From 94241d6c8703a601c1e4dd6e8627e137ffa25426 Mon Sep 17 00:00:00 2001
From: Sarvesh Prakash Nikumbh <snikumbh@mpi-inf.mpg.de>
Date: Mon, 31 Jul 2017 15:19:57 +0200
Subject: [PATCH] Adding readConfigFile function was pending

---
 readConfigFile.m | 76 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 76 insertions(+)
 create mode 100644 readConfigFile.m

diff --git a/readConfigFile.m b/readConfigFile.m
new file mode 100644
index 0000000..ab3a40b
--- /dev/null
+++ b/readConfigFile.m
@@ -0,0 +1,76 @@
+function configParams = readConfigFile(configFilename)
+
+% READCONFIGFILE 
+% Reads all the parameter values given in the config file and returns
+% a structure of all the params
+% 
+% INPUT PARAMS
+% Param 'configFilename' (string)
+% Config filename to read the parameter values from.
+%
+% OUTPUT PARAMS
+% configParams
+% A struct with all variables
+% 
+% ADDITIONAL NOTES
+%
+% Author: snikumbh@mpi-inf.mpg.de
+
+
+fid = fopen(configFilename, 'r');
+
+while feof(fid) == 0
+    l = fgetl(fid);
+    if findstr(l, '##') > 0
+	% skip the comment lines
+    elseif findstr(l, '=') > 0
+	l2 = strsplit(l,'=');
+        switch(l2{1})
+	case 'POSITIVE_FASTA_FILE'
+		configParams.givenPosFastaFilename = l2{2};
+	case 'NEGATIVE_FASTA_FILE'
+		configParams.givenNegFastaFilename = l2{2};
+	case 'NUMBER_OF_POSITIVES'
+		configParams.nPosSequences = str2num(l2{2});
+	case 'NUMBER_OF_NEGATIVES'
+		configParams.nNegSequences = str2num(l2{2});
+	case 'TEST_INDICES'
+		configParams.testIndices = eval(l2{2});
+	case 'OUTPUT_FOLDER'
+		configParams.outputFolder = l2{2};
+	case 'OLIGO_LEN'
+		configParams.oligoLen = eval(l2{2});
+	case 'MAX_DIST'
+		configParams.maxDist = str2num(l2{2});
+	case 'SEGMENT_SIZE_IN_BPS'
+		configParams.segmentSizeInBps = str2num(l2{2});
+	case 'NUMBER_OF_CLUSTERS'
+		configParams.nClusterVals = eval(l2{2});
+	case 'SIGMA_VALUES'
+		configParams.sigmaVals = eval(l2{2});
+	case 'COST_VALUES'
+		configParams.Cs = eval(l2{2});
+	case 'MKL_NORM'
+		configParams.mklNorm = str2num(l2{2});
+	case 'NUMBER_OF_INNER_FOLDS'
+		configParams.nFolds = str2num(l2{2});
+	case 'NUMBER_OF_OUTER_FOLDS'
+		configParams.nOuterFolds = str2num(l2{2});
+	case 'WHETHER_TO_PLOT_HEATMAP'
+		configParams.whetherToPlotHeatmap = l2{2};
+	case 'WHETHER_TO_VISUALIZE_WEIGHT_VECTOR'
+		configParams.whetherToVisualizeWVector = l2{2};
+	case 'DEBUG_LEVEL'
+		configParams.debugLevel = str2num(l2{2});
+	case 'DEBUG_MSG_LOCATION'
+		configParams.debugMsgLocation = l2{2};
+	case 'COMPUTATION_VERSION'
+		configParams.computationVersion = l2{2};
+	end % switch ends
+    else
+
+    end % if-else ends
+end % while ends
+fclose(fid);
+
+end