Merge pull request #136 from CEGRcode/javadoc

Added Javadoc to scriptmanager

Author: owlang

.classpath

@@ -29,4 +29,4 @@
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8/"/>
 	<classpathentry kind="con" path="org.eclipse.buildship.core.gradleclasspathcontainer"/>
 	<classpathentry kind="output" path="bin/default"/>
-</classpath>
+</classpath>

.gitignore

@@ -3,4 +3,4 @@
 /.gradle/
 /build/
 .metadata
-.idea
+.idea

.project

@@ -20,4 +20,4 @@
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.eclipse.buildship.core.gradleprojectnature</nature>
 	</natures>
-</projectDescription>
+</projectDescription>

.settings/org.eclipse.buildship.core.prefs

@@ -1,2 +1,2 @@
 connection.project.dir=
-eclipse.preferences.version=1
+eclipse.preferences.version=1

gradlew

@@ -241,4 +241,4 @@ eval "set -- $(
         tr '\n' ' '
     )" '"$@"'
 
-exec "$JAVACMD" "$@"
+exec "$JAVACMD" "$@"

gradlew.bat

@@ -89,4 +89,4 @@ exit /b %EXIT_CODE%
 :mainEnd
 if "%OS%"=="Windows_NT" endlocal
 
-:omega
+:omega

src/main/java/scriptmanager/charts/CompositePlot.java

@@ -28,6 +28,11 @@
  */
 public class CompositePlot {
 
+	/** 
+	* Creates a new CompositePlot object
+	*/
+	public CompositePlot(){}
+
 	/**
 	 * Create a two-line plot (sense and antisense composites) with a title and
 	 * custom colors. There are no checks on input array lengths (line plot

src/main/java/scriptmanager/charts/Histogram.java

@@ -31,7 +31,7 @@ public class Histogram {
 	 * @param y the list of frequencies
 	 * @param x the list of values that have frequencies (same len as y)
 	 * @return the bar-style histogram chart
-	 * @throws IOException
+	 * @throws IOException Invalid file or parameters
 	 */
 	public static ChartPanel createBarChart(double[] y, int[] x) throws IOException {
 		final XYSeries series = new XYSeries("Frequency");
@@ -54,7 +54,7 @@ public static ChartPanel createBarChart(double[] y, int[] x) throws IOException
 	 * @param x the list of values that have frequencies (same len as y)
 	 * @param output the path of the PNG file to save the chart image to
 	 * @return the bar-style histogram chart
-	 * @throws IOException
+	 * @throws IOException Invalid file or parameters
 	 */
 	public static ChartPanel createBarChart(double[] y, int[] x, File output) throws IOException {
 		final XYSeries series = new XYSeries("Frequency");
@@ -82,7 +82,7 @@ public static ChartPanel createBarChart(double[] y, int[] x, File output) throws
 	 * 
 	 * @param dataset the formatted dataset to plot
 	 * @return the formatted and configured histogram chart
-	 * @throws IOException
+	 * @throws IOException Invalid file or parameters
 	 */
 	private static JFreeChart createChart(IntervalXYDataset dataset) throws IOException {
         final JFreeChart chart = ChartFactory.createXYBarChart(

src/main/java/scriptmanager/charts/LineChart.java

@@ -31,7 +31,7 @@ public class LineChart {
 	 * @param y the duplication rate values
 	 * @param x the domain values
 	 * @return the line plot chart
-	 * @throws IOException
+	 * @throws IOException Invalid file or parameters
 	 */
 	public static ChartPanel createLineChart(ArrayList<Double> y, String[] x) throws IOException {
 		DefaultCategoryDataset dataset = new DefaultCategoryDataset();
@@ -53,7 +53,7 @@ public static ChartPanel createLineChart(ArrayList<Double> y, String[] x) throws
 	 * @param y2 the genome duplication rate values
 	 * @param x  the domain values
 	 * @return the line plot chart
-	 * @throws IOException
+	 * @throws IOException Invalid file or parameters
 	 */
 	public static ChartPanel createLineChart(ArrayList<Double> y1, ArrayList<Double> y2, String[] x) throws IOException {
 		DefaultCategoryDataset dataset = new DefaultCategoryDataset();
@@ -75,7 +75,7 @@ public static ChartPanel createLineChart(ArrayList<Double> y1, ArrayList<Double>
 	 * @param x the domain values
 	 * @param output the path of the PNG file to save the chart image to
 	 * @return the line plot chart
-	 * @throws IOException
+	 * @throws IOException Invalid file or parameters
 	 */
 	public static ChartPanel createLineChart(ArrayList<Double> y, String[] x, File output) throws IOException {
 		DefaultCategoryDataset dataset = new DefaultCategoryDataset();
@@ -102,7 +102,7 @@ public static ChartPanel createLineChart(ArrayList<Double> y, String[] x, File o
 	 * 
 	 * @param dataset the formatted dataset to plot
 	 * @return the line plot chart
-	 * @throws IOException
+	 * @throws IOException Invalid file or parameters
 	 */
 	private static JFreeChart createChart(CategoryDataset dataset) throws IOException {
         final JFreeChart chart = ChartFactory.createLineChart(

src/main/java/scriptmanager/charts/package-info.java

@@ -0,0 +1,7 @@
+/**
+ * Collection of classes containing static methods to generate Components with a
+ * variety of visualizations for data. Used by graphical interfaces
+ * (`window_interface`) and figure making scripts in
+ * {@link scriptmanager.scripts.BAM_Format_Converter}
+ */
+package scriptmanager.charts;