output composite via printstream to fix overwrite

Problem: When the gui wrote the composite output to the
composite_average.out file, runs with multiple BED x BAM combinations
would be sequentially overwritten.

This was fixed by changing the PileupParams composite output object to a
PrintStream that could be initialized at the TagPileupWindow object
before iterating through each BAM and BED file. The get and set methods
for the PileupParams were updated accordingly for all classes that used
the get/setCompositeFile --> get/setCompositePrintStream.

Author: owlang

src/cli/Read_Analysis/TagPileupCLI.java

@@ -11,6 +11,7 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.io.PrintStream;
 
 import util.BAMUtilities;
 import util.ExtensionFileFilter;
@@ -263,7 +264,7 @@ else if(readType.midpoint){
 		p.setOutputCompositeStatus(true);
 
 		//Set COMPOSITE file
-		p.setCompositeFile(outputOptions.outputComposite);
+		p.setCompositePrintStream(new PrintStream(outputOptions.outputComposite));
 
 		//Set READ
 		p.setRead(readType.finalRead);

src/objects/PileupParameters.java

@@ -3,12 +3,13 @@
 import java.awt.Color;
 import java.io.File;
 import java.util.ArrayList;
+import java.io.PrintStream;
 
 public class PileupParameters {
 	//Directory to save matrix and composite into
 	private File OUTPUT = null;
 	//Composite values file if output
-	private String COMPOSITE = null;
+	private PrintStream COMPOSITE = null;
 
 	//Read type:
 	//  0=read1, 1=read2, 2=allreads, 3=midpoint
@@ -126,10 +127,10 @@ public void setPErequire(boolean status) {
 		requirePE = status;
 	}
 
-	public String getCompositeFile() {
+	public PrintStream getCompositePrintStream() {
 		return COMPOSITE;
 	}
-	public void setCompositeFile(String comp) {
+	public void setCompositePrintStream(PrintStream comp) {
 		COMPOSITE = comp;
 	}
 

src/scripts/Read_Analysis/TagPileup.java

@@ -242,13 +242,7 @@ public void run() throws IOException {
 		DOMAIN = DOMAIN_trim;
 
 		// Output composite data file setup
-		if (PARAM.getOutputCompositeStatus()) {
-			try {
-				COMPOSITE = new PrintStream(PARAM.getCompositeFile());
-			} catch (FileNotFoundException e) {
-				e.printStackTrace();
-			}
-		}
+		COMPOSITE = PARAM.getCompositePrintStream();
 
 		// Output composite data to tab-delimited file
 		if (COMPOSITE != null) {

src/window_interface/Read_Analysis/TagPileupOutput.java

@@ -2,7 +2,6 @@
 
 import java.awt.BorderLayout;
 import java.io.File;
-import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.PrintStream;
 import java.util.Vector;
@@ -63,14 +62,6 @@ public TagPileupOutput(Vector<File> be, Vector<File> ba, PileupParameters param)
 	}
 
 	public void run() throws IOException {
-		if (PARAM.getOutputCompositeStatus()) {
-			try {
-				COMPOSITE = new PrintStream(PARAM.getCompositeFile());
-			} catch (FileNotFoundException e) {
-				e.printStackTrace();
-			}
-		}
-
 		// Check if BAI index file exists for all BAM files
 		boolean[] BAMvalid = new boolean[BAMFiles.size()];
 		for (int z = 0; z < BAMFiles.size(); z++) {

src/window_interface/Read_Analysis/TagPileupWindow.java

@@ -12,7 +12,9 @@
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
 import java.io.File;
+import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.io.PrintStream;
 import java.util.Vector;
 
 import javax.swing.ButtonGroup;
@@ -166,7 +168,13 @@ public Void doInBackground() throws IOException, InterruptedException {
 					else { param.setOutputDirectory(OUT_DIR); }
 
 					param.setOutputCompositeStatus(chckbxOutputCompositeData.isSelected()); //Outputs composite plots if check box is selected
-					if(chckbxOutputCompositeData.isSelected()) { param.setCompositeFile(OUT_DIR + File.separator + txtCompositeName.getText()); }
+					if(chckbxOutputCompositeData.isSelected()) {
+						try {
+							param.setCompositePrintStream(new PrintStream(OUT_DIR + File.separator + txtCompositeName.getText()));
+						} catch (FileNotFoundException e) {
+							e.printStackTrace();
+						}
+					}
 
 					if (chckbxOutputData.isSelected()) {
 						if (rdbtnTabdelimited.isSelected()) { param.setOutputType(1); }