JAL-3269 ready for testing embedded interface

[jalview.git] / src / jalview / bin / Jalview.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 047356b..2cf6f37 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -553,8 +553,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
     parseArguments(aparser, true);
   }
 
-  private Object parseArguments(ArgsParser aparser,
-          boolean isStartup)
+  private Object parseArguments(ArgsParser aparser, boolean isStartup)
   {
     boolean isJS = Platform.isJS();
 
@@ -1321,6 +1320,17 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
     JalviewApp app = new JalviewApp()
     {
 
+      // 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
 
       private Hashtable<String, Hashtable<String, String[]>> jsmessages;
@@ -1472,7 +1482,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
       @Override
       public StructureSelectionManagerProvider getStructureSelectionManagerProvider()
       {
-        // TODO Auto-generated method stub
+        // TODO Q: what exactly is this? BH
         return null;
       }
 
@@ -1489,8 +1499,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
               ColumnSelection colsel, HiddenColumns hidden,
               SelectionSource source, Object alignFrame)
       {
-        // TODO Auto-generated method stub
-        return null;
+        return appLoader.getSelectionForListener(getCurrentAlignFrame(),
+                seqsel, colsel, hidden, source, alignFrame);
       }
 
       @Override
@@ -1502,16 +1512,14 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
       @Override
       public Hashtable<String, int[]> getJSHashes()
       {
-        return (jshashes == null
-                ? (jshashes = new Hashtable<>())
+        return (jshashes == null ? (jshashes = new Hashtable<>())
                 : jshashes);
       }
 
       @Override
       public Hashtable<String, Hashtable<String, String[]>> getJSMessages()
       {
-        return (jsmessages == null
-                ? (jsmessages = new Hashtable<>())
+        return (jsmessages == null ? (jsmessages = new Hashtable<>())
                 : jsmessages);
       }
 
@@ -1602,11 +1610,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public void highlightIn(AlignFrameI alf,
-          String sequenceId, String position, String alignedPosition)
+  public void highlightIn(AlignFrameI alf, String sequenceId,
+          String position, String alignedPosition)
   {
-    appLoader.highlightIn(alf, sequenceId, position,
-            alignedPosition);
+    appLoader.highlightIn(alf, sequenceId, position, alignedPosition);
   }
 
   @Override
@@ -1622,15 +1629,14 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public void selectIn(AlignFrameI alf, String sequenceIds,
-          String columns)
+  public void selectIn(AlignFrameI alf, String sequenceIds, String columns)
   {
     selectIn(alf, sequenceIds, columns, null);
   }
 
   @Override
-  public void selectIn(AlignFrameI alf, String sequenceIds,
-          String columns, String sep)
+  public void selectIn(AlignFrameI alf, String sequenceIds, String columns,
+          String sep)
   {
     appLoader.selectIn(alf, sequenceIds, columns, sep);
   }
@@ -1644,8 +1650,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public String getSelectedSequencesAsAlignmentFrom(
-          AlignFrameI alf, String format, String sep)
+  public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+          String format, String sep)
   {
     return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, sep);
   }
@@ -1663,8 +1669,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public String getAlignmentOrderFrom(AlignFrameI alf,
-          String sep)
+  public String getAlignmentOrderFrom(AlignFrameI alf, String sep)
   {
     return appLoader.getAlignmentOrderFrom(alf, sep);
   }
@@ -1682,8 +1687,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public String orderAlignmentBy(AlignFrameI alf,
-          String order, String undoName, String sep)
+  public String orderAlignmentBy(AlignFrameI alf, String order,
+          String undoName, String sep)
   {
     return appLoader.orderAlignmentBy(alf, order, undoName, sep);
   }
@@ -1695,8 +1700,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public String getAlignmentFrom(AlignFrameI alf,
-          String format)
+  public String getAlignmentFrom(AlignFrameI alf, String format)
   {
     return getAlignmentFrom(alf, format, null);
   }
@@ -1708,8 +1712,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public String getAlignmentFrom(AlignFrameI alf,
-          String format, String suffix)
+  public String getAlignmentFrom(AlignFrameI alf, String format,
+          String suffix)
   {
     return appLoader.getAlignmentFrom(alf, format, suffix);
   }
@@ -1717,176 +1721,106 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   @Override
   public void loadAnnotation(String annotation)
   {
-    // TODO Auto-generated method stub
-
+    loadAnnotationFrom(getCurrentAlignFrame(), annotation);
   }
 
   @Override
-  public void loadAnnotationFrom(AlignFrameI alf,
-          String annotation)
+  public void loadAnnotationFrom(AlignFrameI alf, String annotation)
   {
-    // TODO Auto-generated method stub
-
+    appLoader.loadAnnotationFrom(alf, annotation);
   }
 
   @Override
   public void loadFeatures(String features, boolean autoenabledisplay)
   {
-    // TODO Auto-generated method stub
-
+    loadFeaturesFrom(currentAlignFrame, features, autoenabledisplay);
   }
 
   @Override
-  public boolean loadFeaturesFrom(AlignFrameI alf,
-          String features, boolean autoenabledisplay)
+  public boolean loadFeaturesFrom(AlignFrameI alf, String features,
+          boolean autoenabledisplay)
   {
-    // TODO Auto-generated method stub
-    return false;
+    return appLoader.loadFeaturesFrom(alf, features, autoenabledisplay);
   }
 
   @Override
   public String getFeatures(String format)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return getFeaturesFrom(getCurrentAlignFrame(), format);
   }
 
   @Override
-  public String getFeaturesFrom(AlignFrameI alf,
-          String format)
+  public String getFeaturesFrom(AlignFrameI alf, String format)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return appLoader.getFeaturesFrom(alf, format);
   }
 
   @Override
   public String getAnnotation()
   {
-    // TODO Auto-generated method stub
-    return null;
+    return getAnnotationFrom(getCurrentAlignFrame());
   }
 
   @Override
   public String getAnnotationFrom(AlignFrameI alf)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return appLoader.getAnnotationFrom(alf);
   }
 
   @Override
   public AlignFrameI newView()
   {
-    // TODO Auto-generated method stub
-    return null;
+    return newViewFrom(getCurrentAlignFrame(), null);
   }
 
   @Override
   public AlignFrameI newView(String name)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return newViewFrom(getCurrentAlignFrame(), name);
   }
 
   @Override
   public AlignFrameI newViewFrom(AlignFrameI alf)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return newViewFrom(alf, null);
   }
 
   @Override
   public AlignFrameI newViewFrom(AlignFrameI alf, String name)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return appLoader.newViewFrom(alf, name);
   }
 
   @Override
-  public AlignFrameI loadAlignment(String text,
-          String title)
+  public AlignFrameI loadAlignment(String text, String title)
   {
     return appLoader.loadAlignment(text, AlignFrame.DEFAULT_WIDTH,
             AlignFrame.DEFAULT_HEIGHT, title);
   }
 
   @Override
-  public void setMouseoverListener(String listener)
-  {
-    // TODO Auto-generated method stub
-
-  }
-
-  @Override
-  public void setMouseoverListener(AlignFrameI af,
-          String listener)
-  {
-    // TODO Auto-generated method stub
-
-  }
-
-  @Override
-  public void setSelectionListener(String listener)
-  {
-    // TODO Auto-generated method stub
-
-  }
-
-  @Override
-  public void setSelectionListener(AlignFrameI af,
-          String listener)
-  {
-    // TODO Auto-generated method stub
-
-  }
-
-  @Override
-  public void setStructureListener(String listener, String modelSet)
-  {
-    // TODO Auto-generated method stub
-
-  }
-
-  @Override
-  public void removeJavascriptListener(AlignFrameI af,
-          String listener)
-  {
-    // TODO Auto-generated method stub
-
-  }
-
-  @Override
-  public void mouseOverStructure(String pdbResNum, String chain,
-          String pdbfile)
-  {
-    // TODO Auto-generated method stub
-
-  }
-
-  @Override
-  public boolean addPdbFile(AlignFrameI alFrame,
-          String sequenceId, String pdbEntryString, String pdbFile)
+  public boolean addPdbFile(AlignFrameI alFrame, String sequenceId,
+          String pdbEntryString, String pdbFile)
   {
     return appLoader.addPdbFile(alFrame, sequenceId, pdbEntryString,
             pdbFile);
   }
 
   @Override
-  public void scrollViewToIn(AlignFrameI alf,
-          String topRow, String leftHandColumn)
+  public void scrollViewToIn(AlignFrameI alf, String topRow,
+          String leftHandColumn)
   {
     appLoader.scrollViewToIn(alf, topRow, leftHandColumn);
   }
 
   @Override
-  public void scrollViewToRowIn(AlignFrameI alf,
-          String topRow)
+  public void scrollViewToRowIn(AlignFrameI alf, String topRow)
   {
     appLoader.scrollViewToRowIn(alf, topRow);
   }
 
   @Override
-  public void scrollViewToColumnIn(AlignFrameI alf,
-          String leftHandColumn)
+  public void scrollViewToColumnIn(AlignFrameI alf, String leftHandColumn)
   {
     appLoader.scrollViewToColumnIn(alf, leftHandColumn);
   }
@@ -1910,15 +1844,14 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public String getFeatureGroupsOfStateOn(AlignFrameI alf,
-          boolean visible)
+  public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible)
   {
     return appLoader.getFeatureGroupsOfStateOn(alf, visible);
   }
 
   @Override
-  public void setFeatureGroupStateOn(AlignFrameI alf,
-          String groups, boolean state)
+  public void setFeatureGroupStateOn(AlignFrameI alf, String groups,
+          boolean state)
   {
     setFeatureGroupStateOn(alf, groups, state);
   }
@@ -1980,4 +1913,85 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
     return CalculationChooser.openPcaPanel(af, modelName, null);
   }
 
+  @Override
+  public String getSelectedSequencesAsAlignment(String format,
+          boolean suffix)
+  {
+    return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(),
+            format, suffix);
+  }
+
+  @Override
+  public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+          String format, boolean suffix)
+  {
+    return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format,
+            "" + suffix);
+  }
+
+  @Override
+  public String arrayToSeparatorList(String[] array)
+  {
+    return appLoader.arrayToSeparatorList(array);
+  }
+
+  @Override
+  public String[] separatorListToArray(String list)
+  {
+    return appLoader.separatorListToArray(list);
+  }
+
+  //// probably not needed in JalviewJS -- From when Jmol and Jalview did not
+  //// have a direct connection?
+
+  @Override
+  public void setMouseoverListener(String listener)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void setMouseoverListener(AlignFrameI af, String listener)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void setSelectionListener(String listener)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void setSelectionListener(AlignFrameI af, String listener)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void setStructureListener(String listener, String modelSet)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void removeJavascriptListener(AlignFrameI af, String listener)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void mouseOverStructure(String pdbResNum, String chain,
+          String pdbfile)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
 }