Improved consistency between JPredWS and MsaWS

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index a688de2..0d7145c 100755 (executable)
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -12,20 +12,25 @@ import jalview.analysis.AlignSeq;
 import ext.vamsas.*;\r
 \r
 \r
-public class JPredClient\r
+public class JPredClient extends WSClient\r
 {\r
-  int jobsRunning = 0;\r
-  ext.vamsas.JpredSoapBindingStub server;\r
-  WebserviceInfo wsInfo;\r
+  ext.vamsas.JPredWS server;\r
   String altitle = "";\r
   java.util.Hashtable SequenceInfo = null;\r
+  private void setWebService() {\r
+    WebServiceName = "JNetWS";\r
+    WebServiceJobTitle = "JNet secondary structure prediction";\r
+    WebServiceReference="\"Cuff J. A and Barton G.J (1999) Application of enhanced "\r
+        + "multiple sequence alignment profiles to improve protein secondary structure prediction, "\r
+        + "Proteins 40:502-511\".";\r
+    WsURL="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";\r
+  }\r
   public JPredClient(String title, SequenceI[] msf)\r
   {\r
-    wsInfo = new WebserviceInfo("JNet secondary structure prediction on "+title,\r
-          "\"Cuff J. A and Barton G.J (1999) Application of enhanced multiple sequence alignment profiles to improve protein secondary structure prediction, Proteins 40:502-511\".");\r
-\r
+    wsInfo = new WebserviceInfo(WebServiceJobTitle, WebServiceReference);\r
     SequenceI seq = msf[0];\r
-    altitle = "JNet prediction on "+seq.getName()+" using "+title;\r
+    altitle = "JNet prediction on "+seq.getName()+" using alignment from "+title;\r
+\r
     wsInfo.setProgressText("Job details for MSA based prediction ("+title+") on sequence :\n>"\r
                    + seq.getName() + "\n"\r
                    + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n");\r
@@ -35,11 +40,14 @@ public class JPredClient
     JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default\r
     // JBPNote url will be set from properties\r
     try {\r
-      this.server = (JpredSoapBindingStub) loc.getjpred(new java.net.URL("http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred"));\r
+      this.server = loc.getjpred(new java.net.URL(WsURL));\r
     }\r
     catch (Exception ex) {\r
-      wsInfo.setProgressText("Serious! JPred Service location failed\nfor URL :"\r
-                     +loc.getjpredAddress()+"\n"+ex.getMessage());\r
+      JOptionPane.showMessageDialog(Desktop.desktop, "The Secondary Structure Prediction Service named "\r
+                                    +WebServiceName+" at "+WsURL+" couldn't be located.",\r
+                                    "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);\r
+      wsInfo.setProgressText("Serious! "+WebServiceName+" Service location failed\nfor URL :"\r
+                     +WsURL+"\n"+ex.getMessage());\r
     }\r
 \r
     JPredThread jthread = new JPredThread(msf);\r
@@ -48,22 +56,23 @@ public class JPredClient
 \r
   public JPredClient(String title, SequenceI seq)\r
   {\r
-    wsInfo = new WebserviceInfo("JNet secondary structure prediction Job",\r
-                                "\"Cuff J. A and Barton G.J (1999) Application of enhanced multiple sequence alignment profiles to improve protein secondary structure prediction, Proteins 40:502-511\".");\r
-\r
-\r
+    setWebService();\r
+    wsInfo = new WebserviceInfo(WebServiceJobTitle, WebServiceReference);\r
     wsInfo.setProgressText("Job details for prediction on sequence :\n>"\r
                    + seq.getName() + "\n" + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n");\r
     altitle = "JNet prediction for sequence "+seq.getName()+" from "+title;\r
     SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);\r
-// TODO: put proper url in\r
+\r
     JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default\r
     try {\r
-      this.server = (JpredSoapBindingStub) loc.getjpred(new java.net.URL("http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred")); // JBPNote will be set from properties\r
+      this.server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties\r
     }\r
     catch (Exception ex) {\r
-      wsInfo.setProgressText("Serious! JPred Service location failed\nfor URL :"\r
-                     +loc.getjpredAddress()+"\n"+ex.getMessage());\r
+      JOptionPane.showMessageDialog(Desktop.desktop, "The Secondary Structure Prediction Service named "\r
+                                    +WebServiceName+" at "+WsURL+" couldn't be located.",\r
+                                    "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);\r
+      wsInfo.setProgressText("Serious! "+WebServiceName+" Service location failed\nfor URL :"\r
+                     +WsURL+"\n"+ex.getMessage());\r
     }\r
 \r
     JPredThread jthread = new JPredThread(seq);\r
@@ -157,7 +166,7 @@ public class JPredClient
         } else {\r
           jobId = server.predict(sequence);\r
         }\r
-        System.out.println(jobId);\r
+        System.out.println(WsURL+" Job Id '"+jobId+"'");\r
       }\r
       catch (Exception e)\r
       {\r

diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index 1507c12..876c0c1 100755 (executable)
--- a/src/jalview/ws/MsaWSClient.java
+++ b/src/jalview/ws/MsaWSClient.java
@@ -16,20 +16,13 @@ import vamsas.objects.*;
 
 
 public class MsaWSClient
+    extends WSClient
 {
-  int jobsRunning = 0;
-  ext.vamsas.MuscleWS server;
-  WebserviceInfo wsInfo;
-  /**
-   * MsaWSClient
-   *
-   * @param msa SequenceI[]
-   */
-
-  String WebServiceName;
-  String WebServiceJobTitle;
-  String WebServiceReference;
-  String WsURL;
+    /**
+     * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
+     */
+    ext.vamsas.MuscleWS server;
+
   private boolean setWebService(String MsaWSName) {
     if (MsaWServices.info.containsKey(MsaWSName)) {
       WebServiceName = MsaWSName;
@@ -43,9 +36,6 @@ public class MsaWSClient
     }
   }
 
-//  public MsaWSClient(String MsaWSName, SequenceI[] msa) {
-//    MsaWSClient(MsaWSName, msa, true);
-//  }
 
   public MsaWSClient(String MsaWSName, String altitle, SequenceI[] msa, boolean submitGaps, boolean preserveOrder)
   {
@@ -62,8 +52,7 @@ public class MsaWSClient
     // TODO: MuscleWS transmuted to generic MsaWS client
     MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default
     try {
-      this.server = (MuscleWS) loc.getMuscleWS(// JBPNote will be set from properties
-      new java.net.URL(WsURL));
+      this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));
     }
     catch (Exception ex) {
       wsInfo.setProgressText("Serious! "+WebServiceName+" Service location failed\nfor URL :"
@@ -213,7 +202,8 @@ public class MsaWSClient
       {
         vamsas.objects.simple.WsJobId jobsubmit = server.align(seqs);
         if (jobsubmit.getStatus()==1) {
-          System.out.println(jobId=jobsubmit.getJobId());
+          jobId=jobsubmit.getJobId();
+          System.out.println(WsURL+" Job Id '"+jobId+"'");
         } else {
           throw new Exception(jobsubmit.getJobId());
         }

diff --git a/src/jalview/ws/MsaWServices.java b/src/jalview/ws/MsaWServices.java
index 8ea666b..69b5e23 100755 (executable)
--- a/src/jalview/ws/MsaWServices.java
+++ b/src/jalview/ws/MsaWServices.java
@@ -12,6 +12,9 @@ import java.util.Hashtable;
  * @author not attributable
  * @version 1.0
  */
+/**
+ * TODO: MsaWServices will be set from properties and be dynamically discovered.
+ */
 public class MsaWServices {
   public static Hashtable info;
   static