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JAL-2401 code and help tidy for review comments
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Thu, 30 Mar 2017 13:40:56 +0000
(14:40 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Thu, 30 Mar 2017 13:40:56 +0000
(14:40 +0100)
help/html/colourSchemes/user.html
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help/html/colourSchemes/userDefined_java6.gif
[deleted file]
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help/html/colourSchemes/userDefined_java7.gif
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src/jalview/gui/UserDefinedColours.java
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diff --git
a/help/html/colourSchemes/user.html
b/help/html/colourSchemes/user.html
index
fb6c356
..
c2fde1c
100755
(executable)
--- a/
help/html/colourSchemes/user.html
+++ b/
help/html/colourSchemes/user.html
@@
-27,7
+27,7
@@
<strong>User Defined Colours</strong>
</p>
<p>
<strong>User Defined Colours</strong>
</p>
<p>
- <img src="userDefined_java6.gif" width="815" height="402">
+ <img src="userDefined_java7.gif" width="815" height="402">
</p>
<p>
You may define any number of new colour schemes, each with a unique
</p>
<p>
You may define any number of new colour schemes, each with a unique
@@
-41,7
+41,7
@@
The <strong>Case Sensitive</strong> option allows you to choose
distinct colours for upper and lower case residue codes.
<p>
The <strong>Case Sensitive</strong> option allows you to choose
distinct colours for upper and lower case residue codes.
<p>
- The <strong>Lower Case Colour</strong> option allows you to apply a selected colour
+ The <strong>Colour All Lower Case </strong> option allows you to apply a selected colour
to all lower case residues.
<p>
Click <strong>Apply</strong> or <strong>OK</strong> to set your new
to all lower case residues.
<p>
Click <strong>Apply</strong> or <strong>OK</strong> to set your new
@@
-56,11
+56,5
@@
<br> Any saved colour schemes will be automatically loaded the
next time you use Jalview.
<br>
<br> Any saved colour schemes will be automatically loaded the
next time you use Jalview.
<br>
- <br>
- <em>Note: the screenshot shows the appearance when running Java
- version 6. For Java 7 (from Jalview 2.8.2) only the Swatches colour
- chooser is currently supported (for reasons of available screen
- space).</em>
- <p />
</body>
</html>
</body>
</html>
diff --git
a/help/html/colourSchemes/userDefined_java6.gif
b/help/html/colourSchemes/userDefined_java6.gif
deleted file mode 100644
(file)
index
d737e80
..0000000
Binary files a/help/html/colourSchemes/userDefined_java6.gif and /dev/null differ
diff --git
a/help/html/colourSchemes/userDefined_java7.gif
b/help/html/colourSchemes/userDefined_java7.gif
index
f0ced11
..
de80b84
100644
(file)
Binary files a/help/html/colourSchemes/userDefined_java7.gif and b/help/html/colourSchemes/userDefined_java7.gif differ
diff --git
a/src/jalview/gui/UserDefinedColours.java
b/src/jalview/gui/UserDefinedColours.java
index
6e9a121
..
9ab4327
100755
(executable)
--- a/
src/jalview/gui/UserDefinedColours.java
+++ b/
src/jalview/gui/UserDefinedColours.java
@@
-591,11
+591,6
@@
public class UserDefinedColours extends GUserDefinedColours implements
ucs.setLowerCaseColours(newColours);
}
ucs.setLowerCaseColours(newColours);
}
- // if (ap != null)
- // {
- // ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
- // }
-
return ucs;
}
return ucs;
}