FileFormatI further tweaks, clean compile

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

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index aa38540..07a3b25 100755 (executable)
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -94,12 +94,13 @@ 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 +120,8 @@ 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);
@@ -710,7 +712,8 @@ 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 +734,10 @@ 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;
   }
 
   /**