JAL-2256 Corrected AllCols/Rows iterator behaviour for single element

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

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 3ecf22b..dbc707d 100644 (file)
--- 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;
@@ -485,7 +486,8 @@ public class JalviewLite extends Applet implements
         @Override
         public void run()
         {
-          alf.select(sel, csel);
+          alf.select(sel, csel, alf.getAlignViewport().getAlignment()
+                  .getHiddenColumns());
         }
       });
     }
@@ -518,7 +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)
       {
@@ -716,7 +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;
@@ -2256,6 +2258,11 @@ 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
@@ -2268,9 +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;