Merge branch 'develop' into features/JAL-2446NCList

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

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index e22ee0a..f5b5177 100644 (file)
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -74,6 +74,8 @@ import fr.orsay.lri.varna.models.rna.RNA;
  */
 public class StockholmFile extends AlignFile
 {
+  private static final String ANNOTATION = "annotation";
+
   private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
 
   private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
@@ -391,7 +393,7 @@ public class StockholmFile extends AlignFile
               while (j.hasMoreElements())
               {
                 String desc = j.nextElement().toString();
-                if ("annotations".equals(desc) && annotsAdded)
+                if (ANNOTATION.equals(desc) && annotsAdded)
                 {
                   // don't add features if we already added an annotation row
                   continue;
@@ -411,7 +413,7 @@ public class StockholmFile extends AlignFile
                     int new_pos = posmap[k]; // look up nearest seqeunce
                     // position to this column
                     SequenceFeature feat = new SequenceFeature(type, desc,
-                            new_pos, new_pos, 0f, null);
+                            new_pos, new_pos, null);
 
                     seqO.addSequenceFeature(feat);
                   }
@@ -634,7 +636,7 @@ public class StockholmFile extends AlignFile
               content = new Hashtable();
               features.put(this.id2type(type), content);
             }
-            String ns = (String) content.get("annotation");
+            String ns = (String) content.get(ANNOTATION);
 
             if (ns == null)
             {
@@ -642,7 +644,7 @@ public class StockholmFile extends AlignFile
             }
             // finally, append the annotation line
             ns += seq;
-            content.put("annotation", ns);
+            content.put(ANNOTATION, ns);
             // // end of wrapped annotation block.
             // // Now a new row is created with the current set of data
 
@@ -930,10 +932,7 @@ public class StockholmFile extends AlignFile
     while ((in < s.length) && (s[in] != null))
     {
       String tmp = printId(s[in], jvSuffix);
-      if (s[in].getSequence().length > max)
-      {
-        max = s[in].getSequence().length;
-      }
+      max = Math.max(max, s[in].getLength());
 
       if (tmp.length() > maxid)
       {