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‎_wikis/BioJava3:HowTo.md‎

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Original file line numberDiff line numberDiff line change
@@ -22,8 +22,8 @@ All the examples in this section require the biojava-dna module.
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` List`<Symbol>` mySeq = SymbolListFormatter.parseSymbolList(mySeqString);`
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` `
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` // Is it a big list? Don't want to hold it all in memory? Use an iterator instead.`
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` Iterator`<Symbol>` myIterator = SymbolListFormater.parseSymbols(mySeqString);`
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` while (myIterator.hasNext()) {`
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` for (Iterator`<Symbol>` myIterator = SymbolListFormater.parseSymbols(mySeqString);`
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`      myIterator.hasNext(); ) {`
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`   Symbol sym = myIterator.next();`
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` }`
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`  `
@@ -106,8 +106,8 @@ A quality-scored DNA sequence
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### Iterating over the base/score pairs
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` // A 1-indexed iterator and ListIterators are also available.`
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` Iterator`<TaggedSymbol<Integer>`> iter = scoredSeq.taggedSymbolIterator();`
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` while (iter.hasNext()) {`
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` for (Iterator`<TaggedSymbol<Integer>`> iter = scoredSeq.taggedSymbolIterator();`
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`      iter.hasNext(); ) {`
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`   TaggedSymbol`<Integer>` taggedSym = iter.next();`
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`   Symbol sym = taggedSym.getSymbol();`
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`   Integer score = taggedSym.getTag();`
@@ -124,8 +124,7 @@ A quality-scored DNA sequence
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### Iterating over the scores only
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` // A ListIterator is also available, as are 1-indexed iterators.`
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` Iterator`<Integer>` iter = scoredSeq.tagIterator();`
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` while (iter.hasNext()) {`
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` for (Iterator`<Integer>` iter = scoredSeq.tagIterator(); iter.hasNext(); ) {`
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`   Integer score = iter.next();`
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` }`
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@@ -144,9 +143,9 @@ simpler for the most common use-cases.
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### Parsing a FASTA file (the easy way)
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` ThingParser`<FASTA>` parser = ThingParserFactory.`
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`   getReadParser(FASTA.format, new File("/path/to/my/fasta.fa"));`
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` while (parser.hasNext()) {`
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` for (ThingParser`<FASTA>` parser = ThingParserFactory.`
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`        getReadParser(FASTA.format, new File("/path/to/my/fasta.fa"));`
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`      parser.hasNext(); ) {`
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`   FASTA fasta = parser.next(); `
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`   // fasta contains a complete FASTA record.`
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` }`
@@ -156,8 +155,8 @@ simpler for the most common use-cases.
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` FASTAReader reader = new FASTAFileReader(new File("/path/to/my/fasta.fa"));`
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` FASTABuilder builder = new FASTABuilder();`
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` ThingParser`<FASTA>` parser = new ThingParser`<FASTA>`(reader, builder);`
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` while (parser.hasNext()) {`
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` for (ThingParser`<FASTA>` parser = new ThingParser`<FASTA>`(reader, builder);`
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`      parser.hasNext(); ) {`
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`   FASTA fasta = parser.next(); `
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`   // fasta contains a complete FASTA record.`
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` }`

‎_wikis/BioJava3:HowTo.mediawiki‎

Lines changed: 10 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -12,8 +12,8 @@ All the examples in this section require the biojava-dna module.
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List<Symbol> mySeq = SymbolListFormatter.parseSymbolList(mySeqString);
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// Is it a big list? Don't want to hold it all in memory? Use an iterator instead.
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Iterator<Symbol> myIterator = SymbolListFormater.parseSymbols(mySeqString);
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while (myIterator.hasNext()) {
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for (Iterator<Symbol> myIterator = SymbolListFormater.parseSymbols(mySeqString);
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myIterator.hasNext(); ) {
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Symbol sym = myIterator.next();
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}
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@@ -95,8 +95,8 @@ All the examples in this section require the biojava-dna module.
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=== Iterating over the base/score pairs ===
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// A 1-indexed iterator and ListIterators are also available.
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Iterator<TaggedSymbol<Integer>> iter = scoredSeq.taggedSymbolIterator();
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while (iter.hasNext()) {
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for (Iterator<TaggedSymbol<Integer>> iter = scoredSeq.taggedSymbolIterator();
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iter.hasNext(); ) {
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TaggedSymbol<Integer> taggedSym = iter.next();
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Symbol sym = taggedSym.getSymbol();
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Integer score = taggedSym.getTag();
@@ -113,8 +113,7 @@ All the examples in this section require the biojava-dna module.
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=== Iterating over the scores only ===
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// A ListIterator is also available, as are 1-indexed iterators.
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Iterator<Integer> iter = scoredSeq.tagIterator();
117-
while (iter.hasNext()) {
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for (Iterator<Integer> iter = scoredSeq.tagIterator(); iter.hasNext(); ) {
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Integer score = iter.next();
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}
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@@ -128,9 +127,9 @@ Convenience wrapper classes are provided to make the parsing process simpler for
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=== Parsing a FASTA file (the easy way) ===
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131-
ThingParser<FASTA> parser = ThingParserFactory.
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getReadParser(FASTA.format, new File("/path/to/my/fasta.fa"));
133-
while (parser.hasNext()) {
130+
for (ThingParser<FASTA> parser = ThingParserFactory.
131+
getReadParser(FASTA.format, new File("/path/to/my/fasta.fa"));
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parser.hasNext(); ) {
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FASTA fasta = parser.next();
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// fasta contains a complete FASTA record.
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}
@@ -140,8 +139,8 @@ Convenience wrapper classes are provided to make the parsing process simpler for
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FASTAReader reader = new FASTAFileReader(new File("/path/to/my/fasta.fa"));
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FASTABuilder builder = new FASTABuilder();
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ThingParser<FASTA> parser = new ThingParser<FASTA>(reader, builder);
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while (parser.hasNext()) {
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for (ThingParser<FASTA> parser = new ThingParser<FASTA>(reader, builder);
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parser.hasNext(); ) {
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FASTA fasta = parser.next();
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// fasta contains a complete FASTA record.
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}

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