migrated referenced code from other projects to this repository

shenkers · Apr 28, 2014 · 6ea8b91 · 6ea8b91
1 parent a5b0116
commit 6ea8b91
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Showing 6 changed files with 32 additions and 685 deletions.
diff --git a/IsoSCM/.classpath b/IsoSCM/.classpath
@@ -2,9 +2,7 @@
 <classpath>
 	<classpathentry kind="src" path="src"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/Utils"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/itext"/>
-	<classpathentry kind="src" path="/Lai"/>
 	<classpathentry kind="lib" path="lib/colt.jar" sourcepath="lib-src/colt-src.jar"/>
 	<classpathentry kind="lib" path="lib/commons-math3-3.0.jar" sourcepath="lib-src/commons-math3-3.0-sources.jar"/>
 	<classpathentry kind="lib" path="lib/picard-1.106.jar" sourcepath="lib-src/picard-1.106-src.jar"/>

diff --git a/IsoSCM/src/executable/Main.java → IsoSCM/src/executable/IsoSCM.java b/IsoSCM/src/executable/Main.java → IsoSCM/src/executable/IsoSCM.java
@@ -1,7 +1,6 @@
 package executable;
 
 import java.io.File;
-import java.io.FileNotFoundException;
 import java.io.IOException;
 
 import multisample.JointSegmentation;
@@ -15,9 +14,9 @@
 import processing.SlidingWindow;
 import scm.IdentifyChangePoints;
 import splicegraph.ExonSpliceGraph;
-import tools.Strandedness;
 import tools.BEDTools.BEDWriter;
 import tools.GTFTools.GTFWriter;
+import tools.Strandedness;
 import util.IO;
 import util.Util;
 
@@ -28,12 +27,7 @@
 import com.beust.jcommander.converters.FileConverter;
 import com.beust.jcommander.converters.IntegerConverter;
 
-public class Main {
-	enum FileType {}
-
-	public static File getFile(FileType type, File dir, String base){
-		return dir;
-	}
+public class IsoSCM {
 
 	public static void main(String[] args) throws IOException {
 		class AssembleCommand{