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

[jabaws.git] / binaries / src / clustalo / src / clustal-omega.h

diff --git a/binaries/src/clustalo/src/clustal-omega.h b/binaries/src/clustalo/src/clustal-omega.h
index 4f38e6f..d0d483c 100644 (file)
--- a/binaries/src/clustalo/src/clustal-omega.h
+++ b/binaries/src/clustalo/src/clustal-omega.h
@@ -26,6 +26,7 @@
 #ifdef HAVE_OPENMP
 #include <omp.h>
 #endif
+#include <stdbool.h>
 
 #include "clustal-omega-config.h"
 
@@ -62,6 +63,9 @@
 
 extern int iNumberOfThreads;
 
+/* output order */
+enum {INPUT_ORDER = 0, TREE_ORDER};
+
 
 /** user/commandline options
  *
@@ -85,17 +89,31 @@ typedef struct {
      */
     /** clustering type (from cmdline arg) */
     int iClusteringType;
+    /** number of sequences in cluster */
+    int iClustersizes; 
+    /** file with clustering information */
+    char *pcClustfile; 
+    /** use transitivity */
+    int iTransitivity; 
+    /** file with posterior probability information */
+    char *pcPosteriorfile; 
     /** pairwise distance method */
     int iPairDistType;
     /** use mbed-like clustering */
     bool bUseMbed;
     /** use mbed-like clustering also during iteration */
     bool bUseMbedForIteration;
+    /** pile-up flag */
+    bool bPileup;
     /** guidetree output file */
     char *pcGuidetreeOutfile;
     /** guidetree input file */
     char *pcGuidetreeInfile;
-    
+    /** use Kimura corrected distance */
+    bool bUseKimura;
+    /** print percentage identity */
+    bool bPercID;
+
     /* HMMs
      */
     /** HMM input files. index range: 0..iHMMInputFiles */
@@ -103,6 +121,8 @@ typedef struct {
     /** number of provided HMM input files. not really a user
        option but need for ppcHMMInput */
     int iHMMInputFiles;
+    /** HMM batch-file, specify HMMs for individual sequences. FS, r291 -> */
+    char *pcHMMBatch;
 
     /* Iteration
      */
@@ -115,8 +135,7 @@ typedef struct {
     /** max number of guidetree iterations */
        int iMaxGuidetreeIterations;
     
-    /** max MAC RAM (maximum amount of RAM set aside for MAC algorithm) */
-    int iMacRam; /* FS, r240 -> */
+    hhalign_para rHhalignPara;
 
     /* changes here will have to be reflected in FreeAlnOpts(),
         * SetDefaultAlnOpts(), AlnOptsLogicCheck() etc 
@@ -125,8 +144,6 @@ typedef struct {
 
 
 
-
-
 extern void 
 PrintLongVersion(char *pcStr, int iSize);
 
@@ -151,17 +168,19 @@ SequentialAlignmentOrder(int **piOrderLR_p, int iNumSeq);
 extern int
 AlignmentOrder(int **piOrderLR_p, double **pdSeqWeights_p, mseq_t *prMSeq,
                int iPairDistType, char *pcDistmatInfile, char *pcDistmatOutfile,
-               int iClusteringType, char *pcGuidetreeInfile, char *pcGuidetreeOutfile,
-               bool bUseMBed);
+               int iClusteringType, int iClustersizes,
+               char *pcGuidetreeInfile, char *pcGuidetreeOutfile, char *pcClusterFile,
+               bool bUseMBed, bool bPercID);
 
 extern int
 Align(mseq_t *prMSeq, 
       mseq_t *prMSeqProfile,
-         opts_t *prOpts,
-      hhalign_para rHhalignPara);
+         opts_t *prOpts);
 
 extern int
 AlignProfiles(mseq_t *prMSeqProfile1, 
                          mseq_t *prMSeqProfile2, hhalign_para rHhalignPara);
 
 #endif
+extern int
+ReadPseudoCountParams(hhalign_para *rHhalignPara_p, char *pcPseudoFile);