List of usage examples for com.google.common.collect Range contains
public boolean contains(C value)
From source file:io.github.msdk.featdet.chromatogrambuilder.HighestDataPointConnector.java
void addScan(RawDataFile dataFile, MsScan scan) { // Load data points mzBuffer = scan.getMzValues(mzBuffer); intensityBuffer = scan.getIntensityValues(intensityBuffer); numOfDataPoints = scan.getNumberOfDataPoints(); // Sort m/z peaks by descending intensity DataPointSorter.sortDataPoints(mzBuffer, intensityBuffer, numOfDataPoints, SortingProperty.INTENSITY, SortingDirection.DESCENDING); // A set of already connected chromatograms in each iteration connectedChromatograms.clear();// w w w .jav a 2 s. co m for (int i = 0; i < numOfDataPoints; i++) { if (intensityBuffer[i] < noiseLevel) continue; // Search for best chromatogram, which has the highest _last_ data // point BuildingChromatogram bestChromatogram = null; for (BuildingChromatogram testChrom : buildingChromatograms) { Range<Double> toleranceRange = mzTolerance.getToleranceRange(testChrom.getLastMz()); if (toleranceRange.contains(mzBuffer[i])) { if ((bestChromatogram == null) || (testChrom.getLastIntensity() > bestChromatogram.getLastIntensity())) { bestChromatogram = testChrom; } } } // If we found best chromatogram, check if it is already connected. // In such case, we may discard this mass and continue. If we // haven't found a chromatogram, we can create a new one. if (bestChromatogram != null) { if (connectedChromatograms.contains(bestChromatogram)) { continue; } } else { bestChromatogram = new BuildingChromatogram(); } // Add this mzPeak to the chromatogram ChromatographyInfo rt = scan.getChromatographyInfo(); Preconditions.checkNotNull(rt); bestChromatogram.addDataPoint(rt, mzBuffer[i], intensityBuffer[i]); // Move the chromatogram to the set of connected chromatograms connectedChromatograms.add(bestChromatogram); } // Process those chromatograms which were not connected to any m/z peak for (BuildingChromatogram testChrom : buildingChromatograms) { // Skip those which were connected if (connectedChromatograms.contains(testChrom)) { continue; } // Check if we just finished a long-enough segment if (testChrom.getBuildingSegmentLength() >= minimumTimeSpan) { testChrom.commitBuildingSegment(); // Move the chromatogram to the set of connected chromatograms connectedChromatograms.add(testChrom); continue; } // Check if we have any committed segments in the chromatogram if (testChrom.getNumberOfCommittedSegments() > 0) { testChrom.removeBuildingSegment(); // Move the chromatogram to the set of connected chromatograms connectedChromatograms.add(testChrom); continue; } } // All remaining chromatograms in buildingChromatograms are discarded // and buildingChromatograms is replaced with connectedChromatograms buildingChromatograms.clear(); buildingChromatograms.addAll(connectedChromatograms); }
From source file:org.opentestsystem.authoring.testauth.validation.ScoringRuleParameterValidator.java
/** * validate dictionary values/*from w ww .ja v a2 s. com*/ */ private <N extends Number> void validateDictionaryValues( final ComputationRuleParameter computationRuleParameter, final List<ScoringRuleDictionaryElement> dictionaryValues, final Errors errors) { final ComputationRuleType fieldType = computationRuleParameter.getComputationRuleType(); final String paramName = computationRuleParameter.getParameterName(); if (CollectionUtils.isEmpty(dictionaryValues)) { rejectValue(errors, DICTIONARY, getErrorMessageRoot() + DICTIONARY + MSG_REQUIRED, fieldType, paramName); } final Map<String, Collection<ScoringRuleDictionaryElement>> duplicates = Maps.filterEntries( Multimaps.index(dictionaryValues, DICTIONARY_ELEMENT_TO_KEY_TRANSFORMER).asMap(), KEY_DUPLICATE_FILTER); if (!duplicates.isEmpty()) { rejectValue(errors, DICTIONARY, getErrorMessageRoot() + DICTIONARY + MSG_DUPLICATES, paramName, duplicates.keySet().toString()); } for (int i = 0; i < dictionaryValues.size(); i++) { final ScoringRuleDictionaryElement scoringRuleDictionaryElement = dictionaryValues.get(i); String key = scoringRuleDictionaryElement.getKey(); final String value = scoringRuleDictionaryElement.getValue(); try { errors.pushNestedPath(DICTIONARY + "[" + i + "]"); final DictionaryIndexType dictionaryIndex = computationRuleParameter.getDictionaryIndexType(); final boolean indexIsInteger = dictionaryIndex == DictionaryIndexType.INTEGER; if (!rejectIfEmpty(key, errors, KEY, getErrorMessageRoot() + DICTIONARY_KEY, indexIsInteger ? MAX_PARSEABLE_LENGTH : MAX_STRING_LENGTH, fieldType, paramName, i + 1) && indexIsInteger) { if (!StringUtils.isNumeric(key)) { rejectValue(errors, KEY, getErrorMessageRoot() + DICTIONARY_KEY + MSG_INVALID, fieldType, paramName, key, dictionaryIndex); } } key = StringUtils.defaultIfBlank(key, String.valueOf(i + 1)); final boolean valueIsNumeric = NUMERIC_TYPES.contains(fieldType); if (!rejectIfEmpty(value, errors, VALUE, getErrorMessageRoot() + DICTIONARY_VALUE, valueIsNumeric ? MAX_PARSEABLE_LENGTH : MAX_STRING_LENGTH, fieldType, paramName, key) && valueIsNumeric) { final String min = computationRuleParameter.getMinimumValue(); final String max = computationRuleParameter.getMaximumValue(); try { if (fieldType == ComputationRuleType.FLOAT) { final Float floatValue = Float.parseFloat(value); final Range<Float> floatRange = buildFloatRange(min, max); if (floatRange != null && !floatRange.contains(floatValue)) { rejectValue(errors, VALUE, getErrorMessageRoot() + DICTIONARY_VALUE + MSG_RANGE, fieldType, paramName, key, min, max); } } else { final Long longValue = Long.parseLong(value); final Range<Long> longRange = buildLongRange(min, max); if (longRange != null && !longRange.contains(longValue)) { rejectValue(errors, VALUE, getErrorMessageRoot() + DICTIONARY_VALUE + MSG_RANGE, fieldType, paramName, key, min, max); } } } catch (final NumberFormatException e) { rejectValue(errors, VALUE, getErrorMessageRoot() + DICTIONARY_VALUE + MSG_PARSEABLE_NUMBER, fieldType, paramName, key, value); } } else if (ComputationRuleType.BOOLEAN.equals(fieldType) && !Boolean.FALSE.toString().equals(value.toString()) && !Boolean.TRUE.toString().equals(value.toString())) { rejectValue(errors, VALUE, getErrorMessageRoot() + DICTIONARY_VALUE + MSG_PARSEABLE_BOOLEAN, fieldType, paramName, key, value); } } finally { errors.popNestedPath(); } } }
From source file:io.github.mzmine.datamodel.SimpleFeatureTable.java
/** {@inheritDoc} */ @Override//from w w w . j a v a2 s . c o m public List<FeatureTableRow> getRowsInsideRange(Range<Float> rtRange, Range<Double> mzRange) { List<FeatureTableRow> result = new ArrayList<FeatureTableRow>(); for (FeatureTableRow row : featureTableRows) { Float rowRT = row.getRT(); if ((rowRT != null) && rtRange.contains(rowRT) && mzRange.contains(row.getMz())) result.add(row); } return result; }
From source file:net.sf.mzmine.modules.peaklistmethods.identification.customdbsearch.CustomDBSearchTask.java
private void processOneLine(String values[]) { int numOfColumns = Math.min(fieldOrder.length, values.length); String lineID = null, lineName = null, lineFormula = null; double lineMZ = 0, lineRT = 0; for (int i = 0; i < numOfColumns; i++) { if (fieldOrder[i] == FieldItem.FIELD_ID) lineID = values[i];// w ww . ja v a2s . co m if (fieldOrder[i] == FieldItem.FIELD_NAME) lineName = values[i]; if (fieldOrder[i] == FieldItem.FIELD_FORMULA) lineFormula = values[i]; if (fieldOrder[i] == FieldItem.FIELD_MZ) lineMZ = Double.parseDouble(values[i]); if (fieldOrder[i] == FieldItem.FIELD_RT) lineRT = Double.parseDouble(values[i]); } SimplePeakIdentity newIdentity = new SimplePeakIdentity(lineName, lineFormula, dataBaseFile.getName(), lineID, null); for (PeakListRow peakRow : peakList.getRows()) { Range<Double> mzRange = mzTolerance.getToleranceRange(peakRow.getAverageMZ()); Range<Double> rtRange = rtTolerance.getToleranceRange(peakRow.getAverageRT()); boolean mzMatches = (lineMZ == 0d) || mzRange.contains(lineMZ); boolean rtMatches = (lineRT == 0d) || rtRange.contains(lineRT); if (mzMatches && rtMatches) { logger.finest("Found compound " + lineName + " (m/z " + lineMZ + ", RT " + lineRT + ")"); // add new identity to the row peakRow.addPeakIdentity(newIdentity, false); // Notify the GUI about the change in the project MZmineCore.getProjectManager().getCurrentProject().notifyObjectChanged(peakRow, false); } } }
From source file:org.apache.kylin.storage.cache.StreamSQLResult.java
public StreamSQLResult(List<ITuple> rows, Range<Long> timeCovered, TblColRef partitionCol) { sortedRows = Maps.newTreeMap();/* ww w . j a v a 2 s.c o m*/ for (ITuple row : rows) { if (partitionCol != null) { long t = Tuple.getTs(row, partitionCol); //will only cache rows that are within the time range if (timeCovered.contains(t)) { if (!this.sortedRows.containsKey(t)) { this.sortedRows.put(t, Lists.newArrayList(row)); } else { this.sortedRows.get(t).add(row); } } } else { if (!this.sortedRows.containsKey(0L)) { this.sortedRows.put(0L, Lists.<ITuple>newArrayList()); } this.sortedRows.get(0L).add(row); } } this.timeCovered = timeCovered; }
From source file:org.noroomattheinn.visibletesla.stats.StatsRepository.java
public synchronized void loadExistingData(final Recorder r, final Range<Long> period) { loadExistingData(new Recorder() { @Override//from ww w.j a va 2s .c om public void recordElement(long time, String type, double val) { if (period.contains(time)) r.recordElement(time, type, val); } }); }
From source file:com.techshroom.wood.module.ModuleDependencySolver.java
ImmutableList<Module> computeDependencyOrder() {
// Fast-track no module case
if (this.moduleMap.isEmpty()) {
return ImmutableList.of();
}//from w w w . ja va 2s .co m
// If a node goes from A->B, A must be loaded AFTER B
MutableGraph<ModuleMetadata> depGraph = GraphBuilder.directed().allowsSelfLoops(false)
.expectedNodeCount(this.moduleMap.size()).build();
// Insert all nodes before connecting
this.moduleMap.values().stream().map(Module::getMetadata).forEach(depGraph::addNode);
for (Module factory : this.moduleMap.values()) {
ModuleMetadata data = factory.getMetadata();
data.getLoadAfterModules().forEach(dep -> {
Range<SemVer> acceptable = dep.getVersionRange();
// Here, we must load data after meta, put data->meta
depGraph.nodes().stream().filter(meta -> acceptable.contains(meta.getVersion())).findAny()
.ifPresent(meta -> {
// Do a check for existing edges going the other
// way
if (depGraph.edges().contains(EndpointPair.ordered(meta, data))) {
throw new IllegalStateException("Cannot have a two-way dependency. Found between "
+ Modules.getBasicRepresentation(data) + " and "
+ Modules.getBasicRepresentation(meta));
}
depGraph.putEdge(data, meta);
});
});
data.getLoadBeforeModules().forEach(dep -> {
Range<SemVer> acceptable = dep.getVersionRange();
// Here, we must load data before meta, put meta->data
depGraph.nodes().stream().filter(meta -> acceptable.contains(meta.getVersion())).findAny()
.ifPresent(meta -> {
// Do a check for existing edges going the other
// way
if (depGraph.edges().contains(EndpointPair.ordered(data, meta))) {
throw new IllegalStateException("Cannot have a two-way dependency. Found between "
+ Modules.getBasicRepresentation(data) + " and "
+ Modules.getBasicRepresentation(meta));
}
depGraph.putEdge(meta, data);
});
});
data.getRequiredModules().forEach(dep -> {
Range<SemVer> acceptable = dep.getVersionRange();
// Here, we must load data after meta, put data->meta
ModuleMetadata result = depGraph.nodes().stream()
.filter(meta -> acceptable.contains(meta.getVersion())).findAny().orElseThrow(() -> {
return new IllegalStateException("Missing required dependency " + dep);
});
// Do a check for existing edges going the other
// way
if (depGraph.edges().contains(EndpointPair.ordered(result, data))) {
throw new IllegalStateException("Cannot have a two-way dependency. Found between "
+ Modules.getBasicRepresentation(data) + " and "
+ Modules.getBasicRepresentation(result));
}
depGraph.putEdge(data, result);
});
}
// Modules in dependency-loading order
List<ModuleMetadata> dependencyOrder = new LinkedList<>();
// The outDegree is the number of dependencies
Set<ModuleMetadata> noDeps = depGraph.nodes().stream().filter(m -> depGraph.outDegree(m) == 0)
.collect(Collectors.toSet());
checkState(!noDeps.isEmpty(), "There must be at least one module with no dependencies.");
// this set tracks encountered modules (i.e. child nodes)
// that have not been known as satisfied by things in depedencyOrder
Set<ModuleMetadata> encounteredNotSatisfied = new HashSet<>();
// this set tracks satisfied modules
// (but not yet added to dependencyOrder)
// that have not been processed to find other modules
Set<ModuleMetadata> satisfiedNotProcessed = new HashSet<>(noDeps);
// Snapshots the last round hashcode for checks
int lastDepOrderSize = 0;
while (!satisfiedNotProcessed.isEmpty() || lastDepOrderSize != Objects.hash(dependencyOrder,
encounteredNotSatisfied, satisfiedNotProcessed)) {
lastDepOrderSize = Objects.hash(dependencyOrder, encounteredNotSatisfied, satisfiedNotProcessed);
// Process satisfied modules
for (ModuleMetadata node : satisfiedNotProcessed) {
dependencyOrder.add(node);
// Load modules that depend on `node`
// insert them into encountered
depGraph.predecessors(node).forEach(dependent -> {
encounteredNotSatisfied.add(dependent);
});
}
// Clear satisfiedNotProcessed, after processing
satisfiedNotProcessed.clear();
// Process encountered nodes
for (ModuleMetadata node : encounteredNotSatisfied) {
// Calculate the load-after deps that might be satisfiable
// Basically does a ID check against the available
// dependencies.
Set<ModuleDependency> satisfiableLoadAfters = getSatisfiableLoadAfters(depGraph.nodes(),
node.getLoadAfterModules());
Set<ModuleDependency> deps = Sets.union(satisfiableLoadAfters, node.getRequiredModules());
if (allDependenciesSatisified(dependencyOrder, deps)) {
satisfiedNotProcessed.add(node);
}
}
// Remove all satisfied
encounteredNotSatisfied.removeAll(satisfiedNotProcessed);
}
if (encounteredNotSatisfied.size() > 0) {
throw new IllegalStateException("Unsatisfied dependencies: " + encounteredNotSatisfied);
}
return FluentIterable.from(dependencyOrder).transform(ModuleMetadata::getId).transform(this.moduleMap::get)
.toList();
}
From source file:io.github.msdk.datamodel.impl.SimpleFeatureTable.java
/** {@inheritDoc} */ @Override// w w w . j a v a 2 s. c om public List<FeatureTableRow> getRowsInsideRange(Range<Double> rtRange, Range<Double> mzRange) { List<FeatureTableRow> result = new ArrayList<FeatureTableRow>(); for (FeatureTableRow row : featureTableRows) { ChromatographyInfo rowChromatographyInfo = row.getChromatographyInfo(); if (rtRange.contains((double) rowChromatographyInfo.getRetentionTime()) && mzRange.contains(row.getMz())) result.add(row); } return result; }
From source file:org.opentestsystem.authoring.testauth.validation.AbstractDomainValidator.java
/** * when an ItemSelectionAlgorithmParameter is defined as a numeric type (FLOAT or INTEGER), every instance * must be of that numeric type and fall within the range boundary of the ItemSelectionAlgorithmParameter MIN & MAX values *//*from w w w. j a v a 2 s.co m*/ private void rejectIfNotWithinNumericConstraints(final String fieldValue, final String parametersFieldName, final Errors errors, final ItemSelectionAlgorithmParameter parameter, final Object... errorArgs) { try { if (parameter.getItemSelectionType() == ItemSelectionType.FLOAT) { final Float floatValue = Float.parseFloat(fieldValue); final Range<Float> floatRange = buildFloatRange(parameter.getMinimumValue(), parameter.getMaximumValue()); if (floatRange != null && !floatRange.contains(floatValue)) { rejectValue(errors, "", getErrorMessageRoot() + parametersFieldName + MSG_OUT_OF_RANGE, flattenArgs(errorArgs, buildRangeConstraintString(parameter.getMinimumValue(), parameter.getMaximumValue()))); } } else { final Long longValue = Long.parseLong(fieldValue); final Range<Long> longRange = buildLongRange(parameter.getMinimumValue(), parameter.getMaximumValue()); if (longRange != null && !longRange.contains(longValue)) { rejectValue(errors, "", getErrorMessageRoot() + parametersFieldName + MSG_OUT_OF_RANGE, flattenArgs(errorArgs, buildRangeConstraintString(parameter.getMinimumValue(), parameter.getMaximumValue()))); } } } catch (final NumberFormatException e) { rejectValue(errors, "", getErrorMessageRoot() + parametersFieldName + MSG_PARSEABLE_NUMBER, errorArgs); } }
From source file:com.programmablefun.ide.editor.CodeLineStyler.java
private Range findMultiLineComment(int pos) { for (Range r : multiLineComments) { if (r.contains(pos)) { return r; }/*from w w w . ja va 2s.com*/ } return null; }