X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=3d80589a2aac0323ee57911de9151a16b3c759de;hb=cb51e62fe2166b236ef488e0a8f35081fcd71388;hp=b1499118349ab72136665997bc1150c6ef8f2d89;hpb=72fb6df14f1ff426bbafa18dcc9a90450da93018;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index b149911..3d80589 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -858,12 +858,12 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
                     + "] executed successfully!");
             groovyscript = null;
           }
-          while (aparser.getSize() > 0)
-          {
-            System.out.println("Unknown arg: " + aparser.nextValue());
-          }
         }
         checkOutputFile(aparser, af, format);
+        while (aparser.getSize() > 0)
+        {
+          System.out.println("Unknown arg: " + aparser.nextValue());
+        }
       }
     }
     AlignFrame startUpAlframe = null;
@@ -1052,6 +1052,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
       // biojsmsa filename
       String outputFormat = aparser.nextValue();
       String file = aparser.nextValue();
+      System.out.println("format " + outputFormat);
+
       if (outputFormat.equalsIgnoreCase("png"))
       {
         af.createPNG(new File(file));
@@ -1641,6 +1643,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   @Override
   public String getSelectedSequencesFrom(AlignFrameI alf)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return getSelectedSequencesFrom(alf, null);
   }
 
@@ -1652,6 +1658,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   @Override
   public String getSelectedSequencesFrom(AlignFrameI alf, String sep)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return appLoader.getSelectedSequencesFrom(alf, sep);
   }
 
@@ -1664,7 +1674,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public void highlight(String sequenceId, String position,
           String alignedPosition)
   {
-    highlightIn(getCurrentAlignFrame(), sequenceId, position,
+    highlightIn(null, sequenceId, position,
             alignedPosition);
   }
 
@@ -1672,6 +1682,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public void highlightIn(AlignFrameI alf, String sequenceId,
           String position, String alignedPosition)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     appLoader.highlightIn(alf, sequenceId, position, alignedPosition);
   }
 
@@ -1684,7 +1698,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   @Override
   public void select(String sequenceIds, String columns, String sep)
   {
-    selectIn(getCurrentAlignFrame(), sequenceIds, columns, sep);
+    selectIn(null, sequenceIds, columns, sep);
   }
 
   @Override
@@ -1697,6 +1711,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public void selectIn(AlignFrameI alf, String sequenceIds, String columns,
           String sep)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     appLoader.selectIn(alf, sequenceIds, columns, sep);
   }
 
@@ -1704,7 +1722,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public String getSelectedSequencesAsAlignment(String format,
           String suffix)
   {
-    return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(),
+    return getSelectedSequencesAsAlignmentFrom(null,
             format, suffix);
   }
 
@@ -1712,6 +1730,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
           String format, String sep)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, sep);
   }
 
@@ -1730,6 +1752,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   @Override
   public String getAlignmentOrderFrom(AlignFrameI alf, String sep)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return appLoader.getAlignmentOrderFrom(alf, sep);
   }
 
@@ -1749,6 +1775,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public String orderAlignmentBy(AlignFrameI alf, String order,
           String undoName, String sep)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return appLoader.orderAlignmentBy(alf, order, undoName, sep);
   }
 
@@ -1786,6 +1816,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   @Override
   public void loadAnnotationFrom(AlignFrameI alf, String annotation)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     appLoader.loadAnnotationFrom(alf, annotation);
   }
 
@@ -1799,43 +1833,55 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public boolean loadFeaturesFrom(AlignFrameI alf, String features,
           boolean autoenabledisplay)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return appLoader.loadFeaturesFrom(alf, features, autoenabledisplay);
   }
 
   @Override
   public String getFeatures(String format)
   {
-    return getFeaturesFrom(getCurrentAlignFrame(), format);
+    return getFeaturesFrom(null, format);
   }
 
   @Override
   public String getFeaturesFrom(AlignFrameI alf, String format)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return appLoader.getFeaturesFrom(alf, format);
   }
 
   @Override
   public String getAnnotation()
   {
-    return getAnnotationFrom(getCurrentAlignFrame());
+    return getAnnotationFrom(null);
   }
 
   @Override
   public String getAnnotationFrom(AlignFrameI alf)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return appLoader.getAnnotationFrom(alf);
   }
 
   @Override
   public AlignFrameI newView()
   {
-    return newViewFrom(getCurrentAlignFrame(), null);
+    return newViewFrom(null, null);
   }
 
   @Override
   public AlignFrameI newView(String name)
   {
-    return newViewFrom(getCurrentAlignFrame(), name);
+    return newViewFrom(null, name);
   }
 
   @Override
@@ -1847,6 +1893,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   @Override
   public AlignFrameI newViewFrom(AlignFrameI alf, String name)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return appLoader.newViewFrom(alf, name);
   }
 
@@ -1861,6 +1911,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public boolean addPdbFile(AlignFrameI alFrame, String sequenceId,
           String pdbEntryString, String pdbFile)
   {
+    if (alFrame == null)
+    {
+      alFrame = getCurrentAlignFrame();
+    }
     return appLoader.addPdbFile(alFrame, sequenceId, pdbEntryString,
             pdbFile);
   }
@@ -1869,56 +1923,80 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public void scrollViewToIn(AlignFrameI alf, String topRow,
           String leftHandColumn)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     appLoader.scrollViewToIn(alf, topRow, leftHandColumn);
   }
 
   @Override
   public void scrollViewToRowIn(AlignFrameI alf, String topRow)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     appLoader.scrollViewToRowIn(alf, topRow);
   }
 
   @Override
   public void scrollViewToColumnIn(AlignFrameI alf, String leftHandColumn)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     appLoader.scrollViewToColumnIn(alf, leftHandColumn);
   }
 
   @Override
   public String getFeatureGroups()
   {
-    return getFeatureGroupsOn(getCurrentAlignFrame());
+    return getFeatureGroupsOn(null);
   }
 
   @Override
   public String getFeatureGroupsOn(AlignFrameI alf)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return appLoader.getFeatureGroupsOn(alf);
   }
 
   @Override
   public String getFeatureGroupsOfState(boolean visible)
   {
-    return getFeatureGroupsOfStateOn(getCurrentAlignFrame(), visible);
+    return getFeatureGroupsOfStateOn(null, visible);
   }
 
   @Override
   public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return appLoader.getFeatureGroupsOfStateOn(alf, visible);
   }
 
   @Override
-  public void setFeatureGroupStateOn(AlignFrameI alf, String groups,
-          boolean state)
-  {
-    setFeatureGroupStateOn(alf, groups, state);
+  public void setFeatureGroupState(String groups, boolean state)
+  { // JalviewLite API
+    setFeatureGroupStateOn(null, groups, state);
   }
 
   @Override
-  public void setFeatureGroupState(String groups, boolean state)
+  public void setFeatureGroupStateOn(AlignFrameI alf, String groups,
+          boolean state)
   {
-    appLoader.setFeatureGroupStateOn(getCurrentAlignFrame(), groups, state);
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
+    appLoader.setFeatureGroupStateOn(alf, groups, state);
   }
 
   @Override
@@ -1953,7 +2031,11 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   @Override
   public Object openTreePanel(AlignFrame af, String treeType,
           String modelName)
-  {
+  { // JalviewJS api
+    if (af == null)
+    {
+      af = getCurrentAlignFrame();
+    }
     return CalculationChooser.openTreePanel(af, treeType, modelName, null);
   }
 
@@ -1969,6 +2051,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   @Override
   public Object openPcaPanel(AlignFrame af, String modelName)
   {
+    if (af == null)
+    {
+      af = getCurrentAlignFrame();
+    }
     return CalculationChooser.openPcaPanel(af, modelName, null);
   }
 
@@ -1976,7 +2062,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public String getSelectedSequencesAsAlignment(String format,
           boolean suffix)
   {
-    return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(),
+    return getSelectedSequencesAsAlignmentFrom(null,
             format, suffix);
   }
 
@@ -1984,6 +2070,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
           String format, boolean suffix)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format,
             "" + suffix);
   }