本文整理汇总了Java中htsjdk.tribble.readers.AsciiLineReader.readLine方法的典型用法代码示例。如果您正苦于以下问题：Java AsciiLineReader.readLine方法的具体用法？Java AsciiLineReader.readLine怎么用？Java AsciiLineReader.readLine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htsjdk.tribble.readers.AsciiLineReader的用法示例。
在下文中一共展示了AsciiLineReader.readLine方法的15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: writeHeader
import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
@Override
String writeHeader(AsciiLineReader reader, PrintWriter writer) {
String nextLine;
try {
nextLine = reader.readLine();
while (nextLine.startsWith("#")) {
writer.println(nextLine);
nextLine = reader.readLine();
}
} catch (IOException e) {
throw new RuntimeIOException(e);
}
return nextLine;
}
示例2: writeHeader
import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
@Override
String writeHeader(AsciiLineReader reader, PrintWriter writer) throws IOException {
String nextLine = reader.readLine();
if (nextLine.startsWith("psLayout")) {
do {
writer.println(nextLine);
nextLine = reader.readLine();
} while (!nextLine.startsWith("-"));
nextLine = reader.readLine();
}
while (nextLine.startsWith("#") ||
nextLine.startsWith("browser") ||
nextLine.startsWith("track") ||
isEmptyLine(nextLine)) {
writer.println(nextLine);
nextLine = reader.readLine();
}
return nextLine;
}
示例3: writeHeader
import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
@Override
String writeHeader(AsciiLineReader reader, PrintWriter writer) {
try {
String nextLine = reader.readLine();
while (nextLine.startsWith("#")) {
writer.println(nextLine);
nextLine = reader.readLine();
}
return nextLine;
} catch (IOException e) {
LOG.error("Error writing header", e);
return null;
}
}
示例4: writeHeader
import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
@Override
String writeHeader(AsciiLineReader reader, PrintWriter writer) {
try {
String nextLine = reader.readLine();
// TODO -- check "browser" line syntax, is it a multi-line directive?
while (nextLine.startsWith("#")) {
writer.println(nextLine);
nextLine = reader.readLine();
}
return nextLine;
} catch (IOException e) {
log.error("Error writing header", e);
return null;
}
}
示例5: isWiggle
import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
/**
* Utility method. Returns true if this looks like a wiggle locator. The criteria is to scan
* the first 100 lines looking for a valid "track" line. According to UCSC documentation
* track lines must contain a type attribute, which must be equal to "wiggle_0".
*
* @param file
* @return
*/
public static boolean isWiggle(ResourceLocator file) {
AsciiLineReader reader = null;
try {
reader = ParsingUtils.openAsciiReader(file);
String nextLine = null;
int lineNo = 0;
while ((nextLine = reader.readLine()) != null && (nextLine.trim().length() > 0)) {
if (nextLine.startsWith("track") && nextLine.contains("wiggle_0")) {
return true;
}
if (lineNo++ > 100) {
break;
}
}
} catch (IOException e) {
e.printStackTrace();
return false;
} finally {
if (reader != null) {
reader.close();
}
}
return false;
}
示例6: writeHeader
import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
@Override
String writeHeader(AsciiLineReader reader, PrintWriter writer) throws IOException {
String nextLine = reader.readLine();
if (nextLine.startsWith("psLayout")) {
do {
writer.println(nextLine);
nextLine = reader.readLine();
} while (!nextLine.startsWith("-"));
nextLine = reader.readLine();
}
// TODO -- check "browser" line syntax, is it a multi-line directive?
while (nextLine.startsWith("#") ||
nextLine.startsWith("browser") ||
nextLine.startsWith("track") ||
nextLine.trim().length() == 0) {
writer.println(nextLine);
nextLine = reader.readLine();
}
return nextLine;
}
示例7: writeHeader
import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
@Override
String writeHeader(AsciiLineReader reader, PrintWriter writer) {
String nextLine = null;
try {
nextLine = reader.readLine();
while (nextLine.startsWith("#")) {
writer.println(nextLine);
nextLine = reader.readLine();
}
} catch (IOException e) {
e.printStackTrace();
}
return nextLine;
}
示例8: writeHeader
import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
@Override
String writeHeader(AsciiLineReader reader, PrintWriter writer) throws IOException {
String nextLine;
while((nextLine = reader.readLine()) != null) {
writer.println(nextLine);
if (!nextLine.startsWith("#")) {
break;
}
}
return null;
}
示例9: loadFromFile
import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
/**
* Load segmented data from a file could be remote)
* Return a map of trackId -> segment datasource
*
* @return
*/
public SegmentedAsciiDataSet loadFromFile() {
dataset = new SegmentedAsciiDataSet(genome);
if (birdsuite) {
dataset.setTrackType(TrackType.CNV);
}
AsciiLineReader reader = null;
String nextLine = null;
int lineNumber = 0;
IParser<String[], Integer> parser = IParserFactory.getIndexParser(new String[0]);
try {
reader = ParsingUtils.openAsciiReader(locator);
lineNumber = readHeader(reader);
while ((nextLine = reader.readLine()) != null && (nextLine.trim().length() > 0)) {
lineNumber++;
String[] tokens = Globals.tabPattern.split(nextLine, -1);
parseLine(parser, tokens);
}
} catch (IOException e) {
if (nextLine != null && lineNumber != 0) {
throw new ParserException(e.getMessage(), e, lineNumber, nextLine);
} else {
throw new RuntimeException(e);
}
} finally {
if (reader != null) {
reader.close();
}
}
dataset.sortLists();
return dataset;
}
示例10: readHeader
import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
private int readHeader(AsciiLineReader reader) throws IOException {
// Parse comments, if any
String nextLine = reader.readLine();
int lineNumber = 0;
while (nextLine.startsWith("#") || (nextLine.trim().length() == 0)) {
lineNumber++;
if (nextLine.length() > 0) {
parseComment(nextLine, dataset);
}
nextLine = reader.readLine();
}
// Read column headings
headings = nextLine.split("\t");
if (birdsuite) {
//sample sample_index copy_number chr start end confidence
sampleColumn = 0;
dataColumn = 2;
chrColumn = 3;
startColumn = 4;
endColumn = 5;
} else {
sampleColumn = 0;
chrColumn = 1;
startColumn = 2;
endColumn = 3;
dataColumn = headings.length - 1;
}
return lineNumber;
}
示例11: parseHeader
import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
private void parseHeader() {
AsciiLineReader reader = null;
// The DataConsumer interface takes an array of data per position, however wig
// files contain a single data point. Create an "array" once that can
// be resused
try {
reader = ParsingUtils.openAsciiReader(resourceLocator);
while ((nextLine = reader.readLine()) != null && (nextLine.trim().length() > 0)) {
// Skip comment lines
if (nextLine.startsWith("#") || nextLine.startsWith("data") || nextLine.startsWith(
"browser") || nextLine.trim().length() == 0) {
continue;
}
if (nextLine.startsWith("track")) {
trackLine = nextLine;
} else {
return;
}
}
} catch (IOException e) {
e.printStackTrace();
} finally {
if (reader != null) {
reader.close();
}
}
}
示例12: loadKnownSnps
import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
/**
* Load the set of known snps from a tab delimited file, format
* chr < tab> location
* The location is "1 base" (first nucleotide is position 1).
*
* @param snpFile
*/
private static synchronized void loadKnownSnps(String snpFile) {
// This method might get called many times concurrently, but we only want to load these once.
if (knownSnps != null) {
return;
}
knownSnps = new HashMap();
AsciiLineReader reader = null;
try {
reader = ParsingUtils.openAsciiReader(new ResourceLocator(snpFile));
String nextLine = "";
while ((nextLine = reader.readLine()) != null) {
String[] tokens = nextLine.split("\t");
String chr = tokens[0];
Set<Integer> snps = knownSnps.get(chr);
if (snps == null) {
snps = new HashSet(10000);
knownSnps.put(chr, snps);
}
snps.add(new Integer(tokens[1]));
}
} catch (Exception e) {
knownSnps = null;
log.error("", e);
MessageUtils.showMessage("Error loading snps file: " + snpFile + " (" + e.toString() + ")");
} finally {
reader.close();
}
}
示例13: readNextRecord
import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
public DotAlignedAlignment readNextRecord(AsciiLineReader reader) {
String nextLine;
try {
while ((nextLine = reader.readLine()) != null) {
DotAlignedAlignment alignment = createAlignment(nextLine);
if (alignment != null) {
return alignment;
}
}
} catch (IOException e) {
log.error("Error reading line", e);
}
return null;
}
示例14: readNextRecord
import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
public Alignment readNextRecord(AsciiLineReader reader) throws IOException {
String nextLine;
while ((nextLine = reader.readLine()) != null) {
Feature f = codec.decode(nextLine);
if(f != null && f instanceof BasicFeature) {
return new FeatureWrappedAlignment((BasicFeature) f);
}
}
return null;
}
示例15: getFilter
import htsjdk.tribble.readers.AsciiLineReader; //导入方法依赖的package包/类
public static synchronized ReadGroupFilter getFilter() {
PreferenceManager samPrefs = PreferenceManager.getInstance();
if (samPrefs.getAsBoolean(PreferenceManager.SAM_FILTER_ALIGNMENTS)) {
String filterURL = samPrefs.get(PreferenceManager.SAM_FILTER_URL);
ReadGroupFilter filter = filterURL == null ? null : filterCache.get(filterURL);
if (filter == null && filterURL != null && filterURL.trim().length() > 0) {
Set<String> readGroups = new HashSet();
AsciiLineReader reader = null;
try {
reader = ParsingUtils.openAsciiReader(new ResourceLocator(filterURL));
String nextLine;
while ((nextLine = reader.readLine()) != null) {
readGroups.add(nextLine.trim());
}
filter = new ReadGroupFilter(readGroups);
filterCache.put(filterURL, filter);
}
catch (Exception e) {
MessageUtils.showMessage("Error reading read filter list: " + e.getMessage());
}
}
return filter;
}
return null;
}