JAL-2071 further refactoring, optimisation, and house keeping for the generic Free...

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

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 784474e..ab78ad3 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -21,10 +21,14 @@
 package jalview.gui;
 
 import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.fts.service.pdb.PDBFTSPanel;
+import jalview.fts.service.uniprot.UniprotFTSPanel;
+import jalview.io.gff.SequenceOntologyI;
 import jalview.util.DBRefUtils;
 import jalview.util.MessageManager;
 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
@@ -112,6 +116,11 @@ public class SequenceFetcher extends JPanel implements Runnable
 
   int debounceTrap = 0;
 
+  public JTextArea getTextArea()
+  {
+    return textArea;
+  }
+
   /**
    * Blocking method that initialises and returns the shared instance of the
    * SequenceFetcher client
@@ -156,9 +165,9 @@ public class SequenceFetcher extends JPanel implements Runnable
       }
     }
     if (sfetch == null
-            || dasRegistry != jalview.bin.Cache.getDasSourceRegistry()
-            || lastDasSourceRegistry != (jalview.bin.Cache
-                    .getDasSourceRegistry().getDasRegistryURL() + jalview.bin.Cache
+            || dasRegistry != Cache.getDasSourceRegistry()
+            || lastDasSourceRegistry != (Cache.getDasSourceRegistry()
+                    .getDasRegistryURL() + Cache
                     .getDasSourceRegistry().getLocalSourceString())
                     .hashCode())
     {
@@ -173,7 +182,7 @@ public class SequenceFetcher extends JPanel implements Runnable
                 .getString("status.init_sequence_database_fetchers"),
                 Thread.currentThread().hashCode());
       }
-      dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
+      dasRegistry = Cache.getDasSourceRegistry();
       dasRegistry.refreshSources();
 
       jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
@@ -365,15 +374,21 @@ public class SequenceFetcher extends JPanel implements Runnable
       {
         debounceTrap++;
         String currentSelection = database.getSelectedItem();
-        if (!currentSelection.equalsIgnoreCase("pdb"))
-        {
-          otherSourceAction();
-        }
+
         if (currentSelection.equalsIgnoreCase("pdb")
                 && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
         {
           pdbSourceAction();
         }
+        else if (currentSelection.equalsIgnoreCase("uniprot")
+                && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
+        {
+          uniprotSourceAction();
+        }
+        else
+        {
+          otherSourceAction();
+        }
         database.action = -1;
       }
     });
@@ -397,10 +412,16 @@ public class SequenceFetcher extends JPanel implements Runnable
   private void pdbSourceAction()
   {
     databaseButt.setText(database.getSelectedItem());
-    new PDBSearchPanel(this);
+    new PDBFTSPanel(this);
     frame.dispose();
   }
 
+  private void uniprotSourceAction()
+  {
+    databaseButt.setText(database.getSelectedItem());
+    new UniprotFTSPanel(this);
+    frame.dispose();
+  }
   private void otherSourceAction()
   {
     try
@@ -552,7 +573,7 @@ public class SequenceFetcher extends JPanel implements Runnable
                             proxy.getDbName() }), Thread.currentThread()
                         .hashCode());
         isAliSource = proxy.isAlignmentSource();
-        if (proxy.getAccessionSeparator() == null)
+        if (proxy.getMaximumQueryCount() == 1)
         {
           while (en.hasNext())
           {
@@ -592,7 +613,8 @@ public class SequenceFetcher extends JPanel implements Runnable
               }
             } catch (Exception e)
             {
-              jalview.bin.Cache.log.info("Error retrieving " + item
+              Cache.log.info(
+                      "Error retrieving " + item
                       + " from " + proxy.getDbName(), e);
               nextfetch.add(item);
             }
@@ -833,8 +855,13 @@ public class SequenceFetcher extends JPanel implements Runnable
 
         if (preferredFeatureColours != null)
         {
-          af.viewport.applyFeaturesStyle(preferredFeatureColours);
+          af.getViewport().applyFeaturesStyle(preferredFeatureColours);
         }
+        if (Cache.getDefault("HIDE_INTRONS", true))
+        {
+          hideIntronsIfPresent(af);
+        }
+
         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
 
@@ -843,7 +870,7 @@ public class SequenceFetcher extends JPanel implements Runnable
 
         try
         {
-          af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
+          af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN",
                   false));
         } catch (Exception ex)
         {
@@ -857,6 +884,25 @@ 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();