X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=3a238bb0e3f90fc90c201dd2ad7fdcf31172f2b7;hb=8d5cf09fa18cde0cb0d0362adc64571be5b08dc6;hp=1e292bae703bf0690e7d910230df0b9f5988e55a;hpb=48040645e199f64d0bd396cc3a6137035a697737;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 1e292ba..3a238bb 100755
--- 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;
@@ -86,6 +65,7 @@ import jalview.io.NewickFile;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
+import jalview.util.HttpUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.jws2.Jws2Discoverer;
@@ -451,10 +431,8 @@ 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 +628,14 @@ 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 +679,8 @@ 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:");
@@ -710,12 +691,7 @@ public class Jalview
         jalview.bin.Cache.removeProperty("STARTUP_FILE");
       }
 
-      protocol = DataSourceType.FILE;
-
-      if (file.indexOf("http:") > -1)
-      {
-        protocol = DataSourceType.URL;
-      }
+      protocol = AppletFormatAdapter.checkProtocol(file);
 
       if (file.endsWith(".jar"))
       {