Merge branch 'releases/Release_2_11_3_Branch'

[jalview.git] / src / jalview / ws / jws2 / Jws2Client.java

diff --git a/src/jalview/ws/jws2/Jws2Client.java b/src/jalview/ws/jws2/Jws2Client.java
index 0f1a25e..2f996bd 100644 (file)
--- a/src/jalview/ws/jws2/Jws2Client.java
+++ b/src/jalview/ws/jws2/Jws2Client.java
@@ -20,8 +20,19 @@
  */
 package jalview.ws.jws2;
 
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.List;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
+
+import compbio.metadata.Argument;
 import jalview.api.AlignCalcWorkerI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.JvSwingUtils;
@@ -34,18 +45,6 @@ import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.WsParamSetI;
 import jalview.ws.uimodel.AlignAnalysisUIText;
 
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.List;
-
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.event.MenuEvent;
-import javax.swing.event.MenuListener;
-
-import compbio.metadata.Argument;
-
 /**
  * provides metadata for a jabaws2 service instance - resolves names, etc.
  * 
@@ -122,9 +121,10 @@ public abstract class Jws2Client extends jalview.ws.WSClient
       WsParamSetI prset = jobParams.getPreset();
       if (prset == null)
       {
-        paramset = jobParams.isServiceDefaults() ? null
-                : JabaParamStore
-                        .getJabafromJwsArgs(jobParams.getJobParams());
+        paramset =
+                /* JAL-3739 always take values from input form */
+                /* jobParams.isServiceDefaults() ? null : */
+                JabaParamStore.getJabafromJwsArgs(jobParams.getJobParams());
         this.preset = null;
       }
       else
@@ -367,7 +367,7 @@ public abstract class Jws2Client extends jalview.ws.WSClient
       if (service != null
               && !fave.getService().hosturl.equals(service.hosturl))
       {
-        Cache.log.debug("Changing AACon service to " + service.hosturl
+        Console.debug("Changing AACon service to " + service.hosturl
                 + " from " + fave.getService().hosturl);
         fave.setService(service);
       }
@@ -389,7 +389,7 @@ public abstract class Jws2Client extends jalview.ws.WSClient
       if (!service.serviceType.toString()
               .equals(compbio.ws.client.Services.AAConWS.toString()))
       {
-        Cache.log.warn(
+        Console.warn(
                 "Ignoring invalid preferred service for AACon calculations (service type was "
                         + service.serviceType + ")");
         service = null;