JAL-3451 JalviewJS embedded mode not resizing

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index fae2b75..3d80589 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -305,6 +305,15 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
 
     String usrPropsFile = aparser.getValue(ArgsParser.PROPS);
     Cache.loadProperties(usrPropsFile);
+
+    if (aparser.contains(ArgsParser.NODISPLAY)
+            || aparser.contains(ArgsParser.NOGUI)
+            || aparser.contains(ArgsParser.HEADLESS)
+            || "true".equals(System.getProperty("java.awt.headless")))
+    {
+      headless = true;
+    }
+
     if (isJS)
     {
       isJavaAppletTag = aparser.isApplet();
@@ -336,13 +345,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
         showUsage();
         System.exit(0);
       }
-      if (aparser.contains(ArgsParser.NODISPLAY)
-              || aparser.contains(ArgsParser.NOGUI)
-              || aparser.contains(ArgsParser.HEADLESS)
-              || "true".equals(System.getProperty("java.awt.headless")))
-      {
-        headless = true;
-      }
+
 
       // anything else!
 
@@ -398,7 +401,13 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
 
     try
     {
-      UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+      if (!isJS && Platform.isWin())
+       {
+        UIManager.setLookAndFeel(
+                headless ? "javax.swing.plaf.metal.MetalLookAndFeel"
+                        : UIManager.getSystemLookAndFeelClassName());
+//      UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+      }
     } catch (Exception ex)
     {
       System.err.println("Unexpected Look and Feel Exception");
@@ -849,11 +858,11 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
                     + "] executed successfully!");
             groovyscript = null;
           }
-          checkOutputFile(aparser, af, format);
-          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());
         }
       }
     }
@@ -1043,6 +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));
@@ -1632,6 +1643,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   @Override
   public String getSelectedSequencesFrom(AlignFrameI alf)
   {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
     return getSelectedSequencesFrom(alf, null);
   }
 
@@ -1643,6 +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);
   }
 
@@ -1655,7 +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);
   }
 
@@ -1663,6 +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);
   }
 
@@ -1675,7 +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
@@ -1688,6 +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);
   }
 
@@ -1695,7 +1722,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public String getSelectedSequencesAsAlignment(String format,
           String suffix)
   {
-    return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(),
+    return getSelectedSequencesAsAlignmentFrom(null,
             format, suffix);
   }
 
@@ -1703,6 +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);
   }
 
@@ -1721,6 +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);
   }
 
@@ -1740,6 +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);
   }
 
@@ -1777,6 +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);
   }
 
@@ -1790,43 +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
@@ -1838,6 +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);
   }
 
@@ -1852,6 +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);
   }
@@ -1860,56 +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
@@ -1944,7 +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);
   }
 
@@ -1960,6 +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);
   }
 
@@ -1967,7 +2062,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
   public String getSelectedSequencesAsAlignment(String format,
           boolean suffix)
   {
-    return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(),
+    return getSelectedSequencesAsAlignmentFrom(null,
             format, suffix);
   }
 
@@ -1975,6 +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);
   }