JAL-2847 various error popups for db querying now have formatted strings

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 706ed87..02375a4 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -920,6 +920,8 @@ label.updating_vamsas_session = Updating vamsas session
 label.loading_file = Loading File: {0}
 label.edit_params = Edit {0}
 label.as_percentage = As Percentage
+error.database_id_has_letters = Database identifier ({0}) should contain only digits
+error.phyloxml_validation = phyloXML XSD-based validation is turned off (enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file)
 error.not_implemented = Not implemented
 error.no_such_method_as_clone1_for = No such method as clone1 for {0}
 error.null_from_clone1 = Null from clone1!

diff --git a/src/jalview/ext/archaeopteryx/JalviewBinding.java b/src/jalview/ext/archaeopteryx/JalviewBinding.java
index 331e77d..80b2e50 100644 (file)
--- a/src/jalview/ext/archaeopteryx/JalviewBinding.java
+++ b/src/jalview/ext/archaeopteryx/JalviewBinding.java
@@ -1,8 +1,10 @@
 package jalview.ext.archaeopteryx;
 
+import jalview.analysis.AlignmentSorter;
 import jalview.analysis.Conservation;
 import jalview.api.AlignViewportI;
 import jalview.commands.CommandI;
+import jalview.commands.OrderCommand;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceGroup;
@@ -637,16 +639,16 @@ public final class JalviewBinding
 
   public CommandI sortAlignmentIn(AlignmentPanel ap)
   {
-    // // TODO: move to alignment view controller
-    // AlignmentViewport viewport = ap.av;
-    // SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
-    // AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
-    // CommandI undo;
-    // undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
-    //
-    // ap.paintAlignment(true, false);
-    // return undo;
-    return null;
+    // TODO: move to alignment view controller
+    AlignmentViewport viewport = ap.av;
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+    AlignmentSorter.sortByTree(viewport.getAlignment(),
+            treeView.getPhylogeny());
+    CommandI undo;
+    undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
+
+    ap.paintAlignment(true, false);
+    return undo;
   }