From 4c50004b62547992fd7dee166d3f95e7167d1303 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 9 May 2018 14:59:14 +0100
Subject: [PATCH] JAL-2984 add pdb as sequence(s) if associate structure is
 declined

---
 src/jalview/gui/AlignFrame.java |   36 +++++++++++++++++++++++++-----------
 1 file changed, 25 insertions(+), 11 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 9981559..9821e9e 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -4459,17 +4459,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             int assocfiles = 0;
             if (filesmatched.size() > 0)
             {
-              if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
-                      || JvOptionPane.showConfirmDialog(thisaf,
-                              MessageManager.formatMessage(
-                                      "label.automatically_associate_structure_files_with_sequences_same_name",
-                                      new Object[]
-                                      { Integer.valueOf(filesmatched.size())
-                                              .toString() }),
-                              MessageManager.getString(
-                                      "label.automatically_associate_structure_files_by_name"),
-                              JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
-
+              boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
+              if (!autoAssociate)
+              {
+                String msg = MessageManager.formatMessage(
+                        "label.automatically_associate_structure_files_with_sequences_same_name",
+                        new Object[]
+                        { Integer.valueOf(filesmatched.size())
+                                .toString() });
+                String ttl = MessageManager.getString(
+                        "label.automatically_associate_structure_files_by_name");
+                int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
+                        ttl, JvOptionPane.YES_NO_OPTION);
+                autoAssociate = choice == JvOptionPane.YES_OPTION;
+              }
+              if (autoAssociate)
               {
                 for (Object[] fm : filesmatched)
                 {
@@ -4495,6 +4499,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   alignPanel.paintAlignment(true, false);
                 }
               }
+              else
+              {
+                /*
+                 * add declined structures as sequences
+                 */
+                for (Object[] o : filesmatched)
+                {
+                  filesnotmatched.add((String) o[0]);
+                }
+              }
             }
             if (filesnotmatched.size() > 0)
             {
-- 
1.7.10.2