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Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git...
[jalview.git]
/
src
/
jalview
/
schemes
/
PurinePyrimidineColourScheme.java
diff --git
a/src/jalview/schemes/PurinePyrimidineColourScheme.java
b/src/jalview/schemes/PurinePyrimidineColourScheme.java
index
df5e171
..
1b36f30
100644
(file)
--- a/
src/jalview/schemes/PurinePyrimidineColourScheme.java
+++ b/
src/jalview/schemes/PurinePyrimidineColourScheme.java
@@
-1,24
+1,30
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
-import java.awt.*;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.util.Map;
/**
* Class is based off of NucleotideColourScheme
/**
* Class is based off of NucleotideColourScheme
@@
-33,56
+39,29
@@
public class PurinePyrimidineColourScheme extends ResidueColourScheme
public PurinePyrimidineColourScheme()
{
super(ResidueProperties.purinepyrimidineIndex,
public PurinePyrimidineColourScheme()
{
super(ResidueProperties.purinepyrimidineIndex,
- ResidueProperties.purinepyrimidine, 0);
+ ResidueProperties.purinepyrimidine);
}
}
- /**
- * Finds the corresponding color for the type of character inputed
- *
- * @param c
- * Character in sequence
- *
- * @return Color from purinepyrimidineIndex in
- * jalview.schemes.ResidueProperties
- */
- public Color findColour(char c)
+ @Override
+ public boolean isNucleotideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
{
{
- return colors[ResidueProperties.purinepyrimidineIndex[c]];
+ return JalviewColourScheme.PurinePyrimidine.toString();
}
/**
}
/**
- * Returns color based on conservation
- *
- * @param c
- * Character in sequence
- * @param j
- * Threshold
- *
- * @return Color in RGB
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
*/
*/
- public Color findColour(char c, int j)
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ Map<SequenceI, SequenceCollectionI> hrs)
{
{
- Color currentColour;
- if ((threshold == 0) || aboveThreshold(c, j))
- {
- try
- {
- currentColour = colors[ResidueProperties.purinepyrimidineIndex[c]];
- } catch (Exception ex)
- {
- return Color.white;
- }
- }
- else
- {
- return Color.white;
- }
-
- if (conservationColouring)
- {
- currentColour = applyConservation(currentColour, j);
- }
-
- return currentColour;
+ return new PurinePyrimidineColourScheme();
}
}
}
}