From eacce9627f059fc2f9e880c81d8d1bdfbe7fe5b3 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 29 Nov 2005 17:59:29 +0000
Subject: [PATCH] Features added removed from alignment

---
 src/jalview/appletgui/AlignFrame.java      |    1 -
 src/jalview/datamodel/Alignment.java       |    3 ---
 src/jalview/gui/AlignFrame.java            |    5 ++---
 src/jalview/io/SequenceFeatureFetcher.java |    9 +++++----
 4 files changed, 7 insertions(+), 11 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 833a6fe..3d28c34 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -217,7 +217,6 @@ public class AlignFrame extends Frame
       }
 
       viewport.showSequenceFeatures = true;
-      ((Alignment)viewport.alignment).featuresAdded = true;
 
       alignPanel.repaint();
 
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 3a1b44a..d45e9a2 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -42,9 +42,6 @@ public class Alignment implements AlignmentI
     /** DOCUMENT ME!! */
     public AlignmentAnnotation[] annotations;
 
-    /** DOCUMENT ME!! */
-    public boolean featuresAdded = false;
-
     /** Make an alignment from an array of Sequences.
      *
      * @param sequences
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 786f5f9..575746a 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -276,7 +276,6 @@ public class AlignFrame
       }
 
       viewport.showSequenceFeatures = true;
-      ((Alignment)viewport.alignment).featuresAdded = true;
 
       alignPanel.repaint();
 
@@ -1423,7 +1422,7 @@ public class AlignFrame
   {
     viewport.showSequenceFeatures(sequenceFeatures.isSelected());
 
-    if (viewport.showSequenceFeatures &&
+  /*  if (viewport.showSequenceFeatures &&
         ! ( (Alignment) viewport.alignment.getDataset()).featuresAdded)
     {
       System.out.println("new fetcher");
@@ -1431,7 +1430,7 @@ public class AlignFrame
          alignment,
           alignPanel);
     }
-
+*/
     featureSettings.setEnabled(true);
 
     alignPanel.repaint();
diff --git a/src/jalview/io/SequenceFeatureFetcher.java b/src/jalview/io/SequenceFeatureFetcher.java
index b3de0f3..dffe7b9 100755
--- a/src/jalview/io/SequenceFeatureFetcher.java
+++ b/src/jalview/io/SequenceFeatureFetcher.java
@@ -49,7 +49,10 @@ public class SequenceFeatureFetcher implements Runnable
   CutAndPasteTransfer output = new CutAndPasteTransfer();
   StringBuffer sbuffer = new StringBuffer();
 
-  Vector getUniprotEntries(File file)
+  public SequenceFeatureFetcher()
+  {}
+
+  public Vector getUniprotEntries(File file)
   {
 
     UniprotFile uni = new UniprotFile();
@@ -127,7 +130,7 @@ public class SequenceFeatureFetcher implements Runnable
            }
           EBIFetchClient ebi = new EBIFetchClient();
           File file = ebi.fetchDataAsFile(remainingIds.toString(),
-                                          "xml", null);
+                                          "xml", "raw");
 
 
 
@@ -176,8 +179,6 @@ public class SequenceFeatureFetcher implements Runnable
         if(reply == javax.swing.JOptionPane.YES_OPTION)
          new WSWUBlastClient(ap, align, unknownSequences);
       }
-      else
-         ((Alignment)dataset).featuresAdded = true;
 
 
     ap.repaint();
-- 
1.7.10.2