Jalview-JS/JAL-3253 applet param GROUPS

diff --git a/src/jalview/bin/AppletParams.java b/src/jalview/bin/AppletParams.java
index 0ccbdc5..290ae01 100644 (file)
--- a/src/jalview/bin/AppletParams.java
+++ b/src/jalview/bin/AppletParams.java
@@ -125,134 +125,146 @@ public class AppletParams extends HashMap<String, String>
       String arg = args[i].trim();
       if (arg.startsWith("name="))
       {
-        String key = getAttr(arg, "name");
+        String appName = getAttr(arg, "name");
         String value = getAttr(arg, "value");
-        String name = key;
-        switch (name.toLowerCase())
+        String appletName = appName.toLowerCase();
+
+        // note that Application arguments ARE case-sensitive, but
+        // Applet.getParameter() is not.
+
+        switch (appletName)
         {
-        case "alignpdbfiles":
-          break;
-        case "annotationcolour_max":
-          name = "ANNOTATIONCOLOUR_MAX";
+        // tested, working:
+        case "jnetfile":
+          value = resourcePath + value;
+          appName = null;
           break;
-        case "annotationcolour_min":
-          name = "ANNOTATIONCOLOUR_MIN";
+        case "jpredfile":
+          value = resourcePath + value;
+          appName = null;
           break;
-        case "annotations":
-          value = checkTF(value);
+        case "features":
+          value = resourcePath + value;
+          appName = null;
           break;
-        case "application_url":
-          name = "APPLICATION_URL";
+        case "pdbfile":
+          appName = "PDBFILE";
+          value = resourcePath + value;
+          appName = null;
           break;
-        case "automaticscrolling":
-          name = "automaticScrolling";
+        case "tree":
+        case "treefile":
+          appName = "tree";
+          value = resourcePath + value;
+          appletName = null; // taken care of by Jalview
           break;
-        case "centrecolumnlabels":
+        // implemented; not tested:
+        case "annotations":
+          value = resourcePath + value;
+          appName = null;
           break;
         case "defaultcolour":
-          name = "DEFAULT_COLOUR"; // defaultColour
+          appName = "DEFAULT_COLOUR"; // defaultColour
           break;
         case "defaultcolournuc":
-          name = "DEFAULT_COLOUR_NUC";// defaultColourNuc
+          appName = "DEFAULT_COLOUR_NUC";// defaultColourNuc
           break;
         case "defaultcolourprot":
-          name = "DEFAULT_COLOUR_PROT";// defaultColourProt";
+          appName = "DEFAULT_COLOUR_PROT";// defaultColourProt";
+          break;
+        case "annotationcolour_max":
+          appName = "ANNOTATIONCOLOUR_MAX";
+          break;
+        case "annotationcolour_min":
+          appName = "ANNOTATIONCOLOUR_MIN";
+          break;
+        case "centrecolumnlabels":
+          appName = null;
           break;
         case "enablesplitframe":
-          name = "enableSplitFrame";
+          appName = "enableSplitFrame";
           break;
         case "externalstructureviewer":
           break;
-        case "features":
-          value = resourcePath + value;
+        case "alignpdbfiles":
           break;
-        case "format":
+        case "application_url":
+          appName = "APPLICATION_URL";
+          break;
+        case "automaticscrolling":
+          appName = "automaticScrolling";
           break;
         case "heightscale":
-          name = "heightScale";
+          appName = "heightScale";
           break;
         case "hidefeaturegroups":
           break;
         case "jalviewhelpurl":
           break;
-        case "jnetfile":
-          value = resourcePath + value;
-          break;
-        case "jpredfile":
-          value = resourcePath + value;
-          break;
         case "label":
           break;
         case "linklabel_":
-          name = "linkLabel_";
+          appName = "linkLabel_";
           break;
         case "linklabel_1":
-          name = "linkLabel_1";
+          appName = "linkLabel_1";
           break;
         case "linkurl_":
-          name = "linkURL_";
+          appName = "linkURL_";
           break;
         case "nojmol":
           break;
         case "normaliselogo":
-          name = "normaliseLogo";
+          appName = "normaliseLogo";
           break;
         case "normalisesequencelogo":
-          name = "normaliseSequenceLogo";
+          appName = "normaliseSequenceLogo";
           break;
         case "oninit":
           break;
-        case "pdbfile":
-          name = "PDBFILE";
-          break;
         case "pdbseq":
-          name = "PDBSEQ";
+          appName = "PDBSEQ";
           break;
         case "relaxedidmatch":
           break;
         case "resolvetocodebase":
           break;
         case "rgb":
-          name = "RGB";
+          appName = "RGB";
           break;
         case "scaleproteinascdna":
-          name = "scaleProteinAsCdna";
-          break;
-        case "scorefile":
-          name = "scoreFile";
-          value = resourcePath + value;
+          appName = "scaleProteinAsCdna";
           break;
         case "separator":
           break;
         case "sequence":
           break;
         case "sortby":
-          name = "sortBy";
           break;
         case "sortbytree":
           value = checkTF(value);
-          key = null; // taken care of by Jalview
+          appletName = null; // taken care of by Jalview
           break;
-        case "tree":
-        case "treefile":
-          name = "tree";
+        case "format":
+          break;
+        case "scorefile":
+          appName = "scoreFile";
           value = resourcePath + value;
-          key = null; // taken care of by Jalview
           break;
         case "uppercase":
-          name = "upperCase";
+          appName = "upperCase";
           break;
         case "userdefinedcolour":
-          name = "colour";
+          appName = "colour";
           break;
         case "widthscale":
-          name = "widthScale";
+          appName = "widthScale";
           break;
         case "windowheight":
-          name = "windowHeight";
+          appName = "windowHeight";
           break;
         case "windowwidth":
-          name = "windowWidth";
+          appName = "windowWidth";
           break;
         case "wrap":
           break;
@@ -262,7 +274,7 @@ public class AppletParams extends HashMap<String, String>
           value = checkTF(value);
           break;
         case "file":
-          name = "open";
+          appName = "open";
           value = resourcePath + value;
           break;
         case "file2":
@@ -272,69 +284,69 @@ public class AppletParams extends HashMap<String, String>
           value = checkTF(value);
           break;
         case "showannotation":
-          name = "SHOW_ANNOTATIONS";
+          appName = "SHOW_ANNOTATIONS";
           value = checkTF(value);
           break;
         case "showbutton":
           value = checkTF(value);
           break;
         case "showconsensus":
-          name = "SHOW_CONSENSUS_LOGO";
+          appName = "SHOW_CONSENSUS_LOGO";
           value = checkTF(value);
           break;
         case "showconsensushistogram":
-          name = "SHOW_CONSENSUS_HISTOGRAM";
+          appName = "SHOW_CONSENSUS_HISTOGRAM";
           value = checkTF(value);
           break;
         case "showconservation":
-          name = "SHOW_CONSERVATION";
+          appName = "SHOW_CONSERVATION";
           value = checkTF(value);
           break;
         case "showfeaturegroups":
           value = checkTF(value);
           break;
         case "showfeaturesettings":
-          name = "showFeatureSettings";
+          appName = "showFeatureSettings";
           value = checkTF(value);
           break;
         case "showfullid":
-          name = "showFullId";
+          appName = "showFullId";
           value = checkTF(value);
           break;
         case "showgroupconsensus":
-          name = "SHOW_GROUP_CONSENSUS";
+          appName = "SHOW_GROUP_CONSENSUS";
           value = checkTF(value);
           break;
         case "showgroupconservation":
-          name = "SHOW_GROUP_CONSERVATION";
+          appName = "SHOW_GROUP_CONSERVATION";
           value = checkTF(value);
           break;
         case "showoccupancy":
-          name = "SHOW_OCCUPANCY";
+          appName = "SHOW_OCCUPANCY";
           value = checkTF(value);
           break;
         case "showquality":
-          name = "SHOW_QUALITY";
+          appName = "SHOW_QUALITY";
           value = checkTF(value);
           break;
         case "showsequencelogo":
-          name = "showSequenceLogo";
+          appName = "showSequenceLogo";
           value = checkTF(value);
           break;
         case "showtreebootstraps":
-          name = "showTreeBootstraps";
+          appName = "showTreeBootstraps";
           value = checkTF(value);
           break;
         case "showtreedistances":
-          name = "showTreeDistances";
+          appName = "showTreeDistances";
           value = checkTF(value);
           break;
         case "showunconserved":
-          name = "showUnconserved";
+          appName = "showUnconserved";
           value = checkTF(value);
           break;
         case "showunlinkedtreenodes":
-          name = "showUnlinkedTreeNodes";
+          appName = "showUnlinkedTreeNodes";
           value = checkTF(value);
           break;
         default:
@@ -342,7 +354,7 @@ public class AppletParams extends HashMap<String, String>
         }
         if (value != null)
         {
-          vargs.add(name);
+          vargs.add(appName);
           if (value != "true")
           {
             vargs.add(value);
@@ -352,11 +364,12 @@ public class AppletParams extends HashMap<String, String>
         {
           value = "false";
         }
-        System.out.println("AppletParams name=" + name + " value=" + value);
-        Cache.setPropertyNoSave(name, value);
-        if (key != null)
+        System.out.println("AppletParams appName=" + appName + "appletName="
+                + appletName + " value=" + value);
+        Cache.setPropertyNoSave(appName, value);
+        if (appletName != null)
         {
-          appletParams.put(key, value);
+          appletParams.put(appletName, value);
         }
       }
     }

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index f2b790d..ecd9155 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -4928,6 +4928,32 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
+   * Change the display state for the given feature groups -- Added by BH from
+   * JalviewLite
+   * 
+   * @param groups
+   *          list of group strings
+   * @param state
+   *          visible or invisible
+   */
+  public void setFeatureGroupState(String[] groups, boolean state)
+  {
+    jalview.api.FeatureRenderer fr = null;
+    viewport.setShowSequenceFeatures(true);
+    if (alignPanel != null
+            && (fr = alignPanel.getFeatureRenderer()) != null)
+    {
+
+      fr.setGroupVisibility(Arrays.asList(groups), state);
+      alignPanel.getSeqPanel().seqCanvas.repaint();
+      if (alignPanel.overviewPanel != null)
+      {
+        alignPanel.overviewPanel.updateOverviewImage();
+      }
+    }
+  }
+
+  /**
    * Open the dialog for regex description parsing.
    */
   @Override
@@ -5799,4 +5825,5 @@ class PrintThread extends Thread
       }
     }
   }
+
 }