Merge branch 'features/JAL-192_scalerelativetoseq' into develop

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

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index a5f218e..7dcd2b9 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -26,6 +26,8 @@ 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;
@@ -114,6 +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
@@ -367,15 +374,22 @@ 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;
       }
     });
@@ -399,10 +413,16 @@ 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
@@ -840,9 +860,7 @@ public class SequenceFetcher extends JPanel implements Runnable
         }
         if (Cache.getDefault("HIDE_INTRONS", true))
         {
-          af.avc.markColumnsContainingFeatures(true, false, false,
-                  SequenceOntologyI.EXON);
-          af.getViewport().hideSelectedColumns();
+          hideIntronsIfPresent(af);
         }
 
         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
@@ -867,6 +885,25 @@ 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();