From 2cb6da5eef0eb866d7225c20bb44ccda1cab496a Mon Sep 17 00:00:00 2001
From: Hao Cheng <reworkhow@gmail.com>
Date: Fri, 5 Nov 2021 17:42:51 -0700
Subject: [PATCH] update interface

---
 src/1.JWAS/src/JWAS.jl                       | 15 +++++++++++++--
 src/1.JWAS/src/MCMC/MCMC_BayesianAlphabet.jl |  3 ---
 2 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/src/1.JWAS/src/JWAS.jl b/src/1.JWAS/src/JWAS.jl
index 4563b709..8f321f5d 100644
--- a/src/1.JWAS/src/JWAS.jl
+++ b/src/1.JWAS/src/JWAS.jl
@@ -183,8 +183,6 @@ function runMCMC(mme::MME,df;
                 Pi                              = 0.0,
                 estimatePi                      = false,
                 estimateScale                   = false)
-
-
     #Neural Network
     is_nnbayes_partial = (mme.nonlinear_function != false && mme.is_fully_connected==false)
     if mme.nonlinear_function != false #modify data to add phenotypes for hidden nodes
@@ -259,6 +257,19 @@ function runMCMC(mme::MME,df;
         set_marker_hyperparameters_variances_and_pi(mme)
     end
     ############################################################################
+    #fast blocks #now only work for one geno
+    ############################################################################
+    if fast_blocks != false
+        if fast_blocks == true
+            block_size = Int(floor(sqrt(mme.M[1].nObs)))
+        elseif typeof(fast_blocks) <: Number
+            block_size = Int(floor(fast_blocks))
+        end
+        mme.MCMCinfo.fast_blocks  = collect(range(1, step=block_size, stop=mme.M[1].nMarkers))
+        mme.MCMCinfo.chain_length = Int(floor(chain_length/(fast_blocks[2]-fast_blocks[1])))
+    end
+    println("BLOCK SIZE: $block_size")
+    ############################################################################
     # Adhoc functions
     ############################################################################
     #save MCMC samples for all parameters (?seperate function user call)
diff --git a/src/1.JWAS/src/MCMC/MCMC_BayesianAlphabet.jl b/src/1.JWAS/src/MCMC/MCMC_BayesianAlphabet.jl
index a3cac55b..f351bde8 100644
--- a/src/1.JWAS/src/MCMC/MCMC_BayesianAlphabet.jl
+++ b/src/1.JWAS/src/MCMC/MCMC_BayesianAlphabet.jl
@@ -21,9 +21,6 @@ function MCMC_BayesianAlphabet(mme,df)
     is_activation_fcn        = mme.is_activation_fcn
     nonlinear_function       = mme.nonlinear_function
     fast_blocks              = mme.MCMCinfo.fast_blocks
-    if fast_blocks != false
-        chain_length = Int(floor(chain_length/(fast_blocks[2]-fast_blocks[1])))#not flexible
-    end
     ############################################################################
     # Categorical Traits (starting values for maker effects defaulting to 0s)
     ############################################################################