X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSimpleBlastFile.java;h=1b7254593c1f4057be96b9d0ae3a1c09565f7784;hb=fb4028aee26fec7707500b32632ce27521bcf3c4;hp=d0bf651bfac56d5a95cb59f16344ca0e858da88d;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/io/SimpleBlastFile.java b/src/jalview/io/SimpleBlastFile.java
index d0bf651..1b72545 100644
--- a/src/jalview/io/SimpleBlastFile.java
+++ b/src/jalview/io/SimpleBlastFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.
  * 
@@ -20,10 +20,13 @@
  */
 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.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
 
 /**
  * parse a simple blast report. Attempt to cope with query anchored and pairwise
@@ -48,9 +51,10 @@ public class SimpleBlastFile extends AlignFile
   {
   }
 
-  public SimpleBlastFile(String inFile, String type) throws IOException
+  public SimpleBlastFile(String inFile, DataSourceType sourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, sourceType);
   }
 
   public SimpleBlastFile(FileParse source) throws IOException
@@ -58,6 +62,7 @@ public class SimpleBlastFile extends AlignFile
     super(source);
   }
 
+  @Override
   public void initData()
   {
     super.initData();
@@ -66,6 +71,7 @@ public class SimpleBlastFile extends AlignFile
     seqids = new Vector();
   }
 
+  @Override
   public void parse() throws IOException
   {
     String line;
@@ -197,9 +203,8 @@ public class SimpleBlastFile extends AlignFile
             if (seqentry == null)
             {
               padseq = true; // prepend gaps to new sequences in this block
-              seqentry = new Object[]
-              { new StringBuffer(), new long[]
-              { rstart, rend } };
+              seqentry = new Object[] { new StringBuffer(),
+                  new long[] { rstart, rend } };
               seqentries.addElement(seqentry);
               seqhash.put(sqid, seqentry);
 
@@ -284,13 +289,9 @@ public class SimpleBlastFile extends AlignFile
     }
   }
 
-  public String print(SequenceI[] s)
+  @Override
+  public String print(SequenceI[] sqs, boolean jvsuffix)
   {
     return new String("Not Implemented.");
   }
-
-  public String print()
-  {
-    return print(getSeqsAsArray());
-  }
 }