From bfb9d035d37e283762893533bbeef0847b40502b Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 17 Mar 2010 17:39:58 +0000
Subject: [PATCH] simple query anchored blast report parser (shh!) main method
 tester: also tries to output imported alignment as FASTA

---
 src/jalview/io/AppletFormatAdapter.java |   21 ++++++++++++++++++---
 1 file changed, 18 insertions(+), 3 deletions(-)

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 8e05b44..b494dff 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -38,7 +38,7 @@ public class AppletFormatAdapter
    */
   public static final String[] READABLE_FORMATS = new String[]
   { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
-      "PDB", "JnetFile" };
+      "PDB", "JnetFile", "SimpleBLAST" };
 
   /**
    * List of valid format strings for use by callers of the formatSequences
@@ -66,14 +66,14 @@ public class AppletFormatAdapter
    * corresponding to READABLE_FNAMES
    */
   public static final String[] READABLE_EXTENSIONS = new String[]
-  { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar" };
+  { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar", ".blast" };
 
   /**
    * List of readable formats by application in order corresponding to
    * READABLE_EXTENSIONS
    */
   public static final String[] READABLE_FNAMES = new String[]
-  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview" };
+  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview", "SimpleBLAST" };
 
   public static String INVALID_CHARACTERS = "Contains invalid characters";
 
@@ -211,6 +211,10 @@ public class AppletFormatAdapter
       {
         afile = new StockholmFile(inFile, type);
       }
+      else if (format.equals("SimpleBLAST"))
+      {
+        afile = new SimpleBlastFile(inFile,type);
+      }
 
       Alignment al = new Alignment(afile.getSeqsAsArray());
 
@@ -318,6 +322,10 @@ public class AppletFormatAdapter
       {
         afile = new StockholmFile(source);
       }
+      else if (format.equals("SimpleBLAST"))
+      {
+        afile = new SimpleBlastFile(source);
+      }
 
       Alignment al = new Alignment(afile.getSeqsAsArray());
 
@@ -471,6 +479,13 @@ public class AppletFormatAdapter
           {
             System.out.println("Alignment contains " + al.getHeight()
                     + " sequences and " + al.getWidth() + " columns.");
+            try {
+              System.out.println(new AppletFormatAdapter().formatSequences("FASTA", al, true));
+            } catch (Exception e)
+            {
+              System.err.println("Couln't format the alignment for output as a FASTA file.");
+              e.printStackTrace(System.err);
+            }
           }
           else
           {
-- 
1.7.10.2