*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.util.ColorUtils;
* Returns a colour scheme for the given name, with which the given data may
* be coloured. The name is not case-sensitive, and may be one of
* <ul>
+ * <li>any currently registered colour scheme; Jalview by default
+ * provides</li>
+ * <ul>
* <li>Clustal</li>
* <li>Blosum62</li>
* <li>% Identity</li>
* <li>Purine/Pyrimidine</li>
* <li>T-Coffee Scores</li>
* <li>RNA Helices</li>
- * <li>User Defined</li>
+ * </ul>
+ * <li>the name of a programmatically added colour scheme</li>
* <li>an AWT colour name e.g. red</li>
* <li>an AWT hex rgb colour e.g. ff2288</li>
* <li>residue colours list e.g. D,E=red;K,R,H=0022FF;c=yellow</li>
* </ul>
+ *
* If none of these formats is matched, the string is converted to a colour
* using a hashing algorithm. For name "None", returns null.
*
* @param name
* @return
*/
- public static ColourSchemeI getColourScheme(AnnotatedCollectionI forData,
+ public static ColourSchemeI getColourScheme(AlignViewportI view,
+ AnnotatedCollectionI forData,
String name)
{
if (ResidueColourScheme.NONE.equalsIgnoreCase(name))
return null;
}
- JalviewColourScheme scheme = JalviewColourScheme.forName(name);
+
+ /*
+ * if this is the name of a registered colour scheme, just
+ * create a new instance of it
+ */
+ ColourSchemeI scheme = ColourSchemes.getInstance().getColourScheme(name,
+ view,
+ forData, null);
if (scheme != null)
{
- return scheme.getColourScheme(forData);
+ return scheme;
}
/*
* e.g. "red" or "ff00ed",
* or failing that hash the name to a colour
*/
- UserColourScheme ucs = null;
- try
- {
- ucs = new UserColourScheme(name);
- } catch (Exception e)
- {
- // System.err.println("Ignoring exception when parsing colourscheme as applet-parameter");
- }
+ UserColourScheme ucs = new UserColourScheme(name);
return ucs;
}
*/
public static String getColourName(ColourSchemeI cs)
{
- return cs == null ? ResidueColourScheme.NONE : cs
- .getSchemeName();
+ return cs == null ? ResidueColourScheme.NONE : cs.getSchemeName();
}
}