Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e' into develop

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

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index ef48bf9..b490815 100644 (file)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -709,8 +709,8 @@ public class JalviewLite extends Applet implements
    */
   public void loadAnnotationFrom(AlignFrame alf, String annotation)
   {
-    if (new AnnotationFile().readAnnotationFile(alf.getAlignViewport()
-            .getAlignment(), annotation, AppletFormatAdapter.PASTE))
+    if (new AnnotationFile().annotateAlignmentView(alf.getAlignViewport(),
+            annotation, AppletFormatAdapter.PASTE))
     {
       alf.alignPanel.fontChanged();
       alf.alignPanel.setScrollValues(0, 0);
@@ -1269,7 +1269,7 @@ public class JalviewLite extends Applet implements
 
   public static boolean debug = false;
 
-  static String builddate = null, version = null;
+  static String builddate = null, version = null, installation = null;
 
   private static void initBuildDetails()
   {
@@ -1277,6 +1277,7 @@ public class JalviewLite extends Applet implements
     {
       builddate = "unknown";
       version = "test";
+      installation = "Webstart";
       java.net.URL url = JalviewLite.class
               .getResource("/.build_properties");
       if (url != null)
@@ -1296,6 +1297,10 @@ public class JalviewLite extends Applet implements
             {
               builddate = line.substring(line.indexOf("=") + 1);
             }
+            if (line.indexOf("INSTALLATION") > -1)
+            {
+              installation = line.substring(line.indexOf("=") + 1);
+            }
           }
         } catch (Exception ex)
         {
@@ -1311,6 +1316,12 @@ public class JalviewLite extends Applet implements
     return builddate;
   }
 
+  public static String getInstallation()
+  {
+    initBuildDetails();
+    return installation;
+  }
+
   public static String getVersion()
   {
     initBuildDetails();
@@ -1360,6 +1371,7 @@ public class JalviewLite extends Applet implements
 
       System.err.println("JalviewLite Version " + getVersion());
       System.err.println("Build Date : " + getBuildDate());
+      System.err.println("Installation : " + getInstallation());
 
     }
     String externalsviewer = getParameter("externalstructureviewer");
@@ -1987,8 +1999,8 @@ public class JalviewLite extends Applet implements
         {
           param = setProtocolState(param);
 
-          if (new AnnotationFile().readAnnotationFile(
-                  newAlignFrame.viewport.getAlignment(), param, protocol))
+          if (new AnnotationFile().annotateAlignmentView(
+                  newAlignFrame.viewport, param, protocol))
           {
             newAlignFrame.alignPanel.fontChanged();
             newAlignFrame.alignPanel.setScrollValues(0, 0);
@@ -2012,6 +2024,12 @@ public class JalviewLite extends Applet implements
                     param, protocol);
             JnetAnnotationMaker.add_annotation(predictions,
                     newAlignFrame.viewport.getAlignment(), 0, false); // false==do
+            SequenceI repseq = newAlignFrame.viewport.getAlignment()
+                    .getSequenceAt(0);
+            newAlignFrame.viewport.getAlignment().setSeqrep(repseq);
+            ColumnSelection cs = new ColumnSelection();
+            cs.hideInsertionsFor(repseq);
+            newAlignFrame.viewport.setColumnSelection(cs);
             // not
             // add
             // sequence