Java StringUtil.join方法代码示例

import htsjdk.samtools.util.StringUtil; //导入方法依赖的package包/类
/**
 * Given a set of columns assert that all columns conform to the format of an RG header attribute (i.e. 2 letters)
 * the attribute is NOT a member of the rgHeaderTags that are built by default in buildSamHeaderParameters
 *
 * @param rgTagColumns A set of columns that should conform to the rg header attribute format
 */
private void checkRgTagColumns(final Set<String> rgTagColumns) {
    final Set<String> forbiddenHeaders = buildSamHeaderParameters(null).keySet();
    forbiddenHeaders.retainAll(rgTagColumns);

    if (!forbiddenHeaders.isEmpty()) {
        throw new PicardException("Illegal ReadGroup tags in library params(barcode params) file(" + LIBRARY_PARAMS.getAbsolutePath() + ") Offending headers = " + StringUtil.join(", ", forbiddenHeaders));
    }

    for (final String column : rgTagColumns) {
        if (column.length() > 2) {
            throw new PicardException("Column label (" + column + ") unrecognized.  Library params(barcode params) can only contain the columns " +
                    "(OUTPUT, LIBRARY_NAME, SAMPLE_ALIAS, BARCODE, BARCODE_<X> where X is a positive integer) OR two letter RG tags!");
        }
    }
}
 

import htsjdk.samtools.util.StringUtil; //导入方法依赖的package包/类
private void convertParamsFile(String libraryParamsFile, int concatNColumnFields, File testDataDir, File outputDir, File libraryParams, List<File> outputPrefixes) throws FileNotFoundException {
    try (LineReader reader = new BufferedLineReader(new FileInputStream(new File(testDataDir, libraryParamsFile)))) {
        final PrintWriter writer = new PrintWriter(libraryParams);
        final String header = reader.readLine();
        writer.println(header + "\tOUTPUT_PREFIX");
        while (true) {
            final String line = reader.readLine();
            if (line == null) {
                break;
            }
            final String[] fields = line.split("\t");
            final File outputPrefix = new File(outputDir, StringUtil.join("", Arrays.copyOfRange(fields, 0, concatNColumnFields)));
            outputPrefixes.add(outputPrefix);
            writer.println(line + "\t" + outputPrefix);
        }
        writer.close();
    }
}
 

import htsjdk.samtools.util.StringUtil; //导入方法依赖的package包/类
public String listToStr(List<String> result) {
	if(result.size() > 0) {
		return StringUtil.join(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR, result);
	} else {
		return VCFConstants.EMPTY_ALTERNATE_ALLELE_FIELD;
	}
}
 

import htsjdk.samtools.util.StringUtil; //导入方法依赖的package包/类
public String mapTostr() {
	if(valList != null) return StringUtil.join(COMMA, valList);
	else {
		List<String> out = new ArrayList<String>();
		String val;
		for (String string : queryAlts) {
			val = StringUtil.join(COMMA, altValMap.get(string));
			if(!val.equals("")) out.add(val);
		}
		return StringUtil.join(COMMA, out);
	}
}
 

import htsjdk.samtools.util.StringUtil; //导入方法依赖的package包/类
public String toBEDHeader() {
	if(requiredCols == null) {
		getRequiredBEDCols();
		getOthersForBED();
	}
	String header = VCFHeader.HEADER_INDICATOR + VannoUtils.HEADER_CHR + TAB 
			+ VannoUtils.HEADER_FROM + TAB + VannoUtils.HEADER_TO + TAB;
	if(format.refCol > 0) header += VannoUtils.HEADER_REF + TAB;
	if(format.altCol > 0) header += VannoUtils.HEADER_ALT + TAB;
	
	header += StringUtil.join(TAB, otherfields);
	return header;
}
 

import htsjdk.samtools.util.StringUtil; //导入方法依赖的package包/类
private String format(List<Integer> ints) {
    if (ints == null || ints.size() == 0) {
        return "n/a";
    }

    return StringUtil.join(",", ints);
}
 

import htsjdk.samtools.util.StringUtil; //导入方法依赖的package包/类
public String convertQueryToVCF(final BedNode node) {
	String h = basicCols(node, true);
	if(requiredCols.get(3) != -1) h +=  TAB + node.allFieldsMap.get(requiredCols.get(3)); else h += TAB + ".";
	if(requiredCols.get(4) != -1) h +=  TAB + node.allFieldsMap.get(requiredCols.get(4)); else h += TAB + ".";
	if(requiredCols.get(5) != -1) h +=  TAB + node.allFieldsMap.get(requiredCols.get(5)); else h += TAB + ".";
	if(requiredCols.get(6) != -1) h +=  TAB + node.allFieldsMap.get(requiredCols.get(6)); else h += TAB + ".";
	
	h += TAB + StringUtil.join(INFO_FIELD_SEPARATOR, getOtherFieldsVal(node, true));
	return h;
}
 

import htsjdk.samtools.util.StringUtil; //导入方法依赖的package包/类
public String convertQueryToBED(final BedNode node) {
	String h = basicCols(node, false);
	if(requiredCols.get(3) != null) h +=  TAB + node.allFieldsMap.get(requiredCols.get(3));
	if(requiredCols.get(4) != null) h +=  TAB + node.allFieldsMap.get(requiredCols.get(4));
	
	h += TAB + StringUtil.join(TAB, getOtherFieldsVal(node, false));
	return h;
}
 

import htsjdk.samtools.util.StringUtil; //导入方法依赖的package包/类
public String toBEDHeader1() {
	String header = StringUtil.join(TAB, VCFHeader.HEADER_FIELDS.values());
	header = header.replace(HEADER_FIELDS.POS.toString(), VannoUtils.HEADER_FROM);
	header = header.replace(HEADER_FIELDS.ID.toString(), VannoUtils.HEADER_TO);
	header = header.replace(HEADER_FIELDS.INFO.toString(), StringUtil.join(TAB, infoKeys));
	return header;
}
 

import htsjdk.samtools.util.StringUtil; //导入方法依赖的package包/类
private String generate(HashMap<String, String> d) {
    String[] msg = new String[headers.size()];

    for(int i=0; i<msg.length; i++) {
        String value = d.get(headers.get(i));
        if (value == null) { value = ""; }
        msg[i] = value;
    }
    return StringUtil.join(TAB, msg);
}
 

import htsjdk.samtools.util.StringUtil; //导入方法依赖的package包/类
public PerTileParser(final IlluminaFileMap tilesToFiles, final int nextTile) {
    this.tileToFiles = tilesToFiles;
    this.currentTile = null;
    this.nextTile = nextTile;

    if(!tilesToFiles.containsKey(nextTile)) {
        throw new IllegalArgumentException("NextTile (" + nextTile + ") is not contained by tilesToFiles (" + StringUtil.join(",", new ArrayList<Integer>(tilesToFiles.keySet())));
    }
}
 

import htsjdk.samtools.util.StringUtil; //导入方法依赖的package包/类
public void seekToTile(int oneBasedTileNumber) {
    nextTile = oneBasedTileNumber;

    if(!tileToFiles.containsKey(oneBasedTileNumber)) {
        throw new PicardException("PerTileParser does not contain key(" + oneBasedTileNumber +") keys available (" + StringUtil.join(",", new ArrayList<Integer>(tileToFiles.keySet())) + ")");
    }

    if(currentIterator != null) {
        currentIterator.close();
    }
    currentIterator = null;
}
 

import htsjdk.samtools.util.StringUtil; //导入方法依赖的package包/类
public void verifyData(List<Integer> tiles, final int [] cycles) {
    final List<Integer> mapTiles = new ArrayList<Integer>(this.tileToFiles.keySet());
    if(!mapTiles.containsAll(tiles)) {
        throw new PicardException("Missing tiles in PerTileParser expected(" + StringUtil.join(",", tiles) + ") but found (" + StringUtil.join(",", mapTiles) + ")");
    }

    if(!tiles.containsAll(mapTiles)) {
        throw new PicardException("Extra tiles where found in PerTileParser  expected(" + StringUtil.join(",", tiles) + ") but found (" + StringUtil.join(",", mapTiles) + ")");
    }
}
 

import htsjdk.samtools.util.StringUtil; //导入方法依赖的package包/类
/**
 * For each line in the MULTIPLEX_PARAMS file create a FastqRecordsWriter and put it in the sampleBarcodeFastqWriterMap map,
 * where the key to the map is the concatenation of all sampleBarcodes in order for the given line.
 */
private void populateWritersFromMultiplexParams() {
    final TabbedTextFileWithHeaderParser libraryParamsParser = new TabbedTextFileWithHeaderParser(MULTIPLEX_PARAMS);

    final Set<String> expectedColumnLabels = CollectionUtil.makeSet("OUTPUT_PREFIX");
    final List<String> sampleBarcodeColumnLabels = new ArrayList<>();
    for (int i = 1; i <= readStructure.sampleBarcodes.length(); i++) {
        sampleBarcodeColumnLabels.add("BARCODE_" + i);
    }

    expectedColumnLabels.addAll(sampleBarcodeColumnLabels);
    assertExpectedColumns(libraryParamsParser.columnLabels(), expectedColumnLabels);

    for (final TabbedTextFileWithHeaderParser.Row row : libraryParamsParser) {
        List<String> sampleBarcodeValues = null;

        if (!sampleBarcodeColumnLabels.isEmpty()) {
            sampleBarcodeValues = new ArrayList<>();
            for (final String sampleBarcodeLabel : sampleBarcodeColumnLabels) {
                sampleBarcodeValues.add(row.getField(sampleBarcodeLabel));
            }
        }

        final String key = (sampleBarcodeValues == null || sampleBarcodeValues.contains("N")) ? null : StringUtil.join("", sampleBarcodeValues);
        if (sampleBarcodeFastqWriterMap.containsKey(key)) {    //This will catch the case of having more than 1 line in a non-barcoded MULTIPLEX_PARAMS file
            throw new PicardException("Row for barcode " + key + " appears more than once in MULTIPLEX_PARAMS file " +
                    MULTIPLEX_PARAMS);
        }

        final FastqRecordsWriter writer = buildWriter(new File(row.getField("OUTPUT_PREFIX")));
        sampleBarcodeFastqWriterMap.put(key, writer);
    }
    if (sampleBarcodeFastqWriterMap.isEmpty()) {
        throw new PicardException("MULTIPLEX_PARAMS file " + MULTIPLEX_PARAMS + " does have any data rows.");
    }
    libraryParamsParser.close();
}
 

import htsjdk.samtools.util.StringUtil; //导入方法依赖的package包/类
@Override
protected String getProbeSetName() {
    if (BAIT_SET_NAME != null) {
        return BAIT_SET_NAME;
    } else {
        final SortedSet<String> baitSetNames = new TreeSet<String>();
        for (final File file : BAIT_INTERVALS) {
            baitSetNames.add(CollectTargetedMetrics.renderProbeNameFromFile(file));
        }
        return StringUtil.join(".", baitSetNames);
    }
}