From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Thu, 31 May 2012 17:24:21 +0000 (+0000)
Subject: in progress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=519257ef66e0bb653135e77227a16113bdecddf8;p=jalview.git

in progress
---

diff --git a/forester/java/src/org/forester/ws/hmmer/Test.java b/forester/java/src/org/forester/ws/hmmer/Test.java
new file mode 100644
index 0000000..7d53e61
--- /dev/null
+++ b/forester/java/src/org/forester/ws/hmmer/Test.java
@@ -0,0 +1,51 @@
+
+package org.forester.ws.hmmer;
+
+import java.io.BufferedReader;
+import java.io.DataOutputStream;
+import java.io.InputStreamReader;
+import java.net.HttpURLConnection;
+import java.net.URL;
+import java.net.URLEncoder;
+
+public class Test {
+
+    public static void main( final String[] args ) {
+        try {
+            final URL url = new URL( "http://hmmer.janelia.org/search/hmmscan" );
+            final HttpURLConnection connection = ( HttpURLConnection ) url.openConnection();
+            connection.setDoOutput( true );
+            connection.setDoInput( true );
+            connection.setInstanceFollowRedirects( false );
+            connection.setRequestMethod( "POST" );
+            connection.setRequestProperty( "Content-Type", "application/x-www-form-urlencoded" );
+            connection.setRequestProperty( "Accept", "application/json" );
+            //Add the database and the sequence. Add more options as you wish!
+            final String urlParameters = "hmmdb=" + URLEncoder.encode( "pfam", "UTF-8" ) + "&seq="
+                    + ">seq\nEMGPSENDPNLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPV"
+                    + "NSLEKHSWYHGPVSRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEG"
+                    + "RVYHYRINTASDGKLYVSSESRFNTLAELVHHHSTVADGLITTLHYPAP";
+            connection.setRequestProperty( "Content-Length", "" + Integer.toString( urlParameters.getBytes().length ) );
+            //Send request
+            final DataOutputStream wr = new DataOutputStream( connection.getOutputStream() );
+            wr.writeBytes( urlParameters );
+            wr.flush();
+            wr.close();
+            //Now get the redirect URL
+            final URL respUrl = new URL( connection.getHeaderField( "Location" ) );
+            final HttpURLConnection connection2 = ( HttpURLConnection ) respUrl.openConnection();
+            connection2.setRequestMethod( "GET" );
+            connection2.setRequestProperty( "Accept", "text/x-yaml" );
+            //Get the response and print it to the screen
+            final BufferedReader in = new BufferedReader( new InputStreamReader( connection2.getInputStream() ) );
+            String inputLine;
+            while ( ( inputLine = in.readLine() ) != null ) {
+                System.out.println( inputLine );
+            }
+            in.close();
+        }
+        catch ( final Exception e ) {
+            throw new RuntimeException( e );
+        }
+    }
+}