JAL-2609 slightly better updating of left/right scales...

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

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 7f3f93b..798a77e 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("(>|\\])", ")");
@@ -392,7 +394,7 @@ 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;
@@ -412,7 +414,7 @@ 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);
                   }
@@ -635,7 +637,7 @@ 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)
             {
@@ -643,7 +645,7 @@ 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
 
@@ -820,7 +822,7 @@ public class StockholmFile extends AlignFile
     }
     boolean ss = false, posterior = false;
     type = id2type(type);
-    if (type.equals("secondary structure"))
+    if (type.equalsIgnoreCase("secondary structure"))
     {
       ss = true;
     }
@@ -928,10 +930,7 @@ 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)
       {
@@ -1163,10 +1162,10 @@ public class StockholmFile extends AlignFile
     if (typeIds == null)
     {
       typeIds = new Hashtable();
-      typeIds.put("SS", "secondary structure");
-      typeIds.put("SA", "surface accessibility");
+      typeIds.put("SS", "Secondary Structure");
+      typeIds.put("SA", "Surface Accessibility");
       typeIds.put("TM", "transmembrane");
-      typeIds.put("PP", "posterior probability");
+      typeIds.put("PP", "Posterior Probability");
       typeIds.put("LI", "ligand binding");
       typeIds.put("AS", "active site");
       typeIds.put("IN", "intron");
@@ -1177,7 +1176,7 @@ public class StockholmFile extends AlignFile
       typeIds.put("DE", "description");
       typeIds.put("DR", "reference");
       typeIds.put("LO", "look");
-      typeIds.put("RF", "reference positions");
+      typeIds.put("RF", "Reference Positions");
 
     }
   }
@@ -1200,7 +1199,7 @@ public class StockholmFile extends AlignFile
     while (e.hasMoreElements())
     {
       Object ll = e.nextElement();
-      if (typeIds.get(ll).toString().equals(type))
+      if (typeIds.get(ll).toString().equalsIgnoreCase(type))
       {
         key = (String) ll;
         break;