private void setupDecipherAlignment() { algo = null; if (sequenceType.equalsIgnoreCase(AA)) { algo = DecypherAlignment.ALGO_BLASTP; } else if (sequenceType.equalsIgnoreCase(NA)) { algo = DecypherAlignment.ALGO_BLASTN; } else { fireEventOccurred(new WrongParameterEvent( "Selected Program can not Align these types of sequences :" + program + " " + sequenceType + "->" + sequenceType, getCurrentMethodName())); } try { int dcbit = 0; if (bitscore != null) dcbit = bitscore; dcAlign = new DecypherAlignment(net.sourceforge.ondex.config.Config.ondexDir, programDir, cutoff, overlap, evalue, dcbit, 60, true); } catch (Exception e) { e.printStackTrace(); } }
taxids.add(Integer.parseInt(taxid)); } catch (NumberFormatException nfe) { fireEventOccurred(new WrongParameterEvent(taxid + " is no TaxID!", getName())); ccs.add(cc); else fireEventOccurred(new WrongParameterEvent(ccid + " is no ConceptClass!", getName())); cvs.add(dataSource); else fireEventOccurred(new WrongParameterEvent(cvid + " is no DataSource!", getName()));
algo = DecypherAlignment.ALGO_TBLASTN; } else { fireEventOccurred(new WrongParameterEvent("Selected Program can not Align these types of sequences :" + querySequenceType + "->" + targetSequenceType, getCurrentMethodName()));
AttributeName an = graph.getMetaData().getAttributeName(id); if (an == null) fireEventOccurred(new WrongParameterEvent( "AttributeName with id " + id + " not found", "[Export - start]")); DataSource ds = graph.getMetaData().getDataSource(id); if (ds == null) fireEventOccurred(new WrongParameterEvent("DataSource with id " + id + " not found", "[Export - start]")); else {
ONDEXConcept concept = graph.getConcept(rootID); if (concept == null) { fireEventOccurred(new WrongParameterEvent( "There was no valid root concept specified: Aborting", getCurrentMethodName())); RelationType rt = meta.getRelationType(o.toString()); if (rt == null) { fireEventOccurred(new WrongParameterEvent( "Wrong relation type '" + o + "' specified at level '" + arg ConceptClass cc = meta.getConceptClass(o.toString()); if (cc == null) { fireEventOccurred(new WrongParameterEvent( "Wrong concept class '" + o + "' specified at level '" + arg
String[] values = pair.split(","); if (values.length != 2) { fireEventOccurred(new WrongParameterEvent( "Invalid Format for ConceptClass pair " + pair, getCurrentMethodName())); } else { if (fromConceptClass == null) fireEventOccurred(new WrongParameterEvent(values[0] + " is not a valid from ConceptClass.", getCurrentMethodName())); if (toConceptClass == null) fireEventOccurred(new WrongParameterEvent(values[1] + " is not a valid to ConceptClass.", getCurrentMethodName()));
fireEventOccurred(new WrongParameterEvent( "Invalid Format for DataSource pair " + pair, getCurrentMethodName())); } else { if (fromDataSource == null) fireEventOccurred(new WrongParameterEvent(values[0] + " is not a valid from DataSource.", getCurrentMethodName())); if (toDataSource == null) fireEventOccurred(new WrongParameterEvent(values[1] + " is not a valid to DataSource.", getCurrentMethodName()));
} catch (NumberFormatException nfe) { continueRun = false; fireEventOccurred(new WrongParameterEvent("Wrong confidence threshold parameter: " + o, getName())); fireEventOccurred(new WrongParameterEvent("Wrong confidence threshold parameter: " + o, getName())); } catch (NumberFormatException nfe) { continueRun = false; fireEventOccurred(new WrongParameterEvent("Wrong threshold parameter: " + o, getName())); fireEventOccurred(new WrongParameterEvent("Wrong threshold parameter: " + o, getName())); } catch (NumberFormatException nfe) { continueRun = false; fireEventOccurred(new WrongParameterEvent("Wrong intersection cutoff parameter: " + o, getName())); fireEventOccurred(new WrongParameterEvent("Wrong intersection cutoff parameter: " + o, getName())); } catch (NumberFormatException nfe) { continueRun = false; fireEventOccurred(new WrongParameterEvent("Wrong term depth cutoff parameter: " + o, getName())); fireEventOccurred(new WrongParameterEvent("Wrong term depth cutoff parameter: " + o, getName())); if (!file.exists()) { continueRun = false; fireEventOccurred(new WrongParameterEvent("File " + o + "does not exist", getName())); } else { try {
FileArgumentDefinition.EXPORT_FILE); if (output == null) { fireEventOccurred(new WrongParameterEvent( "No output file specified.", getCurrentMethodName())); ready = false;
fireEventOccurred(new WrongParameterEvent( "Parameter for SequenceAlignmentProgram is not recognized :" + program, getCurrentMethodName())); } else { fireEventOccurred(new WrongParameterEvent( "Parameter SequenceAlignmentProgram is not set", getCurrentMethodName()));
"[Filter - setONDEXGraph]")); } else { fireEventOccurred(new WrongParameterEvent(id + " is not a valid RelationType.", "[Filter - setONDEXGraph]")); fireEventOccurred(new WrongParameterEvent( "No target RelationType(s) given.", "[Filter - setONDEXGraph]"));
(String) args.getUniqueValue(PATH_TO_EXEC_ARG)); if (!executable.exists()) { fireEventOccurred(new WrongParameterEvent("Executable " + executable.getAbsolutePath() + "does not exists.", getCurrentMethodName()));
args.getUniqueValue(TARGETRT_ARG).toString()); if (filterOnRt == null) { fireEventOccurred(new WrongParameterEvent(args .getUniqueValue(TARGETRT_ARG) + " is not a valid RelationType.", "[Filter - start]")); args.getUniqueValue(TARGETCC_ARG).toString()); if (filterOnCc == null) { fireEventOccurred(new WrongParameterEvent(args .getUniqueValue(TARGETCC_ARG) + " is not a valid ConceptClass.", "[Filter - start]"));
"[Filter - setONDEXGraph]")); } else { fireEventOccurred(new WrongParameterEvent(id + " is not a valid ConceptClass.", "[Filter - setONDEXGraph]")); fireEventOccurred(new WrongParameterEvent( "No target concept class(es) given.", "[Filter - setONDEXGraph]"));
weightAttributeName = graph.getMetaData().getAttributeName(anArg); if (weightAttributeName == null) { fireEventOccurred(new WrongParameterEvent("Invalid attribute name for edge weight : " + anArg, getCurrentMethodName())); error = true; fireEventOccurred(new WrongParameterEvent("Attribute name for edge weight " + anArg + " does support datatype double!", getCurrentMethodName())); error = true;
String[] split = o.split(","); if (split.length != 2) ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new WrongParameterEvent("Invalid input for class types - should be two, comma delimited.", "[Transformer - setONDEXGraph]")); ConceptClass from = graph.getMetaData().getConceptClass(split[0]); if (from == null) { ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new WrongParameterEvent("Concept class " + split[0] + " is undefined", "[Transformer - setONDEXGraph]")); from = createCC(graph, split[0]); ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new WrongParameterEvent("Concept class " + split[1] + " is undefined", "[Transformer - setONDEXGraph]")); to = createCC(graph, split[1]);
String[] split = o.toString().split(","); if (split.length != 2) ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new WrongParameterEvent("Invalid input for relation typeset(s) - should be two, comma delimited.", "[Transformer - setONDEXGraph]")); RelationType from = graph.getMetaData().getRelationType(split[0]); if (from == null) ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new WrongParameterEvent("Relation type set " + split[0] + " is undefined", "[Transformer - setONDEXGraph]")); RelationType to = graph.getMetaData().getRelationType(split[1]); if (to == null) ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new WrongParameterEvent("Relation type set " + split[1] + " is undefined", "[Transformer - setONDEXGraph]")); if (to != null && from != null) {
dataSource = graph.getMetaData().getDataSource(temp); if (dataSource == null) fireEventOccurred(new WrongParameterEvent("The DataSource " + temp + " does not exist.", getCurrentMethodName())); getCurrentMethodName())); } else { fireEventOccurred(new WrongParameterEvent(id + " is not a valid ConceptClass.", getCurrentMethodName())); fireEventOccurred(new WrongParameterEvent( "No target concept class(es) given.", getCurrentMethodName()));
"[Filter - filterOnGraph]")); } else { fireEventOccurred(new WrongParameterEvent(o + " is not a valid ConceptClass.", "[Filter - filterOnGraph]"));
@Override public void start() throws Exception { setupMetaData(); Map<Integer, Set<Integer>> taxId2CidSet = createTaxIdIndex(); int[] taxIDArray = createTaxIdArray(taxId2CidSet); setupDecipherAlignment(); if (algo != null && dcAlign != null) { runMapping(taxIDArray, taxId2CidSet); } else { fireEventOccurred(new WrongParameterEvent( "Alignment could not be initialized with these parameters. " , getCurrentMethodName())); } }