X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=2d5b23dfa343f3b55284a07b944c6df4563a896e;hb=456e5c765ac1e85336fd9f9b1a35453069bb2298;hp=9b91066e191fded769148b291ae9d68a71993fa0;hpb=b0cee3aaf7d8873910939f97b6acb217d518968d;p=jalview.git
diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 9b91066..2d5b23d 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -20,6 +20,7 @@
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.util.ColorUtils;
@@ -42,7 +43,10 @@ public class ColourSchemeProperty
/**
* Returns a colour scheme for the given name, with which the given data may
- * be coloured. The name may be one of
+ * be coloured. The name is not case-sensitive, and may be one of
+ *
+ * - any currently registered colour scheme; Jalview by default
+ * provides
*
* - Clustal
* - Blosum62
@@ -58,52 +62,50 @@ public class ColourSchemeProperty
* - Purine/Pyrimidine
* - T-Coffee Scores
* - RNA Helices
- * - User Defined
- * - None
+ *
+ * - the name of a programmatically added colour scheme
* - an AWT colour name e.g. red
+ * - an AWT hex rgb colour e.g. ff2288
* - residue colours list e.g. D,E=red;K,R,H=0022FF;c=yellow
*
+ *
* If none of these formats is matched, the string is converted to a colour
- * using a hashing algorithm.
+ * using a hashing algorithm. For name "None", returns null.
*
* @param forData
* @param name
* @return
*/
- public static ColourSchemeI getColour(AnnotatedCollectionI forData,
+ public static ColourSchemeI getColourScheme(AlignViewportI view,
+ AnnotatedCollectionI forData,
String name)
{
- JalviewColourScheme scheme = JalviewColourScheme.forName(name);
- if (scheme != null)
+ if (ResidueColourScheme.NONE.equalsIgnoreCase(name))
{
- // note JalviewColourScheme.None returns null here
- return scheme.getColourScheme(forData);
+ return null;
+
}
- if (name.indexOf('=') == -1)
+ /*
+ * 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)
{
- /*
- * parse the name as a colour specification
- * e.g. "red" or "ff00ed",
- * or failing that hash the name to a colour
- */
- return new UserColourScheme(name);
+ return scheme;
}
/*
* try to parse the string as a residues colour scheme
* e.g. A=red;T,G=blue etc
+ * else parse the name as a colour specification
+ * e.g. "red" or "ff00ed",
+ * or failing that hash the name to a colour
*/
- UserColourScheme ucs = null;
- try
- {
- // fix the launchApp user defined colourscheme transfer bug
- ucs = new UserColourScheme("white");
- ucs.parseAppletParameter(name);
- } catch (Exception e)
- {
- // System.err.println("Ignoring exception when parsing colourscheme as applet-parameter");
- }
+ UserColourScheme ucs = new UserColourScheme(name);
return ucs;
}
@@ -150,8 +152,7 @@ public class ColourSchemeProperty
*/
public static String getColourName(ColourSchemeI cs)
{
- return cs == null ? ResidueColourScheme.NONE : cs
- .getSchemeName();
+ return cs == null ? ResidueColourScheme.NONE : cs.getSchemeName();
}
}