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Text File  |  1996-07-05  |  3KB  |  174 lines
  1. // USeqReader.p 
  2. // by d.g.gilbert, Oct 1990 
  3.  
  4.  
  5. UNIT USeqReader;
  6. INTERFACE
  7.  
  8.  
  9. #ifndef __Types__
  10. #include <Types.h>
  11. #endif
  12.  
  13. #ifndef __Memory__
  14. #include <Memory.h>
  15. #endif
  16.  
  17. #ifndef __QuickDraw__
  18. #include <QuickDraw.h>
  19. #endif
  20.  
  21. #ifndef __ToolUtils__
  22. #include <ToolUtils.h>
  23. #endif
  24.  
  25. #ifndef __OSUtils__
  26. #include <OSUtils.h>
  27. #endif
  28.  
  29. #ifndef __Resources__
  30. #include <Resources.h>
  31. #endif
  32.  
  33. #ifndef __Packages__
  34. #include <Packages.h>
  35. #endif
  36.  
  37. #ifndef __Files__
  38. #include <Files.h>
  39. #endif
  40.  
  41. #ifndef __Printing__
  42. #include <Printing.h>
  43. #endif
  44.  
  45. #ifndef __TextEdit__
  46. #include <TextEdit.h>
  47. #endif
  48.  
  49. #ifndef __Controls__
  50. #include <Controls.h>
  51. #endif
  52.  
  53. #ifndef __Aliases__
  54. #include <Aliases.h>
  55. #endif
  56.  
  57. #ifndef __Editions__
  58. #include <Editions.h>
  59. #endif
  60.  
  61. #ifndef __Events__
  62. #include <Events.h>
  63. #endif
  64.  
  65. #ifndef __Notification__
  66. #include <Notification.h>
  67. #endif
  68.  
  69. #ifndef __AppleEvents__
  70. #include <AppleEvents.h>
  71. #endif
  72.  
  73. #ifndef __Processes__
  74. #include <Processes.h>
  75. #endif
  76.  
  77. #ifndef __Balloons__
  78. #include <Balloons.h>
  79. #endif
  80.  
  81. #ifndef __MacAppTypes__
  82. #include <MacAppTypes.h>
  83. #endif
  84.  
  85. #ifndef __UPascalObject__
  86. #include <UPascalObject.h>
  87. #endif
  88.  
  89. #ifndef __UObject__
  90. #include <UObject.h>
  91. #endif
  92.  
  93. #ifndef __UEventHandler__
  94. #include <UEventHandler.h>
  95. #endif
  96. USES UList, UAdorners, UStream, UGeometry,
  97.     UEvent, UCommand, UCommandHandler,
  98.     UView,  UBehavior, UTEView, UTECommands,
  99.     UMacAppUtilities, UPatch, UFailure, UMacAppGlobals,
  100.         
  101.     UFile, UApplication,
  102.     UPrintHandler, UPrinting,
  103.     UWindow, UMenuMgr, UMemory, UErrorMgr,
  104.         
  105.     /*$U $$Shell(UStd)UStandard.p */ UStandard,
  106.     
  107.     USequence();
  108.  
  109.  
  110. CONST
  111.  
  112.     /*formats*/    
  113.  kIG            ==  1;
  114.  kGenBank       ==  2;
  115.  kNBRF          ==  3;
  116.  kEMBL          ==  4;
  117.  kGCG           ==  5;
  118.  kStrider       ==  6;
  119.  kFitch         ==  7;
  120.  kPearson       ==  8;
  121.  kZuker         ==  9;
  122.  kOlsen         ==  10;
  123.  kPhylip2       ==  11;
  124.  kPhylip4       ==  12;
  125.  kPhylip3       ==  kPhylip4;
  126.  kPhylip        ==  kPhylip4;
  127.  kPlain         ==  13;  // keep this at #13 
  128.  kPIR           ==  14;
  129.  kMSF           ==  15;
  130.  kASN1          ==  16;
  131.  kPAUP          ==  17;
  132.  kPretty        ==  18;
  133.  
  134.  kMaxFormat     ==  18;
  135.  kMinFormat     ==  1;
  136.  kNoformat      ==  -1;    // format not tested 
  137.  kUnknown       ==  0;     // format not determinable 
  138.  
  139.  kASNseqentry   ==  51;
  140.  kASNseqset     ==  52;
  141.  kPhylipInterleave == 61;
  142.  kPhylipSequential == 62;
  143.  
  144.  
  145.  
  146.     pascal integer SeqFileFormatWrapper( longint aRefNum, boolean RefIsHandle) 
  147.     
  148.     pascal integer ReadSeqFile( longint aFileRef, Boolean RefIsHandle, TList aSeqList) 
  149.  
  150.     pascal void    WriteSeqHeader( longint fref, boolean RefIsHandle,
  151.                                 integer        format; integer nseqs,  nbases: longint; Str63 outputName,
  152.                                 Boolean VAR needSameSize, isInterleaved)
  153.                                 
  154.     pascal void    WriteSeqTrailer( longint fref, boolean RefIsHandle,
  155.                                 integer        format, nseqs, nlinesperseq;  longint nbases)
  156.                                 
  157.     pascal void WriteSeqWrapper( fref    : longint; boolean RefIsHandle,
  158.                                 seq        : charsPtr; longint seqlen,
  159.                                 integer        inform;     //format of input seq
  160.                                 integer        outform; //format for output seq
  161.                                 charsPtr seqid)
  162.                                 
  163.     pascal void    DoInterleave( fref    : longint; boolean RefIsHandle,
  164.                                 integer        outform, seqtype, nseqs; longint nbases,
  165.                                 integer        nlines, noutindex; Handle outindex, integer fromFileRef)
  166.                             
  167.         
  168. IMPLEMENTATION
  169.  
  170.         // see USeqReader.cp/.h 
  171.         // $ I USeqReader.inc.p 
  172.  
  173. }
  174.