Commit 98cccd44 authored by tcarver's avatar tcarver
Browse files

Merge pull request #51 from tcarver/master

misc
parents b5bedc1d 62bbbc16
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.
......
......@@ -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);
......
......@@ -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 =
......
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