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support for ends-free alignment

svn path=/bioperl-ext/trunk/; revision=669
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1 parent c233d91 commit c916912f6b46a748d798eeb74bd792ba1a18724a ymc committed Feb 11, 2006
Showing with 411 additions and 28 deletions.
  1. +6 −0 Bio/Ext/Align/Align.xs
  2. +2 −0 Bio/Ext/Align/libs/dpalign.h
  3. +373 −24 Bio/Ext/Align/libs/linspc.c
  4. +30 −4 Bio/Ext/Align/test.pl
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@@ -3326,6 +3326,9 @@ Align_DNA_Sequences(seq1, seq2, match, mismatch, gap, ext, alg)
case 2:
RETVAL = dpAlign_Global_DNA_MillerMyers(seq1, seq2, match, mismatch, gap, ext);
break;
+ case 3:
+ RETVAL = dpAlign_EndsFree_DNA_MillerMyers(seq1, seq2, match, mismatch, gap, ext);
+ break;
default:
RETVAL = dpAlign_Local_DNA_MillerMyers(seq1, seq2, match, mismatch, gap, ext);
break;
@@ -3347,6 +3350,9 @@ Align_Protein_Sequences(seq1, seq2, matrix, alg)
case 2:
RETVAL = dpAlign_Global_Protein_MillerMyers(seq1, seq2, matrix);
break;
+ case 3:
+ RETVAL = dpAlign_EndsFree_Protein_MillerMyers(seq1, seq2, matrix);
+ break;
default:
RETVAL = dpAlign_Local_Protein_MillerMyers(seq1, seq2, matrix);
break;
@@ -51,8 +51,10 @@ typedef struct _dpAlign_ScoringMatrix {
dpAlign_AlignOutput * dpAlign_Local_DNA_MillerMyers(char *, char *, int, int, int, int);
dpAlign_AlignOutput * dpAlign_Global_DNA_MillerMyers(char *, char *, int, int, int, int);
+dpAlign_AlignOutput * dpAlign_EndsFree_DNA_MillerMyers(char *, char *, int, int, int, int);
dpAlign_AlignOutput * dpAlign_Local_Protein_MillerMyers(char *, char *, dpAlign_ScoringMatrix *);
dpAlign_AlignOutput * dpAlign_Global_Protein_MillerMyers(char *, char *, dpAlign_ScoringMatrix *);
+dpAlign_AlignOutput * dpAlign_EndsFree_Protein_MillerMyers(char *, char *, dpAlign_ScoringMatrix *);
dpAlign_SequenceProfile * dpAlign_Protein_Profile(char *, dpAlign_ScoringMatrix *);
int dpAlign_Local_Protein_PhilGreen(dpAlign_SequenceProfile *, char *);
dpAlign_SequenceProfile * dpAlign_DNA_Profile(char *, int, int, int, int);
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