From 984b20fa94376c549b75bda56bf4ec2fecb4cdd6 Mon Sep 17 00:00:00 2001
From: Mungo Carstairs <gmungoc@gmail.com>
Date: Tue, 22 Oct 2019 16:30:18 +0100
Subject: [PATCH] JAL-3253 rename method, add Javadoc

---
 src/jalview/bin/Jalview.java |   29 ++++++++++++++++++++++-------
 1 file changed, 22 insertions(+), 7 deletions(-)

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 3d80589..ff8d52f 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -859,7 +859,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
             groovyscript = null;
           }
         }
-        checkOutputFile(aparser, af, format);
+        createOutputFiles(aparser, af, format);
         while (aparser.getSize() > 0)
         {
           System.out.println("Unknown arg: " + aparser.nextValue());
@@ -1040,19 +1040,34 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
     return haveImport;
   }
 
-  private void checkOutputFile(ArgsParser aparser, AlignFrame af,
+  /**
+   * Writes an output file for each format (if any) specified in the
+   * command-line arguments. Supported formats are currently
+   * <ul>
+   * <li>png</li>
+   * <li>svg</li>
+   * <li>html</li>
+   * <li>biojsmsa</li>
+   * <li>imgMap</li>
+   * <li>eps</li>
+   * </ul>
+   * A format parameter should be followed by a parameter specifying the output
+   * file name. {@code imgMap} parameters should follow those for the
+   * corresponding alignment image output.
+   * 
+   * @param aparser
+   * @param af
+   * @param format
+   */
+  private void createOutputFiles(ArgsParser aparser, AlignFrame af,
           FileFormatI format)
   {
     String imageName = "unnamed.png";
     while (aparser.getSize() > 1)
     {
-      // PNG filename
-      // SVG filename
-      // HTML filename
-      // biojsmsa filename
       String outputFormat = aparser.nextValue();
       String file = aparser.nextValue();
-      System.out.println("format " + outputFormat);
+      // System.out.println("format " + outputFormat);
 
       if (outputFormat.equalsIgnoreCase("png"))
       {
-- 
1.7.10.2