Merge pull request #51 from tcarver/master

misc

ChangeLog

-Version XX
+Version 14
 	Add options in the navigator for searching the forward and 
 	reverse strands individually for base / amino acid patterns.
 	
 	Add an option to the navigator for searching for matches that
-	overlap a seleted region or feature.
+	overlap a selected region or feature.
 	
 	New translation table 24 (Pterobranchia mitochondrial) added.
+	
+	If the BAM index file is missing then Artemis uses the picard library to
+	attempt to create the index.
 
 	Variant (VCF / BCF) filtering now uses the meta-data in the header to
 	enable filtering based on INFO, FILTER and FORMAT columns.

uk/ac/sanger/artemis/components/DbfetchEntrySource.java

@@ -37,6 +37,8 @@ import uk.ac.sanger.artemis.io.EntryInformationException;
 import uk.ac.sanger.artemis.io.SimpleEntryInformation;
 
 import java.io.*;
+import java.util.regex.Pattern;
+
 import javax.swing.*;
 
 /**
@@ -50,7 +52,7 @@ import javax.swing.*;
 public class DbfetchEntrySource
     implements EntrySource 
 {
-
+  private static Pattern REFSEQ_PATTERN = Pattern.compile("[a-zA-Z]{2}?_\\w*");
   /**
    *  Create a new DbfetchEntrySource.
    *  @param frame The component that created this EntrySource.  (Used for
@@ -96,8 +98,12 @@ public class DbfetchEntrySource
 //      new MessageDialog (getFrame (),
 //                         "reading entry - please wait", false);
 
+      String db = "EMBL";
+      if(REFSEQ_PATTERN.matcher(embl_id).matches())
+        db = "refseq";
+      
       final String url_string =
-        "http://www.ebi.ac.uk/cgi-bin/dbfetch?db=EMBL&id=" + embl_id +"&style=raw";
+        "http://www.ebi.ac.uk/cgi-bin/dbfetch?db="+db+"&id=" + embl_id +"&style=raw";
 
       final Document url_document =
         DocumentFactory.makeDocument(url_string);

uk/ac/sanger/artemis/io/IndexFastaStream.java

@@ -257,6 +257,11 @@ public class IndexFastaStream extends StreamSequence
     return fastaIndex;
   }
   
+  public String getContig()
+  {
+    return contig;
+  }
+  
   public static void main(String args[])
   {
     EntryInformation new_entry_information =