Merge branch 'releases/Release_2_11_3_Branch'

[jalview.git] / src / jalview / schemes / ColourSchemes.java

diff --git a/src/jalview/schemes/ColourSchemes.java b/src/jalview/schemes/ColourSchemes.java
index 269811b..303d500 100644 (file)
--- 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 <http://www.gnu.org/licenses/>.
+ * 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 +67,23 @@ 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<String, ColourSchemeI>();
+    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());
+        jalview.bin.Console
+                .errPrintln("Error instantiating colour scheme for "
+                        + cs.toString() + " " + e.getMessage());
+        e.printStackTrace();
+      } catch (ReflectiveOperationException roe)
+      {
+        roe.printStackTrace();
       }
     }
   }
@@ -70,7 +98,7 @@ 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;
     }
 
@@ -78,7 +106,7 @@ 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 +115,19 @@ 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
    * 
@@ -96,16 +137,17 @@ public class ColourSchemes
   {
     if (name != null)
     {
-      schemes.remove(name.toLowerCase());
+      schemes.remove(getColourSchemeShortName(name));
     }
   }
-  
+
   /**
    * 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
@@ -113,7 +155,7 @@ public class ColourSchemes
    *          represent
    * @return
    */
-  public ColourSchemeI getColourScheme(String name,
+  public ColourSchemeI getColourScheme(String name, AlignViewportI viewport,
           AnnotatedCollectionI forData,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
@@ -121,8 +163,8 @@ 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 +180,7 @@ public class ColourSchemes
   public ColourSchemeI getColourScheme(String name,
           AnnotatedCollectionI forData)
   {
-    return getColourScheme(name, forData, null);
+    return getColourScheme(name, null, forData, null);
   }
 
   /**
@@ -165,6 +207,6 @@ public class ColourSchemes
     {
       return false;
     }
-    return schemes.containsKey(name.toLowerCase());
+    return schemes.containsKey(getColourSchemeShortName(name));
   }
 }