2b2874d85add602f6753ae525337a1155d2298ea
braney
  Mon May 25 06:35:18 2020 -0700
allow for fine control of display of non-synonomous changes in mafSnp
display

diff --git src/inc/axt.h src/inc/axt.h
index 5ab86d1..7e6d98a 100644
--- src/inc/axt.h
+++ src/inc/axt.h
@@ -20,30 +20,33 @@
 #ifndef AXT_H
 #define AXT_H
 
 #ifndef LINEFILE_H
 #include "linefile.h"
 #endif 
 
 #ifndef DNASEQ_H
 #include "dnaseq.h"
 #endif
 
 #ifndef CHAIN_H
 #include "chain.h"
 #endif
 
+/*  Matrix made by matblas from blosum62.iij */
+extern char blosumText[];
+
 struct axt
 /* This contains information about one xeno alignment. */
     {
     struct axt *next;
     char *qName;		/* Name of query sequence. */
     int qStart, qEnd;		/* Half open zero=based coordinates. */
     char qStrand;		/* Is this forward or reverse strand + or - */
     char *tName;		/* Name of target. */
     int tStart, tEnd;		/* Target coordinates. */
     char tStrand;               /* Target strand - currently always +. */
     int score;	                /* Score.  Zero for unknown.  Units arbitrary. */
     int symCount;               /* Size of alignments. */
     char *qSym, *tSym;          /* Alignments. */
     int frame;			/* If non-zero then translation frame. */
     };
@@ -256,17 +259,20 @@
 			      struct axtScoreScheme *ss, FILE *f,
 			      boolean reverseTPos, boolean reverseQPos);
 /* Print out an alignment with line-breaks.  If reverseTPos is true, then
  * the sequence has been reverse complemented, so show the coords starting
  * at tEnd and decrementing down to tStart; likewise for reverseQPos. */
 
 double axtIdWithGaps(struct axt *axt);
 /* Return ratio of matching bases to total symbols in alignment. */
 
 double axtCoverage(struct axt *axt, int qSize, int tSize);
 /* Return % of q and t covered. */
 
 void axtOutPretty(struct axt *axt, int lineSize, FILE *f);
 /* Output axt in pretty format. */
 
+struct axtScoreScheme *axtScoreSchemeFromProteinText(char *text, char *fileName);
+/* Parse text into a scoring scheme.  This should be in BLAST protein matrix
+ * format as in blosumText above. */
 #endif /* AXT_H */