JAL-2183 simplified database tree actionPerformed, accept dbl-click

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

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 812bf76..afe6754 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -31,6 +31,7 @@ import jalview.fts.service.uniprot.UniprotFTSPanel;
 import jalview.io.gff.SequenceOntologyI;
 import jalview.util.DBRefUtils;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
@@ -114,8 +115,6 @@ public class SequenceFetcher extends JPanel implements Runnable
 
   private static Thread initingThread = null;
 
-  int debounceTrap = 0;
-
   public JTextArea getTextArea()
   {
     return textArea;
@@ -274,13 +273,13 @@ public class SequenceFetcher extends JPanel implements Runnable
 
     frame = new JInternalFrame();
     frame.setContentPane(this);
-    if (new jalview.util.Platform().isAMac())
+    if (Platform.isAMac())
     {
-      Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
+      Desktop.addInternalFrame(frame, getFrameTitle(), false, 400, 240);
     }
     else
     {
-      Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
+      Desktop.addInternalFrame(frame, getFrameTitle(), false, 400, 180);
     }
   }
 
@@ -363,29 +362,42 @@ public class SequenceFetcher extends JPanel implements Runnable
     jPanel1.add(example);
     jPanel1.add(clear);
     jPanel1.add(close);
-    jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
     jPanel2.setLayout(borderLayout3);
-    databaseButt = database.getDatabaseSelectorButton();
+    databaseButt = /*database.getDatabaseSelectorButton();
+                   final JButton viewdbs =*/new JButton(
+            MessageManager.getString("action.select_ddbb"));
+    databaseButt.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent arg0)
+      {
+        hidePanel();
+        database.showDialog();
+      }
+    });
     databaseButt.setFont(JvSwingUtils.getLabelFont());
     database.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        debounceTrap++;
         String currentSelection = database.getSelectedItem();
+        if (currentSelection == null)
+        {
+          close_actionPerformed(null);
+        }
+
+        showPanel();
 
-        if (currentSelection.equalsIgnoreCase("pdb")
-                && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
+        if ("pdb".equalsIgnoreCase(currentSelection))
         {
           pdbSourceAction();
         }
-        // else if (currentSelection.equalsIgnoreCase("uniprot")
-        // && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) ==
-        // 0)))
-        // {
-        // uniprotSourceAction();
-        // }
+        else if ("uniprot".equalsIgnoreCase(currentSelection))
+        {
+          uniprotSourceAction();
+        }
         else
         {
           otherSourceAction();
@@ -408,6 +420,10 @@ public class SequenceFetcher extends JPanel implements Runnable
     this.add(jPanel2, java.awt.BorderLayout.NORTH);
     jScrollPane1.getViewport().add(textArea);
 
+    /*
+     * open the database tree
+     */
+    database.waitForInput();
   }
 
   private void pdbSourceAction()
@@ -814,10 +830,8 @@ public class SequenceFetcher extends JPanel implements Runnable
       Cache.log.info(
               "Error retrieving " + accession
               + " from " + proxy.getDbName(), e);
-    } finally
-    {
-      return success;
     }
+    return success;
   }
 
   /**
@@ -837,7 +851,6 @@ public class SequenceFetcher extends JPanel implements Runnable
 
     for (String q : queries)
     {
-      DBRefEntry[] found = null;
       DBRefEntry dbr = new DBRefEntry();
       dbr.setSource(proxy.getDbSource());
       dbr.setVersion(null);
@@ -848,8 +861,9 @@ public class SequenceFetcher extends JPanel implements Runnable
       {
         if (rs[r] != null)
         {
-          found = DBRefUtils.searchRefs(rs[r].getDBRefs(), accId);
-          if (found != null && found.length > 0)
+          List<DBRefEntry> found = DBRefUtils.searchRefs(rs[r].getDBRefs(),
+                  accId);
+          if (!found.isEmpty())
           {
             rfound = true;
             break;
@@ -920,7 +934,7 @@ public class SequenceFetcher extends JPanel implements Runnable
         }
         if (Cache.getDefault("HIDE_INTRONS", true))
         {
-          hideIntronsIfPresent(af);
+          af.hideFeatureColumns(SequenceOntologyI.EXON, false);
         }
 
         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
@@ -945,25 +959,6 @@ public class SequenceFetcher extends JPanel implements Runnable
     return al;
   }
 
-  /**
-   * Hide columns not containing 'exon' features, provided there are exon
-   * features on the alignment
-   * 
-   * @param af
-   */
-  public void hideIntronsIfPresent(AlignFrame af)
-  {
-    boolean hasExons = af.avc.markColumnsContainingFeatures(false, false,
-            false,
-            SequenceOntologyI.EXON);
-    if (hasExons)
-    {
-      af.avc.markColumnsContainingFeatures(true, false, true,
-              SequenceOntologyI.EXON);
-      af.getViewport().hideSelectedColumns();
-    }
-  }
-
   void showErrorMessage(final String error)
   {
     resetDialog();
@@ -988,4 +983,22 @@ public class SequenceFetcher extends JPanel implements Runnable
   {
     this.progressIndicator = progressIndicator;
   }
+
+  /**
+   * Make this panel visible (after a selection has been made in the database
+   * chooser)
+   */
+  void showPanel()
+  {
+    frame.setVisible(true);
+  }
+
+  /**
+   * Hide this panel (on clicking the database button to open the database
+   * chooser)
+   */
+  void hidePanel()
+  {
+    frame.setVisible(false);
+  }
 }