X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=a33fdc308a4fd5999052c4b4ec2a31a270268b19;hb=c406d789d51e6ac1ff45e3568d37e9ed53025f03;hp=fc6fb0d0a27d856d8a5dd0e40bac43aaa48b45d3;hpb=27b7c61518e2956d1e23e0ef79033c9cce8c71e8;p=jalview.git

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index fc6fb0d..a33fdc3 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -20,12 +20,11 @@
  */
 package jalview.gui;
 
+import jalview.api.FeatureSettingsI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
-import jalview.io.FormatAdapter;
-import jalview.io.IdentifyFile;
 import jalview.util.DBRefUtils;
 import jalview.util.MessageManager;
 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
@@ -527,6 +526,8 @@ public class SequenceFetcher extends JPanel implements Runnable
             .split(";"));
     Iterator<String> en = Arrays.asList(new String[0]).iterator();
     int nqueries = qries.length;
+
+    FeatureSettingsI preferredFeatureColours = null;
     while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
     {
       if (!en.hasNext() && nextfetch.size() > 0)
@@ -693,6 +694,12 @@ public class SequenceFetcher extends JPanel implements Runnable
       // Stack results ready for opening in alignment windows
       if (aresult != null && aresult.size() > 0)
       {
+        FeatureSettingsI proxyColourScheme = proxy.getFeatureColourScheme();
+        if (proxyColourScheme != null)
+        {
+          preferredFeatureColours = proxyColourScheme;
+        }
+
         AlignmentI ar = null;
         if (isAliSource)
         {
@@ -743,7 +750,8 @@ public class SequenceFetcher extends JPanel implements Runnable
     // process results
     while (presult.size() > 0)
     {
-      parseResult(presult.remove(0), presultTitle.remove(0), null);
+      parseResult(presult.remove(0), presultTitle.remove(0), null,
+              preferredFeatureColours);
     }
     // only remove visual delay after we finished parsing.
     guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
@@ -771,35 +779,6 @@ public class SequenceFetcher extends JPanel implements Runnable
     resetDialog();
   }
 
-  AlignmentI parseResult(String result, String title)
-  {
-    String format = new IdentifyFile().identify(result, "Paste");
-    AlignmentI sequences = null;
-    if (FormatAdapter.isValidFormat(format))
-    {
-      sequences = null;
-      try
-      {
-        sequences = new FormatAdapter().readFile(result.toString(),
-                "Paste", format);
-      } catch (Exception ex)
-      {
-      }
-
-      if (sequences != null)
-      {
-        return parseResult(sequences, title, format);
-      }
-    }
-    else
-    {
-      showErrorMessage("Error retrieving " + textArea.getText() + " from "
-              + database.getSelectedItem());
-    }
-
-    return null;
-  }
-
   /**
    * 
    * @return a standard title for any results retrieved using the currently
@@ -811,7 +790,7 @@ public class SequenceFetcher extends JPanel implements Runnable
   }
 
   AlignmentI parseResult(AlignmentI al, String title,
-          String currentFileFormat)
+          String currentFileFormat, FeatureSettingsI preferredFeatureColours)
   {
 
     if (al != null && al.getHeight() > 0)
@@ -849,6 +828,11 @@ public class SequenceFetcher extends JPanel implements Runnable
 
           }
         }
+
+        if (preferredFeatureColours != null)
+        {
+          af.viewport.applyFeaturesStyle(preferredFeatureColours);
+        }
         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);