Merge branch 'bug/JAL-3633_read_proxy_settings_from_jalview_properties_in_getdown...

[jalview.git] / src / jalview / gui / Preferences.java

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 8eb0664..14063ac 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -31,6 +31,7 @@ import java.awt.event.MouseEvent;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.concurrent.CompletableFuture;
 
 import javax.help.HelpSetException;
 import javax.swing.JComboBox;
@@ -146,10 +147,10 @@ public class Preferences extends GPreferences
 
   /**
    * Holds name and link separated with | character. Sequence IDS and Sequences
-   * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
-   * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
-   * for first and second token specified after a pipe character at end |,|.
-   * (TODO: proper escape for using | to separate ids or sequences
+   * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and $SEQUENCES$
+   * or $SEQUENCES=/.possible | chars ./=$ and separation character for first and
+   * second token specified after a pipe character at end |,|. (TODO: proper
+   * escape for using | to separate ids or sequences
    */
 
   public static List<String> groupURLLinks;
@@ -220,19 +221,27 @@ public class Preferences extends GPreferences
 
   public static void openPreferences()
   {
-    openPreferences(0, null);
+    openPreferences(null, null);
   }
 
-  public static void openPreferences(int selectTab, String message)
+  public static void openPreferences(TabRef selectTab, String message)
   {
     Preferences p = getInstance();
-    p.selectTab(selectTab);
-    p.setMessage(message);
+    if (selectTab != null)
+      p.selectTab(selectTab, message);
     p.frame.show();
     p.frame.moveToFront();
     p.frame.grabFocus();
   }
 
+  public void selectTab(TabRef selectTab, String message)
+  {
+    this.selectTab(selectTab);
+    if (message != null)
+      this.setMessage(message);
+    this.frame.show();
+  }
+
   /**
    * Creates a new Preferences object.
    */
@@ -347,8 +356,8 @@ public class Preferences extends GPreferences
     startupCheckbox
             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
-            Cache.getDefault("www.jalview.org", "http://www.jalview.org")
-                    + "/examples/exampleFile_2_3.jar"));
+            Cache.getDefault("www.jalview.org", "https://www.jalview.org")
+                    + "/examples/exampleFile_2_7.jvp"));
 
     /*
      * Set Colours tab defaults
@@ -388,13 +397,11 @@ public class Preferences extends GPreferences
     /*
      * Set Structure tab defaults
      */
-    final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
+    final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, true);
     structFromPdb.setSelected(structSelected);
-    useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
-    useRnaView.setEnabled(structSelected);
-    addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
+    addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, true));
     addSecondaryStructure.setEnabled(structSelected);
-    addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
+    addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, true));
     addTempFactor.setEnabled(structSelected);
 
     /*
@@ -438,11 +445,27 @@ public class Preferences extends GPreferences
       {
         if (validateViewerPath())
         {
-          Cache.setProperty(
-                  structViewer.getSelectedItem().equals(
-                          ViewerType.CHIMERAX.name()) ? CHIMERAX_PATH
-                                  : CHIMERA_PATH,
-                  structureViewerPath.getText());
+          String path = structureViewerPath.getText();
+          try {
+          ViewerType type = ViewerType.valueOf(viewerType);
+          switch (type)
+          {
+          case JMOL:
+            break;
+          case CHIMERA:
+            Cache.setProperty(CHIMERA_PATH, path);
+            break;
+          case CHIMERAX:
+            Cache.setProperty(CHIMERAX_PATH, path);
+            break;
+          case PYMOL:
+            Cache.setProperty(PYMOL_PATH, path);
+            break;
+          }
+        } catch (IllegalArgumentException x)
+        {
+          Cache.log.error("Failed to set path - unknown viewer type",x);
+        }
         }
       }
     });
@@ -826,8 +849,6 @@ public class Preferences extends GPreferences
             Boolean.toString(addTempFactor.isSelected()));
     Cache.applicationProperties.setProperty(ADD_SS_ANN,
             Boolean.toString(addSecondaryStructure.isSelected()));
-    Cache.applicationProperties.setProperty(USE_RNAVIEW,
-            Boolean.toString(useRnaView.isSelected()));
     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
             Boolean.toString(structFromPdb.isSelected()));
     String viewer = structViewer.getSelectedItem().toString();
@@ -1030,8 +1051,8 @@ public class Preferences extends GPreferences
   }
 
   /**
-   * Do any necessary validation before saving settings. Return focus to the
-   * first tab which fails validation.
+   * Do any necessary validation before saving settings. Return focus to the first
+   * tab which fails validation.
    * 
    * @return
    */
@@ -1085,7 +1106,7 @@ public class Preferences extends GPreferences
    * DOCUMENT ME!
    * 
    * @param e
-   *          DOCUMENT ME!
+   *            DOCUMENT ME!
    */
   @Override
   public void cancel_actionPerformed(ActionEvent e)
@@ -1107,7 +1128,7 @@ public class Preferences extends GPreferences
    * DOCUMENT ME!
    * 
    * @param e
-   *          DOCUMENT ME!
+   *            DOCUMENT ME!
    */
   @Override
   public void annotations_actionPerformed(ActionEvent e)
@@ -1370,8 +1391,8 @@ public class Preferences extends GPreferences
   }
 
   /**
-   * Returns true if structure viewer path is to a valid executable, else shows
-   * an error dialog. Does nothing if the path is empty, as is the case for Jmol
+   * Returns true if structure viewer path is to a valid executable, else shows an
+   * error dialog. Does nothing if the path is empty, as is the case for Jmol
    * (built in to Jalview) or when Jalview is left to try default paths.
    */
   private boolean validateViewerPath()
@@ -1392,8 +1413,8 @@ public class Preferences extends GPreferences
   }
 
   /**
-   * If Chimera or ChimeraX or Pymol is selected, check it can be found on
-   * default or user-specified path, if not show a warning/help dialog
+   * If Chimera or ChimeraX or Pymol is selected, check it can be found on default
+   * or user-specified path, if not show a warning/help dialog
    */
   @Override
   protected void structureViewer_actionPerformed(String selectedItem)
@@ -1460,8 +1481,10 @@ public class Preferences extends GPreferences
                       MessageManager.getString("label.viewer_missing")),
               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
               null, options, options[0]);
+
       if (showHelp == JvOptionPane.NO_OPTION)
       {
+        this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null);
         try
         {
           Help.showHelpWindow(HelpId.StructureViewer);
@@ -1470,6 +1493,24 @@ public class Preferences extends GPreferences
           e.printStackTrace();
         }
       }
+      else if (showHelp == JvOptionPane.OK_OPTION)
+      {
+        this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null);
+        CompletableFuture<Void> cf = CompletableFuture.runAsync(() -> {
+          try
+          {
+            for (int i = 0; i < 3; i++)
+            {
+              structureViewerPath.setBackground(Color.PINK);
+              Thread.sleep(500);
+              structureViewerPath.setBackground(Color.WHITE);
+              Thread.sleep(500);
+            }
+          } catch (InterruptedException e)
+          {
+          }
+        });
+      }
     }
   }