JAL-3446 reorganized JalviewJSApp (accidentally put that in jalview/api)

and
fixes for 2-applet example

- API.md
- follows commit 01717e2 (missing JAL-3446 tag)

diff --git a/doc/JalviewJS-API.md b/doc/JalviewJS-API.md
index 1302021..64cae62 100644 (file)
--- a/doc/JalviewJS-API.md
+++ b/doc/JalviewJS-API.md
@@ -22,7 +22,6 @@
   public String getFeatures(String format);
   public String getFeaturesFrom(AlignFrame alf, String format);
   public Object getFrameForSource(VamsasSource source);
-  public jalview.renderer.seqfeatures.FeatureRenderer getNewFeatureRenderer(AlignViewportI vp);
   public String getParameter(String name);
   public String getSelectedSequences();
   public String getSelectedSequences(String sep);
@@ -30,7 +29,6 @@
   public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, String format, String suffix);
   public String getSelectedSequencesFrom(AlignFrame alf);
   public String getSelectedSequencesFrom(AlignFrame alf, String sep);
-  public Object[] getSelectionForListener(SequenceGroup seqsel, ColumnSelection colsel, HiddenColumns hidden, SelectionSource source, Object alignFrame);
   public String getSeparator();
   public AlignViewportI getViewport();
   public void highlight(String sequenceId, String position, String alignedPosition);
@@ -81,43 +79,43 @@
 - indicate null options
 - use standard arrays; no need for special separators
 - possibly return more actual objects, not just strings
- 
-  public boolean addPdbFile(AlignFrame alFrame, String sequenceId, String pdbEntryString, String pdbFile);
-  public String getAlignment(AlignFrame alf, String format, boolean includeStartEnd);
-  public String[] getAlignmentOrder(AlignFrame alf);
-  public String getAnnotation(AlignFrame alf);
-  public Object getAppletParameter(String name, boolean asString);
-  public URL getCodeBase();
-  public URL getDocumentBase();
-  public String[] getFeatureGroups();
-  public String[] getFeatureGroupsOfState(boolean visible);
-  public String getFeatures(AlignFrame alf, String format);
-  public jalview.renderer.seqfeatures.FeatureRenderer getNewFeatureRenderer(AlignViewportI vp);
-  public String getParameter(String name);
-  public String[] getSelectedSequences(AlignFrame alf);
-  public String[] getSelectedSequencesAsAlignment(AlignFrame alf, String format, boolean includeStartEnd);
-  public Object[] getSelectionForListener(SequenceGroup seqsel, ColumnSelection colsel, HiddenColumns hidden, SelectionSource source, Object alignFrame);
-  public AlignViewportI getViewport();
-  public void highlight(AlignFrame alf, String sequenceId, String position, String alignedPosition);
-  public AlignFrame loadAlignment(String text, String title);
-  public void loadAnnotation(AlignFrame alf, String annotation);
-  public boolean loadFeatures(AlignFrame alf, String features, boolean autoenabledisplay);
-  public boolean loadScoreFile(String sScoreFile) throws IOException;
-  public void newFeatureSettings();
-  public void newStructureView(PDBEntry pdb, SequenceI[] seqs, String[] chains, DataSourceType protocol);
-  public Object openPcaPanel(AlignFrame af, String modelName);
-  public Object openTreePanel(AlignFrame af, String treeType, String modelName);
-  public String[] orderBy(AlignFrame alf, String order, String undoName);
-  public Object parseArguments(String[] args);
-  public boolean parseFeaturesFile(String param, DataSourceType protocol);
-  public void removeSelectionListener(AlignFrame af, String listener);
-  public void scrollViewTo(AlignFrame alf, String topRow, String leftHandColumn);
-  public void select(AlignFrame alf, String[] sequenceIds, String[] columns);
-  public void setFeatureGroupState(AlignFrame alf, String groups, boolean state);
-  public void setSelectionListener(AlignFrame af, String listener);
-  public void showOverview();
-  public void updateForAnnotations();
+- moves AlignFrame to last parameter, as it is likely to be unnecessary
 
+public boolean addPdbFile(String sequenceId, String pdbId, String pdbFile, AlignFrame alFrame);
+public String getAlignment(String format, boolean addSuffix, AlignFrame alf);
+public String[] getAlignmentOrder(AlignFrame alf);
+public String getAnnotation(AlignFrame alf);
+public URL getCodeBase();
+public URL getDocumentBase();
+public String[] getFeatureGroups(AlignFrame alf);
+public String[] getFeatureGroupsOfState(boolean visible, AlignFrame alf);
+public String getFeatures(String format, AlignFrame alf);
+public String getParameter(String name);
+public Object getParameterAsObject(String name);
+public SequenceI[] getSelectedSequences(AlignFrame alf);
+public AlignFrame newView();
+public AlignFrame newView(String name);
+public AlignFrame newViewFrom(AlignFrame alf);
+public AlignFrame newViewFrom(AlignFrame alf, String name);
+public String getSelectedSequencesAsAlignment(String format, boolean addSuffix, AlignFrame alf);
+public void highlight(String sequenceId, String position, String alignedPosition, AlignFrame alf);
+public AlignFrame loadAlignment(String data, String title, int width, int height);
+public void loadAnnotation(String annotation, AlignFrame alf);
+public boolean loadFeatures(String features, boolean autoenabledisplay, AlignFrame alf);
+public boolean loadScoreFile(String sScoreFile, AlignFrame alf);
+public Object openPcaPanel(String modelName, AlignFrame alf);
+public Object openTreePanel(String treeType, String modelName, AlignFrame alf);
+public boolean orderAlignment(String[] ids, String undoName, AlignFrame alf);
+public Object parseArguments(String[] args);
+public void removeSelectionListener(String listener, AlignFrame af);
+public void scrollViewTo(int topRow, int leftHandColumn, AlignFrame alf);
+public void select(String[] sequenceIds, String[] columns, AlignFrame alf);
+public void setFeatureGroupState(String[] groups, boolean state, AlignFrame alf);
+public void setSelectionListener(String listener, AlignFrame alf);
+public void showOverview();
+public void showStructure(String pdbID, String fileType, AlignFrame alf);
+
+ 
 # unknown methods/shouldn't be in interface?
 
   public Object getFrameForSource(VamsasSource source);

diff --git a/src/jalview/api/JalviewJSApi.java b/src/jalview/api/JalviewJSApi.java
new file mode 100644 (file)
index 0000000..895fd15
--- /dev/null
+++ b/src/jalview/api/JalviewJSApi.java
@@ -0,0 +1,412 @@
+package jalview.api;
+
+import java.net.URL;
+
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+
+/**
+ * JAL-3369 JalviewJS API BH 2019.07.17
+ * 
+ * @author hansonr
+ *
+ */
+public interface JalviewJSApi
+{
+
+  /**
+   * bind a pdb file to a sequence in the given AlignFrame.
+   * 
+   * @param sequenceId
+   *          - sequenceId within the dataset or null
+   * @param pdbId
+   *          - the four-character PDB ID
+   * @param pdbFile
+   *          - pdb file - either a URL or a valid PDB file or null.
+   * @param alFrame
+   *          - null or specific AlignFrame. This specifies the dataset that
+   *          will be searched for a seuqence called sequenceId
+   * 
+   * @return true if binding was success
+   */
+  public boolean addPdbFile(String sequenceId, String pdbId, String pdbFile,
+          AlignFrame alFrame);
+
+  /**
+   * Get alignment as format with or without the jalview start-end sequence
+   * suffix appended.
+   * 
+   * @param format
+   * @param addSuffix
+   *          (default false)
+   * @param alf
+   *          (default current)
+   * 
+   * @return
+   */
+  public String getAlignment(String format, boolean addSuffix,
+          AlignFrame alf);
+
+  /**
+   * Get an array of sequence IDs reflecting the order of the alignment in the
+   * specified alignment frame
+   * 
+   * @param alf
+   *          (default current)
+   * @return array of sequence IDs
+   */
+  public String[] getAlignmentOrder(AlignFrame alf);
+
+  /**
+   * Get alignment view alf's annotation as an annotation file
+   * 
+   * @param alf
+   *          (default current)
+   * @return annotation
+   */
+  public String getAnnotation(AlignFrame alf);
+
+  /**
+   * Get the URL for the location where the code is found; typically ending in
+   * "swingjs/j2s".
+   * 
+   * @return web page URL
+   */
+  public URL getCodeBase();
+
+  AlignFrame getCurrentAlignFrame();
+
+  /**
+   * Get the URL for the hosting web page.
+   * 
+   * @return web page URL
+   */
+  public URL getDocumentBase();
+
+  /**
+   * Get the array of feature groups for an alignment frame.
+   * 
+   * @param alf
+   *          AlignFrame to get feature groups for (default current)
+   * @return
+   */
+  public String[] getFeatureGroups(AlignFrame alf);
+
+  /**
+   * Get the array of feature groups for an alignment frame with a specific
+   * on/off state.
+   * 
+   * @param visible
+   *          (default off)
+   * @param alf
+   *          align frame (default current)
+   * 
+   * @return
+   */
+  public String[] getFeatureGroupsOfState(boolean visible, AlignFrame alf);
+
+  /**
+   * Get the sequence features in the alignment frame in the given format
+   * (Jalview or GFF). Two additional options can be added to the format, each
+   * starting with a semicolon:
+   * 
+   * ;includeNonpositional (default) or ;positionalOnly
+   * 
+   * ;includeComplement
+   * 
+   * @param format
+   *          case-insensitive "Jalview" or "GFF" (default "GFF")
+   * @param alf
+   *          (default current)
+   * @return formatted sequence features
+   */
+  public String getFeatures(String format, AlignFrame alf);
+
+  /**
+   * Get an applet parameter as a string.
+   * 
+   * @param name
+   * @return value or null
+   */
+  public String getParameter(String name);
+
+  /**
+   * Get an applet parameter object value.
+   * 
+   * @param name
+   * @return value or null
+   */
+  public Object getParameterAsObject(String name);
+
+  /**
+   * @param alf
+   *          AlignFrame containing selection
+   * @return String list of selected sequence IDs, each terminated by current
+   *         default separator sequence
+   * 
+   */
+  public SequenceI[] getSelectedSequences(AlignFrame alf);
+
+  // BH incompatibility here -- JalviewLite created an AlignFrame; Jalview
+  // creates an AlignmentPanel
+  // /**
+  // * create a new view and return the AlignFrame instance
+  // *
+  // * @return
+  // */
+  //
+  // public AlignFrame newView();
+  //
+  // /**
+  // * create a new view named name and return the AlignFrame instance
+  // *
+  // * @param name
+  // * @return
+  // */
+  //
+  // public AlignFrame newView(String name);
+  //
+  // /**
+  // * create a new view on alf and return the AlignFrame instance
+  // *
+  // * @param alf
+  // * @return
+  // */
+  // public AlignFrame newViewFrom(AlignFrame alf);
+  //
+  // /**
+  // * create a new view named name on alf
+  // *
+  // * @param alf
+  // * @param name
+  // * @return
+  // */
+  // public AlignFrame newViewFrom(AlignFrame alf, String name);
+  //
+
+  /**
+   * get sequences selected in alf and return their alignment in format 'format'
+   * either with or without suffix
+   * 
+   * @param format
+   *          - format of alignment file
+   * @param alf
+   *          - where selection is
+   * @param suffix
+   *          - true to append /start-end string to each sequence ID
+   * 
+   * @return selected sequences as flat file or empty string if there was no
+   *         current selection
+   */
+  public String getSelectedSequencesAsAlignment(String format,
+          boolean addSuffix, AlignFrame alf);
+
+  /**
+   * 
+   * @param sequenceId
+   *          id of sequence to highlight
+   * @param position
+   *          integer position [ tobe implemented or range ] on sequence
+   * @param alignedPosition
+   *          false, blank or something else - indicate if position is an
+   *          alignment column or unaligned sequence position
+   * @param alf
+   *          alignment frame (default current)
+   */
+  public void highlight(String sequenceId, String position,
+          String alignedPosition, AlignFrame alf);
+
+  /**
+   * 
+   * @param data
+   *          alignment data as a string
+   * @param title
+   *          window title
+   * @param width
+   *          desired width or 0 for default width
+   * @param height
+   *          desired height or 0 for default height
+   * @return null or new alignment frame
+   */
+
+  public AlignFrame loadAlignment(String data, String title, int width,
+          int height);
+
+  /**
+   * add the given features or annotation to the given alignment view
+   * 
+   * @param annotation
+   * @param alf
+   *          alignment frame (default current)
+   */
+  public void loadAnnotation(String annotation, AlignFrame alf);
+
+  /**
+   * Parse the given string as a jalview feature or GFF annotation file and
+   * optionally enable feature display on the given AlignFrame.
+   * 
+   * @param features
+   *          - gff or features file
+   * @param autoenabledisplay
+   *          - when true, feature display will be enabled if any features can
+   *          be parsed from the string.
+   * @param alf
+   *          alignment frame (default current)
+   * 
+   * @return true if data parsed as features
+   */
+  public boolean loadFeatures(String features, boolean autoenabledisplay,
+          AlignFrame alf);
+
+  /**
+   * Load a score file.
+   * 
+   * @param sScoreFile
+   * @param alf
+   *          alignment frame (default current)
+   * 
+   * @return
+   */
+  public boolean loadScoreFile(String sScoreFile, AlignFrame alf);
+
+  /**
+   * public static method for JalviewJS API to open a PCAPanel without
+   * necessarily using a dialog.
+   * 
+   * @param modelName
+   * @param alf
+   *          may be null
+   * 
+   * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences"
+   *         if number of sequences selected is inappropriate
+   */
+  public Object openPcaPanel(String modelName, AlignFrame alf);
+
+  /**
+   * Open a new Tree panel on the desktop statically. Params are standard (not
+   * set by Groovy). No dialog is opened.
+   * 
+   * @param treeType
+   * @param modelName
+   * @param alf
+   *          align frame (default current)
+   * 
+   * @return null, or the string "label.you_need_at_least_n_sequences" if number
+   *         of sequences selected is inappropriate
+   */
+  public Object openTreePanel(String treeType, String modelName,
+          AlignFrame alf);
+
+  /**
+   * re-order the given alignment using the given array of sequence IDs
+   * 
+   * @param ids
+   *          array of sequence IDs
+   * @param undoName
+   *          - string to use when referring to ordering action in undo buffer
+   * @param alf
+   *          alignment frame (default current)
+   * 
+   * @return 'true' if alignment was actually reordered. empty string if
+   *         alignment did not contain sequences.
+   */
+  public boolean orderAlignment(String[] ids, String undoName,
+          AlignFrame alf);
+
+  /**
+   * process commandline arguments after the JavaScript application has started
+   *
+   * @param args
+   * @return
+   */
+  public Object parseArguments(String[] args);
+
+  boolean parseFeaturesFile(String filename, AlignFrame alf);
+
+  // Bob's additions:
+
+  /**
+   * remove any callback using the given listener function and associated with
+   * the given AlignFrame (or null for all callbacks);
+   * 
+   * @param listener
+   *          (may be null);
+   * @param alf
+   *          alignment frame (default current)
+   */
+  public void removeSelectionListener(String listener, AlignFrame af);
+
+  /**
+   * adjust horizontal/vertical scroll to make the given location the top left
+   * hand corner for the given view
+   * 
+   * @param topRow
+   *          -1 for current top row
+   * @param leftHandColumn
+   *          -1 for current left-hand column
+   * @param alf
+   *          alignment frame (default current)
+   */
+  public void scrollViewTo(int topRow, int leftHandColumn, AlignFrame alf);
+  /**
+   * select regions of the given alignment frame
+   * 
+   * @param alf
+   *          alignment frame (default current)
+   * @param toselect
+   *          String separated list { column range, seq1...seqn sequence ids }
+   * @param sep
+   *          separator between toselect fields
+   */
+  public void select(String[] sequenceIds, String[] columns,
+          AlignFrame alf);
+  
+  /**
+   * Set the state (visible or not) of the selected feature groups.
+   * 
+   * @param groups
+   * @param state
+   * @param alf
+   *          (default current)
+   */
+  public void setFeatureGroupState(String[] groups, boolean state,
+          AlignFrame alf);
+
+  /**
+   * Register a JavaScript function to handle alignment selection events. Events
+   * are generated when the user completes a selection event, or when the user
+   * deselects all selected regions. The method is called back with the
+   * following arguments:
+   * 
+   * the appletID (such as "Jalview1")
+   * 
+   * the source alignment frame
+   * 
+   * the SelectionSource object (for example, an AlignViewport)
+   * 
+   * the sequence set ID
+   * 
+   * an array of sequence IDs
+   * 
+   * an array of columns (single number or hyphenated range)
+   * 
+   * @param listener
+   *          name of JavaScript function to be called
+   * 
+   * @param alf
+   *          alignment frame (default ALL)
+   */
+  public void setSelectionListener(String listener, AlignFrame alf);
+
+  public void showOverview();
+
+  /**
+   * 
+   * @param pdbID
+   * @param fileType
+   * @param alf
+   *          align frame (default current)
+   */
+  public void showStructure(String pdbID, String fileType, AlignFrame alf);
+
+}

diff --git a/src/jalview/bin/AppletParams.java b/src/jalview/bin/AppletParams.java
index 3abaf72..3642985 100644 (file)
--- a/src/jalview/bin/AppletParams.java
+++ b/src/jalview/bin/AppletParams.java
@@ -185,7 +185,7 @@ public class AppletParams extends HashMap<String, Object>
     case "scorefile":
     case "sequence":
       // setting argName to null indicates that we want
-      // JalviewAppLoader to take care of this.
+      // JalviewJSApp to take care of this using getParameter or getParameterAsObject
       prefName = argName = null;
       value = resourcePath + value;
       break;
@@ -244,7 +244,7 @@ public class AppletParams extends HashMap<String, Object>
     // implemented; not tested:
 
     case "oninit":
-      prefName = null;
+      argName = null;
       break;
     case "annotations":
       value = resourcePath + value;

diff --git a/src/jalview/bin/ArgsParser.java b/src/jalview/bin/ArgsParser.java
index 55e760f..c5c08f6 100644 (file)
--- a/src/jalview/bin/ArgsParser.java
+++ b/src/jalview/bin/ArgsParser.java
@@ -118,14 +118,15 @@ public class ArgsParser
     {
       appletParams = AppletParams.getAppletParams(args, vargs);
     }
-    else if (Platform.isJS() && args.length == 0)
-    {
-      isApplet = true;
-      appletParams = AppletParams
-              .getAppletParams(Platform.getAppletInfoAsMap(), vargs);
-    }
     else
     {
+      if (Platform.isJS())
+
+      {
+        isApplet = true;
+        appletParams = AppletParams
+                .getAppletParams(Platform.getAppletInfoAsMap(), vargs);
+      }
       for (int i = 0; i < args.length; i++)
       {
         String arg = args[i].trim();
@@ -207,7 +208,7 @@ public class ArgsParser
     Object value;
     return (appletParams == null ? null
             : (value = appletParams.get(key.toLowerCase())) == null
-                    ? def : asString ? value.toString()
+                    ? def : asString ? "" + value
                     : value);
   }
 

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 4819d7a..81193e6 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -48,7 +48,6 @@ import com.threerings.getdown.util.LaunchUtil;
 import groovy.lang.Binding;
 import groovy.util.GroovyScriptEngine;
 import jalview.api.AlignCalcWorkerI;
-import jalview.api.JalviewJSApp;
 import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
 import jalview.ext.so.SequenceOntology;
 import jalview.gui.AlignFrame;
@@ -388,8 +387,6 @@ public class Jalview implements ApplicationSingletonI
       System.exit(0);
     }
 
-    desktop = null;
-
     if (!isJS)
     /** @j2sIgnore */
     {
@@ -450,6 +447,8 @@ public class Jalview implements ApplicationSingletonI
       SequenceOntologyFactory.setSequenceOntology(new SequenceOntology());
     }
 
+
+    desktop = null;
     if (!headless)
     {
       desktop = Desktop.getInstance();
@@ -581,7 +580,6 @@ public class Jalview implements ApplicationSingletonI
     FileLoader fileLoader = new FileLoader(!headless);
     FileFormatI format = null;
     // Finally, deal with the remaining input data.
-    JalviewJSApp jsApp = null;
     AlignFrame af = null;
 
     if (file != null)
@@ -822,8 +820,7 @@ public class Jalview implements ApplicationSingletonI
 
         if (isJS)
         {
-          jsApp = new JalviewJSApp(this, aparser);
-          jsApp.load(af);
+          new JalviewJSApp(this, aparser, af);
         }
         else
         /**
@@ -927,10 +924,6 @@ public class Jalview implements ApplicationSingletonI
       desktop.setInBatchMode(false);
     }
 
-    if (isJS && isStartup)
-    {
-      jsApp.callInitCallback();
-    }
   }
   
 

diff --git a/src/jalview/bin/JalviewJSApi.java b/src/jalview/bin/JalviewJSApi.java
deleted file mode 100644 (file)
index 0512841..0000000
--- a/src/jalview/bin/JalviewJSApi.java
+++ /dev/null
@@ -1,622 +0,0 @@
-package jalview.bin;
-
-import java.io.IOException;
-import java.net.URL;
-
-import jalview.api.AlignViewportI;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.io.DataSourceType;
-import jalview.structure.SelectionSource;
-import jalview.structure.VamsasSource;
-
-/**
- * JAL-3369 JalviewJS API BH 2019.07.17
- * 
- * @author hansonr
- *
- */
-public interface JalviewJSApi
-{
-
-  // debug flag - controls output to standard out
-  public static boolean debug = false;
-
-  /**
-   * bind a pdb file to a sequence in the given AlignFrame.
-   * 
-   * @param alFrame
-   *          - null or specific AlignFrame. This specifies the dataset that
-   *          will be searched for a seuqence called sequenceId
-   * @param sequenceId
-   *          - sequenceId within the dataset or null
-   * @param pdbId
-   *          - the four-character PDB ID
-   * @param pdbFile
-   *          - pdb file - either a URL or a valid PDB file or null.
-   * @return true if binding was success
-   */
-  public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
-          String pdbId, String pdbFile);
-
-  /**
-   * The following public methods may be called externally, eg via javascript in
-   * an HTML page.
-   * 
-   * <br>
-   * <em>TODO: introduce interface for jalview.appletgui.AlignFrame</em><br>
-   * 
-   * Most function arguments are strings, which contain serialised versions of
-   * lists. Lists of things are separated by a separator character - either the
-   * default or a user supplied one. Ranges and positions on an alignment or
-   * sequence can be specified as a list, where an item containing a single
-   * number is a single position, and an item like 1-2 specifies columns 1 and 2
-   * as a range.
-   */
-
-  // /**
-  // * @author jimp
-  // *
-  // */
-  // public interface JalviewLiteJsApi
-  // {
-
-  /**
-   * get alignment as format (format names FASTA, BLC, CLUSTAL, MSF, PILEUP,
-   * PFAM - see jalview.io.AppletFormatAdapter for full list);
-   * 
-   * @param format
-   * @return
-   */
-
-  public String getAlignment(String format);
-
-  /**
-   * get alignment as format with jalview start-end sequence suffix appended
-   * 
-   * @param format
-   * @param suffix
-   * @return
-   */
-
-  public String getAlignment(String format, String suffix);
-
-  /**
-   * get alignment displayed in alf as format
-   * 
-   * @param alf
-   * @param format
-   * @return
-   */
-  public String getAlignmentFrom(AlignFrame alf, String format);
-
-  /**
-   * get alignment displayed in alf as format with or without the jalview
-   * start-end sequence suffix appended
-   * 
-   * @param alf
-   * @param format
-   * @param suffix
-   * @return
-   */
-  public String getAlignmentFrom(AlignFrame alf, String format,
-          String suffix);
-
-  /**
-   * get a separator separated list of sequence IDs reflecting the order of the
-   * current alignment
-   * 
-   * @return
-   */
-
-  public String getAlignmentOrder();
-
-  /**
-   * get a separator separated list of sequence IDs reflecting the order of the
-   * alignment in alf
-   * 
-   * @param alf
-   * @return
-   */
-  public String[] getAlignmentOrderFrom(AlignFrame alf);
-
-  /**
-   * get current alignment's annotation as an annotation file
-   * 
-   * @return
-   */
-
-  public String getAnnotation();
-
-  /**
-   * get alignment view alf's annotation as an annotation file
-   * 
-   * @param alf
-   * @return
-   */
-  public String getAnnotationFrom(AlignFrame alf);
-
-  public Object getAppletParameter(String name, boolean asString);
-
-  public URL getCodeBase();
-
-  public URL getDocumentBase();
-
-  /**
-   * 
-   * @return
-   * @see jalview.appletgui.AlignFrame#getFeatureGroups();
-   */
-
-  public String[] getFeatureGroups();
-
-  /**
-   * @param visible
-   * @return
-   * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean);
-   */
-
-  public String[] getFeatureGroupsOfState(boolean visible);
-
-  /**
-   * @param alf
-   *          align frame to get groups of state visible
-   * @param visible
-   * @return
-   * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean);
-   */
-  public String[] getFeatureGroupsOfStateOn(AlignFrame alf,
-          boolean visible);
-
-  /**
-   * @param alf
-   *          AlignFrame to get feature groups on
-   * @return
-   * @see jalview.appletgui.AlignFrame#getFeatureGroups();
-   */
-  public String[] getFeatureGroupsOn(AlignFrame alf);
-
-  /**
-   * get the sequence features in the given format (Jalview or GFF);
-   * 
-   * @param format
-   * @return
-   */
-
-  public String getFeatures(String format);
-
-  /**
-   * get the sequence features in alf in the given format (Jalview or GFF);
-   * 
-   * @param alf
-   * @param format
-   * @return
-   */
-  public String getFeaturesFrom(AlignFrame alf, String format);
-
-  public Object getFrameForSource(VamsasSource source);
-
-  public String getParameter(String name);
-
-  /**
-   * @return String list of selected sequence IDs, each terminated by the
-   *         'boolean not' character (""+0x00AC); or (&#172;);
-   */
-
-  public SequenceI[] getSelectedSequences();
-
-  /**
-   * @param sep
-   *          separator string or null for default
-   * @return String list of selected sequence IDs, each terminated by given
-   *         separator string
-   */
-
-  public SequenceI[] getSelectedSequences(String sep);
-
-  /**
-   * get sequences selected in current AlignFrame and return their alignment in
-   * format 'format' either with or without suffix
-   * 
-   * @param alf
-   *          - where selection is
-   * @param format
-   *          - format of alignment file
-   * @param suffix
-   *          - "true" to append /start-end string to each sequence ID
-   * @return selected sequences as flat file or empty string if there was no
-   *         current selection
-   */
-
-  public String getSelectedSequencesAsAlignment(String format,
-          String suffix);
-
-  /**
-   * get sequences selected in alf and return their alignment in format 'format'
-   * either with or without suffix
-   * 
-   * @param alf
-   *          - where selection is
-   * @param format
-   *          - format of alignment file
-   * @param suffix
-   *          - "true" to append /start-end string to each sequence ID
-   * @return selected sequences as flat file or empty string if there was no
-   *         current selection
-   */
-  public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
-          String format, String suffix);
-
-  /**
-   * @param alf
-   *          AlignFrame containing selection
-   * @return String list of selected sequence IDs, each terminated by current
-   *         default separator sequence
-   * 
-   */
-  public SequenceI[] getSelectedSequencesFrom(AlignFrame alf);
-
-  // BH incompatibility here -- JalviewLite created an AlignFrame; Jalview
-  // creates an AlignmentPanel
-  // /**
-  // * create a new view and return the AlignFrame instance
-  // *
-  // * @return
-  // */
-  //
-  // public AlignFrame newView();
-  //
-  // /**
-  // * create a new view named name and return the AlignFrame instance
-  // *
-  // * @param name
-  // * @return
-  // */
-  //
-  // public AlignFrame newView(String name);
-  //
-  // /**
-  // * create a new view on alf and return the AlignFrame instance
-  // *
-  // * @param alf
-  // * @return
-  // */
-  // public AlignFrame newViewFrom(AlignFrame alf);
-  //
-  // /**
-  // * create a new view named name on alf
-  // *
-  // * @param alf
-  // * @param name
-  // * @return
-  // */
-  // public AlignFrame newViewFrom(AlignFrame alf, String name);
-
-  /**
-   * get list of selected sequence IDs separated by given separator
-   * 
-   * @param alf
-   *          window containing selection
-   * @param sep
-   *          separator string to use - default is 'boolean not'
-   * @return String list of selected sequence IDs, each terminated by the given
-   *         separator
-   */
-  public SequenceI[] getSelectedSequencesFrom(AlignFrame alf, String sep);
-
-  public Object[] getSelectionForListener(SequenceGroup seqsel,
-          ColumnSelection colsel, HiddenColumns hidden,
-          SelectionSource source, Object alignFrame);
-
-  public AlignViewportI getViewport();
-
-  /**
-   * 
-   * @param sequenceId
-   *          id of sequence to highlight
-   * @param position
-   *          integer position [ tobe implemented or range ] on sequence
-   * @param alignedPosition
-   *          true/false/empty string - indicate if position is an alignment
-   *          column or unaligned sequence position
-   */
-
-  public void highlight(String sequenceId, String position,
-          String alignedPosition);
-
-  /**
-   * 
-   * @param sequenceId
-   *          id of sequence to highlight
-   * @param position
-   *          integer position [ tobe implemented or range ] on sequence
-   * @param alignedPosition
-   *          false, blank or something else - indicate if position is an
-   *          alignment column or unaligned sequence position
-   */
-  public void highlightIn(AlignFrame alf, String sequenceId,
-          String position, String alignedPosition);
-
-  /**
-   * 
-   * @param text
-   *          alignment file as a string
-   * @param title
-   *          window title
-   * @return null or new alignment frame
-   */
-
-  public AlignFrame loadAlignment(String text, String title);
-
-  /**
-   * add the given features or annotation to the current alignment
-   * 
-   * @param annotation
-   */
-
-  public void loadAnnotation(String annotation);
-
-  /**
-   * add the given features or annotation to the given alignment view
-   * 
-   * @param alf
-   * @param annotation
-   */
-  public void loadAnnotationFrom(AlignFrame alf, String annotation);
-
-  /**
-   * parse the given string as a jalview feature or GFF annotation file and
-   * optionally enable feature display on the current AlignFrame
-   * 
-   * @param features
-   *          - gff or features file
-   * @param autoenabledisplay
-   *          - when true, feature display will be enabled if any features can
-   *          be parsed from the string.
-   */
-
-  public void loadFeatures(String features, boolean autoenabledisplay);
-
-  /**
-   * parse the given string as a jalview feature or GFF annotation file and
-   * optionally enable feature display on the given AlignFrame.
-   * 
-   * @param alf
-   * @param features
-   *          - gff or features file
-   * @param autoenabledisplay
-   *          - when true, feature display will be enabled if any features can
-   *          be parsed from the string.
-   * @return true if data parsed as features
-   */
-  public boolean loadFeaturesFrom(AlignFrame alf, String features,
-          boolean autoenabledisplay);
-
-  public boolean loadScoreFile(String sScoreFile) throws IOException;
-
-  public void newFeatureSettings();
-
-  public void newStructureView(PDBEntry pdb, SequenceI[] seqs,
-          String[] chains, DataSourceType protocol);
-
-  /// in http://www.jalview.org/examples/jalviewLiteJs.html but missing here
-
-  // get selected sequences as alignment as format with or without start-end
-  // suffix
-
-  /**
-   * re-order the given alignment using the given array of sequence IDs
-   * 
-   * @param alf
-   * @param ids
-   *          array of sequence IDs
-   * @param undoName
-   *          - string to use when referring to ordering action in undo buffer
-   * @return 'true' if alignment was actually reordered. empty string if
-   *         alignment did not contain sequences.
-   */
-  String orderAlignmentBy(AlignFrame alf, String[] ids, String undoName);
-
-  // get a string array from a list
-
-  /**
-   * re-order the current alignment using the given list of sequence IDs
-   * 
-   * @param ids
-   *          array of sequence IDs
-   * @param undoName
-   *          - string to use when referring to ordering action in undo buffer
-   * @return 'true' if alignment was actually reordered. empty string if
-   *         alignment did not contain sequences.
-   */
-
-  public String orderBy(String[] ids, String undoName);
-
-  /**
-   * re-order the current alignment using the given list of sequence IDs
-   * 
-   * @param ids
-   *          array of sequence IDs
-   * @param undoName
-   *          - string to use when referring to ordering action in undo buffer
-   * @param sep
-   * @return 'true' if alignment was actually reordered. empty string if
-   *         alignment did not contain sequences.
-   */
-
-  // public String orderBy(String[] ids, String undoName, String sep);
-  //
-
-  // public boolean getDefaultParameter(String name, boolean def);
-
-  public boolean parseFeaturesFile(String param, DataSourceType protocol);
-
-  /**
-   * remove any callback using the given listener function and associated with
-   * the given AlignFrame (or null for all callbacks);
-   * 
-   * @param af
-   *          (may be null);
-   * @param listener
-   *          (may be null);
-   */
-  public void removeSelectionListener(AlignFrame af, String listener);
-
-  // public void setAlignPdbStructures(boolean defaultParameter);
-
-  /**
-   * adjust horizontal scroll to make the given column the left one in the given
-   * view
-   * 
-   * @param alf
-   * @param leftHandColumn
-   */
-  public void scrollViewToColumnIn(AlignFrame alf, String leftHandColumn);
-
-  /**
-   * adjust horizontal/vertical scroll to make the given location the top left
-   * hand corner for the given view
-   * 
-   * @param alf
-   * @param topRow
-   * @param leftHandColumn
-   */
-  public void scrollViewToIn(AlignFrame alf, String topRow,
-          String leftHandColumn);
-
-  /**
-   * adjust vertical scroll to make the given row the top one for given view
-   * 
-   * @param alf
-   * @param topRow
-   */
-  public void scrollViewToRowIn(AlignFrame alf, String topRow);
-
-  /**
-   * select regions of the currrent alignment frame
-   * 
-   * @param sequenceIds
-   *          String separated list of sequence ids or empty string
-   * @param columns
-   *          String separated list { column range or column, ..} or empty
-   *          string
-   */
-
-  public void select(String sequenceIds, String columns);
-
-  /**
-   * select regions of the currrent alignment frame
-   * 
-   * @param toselect
-   *          String separated list { column range, seq1...seqn sequence ids }
-   * @param sep
-   *          separator between toselect fields
-   */
-
-  public void select(String sequenceIds, String columns, String sep);
-
-  /**
-   * select regions of the given alignment frame
-   * 
-   * @param alf
-   * @param toselect
-   *          String separated list { column range, seq1...seqn sequence ids }
-   * @param sep
-   *          separator between toselect fields
-   */
-  public void selectIn(AlignFrame alf, String sequenceIds, String columns);
-
-  /**
-   * select regions of the given alignment frame
-   * 
-   * @param alf
-   * @param toselect
-   *          String separated list { column range, seq1...seqn sequence ids }
-   * @param sep
-   *          separator between toselect fields
-   */
-  public void selectIn(AlignFrame alf, String sequenceIds, String columns,
-          String sep);
-
-  public void setFeatureGroupState(String groups, boolean state);
-
-  public void setFeatureGroupState(String[] groups, boolean state);
-
-  // public StructureSelectionManagerProvider
-  // getStructureSelectionManagerProvider();
-
-  /**
-   * @param groups
-   *          tab separated list of group names
-   * @param state
-   *          true or false
-   * @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[],
-   *      boolean);
-   */
-  public void setFeatureGroupStateOn(AlignFrame alf, String groups,
-          boolean state);
-
-  public void setSelectionListener(AlignFrame af, String listener);
-
-  /**
-   * register a javascript function to handle any alignment selection events.
-   * Events are generated when the user completes a selection event, or when the
-   * user deselects all selected regions.
-   * 
-   * @param listener
-   *          name of javascript function (called with arguments
-   *          [jalview.appletgui.AlignFrame, String(sequence set id);,
-   *          String(separator separated list of sequences which were
-   *          selected);, String(separator separated list of column ranges (i.e.
-   *          single number or hyphenated range); that were selected);]
-   */
-
-  public void setSelectionListener(String listener);
-
-  public void updateForAnnotations();
-
-  // Bob's additions:
-
-  /**
-   * public static method for JalviewJS API to open a PCAPanel without
-   * necessarily using a dialog.
-   * 
-   * @param af
-   *          may be null
-   * @param modelName
-   * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences"
-   *         if number of sequences selected is inappropriate
-   */
-  public Object openPcaPanel(AlignFrame af, String modelName);
-
-  /**
-   * Open a new Tree panel on the desktop statically. Params are standard (not
-   * set by Groovy). No dialog is opened.
-   * 
-   * @param af
-   *          may be null
-   * @param treeType
-   * @param modelName
-   * @return null, or the string "label.you_need_at_least_n_sequences" if number
-   *         of sequences selected is inappropriate
-   */
-  public Object openTreePanel(AlignFrame af, String treeType,
-          String modelName);
-
-  /**
-   * process commandline arguments after the JavaScript application has started
-   *
-   * @param args
-   * @return
-   */
-  public Object parseArguments(String[] args);
-
-  public void showStructure(AlignFrame af, String pdbID, String fileType);
-
-  public void showOverview();
-
-}

diff --git a/src/jalview/api/JalviewJSApp.java b/src/jalview/bin/JalviewJSApp.java
similarity index 54%
rename from src/jalview/api/JalviewJSApp.java
rename to src/jalview/bin/JalviewJSApp.java
index 5641295..1ba7273 100644 (file)
--- a/src/jalview/api/JalviewJSApp.java
+++ b/src/jalview/bin/JalviewJSApp.java
@@ -1,4 +1,4 @@
-package jalview.api;
+package jalview.bin;
 
 import java.awt.EventQueue;
 //import java.applet.AppletContext;
@@ -9,9 +9,8 @@ import java.util.List;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
-import jalview.bin.ArgsParser;
-import jalview.bin.Jalview;
-import jalview.bin.JalviewJSApi;
+import jalview.api.JalviewJSApi;
+import jalview.api.StructureSelectionManagerProvider;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
@@ -40,16 +39,14 @@ import jalview.io.NewickFile;
 import jalview.structure.SelectionListener;
 import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
-import jalview.structure.VamsasSource;
 import jalview.util.HttpUtils;
-import jalview.util.MessageManager;
 import jalview.util.Platform;
 
-//import netscape.javascript.JSObject;
-
 /**
  * Basically the JalviewLite application, but without JalviewLite
  * 
+ * Processing all "applet parameters" and also all "applet interface" methods.
+ * 
  * @author hansonr
  *
  */
@@ -57,274 +54,121 @@ public class JalviewJSApp implements JalviewJSApi
 {
   private ArgsParser aparser;
 
-  private boolean debug;
-
   private String[] ret = new String[1];
 
+  // private boolean alignPDBStructures; From JalviewLite; not implemented
+
   private String separator = "\u00AC"; // JalviewLite note: the default used to
                                        // be '|', but many sequence IDS include
                                        // pipes.
 
   /**
-   * We maintain a pointer to the jalview instance here, because only with that do we have a direct 
-   * connection from the JavaScript "applet" object to the proper instance of Jalview in case there
-   * are multiple applets on a page.
+   * We maintain a pointer to the jalview instance here, because only with that
+   * do we have a direct connection from the JavaScript "applet" object to the
+   * proper instance of Jalview in case there are multiple applets on a page.
    */
   private Jalview jalview;
 
-
-  public JalviewJSApp(Jalview jalview, ArgsParser aparser)
+  public class JsSelectionListener
+          implements jalview.structure.SelectionListener
   {
-    this.jalview = jalview;
-    this.aparser = aparser;
-    Platform.setAppClass(this);
-  }
 
+    AlignFrame _alf;
 
-  public void load(AlignFrame af)
-  {
-    String sep = (String) getAppletParameter("separator", true);
-    if (sep != null)
+    String _listener;
+
+    public JsSelectionListener(AlignFrame alf, String listener)
     {
-      if (sep.length() > 0)
-      {
-        separator = sep;
-      }
-      else
-      {
-        throw new Error(MessageManager
-                .getString("error.invalid_separator_parameter"));
-      }
+      _alf = alf;
+      _listener = listener;
     }
 
-    loadTree(af);
-    loadScoreFile();
-    loadFeatures(af);
-    loadAnnotations(af);
-    loadJnetFile(af);
-    loadPdbFiles(af);
-  }
-
-  // TODO BH 2019
-  //
-  // These are methods that are in JalviewLite that various classes call
-  // but are not in JalviewLiteJsApi. Or, even if they are, other classes
-  // call
-  // them to JalviewLite directly. Some may not be necessary, but they have
-  // to
-  // be at least mentioned here, or the classes calling them should
-  // reference
-  // JalviewLite itself.
-
-  // private boolean alignPDBStructures; // From JalviewLite; not implemented
-  //
-  
-  @Override
-  public String getParameter(String name)
-  {
-    return (String) getAppletParameter(name, true);
-  }
-
-  @Override
-  public Object getAppletParameter(String name, boolean asString)
-  {
-    return aparser.getAppletValue(name, null, asString);
-  }
-
-  /**
-   * Get the applet-like code base even though this is an application.
-   */
-
-  @Override
-  public URL getCodeBase()
-  {
-    return Platform.getCodeBase();
-  }
-
-  /**
-   * Get the applet-like document base even though this is an application.
-   */
-
-  @Override
-  public URL getDocumentBase()
-  {
-    return Platform.getDocumentBase();
-  }
+    public boolean isFor(AlignFrame alf, String listener)
+    {
+      return (_alf == null || _alf == alf) && _listener.equals(listener);
+    }
 
-  @Override
-  public Object getFrameForSource(VamsasSource source)
-  {
-    if (source != null)
+    @Override
+    public void selection(SequenceGroup seqsel, ColumnSelection colsel,
+            HiddenColumns hidden, SelectionSource source)
     {
-      AlignFrame af;
-      if (source instanceof jalview.gui.AlignViewport
-              && source == (af = Jalview.getCurrentAlignFrame())
-                      .getViewport())
+      // System.err.println("Testing selection event relay to
+      // jsfunction:"+_listener);
+      String setid = "";
+      AlignFrame srcFrame = (_alf == null ? getCurrentAlignFrame() : _alf);
+      if (source != null)
       {
-        // should be valid if it just generated an event!
-        return af;
+        if (source instanceof AlignViewport
+                && srcFrame.getViewport() != source)
+        {
+          return;
+        }
       }
-      // TODO: ensure that if '_af' is specified along with a handler
-      // function, then only events from that alignFrame are sent to that
-      // function
-    }
-    return null;
-  }
-
-  @Override
-  public Object[] getSelectionForListener(SequenceGroup seqsel,
-          ColumnSelection colsel, HiddenColumns hidden,
-          SelectionSource source, Object alignFrame)
-  {
-    return getSelectionForListener(null, seqsel, colsel, hidden, source,
-            alignFrame);
-  }
-
-  /**
-   * scorefile
-   * 
-   */
-
-  @Override
-  public boolean loadScoreFile(String sScoreFile) throws IOException
-  {
-    return loadScoreFile(null, sScoreFile);
-  }
-  
-  public boolean loadScoreFile(AlignFrame af, String sScoreFile) throws IOException
-  {
-    (af == null ? Jalview.getCurrentAlignFrame() : af).loadJalviewDataFile(sScoreFile, null, null, null);
-    return true;
-  }
-
-  public void loadTree(AlignFrame af, NewickFile nf, String treeFile) throws IOException
-  {
-    if (af == null)
-      af = Jalview.getCurrentAlignFrame();
-    af.getViewport()
-            .setCurrentTree(af.showNewickTree(nf, treeFile).getTree());
-  }
-
-  @Override
-  public void newFeatureSettings()
-  {
-    System.err.println(
-            "Jalview applet interface newFeatureSettings not implemented");
-  }
-
-  //
-  //
-  // public void setAlignPdbStructures(boolean defaultParameter)
-  // {
-  // alignPDBStructures = true;
-  // }
-  //
-
-  @Override
-  public void newStructureView(PDBEntry pdb, SequenceI[] seqs,
-          String[] chains, DataSourceType protocol)
-  {
-    newStructureView(null, pdb, seqs, chains, protocol);
-    
-  }
-
-  /**
-   * @j2sAlias showStructure
-   */
-  @Override
-  public void showStructure(AlignFrame af, String pdbID, String fileType) {
-    if (af == null)
-      af = Jalview.getCurrentAlignFrame();
-    PDBEntry pe = null;
-    SequenceI[] seqs = null;
-    if (pdbID == null) {
-      seqs = af.getViewport().getSequenceSelection();
-      if (seqs.length == 0)
-        seqs = af.getViewport().getAlignment().getSequencesArray();
-      for (int i = 0; i < seqs.length; i++) {
-        Vector<PDBEntry> list = seqs[i].getAllPDBEntries();
-        if (list.size() > 0) {
-          pe = list.get(0);
-          break;
+      String[] seqs = new String[] {};
+      String[] cols = new String[] {};
+      int strt = 0, end = (srcFrame == null) ? -1
+              : srcFrame.alignPanel.av.getAlignment().getWidth();
+      if (seqsel != null && seqsel.getSize() > 0)
+      {
+        seqs = new String[seqsel.getSize()];
+        for (int i = 0; i < seqs.length; i++)
+        {
+          seqs[i] = seqsel.getSequenceAt(i).getName();
+        }
+        if (strt < seqsel.getStartRes())
+        {
+          strt = seqsel.getStartRes();
+        }
+        if (end == -1 || end > seqsel.getEndRes())
+        {
+          end = seqsel.getEndRes();
         }
       }
-    }
-    if (pe == null) {
-      if (pdbID == null)
-        return;
-      pe = new PDBEntry(pdbID, null, fileType);
-      List<SequenceI> list = af.getViewport().getAlignment().getSequences();
-      List<SequenceI> tmp = new ArrayList<SequenceI>();
-      for (int i = 0; i < list.size(); i++) {
-        SequenceI seq = list.get(i);
-        if (seq.getPDBEntry(pdbID) != null) {
-          tmp.add(seq);
+      if (colsel != null && !colsel.isEmpty())
+      {
+        if (end == -1)
+        {
+          end = colsel.getMax() + 1;
+        }
+        cols = new String[colsel.getSelected().size()];
+        for (int i = 0; i < cols.length; i++)
+        {
+          cols[i] = "" + (1 + colsel.getSelected().get(i).intValue());
         }
       }
-      seqs = tmp.toArray(new SequenceI[tmp.size()]);
-      af.alignPanel.selectSequences(tmp);
+      else
+      {
+        if (seqsel != null && seqsel.getSize() > 0)
+        {
+          // send a valid range, otherwise we send the empty selection
+          cols = new String[1];
+          cols[0] = "" + (1 + strt) + "-" + (1 + end);
+        }
+      }
+      doSendCallback(_listener,
+              new Object[]
+              { Jalview.getInstance().j2sAppletID, srcFrame, source, setid,
+                  seqs, cols });
     }
-    StructureViewer.launchStructureViewer(
-            af.alignPanel,
-            pe, seqs);
-  }
-  
-  public void newStructureView(AlignFrame af, PDBEntry pdb,
-          SequenceI[] seqs, String[] chains, DataSourceType protocol)
-  {
-    StructureViewer.launchStructureViewer(
-            (af == null ? Jalview.getCurrentAlignFrame() : af).alignPanel,
-            pdb, seqs);
-  }
 
-  /**
-   * features
-   * @param af 
-   * 
-   */
-
-  @Override
-  public boolean parseFeaturesFile(String filename, DataSourceType protocol)
-  {
-    return parseFeaturesFile(null, filename, protocol);
-  }
-  
-  /**
-   * @j2sAlias parseFeatureFile
-   * 
-   * @param af
-   * @param filename
-   * @param protocol
-   * @return
-   */
-  public boolean parseFeaturesFile(AlignFrame af, String filename, DataSourceType protocol)
-  {
-    return (af == null ? Jalview.getCurrentAlignFrame() : af).parseFeaturesFile(filename, protocol);
-  }
-
-  /**
-   * annotations, jpredfile, jnetfile
-   * 
-   */
-
-  @Override
-  public void updateForAnnotations()
-  {
-    updateForAnnotations(null);
   }
 
-  public void updateForAnnotations(AlignFrame af)
+  public JalviewJSApp(Jalview jalview, ArgsParser aparser, AlignFrame alf)
   {
-    (af == null ? Jalview.getCurrentAlignFrame() : af).updateForAnnotations();
+    Platform.setAppClass(this);
+    this.jalview = jalview;
+    this.aparser = aparser;
+    initFromParams(alf);
+    callInitCallback();
   }
 
   @Override
-  public boolean addPdbFile(AlignFrame alf, String sequenceId, String pdbId,
-          String pdbFile)
+  public boolean addPdbFile(String sequenceId, String pdbId, String pdbFile,
+          AlignFrame alf)
   {
     if (alf == null)
     {
-      alf = Jalview.getCurrentAlignFrame();
+      alf = getCurrentAlignFrame();
     }
     SequenceI seq = alf.getViewport().getAlignment().findName(sequenceId);
     if (seq != null)
@@ -362,91 +206,20 @@ public class JalviewJSApp implements JalviewJSApi
     return true;
   }
 
-//  @Override
-//  public String arrayToSeparatorList(String[] array)
-//  {
-//    return arrayToSeparatorList(array, separator);
-//  }
-
-//  /**
-//   * concatenate the list with separator
-//   * 
-//   * @param list
-//   * @param separator
-//   * @return concatenated string
-//   */
-//  public static String arrayToSeparatorList(String[] list, String separator)
-//  {
-//    // TODO use StringUtils version
-//    StringBuffer v = new StringBuffer();
-//    if (list != null && list.length > 0)
-//    {
-//      for (int i = 0, iSize = list.length; i < iSize; i++)
-//      {
-//        if (list[i] != null)
-//        {
-//          if (i > 0)
-//          {
-//            v.append(separator);
-//          }
-//          v.append(list[i]);
-//        }
-//      }
-//      // if (debug)
-//      // {
-//      // System.err
-//      // .println("Returning '" + separator + "' separated List:\n");
-//      // System.err.println(v);
-//      // }
-//      return v.toString();
-//    }
-//    // if (debug)
-//    // {
-//    // System.err.println(
-//    // "Returning empty '" + separator + "' separated List\n");
-//    // }
-//    return "" + separator;
-//  }
-
-  @Override
-  public String getAlignment(String format)
-  {
-    return getAlignmentFrom(null, format, null);
-  }
-
-  /**
-   * suffix string "true"/"false" (default true)
-   *          passed to AlnFile class controls whether /START-END is added to
-   *          sequence names
-   */
-  @Override
-  public String getAlignment(String format, String suffix)
-  {
-    return getAlignmentFrom(Jalview.getCurrentAlignFrame(), format, suffix);
-  }
-
-  @Override
-  public String getAlignmentFrom(AlignFrame alf, String format)
-  {
-    return getAlignmentFrom(alf, format, null);
-  }
-
   @Override
-  public String getAlignmentFrom(AlignFrame alf, String format,
-          String suffix)
+  public String getAlignment(String format, boolean addSuffix,
+          AlignFrame alf)
   {
     try
     {
       if (alf == null)
       {
-        alf = Jalview.getCurrentAlignFrame();
+        alf = getCurrentAlignFrame();
       }
-      boolean seqlimits = (suffix == null
-              || suffix.equalsIgnoreCase("true"));
 
       FileFormatI theFormat = FileFormats.getInstance().forName(format);
       String reply = new AppletFormatAdapter().formatSequences(theFormat,
-              alf.getViewport().getAlignment(), seqlimits);
+              alf.getViewport().getAlignment(), addSuffix);
       return reply;
     } catch (IllegalArgumentException ex)
     {
@@ -457,17 +230,11 @@ public class JalviewJSApp implements JalviewJSApi
   }
 
   @Override
-  public String getAlignmentOrder()
-  {
-    return getAlignmentFrom(Jalview.getCurrentAlignFrame(), null);
-  }
-
-  @Override
-  public String[] getAlignmentOrderFrom(AlignFrame alf)
+  public String[] getAlignmentOrder(AlignFrame alf)
   {
     if (alf == null)
     {
-      alf = Jalview.getCurrentAlignFrame();
+      alf = getCurrentAlignFrame();
     }
     AlignmentI alorder = alf.getViewport().getAlignment();
     String[] order = new String[alorder.getHeight()];
@@ -475,88 +242,95 @@ public class JalviewJSApp implements JalviewJSApi
     {
       order[i] = alorder.getSequenceAt(i).getName();
     }
-    return order;//  arrayToSeparatorList(order, sep);
-  }
-
-  @Override
-  public String getAnnotation()
-  {
-    return getAnnotationFrom(null);
+    return order;// arrayToSeparatorList(order, sep);
   }
 
   @Override
-  public String getAnnotationFrom(AlignFrame alf)
+  public String getAnnotation(AlignFrame alf)
   {
     if (alf == null)
     {
-      alf = Jalview.getCurrentAlignFrame();
+      alf = getCurrentAlignFrame();
     }
     String annotation = new AnnotationFile()
             .printAnnotationsForView(alf.getViewport());
     return annotation;
   }
 
+  /**
+   * Get the applet-like code base even though this is an application.
+   */
+
   @Override
-  public String[] getFeatureGroups()
+  public URL getCodeBase()
   {
-    return getFeatureGroupsOn(null);
+    return Platform.getCodeBase();
   }
 
   @Override
-  public String[] getFeatureGroupsOfState(boolean visible)
+  public AlignFrame getCurrentAlignFrame()
   {
-    return getFeatureGroupsOfStateOn(null, visible);
+    // if (jalview != Jalview.getInstance() || jalview.currentAlignFrame !=
+    // Jalview.getCurrentAlignFrame()) {
+    // /** @j2sNative debugger */
+    // }
+    return jalview.currentAlignFrame;
   }
 
+  /**
+   * Get the applet-like document base even though this is an application.
+   */
+
   @Override
-  public String[] getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
+  public URL getDocumentBase()
   {
-    if (alf == null)
-    {
-      alf = Jalview.getCurrentAlignFrame();
-    }
-    return alf.getFeatureGroupsOfState(visible);
+    return Platform.getDocumentBase();
   }
 
   @Override
-  public String[] getFeatureGroupsOn(AlignFrame alf)
+  public String[] getFeatureGroups(AlignFrame alf)
   {
     if (alf == null)
     {
-      alf = Jalview.getCurrentAlignFrame();
+      alf = getCurrentAlignFrame();
     }
     return alf.getFeatureGroups();
   }
 
   @Override
-  public String getFeatures(String format)
+  public String[] getFeatureGroupsOfState(boolean visible, AlignFrame alf)
   {
-    return getFeaturesFrom(null, format);
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
+    return alf.getFeatureGroupsOfState(visible);
   }
 
   /**
    * JavaScript interface to print the alignment frame
    * 
-   * @param alf
    * @param format
    *          "jalview" or "gff" with or without ";includeComplement" or
    *          ";includeNonpositional"; default with no ";" is
    *          ";includeNonpositional"
+   * @param alf
+   * 
    * @return
    */
   @Override
-  public String getFeaturesFrom(AlignFrame alf, String format)
+  public String getFeatures(String format, AlignFrame alf)
   {
     if (alf == null)
     {
-      alf = Jalview.getCurrentAlignFrame();
+      alf = getCurrentAlignFrame();
     }
     String features;
     FeaturesFile formatter = new FeaturesFile();
     format = format.toLowerCase();
     if (format.indexOf(";") < 0)
       format += ";includenonpositional";
-    boolean nonpos = format.indexOf(";includenonpositional") > 0;
+    boolean nonpos = format.indexOf(";includenonpositional") >= 0;
     boolean compl = format.indexOf(";includecomplement") >= 0;
     if (format.startsWith("jalview"))
     {
@@ -578,7 +352,27 @@ public class JalviewJSApp implements JalviewJSApi
     return features;
 
   }
-  
+
+  /**
+   * Get an applet parameter as a string.
+   * 
+   */
+  @Override
+  public String getParameter(String name)
+  {
+    return (String) aparser.getAppletValue(name, null, true);
+  }
+
+  /**
+   * Get an applet parameter as an Object.
+   */
+
+  @Override
+  public Object getParameterAsObject(String name)
+  {
+    return aparser.getAppletValue(name, null, false);
+  }
+
   /**
    * read sequence1...sequenceN as a raw alignment
    * 
@@ -590,8 +384,7 @@ public class JalviewJSApp implements JalviewJSApi
     StringBuffer data = new StringBuffer("PASTE");
     int i = 1;
     String file = null;
-    while ((file = (String) getAppletParameter("sequence" + i,
-            true)) != null)
+    while ((file = getParameter("sequence" + i)) != null)
     {
       data.append(file.toString() + "\n");
       i++;
@@ -604,43 +397,56 @@ public class JalviewJSApp implements JalviewJSApi
   }
 
   /**
+   * @j2sAlias getSelectedSequences
    * 
-   * @see jalview.appletgui.js.JalviewLiteJsApi#getSelectedSequences()
+   * @see jalview.appletgui.js.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
+   *      .AlignFrame)
    */
   @Override
-  public SequenceI[] getSelectedSequences()
+  public SequenceI[] getSelectedSequences(AlignFrame alf)
   {
-    return getSelectedSequencesFrom(Jalview.getCurrentAlignFrame());
-  }
-
-  /**
-   * 
-   * @see jalview.appletgui.js.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
-   */
-  @Override
-  public SequenceI[] getSelectedSequences(String sep)
-  {
-    return getSelectedSequencesFrom(Jalview.getCurrentAlignFrame(), sep);
+    // return getSelectedSequencesFrom(alf, null);
+    // }
+    //
+    // @Override
+    // public SequenceI[] getSelectedSequencesFrom(AlignFrame alf, String sep)
+    // {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
+    AlignViewport v = alf.getViewport();
+    if (v.getSelectionGroup() != null)
+    {
+      return v.getSelectionGroup().getSequencesInOrder(v.getAlignment());
+    }
+    return null;
   }
+  // /**
+  // *
+  // * @see
+  // jalview.appletgui.js.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
+  // * .AlignFrame, java.lang.String)
+  // */
+  // @Override
+  // public void highlight(String sequenceId, String position,
+  // String alignedPosition)
+  // {
+  // highlightIn(null, sequenceId, position, alignedPosition);
+  // }
 
+  /**
+   * @j2sAlias getSelectedSequencesAsAlignment
+   */
   @Override
   public String getSelectedSequencesAsAlignment(String format,
-          String suffix)
-  {
-    return getSelectedSequencesAsAlignmentFrom(null, format, suffix);
-  }
-
-  @Override
-  public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
-          String format, String suffix)
+          boolean addSuffix, AlignFrame alf)
   {
 
     if (alf == null)
     {
-      alf = Jalview.getCurrentAlignFrame();
+      alf = getCurrentAlignFrame();
     }
-
-    boolean seqlimits = (suffix == null || suffix.equalsIgnoreCase("true"));
     try
     {
       AlignViewport vp = alf.getViewport();
@@ -651,7 +457,7 @@ public class JalviewJSApp implements JalviewJSApi
         // method now returns a full copy of sequence data
         // TODO consider using getSequenceSelection instead here
         String reply = new AppletFormatAdapter().formatSequences(theFormat,
-                new Alignment(vp.getSelectionAsNewSequence()), seqlimits);
+                new Alignment(vp.getSelectionAsNewSequence()), addSuffix);
         return reply;
       }
     } catch (IllegalArgumentException ex)
@@ -663,118 +469,13 @@ public class JalviewJSApp implements JalviewJSApi
     return "";
   }
 
-  /**
-   * 
-   * @see jalview.appletgui.js.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
-   *      .AlignFrame)
-   */
-  @Override
-  public SequenceI[] getSelectedSequencesFrom(AlignFrame alf)
-  {
-    return getSelectedSequencesFrom(alf, null);
-  }
-
-  @Override
-  public SequenceI[] getSelectedSequencesFrom(AlignFrame alf, String sep)
-  {
-    if (alf == null)
-    {
-      alf = Jalview.getCurrentAlignFrame();
-    }
-    AlignViewport v = alf.getViewport();
-    if (v.getSelectionGroup() != null)
-    {
-      return v.getSelectionGroup()
-              .getSequencesInOrder(v.getAlignment());
-    }
-
-    return null;
-  }
-
-  public Object[] getSelectionForListener(AlignFrame alf,
-          SequenceGroup seqsel, ColumnSelection colsel,
-          HiddenColumns hidden, SelectionSource source, Object alignFrame)
-  {
-    if (alf == null)
-    {
-      alf = Jalview.getCurrentAlignFrame();
-    }
-    // System.err.println("Testing selection event relay to
-    // jsfunction:"+_listener);
-    String setid = "";
-    AlignFrame src = (AlignFrame) alignFrame;
-    if (source != null)
-    {
-      if (source instanceof AlignViewport && alf.getViewport() == source)
-      {
-        // should be valid if it just generated an event!
-        src = alf;
-
-      }
-    }
-    String[] seqs = new String[] {};
-    String[] cols = new String[] {};
-    int strt = 0, end = (src == null) ? -1
-            : src.alignPanel.av.getAlignment().getWidth();
-    if (seqsel != null && seqsel.getSize() > 0)
-    {
-      seqs = new String[seqsel.getSize()];
-      for (int i = 0; i < seqs.length; i++)
-      {
-        seqs[i] = seqsel.getSequenceAt(i).getName();
-      }
-      if (strt < seqsel.getStartRes())
-      {
-        strt = seqsel.getStartRes();
-      }
-      if (end == -1 || end > seqsel.getEndRes())
-      {
-        end = seqsel.getEndRes();
-      }
-    }
-    if (colsel != null && !colsel.isEmpty())
-    {
-      if (end == -1)
-      {
-        end = colsel.getMax() + 1;
-      }
-      cols = new String[colsel.getSelected().size()];
-      for (int i = 0; i < cols.length; i++)
-      {
-        cols[i] = "" + (1 + colsel.getSelected().get(i).intValue());
-      }
-    }
-    else
-    {
-      if (seqsel != null && seqsel.getSize() > 0)
-      {
-        // send a valid range, otherwise we send the empty selection
-        cols = new String[2];
-        cols[0] = "" + (1 + strt) + "-" + (1 + end);
-      }
-    }
-    return new Object[] { src, setid, seqs, cols };
-  }
-
-  /**
-   * 
-   * @see jalview.appletgui.js.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
-   *      .AlignFrame, java.lang.String)
-   */
   @Override
   public void highlight(String sequenceId, String position,
-          String alignedPosition)
-  {
-    highlightIn(null, sequenceId, position, alignedPosition);
-  }
-
-  @Override
-  public void highlightIn(AlignFrame alf, final String sequenceId,
-          final String position, final String alignedPosition)
+          String alignedPosition, AlignFrame alf)
   {
     if (alf == null)
     {
-      alf = Jalview.getCurrentAlignFrame();
+      alf = getCurrentAlignFrame();
     }
     // TODO: could try to highlight in all alignments if alf==null
     jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
@@ -823,8 +524,9 @@ public class JalviewJSApp implements JalviewJSApi
     }
   }
 
-  public AlignFrame loadAlignment(String text, int width, int height,
-          String title)
+  @Override
+  public AlignFrame loadAlignment(String text, String title, int width,
+          int height)
   {
     AlignmentI al = null;
 
@@ -836,7 +538,9 @@ public class JalviewJSApp implements JalviewJSApi
               format);
       if (al.getHeight() > 0)
       {
-        return new AlignFrame(al, width, height, title);
+        return new AlignFrame(al,
+                width > 0 ? width : AlignFrame.DEFAULT_WIDTH,
+                height > 0 ? height : AlignFrame.DEFAULT_HEIGHT, title);
       }
     } catch (IOException ex)
     {
@@ -845,36 +549,12 @@ public class JalviewJSApp implements JalviewJSApi
     return null;
   }
 
-  // public void setMouseoverListener(String listener)
-  // {
-  // appLoader.setMouseoverListener(listener);
-  // }
-  //
-  //
-  // public void setMouseoverListener(AlignFrame af, String listener)
-  // {
-  // }
-  //
-
-  @Override
-  public AlignFrame loadAlignment(String text, String title)
-  {
-    return loadAlignment(text, AlignFrame.DEFAULT_WIDTH,
-            AlignFrame.DEFAULT_HEIGHT, title);
-  }
-
-  @Override
-  public void loadAnnotation(String annotation)
-  {
-    loadAnnotationFrom(null, annotation);
-  }
-
   @Override
-  public void loadAnnotationFrom(AlignFrame alf, String annotation)
+  public void loadAnnotation(String annotation, AlignFrame alf)
   {
     if (alf == null)
     {
-      alf = Jalview.getCurrentAlignFrame();
+      alf = getCurrentAlignFrame();
     }
     if (new AnnotationFile().annotateAlignmentView(alf.getViewport(),
             annotation, DataSourceType.PASTE))
@@ -888,580 +568,263 @@ public class JalviewJSApp implements JalviewJSApi
     }
   }
 
-  /**
-   * Load annotations if specified by parameter. Returns true if loaded, else
-   * false.
-   * 
-   * 
-   * @param alignFrame
-   * @return
-   */
-  protected boolean loadAnnotations(AlignFrame af)
+  @Override
+  public boolean loadFeatures(String features, boolean autoenabledisplay,
+          AlignFrame alf)
   {
-    boolean result = false;
-    String param = (String) getAppletParameter("annotations", true);
-    if (param != null)
+    if (alf == null)
     {
-      ret[0] = param;
-      DataSourceType protocol = resolveFileProtocol(ret);
-      param = ret[0];
-      if (new AnnotationFile().annotateAlignmentView(af.getViewport(), param,
-              protocol))
-      {
-        updateForAnnotations();
-        result = true;
-      }
-      else
-      {
-        System.err
-                .println("Annotations were not added from annotation file '"
-                        + param + "'");
-      }
+      alf = getCurrentAlignFrame();
     }
-    return result;
-  }
-
-  //// JalviewJSApi
-
-  /**
-   * Load features file and view settings as specified by parameters. Returns
-   * true if features were loaded, else false.
-   * @param  
-   * 
-   * @param alignFrame
-   * @return
-   */
-  protected boolean loadFeatures(AlignFrame af)
-  {
-    boolean result = false;
-    // ///////////////////////////
-    // modify display of features
-    // we do this before any features have been loaded, ensuring any hidden
-    // groups are hidden when features first displayed
-    //
-    // hide specific groups
-    //
-    String param = (String) getAppletParameter("hidefeaturegroups", true);
-    if (param != null)
+    boolean ret = alf.parseFeaturesFile(features, DataSourceType.PASTE);
+    if (!ret)
     {
-      setFeatureGroupState(af, separatorListToArray(param, separator), false);
-      // setFeatureGroupStateOn(newAlignFrame, param, false);
+      return false;
     }
-    // show specific groups
-    param = (String) getAppletParameter("showfeaturegroups", true);
-    if (param != null)
+    if (autoenabledisplay)
     {
-      setFeatureGroupState(af, separatorListToArray(param, separator), true);
-      // setFeatureGroupStateOn(newAlignFrame, param, true);
+      alf.getViewport().setShowSequenceFeatures(true);
+      // this next was for a checkbox in JalviewLite
+      // ((AlignFrame) alf).getViewport().sequenceFeatures.setState(true);
     }
-    // and now load features
-    param = (String) getAppletParameter("features", true);
-    if (param != null)
-    {
-      ret[0] = param;
-      DataSourceType protocol = resolveFileProtocol(ret);
+    return true;
+  }
 
-      result = parseFeaturesFile(af, ret[0], protocol);
+  @Override
+  public boolean loadScoreFile(String fileName, AlignFrame alf)
+  {
+    try
+    {
+      (alf == null ? getCurrentAlignFrame() : alf)
+              .loadJalviewDataFile(fileName, null, null, null);
+      return true;
+    } catch (Throwable t)
+    {
+      return false;
     }
+  }
 
-    param = (String) getAppletParameter("showFeatureSettings", true);
-    if (param != null && param.equalsIgnoreCase("true"))
+  /**
+   * @j2sAlias openPcaPanel
+   * 
+   *           public static method for JalviewJS API to open a PCAPanel without
+   *           necessarily using a dialog.
+   * @param modelName
+   * @param alf
+   * 
+   * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences"
+   *         if number of sequences selected is inappropriate
+   */
+  @Override
+  public Object openPcaPanel(String modelName, AlignFrame alf)
+  {
+    if (alf == null)
     {
-      newFeatureSettings();
+      alf = getCurrentAlignFrame();
     }
-    return result;
+    return CalculationChooser.openPcaPanel(alf, modelName, null);
   }
 
+  /**
+   * @j2sAlias openTreePanel
+   * 
+   *           Open a new Tree panel on the desktop statically. Params are
+   *           standard (not set by Groovy). No dialog is opened.
+   * @param treeType
+   * @param modelName
+   * @param alf
+   * 
+   * @return null, or the string "label.you_need_at_least_n_sequences" if number
+   *         of sequences selected is inappropriate
+   */
   @Override
-  public void loadFeatures(String features, boolean autoenabledisplay)
+  public Object openTreePanel(String treeType, String modelName,
+          AlignFrame alf)
   {
-    loadFeaturesFrom(null, features, autoenabledisplay);
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
+    return CalculationChooser.openTreePanel(alf, treeType, modelName, null);
   }
 
   @Override
-  public boolean loadFeaturesFrom(AlignFrame alf, String features,
-          boolean autoenabledisplay)
+  public boolean orderAlignment(String[] ids, String undoName,
+          AlignFrame alf)
   {
     if (alf == null)
+      alf = getCurrentAlignFrame();
+    SequenceI[] sqs = null;
+    if (ids != null && ids.length > 0)
     {
-      alf = Jalview.getCurrentAlignFrame();
+      jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+              alf.getViewport().getAlignment().getSequencesArray());
+      int s = 0;
+      sqs = new SequenceI[ids.length];
+      for (int i = 0; i < ids.length; i++)
+      {
+        if (ids[i].trim().length() == 0)
+        {
+          continue;
+        }
+        SequenceI sq = matcher.findIdMatch(ids[i]);
+        if (sq != null)
+        {
+          sqs[s++] = sq;
+        }
+      }
+      if (s > 0)
+      {
+        SequenceI[] sqq = new SequenceI[s];
+        System.arraycopy(sqs, 0, sqq, 0, s);
+        sqs = sqq;
+      }
+      else
+      {
+        sqs = null;
+      }
     }
-    boolean ret = alf.parseFeaturesFile(features, DataSourceType.PASTE);
-    if (!ret)
+    if (sqs == null)
     {
       return false;
     }
-    if (autoenabledisplay)
+    ;
+    final AlignmentOrder aorder = new AlignmentOrder(sqs);
+
+    if (undoName != null && undoName.trim().length() == 0)
     {
-      alf.getViewport().setShowSequenceFeatures(true);
-      // this next was for a checkbox in JalviewLite
-      // ((AlignFrame) alf).getViewport().sequenceFeatures.setState(true);
+      undoName = null;
     }
-    return true;
+    final String _undoName = undoName;
+    // TODO: deal with synchronization here: cannot raise any events until
+    // alfter
+    // this has returned.
+    return alf.sortBy(aorder, _undoName);
   }
 
   /**
-   * Load in a Jnetfile if specified by parameter. Returns true if loaded, else
-   * false.
+   * Allow an outside entity to initiate the second half of argument parsing
+   * (only).
    * 
-   * @param alignFrame
-   * @return
+   * @param args
+   * @return null is good
    */
-  protected boolean loadJnetFile(AlignFrame af)
+  @Override
+  public Object parseArguments(String[] args)
   {
-    boolean result = false;
-    String param = (String) getAppletParameter("jnetfile", true);
-    if (param == null)
+
+    try
     {
-      // jnet became jpred around 2016
-      param = (String) getAppletParameter("jpredfile", true);
-    }
-    if (param != null)
+      jalview.parseArguments(new ArgsParser(args), false);
+      return null;
+    } catch (Throwable t)
     {
-      try
-      {
-        ret[0] = param;
-        DataSourceType protocol = resolveFileProtocol(ret);
-        JPredFile predictions = new JPredFile(ret[0], protocol);
-        JnetAnnotationMaker.add_annotation(predictions,
-                af.getViewport().getAlignment(), 0, false);
-        // false == do not add sequence profile from concise output
-        af.getViewport().getAlignment().setupJPredAlignment();
-        updateForAnnotations();
-        result = true;
-      } catch (Exception ex)
-      {
-        ex.printStackTrace();
-      }
+      return t;
     }
-    return result;
   }
 
   /**
-   * Load PDBFiles if any specified by parameter(s). Returns true if loaded,
-   * else false.
+   * @j2sAlias parseFeatureFile
    * 
-   * @param loaderFrame
+   * @param filename
+   * @param alf
    * @return
    */
-  protected boolean loadPdbFiles(AlignFrame af)
-  {
-    boolean result = false;
-    /*
-     * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6 -
-     * related to JAL-434
-     */
-
-    // not supported (as for JalviewLite)
-    // boolean doAlign = false;//"true".equalsIgnoreCase("" +
-    // getAppletParameter("alignpdbfiles", false));
-    // setAlignPdbStructures(doAlign);
-    /*
-     * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
-     * PDB|1GAQ|1GAQ|C">
-     * 
-     * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
-     * 
-     * <param name="PDBfile3" value="1q0o Q45135_9MICO">
-     */
-
-    // Accumulate pdbs here if they are heading for the same view (if
-    // alignPdbStructures is true)
-    // ArrayList<Object[]> pdbs = new ArrayList<>();
-    // create a lazy matcher if we're asked to
-    boolean relaxed = "true".equalsIgnoreCase(
-            "" + getAppletParameter("relaxedidmatch", false));
-    jalview.analysis.SequenceIdMatcher matcher = relaxed
-            ? new jalview.analysis.SequenceIdMatcher(
-                    af.getViewport().getAlignment().getSequencesArray())
-            : null;
-
-    int pdbFileCount = 0;
-    String param;
-    do
-    {
-      if (pdbFileCount > 0)
-      {
-        param = (String) getAppletParameter("PDBFILE" + pdbFileCount, true);
-      }
-      else
-      {
-        param = (String) getAppletParameter("PDBFILE", true);
-      }
-
-      if (param != null)
-      {
-        PDBEntry pdb = new PDBEntry();
-
-        String seqstring;
-        SequenceI[] seqs = null;
-        String[] chains = null;
-
-        StringTokenizer st = new StringTokenizer(param, " ");
-
-        if (st.countTokens() < 2)
-        {
-          String sequence = (String) getAppletParameter("PDBSEQ", true);
-          if (sequence != null)
-          {
-            seqs = new SequenceI[] { matcher == null
-                    ? (Sequence) af.getViewport().getAlignment()
-                            .findName(sequence)
-                    : matcher.findIdMatch(sequence) };
-          }
-
-        }
-        else
-        {
-          param = st.nextToken();
-          List<SequenceI> tmp = new ArrayList<>();
-          List<String> tmp2 = new ArrayList<>();
-
-          while (st.hasMoreTokens())
-          {
-            seqstring = st.nextToken();
-            StringTokenizer st2 = new StringTokenizer(seqstring, "=");
-            if (st2.countTokens() > 1)
-            {
-              // This is the chain
-              tmp2.add(st2.nextToken());
-              seqstring = st2.nextToken();
-            }
-            tmp.add(matcher == null
-                    ? (Sequence) af.getViewport().getAlignment()
-                            .findName(seqstring)
-                    : matcher.findIdMatch(seqstring));
-          }
-
-          seqs = tmp.toArray(new SequenceI[tmp.size()]);
-          if (tmp2.size() == tmp.size())
-          {
-            chains = tmp2.toArray(new String[tmp2.size()]);
-          }
-        }
-        pdb.setId(param);
-        ret[0] = param;
-        DataSourceType protocol = resolveFileProtocol(ret);
-        // TODO check JAL-357 for files in a jar (CLASSLOADER)
-        pdb.setFile(ret[0]);
-
-        if (seqs != null)
-        {
-          for (int i = 0; i < seqs.length; i++)
-          {
-            if (seqs[i] != null)
-            {
-              ((Sequence) seqs[i]).addPDBId(pdb);
-              StructureSelectionManager
-                      .getStructureSelectionManager(
-                              (StructureSelectionManagerProvider) this)
-                      .registerPDBEntry(pdb);
-            }
-            else
-            {
-              if (debug)
-              {
-                // this may not really be a problem but we give a warning
-                // anyway
-                System.err.println(
-                        "Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
-                                + i + ")");
-              }
-            }
-          }
-
-          // if (doAlign)
-          // {
-          // pdbs.add(new Object[] { pdb, seqs, chains, protocol });
-          // }
-          // else
-          {
-            newStructureView(af, pdb, seqs, chains, protocol);
-          }
-        }
-      }
-
-      pdbFileCount++;
-    } while (param != null || pdbFileCount < 10);
-    //
-    // if (doAlign && pdbs.size() > 0)
-    // {
-    // SequenceI[][] seqs = new SequenceI[pdbs.size()][];
-    // PDBEntry[] pdb = new PDBEntry[pdbs.size()];
-    // String[][] chains = new String[pdbs.size()][];
-    // String[] protocols = new String[pdbs.size()];
-    // for (int pdbsi = 0, pdbsiSize = pdbs
-    // .size(); pdbsi < pdbsiSize; pdbsi++)
-    // {
-    // Object[] o = pdbs.get(pdbsi);
-    // pdb[pdbsi] = (PDBEntry) o[0];
-    // seqs[pdbsi] = (SequenceI[]) o[1];
-    // chains[pdbsi] = (String[]) o[2];
-    // protocols[pdbsi] = (String) o[3];
-    // }
-    //// alignedStructureView(pdb, seqs, chains, protocols);
-    // result = true;
-    // }
-    return result;
-  }
-
-  /**
-   * Load a score file if specified by parameter. Returns true if file was
-   * loaded, else false.
-   * 
-   * @param loaderFrame
-   */
-  protected boolean loadScoreFile()
+  @Override
+  public boolean parseFeaturesFile(String filename, AlignFrame alf)
   {
-    boolean result = false;
-    String sScoreFile = (String) getAppletParameter("scoreFile", true);
-    if (sScoreFile != null && !"".equals(sScoreFile))
-    {
-      try
-      {
-        if (debug)
-        {
-          System.err.println(
-                  "Attempting to load T-COFFEE score file from the scoreFile parameter");
-        }
-        result = loadScoreFile(sScoreFile);
-        if (!result)
-        {
-          System.err.println(
-                  "Failed to parse T-COFFEE parameter as a valid score file ('"
-                          + sScoreFile + "')");
-        }
-      } catch (Exception e)
-      {
-        System.err.printf("Cannot read score file: '%s'. Cause: %s \n",
-                sScoreFile, e.getMessage());
-      }
-    }
-    return result;
+    ret[0] = filename;
+    DataSourceType protocol = resolveFileProtocol(ret);
+    if (protocol == null)
+      return false;
+    return (alf == null ? getCurrentAlignFrame() : alf)
+            .parseFeaturesFile(ret[0], protocol);
   }
 
-  /**
-   * Load a tree for the alignment if specified by parameter. Returns true if a
-   * tree was loaded, else false.
-   * 
-   * @return
-   */
-  protected boolean loadTree(AlignFrame af)
+  @Override
+  public void removeSelectionListener(String listener, AlignFrame alf)
   {
-    boolean result = false;
-    String treeFile = (String) getAppletParameter("tree", true);
-    if (treeFile == null)
-    {
-      treeFile = (String) getAppletParameter("treefile", true);
-    }
 
-    if (treeFile != null)
+    List<SelectionListener> listeners = Desktop
+            .getStructureSelectionManager().getListeners();
+    for (int i = listeners.size(); --i >= 0;)
     {
-      try
-      {
-        ret[0] = treeFile;
-        NewickFile fin = new NewickFile(treeFile, resolveFileProtocol(ret));
-        fin.parse();
-
-        if (fin.getTree() != null)
-        {
-          loadTree(af, fin, ret[0]);
-          result = true;
-          if (debug)
-          {
-            System.out.println("Successfully imported tree.");
-          }
-        }
-        else
-        {
-          if (debug)
-          {
-            System.out.println(
-                    "Tree parameter did not resolve to a valid tree.");
-          }
-        }
-      } catch (Exception ex)
+      SelectionListener l = listeners.get(i);
+      if (l instanceof JsSelectionListener
+              && ((JsSelectionListener) l).isFor(alf, listener))
       {
-        ex.printStackTrace();
+        listeners.remove(i);
+        break;
       }
     }
-    return result;
-  }
-
-  /**
-   * @j2sAlias openPcaPanel
-   * 
-   * public static method for JalviewJS API to open a PCAPanel without
-   * necessarily using a dialog.
-   * 
-   * @param af
-   * @param modelName
-   * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences"
-   *         if number of sequences selected is inappropriate
-   */
-  @Override
-  public Object openPcaPanel(AlignFrame af, String modelName)
-  {
-    if (af == null)
-    {
-      af = Jalview.getCurrentAlignFrame();
-    }
-    return CalculationChooser.openPcaPanel(af, modelName, null);
   }
 
-  /**
-   * @j2sAlias openTreePanel
-   * 
-   * Open a new Tree panel on the desktop statically. Params are standard (not
-   * set by Groovy). No dialog is opened.
-   * 
-   * @param af
-   * @param treeType
-   * @param modelName
-   * @return null, or the string "label.you_need_at_least_n_sequences" if number
-   *         of sequences selected is inappropriate
-   */
-  @Override
-  public Object openTreePanel(AlignFrame af, String treeType,
-          String modelName)
+  private DataSourceType resolveFileProtocol(String[] retPath)
   {
-    if (af == null)
+    String path = retPath[0];
+    /*
+     * is it paste data?
+     */
+    if (path.startsWith("PASTE"))
     {
-      af = Jalview.getCurrentAlignFrame();
+      retPath[0] = path.substring(5);
+      return DataSourceType.PASTE;
     }
-    return CalculationChooser.openTreePanel(af, treeType, modelName, null);
-  }
-
-
-  @Override
-  public String orderBy(String[] ids, String undoName)
-  {
-    return orderAlignmentBy(null, ids, undoName);
-  }
 
-  @Override
-  public String orderAlignmentBy(AlignFrame alf, String[] ids,
-          String undoName)
-  {
-    if (alf == null)
-      alf = Jalview.getCurrentAlignFrame();
-    SequenceI[] sqs = null;
-    if (ids != null && ids.length > 0)
-    {
-      jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
-              alf.getViewport().getAlignment().getSequencesArray());
-      int s = 0;
-      sqs = new SequenceI[ids.length];
-      for (int i = 0; i < ids.length; i++)
-      {
-        if (ids[i].trim().length() == 0)
-        {
-          continue;
-        }
-        SequenceI sq = matcher.findIdMatch(ids[i]);
-        if (sq != null)
-        {
-          sqs[s++] = sq;
-        }
-      }
-      if (s > 0)
-      {
-        SequenceI[] sqq = new SequenceI[s];
-        System.arraycopy(sqs, 0, sqq, 0, s);
-        sqs = sqq;
-      }
-      else
-      {
-        sqs = null;
-      }
-    }
-    if (sqs == null)
+    /*
+     * is it a URL?
+     */
+    if (path.indexOf("://") >= 0)
     {
-      return "";
+      return DataSourceType.URL;
     }
-    ;
-    final AlignmentOrder aorder = new AlignmentOrder(sqs);
 
-    if (undoName != null && undoName.trim().length() == 0)
+    /*
+     * try relative to document root
+     */
+    URL documentBase = getDocumentBase();
+    String withDocBase = resolveUrlForLocalOrAbsolute(path, documentBase);
+    if (HttpUtils.isValidUrl(withDocBase))
     {
-      undoName = null;
+      // if (debug)
+      // {
+      // System.err.println("Prepended document base '" + documentBase
+      // + "' to make: '" + withDocBase + "'");
+      // }
+      retPath[0] = withDocBase;
+      return DataSourceType.URL;
     }
-    final String _undoName = undoName;
-    // TODO: deal with synchronization here: cannot raise any events until after
-    // this has returned.
-    return alf.sortBy(aorder, _undoName) ? "true" : "";
-  }
 
-  /**
-   * Allow an outside entity to initiate the second half of argument parsing
-   * (only).
-   * 
-   * @param args
-   * @return null is good
-   */
-  @Override
-  public Object parseArguments(String[] args)
-  {
-
-    try
-    {
-      jalview.parseArguments(new ArgsParser(args), false);
-      return null;
-    } catch (Throwable t)
+    /*
+     * try relative to codebase (if different to document base)
+     */
+    URL codeBase = getCodeBase();
+    String withCodeBase = resolveUrlForLocalOrAbsolute(path, codeBase);
+    if (!withCodeBase.equals(withDocBase)
+            && HttpUtils.isValidUrl(withCodeBase))
     {
-      return t;
+      // if (debug)
+      // {
+      // System.err.println("Prepended codebase '" + codeBase
+      // + "' to make: '" + withCodeBase + "'");
+      // }
+      retPath[0] = withCodeBase;
+      return DataSourceType.URL;
     }
-  }
 
-  @Override
-  public void removeSelectionListener(AlignFrame af, String listener)
-  {
-
-    List<SelectionListener> listeners = Desktop
-            .getStructureSelectionManager().getListeners();
-    for (int i = listeners.size(); --i >= 0;)
+    /*
+     * try locating by classloader; try this last so files in the directory
+     * are resolved using document base
+     */
+    if (inArchive(getClass(), path))
     {
-      SelectionListener l = listeners.get(i);
-      if (l instanceof JsSelectionListener
-              && ((JsSelectionListener) l).isFor(af, listener))
-      {
-        listeners.remove(i);
-        break;
-      }
+      return DataSourceType.CLASSLOADER;
     }
+    return null;
   }
 
   @Override
-  public void scrollViewToColumnIn(final AlignFrame alf,
-          final String leftHandColumn)
-  {
-    java.awt.EventQueue.invokeLater(new Runnable()
-    {
-
-      @Override
-      public void run()
-      {
-        try
-        {
-          (alf == null ? Jalview.getCurrentAlignFrame() : alf)
-                  .scrollToColumn(
-                          Integer.valueOf(leftHandColumn).intValue());
-
-        } catch (Exception ex)
-        {
-          System.err.println(
-                  "Couldn't parse integer arguments (leftHandColumn='"
-                          + leftHandColumn + "')");
-          ex.printStackTrace();
-        }
-      }
-    });
-
-  }
-
-  @Override
-  public void scrollViewToIn(final AlignFrame alf, final String topRow,
-          final String leftHandColumn)
+  public void scrollViewTo(int topRow, int leftHandColumn, AlignFrame alf)
   {
     // TODO test
     java.awt.EventQueue.invokeLater(new Runnable()
@@ -1471,10 +834,8 @@ public class JalviewJSApp implements JalviewJSApi
       {
         try
         {
-          (alf == null ? Jalview.getCurrentAlignFrame() : alf).scrollTo(
-                  Integer.valueOf(topRow).intValue(),
-                  Integer.valueOf(leftHandColumn).intValue());
-
+          (alf == null ? getCurrentAlignFrame() : alf).scrollTo(topRow,
+                  leftHandColumn);
         } catch (Exception ex)
         {
           System.err.println("Couldn't parse integer arguments (topRow='"
@@ -1487,98 +848,10 @@ public class JalviewJSApp implements JalviewJSApi
   }
 
   @Override
-  public void scrollViewToRowIn(final AlignFrame alf, final String topRow)
-  {
-    // TODO test
-
-    java.awt.EventQueue.invokeLater(new Runnable()
-    {
-      @Override
-      public void run()
-      {
-        try
-        {
-          (alf == null ? Jalview.getCurrentAlignFrame() : alf)
-                  .scrollToRow(Integer.valueOf(topRow).intValue());
-
-        } catch (Exception ex)
-        {
-          System.err.println("Couldn't parse integer arguments (topRow='"
-                  + topRow + "')");
-          ex.printStackTrace();
-        }
-
-      }
-    });
-  }
-
-  @Override
-  public void select(String sequenceIds, String columns)
-  {
-    selectIn(Jalview.getCurrentAlignFrame(), sequenceIds, columns, null);
-  }
-
-  @Override
-  public void select(String sequenceIds, String columns, String sep)
-  {
-    selectIn(null, sequenceIds, columns, sep);
-  }
-
-  // @Override
-  // public AlignFrame newView()
-  // {
-  // return newViewFrom(null, null);
-  // }
-  //
-  // @Override
-  // public AlignFrame newView(String name)
-  // {
-  // return newViewFrom(null, name);
-  // }
-  //
-  // @Override
-  // public AlignFrame newViewFrom(AlignFrame alf)
-  // {
-  // return newViewFrom(alf, null);
-  // }
-  //
-  // @Override
-  // public AlignFrame newViewFrom(AlignFrame alf, String name)
-  // {
-  // if (alf == null)
-  // {
-  // alf = Jalview.getCurrentAlignFrame();
-  // }
-  // return appLoader.newViewFrom(alf, name);
-  // }
-
-  @Override
-  public void selectIn(AlignFrame alf, String sequenceIds, String columns)
-  {
-    selectIn(alf, sequenceIds, columns, null);
-  }
-
-  @Override
-  public void selectIn(AlignFrame af, String sequenceIds, String columns,
-          String sep)
+  public void select(String ids[], String cols[], AlignFrame alf)
   {
-    AlignFrame alf = (af == null ? Jalview.getCurrentAlignFrame() : af);
-
-    if (sep == null || sep.length() == 0)
-    {
-      sep = separator;
-    }
-    else
-    {
-      if (debug)
-      {
-        System.err.println("Selecting region using separator string '"
-                + separator + "'");
-      }
-    }
-    // deparse fields
-    String[] ids = separatorListToArray(sequenceIds, sep);
-    String[] cols = separatorListToArray(columns, sep);
+    if (alf == null)
+      alf = getCurrentAlignFrame();
     final SequenceGroup sel = new SequenceGroup();
     final ColumnSelection csel = new ColumnSelection();
     AlignmentI al = alf.getViewport().getAlignment();
@@ -1674,11 +947,6 @@ public class JalviewJSApp implements JalviewJSApi
                 csel.addElement(r);
               }
             }
-            if (debug)
-            {
-              System.err.println("Range '" + cl + "' deparsed as [" + from
-                      + "," + to + "]");
-            }
           }
           else
           {
@@ -1729,11 +997,6 @@ public class JalviewJSApp implements JalviewJSApi
               }
             }
             csel.addElement(r);
-            if (debug)
-            {
-              System.err.println("Point selection '" + cl
-                      + "' deparsed as [" + r + "]");
-            }
           }
           else
           {
@@ -1762,78 +1025,249 @@ public class JalviewJSApp implements JalviewJSApi
       }
       sel.setStartRes(start);
       sel.setEndRes(end);
+      AlignFrame af = alf;
       EventQueue.invokeLater(new Runnable()
       {
         @Override
         public void run()
         {
-          alf.select(sel, csel,
-                  alf.getCurrentView().getAlignment().getHiddenColumns());
+          af.select(sel, csel,
+                  af.getCurrentView().getAlignment().getHiddenColumns());
         }
       });
     }
   }
 
+  //
+  // @Override
+  // public void setFeatureGroupState(String[] groups, boolean state)
+  // {
+  // setFeatureGroupState(null, groups, state);
+  // }
+  //
+  // @Override
+  // public void setFeatureGroupState(String[] groups, boolean state)
+  // { // JalviewLite API
+  // setFeatureGroupStateOn(null, groups, state);
+  // }
+  //
+  @Override
+  public void setFeatureGroupState(final String[] groups,
+          boolean state, AlignFrame alf)
+  {
+    // setFeatureGroupState(alf, groups, state);
+    // java.awt.EventQueue.invokeLater(new Runnable()
+    // {
+    // @Override
+    // public void run()
+    // {
+    // (alf == null ? getCurrentAlignFrame() : alf)
+    // .setFeatureGroupState(
+    // separatorListToArray(groups, separator), state);
+    // }
+    // });
+    // }
+    //
+    // public void setFeatureGroupState(AlignFrame alf, String[] groups, boolean
+    // state) {
+    (alf == null ? getCurrentAlignFrame() : alf)
+            .setFeatureGroupState(groups, state);
+  }
+
   @Override
-  public void setFeatureGroupState(String[] groups, boolean state)
+  public void setSelectionListener(String listener, AlignFrame alf)
   {
-    setFeatureGroupState(null, groups, state);
+    Desktop.getStructureSelectionManager()
+            .addSelectionListener(new JsSelectionListener(alf, listener));
   }
 
   @Override
-  public void setFeatureGroupState(String groups, boolean state)
-  { // JalviewLite API
-    setFeatureGroupStateOn(null, groups, state);
+  public void showOverview()
+  {
+    getCurrentAlignFrame().overviewMenuItem_actionPerformed(null);
   }
 
+  /**
+   * @j2sAlias showStructure
+   */
   @Override
-  public void setFeatureGroupStateOn(final AlignFrame alf,
-          final String groups, boolean state)
+  public void showStructure(String pdbID, String fileType, AlignFrame alf)
   {
-    setFeatureGroupState(alf, separatorListToArray(groups, separator), state);
-//    java.awt.EventQueue.invokeLater(new Runnable()
-//    {
-//      @Override
-//      public void run()
-//      {
-//        (alf == null ? Jalview.getCurrentAlignFrame() : alf)
-//                .setFeatureGroupState(
-//                        separatorListToArray(groups, separator), state);
-//      }
-//    });
-  }
-
-  public void setFeatureGroupState(AlignFrame af, String[] groups, boolean state) {
-    (af == null ? Jalview.getCurrentAlignFrame() : af).setFeatureGroupState(groups, state);
+    if (alf == null)
+      alf = getCurrentAlignFrame();
+    PDBEntry pe = null;
+    SequenceI[] seqs = null;
+    if (pdbID == null)
+    {
+      seqs = alf.getViewport().getSequenceSelection();
+      if (seqs.length == 0)
+        seqs = alf.getViewport().getAlignment().getSequencesArray();
+      for (int i = 0; i < seqs.length; i++)
+      {
+        Vector<PDBEntry> list = seqs[i].getAllPDBEntries();
+        if (list.size() > 0)
+        {
+          pe = list.get(0);
+          break;
+        }
+      }
+    }
+    if (pe == null)
+    {
+      if (pdbID == null)
+        return;
+      pe = new PDBEntry(pdbID, null, fileType);
+      List<SequenceI> list = alf.getViewport().getAlignment()
+              .getSequences();
+      List<SequenceI> tmp = new ArrayList<SequenceI>();
+      for (int i = 0; i < list.size(); i++)
+      {
+        SequenceI seq = list.get(i);
+        if (seq.getPDBEntry(pdbID) != null)
+        {
+          tmp.add(seq);
+        }
+      }
+      seqs = tmp.toArray(new SequenceI[tmp.size()]);
+      alf.alignPanel.selectSequences(tmp);
+    }
+    StructureViewer.launchStructureViewer(alf.alignPanel, pe, seqs);
   }
 
+  // private or package-private methods
 
-  @Override
-  public void setSelectionListener(AlignFrame af, String listener)
+  /**
+   * form a complete URL given a path to a resource and a reference location on
+   * the same server
+   * 
+   * @param targetPath
+   *          - an absolute path on the same server as localref or a document
+   *          located relative to localref
+   * @param localref
+   *          - a URL on the same server as url
+   * @return a complete URL for the resource located by url
+   */
+  private static String resolveUrlForLocalOrAbsolute(String targetPath,
+          URL localref)
   {
-    Desktop.getStructureSelectionManager()
-            .addSelectionListener(new JsSelectionListener(af, listener));
+    String resolvedPath = "";
+    if (targetPath.startsWith("/"))
+    {
+      String codebase = localref.toString();
+      String localfile = localref.getFile();
+      resolvedPath = codebase.substring(0,
+              codebase.length() - localfile.length()) + targetPath;
+      return resolvedPath;
+    }
+
+    /*
+     * get URL path and strip off any trailing file e.g.
+     * www.jalview.org/examples/index.html#applets?a=b is trimmed to
+     * www.jalview.org/examples/
+     */
+    String urlPath = localref.toString();
+    String directoryPath = urlPath;
+    int lastSeparator = directoryPath.lastIndexOf("/");
+    if (lastSeparator > 0)
+    {
+      directoryPath = directoryPath.substring(0, lastSeparator + 1);
+    }
+
+    if (targetPath.startsWith("/"))
+    {
+      /*
+       * construct absolute URL to a file on the server - this is not allowed?
+       */
+      // String localfile = localref.getFile();
+      // resolvedPath = urlPath.substring(0,
+      // urlPath.length() - localfile.length())
+      // + targetPath;
+      resolvedPath = directoryPath + targetPath.substring(1);
+    }
+    else
+    {
+      resolvedPath = directoryPath + targetPath;
+    }
+    // if (debug)
+    // {
+    // System.err.println(
+    // "resolveUrlForLocalOrAbsolute returning " + resolvedPath);
+    // }
+    return resolvedPath;
   }
 
-  @Override
-  public void setSelectionListener(String listener)
+  /**
+   * parse the string into a list
+   * 
+   * @param list
+   * @param separator
+   * @return elements separated by separator
+   */
+  private static String[] separatorListToArray(String list,
+          String separator)
   {
-    Desktop.getStructureSelectionManager()
-            .addSelectionListener(new JsSelectionListener(null, listener));
+    // TODO use StringUtils version (slightly different...)
+    int seplen = separator.length();
+    if (list == null || list.equals("") || list.equals(separator))
+    {
+      return null;
+    }
+    Vector<String> jv = new Vector<>();
+    int cp = 0, pos;
+    while ((pos = list.indexOf(separator, cp)) > cp)
+    {
+      jv.addElement(list.substring(cp, pos));
+      cp = pos + seplen;
+    }
+    if (cp < list.length())
+    {
+      String c = list.substring(cp);
+      if (!c.equals(separator))
+      {
+        jv.addElement(c);
+      }
+    }
+    if (jv.size() > 0)
+    {
+      String[] v = new String[jv.size()];
+      for (int i = 0; i < v.length; i++)
+      {
+        v[i] = jv.elementAt(i);
+      }
+      jv.removeAllElements();
+      return v;
+    }
+    return null;
   }
 
-  @Override
-  public void showOverview()
+  /**
+   * Discovers whether the given file is in the Applet Archive
+   * 
+   * @param f
+   *          String
+   * @return boolean
+   */
+  private static boolean inArchive(Class<?> c, String f)
   {
-    Jalview.getCurrentAlignFrame().overviewMenuItem_actionPerformed(null);
+    // This might throw a security exception in certain browsers
+    // Netscape Communicator for instance.
+    try
+    {
+      boolean rtn = (c.getResourceAsStream("/" + f) != null);
+      return rtn;
+    } catch (Exception ex)
+    {
+      System.out.println("Exception checking resources: " + f + " " + ex);
+      return false;
+    }
   }
 
   /**
    * Allowing for a JavaScript function here.
    */
-  public void callInitCallback()
+  void callInitCallback()
   {
-    Object initjscallback = getAppletParameter("oninit", false);
+    Object initjscallback = getParameterAsObject("oninit");
     if (initjscallback != null)
     {
       try
@@ -1858,7 +1292,7 @@ public class JalviewJSApp implements JalviewJSApi
    * @param data
    * @return String return from the callback method.
    */
-  public String doSendCallback(Object callback, Object[] data)
+  String doSendCallback(Object callback, Object[] data)
   {
     Jalview me = jalview;
 
@@ -1883,287 +1317,367 @@ public class JalviewJSApp implements JalviewJSApi
     return "";
   }
 
-  private DataSourceType resolveFileProtocol(String[] retPath)
+  /**
+   * Initialize from Info.key/value pairs that match the old JalviewLite applet
+   * parameters.
+   * 
+   * See http://www.jalview.org/old/v2_8/examples/appletParameters.html
+   * 
+   * Note that some of these parameters are handled as command-line arguments,
+   * as determined in ArgsParser.
+   * 
+   * @param alf
+   */
+  private void initFromParams(AlignFrame alf)
   {
-    String path = retPath[0];
-    /*
-     * is it paste data?
-     */
-    if (path.startsWith("PASTE"))
-    {
-      retPath[0] = path.substring(5);
-      return DataSourceType.PASTE;
-    }
-
-    /*
-     * is it a URL?
-     */
-    if (path.indexOf("://") >= 0)
-    {
-      return DataSourceType.URL;
-    }
-
-    /*
-     * try relative to document root
-     */
-    URL documentBase = getDocumentBase();
-    String withDocBase = resolveUrlForLocalOrAbsolute(path, documentBase);
-    if (HttpUtils.isValidUrl(withDocBase))
-    {
-      // if (debug)
-      // {
-      // System.err.println("Prepended document base '" + documentBase
-      // + "' to make: '" + withDocBase + "'");
-      // }
-      retPath[0] = withDocBase;
-      return DataSourceType.URL;
-    }
-
-    /*
-     * try relative to codebase (if different to document base)
-     */
-    URL codeBase = getCodeBase();
-    String withCodeBase = resolveUrlForLocalOrAbsolute(path, codeBase);
-    if (!withCodeBase.equals(withDocBase)
-            && HttpUtils.isValidUrl(withCodeBase))
-    {
-      // if (debug)
-      // {
-      // System.err.println("Prepended codebase '" + codeBase
-      // + "' to make: '" + withCodeBase + "'");
-      // }
-      retPath[0] = withCodeBase;
-      return DataSourceType.URL;
-    }
-
-    /*
-     * try locating by classloader; try this last so files in the directory
-     * are resolved using document base
-     */
-    if (inArchive(getClass(), path))
+    String sep = getParameter("separator");
+    if (sep != null && sep.length() > 0)
     {
-      return DataSourceType.CLASSLOADER;
+      separator = sep;
     }
-    return null;
+    initTree(alf);
+    initScoreFile(alf);
+    initFeatures(alf);
+    initAnnotations(alf);
+    initJnetFile(alf);
+    initPdbFiles(alf);
   }
 
   /**
-   * Discovers whether the given file is in the Applet Archive
+   * Load annotations if specified by parameter. Returns true if loaded, else
+   * false.
    * 
-   * @param f
-   *          String
-   * @return boolean
+   * 
+   * @param alignFrame
+   * @return
    */
-  private static boolean inArchive(Class<?> c, String f)
+  private boolean initAnnotations(AlignFrame alf)
   {
-    // This might throw a security exception in certain browsers
-    // Netscape Communicator for instance.
-    try
-    {
-      boolean rtn = (c.getResourceAsStream("/" + f) != null);
-      return rtn;
-    } catch (Exception ex)
-    {
-      System.out.println("Exception checking resources: " + f + " " + ex);
+
+    String param = getParameter("annotations");
+    if (param == null)
+      return false;
+    ret[0] = param;
+    DataSourceType protocol = resolveFileProtocol(ret);
+    param = ret[0];
+    if (!new AnnotationFile().annotateAlignmentView(alf.getViewport(),
+            param, protocol))
+    {
+      System.err.println("Annotations were not added from annotation file '"
+              + param + "'");
       return false;
     }
+    updateForAnnotations();
+    return true;
   }
 
   /**
-   * form a complete URL given a path to a resource and a reference location on
-   * the same server
-   * 
-   * @param targetPath
-   *          - an absolute path on the same server as localref or a document
-   *          located relative to localref
-   * @param localref
-   *          - a URL on the same server as url
-   * @return a complete URL for the resource located by url
+   * Load features file and view settings as specified by parameters. Returns
+   * true if features were loaded, else false.
+   * 
+   * @param
+   * 
+   * @param alignFrame
+   * @return
    */
-  public static String resolveUrlForLocalOrAbsolute(String targetPath,
-          URL localref)
+  private boolean initFeatures(AlignFrame alf)
   {
-    String resolvedPath = "";
-    if (targetPath.startsWith("/"))
+
+    // ///////////////////////////
+    // modify display of features
+    // we do this before any features have been loaded, ensuring any hidden
+    // groups are hidden when features first displayed
+    //
+    // hide specific groups
+    //
+    String param = getParameter("hidefeaturegroups");
+    if (param != null)
     {
-      String codebase = localref.toString();
-      String localfile = localref.getFile();
-      resolvedPath = codebase.substring(0,
-              codebase.length() - localfile.length()) + targetPath;
-      return resolvedPath;
+      setFeatureGroupState(separatorListToArray(param, separator),
+              false, alf);
+      // setFeatureGroupStateOn(newAlignFrame, param, false);
     }
-
-    /*
-     * get URL path and strip off any trailing file e.g.
-     * www.jalview.org/examples/index.html#applets?a=b is trimmed to
-     * www.jalview.org/examples/
-     */
-    String urlPath = localref.toString();
-    String directoryPath = urlPath;
-    int lastSeparator = directoryPath.lastIndexOf("/");
-    if (lastSeparator > 0)
+    // show specific groups
+    param = getParameter("showfeaturegroups");
+    if (param != null)
     {
-      directoryPath = directoryPath.substring(0, lastSeparator + 1);
+      setFeatureGroupState(separatorListToArray(param, separator),
+              true, alf);
+      // setFeatureGroupStateOn(newAlignFrame, param, true);
     }
-
-    if (targetPath.startsWith("/"))
+    // and now load features
+    param = getParameter("features");
+    if (param == null)
     {
-      /*
-       * construct absolute URL to a file on the server - this is not allowed?
-       */
-      // String localfile = localref.getFile();
-      // resolvedPath = urlPath.substring(0,
-      // urlPath.length() - localfile.length())
-      // + targetPath;
-      resolvedPath = directoryPath + targetPath.substring(1);
+      return false;
     }
-    else
+    if (!parseFeaturesFile(param, alf))
+      return false;
+    param = getParameter("showFeatureSettings");
+    if (param != null && param.equalsIgnoreCase("true"))
     {
-      resolvedPath = directoryPath + targetPath;
+      alf.showFeatureSettingsUI();
     }
-    // if (debug)
-    // {
-    // System.err.println(
-    // "resolveUrlForLocalOrAbsolute returning " + resolvedPath);
-    // }
-    return resolvedPath;
+    return true;
   }
 
   /**
-   * parse the string into a list
+   * Load in a Jnetfile if specified by parameter. Returns true if loaded, else
+   * false.
    * 
-   * @param list
-   * @param separator
-   * @return elements separated by separator
+   * @param alignFrame
+   * @return
    */
-  public static String[] separatorListToArray(String list, String separator)
+  private boolean initJnetFile(AlignFrame alf)
   {
-    // TODO use StringUtils version (slightly different...)
-    int seplen = separator.length();
-    if (list == null || list.equals("") || list.equals(separator))
-    {
-      return null;
-    }
-    Vector<String> jv = new Vector<>();
-    int cp = 0, pos;
-    while ((pos = list.indexOf(separator, cp)) > cp)
+
+    String param = getParameter("jnetfile");
+    if (param == null)
     {
-      jv.addElement(list.substring(cp, pos));
-      cp = pos + seplen;
+      // jnet became jpred around 2016
+      param = getParameter("jpredfile");
     }
-    if (cp < list.length())
+    if (param != null)
     {
-      String c = list.substring(cp);
-      if (!c.equals(separator))
+      try
       {
-        jv.addElement(c);
-      }
-    }
-    if (jv.size() > 0)
-    {
-      String[] v = new String[jv.size()];
-      for (int i = 0; i < v.length; i++)
+        ret[0] = param;
+        DataSourceType protocol = resolveFileProtocol(ret);
+        JPredFile predictions = new JPredFile(ret[0], protocol);
+        JnetAnnotationMaker.add_annotation(predictions,
+                alf.getViewport().getAlignment(), 0, false);
+        // false == do not add sequence profile from concise output
+        alf.getViewport().getAlignment().setupJPredAlignment();
+        updateForAnnotations();
+      } catch (Exception ex)
       {
-        v[i] = jv.elementAt(i);
+        ex.printStackTrace();
+        return false;
       }
-      jv.removeAllElements();
-      return v;
     }
-    return null;
+    return true;
   }
 
-  public class JsSelectionListener
-          implements jalview.structure.SelectionListener
+  /**
+   * Load PDBFiles if any specified by parameter(s). Returns true if loaded,
+   * else false.
+   * 
+   * @param loaderFrame
+   * @return
+   */
+  private boolean initPdbFiles(AlignFrame alf)
   {
 
-    AlignFrame _af;
+    /*
+     * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6 -
+     * related to JAL-434
+     */
 
-    String _listener;
+    // not supported (as for JalviewLite)
+    // boolean doAlign = false;//"true".equalsIgnoreCase("" +
+    // getAppletParameter("alignpdbfiles", false));
+    // setAlignPdbStructures(doAlign);
+    /*
+     * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
+     * PDB|1GAQ|1GAQ|C">
+     * 
+     * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
+     * 
+     * <param name="PDBfile3" value="1q0o Q45135_9MICO">
+     */
+
+    // Accumulate pdbs here if they are heading for the same view (if
+    // alignPdbStructures is true)
+    // ArrayList<Object[]> pdbs = new ArrayList<>();
+    // init a lazy matcher if we're asked to
+    boolean relaxed = "true"
+            .equalsIgnoreCase(getParameter("relaxedidmatch"));
+    jalview.analysis.SequenceIdMatcher matcher = relaxed
+            ? new jalview.analysis.SequenceIdMatcher(
+                    alf.getViewport().getAlignment().getSequencesArray())
+            : null;
 
-    public JsSelectionListener(AlignFrame af, String listener)
+    String param = getParameter("PDBFILE");
+    int plast = (param == null ? 9 : 1);
+    if (param == null && (param = getParameter("PDBFILE1")) == null)
     {
-      _af = af;
-      _listener = listener;
+      return false;
     }
-
-    @Override
-    public void selection(SequenceGroup seqsel, ColumnSelection colsel,
-            HiddenColumns hidden, SelectionSource source)
+    for (int p = 1; p <= plast; p++)
     {
-      // System.err.println("Testing selection event relay to
-      // jsfunction:"+_listener);
-      String setid = "";
-      AlignFrame src = _af;
-      if (source != null)
+      if (p > 1)
       {
-        if (source instanceof AlignViewport
-                && Jalview.getCurrentAlignFrame().getViewport() == source)
-        {
-          src = Jalview.getCurrentAlignFrame();
-          if (src != _af)
-            return;
-        }
+        param = getParameter("PDBFILE" + p);
+        if (param == null)
+          break;
       }
-      String[] seqs = new String[] {};
-      String[] cols = new String[] {};
-      int strt = 0, end = (src == null) ? -1
-              : src.alignPanel.av.getAlignment().getWidth();
-      if (seqsel != null && seqsel.getSize() > 0)
+      PDBEntry pdb = new PDBEntry();
+
+      String seqstring;
+      SequenceI[] seqs = null;
+      String[] chains = null;
+
+      StringTokenizer st = new StringTokenizer(param, " ");
+
+      if (st.countTokens() < 2)
       {
-        seqs = new String[seqsel.getSize()];
-        for (int i = 0; i < seqs.length; i++)
+        String sequence = getParameter("PDBSEQ");
+        if (sequence != null)
         {
-          seqs[i] = seqsel.getSequenceAt(i).getName();
+          seqs = new SequenceI[] { matcher == null
+                  ? (Sequence) alf.getViewport().getAlignment()
+                          .findName(sequence)
+                  : matcher.findIdMatch(sequence) };
         }
-        if (strt < seqsel.getStartRes())
+
+      }
+      else
+      {
+        param = st.nextToken();
+        List<SequenceI> tmp = new ArrayList<>();
+        List<String> tmp2 = new ArrayList<>();
+
+        while (st.hasMoreTokens())
         {
-          strt = seqsel.getStartRes();
+          seqstring = st.nextToken();
+          StringTokenizer st2 = new StringTokenizer(seqstring, "=");
+          if (st2.countTokens() > 1)
+          {
+            // This is the chain
+            tmp2.add(st2.nextToken());
+            seqstring = st2.nextToken();
+          }
+          tmp.add(matcher == null
+                  ? (Sequence) alf.getViewport().getAlignment()
+                          .findName(seqstring)
+                  : matcher.findIdMatch(seqstring));
         }
-        if (end == -1 || end > seqsel.getEndRes())
+
+        seqs = tmp.toArray(new SequenceI[tmp.size()]);
+        if (tmp2.size() == tmp.size())
         {
-          end = seqsel.getEndRes();
+          chains = tmp2.toArray(new String[tmp2.size()]);
         }
       }
-      if (colsel != null && !colsel.isEmpty())
+      pdb.setId(param);
+      ret[0] = param;
+      DataSourceType protocol = resolveFileProtocol(ret);
+      // TODO check JAL-357 for files in a jar (CLASSLOADER)
+      pdb.setFile(ret[0]);
+
+      if (seqs != null)
       {
-        if (end == -1)
+        for (int i = 0; i < seqs.length; i++)
         {
-          end = colsel.getMax() + 1;
+          if (seqs[i] != null)
+          {
+            ((Sequence) seqs[i]).addPDBId(pdb);
+            StructureSelectionManager
+                    .getStructureSelectionManager(
+                            (StructureSelectionManagerProvider) this)
+                    .registerPDBEntry(pdb);
+          }
         }
-        cols = new String[colsel.getSelected().size()];
-        for (int i = 0; i < cols.length; i++)
+
+        // if (doAlign)
+        // {
+        // pdbs.add(new Object[] { pdb, seqs, chains, protocol });
+        // }
+        // else
         {
-          cols[i] = "" + (1 + colsel.getSelected().get(i).intValue());
+          StructureViewer.launchStructureViewer(
+                  (alf == null ? getCurrentAlignFrame() : alf).alignPanel,
+                  pdb, seqs);
         }
       }
-      else
+    }
+    //
+    // if (doAlign && pdbs.size() > 0)
+    // {
+    // SequenceI[][] seqs = new SequenceI[pdbs.size()][];
+    // PDBEntry[] pdb = new PDBEntry[pdbs.size()];
+    // String[][] chains = new String[pdbs.size()][];
+    // String[] protocols = new String[pdbs.size()];
+    // for (int pdbsi = 0, pdbsiSize = pdbs
+    // .size(); pdbsi < pdbsiSize; pdbsi++)
+    // {
+    // Object[] o = pdbs.get(pdbsi);
+    // pdb[pdbsi] = (PDBEntry) o[0];
+    // seqs[pdbsi] = (SequenceI[]) o[1];
+    // chains[pdbsi] = (String[]) o[2];
+    // protocols[pdbsi] = (String) o[3];
+    // }
+    //// alignedStructureView(pdb, seqs, chains, protocols);
+    // result = true;
+    // }
+    return true;
+  }
+
+  /**
+   * Load a score file if specified by parameter. Returns true if file was
+   * loaded, else false.
+   * 
+   * @param loaderFrame
+   */
+  private boolean initScoreFile(AlignFrame alf)
+  {
+
+    String sScoreFile = getParameter("scoreFile");
+    if (sScoreFile != null && !"".equals(sScoreFile))
+    {
+      try
       {
-        if (seqsel != null && seqsel.getSize() > 0)
+        if (loadScoreFile(sScoreFile, alf))
         {
-          // send a valid range, otherwise we send the empty selection
-          cols = new String[1];
-          cols[0] = "" + (1 + strt) + "-" + (1 + end);
+          return true;
         }
-        ;
-
+        System.err.println(
+                "Failed to parse T-COFFEE parameter as a valid score file ('"
+                        + sScoreFile + "')");
+      } catch (Exception e)
+      {
+        System.err.printf("Cannot read score file: '%s'. Cause: %s \n",
+                sScoreFile, e.getMessage());
       }
-
-      doSendCallback(_listener,
-              new Object[]
-              { src, setid, seqs, cols });
     }
+    return false;
+  }
 
-    public boolean isFor(AlignFrame af, String listener)
+  /**
+   * Load a tree for the alignment if specified by parameter. Returns true if a
+   * tree was loaded, else false.
+   * 
+   * @return
+   */
+  private boolean initTree(AlignFrame alf)
+  {
+    String treeFile;
+    if ((treeFile = getParameter("tree")) == null
+            && (treeFile = getParameter("treefile")) == null)
+      return false;
+    if (alf == null)
+      alf = getCurrentAlignFrame();
+    try
     {
-      return _af == af && _listener.contentEquals(listener);
+      ret[0] = treeFile;
+      NewickFile nf = new NewickFile(treeFile, resolveFileProtocol(ret));
+      nf.parse();
+      if (nf.getTree() != null)
+      {
+        treeFile = ret[0];
+        alf.getViewport()
+                .setCurrentTree(alf.showNewickTree(nf, treeFile).getTree());
+        return true;
+      }
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
     }
-
+    return false;
   }
 
-  @Override
-  public AlignViewportI getViewport()
+  private void updateForAnnotations()
   {
-    return Jalview.getCurrentAlignFrame().getViewport();
+    getCurrentAlignFrame().updateForAnnotations();
   }
-
 }

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 4e50439..f74eb32 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -167,6 +167,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 {
 
+  public static int frameCount;
+  
   public static final int DEFAULT_WIDTH = 700;
 
   public static final int DEFAULT_HEIGHT = 500;
@@ -194,6 +196,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   File fileObject;
 
+  private int id;
+
   /**
    * Creates a new AlignFrame object with specific width and height.
    * 
@@ -288,6 +292,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
           int height, String sequenceSetId, String viewId)
   {
+    
+    id = (++frameCount);
+    
     setSize(width, height);
 
     if (al.getDataset() == null)
@@ -5923,6 +5930,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     alignPanel.getSeqPanel().selection(sel, csel, hidden, null);
   }
 
+  
+  public int getID()
+  {
+    return id;
+  }
+
 }
 
 class PrintThread extends Thread

diff --git a/swingjs/SwingJS-site.zip b/swingjs/SwingJS-site.zip
index 90ec5a2..90b1901 100644 (file)
Binary files a/swingjs/SwingJS-site.zip and b/swingjs/SwingJS-site.zip differ

diff --git a/swingjs/timestamp b/swingjs/timestamp
index 5cb9ccc..bf52be2 100644 (file)
--- a/swingjs/timestamp
+++ b/swingjs/timestamp
@@ -1 +1 @@
-20200606223527 
+20200607125736 

diff --git a/swingjs/ver/3.2.9/SwingJS-site.zip b/swingjs/ver/3.2.9/SwingJS-site.zip
index 90ec5a2..90b1901 100644 (file)
Binary files a/swingjs/ver/3.2.9/SwingJS-site.zip and b/swingjs/ver/3.2.9/SwingJS-site.zip differ

diff --git a/swingjs/ver/3.2.9/timestamp b/swingjs/ver/3.2.9/timestamp
index 5cb9ccc..bf52be2 100644 (file)
--- a/swingjs/ver/3.2.9/timestamp
+++ b/swingjs/ver/3.2.9/timestamp
@@ -1 +1 @@
-20200606223527 
+20200607125736 

diff --git a/utils/jalviewjs/site-resources/jalview_bin_JalviewJS_core.html b/utils/jalviewjs/site-resources/_jalview_bin_JalviewJS_core.html
similarity index 100%
rename from utils/jalviewjs/site-resources/jalview_bin_JalviewJS_core.html
rename to utils/jalviewjs/site-resources/_jalview_bin_JalviewJS_core.html

diff --git a/utils/jalviewjs/site-resources/jalview_embedded_example1.html b/utils/jalviewjs/site-resources/_jalview_embedded_example1.html
similarity index 100%
rename from utils/jalviewjs/site-resources/jalview_embedded_example1.html
rename to utils/jalviewjs/site-resources/_jalview_embedded_example1.html

diff --git a/utils/jalviewjs/site-resources/_jalview_embedded_example2.html b/utils/jalviewjs/site-resources/_jalview_embedded_example2.html
new file mode 100644 (file)
index 0000000..89a4f71
--- /dev/null
+++ b/utils/jalviewjs/site-resources/_jalview_embedded_example2.html
@@ -0,0 +1,101 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Embedded JalviewJS Example 2</title><meta charset="utf-8" />
+<script src="swingjs/swingjs2.js"></script>
+<script>
+
+// NOTE: The applet on this page is "Jalview". 
+
+// BH 2019.10.06 adds Tree and Pca functionality
+// BH see issue JAL-3451
+
+if (!self.SwingJS)alert('swingjs2.js was not found. It needs to be in swingjs folder in the same directory as ' + document.location.href)
+Info = {
+  code: null,
+  main: "jalview.bin.JalviewJS2",
+  core: "NONE",
+//     core:"_jalview",
+
+       oninit:function() {$("#links").show();},
+       noannotation: true,
+       
+  readyFunction: null,
+       serverURL: 'https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php',
+       j2sPath: 'swingjs/j2s',
+       console:'sysoutdiv',
+       allowjavascript: true
+}
+
+jvGet = function(what) {
+       switch(what) {
+       case "select1":
+               alert(Jalview1.getApp().getSelectedSequences());
+               break;
+       case "select2":
+               alert(Jalview2.getApp().getSelectedSequences());        
+               break;
+       case "select1fasta":
+               alert(Jalview1.getApp().getSelectedSequencesAsAlignment("fasta",true));
+               break;
+       case "select2fasta":
+               alert(Jalview2.getApp().getSelectedSequencesAsAlignment("fasta",true));
+               break;
+       }
+       
+}
+
+$(document).ready(function() {
+
+         SwingJS.getApplet('Jalview1', Info);
+         SwingJS.getApplet('Jalview2', Info);
+
+});
+
+</script>
+</head>
+<body style="background-image: url(images/coolVeryLightBG.png);">
+<table style="width:1000px;border:2px solid lightblue;border-spacing:0;font-size:16pt;" padding="10" valign="top">
+<tr>
+<td style="font-size:24;font-weight:bold;background-color:lightblue" colspan=2><center>Demonstration of embedded JalviewJS components</center>
+</td>
+
+
+</tr><tr>
+
+
+<td colspan=2 valign=top style="padding:20px;background-color:lightgray">
+this page tests two Jalview apps on the same page.
+<div id="Jalview1-desktop-div" style="width:0px;height:0px;"></div>
+<div id="Jalview2-desktop-div" style="width:0px;height:0px;"></div>
+</td></tr>
+<tr><td style="background-color:lightgray;padding:10px">
+<div id="Jalview1-alignment-div" style="padding:10px;position:relative;width:550px;height:300px">
+</td>
+<td style="background-color:lightgray;padding:10px">
+<div id="Jalview2-alignment-div" style="padding:10px;position:relative;width:550px;height:300px">
+</td>
+</tr>
+<tr><td>
+<div style="display:block;width:500px;height:300px;">
+<div id="sysoutdiv" style="border:1px solid green;width:100%;height:95%;overflow:auto"></div>
+This is System.out. <a href="javascript:J2S.thisApplet._clearConsole()">clear it</a> <br>Add ?j2snocore to URL to see full class list; ?j2sdebug to use uncompressed j2s/core files <br><a href="javascript:getClassList()">get _j2sClassList.txt</a>
+</div>
+
+</td><td valign=top>
+<div id=links style="display:none">
+<a href="javascript:jvGet('select1')">Show Jalview1 selections</a>
+
+<a href="javascript:jvGet('select2')">Show Jalview2 selections</a>
+
+<br>
+<a href="javascript:jvGet('select1fasta')">Show Jalview1 selections (fasta)</a>
+
+<a href="javascript:jvGet('select2fasta')">Show Jalview2 selections (fasta)</a>
+</div>
+</td></tr>
+</table>
+
+
+</body>
+</html>