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Java Pair.getFirst方法代码示例

本文整理汇总了Java中jloda.util.Pair.getFirst方法的典型用法代码示例。如果您正苦于以下问题：Java Pair.getFirst方法的具体用法？Java Pair.getFirst怎么用？Java Pair.getFirst使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类jloda.util.Pair的用法示例。


在下文中一共展示了Pair.getFirst方法的12个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Java代码示例。

示例1: hasNext

import jloda.util.Pair; //导入方法依赖的package包/类
/**
 * Returns <tt>true</tt> if the iteration has more elements. (In other
 * words, returns <tt>true</tt> if <tt>next</tt> would return an element
 * rather than throwing an exception.)
 *
 * @return <tt>true</tt> if the getLetterCodeIterator has more elements.
 */
public boolean hasNext() {
    if (error || currentClass == null)
        return false;
    if (currentCount < currentClass.getFirst())
        return true;
    currentClass = null;
    while (classes.size() > 0) {
        currentCount = 0;
        Pair<Integer, Long> next = classes.remove(0);
        if (next != null && next.getFirst() > 0 && next.getSecond() >= 0) {
            try {
                classDumpReader.seek(next.getSecond());
            } catch (IOException e) {
                Basic.caught(e);
                return false;
            }
            currentClass = next;
            return true;
        }
    }
    return false;
}
开发者ID:danielhuson，项目名称:megan-ce，代码行数:30，代码来源:ReadBlockIteratorRMA2.java

示例2: getSum

import jloda.util.Pair; //导入方法依赖的package包/类
/**
 * get the number associated with a key
 *
 * @param key
 * @return number
 */
public int getSum(Integer key) {
    Pair<Integer, Long> pair = id2SumAndPos.get(key);
    if (pair == null)
        return 0;
    else
        return pair.getFirst();
}
开发者ID:danielhuson，项目名称:megan-ce，代码行数:14，代码来源:ClassificationBlockRMA2.java

示例3: ReadBlockIteratorRMA2

import jloda.util.Pair; //导入方法依赖的package包/类
/**
 * constructor
 *
 * @param wantReadText
 * @param wantMatchData
 * @param wantMatchText
 * @param minScore
 * @param file
 * @throws java.io.IOException
 */
public ReadBlockIteratorRMA2(String classification, Collection<Integer> classIds, boolean wantReadText, boolean wantMatchData, boolean wantMatchText, float minScore, float maxExpected, File file) throws IOException {
    this.wantReadText = wantReadText;
    this.wantMatchData = wantMatchData;
    this.wantMatchText = wantMatchText;
    this.minScore = minScore;
    this.maxExpected = maxExpected;

    RMA2File rma2File = new RMA2File(file);
    dataIndexReader = rma2File.getDataIndexReader();
    InfoSection infoSection = rma2File.loadInfoSection();
    rma2Formatter = infoSection.getRMA2Formatter();

    if (wantReadText || wantMatchText)
        textStorageReader = new TextStorageReader(infoSection.getLocationManager(file));
    else
        textStorageReader = null;

    Map<Integer, Pair<Integer, Long>> map = ClassificationBlockRMA2.getCountAndPos(rma2File, classification);
    for (Integer classId : classIds) {
        Pair<Integer, Long> pair = map.get(classId);
        if (pair != null && pair.getSecond() >= 0) {
            classes.add(pair);
            totalReads += pair.getFirst();
        }
    }

    // if(pair!=null)
    //     System.err.println("classId: "+classId+" size: "+pair.getFirst()+" dumpPos: "+pair.getSecond());

    if (totalReads > 0) {
        currentClass = classes.remove(0);
        currentCount = 0;
        classDumpReader = rma2File.getClassificationDumpReader(classification);
        classDumpReader.seek(currentClass.getSecond());
    } else
        classDumpReader = null;
}
开发者ID:danielhuson，项目名称:megan-ce，代码行数:48，代码来源:ReadBlockIteratorRMA2.java

示例4: ensureArray

import jloda.util.Pair; //导入方法依赖的package包/类
private void ensureArray() {
    if (array == null) {
        synchronized (values) {
            if (array == null) {
                array = new double[values.size()];
                int i = 0;
                for (Pair<Double, String> pair : values) {
                    array[i++] = pair.getFirst();
                }
            }
        }
    }
}
开发者ID:danielhuson，项目名称:megan-ce，代码行数:14，代码来源:WhiskerData.java

示例5: read

import jloda.util.Pair; //导入方法依赖的package包/类
@Override
public void read(IInputReader reader, long startPos) throws IOException {
    reader.seek(startPos);
    setFormatDef(reader.readString());
    FormatDefinition formatDefinition = FormatDefinition.fromString(getFormatDef());
    for (Pair<String, FormatDefinition.Type> pair : formatDefinition.getList()) {
        switch (pair.getFirst()) {
            case "TotalReads":
                setNumberOfReads(reader.readLong());
                break;
            case "TotalMatches":
                setNumberOfMatches(reader.readLong());
                break;
            case "MaxMatchesPerRead":
                setMaxMatchesPerRead(reader.readInt());
                break;
            case "UseKegg":
                setUseKegg(reader.readInt() != 0);
                break;
            case "UseSeed":
                setUseSeed(reader.readInt() != 0);
                break;
            case "UseCog":
                setUseCog(reader.readInt() != 0);
                break;
            case "UsePfam":
                setUsePfam(reader.readInt() != 0);
                break;
            case "ReadFormat":
                setReadFormatDef(reader.readString());
                break;
            case "MatchFormat":
                setMatchFormatDef(reader.readString());
                break;
        }
    }
}
开发者ID:danielhuson，项目名称:megan-ce，代码行数:38，代码来源:MatchFooterRMA3.java

示例6: write

import jloda.util.Pair; //导入方法依赖的package包/类
@Override
public void write(IOutputWriter writer) throws IOException {
    writer.writeString(getFormatDef());
    FormatDefinition formatDefinition = FormatDefinition.fromString(getFormatDef());
    formatDefinition.startWrite();
    for (Pair<String, FormatDefinition.Type> pair : formatDefinition.getList()) {
        switch (pair.getFirst()) {
            case "TotalReads":
                formatDefinition.write(writer, "TotalReads", getNumberOfReads());
                break;
            case "TotalMatches":
                formatDefinition.write(writer, "TotalMatches", getNumberOfMatches());
                break;
            case "MaxMatchesPerRead":
                formatDefinition.write(writer, "MaxMatchesPerRead", getMaxMatchesPerRead());
                break;
            case "UseKegg":
                formatDefinition.write(writer, "UseKegg", isUseKegg() ? 1 : 0);
                break;
            case "UseSeed":
                formatDefinition.write(writer, "UseSeed", isUseSeed() ? 1 : 0);
                break;
            case "UseCog":
                formatDefinition.write(writer, "UseCog", isUseCog() ? 1 : 0);
                break;
            case "UsePfam":
                formatDefinition.write(writer, "UsePfam", isUsePfam() ? 1 : 0);
                break;
            case "ReadFormat":
                formatDefinition.write(writer, "ReadFormat", getReadFormatDef());
                break;
            case "MatchFormat":
                formatDefinition.write(writer, "MatchFormat", getMatchFormatDef());
                break;
        }
    }
    formatDefinition.finishWrite();
}
开发者ID:danielhuson，项目名称:megan-ce，代码行数:39，代码来源:MatchFooterRMA3.java

示例7: processAlignment

import jloda.util.Pair; //导入方法依赖的package包/类
/**
 * compute gap columns for alignment
 *
 * @param alignment
 */
public void processAlignment(Alignment alignment) {
    clear();

    if (alignment != null) {
        LinkedList<Pair<Integer, Integer>> events = new LinkedList<>();
        for (int row = 0; row < alignment.getNumberOfSequences(); row++) {
            Lane lane = alignment.getLane(row);
            Pair<Integer, Integer> startEvent = new Pair<>(lane.getFirstNonGapPosition(), -1);
            events.add(startEvent);
            Pair<Integer, Integer> endEvent = new Pair<>(lane.getLastNonGapPosition(), 1);
            events.add(endEvent);
        }
        Pair<Integer, Integer>[] array = (Pair<Integer, Integer>[]) events.toArray(new Pair[events.size()]);
        Arrays.sort(array);

        int lastStart = 0;
        int coverage = 0;
        for (Pair<Integer, Integer> event : array) {
            if (event.getSecond() == -1) // start
            {
                if (coverage == 0) {
                    if (event.getFirst() - 1 >= 0 && lastStart != -1) {
                        origGapColumns.add(new Pair<>(lastStart, event.getFirst() - 1));
                        orig2jump.put(lastStart, event.getFirst() - lastStart);
                        lastStart = -1;
                    }
                }
                coverage++;
            } else if (event.getSecond() == 1) // end of an interval
            {
                coverage--;
                if (coverage == 0)
                    lastStart = event.getFirst();
            }
        }
        if (lastStart != -1 && lastStart < alignment.getLength()) {
            origGapColumns.add(new Pair<>(lastStart, alignment.getLength()));
            orig2jump.put(lastStart, alignment.getLength() - lastStart);
        }

        originalColumns = alignment.getLength();

        for (Pair<Integer, Integer> col : origGapColumns) {
            layout2jump.put(col.getFirst() - jumped, orig2jump.get(col.getFirst()));
            jumped += orig2jump.get(col.getFirst());
        }

        /*
        for (Pair<Integer, Integer> col : origGapColumns) {
            System.err.println("Original gap column: " + col);
            System.err.println("jump: " + orig2jump.get(col.getFirst()));
        }
        for (Pair<Integer, Integer> col : layoutGapColumns) {
            System.err.println("Layout gap column: " + col);
            System.err.println("jump: " + layout2jump.get(col.getFirst()));
        }
        System.err.println("Original columns: " + getLastOriginalColumn());
        System.err.println("Layout columns:    " + getLastLayoutColumn());
        */
    }
}
开发者ID:danielhuson，项目名称:megan-ce，代码行数:67，代码来源:GapColumnContractor.java

示例8: getPathAndPercent

import jloda.util.Pair; //导入方法依赖的package包/类
/**
 * report the taxonomic path and percent
 *
 * @param readBlock
 * @param activeMatchesForTaxa
 * @param showTaxonIds
 * @param showRank
 * @param useOfficialRanksOnly
 * @throws IOException
 */
public static String getPathAndPercent(IReadBlock readBlock, BitSet activeMatchesForTaxa, boolean showTaxonIds, boolean showRank, boolean useOfficialRanksOnly) {
    final StringBuilder buf = new StringBuilder();
    final List<Pair<Integer, Float>> path = TaxonPathAssignment.computeTaxPath(readBlock, activeMatchesForTaxa);

    final String expectedPath = "dpcofgs";
    int expectedIndex = 0;

    for (Pair<Integer, Float> pair : path) {
        final Integer taxId = pair.getFirst();
        final String taxonName = (showTaxonIds ? "" + taxId : TaxonomyData.getName2IdMap().get(taxId)).replaceAll(";", "\\;");

        if (taxonName.equals("root"))
            continue;

        final int rank = TaxonomyData.getTaxonomicRank(taxId);

        String rankName;
        if (rank != 0) {
            rankName = TaxonomicLevels.getName(rank);
            if (rankName == null)
                rankName = "?";
        } else {
            rankName = "?";
        }
        if (useOfficialRanksOnly && rankName.equals("?"))
            continue;

        if (showRank && !rankName.equals("?")) {
            char letter = Character.toLowerCase(rankName.charAt(0));
            if (rank == 127) // domain
                letter = 'd';

            if (useOfficialRanksOnly) {
                while (expectedIndex < expectedPath.length() && letter != expectedPath.charAt(expectedIndex)) {
                    buf.append(String.format("%c__unknown; %d;", expectedPath.charAt(expectedIndex), (int) (float) pair.getSecond()));
                    expectedIndex++;
                }
                expectedIndex++;
            }

            buf.append(String.format("%c__%s; %d;", letter, taxonName, (int) (float) pair.getSecond()));

        } else
            buf.append(" ").append(taxonName).append("; ").append((int) (float) pair.getSecond()).append(";");
    }
    return buf.toString();
}
开发者ID:danielhuson，项目名称:megan-ce，代码行数:58，代码来源:TaxonPathAssignment.java

示例9: read

import jloda.util.Pair; //导入方法依赖的package包/类
@Override
public void read(IInputReader reader, long startPos) throws IOException {
    reader.seek(startPos);
    setFormatDef(reader.readString());

    doKegg = doSeed = doCog = doPfam = false;

    FormatDefinition formatDefinition = FormatDefinition.fromString(getFormatDef());
    for (Pair<String, FormatDefinition.Type> pair : formatDefinition.getList()) {
        {
            switch (pair.getFirst()) {
                case "ClassificationBlockFormat":
                    setClassificationBlockFormat(reader.readString());
                    break;
                case "TaxStart":
                    setStart(ClassificationType.Taxonomy, reader.readLong());
                    break;
                case "TaxEnd":
                    setEnd(ClassificationType.Taxonomy, reader.readLong());
                    break;
                case "KeggStart":
                    setStart(ClassificationType.KEGG, reader.readLong());
                    doKegg = true;
                    break;
                case "KeggEnd":
                    setEnd(ClassificationType.KEGG, reader.readLong());
                    break;
                case "SeedStart":
                    setStart(ClassificationType.SEED, reader.readLong());
                    doSeed = true;
                    break;
                case "SeedEnd":
                    setEnd(ClassificationType.SEED, reader.readLong());
                    break;
                case "CogStart":
                    setStart(ClassificationType.COG, reader.readLong());
                    doCog = true;
                    break;
                case "CogEnd":
                    setEnd(ClassificationType.COG, reader.readLong());
                    break;
                case "PfamStart":
                    setStart(ClassificationType.PFAM, reader.readLong());
                    doPfam = true;
                    break;
                case "PfamEnd":
                    setEnd(ClassificationType.PFAM, reader.readLong());
                    break;
            }
        }
    }
}
开发者ID:danielhuson，项目名称:megan-ce，代码行数:53，代码来源:ClassificationsFooterRMA3.java

示例10: write

import jloda.util.Pair; //导入方法依赖的package包/类
@Override
public void write(IOutputWriter writer) throws IOException {
    writer.writeString(getFormatDef());

    FormatDefinition formatDefinition = FormatDefinition.fromString(getFormatDef());
    formatDefinition.startWrite();
    for (Pair<String, FormatDefinition.Type> pair : formatDefinition.getList()) {
        {
            switch (pair.getFirst()) {
                case "ClassificationBlockFormat":
                    formatDefinition.write(writer, "ClassificationBlockFormat", getClassificationBlockFormat());
                    break;
                case "TaxStart":
                    formatDefinition.write(writer, "TaxStart", getStart(ClassificationType.Taxonomy));
                    break;
                case "TaxEnd":
                    formatDefinition.write(writer, "TaxEnd", getEnd(ClassificationType.Taxonomy));
                    break;
                case "KeggStart":
                    formatDefinition.write(writer, "KeggStart", getStart(ClassificationType.KEGG));
                    break;
                case "KeggEnd":
                    formatDefinition.write(writer, "KeggEnd", getEnd(ClassificationType.KEGG));
                    break;
                case "SeedStart":
                    formatDefinition.write(writer, "SeedStart", getStart(ClassificationType.SEED));
                    break;
                case "SeedEnd":
                    formatDefinition.write(writer, "SeedEnd", getEnd(ClassificationType.SEED));
                    break;
                case "CogStart":
                    formatDefinition.write(writer, "CogStart", getStart(ClassificationType.COG));
                    break;
                case "CogEnd":
                    formatDefinition.write(writer, "CogEnd", getEnd(ClassificationType.COG));
                    break;
                case "PfamStart":
                    formatDefinition.write(writer, "PfamStart", getStart(ClassificationType.PFAM));
                    break;
                case "PfamEnd":
                    formatDefinition.write(writer, "PfamEnd", getEnd(ClassificationType.PFAM));
                    break;
            }
        }
    }
    formatDefinition.finishWrite();
}
开发者ID:danielhuson，项目名称:megan-ce，代码行数:48，代码来源:ClassificationsFooterRMA3.java

示例11: read

import jloda.util.Pair; //导入方法依赖的package包/类
/**
 * read from an RMA3 file
 *
 * @param reader
 * @throws IOException
 */
public void read(IInputReader reader, long startPos) throws IOException {
    reader.seek(startPos);
    setFormatDef(reader.readString());
    FormatDefinition formatDefinition = FormatDefinition.fromString(getFormatDef());

    for (Pair<String, FormatDefinition.Type> pair : formatDefinition.getList()) {
        switch (pair.getFirst()) {
            case "Creator":
                setCreator(reader.readString());
                break;
            case "CreationDate":
                setCreationDate(reader.readLong());
                break;
            case "AlignmentsFile":
                setAlignmentFile(reader.readString());
                break;
            case "AlignmentFileFormat":
                setAlignmentFileFormat(reader.readString());
                break;
            case "AlignmentFileSize":
                setAlignmentFileSize(reader.readLong());
                break;
            case "ReadsFile":
                setReadsFile(reader.readString());
                break;
            case "ReadsFileFormat":
                setReadsFileFormat(reader.readString());
                break;
            case "ReadsFileSize":
                setReadsFileSize(reader.readLong());
                break;
            case "BlastMode":
                setBlastMode(reader.readString());
                break;
            case "MatchesStart":
                setMatchesStart(reader.readLong());
                break;
            case "MatchesFooter":
                setMatchesFooter(reader.readLong());
                break;
            case "ClassificationsStart":
                setClassificationsStart(reader.readLong());
                break;
            case "ClassificationsFooter":
                setClassificationsFooter(reader.readLong());
                break;
            case "AuxStart":
                setAuxStart(reader.readLong());
                break;
            case "AuxFooter":
                setAuxFooter(reader.readLong());
                break;
            case "FileFooter":
                setFileFooter(reader.readLong());
                break;
        }
    }
}
开发者ID:danielhuson，项目名称:megan-ce，代码行数:65，代码来源:FileFooterRMA3.java

示例12: write

import jloda.util.Pair; //导入方法依赖的package包/类
/**
 * write to an RMA3 file
 *
 * @param writer
 * @return location of fileFooter in file
 * @throws IOException
 */
public void write(IOutputWriter writer) throws IOException {
    writer.writeString(getFormatDef());

    final FormatDefinition formatDefinition = FormatDefinition.fromString(getFormatDef());
    formatDefinition.startWrite();
    for (Pair<String, FormatDefinition.Type> pair : formatDefinition.getList()) {
        {
            switch (pair.getFirst()) {
                case "Creator":
                    formatDefinition.write(writer, "Creator", getCreator());
                    break;
                case "CreationDate":
                    formatDefinition.write(writer, "CreationDate", getCreationDate());
                    break;
                case "AlignmentsFile":
                    formatDefinition.write(writer, "AlignmentsFile", getAlignmentFile());
                    break;
                case "AlignmentFileFormat":
                    formatDefinition.write(writer, "AlignmentFileFormat", getAlignmentFileFormat());
                    break;
                case "AlignmentFileSize":
                    formatDefinition.write(writer, "AlignmentFileSize", getAlignmentFileSize());
                    break;
                case "ReadsFile":
                    formatDefinition.write(writer, "ReadsFile", getReadsFile());
                    break;
                case "ReadsFileFormat":
                    formatDefinition.write(writer, "ReadsFileFormat", getReadsFileFormat());
                    break;
                case "ReadsFileSize":
                    formatDefinition.write(writer, "ReadsFileSize", getReadsFileSize());
                    break;
                case "BlastMode":
                    formatDefinition.write(writer, "BlastMode", getBlastMode());
                    break;
                case "MatchesStart":
                    formatDefinition.write(writer, "MatchesStart", getMatchesStart());
                    break;
                case "MatchesFooter":
                    formatDefinition.write(writer, "MatchesFooter", getMatchesFooter());
                    break;
                case "ClassificationsStart":
                    formatDefinition.write(writer, "ClassificationsStart", getClassificationsStart());
                    break;
                case "ClassificationsFooter":
                    formatDefinition.write(writer, "ClassificationsFooter", getClassificationsFooter());
                    break;
                case "AuxStart":
                    formatDefinition.write(writer, "AuxStart", getAuxStart());
                    break;
                case "AuxFooter":
                    formatDefinition.write(writer, "AuxFooter", getAuxFooter());
                    break;
                case "FileFooter":
                    formatDefinition.write(writer, "FileFooter", getFileFooter());
                    break;
            }
        }
    }
    formatDefinition.finishWrite();
}
开发者ID:danielhuson，项目名称:megan-ce，代码行数:69，代码来源:FileFooterRMA3.java


注：本文中的jloda.util.Pair.getFirst方法示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。