set, if applicable. |
| 838 | |
| 839 | // continue with the entity structure. |
| 840 | String temp; |
| 841 | while (reader.hasNextLine()){ |
| 842 | temp = reader.nextLine(); |
| 843 | |
| 844 | line++; |
| 845 | temp = temp.trim(); |
| 846 | |
| 847 | if (temp.length() == 0 || temp.charAt(0) == '#') |
| 848 | continue; |
| 849 | |
| 850 | if (temp.charAt(temp.length() -1) == '}') |
| 851 | break; |
| 852 | |
| 853 | // now we have a non-comment non-zero line. |
| 854 | // let's do something brilliant with it. |
| 855 | |
| 856 | if(!curly) |
| 857 | if (temp.charAt(0) == '{'){ |
| 858 | curly = true; |
| 859 | temp = temp.substring(1); |
| 860 | if (temp.length() == 0 || temp.charAt(0) == '#') |
| 861 | continue; |
| 862 | } |
| 863 | |
| 864 | if (curly){ |
| 865 | // do the work |
| 866 | |
| 867 | // add the Variables to the Entity |
| 868 | if (temp.startsWith("REAL")){ |
| 869 | temp = temp.substring(4).trim(); |
| 870 | Variable var = parseVariable(file, false, temp, variableMapper, fact); |
| 871 | toAdd.addVariable(var); |
| 872 | variableMapper.put(var.getName(), var); |
| 873 | |
| 874 | } else if (temp.startsWith("INTEGER")){ |
| 875 | temp = temp.substring(7).trim(); |
| 876 | Variable var = parseVariable(file, true, temp, variableMapper, fact); |
| 877 | toAdd.addVariable(var); |
| 878 | variableMapper.put(var.getName(), var); |
| 879 | } else |
| 880 | throw new SyntaxException("Not a variable inside an entity on line " + line); |
| 881 | } |
| 882 | |
| 883 | } |
| 884 | |
| 885 | // link the Entity to the Variables |
| 886 | for (Variable toLinkUp : toAdd.getVariableList()) |
| 887 | toLinkUp.setEntity(toAdd); |
| 888 | |
| 889 | // put the Entity in the map |
| 890 | //System.out.println("Adding: " + toAdd.getName()); |
| 891 | entityMapper.put(toAdd.getName(), toAdd); |
| 892 | // link the Entity to the Model |
| 893 | entityList.add(toAdd); |
| 894 | } |
| 895 | |
| 896 | |
| 897 | /** Reads a simulation parameter file that gives burn-in and thinning. Returns {burn-in, thinning}. |
| 898 | * |
| 899 | * |
| 900 | */ |
| 901 | |
| 902 | private static int[] readSimulation(File file) throws SyntaxException, IOException{ |
| 903 | // reads stuff from the file and return burnIn and thinning. (int[2]) |
| 904 | /* |
| 905 | ?? simulation |
| 906 | ? burn-in |
| 907 | 100 |
| 908 | ? thinning |
| 909 | 100 |
| 910 | */ |
| 911 | return readUnifiedFormatFile(file, "?? simulation", "? burn-in", "? thinning"); |
| 912 | } |
| 913 | |
| 914 | /** Reads the update strategy file, saves individual updates (if any) into the variables in the maps, |
| 915 | @return {String updateStrategy, int iterations} |
| 916 | * |
| 917 | * |
| 918 | */ |
| 919 | private static Object[] readUpdate(File file, HashMap<String, Variable> variableMapper, |
| 920 | String updateStrategy) throws SyntaxException, IOException{ |
| 921 | /* reads the file, parses updateStrategy into the String variable and |
| 922 | returns the number of iterations if updateStrategy == sequential. |
| 923 | else returns -1, and reads the variables' update numbers. |
| 924 | */ |
| 925 | |
| 926 | Object[] toReturn = new Object[2]; |
| 927 | int iterations = -1; |
| 928 | Scanner reader = new Scanner(file); |
| 929 | |
| 930 | line = 0; |
| 931 | String temp = null; |
| 932 | updateStrategy = null; |
| 933 | boolean rightFile = false; |
| 934 | boolean one = false; |
| 935 | boolean strategy = false; |
| 936 | String fileHeader = "?? update"; |
| 937 | String headerOne = "? strategy"; |
| 938 | |
| 939 | while (reader.hasNextLine()){ |
| 940 | temp = reader.nextLine(); |
| 941 | |
| 942 | line++; |
| 943 | temp = temp.trim(); |
| 944 | |
| 945 | if (temp.length() == 0 || temp.charAt(0) == '#') |
| 946 | continue; |
| 947 | |
| 948 | if (temp.equals(fileHeader)){ |
| 949 | rightFile = true; |
| 950 | continue; |
| 951 | } |
| 952 | |
| 953 | if (rightFile){ |
| 954 | if (temp.equals(headerOne)){ |
| 955 | one = true; |
| 956 | continue; |
| 957 | } |
| 958 | |
| 959 | if (one && updateStrategy == null){ // updatestrategy header found, read that |
| 960 | updateStrategy = temp; |
| 961 | if (updateStrategy.equals("sequential")) |
| 962 | iterations = readUpdateValues(true, file, reader, variableMapper); |
| 963 | else if (updateStrategy.equals("random")) |
| 964 | iterations = readUpdateValues(false, file, reader, variableMapper); |
| 965 | else |
| 966 | throw new SyntaxException("In "+ file + ": Unknown update strategy on line " |
| 967 | + line); |
| 968 | |
| 969 | continue; |
| 970 | } else { |
| 971 | throw new SyntaxException("In "+ file + ": Unknown identifier on line " + line); |
| 972 | } |
| 973 | } else throw new SyntaxException(("In "+ file + ": File identifier does not match " + fileHeader)); |
| 974 | } |
| 975 | reader.close(); |
| 976 | |
| 977 | toReturn[0] = updateStrategy; |
| 978 | toReturn[1] = iterations; |
| 979 | return toReturn; |
| 980 | } |
| 981 | |
| 982 | /** Helper for readUpdate. |
| 983 | * |
| 984 | */ |
| 985 | private static int readUpdateValues(boolean sequential, File file, Scanner reader, |
| 986 | HashMap <String, Variable> variableMapper) throws SyntaxException { |
| 987 | boolean seqHeader = false; |
| 988 | String header = null; |
| 989 | String temp = null; |
| 990 | int iterations = -1; |
| 991 | ArrayList<Variable> varArray = new ArrayList<Variable>(variableMapper.values()); |
| 992 | |
| 993 | while (reader.hasNextLine()){ |
| 994 | temp = reader.nextLine(); |
| 995 | |
| 996 | line++; |
| 997 | temp = temp.trim(); |
| 998 | |
| 999 | if (temp.length() == 0 || temp.charAt(0) == '#') |
| 1000 | continue; |
| 1001 | if (sequential){ |
| 1002 | if(temp.equals("? iterations")){ |
| 1003 | seqHeader = true; |
| 1004 | continue; |
| 1005 | } |
| 1006 | |
| 1007 | if(seqHeader && iterations == -1){ // hasn't been set yet |
| 1008 | try{ |
| 1009 | iterations = Integer.parseInt(temp); |
| 1010 | }catch(NumberFormatException e){ |
| 1011 | throw new SyntaxException("In "+ file + ": Not an integer on line " + line); |
| 1012 | } |
| 1013 | } |
| 1014 | } else{ |
| 1015 | // the hard part: |
| 1016 | // expecting: |
| 1017 | // ? updates |
| 1018 | // 500 |
| 1019 | // ? varname |
| 1020 | // 700 |
| 1021 | // ? varname |
| 1022 | // 600 |
| 1023 | // ... |
| 1024 | if (temp.startsWith("?")){ |
| 1025 | header = temp; |
| 1026 | continue; |
| 1027 | } |
| 1028 | if (header != null){ |
| 1029 | int updates = 0; |
| 1030 | try { |
| 1031 | updates = Integer.parseInt(temp); |
| 1032 | }catch(NumberFormatException e){ |
| 1033 | throw new SyntaxException("In "+ file + ": Not an integer on line " + line); |
| 1034 | } |
| 1035 | if (header.equals("? updates")){ |
| 1036 | for (Variable var : varArray){ |
| 1037 | var.setUpdates(updates); |
| 1038 | } |
| 1039 | } else{ |
| 1040 | String name = header.substring(1).trim(); |
| 1041 | if (name.indexOf(' ') > 0) |
| 1042 | name = name.substring(0, name.indexOf(' ')).trim(); |
| 1043 | // if it has "all" or something else after the name |
| 1044 | Variable var = variableMapper.get(name); |
| 1045 | if (var != null) |
| 1046 | var.setUpdates(updates); |
| 1047 | else |
| 1048 | throw new SyntaxException("In "+ file + ": Unknown variable name on line " |
| 1049 | + line); |
| 1050 | } |
| 1051 | |
| 1052 | } |
| 1053 | } |
| 1054 | } |
| 1055 | |
| 1056 | return iterations; |
| 1057 | } |
| 1058 | |
| 1059 | /** Helper for readSimulation. |
| 1060 | * |
| 1061 | */ |
| 1062 | private static int[] readUnifiedFormatFile(File file, String fileHeader, String headerOne, |
| 1063 | String headerTwo) throws SyntaxException, IOException { |
| 1064 | Scanner reader = new Scanner(file); |
| 1065 | |
| 1066 | line = 0; |
| 1067 | String temp = null; |
| 1068 | boolean rightFile = false; |
| 1069 | boolean one = false; |
| 1070 | boolean two = false; |
| 1071 | int[] toReturn = new int[2]; |
| 1072 | |
| 1073 | while (reader.hasNextLine()){ |
| 1074 | temp = reader.nextLine(); |
| 1075 | |
| 1076 | line++; |
| 1077 | temp = temp.trim(); |
| 1078 | |
| 1079 | if (temp.length() == 0 || temp.charAt(0) == '#') |
| 1080 | continue; |
| 1081 | |
| 1082 | if (temp.equals(fileHeader)){ |
| 1083 | rightFile = true; |
| 1084 | continue; |
| 1085 | } |
| 1086 | |
| 1087 | if (rightFile){ |
| 1088 | if (temp.equals(headerOne)){ |
| 1089 | one = true; |
| 1090 | two = false; |
| 1091 | continue; |
| 1092 | } |
| 1093 | |
| 1094 | if (temp.equals(headerTwo)){ |
| 1095 | one = false; |
| 1096 | two = true; |
| 1097 | continue; |
| 1098 | } |
| 1099 | |
| 1100 | if (one){ |
| 1101 | try{ |
| 1102 | toReturn[0] = Integer.parseInt(temp); |
| 1103 | }catch(NumberFormatException e){ |
| 1104 | throw new SyntaxException("In "+ file + ": Not an integer on line " + line); |
| 1105 | } |
| 1106 | } |
| 1107 | |
| 1108 | if (two){ |
| 1109 | try{ |
| 1110 | toReturn[1] = Integer.parseInt(temp); |
| 1111 | }catch(NumberFormatException e){ |
| 1112 | throw new SyntaxException("In "+ file + ": Not an integer on line " + line); |
| 1113 | } |
| 1114 | } |
| 1115 | |
| 1116 | } else throw new SyntaxException(("In "+ file + ": File identifier does not match " + fileHeader)); |
| 1117 | } |
| 1118 | reader.close(); |
| 1119 | |
| 1120 | return toReturn; |
| 1121 | } |
| 1122 | |
| 1123 | /** Reads the parameter names to output -file and sets isPrinted-flags. |
| 1124 | * |
| 1125 | */ |
| 1126 | private static String[] readOutput(File file, HashMap<String, Variable> variableMapper) |
| 1127 | throws SyntaxException, IOException{ |
| 1128 | /* |
| 1129 | reads the variables to be output from the file, |
| 1130 | sets variable.setPrinted() for those variables. |
| 1131 | */ |
| 1132 | |
| 1133 | /* expecting: |
| 1134 | ?? output |
| 1135 | ? alpha |
| 1136 | ? x |
| 1137 | */ |
| 1138 | |
| 1139 | String[] toReturn = new String[2]; |
| 1140 | Scanner reader = new Scanner(file); |
| 1141 | int line = 0; |
| 1142 | String header = null; |
| 1143 | String temp = null; |
| 1144 | boolean rightFile = false; |
| 1145 | String fileHeader = "?? output"; |
| 1146 | |
| 1147 | while (reader.hasNextLine()){ |
| 1148 | temp = reader.nextLine(); |
| 1149 | |
| 1150 | line++; |
| 1151 | temp = temp.trim(); |
| 1152 | |
| 1153 | if (temp.length() == 0 || temp.charAt(0) == '#') |
| 1154 | continue; |
| 1155 | |
| 1156 | if (!rightFile && temp.startsWith(fileHeader)){ |
| 1157 | rightFile = true; |
| 1158 | temp = temp.substring(9); // after ?? output |
| 1159 | if (temp.length() > 0){ |
| 1160 | StringTokenizer tkn = new StringTokenizer(temp, " "); |
| 1161 | if (tkn.countTokens() != 2) |
| 1162 | throw new SyntaxException("In "+ file + ": ?? output outputFileName " + |
| 1163 | "summaryFileName expected on line "+ line); |
| 1164 | toReturn[0] = tkn.nextToken(); |
| 1165 | toReturn[1] = tkn.nextToken(); |
| 1166 | |
| 1167 | } else |
| 1168 | throw new SyntaxException("In "+ file + ": '?? output outputFileName summaryFileName' " + |
| 1169 | "expected on line "+ line); |
| 1170 | continue; |
| 1171 | } |
| 1172 | if (rightFile){ |
| 1173 | if (temp.startsWith("?")){ |
| 1174 | Variable var = null; |
| 1175 | String all = null; |
| 1176 | String name = temp.substring(1).trim(); |
| 1177 | // if it has all after it.. |
| 1178 | if (name.indexOf(' ') > 0){ |
| 1179 | all = name.substring(name.indexOf(' ')).trim(); |
| 1180 | name = name.substring(0, name.indexOf(' ')).trim(); |
| 1181 | if (!all.equals(all)) |
| 1182 | throw new SyntaxException("In "+ file + ": Expecting '? varname all' or " + |
| 1183 | "'? varname' on line "+ line); |
| 1184 | } |
| 1185 | var = variableMapper.get(name); |
| 1186 | if (var != null){ |
| 1187 | // if the user has not specified 'all' for a nonglobal |
| 1188 | if (all == null && var.getEntity() != null){ |
| 1189 | throw new SyntaxException("In "+ file + ": Expecting '? varname all' " + |
| 1190 | "for a non-global variable on line "+ line); |
| 1191 | } |
| 1192 | var.setPrinted(); |
| 1193 | } else |
| 1194 | throw new SyntaxException("In "+ file + ": Unknown variable name on line " + line); |
| 1195 | } |
| 1196 | } else |
| 1197 | throw new SyntaxException(("In "+ file + ": File identifier does not match '" + |
| 1198 | fileHeader +"'")); |
| 1199 | } |
| 1200 | reader.close(); |
| 1201 | return toReturn; |
| 1202 | } |
| 1203 | |
| 1204 | /** Reads the proposal distributions/strategies file, sets them for specified variables. |
| 1205 | * |
| 1206 | */ |
| 1207 | private static void readProposal(File file, HashMap<String, Variable> variableMapper, |
| 1208 | DistributionFactory fact) throws SyntaxException, IOException, |
| 1209 | MissingDistributionException{ |
| 1210 | /* expecting: |
| 1211 | ?? proposal distributions |
| 1212 | ? alpha |
| 1213 | continuous_uniform(-1.0, 1.0) |
| 1214 | ? x all |
| 1215 | discrete_uniform(0,1) |
| 1216 | */ |
| 1217 | Scanner reader = new Scanner(file); |
| 1218 | int line = 0; |
| 1219 | String header = null; |
| 1220 | String temp = null; |
| 1221 | boolean rightFile = false; |
| 1222 | String fileHeader = "?? proposal distributions"; |
| 1223 | |
| 1224 | while (reader.hasNextLine()){ |
| 1225 | temp = reader.nextLine(); |
| 1226 | |
| 1227 | line++; |
| 1228 | temp = temp.trim(); |
| 1229 | |
| 1230 | if (temp.length() == 0 || temp.charAt(0) == '#') |
| 1231 | continue; |
| 1232 | |
| 1233 | if (!rightFile && temp.equals(fileHeader)){ |
| 1234 | rightFile = true; |
| 1235 | continue; |
| 1236 | } |
| 1237 | if (rightFile){ |
| 1238 | if (temp.startsWith("?")){ |
| 1239 | header = temp; |
| 1240 | continue; |
| 1241 | } |
| 1242 | if (header != null){ |
| 1243 | String name = header.substring(1).trim(); |
| 1244 | // if it has "all" or other stuff after it |
| 1245 | if (name.indexOf(' ') > 0) |
| 1246 | name = name.substring(0, name.indexOf(' ')).trim(); |
| 1247 | Variable var = variableMapper.get(name); |
| 1248 | if (var != null){ |
| 1249 | // set the proposal distribution on this line, |
| 1250 | // should match a distribution name. |
| 1251 | // This is copied & modified from parserVariable. |
| 1252 | // allowing proposal distribution parameters to |
| 1253 | // be variables only means uncommenting a few lines. |
| 1254 | // extendability. |
| 1255 | |
| 1256 | String distStr = temp.substring(0, temp.indexOf('(')).trim(); |
| 1257 | Distribution dist = fact.getDistribution(distStr); |
| 1258 | // this might throw a MissingDistributionException. |
| 1259 | |
| 1260 | var.setProposal(dist); |
| 1261 | String strategy = temp.substring(temp.lastIndexOf(')') + 1).trim(); |
| 1262 | if (strategy.equalsIgnoreCase("RW")) |
| 1263 | var.setStrategy("random walk"); |
| 1264 | else |
| 1265 | var.setStrategy("fixed"); |
| 1266 | temp = temp.substring(temp.indexOf('(') +1, temp.lastIndexOf(')')).trim(); |
| 1267 | // Now we have "param1, param2, ..., paramn" |
| 1268 | |
| 1269 | int index = 0; |
| 1270 | while (temp != null){ |
| 1271 | int comma = temp.indexOf(','); |
| 1272 | String param = null; |
| 1273 | if (comma > 0) { |
| 1274 | param = temp.substring(0, comma).trim(); |
| 1275 | // there is a comma, so the next parameter should be before it |
| 1276 | // for the next round: |
| 1277 | temp = temp.substring(comma +1).trim(); |
| 1278 | } else { |
| 1279 | param = temp.trim(); |
| 1280 | // no comma found, so this is the last parameter |
| 1281 | |
| 1282 | // to terminate the loop |
| 1283 | temp = null; |
| 1284 | |
| 1285 | // are there too few parameters in the file? |
| 1286 | if (index+1 != dist.getNumberOfParameters()) |
| 1287 | throw new SyntaxException("Too few parameters on line "+ line); |
| 1288 | } |
| 1289 | |
| 1290 | // are there too many parameters in the file? |
| 1291 | if (dist.getNumberOfParameters() <= index) |
| 1292 | throw new SyntaxException("Too many parameters on line "+ line); |
| 1293 | boolean integer = dist.isInteger(index); |
| 1294 | if (integer){ |
| 1295 | try{ |
| 1296 | int paramInt = Integer.parseInt(param); |
| 1297 | dist.setParameter(index, paramInt); |
| 1298 | // it's a good integer, no need to check for anything else |
| 1299 | |
| 1300 | } catch(NumberFormatException e){ |
| 1301 | // okay, it's not an Integer. |
| 1302 | // it may still be a Variable reference, let's not cry yet |
| 1303 | /* |
| 1304 | Variable paramVar = variableMapper.get(param); |
| 1305 | if (paramVar == null) // run out of tricks |
| 1306 | throw new SyntaxException("Parameter " + (index +1) + " on line " + |
| 1307 | line + " Is not defined before it is used"); |
| 1308 | else{ |
| 1309 | dist.setParameter(index, paramVar); |
| 1310 | paramVar.addAffected(var); |
| 1311 | var.addDependence(paramVar); |
| 1312 | */ |
| 1313 | // and comment this: |
| 1314 | throw new SyntaxException("Proposal distribution has a non-constant " + |
| 1315 | "parameter " + (index +1) +" on line "+ line); |
| 1316 | } |
| 1317 | } else{ |
| 1318 | // not an integer, so it's REAL |
| 1319 | try { |
| 1320 | double paramDouble = Double.parseDouble(param); |
| 1321 | dist.setParameter(index, paramDouble); |
| 1322 | // it's a good double, continue |
| 1323 | |
| 1324 | } catch (NumberFormatException nfe){ |
| 1325 | // okay, not a good double. |
| 1326 | |
| 1327 | // is it a Variable? |
| 1328 | /* |
| 1329 | Variable paramVar = variableMapper.get(param); |
| 1330 | if (paramVar == null) // run out of tricks |
| 1331 | throw new SyntaxException("Parameter " + (index +1) + " on line " |
| 1332 | + line + " Is not defined before it is used"); |
| 1333 | else{ |
| 1334 | dist.setParameter(index, paramVar); |
| 1335 | // paramVar.addAffected(var); |
| 1336 | // var.addDependence(paramVar); |
| 1337 | |
| 1338 | */ |
| 1339 | |
| 1340 | // and comment this |
| 1341 | throw new SyntaxException("Proposal distribution has a non-constant " + |
| 1342 | "parameter " + (index +1) +" on line "+ line); |
| 1343 | } |
| 1344 | } |
| 1345 | |
| 1346 | // if we didn't exit yet, the param is good, let's add the |
| 1347 | // String too |
| 1348 | dist.setParameterString(index, param); |
| 1349 | |
| 1350 | index++; |
| 1351 | } |
| 1352 | |
| 1353 | } else |
| 1354 | throw new SyntaxException("In "+ file + ": Unknown variable name on line " + line); |
| 1355 | } |
| 1356 | } else |
| 1357 | throw new SyntaxException("In "+ file + ": File identifier does not match " + fileHeader); |
| 1358 | } |
| 1359 | reader.close(); |
| 1360 | |
| 1361 | } |
| 1362 | |
| 1363 | /** Reads through entities' data files to see if they are correct. builds the missing values matrix files. |
| 1364 | * |
| 1365 | */ |
| 1366 | private static void readEntityData(LinkedList<Entity> entityList) throws IOException, |
| 1367 | SyntaxException{ |
| 1368 | /* |
| 1369 | Iterate through Entities, all their variables that are data, and |
| 1370 | set the data length(s). Since one Entity only has one dataFile, |
| 1371 | there are either 0 <= Variables with column > 0, |
| 1372 | entailing that only the number of lines in the file counts |
| 1373 | (and that all the lines are of equal length) |
| 1374 | or one Variable |
| 1375 | with column = -1 (taking up the whole dataFile), |
| 1376 | entailing that the Entity's XCoordinate and YCoordinate |
| 1377 | should get the number of columns and number of lines |
| 1378 | as their sizes, respectively. |
| 1379 | */ |
| 1380 | boolean sizeSet = false; |
| 1381 | for(Entity e: entityList){ |
| 1382 | if(e.getDataFile() != null){ |
| 1383 | readData(e); |
| 1384 | } |
| 1385 | } |
| 1386 | } |
| 1387 | |
| 1388 | /** Helper for readEntityData. |
| 1389 | * |
| 1390 | */ |
| 1391 | private static void readData(Entity e) throws IOException, SyntaxException{ |
| 1392 | /* |
| 1393 | reads the data for a single Entity and sets the fields: |
| 1394 | datavar.missingValues, datavar.belongsTo.size |
| 1395 | reads out the missing values and writes the datafile_missing.txt |
| 1396 | to be used by later methods (readInitialValues) |
| 1397 | */ |
| 1398 | |
| 1399 | File dataFile = new File(e.getDataFile()); |
| 1400 | String dataName = e.getDataFile(); |
| 1401 | FileWriter data = null; |
| 1402 | FileWriter missing = null; |
| 1403 | |
| 1404 | if (dataName.indexOf('.') < 0) |
| 1405 | data = new FileWriter(new File(dataName + "_1.txt"), false); |
| 1406 | else |
| 1407 | data = new FileWriter(dataName.substring(0, dataName.indexOf('.')) + "_1.txt", false); |
| 1408 | |
| 1409 | if (dataName.indexOf('.') < 0) |
| 1410 | missing = new FileWriter(dataName + "_missing.txt", false); |
| 1411 | else |
| 1412 | missing = new FileWriter(dataName.substring(0, dataName.indexOf('.')) + "_missing.txt", false); |
| 1413 | Scanner reader = new Scanner(dataFile); |
| 1414 | int dataVars = 0; |
| 1415 | String temp = null; |
| 1416 | |
| 1417 | for(Variable var : e.getVariableList()) |
| 1418 | if (var.isData()) |
| 1419 | dataVars++; |
| 1420 | |
| 1421 | int[][] cols = new int[dataVars][2]; // {column, type} (0-int, 1-double) |
| 1422 | Variable[] dataArray = new Variable[dataVars]; |
| 1423 | |
| 1424 | Variable[] temporary = e.getVariableList().toArray(new Variable[e.getVariableList().size()]); |
| 1425 | |
| 1426 | dataVars = 0; |
| 1427 | for(int i = 0; i < temporary.length; ++i) { |
| 1428 | if (temporary[i].isData()){ |
| 1429 | dataArray[dataVars] = temporary[i]; |
| 1430 | cols[dataVars][0] = temporary[i].getColumn(); |
| 1431 | if (temporary[i].isInteger()) |
| 1432 | cols[dataVars][1] = 0; |
| 1433 | else |
| 1434 | cols[dataVars][1] = 1; |
| 1435 | dataVars++; |
| 1436 | } |
| 1437 | } |
| 1438 | |
| 1439 | // is this dangerous? I guess not. have to take this up. |
| 1440 | for (int i = 0; i < cols.length -1; ++i){ |
| 1441 | for (int j = i +1; j < cols.length; ++j){ |
| 1442 | if (cols[i][0] == cols[j][0]) |
| 1443 | throw new SyntaxException("Entity "+ e.getName() + " has two variables with the same column number"); |
| 1444 | } |
| 1445 | } |
| 1446 | |
| 1447 | |
| 1448 | line = 0; |
| 1449 | int dataline = 0; |
| 1450 | int lineLength = 0; |
| 1451 | |
| 1452 | while (reader.hasNextLine()){ |
| 1453 | temp = reader.nextLine(); |
| 1454 | |
| 1455 | line++; |
| 1456 | temp = temp.trim(); |
| 1457 | |
| 1458 | if (temp.length() == 0 || temp.charAt(0) == '#') |
| 1459 | continue; |
| 1460 | |
| 1461 | StringTokenizer tkn = new StringTokenizer(temp, " "); |
| 1462 | if (dataline != 0 && lineLength != tkn.countTokens()) |
| 1463 | throw new SyntaxException("In " + dataFile + ": Line " + line + |
| 1464 | "is of different length than the others"); |
| 1465 | lineLength = tkn.countTokens(); |
| 1466 | e.setLineLength(lineLength); |
| 1467 | int column = 0; |
| 1468 | int index = 0; |
| 1469 | String token = null; |
| 1470 | while (tkn.hasMoreTokens()){ |
| 1471 | index = 0; |
| 1472 | column++; // columns are numbered starting from 1 |
| 1473 | token = tkn.nextToken(); |
| 1474 | |
| 1475 | |
| 1476 | // there is exactly one variable that can span the whole matrix. |
| 1477 | while (index < cols.length-1 && cols[index][0] != -1 && cols[index][0] != column) |
| 1478 | index++; |
| 1479 | |
| 1480 | if (cols[index][0] != -1 && cols[index][0] != column){ |
| 1481 | // System.out.println("No variable has been defined to use column " + column); |
| 1482 | // write a 0 on its place |
| 1483 | data.write(0 + " "); |
| 1484 | missing.write(1 + " "); |
| 1485 | } else{ |
| 1486 | // the variable that spans the whole matrix must be matched |
| 1487 | // against every column on every line, logically. |
| 1488 | if (cols[index][0] == column || cols[index][0] == -1){ |
| 1489 | // System.out.println("PARSER DEBUG: matching variable on column " + column); |
| 1490 | |
| 1491 | if (cols[index][1] == 0){ // integer |
| 1492 | // System.out.println("PARSER DEBUG: (integer)"); |
| 1493 | if (token.equals("*")){ |
| 1494 | // write a 0 on its place |
| 1495 | data.write(0 + " "); |
| 1496 | missing.write(1 + " "); |
| 1497 | dataArray[index].incrementMissingValues(); |
| 1498 | } else{ |
| 1499 | try{ |
| 1500 | Integer.parseInt(token); |
| 1501 | data.write(token + " "); |
| 1502 | missing.write(0 + " "); |
| 1503 | }catch(NumberFormatException nfe){ |
| 1504 | throw new SyntaxException("In " + dataFile + ": Value on line "+ line + |
| 1505 | " column " + column + " should be an integer"); |
| 1506 | } |
| 1507 | } |
| 1508 | } else{ // decimal(real) |
| 1509 | // System.out.println("PARSER DEBUG: (real)"); |
| 1510 | if (token.equals("*")){ |
| 1511 | // write a 0.0 on its place |
| 1512 | data.write(0.0 + " "); |
| 1513 | missing.write(1 + " "); |
| 1514 | dataArray[index].incrementMissingValues(); |
| 1515 | } else{ |
| 1516 | try{ |
| 1517 | Double.parseDouble(token); |
| 1518 | data.write(token + " "); |
| 1519 | missing.write(0 + " "); |
| 1520 | }catch(NumberFormatException nfe){ |
| 1521 | throw new SyntaxException("In " + dataFile + ": Value on line "+ line + |
| 1522 | " column " + column + " should be a decimal number"); |
| 1523 | } |
| 1524 | } |
| 1525 | } |
| 1526 | } |
| 1527 | } |
| 1528 | |
| 1529 | } |
| 1530 | missing.write("\n"); |
| 1531 | data.write("\n"); |
| 1532 | |
| 1533 | dataline++; // do not count comment lines. |
| 1534 | |
| 1535 | } |
| 1536 | reader.close(); |
| 1537 | missing.close(); |
| 1538 | data.close(); |
| 1539 | |
| 1540 | for (Variable v: dataArray){ |
| 1541 | if (v.getMissingValueCount() > 0){ |
| 1542 | if (v.getDistribution() == null) |
| 1543 | throw new SyntaxException("Variable "+ v.getName() + " has missing values but " + |
| 1544 | "has no distribution"); |
| 1545 | |
| 1546 | if (v.getProposal() == null) |
| 1547 | throw new SyntaxException("Variable "+ v.getName() + " has missing values but " + |
| 1548 | "has no proposal distribution"); |
| 1549 | } |
| 1550 | } |
| 1551 | |
| 1552 | |
| 1553 | if (e.isMatrix()){ |
| 1554 | |
| 1555 | e.getYCoordinate().setSize(dataline); |
| 1556 | e.getXCoordinate().setSize(lineLength); |
| 1557 | e.setSize(-1); |
| 1558 | } else{ |
| 1559 | e.setSize(dataline); |
| 1560 | } |
| 1561 | } |
| 1562 | |
| 1563 | /** Reads the initial values definition file and checks that the format is correct and all missing values of data are present. |
| 1564 | * |
| 1565 | */ |
| 1566 | private static void readInitialValues(File file, HashMap<String, Variable> variableMapper) |
| 1567 | throws IOException, SyntaxException{ |
| 1568 | /* |
| 1569 | Reads through every Entity, |
| 1570 | checks every non-functional Variable that is not data |
| 1571 | that is has getEntity().getSize() or if Entity.isMatrix() |
| 1572 | getEntity().getYCoordinate().getSize() * |
| 1573 | getEntity.getXCoordinate().getSize() initial values in the file. |
| 1574 | Checks also for each non-functional Variable that is data and |
| 1575 | has missingValueCount > 0 |
| 1576 | that it has matching indices of initial values |
| 1577 | that are set as missing |
| 1578 | in the getEntity().dataFile_missing.txt. |
| 1579 | */ |
| 1580 | |
| 1581 | /* |
| 1582 | expecting: |
| 1583 | ?? initial values |
| 1584 | ? alpha |
| 1585 | 0.5 |
| 1586 | ? x 1:21 1:4 |
| 1587 | 1 2 4 5 |
| 1588 | 1 2 4 6 |
| 1589 | ....... |
| 1590 | */ |
| 1591 | |
| 1592 | Scanner reader = new Scanner(file); |
| 1593 | String temp = null; |
| 1594 | line = 0; |
| 1595 | String fileHeader = "?? initial values"; |
| 1596 | String header = null; |
| 1597 | boolean rightFile = false; |
| 1598 | |
| 1599 | |
| 1600 | HashMap<Variable, boolean[][]> missingMap = new HashMap<Variable, boolean[][]>(); |
| 1601 | // every index of the boolean[][] is information if this is found. (false == missing) |
| 1602 | // every variable has got a map like this of its data. |
| 1603 | |
| 1604 | ArrayList <Variable> varList = new ArrayList<Variable>(variableMapper.values()); |
| 1605 | |
| 1606 | for (Variable v : varList){ |
| 1607 | if (v.isFunctional()) |
| 1608 | continue; |
| 1609 | if (v.isData() && v.getMissingValueCount() == 0) |
| 1610 | continue; |
| 1611 | |
| 1612 | if (v.isData()){ |
| 1613 | if (v.getEntity() == null){ |
| 1614 | // global variables cannot be data |
| 1615 | throw new SyntaxException("Global variable "+ v.getName() + " has been defined " + |
| 1616 | "as data"); |
| 1617 | } |
| 1618 | |
| 1619 | // missing values matrix stuff |
| 1620 | Entity entity = v.getEntity(); |
| 1621 | String dataFileName = entity.getDataFile(); |
| 1622 | Scanner missread = new Scanner(new File(dataFileName)); |
| 1623 | String misstemp = null; |
| 1624 | int dataline = 0; |
| 1625 | boolean[][] missing; |
| 1626 | if (entity.isMatrix()) |
| 1627 | missing = new boolean[entity.getYCoordinate().getSize()][entity.getXCoordinate().getSize()]; |
| 1628 | else |
| 1629 | missing = new boolean[entity.getSize()][1]; |
| 1630 | |
| 1631 | while(missread.hasNextLine()){ |
| 1632 | misstemp = missread.nextLine().trim(); |
| 1633 | dataline++; |
| 1634 | int column = 0; |
| 1635 | String token = null; |
| 1636 | StringTokenizer tkn = new StringTokenizer(misstemp, " "); |
| 1637 | while (tkn.hasMoreTokens()){ |
| 1638 | column++; |
| 1639 | token = tkn.nextToken(); |
| 1640 | if (token.equals("*")) |
| 1641 | missing[dataline-1][column-1] = false; // missing |
| 1642 | else |
| 1643 | missing[dataline-1][column-1] = true; // found |
| 1644 | |
| 1645 | } |
| 1646 | } |
| 1647 | |
| 1648 | missingMap.put(v, missing); |
| 1649 | } else{ |
| 1650 | if (v.getEntity() == null){ |
| 1651 | // global, one value |
| 1652 | boolean[][] missing = new boolean[1][1]; |
| 1653 | missing[0][0] = false; // we are missing the one value that has no indices |
| 1654 | missingMap.put(v, missing); |
| 1655 | |
| 1656 | } else if (!v.getEntity().isMatrix()){ |
| 1657 | // one-dim |
| 1658 | int limit = v.getEntity().getSize(); |
| 1659 | // missing every index to size, that is: |
| 1660 | boolean[][] missing = new boolean[limit][1]; |
| 1661 | for (int i = 1; i <= limit; ++i) |
| 1662 | missing[i-1][0] = false; |
| 1663 | missingMap.put(v, missing); |
| 1664 | } else{ |
| 1665 | // two-dim |
| 1666 | int ylimit = v.getEntity().getYCoordinate().getSize(); |
| 1667 | int xlimit = v.getEntity().getXCoordinate().getSize(); |
| 1668 | |
| 1669 | // missing every index to size, that is: |
| 1670 | boolean[][] missing = new boolean[ylimit][xlimit]; |
| 1671 | |
| 1672 | for (int i = 1; i <= ylimit; ++i) |
| 1673 | for (int j = 1; j <= xlimit; ++j) |
| 1674 | missing[i-1][j-1] = false; |
| 1675 | missingMap.put(v, missing); |
| 1676 | } |
| 1677 | } |
| 1678 | } |
| 1679 | |
| 1680 | while (reader.hasNextLine()){ |
| 1681 | temp = reader.nextLine().trim(); |
| 1682 | |
| 1683 | line++; |
| 1684 | |
| 1685 | if (temp.length() == 0 || temp.charAt(0) == '#') |
| 1686 | continue; |
| 1687 | |
| 1688 | if (temp.equals(fileHeader)){ |
| 1689 | rightFile = true; |
| 1690 | continue; |
| 1691 | } |
| 1692 | |
| 1693 | if (rightFile){ |
| 1694 | if (temp.startsWith("?")){ |
| 1695 | header = temp.substring(1).trim(); |
| 1696 | continue; |
| 1697 | } |
| 1698 | if (header != null){ |
| 1699 | // alpha [1:12 [1:54]] |
| 1700 | String name = null; |
| 1701 | if (header.indexOf(' ') != -1){ |
| 1702 | name = header.substring(0, header.indexOf(' ')).trim(); |
| 1703 | header = header.substring(header.indexOf(' ')+1).trim(); |
| 1704 | } else { |
| 1705 | name = header.trim(); |
| 1706 | header = ""; |
| 1707 | } |
| 1708 | // [1:12 [1:54]] |
| 1709 | Variable var = variableMapper.get(name); |
| 1710 | if (var == null) |
| 1711 | throw new SyntaxException("In "+ file + ": Unknown variable name on line " + line); |
| 1712 | else{ |
| 1713 | // cases: a global variable: |
| 1714 | // a one-dimensional entity variable |
| 1715 | // a two-dimensional entity variable |
| 1716 | if (var.isFunctional()) |
| 1717 | throw new SyntaxException("In "+ file + ": Attempting to give an initial " + |
| 1718 | "value to a functional variable on line "+ line); |
| 1719 | if (var.isData() && var.getMissingValueCount() == 0) |
| 1720 | throw new SyntaxException("In "+ file + ": Attempting to give an initial " + |
| 1721 | "value to a data variable on line "+ line); |
| 1722 | |
| 1723 | if (var.getEntity() == null){ |
| 1724 | // global, expecting one value |
| 1725 | if (header.length() > 0) |
| 1726 | throw new SyntaxException("In "+ file + ": Unidentified characters " + |
| 1727 | "after variable name on line "+ line); |
| 1728 | else{ |
| 1729 | if (var.isInteger()){ |
| 1730 | try{ |
| 1731 | Integer.parseInt(temp); |
| 1732 | }catch(NumberFormatException nfe){ |
| 1733 | throw new SyntaxException("In " + file + ": Value on line "+ |
| 1734 | line + " should be an integer"); |
| 1735 | } |
| 1736 | } else{ |
| 1737 | try{ |
| 1738 | Double.parseDouble(temp); |
| 1739 | }catch(NumberFormatException nfe){ |
| 1740 | throw new SyntaxException("In " + file + ": Value on line "+ |
| 1741 | line + " should be a decimal number"); |
| 1742 | } |
| 1743 | } |
| 1744 | // all is well if we didn't exit yet, and we can: |
| 1745 | missingMap.get(var)[0][0] = true; |
| 1746 | } |
| 1747 | } else if(!var.getEntity().isMatrix()){ |
| 1748 | // one-dim |
| 1749 | if (header.indexOf(':') == -1) |
| 1750 | throw new SyntaxException("In " + file + ": '? varname " + |
| 1751 | "startindex:endindex' " + |
| 1752 | "expected on line "+ line); |
| 1753 | |
| 1754 | StringTokenizer limt = new StringTokenizer(header, ": "); |
| 1755 | String one = limt.nextToken(); |
| 1756 | String two = limt.nextToken(); |
| 1757 | int start = -1; |
| 1758 | int end = -1; |
| 1759 | try{ |
| 1760 | start = Integer.parseInt(one); |
| 1761 | end = Integer.parseInt(two); |
| 1762 | if (start <= 0 || end <= 0) |
| 1763 | throw new SyntaxException("In "+ file + ": Boundaries should start from 1 minimum " + |
| 1764 | "on line "+ line); |
| 1765 | }catch(NumberFormatException nfe){ |
| 1766 | throw new SyntaxException("In " + file + ": Boundaries are not integers " + |
| 1767 | "on line "+ line); |
| 1768 | } |
| 1769 | |
| 1770 | readMissing(file, var.isInteger(), start, end, missingMap.get(var), |
| 1771 | temp, reader); |
| 1772 | // reads the values from start to end from temp and reader, checks stuff |
| 1773 | // on missingmap to true ([index][2] = 1;) |
| 1774 | } else { |
| 1775 | // two-dim |
| 1776 | StringTokenizer limt = new StringTokenizer(header, ": "); |
| 1777 | if (header.indexOf(':') == -1 || header.indexOf(':') == |
| 1778 | header.lastIndexOf(':')) |
| 1779 | throw new SyntaxException("In " + file + ": '? varname " + |
| 1780 | "ystartindex:yendindex xstartindex:xendindex' expected on line " |
| 1781 | + line); |
| 1782 | |
| 1783 | String vone = limt.nextToken(); |
| 1784 | String vtwo = limt.nextToken(); |
| 1785 | String hone = limt.nextToken(); |
| 1786 | String htwo = limt.nextToken(); |
| 1787 | |
| 1788 | int vstart = -1; |
| 1789 | int vend = -1; |
| 1790 | int hstart = -1; |
| 1791 | int hend = -1; |
| 1792 | try{ |
| 1793 | vstart = Integer.parseInt(vone); |
| 1794 | vend = Integer.parseInt(vtwo); |
| 1795 | hstart = Integer.parseInt(hone); |
| 1796 | hend = Integer.parseInt(htwo); |
| 1797 | if (vstart <= 0 || vend <= 0 || hstart <= 0 || hend <= 0) |
| 1798 | throw new SyntaxException("In "+ file + ": Boundaries should start from 1 minimum " + |
| 1799 | "on line "+ line); |
| 1800 | }catch(NumberFormatException nfe){ |
| 1801 | throw new SyntaxException("In " + file + ": All boundaries are not " + |
| 1802 | "integers on line "+ line); |
| 1803 | } |
| 1804 | readMissing(file, var.isInteger(), vstart, vend, hstart, hend, |
| 1805 | missingMap.get(var), temp, reader); |
| 1806 | } |
| 1807 | } |
| 1808 | } |
| 1809 | } else |
| 1810 | throw new SyntaxException("In "+ file + ": File identifier does not match " + fileHeader); |
| 1811 | |
| 1812 | } |
| 1813 | |
| 1814 | for (Variable v: varList){ |
| 1815 | if (v.isFunctional()) |
| 1816 | continue; |
| 1817 | if (v.isData() && v.getMissingValueCount() == 0) |
| 1818 | continue; |
| 1819 | |
| 1820 | boolean[][] missing = missingMap.get(v); |
| 1821 | for (int i = 1; i < missing.length; ++i) |
| 1822 | for (int j = 1; j < missing[i].length; ++j) |
| 1823 | if (missing[i-1][j-1] == false){ |
| 1824 | if (v.getEntity() == null) |
| 1825 | throw new SyntaxException("In "+ file + ": Variable "+ v.getName() + " is missing its initial value"); |
| 1826 | else |
| 1827 | throw new SyntaxException("In "+ file + ": Variable "+ v.getName() + " is missing an initial " + |
| 1828 | "value for ("+ i + ", " + j+ ")"); |
| 1829 | } |
| 1830 | } |
| 1831 | |
| 1832 | } |
| 1833 | |
| 1834 | /** Helper for readInitialValues. |
| 1835 | * |
| 1836 | */ |
| 1837 | private static void readMissing(File file, boolean integer, int start, int end, |
| 1838 | boolean[][] missing, String temp, Scanner reader) |
| 1839 | throws SyntaxException{ |
| 1840 | readMissing(file, integer, start, end, -1, -1, missing, temp, reader); |
| 1841 | } |
| 1842 | |
| 1843 | /** Helper for readInitialValues. |
| 1844 | * |
| 1845 | */ |
| 1846 | private static void readMissing(File file, boolean integer, int vstart, int vend, |
| 1847 | int hstart, int hend, boolean[][] missing, String temp, Scanner reader) |
| 1848 | throws SyntaxException{ |
| 1849 | String looptemp = null; |
| 1850 | int dataline = vstart; |
| 1851 | |
| 1852 | while (dataline <= vend){ |
| 1853 | if (temp != null){ |
| 1854 | looptemp = temp; |
| 1855 | temp = null; |
| 1856 | } else{ |
| 1857 | if (!reader.hasNextLine()){ |
| 1858 | if (hstart > 0 && hend > 0) |
| 1859 | throw new SyntaxException("In "+ file +": Not enough initial values, expected "+ vstart +":"+ vend + " "+ hstart + ":" + hend); |
| 1860 | else |
| 1861 | throw new SyntaxException("In "+ file +": Not enough initial values, expected "+ vstart +":"+ vend); |
| 1862 | } |
| 1863 | looptemp = reader.nextLine().trim(); |
| 1864 | line++; |
| 1865 | } |
| 1866 | StringTokenizer tkn = new StringTokenizer(looptemp, " "); |
| 1867 | |
| 1868 | int column = hstart; |
| 1869 | |
| 1870 | while (column <= hend){ |
| 1871 | if (!tkn.hasMoreTokens()){ |
| 1872 | if (hstart > 0 && hend > 0) |
| 1873 | throw new SyntaxException("In "+ file +": Not enough initial values, expected "+ vstart +":"+ vend + " "+ hstart + ":" + hend); |
| 1874 | else |
| 1875 | throw new SyntaxException("In "+ file +": Not enough initial values, expected "+ vstart +":"+ vend); |
| 1876 | } |
| 1877 | |
| 1878 | String token = tkn.nextToken(); |
| 1879 | |
| 1880 | if (integer){ |
| 1881 | try{ |
| 1882 | Integer.parseInt(token); |
| 1883 | }catch(NumberFormatException nfe){ |
| 1884 | throw new SyntaxException("In " + file + ": Value " + dataline +", " + |
| 1885 | column + " on line "+ line + " should be an integer"); |
| 1886 | } |
| 1887 | } else{ |
| 1888 | try{ |
| 1889 | Double.parseDouble(token); |
| 1890 | }catch(NumberFormatException nfe){ |
| 1891 | throw new SyntaxException("In " + file + ": Value " + dataline +", " + |
| 1892 | column + " on line "+ line + " should be a decimal number"); |
| 1893 | } |
| 1894 | } |
| 1895 | |
| 1896 | // it is of the correct type now |
| 1897 | if (column == -1) |
| 1898 | missing[dataline-1][0] = true; |
| 1899 | else |
| 1900 | missing[dataline-1][column -1] = true; |
| 1901 | |
| 1902 | column++; |
| 1903 | } |
| 1904 | // System.out.println("data line " + dataline + " parsed"); |
| 1905 | dataline++; |
| 1906 | } |
| 1907 | |
| 1908 | } |
| 1909 | |
| 1910 | /** Counts the maximum number of spatial neighbours in the model. |
| 1911 | * |
| 1912 | */ |
| 1913 | private static int countNeighbours(LinkedList<Entity> entityList) throws SyntaxException, |
| 1914 | FileNotFoundException{ |
| 1915 | int toReturn = 0; |
| 1916 | int spatialEntities = 0; |
| 1917 | String spatial = null; |
| 1918 | |
| 1919 | for (int i = 0; i < entityList.size(); ++i){ |
| 1920 | Entity e = entityList.get(i); |
| 1921 | if (e.getSpatialMatrixFile() != null){ |
| 1922 | spatial = e.getSpatialMatrixFile(); |
| 1923 | spatialEntities++; |
| 1924 | |
| 1925 | } |
| 1926 | } |
| 1927 | if (spatialEntities > 1) |
| 1928 | throw new SyntaxException("More than one spatial entity defined in the model!"); |
| 1929 | |
| 1930 | if (spatialEntities == 0) |
| 1931 | return toReturn; |
| 1932 | // returning zero, no spatial Entities |
| 1933 | |
| 1934 | // now we have exactly one spatial entity |
| 1935 | // and the matrix filename is at spatial. |
| 1936 | |
| 1937 | Scanner reader = new Scanner(new File(spatial)); |
| 1938 | String temp = null; |
| 1939 | line = 0; |
| 1940 | int maxcount = 0; |
| 1941 | int lineLength = 0; |
| 1942 | int dataline = 0; |
| 1943 | |
| 1944 | while (reader.hasNextLine()){ |
| 1945 | temp = reader.nextLine(); |
| 1946 | |
| 1947 | line++; |
| 1948 | temp = temp.trim(); |
| 1949 | |
| 1950 | if (temp.length() == 0 || temp.charAt(0) == '#') |
| 1951 | continue; |
| 1952 | |
| 1953 | StringTokenizer tkn = new StringTokenizer(temp, " "); |
| 1954 | if (dataline != 0 && lineLength != tkn.countTokens()) |
| 1955 | throw new SyntaxException("In " + spatial + ": Line " + line + " is of different " + |
| 1956 | "length than the others"); |
| 1957 | lineLength = tkn.countTokens(); |
| 1958 | String token = null; |
| 1959 | maxcount = 0; |
| 1960 | while (tkn.hasMoreTokens()){ |
| 1961 | token = tkn.nextToken(); |
| 1962 | |
| 1963 | if (token.equals("1")) |
| 1964 | maxcount++; |
| 1965 | } |
| 1966 | if (maxcount > toReturn){ |
| 1967 | |
| 1968 | toReturn = maxcount; |
| 1969 | } |
| 1970 | dataline++; // don't evaluate comment lines |
| 1971 | |
| 1972 | } |
| 1973 | |
| 1974 | return toReturn; |
| 1975 | } |
| 1976 | |
| 1977 | /** Runs every variable through a sanity check (see Variable.isOk()) |
| 1978 | * |
| 1979 | |
| 1980 | */ |
| 1981 | private static void checkVariablesAreOk(ArrayList<Variable> variableList) |
| 1982 | throws SyntaxException{ |
| 1983 | for (int i = 0; i < variableList.size()-1; ++i){ |
| 1984 | for (int j = i +1; j < variableList.size(); ++j){ |
| 1985 | if (variableList.get(i).equals(variableList.get(j))) |
| 1986 | throw new SyntaxException("Two variables with the same name defined in the model."); |
| 1987 | } |
| 1988 | } |
| 1989 | for(Variable v: variableList){ |
| 1990 | if (v.getProposal() == null){ |
| 1991 | if (!v.isFunctional() && !v.isData()) |
| 1992 | throw new SyntaxException("Stochastic variable "+v.getName() + " has no proposal " + |
| 1993 | "distribution"); |
| 1994 | } |
| 1995 | if(!v.isOk()){ |
| 1996 | System.out.println(v); |
| 1997 | throw new SyntaxException("Variable "+v.getName() + " is NOT ok"); |
| 1998 | } |
| 1999 | } |
| 2000 | } |
| 2001 | |
| 2002 | } |