Merge pull request #94 from CEGRcode/bugfix

Bugfix for #79 #85 #83

Author: WilliamKMLai

.gitignore

@@ -2,3 +2,4 @@
 /bin
 /.gradle/
 /build/
+.metadata

src/cli/Figure_Generation/CompositePlotCLI.java

@@ -5,29 +5,21 @@
 import picocli.CommandLine.Parameters;
 
 import java.awt.Color;
-import java.lang.NullPointerException;
 import java.io.File;
 import java.io.IOException;
-import java.io.OutputStream;
-import java.io.FileOutputStream;
-import java.io.FileNotFoundException;
 import java.util.ArrayList;
-import java.util.Scanner;
 import java.util.concurrent.Callable;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import org.jfree.chart.JFreeChart;
-import org.jfree.chart.ChartUtils;
-import org.jfree.data.xy.XYSeriesCollection;
-import org.jfree.data.xy.XYSeries;
-
-import charts.CompositePlot;
 import objects.ToolDescriptions;
-import util.ExtensionFileFilter;
+import scripts.Figure_Generation.PlotComposite;
 
 /**
- * Figure_GenerationCLI/CompositePlotCLI
+ * Command line interface class for scripts.Figure_Generation.PlotComposite to create line plot images based on the output files of scripts.Figure_Generation.TagPileup.
+ * @author Olivia Lang
+ * @see scripts.Figure_Generation.PlotComposite
+ * @see scripts.Figure_Generation.TagPileup
  */
 @Command(name = "composite-plot", mixinStandardHelpOptions = true,
 	description = ToolDescriptions.composite_description,
@@ -38,10 +30,9 @@
 public class CompositePlotCLI implements Callable<Integer> {
 
 	@Parameters(index = "0", description = "Composite data to plot. (formatted like TagPileup composite output)")
-	private File compositeData;
+	private File inputComposite;
 
-	@Option(names = { "-o",
-			"--output" }, description = "specify output filename, please use PNG extension\n(default=Input filename with \"_compositePlot.png\" appended to the name in working directory of ScriptManager")
+	@Option(names = { "-o", "--output" }, description = "specify output filename, please use PNG extension\n(default=Input filename with \"_compositePlot.png\" appended to the name in working directory of ScriptManager")
 	private File output = null;
 	@Option(names = { "-t", "--title" }, description = "set title (default=<composite-file-name>)")
 	private String title = null;
@@ -55,37 +46,11 @@ public class CompositePlotCLI implements Callable<Integer> {
 			"--custom-colors" }, description = "indicate colors to use for each series. Must indicate a number of colors that matches number of dataseries\n"
 					+ "default behavior:\n" + "if one series input, use black\n"
 					+ "if two series input, use blue(sense) and red(anti)\n"
-					+ "if greater than two series, cycle through a set of 20 preset colors.", arity = "1..")
+					+ "if greater than two series, cycle through a set of 10 preset colors based on Rossi et al, 2021 (PMID:33692541).", arity = "1..")
 	private String[] colors = null;
 
-	XYSeriesCollection xydata = null;
 	private ArrayList<Color> COLORS = new ArrayList<Color>();
 
-	// Colors copied from response on StackOverflow:
-	// https://stackoverflow.com/questions/470690/how-to-automatically-generate-n-distinct-colors
-	String[] KELLY_COLORS_HEX = { "0xFFB300", // Vivid Yellow
-			"0x803E75", // Strong Purple
-			"0xFF6800", // Vivid Orange
-			"0xA6BDD7", // Very Light Blue
-			"0xC10020", // Vivid Red
-			"0xCEA262", // Grayish Yellow
-			"0x817066", // Medium Gray
-			// The following don't work well for people with defective color vision
-			"0x007D34", // Vivid Green
-			"0xF6768E", // Strong Purplish Pink
-			"0x00538A", // Strong Blue
-			"0xFF7A5C", // Strong Yellowish Pink
-			"0x53377A", // Strong Violet
-			"0xFF8E00", // Vivid Orange Yellow
-			"0xB32851", // Strong Purplish Red
-			"0xF4C800", // Vivid Greenish Yellow
-			"0x7F180D", // Strong Reddish Brown
-			"0x93AA00", // Vivid Yellowish Green
-			"0x593315", // Deep Yellowish Brown
-			"0xF13A13", // Vivid Reddish Orange
-			"0x232C16", // Dark Olive Green
-	};
-
 	@Override
 	public Integer call() throws Exception {
 		System.err.println(">CompositePlotCLI.call()");
@@ -97,98 +62,52 @@ public Integer call() throws Exception {
 		}
 
 		// Generate Composite Plot
-		JFreeChart chart = CompositePlot.createChart(xydata, title, COLORS, legend);
-		// Save Composite Plot
-		OutputStream OUT = new FileOutputStream(output);
-		ChartUtils.writeChartAsPNG(OUT, chart, pixelWidth, pixelHeight);
+		PlotComposite.plotCompositeFile(inputComposite, output, true, title, COLORS, legend, pixelWidth, pixelHeight);
 
 		System.err.println("Image Generated.");
 		return (0);
 	}
 
+	/**
+	 * Validate input values and create user-readable error messages.
+	 * @return
+	 * @throws IOException
+	 */
 	private String validateInput() throws IOException {
 		String r = "";
 
-		// check inputs exist
-		if (!compositeData.exists()) {
-			r += "(!)Composite Data file does not exist: " + compositeData.getName() + "\n";
-			return (r);
-		}
-		// check input extensions
-		if (!"out".equals(ExtensionFileFilter.getExtension(compositeData))) {
-			r += "(!)Is this a \".out\" file? Check extension: " + compositeData.getName() + "\n";
+		// Input file check
+		if (!inputComposite.exists()) {
+			r += "(!)Composite Data file does not exist: " + inputComposite.getName() + "\n";
+		} else if (inputComposite.isDirectory()) {
+			r += "(!)Composite Data file is a directory: " + inputComposite.getName() + "\n";
 		}
-		// set default output filename
-		if (output == null) {
-			output = new File(ExtensionFileFilter.stripExtension(compositeData) + "_compositePlot.png");
-			// check output filename is valid
-		} else {
-			// check ext
-			try {
-				if (!"png".equals(ExtensionFileFilter.getExtension(output))) {
-					r += "(!)Use PNG extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output)
-							+ ".png\n";
-				}
-			} catch (NullPointerException e) {
-				r += "(!)Output filename must have extension: use PNG extension for output filename. Try: "
-						+ ExtensionFileFilter.stripExtension(output) + ".png\n";
-			}
-			// check directory
+		
+		// Output file check
+		if (output != null) {
 			if (output.getParent() == null) {
 // 				System.err.println("default to current directory");
 			} else if (!new File(output.getParent()).exists()) {
 				r += "(!)Check output directory exists: " + output.getParent() + "\n";
 			}
 		}
 
-		// check pixel ranges are valid
+		// Pixel ranges must be valid
 		if (pixelHeight <= 0) {
 			r += "(!)Cell height must be a positive integer value! check \"-y\" flag.\"";
 		}
 		if (pixelWidth <= 0) {
 			r += "(!)Cell width must be a positive integer value! check \"-x\" flag.\"";
 		}
 
-		// Parse Datafile
-		try {
-			xydata = parseData();
-			if (xydata == null) {
-				r += "(!)The number of y-values don't match the number of x-values";
-			}
-		} catch (FileNotFoundException e) {
-			e.printStackTrace();
-		}
-
-		// Set Color
-		if (colors == null) { // set defaults based on number of dataseries (n=1 -> black, n=2 -> blue,red,
-								// n=3 -> cycle through kelly colors)
-			if (xydata.getSeriesCount() == 1) {
-				// set color to black default unless otherwise indicated
-				COLORS.add(Color.BLACK);
-			} else if (xydata.getSeriesCount() == 2) {
-				// set colors to blue and red default unless otherwise indicated
-				COLORS.add(Color.BLUE);
-				COLORS.add(Color.RED);
-			} else if (xydata.getSeriesCount() > 2) {
-				// assign a diverse set of colors (as many as there are series)
-				for (int i = 0; i < xydata.getSeriesCount(); i++) {
-					int index = i % KELLY_COLORS_HEX.length;
-					COLORS.add(Color.decode(KELLY_COLORS_HEX[index]));
-				}
-			}
-		} else { // set user specified values and check they match number of data series
-			// assert custom colors have been assigned and length matches number of series
-			if (colors.length != xydata.getSeriesCount()) {
-				r += "(!)Number of colors specified(" + colors.length + ") must match number of dataseries("
-						+ xydata.getSeriesCount() + ")\n";
-			}
+		// Set Colors (customized)
+		if (colors != null) {
 			// check color input format and decode
 			Pattern hexColorPat = Pattern.compile("[0-9A-Fa-f]{6}");
 			for (int i = 0; i < colors.length; i++) {
 				Matcher m = hexColorPat.matcher(colors[i]);
 				if (!m.matches()) {
-					r += "(!)Color(" + colors[i]
-							+ ") must be formatted as a hexidecimal String!\n\tExpected input string format: \"[0-9A-Fa-f]{6}\"\n";
+					r += "(!)Color(" + colors[i] + ") must be formatted as a hexidecimal String!\n\tExpected input string format: \"[0-9A-Fa-f]{6}\"\n";
 				} else {
 					System.err.println("Decoding color: 0x" + colors[i]);
 					COLORS.add(Color.decode("0x" + colors[i]));
@@ -197,55 +116,4 @@ private String validateInput() throws IOException {
 		}
 		return (r);
 	}
-
-	public XYSeriesCollection parseData() throws FileNotFoundException {
-		// parse input into XYDataset obj
-		XYSeriesCollection dataset = new XYSeriesCollection();
-		Scanner scan = new Scanner(compositeData);
-		// parse x values
-		String[] tokens = scan.nextLine().split("\t");
-		if (!tokens[0].equals("")) {
-			scan.close();
-			System.err.println("(!) First row of input file must have an empty first column (as x-values)");
-			return null;
-		}
-		double[] x = new double[tokens.length - 1];
-		for (int i = 1; i < tokens.length; i++) {
-			x[i - 1] = Double.parseDouble(tokens[i]);
-		}
-
-		XYSeries s;
-		// line-by-line through file
-		while (scan.hasNextLine()) {
-			tokens = scan.nextLine().split("\t");
-			// check for format consistency: number of x-values matches y-values
-			if (tokens.length - 1 != x.length) {
-				System.err.println("(!) Check number of x-values matches number of y-values");
-				scan.close();
-				return null;
-			}
-			// skip any rows with blank labels
-			if (tokens[0].equals("")) {
-				for (int i = 1; i < tokens.length; i++) {
-					if (x[i - 1] != Double.parseDouble(tokens[i])) {
-						System.err.println(x[i - 1]);
-						System.err.println(tokens[i]);
-						System.err.println("(!) Check dataseries based on same x-scale file");
-						scan.close();
-						return null;
-					}
-				}
-				continue;
-			}
-			// initialize series based on rowname column of input file
-			s = new XYSeries(tokens[0]);
-			// parse y-values of current row
-			for (int i = 1; i < tokens.length; i++) {
-				s.add(x[i - 1], Double.parseDouble(tokens[i]));
-			}
-			dataset.addSeries(s);
-		}
-		scan.close();
-		return (dataset);
-	}
 }

src/cli/Figure_Generation/TwoColorHeatMapCLI.java

@@ -108,13 +108,9 @@ private String validateInput() throws IOException {
 			r += "(!)CDT file does not exist: " + CDT.getName() + "\n";
 			return (r);
 		}
-		// check input extensions
-		if (!"cdt".equals(ExtensionFileFilter.getExtension(CDT))) {
-			r += "(!)Is this a CDT file? Check extension: " + CDT.getName() + "\n";
-		}
 		// set default output filename
 		if (output == null) {
-			String NAME = ExtensionFileFilter.stripExtension(CDT);
+			String NAME = ExtensionFileFilter.stripExtensionIgnoreGZ(CDT);
 			output = new File(NAME + "_" + scaleType + ".png");
 			// check output filename is valid
 		} else {

src/cli/Read_Analysis/TagPileupCLI.java

@@ -218,6 +218,7 @@ else if(readType.midpoint){
 
 		//validate smooth params
 		if(smoothType.winVals!=-9999 && smoothType.winVals<1){ r += "(!)Invalid Smoothing Window Size. Must be larger than 0 bins, winSize=" + smoothType.winVals + "\n"; }
+		if(smoothType.winVals!=-9999 && smoothType.winVals%2==0){ r += "(!)Invalid Smoothing Window Size. Must be odd for symmetrical smoothing (so that the window is centered properly), winSize=" + smoothType.winVals + "\n"; }
 		if(smoothType.gaussVals[0]!=-9999 && smoothType.gaussVals[0]<1){ r += "(!)Invalid Standard Deviation Size. Must be larger than 0 bins, stdSize=" + smoothType.gaussVals[0] + "\n"; }
 		if(smoothType.gaussVals[1]!=-9999 && smoothType.gaussVals[1]<1){ r += "(!)Invalid Number of Standard Deviations. Must be larger than 0 standard deviations, stdNum=" + smoothType.gaussVals[1] + "\n"; }
 

src/main/ScriptManagerGUI.java

@@ -58,6 +58,7 @@
 import window_interface.Figure_Generation.TwoColorHeatMapWindow;
 import window_interface.Figure_Generation.ThreeColorHeatMapWindow;
 import window_interface.Figure_Generation.MergeHeatMapWindow;
+import window_interface.Figure_Generation.PlotCompositeWindow;
 import window_interface.Figure_Generation.LabelHeatMapWindow;
 
 public class ScriptManagerGUI {
@@ -1405,12 +1406,40 @@ public void run() {
 				});
 			}
 		});
-		sl_pnlFigure.putConstraint(SpringLayout.NORTH, btncolorSequencePlot, 0, SpringLayout.NORTH,
-				txtcolorSequencePlot);
+		sl_pnlFigure.putConstraint(SpringLayout.NORTH, btncolorSequencePlot, 0, SpringLayout.NORTH, txtcolorSequencePlot);
 		sl_pnlFigure.putConstraint(SpringLayout.WEST, btncolorSequencePlot, 10, SpringLayout.WEST, pnlFigure);
-		sl_pnlFigure.putConstraint(SpringLayout.WEST, txtcolorSequencePlot, 10, SpringLayout.EAST,
-				btncolorSequencePlot);
+		sl_pnlFigure.putConstraint(SpringLayout.WEST, txtcolorSequencePlot, 10, SpringLayout.EAST, btncolorSequencePlot);
 		pnlFigure.add(btncolorSequencePlot);
+		
+
+		// >FourColorPlot
+		JTextArea txtMakeCompositePlot = new JTextArea();
+		initializeTextArea(txtMakeCompositePlot);
+		txtMakeCompositePlot.setText(ToolDescriptions.composite_description);
+		sl_pnlFigure.putConstraint(SpringLayout.NORTH, txtMakeCompositePlot, 10, SpringLayout.SOUTH, txtcolorSequencePlot);
+		sl_pnlFigure.putConstraint(SpringLayout.NORTH, txtMakeCompositePlot, 10, SpringLayout.SOUTH, btncolorSequencePlot);
+		sl_pnlFigure.putConstraint(SpringLayout.EAST, txtMakeCompositePlot, -10, SpringLayout.EAST, pnlFigure);
+		pnlFigure.add(txtMakeCompositePlot);
+
+		JButton btnMakeCompositePlot = new JButton("Composite Plot");
+		btnMakeCompositePlot.addActionListener(new ActionListener() {
+			public void actionPerformed(ActionEvent e) {
+				EventQueue.invokeLater(new Runnable() {
+					public void run() {
+						try {
+							PlotCompositeWindow frame = new PlotCompositeWindow();
+							frame.setVisible(true);
+						} catch (Exception e) {
+							e.printStackTrace();
+						}
+					}
+				});
+			}
+		});
+		sl_pnlFigure.putConstraint(SpringLayout.NORTH, btnMakeCompositePlot, 0, SpringLayout.NORTH, txtMakeCompositePlot);
+		sl_pnlFigure.putConstraint(SpringLayout.WEST, btnMakeCompositePlot, 10, SpringLayout.WEST, pnlFigure);
+		sl_pnlFigure.putConstraint(SpringLayout.WEST, txtMakeCompositePlot, 10, SpringLayout.EAST, btnMakeCompositePlot);
+		pnlFigure.add(btnMakeCompositePlot);
 
 		// Set default tab to open to...
 		// 0=BAM_Statistics 5=Peak_Analysis