X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFeaturesFile.java;h=7299628f8ddcb6edf5d40162e432b703abd9b124;hb=37a5dfc3c72a42689e90ad8a0e118e8855d9868b;hp=943101156c7d38fd1e281181b14e612e956c294e;hpb=bceadbb394604c88ac18e2dcf4b33e735377d7ac;p=jalview.git

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 9431011..7299628 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -40,15 +40,6 @@ public class FeaturesFile extends AlignFile
     {
     }
 
-    /**
-     * Creates a new FeaturesFile object.
-     *
-     * @param inStr DOCUMENT ME!
-     */
-    public FeaturesFile(String inStr)
-    {
-        super(inStr);
-    }
 
     /**
      * Creates a new FeaturesFile object.
@@ -165,7 +156,7 @@ public class FeaturesFile extends AlignFile
                 end = Integer.parseInt(st.nextToken());
                 try
                 {
-                  score = Float.parseFloat(st.nextToken());
+                  score =  new Float(st.nextToken()).floatValue();
                 }
                 catch (NumberFormatException ex)
                 {
@@ -182,7 +173,17 @@ public class FeaturesFile extends AlignFile
                 catch (Exception ex)
                 {}
 
-                seq.getDatasetSequence().addSequenceFeature(sf);
+                if(st.hasMoreTokens())
+                {
+                  StringBuffer attributes = new StringBuffer();
+                  while (st.hasMoreTokens())
+                  {
+                    attributes.append("\t"+st.nextElement());
+                  }
+                  sf.setValue("ATTRIBUTES", attributes.toString());
+                }
+
+                seq.addSequenceFeature(sf);
 
                 break;
               }
@@ -412,6 +413,7 @@ public class FeaturesFile extends AlignFile
     {
       StringBuffer out = new StringBuffer();
       SequenceFeature [] next;
+      String source;
 
       for(int i=0; i<seqs.length; i++)
       {
@@ -423,8 +425,12 @@ public class FeaturesFile extends AlignFile
             if(!visible.containsKey(next[j].type))
               continue;
 
+            source = next[j].featureGroup;
+            if(source==null)
+              source = next[j].getDescription();
+
             out.append(seqs[i].getName() + "\t"
-                       + next[j].description + "\t"
+                       + source + "\t"
                        + next[j].type  + "\t"
                        + next[j].begin + "\t"
                        + next[j].end   + "\t"
@@ -435,10 +441,16 @@ public class FeaturesFile extends AlignFile
               out.append(next[j].getValue("STRAND")+"\t");
             else
               out.append(".\t");
+
             if(next[j].getValue("FRAME")!=null)
-              out.append(next[j].getValue("FRAME")+"\n");
+              out.append(next[j].getValue("FRAME"));
             else
-              out.append(".\n");
+              out.append(".");
+
+            if(next[j].getValue("ATTRIBUTES")!=null)
+              out.append(next[j].getValue("ATTRIBUTES"));
+
+            out.append("\n");
 
           }
         }