Merge pull request #67 from CEGRcode/hotfix

bugfix batch PEStat in GUI interface

Author: WilliamKMLai

src/scripts/BAM_Statistics/PEStats.java

@@ -27,7 +27,6 @@
 public class PEStats {
 
 	public static Vector<ChartPanel> getPEStats( File out_basename, File bamFile, boolean DUP_STATUS, int MIN_INSERT, int MAX_INSERT, PrintStream PS_INSERT, PrintStream PS_DUP, boolean SUM_STATUS ){
-		System.out.println("getPEStats called");
 		final SamReaderFactory factory = SamReaderFactory.makeDefault().enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS, SamReaderFactory.Option.VALIDATE_CRC_CHECKSUMS).validationStringency(ValidationStringency.SILENT);
 
 		// Output Vecotr of Charts to be returned
@@ -40,6 +39,7 @@ public static Vector<ChartPanel> getPEStats( File out_basename, File bamFile, bo
 		PrintStream OUT_DUP = null;
 		File OUT_DUPPNG = null;
 
+		// Set output PrintStreams and PNG file objects
 		if( out_basename!=null ) {
 			try {
 				OUT_INSERT = new PrintStream(new File( out_basename.getCanonicalPath() + "_InsertHistogram.out"));
@@ -60,9 +60,7 @@ public static Vector<ChartPanel> getPEStats( File out_basename, File bamFile, bo
 		printBoth( null, OUT_INSERT_SUM, time );
 		printBoth( PS_INSERT, OUT_INSERT, time );
 		printBoth( PS_DUP, OUT_DUP, time );
-		
-		if(PS_DUP!=null){ PS_DUP.println("YO!"); }
-		
+
 		//Check if BAI index file exists
 		File f = new File(bamFile + ".bai");
 		if(f.exists() && !f.isDirectory()) {
@@ -77,6 +75,7 @@ public static Vector<ChartPanel> getPEStats( File out_basename, File bamFile, bo
 			//Code to get individual chromosome stats
 			SamReader reader = factory.open(bamFile);
 			AbstractBAMFileIndex bai = (AbstractBAMFileIndex) reader.indexing().getIndex();
+			System.out.println(bamFile);
 
 			//Variables to keep track of insert size histogram
 			double InsertAverage = 0;
@@ -197,13 +196,13 @@ public static Vector<ChartPanel> getPEStats( File out_basename, File bamFile, bo
 			try{
 				charts.add( 0, Histogram.createBarChart(HIST, DOMAIN, OUT_INSPNG) );
 			}catch( IOException e ){ e.printStackTrace(); }
-			
+
+			//Duplication statistics
 			if(DUP_STATUS) {
-				//Duplication statistics
 				double UNIQUE_MOLECULES = 0;
 				String[] BIN_NAME = initializeBIN_Names();
 				ArrayList<Double> BIN = new ArrayList<Double>();
-				initializeBINS(BIN);	
+				initializeBINS(BIN);
 
 				Iterator<Integer> keys = ALL_COMPLEXITY.keySet().iterator();
 				while(keys.hasNext()) {
@@ -223,14 +222,13 @@ public static Vector<ChartPanel> getPEStats( File out_basename, File bamFile, bo
 					charts.add( 1, LineChart.createLineChart(BIN, BIN_NAME, OUT_DUPPNG) );
 				}catch( IOException e ){ e.printStackTrace(); }
 			}
-			
 		} else {
+			charts.add(0, new ChartPanel(null));
+			charts.add(1, new ChartPanel(null));
 			printBoth( PS_INSERT, OUT_INSERT, "BAI Index File does not exist for: " + bamFile.getName() );
 			printBoth( System.err, OUT_INSERT_SUM, "BAI Index File does not exist for: " + bamFile.getName() );
 			printBoth( PS_DUP, OUT_DUP, "BAI Index File does not exist for: " + bamFile.getName() );
 		}
-		if(PS_INSERT != null){ PS_INSERT.close(); }
-		if(PS_DUP!=null){ PS_DUP.close(); }
 
 		if(OUT_INSERT != null){ OUT_INSERT.close(); }
 		if(OUT_INSERT_SUM!=null){ OUT_INSERT_SUM.close(); }

src/window_interface/BAM_Statistics/PEStatOutput.java

@@ -23,7 +23,7 @@
 public class PEStatOutput extends JFrame {
 
 	Vector<File> bamFiles = null;
-	private File OUTPUT_PATH = null;
+	private File OUT_DIR = null;
 	private boolean OUTPUT_STATUS = false;
 	private boolean DUP_STATUS = false;
 	private static int MIN_INSERT = 0;
@@ -54,7 +54,7 @@ public PEStatOutput(Vector<File> input, File o, boolean out, boolean dup, int mi
 		layeredPane.add(tabbedPane);
 
 		bamFiles = input;
-		OUTPUT_PATH = o;
+		OUT_DIR = o;
 		OUTPUT_STATUS = out;
 		DUP_STATUS = dup;
 		MIN_INSERT = min;
@@ -76,17 +76,17 @@ public PEStatOutput(Vector<File> input, File o, boolean out, boolean dup, int mi
 	public void run() throws IOException {
 		//Iterate through all BAM files in Vector	
 		for(int x = 0; x < bamFiles.size(); x++) {
-			
 			// Construct Basename
-			File NAME = null;
+			File OUT_BASENAME = null;
 			if(OUTPUT_STATUS){
 				try{
-					NAME = new File( bamFiles.get(x).getName().split("\\.")[0] );
-					if(OUTPUT_PATH != null){ NAME = new File( OUTPUT_PATH.getCanonicalPath() + File.separator + NAME.getCanonicalPath() ); }
+					if(OUT_DIR == null) { OUT_BASENAME = new File(bamFiles.get(x).getName().split("\\.")[0]); }
+					else { OUT_BASENAME = new File( OUT_DIR.getCanonicalPath() + File.separator + bamFiles.get(x).getName().split("\\.")[0] ); }
 				}
 				catch (FileNotFoundException e) { e.printStackTrace(); }
 // 				catch (IOException e) {	e.printStackTrace(); }
 			}
+			
 			// Initialize PrintStream and TextArea for PE stats (insert sizes)
 			PrintStream ps_insert = null;
 			JTextArea PE_STATS = new JTextArea();
@@ -99,9 +99,9 @@ public void run() throws IOException {
 				DUP_STATS.setEditable(false);
 				ps_dup = new PrintStream(new CustomOutputStream( DUP_STATS ));
 			}
-			
+
 			//Call public static method from scripts
-			Vector<ChartPanel> charts = PEStats.getPEStats( NAME, bamFiles.get(x), DUP_STATUS, MIN_INSERT, MAX_INSERT, ps_insert, ps_dup, false );
+			Vector<ChartPanel> charts = PEStats.getPEStats( OUT_BASENAME, bamFiles.get(x), DUP_STATUS, MIN_INSERT, MAX_INSERT, ps_insert, ps_dup, false );
 
 			//Add pe stats to tabbed pane
 			PE_STATS.setCaretPosition(0);
@@ -117,7 +117,7 @@ public void run() throws IOException {
 				tabbedPane_Duplication.add(bamFiles.get(x).getName(), charts.get(1));
 			}
 
-			ps_dup.close();
+			if(ps_dup!=null) { ps_dup.close(); }
 			ps_insert.close();
 
 			firePropertyChange("bam",x, x + 1);	

src/window_interface/BAM_Statistics/PEStatWindow.java

@@ -52,7 +52,7 @@ public class PEStatWindow extends JFrame implements ActionListener, PropertyChan
 
 	final DefaultListModel<String> expList;
 	Vector<File> BAMFiles = new Vector<File>();
-	private File OUTPUT_PATH = null;
+	private File OUTPUT_PATH = new File(System.getProperty("user.dir"));
 
 	JProgressBar progressBar;
 	public Task task;
@@ -72,7 +72,7 @@ public void propertyChange(PropertyChangeEvent propertyChangeEvent) {
 			        	setProgress(percentComplete);
 				     }
 				 });
-				stat.setVisible(true);				
+				stat.setVisible(true);
 				stat.run();
 			} catch(NumberFormatException nfe){
 				JOptionPane.showMessageDialog(null, "Input Fields Must Contain Integers");