org.biojava.nbio.ontology.obo.OboFileParser 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/
*
* Created on Jan 18, 2008
*
*/
package org.biojava.nbio.ontology.obo;
import org.biojava.nbio.ontology.Synonym;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.BufferedReader;
import java.io.IOException;
import java.text.SimpleDateFormat;
import java.util.*;
/** A class to parse the content of an OBO file. It delegates handling of the
* content to the OBOFileEventListener implementation.
*
* This file contains parts of the OBO-Edit file OBOParseEngine, (particularly the encoding and decoding part)
*
* http://geneontology.cvs.sourceforge.net/geneontology/go-dev/java/oboedit/sources/org/geneontology/oboedit/dataadapter/OBOParseEngine.java?revision=1.10&view=markup
* Thanks to the OboEdit developers for giving permission to release this in BioJava.
*
*
* @author Andreas Prlic
* @author John Day Richter
* @since 1.6
*/
public class OboFileParser {
private static final Logger logger = LoggerFactory.getLogger(OboFileParser.class);
List listeners;
protected String line;
protected int linenum = 0;
protected int totalSize = 0;
protected int bytesRead = 0;
protected StringBuffer tempBuffer = new StringBuffer();
protected SimpleDateFormat dateFormat = new SimpleDateFormat("dd:MM:yyyy HH:mm", Locale.US);
protected static final Map escapeChars =
new HashMap();
protected static final Map unescapeChars =
new HashMap();
static {
escapeChars.put(new Character('n'), new Character('\n'));
escapeChars.put(new Character('W'), new Character(' '));
escapeChars.put(new Character('t'), new Character('\t'));
escapeChars.put(new Character(':'), new Character(':'));
escapeChars.put(new Character(','), new Character(','));
escapeChars.put(new Character('"'), new Character('"'));
escapeChars.put(new Character('\''), new Character('\''));
escapeChars.put(new Character('\\'), new Character('\\'));
escapeChars.put(new Character('{'), new Character('{'));
escapeChars.put(new Character('}'), new Character('}'));
escapeChars.put(new Character('('), new Character('('));
escapeChars.put(new Character(')'), new Character(')'));
escapeChars.put(new Character('['), new Character('['));
escapeChars.put(new Character(']'), new Character(']'));
escapeChars.put(new Character('!'), new Character('!'));
Iterator it = escapeChars.keySet().iterator();
while (it.hasNext()) {
Character key = it.next();
Character value = escapeChars.get(key);
unescapeChars.put(value, key);
}
}
public static class SOPair {
public String str = null;
public int index = -1;
public int endIndex = -1;
public SOPair(String str, int index) {
this(str, index, -1);
}
public SOPair(String str, int index, int endIndex) {
this.str = str;
this.index = index;
this.endIndex = endIndex;
}
}
public OboFileParser(){
listeners = new ArrayList();
}
public void addOboFileEventListener(OboFileEventListener listener){
listeners.add(listener);
}
public List getOboFileEventListener(){
return listeners;
}
/** parse an ontology file
*
* @param oboFile
* @throws IOException
* @throws IOException
*/
public void parseOBO(BufferedReader oboFile) throws IOException{
String line;
String currentStanza;
while ((line = oboFile.readLine()) != null) {
if (line.length() == 0)
continue;
if ( line.charAt(0) == '[') {
if (line.charAt(line.length() - 1) != ']')
throw new IOException("Unclosed stanza: \"" + line + "\"" );
String stanzaname = line.substring(1, line.length() - 1);
if (stanzaname.length() < 1)
throw new IOException("Empty stanza: \"" +line+"\"");
currentStanza = stanzaname;
//logger.info("stanza: {}", currentStanza);
triggerNewStanza(currentStanza);
} else {
// a content line
SOPair pair;
pair = unescape(line, ':', 0, true);
//logger.info(pair);
String name = pair.str;
int lineEnd = findUnescaped(line, '!', 0, line.length(), true);
if (lineEnd == -1)
lineEnd = line.length();
// find nested values
NestedValue nv = null;
int trailingStartIndex = -1;
int trailingEndIndex = -1;
for (int i = lineEnd - 1; i >= 0; i--) {
if (Character.isWhitespace(line.charAt(i))) {
// keep going until we see non-whitespace
} else if (line.charAt(i) == '}') {
// if the first thing we see is a closing brace,
// we have a trailing modifier
if (i >= 1 && line.charAt(i - 1) == '\\')
continue;
trailingEndIndex = i;
break;
} else
break;
}
if (trailingEndIndex != -1) {
for (int i = trailingEndIndex - 1; i >= 0; i--) {
if (line.charAt(i) == '{') {
if (i >= 1 && line.charAt(i - 1) == '\\')
continue;
trailingStartIndex = i + 1;
}
}
}
int valueStopIndex;
if (trailingStartIndex == -1 && trailingEndIndex != -1)
throw new IOException("Unterminated trailing modifier. " + line);
else if (trailingStartIndex != -1) {
valueStopIndex = trailingStartIndex - 1;
String trailing = line.substring(trailingStartIndex,
trailingEndIndex).trim();
nv = new NestedValue();
getNestedValue(nv, trailing, 0);
} else
valueStopIndex = lineEnd;
String value = line.substring(pair.index + 1, valueStopIndex).trim();
/*
* if (nv != null) logger.warn("nv = "+nv+", value =
* |"+value+"|");
*/
if (value.length() == 0)
throw new IOException("Tag found with no value "+ line);
if ( isSynonym(name)){
Synonym synonym = parseSynonym(name,value);
triggerNewSynonym(synonym);
} else {
//logger.info("new key:" + name + " " + value);
triggerNewKey(name,value);
}
//logger.info("parsed key: " + name +" value: " + value + " nv: " + nv);
}
}
}
private boolean isSynonym(String key){
if ( key.equals(OboFileHandler.SYNONYM) || key.equals(OboFileHandler.EXACT_SYNONYM))
return true;
return false;
}
/** parse the Synonym String from the Term.
* value can be:
* "ca_bind" RELATED [uniprot:curation]
* @param value
* @return the synonym text
*/
private Synonym parseSynonym(String key, String value) throws IOException{
//logger.info("PARSE SYNONYM " + key + " " + value);
int startIndex = findUnescaped(value, '"', 0, value.length());
if (startIndex == -1)
throw new IOException("Expected \"" + line + " " + linenum);
SOPair p = unescape(value, '"', startIndex + 1, value.length(),
true);
int defIndex = findUnescaped(value, '[', p.index, value.length());
if (defIndex == -1) {
throw new IOException("Badly formatted synonym. "
+ "No dbxref list found." + line + " " + linenum );
}
String leftovers = value.substring(p.index + 1, defIndex).trim();
StringTokenizer tokenizer = new StringTokenizer(leftovers, " \t");
int scope = Synonym.RELATED_SYNONYM;
if ( key.equals(OboFileHandler.EXACT_SYNONYM))
scope = Synonym.EXACT_SYNONYM;
else if ( key.equals(OboFileHandler.BROAD_SYNONYM))
scope = Synonym.BROAD_SYNONYM;
else if ( key.equals(OboFileHandler.NARROW_SYNONYM))
scope = Synonym.NARROW_SYNONYM;
String catID = null;
for (int i = 0; tokenizer.hasMoreTokens(); i++) {
String token = tokenizer.nextToken();
//logger.info("TOKEN:" +token);
if (i == 0) {
if (token.equals("RELATED"))
scope = Synonym.RELATED_SYNONYM;
else if (token.equals("UNSPECIFIED"))
scope = Synonym.RELATED_SYNONYM;
else if (token.equals("EXACT"))
scope = Synonym.EXACT_SYNONYM;
else if (token.equals("BROAD"))
scope = Synonym.BROAD_SYNONYM;
else if (token.equals("NARROW"))
scope = Synonym.NARROW_SYNONYM;
else
throw new IOException("Found unexpected scope "
+ "identifier " + token + line);
} else if (i == 1) {
catID = token;
} else
throw new IOException("Expected dbxref list,"
+ " instead found " + token + line );
}
Synonym synonym = new Synonym();
synonym.setScope(scope);
synonym.setCategory(catID);
synonym.setName(p.str);
//logger.info("SYNONYM: " + p.str +" " + synonym.getCategory() + " " + synonym.getScope());
Map[] refs = getDbxrefList(value,defIndex + 1, value.length());
// set the refs in the synonym
for (Map ref : refs){
@SuppressWarnings("unused")
String xref = (String) ref.get("xref");
@SuppressWarnings("unused")
String desc = (String) ref.get("desc");
//logger.info(xref + " " + desc);
@SuppressWarnings("unused")
NestedValue nv = (NestedValue) ref.get("nv");
//TODO: add implementation for this...
}
return synonym;
}
protected Map[] getDbxrefList(String line, int startoffset, int endoffset) throws IOException {
Vector> temp = new Vector>();
boolean stop = false;
while (!stop) {
int braceIndex = findUnescaped(line, '{', startoffset, endoffset);
int endIndex = findUnescaped(line, ',', startoffset, endoffset,
true);
boolean trailing = false;
if (endIndex == -1) {
endIndex = findUnescaped(line, ']', startoffset, endoffset,
true);
if (endIndex == -1) {
throw new IOException("Unterminated xref list " + line);
}
stop = true;
}
if (braceIndex != -1 && braceIndex < endIndex) {
endIndex = braceIndex;
trailing = true;
}
Map pair = parseXref(line,
startoffset,
endIndex);
if (pair == null) {
startoffset++;
continue;
}
NestedValue nv = null;
if (trailing) {
nv = new NestedValue();
endIndex = getNestedValue(nv, line, endIndex + 1);
if (endIndex == -1) {
throw new IOException("Badly formatted "
+ "trailing properties " + line);
}
pair.put("nv",nv);
}
temp.add(pair);
startoffset = endIndex + 1;
}
Map[] out = new HashMap[temp.size()];
for (int i = 0; i < temp.size(); i++) {
Map pair = temp.get(i);
out[i] = pair;
}
return out;
}
protected Map parseXref(String line,
int startoffset, int endoffset) throws IOException {
String xref_str = null;
String desc_str = null;
SOPair xref = unescape(line, '"', startoffset, endoffset, false);
xref_str = xref.str.trim();
if (xref_str.length() == 0)
return null;
if (xref.index != -1) {
SOPair desc = unescape(line, '"', xref.index + 1, endoffset, true);
desc_str = desc.str.trim();
}
Map m = new HashMap();
m.put("xref",xref_str);
m.put("desc",desc_str);
return m;
}
private void triggerNewStanza(String stanza){
Iterator iter = listeners.iterator();
while (iter.hasNext()){
OboFileEventListener li = iter.next();
li.newStanza(stanza);
}
}
private void triggerNewKey(String key, String value){
Iterator iter = listeners.iterator();
while (iter.hasNext()){
OboFileEventListener li = iter.next();
li.newKey(key, value);
}
}
private void triggerNewSynonym(Synonym synonym){
Iterator iter = listeners.iterator();
while (iter.hasNext()){
OboFileEventListener li = iter.next();
li.newSynonym(synonym);
}
}
public static String escape(String str, boolean escapespaces) {
StringBuffer out = new StringBuffer();
for (int i = 0; i < str.length(); i++) {
char c = str.charAt(i);
Object o = unescapeChars.get(new Character(c));
if (o == null)
out.append(c);
else {
if (escapespaces || (!escapespaces && c != ' ' && c != '\t')) {
out.append("\\" + o);
} else
out.append(c);
}
}
return out.toString();
}
public String unescape(String str) throws IOException {
return unescape(str, '\0', 0, str.length(), false).str;
}
public SOPair unescape(String str, char toChar, int startindex,
boolean mustFindChar) throws IOException {
return unescape(str, toChar, startindex, str.length(), mustFindChar);
}
public SOPair unescape(String str, char toChar, int startindex,
int endindex, boolean mustFindChar) throws IOException {
StringBuffer out = new StringBuffer();
int endValue = -1;
for (int i = startindex; i < endindex; i++) {
char c = str.charAt(i);
if (c == '\\') {
i++;
c = str.charAt(i);
Character mapchar = escapeChars
.get(new Character(c));
if (mapchar == null)
throw new IOException("Unrecognized escape"
+ " character " + c + " found.");
out.append(mapchar);
} else if (c == toChar) {
endValue = i;
break;
} else {
out.append(c);
}
}
if (endValue == -1 && mustFindChar) {
throw new IOException("Expected " + toChar + "." + str);
}
return new SOPair(out.toString(), endValue);
}
public static int findUnescaped(String str, char toChar) {
return findUnescaped(str, toChar, 0, str.length());
}
public static int findUnescaped(String str, char toChar, int startIndex,
int endIndex) {
return findUnescaped(str, toChar, startIndex, endIndex, false);
}
public static int findUnescaped(String str, char toChar, int startindex,
int endindex, boolean honorQuotes) {
boolean inQuotes = false;
char quoteChar = '\0';
for (int i = startindex; i < endindex; i++) {
char c = str.charAt(i);
if (c == '\\') {
i++;
continue;
} else if (inQuotes) {
if (c == quoteChar)
inQuotes = false;
continue;
} else if (c == toChar) {
return i;
} else if (honorQuotes && isQuote(c)) {
inQuotes = true;
quoteChar = c;
}
}
return -1;
}
public static boolean isEscapeStarter(char c) {
return c == '\\';
}
public static boolean isQuote(char c) {
return c == '"';
}
protected StringBuffer getTempBuffer() {
tempBuffer.delete(0, tempBuffer.length());
return tempBuffer;
}
protected SOPair readQuotedString(String value, int startIndex,
int stopIndex, char terminatingChar, boolean requireQuotes,
boolean legalEndOfLine) throws IOException {
char quoteChar = '\0';
StringBuffer out = getTempBuffer();
int i = startIndex;
boolean useQuotes = false;
for (; i < stopIndex; i++) {
// burn through any leading whitespace
if (Character.isWhitespace(value.charAt(i)))
continue;
// if the first non-whitespace character is not a quote,
// proceed in non-quoted mode
else if (!isQuote(value.charAt(i))) {
if (requireQuotes)
throw new IOException(
"Expected start of quoted string. " +
line + " " + value+ " at linenr " + linenum);
useQuotes = false;
break;
} else {
useQuotes = true;
quoteChar = value.charAt(i);
i++;
break;
}
}
// look for a closing quote or final delimiter
for (; i < stopIndex; i++) {
if (isEscapeStarter(value.charAt(i))) {
i++;
if (i >= value.length())
throw new IOException("Incomplete escape sequence. " + line);
out.append(value.charAt(i));
} else if ((useQuotes && value.charAt(i) == quoteChar)
|| (!useQuotes && value.charAt(i) == terminatingChar)) {
if (!useQuotes)
return new SOPair(out.toString().trim(), startIndex, i - 1);
else
return new SOPair(out.toString(), startIndex, i);
} else {
out.append(value.charAt(i));
}
}
if (!useQuotes && legalEndOfLine)
return new SOPair(out.toString().trim(), startIndex, i);
else
throw new IOException("Unterminated quoted string. " +line);
}
protected int getNestedValue(NestedValue nv, String str, int startIndex)
throws IOException {
while (startIndex < str.length()) {
int equalsIndex = findUnescaped(str, '=', startIndex, str.length());
if (equalsIndex == -1)
throw new IOException("Expected = in trailing modifier " +line);
String name = str.substring(startIndex, equalsIndex).trim();
SOPair value = readQuotedString(str, equalsIndex + 1, str.length(),
',', false, true);
Properties pv = new Properties();
pv.setProperty(unescape(name),value.str);
nv.addPropertyValue(pv);
startIndex = value.endIndex + 1;
for (; startIndex < str.length(); startIndex++) {
if (Character.isWhitespace(str.charAt(startIndex)))
continue;
else if (str.charAt(startIndex) == ',') {
startIndex++;
break;
} else {
logger.error("found character |{}|", str.charAt(startIndex));
throw new IOException("Expected comma in trailing modifier. " +
line + " linenr: " + linenum);
}
}
}
return str.length();
}
}
class NestedValue {
protected Properties propertyValues = new Properties();
protected String name;
protected String suggestedComment;
public NestedValue() {
}
@Override
public String toString(){
String txt = "NestedValue: " ;
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