JAL-1691 linked scrollling in split frame (Desktop)

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

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index f28ef68..3a54cc1 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -1,4 +1,5 @@
 /*
+
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * Copyright (C) 2014 The Jalview Authors
  * 
@@ -37,12 +38,13 @@ import java.awt.event.ItemEvent;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
+import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Vector;
 
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
-import javax.swing.ListSelectionModel;
+import javax.swing.JLabel;
 
 /**
  * Provides the behaviors for the Structure chooser Panel
@@ -61,9 +63,9 @@ public class StructureChooser extends GStructureChooser
 
   private IProgressIndicator progressIndicator;
 
-  private Collection<PDBResponseSummary> discoveredStructuresSet = new HashSet<PDBResponseSummary>();
+  private Collection<PDBResponseSummary> discoveredStructuresSet;
 
-  private PDBRestRequest pdbRequest;
+  private PDBRestRequest lastPdbRequest;
 
   private PDBRestClient pdbRestCleint;
 
@@ -130,17 +132,19 @@ public class StructureChooser extends GStructureChooser
     Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
             .getStructureSummaryFields();
 
-    pdbRequest = new PDBRestRequest();
-    pdbRequest.setAllowEmptySeq(false);
-    pdbRequest.setResponseSize(500);
-    pdbRequest.setFieldToSearchBy("(text:");
-    pdbRequest.setWantedFields(wantedFields);
+    discoveredStructuresSet = new LinkedHashSet<PDBResponseSummary>();
     for (SequenceI seq : selectedSequences)
     {
+      PDBRestRequest pdbRequest = new PDBRestRequest();
+      pdbRequest.setAllowEmptySeq(false);
+      pdbRequest.setResponseSize(500);
+      pdbRequest.setFieldToSearchBy("(text:");
+      pdbRequest.setWantedFields(wantedFields);
       pdbRequest.setSearchTerm(buildQuery(seq) + ")");
       pdbRequest.setAssociatedSequence(seq.getName());
       pdbRestCleint = new PDBRestClient();
       PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
+      lastPdbRequest = pdbRequest;
       if (resultList.getSearchSummary() != null
               && !resultList.getSearchSummary().isEmpty())
       {
@@ -153,7 +157,7 @@ public class StructureChooser extends GStructureChooser
     if (discoveredStructuresSet != null
             && !discoveredStructuresSet.isEmpty())
     {
-      tbl_summary.setModel(PDBRestResponse.getTableModel(pdbRequest,
+      tbl_summary.setModel(PDBRestResponse.getTableModel(lastPdbRequest,
               discoveredStructuresSet));
       structuresDiscovered = true;
       noOfStructuresFound = discoveredStructuresSet.size();
@@ -243,19 +247,25 @@ public class StructureChooser extends GStructureChooser
         try
         {
           lbl_loading.setVisible(true);
-          pdbRequest.setResponseSize(1);
-          pdbRequest.setFieldToSearchBy("(text:");
-          pdbRequest.setFieldToSortBy(fieldToFilterBy,
-                  !chk_invertFilter.isSelected());
 
+          Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
+                  .getStructureSummaryFields();
           Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
           for (SequenceI seq : selectedSequences)
           {
+            PDBRestRequest pdbRequest = new PDBRestRequest();
+            pdbRequest.setAllowEmptySeq(false);
+            pdbRequest.setResponseSize(1);
+            pdbRequest.setFieldToSearchBy("(text:");
+            pdbRequest.setFieldToSortBy(fieldToFilterBy,
+                    !chk_invertFilter.isSelected());
             pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+            pdbRequest.setWantedFields(wantedFields);
             pdbRequest.setAssociatedSequence(seq.getName());
             pdbRestCleint = new PDBRestClient();
             PDBRestResponse resultList = pdbRestCleint
                     .executeRequest(pdbRequest);
+            lastPdbRequest = pdbRequest;
             if (resultList.getSearchSummary() != null
                     && !resultList.getSearchSummary().isEmpty())
             {
@@ -263,50 +273,37 @@ public class StructureChooser extends GStructureChooser
             }
           }
 
-          if (filteredResponse != null)
+          if (!filteredResponse.isEmpty())
           {
-            int filterResponseCount = filteredResponse.size();
-            List<PDBResponseSummary> originalDiscoveredStructuresList = new ArrayList<PDBResponseSummary>(
-                    discoveredStructuresSet);
-            originalDiscoveredStructuresList.removeAll(filteredResponse);
-            Collection<PDBResponseSummary> reorderedStructuresSet = new ArrayList<PDBResponseSummary>();
+            final int filterResponseCount = filteredResponse.size();
+            Collection<PDBResponseSummary> reorderedStructuresSet = new LinkedHashSet<PDBResponseSummary>();
             reorderedStructuresSet.addAll(filteredResponse);
-            reorderedStructuresSet.addAll(originalDiscoveredStructuresList);
+            reorderedStructuresSet.addAll(discoveredStructuresSet);
+            tbl_summary.setModel(PDBRestResponse.getTableModel(
+                    lastPdbRequest, reorderedStructuresSet));
 
-            tbl_summary.setModel(PDBRestResponse.getTableModel(pdbRequest,
-                    reorderedStructuresSet));
-
-            ListSelectionModel model = tbl_summary.getSelectionModel();
-            model.clearSelection();
-            for (int x = 0; x < filterResponseCount; x++)
-            {
-              model.addSelectionInterval(x, x);
-            }
+            // Update table selection model here
+            tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
 
-            // Discard unwanted objects to make them eligible for garbage
-            // collection
-            originalDiscoveredStructuresList = null;
-            reorderedStructuresSet = null;
           }
 
           lbl_loading.setVisible(false);
+          String totalTime = (System.currentTimeMillis() - startTime)
+                  + " milli secs";
+          mainFrame.setTitle("Structure Chooser - Filter time ("
+                  + totalTime + ")");
+
+          validateSelections();
         } catch (Exception e)
         {
           e.printStackTrace();
         }
-        String totalTime = (System.currentTimeMillis() - startTime)
-                + " milli secs";
-        mainFrame.setTitle("Structure Chooser - Filter time (" + totalTime
-                + ")");
-
-        validateSelections();
       }
     });
     filterThread.start();
   }
 
 
-
   /**
    * Handles action event for btn_pdbFromFile
    */
@@ -409,7 +406,6 @@ public class StructureChooser extends GStructureChooser
     {
       validateAssociationFromFile();
     }
-
   }
 
   /**
@@ -504,7 +500,7 @@ public class StructureChooser extends GStructureChooser
     if (currentView == VIEWS_FILTER)
     {
       int pdbIdCol = PDBRestClient.getPDBIdColumIndex(
-              pdbRequest.getWantedFields(), true);
+              lastPdbRequest.getWantedFields(), true);
       int[] selectedRows = tbl_summary.getSelectedRows();
       PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
       int count = 0;
@@ -551,12 +547,13 @@ public class StructureChooser extends GStructureChooser
    * a unique sequence when more than one sequence selection is made.
    */
   public void populateCmbAssociateSeqOptions(
-          JComboBox<AssociateSeqOptions> cmb_assSeq)
+          JComboBox<AssociateSeqOptions> cmb_assSeq, JLabel lbl_associateSeq)
   {
     cmb_assSeq.removeAllItems();
     cmb_assSeq.addItem(new AssociateSeqOptions("-Select Associated Seq-",
             null));
     // cmb_assSeq.addItem(new AssociateSeqOptions("Auto Detect", null));
+    lbl_associateSeq.setVisible(false);
     if (selectedSequences.length > 1)
     {
       for (SequenceI seq : selectedSequences)
@@ -566,6 +563,10 @@ public class StructureChooser extends GStructureChooser
     }
     else
     {
+      String seqName = selectedSequence.getDisplayId(false);
+      seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
+      lbl_associateSeq.setText(seqName);
+      lbl_associateSeq.setVisible(true);
       cmb_assSeq.setVisible(false);
     }
   }
@@ -593,7 +594,7 @@ public class StructureChooser extends GStructureChooser
     {
       List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
       wantedFields.add(PDBDocField.PDB_ID);
-      pdbRequest = new PDBRestRequest();
+      PDBRestRequest pdbRequest = new PDBRestRequest();
       pdbRequest.setAllowEmptySeq(false);
       pdbRequest.setResponseSize(1);
       pdbRequest.setFieldToSearchBy("(pdb_id:");
@@ -611,4 +612,23 @@ public class StructureChooser extends GStructureChooser
     validateSelections();
   }
 
+  @Override
+  public void tabRefresh()
+  {
+    if (selectedSequences != null)
+    {
+      Thread refreshThread = new Thread(new Runnable()
+      {
+        @Override
+        public void run()
+        {
+          fetchStructuresMetaData();
+          filterResultSet(((FilterOption) cmb_filterOption
+                  .getSelectedItem()).getValue());
+        }
+      });
+      refreshThread.start();
+    }
+  }
+
 }