Changed default to use joinAlernate. Seems to be working much better …

…now that final states assignment issue was fixed
amnh · Jul 4, 2023 · b21f8e9 · b21f8e9
1 parent 61da923
commit b21f8e9
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Showing 5 changed files with 10 additions and 8 deletions.
diff --git a/pkg/PhyGraph/Search/GeneticAlgorithm.hs b/pkg/PhyGraph/Search/GeneticAlgorithm.hs
@@ -103,7 +103,7 @@ geneticAlgorithm inGS inData rSeed doElitist maxNetEdges keepNum popSize generat
             recombineSwap = getRandomElement (seedList !! 4) [None, NNI, SPR] --  these take too long, "tbr", "alternate"]
 
             -- options to join via union choices or all in fuse
-            joinType =  getRandomElement (seedList !! 6) [JoinPruned, JoinAll ]
+            joinType =  getRandomElement (seedList !! 6) [JoinAlternate, JoinAll ]
 
             doSteepest = True
             returnBest = False

diff --git a/pkg/PhyGraph/Search/Refinement.hs b/pkg/PhyGraph/Search/Refinement.hs
@@ -252,7 +252,7 @@ fuseGraphs inArgs inGS inData rSeed inGraphList
                joinType
                  | any ((=="joinall").fst) lcArgList = JoinAll
                  | any ((=="joinpruned").fst) lcArgList = JoinPruned
-                 | otherwise = JoinAll
+                 | otherwise = JoinAlternate
 
                -- set implied alignment swapping
                doIA' = any ((=="ia").fst) lcArgList

diff --git a/pkg/PhyGraph/Search/SwapMaster.hs b/pkg/PhyGraph/Search/SwapMaster.hs
@@ -102,7 +102,7 @@ swapMaster inArgs inGS inData rSeed inGraphListInput =
                  | any ((=="joinall").fst) lcArgList = JoinAll
                  | any ((=="joinpruned").fst) lcArgList = JoinPruned
                  | any ((=="joinalternate").fst) lcArgList = JoinAlternate
-                 | otherwise = JoinAll --others miss too much--need to refine unions
+                 | otherwise = JoinAlternate 
 
 
                -- randomize split graph and rejoin edges, defualt to randomize

diff --git a/pkg/PhyGraph/Utilities/Utilities.hs b/pkg/PhyGraph/Utilities/Utilities.hs
@@ -71,7 +71,7 @@ import qualified Utilities.LocalGraph        as LG
 -- assumes all indexing is the same between the simple and decorated graph
 -- done recusively until no minLength == zero edges so edges renumbered properly
 -- network edges, pendant edges and root edges, are not collapsed
--- this wierd thype is to allow for polymorphism in graph type--basiclly a general phylogenetic graph
+-- this wierd thype is to allow for polymorphism in graph type--basically a general phylogenetic graph
 collapseGraph :: GenPhyloGraph a b 
                  -> GenPhyloGraph a b
 collapseGraph inPhylograph@(inSimple, inC, inDecorated, inD, inE, inF) =

diff --git a/testData/charWag.pg b/testData/charWag.pg
@@ -28,12 +28,12 @@ set(seed:1666899539)
 
 --set(dynamicEpsilon:0.0)
 
-set(useIA:False)
+--set(useIA:False)
 
 -- For network testing
 --set (outgroup:"one")
 --set(graphtype:hardwired)
-set(graphtype:softwired)
+--set(graphtype:softwired)
 --Set(Compressresolutions:True)
 --set(graphFactor:NoPenalty)
 --set(rootcost:ml)
@@ -49,9 +49,11 @@ build(replicates:10)
 
 --set(multitraverse:false)
 
+fuse(tbr)
+
 --search(minutes:1)
 --build(replicates:10)
-refine(netadd, atrandom, maxnetedges:5)
+--refine(netadd, atrandom, maxnetedges:5)
 --fuse(tbr)
 --swap()
 
@@ -64,7 +66,7 @@ refine(netadd, atrandom, maxnetedges:5)
 select(best)
 report("test0-data.csv", data, overwrite)
 report("test0-crossrefs.csv", crossrefs, overwrite)
-report("test0-serach.csv", search, overwrite)
+report("test0-search.csv", search, overwrite)
 --report("test0-wag.txt", overwrite, graphs, ascii)
 report("test0-wag.dot", overwrite, graphs, dotpdf, nocollapse)
 --report("test0-wag.tre", overwrite, graphs, newick, nohtulabels, nobraNCHLENGTHS, collapse)