Java ComboCondition.addCondition方法代码示例

import com.healthmarketscience.sqlbuilder.ComboCondition; //导入方法依赖的package包/类
/**
 * Build the standard pharmacogenomic condition to be used when retrieving 
 * variants for any patient's analysis.
 * @return the ComboCondition to be used for all analyses
 * @deprecated This method creates a mega condition that retrieves all PGx
 *		variants from the DB. However, as the PGx DB grows, this condition
 *		will become unreasonably large, and is limited by the
 *		'max_allowed_packet' property in MySQL. Replaced by {@link #buildConditionList()}
 */
@Deprecated
private static ComboCondition buildCondition() {
	ComboCondition query= new ComboCondition(ComboCondition.Op.OR);
	
	/* Get all relevant genes. */
	List<String> genes= new LinkedList<String>();
	try {
		genes= PGXDBFunctions.getGenes();
	} catch (SQLException se) {
		se.printStackTrace();
	}
	
	/* Get all relevant markers. */
	List<String> markers= new LinkedList<String>();
	try {
		for (String g : genes) {
			markers.addAll(PGXDBFunctions.getMarkers(g));
		}
		} catch (Exception pe) {
		pe.printStackTrace();
	}
	
	
	/* Add all markers to the ComboCondition.
	 * NOTE: this is hardcoded for now, but will need to be changed if the
	 * dbSNP annotation DB is updated. */
	for (String m : markers) {
		query.addCondition(
			BinaryCondition.equalTo(ts.getDBColumn(columns.get(DBSNP_COLUMN)), m));
	}
	
	return query;		
}
 

import com.healthmarketscience.sqlbuilder.ComboCondition; //导入方法依赖的package包/类
/**
 * Build the standard pharmacogenomic conditions to be used when retrieving 
 * variants for any patient's analysis and store these in a list.
 * @return a Map of Conditions to be used for all PGx analyses
 * @throws SQLException
 */
private static Map<String, Condition> buildConditionList() throws SQLException {
	Map<String, Condition> queryMap= new HashMap<String, Condition>();
	
	/* Get all relevant markers for a particular gene and create a
	 * ComboCondition for that set. Then add it to the List. */
		for (String g : PGXDBFunctions.getGenes()) {
			// generate a new query for this gene
			ComboCondition query= new ComboCondition(ComboCondition.Op.OR);
			
			try {
				/* Add all the marker positions for this gene.
				 * NOTE: You can also search for variants using the dbSNP rsID,
				 * however, then you rely on the DB to be up-to-date and annotated
				 * correctly, which is not always the case. It's better to query
				 * variants by chromosomal coordinates. Original code is commented
				 * out below. */
				for (PGXMarker pgxm : PGXDBFunctions.getMarkerInfo(g)) {
					ComboCondition variantCondition= new ComboCondition(ComboCondition.Op.AND);
					variantCondition.addCondition(
						BinaryCondition.equalTo(ts.getDBColumn(BasicVariantColumns.CHROM), pgxm.chromosome));
					variantCondition.addCondition(
						BinaryCondition.equalTo(ts.getDBColumn(BasicVariantColumns.START_POSITION), Integer.parseInt(pgxm.position)));	
					
					query.addCondition(variantCondition);
				}
			} catch (Exception e) {
				e.printStackTrace();
			}
			
			// add this gene-query pair to the list
			queryMap.put(g, query);
		}
	
	return queryMap;		
}
 

import com.healthmarketscience.sqlbuilder.ComboCondition; //导入方法依赖的package包/类
/** 
 * Build the standard pharmacogenomic conditions for NOVEL variants.
 * @return a List of Conditions to be used for all PGx analyses of novel variants
 * @throws SQLException
 */
private static List<Condition> buildNovelConditionList() throws SQLException, RemoteException, SessionExpiredException {
		List<Condition> output= new LinkedList<Condition>();
	
		/* Get all genic non-synonymous variants. */
		ComboCondition mutationCondition= new ComboCondition(ComboCondition.Op.OR);
		for (String mutationEffect : NOVEL_MUTATIONS) {
			mutationCondition.addCondition(
				BinaryCondition.iLike(ts.getDBColumn(BasicVariantColumns.JANNOVAR_EFFECT), mutationEffect + "%"));
		}
		output.add(mutationCondition);	
		
		/* For each of the allele frequency columns, check if the allele 
		 * frequency is below threshold. If allele frequency at the position
		 * is null, also report it. */
		ComboCondition afCondition= new ComboCondition(ComboCondition.Op.OR);
		AnnotationManagerAdapter am= MedSavantClient.AnnotationManagerAdapter;
		Map<String, Set<CustomField>> fieldMap= 
			am.getAnnotationFieldsByTag(LoginController.getInstance().getSessionID(), true);
		Set<CustomField> columnNames= fieldMap.get(CustomField.ALLELE_FREQUENCY_TAG);
		for (CustomField cf : columnNames) {
			DbColumn afColumn= ts.getDBColumn(cf.getColumnName());
			// include variant if AF is below threshold
			afCondition.addCondition(
				BinaryCondition.lessThan(afColumn, AF_THRESHOLD, true));
			// include variant even if AF information is missing
			afCondition.addCondition(UnaryCondition.isNull(afColumn));
		}
		output.add(afCondition);
		
		return output;
}
 

import com.healthmarketscience.sqlbuilder.ComboCondition; //导入方法依赖的package包/类
/**
 * Get all pharmacogenomic variants for this individual.
 */
private void queryVariants() throws SQLException, RemoteException, SessionExpiredException {
	/* Iterate through all gene conditions. */
	List<String> allGeneKeys= new ArrayList<String>(standardPGXConditions.keySet());
	// Sort the list of genes by gene symbol for convenience later
	Collections.sort(allGeneKeys);
	for (String geneKey : allGeneKeys) {
		/* The variants for this gene. */
		PGXGene pgxVariants= new PGXGene(geneKey);
		
		/* Take the standard combocondition and AND it to the DNA ID for this
		 * individual before submitting for variants. */
		ComboCondition query= new ComboCondition(ComboCondition.Op.AND);
		query.addCondition(
			BinaryCondition.equalTo(ts.getDBColumn(BasicVariantColumns.DNA_ID), dnaID));
		query.addCondition(standardPGXConditions.get(geneKey));
		
		/* Once query is built, run it on the remote server. */
		List<Variant> retrievedVariants= runRemoteQuery(query);			
		
		/* Add variants to the list for this PGx gene. */
		for (Variant var : retrievedVariants) {
			pgxVariants.addVariant(var);
		}
		
		/* Add the current gene-variant object to the list. */
		pgxGenes.add(pgxVariants);
		
		/* If analysis has been cancelled, stop querying. */
		if (isCancelled) {
			return;
		}
	}
}
 

import com.healthmarketscience.sqlbuilder.ComboCondition; //导入方法依赖的package包/类
private void applyFilters(SelectQuery query) {
    if(this.filters != null && this.filters.length > 0) {
        ComboCondition comboCondition = new ComboCondition(ComboCondition.Op.AND);
        if (filters.length > 0) {
            for(int i=0; i<filters.length; i++) {
                Filter filter = filters[i];
                FilterType filterType = filter.getFilterType();
                DbColumn filterColumn = new DbColumn(dbTable, filter.getField(), "",null,null);
                if(filterType.equals(FilterType.EQ)) {
                    comboCondition.addCondition(BinaryCondition.equalTo(filterColumn, filter.getValue()));
                } else if(filterType.equals(FilterType.GT)) {
                    comboCondition.addCondition(BinaryCondition.greaterThan(filterColumn, filter.getValue(), false));
                } else if(filterType.equals(FilterType.LT)) {
                    comboCondition.addCondition(BinaryCondition.lessThan(filterColumn, filter.getValue(), false));
                } else if(filterType.equals(FilterType.GTE)) {
                    comboCondition.addCondition(BinaryCondition.greaterThan(filterColumn, filter.getValue(), true));
                } else if(filterType.equals(FilterType.LTE)) {
                    comboCondition.addCondition(BinaryCondition.lessThan(filterColumn, filter.getValue(), true));
                } else if(filterType.equals(FilterType.NEQ)) {
                    comboCondition.addCondition(BinaryCondition.notEqualTo(filterColumn, filter.getValue()));
                } else if(filterType.equals(FilterType.IN)) {
                    ComboCondition comboConditionOR = new ComboCondition(ComboCondition.Op.OR);
                    String[] condicion =filter.getValue().toString().split(",");
                    for (int z=0; z < condicion.length ; z++) {
                        comboConditionOR.addCondition(BinaryCondition.equalTo(filterColumn, condicion[z]));
                    }
                    comboCondition.addCondition(comboConditionOR);
                }
                else {
                    throw new UnsupportedOperationException("Currently, the filter operation " + filterType + " is not supported");
                }
            }
        }
        query.addCondition(comboCondition);
    }
}
 

import com.healthmarketscience.sqlbuilder.ComboCondition; //导入方法依赖的package包/类
/**
 * Get all novel and rare pharmacogenomic variants for this individual.
 * @precondition	pgxGenes must already have been initialized by running queryVariants()
 */
private void getNovelVariants() throws SQLException, RemoteException, SessionExpiredException, PGXException {
	/* If analysis has been cancelled, stop. */
	if (isCancelled) {
		return;
	}
	
	/* Iterate through all previously stored PGXGene objects and get all 
	 * low allele frequency variants for these genes. */
	for (PGXGene pg : pgxGenes) {
		String geneSymbol= pg.getGene();
		List<PGXMarker> existingMarkers= PGXDBFunctions.getMarkerInfo(geneSymbol);
	
		ComboCondition query= new ComboCondition(ComboCondition.Op.AND);
		
		/* Get variants for this patient/DNA ID and this PGx gene. */
		query.addCondition(
			BinaryCondition.equalTo(ts.getDBColumn(BasicVariantColumns.DNA_ID), dnaID));
		query.addCondition(
			BinaryCondition.iLike(ts.getDBColumn(BasicVariantColumns.JANNOVAR_SYMBOL), geneSymbol + "%"));
		
		/* Ensure that the patient actually has this variant, and is not
		 * homozygous for the reference. This is important if reference 
		 * positions are reported, which happens in a pgx analysis. In
		 * general, VCF files do not report homozygous ref positions. */
		query.addCondition(
			BinaryCondition.notiLike(ts.getDBColumn(BasicVariantColumns.GT), "0%0"));
		
		/* Add all default novel Conditions to this query. */
		for (Condition c : novelPGXConditions) {
			query.addCondition(c);
		}
		
		/* Once query is built, run it on the remote server. */
		List<Variant> potentialNovelVariants= runRemoteQuery(query);
		
		/* Check if returned variants are NOT PGx markers and then add to
		 * the novel variants. */
		for (Variant var : potentialNovelVariants) {
			if (!isKnownPGXMarker(var.getChromosome(), Long.toString(var.getStart()))) {	
				pg.addNovelVariant(var);
			}
		}
	}
}