diff --git a/uk/ac/sanger/artemis/components/BioJavaEntrySource.java b/uk/ac/sanger/artemis/components/BioJavaEntrySource.java index 8f9a64ce7cbf0db3e1d8d4d89c45440407d63214..ca1c454014268b0febef7f0557ed724138c7d1c7 100644 --- a/uk/ac/sanger/artemis/components/BioJavaEntrySource.java +++ b/uk/ac/sanger/artemis/components/BioJavaEntrySource.java @@ -25,29 +25,12 @@ package uk.ac.sanger.artemis.components; -import java.net.*; import java.io.*; -import java.util.*; -import java.lang.RuntimeException; -import org.biojava.bio.program.das.*; -import org.biojava.bio.BioException; -import org.biojava.bio.seq.io.SequenceBuilderFactory; -import org.biojava.bio.seq.io.EmblProcessor; -import org.biojava.bio.seq.io.SmartSequenceBuilder; -import org.biojava.bio.seq.io.SymbolTokenization; -import org.biojava.bio.seq.io.StreamReader; -import org.biojava.bio.seq.io.SequenceFormat; import org.biojava.bio.seq.io.EmblLikeFormat; -import org.biojava.bio.seq.SequenceIterator; -import org.biojava.bio.symbol.Alphabet; -import org.biojava.bio.seq.DNATools; import uk.ac.sanger.artemis.util.*; import uk.ac.sanger.artemis.io.BioJavaEntry; -import uk.ac.sanger.artemis.io.EntryInformation; -import uk.ac.sanger.artemis.io.SimpleEntryInformation; - import uk.ac.sanger.artemis.*; import uk.ac.sanger.artemis.sequence.*; @@ -145,50 +128,6 @@ public class BioJavaEntrySource implements EntrySource public Entry getEntry (final boolean show_progress) throws OutOfRangeException, NoSequenceException, IOException { -// DASSequence dasSeq = null; - -// try { -// final URL dbURL = -// new URL("http://genome.ornl.gov/das/das.cgi/ecoli"); -// // new URL("http://genome.cse.ucsc.edu:80/cgi-bin/das/cb1"); -// // new URL("http://servlet.sanger.ac.uk:8080/das/ens1131cds/"); -// final DASSequenceDB dasDB = new DASSequenceDB (dbURL); - -// final Set ids = dasDB.ids(); - -// for (Iterator i = ids.iterator(); i.hasNext(); ) { -// System.out.println(i.next().toString()); -// } - -// // dasSeq = (DASSequence) dasDB.getSequence((String) ids.iterator().next()); - -// SequenceIterator si = dasDB.sequenceIterator(); - -// if (si.hasNext()) { -// dasSeq = (DASSequence) si.nextSequence(); - -// System.err.println("Got: " + dasSeq); - -// final BioJavaEntry bioJavaEntry = new BioJavaEntry (dasSeq); - -// return new Entry (bioJavaEntry); -// } else { -// System.err.println("No more sequences..."); -// } - - -// // final BioJavaEntry emblEntry = -// // new BioJavaEntry (document, new EmblLikeFormat ()); - -// // return new Entry (emblEntry); -// } catch (MalformedURLException mue) { -// mue.printStackTrace(); -// } catch (BioException be) { -// be.printStackTrace(); -// } - -// return null; - final String fileName = "/nfs/team81/kmr/pow/java2/AE002734.game"; final FileDocument document = new FileDocument (new File (fileName)); @@ -196,14 +135,6 @@ public class BioJavaEntrySource implements EntrySource new BioJavaEntry (document, new EmblLikeFormat ()); return new Entry (emblEntry); - -// final String fileName = "/nfs/team81/kmr/pow/java2/AB000095.embl"; -// final FileDocument document = new FileDocument (new File (fileName)); - -// final BioJavaEntry emblEntry = -// new BioJavaEntry (document, new EmblLikeFormat ()); - -// return new Entry (emblEntry); } /**