X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSimpleBlastFile.java;h=b59a4b5b0389d415dc8f4a6e55efa5915ab0bb6c;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=502ecedcebd1c9ce7cfd3025157baad2720a2550;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git diff --git a/src/jalview/io/SimpleBlastFile.java b/src/jalview/io/SimpleBlastFile.java index 502eced..b59a4b5 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 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * Copyright (C) 2015 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 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);