JAL-1793 spike branch updated to latest

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

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index da10e3f..20f4a49 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -157,8 +157,8 @@ public class StructureChooser extends GStructureChooser
     Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
             .getStructureSummaryFields();
 
-    discoveredStructuresSet = new LinkedHashSet<FTSData>();
-    HashSet<String> errors = new HashSet<String>();
+    discoveredStructuresSet = new LinkedHashSet<>();
+    HashSet<String> errors = new HashSet<>();
     for (SequenceI seq : selectedSequences)
     {
       FTSRestRequest pdbRequest = new FTSRestRequest();
@@ -223,7 +223,7 @@ public class StructureChooser extends GStructureChooser
 
   public void loadLocalCachedPDBEntries()
   {
-    ArrayList<CachedPDB> entries = new ArrayList<CachedPDB>();
+    ArrayList<CachedPDB> entries = new ArrayList<>();
     for (SequenceI seq : selectedSequences)
     {
       if (seq.getDatasetSequence() != null
@@ -257,7 +257,7 @@ public class StructureChooser extends GStructureChooser
     boolean isPDBRefsFound = false;
     boolean isUniProtRefsFound = false;
     StringBuilder queryBuilder = new StringBuilder();
-    Set<String> seqRefs = new LinkedHashSet<String>();
+    Set<String> seqRefs = new LinkedHashSet<>();
 
     if (seq.getAllPDBEntries() != null
             && queryBuilder.length() < MAX_QLENGTH)
@@ -401,8 +401,8 @@ public class StructureChooser extends GStructureChooser
         lbl_loading.setVisible(true);
         Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
                 .getStructureSummaryFields();
-        Collection<FTSData> filteredResponse = new HashSet<FTSData>();
-        HashSet<String> errors = new HashSet<String>();
+        Collection<FTSData> filteredResponse = new HashSet<>();
+        HashSet<String> errors = new HashSet<>();
 
         for (SequenceI seq : selectedSequences)
         {
@@ -453,7 +453,7 @@ public class StructureChooser extends GStructureChooser
         if (!filteredResponse.isEmpty())
         {
           final int filterResponseCount = filteredResponse.size();
-          Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<FTSData>();
+          Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<>();
           reorderedStructuresSet.addAll(filteredResponse);
           reorderedStructuresSet.addAll(discoveredStructuresSet);
           getResultTable().setModel(FTSRestResponse
@@ -725,11 +725,10 @@ public class StructureChooser extends GStructureChooser
   @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);
+
     new Thread(new Runnable()
     {
       @Override
@@ -747,7 +746,7 @@ public class StructureChooser extends GStructureChooser
           int[] selectedRows = getResultTable().getSelectedRows();
           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
           int count = 0;
-          List<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+          List<SequenceI> selectedSeqsToView = new ArrayList<>();
           for (int row : selectedRows)
           {
             String pdbIdStr = getResultTable()
@@ -761,6 +760,7 @@ public class StructureChooser extends GStructureChooser
               pdbEntry = getFindEntry(pdbIdStr,
                       selectedSeq.getAllPDBEntries());
             }
+
             if (pdbEntry == null)
             {
               pdbEntry = new PDBEntry();
@@ -783,7 +783,7 @@ public class StructureChooser extends GStructureChooser
                   .getModelIndex();
           int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
                   .getModelIndex();
-          List<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+          List<SequenceI> selectedSeqsToView = new ArrayList<>();
           for (int row : selectedRows)
           {
             PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
@@ -805,7 +805,6 @@ public class StructureChooser extends GStructureChooser
           {
             selectedSequence = userSelectedSeq;
           }
-
           String pdbIdStr = txt_search.getText();
           PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
           if (pdbEntry == null)
@@ -847,6 +846,7 @@ public class StructureChooser extends GStructureChooser
                   { selectedSequence });
         }
         closeAction(preferredHeight);
+        mainFrame.dispose();
       }
     }).start();
   }
@@ -870,13 +870,15 @@ public class StructureChooser extends GStructureChooser
           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())
     {
-      List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
+      List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
       int p = 0;
       // 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
@@ -907,41 +909,43 @@ public class StructureChooser extends GStructureChooser
       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);
+
+        setProgressBar("Fetch complete.", progressId); // todo i18n
       }
     }
     if (pdbEntriesToView.length > 1)
     {
-      ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
+      ArrayList<SequenceI[]> seqsMap = new ArrayList<>();
       for (SequenceI seq : sequences)
       {
         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);
   }
 
   /**
@@ -1000,7 +1004,7 @@ public class StructureChooser extends GStructureChooser
           String searchTerm = txt_search.getText().toLowerCase();
           searchTerm = searchTerm.split(":")[0];
           // System.out.println(">>>>> search term : " + searchTerm);
-          List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
+          List<FTSDataColumnI> wantedFields = new ArrayList<>();
           FTSRestRequest pdbRequest = new FTSRestRequest();
           pdbRequest.setAllowEmptySeq(false);
           pdbRequest.setResponseSize(1);
@@ -1062,7 +1066,7 @@ public class StructureChooser extends GStructureChooser
 
     public PDBEntryTableModel(List<CachedPDB> pdbEntries)
     {
-      this.pdbEntries = new ArrayList<CachedPDB>(pdbEntries);
+      this.pdbEntries = new ArrayList<>(pdbEntries);
     }
 
     @Override