JAL-976 fix AACon name typo in source and GUI

[jalview.git] / src / jalview / ws / jws2 / dm / AAConSettings.java

diff --git a/src/jalview/ws/jws2/dm/AAConSettings.java b/src/jalview/ws/jws2/dm/AAConSettings.java
new file mode 100644 (file)
index 0000000..f226ce1
--- /dev/null
+++ b/src/jalview/ws/jws2/dm/AAConSettings.java
@@ -0,0 +1,126 @@
+package jalview.ws.jws2.dm;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import compbio.metadata.Argument;
+import compbio.metadata.Option;
+import compbio.metadata.Preset;
+
+import jalview.ws.jws2.JabaParamStore;
+import jalview.ws.jws2.JabaPreset;
+import jalview.ws.jws2.ParameterUtils;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.ParamManager;
+import jalview.ws.params.WsParamSetI;
+
+/**
+ * preferences for running AACon service
+ * 
+ * @author jprocter TODO: refactor to a generic 'last job and service run'
+ *         container ?
+ */
+public class AAConSettings extends jalview.ws.params.AutoCalcSetting 
+{
+  Jws2Instance service;
+
+  public AAConSettings(boolean autoUpdate, Jws2Instance service,
+          WsParamSetI preset, List<ArgumentI> jobArgset)
+  {
+    super(preset, jobArgset, autoUpdate);
+    this.service = service;
+  }
+
+  public Jws2Instance getService()
+  {
+    return service;
+  }
+
+  public void setService(Jws2Instance service)
+  {
+    this.service = service;
+    if (preset != null)
+    {
+      // migrate preset to new service
+      for (String url : preset.getApplicableUrls())
+      {
+        if (url.equals(service.getUri()))
+        {
+          return;
+        }
+      }
+      WsParamSetI pr = service.getParamStore().getPreset(preset.getName());
+      if (pr instanceof JabaPreset && preset instanceof JabaPreset)
+      {
+        // easy - Presets are identical (we assume)
+        preset = pr;
+        return;
+      }
+      List<ArgumentI> oldargs = new ArrayList<ArgumentI>(), newargs = new ArrayList<ArgumentI>();
+      oldargs.addAll(preset.getArguments());
+      // need to compare parameters
+      for (ArgumentI newparg : pr.getArguments())
+      {
+        if (!oldargs.remove(newparg))
+        {
+          newargs.add(newparg);
+        }
+      }
+      if (oldargs.size() == 0 && newargs.size() == 0)
+      {
+        // exact match.
+        preset = pr;
+        return;
+      }
+      // Try even harder to migrate arguments.
+      throw new Error("Parameter migration not implemented yet");
+    }
+  }
+
+  public List<Argument> getJobArgset()
+  {
+    return jobArgset==null ? null : JabaParamStore.getJabafromJwsArgs(jobArgset);
+  }
+
+  public void setJobArgset(List<Argument> jobArgset)
+  {
+    // TODO: test if parameters valid for service
+    this.jobArgset = jobArgset==null ? null : JabaParamStore.getJwsArgsfromJaba(jobArgset);
+  }
+
+  public String getWsParamFile()
+  {
+    List<Option> opts=null;
+    if (jobArgset!=null)
+    {
+      opts = JabaParamStore.getJabafromJwsArgs(jobArgset);
+    } else {
+      if (preset!=null)
+      {
+        opts = JabaParamStore.getJabafromJwsArgs(preset.getArguments());
+      }
+    }
+    if (opts==null  || opts.size()==0)
+    {
+      return "";
+    }
+    StringBuffer pset=new StringBuffer();
+    for (String ps:ParameterUtils.writeParameterSet(opts, " "))
+    {
+      pset.append(ps); pset.append("\n");
+    }
+    return pset.toString();
+  }
+
+  @Override
+  public String getServiceURI()
+  {
+    return service.getServiceTypeURI();
+  }
+  @Override
+  public String[] getServiceURLs()
+  {
+    return new String[] { service.getUri() };
+  }
+}