Merge branch 'develop' into spike/matrix_annot

[jalview.git] / src / jalview / renderer / AnnotationRenderer.java

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 1928ba3..f5562d7 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -32,7 +32,9 @@ import jalview.datamodel.ProfilesI;
 import jalview.renderer.api.AnnotationRendererFactoryI;
 import jalview.renderer.api.AnnotationRowRendererI;
 import jalview.schemes.ColourSchemeI;
+import jalview.schemes.NucleotideColourScheme;
 import jalview.schemes.ResidueProperties;
+import jalview.schemes.ZappoColourScheme;
 import jalview.util.Platform;
 
 import java.awt.BasicStroke;
@@ -72,7 +74,7 @@ public class AnnotationRenderer
   boolean av_renderHistogram = true, av_renderProfile = true,
           av_normaliseProfile = false;
 
-  ColourSchemeI profcolour = null;
+  ResidueShaderI profcolour = null;
 
   private ColumnSelection columnSelection;
 
@@ -316,13 +318,17 @@ public class AnnotationRenderer
     av_renderHistogram = av.isShowConsensusHistogram();
     av_renderProfile = av.isShowSequenceLogo();
     av_normaliseProfile = av.isNormaliseSequenceLogo();
-    profcolour = av.getGlobalColourScheme();
-    if (profcolour == null)
+    profcolour = av.getResidueShading();
+    if (profcolour == null || profcolour.getColourScheme() == null)
     {
-      // Set the default colour for sequence logo if the alignnent has no
-      // colourscheme set
-      profcolour = av.getAlignment().isNucleotide() ? new jalview.schemes.NucleotideColourScheme()
-              : new jalview.schemes.ZappoColourScheme();
+      /*
+       * Use default colour for sequence logo if 
+       * the alignment has no colourscheme set
+       * (would like to use user preference but n/a for applet)
+       */
+      ColourSchemeI col = av.getAlignment().isNucleotide() ? new NucleotideColourScheme()
+              : new ZappoColourScheme();
+      profcolour = new ResidueShader(col);
     }
     columnSelection = av.getColumnSelection();
     hconsensus = av.getSequenceConsensusHash();