X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemes.java;h=698769c9a95d7a7007eba5792526f118b9a1c15d;hb=d4271d32477e99e9fbbfa5db3e11f1b79324e60d;hp=b28139fd430454fe2bbf957e62b5f32def957fa1;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git
diff --git a/src/jalview/schemes/ColourSchemes.java b/src/jalview/schemes/ColourSchemes.java
index b28139f..698769c 100644
--- a/src/jalview/schemes/ColourSchemes.java
+++ b/src/jalview/schemes/ColourSchemes.java
@@ -1,12 +1,34 @@
+/*
+ * 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 java.util.LinkedHashMap;
+import java.util.Locale;
+import java.util.Map;
+
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
-import java.util.LinkedHashMap;
-import java.util.Map;
-
public class ColourSchemes
{
/*
@@ -45,17 +67,22 @@ 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();
}
}
}
@@ -78,7 +105,7 @@ public class ColourSchemes
* name is lower-case for non-case-sensitive lookup
* (name in the colour keeps its true case)
*/
- String lower = name.toLowerCase();
+ String lower = getColourSchemeShortName(cs);
if (schemes.containsKey(lower))
{
System.err
@@ -87,6 +114,19 @@ public class ColourSchemes
schemes.put(lower, cs);
}
+ private String getColourSchemeShortName(ColourSchemeI cs)
+ {
+ return getColourSchemeShortName(cs.getSchemeName());
+ }
+
+ private String getColourSchemeShortName(String name)
+ {
+ if (name == null)
+ return null;
+ return name.toLowerCase(Locale.ROOT).replaceAll("%", "pc")
+ .replaceAll("[^a-z0-9]", "-").replaceAll("--+", "-");
+ }
+
/**
* Removes a colour scheme by name
*
@@ -96,7 +136,7 @@ public class ColourSchemes
{
if (name != null)
{
- schemes.remove(name.toLowerCase());
+ schemes.remove(getColourSchemeShortName(name));
}
}
@@ -106,6 +146,7 @@ public class ColourSchemes
*
* @param name
* name of the colour scheme
+ * @param viewport
* @param forData
* the data to be coloured
* @param optional
@@ -113,7 +154,7 @@ public class ColourSchemes
* represent
* @return
*/
- public ColourSchemeI getColourScheme(String name,
+ public ColourSchemeI getColourScheme(String name, AlignViewportI viewport,
AnnotatedCollectionI forData,
Map hiddenRepSequences)
{
@@ -121,8 +162,8 @@ public class ColourSchemes
{
return null;
}
- ColourSchemeI cs = schemes.get(name.toLowerCase());
- return cs == null ? null : cs.getInstance(forData, hiddenRepSequences);
+ ColourSchemeI cs = schemes.get(getColourSchemeShortName(name));
+ return cs == null ? null : cs.getInstance(viewport, forData);
}
/**
@@ -138,7 +179,7 @@ public class ColourSchemes
public ColourSchemeI getColourScheme(String name,
AnnotatedCollectionI forData)
{
- return getColourScheme(name, forData, null);
+ return getColourScheme(name, null, forData, null);
}
/**
@@ -165,6 +206,6 @@ public class ColourSchemes
{
return false;
}
- return schemes.containsKey(name.toLowerCase());
+ return schemes.containsKey(getColourSchemeShortName(name));
}
}