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 b95cf1f..1b93892 100755 (executable)
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -1,27 +1,30 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 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!
@@ -45,15 +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
@@ -64,6 +68,7 @@ public class BLCFile extends AlignFile
   /**
    * DOCUMENT ME!
    */
+  @Override
   public void initData()
   {
     super.initData();
@@ -86,6 +91,7 @@ public class BLCFile extends AlignFile
   /**
    * DOCUMENT ME!
    */
+  @Override
   public void parse() throws IOException
   {
     StringBuffer headerLines = new StringBuffer();
@@ -113,7 +119,9 @@ public class BLCFile extends AlignFile
       {
         line = nextLine();
         if (line == null)
+        {
           break;
+        }
         // seek end of ids
         if (line.indexOf("*") > -1)
         {
@@ -148,7 +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()];
 
@@ -196,9 +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);
     }
   }
@@ -206,22 +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();
     /**
@@ -235,7 +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());
@@ -243,10 +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++;
     }