website/archive/binaries/mac/src/clustalw/src/interface/InteractiveMenu.cpp

   1 /**
   2  * Author: Mark Larkin
   3  *
   4  * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
   5  */
   6 /**
   7  * Mark Larkin Dec 12 2005.
   8  * This provides the implementation of the interactive menu functions.
   9  * Changes:
  10  * 15-5-07: Added changes to clustering algorithm choice in function phylogenticTreeMenu
  11  *          Added iteration to the multipleAlignMenu function.
  12  */
  13 #ifdef HAVE_CONFIG_H
  14     #include "config.h"
  15 #endif
  16 #include <stdio.h>
  17 #include <string>
  18 #include <ctype.h>
  19 #include <cstdlib>
  20 #include <iostream>
  21 #include <iomanip>
  22 #include <stdarg.h>
  23 #include "InteractiveMenu.h"
  24
  25 namespace clustalw
  26 {
  27 using namespace std;
  28
  29 InteractiveMenu::InteractiveMenu()
  30 {
  31     try
  32     {
  33         clustalObj = new Clustal();
  34         lin1 = "";
  35
  36         secStructOutputTxt[0] = string("Secondary Structure");
  37         secStructOutputTxt[1] = string("Gap Penalty Mask");
  38         secStructOutputTxt[2] = string("Structure and Penalty Mask");
  39         secStructOutputTxt[3] = string("None");
  40     }
  41     catch(bad_alloc)
  42     {
  43         cerr<<"The memory heap is exhausted. The program must terminate now\n";
  44         exit(1);
  45     }
  46
  47     /* Initialise the menu structs */
  48     matrixMenu.noptions = 5;
  49     strcpy(matrixMenu.opt[AABLOSUM].title, "BLOSUM series");
  50     strcpy(matrixMenu.opt[AABLOSUM].string, "blosum");
  51     strcpy(matrixMenu.opt[AAPAM].title, "PAM series");
  52     strcpy(matrixMenu.opt[AAPAM].string, "pam");
  53     strcpy(matrixMenu.opt[AAGONNET].title, "Gonnet series");
  54     strcpy(matrixMenu.opt[AAGONNET].string, "gonnet");
  55     strcpy(matrixMenu.opt[AAIDENTITY].title, "Identity matrix");
  56     strcpy(matrixMenu.opt[AAIDENTITY].string, "id");
  57     strcpy(matrixMenu.opt[AAUSERDEFINED].title, "User defined");
  58     strcpy(matrixMenu.opt[AAUSERDEFINED].string, "");
  59
  60     dnaMatrixMenu.noptions = 3;
  61     strcpy(dnaMatrixMenu.opt[DNAIUB].title, "IUB");
  62     strcpy(dnaMatrixMenu.opt[DNAIUB].string, "iub");
  63     strcpy(dnaMatrixMenu.opt[DNACLUSTALW].title, "CLUSTALW(1.6)");
  64     strcpy(dnaMatrixMenu.opt[DNACLUSTALW].string, "clustalw");
  65     strcpy(dnaMatrixMenu.opt[DNAUSERDEFINED].title, "User defined");
  66     strcpy(dnaMatrixMenu.opt[DNAUSERDEFINED].string, "");
  67
  68     pwMatrixMenu.noptions = 5;
  69     strcpy(pwMatrixMenu.opt[PWAABLOSUM].title, "BLOSUM 30");
  70     strcpy(pwMatrixMenu.opt[PWAABLOSUM].string, "blosum");
  71     strcpy(pwMatrixMenu.opt[PWAAPAM].title, "PAM 350");
  72     strcpy(pwMatrixMenu.opt[PWAAPAM].string, "pam");
  73     strcpy(pwMatrixMenu.opt[PWAAGONNET].title, "Gonnet 250");
  74     strcpy(pwMatrixMenu.opt[PWAAGONNET].string, "gonnet");
  75     strcpy(pwMatrixMenu.opt[PWAAIDENTITY].title, "Identity matrix");
  76     strcpy(pwMatrixMenu.opt[PWAAIDENTITY].string, "id");
  77     strcpy(pwMatrixMenu.opt[PWAAUSER].title, "User defined");
  78     strcpy(pwMatrixMenu.opt[PWAAUSER].string, "");
  79
  80 }
  81
  82 InteractiveMenu::~InteractiveMenu()
  83 {
  84     delete clustalObj;
  85 }
  86
  87 void InteractiveMenu::mainMenu()
  88 {
  89     while (true)
  90     {
  91         lin1 = "";
  92         cout<<"\n\n\n";
  93         cout<<" **************************************************************\n";
  94         cout<<" ******** CLUSTAL "
  95             << userParameters->getRevisionLevel()
  96             <<" Multiple Sequence Alignments  ********\n";
  97         cout<<" **************************************************************\n";
  98         cout<<"\n\n";
  99
 100         cout<<"     1. Sequence Input From Disc\n";
 101         cout<<"     2. Multiple Alignments\n";
 102         cout<<"     3. Profile / Structure Alignments\n";
 103         cout<<"     4. Phylogenetic trees\n\n";
 104         cout<<"     S. Execute a system command\n";
 105         cout<<"     H. HELP\n";
 106         cout<<"     X. EXIT (leave program)\n\n\n";
 107
 108         choice = utilityObject->getChoice(string("Your choice"));
 109
 110         string offendingSeq; // unused here
 111         switch (toupper(choice))
 112         {
 113             case '1':
 114                 clustalObj->sequenceInput(false, &offendingSeq);
 115                 break;
 116             case '2':
 117                 multipleAlignMenu();
 118                 break;
 119             case '3':
 120                 profileAlignMenu();
 121                 break;
 122             case '4':
 123                 phylogeneticTreeMenu();
 124                 break;
 125             case 'S':
 126                 doSystem();
 127                 break;
 128             case '?':
 129             case 'H':
 130                 clustalObj->getHelp('1');
 131                 break;
 132             case 'Q':
 133             case 'X':
 134                 exit(0);
 135                 break;
 136             default:
 137                 cout<<"\n\nUnrecognised Command\n\n";
 138                 break;
 139         }
 140     }
 141 }
 142 void InteractiveMenu::multipleAlignMenu()
 143 {
 144     while (true)
 145     {
 146         lin1 = "";
 147         cout<<"\n\n\n";
 148         cout<<"****** MULTIPLE ALIGNMENT MENU ******\n\n\n";
 149
 150         cout<<"    1.  Do complete multiple alignment now "
 151             <<(!userParameters->getQuickPairAlign() ? "Slow/Accurate" : "Fast/Approximate")
 152             <<"\n";
 153         cout<<"    2.  Produce guide tree file only\n";
 154         cout<<"    3.  Do alignment using old guide tree file\n\n";
 155         cout<<"    4.  Toggle Slow/Fast pairwise alignments = "
 156             <<((!userParameters->getQuickPairAlign()) ? "SLOW" : "FAST")
 157             <<"\n\n";
 158         cout<<"    5.  Pairwise alignment parameters\n";
 159         cout<<"    6.  Multiple alignment parameters\n\n";
 160         cout<<"    7.  Reset gaps before alignment?";
 161
 162         if (userParameters->getResetAlignmentsNew())
 163         {
 164             cout<<" = ON\n";
 165         }
 166         else
 167         {
 168             cout<<" = OFF\n";
 169         }
 170
 171         cout<<"    8.  Toggle screen display          = "
 172             <<((!userParameters->getShowAlign()) ? "OFF" : "ON")
 173             <<"\n";
 174         cout<<"    9.  Output format options\n";
 175         cout<<"    I. Iteration = ";
 176
 177         if(userParameters->getDoRemoveFirstIteration() == ALIGNMENT)
 178         {
 179             cout << "ALIGNMENT\n\n";
 180         }
 181         else if(userParameters->getDoRemoveFirstIteration() == TREE)
 182         {
 183             cout << "TREE\n\n";
 184         }
 185         else
 186         {
 187             cout << "NONE\n\n";
 188         }
 189
 190         cout<<"    S.  Execute a system command\n";
 191         cout<<"    H.  HELP\n";
 192         cout<<"    or press [RETURN] to go back to main menu\n\n\n";
 193
 194         choice = utilityObject->getChoice(string("Your choice"));
 195         if (choice == '\n')
 196         {
 197             return ;
 198         }
 199
 200         switch (toupper(choice))
 201         {
 202             case '1':
 203                 clustalObj->align(&phylipName);
 204                 break;
 205             case '2':
 206                 clustalObj->doGuideTreeOnly(&phylipName);
 207                 break;
 208             case '3':
 209                 clustalObj->doAlignUseOldTree(&phylipName);
 210                 break;
 211             case '4':
 212                 userParameters->toggleQuickPairAlign();
 213                 break;
 214             case '5':
 215                 pairwiseMenu();
 216                 break;
 217             case '6':
 218                 multiMenu();
 219                 break;
 220             case '7':
 221                 userParameters->toggleResetAlignmentsNew();
 222                 if (userParameters->getResetAlignmentsNew() == true)
 223                 {
 224                     userParameters->setResetAlignmentsAll(false);
 225                 }
 226                 break;
 227             case '8':
 228                 userParameters->toggleShowAlign();
 229                 break;
 230             case '9':
 231                 formatOptionsMenu();
 232                 break;
 233             case 'I':
 234                 iterationMenu();
 235                 break;
 236             case 'S':
 237                 doSystem();
 238                 break;
 239             case '?':
 240             case 'H':
 241                 clustalObj->getHelp('2');
 242                 break;
 243             case 'Q':
 244             case 'X':
 245                 return ;
 246
 247             default:
 248                 fprintf(stdout, "\n\nUnrecognised Command\n\n");
 249                 break;
 250         }
 251     }
 252 }
 253
 254 void InteractiveMenu::profileAlignMenu(void)
 255 {
 256     while (true)
 257     {
 258         lin1 = "";
 259         cout<<"\n\n\n";
 260         cout<<"****** PROFILE AND STRUCTURE ALIGNMENT MENU ******\n\n\n";
 261
 262         cout<<"    1.  Input 1st. profile             ";
 263
 264         if (!userParameters->getProfile1Empty())
 265         {
 266             cout<<"(loaded)";
 267         }
 268
 269         cout<<"\n";
 270         cout<<"    2.  Input 2nd. profile/sequences   ";
 271
 272         if (!userParameters->getProfile2Empty())
 273         {
 274             cout<<"(loaded)";
 275         }
 276
 277         cout<<"\n\n";
 278         cout<<"    3.  Align 2nd. profile to 1st. profile\n";
 279
 280         cout<<"    4.  Align sequences to 1st. profile "
 281             <<((!userParameters->getQuickPairAlign())
 282                 ? "(Slow/Accurate)\n\n" : "(Fast/Approximate)\n\n");
 283
 284         cout<<"    5.  Toggle Slow/Fast pairwise alignments = "
 285             <<((!userParameters->getQuickPairAlign())
 286                    ? "SLOW\n\n" : "FAST\n\n");
 287
 288         cout<<"    6.  Pairwise alignment parameters\n";
 289         cout<<"    7.  Multiple alignment parameters\n\n";
 290
 291         cout<<"    8.  Toggle screen display                = "
 292             <<((!userParameters->getShowAlign()) ? "OFF\n" : "ON\n");
 293
 294         cout<<"    9.  Output format options\n";
 295         cout<<"    0.  Secondary structure options\n\n";
 296         cout<<"    S.  Execute a system command\n";
 297         cout<<"    H.  HELP\n";
 298         cout<<"    or press [RETURN] to go back to main menu\n\n\n";
 299
 300         choice = utilityObject->getChoice(string("Your choice"));
 301         if (choice == '\n')
 302         {
 303             return ;
 304         }
 305
 306         switch (toupper(choice))
 307         {
 308             case '1':
 309                 clustalObj->profile1Input();
 310                 break;
 311             case '2':
 312                 clustalObj->profile2Input();
 313                 break;
 314             case '3':
 315                 clustalObj->profileAlign(&p1TreeName, &p2TreeName);
 316                 break;
 317             case '4':
 318                 /* align new sequences to profile 1 */
 319                 clustalObj->sequencesAlignToProfile(&phylipName);
 320                 break;
 321             case '5':
 322                 userParameters->toggleQuickPairAlign();
 323                 break;
 324             case '6':
 325                 pairwiseMenu();
 326                 break;
 327             case '7':
 328                 multiMenu();
 329                 break;
 330             case '8':
 331                 userParameters->toggleShowAlign();
 332                 break;
 333             case '9':
 334                 formatOptionsMenu();
 335                 break;
 336             case '0':
 337                 ssOptionsMenu();
 338                 break;
 339             case 'S':
 340                 doSystem();
 341                 break;
 342             case '?':
 343             case 'H':
 344                 clustalObj->getHelp('6');
 345                 break;
 346             case 'Q':
 347             case 'X':
 348                 return ;
 349
 350             default:
 351                 cout<<"\n\nUnrecognised Command\n\n";
 352                 break;
 353         }
 354     }
 355 }
 356
 357 void InteractiveMenu::ssOptionsMenu()
 358 {
 359     while (true)
 360     {
 361         lin1 = "";
 362         cout<<"\n\n\n";
 363         cout<<" ********* SECONDARY STRUCTURE OPTIONS *********\n\n\n";
 364
 365         cout<<"     1. Use profile 1 secondary structure / penalty mask  ";
 366         if (userParameters->getUseSS1())
 367         {
 368             cout<<"= YES\n";
 369         }
 370         else
 371         {
 372             cout<<"= NO\n";
 373         }
 374
 375         cout<<"     2. Use profile 2 secondary structure / penalty mask  ";
 376         if (userParameters->getUseSS2())
 377         {
 378             cout<<"= YES\n\n";
 379         }
 380         else
 381         {
 382             cout<<"= NO\n\n";
 383         }
 384
 385         cout<<"     3. Output in alignment  ";
 386         cout<<"= "<< secStructOutputTxt[userParameters->getOutputStructPenalties()] <<"\n\n";
 387
 388         cout<<"     4. Helix gap penalty                     : "
 389             <<userParameters->getHelixPenalty()<<"\n";
 390         cout<<"     5. Strand gap penalty                    : "
 391             <<userParameters->getStrandPenalty()<<"\n";
 392         cout<<"     6. Loop gap penalty                      : "
 393             <<userParameters->getLoopPenalty()<<"\n";
 394         cout<<"     7. Secondary structure terminal penalty  : "
 395             <<userParameters->getHelixEndPenalty()<<"\n";
 396         cout<<"     8. Helix terminal positions       within : "
 397             <<userParameters->getHelixEndMinus()
 398             <<"      outside : "
 399             <<userParameters->getHelixEndPlus()<<"\n";
 400         cout<<"     9. Strand terminal positions      within : "
 401             <<userParameters->getStrandEndMinus()
 402             <<"      outside : "
 403             <<userParameters->getStrandEndPlus()<<"\n\n\n";
 404         cout<<"     H. HELP\n\n\n";
 405
 406         choice = utilityObject->getChoice(string("Enter number (or [RETURN] to exit)"));
 407         if (choice == '\n')
 408         {
 409             return ;
 410         }
 411
 412         switch (toupper(choice))
 413         {
 414             case '1':
 415                 userParameters->toggleUseSS1();
 416                 break;
 417             case '2':
 418                 userParameters->toggleUseSS2();
 419                 break;
 420             case '3':
 421                 userParameters->setOutputStructPenalties(secStrOutputOptions());
 422                 break;
 423             case '4':
 424                 cout<<"Helix Penalty Currently: "
 425                     << userParameters->getHelixPenalty()<<"\n";
 426                 userParameters->setHelixPenalty(utilityObject->getInt("Enter number",
 427                                                   1,9, userParameters->getHelixPenalty()));
 428                 break;
 429             case '5':
 430                 cout<<"Strand Gap Penalty Currently: "
 431                     << userParameters->getStrandPenalty() <<"\n";
 432                 userParameters->setStrandPenalty(utilityObject->getInt("Enter number",
 433                                                   1,9, userParameters->getStrandPenalty()));
 434                 break;
 435             case '6':
 436                 cout<<"Loop Gap Penalty Currently: "
 437                     << userParameters->getLoopPenalty() <<"\n";
 438                 userParameters->setLoopPenalty(utilityObject->getInt("Enter number",
 439                                                  1, 9, userParameters->getLoopPenalty()));
 440                 break;
 441             case '7':
 442                 cout<<"Secondary Structure Terminal Penalty Currently: "
 443                     << userParameters->getHelixEndPenalty() <<"\n";
 444                 userParameters->setHelixEndPenalty(utilityObject->getInt("Enter number",
 445                                                1, 9,userParameters->getHelixEndPenalty()));
 446                 userParameters->setStrandEndPenalty(userParameters->getHelixEndPenalty());
 447                 break;
 448             case '8':
 449                 cout<<"Helix Terminal Positions Currently: \n";
 450                 cout<<"        within helix: "
 451                     << userParameters->getHelixEndMinus()
 452                     << "      outside helix: "
 453                     << userParameters->getHelixEndPlus() <<"\n";
 454
 455                 userParameters->setHelixEndMinus(utilityObject->getInt(
 456                                  "Enter number of residues within helix",
 457                                  0, 3, userParameters->getHelixEndMinus()));
 458                 userParameters->setHelixEndPlus(utilityObject->getInt(
 459                                  "Enter number of residues outside helix", 0, 3,
 460                                  userParameters->getHelixEndPlus()));
 461                 break;
 462             case '9':
 463                 cout<<"Strand Terminal Positions Currently: \n";
 464                 cout<<"        within strand: "
 465                     << userParameters->getStrandEndMinus()
 466                     << "      outside strand: "
 467                     << userParameters->getStrandEndPlus() <<"\n";
 468                 userParameters->setStrandEndMinus(utilityObject->getInt(
 469                                  "Enter number of residues within strand", 0, 3,
 470                                  userParameters->getStrandEndMinus()));
 471                 userParameters->setStrandEndPlus(utilityObject->getInt(
 472                                  "Enter number of residues outside strand", 0, 3,
 473                                  userParameters->getStrandEndPlus()));
 474                 break;
 475             case '?':
 476             case 'H':
 477                 clustalObj->getHelp('B');
 478                 break;
 479             default:
 480                 cout<<"\n\nUnrecognised Command\n\n";
 481                 break;
 482         }
 483     }
 484 }
 485 int InteractiveMenu::secStrOutputOptions()
 486 {
 487     while (true)
 488     {
 489         lin1 = "";
 490         cout<<"\n\n\n";
 491         cout<<" ********* Secondary Structure Output Menu *********\n\n\n";
 492
 493         cout<<"     1. "<< secStructOutputTxt[0] <<"\n";
 494         cout<<"     2. "<< secStructOutputTxt[1] <<"\n";
 495         cout<<"     3. "<< secStructOutputTxt[2] <<"\n";
 496         cout<<"     4. "<< secStructOutputTxt[3] <<"\n";
 497         cout<<"     H. HELP\n\n";
 498         cout<<"     -- Current output is "
 499             << secStructOutputTxt[userParameters->getOutputStructPenalties()];
 500         cout<<" --\n";
 501
 502         choice = utilityObject->getChoice(string("Enter number (or [RETURN] to exit)"));
 503         if (choice == '\n')
 504         {
 505             return (userParameters->getOutputStructPenalties());;
 506         }
 507
 508         switch (toupper(choice))
 509         {
 510             case '1':
 511                 return (OUTSECST);
 512             case '2':
 513                 return (OUTGAP);
 514             case '3':
 515                 return (OUTBOTH);
 516             case '4':
 517                 return (OUTNONE);
 518             case '?':
 519             case 'H':
 520                 clustalObj->getHelp('C');
 521             case 'Q':
 522             case 'X':
 523                 return (0);
 524
 525             default:
 526                 cout<< "\n\nUnrecognised Command\n\n";
 527                 break;
 528         }
 529     }
 530 }
 531
 532 void InteractiveMenu::phylogeneticTreeMenu()
 533 {
 534     while (true)
 535     {
 536         lin1 = "";
 537         cout<<"\n\n\n";
 538         cout<<"****** PHYLOGENETIC TREE MENU ******\n\n\n";
 539
 540         cout<<"    1.  Input an alignment\n";
 541         cout<<"    2.  Exclude positions with gaps?        ";
 542
 543         if (userParameters->getTossGaps())
 544         {
 545             cout<<"= ON\n";
 546         }
 547         else
 548         {
 549             cout<<"= OFF\n";
 550         }
 551
 552         cout<<"    3.  Correct for multiple substitutions? ";
 553
 554         if (userParameters->getKimura())
 555         {
 556             cout<<"= ON\n";
 557         }
 558         else
 559         {
 560             cout<<"= OFF\n";
 561         }
 562
 563         cout<<"    4.  Draw tree now\n";
 564         cout<<"    5.  Bootstrap tree\n";
 565         cout<<"    6.  Output format options\n";
 566         cout<<"    7.  Clustering algorithm = "; // Mark change 15-5-2007
 567         if(userParameters->getClusterAlgorithm() == NJ)
 568         {
 569             cout << "NJ\n\n";
 570         }
 571         else
 572         {
 573             cout << "UPGMA\n\n";
 574         }
 575         cout<<"    S.  Execute a system command\n";
 576         cout<<"    H.  HELP\n";
 577         cout<<"    or press [RETURN] to go back to main menu\n\n\n";
 578
 579         choice = utilityObject->getChoice(string("Your choice"));
 580         if (choice == '\n')
 581         {
 582             return ;
 583         }
 584
 585         string offendingSeq; // unused here
 586         switch (toupper(choice))
 587         {
 588             case '1':
 589                 clustalObj->sequenceInput(false, &offendingSeq);
 590                 break;
 591             case '2':
 592                 userParameters->toggleTossGaps();
 593                 break;
 594             case '3':
 595                 userParameters->toggleKimura();
 596                 break;
 597             case '4':
 598                 clustalObj->phylogeneticTree(&phylipName, &clustalName, &distName,
 599                     &nexusName, "amenu.pim");
 600                 break;
 601             case '5':
 602                 clustalObj->bootstrapTree(&phylipName, &clustalName, &nexusName);
 603                 break;
 604             case '6':
 605                 treeFormatOptionsMenu();
 606                 break;
 607             case '7':
 608                 clusteringAlgorithmMenu();
 609                 break;
 610             case 'S':
 611                 doSystem();
 612                 break;
 613             case '?':
 614             case 'H':
 615                 clustalObj->getHelp('7');
 616                 break;
 617             case 'Q':
 618             case 'X':
 619                 return ;
 620
 621             default:
 622                 cout<<"\n\nUnrecognised Command\n\n";
 623                 break;
 624         }
 625     }
 626 }
 627
 628 void InteractiveMenu::treeFormatOptionsMenu()
 629 {
 630     while (true)
 631     {
 632         lin1 = "";
 633         cout<< "\n\n\n";
 634         cout<<" ****** Format of Phylogenetic Tree Output ******\n\n\n";
 635         cout<<"     1. Toggle CLUSTAL format tree output    =  "
 636             << ((!userParameters->getOutputTreeClustal()) ? "OFF" : "ON")<<"\n";
 637         cout<<"     2. Toggle Phylip format tree output     =  "
 638             << ((!userParameters->getOutputTreePhylip()) ? "OFF" : "ON")<<"\n";
 639         cout<<"     3. Toggle Phylip distance matrix output =  "
 640             << ((!userParameters->getOutputTreeDistances()) ? "OFF" : "ON")<<"\n";
 641         cout<<"     4. Toggle Nexus format tree output      =  "
 642             << ((!userParameters->getOutputTreeNexus()) ? "OFF" : "ON")<<"\n\n";
 643         cout<<"     5. Toggle Phylip bootstrap positions    =  "
 644             <<((userParameters->getBootstrapFormat() == BS_NODE_LABELS) ? "NODE LABELS" :
 645             "BRANCH LABELS") <<"\n\n\n";
 646         cout<<"     H. HELP\n\n\n";
 647
 648         choice = utilityObject->getChoice(string("Enter number (or [RETURN] to exit)"));
 649         if (choice == '\n')
 650         {
 651             return ;
 652         }
 653         switch (toupper(choice))
 654         {
 655             case '1':
 656                 userParameters->toggleOutputTreeClustal();
 657                 break;
 658             case '2':
 659                 userParameters->toggleOutputTreePhylip();
 660                 break;
 661             case '3':
 662                 userParameters->toggleOutputTreeDistances();
 663                 break;
 664             case '4':
 665                 userParameters->toggleOutputTreeNexus();
 666                 break;
 667             case '5':
 668                 userParameters->toggleBootstrapFormat();
 669                 break;
 670             case '?':
 671             case 'H':
 672                 clustalObj->getHelp('0');
 673                 break;
 674             default:
 675                 cout<< "\n\nUnrecognised Command\n\n";
 676                 break;
 677         }
 678     }
 679
 680 }
 681
 682 void InteractiveMenu::formatOptionsMenu()
 683 {
 684
 685     while (true)
 686     {
 687         lin1 = "";
 688         cout<<"\n\n\n";
 689         cout<<" ********* Format of Alignment Output *********\n\n\n";
 690         cout<<"     F. Toggle FASTA format output       =  "
 691             << ((!userParameters->getOutputFasta()) ? "OFF" : "ON") <<"\n\n";
 692         cout<<"     1. Toggle CLUSTAL format output     =  "
 693             << ((!userParameters->getOutputClustal()) ? "OFF" : "ON") <<"\n";
 694         cout<<"     2. Toggle NBRF/PIR format output    =  "
 695             << ((!userParameters->getOutputNbrf()) ? "OFF" : "ON") << "\n";
 696         cout<<"     3. Toggle GCG/MSF format output     =  "
 697             << ((!userParameters->getOutputGCG()) ? "OFF" : "ON") << "\n";
 698         cout<<"     4. Toggle PHYLIP format output      =  "
 699             << ((!userParameters->getOutputPhylip()) ? "OFF" : "ON") << "\n";
 700         cout<<"     5. Toggle NEXUS format output       =  "
 701             << ((!userParameters->getOutputNexus()) ? "OFF" : "ON") << "\n";
 702         cout<<"     6. Toggle GDE format output         =  "
 703             << ((!userParameters->getOutputGde()) ? "OFF" : "ON") << "\n\n";
 704         cout<<"     7. Toggle GDE output case           =  "
 705             << ((!userParameters->getLowercase()) ? "UPPER" : "LOWER") << "\n";
 706
 707         cout<<"     8. Toggle CLUSTALW sequence numbers =  "
 708             << ((!userParameters->getClSeqNumbers()) ? "OFF" : "ON") << "\n";
 709         cout<<"     9. Toggle output order              =  "
 710             << ((userParameters->getOutputOrder() == 0) ? "INPUT FILE" : "ALIGNED")
 711             <<"\n\n";
 712
 713         cout<<"     0. Create alignment output file(s) now?\n\n";
 714         cout<<"     T. Toggle parameter output          = "
 715             << ((!userParameters->getSaveParameters()) ? "OFF" : "ON") << "\n";
 716         cout<<"     R. Toggle sequence range numbers =  "
 717             <<((!userParameters->getSeqRange()) ? "OFF" : "ON") << "\n\n";
 718
 719         cout<<"     H. HELP\n\n\n";
 720
 721         choice = utilityObject->getChoice(string("Enter number (or [RETURN] to exit)"));
 722         if (choice == '\n')
 723         {
 724             return ;
 725         }
 726         switch (toupper(choice))
 727         {
 728             case '1':
 729                 userParameters->toggleOutputClustal();
 730                 break;
 731             case '2':
 732                 userParameters->toggleOutputNbrf();
 733                 break;
 734             case '3':
 735                 userParameters->toggleOutputGCG();
 736                 break;
 737             case '4':
 738                 userParameters->toggleOutputPhylip();
 739                 break;
 740             case '5':
 741                 userParameters->toggleOutputNexus();
 742                 break;
 743             case '6':
 744                 userParameters->toggleOutputGde();
 745                 break;
 746             case '7':
 747                 userParameters->toggleLowercase();
 748                 break;
 749             case '8':
 750                 userParameters->toggleClSeqNumbers();
 751                 break;
 752             case '9':
 753                 userParameters->toggleOutputOrder();
 754                 break;
 755             case 'F':
 756                 userParameters->toggleOutputFasta();
 757                 break;
 758             case 'R':
 759                 userParameters->toggleSeqRange();
 760                 break;
 761             case '0':
 762                 clustalObj->outputNow();
 763                 break;
 764             case 'T':
 765                 userParameters->toggleSaveParameters();
 766                 break;
 767             case '?':
 768             case 'H':
 769                 clustalObj->getHelp('5');
 770                 break;
 771             default:
 772                 cout<<"\n\nUnrecognised Command\n\n";
 773                 break;
 774         }
 775     }
 776 }
 777
 778 void InteractiveMenu::pairwiseMenu()
 779 {
 780     if (userParameters->getDNAFlag())
 781     {
 782         userParameters->setPWParamToDNA();
 783     }
 784     else
 785     {
 786         userParameters->setPWParamToProtein();
 787     }
 788
 789     while (true)
 790     {
 791         lin1 = "";
 792         cout<<"\n\n\n";
 793         cout<<" ********* PAIRWISE ALIGNMENT PARAMETERS *********\n\n\n";
 794
 795         cout<<"     Slow/Accurate alignments:\n\n";
 796
 797         cout<<"     1. Gap Open Penalty       : "
 798             << fixed << setprecision(2) << userParameters->getPWGapOpen() << "\n";
 799         cout<<"     2. Gap Extension Penalty  : "
 800             << fixed << setprecision(2) << userParameters->getPWGapExtend() << "\n";
 801         cout<< "     3. Protein weight matrix  :"
 802             << matrixMenu.opt[subMatrix->getPWMatrixNum() - 1].title
 803             << "\n";
 804         cout<<"     4. DNA weight matrix      :"
 805             << dnaMatrixMenu.opt[subMatrix->getPWDNAMatrixNum() - 1].title
 806             << "\n\n";
 807
 808         cout<<"     Fast/Approximate alignments:\n\n";
 809
 810         cout<<"     5. Gap penalty            :"
 811             << userParameters->getWindowGap() << "\n";
 812         cout<<"     6. K-tuple (word) size    :"
 813             << userParameters->getKtup() << "\n";
 814         cout<<"     7. No. of top diagonals   :"
 815             << userParameters->getSignif() << "\n";
 816         cout<<"     8. Window size            :"
 817             << userParameters->getWindow() << "\n\n";
 818
 819         cout<<"     9. Toggle Slow/Fast pairwise alignments ";
 820         if (userParameters->getQuickPairAlign())
 821         {
 822             cout<<"= FAST\n\n";
 823         }
 824         else
 825         {
 826             cout<<"= SLOW\n\n";
 827         }
 828
 829
 830         cout<<"     H. HELP\n\n\n";
 831         choice = utilityObject->getChoice(string("Enter number (or [RETURN] to exit)"));
 832         if (choice == '\n')
 833         {
 834             if (userParameters->getDNAFlag())
 835             {
 836                 userParameters->setPWDNAParam();
 837             }
 838             else
 839             {
 840                 userParameters->setPWProteinParam();
 841             }
 842
 843             return ;
 844         }
 845
 846
 847         switch (toupper(choice))
 848         {
 849             case '1':
 850                 cout<<"Gap Open Penalty Currently: "
 851                     << userParameters->getPWGapOpen() << "\n";
 852                 userParameters->setPWGapOpen(
 853                               (float)utilityObject->getReal("Enter number", (double)0.0,
 854                               (double)100.0, (double)userParameters->getPWGapOpen()));
 855                 break;
 856             case '2':
 857                 cout<<"Gap Extension Penalty Currently: "
 858                     << userParameters->getPWGapExtend() << "\n";
 859                 userParameters->setPWGapExtend(
 860                               (float)utilityObject->getReal("Enter number", (double)0.0,
 861                               (double)10.0, (double)userParameters->getPWGapExtend()));
 862                 break;
 863             case '3':
 864                 readMatrix(Protein, Pairwise, pwMatrixMenu);
 865                 break;
 866             case '4':
 867                 readMatrix(DNA, Pairwise, dnaMatrixMenu);
 868                 break;
 869             case '5':
 870                 cout<<"Gap Penalty Currently: "
 871                     << userParameters->getWindowGap() << "\n";
 872                 userParameters->setWindowGap(
 873                                  utilityObject->getInt("Enter number", 1, 500,
 874                                                 userParameters->getWindowGap()));
 875                 break;
 876             case '6':
 877                 cout<<"K-tuple Currently: "
 878                     << userParameters->getKtup() << "\n";
 879                 if (userParameters->getDNAFlag())
 880                 {
 881                     int _ktup = utilityObject->getInt("Enter number", 1, 4,
 882                                                       userParameters->getKtup());
 883                     userParameters->setKtup(_ktup);
 884                     // see bug 185
 885                     userParameters->setDNAKtup(_ktup);
 886                     userParameters->setWindowGap(_ktup + 4);
 887                     userParameters->setDNAWindowGap(_ktup + 4);
 888
 889                 }
 890                 else
 891                 {
 892                     int _ktup = utilityObject->getInt("Enter number", 1, 2,
 893                                                       userParameters->getKtup());
 894                     userParameters->setKtup(_ktup);
 895                     // see bug 185
 896                     userParameters->setAAKtup(_ktup);
 897                     userParameters->setWindowGap(_ktup + 3);
 898                     userParameters->setAAWindowGap(_ktup + 3);
 899
 900                 }
 901                 break;
 902             case '7':
 903                 cout<<"Top diagonals Currently: "
 904                     << userParameters->getSignif() << "\n";
 905                 userParameters->setSignif(
 906                                 utilityObject->getInt("Enter number", 1, 50,
 907                                           userParameters->getSignif()));
 908                 break;
 909             case '8':
 910                 cout<<"Window size Currently: "
 911                     << userParameters->getWindow() << "\n";
 912                 userParameters->setWindow(
 913                                 utilityObject->getInt("Enter number", 1, 50,
 914                                            userParameters->getWindow()));
 915                 break;
 916             case '9':
 917                 userParameters->toggleQuickPairAlign();
 918                 break;
 919             case '?':
 920             case 'H':
 921                 clustalObj->getHelp('3');
 922                 break;
 923             default:
 924                 cout<< "\n\nUnrecognised Command\n\n";
 925                 break;
 926         }
 927     }
 928 }
 929
 930 void InteractiveMenu::multiMenu()
 931 {
 932     if (userParameters->getDNAFlag())
 933     {
 934         userParameters->setDNAMultiGap();
 935     }
 936     else
 937     {
 938         userParameters->setProtMultiGap();
 939     }
 940
 941     while (true)
 942     {
 943         lin1 = "";
 944         cout<<"\n\n\n ********* MULTIPLE ALIGNMENT PARAMETERS *********\n\n\n";
 945         cout<<"     1. Gap Opening Penalty              :"
 946             << fixed << setprecision(2) << userParameters->getGapOpen() << "\n";
 947         cout<<"     2. Gap Extension Penalty            :"
 948             << fixed << setprecision(2) << userParameters->getGapExtend() << "\n";
 949
 950         cout<<"     3. Delay divergent sequences        :"
 951             << userParameters->getDivergenceCutoff() << " %\n\n";
 952
 953         cout<<"     4. DNA Transitions Weight           :"
 954             << fixed << setprecision(2) << userParameters->getTransitionWeight() << "\n\n";
 955         cout<<"     5. Protein weight matrix            :"
 956             << matrixMenu.opt[subMatrix->getMatrixNum() - 1].title
 957             << "\n";
 958         cout<<"     6. DNA weight matrix                :"
 959             << dnaMatrixMenu.opt[subMatrix->getDNAMatrixNum() - 1].title
 960             << "\n";
 961         cout<<"     7. Use negative matrix              :"
 962             << ((!userParameters->getUseNegMatrix()) ? "OFF" : "ON") << "\n\n";
 963         cout<<"     8. Protein Gap Parameters\n\n";
 964         cout<<"     H. HELP\n\n\n";
 965
 966         choice = utilityObject->getChoice(string("Enter number (or [RETURN] to exit)"));
 967         if (choice == '\n')
 968         {
 969             if (userParameters->getDNAFlag())
 970             {
 971                 //userParameters->setDNAMultiGap();
 972                 userParameters->setDNAGapOpen(userParameters->getGapOpen());
 973                 userParameters->setDNAGapExtend(userParameters->getGapExtend());
 974             }
 975             else
 976             {
 977                 //userParameters->setProtMultiGap();
 978                 userParameters->setAAGapOpen(userParameters->getGapOpen());
 979                 userParameters->setAAGapExtend(userParameters->getGapExtend());
 980             }
 981             return ;
 982         }
 983
 984
 985         switch (toupper(choice))
 986         {
 987             case '1':
 988                 cout<<"Gap Opening Penalty Currently: "
 989                     << userParameters->getGapOpen() << "\n";
 990                 userParameters->setGapOpen(
 991                                   (float)utilityObject->getReal("Enter number", (double)0.0,
 992                                   (double)100.0, (double)userParameters->getGapOpen()));
 993                 break;
 994             case '2':
 995                 cout<<"Gap Extension Penalty Currently: "
 996                     << userParameters->getGapExtend() << "\n";
 997                 userParameters->setGapExtend(
 998                                 (float)utilityObject->getReal("Enter number", (double)0.0,
 999                                 (double)10.0, (double)userParameters->getGapExtend()));
1000                 break;
1001             case '3':
1002                 cout<<"Min Identity Currently: "
1003                     << userParameters->getDivergenceCutoff() << "\n";
1004                 userParameters->setDivergenceCutoff(
1005                                      utilityObject->getInt("Enter number", 0, 100,
1006                                      userParameters->getDivergenceCutoff()));
1007                 break;
1008             case '4':
1009                 cout<<"Transition Weight Currently: "
1010                     << userParameters->getTransitionWeight() << "\n";
1011                 userParameters->setTransitionWeight(
1012                                 (float)utilityObject->getReal("Enter number", (double)0.0,
1013                                 (double)1.0,
1014                                 (double)userParameters->getTransitionWeight()));
1015                 break;
1016             case '5':
1017                 readMatrix(Protein, MultipleAlign, matrixMenu);
1018                 break;
1019             case '6':
1020                 readMatrix(DNA, MultipleAlign, dnaMatrixMenu);
1021                 break;
1022             case '7':
1023                 userParameters->toggleUseNegMatrix();
1024                 break;
1025             case '8':
1026                 gapPenaltiesMenu();
1027                 break;
1028             case '?':
1029             case 'H':
1030                 //clustalObj->getHelp('4');
1031                 break;
1032             default:
1033                 cout<< "\n\nUnrecognised Command\n\n";
1034                 break;
1035         }
1036     }
1037 }
1038
1039 void InteractiveMenu::gapPenaltiesMenu()
1040 {
1041
1042     while (true)
1043     {
1044         lin1 = "";
1045         cout<< "\n\n\n ********* PROTEIN GAP PARAMETERS *********\n\n\n\n";
1046         cout<<"     1. Toggle Residue-Specific Penalties :"
1047             << ((userParameters->getNoPrefPenalties()) ? "OFF" : "ON") << "\n\n";
1048         cout<<"     2. Toggle Hydrophilic Penalties      :"
1049             << ((userParameters->getNoHydPenalties()) ? "OFF" : "ON") << "\n";
1050         cout<<"     3. Hydrophilic Residues              :"
1051             << userParameters->getHydResidues() << "\n\n";
1052         cout<<"     4. Gap Separation Distance           :"
1053             << userParameters->getGapDist() << "\n";
1054         cout<<"     5. Toggle End Gap Separation         :"
1055             << ((!userParameters->getUseEndGaps()) ? "OFF" : "ON") << "\n\n";
1056         cout<<"     H. HELP\n\n\n";
1057
1058         choice = utilityObject->getChoice(string("Enter number (or [RETURN] to exit)"));
1059         if (choice == '\n')
1060         {
1061             return ;
1062         }
1063
1064         switch (toupper(choice))
1065         {
1066             case '1':
1067                 userParameters->toggleNoPrefPenalties();
1068                 break;
1069             case '2':
1070                 userParameters->toggleNoHydPenalties();
1071                 break;
1072             case '3':
1073                 cout<<"Hydrophilic Residues Currently: "
1074                     << userParameters->getHydResidues() << "\n";
1075                 lin1 = "";
1076                 utilityObject->getStr(string("Enter residues (or [RETURN] to quit)"), lin1);
1077                 if (lin1.size() > 0)
1078                 {
1079                     userParameters->setHydResidues(lin1);
1080                 }
1081                 break;
1082             case '4':
1083                 cout<<"Gap Separation Distance Currently: "
1084                     << userParameters->getGapDist() << "\n";
1085                 userParameters->setGapDist(
1086                                 utilityObject->getInt("Enter number", 0, 100,
1087                                 userParameters->getGapDist()));
1088                 break;
1089             case '5':
1090                 userParameters->toggleUseEndGaps();
1091                 break;
1092             case '?':
1093             case 'H':
1094                 clustalObj->getHelp('A');
1095                 break;
1096             default:
1097                 cout<< "\n\nUnrecognised Command\n\n";
1098                 break;
1099         }
1100     }
1101 }
1102
1103 /*
1104  * This function displays the menu for selecting the weight matrix to use.
1105  * It is used for both the protein and DNA menu for pairwise and Multiple alignment.
1106  * This is why it requires the MatMenu struct.
1107  */
1108 int InteractiveMenu::readMatrix(int alignResidueType, int alignType, MatMenu menu)
1109 {
1110     static char userFile[FILENAMELEN + 1];
1111     int i, option;
1112     char title[10];
1113     int matn; // Used to show which is the current matrix.
1114
1115     if(alignResidueType == Protein)
1116     {
1117         strcpy(title, "PROTEIN");
1118     }
1119     else // DNA
1120     {
1121         strcpy(title, "DNA");
1122     }
1123
1124     while (true)
1125     {
1126         lin1 = "";
1127         cout<<"\n\n\n ********* "<< title <<" WEIGHT MATRIX MENU *********\n\n\n";
1128
1129         // Find out what the currently selected matrix is.
1130         matn = subMatrix->getMatrixNumForMenu(alignResidueType, alignType);
1131
1132         for (i = 0; i < menu.noptions; i++)
1133         {
1134             cout<< "     " << i + 1 << ". " << menu.opt[i].title << "\n";
1135         }
1136
1137         cout<<"     H. HELP\n\n";
1138         cout<<"     -- Current matrix is the "
1139             << menu.opt[matn -1].title << " ";
1140
1141         if (matn == menu.noptions)
1142         {
1143             cout<<"(file = "<< userFile <<")";;
1144         }
1145
1146         cout<<"--\n";
1147         choice = utilityObject->getChoice(string("Enter number (or [RETURN] to exit)"));
1148         if (choice == '\n')
1149         {
1150             return matn;
1151         }
1152
1153         option = toupper(choice) - '0';
1154         // Select the matrix series to be using
1155         if (option > 0 && option < menu.noptions)
1156         {
1157             subMatrix->setCurrentNameAndNum(string(menu.opt[i - 1].string), option,
1158                                             alignResidueType, alignType);
1159         }
1160         else if (option == menu.noptions) // Read in a User defined matrix.
1161         {
1162             // NOTE this will be changed to deal with matrix series.
1163             if (subMatrix->getUserMatFromFile(userFile, alignResidueType, alignType))
1164             {
1165                 subMatrix->setCurrentNameAndNum(userFile, option,
1166                                             alignResidueType, alignType);
1167             }
1168         }
1169         else
1170         switch (toupper(choice))
1171         {
1172             case '?':
1173             case 'H':
1174                 clustalObj->getHelp('8');
1175                 break;
1176             default:
1177                 cout<< "\n\nUnrecognised Command\n\n";
1178                 break;
1179         }
1180     }
1181 }
1182
1183 void InteractiveMenu::doSystem()
1184 {
1185     lin1 = "";
1186     utilityObject->getStr(string("\n\nEnter system command"), lin1);
1187
1188     if (lin1.size() > 0)
1189     {
1190         system(lin1.c_str());
1191     }
1192     cout<< "\n\n";
1193 }
1194
1195 void InteractiveMenu::clusteringAlgorithmMenu()
1196 {
1197     string currentAlgorithm = "";
1198     cout<<"****** CLUSTERING ALGORITHM MENU ******\n\n\n";
1199     while (true)
1200     {
1201         if(userParameters->getClusterAlgorithm() == NJ)
1202         {
1203             currentAlgorithm = "Neighbour Joining";
1204         }
1205         else
1206         {
1207             currentAlgorithm = "UPGMA";
1208         }
1209         lin1 = "";
1210         cout<< "\n\n\n";
1211         cout<<" ****** Clustering Algorithms ******\n\n\n";
1212         cout<<"     1. Neighbour Joining \n";
1213         cout<<"     2. UPGMA \n";
1214         cout << "-- Current algorithm is "<< currentAlgorithm << " --\n\n\n";
1215
1216
1217         choice = utilityObject->getChoice(string("Enter number (or [RETURN] to exit)"));
1218         if (choice == '\n')
1219         {
1220             return ;
1221         }
1222         switch (toupper(choice))
1223         {
1224             case '1':
1225                 userParameters->setClusterAlgorithm(NJ);
1226                 break;
1227             case '2':
1228                 userParameters->setClusterAlgorithm(UPGMA);
1229                 break;
1230             default:
1231                 cout<< "\n\nUnrecognised Command\n\n";
1232                 break;
1233         }
1234     }
1235 }
1236
1237 void InteractiveMenu::iterationMenu()
1238 {
1239     string currentIteration = "";
1240     cout<<"****** ITERATION MENU ******\n\n\n";
1241     while (true)
1242     {
1243         if(userParameters->getDoRemoveFirstIteration() == ALIGNMENT)
1244         {
1245             currentIteration = "Alignment iteration";
1246         }
1247         else if(userParameters->getDoRemoveFirstIteration() == TREE)
1248         {
1249             currentIteration = "Tree based iteration";
1250         }
1251         else
1252         {
1253             currentIteration = "None";
1254         }
1255         lin1 = "";
1256         cout<< "\n\n\n";
1257         cout<<" ****** Iteration Choices ******\n\n\n";
1258         cout<<"     1. Off \n";
1259         cout<<"     2. Tree based iteration (iterates each profile alignment step) \n";
1260         cout<<"     3. Alignment iteration (iterates final alignment only) \n\n";
1261         cout << "-- Current selection is "<< currentIteration << " --\n\n\n";
1262
1263
1264         choice = utilityObject->getChoice(string("Enter number (or [RETURN] to exit)"));
1265         if (choice == '\n')
1266         {
1267             return ;
1268         }
1269         switch (toupper(choice))
1270         {
1271             case '1':
1272                 userParameters->setDoRemoveFirstIteration(NONE);
1273                 break;
1274             case '2':
1275                 userParameters->setDoRemoveFirstIteration(TREE);
1276                 break;
1277             case '3':
1278                 userParameters->setDoRemoveFirstIteration(ALIGNMENT);
1279                 break;
1280             default:
1281                 cout<< "\n\nUnrecognised Command\n\n";
1282                 break;
1283         }
1284     }
1285 }
1286
1287 }
1288