JAL-3390 first pass refactoring for JalviewJmolBinding.showStructures

[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 c981165..e3625fa 100644 (file)
--- a/src/jalview/ext/jmol/JmolCommands.java
+++ b/src/jalview/ext/jmol/JmolCommands.java
@@ -27,6 +27,7 @@ import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
+import jalview.ext.rbvi.chimera.AtomSpecModel;
 import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureMappingcommandSet;
@@ -36,6 +37,7 @@ import jalview.structures.models.AAStructureBindingModel;
 import java.awt.Color;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Map;
 
 /**
  * Routines for generating Jmol commands for Jalview/Jmol binding another
@@ -47,6 +49,8 @@ import java.util.List;
 public class JmolCommands
 {
 
+  private static final String COMMA = ",";
+
   /**
    * Jmol utility which constructs the commands to colour chains by the given
    * alignment
@@ -138,7 +142,7 @@ public class JmolCommands
               String newSelcom = (mapping[m].getChain() != " "
                       ? ":" + mapping[m].getChain()
                       : "") + "/" + (pdbfnum + 1) + ".1" + ";color["
-                      + col.getRed() + "," + col.getGreen() + ","
+                      + col.getRed() + COMMA + col.getGreen() + COMMA
                       + col.getBlue() + "]";
               if (command.length() > newSelcom.length() && command
                       .substring(command.length() - newSelcom.length())
@@ -217,4 +221,77 @@ public class JmolCommands
     return sb;
   }
 
+  /**
+   * Answers a Jmol 'color' command to colour residues as described by the given
+   * map of {@code <Color, AtomSpecModel>}
+   * 
+   * @param map
+   * @return
+   */
+  public static String[] getColourBySequenceCommand(
+          Map<Object, AtomSpecModel> map)
+  {
+    String[] cmds = new String[map.keySet().size()];
+
+    int i = 0;
+    for (Object o : map.keySet())
+    {
+      StringBuilder cmd = new StringBuilder(128);
+      Color c = (Color) o;
+      String atomSpec = getAtomSpec(map.get(o));
+      cmd.append("select ").append(atomSpec).append(";color[")
+              .append(c.getRed()).append(COMMA).append(c.getGreen())
+              .append(COMMA).append(c.getBlue()).append("];");
+      cmds[i] = cmd.toString();
+      i++;
+    }
+
+    return cmds;
+  }
+
+  /**
+   * Builds a Jmol syntax selection expression from the given model, for example
+   * 
+   * <pre>
+   * 61-64,70:A/1.1,12-25,41-44:B/1.1,12:A/2.1
+   * for model 1, chain A, residues 61-64 and 70, chain B residues 12-25 and 41-44, model 2 chain A residue 12
+   * </pre>
+   * 
+   * @param atomSpecModel
+   * @return
+   */
+  public static String getAtomSpec(AtomSpecModel atomSpecModel)
+  {
+    StringBuilder sb = new StringBuilder(64);
+    for (int model : atomSpecModel.getModels())
+    {
+      for (String chain : atomSpecModel.getChains(model))
+      {
+        if (sb.length() > 0)
+        {
+          sb.append(COMMA);
+        }
+        boolean firstRange = true;
+        for (int[] range : atomSpecModel.getRanges(model, chain))
+        {
+          if (!firstRange)
+          {
+            sb.append(COMMA);
+          }
+          firstRange = false;
+          sb.append(range[0]);
+          if (range[1] != range[0])
+          {
+            sb.append("-").append(range[1]);
+          }
+        }
+        sb.append(":").append(chain).append("/")
+                .append(String.valueOf(model + 1))
+                .append(".1");
+      }
+    }
+
+    return sb.toString();
+  }
+
 }