X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FAnnotate3D.java;h=022ae6d6ff399be4ee3f8a1a6bb03ef27c3eea06;hb=0df37dd0eaf85aac817e0a5f747819b49f405024;hp=509d4ae91f1487d941fa56fa5100c7abd5803ed9;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git diff --git a/src/jalview/ws/jws1/Annotate3D.java b/src/jalview/ws/jws1/Annotate3D.java index 509d4ae..022ae6d 100644 --- a/src/jalview/ws/jws1/Annotate3D.java +++ b/src/jalview/ws/jws1/Annotate3D.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,8 +20,8 @@ */ package jalview.ws.jws1; -import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; +import jalview.io.FileFormat; import jalview.io.FileParse; import jalview.io.FormatAdapter; import jalview.io.InputStreamParser; @@ -86,8 +86,10 @@ public class Annotate3D AlignmentI al = null; while (r.hasNext()) { - FileParse fp = new InputStreamParser(r.next(), source.getDataName()); - AlignmentI nal = new FormatAdapter().readFromFile(fp, "RNAML"); + FileParse fp = new InputStreamParser(r.next(), + source.getDataName()); + AlignmentI nal = new FormatAdapter().readFromFile(fp, + FileFormat.Rnaml); if (al == null) { al = nal; @@ -106,7 +108,8 @@ public class Annotate3D } else { - throw new IOException(MessageManager.getString("exception.unexpected_handling_rnaml_translation_for_pdb"), + throw new IOException(MessageManager.getString( + "exception.unexpected_handling_rnaml_translation_for_pdb"), x); } } @@ -177,8 +180,8 @@ public class Annotate3D URL url = new URL( "http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data=" + content); - BufferedReader is = new BufferedReader(new InputStreamReader( - url.openStream())); + BufferedReader is = new BufferedReader( + new InputStreamReader(url.openStream())); String str4; while ((str4 = is.readLine()) != null) {