X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=ab9b1d9b6e6370b876f110e5973fc6e2fc07c1c6;hb=8bdcb5fb1d1fc9fccd8c6c97a17eb3ee4ceaa4d0;hp=941891398d2e4ca207499f9ccc25de147e571aa5;hpb=25e36b8f366dab01f838d8175e59e9148628eb68;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 9418913..ab9b1d9 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -21,7 +21,6 @@
 package jalview.bin;
 
 import jalview.api.AlignCalcWorkerI;
-import jalview.api.AlignFrameI;
 import jalview.api.AlignViewportI;
 import jalview.api.JalviewApp;
 import jalview.api.StructureSelectionManagerProvider;
@@ -287,9 +286,13 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
    * @param args
    *          open <em>filename</em>
    */
+  @SuppressWarnings("unused")
   public static void main(String[] args)
   {
-    // Platform.startJavaLogging();
+    if (false)
+    {
+      Platform.startJavaLogging();
+    }
     getInstance().doMain(args);
   }
 
@@ -1672,7 +1675,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
    *      .AlignFrame)
    */
   @Override
-  public String getSelectedSequencesFrom(AlignFrameI alf)
+  public String getSelectedSequencesFrom(AlignFrame alf)
   {
     if (alf == null)
     {
@@ -1687,7 +1690,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
    *      .AlignFrame, java.lang.String)
    */
   @Override
-  public String getSelectedSequencesFrom(AlignFrameI alf, String sep)
+  public String getSelectedSequencesFrom(AlignFrame alf, String sep)
   {
     if (alf == null)
     {
@@ -1710,7 +1713,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public void highlightIn(AlignFrameI alf, String sequenceId,
+  public void highlightIn(AlignFrame alf, String sequenceId,
           String position, String alignedPosition)
   {
     if (alf == null)
@@ -1733,13 +1736,13 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public void selectIn(AlignFrameI alf, String sequenceIds, String columns)
+  public void selectIn(AlignFrame alf, String sequenceIds, String columns)
   {
     selectIn(alf, sequenceIds, columns, null);
   }
 
   @Override
-  public void selectIn(AlignFrameI alf, String sequenceIds, String columns,
+  public void selectIn(AlignFrame alf, String sequenceIds, String columns,
           String sep)
   {
     if (alf == null)
@@ -1758,7 +1761,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+  public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
           String format, String sep)
   {
     if (alf == null)
@@ -1775,13 +1778,13 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public String getAlignmentOrderFrom(AlignFrameI alf)
+  public String getAlignmentOrderFrom(AlignFrame alf)
   {
     return getAlignmentFrom(alf, null);
   }
 
   @Override
-  public String getAlignmentOrderFrom(AlignFrameI alf, String sep)
+  public String getAlignmentOrderFrom(AlignFrame alf, String sep)
   {
     if (alf == null)
     {
@@ -1803,7 +1806,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public String orderAlignmentBy(AlignFrameI alf, String order,
+  public String orderAlignmentBy(AlignFrame alf, String order,
           String undoName, String sep)
   {
     if (alf == null)
@@ -1820,7 +1823,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public String getAlignmentFrom(AlignFrameI alf, String format)
+  public String getAlignmentFrom(AlignFrame alf, String format)
   {
     return getAlignmentFrom(alf, format, null);
   }
@@ -1832,7 +1835,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public String getAlignmentFrom(AlignFrameI alf, String format,
+  public String getAlignmentFrom(AlignFrame alf, String format,
           String suffix)
   {
     return appLoader.getAlignmentFrom(alf, format, suffix);
@@ -1845,7 +1848,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public void loadAnnotationFrom(AlignFrameI alf, String annotation)
+  public void loadAnnotationFrom(AlignFrame alf, String annotation)
   {
     if (alf == null)
     {
@@ -1861,7 +1864,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public boolean loadFeaturesFrom(AlignFrameI alf, String features,
+  public boolean loadFeaturesFrom(AlignFrame alf, String features,
           boolean autoenabledisplay)
   {
     if (alf == null)
@@ -1878,7 +1881,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public String getFeaturesFrom(AlignFrameI alf, String format)
+  public String getFeaturesFrom(AlignFrame alf, String format)
   {
     if (alf == null)
     {
@@ -1894,7 +1897,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public String getAnnotationFrom(AlignFrameI alf)
+  public String getAnnotationFrom(AlignFrame alf)
   {
     if (alf == null)
     {
@@ -1903,43 +1906,43 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
     return appLoader.getAnnotationFrom(alf);
   }
 
-  @Override
-  public AlignFrameI newView()
-  {
-    return newViewFrom(null, null);
-  }
-
-  @Override
-  public AlignFrameI newView(String name)
-  {
-    return newViewFrom(null, name);
-  }
-
-  @Override
-  public AlignFrameI newViewFrom(AlignFrameI alf)
-  {
-    return newViewFrom(alf, null);
-  }
+  // @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 AlignFrameI newViewFrom(AlignFrameI alf, String name)
-  {
-    if (alf == null)
-    {
-      alf = getCurrentAlignFrame();
-    }
-    return appLoader.newViewFrom(alf, name);
-  }
+  // @Override
+  // public AlignFrame newViewFrom(AlignFrame alf, String name)
+  // {
+  // if (alf == null)
+  // {
+  // alf = getCurrentAlignFrame();
+  // }
+  // return appLoader.newViewFrom(alf, name);
+  // }
 
   @Override
-  public AlignFrameI loadAlignment(String text, String title)
+  public AlignFrame loadAlignment(String text, String title)
   {
     return appLoader.loadAlignment(text, AlignFrame.DEFAULT_WIDTH,
             AlignFrame.DEFAULT_HEIGHT, title);
   }
 
   @Override
-  public boolean addPdbFile(AlignFrameI alFrame, String sequenceId,
+  public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
           String pdbEntryString, String pdbFile)
   {
     if (alFrame == null)
@@ -1951,7 +1954,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public void scrollViewToIn(AlignFrameI alf, String topRow,
+  public void scrollViewToIn(AlignFrame alf, String topRow,
           String leftHandColumn)
   {
     if (alf == null)
@@ -1962,7 +1965,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public void scrollViewToRowIn(AlignFrameI alf, String topRow)
+  public void scrollViewToRowIn(AlignFrame alf, String topRow)
   {
     if (alf == null)
     {
@@ -1972,7 +1975,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public void scrollViewToColumnIn(AlignFrameI alf, String leftHandColumn)
+  public void scrollViewToColumnIn(AlignFrame alf, String leftHandColumn)
   {
     if (alf == null)
     {
@@ -1988,7 +1991,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public String getFeatureGroupsOn(AlignFrameI alf)
+  public String getFeatureGroupsOn(AlignFrame alf)
   {
     if (alf == null)
     {
@@ -2004,7 +2007,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible)
+  public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
   {
     if (alf == null)
     {
@@ -2020,7 +2023,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public void setFeatureGroupStateOn(AlignFrameI alf, String groups,
+  public void setFeatureGroupStateOn(AlignFrame alf, String groups,
           boolean state)
   {
     if (alf == null)
@@ -2098,7 +2101,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+  public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
           String format, boolean suffix)
   {
     if (alf == null)
@@ -2132,7 +2135,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public void setMouseoverListener(AlignFrameI af, String listener)
+  public void setMouseoverListener(AlignFrame af, String listener)
   {
     // TODO Auto-generated method stub
 
@@ -2146,7 +2149,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public void setSelectionListener(AlignFrameI af, String listener)
+  public void setSelectionListener(AlignFrame af, String listener)
   {
     // TODO Auto-generated method stub
 
@@ -2160,7 +2163,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   }
 
   @Override
-  public void removeJavascriptListener(AlignFrameI af, String listener)
+  public void removeJavascriptListener(AlignFrame af, String listener)
   {
     // TODO Auto-generated method stub