Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons

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

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 646a7f1..caecbba 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -27,6 +27,7 @@ import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceI;
 import jalview.fts.core.GFTSPanel;
 import jalview.fts.service.pdb.PDBFTSPanel;
+import jalview.fts.service.threedbeacons.TDBeaconsFTSPanel;
 import jalview.fts.service.uniprot.UniprotFTSPanel;
 import jalview.io.FileFormatI;
 import jalview.io.gff.SequenceOntologyI;
@@ -195,6 +196,11 @@ 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();
@@ -436,6 +442,14 @@ public class SequenceFetcher extends JPanel implements Runnable
       resetDialog();
       return;
     }
+    if (database.getSelectedIndex() == 0)
+    {
+      // todo i18n
+      showErrorMessage("Please choose a database");
+      resetDialog();
+      return;
+    }
+
     exampleBtn.setEnabled(false);
     textArea.setEnabled(false);
     okBtn.setEnabled(false);
@@ -789,8 +803,15 @@ public class SequenceFetcher extends JPanel implements Runnable
   {
     return "Retrieved from " + database.getSelectedItem();
   }
-
-  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)
   {
@@ -823,10 +844,7 @@ public class SequenceFetcher extends JPanel implements Runnable
           }
         }
 
-        if (preferredFeatureColours != null)
-        {
-          af.getViewport().applyFeaturesStyle(preferredFeatureColours);
-        }
+        af.getViewport().applyFeaturesStyle(preferredFeatureColours);
         if (Cache.getDefault("HIDE_INTRONS", true))
         {
           af.hideFeatureColumns(SequenceOntologyI.EXON, false);