X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemes.java;h=99e97592c55bb2c8f52de2a32c1f9ad908825391;hb=8956fdfd008d0d949814c4680a7b3a55969e39e1;hp=817fb0136767e4106fd656db2d554faea0e0c58a;hpb=8b55eedb9d76a8c65b80f756c4412bf029906bf7;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemes.java b/src/jalview/schemes/ColourSchemes.java
index 817fb01..99e9759 100644
--- a/src/jalview/schemes/ColourSchemes.java
+++ b/src/jalview/schemes/ColourSchemes.java
@@ -1,14 +1,29 @@
+/*
+ * 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 jalview.binding.JalviewUserColours;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
-import java.awt.Color;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.InputStreamReader;
 import java.util.LinkedHashMap;
 import java.util.Map;
 
@@ -20,7 +35,7 @@ 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<String, ColourSchemeI> schemes;
 
@@ -99,9 +114,12 @@ 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
@@ -167,124 +185,6 @@ public class ColourSchemes
     {
       return false;
     }
-    name = name.toLowerCase();
-    for (ColourSchemeI scheme : getColourSchemes())
-    {
-      if (name.equals(scheme.getSchemeName().toLowerCase()))
-      {
-        return true;
-      }
-    }
-    return false;
-  }
-
-  /**
-   * Loads a user defined colour scheme from file. The file should contain a
-   * definition of residue colours in XML format as defined in
-   * JalviewUserColours.xsd.
-   * 
-   * @param filePath
-   * 
-   * @return
-   */
-  public static UserColourScheme loadColourScheme(String filePath)
-  {
-    UserColourScheme ucs = null;
-    Color[] newColours = null;
-    File file = new File(filePath);
-    try
-    {
-      InputStreamReader in = new InputStreamReader(
-              new FileInputStream(file), "UTF-8");
-  
-      jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
-  
-      org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
-              jucs);
-      jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar
-              .unmarshal(in);
-  
-      /*
-       * non-case-sensitive colours are for 20 amino acid codes,
-       * B, Z, X and Gap
-       * optionally, lower-case alternatives for all except Gap
-       */
-      newColours = new Color[24];
-      Color[] lowerCase = new Color[23];
-      boolean caseSensitive = false;
-  
-      String name;
-      int index;
-      for (int i = 0; i < jucs.getColourCount(); i++)
-      {
-        name = jucs.getColour(i).getName();
-        if (ResidueProperties.aa3Hash.containsKey(name))
-        {
-          index = ResidueProperties.aa3Hash.get(name).intValue();
-        }
-        else
-        {
-          index = ResidueProperties.aaIndex[name.charAt(0)];
-        }
-        if (index == -1)
-        {
-          continue;
-        }
-  
-        Color color = new Color(Integer.parseInt(jucs.getColour(i)
-                .getRGB(), 16));
-        if (name.toLowerCase().equals(name))
-        {
-          caseSensitive = true;
-          lowerCase[index] = color;
-        }
-        else
-        {
-          newColours[index] = color;
-        }
-      }
-  
-      /*
-       * instantiate the colour scheme
-       */
-      ucs = new UserColourScheme(newColours);
-      ucs.setName(jucs.getSchemeName());
-      if (caseSensitive)
-      {
-        ucs.setLowerCaseColours(lowerCase);
-      }
-    } catch (Exception ex)
-    {
-      // Could be old Jalview Archive format
-      try
-      {
-        InputStreamReader in = new InputStreamReader(new FileInputStream(
-                file), "UTF-8");
-  
-        jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
-  
-        jucs = JalviewUserColours.unmarshal(in);
-  
-        newColours = new Color[jucs.getColourCount()];
-  
-        for (int i = 0; i < 24; i++)
-        {
-          newColours[i] = new Color(Integer.parseInt(jucs.getColour(i)
-                  .getRGB(), 16));
-        }
-        ucs = new UserColourScheme(newColours);
-        ucs.setName(jucs.getSchemeName());
-      } catch (Exception ex2)
-      {
-        ex2.printStackTrace();
-      }
-  
-      if (newColours == null)
-      {
-        System.out.println("Error loading User ColourFile\n" + ex);
-      }
-    }
-  
-    return ucs;
+    return schemes.containsKey(name.toLowerCase());
   }
 }