Merge branch 'develop' into patch/JAL-3921_jmol_session_save

[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 25f6aec..1fb8761 100644 (file)
--- a/src/jalview/ext/jmol/JmolCommands.java
+++ b/src/jalview/ext/jmol/JmolCommands.java
@@ -54,7 +54,8 @@ 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;");
@@ -112,7 +113,8 @@ 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);
@@ -146,7 +148,8 @@ 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]);
       }
     }
 
@@ -178,7 +181,7 @@ 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();
@@ -190,18 +193,35 @@ 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()));
+  }
 
+  @Override
+  public List<StructureCommandI> centerViewOn(List<AtomSpecModel> residues)
+  {
+    StringBuilder sb = new StringBuilder(64);
+    sb.append("center ");
+    for (AtomSpecModel ranges : residues)
+    {
+      if (sb.length() > 9)
+      {
+        sb.append(" or ");
+      }
+      sb.append(getAtomSpec(ranges, AtomSpecType.RESIDUE_ONLY));
+    }
     return Arrays.asList(new StructureCommand(sb.toString()));
   }
 
@@ -221,13 +241,15 @@ public class JmolCommands extends StructureCommandsBase
     /*
      * https://chemapps.stolaf.edu/jmol/docs/#writemodel
      */
-    return new StructureCommand("write STATE \"" + filepath + "\"");
+    StructureCommand sc = new StructureCommand("write STATE \"" + filepath + "\"");
+    sc.setWaitNeeded(true);
+    return sc;
   }
 
   @Override
   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());
@@ -250,7 +272,7 @@ 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);
 
@@ -293,10 +315,41 @@ public class JmolCommands extends StructureCommandsBase
   public StructureCommandI loadFile(String file)
   {
     // https://chemapps.stolaf.edu/jmol/docs/#loadfiles
-    return new StructureCommand("load FILES \"" + 
-            Platform.escapeBackslashes(file) + "\"");
+    return new StructureCommand(
+            "load FILES \"" + Platform.escapeBackslashes(file) + "\"");
+  }
+  @Override
+  public StructureCommandI restoreSession(String filePath)
+  {
+    return new StructureCommand(
+            "restore STATE \"" + Platform.escapeBackslashes(filePath) + "\"");
   }
 
+  @Override
+  public List<StructureCommandI> showHetatms(List<String> toShow)
+  {
+    // always clear the current hetero cpk display
+    
+    StringBuilder sb = new StringBuilder();
+    sb.append("select hetero; cpk off;");
+    
+    if (toShow != null && !toShow.isEmpty())
+    {
+      // select what was requested
+      sb.append("select ");
+      boolean or = false;
+      for (String k : toShow)
+      {
+        sb.append(or ? " or " : " ");
+        sb.append(k);
+        or = true;
+      }
+      // and show as
+      sb.append("; cpk;");
+    }
+    
+    return Arrays.asList(new StructureCommand(sb.toString()));
+  }
   /**
    * Obsolete method, only referenced from
    * jalview.javascript.MouseOverStructureListener
@@ -433,8 +486,7 @@ public class JmolCommands extends StructureCommandsBase
    * @return
    */
   @Deprecated
-  private static StringBuilder condenseCommand(
-          StringBuilder command,
+  private static StringBuilder condenseCommand(StringBuilder command,
           int pos)
   {