merge showTargetCoor

lancelothk · Feb 10, 2016 · e022fa9
1 parent c5246d8
commit e022fa9
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Showing 6 changed files with 11 additions and 10 deletions.
diff --git a/.idea/artifacts/BSPAT.xml b/.idea/artifacts/BSPAT.xml
diff --git a/.idea/artifacts/BSPAT_war_exploded.xml b/.idea/artifacts/BSPAT_war_exploded.xml
diff --git a/BSPAT/BSPAT.iml b/BSPAT/BSPAT.iml
@@ -42,7 +42,6 @@
         <SOURCES />
       </library>
     </orderEntry>
-    <orderEntry type="library" name="apache http" level="project" />
     <orderEntry type="library" name="jstl-1.2.1" level="project" />
     <orderEntry type="module-library" scope="TEST">
       <library name="JUnit4">
@@ -54,6 +53,7 @@
         <SOURCES />
       </library>
     </orderEntry>
+    <orderEntry type="library" name="apache http" level="project" />
   </component>
   <component name="org.twodividedbyzero.idea.findbugs">
     <option name="_basePreferences">

diff --git a/BSPAT/src/edu/cwru/cbc/BSPAT/core/DrawPattern.java b/BSPAT/src/edu/cwru/cbc/BSPAT/core/DrawPattern.java
@@ -180,8 +180,8 @@ public void drawPattern(PatternLink patternLink) throws IOException {
 		patternLink.setGBResultLink(methylWriter.getGBLinkFileName());
 		patternLink.setFigureResultLink(methylWriter.getFigureName());
 
-		buildFigureFrame(methylWriter.getGraphWriter(), imageHeight, imageWidth, height, left, coordinate, targetLength,
-				statList);
+		buildFigureFrame(methylWriter.getGraphWriter(), imageHeight, imageWidth, height, left, chr,
+				String.valueOf(beginCoor), String.valueOf(endCoor), targetLength, statList);
 
 		// 4. add CpG sites
 		DecimalFormat percent = new DecimalFormat("##.00%");
@@ -274,8 +274,8 @@ public void drawASMPattern(ReportSummary reportSummary, PatternResult patternWit
 		reportSummary.setASMGBLink(ASMWriter.getGBLinkFileName());
 		reportSummary.setASMFigureLink(ASMWriter.getFigureName());
 
-		buildFigureFrame(ASMWriter.getGraphWriter(), imageHeight, imageWidth, height, left, coordinate, refLength,
-				statList);
+		buildFigureFrame(ASMWriter.getGraphWriter(), imageHeight, imageWidth, height, left, chr,
+				String.valueOf(beginCoor), String.valueOf(endCoor), refLength, statList);
 
 		DecimalFormat percent = new DecimalFormat("##.00%");
 
@@ -321,7 +321,7 @@ public void drawASMPattern(ReportSummary reportSummary, PatternResult patternWit
 				height + HEIGHT_INTERVAL, left);
 		// set snp info
 		if (patternWithAllele.hasAllele()) {
-			int snpQueryPos;
+			long snpQueryPos;
 			switch (strand) {
 				case "+":
 					snpQueryPos = convertCoordinates(chr, coordinateMap.get(region).getStart(), "hg38",

diff --git a/BSPAT/web/WEB-INF/config.properties b/BSPAT/web/WEB-INF/config.properties
@@ -1,6 +1,6 @@
 gmailUsername=username
 gmailPassword=password
-bismarkPath=/path/bismark_v0.14.2_noSleep/
-bowtiePath=/path/bowtie-1.1.1/
+bismarkPath=/home/lancelothk/software/bismark_v0.14.2_noSleep/
+bowtiePath=/home/lancelothk/software/bowtie-1.1.1/
 figure_font=Arial
 useSingleThread=FALSE
diff --git a/BSPAT_analysis/BSPAT_analysis.iml b/BSPAT_analysis/BSPAT_analysis.iml