X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FColourSchemes.java;h=e2a8cb31425ababfe725c11473bc4f7314894217;hb=155a17a423e980849fd4dc5f857da1a72b0010b9;hp=21faa2a43e8165817df5be5d1468c530931eadc3;hpb=94379c810f9115b8564ee7bac46ed119218d5fd2;p=jalview.git
diff --git a/src/jalview/schemes/ColourSchemes.java b/src/jalview/schemes/ColourSchemes.java
index 21faa2a..e2a8cb3 100644
--- a/src/jalview/schemes/ColourSchemes.java
+++ b/src/jalview/schemes/ColourSchemes.java
@@ -1,11 +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 jalview.api.AlignViewportI;
-import jalview.datamodel.AnnotatedCollectionI;
-
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;
+
public class ColourSchemes
{
/*
@@ -14,7 +37,7 @@ 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;
@@ -44,17 +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 "
+ jalview.bin.Console.errPrintln("Error instantiating colour scheme for "
+ cs.toString() + " " + e.getMessage());
+ e.printStackTrace();
+ } catch (ReflectiveOperationException roe)
+ {
+ roe.printStackTrace();
}
}
}
@@ -69,7 +97,7 @@ public class ColourSchemes
String name = cs.getSchemeName();
if (name == null)
{
- System.err.println("ColourScheme name may not be null");
+ jalview.bin.Console.errPrintln("ColourScheme name may not be null");
return;
}
@@ -77,7 +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
@@ -86,6 +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
*
@@ -93,9 +134,12 @@ public class ColourSchemes
*/
public void removeColourScheme(String name)
{
- schemes.remove(name);
+ if (name != null)
+ {
+ schemes.remove(getColourSchemeShortName(name));
+ }
}
-
+
/**
* Returns an instance of the colour scheme with which the given view may be
* coloured
@@ -103,32 +147,39 @@ public class ColourSchemes
* @param name
* name of the colour scheme
* @param viewport
+ * @param forData
+ * the data to be coloured
+ * @param optional
+ * map from hidden representative sequences to the sequences they
+ * represent
* @return
*/
- public ColourSchemeI getColourScheme(String name, AlignViewportI viewport)
+ public ColourSchemeI getColourScheme(String name, AlignViewportI viewport,
+ AnnotatedCollectionI forData,
+ Map hiddenRepSequences)
{
if (name == null)
{
return null;
}
- ColourSchemeI cs = schemes.get(name.toLowerCase());
- return cs == null ? null : cs.getInstance(viewport.getAlignment(),
- viewport.getHiddenRepSequences());
+ ColourSchemeI cs = schemes.get(getColourSchemeShortName(name));
+ return cs == null ? null : cs.getInstance(viewport, forData);
}
/**
- * Returns an instance of the colour scheme with which the given data may be
+ * Returns an instance of the colour scheme with which the given view may be
* coloured
*
* @param name
+ * name of the colour scheme
* @param forData
+ * the data to be coloured
* @return
*/
public ColourSchemeI getColourScheme(String name,
AnnotatedCollectionI forData)
{
- ColourSchemeI cs = schemes.get(name.toLowerCase());
- return cs == null ? null : cs.getInstance(forData, null);
+ return getColourScheme(name, null, forData, null);
}
/**
@@ -141,4 +192,20 @@ public class ColourSchemes
{
return schemes.values();
}
+
+ /**
+ * Answers true if there is a scheme with the given name, else false. The test
+ * is not case-sensitive.
+ *
+ * @param name
+ * @return
+ */
+ public boolean nameExists(String name)
+ {
+ if (name == null)
+ {
+ return false;
+ }
+ return schemes.containsKey(getColourSchemeShortName(name));
+ }
}