fix unhandled ScriptManagerException

The exception thrown when input FASTA has N-containing sequences is not properly handled. This commit adds appropriate `throws` and `catch` statements

src/main/java/scriptmanager/window_interface/Sequence_Analysis/DNAShapefromFASTAOutput.java

@@ -19,6 +19,7 @@
 import scriptmanager.objects.CustomOutputStream;
 import scriptmanager.objects.LogItem;
 import scriptmanager.objects.Exceptions.OptionException;
+import scriptmanager.objects.Exceptions.ScriptManagerException;
 import scriptmanager.util.ExtensionFileFilter;
 
 import scriptmanager.cli.Sequence_Analysis.DNAShapefromFASTACLI;
@@ -100,7 +101,7 @@ public DNAShapefromFASTAOutput(ArrayList<File> fa, File out_dir, boolean[] type,
 	 * @throws IOException Invalid file or parameters
 	 * @throws InterruptedException Thrown when more than one script is run at the same time
 	 */
-	public void run() throws OptionException, FileNotFoundException, IOException, InterruptedException {
+	public void run() throws ScriptManagerException, OptionException, FileNotFoundException, IOException, InterruptedException {
 			LogItem old_li = null;
 			// Move through each BED File
 			for (int x = 0; x < FASTA.size(); x++) {

src/main/java/scriptmanager/window_interface/Sequence_Analysis/DNAShapefromFASTAWindow.java

@@ -36,6 +36,7 @@
 import javax.swing.border.TitledBorder;
 
 import scriptmanager.objects.Exceptions.OptionException;
+import scriptmanager.objects.Exceptions.ScriptManagerException;
 import scriptmanager.objects.ToolDescriptions;
 import scriptmanager.util.ExtensionFileFilter;
 import scriptmanager.util.FileSelection;
@@ -136,6 +137,8 @@ public void propertyChange(PropertyChangeEvent evt) {
 					output_obj.setVisible(true);
 					output_obj.run();
 				}
+			} catch (ScriptManagerException sme) {
+				JOptionPane.showMessageDialog(null, sme.getMessage());
 			} catch (OptionException oe) {
 				JOptionPane.showMessageDialog(null, oe.getMessage());
 			} catch (NumberFormatException nfe) {