Merge branch 'develop' into features/JAL-2349_matrixvis

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

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index f5562d7..8f751b6 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -28,6 +28,7 @@ import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.ProfilesI;
 import jalview.renderer.api.AnnotationRendererFactoryI;
 import jalview.renderer.api.AnnotationRowRendererI;
@@ -77,6 +78,8 @@ public class AnnotationRenderer
   ResidueShaderI profcolour = null;
 
   private ColumnSelection columnSelection;
+  
+  private HiddenColumns hiddenColumns;
 
   private ProfilesI hconsensus;
 
@@ -311,7 +314,7 @@ public class AnnotationRenderer
   public void updateFromAlignViewport(AlignViewportI av)
   {
     charWidth = av.getCharWidth();
-    endRes = av.getEndRes();
+    endRes = av.getRanges().getEndRes();
     charHeight = av.getCharHeight();
     hasHiddenColumns = av.hasHiddenColumns();
     validCharWidth = av.isValidCharWidth();
@@ -331,6 +334,7 @@ public class AnnotationRenderer
       profcolour = new ResidueShader(col);
     }
     columnSelection = av.getColumnSelection();
+    hiddenColumns = av.getAlignment().getHiddenColumns();
     hconsensus = av.getSequenceConsensusHash();
     complementConsensus = av.getComplementConsensusHash();
     hStrucConsensus = av.getRnaStructureConsensusHash();
@@ -594,7 +598,7 @@ public class AnnotationRenderer
         {
           if (hasHiddenColumns)
           {
-            column = columnSelection.adjustForHiddenColumns(startRes + x);
+            column = hiddenColumns.adjustForHiddenColumns(startRes + x);
             if (column > row_annotations.length - 1)
             {
               break;
@@ -1052,8 +1056,8 @@ public class AnnotationRenderer
             if (renderer != null)
             {
               renderer.renderRow(g, charWidth, charHeight,
-                      hasHiddenColumns, av, columnSelection, row,
-                      row_annotations, startRes, endRes, row.graphMin,
+                      hasHiddenColumns, av, hiddenColumns, columnSelection,
+                      row, row_annotations, startRes, endRes, row.graphMin,
                       row.graphMax, y);
             }
             if (debugRedraw)
@@ -1262,7 +1266,7 @@ public class AnnotationRenderer
       column = sRes + x;
       if (hasHiddenColumns)
       {
-        column = columnSelection.adjustForHiddenColumns(column);
+        column = hiddenColumns.adjustForHiddenColumns(column);
       }
 
       if (column > aaMax)
@@ -1341,7 +1345,7 @@ public class AnnotationRenderer
       column = sRes + x;
       if (hasHiddenColumns)
       {
-        column = columnSelection.adjustForHiddenColumns(column);
+        column = hiddenColumns.adjustForHiddenColumns(column);
       }
 
       if (column > aaMax)