JAL-2629 add simple jackhmmer functionality

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

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 3afb967..f7a2df2 100644 (file)
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -28,7 +28,6 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
@@ -43,12 +42,10 @@ import java.io.FileReader;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Enumeration;
-import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.Map.Entry;
 import java.util.Vector;
 
 import com.stevesoft.pat.Regex;
@@ -1029,36 +1026,40 @@ public class StockholmFile extends AlignFile
       if (alAnot != null)
       {
         Annotation[] ann;
+
         for (int j = 0; j < alAnot.length; j++)
         {
-
-          String key = type2id(alAnot[j].label);
-          boolean isrna = alAnot[j].isValidStruc();
-
-          if (isrna)
-          {
-            // hardwire to secondary structure if there is RNA secondary
-            // structure on the annotation
-            key = "SS";
-          }
-          if (key == null)
+          if (alAnot[j].annotations != null)
           {
+            String key = type2id(alAnot[j].label);
+            boolean isrna = alAnot[j].isValidStruc();
 
-            continue;
-          }
+            if (isrna)
+            {
+              // hardwire to secondary structure if there is RNA secondary
+              // structure on the annotation
+              key = "SS";
+            }
+            if (key == null)
+            {
 
-          // out.append("#=GR ");
-          out.append(new Format("%-" + maxid + "s").form(
-                  "#=GR " + printId(s[i], jvSuffix) + " " + key + " "));
-          ann = alAnot[j].annotations;
-          String seq = "";
-          for (int k = 0; k < ann.length; k++)
-          {
-            seq += outputCharacter(key, k, isrna, ann, s[i]);
+              continue;
+            }
+
+            // out.append("#=GR ");
+            out.append(new Format("%-" + maxid + "s").form(
+                    "#=GR " + printId(s[i], jvSuffix) + " " + key + " "));
+            ann = alAnot[j].annotations;
+            String seq = "";
+            for (int k = 0; k < ann.length; k++)
+            {
+              seq += outputCharacter(key, k, isrna, ann, s[i]);
+            }
+            out.append(seq);
+            out.append(newline);
           }
-          out.append(seq);
-          out.append(newline);
         }
+
       }
 
       out.append(new Format("%-" + maxid + "s")