From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 15 May 2020 06:29:55 +0000 (+0100)
Subject: JAL-3551 raise label on ('highlight') structure residue (wip)
X-Git-Tag: Release_2_11_2_0~37^2~18
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=b145d2b4a617f452801953c1b49dae6b65521f14

JAL-3551 raise label on ('highlight') structure residue (wip)
---

diff --git a/src/jalview/gui/PymolBindingModel.java b/src/jalview/gui/PymolBindingModel.java
index 6787c8a..fcf586a 100644
--- a/src/jalview/gui/PymolBindingModel.java
+++ b/src/jalview/gui/PymolBindingModel.java
@@ -12,12 +12,20 @@ import jalview.ext.pymol.PymolCommands;
 import jalview.ext.pymol.PymolManager;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.structure.AtomSpec;
+import jalview.structure.StructureCommand;
 import jalview.structure.StructureCommandI;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
 
 public class PymolBindingModel extends AAStructureBindingModel
 {
+  /*
+   * format for labels shown on structures when mousing over sequence;
+   * see https://pymolwiki.org/index.php/Label#examples
+   * left not final so customisable e.g. with a Groovy script
+   */
+  private static String LABEL_FORMAT = "\"%s %s\" % (resn,resi)";
+
   private PymolManager pymolManager;
 
   private Thread pymolMonitor;
@@ -32,6 +40,8 @@ public class PymolBindingModel extends AAStructureBindingModel
    */
   Map<String, String> pymolObjects = new HashMap<>();
 
+  private String lastLabelSpec;
+
   /**
    * Constructor
    * 
@@ -59,6 +69,37 @@ public class PymolBindingModel extends AAStructureBindingModel
   @Override
   public void highlightAtoms(List<AtomSpec> atoms)
   {
+    /*
+     * https://pymolwiki.org/index.php/Label#examples
+     */
+    StringBuilder sb = new StringBuilder();
+    for (AtomSpec atom : atoms)
+    {
+      // todo promote to StructureCommandsI.showLabel()
+      // todo handle CA|P correctly
+      String modelId = getModelIdForFile(atom.getPdbFile());
+      sb.append(String.format(" %s//%s/%d/CA", modelId,
+              atom.getChain(),
+              atom.getPdbResNum()));
+    }
+    String labelSpec = sb.toString();
+    if (labelSpec.equals(lastLabelSpec))
+    {
+      return;
+    }
+    StructureCommandI command = new StructureCommand("label", labelSpec, LABEL_FORMAT);
+    executeCommand(command, false);
+
+    /*
+     * and remove the label(s) previously shown
+     */
+    if (lastLabelSpec != null)
+    {
+      command = new StructureCommand("label", lastLabelSpec, "");
+      executeCommand(command, false);
+    }
+
+    lastLabelSpec = labelSpec;
   }
 
   @Override