public void parseEntityFrame(OBODoc obodoc) throws OBOFormatParserException { parseZeroOrMoreWsOptCmtNl(); String rest = s.rest(); if (rest != null && rest.startsWith("[Term]")) { parseTermFrame(obodoc); } else { parseTypedefFrame(obodoc); } }
/** * @param obodoc obodoc * @throws OBOFormatParserException parser exception */ public void parseEntityFrame(OBODoc obodoc) { parseZeroOrMoreWsOptCmtNl(); String rest = stream.rest(); if (rest.startsWith("[Term]")) { parseTermFrame(obodoc); } else if (rest.startsWith("[Instance]")) { LOG.error("Error: Instance frames are not supported yet. Parsing stopped at line: {}", Integer.valueOf( stream.getLineNo())); while (!stream.eof()) { stream.advanceLine(); } } else { parseTypedefFrame(obodoc); } }
/** * @param obodoc obodoc * @throws OBOFormatParserException parser exception */ public void parseEntityFrame(OBODoc obodoc) { parseZeroOrMoreWsOptCmtNl(); String rest = stream.rest(); if (rest.startsWith("[Term]")) { parseTermFrame(obodoc); } else if (rest.startsWith("[Instance]")) { LOG.error("Error: Instance frames are not supported yet. Parsing stopped at line: {}", Integer.valueOf( stream.getLineNo())); while (!stream.eof()) { stream.advanceLine(); } } else { parseTypedefFrame(obodoc); } }
/** * @param obodoc obodoc * @throws OBOFormatParserException parser exception */ public void parseEntityFrame(OBODoc obodoc) { parseZeroOrMoreWsOptCmtNl(); String rest = stream.rest(); if (rest.startsWith("[Term]")) { parseTermFrame(obodoc); } else if (rest.startsWith("[Instance]")) { LOG.error("Error: Instance frames are not supported yet. Parsing stopped at line: {}", Integer.valueOf( stream.getLineNo())); while (!stream.eof()) { stream.advanceLine(); } } else { parseTypedefFrame(obodoc); } }
/** * @param obodoc obodoc * @throws OBOFormatParserException parser exception */ public void parseEntityFrame(OBODoc obodoc) { parseZeroOrMoreWsOptCmtNl(); String rest = stream.rest(); if (rest.startsWith("[Term]")) { parseTermFrame(obodoc); } else if (rest.startsWith("[Instance]")) { LOG.error("Error: Instance frames are not supported yet. Parsing stopped at line: {}", Integer.valueOf( stream.getLineNo())); while (!stream.eof()) { stream.advanceLine(); } } else { parseTypedefFrame(obodoc); } }
/** * header-clause ::= format-version-TVP | ... | ... * * @param h header frame * @return false if there are no more header clauses, other wise true * @throws OBOFormatParserException */ protected boolean parseHeaderClauseNl(Frame h) throws OBOFormatParserException { parseZeroOrMoreWsOptCmtNl(); if (s.peekCharIs('[') || s.eof()) { return false; } parseHeaderClause(h); forceParseNlOrEof(); return true; }
parseZeroOrMoreWsOptCmtNl(); if (s.consume("[Term]")) { forceParseNlOrEof(); parseIdLine(f); parseZeroOrMoreWsOptCmtNl(); while (true) { if (s.eof() || s.peekCharIs('[')) { parseZeroOrMoreWsOptCmtNl();
/** * header-clause ::= format-version-TVP | ... | ... * * @param h header frame * @return false if there are no more header clauses, other wise true * @throws OBOFormatParserException parser exception */ protected boolean parseHeaderClauseNl(Frame h) { parseZeroOrMoreWsOptCmtNl(); if (stream.peekCharIs('[') || stream.eof()) { return false; } parseHeaderClause(h); parseHiddenComment(); forceParseNlOrEof(); return true; }
parseZeroOrMoreWsOptCmtNl(); if (stream.consume("[Typedef]")) { forceParseNlOrEof(); parseIdLine(f); parseZeroOrMoreWsOptCmtNl(); while (true) { if (stream.eof() || stream.peekCharIs('[')) { parseZeroOrMoreWsOptCmtNl();
parseZeroOrMoreWsOptCmtNl(); if (stream.consume("[Term]")) { forceParseNlOrEof(); parseIdLine(f); parseZeroOrMoreWsOptCmtNl(); while (true) { if (stream.eof() || stream.peekCharIs('[')) { parseZeroOrMoreWsOptCmtNl();
parseZeroOrMoreWsOptCmtNl(); if (stream.consume("[Term]")) { forceParseNlOrEof(); parseIdLine(f); parseZeroOrMoreWsOptCmtNl(); while (true) { if (stream.eof() || stream.peekCharIs('[')) { parseZeroOrMoreWsOptCmtNl();
parseZeroOrMoreWsOptCmtNl(); if (stream.consume("[Term]")) { forceParseNlOrEof(); parseIdLine(f); parseZeroOrMoreWsOptCmtNl(); while (true) { if (stream.eof() || stream.peekCharIs('[')) { parseZeroOrMoreWsOptCmtNl();
/** * header-clause ::= format-version-TVP | ... | ... * * @param h header frame * @return false if there are no more header clauses, other wise true * @throws OBOFormatParserException parser exception */ protected boolean parseHeaderClauseNl(Frame h) { parseZeroOrMoreWsOptCmtNl(); if (stream.peekCharIs('[') || stream.eof()) { return false; } parseHeaderClause(h); parseHiddenComment(); forceParseNlOrEof(); return true; }
/** * header-clause ::= format-version-TVP | ... | ... * * @param h header frame * @return false if there are no more header clauses, other wise true * @throws OBOFormatParserException parser exception */ protected boolean parseHeaderClauseNl(Frame h) { parseZeroOrMoreWsOptCmtNl(); if (stream.peekCharIs('[') || stream.eof()) { return false; } parseHeaderClause(h); parseHiddenComment(); forceParseNlOrEof(); return true; }
/** * header-clause ::= format-version-TVP | ... | ... * * @param h header frame * @return false if there are no more header clauses, other wise true * @throws OBOFormatParserException parser exception */ protected boolean parseHeaderClauseNl(Frame h) { parseZeroOrMoreWsOptCmtNl(); if (stream.peekCharIs('[') || stream.eof()) { return false; } parseHeaderClause(h); parseHiddenComment(); forceParseNlOrEof(); return true; }
public void parseOBODoc(OBODoc obodoc) throws OBOFormatParserException { Frame h = new Frame(FrameType.HEADER); obodoc.setHeaderFrame(h); parseHeaderFrame(h); parseZeroOrMoreWsOptCmtNl(); while (s.eof() == false) { parseEntityFrame(obodoc); parseZeroOrMoreWsOptCmtNl(); } // set OBO namespace in frames final String defaultOboNamespace = h.getTagValue(OboFormatTag.TAG_DEFAULT_NAMESPACE, String.class); if (defaultOboNamespace != null) { addOboNamespace(obodoc.getTermFrames(), defaultOboNamespace); addOboNamespace(obodoc.getTypedefFrames(), defaultOboNamespace); addOboNamespace(obodoc.getInstanceFrames(), defaultOboNamespace); } }
/** * @param obodoc obodoc * @throws OBOFormatParserException parser exception */ public void parseOBODoc(OBODoc obodoc) { Frame h = new Frame(FrameType.HEADER); obodoc.setHeaderFrame(h); parseHeaderFrame(h); h.freeze(); parseZeroOrMoreWsOptCmtNl(); while (!stream.eof()) { parseEntityFrame(obodoc); parseZeroOrMoreWsOptCmtNl(); } // set OBO namespace in frames String defaultOboNamespace = h .getTagValue(OboFormatTag.TAG_DEFAULT_NAMESPACE, String.class); if (defaultOboNamespace != null) { addOboNamespace(obodoc.getTermFrames(), defaultOboNamespace); addOboNamespace(obodoc.getTypedefFrames(), defaultOboNamespace); addOboNamespace(obodoc.getInstanceFrames(), defaultOboNamespace); } }
/** * @param obodoc obodoc * @throws OBOFormatParserException parser exception */ public void parseOBODoc(OBODoc obodoc) { Frame h = new Frame(FrameType.HEADER); obodoc.setHeaderFrame(h); parseHeaderFrame(h); h.freeze(); parseZeroOrMoreWsOptCmtNl(); while (!stream.eof()) { parseEntityFrame(obodoc); parseZeroOrMoreWsOptCmtNl(); } // set OBO namespace in frames String defaultOboNamespace = h .getTagValue(OboFormatTag.TAG_DEFAULT_NAMESPACE, String.class); if (defaultOboNamespace != null) { addOboNamespace(obodoc.getTermFrames(), defaultOboNamespace); addOboNamespace(obodoc.getTypedefFrames(), defaultOboNamespace); addOboNamespace(obodoc.getInstanceFrames(), defaultOboNamespace); } }
/** * @param obodoc obodoc * @throws OBOFormatParserException parser exception */ public void parseOBODoc(OBODoc obodoc) { Frame h = new Frame(FrameType.HEADER); obodoc.setHeaderFrame(h); parseHeaderFrame(h); h.freeze(); parseZeroOrMoreWsOptCmtNl(); while (!stream.eof()) { parseEntityFrame(obodoc); parseZeroOrMoreWsOptCmtNl(); } // set OBO namespace in frames String defaultOboNamespace = h .getTagValue(OboFormatTag.TAG_DEFAULT_NAMESPACE, String.class); if (defaultOboNamespace != null) { addOboNamespace(obodoc.getTermFrames(), defaultOboNamespace); addOboNamespace(obodoc.getTypedefFrames(), defaultOboNamespace); addOboNamespace(obodoc.getInstanceFrames(), defaultOboNamespace); } }
/** * @param obodoc obodoc * @throws OBOFormatParserException parser exception */ public void parseOBODoc(OBODoc obodoc) { Frame h = new Frame(FrameType.HEADER); obodoc.setHeaderFrame(h); parseHeaderFrame(h); h.freeze(); parseZeroOrMoreWsOptCmtNl(); while (!stream.eof()) { parseEntityFrame(obodoc); parseZeroOrMoreWsOptCmtNl(); } // set OBO namespace in frames String defaultOboNamespace = h .getTagValue(OboFormatTag.TAG_DEFAULT_NAMESPACE, String.class); if (defaultOboNamespace != null) { addOboNamespace(obodoc.getTermFrames(), defaultOboNamespace); addOboNamespace(obodoc.getTypedefFrames(), defaultOboNamespace); addOboNamespace(obodoc.getInstanceFrames(), defaultOboNamespace); } }