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Merge branch 'doc/JAL-4090_Release_2_11_3_0' into develop
[jalview.git]
/
src
/
jalview
/
gui
/
AppVarnaBinding.java
diff --git
a/src/jalview/gui/AppVarnaBinding.java
b/src/jalview/gui/AppVarnaBinding.java
index
0a3685e
..
8951df0
100644
(file)
--- a/
src/jalview/gui/AppVarnaBinding.java
+++ b/
src/jalview/gui/AppVarnaBinding.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-281,8
+281,8
@@
public class AppVarnaBinding extends JalviewVarnaBinding
String name = r.getName();
if (name.equals(""))
{
String name = r.getName();
if (name.equals(""))
{
- name = path.substring(path
- .lastIndexOf(File.separatorChar) + 1);
+ name = path.substring(
+ path.lastIndexOf(File.separatorChar) + 1);
}
if (mdls.size() > 1)
{
}
if (mdls.size() > 1)
{
@@
-290,6
+290,8
@@
public class AppVarnaBinding extends JalviewVarnaBinding
}
_rnaList.add(varnaPanel.getConfig().clone(), r, name,
true);
}
_rnaList.add(varnaPanel.getConfig().clone(), r, name,
true);
+ // BH 2018 SwingJS clone of varnaPanel or its config will
+ // be the object itself, not a clone
}
}
}
}
}
}
@@
-374,9
+376,9
@@
public class AppVarnaBinding extends JalviewVarnaBinding
_sideList.ensureIndexIsVisible(index);
/*
_sideList.ensureIndexIsVisible(index);
/*
- * TODO Object newName = JOptionPane.showInputDialog( this,
+ * TODO Object newName = JvOptionPane.showInputDialog( this,
* "Specify a new name for this RNA", "Rename RNA",
* "Specify a new name for this RNA", "Rename RNA",
- * JOptionPane.QUESTION_MESSAGE, (Icon)null, null, item.toString()); if
+ * JvOptionPane.QUESTION_MESSAGE, (Icon)null, null, item.toString()); if
* (newName!=null) { item.name = newName.toString();
* this._sideList.repaint(); }
*/
* (newName!=null) { item.name = newName.toString();
* this._sideList.repaint(); }
*/
@@
-384,7
+386,7
@@
public class AppVarnaBinding extends JalviewVarnaBinding
}
@Override
}
@Override
- public String[] getPdbFile()
+ public String[] getStructureFiles()
{
return null;
}
{
return null;
}
@@
-545,7
+547,8
@@
public class AppVarnaBinding extends JalviewVarnaBinding
*/
public void addStructure(RNA rna)
{
*/
public void addStructure(RNA rna)
{
- VARNAConfig config = vp.getConfig().clone();
+ VARNAConfig config = vp.getConfig().clone(); // BH 2018 this will NOT be a
+ // clone in SwingJS
addStructure(rna, config);
}
addStructure(rna, config);
}
@@
-571,7
+574,7
@@
public class AppVarnaBinding extends JalviewVarnaBinding
} catch (ExceptionNAViewAlgorithm e)
{
// only throwable for draw mode = 3 NAView
} catch (ExceptionNAViewAlgorithm e)
{
// only throwable for draw mode = 3 NAView
- System.err.println("Error drawing RNA: " + e.getMessage());
+ jalview.bin.Console.errPrintln("Error drawing RNA: " + e.getMessage());
}
}
}
}
}
}