X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FColourSchemes.java;h=d31fbba4c752c19aaffd3be8c6def41e13b3c1ac;hb=5f14ca65f127ffbe8ca3c043ac46730fe5a00423;hp=dc7e40335b72bfe256ab08c0becb873165345fdc;hpb=d7fd122bbdef3ab11f43ed6058fe37872d1d368e;p=jalview.git
diff --git a/src/jalview/schemes/ColourSchemes.java b/src/jalview/schemes/ColourSchemes.java
index dc7e403..d31fbba 100644
--- a/src/jalview/schemes/ColourSchemes.java
+++ b/src/jalview/schemes/ColourSchemes.java
@@ -1,5 +1,26 @@
+/*
+ * 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
+ * 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.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
@@ -15,7 +36,7 @@ public class ColourSchemes
private static ColourSchemes instance = new ColourSchemes();
/*
- * a map from scheme name to an instance of it
+ * a map from scheme name (lower-cased) to an instance of it
*/
private Map schemes;
@@ -45,17 +66,22 @@ public class ColourSchemes
* store in an order-preserving map, so items can be added to menus
* in the order in which they are 'discovered'
*/
- schemes = new LinkedHashMap();
+ schemes = new LinkedHashMap<>();
for (JalviewColourScheme cs : JalviewColourScheme.values())
{
try
{
- registerColourScheme(cs.getSchemeClass().newInstance());
+ registerColourScheme(
+ cs.getSchemeClass().getDeclaredConstructor().newInstance());
} catch (InstantiationException | IllegalAccessException e)
{
System.err.println("Error instantiating colour scheme for "
+ cs.toString() + " " + e.getMessage());
+ e.printStackTrace();
+ } catch (ReflectiveOperationException roe)
+ {
+ roe.printStackTrace();
}
}
}
@@ -94,15 +120,19 @@ public class ColourSchemes
*/
public void removeColourScheme(String name)
{
- schemes.remove(name);
+ if (name != null)
+ {
+ schemes.remove(name.toLowerCase());
+ }
}
-
+
/**
* Returns an instance of the colour scheme with which the given view may be
* coloured
*
* @param name
* name of the colour scheme
+ * @param viewport
* @param forData
* the data to be coloured
* @param optional
@@ -111,7 +141,7 @@ public class ColourSchemes
* @return
*/
public ColourSchemeI getColourScheme(String name,
- AnnotatedCollectionI forData,
+ AlignViewportI viewport, AnnotatedCollectionI forData,
Map hiddenRepSequences)
{
if (name == null)
@@ -119,7 +149,8 @@ public class ColourSchemes
return null;
}
ColourSchemeI cs = schemes.get(name.toLowerCase());
- return cs == null ? null : cs.getInstance(forData, hiddenRepSequences);
+ return cs == null ? null
+ : cs.getInstance(viewport, forData);
}
/**
@@ -135,7 +166,7 @@ public class ColourSchemes
public ColourSchemeI getColourScheme(String name,
AnnotatedCollectionI forData)
{
- return getColourScheme(name, forData, null);
+ return getColourScheme(name, null, forData, null);
}
/**
@@ -162,14 +193,6 @@ public class ColourSchemes
{
return false;
}
- name = name.toLowerCase();
- for (ColourSchemeI scheme : getColourSchemes())
- {
- if (name.equals(scheme.getSchemeName().toLowerCase()))
- {
- return true;
- }
- }
- return false;
+ return schemes.containsKey(name.toLowerCase());
}
}