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

diff --git a/src/jalview/api/structures/JalviewStructureDisplayI.java b/src/jalview/api/structures/JalviewStructureDisplayI.java
index 0ca9061..cbd2131 100644 (file)
--- a/src/jalview/api/structures/JalviewStructureDisplayI.java
+++ b/src/jalview/api/structures/JalviewStructureDisplayI.java
@@ -23,7 +23,6 @@ package jalview.api.structures;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
 import jalview.structures.models.AAStructureBindingModel;
 
 public interface JalviewStructureDisplayI
@@ -59,13 +58,6 @@ public interface JalviewStructureDisplayI
   void closeViewer(boolean closeExternalViewer);
 
   /**
-   * apply a colourscheme to the structures in the viewer
-   * 
-   * @param colourScheme
-   */
-  void setJalviewColourScheme(ColourSchemeI colourScheme);
-
-  /**
    * 
    * @return true if all background sequence/structure binding threads have
    *         completed for this viewer instance

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index fc6dd26..216320f 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -899,7 +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);
@@ -912,9 +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);

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index ec51943..8eaeed2 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -779,12 +779,6 @@ public abstract class StructureViewerBase extends GStructureViewer
     buildColourMenu();
   }
 
-  @Override
-  public void setJalviewColourScheme(ColourSchemeI cs)
-  {
-    getBinding().setJalviewColourScheme(cs);
-  }
-
   /**
    * Sends commands to the structure viewer to superimpose structures based on
    * currently associated alignments. May optionally return an error message for

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index ef4fed3..d2fff3f 100644 (file)
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -819,10 +819,18 @@ public abstract class AAStructureBindingModel
     {
       return;
     }
-    // todo: property change event for visibleAlignment
-    // to avoid unnecessary redraws here
-    if (!colourBySequence && !isShowAlignmentOnly())
+
+    /*
+     * if structure is not coloured by sequence, but restricted to the alignment,
+     * then redraw it (but don't recolour it) in case hidden regions have changed
+     * (todo: specific messaging for change of hidden region only)
+     */
+    if (!colourBySequence)
     {
+      if (isShowAlignmentOnly())
+      {
+        showStructures(alignmentv.getAlignViewport(), false);
+      }
       return;
     }
     if (getSsm() == null)