Java Code Examples for org.apache.commons.compress.utils.Lists#newArrayList()

private List<String> getLogs(JSONObject logInfo) {
    List<String> logs = Lists.newArrayList();
    if (logInfo.has("log")) {
        try {
            JSONArray logArray = logInfo.getJSONArray("log");

            for (int i=0; i<logArray.length(); i++) {
                logs.add(logArray.getString(i));
            }

        } catch (JSONException e) {
            e.printStackTrace();
        }
    }
    return logs;
}
 

/**
 * 准备(界面字段等)
 */
@Override
public void prepare() {
    templateId = Integer.parseInt(TxYunMsgForm.getInstance().getMsgTemplateIdTextField().getText());

    if (TxYunMsgForm.getInstance().getTemplateMsgDataTable().getModel().getRowCount() == 0) {
        TxYunMsgForm.initTemplateDataTable();
    }

    DefaultTableModel tableModel = (DefaultTableModel) TxYunMsgForm.getInstance().getTemplateMsgDataTable().getModel();
    int rowCount = tableModel.getRowCount();
    paramList = Lists.newArrayList();
    for (int i = 0; i < rowCount; i++) {
        String value = ((String) tableModel.getValueAt(i, 1));
        paramList.add(value);
    }
}
 

/**
 * 准备(界面字段等)
 */
@Override
public void prepare() {
    templateId = MaTemplateMsgForm.getInstance().getMsgTemplateIdTextField().getText().trim();
    templateUrl = MaTemplateMsgForm.getInstance().getMsgTemplateUrlTextField().getText().trim();
    templateKeyWord = MaTemplateMsgForm.getInstance().getMsgTemplateKeyWordTextField().getText().trim() + ".DATA";

    if (MaTemplateMsgForm.getInstance().getTemplateMsgDataTable().getModel().getRowCount() == 0) {
        MaTemplateMsgForm.initTemplateDataTable();
    }

    DefaultTableModel tableModel = (DefaultTableModel) MaTemplateMsgForm.getInstance().getTemplateMsgDataTable().getModel();
    int rowCount = tableModel.getRowCount();
    TemplateData templateData;
    templateDataList = Lists.newArrayList();
    for (int i = 0; i < rowCount; i++) {
        String name = ((String) tableModel.getValueAt(i, 0)).trim();
        String value = ((String) tableModel.getValueAt(i, 1)).trim();
        String color = ((String) tableModel.getValueAt(i, 2)).trim();
        templateData = new TemplateData();
        templateData.setName(name);
        templateData.setValue(value);
        templateData.setColor(color);
        templateDataList.add(templateData);
    }
}
 

public static void setupNew3DVisualizer(final RawDataFile dataFile, final Range<Double> mzRange,
    final Range<Double> rtRange, final Feature featureToShow) {

  final ParameterSet myParameters =
      MZmineCore.getConfiguration().getModuleParameters(Fx3DVisualizerModule.class);
  final Fx3DVisualizerModule myInstance =
      MZmineCore.getModuleInstance(Fx3DVisualizerModule.class);
  myParameters.getParameter(Fx3DVisualizerParameters.dataFiles)
      .setValue(RawDataFilesSelectionType.SPECIFIC_FILES, new RawDataFile[] {dataFile});
  myParameters.getParameter(Fx3DVisualizerParameters.scanSelection)
      .setValue(new ScanSelection(rtRange, 1));
  myParameters.getParameter(Fx3DVisualizerParameters.mzRange).setValue(mzRange);
  
  List<FeatureSelection> featuresList = Lists.newArrayList();
  if (featureToShow != null) {
    FeatureSelection selectedFeature = new FeatureSelection(null, featureToShow, null, null);
    featuresList.add(selectedFeature);
  }
  
  myParameters.getParameter(Fx3DVisualizerParameters.features).setValue(featuresList);
  if (myParameters.showSetupDialog(MZmineCore.getDesktop().getMainWindow(),
      true) == ExitCode.OK) {
    myInstance.runModule(MZmineCore.getProjectManager().getCurrentProject(),
        myParameters.cloneParameterSet(), new ArrayList<Task>());
  }
}
 

ColumnRowType buildColumnRowType() {
    OLAPRel olapChild = (OLAPRel) getInput(0);
    ColumnRowType inputColumnRowType = olapChild.getColumnRowType();

    List<TblColRef> columns = new ArrayList<>();
    // the input col always be collected by left
    columns.addAll(inputColumnRowType.getAllColumns());

    // add window aggregate calls column
    for (Group group : groups) {
        List<TupleExpression> sourceColOuter = Lists.newArrayList();
        group.keys.asSet().stream().map(inputColumnRowType::getTupleExpressionByIndex).forEach(sourceColOuter::add);
        group.orderKeys.getFieldCollations().stream().map(RelFieldCollation::getFieldIndex)
                .map(inputColumnRowType::getTupleExpressionByIndex).forEach(sourceColOuter::add);
        for (AggregateCall aggrCall : group.getAggregateCalls(this)) {
            TblColRef aggrCallCol = TblColRef.newInnerColumn(aggrCall.getName(),
                    TblColRef.InnerDataTypeEnum.LITERAL);
            List<TupleExpression> sourceColInner = Lists.newArrayList(sourceColOuter.iterator());
            aggrCall.getArgList().stream().filter(i -> i < inputColumnRowType.size())
                    .map(inputColumnRowType::getTupleExpressionByIndex).forEach(sourceColInner::add);
            aggrCallCol.setSubTupleExps(sourceColInner);
            columns.add(aggrCallCol);
        }
    }
    return new ColumnRowType(columns);
}
 

/**
 * 准备(界面字段等)
 */
@Override
public void prepare() {
    templateId = UpYunMsgForm.getInstance().getMsgTemplateIdTextField().getText();

    if (UpYunMsgForm.getInstance().getTemplateMsgDataTable().getModel().getRowCount() == 0) {
        UpYunMsgForm.initTemplateDataTable();
    }

    DefaultTableModel tableModel = (DefaultTableModel) UpYunMsgForm.getInstance().getTemplateMsgDataTable().getModel();
    int rowCount = tableModel.getRowCount();
    paramList = Lists.newArrayList();
    for (int i = 0; i < rowCount; i++) {
        String value = ((String) tableModel.getValueAt(i, 1));
        paramList.add(value);
    }
}
 

/**
 * 准备(界面字段等)
 */
@Override
public void prepare() {
    templateId = AliYunMsgForm.getInstance().getMsgTemplateIdTextField().getText();

    if (AliYunMsgForm.getInstance().getTemplateMsgDataTable().getModel().getRowCount() == 0) {
        AliYunMsgForm.initTemplateDataTable();
    }

    DefaultTableModel tableModel = (DefaultTableModel) AliYunMsgForm.getInstance().getTemplateMsgDataTable().getModel();
    int rowCount = tableModel.getRowCount();
    TemplateData templateData;
    templateDataList = Lists.newArrayList();
    for (int i = 0; i < rowCount; i++) {
        String name = ((String) tableModel.getValueAt(i, 0)).trim();
        String value = ((String) tableModel.getValueAt(i, 1)).trim();
        templateData = new TemplateData();
        templateData.setName(name);
        templateData.setValue(value);
        templateDataList.add(templateData);
    }

}
 

@Override
public SendResult send(String[] msgData) {
    SendResult sendResult = new SendResult();

    try {
        MailMsg mailMsg = mailMsgMaker.makeMsg(msgData);
        List<String> tos = Lists.newArrayList();
        tos.add(msgData[0]);
        if (PushControl.dryRun) {
            sendResult.setSuccess(true);
            return sendResult;
        } else {
            List<String> ccList = null;
            if (StringUtils.isNotBlank(mailMsg.getMailCc())) {
                ccList = Lists.newArrayList();
                ccList.add(mailMsg.getMailCc());
            }
            if (StringUtils.isEmpty(mailMsg.getMailFiles())) {
                MailUtil.send(mailAccount, tos, ccList, null, mailMsg.getMailTitle(), mailMsg.getMailContent(), true);
            } else {
                MailUtil.send(mailAccount, tos, ccList, null, mailMsg.getMailTitle(), mailMsg.getMailContent(), true, FileUtil.file(mailMsg.getMailFiles()));
            }
            sendResult.setSuccess(true);
        }
    } catch (Exception e) {
        sendResult.setSuccess(false);
        sendResult.setInfo(e.getMessage());
        log.error(ExceptionUtils.getStackTrace(e));
    }

    return sendResult;
}
 

private static List<TransExonRef> parseTransExonRefs(final String data)
{
    List<TransExonRef> transExonRefs = Lists.newArrayList();

    for(String ref : data.split(ITEM_DELIM, -1))
    {
        String[] items = ref.split(":");
        if(items.length != 4)
            continue;

        transExonRefs.add(new TransExonRef(items[0], Integer.parseInt(items[1]), items[2], Integer.parseInt(items[3])));
    }

    return transExonRefs;
}
 

public String[] getBlockLocations(long start, long end) {
  List<String> hosts = Lists.newArrayList();
  try {
    for (BlockLocation location : fs.getFileBlockLocations(path, start, end)) {
      Collections.addAll(hosts, location.getHosts());
    }

    return hosts.toArray(NO_LOCATION_PREFERENCE);

  } catch (IOException e) {
    throw new RuntimeIOException(e, "Failed to get block locations for path: %s", path);
  }
}
 

@Override
public SingleData<ConnectionsData> serialize(File file) throws IOException {
    ConnectionsDataSet dataSet = reader.read(file);

    final Map<Date, ConnectionsData> stats = dataSet.getSummary();
    final List<Date> periods = Lists.newArrayList(stats.keySet().iterator());
    final List<ConnectionsData> values = Lists.newArrayList(stats.values().iterator());

    SingleData<ConnectionsData> ret = new SingleData<>();

    ret.setPeriods(periods);
    ret.setValues(values);

    return ret;
}
 

/**
 * Example command line: {@code tf delete dir/file.txt}
 * <p>
 * Example stdout:<br>
 * <pre>{@code dir:
 * file.txt}</pre>
 * <p>
 * Example stderr:<br>
 * <pre>{@code The item C:\FullPath\dir\file.txt could not be found in your workspace, or you do not have permission to access it.}</pre>
 */
@Override
public TfvcCheckoutResult parseOutput(String stdout, String stderr) {
    List<TfsLocalPath> checkedOutFiles = Lists.newArrayList();
    List<TfsLocalPath> notFoundFiles = Lists.newArrayList();
    List<String> errorMessages = Lists.newArrayList();

    parseStdErr(stderr, notFoundFiles, errorMessages);
    parseStdOut(stdout, checkedOutFiles);

    return new TfvcCheckoutResult(checkedOutFiles, notFoundFiles, errorMessages);
}
 

public CfSampleData(final String sampleId)
{
    SampleId = sampleId;
    Chains = Maps.newHashMap();
    CfSvList = Lists.newArrayList();
    UnchainedSvList = Lists.newArrayList();
    ClusterChainOverlaps = Lists.newArrayList();
    SvProximityDistance = Maps.newHashMap();
}
 

/**
 * @see BaseService#findAllById(Iterable)
 */
@Override
public List<T> findAllById(Iterable<K> ids) {
    return Lists.newArrayList(this.repository.findAllById(ids).iterator());
}
 

public static Map<String,List<ReadRecord>> loadChimericReads(final String inputFile)
{
    Map<String,List<ReadRecord>> readsMap = Maps.newHashMap();

    if(!Files.exists(Paths.get(inputFile)))
    {
        ISF_LOGGER.error("invalid chimeric reads file: {}", inputFile);
        return readsMap;
    }

    try
    {
        BufferedReader fileReader = new BufferedReader(new FileReader(inputFile));

        // skip field names
        String line = fileReader.readLine();

        if (line == null)
        {
            ISF_LOGGER.error("empty chimeric reads file: {}", inputFile);
            return readsMap;
        }

        final Map<String,Integer> fieldsMap  = createFieldsIndexMap(line, DELIMITER);
        String currentReadId = "";
        List<ReadRecord> currentReads = null;

        int readId = fieldsMap.get("ReadId");
        int chr = fieldsMap.get("Chromosome");
        int posStart = fieldsMap.get("PosStart");
        int posEnd = fieldsMap.get("PosEnd");
        int cigar = fieldsMap.get("Cigar");
        int insertSize = fieldsMap.get("InsertSize");
        int flags = fieldsMap.get("Flags");
        int suppAlgn = fieldsMap.get("SuppAlign");
        int bases = fieldsMap.get("Bases");
        int mateChr = fieldsMap.get("MateChr");
        int matePosStart = fieldsMap.get("MatePosStart");
        int geneSet = fieldsMap.get("GeneSet");
        int bestMatch = fieldsMap.get("BestMatch");
        int transExonData = fieldsMap.get("TransExonData");

        while ((line = fileReader.readLine()) != null)
        {
            String[] items = line.split(DELIMITER, -1);

            ReadRecord read = new ReadRecord(
                    items[readId],
                    items[chr],
                    Integer.parseInt(items[posStart]),
                    Integer.parseInt(items[posEnd]),
                    items[bases],
                    cigarFromStr((items[cigar])),
                    Integer.parseInt(items[insertSize]),
                    Integer.parseInt(items[flags]),
                    items[mateChr],
                    Integer.parseInt(items[matePosStart]));

            String saData = items[suppAlgn];

            if(!saData.equals("NONE"))
                read.setSuppAlignment(saData);

            read.setGeneCollection(SE_START,Integer.parseInt(items[geneSet]), true);
            read.setGeneCollection(SE_END,Integer.parseInt(items[geneSet]), true);

            RegionMatchType matchType = RegionMatchType.valueOf(items[bestMatch]);

            if(matchType != NONE)
            {
                List<TransExonRef> transExonRefs = parseTransExonRefs(items[transExonData]);
                read.getTransExonRefs().put(matchType, transExonRefs);
            }

            if(!read.Id.equals(currentReadId))
            {
                currentReadId = read.Id;
                currentReads = Lists.newArrayList();
                readsMap.put(read.Id, currentReads);
            }

            currentReads.add(read);
        }

        ISF_LOGGER.info("loaded {} chimeric fragment reads from file({})", readsMap.size(), inputFile);
    }
    catch (IOException e)
    {
        ISF_LOGGER.warn("failed to load chimeric reads file({}): {}", inputFile, e.toString());
    }

    return readsMap;
}
 

@Override
public List collectToList(Object table) throws Exception {
  return Lists.newArrayList(((Table) table).execute().collect());
}
 

@NotNull
private static List<String> extractCandidateAlternativeCodonsFromMessageField(@NotNull String messageField) {
    String fieldValue = extractOptionalValueFromMessageField(messageField, "candidate_alternative_sequence");

    return fieldValue != null ? Arrays.asList(fieldValue.split("/")) : Lists.newArrayList();
}
 

private List<Entry<String, JsonNode>> getJsonEntries(String json) throws Exception {
    JsonNode jsonNode = JSONTestHelper.getMapper().readValue(json, JsonNode.class);
    return Lists.newArrayList(jsonNode.fields());
}
 

public SendResult sendRobotMsg(String[] msgData) {
    SendResult sendResult = new SendResult();

    try {
        DingTalkClient client = getRobotClient();
        OapiRobotSendRequest request2 = new OapiRobotSendRequest();
        DingMsg dingMsg = dingMsgMaker.makeMsg(msgData);
        if ("文本消息".equals(DingMsgMaker.msgType)) {
            request2.setMsgtype("text");
            OapiRobotSendRequest.Text text = new OapiRobotSendRequest.Text();
            text.setContent(dingMsg.getContent());
            request2.setText(text);
            OapiRobotSendRequest.At at = new OapiRobotSendRequest.At();
            if (msgData != null && StringUtils.isNotBlank(msgData[0])) {
                List<String> mobiles = Lists.newArrayList();
                mobiles.add(msgData[0]);
                at.setAtMobiles(mobiles);
            } else {
                at.setIsAtAll("true");
            }
            request2.setAt(at);
        } else if ("链接消息".equals(DingMsgMaker.msgType)) {
            request2.setMsgtype("link");
            OapiRobotSendRequest.Link link = new OapiRobotSendRequest.Link();
            link.setMessageUrl(dingMsg.getUrl());
            link.setPicUrl(dingMsg.getPicUrl());
            link.setTitle(dingMsg.getTitle());
            link.setText(dingMsg.getContent());
            request2.setLink(link);
        } else if ("markdown消息".equals(DingMsgMaker.msgType)) {
            request2.setMsgtype("markdown");
            OapiRobotSendRequest.Markdown markdown = new OapiRobotSendRequest.Markdown();
            markdown.setTitle(dingMsg.getTitle());
            markdown.setText(dingMsg.getContent());
            request2.setMarkdown(markdown);
        } else if ("卡片消息".equals(DingMsgMaker.msgType)) {
            request2.setMsgtype("actionCard");
            OapiRobotSendRequest.Actioncard actionCard = new OapiRobotSendRequest.Actioncard();
            actionCard.setTitle(dingMsg.getTitle());
            actionCard.setText(dingMsg.getContent());
            actionCard.setSingleTitle(dingMsg.getBtnTxt());
            actionCard.setSingleURL(dingMsg.getBtnUrl());
            request2.setActionCard(actionCard);
        }

        if (PushControl.dryRun) {
            sendResult.setSuccess(true);
            return sendResult;
        } else {
            OapiRobotSendResponse response2 = client.execute(request2);
            if (response2.getErrcode() != 0) {
                sendResult.setSuccess(false);
                sendResult.setInfo(response2.getErrmsg());
                log.error(response2.getErrmsg());
                return sendResult;
            }
        }
    } catch (Exception e) {
        sendResult.setSuccess(false);
        sendResult.setInfo(e.getMessage());
        log.error(e.toString());
        return sendResult;
    }

    sendResult.setSuccess(true);
    return sendResult;
}
 

@NotNull
public static List<VariantHotspot> moveLeft(boolean delete, int position, int indelLength, int readIndex, byte[] readBases,
        int refIndex, byte[] refBases) {
    int absIndelLength = Math.abs(indelLength);
    int minReadIndex = Math.max(0, readIndex - absIndelLength);
    int maxRefIndex = Math.max(0, refIndex - absIndelLength);

    int indelIndex = readIndex + absIndelLength - 1;

    int sameBases = 0;
    while (refIndex >= maxRefIndex && indelIndex >= minReadIndex && readBases[indelIndex] == refBases[refIndex]) {
        sameBases++;
        indelIndex--;
        refIndex--;
    }

    int snvLength = 0;
    while (refIndex >= maxRefIndex && indelIndex >= minReadIndex && readBases[indelIndex] != refBases[refIndex]) {
        snvLength++;
        indelIndex--;
        refIndex--;
    }

    int sameBases2 = 0;
    while (refIndex >= maxRefIndex && indelIndex >= minReadIndex && readBases[indelIndex] == refBases[refIndex]) {
        sameBases2++;
        indelIndex--;
        refIndex--;
    }

    if (sameBases == 0 || snvLength == 0 || sameBases2 == 0 || snvLength > MAX_MNV_LENGTH) {
        return Collections.emptyList();
    }

    int indelShift = sameBases + snvLength + sameBases2;

    final List<VariantHotspot> result = Lists.newArrayList();

    final String indelRef = new String(refBases, refIndex, 1);
    final String indelAlt = new String(readBases, readIndex - indelShift, absIndelLength);

    VariantHotspot indel = ImmutableVariantHotspotImpl.builder()
            .chromosome("1")
            .position(position - indelShift)
            .ref(delete ? indelAlt : indelRef)
            .alt(delete ? indelRef : indelAlt)
            .build();
    result.add(indel);

    final String snvRef = new String(refBases, refIndex + sameBases2 + 1, snvLength);
    final String snvAlt = new String(readBases, refIndex + sameBases2 + 1 + absIndelLength - 1, snvLength);

    VariantHotspot snv = ImmutableVariantHotspotImpl.builder()
            .chromosome("1")
            .position(position - indelShift + sameBases2 + 1 + (delete ? absIndelLength - 1 : 0))
            .ref(delete ? snvAlt : snvRef)
            .alt(delete ? snvRef : snvAlt)
            .build();
    result.add(snv);

    return result;
}