--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23/src/tigr/show-aligns.cc	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,635 @@
+//------------------------------------------------------------------------------
+//   Programmer: Adam M Phillippy, The Institute for Genomic Research
+//         File: show-aligns.cc
+//         Date: 10 / 18 / 2002
+//
+//        Usage: show-aligns [options] <deltafile>
+//               Try 'show-aligns -h' for more information
+//
+//  Description: For use in conjunction with the MUMmer package.
+//              "show-aligns" displays human readable information from the
+//             .delta output of the "nucmer" and "promer" programs. Outputs
+//            pairwise alignments to stdout. Works for both nucleotide and
+//           amino-acid alignments.
+//
+//------------------------------------------------------------------------------
+
+#include "delta.hh"
+#include "tigrinc.hh"
+#include "translate.hh"
+#include "sw_alignscore.hh"
+#include <vector>
+#include <algorithm>
+using namespace std;
+
+//------------------------------------------------------------- Constants ----//
+
+const char NUCMER_MISMATCH_CHAR = '^';
+const char NUCMER_MATCH_CHAR = ' ';
+const char PROMER_SIM_CHAR = '+';
+const char PROMER_MISMATCH_CHAR = ' ';
+
+//-- Note: if coord exceeds LINE_PREFIX_LEN - 1 digits,
+//         increase these accordingly
+#define LINE_PREFIX_LEN 11
+#define PREFIX_FORMAT "%-10ld "
+
+#define DEFAULT_SCREEN_WIDTH 60
+int Screen_Width = DEFAULT_SCREEN_WIDTH;
+
+
+
+//------------------------------------------------------ Type Definitions ----//
+struct AlignStats
+     //-- Alignment statistics data structure
+{
+  long int sQ, eQ, sR, eR;              // start and end in Query and Reference
+                                        // relative to the directional strand
+  vector<long int> Delta;               // delta information
+};
+
+
+
+struct sR_Sort
+//-- For sorting alignments by their sR coordinate
+{
+  bool operator( ) (const AlignStats & pA, const AlignStats & pB)
+  {
+    //-- sort sR
+    if ( pA.sR < pB.sR )
+      return true;
+    else
+      return false;
+  }
+};
+
+
+
+struct sQ_Sort
+//-- For sorting alignments by their sQ coordinate
+{
+  bool operator( ) (const AlignStats & pA, const AlignStats & pB)
+  {
+    //-- sort sQ
+    if ( pA.sQ < pB.sQ )
+      return true;
+    else
+      return false;
+  }
+};
+
+
+
+
+//------------------------------------------------------ Global Variables ----//
+bool isSortByQuery = false;              // -q option
+bool isSortByReference = false;          // -r option
+
+int DATA_TYPE = NUCMER_DATA;
+int MATRIX_TYPE = BLOSUM62;
+
+char InputFileName [MAX_LINE];
+char RefFileName [MAX_LINE], QryFileName [MAX_LINE];
+
+
+
+//------------------------------------------------- Function Declarations ----//
+long int toFwd
+     (long int coord, long int len, int frame);
+
+void parseDelta
+     (vector<AlignStats> & Aligns, char * IdR, char * IdQ);
+
+void printAlignments
+     (vector<AlignStats> Aligns, char * R, char * Q);
+
+void printHelp
+     (const char * s);
+
+void printUsage
+     (const char * s);
+
+long int revC
+     (long int coord, long int len);
+
+
+
+//-------------------------------------------------- Function Definitions ----//
+int main
+     (int argc, char ** argv)
+{
+  long int i;
+
+  FILE * RefFile = NULL;
+  FILE * QryFile = NULL;
+
+  vector<AlignStats> Aligns;
+
+  char * R, * Q;
+
+  long int InitSize = INIT_SIZE;
+  char Id [MAX_LINE], IdR [MAX_LINE], IdQ [MAX_LINE];
+
+  //-- Parse the command line arguments
+  {
+    int ch, errflg = 0;
+    optarg = NULL;
+
+    while ( !errflg  &&  ((ch = getopt
+                           (argc, argv, "hqrw:x:")) != EOF) )
+      switch (ch)
+        {
+        case 'h' :
+	  printHelp (argv[0]);
+	  exit (EXIT_SUCCESS);
+          break;
+
+	case 'q' :
+	  isSortByQuery = true;
+	  break;
+
+	case 'r' :
+	  isSortByReference = true;
+	  break;
+
+	case 'w' :
+	  Screen_Width = atoi (optarg);
+	  if ( Screen_Width <= LINE_PREFIX_LEN )
+	    {
+	      fprintf(stderr,
+		      "WARNING: invalid screen width %d, using default\n",
+		      DEFAULT_SCREEN_WIDTH);
+	      Screen_Width = DEFAULT_SCREEN_WIDTH;
+	    }
+	  break;
+
+	case 'x' :
+	  MATRIX_TYPE = atoi (optarg);
+	  if ( MATRIX_TYPE < 1 || MATRIX_TYPE > 3 )
+	    {
+	      fprintf(stderr,
+		      "WARNING: invalid matrix type %d, using default\n",
+		      MATRIX_TYPE);
+	      MATRIX_TYPE = BLOSUM62;
+	    }
+	  break;
+
+        default :
+          errflg ++;
+        }
+
+    if ( errflg > 0  ||  argc - optind != 3 )
+      {
+        printUsage (argv[0]);
+        exit (EXIT_FAILURE);
+      }
+
+    if ( isSortByQuery  &&  isSortByReference )
+      fprintf (stderr,
+               "WARNING: both -r and -q were passed, -q ignored\n");
+  }
+
+  strcpy (InputFileName, argv[optind ++]);
+  strcpy (IdR, argv[optind ++]);
+  strcpy (IdQ, argv[optind ++]);
+
+  //-- Read in the alignment data
+  parseDelta (Aligns, IdR, IdQ);
+
+  //-- Find, and read in the reference sequence
+  RefFile = File_Open (RefFileName, "r");
+  InitSize = INIT_SIZE;
+  R = (char *) Safe_malloc ( sizeof(char) * InitSize );
+  while ( Read_String (RefFile, R, InitSize, Id, FALSE) )
+    if ( strcmp (Id, IdR) == 0 )
+      break;
+  fclose (RefFile);
+  if ( strcmp (Id, IdR) != 0 )
+    {
+      fprintf(stderr,"ERROR: Could not find %s in the reference file\n", IdR);
+      exit (EXIT_FAILURE);
+    }
+
+
+  //-- Find, and read in the query sequence
+  QryFile = File_Open (QryFileName, "r");
+  InitSize = INIT_SIZE;
+  Q = (char *) Safe_malloc ( sizeof(char) * InitSize );
+  while ( Read_String (QryFile, Q, InitSize, Id, FALSE) )
+    if ( strcmp (Id, IdQ) == 0 )
+      break;
+  fclose (QryFile);
+  if ( strcmp (Id, IdQ) != 0 )
+    {
+      fprintf(stderr,"ERROR: Could not find %s in the query file\n", IdQ);
+      exit (EXIT_FAILURE);
+    }
+
+  //-- Sort the alignment regions if user passed -r or -q option
+  if ( isSortByReference )
+    sort (Aligns.begin( ), Aligns.end( ), sR_Sort( ));
+  else if ( isSortByQuery )
+    sort (Aligns.begin( ), Aligns.end( ), sQ_Sort( ));
+
+
+  //-- Output the alignments to stdout
+  printf("%s %s\n\n", RefFileName, QryFileName);
+  for ( i = 0; i < Screen_Width; i ++ ) printf("=");
+  printf("\n-- Alignments between %s and %s\n\n", IdR, IdQ);
+  printAlignments (Aligns, R, Q);
+  printf("\n");
+  for ( i = 0; i < Screen_Width; i ++ ) printf("=");
+  printf("\n");
+
+  return EXIT_SUCCESS;
+}
+
+
+
+
+long int toFwd
+     (long int coord, long int len, int frame)
+
+     // Switch relative coordinate to reference forward DNA strand
+
+{
+  long int newc = coord;
+
+  if ( DATA_TYPE == PROMER_DATA )
+    newc = newc * 3 - (3 - labs(frame));
+
+  if ( frame < 0 )
+    return revC ( newc, len );
+  else
+    return newc;
+}
+
+
+
+
+void parseDelta
+     (vector<AlignStats> & Aligns, char * IdR, char * IdQ)
+
+     // Read in the alignments from the desired region
+
+{
+  AlignStats aStats;                     //  single alignment region
+  bool found = false;
+
+  DeltaReader_t dr;
+  dr.open (InputFileName);
+  DATA_TYPE = dr.getDataType( ) == NUCMER_STRING ?
+    NUCMER_DATA : PROMER_DATA;
+  strcpy (RefFileName, dr.getReferencePath( ).c_str( ));
+  strcpy (QryFileName, dr.getQueryPath( ).c_str( ));
+
+  while ( dr.readNext( ) )
+    {
+      if ( dr.getRecord( ).idR == IdR  &&
+	   dr.getRecord( ).idQ == IdQ )
+	{
+	  found = true;
+	  break;
+	}
+    }
+  if ( !found )
+    {
+      fprintf(stderr, "ERROR: Could not find any alignments for %s and %s\n",
+	      IdR, IdQ);
+      exit (EXIT_FAILURE);
+    }
+
+  for ( unsigned int i = 0; i < dr.getRecord( ).aligns.size( ); i ++ )
+    {
+      aStats.sR = dr.getRecord( ).aligns[i].sR;
+      aStats.eR = dr.getRecord( ).aligns[i].eR;
+      aStats.sQ = dr.getRecord( ).aligns[i].sQ;
+      aStats.eQ = dr.getRecord( ).aligns[i].eQ;
+
+      aStats.Delta = dr.getRecord( ).aligns[i].deltas;
+
+      //-- Add the new alignment
+      Aligns.push_back (aStats);
+    }
+  dr.close( );
+
+  return;
+}
+
+
+
+
+void printAlignments
+     (vector<AlignStats> Aligns, char * R, char * Q)
+
+     // Print the alignments to the screen
+
+{
+  vector<AlignStats>::iterator Ap;
+  vector<long int>::iterator Dp;
+
+  char * A[7] = {NULL, NULL, NULL, NULL, NULL, NULL, NULL};
+  char * B[7] = {NULL, NULL, NULL, NULL, NULL, NULL, NULL};
+  int Ai, Bi, i;
+
+  char Buff1 [Screen_Width + 1],
+       Buff2 [Screen_Width + 1],
+       Buff3 [Screen_Width + 1];
+
+  int Sign;
+  long int Delta;
+  long int Total, Errors, Remain;
+  long int Pos;
+
+  long int sR, eR, sQ, eQ;
+  long int Apos, Bpos;
+  long int SeqLenR, SeqLenQ;
+  int frameR, frameQ;
+
+  for ( i = 0; i < LINE_PREFIX_LEN; i ++ )
+    Buff3[i] = ' ';
+
+  SeqLenR = strlen (R + 1);
+  SeqLenQ = strlen (Q + 1);
+
+  if ( DATA_TYPE == NUCMER_DATA )
+    {
+      A[1] = R;
+      A[4] = (char *) Safe_malloc ( sizeof(char) * (SeqLenR + 2) );
+      strcpy ( A[4] + 1, A[1] + 1 );
+      A[4][0] = '\0';
+      Reverse_Complement ( A[4], 1, SeqLenR );
+
+      B[1] = Q;
+      B[4] = (char *) Safe_malloc ( sizeof(char) * (SeqLenQ + 2) );
+      strcpy ( B[4] + 1, B[1] + 1 );
+      B[4][0] = '\0';
+      Reverse_Complement ( B[4], 1, SeqLenQ );
+    }
+
+  for ( Ap = Aligns.begin( ); Ap < Aligns.end( ); Ap ++ )
+    {
+      sR = Ap->sR;
+      eR = Ap->eR;
+      sQ = Ap->sQ;
+      eQ = Ap->eQ;
+
+      //-- Get the coords and frame right
+      frameR = 1;
+      if ( sR > eR )
+	{
+	  sR = revC (sR, SeqLenR);
+	  eR = revC (eR, SeqLenR);
+	  frameR += 3;
+	}
+      frameQ = 1;
+      if ( sQ > eQ )
+	{
+	  sQ = revC (sQ, SeqLenQ);
+	  eQ = revC (eQ, SeqLenQ);
+	  frameQ += 3;
+	}
+
+      if ( DATA_TYPE == PROMER_DATA )
+	{
+	  frameR += (sR + 2) % 3;
+	  frameQ += (sQ + 2) % 3;
+
+	  //-- Translate the coordinates from DNA to Amino Acid
+	  //   remeber that eR and eQ point to the last nucleotide in the codon
+	  sR = (sR + 2) / 3;
+	  eR = eR / 3;
+	  sQ = (sQ + 2) / 3;
+	  eQ = eQ / 3;
+	}
+      Ai = frameR;
+      Bi = frameQ;
+      if ( frameR > 3 )
+	frameR = -(frameR - 3);
+      if ( frameQ > 3 )
+	frameQ = -(frameQ - 3);
+
+      //-- Get the sequence
+      if ( A[Ai] == NULL )
+	{
+	  assert ( DATA_TYPE == PROMER_DATA );
+	  A[Ai] = (char *) Safe_malloc ( sizeof(char) * ( SeqLenR / 3 + 2 ) );
+	  A[Ai][0] = '\0';
+	  Translate_DNA ( R, A[Ai], Ai );
+	}
+      if ( B[Bi] == NULL )
+	{
+	  assert ( DATA_TYPE == PROMER_DATA );
+	  B[Bi] = (char *) Safe_malloc ( sizeof(char) * ( SeqLenQ / 3 + 2 ) );
+	  B[Bi][0] = '\0';
+	  Translate_DNA ( Q, B[Bi], Bi );
+	}
+
+
+      //-- Generate the alignment
+      printf("-- BEGIN alignment [ %s%d %ld - %ld | %s%d %ld - %ld ]\n\n\n",
+	     frameR > 0 ? "+" : "-", abs(frameR), Ap->sR, Ap->eR,
+	     frameQ > 0 ? "+" : "-", abs(frameQ), Ap->sQ, Ap->eQ);
+
+      Apos = sR;
+      Bpos = sQ;
+
+      Errors = 0;
+      Total = 0;
+      Remain = eR - sR + 1;
+
+      sprintf(Buff1, PREFIX_FORMAT, toFwd (Apos, SeqLenR, frameR));
+      sprintf(Buff2, PREFIX_FORMAT, toFwd (Bpos, SeqLenQ, frameQ));
+      Pos = LINE_PREFIX_LEN;
+
+      for ( Dp = Ap->Delta.begin( );
+	    Dp < Ap->Delta.end( ) &&
+	    *Dp != 0; Dp ++ )
+	{
+	  Delta = *Dp;
+	  Sign = Delta > 0 ? 1 : -1;
+	  Delta = labs ( Delta );
+
+
+	  //-- For all the bases before the next indel
+	  for ( i = 1; i < Delta; i ++ )
+	    {
+	      if ( Pos >= Screen_Width )
+		{
+		  Buff1[Pos] = Buff2[Pos] = Buff3[Pos] = '\0';
+		  if ( DATA_TYPE == NUCMER_DATA )
+		    printf("%s\n%s\n%s\n\n", Buff1, Buff2, Buff3);
+		  else
+		    printf("%s\n%s\n%s\n\n", Buff1, Buff3, Buff2);
+		  sprintf(Buff1, PREFIX_FORMAT, toFwd (Apos, SeqLenR, frameR));
+		  sprintf(Buff2, PREFIX_FORMAT, toFwd (Bpos, SeqLenQ, frameQ));
+		  Pos = LINE_PREFIX_LEN;
+		}
+
+	      if ( DATA_TYPE == NUCMER_DATA )
+		Buff3[Pos] = A[Ai][Apos] == B[Bi][Bpos] ?
+		  NUCMER_MATCH_CHAR : NUCMER_MISMATCH_CHAR;
+	      else if ( A[Ai][Apos] == B[Bi][Bpos] )
+		Buff3[Pos] = A[Ai][Apos];
+	      else
+		Buff3[Pos] = MATCH_SCORE
+		  [MATRIX_TYPE]
+		  [toupper(A[Ai][Apos]) - 'A']
+		  [toupper(B[Bi][Bpos]) - 'A'] > 0 ?
+		  PROMER_SIM_CHAR : PROMER_MISMATCH_CHAR;
+	      Buff1[Pos] = A[Ai][Apos ++];
+	      Buff2[Pos ++] = B[Bi][Bpos ++];
+	    }
+
+
+	  //-- For the indel
+	  Remain -= i - 1;
+
+	  if ( Pos >= Screen_Width )
+	    {
+	      Buff1[Pos] = Buff2[Pos] = Buff3[Pos] = '\0';
+	      if ( DATA_TYPE == NUCMER_DATA )
+		printf("%s\n%s\n%s\n\n", Buff1, Buff2, Buff3);
+	      else
+		printf("%s\n%s\n%s\n\n", Buff1, Buff3, Buff2);
+	      sprintf(Buff1, PREFIX_FORMAT, toFwd (Apos, SeqLenR, frameR));
+	      sprintf(Buff2, PREFIX_FORMAT, toFwd (Bpos, SeqLenQ, frameQ));
+	      Pos = LINE_PREFIX_LEN;
+	    }
+
+	  if ( Sign == 1 )
+	    {
+	      if ( DATA_TYPE == NUCMER_DATA )
+		Buff3[Pos] = NUCMER_MISMATCH_CHAR;
+	      else
+		Buff3[Pos] = PROMER_MISMATCH_CHAR;
+	      Buff1[Pos] = A[Ai][Apos ++];
+	      Buff2[Pos ++] = '.';
+	      Remain --;
+	    }
+	  else
+	    {
+	      if ( DATA_TYPE == NUCMER_DATA )
+		Buff3[Pos] = NUCMER_MISMATCH_CHAR;
+	      else
+		Buff3[Pos] = PROMER_MISMATCH_CHAR;
+	      Buff1[Pos] = '.';
+	      Buff2[Pos ++] = B[Bi][Bpos ++];
+	      Total ++;
+	    }
+	}
+
+
+      //-- For all the bases remaining after the last indel
+      for ( i = 0; i < Remain; i ++ )
+	{
+	  if ( Pos >= Screen_Width )
+	    {
+	      Buff1[Pos] = Buff2[Pos] = Buff3[Pos] = '\0';
+	      if ( DATA_TYPE == NUCMER_DATA )
+		printf("%s\n%s\n%s\n\n", Buff1, Buff2, Buff3);
+	      else
+		printf("%s\n%s\n%s\n\n", Buff1, Buff3, Buff2);
+	      sprintf(Buff1, PREFIX_FORMAT, toFwd (Apos, SeqLenR, frameR));
+	      sprintf(Buff2, PREFIX_FORMAT, toFwd (Bpos, SeqLenQ, frameQ));
+	      Pos = LINE_PREFIX_LEN;
+	    }
+	  
+	  if ( DATA_TYPE == NUCMER_DATA )
+	    Buff3[Pos] = A[Ai][Apos] == B[Bi][Bpos] ?
+	      NUCMER_MATCH_CHAR : NUCMER_MISMATCH_CHAR;
+	  else if ( A[Ai][Apos] == B[Bi][Bpos] )
+	    Buff3[Pos] = A[Ai][Apos];
+	  else
+	    Buff3[Pos] = MATCH_SCORE
+	      [MATRIX_TYPE]
+	      [toupper(A[Ai][Apos]) - 'A']
+	      [toupper(B[Bi][Bpos]) - 'A'] > 0 ?
+	      PROMER_SIM_CHAR : PROMER_MISMATCH_CHAR;
+	  Buff1[Pos] = A[Ai][Apos ++];
+	  Buff2[Pos ++] = B[Bi][Bpos ++];
+	}
+
+
+      //-- For the remaining buffered output
+      if ( Pos > LINE_PREFIX_LEN )
+	{
+	  Buff1[Pos] = Buff2[Pos] = Buff3[Pos] = '\0';
+	  if ( DATA_TYPE == NUCMER_DATA )
+	    printf("%s\n%s\n%s\n\n", Buff1, Buff2, Buff3);
+	  else
+	    printf("%s\n%s\n%s\n\n", Buff1, Buff3, Buff2);
+	  sprintf(Buff1, PREFIX_FORMAT, toFwd (Apos, SeqLenR, frameR));
+	  sprintf(Buff2, PREFIX_FORMAT, toFwd (Bpos, SeqLenQ, frameQ));
+	  Pos = LINE_PREFIX_LEN;
+	}
+
+      printf("\n--   END alignment [ %s%d %ld - %ld | %s%d %ld - %ld ]\n",
+	     frameR > 0 ? "+" : "-", abs(frameR), Ap->sR, Ap->eR,
+	     frameQ > 0 ? "+" : "-", abs(frameQ), Ap->sQ, Ap->eQ);
+    }
+
+  //-- Free the sequences, except for the originals
+  for ( i = 0; i < 7; i ++ )
+    {
+      if ( (DATA_TYPE != NUCMER_DATA || i != 1)  &&  A[i] != NULL )
+	free ( A[i] );
+      if ( (DATA_TYPE != NUCMER_DATA || i != 1)  &&  B[i] != NULL )
+	free ( B[i] );
+    }
+
+  return;
+}
+
+
+
+
+void printHelp
+     (const char * s)
+
+      //  Display the program's help information to stderr
+
+{
+  fprintf (stderr,
+           "\nUSAGE: %s  [options]  <deltafile>  <ref ID>  <qry ID>\n\n", s);
+  fprintf (stderr,
+       "-h            Display help information\n"
+       "-q            Sort alignments by the query start coordinate\n"
+       "-r            Sort alignments by the reference start coordinate\n"
+       "-w int        Set the screen width - default is 60\n"
+       "-x int        Set the matrix type - default is 2 (BLOSUM 62),\n"
+       "              other options include 1 (BLOSUM 45) and 3 (BLOSUM 80)\n"
+       "              note: only has effect on amino acid alignments\n\n");
+  fprintf (stderr,
+       "  Input is the .delta output of either the \"nucmer\" or the\n"
+       "\"promer\" program passed on the command line.\n"
+       "  Output is to stdout, and consists of all the alignments between the\n"
+       "query and reference sequences identified on the command line.\n"
+       "  NOTE: No sorting is done by default, therefore the alignments\n"
+       "will be ordered as found in the <deltafile> input.\n\n");
+  return;
+}
+
+
+
+
+void printUsage
+     (const char * s)
+
+      //  Display the program's usage information to stderr.
+
+{
+  fprintf (stderr,
+           "\nUSAGE: %s  [options]  <deltafile>  <ref ID>  <qry ID>\n\n", s);
+  fprintf (stderr, "Try '%s -h' for more information.\n", s);
+  return;
+}
+
+
+
+
+long int revC
+     (long int coord, long int len)
+{
+  return len - coord + 1;
+}