From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 29 Sep 2016 11:56:51 +0000 (+0100)
Subject: JAL-2237 apply default filter as sort in initial search
X-Git-Tag: Release_2_10_0~29
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=32e495296239f89190828a16d8893c1e143e0a12;p=jalview.git

JAL-2237 apply default filter as sort in initial search
---

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 7d8f1bf..af8b2f3 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -65,8 +65,6 @@ import javax.swing.table.AbstractTableModel;
 public class StructureChooser extends GStructureChooser implements
         IProgressIndicator
 {
-  private boolean structuresDiscovered = false;
-
   private SequenceI selectedSequence;
 
   private SequenceI[] selectedSequences;
@@ -103,6 +101,8 @@ public class StructureChooser extends GStructureChooser implements
       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
     }
 
+    // ensure a filter option is in force for search
+    populateFilterComboBox(true);
     Thread discoverPDBStructuresThread = new Thread(new Runnable()
     {
       @Override
@@ -117,7 +117,8 @@ public class StructureChooser extends GStructureChooser implements
                 .getString("status.searching_for_pdb_structures"),
                 startTime);
         fetchStructuresMetaData();
-        populateFilterComboBox();
+        // revise filter options if no results were found
+        populateFilterComboBox(isStructuresDiscovered());
         updateProgressIndicator(null, startTime);
         mainFrame.setVisible(true);
         updateCurrentView();
@@ -161,6 +162,10 @@ public class StructureChooser extends GStructureChooser implements
       pdbRequest.setAllowEmptySeq(false);
       pdbRequest.setResponseSize(500);
       pdbRequest.setFieldToSearchBy("(");
+      FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+              .getSelectedItem());
+      pdbRequest.setFieldToSortBy(selectedFilterOpt.getValue(),
+              !chk_invertFilter.isSelected());
       pdbRequest.setWantedFields(wantedFields);
       pdbRequest.setSearchTerm(buildQuery(seq) + ")");
       pdbRequest.setAssociatedSequence(seq);
@@ -191,7 +196,6 @@ public class StructureChooser extends GStructureChooser implements
       getResultTable().setModel(
               FTSRestResponse.getTableModel(lastPdbRequest,
               discoveredStructuresSet));
-      structuresDiscovered = true;
       noOfStructuresFound = discoveredStructuresSet.size();
       mainFrame.setTitle(MessageManager.formatMessage(
               "label.structure_chooser_no_of_structures",
@@ -524,10 +528,15 @@ public class StructureChooser extends GStructureChooser implements
    * Populates the filter combo-box options dynamically depending on discovered
    * structures
    */
-  @Override
-  protected void populateFilterComboBox()
+  protected void populateFilterComboBox(boolean haveData)
   {
-    if (isStructuresDiscovered())
+    /*
+     * temporarily suspend the change listener behaviour
+     */
+    cmb_filterOption.removeItemListener(this);
+
+    cmb_filterOption.removeAllItems();
+    if (haveData)
     {
       cmb_filterOption.addItem(new FilterOption("Best Quality",
               "overall_quality", VIEWS_FILTER));
@@ -546,12 +555,13 @@ public class StructureChooser extends GStructureChooser implements
             VIEWS_FROM_FILE));
     cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-",
             VIEWS_LOCAL_PDB));
+
+    cmb_filterOption.addItemListener(this);
   }
 
   /**
    * Updates the displayed view based on the selected filter option
    */
-  @Override
   protected void updateCurrentView()
   {
     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
@@ -963,12 +973,8 @@ public class StructureChooser extends GStructureChooser implements
 
   public boolean isStructuresDiscovered()
   {
-    return structuresDiscovered;
-  }
-
-  public void setStructuresDiscovered(boolean structuresDiscovered)
-  {
-    this.structuresDiscovered = structuresDiscovered;
+    return discoveredStructuresSet != null
+            && !discoveredStructuresSet.isEmpty();
   }
 
   public Collection<FTSData> getDiscoveredStructuresSet()
diff --git a/src/jalview/jbgui/GStructureChooser.java b/src/jalview/jbgui/GStructureChooser.java
index ec12b26..4d66a18 100644
--- a/src/jalview/jbgui/GStructureChooser.java
+++ b/src/jalview/jbgui/GStructureChooser.java
@@ -802,10 +802,6 @@ public abstract class GStructureChooser extends JPanel implements
 
   protected abstract void stateChanged(ItemEvent e);
 
-  protected abstract void updateCurrentView();
-
-  protected abstract void populateFilterComboBox();
-
   protected abstract void ok_ActionPerformed();
 
   protected abstract void pdbFromFile_actionPerformed();
diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java
index bad536b..4c7df46 100644
--- a/test/jalview/gui/StructureChooserTest.java
+++ b/test/jalview/gui/StructureChooserTest.java
@@ -105,24 +105,16 @@ public class StructureChooserTest
   }
 
   @Test(groups = { "Functional" })
-  public void populateFilterComboBoxTest()
+  public void populateFilterComboBoxTest() throws InterruptedException
   {
     SequenceI[] selectedSeqs = new SequenceI[] { seq };
     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
-    sc.populateFilterComboBox();
+    sc.populateFilterComboBox(false);
     int optionsSize = sc.getCmbFilterOption().getItemCount();
     assertEquals(3, optionsSize); // if structures are not discovered then don't
                                   // populate filter options
 
-    sc.setStructuresDiscovered(true);
-    sc.populateFilterComboBox();
-    try
-    {
-      Thread.sleep(2000);
-    } catch (InterruptedException e)
-    {
-      e.printStackTrace();
-    }
+    sc.populateFilterComboBox(true);
     optionsSize = sc.getCmbFilterOption().getItemCount();
     assertTrue(optionsSize > 3); // if structures are found, filter options
                                  // should be populated