JAL-3633 ensure check both http:// or https:// for urls

[jalview.git] / src / jalview / bin / Jalview.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 1e292ba..eaa5fa8 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,28 +20,6 @@
  */
 package jalview.bin;
 
-import jalview.ext.so.SequenceOntology;
-import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.gui.PromptUserConfig;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.BioJsHTMLOutput;
-import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
-import jalview.io.FileFormatException;
-import jalview.io.FileFormatI;
-import jalview.io.FileFormats;
-import jalview.io.FileLoader;
-import jalview.io.HtmlSvgOutput;
-import jalview.io.IdentifyFile;
-import jalview.io.NewickFile;
-import jalview.io.gff.SequenceOntologyFactory;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.ws.jws2.Jws2Discoverer;
-
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileOutputStream;
@@ -79,6 +57,7 @@ import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FileFormatException;
 import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
 import jalview.io.FileLoader;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
@@ -451,10 +430,8 @@ public class Jalview
       }
       System.out.println("CMD [-open " + file + "] executed successfully!");
 
-      
-
       protocol = AppletFormatAdapter.checkProtocol(file);
-      
+
       if (protocol == DataSourceType.FILE)
       {
         if (!(new File(file)).exists())
@@ -650,11 +627,14 @@ public class Jalview
             af.createEPS(outputFile);
             continue;
           }
-          FileFormatI outFormat=null;
-          try {
+          FileFormatI outFormat = null;
+          try
+          {
             outFormat = FileFormats.getInstance().forName(outputFormat);
-          } catch (Exception formatP) {
-            System.out.println("Couldn't parse "+outFormat+" as a valid Jalview format string.");
+          } catch (Exception formatP)
+          {
+            System.out.println("Couldn't parse " + outFormat
+                    + " as a valid Jalview format string.");
           }
           if (outFormat != null)
           {
@@ -698,8 +678,8 @@ public class Jalview
               jalview.bin.Cache.getDefault("www.jalview.org",
                       "https://www.jalview.org")
                       + "/examples/exampleFile_2_7.jvp");
-      if (file.equals(
-              "http://www.jalview.org/examples/exampleFile_2_3.jar") || file.equals(
+      if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
+              || file.equals(
                       "http://www.jalview.org/examples/exampleFile_2_7.jar"))
       {
         file.replace("http:", "https:");