JAL-4389 Adjust preferences menu to work with any WSDiscoverer

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 19d929e..67b45e3 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -40,6 +40,7 @@ import javax.swing.JComboBox;
 import javax.swing.JFileChooser;
 import javax.swing.JInternalFrame;
 import javax.swing.JPanel;
+import javax.swing.JTabbedPane;
 import javax.swing.JTextField;
 import javax.swing.ListSelectionModel;
 import javax.swing.RowFilter;
@@ -58,7 +59,6 @@ import jalview.hmmer.HmmerCommand;
 import jalview.util.FileUtils;
 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.bin.ApplicationSingletonProvider;
 import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
 import jalview.bin.Cache;
 import jalview.bin.Console;
@@ -84,6 +84,10 @@ import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.util.UrlConstants;
 import jalview.ws.sifts.SiftsSettings;
+import jalview.ws2.client.api.WebServiceDiscovererI;
+import jalview.ws2.client.ebi.JobDispatcherWSDiscoverer;
+import jalview.ws2.client.jpred4.JPred4WSDiscoverer;
+import jalview.ws2.client.slivka.SlivkaWSDiscoverer;
 
 /**
  * DOCUMENT ME!
@@ -297,7 +301,6 @@ public class Preferences extends GPreferences implements ApplicationSingletonI
 
   private WsPreferences wsPrefs;
 
-  private SlivkaPreferences slivkaPrefs;
   private OptionsParam promptEachTimeOpt = new OptionsParam(
           MessageManager.getString("label.prompt_each_time"),
           "Prompt each time");
@@ -373,9 +376,13 @@ public class Preferences extends GPreferences implements ApplicationSingletonI
       wsTab.add(wsPrefs, BorderLayout.CENTER);
     }
 
-    slivkaPrefs = new SlivkaPreferences();
-    slivkaTab.add(slivkaPrefs, BorderLayout.CENTER);
-   
+    if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true))
+      addWebServiceTab(tabbedPane, SlivkaWSDiscoverer.getInstance());
+    if (Cache.getDefault("SHOW_EBI_SERVICES", true))
+      addWebServiceTab(tabbedPane, JobDispatcherWSDiscoverer.getInstance());
+    if (Cache.getDefault("SHOW_JPRED4_SERVICES", true))
+      addWebServiceTab(tabbedPane, JPred4WSDiscoverer.getInstance());
+
     int width = 500, height = 450;
     if (Platform.isAMacAndNotJS())
     {
@@ -870,6 +877,16 @@ public class Preferences extends GPreferences implements ApplicationSingletonI
     loadLastSavedBackupsOptions();
   }
 
+  
+  private void addWebServiceTab(JTabbedPane tabs, WebServiceDiscovererI discoverer)
+  {
+    String name = discoverer.getName();
+    JPanel tab = new JPanel();
+    tab.setLayout(new BorderLayout());
+    tab.add(new WS2PreferencesPanel(discoverer), BorderLayout.CENTER);
+    tabs.add(tab, name + " services");
+  }
+  
   /**
    * A helper method that sets the items and initial selection in a character
    * rendering option list (Prompt each time/Lineart/Text)

diff --git a/src/jalview/gui/SlivkaPreferences.java b/src/jalview/gui/WS2PreferencesPanel.java
similarity index 98%
rename from src/jalview/gui/SlivkaPreferences.java
rename to src/jalview/gui/WS2PreferencesPanel.java
index 5f2e106..d5dc39e 100644 (file)
--- a/src/jalview/gui/SlivkaPreferences.java
+++ b/src/jalview/gui/WS2PreferencesPanel.java
@@ -39,7 +39,7 @@ import jalview.ws2.client.api.WebServiceDiscovererI;
 import jalview.ws2.client.slivka.SlivkaWSDiscoverer;
 
 @SuppressWarnings("serial")
-public class SlivkaPreferences extends JPanel
+public class WS2PreferencesPanel extends JPanel
 {
   {
     setLayout(new BoxLayout(this, BoxLayout.PAGE_AXIS));
@@ -202,8 +202,8 @@ public class SlivkaPreferences extends JPanel
     final int i = urlListTable.getSelectedRow();
     if (i >= 0)
     {
-      urls.remove(i);
-      statuses.remove(i);
+      URL url = urls.remove(i);
+      statuses.remove(url);
       urlTableModel.fireTableRowsDeleted(i, i);
       discoverer.setUrls(urls);
     }
@@ -286,7 +286,6 @@ public class SlivkaPreferences extends JPanel
   private void moveTableRow(int fromIndex, int toIndex)
   {
     URL url = urls.get(fromIndex);
-    int status = statuses.get(fromIndex);
     urls.set(fromIndex, urls.get(toIndex));
     urls.set(toIndex, url);
     if (urlListTable.getSelectedRow() == fromIndex)
@@ -360,10 +359,10 @@ public class SlivkaPreferences extends JPanel
     add(progressBar);
   }
 
-  SlivkaPreferences()
+  WS2PreferencesPanel(WebServiceDiscovererI discoverer)
   {
     // Initial URLs loading
-    discoverer = SlivkaWSDiscoverer.getInstance();
+    this.discoverer = discoverer;
     urls.addAll(discoverer.getUrls());
     for (URL url : urls)
     {

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index dfe08ed..099f75c 100755 (executable)
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -358,7 +358,6 @@ public class GPreferences extends JPanel
    */
   protected JPanel wsTab = new JPanel();
 
-  protected JPanel slivkaTab = new JPanel();
   /*
    * Backups tab components
    * a lot of these are member variables instead of local variables only so that they
@@ -405,7 +404,7 @@ public class GPreferences extends JPanel
 
   protected JTextArea backupfilesExampleLabel = new JTextArea();
 
-  private final JTabbedPane tabbedPane = new JTabbedPane();
+  protected final JTabbedPane tabbedPane = new JTabbedPane();
 
   private JLabel messageLabel = new JLabel("", JLabel.CENTER);
 
@@ -502,11 +501,8 @@ public class GPreferences extends JPanel
       tabbedPane.add(initStartupTab(),
               MessageManager.getString("label.startup"));
       wsTab.setLayout(new BorderLayout());
-      tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
+      tabbedPane.add(wsTab, "JABAWS " + MessageManager.getString("label.web_services"));
     }
-    
-    slivkaTab.setLayout(new BorderLayout());
-    tabbedPane.add(slivkaTab, "Slivka Services");
 
     /*
      * Handler to validate a tab before leaving it - currently only for

diff --git a/src/jalview/ws2/client/api/AbstractWebServiceDiscoverer.java b/src/jalview/ws2/client/api/AbstractWebServiceDiscoverer.java
index c2c7db1..6e32d48 100644 (file)
--- a/src/jalview/ws2/client/api/AbstractWebServiceDiscoverer.java
+++ b/src/jalview/ws2/client/api/AbstractWebServiceDiscoverer.java
@@ -16,7 +16,7 @@ import jalview.ws2.actions.api.ActionI;
 import jalview.ws2.api.WebService;
 
 public abstract class AbstractWebServiceDiscoverer implements WebServiceDiscovererI
-{
+{  
   // TODO: we can use linked hash map to group and retrieve services by type.
   protected List<WebService<?>> services = List.of();
 

diff --git a/src/jalview/ws2/client/api/WebServiceDiscovererI.java b/src/jalview/ws2/client/api/WebServiceDiscovererI.java
index 4a09ef7..f5a73c0 100644 (file)
--- a/src/jalview/ws2/client/api/WebServiceDiscovererI.java
+++ b/src/jalview/ws2/client/api/WebServiceDiscovererI.java
@@ -25,6 +25,13 @@ public interface WebServiceDiscovererI extends WebServiceProviderI
   public static final int STATUS_UNKNOWN = -2;
 
   /**
+   * Get the short name of the discoverer.
+   * 
+   * @return discoverer name
+   */
+  String getName();
+  
+  /**
    * List the urls used by this discoverer.
    */
   List<URL> getUrls();

diff --git a/src/jalview/ws2/client/ebi/JobDispatcherWSDiscoverer.java b/src/jalview/ws2/client/ebi/JobDispatcherWSDiscoverer.java
index 48d0ba5..e357479 100644 (file)
--- a/src/jalview/ws2/client/ebi/JobDispatcherWSDiscoverer.java
+++ b/src/jalview/ws2/client/ebi/JobDispatcherWSDiscoverer.java
@@ -41,6 +41,11 @@ public final class JobDispatcherWSDiscoverer extends AbstractWebServiceDiscovere
     return instance;
   }
   
+  public String getName()
+  {
+    return "Job Dispatcher";
+  }
+
   public static void setParamManager(ParamManager manager)
   {
     paramManager = manager;

diff --git a/src/jalview/ws2/client/jpred4/JPred4WSDiscoverer.java b/src/jalview/ws2/client/jpred4/JPred4WSDiscoverer.java
index ada0d2f..8daa3b6 100644 (file)
--- a/src/jalview/ws2/client/jpred4/JPred4WSDiscoverer.java
+++ b/src/jalview/ws2/client/jpred4/JPred4WSDiscoverer.java
@@ -44,6 +44,11 @@ public class JPred4WSDiscoverer extends AbstractWebServiceDiscoverer
     return instance;
   }
 
+  public String getName()
+  {
+    return "JPred4";
+  }
+
   public static void setParamManager(ParamManager manager)
   {
     paramManager = manager;

diff --git a/src/jalview/ws2/client/slivka/SlivkaWSDiscoverer.java b/src/jalview/ws2/client/slivka/SlivkaWSDiscoverer.java
index 51e27ad..165226f 100644 (file)
--- a/src/jalview/ws2/client/slivka/SlivkaWSDiscoverer.java
+++ b/src/jalview/ws2/client/slivka/SlivkaWSDiscoverer.java
@@ -53,6 +53,11 @@ public class SlivkaWSDiscoverer extends AbstractWebServiceDiscoverer
     return instance;
   }
 
+  public String getName()
+  {
+    return "Slivka";
+  }
+
   public static void setParamManager(ParamManager manager)
   {
     paramManager = manager;