Fixed files that weren't meant to be modified

benjaminbeer256 · benjaminbeer256 · commit 0fa37dfd434c · 2023-08-04T10:40:06.000-04:00
diff --git a/.classpath b/.classpath
@@ -6,6 +6,20 @@
 			<attribute name="gradle_used_by_scope" value="main,test"/>
 		</attributes>
 	</classpathentry>
+	<classpathentry kind="src" output="bin/test" path="src/test/java">
+		<attributes>
+			<attribute name="gradle_scope" value="test"/>
+			<attribute name="gradle_used_by_scope" value="test"/>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="bin/test" path="src/test/resources">
+		<attributes>
+			<attribute name="gradle_scope" value="test"/>
+			<attribute name="gradle_used_by_scope" value="test"/>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="src" output="bin/main" path="src/main/java">
 		<attributes>
 			<attribute name="gradle_scope" value="main"/>
@@ -15,4 +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>
diff --git a/.gitignore b/.gitignore
@@ -3,5 +3,4 @@
 /.gradle/
 /build/
 .metadata
-.idea
-/doc
+.idea
diff --git a/.project b/.project
@@ -20,15 +20,4 @@
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.eclipse.buildship.core.gradleprojectnature</nature>
 	</natures>
-	<filteredResources>
-		<filter>
-			<id>1687870327349</id>
-			<name></name>
-			<type>30</type>
-			<matcher>
-				<id>org.eclipse.core.resources.regexFilterMatcher</id>
-				<arguments>node_modules|\.git|__CREATED_BY_JAVA_LANGUAGE_SERVER__</arguments>
-			</matcher>
-		</filter>
-	</filteredResources>
-</projectDescription>
+</projectDescription>
diff --git a/.settings/org.eclipse.buildship.core.prefs b/.settings/org.eclipse.buildship.core.prefs
@@ -1,13 +1,2 @@
-arguments=--init-script /var/folders/32/shfmy9512bncl3tdq6z2z4v00000gs/T/d146c9752a26f79b52047fb6dc6ed385d064e120494f96f08ca63a317c41f94c.gradle --init-script /var/folders/32/shfmy9512bncl3tdq6z2z4v00000gs/T/52cde0cfcf3e28b8b7510e992210d9614505e0911af0c190bd590d7158574963.gradle
-auto.sync=false
-build.scans.enabled=false
-connection.gradle.distribution=GRADLE_DISTRIBUTION(WRAPPER)
 connection.project.dir=
-eclipse.preferences.version=1
-gradle.user.home=
-java.home=/Library/Java/JavaVirtualMachines/jdk-18.0.2.jdk/Contents/Home
-jvm.arguments=
-offline.mode=false
-override.workspace.settings=true
-show.console.view=true
-show.executions.view=true
+eclipse.preferences.version=1
diff --git a/gradlew b/gradlew
@@ -22,7 +22,7 @@
 #
 #   Important for running:
 #
-#   (1) You need a POSIX-compliant shell to run this script If your /bin/sh is
+#   (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is
 #       noncompliant, but you have some other compliant shell such as ksh or
 #       bash, then to run this script, type that shell name before the whole
 #       command line, like:
@@ -85,7 +85,7 @@ done
 APP_BASE_NAME=${0##*/}
 APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
 
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
 DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
@@ -241,4 +241,4 @@ eval "set -- $(
         tr '\n' ' '
     )" '"$@"'
 
-exec "$JAVACMD" "$@"
+exec "$JAVACMD" "$@"
diff --git a/gradlew.bat b/gradlew.bat
@@ -33,7 +33,7 @@ set APP_HOME=%DIRNAME%
 @rem Resolve any "." and ".." in APP_HOME to make it shorter.
 for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
 
-@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script
+@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
 set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
 
 @rem Find java.exe
@@ -89,4 +89,4 @@ exit /b %EXIT_CODE%
 :mainEnd
 if "%OS%"=="Windows_NT" endlocal
 
-:omega
+:omega
diff --git a/src/main/java/scriptmanager/cli/BAM_Manipulation/BAIIndexerCLI.java b/src/main/java/scriptmanager/cli/BAM_Manipulation/BAIIndexerCLI.java
@@ -7,7 +7,7 @@
 import scriptmanager.objects.ToolDescriptions;
 
 /**
- * Print a message redirecting user to the original CLI tool.
+ * Prints a message redirecting user to the original CLI tool.
  * 
  * @author Olivia Lang
  * @see scriptmanager.scripts.BAM_Manipulation.BAIIndexer
diff --git a/src/main/java/scriptmanager/cli/BAM_Manipulation/BAMRemoveDupCLI.java b/src/main/java/scriptmanager/cli/BAM_Manipulation/BAMRemoveDupCLI.java
@@ -9,7 +9,7 @@
 import scriptmanager.objects.ToolDescriptions;
 
 /**
- * Print a message redirecting user to the original CLI tool.
+ * Prints a message redirecting user to the original CLI tool.
  * 
  * @author Olivia Lang
  * @see scriptmanager.scripts.BAM_Manipulation.BAMMarkDuplicates
diff --git a/src/main/java/scriptmanager/cli/BAM_Manipulation/MergeBAMCLI.java b/src/main/java/scriptmanager/cli/BAM_Manipulation/MergeBAMCLI.java
@@ -7,7 +7,7 @@
 import scriptmanager.objects.ToolDescriptions;
 
 /**
- * Print a message redirecting user to the original CLI tool.
+ * Prints a message redirecting user to the original CLI tool.
  * 
  * @author Olivia Lang
  * @see scriptmanager.scripts.BAM_Manipulation.MergeBAM
diff --git a/src/main/java/scriptmanager/cli/BAM_Manipulation/SortBAMCLI.java b/src/main/java/scriptmanager/cli/BAM_Manipulation/SortBAMCLI.java
@@ -8,7 +8,7 @@
 import scriptmanager.objects.ToolDescriptions;
 
 /**
- * Print a message redirecting user to the original CLI tool.
+ * Prints a message redirecting user to the original CLI tool.
  * 
  * @author Olivia Lang
  * @see scriptmanager.scripts.BAM_Manipulation.BAMFileSort
diff --git a/src/main/java/scriptmanager/cli/Figure_Generation/MergeHeatMapCLI.java b/src/main/java/scriptmanager/cli/Figure_Generation/MergeHeatMapCLI.java
@@ -17,7 +17,7 @@
  * Command line interface class for merging two heat maps
  * 
  * @author Olivia Lang
- * @see scriptmanager.scripts.Figure_Generation.FourColorPlot
+ * @see scriptmanager.scripts.Figure_Generation.MergeHeatMapPlot
  */
 @Command(name = "merge-heatmap",
 	mixinStandardHelpOptions = true,
diff --git a/src/main/java/scriptmanager/cli/Figure_Generation/ThreeColorHeatMapCLI.java b/src/main/java/scriptmanager/cli/Figure_Generation/ThreeColorHeatMapCLI.java
@@ -23,7 +23,7 @@
  * Command line interface class for generating three color heat maps
  * 
  * @author Olivia Lang
- * @see scriptmanager.scripts.Figure_Generation.FourColorPlot
+ * @see scriptmanager.scripts.Figure_Generation.ThreeColorHeatMap
  */
 @Command(name = "three-color", mixinStandardHelpOptions = true,
 	description = ToolDescriptions.threecolorheatmap_description,
diff --git a/src/main/java/scriptmanager/cli/Figure_Generation/TwoColorHeatMapCLI.java b/src/main/java/scriptmanager/cli/Figure_Generation/TwoColorHeatMapCLI.java
@@ -22,7 +22,7 @@
  * sequence plots.
  * 
  * @author Olivia Lang
- * @see scriptmanager.scripts.Figure_Generation.FourColorPlot
+ * @see scriptmanager.scripts.Figure_Generation.TwoColorHeatMap
  */
 @Command(name = "heatmap",
 	mixinStandardHelpOptions = true,
diff --git a/src/main/java/scriptmanager/cli/File_Utilities/ConvertBEDChrNamesCLI.java b/src/main/java/scriptmanager/cli/File_Utilities/ConvertBEDChrNamesCLI.java
@@ -14,7 +14,7 @@
 import scriptmanager.scripts.File_Utilities.ConvertChrNames;
 
 /**
- * Command line interface class for converting chromsome names of BED file by
+ * Command line interface class for converting chromsome names of BED files by
  * calling method implemented in the scripts package.
  * 
  * @author Olivia Lang
diff --git a/src/main/java/scriptmanager/cli/File_Utilities/ConvertGFFChrNamesCLI.java b/src/main/java/scriptmanager/cli/File_Utilities/ConvertGFFChrNamesCLI.java
@@ -14,7 +14,7 @@
 import scriptmanager.scripts.File_Utilities.ConvertChrNames;
 
 /**
- * Command line interface class for converting chromsome names of GFF file by
+ * Command line interface class for converting chromsome names of GFF files by
  * calling method implemented in the scripts package.
  * 
  * @author Olivia Lang
diff --git a/src/main/java/scriptmanager/cli/File_Utilities/MD5ChecksumCLI.java b/src/main/java/scriptmanager/cli/File_Utilities/MD5ChecksumCLI.java
@@ -13,7 +13,7 @@
 import scriptmanager.scripts.File_Utilities.MD5Checksum;
 
 /**
- * Print a message redirecting user to the original CLI tool.
+ * Prints a message redirecting user to the original CLI tool.
  * 
  * @author Olivia Lang
  * @see scriptmanager.scripts.File_Utilities.MD5Checksum
diff --git a/src/main/java/scriptmanager/scripts/BAM_Statistics/CorrelationScripts/CorrelationExtract.java b/src/main/java/scriptmanager/scripts/BAM_Statistics/CorrelationScripts/CorrelationExtract.java
@@ -35,10 +35,10 @@ public class CorrelationExtract implements Runnable {
 	 * @param r Which reads to correlate 
 	 * @param s The tag shift in #of base pairs
 	 * @param b The bin size in #of base pairs
-	 * @param current Specifies the current  
-	 * @param sub ️
-	 * @param e1 First SAM file
-	 * @param e2 Second SAM file
+	 * @param current Specifies the starting index
+	 * @param sub ️The subset size
+	 * @param e1 First BAM file
+	 * @param e2 Second BAM file
 	 */
 	public CorrelationExtract(Vector<CorrelationCoord> win, int r, int s, int b, int current, int sub, File e1, File e2) {
 		ALLNodes = win;
@@ -52,7 +52,7 @@ public CorrelationExtract(Vector<CorrelationCoord> win, int r, int s, int b, int
 	}
 	
 	/**
-	 * Runs the correlation analysis between the two SAM files
+	 * Runs the correlation analysis between the two BAM files
 	 */
 	public void run() {
 		for(int x = INDEX; x < INDEX + SUBSETSIZE; x++) {
diff --git a/src/main/java/scriptmanager/scripts/BAM_Statistics/package-info.java b/src/main/java/scriptmanager/scripts/BAM_Statistics/package-info.java
@@ -1,4 +1,4 @@
 /**
- * Package containing scripts necessary for BAM file analysis
+ * Package containing scripts for BAM file analysis
  */
 package scriptmanager.scripts.BAM_Statistics;
diff --git a/src/main/java/scriptmanager/scripts/Coordinate_Manipulation/package-info.java b/src/main/java/scriptmanager/scripts/Coordinate_Manipulation/package-info.java
@@ -1,4 +1,4 @@
 /**
- * Package containing scripts necessary for coordinate manipulation of BED and GFF files
+ * Package containing scripts necessary for manipulation of BED and GFF files
  */
 package scriptmanager.scripts.Coordinate_Manipulation;
diff --git a/src/main/java/scriptmanager/scripts/Peak_Analysis/FilterBEDbyProximity.java b/src/main/java/scriptmanager/scripts/Peak_Analysis/FilterBEDbyProximity.java
@@ -28,6 +28,14 @@ public class FilterBEDbyProximity{
 	private PrintStream OUT_Cluster = null;
 	private PrintStream PS = null;
 	
+	/**
+	 * Creates a new instance of a FilterBEDbyProximity script
+	 * @param input BED file to filter
+	 * @param cutoff Exclusion distance (bp)
+	 * @param outputBase Base name for the output files
+	 * @param ps Output PrintStream
+	 * @throws IOException Invalid file or parameters
+	 */
 	public FilterBEDbyProximity(File input, int cutoff, String outputBase, PrintStream ps) throws IOException {
 		CUTOFF = cutoff;
 		PS = ps;
diff --git a/src/main/java/scriptmanager/scripts/Read_Analysis/ScalingFactor.java b/src/main/java/scriptmanager/scripts/Read_Analysis/ScalingFactor.java
@@ -532,6 +532,11 @@ public int compare(PairedCounts o1, PairedCounts o2) {
 	public static class PairedCounts implements Comparable<PairedCounts> {
 		public Double x, y;
 
+		/**
+		 * Creates a new PaireCounts object
+		 * @param a The value of X
+		 * @param b The value of Y
+		 */
 		public PairedCounts(double a, double b) {
 			x = a;
 			y = b;
diff --git a/src/main/java/scriptmanager/scripts/Read_Analysis/SimilarityMatrix.java b/src/main/java/scriptmanager/scripts/Read_Analysis/SimilarityMatrix.java
@@ -158,7 +158,7 @@ public void outputMatrixLoadFail() throws FileNotFoundException, IOException {
 	/**
 	 * Outputs resulting matrix to same directory as original matrix
 	 * @param matrix Matrix to output
-	 * @param id
+	 * @param id ID's of rows and columns
 	 * @throws IOException Invalid file or parameters
 	 */
 	public void outputMatrix(double[][] matrix, ArrayList<String> id) throws IOException {
diff --git a/src/main/java/scriptmanager/util/FileSelection.java b/src/main/java/scriptmanager/util/FileSelection.java
@@ -17,7 +17,7 @@ public class FileSelection {
 	 * Generic multi-file FileSelector without extension restrictions (commonly
 	 * TAB-delimited file formats like matrix/table data).
 	 * 
-	 * @param fc
+	 * @param fc FileChooser that provides all files and displays appropriate files
 	 * @return array of File objects from selector UI
 	 */
 	public static File[] getGenericFiles(JFileChooser fc){
@@ -36,7 +36,7 @@ public static File[] getGenericFiles(JFileChooser fc){
 	/**
 	 * Generic single-file FileSelector for retrieving directories.
 	 * 
-	 * @param fc
+	 * @param fc FileChooser that provides all files and displays appropriate files
 	 * @return a directory-type file
 	 */
 	public static File getOutputDir(JFileChooser fc) {
@@ -54,7 +54,7 @@ public static File getOutputDir(JFileChooser fc) {
 	 * Extension-based single-file FileSelector for retrieving a single file with a
 	 * specific extension.
 	 * 
-	 * @param fc
+	 * @param fc FileChooser that provides all files and displays appropriate files
 	 * @param ext the extension to restrict file selection options by
 	 * @return a single file with a specific extension (see "ext")
 	 */
@@ -66,7 +66,7 @@ public static File getFile(JFileChooser fc, String ext){
 	 * Extension-based single-file FileSelector for retrieving a single file with a
 	 * specific extension where ignoring ".gz" extensions can be toggled.
 	 * 
-	 * @param fc
+	 * @param fc FileChooser that provides all files and displays appropriate files
 	 * @param ext       the extension to restrict file selection options by
 	 * @param includeGZ true value means ignore the ".gz" if present when checking
 	 *                  the extension
@@ -90,7 +90,7 @@ public static File getFile(JFileChooser fc, String ext, boolean includeGZ){
 	 * Extension-based multi-file FileSelector for retrieving a set of files with a
 	 * specific extension.
 	 * 
-	 * @param fc
+	 * @param fc FileChooser that provides all files and displays appropriate files
 	 * @param ext the extension to restrict file selection options by
 	 * @return a list of files with a specific extension (see "ext")
 	 */
@@ -102,7 +102,7 @@ public static File[] getFiles(JFileChooser fc, String ext){
 	 * Extension-based multi-file FileSelector for retrieving a set of files with a
 	 * specific extension where ignoring ".gz" extensions can be toggled.
 	 * 
-	 * @param fc
+	 * @param fc FileChooser that provides all files and displays appropriate files
 	 * @param ext       the extension to restrict file selection options by
 	 * @param includeGZ true value means ignore the ".gz" if present when checking
 	 *                  the extension
diff --git a/src/main/java/scriptmanager/window_interface/BAM_Manipulation/BAIIndexerWindow.java b/src/main/java/scriptmanager/window_interface/BAM_Manipulation/BAIIndexerWindow.java
@@ -32,8 +32,8 @@
 
 /**
  * Graphical window for user argument selection and execution of the BAIIndexer script
+ * @see scriptmanager.scripts.BAM_Manipulation.BAIIndexer
  * @see scriptmanager.cli.BAM_Manipulation.BAIIndexerCLI
- * @see scriptmanager.window_interface.BAM_Manipulation.BAIIndexerWindow
  */
 @SuppressWarnings("serial")
 public class BAIIndexerWindow extends JFrame implements ActionListener, PropertyChangeListener {
diff --git a/src/main/java/scriptmanager/window_interface/BAM_Manipulation/FilterforPIPseqWindow.java b/src/main/java/scriptmanager/window_interface/BAM_Manipulation/FilterforPIPseqWindow.java
@@ -38,7 +38,7 @@
 /**
  * Graphical window for user argument selection and execution of the FilterforPIPseq script
  * @see scriptmanager.scripts.BAM_Manipulation.FilterforPIPseq
- * @see scriptmanager.window_interface.BAM_Manipulation.FilterforPIPseqWindow
+ * @see scriptmanager.window_interface.BAM_Manipulation.FilterforPIPseqOutput
  */
 @SuppressWarnings("serial")
 public class FilterforPIPseqWindow extends JFrame implements ActionListener, PropertyChangeListener {
diff --git a/src/main/java/scriptmanager/window_interface/BAM_Statistics/PEStatOutput.java b/src/main/java/scriptmanager/window_interface/BAM_Statistics/PEStatOutput.java
@@ -21,10 +21,9 @@
 import scriptmanager.scripts.BAM_Statistics.PEStats;
 
 /**
- * Graphical window for viewing results form the PEStats script
- * @see scriptmanager.scripts.BAM_Statistics.SEStats
- * @see scriptmanager.window_interface.BAM_Statistics.SEStatWindow
- * @see scriptmanager.window_interface.BAM_Statistics.SEStatOutput
+ * Graphical window for running and viewing results form the PEStats script
+ * @see scriptmanager.scripts.BAM_Statistics.PEStats
+ * @see scriptmanager.window_interface.BAM_Statistics.PEStatOutput
  */
 @SuppressWarnings("serial")
 public class PEStatOutput extends JFrame {
diff --git a/src/main/java/scriptmanager/window_interface/BAM_Statistics/PEStatWindow.java b/src/main/java/scriptmanager/window_interface/BAM_Statistics/PEStatWindow.java
@@ -37,8 +37,8 @@
 
 /**
  * Graphical window for user argument selection and execution of the PEStats script
- * @see scriptmanager.scripts.BAM_Statistics.SEStats
- * @see scriptmanager.window_interface.BAM_Statistics.SEStatOutput
+ * @see scriptmanager.scripts.BAM_Statistics.PEStats
+ * @see scriptmanager.window_interface.BAM_Statistics.PEStatOutput
  */
 @SuppressWarnings("serial")
 public class PEStatWindow extends JFrame implements ActionListener, PropertyChangeListener {
diff --git a/src/main/java/scriptmanager/window_interface/Figure_Generation/LabelHeatMapOutput.java b/src/main/java/scriptmanager/window_interface/Figure_Generation/LabelHeatMapOutput.java
@@ -19,7 +19,7 @@
 
 /**
  * Output wrapper for running LabelHeatMap script and reporting when the process is completed
- * @see scriptmanager.scripts.Figure_Generation
+ * @see scriptmanager.scripts.Figure_Generation.LabelHeatMap
  * @see scriptmanager.window_interface.Figure_Generation.LabelHeatMapWindow
  */
 @SuppressWarnings("serial")
diff --git a/src/main/java/scriptmanager/window_interface/Figure_Generation/LabelHeatMapWindow.java b/src/main/java/scriptmanager/window_interface/Figure_Generation/LabelHeatMapWindow.java
@@ -44,8 +44,8 @@
  * into a user-friendly layout of fields and labels.
  * 
  * @author Olivia Lang
- * @see scriptmanager.scripts.Figure_Generation.PlotComposite
- * @see scriptmanager.window_interface.Figure_Generation.PlotCompositeOutput
+ * @see scriptmanager.scripts.Figure_Generation.LabelHeatMap
+ * @see scriptmanager.window_interface.Figure_Generation.LabelHeatMapOutput
  */
 @SuppressWarnings("serial")
 public class LabelHeatMapWindow extends JFrame implements ActionListener, PropertyChangeListener {
diff --git a/src/main/java/scriptmanager/window_interface/File_Utilities/CompressFileWindow.java b/src/main/java/scriptmanager/window_interface/File_Utilities/CompressFileWindow.java
diff --git a/src/main/java/scriptmanager/window_interface/File_Utilities/DecompressGZFileWindow.java b/src/main/java/scriptmanager/window_interface/File_Utilities/DecompressGZFileWindow.java
diff --git a/src/main/java/scriptmanager/window_interface/Peak_Analysis/BEDPeakAligntoRefOutput.java b/src/main/java/scriptmanager/window_interface/Peak_Analysis/BEDPeakAligntoRefOutput.java
diff --git a/src/main/java/scriptmanager/window_interface/Peak_Analysis/BEDPeakAligntoRefWindow.java b/src/main/java/scriptmanager/window_interface/Peak_Analysis/BEDPeakAligntoRefWindow.java
diff --git a/src/main/java/scriptmanager/window_interface/Peak_Analysis/FilterBEDbyProximityOutput.java b/src/main/java/scriptmanager/window_interface/Peak_Analysis/FilterBEDbyProximityOutput.java
diff --git a/src/main/java/scriptmanager/window_interface/Peak_Analysis/FilterBEDbyProximityWindow.java b/src/main/java/scriptmanager/window_interface/Peak_Analysis/FilterBEDbyProximityWindow.java

Original file line number	Diff line number	Diff line change
`@@ -7,7 +7,7 @@`
`7`	`7`	`import scriptmanager.objects.ToolDescriptions;`
`8`	`8`
`9`	`9`	`/**`
`10`		`- * Print a message redirecting user to the original CLI tool.`
	`10`	`+ * Prints a message redirecting user to the original CLI tool.`
`11`	`11`	`*`
`12`	`12`	`* @author Olivia Lang`
`13`	`13`	`* @see scriptmanager.scripts.BAM_Manipulation.BAIIndexer`
Original file line number	Diff line number	Diff line change
`@@ -9,7 +9,7 @@`
`9`	`9`	`import scriptmanager.objects.ToolDescriptions;`
`10`	`10`
`11`	`11`	`/**`
`12`		`- * Print a message redirecting user to the original CLI tool.`
	`12`	`+ * Prints a message redirecting user to the original CLI tool.`
`13`	`13`	`*`
`14`	`14`	`* @author Olivia Lang`
`15`	`15`	`* @see scriptmanager.scripts.BAM_Manipulation.BAMMarkDuplicates`
Original file line number	Diff line number	Diff line change
`@@ -8,7 +8,7 @@`
`8`	`8`	`import scriptmanager.objects.ToolDescriptions;`
`9`	`9`
`10`	`10`	`/**`
`11`		`- * Print a message redirecting user to the original CLI tool.`
	`11`	`+ * Prints a message redirecting user to the original CLI tool.`
`12`	`12`	`*`
`13`	`13`	`* @author Olivia Lang`
`14`	`14`	`* @see scriptmanager.scripts.BAM_Manipulation.BAMFileSort`