file format enum wip changes

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

diff --git a/src/jalview/io/SimpleBlastFile.java b/src/jalview/io/SimpleBlastFile.java
index ec1cbd0..a3fc716 100644 (file)
--- a/src/jalview/io/SimpleBlastFile.java
+++ b/src/jalview/io/SimpleBlastFile.java
@@ -1,27 +1,32 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 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 jalview.util.*;
+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
@@ -46,9 +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
@@ -56,6 +62,7 @@ public class SimpleBlastFile extends AlignFile
     super(source);
   }
 
+  @Override
   public void initData()
   {
     super.initData();
@@ -64,6 +71,7 @@ public class SimpleBlastFile extends AlignFile
     seqids = new Vector();
   }
 
+  @Override
   public void parse() throws IOException
   {
     String line;
@@ -195,9 +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);
 
@@ -287,6 +294,7 @@ public class SimpleBlastFile extends AlignFile
     return new String("Not Implemented.");
   }
 
+  @Override
   public String print()
   {
     return print(getSeqsAsArray());