JWS-112 Bumping version of ClustalO (src, binaries and windows) to version 1.2.4.

[jabaws.git] / binaries / src / clustalo / src / clustal / seq.h

diff --git a/binaries/src/clustalo/src/clustal/seq.h b/binaries/src/clustalo/src/clustal/seq.h
index af2c98a..8f9fe1b 100644 (file)
--- a/binaries/src/clustalo/src/clustal/seq.h
+++ b/binaries/src/clustalo/src/clustal/seq.h
@@ -13,7 +13,7 @@
  ********************************************************************/
 
 /*
- *  RCS $Id: seq.h 234 2011-04-13 05:26:16Z andreas $
+ *  RCS $Id: seq.h 296 2014-10-07 12:15:41Z fabian $
  */
 
 #ifndef CLUSTALO_SEQ_H
@@ -62,6 +62,10 @@ typedef struct {
      */
     char **orig_seq;
     
+  /** order in which sequences appear in guide-tree
+   */
+  int *tree_order;
+
     /**
      * @brief Squid's sequence info structure.
      * Index range: 0--nseq-1.
@@ -107,6 +111,10 @@ typedef struct {
      *
      */
     SQINFO *sqinfo; 
+
+  /* HMM batch information */
+  char ***pppcHMMBNames;
+  int **ppiHMMBindex;
 } mseq_t;
 
 extern void
@@ -125,8 +133,9 @@ extern const char *
 SeqTypeToStr(int seqtype);
 
 extern int
-ReadSequences(mseq_t *prMSeq_p, char *pcSeqFile, int iSeqType,
-  int iMaxNumSeq, int iMaxSeqLen);
+ReadSequences(mseq_t *prMSeq_p, char *pcSeqFile, 
+              int iSeqType,  int iSeqFmt, bool bIsProfile, bool bDealignInputSeqs, 
+              int iMaxNumSeq, int iMaxSeqLen, char *pcHMMBatch);
 
 extern void
 NewMSeq(mseq_t **mseq);
@@ -144,7 +153,7 @@ extern int
 FindSeqName(char *seqname, mseq_t *mseq);
 
 extern int
-WriteAlignment(mseq_t *mseq, const char *aln_outfile, int msafile_format);
+WriteAlignment(mseq_t *mseq, const char *aln_outfile, int msafile_format, int iWrap, bool bResno);
 
 extern void
 DealignSeq(char *seq);
@@ -159,6 +168,6 @@ void
 JoinMSeqs(mseq_t **prMSeqDest_p, mseq_t *prMSeqToAdd);
 
 bool
-SeqsAreAligned(mseq_t *prMSeq);
+SeqsAreAligned(mseq_t *prMSeq, bool bIsProfile, bool bDealignInputSeqs);
 
 #endif