JAL-3210 Barebones gradle/buildship/eclipse. See README

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

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index aa21b0f..5f68099 100755 (executable)
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -441,7 +441,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
       float score = Float.NaN;
       try
       {
-        score = new Float(gffColumns[6]).floatValue();
+        score = Float.valueOf(gffColumns[6]).floatValue();
       } catch (NumberFormatException ex)
       {
         sf = new SequenceFeature(ft, desc, startPos, endPos, featureGroup);
@@ -829,15 +829,14 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
     AlignViewportI av = getViewport();
     if (av != null)
     {
-      AlignmentI a = av.getAlignment();
-      if (a != null)
+      if (av.getAlignment() != null)
       {
-        dataset = a.getDataset();
+        dataset = av.getAlignment().getDataset();
       }
       if (dataset == null)
       {
         // working in the applet context ?
-        dataset = a;
+        dataset = av.getAlignment();
       }
     }
     else
@@ -891,8 +890,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
 
     StringBuilder out = new StringBuilder(256);
 
-    out.append(String.format("%s %d" + newline, GFF_VERSION,
-            gffVersion == 0 ? 2 : gffVersion));
+    out.append(String.format("%s %d\n", GFF_VERSION, gffVersion == 0 ? 2 : gffVersion));
 
     if (!includeNonPositionalFeatures
             && (visibleColours == null || visibleColours.isEmpty()))