X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSimpleBlastFile.java;h=f4dc5a2a89a3383384d452a21b9e63b05a464f66;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=2f4f2e2f58faf188d0a5682b76934d0151b74d5b;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git diff --git a/src/jalview/io/SimpleBlastFile.java b/src/jalview/io/SimpleBlastFile.java index 2f4f2e2..f4dc5a2 100644 --- a/src/jalview/io/SimpleBlastFile.java +++ b/src/jalview/io/SimpleBlastFile.java @@ -1,27 +1,32 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.io; -import java.io.*; -import java.util.*; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceI; -import jalview.datamodel.*; -import jalview.util.*; +import java.io.IOException; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.Vector; /** * parse a simple blast report. Attempt to cope with query anchored and pairwise @@ -195,9 +200,8 @@ public class SimpleBlastFile extends AlignFile if (seqentry == null) { padseq = true; // prepend gaps to new sequences in this block - seqentry = new Object[] - { new StringBuffer(), new long[] - { rstart, rend } }; + seqentry = new Object[] { new StringBuffer(), + new long[] { rstart, rend } }; seqentries.addElement(seqentry); seqhash.put(sqid, seqentry);