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JAL-2089 patch broken merge to master for Release 2.10.0b1
[jalview.git]
/
src
/
jalview
/
gui
/
AppVarna.java
diff --git
a/src/jalview/gui/AppVarna.java
b/src/jalview/gui/AppVarna.java
index
99bcff4
..
f4a4f4d
100644
(file)
--- a/
src/jalview/gui/AppVarna.java
+++ b/
src/jalview/gui/AppVarna.java
@@
-64,8
+64,8
@@
public class AppVarna extends JInternalFrame implements SelectionListener,
SecondaryStructureListener, InterfaceVARNASelectionListener,
VamsasSource
{
SecondaryStructureListener, InterfaceVARNASelectionListener,
VamsasSource
{
- private static final byte[] PAIRS = new byte[]
- { '(', ')', '[', ']', '{', '}', '<', '>' };
+ private static final byte[] PAIRS = new byte[] { '(', ')', '[', ']', '{',
+ '}', '<', '>' };
private AppVarnaBinding vab;
private AppVarnaBinding vab;
@@
-181,8
+181,7
@@
public class AppVarna extends JInternalFrame implements SelectionListener,
String theTitle = sname
+ (aa.sequenceRef == null ? " trimmed to " + seq.getName() : "");
theTitle = MessageManager.formatMessage("label.varna_params",
String theTitle = sname
+ (aa.sequenceRef == null ? " trimmed to " + seq.getName() : "");
theTitle = MessageManager.formatMessage("label.varna_params",
- new String[]
- { theTitle });
+ new String[] { theTitle });
setTitle(theTitle);
String gappedTitle = sname + " (with gaps)";
setTitle(theTitle);
String gappedTitle = sname + " (with gaps)";
@@
-195,7
+194,6
@@
public class AppVarna extends JInternalFrame implements SelectionListener,
vab.setSelectedIndex(0);
}
vab.setSelectedIndex(0);
}
-
/**
* Constructor that links the viewer to a parent panel (but has no structures
* yet - use addModel to add them)
/**
* Constructor that links the viewer to a parent panel (but has no structures
* yet - use addModel to add them)
@@
-677,7
+675,6
@@
public class AppVarna extends JInternalFrame implements SelectionListener,
vab.setSelectedIndex(selectedIndex);
}
vab.setSelectedIndex(selectedIndex);
}
-
/**
* Add a model with associated Varna session file
*
/**
* Add a model with associated Varna session file
*
@@
-716,7
+713,6
@@
public class AppVarna extends JInternalFrame implements SelectionListener,
}
}
}
}
-
/**
* Replace everything except RNA secondary structure characters with a period
*
/**
* Replace everything except RNA secondary structure characters with a period
*