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Any character non aa or nucleotide is a space
[jalview.git] / src / jalview / io / FeaturesFile.java
diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index d81141c..2c0b6d7 100755 (executable)
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -125,7 +125,7 @@ public class FeaturesFile extends AlignFile
             else\r
             {\r
               UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
-              colours.put(type, ucs.findColour("A"));\r
+              colours.put(type, ucs.findColour('A'));\r
               if (st.hasMoreElements())\r
               {\r
                 String link = st.nextToken();\r
@@ -230,7 +230,7 @@ public class FeaturesFile extends AlignFile
             {\r
               // Probably the old style groups file\r
               UserColourScheme ucs = new UserColourScheme(type);\r
-              colours.put(type, ucs.findColour("A"));\r
+              colours.put(type, ucs.findColour('A'));\r
             }\r
 \r
             sf = new SequenceFeature(type, desc, "", start, end, featureGroup);\r
@@ -267,6 +267,9 @@ public class FeaturesFile extends AlignFile
 \r
     public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)\r
     {\r
+      if(sf.getDescription()==null)\r
+        return;\r
+\r
       if(removeHTML && sf.getDescription().toUpperCase().indexOf("<HTML>")==-1)\r
         removeHTML = false;\r
 \r
@@ -410,6 +413,10 @@ public class FeaturesFile extends AlignFile
                   out.append(next[j].type+"\t");\r
                 else\r
                 {\r
+                  if(next[j].links!=null\r
+                     && next[j].getDescription().indexOf("<html>")==-1)\r
+                    out.append("<html>");\r
+\r
                   out.append(next[j].description+" ");\r
                   if(next[j].links!=null)\r
                     {\r
@@ -428,7 +435,12 @@ public class FeaturesFile extends AlignFile
                                      + "</a>");\r
                         }\r
                       }\r
+\r
+                      if (next[j].getDescription().indexOf("</html>") == -1)\r
+                        out.append("</html>");\r
                     }\r
+\r
+\r
                    out.append("\t");\r
                 }\r
 \r