X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=98e90bdf769f07363b4b8bb598d97a5edf6d3db2;hb=2bb9cad4fa36d64cebbe09bc63732e8dbb4dcb32;hp=53e9b60a81e6e14bb701c8c2232fedf7bf8530ae;hpb=94379c810f9115b8564ee7bac46ed119218d5fd2;p=jalview.git
diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 53e9b60..98e90bd 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;
@@ -44,6 +45,9 @@ public class ColourSchemeProperty
* 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
*
+ * - any currently registered colour scheme; Jalview by default
+ * provides
+ *
* - Clustal
* - Blosum62
* - % Identity
@@ -58,11 +62,13 @@ public class ColourSchemeProperty
* - Purine/Pyrimidine
* - T-Coffee Scores
* - RNA Helices
- * - User Defined
+ *
+ * - 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. For name "None", returns null.
*
@@ -70,8 +76,8 @@ public class ColourSchemeProperty
* @param name
* @return
*/
- public static ColourSchemeI getColourScheme(AnnotatedCollectionI forData,
- String name)
+ public static ColourSchemeI getColourScheme(AlignViewportI view,
+ AnnotatedCollectionI forData, String name)
{
if (ResidueColourScheme.NONE.equalsIgnoreCase(name))
{
@@ -83,8 +89,8 @@ public class ColourSchemeProperty
* if this is the name of a registered colour scheme, just
* create a new instance of it
*/
- ColourSchemeI scheme = ColourSchemes.getInstance().getColourScheme(
- name, forData);
+ ColourSchemeI scheme = ColourSchemes.getInstance().getColourScheme(name,
+ view, forData, null);
if (scheme != null)
{
return scheme;
@@ -144,8 +150,7 @@ public class ColourSchemeProperty
*/
public static String getColourName(ColourSchemeI cs)
{
- return cs == null ? ResidueColourScheme.NONE : cs
- .getSchemeName();
+ return cs == null ? ResidueColourScheme.NONE : cs.getSchemeName();
}
}