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Fix for RT ticket #642944. ACT can now handle NCBI Blast web site com…
…parison files. This is a workaround for the fact that DoubleACT and WebACT are currently down
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src/main/java/uk/ac/sanger/artemis/BlastWebSiteHitTableComparisonData.java
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| /* BlastServerTableComparisonData.java | ||
| * | ||
| * This file is part of Artemis | ||
| * | ||
| * Copyright (C) 2018 Genome Research Limited | ||
| * | ||
| * 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 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. | ||
| * | ||
| * 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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. | ||
| * | ||
| */ | ||
|
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| package uk.ac.sanger.artemis; | ||
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| import uk.ac.sanger.artemis.util.LinePushBackReader; | ||
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| import java.io.*; | ||
| import java.util.List; | ||
| import java.util.StringTokenizer; | ||
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| /** | ||
| * This class implements the SimpleComparisonData interface | ||
| * for blast web site hit table output. | ||
| * | ||
| * @author kp11 | ||
| */ | ||
| public class BlastWebSiteHitTableComparisonData extends SimpleComparisonData { | ||
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| /** Min number of fields in web site blastn/tblastx file. */ | ||
| public static final int MIN_NUM_FIELDS = 12; | ||
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| /** Max number of fields in web site blastn/tblastx file. */ | ||
| public static final int MAX_NUM_FIELDS = 14; | ||
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| /** Comparison file descriptive type. */ | ||
| public static final String TYPE = "Blast web site hit table comparison data"; | ||
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| /** | ||
| * Create a new BlastWebSiteHitTableComparisonData by reading from the given | ||
| * LinePushBackReader. | ||
| */ | ||
| public BlastWebSiteHitTableComparisonData (final LinePushBackReader stream) | ||
| throws IOException { | ||
| super (stream); | ||
| } | ||
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| /** | ||
| * Create a new, empty instance of BlastServerTableComparisonData. | ||
| */ | ||
| public BlastWebSiteHitTableComparisonData () { | ||
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| } | ||
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| /** | ||
| * Returns a new, empty instance of this type of object; | ||
| */ | ||
| protected SimpleComparisonData getNewSimpleComparisonData () { | ||
| return new BlastWebSiteHitTableComparisonData (); | ||
| } | ||
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| /** | ||
| * Make an AlignMatch object from the given String. | ||
| */ | ||
| private static AlignMatch makeMatchFromStringStatic (String line) | ||
| throws IOException { | ||
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| if (line.trim ().length () == 0 || line.startsWith ("#")) { | ||
| return null; | ||
| } | ||
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| final StringTokenizer tokenizer = new StringTokenizer (line, "\t"); | ||
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| int numTokens = tokenizer.countTokens (); | ||
| if ( | ||
| numTokens < BlastWebSiteHitTableComparisonData.MIN_NUM_FIELDS || | ||
| numTokens > BlastWebSiteHitTableComparisonData.MAX_NUM_FIELDS) { | ||
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| final String message = "while reading " + | ||
| BlastWebSiteHitTableComparisonData.TYPE + | ||
| ": unexpected number of fields for this line: " + line; | ||
| throw new ComparisonDataParseException (message); | ||
|
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| } | ||
|
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| // Parse fields from line... | ||
|
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| // throw away the query name | ||
| tokenizer.nextToken (); | ||
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| // throw away the subject name | ||
| tokenizer.nextToken (); | ||
|
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| // % ident | ||
| final String percentIdentToken = tokenizer.nextToken (); | ||
|
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| // throw away alignment length | ||
| tokenizer.nextToken (); | ||
|
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| // throw away mismatches | ||
| tokenizer.nextToken (); | ||
|
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| // throw away gap opens | ||
| tokenizer.nextToken (); | ||
|
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| // Query start/end | ||
| final String qStartToken = tokenizer.nextToken (); | ||
| final String qEndToken = tokenizer.nextToken (); | ||
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| final String sStartToken = tokenizer.nextToken (); | ||
| final String sEndToken = tokenizer.nextToken (); | ||
|
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| // throw away evalue | ||
| tokenizer.nextToken (); | ||
|
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| // % bit score | ||
| final String scoreToken = tokenizer.nextToken (); | ||
|
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| // And ignore all the end fields for tblastx | ||
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| try { | ||
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| final int score = (int)(Float.valueOf (scoreToken).floatValue ()); | ||
| final int percentIdent = (int)(Float.valueOf (percentIdentToken).floatValue ()); | ||
| final int qStart = Integer.valueOf (qStartToken).intValue (); | ||
| final int qEnd = Integer.valueOf (qEndToken).intValue (); | ||
| final int sStart = Integer.valueOf (sStartToken).intValue (); | ||
| final int sEnd = Integer.valueOf (sEndToken).intValue (); | ||
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| return makeAlignMatch (sStart, sEnd, qStart, qEnd, score, | ||
| percentIdent); | ||
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| } catch (NumberFormatException e) { | ||
| throw new IOException ("while reading " + | ||
| BlastWebSiteHitTableComparisonData.TYPE + | ||
| ": failed to parse a number from this string: " + | ||
| e.getMessage ()); | ||
| } | ||
| } | ||
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| /** | ||
| * Make an AlignMatch object from the given String. The String must be in | ||
| * a format appropriate for this object. | ||
| */ | ||
| @Override | ||
| protected AlignMatch makeMatchFromString (final String line) | ||
| throws IOException { | ||
| return makeMatchFromStringStatic (line); | ||
| } | ||
|
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| /** | ||
| * Returns true if and only if the given line is in the correct format for | ||
| * this type of ComparisonData. This should be as strict as possible. | ||
| */ | ||
| public static boolean formatCorrect (final List<String> headers) { | ||
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| boolean result = false; | ||
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| if (headers.size() >= 4) { | ||
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| String blastTypeHeader = headers.get(0); | ||
| String iterationHeader = headers.get(1); | ||
| String queryHeader = headers.get(2); | ||
| String ridHeader = headers.get(3); | ||
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| if ( | ||
| (blastTypeHeader.startsWith ("# tblastx") || blastTypeHeader.startsWith ("# blastn")) && | ||
| iterationHeader.startsWith ("# Iteration:") && | ||
| queryHeader.startsWith ("# Query:") && | ||
| ridHeader.startsWith ("# RID:")) { | ||
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| result = true; | ||
| } | ||
| } | ||
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| return result; | ||
| } | ||
|
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| } |
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