+/*
+ * 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.Locale;
+
import jalview.api.AlignViewportI;
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+import jalview.util.ColorUtils;
+import java.awt.Color;
import java.util.LinkedHashMap;
import java.util.Map;
-public class ColourSchemes
+public class ColourSchemes implements ApplicationSingletonI
{
- /*
- * singleton instance of this class
- */
- private static ColourSchemes instance = new ColourSchemes();
-
- /*
- * a map from scheme name to an instance of it
- */
- private Map<String, ColourSchemeI> schemes;
/**
* Returns the singleton instance of this class
*/
public static ColourSchemes getInstance()
{
- return instance;
+ return (ColourSchemes) ApplicationSingletonProvider
+ .getInstance(ColourSchemes.class);
}
private ColourSchemes()
}
/**
+ * ColourSchemeProperty "static"
+ */
+ public Color[] rnaHelices = null;
+
+ /**
+ * delete the existing cached RNA helices colours
+ */
+ public static void resetRnaHelicesShading()
+ {
+ getInstance().rnaHelices = null;
+ }
+
+ public static void initRnaHelicesShading(int n)
+ {
+ int i = 0;
+ ColourSchemes j = getInstance();
+
+ if (j.rnaHelices == null)
+ {
+ j.rnaHelices = new Color[n + 1];
+ }
+ else if (j.rnaHelices != null && j.rnaHelices.length <= n)
+ {
+ Color[] t = new Color[n + 1];
+ System.arraycopy(j.rnaHelices, 0, t, 0, j.rnaHelices.length);
+ i = j.rnaHelices.length;
+ j.rnaHelices = t;
+ }
+ else
+ {
+ return;
+ }
+ // Generate random colors and store
+ for (; i <= n; i++)
+ {
+ j.rnaHelices[i] = ColorUtils.generateRandomColor(Color.white);
+ }
+ }
+
+ /**
+ * a map from scheme name (lower-cased) to an instance of it
+ */
+ private Map<String, ColourSchemeI> schemes;
+
+ /**
* Loads an instance of each standard or user-defined colour scheme
*
* @return
* 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());
+ e.printStackTrace();
+ } catch (ReflectiveOperationException roe)
+ {
+ roe.printStackTrace();
}
}
}
* name is lower-case for non-case-sensitive lookup
* (name in the colour keeps its true case)
*/
- String lower = name.toLowerCase();
+ String lower = name.toLowerCase(Locale.ROOT);
if (schemes.containsKey(lower))
{
System.err
*/
public void removeColourScheme(String name)
{
- schemes.remove(name);
+ if (name != null)
+ {
+ schemes.remove(name.toLowerCase(Locale.ROOT));
+ }
}
-
+
/**
* 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
+ * 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<SequenceI, SequenceCollectionI> 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(name.toLowerCase(Locale.ROOT));
+ 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);
}
/**
{
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(Locale.ROOT));
+ }
}
git://source.jalview.org / jalview.git / blobdiff