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JAL-2018 export graduated feature colours correctly
[jalview.git] / src / jalview / io / FeaturesFile.java
diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 2dd5f26..372d905 100755 (executable)
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -842,12 +842,12 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
         features = sequences[i].getSequenceFeatures();
         if (features != null)
         {
-          for (int j = 0; j < features.length; j++)
+          for (SequenceFeature sequenceFeature : features)
           {
-            isnonpos = features[j].begin == 0 && features[j].end == 0;
+            isnonpos = sequenceFeature.begin == 0 && sequenceFeature.end == 0;
             if ((!nonpos && isnonpos)
                     || (!isnonpos && visOnly && !visible
-                            .containsKey(features[j].type)))
+                            .containsKey(sequenceFeature.type)))
             {
               // skip if feature is nonpos and we ignore them or if we only
               // output visible and it isn't non-pos and it's not visible
@@ -855,47 +855,48 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
             }
 
             if (group != null
-                    && (features[j].featureGroup == null || !features[j].featureGroup
+                    && (sequenceFeature.featureGroup == null || !sequenceFeature.featureGroup
                             .equals(group)))
             {
               continue;
             }
 
-            if (group == null && features[j].featureGroup != null)
+            if (group == null && sequenceFeature.featureGroup != null)
             {
               continue;
             }
             // we have features to output
             featuresGen = true;
-            if (features[j].description == null
-                    || features[j].description.equals(""))
+            if (sequenceFeature.description == null
+                    || sequenceFeature.description.equals(""))
             {
-              out.append(features[j].type).append(TAB);
+              out.append(sequenceFeature.type).append(TAB);
             }
             else
             {
-              if (features[j].links != null
-                      && features[j].getDescription().indexOf("<html>") == -1)
+              if (sequenceFeature.links != null
+                      && sequenceFeature.getDescription().indexOf("<html>") == -1)
               {
                 out.append("<html>");
               }
 
-              out.append(features[j].description + " ");
-              if (features[j].links != null)
+              out.append(sequenceFeature.description);
+              if (sequenceFeature.links != null)
               {
-                for (int l = 0; l < features[j].links.size(); l++)
+                for (int l = 0; l < sequenceFeature.links.size(); l++)
                 {
-                  String label = features[j].links.elementAt(l).toString();
+                  String label = sequenceFeature.links.elementAt(l);
                   String href = label.substring(label.indexOf("|") + 1);
                   label = label.substring(0, label.indexOf("|"));
 
-                  if (features[j].description.indexOf(href) == -1)
+                  if (sequenceFeature.description.indexOf(href) == -1)
                   {
-                    out.append("<a href=\"" + href + "\">" + label + "</a>");
+                    out.append(" <a href=\"" + href + "\">" + label
+                            + "</a>");
                   }
                 }
 
-                if (features[j].getDescription().indexOf("</html>") == -1)
+                if (sequenceFeature.getDescription().indexOf("</html>") == -1)
                 {
                   out.append("</html>");
                 }
@@ -905,15 +906,15 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
             }
             out.append(sequences[i].getName());
             out.append("\t-1\t");
-            out.append(features[j].begin);
+            out.append(sequenceFeature.begin);
             out.append(TAB);
-            out.append(features[j].end);
+            out.append(sequenceFeature.end);
             out.append(TAB);
-            out.append(features[j].type);
-            if (!Float.isNaN(features[j].score))
+            out.append(sequenceFeature.type);
+            if (!Float.isNaN(sequenceFeature.score))
             {
               out.append(TAB);
-              out.append(features[j].score);
+              out.append(sequenceFeature.score);
             }
             out.append(newline);
           }
@@ -1024,7 +1025,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
           boolean includeNonPositionalFeatures)
   {
     StringBuilder out = new StringBuilder(256);
-    out.append(String.format("%s %d\n", GFF_VERSION, gffVersion));
+    int version = gffVersion == 0 ? 2 : gffVersion;
+    out.append(String.format("%s %d\n", GFF_VERSION, version));
     String source;
     boolean isnonpos;
     for (SequenceI seq : sequences)