JAL-3390 new View menu option to hide hidden regions in structure

[jalview.git] / src / jalview / ext / jmol / JmolCommands.java

diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java
index 8fb0de6..c981165 100644 (file)
--- a/src/jalview/ext/jmol/JmolCommands.java
+++ b/src/jalview/ext/jmol/JmolCommands.java
@@ -31,6 +31,7 @@ import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
 
 import java.awt.Color;
 import java.util.ArrayList;
@@ -55,6 +56,15 @@ public class JmolCommands
    */
   public static StructureMappingcommandSet[] getColourBySequenceCommand(
           StructureSelectionManager ssm, String[] files,
+          AAStructureBindingModel binding, AlignmentViewPanel viewPanel)
+  {
+    SequenceRenderer sr = binding.getSequenceRenderer(viewPanel);
+    SequenceI[][] sequence = binding.getSequence();
+    return getColourBySequenceCommand(ssm, files, sequence, sr, viewPanel);
+  }
+
+  public static StructureMappingcommandSet[] getColourBySequenceCommand(
+          StructureSelectionManager ssm, String[] files,
           SequenceI[][] sequence, SequenceRenderer sr,
           AlignmentViewPanel viewPanel)
   {
@@ -63,14 +73,14 @@ public class JmolCommands
     AlignViewportI viewport = viewPanel.getAlignViewport();
     HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
     AlignmentI al = viewport.getAlignment();
-    List<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
+    List<StructureMappingcommandSet> cset = new ArrayList<>();
 
     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
     {
       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
       StringBuffer command = new StringBuffer();
       StructureMappingcommandSet smc;
-      ArrayList<String> str = new ArrayList<String>();
+      ArrayList<String> str = new ArrayList<>();
 
       if (mapping == null || mapping.length < 1)
       {