diff --git a/ChangeLog.md b/ChangeLog.md
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -5,6 +5,13 @@
## Unreleased changes
+## Version 0.6.1.1
+
+- Remove plotting functionality (gnuplot incompatible with ghc921).
+- Read files strictly.
+- Refactor; flatten model hierarchy.
+
+
## Version 0.6.1.0
- Split `ELynx.Tools` into separate modules because the package will be reduced.
diff --git a/README.md b/README.md
--- a/README.md
+++ b/README.md
@@ -2,7 +2,7 @@
# The ELynx Suite
-Version: 0.6.0.0.
+Version: 0.6.1.1.
Reproducible evolution made easy.
@@ -69,15 +69,16 @@
# Get help
- cabal exec slynx -- --help
+ cabal run slynx -- --help
# OR: stack exec slynx -- --help
# OR: slynx --help
- ELynx Suite version 0.6.0.0.
+ Up to date
+ ELynx Suite version 0.6.1.1.
Developed by Dominik Schrempf.
- Compiled on September 4, 2021, at 12:58 pm, UTC.
+ Compiled on February 22, 2022, at 15:10 pm, UTC.
- Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME]
+ Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME]
[-f|--force] [--no-elynx-file] COMMAND
Analyze, and simulate multi sequence alignments.
@@ -138,18 +139,19 @@
The documentation of sub commands can be accessed separately:
- cabal exec slynx -- simulate --help
+ cabal run slynx -- simulate --help
# OR: stack exec slynx -- simulate --help
# OR: slynx simulate --help
- ELynx Suite version 0.6.0.0.
+ Up to date
+ ELynx Suite version 0.6.1.1.
Developed by Dominik Schrempf.
- Compiled on September 4, 2021, at 12:58 pm, UTC.
+ Compiled on February 22, 2022, at 15:10 pm, UTC.
- Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL]
- [-m|--mixture-model MODEL] [-e|--edm-file NAME]
- [-p|--siteprofile-files NAMES]
- [-w|--mixture-model-weights "[DOUBLE,DOUBLE,...]"]
+ Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL]
+ [-m|--mixture-model MODEL] [-e|--edm-file NAME]
+ [-p|--siteprofile-files NAMES]
+ [-w|--mixture-model-weights "[DOUBLE,DOUBLE,...]"]
[-g|--gamma-rate-heterogeneity "(NCAT,SHAPE)"]
(-l|--length NUMBER) [-S|--seed [INT]]
Simulate multi sequence alignments.
diff --git a/src/TLynx/Compare/Compare.hs b/src/TLynx/Compare/Compare.hs
--- a/src/TLynx/Compare/Compare.hs
+++ b/src/TLynx/Compare/Compare.hs
@@ -31,7 +31,6 @@
import ELynx.Tools.Logger
import ELynx.Tools.Options
import ELynx.Tree
-import Graphics.Gnuplot.Simple
import System.IO
import TLynx.Compare.Options
import TLynx.Parsers
@@ -91,11 +90,13 @@
(t1, t2) <-
if argsIntersect l
then do
- let [x, y] = either error id $ intersect [tr1, tr2]
- liftIO $ hPutStrLn outH "Intersected trees are:"
- liftIO $ BL.hPutStrLn outH $ toNewick x
- liftIO $ BL.hPutStrLn outH $ toNewick y
- return (x, y)
+ case either error id $ intersect [tr1, tr2] of
+ [x, y] -> do
+ liftIO $ hPutStrLn outH "Intersected trees are:"
+ liftIO $ BL.hPutStrLn outH $ toNewick x
+ liftIO $ BL.hPutStrLn outH $ toNewick y
+ return (x, y)
+ _ -> error "compareCmd: Could not intersect trees."
else return (tr1, tr2)
-- Distances.
@@ -230,14 +231,16 @@
case bn of
Nothing ->
logInfoS "No output file name provided. Do not generate plots."
- Just fn -> do
- let compareCommonBps =
- [ (bpToBrLen1 M.! b, bpToBrLen2 M.! b)
- | b <- S.toList bpCommon
- ]
- liftIO $ epspdfPlot fn (plotBps compareCommonBps)
- logInfoS
- "Comparison of branch lengths plot generated (EPS and PDF)"
+ -- Just fn -> do
+ -- let compareCommonBps =
+ -- [ (bpToBrLen1 M.! b, bpToBrLen2 M.! b)
+ -- | b <- S.toList bpCommon
+ -- ]
+ -- liftIO $ epspdfPlot fn (plotBps compareCommonBps)
+ -- logInfoS
+ -- "Comparison of branch lengths plot generated (EPS and PDF)"
+ Just _ -> do
+ logInfoS "No plot generated (no Gnuplot with GHC 9.2.1)"
_ -> logWarnS "Not all branches have a length! Can not analyze bipartitions."
header :: String
@@ -270,19 +273,22 @@
rd = 2 * d / (l1 + l2)
s = bpHuman p
-plotBps :: [(Double, Double)] -> [Attribute] -> IO ()
-plotBps xs as = plotPathsStyle as' [(ps1, xs), (ps2, line)]
- where
- as' =
- as
- ++ [ Title "Comparison of branch lengths of common branches",
- XLabel "Branch lengths, tree 1",
- YLabel "Branch lengths, tree 2"
- ]
- ps1 = PlotStyle Points (DefaultStyle 1)
- -- m = minimum $ map fst xs ++ map snd xs
- mx = maximum $ map fst xs
- my = maximum $ map snd xs
- m = min mx my
- line = [(0, 0), (m, m)]
- ps2 = PlotStyle Lines (DefaultStyle 1)
+-- -- NOTE: I removed the plotting functionality because Gnuplot does not
+-- -- support GHC 9.2.1.
+--
+-- plotBps :: [(Double, Double)] -> [Attribute] -> IO ()
+-- plotBps xs as = plotPathsStyle as' [(ps1, xs), (ps2, line)]
+-- where
+-- as' =
+-- as
+-- ++ [ Title "Comparison of branch lengths of common branches",
+-- XLabel "Branch lengths, tree 1",
+-- YLabel "Branch lengths, tree 2"
+-- ]
+-- ps1 = PlotStyle Points (DefaultStyle 1)
+-- -- m = minimum $ map fst xs ++ map snd xs
+-- mx = maximum $ map fst xs
+-- my = maximum $ map snd xs
+-- m = min mx my
+-- line = [(0, 0), (m, m)]
+-- ps2 = PlotStyle Lines (DefaultStyle 1)
diff --git a/src/TLynx/Distance/Distance.hs b/src/TLynx/Distance/Distance.hs
--- a/src/TLynx/Distance/Distance.hs
+++ b/src/TLynx/Distance/Distance.hs
@@ -1,5 +1,5 @@
{-# LANGUAGE OverloadedStrings #-}
-{-# LANGUAGE TemplateHaskell #-}
+{-# LANGUAGE TemplateHaskellQuotes #-}
-- |
-- Description : Compute distances between trees
@@ -153,9 +153,9 @@
let distanceMeasure =
if argsIntersect l
then
- ( \t1 t2 ->
- let [t1', t2'] = either error id $ intersect [t1, t2]
- in distanceMeasure' t1' t2'
+ ( \t1 t2 -> case either error id $ intersect [t1, t2] of
+ [t1', t2'] -> distanceMeasure' t1' t2'
+ _ -> error "distance: Could not intersect trees."
)
else distanceMeasure'
-- Possibly normalize trees.
diff --git a/tlynx.cabal b/tlynx.cabal
--- a/tlynx.cabal
+++ b/tlynx.cabal
@@ -1,6 +1,6 @@
-cabal-version: 2.2
+cabal-version: 3.0
name: tlynx
-version: 0.6.1.0
+version: 0.6.1.1
synopsis: Handle phylogenetic trees
description: Examine, compare, and simulate phylogenetic trees in a reproducible way. Please see the README on GitHub at .
category: Bioinformatics
@@ -56,7 +56,6 @@
, data-default-class
, elynx-tools
, elynx-tree
- , gnuplot
, mwc-random
, optparse-applicative
, parallel