biojava#276 updating to latest version of HMMER API. Incorporating some feedback from Rob Finn to match more closely what is being reported at the Pfam website.

andreasprlic · andreasprlic · commit dd61ec1803bb · 2015-06-11T13:38:33.000-07:00
diff --git a/biojava-ws/src/main/java/demo/HmmerDemo.java b/biojava-ws/src/main/java/demo/HmmerDemo.java
@@ -42,17 +42,15 @@ public static void main(String[] args){
 
 		try {
 			// first we get a UniProt sequence
-			String uniProtID = "P26663";
+			String uniProtID = "P08487";
 			ProteinSequence seq = getUniprot(uniProtID);
 
 			
 			// now we submit this sequence to the Hmmer web site
-			HmmerScan hmmer = new RemoteHmmerScan();
+			RemoteHmmerScan hmmer = new RemoteHmmerScan();
 
 			SortedSet<HmmerResult> results = hmmer.scan(seq);
 
-			
-			
 			// and now let's print out the obtained annotations
 			
 			System.out.println(String.format("#\t%15s\t%10s\t%s\t%s\t%8s\t%s",
@@ -68,7 +66,7 @@ public static void main(String[] args){
 							counter,
 							hmmerResult.getName(), domain.getHmmAcc(), 
 							domain.getSqFrom(),domain.getSqTo(),
-							hmmerResult.getEvalue(), hmmerResult.getDesc()
+							domain.getEvalue(), hmmerResult.getDesc()
 							));
 
 				}
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerDomain.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerDomain.java
@@ -44,6 +44,15 @@ public class HmmerDomain implements Comparable<HmmerDomain>, Serializable{
 	String hmmName;
 	String hmmDesc;
 	String hmmAcc;
+	Float evalue;
+
+	public Float getEvalue() {
+		return evalue;
+	}
+	public void setEvalue(Float evalue) {
+		this.evalue = evalue;
+	}
+
 	public Integer getSqFrom() {
 		return sqFrom;
 	}
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
@@ -41,16 +41,11 @@ public class RemoteHmmerScan implements HmmerScan {
 
 	public static String HMMER_SERVICE = "http://www.ebi.ac.uk/Tools/hmmer/search/hmmscan";
 
-	// The Gathering threshold indicates to HMMER to use the threshold defined in the HMM file to be searched.
-	// This ensures that there are no false positive results.
-
-	public boolean DEFAULT_SEARCH_CUT_GA = true;
-
-	private boolean searchWithCutGA;
 	public RemoteHmmerScan(){
-		searchWithCutGA = DEFAULT_SEARCH_CUT_GA;
+
 	}
 
+
 	@Override
 	public  SortedSet<HmmerResult> scan(ProteinSequence sequence) throws IOException {
 
@@ -73,8 +68,12 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
 
 		postContent.append("hmmdb=pfam");
 
-		if ( searchWithCutGA )
-			postContent.append("&cut_ga=1");
+
+		// by default hmmscan runs with the HMMER3 cut_ga parameter enabled, the "gathering freshold", which depends on
+		// the cutoffs defined in the underlying HMM files.
+		// to request a different cutoff by e-value this could be enabled:
+		//postContent.append("&E=1");
+
 
 		postContent.append("&seq=");
 		postContent.append(sequence.getSequenceAsString());
@@ -90,7 +89,6 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
 
 		connection.setRequestProperty("Accept:","application/json");
 
-
 		connection.setRequestProperty("Content-Length", "" +
 				Integer.toString(postContent.toString().getBytes().length));
 
@@ -102,8 +100,6 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
 		wr.close ();
 
 
-
-
 //		//Now get the redirect URL
 		URL respUrl = new URL( connection.getHeaderField( "Location" ));
 
@@ -158,7 +154,8 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
 				} else if ( dclO instanceof Integer){
 					dcl = (Integer) dclO;
 				} 
-				
+
+
 				hmmResult.setAcc((String)hit.get("acc"));
 				hmmResult.setDcl(dcl);
 				hmmResult.setDesc((String)hit.get("desc"));
@@ -175,9 +172,34 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
 				for ( int j= 0 ; j < hmmdomains.size() ; j++){
 					JSONObject d = hmmdomains.getJSONObject(j);
 					//System.out.println(d);
-					Integer is_reported = getInteger(d.get("is_reported"));
-					if ( is_reported != 1) {
-						//System.out.println("excluding: " + d);
+					Integer is_included = getInteger(d.get("is_included"));
+					if ( is_included == 0) {
+//						System.out.println("  excluding: " + d.get("alihmmdesc") + " " + d.get("alihmmname") + " " +
+//								hit.get("evalue") + " " +
+//								d.get("alisqfrom") + " " +
+//								d.get("alisqto"));
+						continue;
+					}
+
+
+					// this filters out multiple hits to the same clan
+					Integer outcompeted = getInteger(d.get("outcompeted"));
+					if ( outcompeted != null && outcompeted == 1) {
+//						System.out.println("  outcompeted: " + d.get("alihmmdesc") + " " + d.get("alihmmname")+ " " +
+//								hit.get("evalue") + " " +
+//								d.get("alisqfrom") + " " +
+//								d.get("alisqto")
+//						);
+						continue;
+					}
+
+					Integer significant = getInteger(d.get("significant"));
+
+					if (  significant != 1) {
+//						System.out.println("  not significant: " + d.get("alihmmdesc") + " " + d.get("alihmmname")+ " " +
+//								hit.get("evalue") + " " +
+//								d.get("alisqfrom") + " " +
+//								d.get("alisqto"));
 						continue;
 					}
 
@@ -188,13 +210,15 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
 
 					dom.setHmmFrom(getInteger(d.get("alihmmfrom")));
 					dom.setHmmTo(getInteger(d.get("alihmmto")));
-					dom.setSimCount((Integer)d.get("aliSimCount"));
+					dom.setSimCount((Integer) d.get("aliSimCount"));
 					dom.setSqFrom(getInteger(d.get("alisqfrom")));
 					dom.setSqTo(getInteger(d.get("alisqto")));
 					dom.setHmmName((String)d.get("alihmmname"));
+					dom.setEvalue(Float.parseFloat((String)d.get("ievalue")));
+
 					domains.add(dom);
 
-					System.out.println(d.get("alicsline"));
+
 				}
 
 				hmmResult.setDomains(domains);
