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 0376c2c..1b93892 100755 (executable)
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -20,10 +20,11 @@
  */
 package jalview.io;
 
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.io.IOException;
+import java.util.Vector;
 
 /**
  * DOCUMENT ME!
@@ -47,15 +48,16 @@ public class BLCFile extends AlignFile
    * 
    * @param inFile
    *          DOCUMENT ME!
-   * @param type
+   * @param sourceType
    *          DOCUMENT ME!
    * 
    * @throws IOException
    *           DOCUMENT ME!
    */
-  public BLCFile(String inFile, String type) throws IOException
+  public BLCFile(String inFile, DataSourceType sourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, sourceType);
   }
 
   public BLCFile(FileParse source) throws IOException
@@ -66,6 +68,7 @@ public class BLCFile extends AlignFile
   /**
    * DOCUMENT ME!
    */
+  @Override
   public void initData()
   {
     super.initData();
@@ -88,6 +91,7 @@ public class BLCFile extends AlignFile
   /**
    * DOCUMENT ME!
    */
+  @Override
   public void parse() throws IOException
   {
     StringBuffer headerLines = new StringBuffer();
@@ -115,7 +119,9 @@ public class BLCFile extends AlignFile
       {
         line = nextLine();
         if (line == null)
+        {
           break;
+        }
         // seek end of ids
         if (line.indexOf("*") > -1)
         {
@@ -150,7 +156,9 @@ public class BLCFile extends AlignFile
         }
       } while (!idsFound);
       if (line == null)
+      {
         break; // end of file.
+      }
       int starCol = line.indexOf("*");
       seqstrings = new StringBuffer[seqs.size()];
 
@@ -198,9 +206,11 @@ public class BLCFile extends AlignFile
     }
     if (seqs.size() > 0)
     {
-      if (headerLines.length() > 1 + numHeaderLines) // could see if buffer is
+      if (headerLines.length() > 1 + numHeaderLines)
+      {
         // just whitespace or not.
         setAlignmentProperty("Comments", headerLines.toString());
+      }
       setAlignmentProperty("iteration", "" + iterationCount);
     }
   }
@@ -208,22 +218,13 @@ public class BLCFile extends AlignFile
   /**
    * DOCUMENT ME!
    * 
-   * @return DOCUMENT ME!
-   */
-  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();
     /**
@@ -237,7 +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());
@@ -245,10 +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++;
     }