biojava
diff --git a/‎alignment/smithwaterman.md‎
Lines changed: 1 addition & 1 deletion b/‎alignment/smithwaterman.md‎
Lines changed: 1 addition & 1 deletion
diff --git a/‎core/readwrite.md‎
Lines changed: 1 addition & 1 deletion b/‎core/readwrite.md‎
Lines changed: 1 addition & 1 deletion
diff --git a/‎core/translating.md‎
Lines changed: 1 addition & 1 deletion b/‎core/translating.md‎
Lines changed: 1 addition & 1 deletion
@@ -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();
 
@@ -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();
 
@@ -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();