Merge pull request #32 from lemora/fix/repair-broken-examples

josemduarte · web-flow · commit ac806c269485 · 2021-11-06T20:52:42.000-07:00
Fix broken examples
diff --git a/alignment/smithwaterman.md b/alignment/smithwaterman.md
@@ -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();
diff --git a/core/readwrite.md b/core/readwrite.md
@@ -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();
diff --git a/core/translating.md b/core/translating.md
@@ -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>(

Original file line number	Diff line number	Diff line change
`@@ -36,7 +36,7 @@ public static void main(String[] args) throws Exception {`
`36`	`36`	`}`
`37`	`37`
`38`	`38`	`private static ProteinSequence getSequenceForId(String uniProtId) throws Exception {`
`39`		`- URL uniprotFasta = new URL(String.format("http://www.uniprot.org/uniprot/%s.fasta", uniProtId));`
	`39`	`+ URL uniprotFasta = new URL(String.format("https://www.uniprot.org/uniprot/%s.fasta", uniProtId));`
`40`	`40`	`ProteinSequence seq = FastaReaderHelper.readFastaProteinSequence(uniprotFasta.openStream()).get(uniProtId);`
`41`	`41`	`System.out.printf("id : %s %s%s%s", uniProtId, seq, System.getProperty("line.separator"), seq.getOriginalHeader());`
`42`	`42`	`System.out.println();`