Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

[jalview.git] / src / jalview / io / FeaturesFile.java

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 73783e5..48eeee3 100755 (executable)
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -35,11 +35,12 @@ import jalview.io.gff.GffHelperBase;
 import jalview.io.gff.GffHelperFactory;
 import jalview.io.gff.GffHelperI;
 import jalview.schemes.FeatureColour;
-import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
 import jalview.util.MapList;
 import jalview.util.ParseHtmlBodyAndLinks;
 import jalview.util.StringUtils;
 
+import java.awt.Color;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -94,12 +95,13 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
    * Constructor which does not parse the file immediately
    * 
    * @param inFile
-   * @param type
+   * @param paste
    * @throws IOException
    */
-  public FeaturesFile(String inFile, String type) throws IOException
+  public FeaturesFile(String inFile, DataSourceType paste)
+          throws IOException
   {
-    super(false, inFile, type);
+    super(false, inFile, paste);
   }
 
   /**
@@ -119,7 +121,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
    * @param type
    * @throws IOException
    */
-  public FeaturesFile(boolean parseImmediately, String inFile, String type)
+  public FeaturesFile(boolean parseImmediately, String inFile,
+          DataSourceType type)
           throws IOException
   {
     super(parseImmediately, inFile, type);
@@ -353,8 +356,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
        * Perhaps an old style groups file with no colours -
        * synthesize a colour from the feature type
        */
-      UserColourScheme ucs = new UserColourScheme(ft);
-      featureColours.put(ft, new FeatureColour(ucs.findColour('A')));
+      Color colour = ColorUtils.createColourFromName(ft);
+      featureColours.put(ft, new FeatureColour(colour));
     }
     SequenceFeature sf = new SequenceFeature(ft, desc, "", startPos,
             endPos, featureGroup);
@@ -710,7 +713,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
       dataset = new Alignment(new SequenceI[] {});
     }
 
-    boolean parseResult = parse(dataset, null, false, true);
+    Map<String, FeatureColourI> featureColours = new HashMap<String, FeatureColourI>();
+    boolean parseResult = parse(dataset, featureColours, false, true);
     if (!parseResult)
     {
       // pass error up somehow
@@ -731,9 +735,10 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
    * @return error message
    */
   @Override
-  public String print()
+  public String print(SequenceI[] sqs, boolean jvsuffix)
   {
-    return "Use printGffFormat() or printJalviewFormat()";
+    System.out.println("Use printGffFormat() or printJalviewFormat()");
+    return null;
   }
 
   /**