Uniprot has switched to https

josemduarte · josemduarte · commit 7a36714aa966 · 2018-07-02T09:57:03.000-07:00
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java
@@ -76,7 +76,9 @@ public class UniprotProxySequenceReader<C extends Compound> implements ProxySequ
 	private static final String TREMBLID_PATTERN = "[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}";
 	public static final Pattern UP_AC_PATTERN = Pattern.compile("(" + SPID_PATTERN + "|" + TREMBLID_PATTERN + ")");
 
-	private static String uniprotbaseURL = "http://www.uniprot.org"; //"http://pir.uniprot.org";
+	public static final String DEFAULT_UNIPROT_BASE_URL = "https://www.uniprot.org";
+
+	private static String uniprotbaseURL = DEFAULT_UNIPROT_BASE_URL;
 	private static String uniprotDirectoryCache = null;
 	private String sequence;
 	private CompoundSet<C> compoundSet;
diff --git a/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java b/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java
@@ -84,7 +84,8 @@ private void testUniprot(String uniprotID) throws CompoundNotFoundException, IOE
 
 	}
 
-	/** Fetch a protein sequence from the UniProt web site
+	/**
+	 * Fetch a protein sequence from the UniProt web site
 	 *
 	 * @param uniProtID
 	 * @return a Protein Sequence

Original file line number	Diff line number	Diff line change
`@@ -84,7 +84,8 @@ private void testUniprot(String uniprotID) throws CompoundNotFoundException, IOE`
`84`	`84`
`85`	`85`	`}`
`86`	`86`
`87`		`- /** Fetch a protein sequence from the UniProt web site`
	`87`	`+ /**`
	`88`	`+ * Fetch a protein sequence from the UniProt web site`
`88`	`89`	`*`
`89`	`90`	`* @param uniProtID`
`90`	`91`	`* @return a Protein Sequence`