Merge branch 'develop' into trial_merge/JAL-1950

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

diff --git a/src/jalview/schemes/ColourSchemes.java b/src/jalview/schemes/ColourSchemes.java
new file mode 100644 (file)
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+++ b/src/jalview/schemes/ColourSchemes.java
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+/*
+ * 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.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.util.LinkedHashMap;
+import java.util.Map;
+
+public class ColourSchemes
+{
+  /*
+   * singleton instance of this class
+   */
+  private static ColourSchemes instance = new ColourSchemes();
+
+  /*
+   * a map from scheme name (lower-cased) to an instance of it
+   */
+  private Map<String, ColourSchemeI> schemes;
+
+  /**
+   * Returns the singleton instance of this class
+   * 
+   * @return
+   */
+  public static ColourSchemes getInstance()
+  {
+    return instance;
+  }
+
+  private ColourSchemes()
+  {
+    loadColourSchemes();
+  }
+
+  /**
+   * Loads an instance of each standard or user-defined colour scheme
+   * 
+   * @return
+   */
+  void loadColourSchemes()
+  {
+    /*
+     * 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>();
+
+    for (JalviewColourScheme cs : JalviewColourScheme.values())
+    {
+      try
+      {
+        registerColourScheme(cs.getSchemeClass().newInstance());
+      } catch (InstantiationException | IllegalAccessException e)
+      {
+        System.err.println("Error instantiating colour scheme for "
+                + cs.toString() + " " + e.getMessage());
+      }
+    }
+  }
+
+  /**
+   * Registers a colour scheme
+   * 
+   * @param cs
+   */
+  public void registerColourScheme(ColourSchemeI cs)
+  {
+    String name = cs.getSchemeName();
+    if (name == null)
+    {
+      System.err.println("ColourScheme name may not be null");
+      return;
+    }
+
+    /*
+     * name is lower-case for non-case-sensitive lookup
+     * (name in the colour keeps its true case)
+     */
+    String lower = name.toLowerCase();
+    if (schemes.containsKey(lower))
+    {
+      System.err
+              .println("Warning: overwriting colour scheme named " + name);
+    }
+    schemes.put(lower, cs);
+  }
+
+  /**
+   * Removes a colour scheme by name
+   * 
+   * @param name
+   */
+  public void removeColourScheme(String 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 forData
+   *          the data to be coloured
+   * @param optional
+   *          map from hidden representative sequences to the sequences they
+   *          represent
+   * @return
+   */
+  public ColourSchemeI getColourScheme(String name,
+          AnnotatedCollectionI forData,
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  {
+    if (name == null)
+    {
+      return null;
+    }
+    ColourSchemeI cs = schemes.get(name.toLowerCase());
+    return cs == null ? null : cs.getInstance(forData, hiddenRepSequences);
+  }
+
+  /**
+   * 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)
+  {
+    return getColourScheme(name, forData, null);
+  }
+
+  /**
+   * Returns an iterable set of the colour schemes, in the order in which they
+   * were added
+   * 
+   * @return
+   */
+  public Iterable<ColourSchemeI> getColourSchemes()
+  {
+    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(name.toLowerCase());
+  }
+}