Example usage for java.util Comparator comparing

Usage

From source file:main.java.RMDupper.java

/**
 * This Method reads a SAM File and parses the input
 * Currently, only merged Reads with the "M" Flag in front are checked for Duplicates.
 * R/F Flags are simply written into output File, also other "non-flagged" ones.
 *///from  w  w  w  .ja  v a2s  .  co  m
public void readSAMFile() {
    Comparator<SAMRecord> samRecordComparatorForRecordBuffer = new SAMRecordPositionAndQualityComparator();
    Comparator<SAMRecord> samRecordComparatorForDuplicateBuffer;

    if (this.allReadsAsMerged) {
        samRecordComparatorForDuplicateBuffer = new SAMRecordQualityComparator();
    } else {
        samRecordComparatorForDuplicateBuffer = new SAMRecordQualityComparatorPreferMerged();
    }

    PriorityQueue<ImmutableTriple<Integer, Integer, SAMRecord>> recordBuffer = new PriorityQueue<ImmutableTriple<Integer, Integer, SAMRecord>>(
            1000, Comparator.comparing(ImmutableTriple<Integer, Integer, SAMRecord>::getRight,
                    samRecordComparatorForRecordBuffer));
    PriorityQueue<ImmutableTriple<Integer, Integer, SAMRecord>> duplicateBuffer = new PriorityQueue<ImmutableTriple<Integer, Integer, SAMRecord>>(
            1000, Comparator.comparing(ImmutableTriple<Integer, Integer, SAMRecord>::getRight,
                    samRecordComparatorForDuplicateBuffer.reversed()));
    Set<String> discardSet = new HashSet<String>(1000);
    String referenceName = SAMRecord.NO_ALIGNMENT_REFERENCE_NAME;

    Iterator it = inputSam.iterator();
    while (it.hasNext()) {
        SAMRecord curr = (SAMRecord) it.next();
        if (curr.getReferenceName() == SAMRecord.NO_ALIGNMENT_REFERENCE_NAME) {
            this.outputSam.addAlignment(curr);
        } else {
            if (referenceName == curr.getReferenceName()) {
                queueOrOutput(this.dupStats, this.oc, this.outputSam, this.allReadsAsMerged, recordBuffer,
                        duplicateBuffer, discardSet, curr);
            } else {
                flushQueue(this.dupStats, this.oc, this.outputSam, this.allReadsAsMerged, recordBuffer,
                        duplicateBuffer, discardSet);
                queueOrOutput(this.dupStats, this.oc, this.outputSam, this.allReadsAsMerged, recordBuffer,
                        duplicateBuffer, discardSet, curr);
                referenceName = curr.getReferenceName();
            }
        }

        this.dupStats.total++;
        if (this.dupStats.total % 100000 == 0) {
            if (!piped) {
                System.err.println("Reads treated: " + this.dupStats.total);
            }
        }
    }
    flushQueue(this.dupStats, this.oc, this.outputSam, this.allReadsAsMerged, recordBuffer, duplicateBuffer,
            discardSet);
}

From source file:org.eclipse.sw360.datahandler.common.CommonUtils.java

public static Optional<Attachment> getBestClearingReport(Release release) {
    return nullToEmptyCollection(release.getAttachments()).stream()
            .filter(att -> att.getAttachmentType() == AttachmentType.CLEARING_REPORT)
            .max(Comparator.comparing(Attachment::getCheckStatus, CHECK_STATUS_COMPARATOR));
}

From source file:com.evolveum.midpoint.prism.marshaller.PrismBeanInspector.java

@NotNull
public <T> Class<? extends T> findMatchingSubclass(Class<T> beanClass, Collection<QName> fields)
        throws SchemaException {
    SchemaRegistry schemaRegistry = prismContext.getSchemaRegistry();
    TypeDefinition typeDef = schemaRegistry.findTypeDefinitionByCompileTimeClass(beanClass,
            TypeDefinition.class);
    if (typeDef == null) {
        throw new SchemaException("No type definition for " + beanClass);
    }//  w  ww  .j a  v  a  2  s.c o m
    List<TypeDefinition> subTypes = new ArrayList<>(typeDef.getStaticSubTypes());
    subTypes.sort(Comparator.comparing(TypeDefinition::getInstantiationOrder, nullsLast(naturalOrder())));
    TypeDefinition matchingDefinition = null;
    for (TypeDefinition subType : subTypes) {
        if (matchingDefinition != null && !Objects.equals(matchingDefinition.getInstantiationOrder(),
                subType.getInstantiationOrder())) {
            break; // found something and went to lower orders -> we can stop searching
        }
        if (matches(subType, fields)) {
            if (matchingDefinition != null) {
                throw new SchemaException("Couldn't unambiguously determine a subclass for " + beanClass
                        + " instantiation (fields: " + fields + "). Candidates: " + matchingDefinition + ", "
                        + subType);
            }
            matchingDefinition = subType;
        }
    }
    if (matchingDefinition == null) {
        final int MAX = 5;
        throw new SchemaException("Couldn't find a subclass of " + beanClass + " that would contain fields "
                + fields + ". Considered " + subTypes.subList(0, Math.min(subTypes.size(), MAX))
                + (subTypes.size() >= MAX ? " (...)" : ""));
    }
    //noinspection unchecked
    Class<? extends T> compileTimeClass = (Class<? extends T>) matchingDefinition.getCompileTimeClass();
    if (compileTimeClass != null) {
        return compileTimeClass;
    } else {
        throw new SchemaException("No compile time class defined for " + matchingDefinition);
    }
}

From source file:org.kitodo.production.services.data.ProcessService.java

/**
 * Filter and sort after creation date list of process properties for
 * correction and solution messages.//from ww w .  j  a v a2 s  .com
 *
 * @return list of ProcessProperty objects
 */
public List<PropertyDTO> getSortedCorrectionSolutionMessages(ProcessDTO process) {
    List<PropertyDTO> filteredList = filterForCorrectionSolutionMessages(process.getProperties());

    if (filteredList.size() > 1) {
        filteredList.sort(Comparator.comparing(PropertyDTO::getCreationDate,
                Comparator.nullsFirst(Comparator.naturalOrder())));
    }

    return filteredList;
}

From source file:sg.ncl.MainController.java

@RequestMapping("/admin/usage")
public String adminTeamUsage(Model model, @RequestParam(value = "start", required = false) String start,
        @RequestParam(value = "end", required = false) String end,
        @RequestParam(value = "organizationType", required = false) String organizationType,
        @RequestParam(value = "team", required = false) String team,
        final RedirectAttributes redirectAttributes, HttpSession session)
        throws IOException, WebServiceRuntimeException {
    if (!validateIfAdmin(session)) {
        return NO_PERMISSION_PAGE;
    }/*from w  w w .j  a va  2s  .c  o  m*/

    DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd");
    ZonedDateTime nowDate = ZonedDateTime.now();
    String now = nowDate.format(formatter);
    if (start == null) {
        start = nowDate.with(firstDayOfMonth()).format(formatter);
    }
    if (end == null) {
        end = now;
    }
    if (now.compareTo(start) < 0 || now.compareTo(end) < 0) {
        redirectAttributes.addFlashAttribute(MESSAGE, "Period selected is beyond current date (today).");
        return REDIRECT_TEAM_USAGE;
    }

    // get list of teamids
    HttpEntity<String> request = createHttpEntityHeaderOnly();
    ResponseEntity responseEntity = restTemplate.exchange(properties.getSioTeamsUrl(), HttpMethod.GET, request,
            String.class);
    JSONArray jsonArray = new JSONArray(responseEntity.getBody().toString());

    List<Team2> searchTeams = new ArrayList<>();
    TeamManager2 teamManager2 = new TeamManager2();
    getSearchTeams(organizationType, team, jsonArray, searchTeams, teamManager2);

    if (!searchTeams.isEmpty()) {
        List<String> dates = getDates(start, end, formatter);

        Map<String, List<Long>> teamUsages = new HashMap<>();
        Long totalUsage = 0L;
        for (Team2 team2 : searchTeams) {
            try {
                List<Long> usages = new ArrayList<>();
                totalUsage += getTeamUsageStatistics(team2, start, end, request, usages);
                teamUsages.put(team2.getName(), usages);
            } catch (RestClientException rce) {
                log.warn("Error connecting to sio analytics service for team usage: {}", rce);
                redirectAttributes.addFlashAttribute(MESSAGE, ERR_SERVER_OVERLOAD);
                return REDIRECT_TEAM_USAGE;
            } catch (StartDateAfterEndDateException sde) {
                redirectAttributes.addFlashAttribute(MESSAGE, ERR_START_DATE_AFTER_END_DATE);
                return REDIRECT_TEAM_USAGE;
            }
        }
        model.addAttribute("dates", dates);
        model.addAttribute("teamUsages", teamUsages);
        model.addAttribute("totalUsage", totalUsage);
    }

    List<Team2> allTeams = new ArrayList<>(teamManager2.getTeamMap().values());
    allTeams.sort(Comparator.comparing(Team2::getName, String.CASE_INSENSITIVE_ORDER));
    model.addAttribute(ALL_TEAMS, allTeams);
    model.addAttribute("start", start);
    model.addAttribute("end", end);
    model.addAttribute("organizationType", organizationType);
    model.addAttribute("team", team);
    return "usage_statistics";
}

From source file:sg.ncl.MainController.java

/**
 * Allows admins to:/*from w ww  .  ja  va 2s.c  o  m*/
 * view reservations
 * reserve nodes
 * release nodes
 */
@GetMapping("/admin/nodesReservation")
public String adminNodesReservation(
        @ModelAttribute("reservationStatusForm") ReservationStatusForm reservationStatusForm, Model model,
        HttpSession session) {
    if (!validateIfAdmin(session)) {
        return NO_PERMISSION_PAGE;
    }

    List<Team2> allTeams = new ArrayList<>(getTeamMap().values());
    allTeams.sort(Comparator.comparing(Team2::getName, String.CASE_INSENSITIVE_ORDER));
    model.addAttribute(ALL_TEAMS, allTeams);
    model.addAttribute(RESERVATION_STATUS_FORM, reservationStatusForm);

    return "node_reservation";
}

From source file:sg.ncl.MainController.java

@PostMapping("/admin/nodesReservation")
public String adminNodesReservation(
        @ModelAttribute("reservationStatusForm") ReservationStatusForm reservationStatusForm,
        BindingResult bindingResult, RedirectAttributes redirectAttributes, Model model) {
    List<Team2> allTeams = new ArrayList<>(getTeamMap().values());
    allTeams.sort(Comparator.comparing(Team2::getName, String.CASE_INSENSITIVE_ORDER));
    model.addAttribute(ALL_TEAMS, allTeams);

    // sanitization
    if (bindingResult.hasErrors()) {
        model.addAttribute(ALL_TEAMS, allTeams);
        model.addAttribute(RESERVATION_STATUS_FORM, reservationStatusForm);
        model.addAttribute(STATUS, NODES_RESERVATION_FAIL);
        model.addAttribute(MESSAGE, "form errors");
        return "node_reservation";
    }/*from  w w w.  j a  v a 2s. c  o  m*/

    switch (reservationStatusForm.getAction()) {
    case "release":
        releaseNodes(reservationStatusForm, redirectAttributes);
        break;
    case "reserve":
        reserveNodes(reservationStatusForm, redirectAttributes);
        break;
    case "check":
        checkReservation(reservationStatusForm, redirectAttributes);
        break;
    default:
        // error
        redirectAttributes.addFlashAttribute(STATUS, NODES_RESERVATION_FAIL);
        redirectAttributes.addFlashAttribute(MESSAGE, ERR_SERVER_OVERLOAD);
        break;
    }

    redirectAttributes.addFlashAttribute(RESERVATION_STATUS_FORM, reservationStatusForm);
    redirectAttributes.addFlashAttribute(ALL_TEAMS, allTeams);

    return "redirect:/admin/nodesReservation";
}

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