Features added removed from alignment

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 833a6fe..3d28c34 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -217,7 +217,6 @@ public class AlignFrame extends Frame
       }\r
 \r
       viewport.showSequenceFeatures = true;\r
-      ((Alignment)viewport.alignment).featuresAdded = true;\r
 \r
       alignPanel.repaint();\r
 \r

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 3a1b44a..d45e9a2 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -42,9 +42,6 @@ public class Alignment implements AlignmentI
     /** DOCUMENT ME!! */\r
     public AlignmentAnnotation[] annotations;\r
 \r
-    /** DOCUMENT ME!! */\r
-    public boolean featuresAdded = false;\r
-\r
     /** Make an alignment from an array of Sequences.\r
      *\r
      * @param sequences\r

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 786f5f9..575746a 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -276,7 +276,6 @@ public class AlignFrame
       }\r
 \r
       viewport.showSequenceFeatures = true;\r
-      ((Alignment)viewport.alignment).featuresAdded = true;\r
 \r
       alignPanel.repaint();\r
 \r
@@ -1423,7 +1422,7 @@ public class AlignFrame
   {\r
     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
 \r
-    if (viewport.showSequenceFeatures &&\r
+  /*  if (viewport.showSequenceFeatures &&\r
         ! ( (Alignment) viewport.alignment.getDataset()).featuresAdded)\r
     {\r
       System.out.println("new fetcher");\r
@@ -1431,7 +1430,7 @@ public class AlignFrame
          alignment,\r
           alignPanel);\r
     }\r
-\r
+*/\r
     featureSettings.setEnabled(true);\r
 \r
     alignPanel.repaint();\r

diff --git a/src/jalview/io/SequenceFeatureFetcher.java b/src/jalview/io/SequenceFeatureFetcher.java
index b3de0f3..dffe7b9 100755 (executable)
--- 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();\r
   StringBuffer sbuffer = new StringBuffer();\r
 \r
-  Vector getUniprotEntries(File file)\r
+  public SequenceFeatureFetcher()\r
+  {}\r
+\r
+  public Vector getUniprotEntries(File file)\r
   {\r
 \r
     UniprotFile uni = new UniprotFile();\r
@@ -127,7 +130,7 @@ public class SequenceFeatureFetcher implements Runnable
            }\r
           EBIFetchClient ebi = new EBIFetchClient();\r
           File file = ebi.fetchDataAsFile(remainingIds.toString(),\r
-                                          "xml", null);\r
+                                          "xml", "raw");\r
 \r
 \r
 \r
@@ -176,8 +179,6 @@ public class SequenceFeatureFetcher implements Runnable
         if(reply == javax.swing.JOptionPane.YES_OPTION)\r
          new WSWUBlastClient(ap, align, unknownSequences);\r
       }\r
-      else\r
-         ((Alignment)dataset).featuresAdded = true;\r
 \r
 \r
     ap.repaint();\r