JAL-3390 redraw structures if alignment only and hidden regions change

[jalview.git] / src / jalview / ext / rbvi / chimera / JalviewChimeraBinding.java

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 1731a05..216320f 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -22,7 +22,6 @@ package jalview.ext.rbvi.chimera;
 
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
-import jalview.api.SequenceRenderer;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
@@ -667,16 +666,15 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 
   /**
    * @param files
-   * @param sr
    * @param viewPanel
    * @return
    */
   @Override
   protected StructureMappingcommandSet[] getColourBySequenceCommands(
-          String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
+          String[] files, AlignmentViewPanel viewPanel)
   {
     return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
-            getSequence(), sr, viewPanel);
+            this, viewPanel);
   }
 
   /**
@@ -901,7 +899,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       return;
     }
 
-    // Chimera expects RBG values in the range 0-1
+    // Chimera expects RGB values in the range 0-1
     final double normalise = 255D;
     viewerCommandHistory(false);
     StringBuilder command = new StringBuilder(128);
@@ -914,9 +912,11 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
               ? ResidueProperties.getSingleCharacterCode(resName)
               : resName.charAt(0);
       Color col = cs.findColour(res, 0, null, null, 0f);
-      command.append("color " + col.getRed() / normalise + ","
-              + col.getGreen() / normalise + "," + col.getBlue() / normalise
-              + " ::" + resName + ";");
+      command.append("color ")
+              .append(String.valueOf(col.getRed() / normalise)).append(",")
+              .append(String.valueOf(col.getGreen() / normalise))
+              .append(",").append(String.valueOf(col.getBlue() / normalise))
+              .append(" ::").append(resName).append(";");
     }
 
     sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA);
@@ -1350,7 +1350,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
               continue;
             }
             Iterator<int[]> visible;
-            if (isShowAlignmentOnly())
+            if (isShowAlignmentOnly() && isHideHiddenRegions())
             {
               visible = alignment.getHiddenColumns()
                     .getVisContigsIterator(0, width, true);