Improved consistency between JPredWS and MsaWS

[jalview.git] / src / jalview / ws / JPredClient.java

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