JAL-1569 formatting

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

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 1c84f00..85f9455 100644 (file)
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -40,7 +40,9 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.Hashtable;
+import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
@@ -185,7 +187,7 @@ public class StockholmFile extends AlignFile
     String version;
     // String id;
     Hashtable seqAnn = new Hashtable(); // Sequence related annotations
-    Hashtable seqs = new Hashtable();
+    LinkedHashMap<String, String> seqs = new LinkedHashMap<String, String>();
     Regex p, r, rend, s, x;
     // Temporary line for processing RNA annotation
     // String RNAannot = "";
@@ -197,7 +199,9 @@ public class StockholmFile extends AlignFile
     r = new Regex("# STOCKHOLM ([\\d\\.]+)");
     if (!r.search(nextLine()))
     {
-      throw new IOException(MessageManager.getString("exception.stockholm_invalid_format"));
+      throw new IOException(
+              MessageManager
+                      .getString("exception.stockholm_invalid_format"));
     }
     else
     {
@@ -257,12 +261,11 @@ public class StockholmFile extends AlignFile
           }
         }
         // logger.debug("Number of sequences: " + this.noSeqs);
-        Enumeration accs = seqs.keys();
-        while (accs.hasMoreElements())
+        for (Map.Entry<String, String> skey : seqs.entrySet())
         {
-          String acc = (String) accs.nextElement();
           // logger.debug("Processing sequence " + acc);
-          String seq = (String) seqs.remove(acc);
+          String acc = skey.getKey();
+          String seq = skey.getValue();
           if (maxLength < seq.length())
           {
             maxLength = seq.length();
@@ -366,6 +369,7 @@ public class StockholmFile extends AlignFile
                     AlignmentAnnotation an = (AlignmentAnnotation) vv
                             .elementAt(ii);
                     seqO.addAlignmentAnnotation(an);
+                    annotations.add(an);
                   }
                 }
               }
@@ -415,9 +419,11 @@ public class StockholmFile extends AlignFile
         if (!x.search(line))
         {
           // logger.error("Could not parse sequence line: " + line);
-          throw new IOException(MessageManager.formatMessage("exception.couldnt_parse_sequence_line", new String[]{line}));
+          throw new IOException(MessageManager.formatMessage(
+                  "exception.couldnt_parse_sequence_line", new String[]
+                  { line }));
         }
-        String ns = (String) seqs.get(x.stringMatched(1));
+        String ns = seqs.get(x.stringMatched(1));
         if (ns == null)
         {
           ns = "";
@@ -527,7 +533,9 @@ public class StockholmFile extends AlignFile
           }
           else
           {
-            throw new IOException(MessageManager.formatMessage("exception.error_parsing_line", new String[]{line}));
+            throw new IOException(MessageManager.formatMessage(
+                    "exception.error_parsing_line", new String[]
+                    { line }));
           }
         }
         else if (annType.equals("GC"))
@@ -635,9 +643,13 @@ public class StockholmFile extends AlignFile
               strucAnn = new Hashtable();
             }
 
-            Vector newStruc = new Vector();
+            Vector<AlignmentAnnotation> newStruc = new Vector<AlignmentAnnotation>();
             parseAnnotationRow(newStruc, type, ns);
-
+            for (AlignmentAnnotation alan : newStruc)
+            {
+              alan.visible = false;
+            }
+            // annotations.addAll(newStruc);
             strucAnn.put(type, newStruc);
             seqAnn.put(acc, strucAnn);
           }
@@ -652,7 +664,9 @@ public class StockholmFile extends AlignFile
         }
         else
         {
-          throw new IOException(MessageManager.formatMessage("exception.unknown_annotation_detected", new String[]{annType,annContent}));
+          throw new IOException(MessageManager.formatMessage(
+                  "exception.unknown_annotation_detected", new String[]
+                  { annType, annContent }));
         }
       }
     }
@@ -1041,11 +1055,12 @@ public class StockholmFile extends AlignFile
 
         out.append(new Format("%-" + maxid + "s").form("#=GC " + label
                 + " "));
+        boolean isrna = aa.isValidStruc();
         for (int j = 0; j < aa.annotations.length; j++)
         {
           String ch = (aa.annotations[j] == null) ? "-"
                   : aa.annotations[j].displayCharacter;
-          if (ch.length() == 0)
+          if (ch.length() == 0 || isrna)
           {
             char ll = aa.annotations[j].secondaryStructure;
             if (Character.toString(ll).equals(" "))