JAL-2698 spawn a thread to test for and raise auto associate dialogs for PDB file...

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index c78abdc..434e2b4 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -4387,7 +4387,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // Java's Transferable for native dnd
     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
     Transferable t = evt.getTransferable();
-    List<String> files = new ArrayList<>();
+    final AlignFrame thisaf = this;
+    final List<String> files = new ArrayList<>();
     List<DataSourceType> protocols = new ArrayList<>();
 
     try
@@ -4399,133 +4400,144 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     if (files != null)
     {
-      try
+      new Thread(new Runnable()
       {
-        // check to see if any of these files have names matching sequences in
-        // the alignment
-        SequenceIdMatcher idm = new SequenceIdMatcher(
-                viewport.getAlignment().getSequencesArray());
-        /**
-         * Object[] { String,SequenceI}
-         */
-        ArrayList<Object[]> filesmatched = new ArrayList<>();
-        ArrayList<String> filesnotmatched = new ArrayList<>();
-        for (int i = 0; i < files.size(); i++)
+        @Override
+        public void run()
         {
-          String file = files.get(i).toString();
-          String pdbfn = "";
-          DataSourceType protocol = FormatAdapter.checkProtocol(file);
-          if (protocol == DataSourceType.FILE)
-          {
-            File fl = new File(file);
-            pdbfn = fl.getName();
-          }
-          else if (protocol == DataSourceType.URL)
-          {
-            URL url = new URL(file);
-            pdbfn = url.getFile();
-          }
-          if (pdbfn.length() > 0)
+          try
           {
-            // attempt to find a match in the alignment
-            SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
-            int l = 0, c = pdbfn.indexOf(".");
-            while (mtch == null && c != -1)
+            // check to see if any of these files have names matching sequences
+            // in
+            // the alignment
+            SequenceIdMatcher idm = new SequenceIdMatcher(
+                    viewport.getAlignment().getSequencesArray());
+            /**
+             * Object[] { String,SequenceI}
+             */
+            ArrayList<Object[]> filesmatched = new ArrayList<>();
+            ArrayList<String> filesnotmatched = new ArrayList<>();
+            for (int i = 0; i < files.size(); i++)
             {
-              do
+              String file = files.get(i).toString();
+              String pdbfn = "";
+              DataSourceType protocol = FormatAdapter.checkProtocol(file);
+              if (protocol == DataSourceType.FILE)
               {
-                l = c;
-              } while ((c = pdbfn.indexOf(".", l)) > l);
-              if (l > -1)
-              {
-                pdbfn = pdbfn.substring(0, l);
+                File fl = new File(file);
+                pdbfn = fl.getName();
               }
-              mtch = idm.findAllIdMatches(pdbfn);
-            }
-            if (mtch != null)
-            {
-              FileFormatI type = null;
-              try
+              else if (protocol == DataSourceType.URL)
               {
-                type = new IdentifyFile().identify(file, protocol);
-              } catch (Exception ex)
-              {
-                type = null;
+                URL url = new URL(file);
+                pdbfn = url.getFile();
               }
-              if (type != null && type.isStructureFile())
+              if (pdbfn.length() > 0)
               {
-                filesmatched.add(new Object[] { file, protocol, mtch });
-                continue;
+                // attempt to find a match in the alignment
+                SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
+                int l = 0, c = pdbfn.indexOf(".");
+                while (mtch == null && c != -1)
+                {
+                  do
+                  {
+                    l = c;
+                  } while ((c = pdbfn.indexOf(".", l)) > l);
+                  if (l > -1)
+                  {
+                    pdbfn = pdbfn.substring(0, l);
+                  }
+                  mtch = idm.findAllIdMatches(pdbfn);
+                }
+                if (mtch != null)
+                {
+                  FileFormatI type = null;
+                  try
+                  {
+                    type = new IdentifyFile().identify(file, protocol);
+                  } catch (Exception ex)
+                  {
+                    type = null;
+                  }
+                  if (type != null && type.isStructureFile())
+                  {
+                    filesmatched.add(new Object[] { file, protocol, mtch });
+                    continue;
+                  }
+                }
+                // File wasn't named like one of the sequences or wasn't a PDB
+                // file.
+                filesnotmatched.add(file);
               }
             }
-            // File wasn't named like one of the sequences or wasn't a PDB file.
-            filesnotmatched.add(file);
-          }
-        }
-        int assocfiles = 0;
-        if (filesmatched.size() > 0)
-        {
-          if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
-                  || JvOptionPane.showConfirmDialog(this,
-                          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)
-
-          {
-            for (Object[] fm : filesmatched)
+            int assocfiles = 0;
+            if (filesmatched.size() > 0)
             {
-              // try and associate
-              // TODO: may want to set a standard ID naming formalism for
-              // associating PDB files which have no IDs.
-              for (SequenceI toassoc : (SequenceI[]) fm[2])
+              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)
+
               {
-                PDBEntry pe = new AssociatePdbFileWithSeq()
-                        .associatePdbWithSeq((String) fm[0],
-                                (DataSourceType) fm[1], toassoc, false,
-                                Desktop.instance);
-                if (pe != null)
+                for (Object[] fm : filesmatched)
                 {
-                  System.err.println("Associated file : " + ((String) fm[0])
-                          + " with " + toassoc.getDisplayId(true));
-                  assocfiles++;
+                  // try and associate
+                  // TODO: may want to set a standard ID naming formalism for
+                  // associating PDB files which have no IDs.
+                  for (SequenceI toassoc : (SequenceI[]) fm[2])
+                  {
+                    PDBEntry pe = new AssociatePdbFileWithSeq()
+                            .associatePdbWithSeq((String) fm[0],
+                                    (DataSourceType) fm[1], toassoc, false,
+                                    Desktop.instance);
+                    if (pe != null)
+                    {
+                      System.err.println("Associated file : "
+                              + ((String) fm[0]) + " with "
+                              + toassoc.getDisplayId(true));
+                      assocfiles++;
+                    }
+                  }
+                  alignPanel.paintAlignment(true);
                 }
               }
-              alignPanel.paintAlignment(true);
             }
-          }
-        }
-        if (filesnotmatched.size() > 0)
-        {
-          if (assocfiles > 0 && (Cache.getDefault(
-                  "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
-                  || JvOptionPane.showConfirmDialog(this,
-                          "<html>" + MessageManager.formatMessage(
-                                  "label.ignore_unmatched_dropped_files_info",
-                                  new Object[]
-                                  { Integer.valueOf(filesnotmatched.size())
-                                          .toString() })
-                                  + "</html>",
-                          MessageManager.getString(
-                                  "label.ignore_unmatched_dropped_files"),
-                          JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
-          {
-            return;
-          }
-          for (String fn : filesnotmatched)
+            if (filesnotmatched.size() > 0)
+            {
+              if (assocfiles > 0 && (Cache.getDefault(
+                      "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
+                      || JvOptionPane.showConfirmDialog(thisaf,
+                              "<html>" + MessageManager.formatMessage(
+                                      "label.ignore_unmatched_dropped_files_info",
+                                      new Object[]
+                                      { Integer.valueOf(
+                                              filesnotmatched.size())
+                                              .toString() })
+                                      + "</html>",
+                              MessageManager.getString(
+                                      "label.ignore_unmatched_dropped_files"),
+                              JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
+              {
+                return;
+              }
+              for (String fn : filesnotmatched)
+              {
+                loadJalviewDataFile(fn, null, null, null);
+              }
+
+            }
+          } catch (Exception ex)
           {
-            loadJalviewDataFile(fn, null, null, null);
+            ex.printStackTrace();
           }
-
         }
-      } catch (Exception ex)
-      {
-        ex.printStackTrace();
-      }
+      }).start();
     }
   }