JAL-2136 merged and resolved conflicts with 80edaa84d6d9beac9f0d2c71b50b7b56fd393427

[jalview.git] / src / jalview / gui / StructureChooser.java

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 4d59d45..bff6d6f 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -771,11 +771,8 @@ public class StructureChooser extends GStructureChooser implements
   @Override
   public void ok_ActionPerformed()
   {
-    final long progressSessionId = System.currentTimeMillis();
     final StructureSelectionManager ssm = ap.getStructureSelectionManager();
     final int preferredHeight = pnl_filter.getHeight();
-    ssm.setProgressIndicator(this);
-    ssm.setProgressSessionId(progressSessionId);
     ssm.setMappingForPhyre2Model(false);
     new Thread(new Runnable()
     {
@@ -853,6 +850,7 @@ public class StructureChooser extends GStructureChooser implements
             selectedSequence = userSelectedSeq;
           }
 
+
           String pdbIdStr = txt_search.getText();
           PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
           if (pdbEntry == null)
@@ -888,7 +886,8 @@ public class StructureChooser extends GStructureChooser implements
                           DataSourceType.FILE,
                       selectedSequence, true, Desktop.instance);
 
-          launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
+          launchStructureViewer(ssm,
+                  new PDBEntry[] { fileEntry }, ap,
                   new SequenceI[] { selectedSequence });
         }
         else if (currentView == VIEWS_PHYRE2_PREDICTION)
@@ -994,9 +993,11 @@ public class StructureChooser extends GStructureChooser implements
           final PDBEntry[] pdbEntriesToView,
           final AlignmentPanel alignPanel, SequenceI[] sequences)
   {
-    ssm.setProgressBar(MessageManager
-            .getString("status.launching_3d_structure_viewer"));
+    long progressId = sequences.hashCode();
+    setProgressBar(MessageManager
+            .getString("status.launching_3d_structure_viewer"), progressId);
     final StructureViewer sViewer = new StructureViewer(ssm);
+    setProgressBar(null, progressId);
 
     if (SiftsSettings.isMapWithSifts())
     {
@@ -1005,6 +1006,7 @@ public class StructureChooser extends GStructureChooser implements
       // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
       // real PDB ID. For moment, we can also safely do this if there is already
       // a known mapping between the PDBEntry and the sequence.
+
       for (SequenceI seq : sequences)
       {
         PDBEntry pdbe = pdbEntriesToView[p++];
@@ -1031,18 +1033,17 @@ public class StructureChooser extends GStructureChooser implements
       if (!seqsWithoutSourceDBRef.isEmpty())
       {
         int y = seqsWithoutSourceDBRef.size();
-        ssm.setProgressBar(null);
-        ssm.setProgressBar(MessageManager.formatMessage(
+        setProgressBar(MessageManager.formatMessage(
                 "status.fetching_dbrefs_for_sequences_without_valid_refs",
-                y));
+                y), progressId);
         SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
         int x = 0;
         for (SequenceI fSeq : seqsWithoutSourceDBRef)
         {
           seqWithoutSrcDBRef[x++] = fSeq;
         }
-        DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
-        dbRefFetcher.fetchDBRefs(true);
+        new DBRefFetcher(seqWithoutSrcDBRef).fetchDBRefs(true);
+        setProgressBar("Fetch complete.", progressId); // todo i18n
       }
     }
     if (pdbEntriesToView.length > 1)
@@ -1053,19 +1054,18 @@ public class StructureChooser extends GStructureChooser implements
         seqsMap.add(new SequenceI[] { seq });
       }
       SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
-      ssm.setProgressBar(null);
-      ssm.setProgressBar(MessageManager
-              .getString("status.fetching_3d_structures_for_selected_entries"));
+      setProgressBar(MessageManager
+                    .getString("status.fetching_3d_structures_for_selected_entries"), progressId);
       sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
     }
     else
     {
-      ssm.setProgressBar(null);
-      ssm.setProgressBar(MessageManager.formatMessage(
+      setProgressBar(MessageManager.formatMessage(
               "status.fetching_3d_structures_for",
-              pdbEntriesToView[0].getId()));
+              pdbEntriesToView[0].getId()),progressId);
       sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
     }
+    setProgressBar(null, progressId);
   }
 
   /**