org.biojava.bio.program.sax.FastaSearchSAXParser Maven / Gradle / Ivy
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.bio.program.sax;
import java.io.BufferedReader;
import java.io.IOException;
import java.text.DecimalFormat;
import java.text.NumberFormat;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
import java.util.Set;
import org.biojava.bio.BioException;
import org.biojava.bio.search.SearchContentHandler;
import org.biojava.utils.ParserException;
import org.xml.sax.Attributes;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
import org.xml.sax.helpers.AttributesImpl;
/**
* FastaSearchSAXParser is a SAX2 compliant parser for
* '-m 10' format output from the the Fasta search program (see the
* Fasta documentation for details of this format).
*
* Versions of Fasta supported are as follows. Note that the compile
* time option -DM10_CONS should be used to allow correct reporting of
* the number of matches in HSPSummary elements
*
*
* - 33t07
* - 33t08 (current tests are against output from this version)
*
*
* The SAX2 events produced are as if the input to the parser was
* an XML file validating against the BioJava
* BlastLikeDataSetCollection DTD. There is no requirement for an
* intermediate conversion of native output to XML format.
*
* @author Keith James
* @since 1.2
*/
public class FastaSearchSAXParser extends AbstractNativeAppSAXParser
implements SearchContentHandler
{
private FastaSearchParser fastaParser;
private Map searchProperties;
private Map hitProperties;
private String queryID;
private String databaseID;
private AttributesImpl attributes;
private QName qName;
private boolean firstHit = true;
// Set/reset by callback from main parser
private boolean moreSearchesAvailable = true;
// For formatting rounded numbers
private NumberFormat nFormat;
// Platform independent linebreaks
private String nl;
// For creating character events
private StringBuffer props;
private StringBuffer seqTokens;
private String stringOut;
private char [] charOut;
/**
* Creates a new FastaSearchSAXParser instance.
*/
public FastaSearchSAXParser()
{
this.setNamespacePrefix("biojava");
this.addPrefixMapping("biojava", "http://www.biojava.org");
fastaParser = new FastaSearchParser();
attributes = new AttributesImpl();
qName = new QName(this);
nFormat = new DecimalFormat("###.0");
props = new StringBuffer(1024);
seqTokens = new StringBuffer(2048);
nl = System.getProperty("line.separator");
}
public void parse(InputSource source)
throws IOException, SAXException
{
BufferedReader content = getContentStream(source);
if (oHandler == null)
throw new SAXException("Running FastaSearchSAXParser with null ContentHandler");
try
{
attributes.clear();
// Namespace attribute
qName.setQName("xmlns");
attributes.addAttribute(qName.getURI(),
qName.getLocalName(),
qName.getQName(),
"CDATA",
"");
// Namespace attribute
qName.setQName("xmlns:biojava");
attributes.addAttribute(qName.getURI(),
qName.getLocalName(),
qName.getQName(),
"CDATA",
"http://www.biojava.org");
// Start the BlastLikeDataSetCollection
startElement(new QName(this, this.prefix("BlastLikeDataSetCollection")),
(Attributes) attributes);
while (moreSearchesAvailable)
{
// This method returns once a single result is
// parsed. The parser also informs us of subsequent
// results via the setMoreSearches() method.
fastaParser.parseSearch(content, this);
}
// End the BlastLikeDataSetCollection
endElement(new QName(this, this.prefix("BlastLikeDataSetCollection")));
}
catch (BioException be)
{
throw new SAXException(be);
}
catch (ParserException pe)
{
throw new SAXException(pe);
}
}
public boolean getMoreSearches()
{
return moreSearchesAvailable;
}
public void setMoreSearches(boolean value)
{
moreSearchesAvailable = value;
}
/**
* setQuerySeq identifies the query sequence by a
* name, ID or URN.
*
* @param identifier a String which should be an
* unique identifer for the sequence.
*
* @deprecated use setQueryID instead.
*/
public void setQuerySeq(String identifier)
{
setQueryID(identifier);
}
public void setQueryID(String queryID)
{
this.queryID = queryID;
}
/**
* setSubjectDB identifies the database searched by a
* name, ID or URN.
*
* @param identifier a String which should be an unique
* identifier for the database searched.
*
* @deprecated use setDatabaseID instead.
*/
public void setSubjectDB(String identifier)
{
setDatabaseID(identifier);
}
public void setDatabaseID(String databaseID)
{
this.databaseID = databaseID;
}
public void startSearch()
{
searchProperties = new HashMap();
}
public void addSearchProperty(Object key, Object value)
{
searchProperties.put(key, value);
}
public void endSearch()
{
try
{
// If we found any hits then we need to close a Detail
// element too
if (! firstHit)
{
endElement(new QName(this, this.prefix("Detail")));
// Prime to get next firstHit
firstHit = true;
}
endElement(new QName(this, this.prefix("BlastLikeDataSet")));
}
catch (SAXException se)
{
System.err.println("An error occurred while creating an endElement SAX event: ");
se.printStackTrace();
}
}
public void startHeader() { }
public void endHeader()
{
try
{
attributes.clear();
// Program name attribute
qName.setQName("program");
attributes.addAttribute(qName.getURI(),
qName.getLocalName(),
qName.getQName(),
"CDATA",
(String) searchProperties.get("pg_name"));
// Program version attribute
qName.setQName("version");
attributes.addAttribute(qName.getURI(),
qName.getLocalName(),
qName.getQName(),
"CDATA",
(String) searchProperties.get("pg_ver"));
// Start the BlastLikeDataSet
startElement(new QName(this, this.prefix("BlastLikeDataSet")),
(Attributes) attributes);
attributes.clear();
// Start the Header
startElement(new QName(this, this.prefix("Header")),
(Attributes) attributes);
attributes.clear();
// Query id attribute
qName.setQName("id");
attributes.addAttribute(qName.getURI(),
qName.getLocalName(),
qName.getQName(),
"CDATA",
queryID);
// metaData attribute for QueryId
qName.setQName("metaData");
attributes.addAttribute(qName.getURI(),
qName.getLocalName(),
qName.getQName(),
"CDATA",
"none");
// Start the QueryId
startElement(new QName(this, this.prefix("QueryId")),
(Attributes) attributes);
// End the QueryId
endElement(new QName(this, this.prefix("QueryId")));
attributes.clear();
// id attribute for DatabaseId
qName.setQName("id");
attributes.addAttribute(qName.getURI(),
qName.getLocalName(),
qName.getQName(),
"CDATA",
databaseID);
// metaData attribute for DatabaseId
qName.setQName("metaData");
attributes.addAttribute(qName.getURI(),
qName.getLocalName(),
qName.getQName(),
"CDATA",
"none");
// Start the DatabaseId
startElement(new QName(this, this.prefix("DatabaseId")),
(Attributes) attributes);
// End the DatabaseId
endElement(new QName(this, this.prefix("DatabaseId")));
attributes.clear();
// Whitespace attribute for raw data
qName.setQName("xml:space");
attributes.addAttribute(qName.getURI(),
qName.getLocalName(),
qName.getQName(),
"CDATA",
"preserve");
// Start the RawOutput
startElement(new QName(this, this.prefix("RawOutput")),
(Attributes) attributes);
// Reconstitute the 'raw' header from the properties Map
Set spKeys = searchProperties.keySet();
String [] searchPropKeys =
(String []) spKeys.toArray(new String [spKeys.size() - 1]);
Arrays.sort(searchPropKeys);
// Clear StringBuffer
props.setLength(0);
props.append(nl);
for (int i = 0; i < searchPropKeys.length; i++)
{
props.append(searchPropKeys[i] + ": ");
props.append((String) searchProperties.get(searchPropKeys[i]) + nl);
}
charOut = new char [props.length()];
props.getChars(0, props.length(), charOut, 0);
// Characters of raw header
characters(charOut, 0, charOut.length);
// End the RawOutput
endElement(new QName(this, this.prefix("RawOutput")));
// End the Header
endElement(new QName(this, this.prefix("Header")));
}
catch (SAXException se)
{
System.err.println("An error occurred while creating SAX events from header data: ");
se.printStackTrace();
}
}
public void startHit()
{
// Hit elements must be wrapped in a Detail element so we
// start one at the first hit
if (firstHit)
{
firstHit = false;
attributes.clear();
try
{
startElement(new QName(this, this.prefix("Detail")),
(Attributes) attributes);
}
catch (SAXException se)
{
System.err.println("An error occurred while creating startElement SAX event from hit data: ");
se.printStackTrace();
}
}
hitProperties = new HashMap();
}
public void addHitProperty(Object key, Object value)
{
hitProperties.put(key, value);
}
public void endHit() { }
public void startSubHit() { }
public void addSubHitProperty(Object key, Object value)
{
hitProperties.put(key, value);
}
public void endSubHit()
{
attributes.clear();
// Query sequence length attribute
qName.setQName("sequenceLength");
attributes.addAttribute(qName.getURI(),
qName.getLocalName(),
qName.getQName(),
"CDATA",
(String) hitProperties.get("subject_sq_len"));
try
{
// Start the Hit
startElement(new QName(this, this.prefix("Hit")),
(Attributes) attributes);
attributes.clear();
// Hit id attribute
qName.setQName("id");
attributes.addAttribute(qName.getURI(),
qName.getLocalName(),
qName.getQName(),
"CDATA",
(String) hitProperties.get("id"));
// Metadata attribute
qName.setQName("metaData");
attributes.addAttribute(qName.getURI(),
qName.getLocalName(),
qName.getQName(),
"CDATA",
"none");
// Start the HitId
startElement(new QName(this, this.prefix("HitId")),
(Attributes) attributes);
// End the HitId
endElement(new QName(this, this.prefix("HitId")));
attributes.clear();
// Start the HitDescription
startElement(new QName(this, this.prefix("HitDescription")),
(Attributes) attributes);
stringOut = (String) hitProperties.get("desc");
charOut = new char [stringOut.length()];
stringOut.getChars(0, stringOut.length(), charOut, 0);
// Characters of description
characters(charOut, 0, charOut.length);
// End the HitDescription
endElement(new QName(this, this.prefix("HitDescription")));
// Start the HSPCollection
startElement(new QName(this, this.prefix("HSPCollection")),
(Attributes) attributes);
// Start the HSP (for Fasta, we use one "HSP" to represent the hit
startElement(new QName(this, this.prefix("HSP")),
(Attributes) attributes);
String score;
if (hitProperties.containsKey("fa_z-score"))
score = (String) hitProperties.get("fa_z-score");
else
throw new SAXException("Failed to retrieve hit z-score from search data");
// Score attribute
qName.setQName("score");
attributes.addAttribute(qName.getURI(),
qName.getLocalName(),
qName.getQName(),
"CDATA",
score);
// expectValue attribute
qName.setQName("expectValue");
attributes.addAttribute(qName.getURI(),
qName.getLocalName(),
qName.getQName(),
"CDATA",
(String) hitProperties.get("fa_expect"));
// numberOfIdentities attribute
qName.setQName("numberOfIdentities");
attributes.addAttribute(qName.getURI(),
qName.getLocalName(),
qName.getQName(),
"CDATA",
countTokens(':', (String) hitProperties.get("matchTokens")));
String overlap;
if (hitProperties.containsKey("fa_overlap"))
overlap = hitProperties.get("fa_overlap").toString();
else if (hitProperties.containsKey("sw_overlap"))
overlap = hitProperties.get("sw_overlap").toString();
else
throw new SAXException("Failed to retrieve hit overlap from search data");
// alignmentSize attribute
qName.setQName("alignmentSize");
attributes.addAttribute(qName.getURI(),
qName.getLocalName(),
qName.getQName(),
"CDATA",
overlap);
float percentId;
if (hitProperties.containsKey("fa_ident"))
percentId = Float.parseFloat((String) hitProperties.get("fa_ident"));
else
percentId = Float.parseFloat((String) hitProperties.get("sw_ident"));
// percentageIdentity attribute
qName.setQName("percentageIdentity");
attributes.addAttribute(qName.getURI(),
qName.getLocalName(),
qName.getQName(),
"CDATA",
nFormat.format(percentId * 100));
// Maybe proper RNA check? Should be same for query and subject
String seqType;
if (hitProperties.get("query_sq_type").equals("dna"))
seqType = "dna";
else
seqType = "protein";
// querySequenceType attribute
qName.setQName("querySequenceType");
attributes.addAttribute(qName.getURI(),
qName.getLocalName(),
qName.getQName(),
"CDATA",
seqType);
// Maybe proper RNA check? Maybe raise exception if not
// same as query type?
if (hitProperties.get("subject_sq_type").equals("dna"))
seqType = "dna";
else
seqType = "protein";
// hitSequenceType attribute
qName.setQName("hitSequenceType");
attributes.addAttribute(qName.getURI(),
qName.getLocalName(),
qName.getQName(),
"CDATA",
seqType);
// Strand information only valid for DNA
if (seqType.equals("dna"))
{
// queryStrand attribute (always plus for Fasta)
qName.setQName("queryStrand");
attributes.addAttribute(qName.getURI(),
qName.getLocalName(),
qName.getQName(),
"CDATA",
"plus");
String strand;
if (hitProperties.get("fa_frame").equals("f"))
strand = "plus";
else
strand = "minus";
// hitStrand attribute (may be minus for Fasta vs. nt sequence)
qName.setQName("hitStrand");
attributes.addAttribute(qName.getURI(),
qName.getLocalName(),
qName.getQName(),
"CDATA",
strand);
}
// Start the HSPSummary
startElement(new QName(this, this.prefix("HSPSummary")),
(Attributes) attributes);
attributes.clear();
// Start the RawOutput
startElement(new QName(this, this.prefix("RawOutput")),
(Attributes) attributes);
// Reconstitute the 'raw' header from the properties Map
Set hpKeys = hitProperties.keySet();
String [] hitPropKeys =
(String []) hpKeys.toArray(new String [hpKeys.size() - 1]);
Arrays.sort(hitPropKeys);
// Clear StringBuffer
props.setLength(0);
props.append(nl);
for (int i = 0; i < hitPropKeys.length; i++)
{
// Skip the sequence and consensus tokens
if (hitPropKeys[i].endsWith("Tokens"))
continue;
props.append(hitPropKeys[i] + ": ");
props.append((String) hitProperties.get(hitPropKeys[i]) + nl);
}
charOut = new char [props.length()];
props.getChars(0, props.length(), charOut, 0);
// Characters of raw header
characters(charOut, 0, charOut.length);
// End the RawOutput
endElement(new QName(this, this.prefix("RawOutput")));
// End the HSPSummary
endElement(new QName(this, this.prefix("HSPSummary")));
// Start the BlastLikeAlignment
startElement(new QName(this, this.prefix("BlastLikeAlignment")),
(Attributes) attributes);
String alStart = (String) hitProperties.get("query_al_start");
String alStop = (String) hitProperties.get("query_al_stop");
String alDispStart = (String) hitProperties.get("query_al_display_start");
// Query sequence startPosition attribute
qName.setQName("startPosition");
attributes.addAttribute(qName.getURI(),
qName.getLocalName(),
qName.getQName(),
"CDATA",
alStart);
// Query sequence stopPosition attribute
qName.setQName("stopPosition");
attributes.addAttribute(qName.getURI(),
qName.getLocalName(),
qName.getQName(),
"CDATA",
alStop);
// Start the QuerySequence
startElement(new QName(this, this.prefix("QuerySequence")),
(Attributes) attributes);
seqTokens.setLength(0);
seqTokens.append((String) hitProperties.get("querySeqTokens"));
// Fasta includes context sequence which we need to trim
stringOut = prepSeqTokens(seqTokens,
Integer.parseInt(alStart),
Integer.parseInt(alStop),
Integer.parseInt(alDispStart));
charOut = new char [stringOut.length()];
stringOut.getChars(0, stringOut.length(), charOut, 0);
// Characters of QuerySequence
characters(charOut, 0, charOut.length);
// End the QuerySequence
endElement(new QName(this, this.prefix("QuerySequence")));
attributes.clear();
// Whitespace attribute for MatchConsensus
qName.setQName("xml:space");
attributes.addAttribute(qName.getURI(),
qName.getLocalName(),
qName.getQName(),
"CDATA",
"preserve");
// Start the MatchConsensus
startElement(new QName(this, this.prefix("MatchConsensus")),
(Attributes) attributes);
stringOut = ((String) hitProperties.get("matchTokens")).trim();
charOut = new char [stringOut.length()];
stringOut.getChars(0, stringOut.length(), charOut, 0);
// Characters of MatchConsensus
characters(charOut, 0, charOut.length);
// End the MatchConsensus
endElement(new QName(this, this.prefix("MatchConsensus")));
alStart = (String) hitProperties.get("subject_al_start");
alStop = (String) hitProperties.get("subject_al_stop");
alDispStart = (String) hitProperties.get("subject_al_display_start");
attributes.clear();
// Hit sequence startPosition attribute
qName.setQName("startPosition");
attributes.addAttribute(qName.getURI(),
qName.getLocalName(),
qName.getQName(),
"CDATA",
alStart);
// Hit sequence stopPosition attribute
qName.setQName("stopPosition");
attributes.addAttribute(qName.getURI(),
qName.getLocalName(),
qName.getQName(),
"CDATA",
alStop);
// Start the HitSequence
startElement(new QName(this, this.prefix("HitSequence")),
(Attributes) attributes);
seqTokens.setLength(0);
seqTokens.append((String) hitProperties.get("subjectSeqTokens"));
// Fasta includes context sequence which we need to trim
stringOut = prepSeqTokens(seqTokens,
Integer.parseInt(alStart),
Integer.parseInt(alStop),
Integer.parseInt(alDispStart));
charOut = new char [stringOut.length()];
stringOut.getChars(0, stringOut.length(), charOut, 0);
// Characters of HitSequence
characters(charOut, 0, charOut.length);
// End the HitSequence
endElement(new QName(this, this.prefix("HitSequence")));
// End the BlastLikeAlignment
endElement(new QName(this, this.prefix("BlastLikeAlignment")));
// End the HSP
endElement(new QName(this, this.prefix("HSP")));
// End the HSPCollection
endElement(new QName(this, this.prefix("HSPCollection")));
// End the hit
endElement(new QName(this, this.prefix("Hit")));
}
catch (SAXException se)
{
System.err.println("An error occurred while creating SAX events from hit data: ");
se.printStackTrace();
}
}
/**
* countTokens counts up the occurrences of a char in
* a String.
*
* @param token a char to count.
* @param string a String to count within.
*
* @return a String representation of the total count.
*/
private String countTokens(char token, String string)
{
int count = 0;
for (int i = string.length(); --i >= 0;)
{
if (string.charAt(i) == token)
count++;
}
return String.valueOf(count);
}
/**
* The prepSeqTokens method prepares the sequence
* data extracted from the Fasta output. Two things need to be
* done; firstly, the leading gaps are removed from the sequence
* (these are just format padding and not really part of the
* alignment) and secondly, as Fasta supplies some flanking
* sequence context for its alignments, this must be removed
* too. See the Fasta documentation for an explanation of the
* format.
*
* @param name a StringBuffer containing the
* unprepared sequence tokens.
* @param alStart an int indicating the start
* position of the alignment in the original sequence.
* @param alStop an int indicating the stop
* position of the alignment in the original sequence.
* @param alDispStart an int indicating the start
* of a flanking context in the original sequence.
*
* @return a String value consisting of a subsequence
* containing only the interesting alignment.
*/
private String prepSeqTokens(StringBuffer seqTokens,
int alStart,
int alStop,
int alDispStart)
{
// Strip leading gap characters
while (seqTokens.charAt(0) == '-')
seqTokens.deleteCharAt(0);
int gapCount = 0;
// Count gaps to add to number of chars returned
for (int i = seqTokens.length(); --i >= 0;)
{
if (seqTokens.charAt(i) == '-')
gapCount++;
}
// Calculate the position at which the real alignment
// starts/stops, allowing for the gaps, which are not counted
// in the numbering system
return seqTokens.substring(alStart - alDispStart,
alStop - alDispStart + gapCount + 1);
}
}