JAL-2507 output secondary structure regardless of presence of dataset sequence

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

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index a5cd401..32e6ff7 100644 (file)
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -97,7 +97,8 @@ public class StockholmFile extends AlignFile
     this.al = al;
   }
 
-  public StockholmFile(String inFile, String type) throws IOException
+  public StockholmFile(String inFile, DataSourceType type)
+          throws IOException
   {
     super(inFile, type);
   }
@@ -540,8 +541,7 @@ public class StockholmFile extends AlignFile
           }
           else
           {
-            // throw new IOException(MessageManager.formatMessage(
-            // "exception.error_parsing_line", new String[] { line }));
+            // throw new IOException("Error parsing " + line);
             System.err.println(">> missing annotation: " + line);
           }
         }
@@ -800,9 +800,9 @@ public class StockholmFile extends AlignFile
   {
     String convert1, convert2 = null;
 
-    convert1 = OPEN_PAREN.replaceAll(annots);
-    convert2 = CLOSE_PAREN.replaceAll(convert1);
-    annots = convert2;
+    // convert1 = OPEN_PAREN.replaceAll(annots);
+    // convert2 = CLOSE_PAREN.replaceAll(convert1);
+    // annots = convert2;
 
     String type = label;
     if (label.contains("_cons"))
@@ -830,8 +830,7 @@ public class StockholmFile extends AlignFile
         {
           if (DETECT_BRACKETS.search(pos))
           {
-            ann.secondaryStructure = Rna.getRNASecStrucState(
-                    pos).charAt(0);
+            ann.secondaryStructure = Rna.getRNASecStrucState(pos).charAt(0);
           }
           else
           {
@@ -882,8 +881,13 @@ public class StockholmFile extends AlignFile
     return annot;
   }
 
-  public String print(SequenceI[] s)
+  @Override
+  public String print(SequenceI[] s, boolean jvSuffix)
   {
+    out = new StringBuffer();
+    out.append("# STOCKHOLM 1.0");
+    out.append(newline);
+
     // find max length of id
     int max = 0;
     int maxid = 0;
@@ -891,7 +895,7 @@ public class StockholmFile extends AlignFile
     Hashtable dataRef = null;
     while ((in < s.length) && (s[in] != null))
     {
-      String tmp = printId(s[in]);
+      String tmp = printId(s[in], jvSuffix);
       if (s[in].getSequence().length > max)
       {
         max = s[in].getSequence().length;
@@ -962,47 +966,44 @@ public class StockholmFile extends AlignFile
     // output annotations
     while (i < s.length && s[i] != null)
     {
-      if (s[i].getDatasetSequence() != null)
+      AlignmentAnnotation[] alAnot = s[i].getAnnotation();
+      if (alAnot != null)
       {
-        SequenceI ds = s[i].getDatasetSequence();
-        AlignmentAnnotation[] alAnot;
         Annotation[] ann;
-        Annotation annot;
-        alAnot = s[i].getAnnotation();
-        String feature = "";
-        if (alAnot != null)
+        for (int j = 0; j < alAnot.length; j++)
         {
-          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 (ds.getSequenceFeatures() != null)
-            {
-              feature = ds.getSequenceFeatures()[0].type;
-            }
-            // ?bug - feature may still have previous loop value
-            String key = type2id(feature);
 
-            if (key == null)
-            {
-              continue;
-            }
+            continue;
+          }
 
-            // out.append("#=GR ");
-            out.append(new Format("%-" + maxid + "s").form("#=GR "
-                    + printId(s[i]) + " " + key + " "));
-            ann = alAnot[j].annotations;
-            boolean isrna = alAnot[j].isValidStruc();
-            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("#=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(new Format("%-" + maxid + "s").form(printId(s[i]) + " "));
+      out.append(new Format("%-" + maxid + "s")
+              .form(printId(s[i], jvSuffix) + " "));
       out.append(s[i].getSequenceAsString());
       out.append(newline);
       i++;
@@ -1055,6 +1056,10 @@ public class StockholmFile extends AlignFile
         out.append(newline);
       }
     }
+
+    out.append("//");
+    out.append(newline);
+
     return out.toString();
   }
 
@@ -1107,13 +1112,12 @@ public class StockholmFile extends AlignFile
     return seq;
   }
 
-  @Override
   public String print()
   {
     out = new StringBuffer();
     out.append("# STOCKHOLM 1.0");
     out.append(newline);
-    print(getSeqsAsArray());
+    print(getSeqsAsArray(), false);
 
     out.append("//");
     out.append(newline);