first jemboss clustalw client for jalview.

diff --git a/src/jalview/ws/Jemboss.java b/src/jalview/ws/Jemboss.java
new file mode 100755 (executable)
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--- /dev/null
+++ b/src/jalview/ws/Jemboss.java
@@ -0,0 +1,161 @@
+package jalview.ws;
+
+/**
+ * <p>Title: JalviewX</p>
+ * <p>Description: Jalview Re-engineered</p>
+ * <p>Copyright: Copyright (c) 2004</p>
+ * <p>Company: Dundee University</p>
+ * @author not attributable
+ * @version 1.0
+ * Commenced 14th January 2005, Jim Procter
+ * Contains and depends on GPL-2 jemboss classes
+ * see http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Jemboss/index.html
+ */
+
+/**
+ * Philosophy
+ * Jemboss webservices are implemented here as re-entrant synchronous SOAP
+ * exchanges. It is up to the user of the class whether these exchanges
+ * are executed in their own thread to effect background processing
+ * functionality.
+ *
+ * Things to do
+ * Test threadability
+ * Standardise the exceptions (currently errors are output on stdout)
+ * Allow server configuration
+ */
+
+import jalview.io.*;
+import jalview.datamodel.*;
+import ext.jemboss.*;
+import ext.jemboss.soap.*;
+import java.io.*;
+import java.net.*;
+import java.util.Hashtable;
+import java.util.Enumeration;
+import java.security.Security;
+
+
+public class Jemboss
+{
+  private static ext.jemboss.JembossParams vamsas_server;
+
+  public Jemboss()
+  {
+    // Set up default jalview-jemboss server properties
+    //
+    vamsas_server = new JembossParams();
+    System.out.println("Jemboss Server Init\n"
+                       + vamsas_server.serverDescription()
+                       + "\nUser Authorisation ? "
+                       + vamsas_server.getUseAuth()
+                       +"\n");
+  }
+
+  /* public void updateServer(JembossParams props)
+  {
+    vamsas_server.updateJembossPropStrings (
+      props.getEmbossEnvironmentArray());
+  }
+  */
+
+  public SequenceI[] clustalW(SequenceI[] sequences)
+  {
+
+    // Simplest client call - with gumph from jemboss.server.TestPrivateServer
+    if (vamsas_server.getPublicSoapURL().startsWith("https"))
+    {
+      //SSL settings
+      //    System.setProperty ("javax.net.debug", "all");
+      com.sun.net.ssl.internal.ssl.Provider p =
+          new com.sun.net.ssl.internal.ssl.Provider();
+      Security.addProvider(p);
+
+      //have to do it this way to work with JNLP
+      URL.setURLStreamHandlerFactory( new URLStreamHandlerFactory()
+      {
+        public URLStreamHandler createURLStreamHandler(final String protocol)
+        {
+          if(protocol != null && protocol.compareTo("https") == 0)
+          {
+            return new com.sun.net.ssl.internal.www.protocol.https.Handler();
+          }
+          return null;
+        }
+      });
+
+      //location of keystore
+      System.setProperty("javax.net.ssl.trustStore",
+                         "resources/client.keystore");
+
+      String jembossClientKeyStore = System.getProperty("user.home") +
+          "/.jembossClientKeystore";
+
+      try
+      {
+        new JembossJarUtil("resources/client.jar").writeByteFile(
+      "client.keystore",jembossClientKeyStore);
+        System.setProperty("javax.net.ssl.trustStore",
+                           jembossClientKeyStore);
+      }
+      catch(Exception exp){}
+
+    }
+
+    Hashtable filesToMove = new Hashtable();
+    String embossCommand = "emma -sequence jalseqs.fasta -auto";
+    // Load sequence file into hash
+    filesToMove.put("jalseqs.fasta",
+                    jalview.io.FastaFile.print(sequences,124,false).getBytes());
+
+    if(vamsas_server.getUseAuth() == true)
+      if(vamsas_server.getServiceUserName() == null)
+        System.out.println("jalview.Jemboss: OOPS! Authentication required!");
+
+    // submit to private server
+    try
+    {
+      JembossRun thisrun = new JembossRun(embossCommand,"",
+                                          filesToMove,vamsas_server);
+      Hashtable h = thisrun.hash();
+      Enumeration enum = h.keys();
+      // Find the alignment generated and parse it
+      while (enum.hasMoreElements())
+      {
+        String thiskey = (String)enum.nextElement().toString();
+        if (thiskey.endsWith(".aln"))
+        {
+          // FormatAdapter, and IdentifyFile use a protocol string
+          // to work out what 'file' is - file/url/Alignmentasastring
+          String alfile = h.get(thiskey).toString();
+          String format = IdentifyFile.Identify(alfile, "Paste");
+          SequenceI[] alignment = null;
+
+          if (FormatProperties.contains(format))
+            alignment = FormatAdapter.read(alfile, "Paste", format);
+          else
+            System.out.println("jalview.Jemboss: Unknown format "+format+"\n");
+          if (alignment == null)
+            System.out.println("jalview.Jemboss: Couldn't read response:\n"
+                               + alfile + "\n---EOF\n");
+          else
+            return alignment;
+        }
+
+      }
+
+    }
+    catch (JembossSoapException eae)
+    {
+      System.out.println("jalview.Jemboss: SOAP ERROR :"+embossCommand
+                         + "\n" + eae);
+    }
+    catch (Exception e) {
+      System.out.println("jalview.Jemboss: Some other failure :\n"
+                         +e.getMessage()+"\n");
+    }
+
+    return null;
+  }
+}
+