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JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...
[jalview.git]
/
src
/
jalview
/
io
/
VamsasAppDatastore.java
diff --git
a/src/jalview/io/VamsasAppDatastore.java
b/src/jalview/io/VamsasAppDatastore.java
index
adf4447
..
84d31f0
100644
(file)
--- a/
src/jalview/io/VamsasAppDatastore.java
+++ b/
src/jalview/io/VamsasAppDatastore.java
@@
-389,7
+389,6
@@
public class VamsasAppDatastore
{
dssmods.addElement(sequence);
}
{
dssmods.addElement(sequence);
}
- ;
}
if (dssmods.size() > 0)
{
}
if (dssmods.size() > 0)
{
@@
-585,7
+584,6
@@
public class VamsasAppDatastore
(AlignmentSequence) alsref, aa[i]);
break;
}
(AlignmentSequence) alsref, aa[i]);
break;
}
- ;
}
}
}
}
}
}
@@
-720,9
+718,9
@@
public class VamsasAppDatastore
// /SAVE THE TREES
// /////////////////////////////////
// FIND ANY ASSOCIATED TREES
// /SAVE THE TREES
// /////////////////////////////////
// FIND ANY ASSOCIATED TREES
- if (Desktop.desktop != null)
+ if (Desktop.getDesktopPane() != null)
{
{
- javax.swing.JInternalFrame[] frames = Desktop.instance
+ javax.swing.JInternalFrame[] frames = Desktop.getInstance()
.getAllFrames();
for (int t = 0; t < frames.length; t++)
.getAllFrames();
for (int t = 0; t < frames.length; t++)
@@
-1478,8
+1476,7
@@
public class VamsasAppDatastore
// active
if (mappings != null)
{
// active
if (mappings != null)
{
- jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance)
+ Desktop.getStructureSelectionManager()
.registerMappings(mappings);
}
}
.registerMappings(mappings);
}
}
@@
-2020,17
+2017,17
@@
public class VamsasAppDatastore
}
// bitfields - should be a template in j1.5
}
// bitfields - should be a template in j1.5
- private static int HASSECSTR = 0;
+ private static final int HASSECSTR = 0;
- private static int HASVALS = 1;
+ private static final int HASVALS = 1;
- private static int HASHPHOB = 2;
+ private static final int HASHPHOB = 2;
- private static int HASDC = 3;
+ private static final int HASDC = 3;
- private static int HASDESCSTR = 4;
+ private static final int HASDESCSTR = 4;
- private static int HASTWOSTATE = 5; // not used yet.
+ private static final int HASTWOSTATE = 5; // not used yet.
/**
* parses the AnnotationElements - if they exist - into
/**
* parses the AnnotationElements - if they exist - into