From d65b2d32d1d06ed3ed31ee806f4d5a0ee8ceb1cc Mon Sep 17 00:00:00 2001 From: weisburd Date: Wed, 19 May 2010 03:39:34 +0000 Subject: [PATCH] Removed AnnotatorROD which has been ported to Tribble git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3387 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/refdata/AnnotatorROD.java | 292 ------------------ 1 file changed, 292 deletions(-) delete mode 100755 java/src/org/broadinstitute/sting/gatk/refdata/AnnotatorROD.java diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/AnnotatorROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/AnnotatorROD.java deleted file mode 100755 index 74f8c9dd5..000000000 --- a/java/src/org/broadinstitute/sting/gatk/refdata/AnnotatorROD.java +++ /dev/null @@ -1,292 +0,0 @@ -/* - * Copyright (c) 2010 The Broad Institute - * - * Permission is hereby granted, free of charge, to any person - * obtaining a copy of this software and associated documentation - * files (the "Software"), to deal in the Software without - * restriction, including without limitation the rights to use, - * copy, modify, merge, publish, distribute, sublicense, and/or sell - * copies of the Software, and to permit persons to whom the - * Software is furnished to do so, subject to the following - * conditions: - * - * The above copyright notice and this permission notice shall be - * included in all copies or substantial portions of the Software. - * - * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, - * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES - * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND - * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT - * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, - * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING - * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR - * THE USE OR OTHER DEALINGS IN THE SOFTWARE. - */ - -package org.broadinstitute.sting.gatk.refdata; - -import java.io.File; -import java.io.FileNotFoundException; -import java.io.IOException; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.HashMap; -import java.util.Map; - -import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.text.XReadLines; - -/** - * 
- * This slightly modified TabularROD format is used as input to the
- * GenomicAnnotator.
- * The main differences from TabularROD are:
- * - the delimiter is \t instead of \s+
- * - incomplete records are allowed (eg. where some values are left blank)
- * - the header column is just the first non-comment, non-empty row in the file.
- *    It no longer has to start with the "HEADER" keyword.
- *
- * - * More details can be found here: http://www.broadinstitute.org/gsa/wiki/index.php/GenomicAnnotator - */ -public class AnnotatorROD extends TabularROD { - - private static Logger logger = Logger.getLogger(AnnotatorROD.class); - - /** Special column names */ - public static final String CHRPOS_COLUMN = "chrpos"; - public static final String HAPLOTYPE_REFERENCE_COLUMN = "haplotypeReference"; - public static final String HAPLOTYPE_ALTERNATE_COLUMN = "haplotypeAlternate"; - public static final String HAPLOTYPE_STRAND_COLUMN = "haplotypeStrand"; - - private static int parsedRecords = 0; - - // Temporary attributes were added to make it easier to implement certain - // optimizations for RODs that span an interval. For example, if a Walker - // needs to do a time-consuming computation on data from a ROD, it would normally - // have to repeat this computation every time its map(..) method is called. - // If a ROD spans an interval, the Walker's map(..) method will be called for every position in ROD. - // However, many computations (including validation and parsing) are done per ROD rather than - // per position. Therefore, substantial optimizations are possible if the result - // of the first computation is cached and reused on subsequent map(..) calls. - // Temporary attributes provide a convenient place to store these results, - // freeing the Walkers from having to maintain their own ROD -> result hashmaps. - private Map temporaryAttributes; - - /** - * Constructor. - * - * @param name The binding name provided as the first in the list of -B args. - */ - public AnnotatorROD(String name) { - super(name, new ArrayList()); - - setDelimiter("\t", "\\t"); - } - - - /** - * Walks through the source files looking for the header line, which it - * returns as a list of strings. - * - * @param source - * @return - */ - public Object initialize(final File source) throws FileNotFoundException { - ArrayList header = AnnotatorROD.readHeader(source); - return header; - } - - - - - /** - * Finds and parses the header string in the file. - * @param source The source file. - * @return A List of the column names parsed out of the header. - * @throws FileNotFoundException - */ - public static ArrayList readHeader(final File source) throws FileNotFoundException { - ArrayList header = null; - XReadLines reader = new XReadLines(source); - - //find the 1st line that's non-empty and not a comment - for ( String line : reader ) { - line = line.trim(); - if ( line.isEmpty() || line.startsWith("#") ) { - continue; - } - - header = new ArrayList(Arrays.asList(line.split(DELIMITER_REGEX))); - break; - } - - // check that we found the header - if ( header == null ) { - throw new RuntimeException("No header in " + source + ". All lines are either comments or empty."); - } - - logger.info(String.format("Found header line containing %d columns:\n[%s]", header.size(), Utils.join("\t", header))); - - try { - reader.close(); - } catch ( IOException e ) { - throw new RuntimeException(e); - } - - return header; - } - - - /** - * Used by ROD management system to set the data in this ROD associated with a line in a rod - * - * @param headerObj - * @param parts - * @return - * @throws IOException - */ - public boolean parseLine(final Object headerObj, final String[] parts) throws IOException { - ArrayList header = (ArrayList)(headerObj); - - //save the header in the super-class - getHeader().addAll(header); - - if ( parts.length == 0 || parts[0].startsWith("#") || header.get(0).equals(parts[0]) /* Skip the header line */ ) - return false; - - - if ( header.size() < parts.length) { - throw new IOException(String.format("Encountered line with more columns than have names in the header. Header has %d columns, this line has %d columns.", header.size(), parts.length)); - } - - for ( int i = 0; i < parts.length; i++ ) { - put(header.get(i), parts[i]); - } - - if ( printRecordsParsed ) System.out.printf("Parsed %d records %s%n", ++parsedRecords, this); - - return true; - } - - - // ---------------------------------------------------------------------- - // - // ROD accessors - // - // ---------------------------------------------------------------------- - public GenomeLoc getLocation() { - if ( loc == null ) { - String s = get(getHeader().get(0)); - if(s == null) { - throw new RuntimeException("Location not set.."); //this should never happen unless the line in the file is empty - } - loc = GenomeLocParser.parseGenomeLoc(s); - } - - return loc; - } - - - /** - * Checks whether an attribute has been set for the given key. - * - * Temporary attributes make it easier to implement certain - * optimizations for RODs that span an interval. For example, if a Walker - * needs to do a time-consuming computation on data from a ROD, it would normally - * have to repeat this computation every time its map(..) method is called. - * If a ROD spans an interval, the Walker's map(..) method will be called for every position in ROD. - * However, many computations (including validation and parsing) are done per ROD rather than - * per position. Therefore, substantial optimizations are possible if the result - * of the first computation is cached and reused on subsequent map(..) calls. - * Temporary attributes provide a convenient place to store these results, - * freeing the Walkers from having to maintain their own ROD -> result hashmaps. - * - * @param key key - * @return True if an attribute has been set for this key. - */ - public boolean containsTemporaryAttribute(Object key) { - if(temporaryAttributes != null) { - return temporaryAttributes.containsKey(key); - } - return false; - } - - /** - * Sets the key to the given value, replacing any previous value. The previous - * value is returned. - * - * Temporary attributes make it easier to implement certain - * optimizations for RODs that span an interval. For example, if a Walker - * needs to do a time-consuming computation on data from a ROD, it would normally - * have to repeat this computation every time its map(..) method is called. - * If a ROD spans an interval, the Walker's map(..) method will be called for every position in ROD. - * However, many computations (including validation and parsing) are done per ROD rather than - * per position. Therefore, substantial optimizations are possible if the result - * of the first computation is cached and reused on subsequent map(..) calls. - * Temporary attributes provide a convenient place to store these results, - * freeing the Walkers from having to maintain their own ROD -> result hashmaps. - * - * @param key key - * @param value value - * @return attribute - */ - public Object setTemporaryAttribute(Object key, Object value) { - if(temporaryAttributes == null) { - temporaryAttributes = new HashMap(); - } - return temporaryAttributes.put(key, value); - } - - /** - * Looks up the value associated with the given key. - * - * Temporary attributes make it easier to implement certain - * optimizations for RODs that span an interval. For example, if a Walker - * needs to do a time-consuming computation on data from a ROD, it would normally - * have to repeat this computation every time its map(..) method is called. - * If a ROD spans an interval, the Walker's map(..) method will be called for every position in ROD. - * However, many computations (including validation and parsing) are done per ROD rather than - * per position. Therefore, substantial optimizations are possible if the result - * of the first computation is cached and reused on subsequent map(..) calls. - * Temporary attributes provide a convenient place to store these results, - * freeing the Walkers from having to maintain their own ROD -> result hashmaps. - * - * @param key key - * @return The value, or null. - */ - public Object getTemporaryAttribute(Object key) { - if(temporaryAttributes != null) { - return temporaryAttributes.get(key); - } - return null; - } - - /** - * Removes the attribute that has the given key. - * - * Temporary attributes make it easier to implement certain - * optimizations for RODs that span an interval. For example, if a Walker - * needs to do a time-consuming computation on data from a ROD, it would normally - * have to repeat this computation every time its map(..) method is called. - * If a ROD spans an interval, the Walker's map(..) method will be called for every position in ROD. - * However, many computations (including validation and parsing) are done per ROD rather than - * per position. Therefore, substantial optimizations are possible if the result - * of the first computation is cached and reused on subsequent map(..) calls. - * Temporary attributes provide a convenient place to store these results, - * freeing the Walkers from having to maintain their own ROD -> result hashmaps. - * - * @param key key - * @return The value that was associated with this key, or null. - */ - public Object removeTemporaryAttribute(Object key) { - if(temporaryAttributes != null) { - return temporaryAttributes.remove(key); - } - return null; - } - -}