From 012a3c8c6325831cc998052029008904b5e239e3 Mon Sep 17 00:00:00 2001
From: lancelothk <lancelothk@gmail.com>
Date: Sat, 11 Aug 2018 12:24:43 -0700
Subject: [PATCH] Bug fix: incorrect order of pattern in figure drawing Draw
 pattern with allele first, which is consistent with assumption in
 drawASMFigure. Add test for this issue.

---
 .../cwru/cbc/BSPAT/MethylFigure/IOUtils.java  |  5 ++--
 .../BSPAT/MethylFigure/MethylFigurePgm.java   |  8 ++---
 .../cbc/BSPAT/MethylFigure/IOUtilsTest.java   | 29 +++++++++++++++++++
 3 files changed, 36 insertions(+), 6 deletions(-)
 create mode 100644 BSPAT_standAlone/src/test/java/edu/cwru/cbc/BSPAT/MethylFigure/IOUtilsTest.java

diff --git a/BSPAT_standAlone/src/main/java/edu/cwru/cbc/BSPAT/MethylFigure/IOUtils.java b/BSPAT_standAlone/src/main/java/edu/cwru/cbc/BSPAT/MethylFigure/IOUtils.java
index f03ff3f..ad67ed6 100644
--- a/BSPAT_standAlone/src/main/java/edu/cwru/cbc/BSPAT/MethylFigure/IOUtils.java
+++ b/BSPAT_standAlone/src/main/java/edu/cwru/cbc/BSPAT/MethylFigure/IOUtils.java
@@ -42,9 +42,10 @@ static List<PatternResult> readASMPatterns(String ASMPatternFileName) throws IOE
 				cpg.setMethylLevel(methylLevel);
 			}
 
-			patternResultLists.add(patternWithoutAllele);
+			// First result in patternResultLists is the one with allele.
+			// Should be consistent with implementation in MethylFigurePgm.drawASMFigure
 			patternResultLists.add(patternWithAllele);
-			patternBuffReader.close();
+			patternResultLists.add(patternWithoutAllele);
 		}
 		return patternResultLists;
 	}
diff --git a/BSPAT_standAlone/src/main/java/edu/cwru/cbc/BSPAT/MethylFigure/MethylFigurePgm.java b/BSPAT_standAlone/src/main/java/edu/cwru/cbc/BSPAT/MethylFigure/MethylFigurePgm.java
index 657e2be..a23779c 100644
--- a/BSPAT_standAlone/src/main/java/edu/cwru/cbc/BSPAT/MethylFigure/MethylFigurePgm.java
+++ b/BSPAT_standAlone/src/main/java/edu/cwru/cbc/BSPAT/MethylFigure/MethylFigurePgm.java
@@ -104,7 +104,8 @@ private static void drawASMFigure(String regionName, String ASMPatternFileName,
 		methylWriter.getGraphWriter().drawString(regionName, REGION_NAME_LEFTSTART, height);
 		methylWriter.getGraphWriter().setFont(new Font(figureFont, Font.PLAIN, COMMON_FONT_SIZE));
 
-		// pattern with allele
+		// order of drawing should be consistent with IOUtils.readASMPatterns.
+		// pattern with allele first
 		addAverage(methylWriter.getGraphWriter(), figureFont, patternResultList.get(0).getCpGList(), height, left);
 		addAllele(patternResultList.get(0), methylWriter.getGraphWriter(), height + HEIGHT_INTERVAL, left);
 		height += 2 * HEIGHT_INTERVAL;
@@ -169,8 +170,7 @@ private static void drawFigure(String regionName, String patternFileName, String
 		methylWriter.close();
 	}
 
-	private static void addAllele(PatternResult patternResult, Graphics2D graphWriter, int height, int left) throws
-			IOException {
+	private static void addAllele(PatternResult patternResult, Graphics2D graphWriter, int height, int left) {
 		if (patternResult.getSnp() != null) {
 			graphWriter.setPaint(Color.BLUE);
 			graphWriter.fill(new Rectangle2D.Double(left + (patternResult.getSnp().getPosition() * BPWIDTH), height,
@@ -180,7 +180,7 @@ private static void addAllele(PatternResult patternResult, Graphics2D graphWrite
 	}
 
 	private static void addAverage(Graphics2D graphWriter, String fontChoice, List<? extends CpG> cpgList, int height,
-	                               int left) throws IOException {
+	                               int left) {
 		// 5. add average
 		DecimalFormat percentSmall = new DecimalFormat("##%");
 		height += HEIGHT_INTERVAL;
diff --git a/BSPAT_standAlone/src/test/java/edu/cwru/cbc/BSPAT/MethylFigure/IOUtilsTest.java b/BSPAT_standAlone/src/test/java/edu/cwru/cbc/BSPAT/MethylFigure/IOUtilsTest.java
new file mode 100644
index 0000000..eefeefd
--- /dev/null
+++ b/BSPAT_standAlone/src/test/java/edu/cwru/cbc/BSPAT/MethylFigure/IOUtilsTest.java
@@ -0,0 +1,29 @@
+package edu.cwru.cbc.BSPAT.MethylFigure;
+
+import edu.cwru.cbc.BSPAT.commons.PatternResult;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import java.io.IOException;
+import java.util.List;
+
+import static org.testng.Assert.*;
+
+public class IOUtilsTest {
+	private String testResourcePath;
+
+	@BeforeMethod
+	public void setUp() {
+		String root = this.getClass().getClassLoader().getResource("").getFile();
+		assertNotNull(root);
+		testResourcePath = root + "integration/";
+	}
+
+	@Test
+	public void testReadASMPatterns() throws IOException {
+		String ASMPatternFileName = testResourcePath + "/demoExpected/demoRef-10-96-test-plus_bismark.analysis_ASM.txt";
+		List<PatternResult> patternResultList = IOUtils.readASMPatterns(ASMPatternFileName);
+		assertNotNull(patternResultList.get(0).getSnp(), "First ASM pattern should be the one with allele");
+		assertNull(patternResultList.get(1).getSnp(), "Second ASM pattern should be the one without allele");
+	}
+}
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