JAL-3390 unit tests and command and menu refinements

[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 09f3876..d5a0347 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -39,7 +39,6 @@ import org.jmol.api.JmolViewer;
 import org.jmol.c.CBK;
 import org.jmol.viewer.Viewer;
 
-import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
@@ -51,7 +50,6 @@ import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
 import jalview.structure.AtomSpec;
-import jalview.structure.AtomSpecModel;
 import jalview.structure.StructureCommand;
 import jalview.structure.StructureCommandI;
 import jalview.structure.StructureSelectionManager;
@@ -1000,75 +998,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     showConsole(false);
   }
 
-  @Override
-  public void showStructures(AlignViewportI av, boolean refocus)
-  {
-    String cmd = buildShowStructuresCommand(av, refocus);
-    executeCommand(new StructureCommand(cmd), false);
-  }
-
-  /**
-   * Builds a command to show parts of the structure, depending on whether
-   * <ul>
-   * <li>all structures or regions mapped to alignment only are shown</li>
-   * <li>all chains or only selected chains are shown</li>
-   * </ul>
-   * 
-   * @param av
-   * @param refocus
-   * @return
-   */
-  protected String buildShowStructuresCommand(AlignViewportI av,
-          boolean refocus)
-  {
-    StringBuilder cmd = new StringBuilder(128);
-    if (!isShowAlignmentOnly())
-    {
-      cmd.append("display *");
-    }
-    else
-    {
-      AtomSpecModel model = getShownResidues(av);
-      String atomSpec = getCommandGenerator().getAtomSpec(model, false);
-
-      cmd.append("hide *;display ").append(atomSpec)
-              .append("; select displayed");
-    }
-
-    /*
-     * hide any chains not selected to be shown
-     */
-    if (!chainsToHide.isEmpty())
-    {
-      cmd.append("; hide add ");
-      boolean firstHide = true;
-      for (String pdbChain : chainsToHide)
-      {
-        String[] toks = pdbChain.split(":");
-        String chainId = toks[1];
-        String modelNo = getModelIdForFile(getFileForChain(pdbChain));
-        if ("".equals(modelNo))
-        {
-          continue;
-        }
-        if (!firstHide)
-        {
-          cmd.append(",");
-        }
-        firstHide = false;
-        cmd.append(":").append(chainId).append("/")
-                .append(String.valueOf(modelNo)).append(".1");
-      }
-    }
-
-    cmd.append("; cartoon only");
-    if (refocus)
-    {
-      cmd.append("; zoom 0");
-    }
-    return 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.