JAL-3551 working proof of concept of Jalview driving PyMOL

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

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
index 5eba203..9636a6a 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
@@ -21,12 +21,12 @@
 package jalview.ext.rbvi.chimera;
 
 import jalview.structure.AtomSpecModel;
+import jalview.structure.StructureCommand;
+import jalview.structure.StructureCommandI;
 import jalview.util.ColorUtils;
-import jalview.util.IntRangeComparator;
 
 import java.awt.Color;
-import java.util.Collections;
-import java.util.Iterator;
+import java.util.Arrays;
 import java.util.List;
 
 /**
@@ -34,12 +34,19 @@ import java.util.List;
  */
 public class ChimeraXCommands extends ChimeraCommands
 {
-  private static final String CMD_COLOUR_BY_CHARGE = "color white;color :ASP,GLU red;color :LYS,ARG blue;color :CYS yellow";
+  private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
+          "~display all;show @CA|P pbonds");
+
+  private static final StructureCommand FOCUS_VIEW = new StructureCommand(
+          "view");
+
+  private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand(
+          "color white;color :ASP,GLU red;color :LYS,ARG blue;color :CYS yellow");
 
   @Override
-  public String colourByCharge()
+  public List<StructureCommandI> colourByCharge()
   {
-    return CMD_COLOUR_BY_CHARGE;
+    return Arrays.asList(COLOUR_BY_CHARGE);
   }
 
   @Override
@@ -49,26 +56,26 @@ public class ChimeraXCommands extends ChimeraCommands
   }
 
   @Override
-  public String setBackgroundColour(Color col)
+  public StructureCommandI setBackgroundColour(Color col)
   {
     // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/set.html
-    return "set bgColor " + ColorUtils.toTkCode(col);
+    return new StructureCommand("set bgColor " + ColorUtils.toTkCode(col));
   }
 
   @Override
-  public String getColourCommand(String atomSpec, Color colour)
+  public StructureCommandI getColourCommand(String atomSpec, Color colour)
   {
     // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html
     String colourCode = getColourString(colour);
 
-    return "color " + atomSpec + " " + colourCode;
+    return new StructureCommand("color " + atomSpec + " " + colourCode);
   }
 
   @Override
-  public String focusView()
+  public StructureCommandI focusView()
   {
     // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/view.html
-    return "view";
+    return FOCUS_VIEW;
   }
 
   /**
@@ -96,7 +103,7 @@ public class ChimeraXCommands extends ChimeraCommands
    * @return
    */
   @Override
-  protected String setAttribute(String attributeName,
+  protected StructureCommandI setAttribute(String attributeName,
           String attributeValue, AtomSpecModel atomSpecModel)
   {
     StringBuilder sb = new StringBuilder(128);
@@ -104,21 +111,21 @@ public class ChimeraXCommands extends ChimeraCommands
     sb.append(" res ").append(attributeName).append(" '")
             .append(attributeValue).append("'");
     sb.append(" create true");
-    return sb.toString();
+    return new StructureCommand(sb.toString());
   }
 
   @Override
-  public String openCommandFile(String path)
+  public StructureCommandI openCommandFile(String path)
   {
     // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html
-    return "open " + path;
+    return new StructureCommand("open " + path);
   }
 
   @Override
-  public String saveSession(String filepath)
+  public StructureCommandI saveSession(String filepath)
   {
     // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html
-    return "save session " + filepath;
+    return new StructureCommand("save session " + filepath);
   }
 
   /**
@@ -133,7 +140,7 @@ public class ChimeraXCommands extends ChimeraCommands
   {
     StringBuilder sb = new StringBuilder(128);
     boolean firstModel = true;
-    for (Integer model : atomSpec.getModels())
+    for (String model : atomSpec.getModels())
     {
       if (!firstModel)
       {
@@ -157,7 +164,7 @@ public class ChimeraXCommands extends ChimeraCommands
    * @param model
    * @param atomSpec
    */
-  protected void appendModel(StringBuilder sb, Integer model,
+  protected void appendModel(StringBuilder sb, String model,
           AtomSpecModel atomSpec)
   {
     sb.append("#").append(model);
@@ -167,59 +174,29 @@ public class ChimeraXCommands extends ChimeraCommands
       boolean firstPositionForChain = true;
       sb.append("/").append(chain.trim()).append(":");
       List<int[]> rangeList = atomSpec.getRanges(model, chain);
-
-      /*
-       * sort ranges into ascending start position order
-       */
-      Collections.sort(rangeList, IntRangeComparator.ASCENDING);
-
-      int start = rangeList.isEmpty() ? 0 : rangeList.get(0)[0];
-      int end = rangeList.isEmpty() ? 0 : rangeList.get(0)[1];
-
-      Iterator<int[]> iterator = rangeList.iterator();
-      while (iterator.hasNext())
+      boolean first = true;
+      for (int[] range : rangeList)
       {
-        int[] range = iterator.next();
-        if (range[0] <= end + 1)
+        if (!first)
         {
-          /*
-           * range overlaps or is contiguous with the last one
-           * - so just extend the end position, and carry on
-           * (unless this is the last in the list)
-           */
-          end = Math.max(end, range[1]);
+          sb.append(",");
         }
-        else
-        {
-          /*
-           * we have a break so append the last range
-           */
-          appendRange(sb, start, end, chain, firstPositionForChain, true);
-          start = range[0];
-          end = range[1];
-          firstPositionForChain = false;
-        }
-      }
-
-      /*
-       * and append the last range
-       */
-      if (!rangeList.isEmpty())
-      {
-        appendRange(sb, start, end, chain, firstPositionForChain, true);
+        first = false;
+        appendRange(sb, range[0], range[1], chain, firstPositionForChain,
+                true);
       }
-      firstPositionForChain = false;
     }
   }
 
   @Override
-  public String showBackbone()
+  public List<StructureCommandI> showBackbone()
   {
-    return "~display all;show @CA|P pbonds";
+    return Arrays.asList(SHOW_BACKBONE);
   }
 
   @Override
-  public String superposeStructures(AtomSpecModel spec, AtomSpecModel ref)
+  public List<StructureCommandI> superposeStructures(AtomSpecModel spec,
+          AtomSpecModel ref)
   {
     /*
      * Form ChimeraX match command to match spec to ref
@@ -242,7 +219,7 @@ public class ChimeraXCommands extends ChimeraCommands
     cmd.append(getAtomSpec(spec, false)).append("|");
     cmd.append(getAtomSpec(ref, false)).append("; view");
 
-    return cmd.toString();
+    return Arrays.asList(new StructureCommand(cmd.toString()));
   }
 
 }