Skip to content

Commit 586b9d2

Browse files
heuermhheuermh
authored
Update BioJava_CookBook3_FASTQ.md
Code style fixes
1 parent 413f6a3 commit 586b9d2

File tree

1 file changed

+25
-50
lines changed

1 file changed

+25
-50
lines changed

‎_wiki/BioJava_CookBook3_FASTQ.md‎

Lines changed: 25 additions & 50 deletions
Original file line numberDiff line numberDiff line change
@@ -33,8 +33,7 @@ FastqWriter fastqWriter = new SangerFastqWriter();
3333
FileWriter fileWriter = new FileWriter(new File("sanger.fastq"))));
3434

3535
for (Fastq fastq : fastqReader.read(new File("illumina.fastq"))) {
36-
if (fastq.getSequence().length() > 16)
37-
{
36+
if (fastq.getSequence().length() > 16) {
3837
fastqWriter.append(fileWriter, fastq);`
3938
}
4039
}
@@ -48,11 +47,9 @@ BufferedReader reader = new BufferedReader(new FileReader(new File("illumina.fas
4847
final FastqWriter fastqWriter = new SangerFastqWriter();
4948
final FileWriter fileWriter = new FileWriter(new File("sanger.fastq"))));
5049

51-
fastqReader.stream(reader, new StreamListener()
52-
{
50+
fastqReader.stream(reader, new StreamListener() {
5351
@Override
54-
public void fastq(final Fastq fastq)
55-
{
52+
public void fastq(final Fastq fastq) {
5653
   fastqWriter.append(fileWriter, fastq);
5754
}
5855
});
@@ -66,13 +63,10 @@ BufferedReader reader = new BufferedReader(new FileReader(new File("illumina.fas
6663
FastqWriter fastqWriter = new SangerFastqWriter();
6764
FileWriter fileWriter = new FileWriter(new File("sanger.fastq"))));
6865

69-
fastqReader.stream(reader, new StreamListener()
70-
{
66+
fastqReader.stream(reader, new StreamListener() {
7167
  @Override
72-
  public void fastq(final Fastq fastq)
73-
  {
74-
    if (fastq.getSequence().length() > 16)
75-
    {
68+
  public void fastq(final Fastq fastq) {
69+
    if (fastq.getSequence().length() > 16) {
7670
      fastqWriter.append(fileWriter, fastq);
7771
    }
7872
  }
@@ -98,11 +92,9 @@ FastqReader fastqReader = new IlluminaFastqReader();
9892
BufferedReader reader = new BufferedReader(new FileReader(new File("illumina.fastq")));
9993

10094
final AtomicInteger count = new AtomicInteger();
101-
fastqReader.stream(reader, new StreamListener()
102-
{
95+
fastqReader.stream(reader, new StreamListener() {
10396
  @Override
104-
  public void fastq(final Fastq fastq)
105-
  {
97+
  public void fastq(final Fastq fastq) {
10698
    count.incrementAndGet();
10799
  }
108100
});
@@ -117,11 +109,9 @@ FastqReader fastqReader = new IlluminaFastqReader();
117109
BufferedReader reader = new BufferedReader(new FileReader(new File("illumina.fastq")));
118110

119111
final AtomicInteger count = new AtomicInteger();
120-
fastqReader.parse(reader, new ParseAdapter()
121-
{
112+
fastqReader.parse(reader, new ParseAdapter() {
122113
  @Override
123-
  public void complete() throws IOException
124-
  {
114+
  public void complete() throws IOException {
125115
    count.incrementAndGet();
126116
  }
127117
});
@@ -136,13 +126,10 @@ final Pattern pattern = Pattern.compile("^HWUSI-EAS100R:.\*$");
136126
FastqReader fastqReader = new IlluminaFastqReader();
137127
BufferedReader reader = new BufferedReader(new FileReader(new File("illumina.fastq")));
138128

139-
fastqReader.parse(reader, new ParseAdapter()
140-
{
129+
fastqReader.parse(reader, new ParseAdapter() {
141130
  @Override
142-
  public void description(final String description) throws IOException
143-
  {
144-
    if (pattern.matches(description))
145-
    {
131+
  public void description(final String description) throws IOException {
132+
    if (pattern.matches(description)) {
146133
      System.out.println(description);
147134
    }
148135
  }
@@ -189,11 +176,9 @@ FastqReader fastqReader = new SangerFastqReader();
189176
BufferedReader reader = new BufferedReader(new FileReader(new File("sanger.fastq")));
190177
List<DNASequence> sequences = new ArrayList<DNASequence>();
191178

192-
fastqReader.stream(reader, new StreamListener()
193-
{
179+
fastqReader.stream(reader, new StreamListener() {
194180
  @Override
195-
  public void fastq(final Fastq fastq)
196-
  {
181+
  public void fastq(final Fastq fastq) {
197182
    sequences.add(FastqTools.createDNASequence(fastq));
198183
  }
199184
});
@@ -206,11 +191,9 @@ FastqReader fastqReader = new SangerFastqReader();
206191
BufferedReader reader = new BufferedReader(new FileReader(new File("sanger.fastq")));
207192
List<DNASequence> sequences = new ArrayList<DNASequence>();
208193

209-
fastqReader.stream(inputSupplier, new StreamListener()
210-
{
194+
fastqReader.stream(inputSupplier, new StreamListener() {
211195
  @Override
212-
  public void fastq(final Fastq fastq)
213-
  {
196+
  public void fastq(final Fastq fastq) {
214197
    sequences.add(FastqTools.createDNASequenceWithQualityScores(fastq));
215198
  }
216199
});
@@ -223,11 +206,9 @@ FastqReader fastqReader = new SangerFastqReader();
223206
BufferedReader reader = new BufferedReader(new FileReader(new File("sanger.fastq")));
224207
List<DNASequence> sequences = new ArrayList<DNASequence>();
225208

226-
fastqReader.stream(reader, new StreamListener()
227-
{
209+
fastqReader.stream(reader, new StreamListener() {
228210
  @Override
229-
  public void fastq(final Fastq fastq)
230-
{
211+
  public void fastq(final Fastq fastq) {
231212
    sequences.add(FastqTools.createDNASequenceWithQualityScoresAndErrorProbabilities(fastq));
232213
  }
233214
});
@@ -241,14 +222,11 @@ BufferedReader reader = new BufferedReader(new FileReader(new File("sanger.fastq
241222
SummaryStatistics stats = new SummaryStatistics();
242223
StringBuilder sb = new StringBuilder(512);
243224

244-
fastqReader.stream(reader, new StreamListener()
245-
{
225+
fastqReader.stream(reader, new StreamListener() {
246226
  @Override
247-
  public void fastq(final Fastq fastq)
248-
  {
227+
  public void fastq(final Fastq fastq) {
249228
    stats.clear();
250-
    for (Double errorProbability : FastqTools.errorProbabilities(fastq))
251-
    {
229+
    for (Double errorProbability : FastqTools.errorProbabilities(fastq)) {
252230
      stats.addValue(errorProbability);
253231
    }
254232
    sb.delete(0, sb.length());
@@ -270,16 +248,13 @@ BufferedReader reader = new BufferedReader(new FileReader(new File("sanger.fastq
270248
SummaryStatistics stats = new SummaryStatistics();
271249
StringBuilder sb = new StringBuilder(512);
272250

273-
fastqReader.stream(reader, new StreamListener()
274-
{
251+
fastqReader.stream(reader, new StreamListener() {
275252
  @Override
276-
  public void fastq(final Fastq fastq)
277-
  {
253+
  public void fastq(final Fastq fastq) {
278254
    stats.clear();
279255
    int size = fastq.getSequence().length();
280256
    double[] errorProbabilities = FastqTools.errorProbabilties(fastq, new double[size]);
281-
    for (int i = 0; i < size; i++)
282-
    {
257+
    for (int i = 0; i < size; i++) {
283258
      stats.addValue(errorProbabilities[i]);
284259
    }
285260
    sb.delete(0, sb.length());

0 commit comments

Comments
 (0)