From e986fde3ae4b511e4c5eccfc1a6e4591a5e77661 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 17 Nov 2005 18:18:55 +0000
Subject: [PATCH] Hidden tabs and vamsas refs for beta release

---
 src/jalview/gui/AlignFrame.java       |   12 ++++++++----
 src/jalview/gui/Desktop.java          |    4 ++--
 src/jalview/gui/SequenceFetcher.java  |   18 +++++++++++-------
 src/jalview/gui/SequenceRenderer.java |    3 ++-
 4 files changed, 23 insertions(+), 14 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 65b9a08..74f081b 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -98,7 +98,7 @@ public class AlignFrame
    // remove(tabbedPane);
     getContentPane().add(alignPanel, BorderLayout.CENTER);
 
-    setGUINucleotide(al.isNucleotide());
+
 
   //  tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);
 
@@ -127,8 +127,12 @@ public class AlignFrame
      }
    });
 
-	if(Desktop.desktop!=null)
+
+  if (Desktop.desktop != null)
+  {
     addServiceListeners();
+    setGUINucleotide(al.isNucleotide());
+  }
   }
 
   /* Set up intrinsic listeners for dynamically generated GUI bits. */
@@ -2492,7 +2496,7 @@ public class AlignFrame
     // TODO: group services by location as well as function.
   }
 
-  public void vamsasStore_actionPerformed(ActionEvent e)
+ /* public void vamsasStore_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
         getProperty("LAST_DIRECTORY"));
@@ -2509,7 +2513,7 @@ public class AlignFrame
       //vs.store(chooser.getSelectedFile().getAbsolutePath()   );
       vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
     }
-  }
+  }*/
 
   public void featureSettings_actionPerformed(ActionEvent e)
   {
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index cc720fe..8323320 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -550,7 +550,7 @@ public class Desktop extends jalview.jbgui.GDesktop
         }
     }
 
-    public void vamsasLoad_actionPerformed(ActionEvent e)
+  /*  public void vamsasLoad_actionPerformed(ActionEvent e)
     {
       JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
           getProperty("LAST_DIRECTORY"));
@@ -569,7 +569,7 @@ public class Desktop extends jalview.jbgui.GDesktop
             );
       }
 
-    }
+    }*/
 
 
     public void inputSequence_actionPerformed(ActionEvent e)
diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 4fa215f..adadf14 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -127,6 +127,7 @@ public class SequenceFetcher
 
   public void run()
   {
+    String error = null;
     StringBuffer result = new StringBuffer();
       if (database.getSelectedItem().equals("Uniprot")
           || database.getSelectedItem().equals("EMBL")
@@ -160,13 +161,11 @@ public class SequenceFetcher
           }
         }catch(Exception ex)// Problem parsing PDB file
         {
-          JOptionPane.showInternalMessageDialog(Desktop.desktop,
-         "Error retrieving "+textfield.getText()+" from "+database.getSelectedItem(),
-         "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);
+          error = "Error retrieving "+textfield.getText()+" from "+database.getSelectedItem();
         }
       }
 
-    if (result.length() > 0)
+    if (result.length() > 0 && error!=null)
     {
       String format = IdentifyFile.Identify(result.toString(), "Paste");
       SequenceI[] sequences = null;
@@ -228,9 +227,9 @@ public class SequenceFetcher
 
         }
         else
-          JOptionPane.showInternalMessageDialog(Desktop.desktop,
-         "Error retrieving "+textfield.getText()+" from "+database.getSelectedItem(),
-         "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);
+          error = "Error retrieving "+textfield.getText()+" from "+database.getSelectedItem();
+
+
 
       }
     }
@@ -240,6 +239,11 @@ public class SequenceFetcher
     ok.setEnabled(true);
     cancel.setEnabled(true);
     frame.setTitle("Sequence Fetcher");
+
+    if(error!=null)
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+         error, "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);
+
   }
 }
 
diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index f70a9fa..e95ca02 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -86,7 +86,8 @@ public class SequenceRenderer
 
       graphics = bi.getGraphics();
 
-      bi.setRGB(0,0, initialCol.getRGB());
+      if(initialCol!=null)
+        bi.setRGB(0,0, initialCol.getRGB());
 
       allGroups = av.alignment.findAllGroups(seq);
 
-- 
1.7.10.2