separate chart generation from script TagPileup

Only the GUI version of TagPileup generates the composite chart so the
classes for this tool arre restuctured in this commit so that the chart
is generated by the window_interface/TagPileupOutput class. This results
in one less argument input to the script so the CLI class was also
minorly affected by this commit.

Author: owlang

src/cli/Read_Analysis/TagPileupCLI.java

@@ -139,7 +139,7 @@ public Integer call() throws Exception {
 			System.exit(1);
 		}
 
-		TagPileup script_obj = new TagPileup(bedFile, bamFile, p, null, outputOptions.outputMatrix.get(0), false);
+		TagPileup script_obj = new TagPileup(bedFile, bamFile, p, null, outputOptions.outputMatrix.get(0));
 		script_obj.run();
 
 		System.err.println( "Calculations complete" );

src/scripts/Read_Analysis/TagPileup.java

@@ -19,7 +19,6 @@
 import java.util.concurrent.Executors;
 import java.util.zip.GZIPOutputStream;
 
-import charts.CompositePlot;
 import htsjdk.samtools.AbstractBAMFileIndex;
 import htsjdk.samtools.SamReader;
 import htsjdk.samtools.SamReaderFactory;
@@ -34,6 +33,9 @@ public class TagPileup {
 	File BAM = null;
 
 	PileupParameters PARAM = null;
+	public double[] DOMAIN = null;
+	public double[] AVG_S1 = null;
+	public double[] AVG_S2 = null;
 
 	PrintStream COMPOSITE = null;
 	// Generic print stream to accept PrintStream of GZIPOutputStream
@@ -46,16 +48,12 @@ public class TagPileup {
 
 	String outMatrixBasename;
 
-	boolean GUI = false;
-
-	public TagPileup(File be, File ba, PileupParameters param, PrintStream outputwindow_ps, String outMat,
-			boolean guiStatus) {
+	public TagPileup(File be, File ba, PileupParameters param, PrintStream outputwindow_ps, String outMat) {
 		BED = be;
 		BAM = ba;
 		PARAM = param;
 		PS = outputwindow_ps;
 		outMatrixBasename = outMat;
-		GUI = guiStatus;
 	}
 
 	public void run() throws IOException {
@@ -133,11 +131,11 @@ public void run() throws IOException {
 		while (!parseMaster.isTerminated()) {
 		}
 
-		double[] AVG_S1 = new double[getMaxBEDSize(INPUT)];
-		double[] AVG_S2 = null;
+		DOMAIN = new double[getMaxBEDSize(INPUT)];
+		AVG_S1 = new double[DOMAIN.length];
+		AVG_S2 = null;
 		if (STRAND == 0)
-			AVG_S2 = new double[AVG_S1.length];
-		double[] DOMAIN = new double[AVG_S1.length];
+			AVG_S2 = new double[DOMAIN.length];
 
 		// Account for the shifted oversized window produced by binning and smoothing
 		int OUTSTART = 0;
@@ -278,16 +276,6 @@ public void run() throws IOException {
 			}
 		}
 
-		// Make composite plots
-		if (GUI) {
-			if (STRAND == 0) {
-				compositePlot = CompositePlot.createCompositePlot(DOMAIN, AVG_S1, AVG_S2, BED.getName(),
-						PARAM.getColors());
-			} else {
-				compositePlot = CompositePlot.createCompositePlot(DOMAIN, AVG_S1, BED.getName(), PARAM.getColors());
-			}
-		}
-
 		// Output JTV files
 		if (OUT_S1 != null) {
 			if (PARAM.getOutputJTV() && PARAM.getOutputType() == 2) {

src/window_interface/Read_Analysis/TagPileupOutput.java

@@ -15,6 +15,7 @@
 import javax.swing.JTabbedPane;
 import javax.swing.SpringLayout;
 
+import charts.CompositePlot;
 import objects.PileupParameters;
 import objects.CustomOutputStream;
 import scripts.Read_Analysis.TagPileup;
@@ -104,10 +105,15 @@ public void run() throws IOException {
 					STATS.setEditable(false); // Make it un-editable
 					PrintStream ps = new PrintStream(new CustomOutputStream(STATS));
 
-					TagPileup script_obj = new TagPileup(BEDFiles.get(BED_Index), BAM, PARAM, ps, null, true);
+					TagPileup script_obj = new TagPileup(BEDFiles.get(BED_Index), BAM, PARAM, ps, null);
 					script_obj.run();
 
-					tabbedPane_Scatterplot.add(BAM.getName(), script_obj.getCompositePlot());
+					// Make composite plots
+					if (PARAM.getStrand() == 0) {
+						tabbedPane_Scatterplot.add(BAM.getName(), CompositePlot.createCompositePlot(script_obj.DOMAIN, script_obj.AVG_S1, script_obj.AVG_S2, BEDFiles.get(BED_Index).getName(), PARAM.getColors()));
+					} else {
+						tabbedPane_Scatterplot.add(BAM.getName(), CompositePlot.createCompositePlot(script_obj.DOMAIN, script_obj.AVG_S1, BEDFiles.get(BED_Index).getName(), PARAM.getColors()));
+					}
 
 					STATS.setCaretPosition(0);
 					JScrollPane newpane = new JScrollPane(STATS, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS,