X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSimpleBlastFile.java;h=ba6b2f3606db2758e4ecffc444318a3b7aec9f0f;hb=9135cbb74bbff06ea60485540194515ebcc018b0;hp=03f76ead979850889f5a8afe995b4753962713ef;hpb=539476a37ccaae7b2b665c9f9ccc817320582781;p=jalview.git diff --git a/src/jalview/io/SimpleBlastFile.java b/src/jalview/io/SimpleBlastFile.java index 03f76ea..ba6b2f3 100644 --- a/src/jalview/io/SimpleBlastFile.java +++ b/src/jalview/io/SimpleBlastFile.java @@ -1,28 +1,32 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * - * This program 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 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program 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. + * 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. + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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 @@ -37,17 +41,20 @@ public class SimpleBlastFile extends AlignFile * header and footer info goes into alignment annotation. */ StringBuffer headerLines, footerLines; + /** * hold sequence ids in order of appearance in file */ Vector seqids; + public SimpleBlastFile() { } - public SimpleBlastFile(String inFile, String type) throws IOException + public SimpleBlastFile(String inFile, DataSourceType sourceType) + throws IOException { - super(inFile, type); + super(inFile, sourceType); } public SimpleBlastFile(FileParse source) throws IOException @@ -55,6 +62,7 @@ public class SimpleBlastFile extends AlignFile super(source); } + @Override public void initData() { super.initData(); @@ -63,6 +71,7 @@ public class SimpleBlastFile extends AlignFile seqids = new Vector(); } + @Override public void parse() throws IOException { String line; @@ -87,6 +96,8 @@ public class SimpleBlastFile extends AlignFile continue; } // parse out the sequences + // query anchored means that we use the query sequence as the + // alignment ruler if (line.indexOf("Query") == 0) { padding = -1; @@ -104,7 +115,7 @@ public class SimpleBlastFile extends AlignFile { numcol = p; } - else if (aligcol!=-1 && lastcol == -1) + else if (aligcol != -1 && lastcol == -1) { lastcol = p; } @@ -133,7 +144,8 @@ public class SimpleBlastFile extends AlignFile padding = aligcol; } } - if (line.indexOf("Database:")>-1 || (aligcol == -1 || numcol == -1 || lastcol == -1) + if (line.indexOf("Database:") > -1 + || (aligcol == -1 || numcol == -1 || lastcol == -1) || line.length() < lastcol) { inAlignments = false; @@ -153,7 +165,8 @@ public class SimpleBlastFile extends AlignFile rstart = Long.parseLong(stindx); } catch (Exception e) { - System.err.println("Couldn't parse '"+stindx+"' as start of row"); + System.err.println( + "Couldn't parse '" + stindx + "' as start of row"); // inAlignments = false; // warn for this line } @@ -162,22 +175,40 @@ public class SimpleBlastFile extends AlignFile rend = Long.parseLong(endindx); } catch (Exception e) { - System.err.println("Couldn't parse '"+endindx+"' as end of row"); + System.err.println( + "Couldn't parse '" + endindx + "' as end of row"); // inAlignments = false; // warn for this line } - Object[] seqentry = (Object[]) seqhash.get(sqid); + Vector seqentries = (Vector) seqhash.get(sqid); + if (seqentries == null) + { + seqentries = new Vector(); + seqhash.put(sqid, seqentries); + seqids.addElement(sqid); + } + + Object[] seqentry = null; + Enumeration sqent = seqentries.elements(); + while (seqentry == null && sqent.hasMoreElements()) + { + seqentry = (Object[]) sqent.nextElement(); + if (((long[]) seqentry[1])[1] + 1 != rstart) + { + seqentry = null; + } + } padseq = false; 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); - seqids.addElement(sqid); - + } if (sqid.equals("Query")) { @@ -228,7 +259,7 @@ public class SimpleBlastFile extends AlignFile { Sequence newseq = new Sequence(idstring, - ((StringBuffer) seqentry[0]).toString(), + ((StringBuffer) seqentry[0]).toString(), (int) ((long[]) seqentry[1])[0], (int) ((long[]) seqentry[1])[1]); if (newseq.getEnd() == 0) @@ -259,13 +290,9 @@ public class SimpleBlastFile extends AlignFile } } - public String print(SequenceI[] s) + @Override + public String print(SequenceI[] sqs, boolean jvsuffix) { return new String("Not Implemented."); } - - public String print() - { - return print(getSeqsAsArray()); - } }