From 94466a15aaf38cf715a4f6a607365680ea76faf1 Mon Sep 17 00:00:00 2001
From: Sarvesh Prakash Nikumbh <snikumbh@mpi-inf.mpg.de>
Date: Wed, 19 Jul 2017 17:58:58 +0200
Subject: [PATCH] Minor cleaning.

---
 get_colored.m             |  8 ++------
 performMKLWithSimpleMKL.m | 22 ----------------------
 2 files changed, 2 insertions(+), 28 deletions(-)
 delete mode 100644 performMKLWithSimpleMKL.m

diff --git a/get_colored.m b/get_colored.m
index d7007b5..6f09d16 100644
--- a/get_colored.m
+++ b/get_colored.m
@@ -1,14 +1,12 @@
 function [colored_string] = get_colored(given_string, oligoLen)
 
+% Colors the given string (DNA motif) using the IUPAC color scheme for the nucleotides A, C, G, T.
+
 given_string = char(given_string);
-%disp(size(given_string, 2));
-%disp(given_string(1,3));
 alphabet = upper('acgt');
 colored_string = [];
 for i=1:size(given_string, 2)
-    %fprintf('%d--\n',i);
     if isscalar(given_string(1,i))
-    %fprintf('YES SCALAR\n');
     if oligoLen~= 0 && i == oligoLen+1
 	colored_string = strcat(colored_string, '\color{black}|');
     end
@@ -25,7 +23,5 @@
     end
 end
 
-%title(['\fontsize{16}black {\color{magenta}magenta '...
-%'\color[rgb]{0 .5 .5}teal \color{red}red} black again'])
 
 end
diff --git a/performMKLWithSimpleMKL.m b/performMKLWithSimpleMKL.m
deleted file mode 100644
index 2c58a9a..0000000
--- a/performMKLWithSimpleMKL.m
+++ /dev/null
@@ -1,22 +0,0 @@
-function [w, alpha, b] = performMklWithSimpleMKL(Cval, Y, allSeqsNonShiftedStdSetKernel, allSeqsShiftedStdSetKernel, allSeqsNonShiftedConformedSetKernel, allSeqsShiftedConformedSetKernel)
-
-%
-% We are using SimpleMKL here for performing multiple kernel learning
-% update Dec 03, 2016: SimpleMKL was part of the plan earlier. 
-% As of now, we are using a Shogun implementation of MKL. 
-%
-%
-fprintf('Setting up things for MKL run...\n');
-for k=1:size(allSeqsNonShiftedConformedSetKernel, 2)
-    Ks(:,:,k) = allSeqsNonShiftedConformedSetKernel(1,k);
-end
-fprintf('Using %d different kernels\n',size(Ks,3));
-
-[w, alpha, b] = simplemkl(Y, Ks, Cval);
-
-fprintf('Algorithm selected %d kernels\n',sum(w>1e-4));
-
-[ignore,ind]= max(w);
-fprintf('most active kernel (w=%.2g) = %.2f\n', w(ind), ind);
-
-end