Merge branch 'development'

mbrazeau · Mar 16, 2018 · cff054e · cff054e
2 parents 21726e7 + d3ab3e7
commit cff054e
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Showing 3 changed files with 63 additions and 24 deletions.
diff --git a/src/fitch.c b/src/fitch.c
@@ -197,6 +197,57 @@ int mpl_nadown1_simpl
 }
 
 
+int mpl_nadown2_simpl
+(MPLndsets* lset, MPLndsets* rset, MPLndsets* nset, MPLpartition* part)
+{
+    int             i       = 0;
+    int             j       = 0;
+    int             steps   = 0;
+    const int*      indices = part->charindices;
+    int             nchars  = part->ncharsinpart;
+    MPLstate*       left    = lset->downpass2;
+    MPLstate*       right   = rset->downpass2;
+    MPLstate*       setstat = nset->uppass1;
+    MPLstate*       npre    = nset->downpass2;
+    MPLstate*       stacts  = nset->subtree_actives;
+    MPLstate*       tstatcs = nset->temp_subtr_actives;
+    MPLstate*       lacts   = lset->subtree_actives;
+    MPLstate*       racts   = rset->subtree_actives;
+    MPLstate        temp    = 0;
+    unsigned long*  weights = part->intwts;
+
+    for (i = 0; i < nchars; ++i) {
+
+        j = indices[i];
+
+        // TODO: Extend and test
+        if (setstat[j] != NA) { // If the node is not in the inapplicable state
+            // Do regular Fitch parsimony (sort of)
+            if ((temp = (left[j] & right[j]) & ISAPPLIC)) {
+                npre[j] = temp;
+            }
+            else {
+                npre[j] = (left[j] | right[j]);
+                if (left[j] & ISAPPLIC && right[j] & ISAPPLIC) {
+                    if (!(npre[j] & NA)) {
+                        steps += weights[j];
+                    }
+                }
+            }
+        }
+        else {
+            npre[j] = NA;
+        }
+
+#ifdef DEBUG
+        assert(npre[j]);
+#endif
+    }
+
+    return 0;
+}
+
+
 int mpl_NA_fitch_first_update_downpass
 (MPLndsets* lset, MPLndsets* rset, MPLndsets* nset, MPLpartition* part)
 {
@@ -327,24 +378,12 @@ int mpl_naupp1_simpl
 
         j = indices[i];
 
-        // TODO: Rewrite this
-        if (anc[j] == NA) {
-            nifin[j] = npre[j];
-            if (left[j] & right[j] & NA) {
-                nifin[j] = NA;
-            }
+        if (anc[j] == NA && npre[j] & NA) {
+            nifin[j] = NA;
         }
         else {
-            nifin[j] = npre[j] & anc[j];
-
-            if (nifin[j] != anc[j]) {
-                nifin[j] = (npre[j] | (anc[j] & (left[j] | right[j])));
-            }
-            else {
-                nifin[j] = nifin[j] | anc[j];
-            }
+            nifin[j] = nifin[j] & ISAPPLIC;
         }
-
         // Store the set for restoration during tree searches.
         nfint[j] = nifin[j];
 

diff --git a/src/morphydefs.h b/src/morphydefs.h
@@ -27,12 +27,14 @@ typedef double Mflt;
 
 typedef unsigned int MPLstate;
 
-#define NA              ((MPLstate)0b1)
+#define NA              ((MPLstate)1)
 #define MISSING         ((MPLstate)~0)
 #define ISAPPLIC        (((MPLstate)~0)^NA)
+#define UNKNOWN         ISAPPLIC
 #define MAXSTATES       (CHAR_BIT * sizeof(MPLstate))
 #define DEFAULTGAP      '-'
 #define DEFAULTMISSING  '?'
+#define DEFAULTUNKNOWN  '+'
 #define DEFAULCHARTYPE  FITCH_T
 #define DEFAULTWTBASE   1
 #define NACUTOFF        2   // The max number of NA tokens that can be ignored
@@ -45,7 +47,7 @@ typedef unsigned int MPLstate;
                                                steer pretty clear of epsilon */
 
 typedef struct MPLndsets MPLndsets;
-typedef struct partition_s MPLpartition;
+typedef struct MPLpartition MPLpartition;
 // Evaluator function pointers
 typedef int (*MPLdownfxn)
             (MPLndsets*     lset,
@@ -110,8 +112,7 @@ typedef struct {
 } MPLcupdate;
 
 
-typedef struct partition_s MPLpartition;
-typedef struct partition_s {
+struct MPLpartition {
 
     MPLchtype       chtype;         /*!< The optimality type used for this partition. */
     bool            isNAtype;       /*!< This character should be treated as having inapplicable data. */ 
@@ -145,11 +146,10 @@ typedef struct partition_s {
     MPLloclfxn      loclfxn;
     MPLpartition*   next;
 
-} MPLpartition;
-
+};
 
 
-typedef struct MPLndsets {
+struct MPLndsets {
 
     bool        updated;
     int         steps_to_recall;
@@ -169,7 +169,7 @@ typedef struct MPLndsets {
     char**      upp1str;
     char**      upp2str;
 
-} MPLndsets;
+};
 
 
 typedef struct mpl_matrix_s {

diff --git a/src/statedata.c b/src/statedata.c
@@ -561,7 +561,7 @@ int mpl_set_gap_push(Morphyp handl)
 int mpl_get_uncorrected_shift_value(char symb, Morphyp handl)
 {
     // Gets the raw shift value as determined by the order in the symbols list
-    assert(symb != DEFAULTGAP && symb != DEFAULTMISSING);
+    assert(symb != DEFAULTGAP && symb != DEFAULTMISSING && symb != DEFAULTUNKNOWN);
     int shift = 0;
     char* symbols = mpl_get_symbols((Morphy)handl);