binaries/src/muscle/params.cpp

   1 #include "muscle.h"\r
   2 #include "objscore.h"\r
   3 #include "profile.h"\r
   4 #include "enumopts.h"\r
   5 \r
   6 const double DEFAULT_MAX_MB_FRACT = 0.8;\r
   7 \r
   8 SCORE g_scoreCenter = 0;\r
   9 SCORE g_scoreGapExtend = 0;\r
  10 SCORE g_scoreGapOpen2 = MINUS_INFINITY;\r
  11 SCORE g_scoreGapExtend2 = MINUS_INFINITY;\r
  12 SCORE g_scoreGapAmbig = 0;\r
  13 SCORE g_scoreAmbigFactor = 0;\r
  14 \r
  15 extern SCOREMATRIX VTML_LA;\r
  16 extern SCOREMATRIX PAM200;\r
  17 extern SCOREMATRIX PAM200NoCenter;\r
  18 extern SCOREMATRIX VTML_SP;\r
  19 extern SCOREMATRIX VTML_SPNoCenter;\r
  20 extern SCOREMATRIX NUC_SP;\r
  21 \r
  22 PTR_SCOREMATRIX g_ptrScoreMatrix;\r
  23 \r
  24 const char *g_pstrInFileName = "-";\r
  25 const char *g_pstrOutFileName = "-";\r
  26 const char *g_pstrFASTAOutFileName = 0;\r
  27 const char *g_pstrMSFOutFileName = 0;\r
  28 const char *g_pstrClwOutFileName = 0;\r
  29 const char *g_pstrClwStrictOutFileName = 0;\r
  30 const char *g_pstrHTMLOutFileName = 0;\r
  31 const char *g_pstrPHYIOutFileName = 0;\r
  32 const char *g_pstrPHYSOutFileName = 0;\r
  33 const char *g_pstrDistMxFileName1 = 0;\r
  34 const char *g_pstrDistMxFileName2 = 0;\r
  35 \r
  36 const char *g_pstrFileName1 = 0;\r
  37 const char *g_pstrFileName2 = 0;\r
  38 \r
  39 const char *g_pstrSPFileName = 0;\r
  40 const char *g_pstrMatrixFileName = 0;\r
  41 \r
  42 const char *g_pstrUseTreeFileName = 0;\r
  43 bool g_bUseTreeNoWarn = false;\r
  44 \r
  45 const char *g_pstrComputeWeightsFileName;\r
  46 const char *g_pstrScoreFileName;\r
  47 \r
  48 const char *g_pstrProf1FileName = 0;\r
  49 const char *g_pstrProf2FileName = 0;\r
  50 \r
  51 unsigned g_uSmoothWindowLength = 7;\r
  52 unsigned g_uAnchorSpacing = 32;\r
  53 unsigned g_uMaxTreeRefineIters = 1;\r
  54 \r
  55 unsigned g_uRefineWindow = 200;\r
  56 unsigned g_uWindowFrom = 0;\r
  57 unsigned g_uWindowTo = 0;\r
  58 unsigned g_uSaveWindow = uInsane;\r
  59 unsigned g_uWindowOffset = 0;\r
  60 \r
  61 unsigned g_uMaxSubFamCount = 5;\r
  62 \r
  63 unsigned g_uHydrophobicRunLength = 5;\r
  64 float g_dHydroFactor = (float) 1.2;\r
  65 \r
  66 unsigned g_uMinDiagLength = 24; // TODO alpha -- should depend on alphabet?\r
  67 unsigned g_uMaxDiagBreak = 1;\r
  68 unsigned g_uDiagMargin = 5;\r
  69 \r
  70 float g_dSUEFF = (float) 0.1;\r
  71 \r
  72 bool g_bPrecompiledCenter = true;\r
  73 bool g_bNormalizeCounts = false;\r
  74 bool g_bDiags1 = false;\r
  75 bool g_bDiags2 = false;\r
  76 bool g_bAnchors = true;\r
  77 bool g_bQuiet = false;\r
  78 bool g_bVerbose = false;\r
  79 bool g_bRefine = false;\r
  80 bool g_bRefineW = false;\r
  81 bool g_bProfDB = false;\r
  82 bool g_bLow = false;\r
  83 bool g_bSW = false;\r
  84 bool g_bClusterOnly = false;\r
  85 bool g_bProfile = false;\r
  86 bool g_bPPScore = false;\r
  87 bool g_bBrenner = false;\r
  88 bool g_bDimer = false;\r
  89 bool g_bVersion = false;\r
  90 bool g_bStable = false;\r
  91 bool g_bFASTA = false;\r
  92 bool g_bPAS = false;\r
  93 bool g_bTomHydro = false;\r
  94 bool g_bMakeTree = false;\r
  95 \r
  96 #if     DEBUG\r
  97 bool g_bCatchExceptions = false;\r
  98 #else\r
  99 bool g_bCatchExceptions = true;\r
 100 #endif\r
 101 \r
 102 bool g_bMSF = false;\r
 103 bool g_bAln = false;\r
 104 bool g_bClwStrict = false;\r
 105 bool g_bHTML = false;\r
 106 bool g_bPHYI = false;\r
 107 bool g_bPHYS = false;\r
 108 \r
 109 unsigned g_uMaxIters = 8;\r
 110 unsigned long g_ulMaxSecs = 0;\r
 111 unsigned g_uMaxMB = 500;\r
 112 \r
 113 PPSCORE g_PPScore = PPSCORE_LE;\r
 114 OBJSCORE g_ObjScore = OBJSCORE_SPM;\r
 115 \r
 116 SEQWEIGHT g_SeqWeight1 = SEQWEIGHT_ClustalW;\r
 117 SEQWEIGHT g_SeqWeight2 = SEQWEIGHT_ClustalW;\r
 118 \r
 119 DISTANCE g_Distance1 = DISTANCE_Kmer6_6;\r
 120 DISTANCE g_Distance2 = DISTANCE_PctIdKimura;\r
 121 \r
 122 CLUSTER g_Cluster1 = CLUSTER_UPGMB;\r
 123 CLUSTER g_Cluster2 = CLUSTER_UPGMB;\r
 124 \r
 125 ROOT g_Root1 = ROOT_Pseudo;\r
 126 ROOT g_Root2 = ROOT_Pseudo;\r
 127 \r
 128 bool g_bDiags;\r
 129 \r
 130 SEQTYPE g_SeqType = SEQTYPE_Auto;\r
 131 \r
 132 TERMGAPS g_TermGaps = TERMGAPS_Half;\r
 133 \r
 134 //------------------------------------------------------\r
 135 // These parameters depending on the chosen prof-prof\r
 136 // score (g_PPScore), initialized to "Undefined".\r
 137 float g_dSmoothScoreCeil = fInsane;\r
 138 float g_dMinBestColScore = fInsane;\r
 139 float g_dMinSmoothScore = fInsane;\r
 140 SCORE g_scoreGapOpen = fInsane;\r
 141 //------------------------------------------------------\r
 142 \r
 143 static unsigned atou(const char *s)\r
 144         {\r
 145         return (unsigned) atoi(s);\r
 146         }\r
 147 \r
 148 const char *MaxSecsToStr()\r
 149         {\r
 150         if (0 == g_ulMaxSecs)\r
 151                 return "(No limit)";\r
 152         return SecsToStr(g_ulMaxSecs);\r
 153         }\r
 154 \r
 155 void ListParams()\r
 156         {\r
 157         Log("\n");\r
 158         Log("%s\n", MUSCLE_LONG_VERSION);\r
 159         Log("http://www.drive5.com/muscle\n");\r
 160         Log("\n");\r
 161         Log("Profile-profile score    %s\n", PPSCOREToStr(g_PPScore));\r
 162         Log("Max iterations           %u\n", g_uMaxIters);\r
 163         Log("Max trees                %u\n", g_uMaxTreeRefineIters);\r
 164         Log("Max time                 %s\n", MaxSecsToStr());\r
 165         Log("Max MB                   %u\n", g_uMaxMB);\r
 166         Log("Gap open                 %g\n", g_scoreGapOpen);\r
 167         Log("Gap extend (dimer)       %g\n", g_scoreGapExtend);\r
 168         Log("Gap ambig factor         %g\n", g_scoreAmbigFactor);\r
 169         Log("Gap ambig penalty        %g\n", g_scoreGapAmbig);\r
 170         Log("Center (LE)              %g\n", g_scoreCenter);\r
 171         Log("Term gaps                %s\n", TERMGAPSToStr(g_TermGaps));\r
 172 \r
 173         Log("Smooth window length     %u\n", g_uSmoothWindowLength);\r
 174         Log("Refine window length     %u\n", g_uRefineWindow);\r
 175         Log("Min anchor spacing       %u\n", g_uAnchorSpacing);\r
 176         Log("Min diag length (lambda) %u\n", g_uMinDiagLength);\r
 177         Log("Diag margin (mu)         %u\n", g_uDiagMargin);\r
 178         Log("Min diag break           %u\n", g_uMaxDiagBreak);\r
 179         Log("Hydrophobic window       %u\n", g_uHydrophobicRunLength);\r
 180 \r
 181         Log("Hydrophobic gap factor   %g\n", g_dHydroFactor);\r
 182         Log("Smooth score ceiling     %g\n", g_dSmoothScoreCeil);\r
 183         Log("Min best col score       %g\n", g_dMinBestColScore);\r
 184         Log("Min anchor score         %g\n", g_dMinSmoothScore);\r
 185         Log("SUEFF                    %g\n", g_dSUEFF);\r
 186 \r
 187         Log("Brenner root MSA         %s\n", BoolToStr(g_bBrenner));\r
 188         Log("Normalize counts         %s\n", BoolToStr(g_bNormalizeCounts));\r
 189         Log("Diagonals (1)            %s\n", BoolToStr(g_bDiags1));\r
 190         Log("Diagonals (2)            %s\n", BoolToStr(g_bDiags2));\r
 191         Log("Anchors                  %s\n", BoolToStr(g_bAnchors));\r
 192         Log("MSF output format        %s\n", BoolToStr(g_bMSF));\r
 193         Log("Phylip interleaved       %s\n", BoolToStr(g_bPHYI));\r
 194         Log("Phylip sequential        %s\n", BoolToStr(g_bPHYS));\r
 195         Log("ClustalW output format   %s\n", BoolToStr(g_bAln));\r
 196         Log("Catch exceptions         %s\n", BoolToStr(g_bCatchExceptions));\r
 197         Log("Quiet                    %s\n", BoolToStr(g_bQuiet));\r
 198         Log("Refine                   %s\n", BoolToStr(g_bRefine));\r
 199         Log("ProdfDB                  %s\n", BoolToStr(g_bProfDB));\r
 200         Log("Low complexity profiles  %s\n", BoolToStr(g_bLow));\r
 201 \r
 202         Log("Objective score          %s\n", OBJSCOREToStr(g_ObjScore));\r
 203 \r
 204         Log("Distance method (1)      %s\n", DISTANCEToStr(g_Distance1));\r
 205         Log("Clustering method (1)    %s\n", CLUSTERToStr(g_Cluster1));\r
 206         Log("Root method (1)          %s\n", ROOTToStr(g_Root1));\r
 207         Log("Sequence weighting (1)   %s\n", SEQWEIGHTToStr(g_SeqWeight1));\r
 208 \r
 209         Log("Distance method (2)      %s\n", DISTANCEToStr(g_Distance2));\r
 210         Log("Clustering method (2)    %s\n", CLUSTERToStr(g_Cluster2));\r
 211         Log("Root method (2)          %s\n", ROOTToStr(g_Root2));\r
 212         Log("Sequence weighting (2)   %s\n", SEQWEIGHTToStr(g_SeqWeight2));\r
 213 \r
 214         Log("\n");\r
 215         }\r
 216 \r
 217 static void SetDefaultsLE()\r
 218         {\r
 219         g_ptrScoreMatrix = &VTML_LA;\r
 220 \r
 221         //g_scoreGapOpen = (SCORE) -3.00;\r
 222         //g_scoreCenter = (SCORE) -0.55;\r
 223         g_scoreGapOpen = (SCORE) -2.9;\r
 224         g_scoreCenter = (SCORE) -0.52;\r
 225 \r
 226         g_bNormalizeCounts = true;\r
 227 \r
 228         //g_dSmoothScoreCeil = 5.0;\r
 229         //g_dMinBestColScore = 4.0;\r
 230         //g_dMinSmoothScore = 2.0;\r
 231         g_dSmoothScoreCeil = 3.0;\r
 232         g_dMinBestColScore = 2.0;\r
 233         g_dMinSmoothScore = 1.0;\r
 234 \r
 235         g_Distance1 = DISTANCE_Kmer6_6;\r
 236         g_Distance2 = DISTANCE_PctIdKimura;\r
 237         }\r
 238 \r
 239 static void SetDefaultsSP()\r
 240         {\r
 241         g_ptrScoreMatrix = &PAM200;\r
 242 \r
 243         g_scoreGapOpen = -1439;\r
 244         g_scoreCenter = 0.0;    // center pre-added into score mx\r
 245 \r
 246         g_bNormalizeCounts = false;\r
 247 \r
 248         g_dSmoothScoreCeil = 200.0;\r
 249         g_dMinBestColScore = 300.0;\r
 250         g_dMinSmoothScore = 125.0;\r
 251 \r
 252         g_Distance1 = DISTANCE_Kmer6_6;\r
 253         g_Distance2 = DISTANCE_PctIdKimura;\r
 254         }\r
 255 \r
 256 static void SetDefaultsSV()\r
 257         {\r
 258         g_ptrScoreMatrix = &VTML_SP;\r
 259 \r
 260         g_scoreGapOpen = -300;\r
 261         g_scoreCenter = 0.0;    // center pre-added into score mx\r
 262 \r
 263         g_bNormalizeCounts = false;\r
 264 \r
 265         g_dSmoothScoreCeil = 90.0;\r
 266         g_dMinBestColScore = 130.0;\r
 267         g_dMinSmoothScore = 40.0;\r
 268 \r
 269         g_Distance1 = DISTANCE_Kmer6_6;\r
 270         g_Distance2 = DISTANCE_PctIdKimura;\r
 271         }\r
 272 \r
 273 //static void SetDefaultsSPN()\r
 274 //      {\r
 275 //      g_ptrScoreMatrix = &NUC_SP;\r
 276 //\r
 277 //      g_scoreGapOpen = -400;\r
 278 //      g_scoreCenter = 0.0;    // center pre-added into score mx\r
 279 //\r
 280 //      g_bNormalizeCounts = false;\r
 281 //\r
 282 //      g_dSmoothScoreCeil = 999.0;             // disable\r
 283 //      g_dMinBestColScore = 90;\r
 284 //      g_dMinSmoothScore = 90;\r
 285 //\r
 286 //      g_Distance1 = DISTANCE_Kmer4_6;\r
 287 //      g_Distance2 = DISTANCE_PctIdKimura;\r
 288 //      }\r
 289 \r
 290 static void SetDefaultsSPN_DNA()\r
 291         {\r
 292         g_ptrScoreMatrix = &NUC_SP;\r
 293 \r
 294         g_scoreGapOpen = -400;\r
 295         g_scoreCenter = 0.0;    // center pre-added into score mx\r
 296         g_scoreGapExtend = 0.0;\r
 297 \r
 298         g_bNormalizeCounts = false;\r
 299 \r
 300         g_dSmoothScoreCeil = 999.0;             // disable\r
 301         g_dMinBestColScore = 90;\r
 302         g_dMinSmoothScore = 90;\r
 303 \r
 304         g_Distance1 = DISTANCE_Kmer4_6;\r
 305         g_Distance2 = DISTANCE_PctIdKimura;\r
 306         }\r
 307 \r
 308 static void SetDefaultsSPN_RNA()\r
 309         {\r
 310         g_ptrScoreMatrix = &NUC_SP;\r
 311 \r
 312         g_scoreGapOpen = -420;\r
 313         g_scoreCenter = -300;   // total center = NUC_EXTEND - 300 \r
 314         g_scoreGapExtend = 0.0;\r
 315 \r
 316         g_bNormalizeCounts = false;\r
 317 \r
 318         g_dSmoothScoreCeil = 999.0;             // disable\r
 319         g_dMinBestColScore = 90;\r
 320         g_dMinSmoothScore = 90;\r
 321 \r
 322         g_Distance1 = DISTANCE_Kmer4_6;\r
 323         g_Distance2 = DISTANCE_PctIdKimura;\r
 324         }\r
 325 \r
 326 static void FlagParam(const char *OptName, bool *ptrParam, bool bValueIfFlagSet)\r
 327         {\r
 328         bool bIsSet = FlagOpt(OptName);\r
 329         if (bIsSet)\r
 330                 *ptrParam = bValueIfFlagSet;\r
 331         }\r
 332 \r
 333 static void StrParam(const char *OptName, const char **ptrptrParam)\r
 334         {\r
 335         const char *opt = ValueOpt(OptName);\r
 336         if (0 != opt)\r
 337                 *ptrptrParam = opt;\r
 338         }\r
 339 \r
 340 static void FloatParam(const char *OptName, float *ptrParam)\r
 341         {\r
 342         const char *opt = ValueOpt(OptName);\r
 343         if (0 != opt)\r
 344                 *ptrParam = (float) atof(opt);\r
 345         }\r
 346 \r
 347 static void UintParam(const char *OptName, unsigned *ptrParam)\r
 348         {\r
 349         const char *opt = ValueOpt(OptName);\r
 350         if (0 != opt)\r
 351                 *ptrParam = atou(opt);\r
 352         }\r
 353 \r
 354 static void EnumParam(const char *OptName, EnumOpt *Opts, int *Param)\r
 355         {\r
 356         const char *Value = ValueOpt(OptName);\r
 357         if (0 == Value)\r
 358                 return;\r
 359 \r
 360         for (;;)\r
 361                 {\r
 362                 if (0 == Opts->pstrOpt)\r
 363                         Quit("Invalid parameter -%s %s", OptName, Value);\r
 364                 if (0 == stricmp(Value, Opts->pstrOpt))\r
 365                         {\r
 366                         *Param = Opts->iValue;\r
 367                         return;\r
 368                         }\r
 369                 ++Opts;\r
 370                 }\r
 371         }\r
 372 \r
 373 static void SetPPDefaultParams()\r
 374         {\r
 375         switch (g_PPScore)\r
 376                 {\r
 377         case PPSCORE_SP:\r
 378                 SetDefaultsSP();\r
 379                 break;\r
 380 \r
 381         case PPSCORE_LE:\r
 382                 SetDefaultsLE();\r
 383                 break;\r
 384 \r
 385         case PPSCORE_SV:\r
 386                 SetDefaultsSV();\r
 387                 break;\r
 388 \r
 389         case PPSCORE_SPN:\r
 390                 switch (g_Alpha)\r
 391                         {\r
 392                 case ALPHA_DNA:\r
 393                         SetDefaultsSPN_DNA();\r
 394                         break;\r
 395                 case ALPHA_RNA:\r
 396                         SetDefaultsSPN_RNA();\r
 397                         break;\r
 398                 default:\r
 399                         Quit("Invalid alpha %d", g_Alpha);\r
 400                         }\r
 401                 break;\r
 402 \r
 403         default:\r
 404                 Quit("Invalid g_PPScore");\r
 405                 }\r
 406         }\r
 407 \r
 408 static void SetPPCommandLineParams()\r
 409         {\r
 410         FloatParam("GapOpen", &g_scoreGapOpen);\r
 411         FloatParam("GapOpen2", &g_scoreGapOpen2);\r
 412         FloatParam("GapExtend", &g_scoreGapExtend);\r
 413         FloatParam("GapExtend2", &g_scoreGapExtend2);\r
 414         FloatParam("GapAmbig", &g_scoreAmbigFactor);\r
 415         FloatParam("Center", &g_scoreCenter);\r
 416         FloatParam("SmoothScoreCeil", &g_dSmoothScoreCeil);\r
 417         FloatParam("MinBestColScore", &g_dMinBestColScore);\r
 418         FloatParam("MinSmoothScore", &g_dMinSmoothScore);\r
 419 \r
 420         EnumParam("Distance", DISTANCE_Opts, (int *) &g_Distance1);\r
 421         EnumParam("Distance", DISTANCE_Opts, (int *) &g_Distance2);\r
 422 \r
 423         EnumParam("Distance1", DISTANCE_Opts, (int *) &g_Distance1);\r
 424         EnumParam("Distance2", DISTANCE_Opts, (int *) &g_Distance2);\r
 425         }\r
 426 \r
 427 void SetPPScore(bool bRespectFlagOpts)\r
 428         {\r
 429         if (bRespectFlagOpts)\r
 430                 {\r
 431                 if (FlagOpt("SP"))\r
 432                         g_PPScore = PPSCORE_SP;\r
 433                 else if (FlagOpt("LE"))\r
 434                         g_PPScore = PPSCORE_LE;\r
 435                 else if (FlagOpt("SV"))\r
 436                         g_PPScore = PPSCORE_SV;\r
 437                 else if (FlagOpt("SPN"))\r
 438                         g_PPScore = PPSCORE_SPN;\r
 439                 }\r
 440 \r
 441         switch (g_PPScore)\r
 442                 {\r
 443         case PPSCORE_LE:\r
 444         case PPSCORE_SP:\r
 445         case PPSCORE_SV:\r
 446                 if (ALPHA_RNA == g_Alpha || ALPHA_DNA == g_Alpha)\r
 447                         g_PPScore = PPSCORE_SPN;\r
 448                 break;\r
 449         case PPSCORE_SPN:\r
 450                 if (ALPHA_Amino == g_Alpha)\r
 451                         g_PPScore = PPSCORE_LE;\r
 452                 break;\r
 453                 }\r
 454 \r
 455         SetPPDefaultParams();\r
 456         SetPPCommandLineParams();\r
 457 \r
 458         if (g_bVerbose)\r
 459                 ListParams();\r
 460         }\r
 461 \r
 462 void SetPPScore(PPSCORE p)\r
 463         {\r
 464         g_PPScore = p;\r
 465         SetPPScore(true);\r
 466         }\r
 467 \r
 468 static void SetMaxSecs()\r
 469         {\r
 470         float fMaxHours = 0.0;\r
 471         FloatParam("MaxHours", &fMaxHours);\r
 472         if (0.0 == fMaxHours)\r
 473                 return;\r
 474         g_ulMaxSecs = (unsigned long) (fMaxHours*60*60);\r
 475         }\r
 476 \r
 477 static bool CanDoLowComplexity()\r
 478         {\r
 479         if (g_SeqWeight1 != SEQWEIGHT_ClustalW)\r
 480                 return false;\r
 481         if (1 == g_uMaxIters)\r
 482                 return true;\r
 483         return g_SeqWeight2 == SEQWEIGHT_ClustalW;\r
 484         }\r
 485 \r
 486 bool MissingCommand()\r
 487         {\r
 488         if (strcmp(g_pstrInFileName, "-"))\r
 489                 return false;\r
 490         if (0 != g_pstrFileName1)\r
 491                 return false;\r
 492         if (0 != g_pstrSPFileName)\r
 493                 return false;\r
 494         return true;\r
 495         }\r
 496 \r
 497 void SetParams()\r
 498         {\r
 499         SetMaxSecs();\r
 500 \r
 501         StrParam("in", &g_pstrInFileName);\r
 502         StrParam("out", &g_pstrOutFileName);\r
 503 \r
 504         StrParam("FASTAOut", &g_pstrFASTAOutFileName);\r
 505         StrParam("ClwOut", &g_pstrClwOutFileName);\r
 506         StrParam("ClwStrictOut", &g_pstrClwStrictOutFileName);\r
 507         StrParam("HTMLOut", &g_pstrHTMLOutFileName);\r
 508         StrParam("PHYIOut", &g_pstrPHYIOutFileName);\r
 509         StrParam("PHYSOut", &g_pstrPHYSOutFileName);\r
 510         StrParam("MSFOut", &g_pstrMSFOutFileName);\r
 511 \r
 512         StrParam("in1", &g_pstrFileName1);\r
 513         StrParam("in2", &g_pstrFileName2);\r
 514 \r
 515         StrParam("Matrix", &g_pstrMatrixFileName);\r
 516         StrParam("SPScore", &g_pstrSPFileName);\r
 517 \r
 518         StrParam("UseTree_NoWarn", &g_pstrUseTreeFileName);\r
 519         if (0 != g_pstrUseTreeFileName)\r
 520                 g_bUseTreeNoWarn = true;\r
 521 \r
 522         StrParam("UseTree", &g_pstrUseTreeFileName);\r
 523         StrParam("ComputeWeights", &g_pstrComputeWeightsFileName);\r
 524         StrParam("ScoreFile", &g_pstrScoreFileName);\r
 525         StrParam("DistMx1", &g_pstrDistMxFileName1);\r
 526         StrParam("DistMx2", &g_pstrDistMxFileName2);\r
 527 \r
 528         FlagParam("Core", &g_bCatchExceptions, false);\r
 529         FlagParam("NoCore", &g_bCatchExceptions, true);\r
 530 \r
 531         FlagParam("Diags1", &g_bDiags1, true);\r
 532         FlagParam("Diags2", &g_bDiags2, true);\r
 533 \r
 534         bool Diags = false;\r
 535         FlagParam("Diags", &Diags, true);\r
 536         if (Diags)\r
 537                 {\r
 538                 g_bDiags1 = true;\r
 539                 g_bDiags2 = true;\r
 540                 }\r
 541 \r
 542         FlagParam("Anchors", &g_bAnchors, true);\r
 543         FlagParam("NoAnchors", &g_bAnchors, false);\r
 544 \r
 545         FlagParam("Quiet", &g_bQuiet, true);\r
 546         FlagParam("Verbose", &g_bVerbose, true);\r
 547         FlagParam("Version", &g_bVersion, true);\r
 548         FlagParam("Stable", &g_bStable, true);\r
 549         FlagParam("Group", &g_bStable, false);\r
 550         FlagParam("Refine", &g_bRefine, true);\r
 551         FlagParam("RefineW", &g_bRefineW, true);\r
 552         FlagParam("ProfDB", &g_bProfDB, true);\r
 553         FlagParam("SW", &g_bSW, true);\r
 554         FlagParam("ClusterOnly", &g_bClusterOnly, true);\r
 555         FlagParam("Profile", &g_bProfile, true);\r
 556         FlagParam("PPScore", &g_bPPScore, true);\r
 557         FlagParam("Brenner", &g_bBrenner, true);\r
 558         FlagParam("Dimer", &g_bDimer, true);\r
 559 \r
 560         FlagParam("MSF", &g_bMSF, true);\r
 561         FlagParam("PHYI", &g_bPHYI, true);\r
 562         FlagParam("PHYS", &g_bPHYS, true);\r
 563         FlagParam("clw", &g_bAln, true);\r
 564         FlagParam("HTML", &g_bHTML, true);\r
 565         FlagParam("FASTA", &g_bFASTA, true);\r
 566         FlagParam("PAS", &g_bPAS, true);\r
 567         FlagParam("MakeTree", &g_bMakeTree, true);\r
 568 \r
 569         bool b = false;\r
 570         FlagParam("clwstrict", &b, true);\r
 571         if (b)\r
 572                 {\r
 573                 g_bAln = true;\r
 574                 g_bClwStrict = true;\r
 575                 }\r
 576 \r
 577         UintParam("MaxIters", &g_uMaxIters);\r
 578         UintParam("MaxTrees", &g_uMaxTreeRefineIters);\r
 579         UintParam("SmoothWindow", &g_uSmoothWindowLength);\r
 580         UintParam("RefineWindow", &g_uRefineWindow);\r
 581         UintParam("FromWindow", &g_uWindowFrom);\r
 582         UintParam("ToWindow", &g_uWindowTo);\r
 583         UintParam("SaveWindow", &g_uSaveWindow);\r
 584         UintParam("WindowOffset", &g_uWindowOffset);\r
 585         UintParam("AnchorSpacing", &g_uAnchorSpacing);\r
 586         UintParam("DiagLength", &g_uMinDiagLength);\r
 587         UintParam("DiagMargin", &g_uDiagMargin);\r
 588         UintParam("DiagBreak", &g_uMaxDiagBreak);\r
 589         UintParam("MaxSubFam", &g_uMaxSubFamCount);\r
 590 \r
 591         UintParam("Hydro", &g_uHydrophobicRunLength);\r
 592         FlagParam("TomHydro", &g_bTomHydro, true);\r
 593         if (g_bTomHydro)\r
 594                 g_uHydrophobicRunLength = 0;\r
 595 \r
 596         FloatParam("SUEFF", &g_dSUEFF);\r
 597         FloatParam("HydroFactor", &g_dHydroFactor);\r
 598 \r
 599         EnumParam("ObjScore", OBJSCORE_Opts, (int *) &g_ObjScore);\r
 600         EnumParam("TermGaps", TERMGAPS_Opts, (int *) &g_TermGaps);\r
 601 \r
 602         EnumParam("Weight", SEQWEIGHT_Opts, (int *) &g_SeqWeight1);\r
 603         EnumParam("Weight", SEQWEIGHT_Opts, (int *) &g_SeqWeight2);\r
 604 \r
 605         EnumParam("Weight1", SEQWEIGHT_Opts, (int *) &g_SeqWeight1);\r
 606         EnumParam("Weight2", SEQWEIGHT_Opts, (int *) &g_SeqWeight2);\r
 607 \r
 608         EnumParam("Cluster", CLUSTER_Opts, (int *) &g_Cluster1);\r
 609         EnumParam("Cluster", CLUSTER_Opts, (int *) &g_Cluster2);\r
 610 \r
 611         EnumParam("Cluster1", CLUSTER_Opts, (int *) &g_Cluster1);\r
 612         EnumParam("Cluster2", CLUSTER_Opts, (int *) &g_Cluster2);\r
 613 \r
 614         EnumParam("Root1", ROOT_Opts, (int *) &g_Root1);\r
 615         EnumParam("Root2", ROOT_Opts, (int *) &g_Root2);\r
 616 \r
 617         EnumParam("SeqType", SEQTYPE_Opts, (int *) &g_SeqType);\r
 618 \r
 619         g_scoreGapAmbig = g_scoreGapOpen*g_scoreAmbigFactor;\r
 620         g_bLow = CanDoLowComplexity();\r
 621 \r
 622         if (g_bDimer)\r
 623                 g_bPrecompiledCenter = false;\r
 624 \r
 625         UintParam("MaxMB", &g_uMaxMB);\r
 626         if (0 == ValueOpt("MaxMB"))\r
 627                 g_uMaxMB = (unsigned) (GetRAMSizeMB()*DEFAULT_MAX_MB_FRACT);\r
 628         }\r