JAL-3365 expand range of allowed DSSP secondary structure symbols in Stockholm files

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

diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index c0ecd58..1b93892 100755 (executable)
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -218,23 +218,13 @@ public class BLCFile extends AlignFile
   /**
    * DOCUMENT ME!
    * 
-   * @return DOCUMENT ME!
-   */
-  @Override
-  public String print()
-  {
-    return print(getSeqsAsArray());
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
    * @param s
    *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
-  public String print(SequenceI[] s)
+  @Override
+  public String print(SequenceI[] s, boolean jvsuffix)
   {
     StringBuffer out = new StringBuffer();
     /**
@@ -248,7 +238,7 @@ public class BLCFile extends AlignFile
 
     while ((i < s.length) && (s[i] != null))
     {
-      out.append(">" + printId(s[i]));
+      out.append(">" + printId(s[i], jvsuffix));
       if (s[i].getDescription() != null)
       {
         out.append(" " + s[i].getDescription());
@@ -256,10 +246,7 @@ public class BLCFile extends AlignFile
 
       out.append(newline);
 
-      if (s[i].getSequence().length > max)
-      {
-        max = s[i].getSequence().length;
-      }
+      max = Math.max(max, s[i].getLength());
 
       i++;
     }