X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FAppletParams.java;h=726734d3c832126ff3b91629e3f218aa7fe09fd3;hb=eb349b848556f0d8537755d5d869366479364d45;hp=a6c87b1939b286a4c5f285862b36cc4941ebe21f;hpb=af83e7d123133d2bb44b0bcafe538e300304a1b1;p=jalview.git

diff --git a/src/jalview/bin/AppletParams.java b/src/jalview/bin/AppletParams.java
index a6c87b1..726734d 100644
--- a/src/jalview/bin/AppletParams.java
+++ b/src/jalview/bin/AppletParams.java
@@ -8,7 +8,15 @@ import java.util.Map;
 import jalview.gui.Preferences;
 
 /**
- * Collection of all known applet tags from JalviewLite
+ * Collection of all known applet tags from JalviewLite.
+ * Three cases; can be one or more of these:
+ * 
+ * CASE I. args[] name and value for ArgsParser
+ * 
+ * CASE II. applet parameter for JalviewJSApp
+ * 
+ * CASE III. mapped to a Preference
+ * 
  * 
  * @author hansonr
  *
@@ -17,8 +25,9 @@ import jalview.gui.Preferences;
 public class AppletParams extends HashMap<String, Object>
 {
 
-  private final static String[] params = { "alignpdbfiles",
-      Preferences.ANNOTATIONCOLOUR_MAX, Preferences.ANNOTATIONCOLOUR_MIN,
+  private final static String[] params = { 
+      "alignpdbfiles",
+      "ANNOTATIONCOLOUR_MAX", "ANNOTATIONCOLOUR_MIN",
       "annotations",
       "APPLICATION_URL", "automaticScrolling", "centrecolumnlabels",
       "debug", "defaultColour", "defaultColourNuc", "defaultColourProt",
@@ -162,14 +171,20 @@ public class AppletParams extends HashMap<String, Object>
     // note that Application arguments ARE case-sensitive, but
     // Applet.getParameter() is not.
 
-    String appletName = prefName.toLowerCase();
-    String argName = prefName;
+    // prefName // CASE III
+
+    String argName = null;  // CASE I                
+
+    String appletName = prefName.toLowerCase();   // CASE II
+
+    // by nulling one or more of these names, that route will not be used.
+    
     switch (appletName)
     {
 
     case "file":
       argName = "open";
-      appletName = null;
+      prefName = null;
       value = resourcePath + value;
       break;
     case "file2":
@@ -177,27 +192,34 @@ public class AppletParams extends HashMap<String, Object>
       prefName = null;
       value = resourcePath + value;
       break;
-    case "features":
-    case "jnetfile":
-    case "jpredfile":
-    case "pdbfile":
-    case "scorefile":
-    case "sequence":
+    case "oninit":
+    case "hidefeaturegroups":
+      // applet parameter only
       // setting argName to null indicates that we want
-      // JalviewAppLoader to take care of this.
-      prefName = argName = null;
-      value = resourcePath + value;
+      // JalviewJSApp to take care of this using getParameter or getParameterAsObject      
+     prefName = argName = null;
       break;
     case "tree":
     case "treefile":
       // setting appletName to null indicates that we want
       // Jalview.doMain to taken care of this as Jalview args
       argName = "tree";
-      appletName = null;
+      prefName = null;
+      value = resourcePath + value;
+      break;
+
+    case "features":
+    case "jnetfile":
+    case "jpredfile":
+    case "pdbfile":
+    case "scorefile":
+    case "sequence":
+    case "annotations":
+      prefName = argName = null;
       value = resourcePath + value;
       break;
 
-    // non-loading preferences
+      // non-loading preferences
 
     case "defaultcolour":
       prefName = Preferences.DEFAULT_COLOUR;
@@ -239,33 +261,23 @@ public class AppletParams extends HashMap<String, Object>
     case "wrap":
       prefName = Preferences.WRAP_ALIGNMENT;
       break;
+    case "sortbytree":
+      argName = prefName;
+      prefName = Preferences.SORT_BY_TREE;
+      value = checkTF(value);
+      break;
 
     // implemented; not tested:
 
-    case "oninit":
-      prefName = null;
-      break;
-    case "annotations":
-      value = resourcePath + value;
-      argName = null;
-      break;
-    case "hidefeaturegroups":
-      // TODO
-      break;
     case "pdbseq":
-      argName = prefName = null;
-      break;
-    case "sortbytree":
-      prefName = Preferences.SORT_BY_TREE;
-      value = checkTF(value);
-      appletName = null; // taken care of by Jalview
+    case "alignpdbfiles":
+      prefName = null;
       break;
     case "format":
-      break;
-    case "alignpdbfiles":
-      argName = prefName = null;
+      argName = prefName;
       break;
     case "separator":
+      argName = prefName;
       break;
 
     // TODO: probably not relevant?
@@ -304,17 +316,13 @@ public class AppletParams extends HashMap<String, Object>
     case "widthscale":
     case "windowheight":
     case "windowwidth":
-      argName = prefName = null;
+      prefName = null;
       break;
 
     // TRUE/FALSE
 
     case "debug":
-      value = checkTF(value);
-      break;
     case "embedded":
-      value = checkTF(value);
-      break;
     case "showbutton":
       value = checkTF(value);
       break;
@@ -354,25 +362,15 @@ public class AppletParams extends HashMap<String, Object>
       prefName = Preferences.SHOW_CONSENSUS_LOGO;
       value = checkTF(value);
       break;
-    case "showfeaturegroups":
+    case "showunconserved":
+      prefName = Preferences.SHOW_UNCONSERVED;
       value = checkTF(value);
       break;
+    case "showfeaturegroups":
     case "showfeaturesettings":
-      value = checkTF(value);
-      break;
     case "showfullid":
-      value = checkTF(value);
-      break;
     case "showtreebootstraps":
-      value = checkTF(value);
-      break;
     case "showtreedistances":
-      value = checkTF(value);
-      break;
-    case "showunconserved":
-      prefName = Preferences.SHOW_UNCONSERVED;
-      value = checkTF(value);
-      break;
     case "showunlinkedtreenodes":
       value = checkTF(value);
       break;
@@ -390,6 +388,9 @@ public class AppletParams extends HashMap<String, Object>
       break;
     }
 
+    // CASE I.  args[] name and value for ArgsParser
+    //
+    // If given an argument name, 
     // put name and value into application args
     if (value != null && argName != null)
     {
@@ -399,16 +400,22 @@ public class AppletParams extends HashMap<String, Object>
         vargs.add(value.toString());
       }
     }
+    
+    // CASE II.   applet parameter for JalviewJSApp
+    
     if (value == null)
     {
       value = "false";
     }
     System.out.println("AppletParams propName=" + prefName + " argName="
-            + argName + " appletName=" + appletName + " value=" + value);
+            + argName + " appletName=" + appletName + " value=" + value);    
     if (appletName != null)
     {
       appletParams.put(appletName, value);
     }
+    
+    // CASE III.  mapped to a Preference
+    
     if (prefName != null)
     {
       Cache.setPropertyNoSave(prefName, value.toString());