org.biojava.bio.program.sax.FastaSearchParser 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.util.HashSet;
import java.util.Set;
import java.util.StringTokenizer;
import org.biojava.bio.BioException;
import org.biojava.bio.search.SearchContentHandler;
import org.biojava.utils.ParserException;
/**
* FastaSearchParser objects provide Fasta search
* parsing functionality for the '-m 10' output format (see the Fasta
* documentation). Data are passed to a SearchContentHandler which
* coordinates its interpretation and creation of objects representing
* the result.
*
* If the search output contains no hits only the header data will
* be sent to the handler before the dataset ends. The handler is
* responsible for dealing with this state.
*
* This class was originally used outside of the BioJava SAX
* framework, but is now only used to provide functionality for
* FastaSearchSAXParser.
*
* @author Keith James
* @author Greg Cox
* @since 1.1
*/
class FastaSearchParser
{
private static final int NODATA = 0;
private static final int INHEADER = 1;
private static final int INHIT = 2;
private static final int INQUERY = 3;
private static final int INSUBJECT = 4;
private static final int INALIGN = 5;
// Valid line identifiers for result annotation
private static HashSet resultAnnoTokens =
(HashSet) fillSet(new String [] { "mp_name", "mp_ver",
"mp_argv", "mp_extrap",
"mp_stats", "mp_KS",
"pg_name", "pg_ver",
"pg_optcut", "pg_cgap" },
new HashSet());
// Valid line identifiers for search parameters
private static HashSet resultSearchParmTokens =
(HashSet) fillSet(new String [] { "pg_matrix", "pg_ktup",
"pg_gap-pen" },
new HashSet());
// Valid line identifiers for hit annotation
private static HashSet hitAnnoTokens =
(HashSet) fillSet(new String [] { "fa_frame", "fa_initn",
"fa_init1", "fa_opt",
"fa_bits", "sw_score",
"sw_ident", "sw_gident",
"sw_overlap", "fa_ident",
"fa_gident", "fa_overlap",
"fa_score" },
new HashSet());
// Valid line identifiers for hit data
private static HashSet hitDataTokens =
(HashSet) fillSet(new String [] { "fa_expect", "fa_z-score" },
new HashSet());
private int searchStatus = NODATA;
private boolean searchParsed = false;
private SearchContentHandler handler;
private String line;
private int lineNumber;
StringBuffer querySeqTokens = new StringBuffer(1024);
StringBuffer subjectSeqTokens = new StringBuffer(1024);
StringBuffer matchTokens = new StringBuffer(1024);
/**
* The parseSearch method performs the core parsing
* operations. It parses one result from the stream before
* returning. The handler is informed whether or not there are
* further searches in the stream.
*
* @param reader a BufferedReader to read from.
* @param handler a SearchContentHandler to notify
* of events.
*
* @exception IOException if the BufferedReader fails.
* @exception BioException if the parser (via the registered
* SearchContentHandler) fails to resolve a query sequence and
* target database.
* @exception ParserException if the parser fails to parse a
* line.
*/
public void parseSearch(BufferedReader reader,
SearchContentHandler handler)
throws IOException, BioException, ParserException
{
lineNumber = 0;
this.handler = handler;
LINE:
while ((line = reader.readLine()) != null)
{
lineNumber++;
// This token indicates the end of the formatted search
// data. Some outputs don't have any alignment consensus
// tokens, so we need to check here as well as INALIGN
if (line.startsWith(">>><<<"))
{
// If we got here while INHEADER then the search had
// no hits
if (searchStatus == INHEADER)
{
// Inform of end of header and search
handler.endHeader();
handler.endSearch();
searchParsed = true;
searchStatus = NODATA;
continue LINE;
}
// Pass final data to handler
handler.addSubHitProperty("querySeqTokens", querySeqTokens.substring(0));
handler.addSubHitProperty("subjectSeqTokens", subjectSeqTokens.substring(0));
handler.addSubHitProperty("matchTokens", matchTokens.substring(0));
handler.endSubHit();
handler.endSearch();
searchParsed = true;
searchStatus = NODATA;
// Continue getting lines to look for start of another
// search. This allows setMoreSearches(boolean flag)
// to be called on the handler. When true it will know
// to expect more.
continue LINE;
}
STATUS:
switch (searchStatus)
{
case NODATA:
// This token marks the line describing the query
// sequence file and database searched. It is
// followed by header lines containing data about
// the search
if (line.startsWith(">>>"))
{
searchStatus = INHEADER;
handler.setQueryID(parseQueryID(line));
handler.setDatabaseID(parseDatabaseID(line));
handler.startSearch();
handler.startHeader();
// If we already saw an end of search token
// then this is the start of another
// dataset. We break from the loop and return
// that the stream is not empty
if (searchParsed)
{
searchParsed = false;
handler.setMoreSearches(true);
// We have parsed one result, so return
return;
}
else
// We break out and setMoreSearches(false)
// is called below
break STATUS;
}
else
// Continue getting lines to look for start of another
// search. This allows setMoreSearches(boolean flag)
// to be called on the handler. When true it will know
// to expect more.
continue LINE;
case INHEADER:
// This token marks the line describing a hit. It
// is followed by header lines containing data
// about the hit
if (line.startsWith(">>"))
{
searchStatus = INHIT;
handler.endHeader();
handler.startHit();
querySeqTokens.setLength(0);
subjectSeqTokens.setLength(0);
matchTokens.setLength(0);
handler.addHitProperty("id", parseID(line));
handler.addHitProperty("desc", parseDesc(line));
}
else
{
if (! parseHeaderLine(line, resultAnnoTokens))
if (! parseHeaderLine(line, resultSearchParmTokens))
throw new ParserException("Fasta parser failed to recognise line type",
null,
lineNumber,
line);
}
break STATUS;
case INHIT:
// This token marks the line describing the query
// sequence.
if (line.startsWith(">"))
{
searchStatus = INQUERY;
handler.endHit();
handler.startSubHit();
}
else
{
if (! parseHitLine(line, hitAnnoTokens))
if (! parseHitLine(line, hitDataTokens))
throw new ParserException("Fasta parser failed to recognise line type",
null,
lineNumber,
line);
}
break STATUS;
case INQUERY:
// This token marks the line describing the
// subject sequence.
if (line.startsWith(">"))
{
searchStatus = INSUBJECT;
}
else
{
parseQuerySequence(line);
}
break STATUS;
case INSUBJECT:
// This token marks the start of lines containing
// the consensus symbols from the Fasta alignment,
// which we ignore
if (line.startsWith("; al_cons:"))
{
searchStatus = INALIGN;
}
else if (line.startsWith(">>"))
{
searchStatus = INHIT;
// Pass data to handler
handler.addSubHitProperty("querySeqTokens", querySeqTokens.substring(0));
handler.addSubHitProperty("subjectSeqTokens", subjectSeqTokens.substring(0));
handler.addSubHitProperty("matchTokens", matchTokens.substring(0));
handler.endSubHit();
handler.startHit();
querySeqTokens.setLength(0);
subjectSeqTokens.setLength(0);
matchTokens.setLength(0);
handler.addHitProperty("id", parseID(line));
handler.addHitProperty("desc", parseDesc(line));
}
else
{
parseSubjectSequence(line);
}
break STATUS;
case INALIGN:
if (line.startsWith(">>"))
{
searchStatus = INHIT;
// Pass data to handler
handler.addSubHitProperty("querySeqTokens", querySeqTokens.substring(0));
handler.addSubHitProperty("subjectSeqTokens", subjectSeqTokens.substring(0));
handler.addSubHitProperty("matchTokens", matchTokens.substring(0));
handler.endSubHit();
handler.startHit();
querySeqTokens.setLength(0);
subjectSeqTokens.setLength(0);
matchTokens.setLength(0);
handler.addHitProperty("id", parseID(line));
handler.addHitProperty("desc", parseDesc(line));
}
else if (line.startsWith(">>><<<"))
{
searchStatus = NODATA;
// Pass final data to handler
handler.addSubHitProperty("querySeqTokens", querySeqTokens.substring(0));
handler.addSubHitProperty("subjectSeqTokens", subjectSeqTokens.substring(0));
handler.addSubHitProperty("matchTokens", matchTokens.substring(0));
handler.endSubHit();
handler.endSearch();
searchParsed = true;
handler.setMoreSearches(true);
continue LINE;
}
else
{
matchTokens.append(line);
}
break STATUS;
default:
break STATUS;
} // end switch
} // end while
// This is false if we reach here and return
handler.setMoreSearches(false);
}
/**
* The fillSet method populates a Set
* with the elements of an array.
*
* @param tokenArray a String [] array.
* @param set a Set to fill.
*
* @return a Set.
*/
private static Set fillSet(String [] tokenArray, Set set)
{
for (int i = 0; i < tokenArray.length; i++)
set.add(tokenArray[i]);
return set;
}
/**
* The parseID method parses sequence IDs from
* lines starting with '>' and '>>'.
*
* @param line a String to be parsed.
*
* @return a String containing the ID.
*
* @exception ParserException if an error occurs.
*/
private String parseID(String line)
throws ParserException
{
String trimmed = line.trim();
int firstSpace = trimmed.indexOf(' ');
// For Hit header lines (always start with >>)
if (trimmed.startsWith(">>"))
{
if (trimmed.length() == 2)
throw new ParserException("Fasta parser encountered a sequence with no Id",
null,
lineNumber,
line);
if (firstSpace == -1)
return trimmed.substring(2);
else
return trimmed.substring(2, firstSpace);
}
// For SubHit header lines (always start with >)
else
{
if (trimmed.length() == 1)
throw new ParserException("Fasta parser encountered a sequence with no Id",
null,
lineNumber,
line);
if (firstSpace == -1)
return trimmed.substring(1);
else
return trimmed.substring(1, firstSpace);
}
}
/**
* The parseDesc method parses the sequence
* description from subject header lines.
*
* @param line a String to be parsed.
*
* @return a String containing the description.
*/
private String parseDesc(String line)
{
String trimmed = line.trim();
int firstSpace = trimmed.indexOf(' ');
if (firstSpace == -1)
return "No description";
return trimmed.substring(firstSpace + 1);
}
/**
* Creates a new parseQueryID instance.
*
* @param line a String to be parsed.
*
* @return a String.
*
* @exception ParserException if an error occurs
*/
private String parseQueryID(String line)
throws ParserException
{
int firstComma = line.indexOf(",");
if (firstComma == -1)
throw new ParserException("Fasta parser failed to parse a query ID",
null,
lineNumber,
line);
// return string between >>> and ,
return line.substring(3, firstComma).trim();
}
/**
* The parseDatabaseID method parses a database
* filename from the relevant output line.
*
* @param line a String to be parsed.
*
* @return a String.
*
* @exception ParserException if an error occurs.
*/
private String parseDatabaseID(String line)
throws ParserException
{
StringTokenizer st = new StringTokenizer(line);
String id = null;
int count = st.countTokens();
for (int i = 0; i < count - 1; i++)
{
id = st.nextToken();
}
if (id == null)
throw new ParserException("Fasta parser failed to parse a database ID",
null,
lineNumber,
line);
return id;
}
private boolean parseHeaderLine(String line,
Set tokenSet)
throws ParserException
{
String [] data = parseLine(line, tokenSet);
if (data.length > 0)
{
handler.addSearchProperty(data[0], data[1]);
return true;
}
else
{
return false;
}
}
private boolean parseHitLine(String line,
Set tokenSet)
throws ParserException
{
String [] data = parseLine(line, tokenSet);
if (data.length > 0)
{
handler.addHitProperty(data[0], data[1]);
return true;
}
return false;
}
private String [] parseLine(String line,
Set tokenSet)
throws ParserException
{
int idTokenStart = line.indexOf(";");
int idTokenEnd = line.indexOf(":");
String idToken = line.substring(idTokenStart + 1, idTokenEnd);
idToken = idToken.trim();
String idValue = line.substring(idTokenEnd + 1);
idValue = idValue.trim();
if (tokenSet.contains(idToken))
return new String [] { idToken, idValue };
else
return new String [0];
}
private void parseQuerySequence(String line)
{
String [] data = parseSequence(line);
if (data.length > 0)
{
// We have a key/value pair
handler.addSubHitProperty("query" + data[0], data[1]);
}
else
{
// We have a line of sequence tokens
querySeqTokens.append(line);
}
}
private void parseSubjectSequence(String line)
{
String [] data = parseSequence(line);
if (data.length > 0)
{
// We have a key/value pair
handler.addSubHitProperty("subject" + data[0], data[1]);
}
else
{
// We have a line of sequence tokens
subjectSeqTokens.append(line);
}
}
private String [] parseSequence(String line)
{
if (line.startsWith(";"))
{
// Check the sequence type given by the report
if (line.equals("; sq_type: p"))
{
return new String [] { "_sq_type", "protein"};
}
else if (line.equals("; sq_type: D"))
{
return new String [] { "_sq_type", "dna"};
}
// Record the coordinates and offset of the alignment
if (line.startsWith("; al_start:"))
{
return new String [] { "_al_start", parseCoord(line) };
}
else if (line.startsWith("; al_stop:"))
{
return new String [] { "_al_stop", parseCoord(line) };
}
else if (line.startsWith("; al_display_start:"))
{
return new String [] {"_al_display_start", parseCoord(line) };
}
else if (line.startsWith("; sq_len:"))
{
return new String [] { "_sq_len", parseCoord(line) };
}
else if (line.startsWith("; sq_offset:"))
{
return new String [] { "_sq_offset", parseCoord(line) };
}
}
return new String [0];
}
/**
* The parseCoord method extracts integer coordinates
* from Fasta output lines.
*
* @param line a String to parse.
*
* @return a String coordinate.
*/
private String parseCoord(String line)
{
int sepIndex = line.lastIndexOf(":");
return line.substring(sepIndex + 1).trim();
}
}