better preferences/properties

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index facc826..359eabe 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -871,6 +871,43 @@ public class Preferences extends GPreferences
     }
   }
 
+  public static void setAppletDefaults()
+  {
+
+    // http://www.jalview.org/old/v2_8/examples/appletParameters.html
+
+    // showConservation true or false Default is true.
+    // showQuality true or false Default is true.
+    // showConsensus true or false Default is true.
+    // showFeatureSettings true or false Shows the feature settings window when
+    // startin
+    // showTreeBootstraps true or false (default is true) show or hide branch
+    // bootstraps
+    // showTreeDistances true or false (default is true) show or hide branch
+    // lengths
+    // showUnlinkedTreeNodes true or false (default is false) indicate if
+    // unassociated nodes should be highlighted in the tree view
+    // showUnconserved true of false (default is false) When true, only gaps and
+    // symbols different to the consensus sequence ions of the alignment
+    // showGroupConsensus true of false (default is false) When true, shows
+    // consensus annotation row for any groups on the alignment. (since 2.7)
+    // showGroupConservation true of false (default is false) When true, shows
+    // amino-acid property conservation annotation row for any groups on the
+    // showConsensusHistogram true of false (default is true) When true, shows
+    // the percentage occurence of the consensus symbol for each column as a
+    // showSequenceLogo true of false (default is false) When true, shows a
+    // sequence logo above the consensus sequence (overlaid above the Consensus
+
+    Cache.setPropertyNoSave("SHOW_CONSERVATION", "true");
+    Cache.setPropertyNoSave("SHOW_QUALITY", "false");
+    Cache.setPropertyNoSave("SHOW_CONCENSUS", "true");
+    Cache.setPropertyNoSave("SHOW_UNCONSERVED", "false");
+    Cache.setPropertyNoSave("SHOW_GROUP_CONSERVATION", "false");
+    Cache.setPropertyNoSave("SHOW_GROUP_CONCENSUS", "false");
+
+    // TODO -- just a start here
+  }
+
   /**
    * Do any necessary validation before saving settings. Return focus to the
    * first tab which fails validation.

diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index c0f65c4..e4e0b6c 100644 (file)
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -517,7 +517,7 @@ public class Tree extends DatastoreItem
    * referenced in input data has already been associated with jalview objects.
    * 
    * @param tp
-   * @param alignFrame
+   * @param loaderFrame
    * @return Object[] { AlignmentView, AlignmentI - reference alignment for
    *         input }
    */

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index de20556..dbe46f6 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -25,6 +25,7 @@ import jalview.analysis.GeneticCodeI;
 import jalview.analysis.GeneticCodes;
 import jalview.api.SplitContainerI;
 import jalview.bin.Cache;
+import jalview.bin.Jalview;
 import jalview.gui.JvSwingUtils;
 import jalview.gui.Preferences;
 import jalview.io.FileFormats;
@@ -221,7 +222,7 @@ public class GAlignFrame extends JInternalFrame
     {
 
       // for Web-page embedding using id=align-frame-div
-      setName("jalview-alignment");
+      setName(Jalview.getAppID("alignment"));
 
       jbInit();
       setJMenuBar(alignFrameMenuBar);

diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java
index 943e705..051bac7 100755 (executable)
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@ -21,6 +21,7 @@
 package jalview.jbgui;
 
 import jalview.api.AlignmentViewPanel;
+import jalview.bin.Jalview;
 import jalview.io.FileFormatException;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -150,7 +151,7 @@ public abstract class GDesktop extends JFrame
    */
   private void jbInit() throws Exception
   {
-    setName("jalview-desktop");
+    setName(Jalview.getAppID("desktop"));
     FileMenu.setText(MessageManager.getString("action.file"));
     HelpMenu.setText(MessageManager.getString("action.help"));
     VamsasMenu.setText("Vamsas");

diff --git a/src/jalview/jbgui/GPCAPanel.java b/src/jalview/jbgui/GPCAPanel.java
index a6498d2..04aab37 100755 (executable)
--- a/src/jalview/jbgui/GPCAPanel.java
+++ b/src/jalview/jbgui/GPCAPanel.java
@@ -20,6 +20,7 @@
  */
 package jalview.jbgui;
 
+import jalview.bin.Jalview;
 import jalview.util.ImageMaker.TYPE;
 import jalview.util.MessageManager;
 
@@ -88,8 +89,8 @@ public class GPCAPanel extends JInternalFrame
 
   private void jbInit() throws Exception
   {
-    setName("jalview-pca");
-    this.getContentPane().setLayout(new BorderLayout());
+    setName(Jalview.getAppID("pca"));
+    getContentPane().setLayout(new BorderLayout());
     JPanel jPanel2 = new JPanel();
     jPanel2.setLayout(new FlowLayout());
     JLabel jLabel1 = new JLabel();

diff --git a/src/jalview/jbgui/GRnaStructureViewer.java b/src/jalview/jbgui/GRnaStructureViewer.java
index e0bec25..a90bd48 100644 (file)
--- a/src/jalview/jbgui/GRnaStructureViewer.java
+++ b/src/jalview/jbgui/GRnaStructureViewer.java
@@ -20,6 +20,8 @@
  */
 package jalview.jbgui;
 
+import jalview.bin.Jalview;
+
 import javax.swing.JInternalFrame;
 
 @SuppressWarnings("serial")
@@ -38,9 +40,7 @@ public class GRnaStructureViewer extends JInternalFrame
 
   private void jbInit() throws Exception
   {
-    
-    setName("jalview-rnastructureviewer");
-
+    setName(Jalview.getAppID("rnastructureviewer"));
   }
 
 }

diff --git a/src/jalview/jbgui/GSplitFrame.java b/src/jalview/jbgui/GSplitFrame.java
index a75760d..ed715c8 100644 (file)
--- a/src/jalview/jbgui/GSplitFrame.java
+++ b/src/jalview/jbgui/GSplitFrame.java
@@ -20,6 +20,7 @@
  */
 package jalview.jbgui;
 
+import jalview.bin.Jalview;
 import jalview.util.Platform;
 
 import java.awt.Component;
@@ -57,7 +58,7 @@ public class GSplitFrame extends JInternalFrame
    */
   public GSplitFrame(GAlignFrame top, GAlignFrame bottom)
   {
-    setName("jalview-splitframe");
+    setName(Jalview.getAppID("splitframe"));
     this.topFrame = top;
     this.bottomFrame = bottom;
 

diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java
index dfee3e2..e16d63a 100644 (file)
--- a/src/jalview/jbgui/GStructureViewer.java
+++ b/src/jalview/jbgui/GStructureViewer.java
@@ -21,6 +21,7 @@
 package jalview.jbgui;
 
 import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Jalview;
 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 import jalview.util.ImageMaker.TYPE;
 import jalview.util.MessageManager;
@@ -89,7 +90,7 @@ public abstract class GStructureViewer extends JInternalFrame
   private void jbInit() throws Exception
   {
 
-    setName("jalview-structureviewer");
+    setName(Jalview.getAppID("structureviewer"));
 
     JMenuBar menuBar = new JMenuBar();
     this.setJMenuBar(menuBar);

diff --git a/src/jalview/jbgui/GTreePanel.java b/src/jalview/jbgui/GTreePanel.java
index d184e76..0f9c2a2 100755 (executable)
--- a/src/jalview/jbgui/GTreePanel.java
+++ b/src/jalview/jbgui/GTreePanel.java
@@ -20,6 +20,7 @@
  */
 package jalview.jbgui;
 
+import jalview.bin.Jalview;
 import jalview.util.ImageMaker.TYPE;
 import jalview.util.MessageManager;
 
@@ -92,7 +93,7 @@ public class GTreePanel extends JInternalFrame
 
   private void jbInit() throws Exception
   {
-    setName("jalview-tree");
+    setName(Jalview.getAppID("tree"));
     this.getContentPane().setLayout(borderLayout1);
     this.setBackground(Color.white);
     this.setFont(new java.awt.Font("Verdana", 0, 12));

diff --git a/src/jalview/util/Platform.java b/src/jalview/util/Platform.java
index 66ce556..96940e5 100644 (file)
--- a/src/jalview/util/Platform.java
+++ b/src/jalview/util/Platform.java
@@ -32,6 +32,7 @@ import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.Reader;
+import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.Properties;
 
@@ -458,7 +459,7 @@ public class Platform
 
     System.out.println(
             "Platform id=" + id + " reading Info." + key + " = " + value);
-    p.put(id + "_" + key, value);
+    p.put(key, value);
 
     /**
      * @j2sNative
@@ -612,4 +613,34 @@ public class Platform
 
   }
 
+  public static URL getDocumentBase()
+  {
+    try
+    {
+      return (isJS() ? new URL(/**
+                                * @j2sNative J2S.thisApplet._applet.appletViewer.appletDocumentBase
+                                *            ||
+                                */
+              "") : null);
+    } catch (MalformedURLException e)
+    {
+      return null;
+    }
+  }
+
+  public static URL getCodeBase()
+  {
+    try
+    {
+      return (isJS() ? new URL(/**
+                                * @j2sNative J2S.thisApplet._applet.appletViewer.appletCodeBase
+                                *            ||
+                                */
+              "") : null);
+    } catch (MalformedURLException e)
+    {
+      return null;
+    }
+  }
+
 }