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Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into...
[jalview.git]
/
src
/
jalview
/
schemes
/
UserColourScheme.java
diff --git
a/src/jalview/schemes/UserColourScheme.java
b/src/jalview/schemes/UserColourScheme.java
index
bf62e45
..
ec0f008
100755
(executable)
--- a/
src/jalview/schemes/UserColourScheme.java
+++ b/
src/jalview/schemes/UserColourScheme.java
@@
-20,9
+20,10
@@
*/
package jalview.schemes;
*/
package jalview.schemes;
+import java.util.Locale;
+
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
import jalview.util.ColorUtils;
import jalview.util.StringUtils;
import jalview.util.ColorUtils;
import jalview.util.StringUtils;
@@
-56,8
+57,8
@@
public class UserColourScheme extends ResidueColourScheme
}
@Override
}
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI sg,
- Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI sg)
{
return new UserColourScheme(this);
}
{
return new UserColourScheme(this);
}
@@
-107,7
+108,7
@@
public class UserColourScheme extends ResidueColourScheme
if (col == null)
{
if (col == null)
{
- System.out.println("Making colour from name: " + colour);
+ jalview.bin.Console.outPrintln("Making colour from name: " + colour);
col = ColorUtils.createColourFromName(colour);
}
col = ColorUtils.createColourFromName(colour);
}
@@
-216,7
+217,7
@@
public class UserColourScheme extends ResidueColourScheme
continue;
}
continue;
}
- if (residue.equals(residue.toLowerCase()))
+ if (residue.equals(residue.toLowerCase(Locale.ROOT)))
{
if (lowerCaseColours == null)
{
{
if (lowerCaseColours == null)
{
@@
-233,7
+234,7
@@
public class UserColourScheme extends ResidueColourScheme
}
} catch (Exception ex)
{
}
} catch (Exception ex)
{
- System.out.println(
+ jalview.bin.Console.outPrintln(
"Error parsing userDefinedColours:\n" + token + "\n" + ex);
}
"Error parsing userDefinedColours:\n" + token + "\n" + ex);
}
@@
-307,7
+308,7
@@
public class UserColourScheme extends ResidueColourScheme
c = lowerCaseColours[index];
if (c != null && !c.equals(Color.white))
{
c = lowerCaseColours[index];
if (c != null && !c.equals(Color.white))
{
- residue = residue.toLowerCase();
+ residue = residue.toLowerCase(Locale.ROOT);
if (colours.get(c) == null)
{
colours.put(c, new ArrayList<String>());
if (colours.get(c) == null)
{
colours.put(c, new ArrayList<String>());