From 7713b430384995e970ec67129c0ce9a9ad2c9855 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 29 Oct 2010 16:11:04 +0000
Subject: [PATCH] refactored so public interfaces take instances of
 WsParamSetI, and ensured that name of preset is logged in
 job output (JAL-667)

---
 src/jalview/ws/jws2/MsaWSClient.java |   11 +++--
 src/jalview/ws/jws2/MsaWSThread.java |   85 ++++++++++++++++++++++++++++------
 2 files changed, 77 insertions(+), 19 deletions(-)

diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java
index 92f0a3e..8a352bf 100644
--- a/src/jalview/ws/jws2/MsaWSClient.java
+++ b/src/jalview/ws/jws2/MsaWSClient.java
@@ -50,7 +50,7 @@ public class MsaWSClient extends Jws2Client
 
   AlignFrame alignFrame;
 
-  private Preset preset;
+  private WsParamSetI preset;
 
   private List<Argument> paramset;
 
@@ -112,10 +112,11 @@ public class MsaWSClient extends Jws2Client
       return;
     }
     server = sh.service;
+    this.preset=preset;
     if (preset != null)
     {
-      if (preset instanceof JabaPreset)
-      {
+      if (!((preset instanceof JabaPreset) || preset instanceof JabaWsParamSet)) {
+      /*{
         this.preset = ((JabaPreset) preset).p;
       }
       else if (preset instanceof JabaWsParamSet)
@@ -137,7 +138,7 @@ public class MsaWSClient extends Jws2Client
         paramset = newargs;
       }
       else
-      {
+      {*/
         throw new Error(
                 "Implementation error: Can only instantiate Jaba parameter sets.");
       }
@@ -167,7 +168,7 @@ public class MsaWSClient extends Jws2Client
       }
       else
       {
-        this.preset = ((JabaPreset) prset).p;
+        this.preset = prset; // ((JabaPreset) prset).p;
         paramset = null; // no user supplied parameters.
       }
     }
diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index 6f06731..bd86bf0 100644
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -34,6 +34,8 @@ import jalview.gui.*;
 import jalview.ws.AWsJob;
 import jalview.ws.WSClientI;
 import jalview.ws.JobStateSummary;
+import jalview.ws.jws2.dm.JabaWsParamSet;
+import jalview.ws.params.WsParamSetI;
 
 /**
  * <p>
@@ -69,7 +71,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
   {
     long lastChunk = 0;
 
-    Preset preset = null;
+    WsParamSetI preset = null;
 
     List<Argument> arguments = null;
 
@@ -373,6 +375,67 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       return alignmentProgram;
     }
 
+    public boolean hasArguments()
+    {
+      return (arguments != null && arguments.size() > 0)
+              || (preset != null && preset instanceof JabaWsParamSet);
+    }
+
+    public List<Argument> getJabaArguments()
+    {
+      List<Argument> newargs = new ArrayList<Argument>();
+      if (preset != null && preset instanceof JabaWsParamSet)
+      {
+        newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
+      }
+      if (arguments != null && arguments.size() > 0)
+      {
+        newargs.addAll(arguments);
+      }
+      return newargs;
+    }
+
+    /**
+     * add a progess header to status string containing presets/args used
+     */
+    public void addInitialStatus()
+    {
+      if (preset != null)
+      {
+        jobProgress.append("Using "
+                + (preset instanceof JabaPreset ? "Server" : "User")
+                + "Preset: " + preset.getName());
+        if (preset instanceof JabaWsParamSet)
+        {
+          for (Argument opt : ((JabaWsParamSet) preset).getjabaArguments())
+          {
+            jobProgress.append(opt.getName() + " " + opt.getDefaultValue()
+                    + "\n");
+          }
+        }
+      }
+      if (arguments != null && arguments.size() > 0)
+      {
+        jobProgress.append("With custom parameters : \n");
+        // merge arguments with preset's own arguments.
+        for (Argument opt : arguments)
+        {
+          jobProgress.append(opt.getName() + " " + opt.getDefaultValue()
+                  + "\n");
+        }
+      }
+      jobProgress.append("\nJob Output:\n");
+    }
+
+    public boolean isPresetJob()
+    {
+      return preset != null && preset instanceof JabaPreset;
+    }
+
+    public Preset getServerPreset()
+    {
+      return (isPresetJob()) ? ((JabaPreset) preset).p : null;
+    }
   }
 
   String alTitle; // name which will be used to form new alignment window.
@@ -416,7 +479,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
    * @param seqset
    *          Alignment
    */
-  MsaWSThread(MsaWS server2, Preset preset, List<Argument> paramset,
+  MsaWSThread(MsaWS server2, WsParamSetI preset, List<Argument> paramset,
           String wsUrl, WebserviceInfo wsinfo,
           jalview.gui.AlignFrame alFrame, String wsname, String title,
           AlignmentView _msa, boolean subgaps, boolean presorder,
@@ -580,21 +643,15 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     }
     try
     {
-      // TODO: get the parameters (if any) for this job and submit the job
-      if (j.arguments != null && j.arguments.size() > 0)
+      j.addInitialStatus(); // list the presets/parameters used for the job in
+                            // status
+      if (j.isPresetJob())
       {
-        StringBuffer pset = new StringBuffer();
-        for (Argument arg : j.arguments)
-        {
-          pset.append(arg.getName() + " " + arg.getDefaultValue() + "\n");
-        }
-        j.setStatus("Custom Parameters:\n" + pset.toString()
-                + "\nJob Output:\n");
-        j.setJobId(server.customAlign(j.seqs, j.arguments));
+        j.setJobId(server.presetAlign(j.seqs, j.getServerPreset()));
       }
-      else if (j.preset != null)
+      else if (j.hasArguments())
       {
-        j.setJobId(server.presetAlign(j.seqs, j.preset));
+        j.setJobId(server.customAlign(j.seqs,j.getJabaArguments()));
       }
       else
       {
-- 
1.7.10.2