X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=7fa514710dbf1cfbfeca9faed7d1c98beffe759b;hb=7d6bf4ac01167499c0f4e07de63edcdd72a6d595;hp=7f15b3e1fd7247d234af3cb22639db3d14cb55f7;hpb=8b27085fa7fc5f2877e078421284c2636b85b8c6;p=jalview.git

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 7f15b3e..7fa5147 100644
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -38,8 +38,8 @@ import jalview.datamodel.SequenceI;
 import jalview.io.AnnotationFile;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
 import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
 import jalview.io.FileParse;
 import jalview.io.IdentifyFile;
 import jalview.io.JPredFile;
@@ -51,6 +51,7 @@ import jalview.javascript.JsCallBack;
 import jalview.javascript.MouseOverStructureListener;
 import jalview.structure.SelectionListener;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.ColorUtils;
 import jalview.util.HttpUtils;
 import jalview.util.MessageManager;
 
@@ -470,7 +471,7 @@ public class JalviewLite extends Applet implements
         SequenceI rs = sel.getSequenceAt(0);
         start = rs.findIndex(start);
         end = rs.findIndex(end);
-        List<Integer> cs = csel.getSelected();
+        List<Integer> cs = new ArrayList<Integer>(csel.getSelected());
         csel.clear();
         for (Integer selectedCol : cs)
         {
@@ -517,7 +518,7 @@ public class JalviewLite extends Applet implements
   {
     try
     {
-      FileFormatI theFormat = FileFormat.valueOf(format);
+      FileFormatI theFormat = FileFormats.getInstance().forName(format);
       boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
       if (alf.viewport.getSelectionGroup() != null)
       {
@@ -715,7 +716,7 @@ public class JalviewLite extends Applet implements
     {
       boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
 
-      FileFormatI theFormat = FileFormat.valueOf(format);
+      FileFormatI theFormat = FileFormats.getInstance().forName(format);
       String reply = new AppletFormatAdapter().formatSequences(theFormat,
               alf.viewport.getAlignment(), seqlimits);
       return reply;
@@ -2255,6 +2256,11 @@ public class JalviewLite extends Applet implements
     {
       boolean result = false;
       String param = applet.getParameter("jnetfile");
+      if (param == null)
+      {
+        // jnet became jpred around 2016
+        param = applet.getParameter("jpredfile");
+      }
       if (param != null)
       {
         try
@@ -2883,22 +2889,13 @@ public class JalviewLite extends Applet implements
     {
       return defcolour;
     }
-    Color col = jalview.schemes.ColourSchemeProperty
-            .getAWTColorFromName(colprop);
+    Color col = ColorUtils.parseColourString(colprop);
     if (col == null)
     {
-      try
-      {
-        col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
-      } catch (Exception ex)
-      {
-        System.err.println("Couldn't parse '" + colprop
-                + "' as a colour for " + colparam);
-        col = null;
-      }
+      System.err.println("Couldn't parse '" + colprop
+              + "' as a colour for " + colparam);
     }
     return (col == null) ? defcolour : col;
-
   }
 
   public void openJalviewHelpUrl()