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 54aefc4..d225e42 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -20,6 +20,21 @@
  */
 package jalview.gui;
 
+import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceI;
+import jalview.fts.core.GFTSPanel;
+import jalview.fts.service.pdb.PDBFTSPanel;
+import jalview.fts.service.uniprot.UniprotFTSPanel;
+import jalview.io.FileFormatI;
+import jalview.io.gff.SequenceOntologyI;
+import jalview.util.DBRefUtils;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
 import java.awt.BorderLayout;
 import java.awt.Font;
 import java.awt.event.ActionEvent;
@@ -42,22 +57,6 @@ import javax.swing.JScrollPane;
 import javax.swing.JTextArea;
 import javax.swing.SwingConstants;
 
-import jalview.api.FeatureSettingsModelI;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
-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;
-import jalview.util.DBRefUtils;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.ws.seqfetcher.DbSourceProxy;
-
 /**
  * A panel where the use may choose a database source, and enter one or more
  * accessions, to retrieve entries from the database.
@@ -105,7 +104,6 @@ public class SequenceFetcher extends JPanel implements Runnable
       return other.key == this.key;
     }
   }
-
   private static jalview.ws.SequenceFetcher sfetch = null;
 
   JLabel exampleAccession;
@@ -185,8 +183,8 @@ public class SequenceFetcher extends JPanel implements Runnable
 
     frame = new JInternalFrame();
     frame.setContentPane(this);
-    Desktop.addInternalFrame(frame, getFrameTitle(), true, 400,
-            Platform.isAMacAndNotJS() ? 240 : 180);
+    Desktop.addInternalFrame(frame, getFrameTitle(), Desktop.FRAME_MAKE_VISIBLE, 400, 
+               Platform.isAMacAndNotJS() ? 240 : 180, Desktop.FRAME_ALLOW_RESIZE, Desktop.FRAME_SET_MIN_SIZE_300);
   }
 
   private String getFrameTitle()
@@ -372,7 +370,6 @@ public class SequenceFetcher extends JPanel implements Runnable
       }
     }
   }
-
   /**
    * Answers a semi-colon-delimited string with the example query or queries for
    * the selected database
@@ -494,9 +491,9 @@ public class SequenceFetcher extends JPanel implements Runnable
       text = text.replace(",", ";");
     }
     text = text.replaceAll("(\\s|[; ])+", ";");
-    if (!t0.equals(text))
+    if (!t0.equals(text)) 
     {
-      textArea.setText(text);
+         textArea.setText(text);
     }
     if (text.isEmpty())
     {
@@ -834,12 +831,12 @@ public class SequenceFetcher extends JPanel implements Runnable
 
     for (String q : queries)
     {
-      // BH 2019.01.25 dbr is never used.
-      // DBRefEntry dbr = new DBRefEntry();
-      // dbr.setSource(proxy.getDbSource());
-      // dbr.setVersion(null);
+       // BH 2019.01.25 dbr is never used.
+//      DBRefEntry dbr = new DBRefEntry();
+//      dbr.setSource(proxy.getDbSource());
+//      dbr.setVersion(null);
       String accId = proxy.getAccessionIdFromQuery(q);
-      // dbr.setAccessionId(accId);
+//      dbr.setAccessionId(accId);
       boolean rfound = false;
       for (int r = 0, nr = rs.length; r < nr; r++)
       {
@@ -914,7 +911,10 @@ public class SequenceFetcher extends JPanel implements Runnable
           }
         }
 
-        af.getViewport().applyFeaturesStyle(preferredFeatureColours);
+        if (preferredFeatureColours != null)
+        {
+          af.getViewport().applyFeaturesStyle(preferredFeatureColours);
+        }
         if (Cache.getDefault("HIDE_INTRONS", true))
         {
           af.hideFeatureColumns(SequenceOntologyI.EXON, false);
@@ -948,7 +948,7 @@ public class SequenceFetcher extends JPanel implements Runnable
       @Override
       public void run()
       {
-        JvOptionPane.showInternalMessageDialog(Desktop.desktop, error,
+        JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), error,
                 MessageManager.getString("label.error_retrieving_data"),
                 JvOptionPane.WARNING_MESSAGE);
       }