JAL-3404 explicit getModelForPdbFile lookup

[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 c727baf..2645980 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -37,6 +37,7 @@ import jalview.structure.AtomSpec;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MessageManager;
+import jalview.util.StructureCommands;
 
 import java.awt.Color;
 import java.awt.Container;
@@ -58,7 +59,6 @@ import org.jmol.api.JmolSelectionListener;
 import org.jmol.api.JmolStatusListener;
 import org.jmol.api.JmolViewer;
 import org.jmol.c.CBK;
-import org.jmol.script.T;
 import org.jmol.viewer.Viewer;
 
 public abstract class JalviewJmolBinding extends AAStructureBindingModel
@@ -458,7 +458,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       }
       // System.out.println("Select regions:\n" + selectioncom.toString());
       evalStateCommand("select *; cartoons off; backbone; select ("
-              + selectioncom.toString() + "); cartoons; ");
+              + selectioncom.toString() + "); cartoons; zoom 0");
       // evalStateCommand("select *; backbone; select "+selcom.toString()+";
       // cartoons; center "+selcom.toString());
     }
@@ -485,8 +485,13 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    * @param commands
    */
   @Override
-  protected void colourBySequence(final String[] commands)
+  protected void colourBySequence(AlignmentViewPanel viewPanel)
   {
+    Map<Object, AtomSpecModel> map = StructureCommands.buildColoursMap(this,
+            viewPanel);
+
+    String[] commands = JmolCommands.getColourBySequenceCommand(map);
+
     if (colourby != null)
     {
       colourby.interrupt();
@@ -507,20 +512,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   /**
-   * @param files
-   * @param viewPanel
-   * @return
-   */
-  @Override
-  protected String[] getColourBySequenceCommands(
-          String[] files, AlignmentViewPanel viewPanel)
-  {
-    Map<Object, AtomSpecModel> map = buildColoursMap(viewPanel);
-
-    return JmolCommands.getColourBySequenceCommand(map);
-  }
-
-  /**
    * @param command
    */
   protected void executeWhenReady(String command)
@@ -566,19 +557,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     return null;
   }
 
-  public Color getColour(int atomIndex, int pdbResNum, String chain,
-          String pdbfile)
-  {
-    if (getModelNum(pdbfile) < 0)
-    {
-      return null;
-    }
-    // TODO: verify atomIndex is selecting correct model.
-    // return new Color(viewer.getAtomArgb(atomIndex)); Jmol 12.2.4
-    int colour = viewer.ms.at[atomIndex].atomPropertyInt(T.color);
-    return new Color(colour);
-  }
-
   /**
    * instruct the Jalview binding to update the pdbentries vector if necessary
    * prior to matching the jmol view's contents to the list of structure files
@@ -613,7 +591,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   @Override
   public synchronized String[] getStructureFiles()
   {
-    List<String> mset = new ArrayList<>();
     if (viewer == null)
     {
       return new String[0];
@@ -621,6 +598,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
     if (modelFileNames == null)
     {
+      List<String> mset = new ArrayList<>();
       int modelCount = viewer.ms.mc;
       String filePath = null;
       for (int i = 0; i < modelCount; ++i)
@@ -1430,21 +1408,19 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   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);
+      cmd.append("hide *;display ").append(atomSpec)
+              .append("; select displayed");
     }
     else
     {
-      cmd.append("display *");
+      cmd.append(";display *");
     }
-    cmd.append("; cartoon");
+    cmd.append("; cartoon only");
     if (refocus)
     {
       cmd.append("; zoom 0");
@@ -1461,4 +1437,23 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   {
     return String.valueOf(model + 1) + ".1";
   }
+
+  /**
+   * Sends a command to recentre the display
+   */
+  @Override
+  public void focusView()
+  {
+    /*
+     * don't use evalStateCommand because it ignores a command that is the same
+     * as the last command (why?); but user may have adjusted the display since
+     */
+    viewer.evalString("zoom 0");
+  }
+
+  @Override
+  public int getModelForPdbFile(String fileName, int fileIndex)
+  {
+    return fileIndex;
+  }
 }