From 5808cfcdd5c3fcb7fc6b4b1cb12bfb0c9f75235d Mon Sep 17 00:00:00 2001 From: kjvdheide Date: Tue, 5 Dec 2017 14:21:04 +0000 Subject: [PATCH] JAL-2847 various error popups for db querying now have formatted strings --- resources/lang/Messages.properties | 2 ++ src/jalview/ext/archaeopteryx/JalviewBinding.java | 22 +++++++++++---------- 2 files changed, 14 insertions(+), 10 deletions(-) diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 706ed87..02375a4 100644 --- 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 --- 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; } -- 1.7.10.2