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Commit cd4820c

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andreasprlicandreasprlic
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biojava#276 updating to latest location of HMMER web services, now at EBI.
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+30-37Lines changed: 30 additions & 37 deletions

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‎biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java‎

Copy file name to clipboardExpand all lines: biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
+30-37Lines changed: 30 additions & 37 deletions
Original file line numberDiff line numberDiff line change
@@ -32,14 +32,17 @@
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import java.util.TreeSet;
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/** Makes remote calls to the Hmmer3 web site and returns Pfam domain annotations for an input protein sequence.
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/** Makes remote calls to the HMMER web service at the EBI web site and returns Pfam domain annotations for an input protein sequence.
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*
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* @author Andreas Prlic
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* @since 3.0.3
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*/
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public class RemoteHmmerScan implements HmmerScan {
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public static String HMMER_SERVICE = "http://hmmer.janelia.org/search/hmmscan";
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public static String HMMER_SERVICE = "http://www.ebi.ac.uk/Tools/hmmer/search/hmmscan";
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// The Gathering threshold indicates to HMMER to use the threshold defined in the HMM file to be searched.
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// This ensures that there are no false positive results.
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public boolean DEFAULT_SEARCH_CUT_GA = true;
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@@ -66,8 +69,16 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence) throws IOException
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*/
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public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation) throws IOException{
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StringBuffer postContent = new StringBuffer();
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postContent.append("hmmdb=pfam");
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if ( searchWithCutGA )
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postContent.append("&cut_ga=1");
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postContent.append("&seq=");
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postContent.append(sequence.getSequenceAsString());
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String urlparameters = prepareParameters(sequence, searchWithCutGA);
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HttpURLConnection connection = (HttpURLConnection) serviceLocation.openConnection();
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connection.setDoOutput(true);
@@ -76,24 +87,29 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
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connection.setInstanceFollowRedirects(false);
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connection.setRequestMethod("POST");
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connection.setRequestProperty("Content-Type", "application/x-www-form-urlencoded");
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connection.setRequestProperty("Accept", "application/json");
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connection.setRequestProperty("Accept:","application/json");
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connection.setRequestProperty("Content-Length", "" +
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Integer.toString(urlparameters.toString().getBytes().length));
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Integer.toString(postContent.toString().getBytes().length));
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//Send request
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DataOutputStream wr = new DataOutputStream (
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connection.getOutputStream ());
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wr.writeBytes (urlparameters);
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wr.write(postContent.toString().getBytes());
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wr.flush ();
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wr.close ();
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//Now get the redirect URL
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// //Now get the redirect URL
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URL respUrl = new URL( connection.getHeaderField( "Location" ));
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int responseCode = connection.getResponseCode();
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if ( responseCode == 500){
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System.err.println("something went wrong!" + urlparameters);
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System.err.println("something went wrong!" + serviceLocation);
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System.err.println(connection.getResponseMessage());
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}
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@@ -110,8 +126,11 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
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String inputLine;
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StringBuffer result = new StringBuffer();
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while ((inputLine = in.readLine()) != null)
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while ((inputLine = in.readLine()) != null) {
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//System.out.println(inputLine);
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result.append(inputLine);
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}
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in.close();
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// process the response and build up a container for the data.
@@ -174,6 +193,8 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
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dom.setSqTo(getInteger(d.get("alisqto")));
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dom.setHmmName((String)d.get("alihmmname"));
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domains.add(dom);
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System.out.println(d.get("alicsline"));
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}
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hmmResult.setDomains(domains);
@@ -188,34 +209,6 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
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}
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private String prepareParameters(ProteinSequence sequence,
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boolean searchWithCutGA) throws UnsupportedEncodingException {
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StringBuffer urlParameters = new StringBuffer();
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urlParameters.append("hmmdb=");
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urlParameters.append(URLEncoder.encode("pfam","UTF-8"));
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// search by cut_ga, not e-values
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//cut_ga' : '',
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if ( searchWithCutGA ) {
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urlParameters.append("&cut_ga=");
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//urlParameters.append(URLEncoder.encode("1","UTF-8"));
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}
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urlParameters.append("&seq=");
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urlParameters.append(URLEncoder.encode(">seq\n"+sequence.toString(), "UTF-8"));
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return urlParameters.toString();
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}
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private Integer getInteger(Object object) {
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if ( object instanceof Integer)

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