X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolCommands.java;h=58b69efbb07f9201dec6f1a685f62afd1ee1fa5b;hb=b9b1f47cc74bbec8c28b75776e1d00c258215dfb;hp=3e0afd705a2c14e56d8054cbdcd6e3912c4e69ac;hpb=4f30214e8098748469c6a4269ac2ed6c5750e4b0;p=jalview.git

diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java
index 3e0afd7..58b69ef 100644
--- a/src/jalview/ext/jmol/JmolCommands.java
+++ b/src/jalview/ext/jmol/JmolCommands.java
@@ -40,7 +40,9 @@ import jalview.structure.StructureCommandI;
 import jalview.structure.StructureCommandsBase;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
+import jalview.structure.StructureCommandsI.AtomSpecType;
 import jalview.util.Comparison;
+import jalview.util.Platform;
 
 /**
  * Routines for generating Jmol commands for Jalview/Jmol binding
@@ -53,7 +55,8 @@ public class JmolCommands extends StructureCommandsBase
   private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
           "select *; cartoons off; backbone");
 
-  private static final StructureCommand FOCUS_VIEW = new StructureCommand("zoom 0");
+  private static final StructureCommand FOCUS_VIEW = new StructureCommand(
+          "zoom 0");
 
   private static final StructureCommand COLOUR_ALL_WHITE = new StructureCommand(
           "select *;color white;");
@@ -111,7 +114,8 @@ public class JmolCommands extends StructureCommandsBase
   }
 
   @Override
-  public List<StructureCommandI> colourByResidues(Map<String, Color> colours)
+  public List<StructureCommandI> colourByResidues(
+          Map<String, Color> colours)
   {
     List<StructureCommandI> cmds = super.colourByResidues(colours);
     cmds.add(0, COLOUR_ALL_WHITE);
@@ -145,7 +149,8 @@ public class JmolCommands extends StructureCommandsBase
           atomSpec.append(" or ");
         }
         first = false;
-        atomSpec.append(":").append(tokens[1]).append(" /").append(tokens[0]);
+        atomSpec.append(":").append(tokens[1]).append(" /")
+                .append(tokens[0]);
       }
     }
 
@@ -177,7 +182,7 @@ public class JmolCommands extends StructureCommandsBase
    */
   @Override
   public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
-          AtomSpecModel atomSpec)
+          AtomSpecModel atomSpec, AtomSpecType backbone)
   {
     StringBuilder sb = new StringBuilder(64);
     String refModel = refAtoms.getModels().iterator().next();
@@ -189,17 +194,19 @@ public class JmolCommands extends StructureCommandsBase
      * command examples don't include modelspec with atoms, getAtomSpec does;
      * it works, so leave it as it is for simplicity
      */
-    sb.append(getAtomSpec(atomSpec, true)).append("}{");
-    sb.append(getAtomSpec(refAtoms, true)).append("}");
+    sb.append(getAtomSpec(atomSpec, backbone)).append("}{");
+    sb.append(getAtomSpec(refAtoms, backbone)).append("}");
     sb.append(" ROTATE TRANSLATE ");
     sb.append(getCommandSeparator());
 
     /*
      * show residues used for superposition as ribbon
      */
-    sb.append("select ").append(getAtomSpec(atomSpec, false)).append("|");
-    sb.append(getAtomSpec(refAtoms, false)).append(getCommandSeparator())
-            .append("cartoons");
+    sb.append("select ")
+            .append(getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY))
+            .append("|");
+    sb.append(getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY))
+            .append(getCommandSeparator()).append("cartoons");
 
     return Arrays.asList(new StructureCommand(sb.toString()));
   }
@@ -224,9 +231,9 @@ public class JmolCommands extends StructureCommandsBase
   }
 
   @Override
-  protected StructureCommandI getColourCommand(String atomSpec, Color colour)
+  protected StructureCommandI colourResidues(String atomSpec, Color colour)
   {
-    StringBuilder sb = new StringBuilder(atomSpec.length()+20);
+    StringBuilder sb = new StringBuilder(atomSpec.length() + 20);
     sb.append("select ").append(atomSpec).append(getCommandSeparator())
             .append("color").append(getColourString(colour));
     return new StructureCommand(sb.toString());
@@ -249,7 +256,7 @@ public class JmolCommands extends StructureCommandsBase
    * a separate clause in the {@code compare} (superposition) command.
    */
   @Override
-  public String getAtomSpec(AtomSpecModel model, boolean alphaOnly)
+  public String getAtomSpec(AtomSpecModel model, AtomSpecType specType)
   {
     StringBuilder sb = new StringBuilder(128);
 
@@ -291,7 +298,9 @@ public class JmolCommands extends StructureCommandsBase
   @Override
   public StructureCommandI loadFile(String file)
   {
-    return null;
+    // https://chemapps.stolaf.edu/jmol/docs/#loadfiles
+    return new StructureCommand(
+            "load FILES \"" + Platform.escapeBackslashes(file) + "\"");
   }
 
   /**
@@ -430,8 +439,7 @@ public class JmolCommands extends StructureCommandsBase
    * @return
    */
   @Deprecated
-  private static StringBuilder condenseCommand(
-          StringBuilder command,
+  private static StringBuilder condenseCommand(StringBuilder command,
           int pos)
   {
 
@@ -466,4 +474,16 @@ public class JmolCommands extends StructureCommandsBase
 
     return sb;
   }
+
+  @Override
+  public StructureCommandI openSession(String filepath)
+  {
+    return loadFile(filepath);
+  }
+
+  @Override
+  public StructureCommandI closeViewer()
+  {
+    return null; // not an external viewer
+  }
 }