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Fix broken examples #32

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Merged
josemduarte merged 1 commit into from
Nov 7, 2021
Merged

Fix broken examples #32

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2 changes: 1 addition & 1 deletion 2 alignment/smithwaterman.md
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ public static void main(String[] args) throws Exception {
}

private static ProteinSequence getSequenceForId(String uniProtId) throws Exception {
URL uniprotFasta = new URL(String.format("http://www.uniprot.org/uniprot/%s.fasta", uniProtId));
URL uniprotFasta = new URL(String.format("https://www.uniprot.org/uniprot/%s.fasta", uniProtId));
ProteinSequence seq = FastaReaderHelper.readFastaProteinSequence(uniprotFasta.openStream()).get(uniProtId);
System.out.printf("id : %s %s%s%s", uniProtId, seq, System.getProperty("line.separator"), seq.getOriginalHeader());
System.out.println();
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2 changes: 1 addition & 1 deletion 2 core/readwrite.md
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Expand Up @@ -13,7 +13,7 @@ Here an example that parses a UniProt FASTA file into a protein sequence.

```java
public static ProteinSequence getSequenceForId(String uniProtId) throws Exception {
URL uniprotFasta = new URL(String.format("http://www.uniprot.org/uniprot/%s.fasta", uniProtId));
URL uniprotFasta = new URL(String.format("https://www.uniprot.org/uniprot/%s.fasta", uniProtId));
ProteinSequence seq = FastaReaderHelper.readFastaProteinSequence(uniprotFasta.openStream()).get(uniProtId);
System.out.printf("id : %s %s%s%s", uniProtId, seq, System.getProperty("line.separator"), seq.getOriginalHeader());
System.out.println();
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2 changes: 1 addition & 1 deletion 2 core/translating.md
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Expand Up @@ -63,7 +63,7 @@ An example for how to parse a sequence from a String and using the Translation e

// define the Ambiguity Compound Sets
AmbiguityDNACompoundSet ambiguityDNACompoundSet = AmbiguityDNACompoundSet.getDNACompoundSet();
CompoundSet<NucleotideCompound> nucleotideCompoundSet = AmbiguityRNACompoundSet.getDNACompoundSet();
CompoundSet<NucleotideCompound> nucleotideCompoundSet = AmbiguityRNACompoundSet.getRNACompoundSet();

FastaReader<DNASequence, NucleotideCompound> proxy =
new FastaReader<DNASequence, NucleotideCompound>(
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