JAL-3390 first pass refactoring for JalviewJmolBinding.showStructures

[jalview.git] / src / jalview / ext / jmol / JalviewJmolBinding.java

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 762b08e..8cecf6e 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -23,18 +23,17 @@ package jalview.ext.jmol;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.ext.rbvi.chimera.AtomSpecModel;
 import jalview.gui.IProgressIndicator;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.AtomSpec;
-import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MessageManager;
@@ -135,15 +134,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   /**
    * prepare the view for a given set of models/chains. chainList contains
    * strings of the form 'pdbfilename:Chaincode'
-   * 
-   * @param chainList
-   *          list of chains to make visible
    */
-  public void centerViewer(Vector<String> chainList)
+  public void centerViewer()
   {
     StringBuilder cmd = new StringBuilder(128);
     int mlength, p;
-    for (String lbl : chainList)
+    for (String lbl : chainsToShow)
     {
       mlength = 0;
       do
@@ -159,7 +155,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     {
       cmd.setLength(cmd.length() - 4);
     }
-    evalStateCommand("select *;restrict " + cmd + ";cartoon;center " + cmd);
+    String command = "select *;restrict " + cmd + ";cartoon;center " + cmd;
+    evalStateCommand(command);
   }
 
   public void closeViewer()
@@ -479,14 +476,14 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   Thread colourby = null;
+  
   /**
    * Sends a set of colour commands to the structure viewer
    * 
-   * @param colourBySequenceCommands
+   * @param commands
    */
   @Override
-  protected void colourBySequence(
-          final StructureMappingcommandSet[] colourBySequenceCommands)
+  protected void colourBySequence(final String[] commands)
   {
     if (colourby != null)
     {
@@ -498,12 +495,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       @Override
       public void run()
       {
-        for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
+        for (String cmd : commands)
         {
-          for (String cbyseq : cpdbbyseq.commands)
-          {
-            executeWhenReady(cbyseq);
-          }
+          executeWhenReady(cmd);
         }
       }
     });
@@ -512,16 +506,16 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   /**
    * @param files
-   * @param sr
    * @param viewPanel
    * @return
    */
   @Override
-  protected StructureMappingcommandSet[] getColourBySequenceCommands(
-          String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
+  protected String[] getColourBySequenceCommands(
+          String[] files, AlignmentViewPanel viewPanel)
   {
-    return JmolCommands.getColourBySequenceCommand(getSsm(), files,
-            getSequence(), sr, viewPanel);
+    Map<Object, AtomSpecModel> map = buildColoursMap(viewPanel);
+
+    return JmolCommands.getColourBySequenceCommand(map);
   }
 
   /**
@@ -1419,8 +1413,38 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   @Override
-  public void showStructures(AlignViewportI av)
+  public void showStructures(AlignViewportI av, boolean refocus)
+  {
+    StringBuilder cmd = new StringBuilder(128);
+
+    if (isShowAlignmentOnly())
+    {
+      cmd.append("hide *;");
+
+    AtomSpecModel model = getShownResidues(av);
+    String atomSpec = JmolCommands.getAtomSpec(model);
+
+    cmd.append("display ").append(atomSpec);
+    }
+    else
+    {
+      cmd.append("display *");
+    }
+    cmd.append("; cartoon");
+    if (refocus)
+    {
+      cmd.append("; zoom 100");
+    }
+    evalStateCommand(cmd.toString());
+  }
+
+  /**
+   * Answers a Jmol syntax style structure model specification. Model number 0, 1,
+   * 2... is formatted as "1.1", "2.1", "3.1" etc.
+   */
+  @Override
+  public String getModelSpec(int model)
   {
-    // TODO show Jmol structure optionally restricted to visible alignment
+    return String.valueOf(model + 1) + ".1";
   }
 }