3253-omnibus save

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

diff --git a/src/jalview/bin/JalviewAppLoader.java b/src/jalview/bin/JalviewAppLoader.java
index 51a0330..834a30f 100644 (file)
--- a/src/jalview/bin/JalviewAppLoader.java
+++ b/src/jalview/bin/JalviewAppLoader.java
@@ -31,7 +31,6 @@ import jalview.structure.StructureSelectionManager;
 import jalview.util.HttpUtils;
 import jalview.util.MessageManager;
 
-import java.awt.EventQueue;
 import java.io.IOException;
 import java.net.URL;
 import java.util.ArrayList;
@@ -787,7 +786,7 @@ public class JalviewAppLoader
   public void setFeatureGroupStateOn(final AlignFrameI alf,
           final String groups, boolean state)
   {
-    java.awt.EventQueue.invokeLater(new Runnable()
+    Jalview.execRunnable(new Runnable()
     {
       @Override
       public void run()
@@ -807,7 +806,7 @@ public class JalviewAppLoader
   public void scrollViewToIn(final AlignFrameI alf, final String topRow,
           final String leftHandColumn)
   {
-    java.awt.EventQueue.invokeLater(new Runnable()
+    Jalview.execRunnable(new Runnable()
     {
       @Override
       public void run()
@@ -831,7 +830,7 @@ public class JalviewAppLoader
   public void scrollViewToRowIn(final AlignFrameI alf, final String topRow)
   {
 
-    java.awt.EventQueue.invokeLater(new Runnable()
+    Jalview.execRunnable(new Runnable()
     {
       @Override
       public void run()
@@ -854,7 +853,7 @@ public class JalviewAppLoader
   public void scrollViewToColumnIn(final AlignFrameI alf,
           final String leftHandColumn)
   {
-    java.awt.EventQueue.invokeLater(new Runnable()
+    Jalview.execRunnable(new Runnable()
     {
 
       @Override
@@ -982,7 +981,7 @@ public class JalviewAppLoader
       if (alignedPosition != null && (alignedPosition.trim().length() == 0
               || alignedPosition.toLowerCase().indexOf("false") > -1))
       {
-        java.awt.EventQueue.invokeLater(new Runnable()
+        Jalview.execRunnable(new Runnable()
         {
           @Override
           public void run()
@@ -995,7 +994,7 @@ public class JalviewAppLoader
       }
       else
       {
-        java.awt.EventQueue.invokeLater(new Runnable()
+        Jalview.execRunnable(new Runnable()
         {
           @Override
           public void run()
@@ -1211,7 +1210,7 @@ public class JalviewAppLoader
       }
       sel.setStartRes(start);
       sel.setEndRes(end);
-      EventQueue.invokeLater(new Runnable()
+      Jalview.execRunnable(new Runnable()
       {
         @Override
         public void run()
@@ -1305,7 +1304,6 @@ public class JalviewAppLoader
     {
       return "";
     }
-    ;
     final AlignmentOrder aorder = new AlignmentOrder(sqs);
 
     if (undoName != null && undoName.trim().length() == 0)
@@ -1372,7 +1370,8 @@ public class JalviewAppLoader
     return true;
   }
 
-  public String getFeaturesFrom(AlignFrameI alf, String format)
+  public String getFeaturesFrom(AlignFrameI alf, String format,
+          boolean includeNonpositionsFeatures, boolean includeComplement)
   {
     AlignFrame f = ((AlignFrame) alf);
 
@@ -1382,13 +1381,15 @@ public class JalviewAppLoader
     {
       features = formatter.printJalviewFormat(
               f.getViewport().getAlignment().getSequencesArray(),
-              f.alignPanel.getFeatureRenderer(), true);
+              f.alignPanel.getFeatureRenderer(),
+              includeNonpositionsFeatures, includeComplement);
     }
     else
     {
       features = formatter.printGffFormat(
               f.getViewport().getAlignment().getSequencesArray(),
-              f.alignPanel.getFeatureRenderer(), true);
+              f.alignPanel.getFeatureRenderer(),
+              includeNonpositionsFeatures, includeComplement);
     }
 
     if (features == null)