Jalview-JS/JAL-3253 applet params jpredfile, jnetfile

debug comments out, fixes for missing annotation file post-load tasks

diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java
index 404c497..6caa1c7 100644 (file)
--- a/src/jalview/api/FeatureRenderer.java
+++ b/src/jalview/api/FeatureRenderer.java
@@ -125,7 +125,7 @@ public interface FeatureRenderer
   List<String> getFeatureGroups();
 
   /**
-   * get groups that are visible/invisible
+   * get groups that are visible/invisible -- JalviewLite only?
    * 
    * @param visible
    * @return
@@ -133,7 +133,7 @@ public interface FeatureRenderer
   List<String> getGroups(boolean visible);
 
   /**
-   * Set visibility for a list of groups
+   * Set visibility for a list of groups -- JalviewLite only?
    * 
    * @param toset
    * @param visible

diff --git a/src/jalview/api/JalviewApp.java b/src/jalview/api/JalviewApp.java
index 1d67bc2..7215227 100644 (file)
--- a/src/jalview/api/JalviewApp.java
+++ b/src/jalview/api/JalviewApp.java
@@ -26,7 +26,7 @@ public interface JalviewApp
   public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs,
           String[][] chains, String[] protocols);
 
-  public void updateForLoader();
+  public void updateForAnnotations();
 
   public AlignViewportI getViewport();
 

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 402f9bf..7bf0c72 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1177,13 +1177,18 @@ public class Jalview implements ApplicationSingletonI
     return id + (frameType == null ? "" : "-" + frameType);
   }
 
+  /**
+   * Handle all JalviewLite applet parameters
+   * 
+   * @param aparser
+   * @param af
+   */
   private void loadAppletParams(ArgsParser aparser, AlignFrame af)
   {
     Jalview me = this;
     JalviewApp app = new JalviewApp()
     {
 
-
       @Override
       public String getParameter(String name)
       {
@@ -1198,12 +1203,18 @@ public class Jalview implements ApplicationSingletonI
                 : "true".equalsIgnoreCase(stn));
       }
 
+      /**
+       * Get the applet-like document base even though this is an application.
+       */
       @Override
       public URL getDocumentBase()
       {
         return Platform.getDocumentBase();
       }
 
+      /**
+       * Get the applet-like code base even though this is an application.
+       */
       @Override
       public URL getCodeBase()
       {
@@ -1216,6 +1227,21 @@ public class Jalview implements ApplicationSingletonI
         return Jalview.getCurrentAlignFrame().getViewport();
       }
 
+      /**
+       * features
+       * 
+       */
+      @Override
+      public boolean parseFeaturesFile(String filename,
+              DataSourceType protocol)
+      {
+        return af.parseFeaturesFile(filename, protocol);
+      }
+
+      /**
+       * scorefile
+       * 
+       */
       @Override
       public boolean loadScoreFile(String sScoreFile) throws IOException
       {
@@ -1224,18 +1250,21 @@ public class Jalview implements ApplicationSingletonI
         return true;
       }
 
+      /**
+       * annotations, jpredfile, jnetfile
+       * 
+       */
       @Override
-      public boolean parseFeaturesFile(String filename,
-              DataSourceType protocol)
+      public void updateForAnnotations()
       {
-        return af.parseFeaturesFile(filename, protocol);
+        Jalview.getCurrentAlignFrame().updateForAnnotations();
       }
 
       @Override
       public void loadTree(NewickFile fin, String treeFile)
               throws IOException
       {
-        // n/a -- already done
+        // n/a -- already done by standard Jalview command line processing
       }
 
       @Override
@@ -1262,13 +1291,6 @@ public class Jalview implements ApplicationSingletonI
       }
 
       @Override
-      public void updateForLoader()
-      {
-        // TODO Auto-generated method stub
-
-      }
-
-      @Override
       public void setFeatureGroupState(String[] groups, boolean state)
       {
         // TODO Auto-generated method stub

diff --git a/src/jalview/bin/JalviewAppLoader.java b/src/jalview/bin/JalviewAppLoader.java
index 194d619..4ac4ffd 100644 (file)
--- a/src/jalview/bin/JalviewAppLoader.java
+++ b/src/jalview/bin/JalviewAppLoader.java
@@ -260,7 +260,7 @@ public class JalviewAppLoader
                 app.getViewport().getAlignment(), 0, false);
         // false == do not add sequence profile from concise output
         app.getViewport().getAlignment().setupJPredAlignment();
-        app.updateForLoader();
+        app.updateForAnnotations();
         result = true;
       } catch (Exception ex)
       {
@@ -290,7 +290,7 @@ public class JalviewAppLoader
       if (new AnnotationFile().annotateAlignmentView(app.getViewport(),
               param, protocol))
       {
-        app.updateForLoader();
+        app.updateForAnnotations();
         result = true;
       }
       else

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 5cb599f..8c251cc 100644 (file)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -2484,7 +2484,7 @@ public class JalviewLite extends Applet
   }
 
   @Override
-  public void updateForLoader()
+  public void updateForAnnotations()
   {
     loaderFrame.alignPanel.fontChanged();
     loaderFrame.alignPanel.setScrollValues(0, 0);

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 343dfbe..f2b790d 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -4805,11 +4805,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
       if (isAnnotation)
       {
-
-        alignPanel.adjustAnnotationHeight();
-        viewport.updateSequenceIdColours();
-        buildSortByAnnotationScoresMenu();
-        alignPanel.paintAlignment(true, true);
+        updateForAnnotations();
       }
     } catch (Exception ex)
     {
@@ -4838,6 +4834,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
+   * Do all updates necessary after an annotation file such as jnet. Also called
+   * from Jalview.loadAppletParams for "annotations", "jnetFile"
+   */
+  public void updateForAnnotations()
+  {
+    alignPanel.adjustAnnotationHeight();
+    viewport.updateSequenceIdColours();
+    buildSortByAnnotationScoresMenu();
+    alignPanel.paintAlignment(true, true);
+  }
+
+  /**
    * Method invoked by the ChangeListener on the tabbed pane, in other words
    * when a different tabbed pane is selected by the user or programmatically.
    */