X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=dbc707d387ca807e2fc9dc9397694767d0d96feb;hb=9ba5a485b66e9c5a86b12dedc7b32616f3ef6db8;hp=de011ea45fcabb9e037f5ca8ab77ebf2e7835d7c;hpb=cd4e2687751aab1c9c5974e6966e610a3332236b;p=jalview.git

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index de011ea..dbc707d 100644
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -31,6 +31,7 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
@@ -38,8 +39,8 @@ 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 +52,7 @@ 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;
 
@@ -484,7 +486,8 @@ public class JalviewLite extends Applet implements
         @Override
         public void run()
         {
-          alf.select(sel, csel);
+          alf.select(sel, csel, alf.getAlignViewport().getAlignment()
+                  .getHiddenColumns());
         }
       });
     }
@@ -517,7 +520,7 @@ 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 +718,7 @@ 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;
@@ -2272,9 +2275,9 @@ public class JalviewLite extends Applet implements
           SequenceI repseq = alignFrame.viewport.getAlignment()
                   .getSequenceAt(0);
           alignFrame.viewport.getAlignment().setSeqrep(repseq);
-          ColumnSelection cs = new ColumnSelection();
+          HiddenColumns cs = new HiddenColumns();
           cs.hideInsertionsFor(repseq);
-          alignFrame.viewport.setColumnSelection(cs);
+          alignFrame.viewport.getAlignment().setHiddenColumns(cs);
           alignFrame.alignPanel.fontChanged();
           alignFrame.alignPanel.setScrollValues(0, 0);
           result = true;
@@ -2888,22 +2891,13 @@ 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()