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 6bf7010..e3625fa 100644 (file)
--- a/src/jalview/ext/jmol/JmolCommands.java
+++ b/src/jalview/ext/jmol/JmolCommands.java
@@ -27,14 +27,17 @@ 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;
 import jalview.structure.StructureSelectionManager;
+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
@@ -46,6 +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
@@ -55,6 +60,15 @@ 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)
   {
@@ -63,21 +77,20 @@ 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)
       {
         continue;
       }
 
-      int lastPos = -1;
       for (int s = 0; s < sequence[pdbfnum].length; s++)
       {
         for (int sp, m = 0; m < mapping.length; m++)
@@ -85,6 +98,7 @@ public class JmolCommands
           if (mapping[m].getSequence() == sequence[pdbfnum][s]
                   && (sp = al.findIndex(sequence[pdbfnum][s])) > -1)
           {
+            int lastPos = StructureMapping.UNASSIGNED_VALUE;
             SequenceI asp = al.getSequenceAt(sp);
             for (int r = 0; r < asp.getLength(); r++)
             {
@@ -95,10 +109,22 @@ public class JmolCommands
               }
               int pos = mapping[m].getPDBResNum(asp.findPosition(r));
 
-              if (pos < 1 || pos == lastPos)
+              if (pos == lastPos)
               {
                 continue;
               }
+              if (pos == StructureMapping.UNASSIGNED_VALUE)
+              {
+                // terminate current colour op
+                if (command.length() > 0
+                        && command.charAt(command.length() - 1) != ';')
+                {
+                  command.append(";");
+                }
+                // reset lastPos
+                lastPos = StructureMapping.UNASSIGNED_VALUE;
+                continue;
+              }
 
               lastPos = pos;
 
@@ -116,7 +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())
@@ -128,7 +154,12 @@ public class JmolCommands
               // TODO: deal with case when buffer is too large for Jmol to parse
               // - execute command and flush
 
-              command.append(";");
+              if (command.length() > 0
+                      && command.charAt(command.length() - 1) != ';')
+              {
+                command.append(";");
+              }
+
               if (command.length() > 51200)
               {
                 // add another chunk
@@ -190,4 +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();
+  }
+
 }