Merge pull request #722 from josemduarte/master

josemduarte · web-flow · commit 4c5f7f9e570d · 2018-01-17T09:35:14.000-08:00
Fixing hmmer scan web service and adding test for it
diff --git a/biojava-ws/src/main/java/demo/HmmerDemo.java b/biojava-ws/src/main/java/demo/HmmerDemo.java
@@ -30,55 +30,54 @@
 
 import java.util.SortedSet;
 
-/** The cookbook recipe for how to request Pfam annotations for a protein sequence using the Hmmer3 service
+/** 
+ * The cookbook recipe for how to request Pfam annotations for a protein sequence using the Hmmer3 service
  *
  * @author Andreas Prlic
  * @since 3.0.3
  */
 public class HmmerDemo {
 
-	public static void main(String[] args){
+	public static void main(String[] args) throws Exception {
 
-		try {
-			// first we get a UniProt sequence
-			String uniProtID = "P08487";
-			ProteinSequence seq = getUniprot(uniProtID);
 
+		// first we get a UniProt sequence
+		String uniProtID = "P08487";
+		ProteinSequence seq = getUniprot(uniProtID);
 
-			// now we submit this sequence to the Hmmer web site
-			RemoteHmmerScan hmmer = new RemoteHmmerScan();
 
-			SortedSet<HmmerResult> results = hmmer.scan(seq);
+		// now we submit this sequence to the Hmmer web site
+		RemoteHmmerScan hmmer = new RemoteHmmerScan();
 
-			// and now let's print out the obtained annotations
+		SortedSet<HmmerResult> results = hmmer.scan(seq);
 
-			System.out.println(String.format("#\t%15s\t%10s\t%s\t%s\t%8s\t%s",
-					"Domain","ACC", "Start","End","eValue","Description"));
+		// and now let's print out the obtained annotations
 
-			int counter = 0;
-			for (HmmerResult hmmerResult : results) {
-				//System.out.println(hmmerResult);
+		System.out.println(String.format("#\t%15s\t%10s\t%s\t%s\t%8s\t%s",
+				"Domain","ACC", "Start","End","eValue","Description"));
 
-				for ( HmmerDomain domain : hmmerResult.getDomains()) {
-					counter++;
-					System.out.println(String.format("%d\t%15s\t%10s\t%5d\t%5d\t%.2e\t%s",
-							counter,
-							hmmerResult.getName(), domain.getHmmAcc(),
-							domain.getSqFrom(),domain.getSqTo(),
-							domain.getEvalue(), hmmerResult.getDesc()
-							));
+		int counter = 0;
+		for (HmmerResult hmmerResult : results) {
+			//System.out.println(hmmerResult);
 
-				}
+			for ( HmmerDomain domain : hmmerResult.getDomains()) {
+				counter++;
+				System.out.println(String.format("%d\t%15s\t%10s\t%5d\t%5d\t%.2e\t%s",
+						counter,
+						hmmerResult.getName(), domain.getHmmAcc(),
+						domain.getSqFrom(),domain.getSqTo(),
+						domain.getEvalue(), hmmerResult.getDesc()
+						));
 
 			}
 
-		} catch (Exception e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
 		}
+
+
 	}
 
-	/** Fetch a protein sequence from the UniProt web site
+	/** 
+	 * Fetch a protein sequence from the UniProt web site
 	 *
 	 * @param uniProtID
 	 * @return a Protein Sequence
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
@@ -43,7 +43,7 @@ public class RemoteHmmerScan implements HmmerScan {
 
 	private static final Logger LOGGER = LoggerFactory.getLogger(RemoteHmmerScan.class);
 	
-	public static final String HMMER_SERVICE = "http://www.ebi.ac.uk/Tools/hmmer/search/hmmscan";
+	public static final String HMMER_SERVICE = "https://www.ebi.ac.uk/Tools/hmmer/search/hmmscan";
 
 	public RemoteHmmerScan(){
 
diff --git a/biojava-ws/src/test/java/org/biojava/nbio/ws/hmmer/TestRemoteHmmerScan.java b/biojava-ws/src/test/java/org/biojava/nbio/ws/hmmer/TestRemoteHmmerScan.java
@@ -0,0 +1,42 @@
+package org.biojava.nbio.ws.hmmer;
+
+import java.util.SortedSet;
+
+import org.biojava.nbio.core.sequence.ProteinSequence;
+import org.junit.Test;
+import static org.junit.Assert.*;
+
+public class TestRemoteHmmerScan {
+	
+	/**
+	 * Sequence for UniProt id P30340 (PDB 1SMT)
+	 */
+	private static final String TEST_SEQ = "MTKPVLQDGETVVCQGTHAAIASELQAIAPEVAQSLAEFFAVLADPNRLRLLSLLARSEL" + 
+			"CVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQGRHVYYQLQDHHIVALYQNALDHLQE" + 
+			"CR";
+	
+	@Test
+	public void testHmmerWs() throws Exception {
+
+		ProteinSequence seq = new ProteinSequence(TEST_SEQ);
+
+		// now we submit this sequence to the Hmmer web site
+		RemoteHmmerScan hmmer = new RemoteHmmerScan();
+
+		SortedSet<HmmerResult> results = hmmer.scan(seq);
+		
+		assertNotNull(results);
+		// 2 results (domains) for P30340 (PDB 1smt) as of Jan 2018
+		assertEquals(2, results.size());
+
+		boolean gotSh2Domain = false;
+		
+		for (HmmerResult hmmerResult : results) {
+			if (hmmerResult.getName().equals("HTH_5")) {
+				gotSh2Domain = true;
+			}
+		}
+		
+		assertTrue("A HTH_5 domain should be present as one of the hmmer scan matches",gotSh2Domain);
+	}
+}
