Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

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

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 3d09f99..d225e42 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -66,11 +66,49 @@ import javax.swing.SwingConstants;
  */
 public class SequenceFetcher extends JPanel implements Runnable
 {
+  private class StringPair
+  {
+    private String key;
+
+    private String display;
+
+    public StringPair(String s1, String s2)
+    {
+      key = s1;
+      display = s2;
+    }
+
+    public StringPair(String s)
+    {
+      this(s, s);
+    }
+
+    public String getKey()
+    {
+      return key;
+    }
+
+    public String getDisplay()
+    {
+      return display;
+    }
+
+    @Override
+    public String toString()
+    {
+      return display;
+    }
+
+    public boolean equals(StringPair other)
+    {
+      return other.key == this.key;
+    }
+  }
   private static jalview.ws.SequenceFetcher sfetch = null;
 
   JLabel exampleAccession;
 
-  JComboBox<String> database;
+  JComboBox<StringPair> database;
 
   JCheckBox replacePunctuation;
 
@@ -163,15 +201,25 @@ public class SequenceFetcher extends JPanel implements Runnable
 
     database = new JComboBox<>();
     database.setFont(JvSwingUtils.getLabelFont());
-    database.setPrototypeDisplayValue("ENSEMBLGENOMES   ");
+    StringPair instructionItem = new StringPair(
+            MessageManager.getString("action.select_ddbb"));
+    database.setPrototypeDisplayValue(instructionItem);
     String[] sources = new jalview.ws.SequenceFetcher().getSupportedDb();
     Arrays.sort(sources, String.CASE_INSENSITIVE_ORDER);
-    database.addItem(MessageManager.getString("action.select_ddbb"));
+    database.addItem(instructionItem);
     for (String source : sources)
     {
-      database.addItem(source);
+      List<DbSourceProxy> slist = sfetch.getSourceProxy(source);
+      if (slist.size() == 1 && slist.get(0) != null)
+      {
+        database.addItem(new StringPair(source, slist.get(0).getDbName()));
+      }
+      else
+      {
+        database.addItem(new StringPair(source));
+      }
     }
-    database.setSelectedItem(selectedDb);
+    setDatabaseSelectedItem(selectedDb);
     if (database.getSelectedIndex() == -1)
     {
       database.setSelectedIndex(0);
@@ -182,7 +230,8 @@ public class SequenceFetcher extends JPanel implements Runnable
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        String currentSelection = (String) database.getSelectedItem();
+        String currentSelection = ((StringPair) database.getSelectedItem())
+                .getKey();
         updateExampleQuery(currentSelection);
 
         if ("pdb".equalsIgnoreCase(currentSelection))
@@ -195,6 +244,11 @@ public class SequenceFetcher extends JPanel implements Runnable
           frame.dispose();
           new UniprotFTSPanel(SequenceFetcher.this);
         }
+        else if ("3d-beacons".equalsIgnoreCase(currentSelection))
+        {
+          frame.dispose();
+          new TDBeaconsFTSPanel(SequenceFetcher.this);
+        }
         else
         {
           otherSourceAction();
@@ -304,6 +358,18 @@ public class SequenceFetcher extends JPanel implements Runnable
     this.add(databasePanel, BorderLayout.NORTH);
   }
 
+  private void setDatabaseSelectedItem(String db)
+  {
+    for (int i = 0; i < database.getItemCount(); i++)
+    {
+      StringPair sp = database.getItemAt(i);
+      if (sp != null && db != null && db.equals(sp.getKey()))
+      {
+        database.setSelectedIndex(i);
+        return;
+      }
+    }
+  }
   /**
    * Answers a semi-colon-delimited string with the example query or queries for
    * the selected database
@@ -375,7 +441,8 @@ public class SequenceFetcher extends JPanel implements Runnable
    */
   protected void example_actionPerformed()
   {
-    String eq = getExampleQueries((String) database.getSelectedItem());
+    String eq = getExampleQueries(
+            ((StringPair) database.getSelectedItem()).getKey());
     textArea.setText(eq);
     repaint();
   }
@@ -471,8 +538,8 @@ public class SequenceFetcher extends JPanel implements Runnable
     List<String> presultTitle = new ArrayList<>();
     List<AlignmentI> presult = new ArrayList<>();
     List<AlignmentI> aresult = new ArrayList<>();
-    List<DbSourceProxy> sources = sfetch
-            .getSourceProxy((String) database.getSelectedItem());
+    List<DbSourceProxy> sources = sfetch.getSourceProxy(
+            ((StringPair) database.getSelectedItem()).getKey());
     Iterator<DbSourceProxy> proxies = sources.iterator();
     String[] qries = textArea.getText().trim().split(";");
     List<String> nextFetch = Arrays.asList(qries);
@@ -524,23 +591,25 @@ public class SequenceFetcher extends JPanel implements Runnable
       } catch (Exception e)
       {
         showErrorMessage("Error retrieving " + textArea.getText() + " from "
-                + database.getSelectedItem());
+                + ((StringPair) database.getSelectedItem()).getDisplay());
         // error
         // +="Couldn't retrieve sequences from "+database.getSelectedItem();
         System.err.println("Retrieval failed for source ='"
-                + database.getSelectedItem() + "' and query\n'"
-                + textArea.getText() + "'\n");
+                + ((StringPair) database.getSelectedItem()).getDisplay()
+                + "' and query\n'" + textArea.getText() + "'\n");
         e.printStackTrace();
       } catch (OutOfMemoryError e)
       {
         showErrorMessage("Out of Memory when retrieving "
-                + textArea.getText() + " from " + database.getSelectedItem()
+                + textArea.getText() + " from "
+                + ((StringPair) database.getSelectedItem()).getDisplay()
                 + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
         e.printStackTrace();
       } catch (Error e)
       {
         showErrorMessage("Serious Error retrieving " + textArea.getText()
-                + " from " + database.getSelectedItem());
+                + " from "
+                + ((StringPair) database.getSelectedItem()).getDisplay());
         e.printStackTrace();
       }
 
@@ -687,7 +756,8 @@ public class SequenceFetcher extends JPanel implements Runnable
     } catch (OutOfMemoryError oome)
     {
       new OOMWarning("fetching " + multiacc + " from "
-              + database.getSelectedItem(), oome, this);
+              + ((StringPair) database.getSelectedItem()).getDisplay(),
+              oome, this);
     }
   }
 
@@ -795,10 +865,20 @@ public class SequenceFetcher extends JPanel implements Runnable
    */
   public String getDefaultRetrievalTitle()
   {
-    return "Retrieved from " + database.getSelectedItem();
+    return "Retrieved from "
+            + ((StringPair) database.getSelectedItem()).getDisplay();
   }
 
-  AlignmentI parseResult(AlignmentI al, String title,
+  /**
+   * constructs an alignment frame given the data and metadata
+   * 
+   * @param al
+   * @param title
+   * @param currentFileFormat
+   * @param preferredFeatureColours
+   * @return the alignment
+   */
+  public AlignmentI parseResult(AlignmentI al, String title,
           FileFormatI currentFileFormat,
           FeatureSettingsModelI preferredFeatureColours)
   {