From 8e98fa5a09e06ac59c965d030ed71b0158178a24 Mon Sep 17 00:00:00 2001
From: BobHanson <hansonr@stolaf.edu>
Date: Mon, 1 Jun 2020 22:27:37 -0500
Subject: [PATCH] SO option true for Java (from Jalview-JS/develop)

---
 src/jalview/bin/Jalview.java |  113 ++++--------------------------------------
 1 file changed, 9 insertions(+), 104 deletions(-)

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index ab9b1d9..74babbb 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -474,7 +474,9 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
      * configure 'full' SO model if preferences say to, 
      * else use the default (SO Lite)
      */
-    if (Cache.getDefault(Preferences.USE_FULL_SO, false))
+    // BH NOTE 2020.06.01 Jalview-JS/develop has this true for Java, false for
+    // JavaScript
+    if (Cache.getDefault(Preferences.USE_FULL_SO, !isJS))
     {
       SequenceOntologyFactory.setSequenceOntology(new SequenceOntology());
     }
@@ -562,7 +564,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
     try
     {
       ArgsParser aparser = new ArgsParser(args);
-      return parseArguments(aparser, false);
+      parseArguments(aparser, false);
+      return null;
     } catch (Throwable t)
     {
       return t;
@@ -573,9 +576,9 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
    * 
    * @param aparser
    * @param isStartup
-   * @return
+   * @return null, indicating no error
    */
-  private Object parseArguments(ArgsParser aparser, boolean isStartup)
+  private void parseArguments(ArgsParser aparser, boolean isStartup)
   {
     boolean isJS = Platform.isJS();
 
@@ -599,7 +602,6 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
       System.out.println("No files to open!");
       System.exit(1);
     }
-    boolean haveImport = checkStartVamas(aparser);
     // Finally, deal with the remaining input data.
     long progress = -1;
     if (file == null && isJavaAppletTag)
@@ -729,11 +731,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
                     "CMD [-open2 " + file2 + "] executed successfully!");
           }
         }
-
         setCurrentAlignFrame(af);
 
-        // TODO: file2 How to implement file2 for the applet spit screen?
-
         data = aparser.getValue(ArgsParser.COLOUR, true);
         if (data != null)
         {
@@ -885,12 +884,13 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
         }
       }
     }
+
     AlignFrame startUpAlframe = null;
     // We'll only open the default file if the desktop is visible.
     // And the user
     // ////////////////////
 
-    if (!isJS && !headless && file == null && !haveImport
+    if (!isJS && !headless && file == null
             && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
     /**
      * Java only
@@ -963,100 +963,6 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
       desktop.setInBatchMode(false);
     }
 
-    return null;
-  }
-
-  private boolean checkStartVamas(ArgsParser aparser)
-  {
-    String vamsasImport = aparser.getValue(ArgsParser.VDOC);
-    String vamsasSession = aparser.getValue(ArgsParser.VSESS);
-    if (vamsasImport == null && vamsasSession == null)
-    {
-      return false;
-    }
-    if (desktop == null || headless)
-    {
-      System.out.println(
-              "Headless vamsas sessions not yet supported. Sorry.");
-      System.exit(1);
-    }
-    boolean haveImport = (vamsasImport != null);
-    if (haveImport)
-    {
-      // if we have a file, start a new session and import it.
-      boolean inSession = false;
-      try
-      {
-        DataSourceType viprotocol = AppletFormatAdapter
-                .checkProtocol(vamsasImport);
-        if (viprotocol == DataSourceType.FILE)
-        {
-          inSession = desktop.vamsasImport(new File(vamsasImport));
-        }
-        else if (viprotocol == DataSourceType.URL)
-        {
-          inSession = desktop.vamsasImport(new URL(vamsasImport));
-        }
-
-      } catch (Exception e)
-      {
-        System.err.println("Exeption when importing " + vamsasImport
-                + " as a vamsas document.");
-        e.printStackTrace();
-      }
-      if (!inSession)
-      {
-        System.err.println("Failed to import " + vamsasImport
-                + " as a vamsas document.");
-      }
-      else
-      {
-        System.out.println("Imported Successfully into new session "
-                + desktop.getVamsasApplication().getCurrentSession());
-      }
-    }
-    if (vamsasSession != null)
-    {
-      if (vamsasImport != null)
-      {
-        // close the newly imported session and import the Jalview specific
-        // remnants into the new session later on.
-        desktop.vamsasStop_actionPerformed(null);
-      }
-      // now join the new session
-      try
-      {
-        if (desktop.joinVamsasSession(vamsasSession))
-        {
-          System.out.println(
-                  "Successfully joined vamsas session " + vamsasSession);
-        }
-        else
-        {
-          System.err.println("WARNING: Failed to join vamsas session "
-                  + vamsasSession);
-        }
-      } catch (Exception e)
-      {
-        System.err.println(
-                "ERROR: Failed to join vamsas session " + vamsasSession);
-        e.printStackTrace();
-      }
-      if (vamsasImport != null)
-      {
-        // the Jalview specific remnants can now be imported into the new
-        // session at the user's leisure.
-        Cache.log.info(
-                "Skipping Push for import of data into existing vamsas session.");
-        // TODO:
-        // enable
-        // this
-        // when
-        // debugged
-        // desktop.getVamsasApplication().push_update();
-      }
-    }
-    return haveImport;
   }
 
   /**
@@ -1109,7 +1015,6 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
         imageName = imageFile.getName();
         HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
         htmlSVG.exportHTML(file);
-
         System.out.println("Creating HTML image: " + file);
         continue;
       }
-- 
1.7.10.2