JAL-2422 general pull-up/removal of common or unused fields and methods

[jalview.git] / src / jalview / ext / rbvi / chimera / JalviewChimeraBinding.java

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index d7bcc66..0192993 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -82,32 +82,12 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   private AbstractRequestHandler chimeraListener;
 
   /*
-   * set if chimera state is being restored from some source - instructs binding
-   * not to apply default display style when structure set is updated for first
-   * time.
-   */
-  private boolean loadingFromArchive = false;
-
-  /*
-   * flag to indicate if the Chimera viewer should ignore sequence colouring
-   * events from the structure manager because the GUI is still setting up
-   */
-  private boolean loadingFinished = true;
-
-  /*
    * Map of ChimeraModel objects keyed by PDB full local file name
    */
   private Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<>();
 
   String lastHighlightCommand;
 
-  /*
-   * incremented every time a load notification is successfully handled -
-   * lightweight mechanism for other threads to detect when they can start
-   * referring to new structures.
-   */
-  private long loadNotifiesHandled = 0;
-
   private Thread chimeraMonitor;
 
   /**
@@ -631,9 +611,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 
   /**
    * Send a command to Chimera, and optionally log and return any responses.
-   * <p>
-   * Does nothing, and returns null, if the command is the same as the last one
-   * sent [why?].
    * 
    * @param command
    * @param getResponse
@@ -648,23 +625,17 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       return null;
     }
     List<String> reply = null;
-    viewerCommandHistory(false);
-    if (true /*lastCommand == null || !lastCommand.equals(command)*/)
+    // trim command or it may never find a match in the replyLog!!
+    List<String> lastReply = chimeraManager
+            .sendChimeraCommand(command.trim(), getResponse);
+    if (getResponse)
     {
-      // trim command or it may never find a match in the replyLog!!
-      List<String> lastReply = chimeraManager.sendChimeraCommand(command.trim(),
-              getResponse);
-      if (getResponse)
+      reply = lastReply;
+      if (debug)
       {
-        reply = lastReply;
-        if (debug)
-        {
-          log("Response from command ('" + command + "') was:\n"
-                  + lastReply);
-        }
+        log("Response from command ('" + command + "') was:\n" + lastReply);
       }
     }
-    viewerCommandHistory(true);
 
     return reply;
   }
@@ -706,13 +677,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   // //////////////////////////
 
   /**
-   * instruct the Jalview binding to update the pdbentries vector if necessary
-   * prior to matching the viewer's contents to the list of structure files
-   * Jalview knows about.
-   */
-  public abstract void refreshPdbEntries();
-
-  /**
    * map between index of model filename returned from getPdbFile and the first
    * index of models from this file in the viewer. Note - this is not trimmed -
    * use getPdbFile to get number of unique models.
@@ -889,53 +853,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     System.err.println("## Chimera log: " + message);
   }
 
-  private void viewerCommandHistory(boolean enable)
-  {
-    // log("(Not yet implemented) History "
-    // + ((debug || enable) ? "on" : "off"));
-  }
-
-  public long getLoadNotifiesHandled()
-  {
-    return loadNotifiesHandled;
-  }
-
-  /**
-   * called when the binding thinks the UI needs to be refreshed after a Chimera
-   * state change. this could be because structures were loaded, or because an
-   * error has occurred.
-   */
-  public abstract void refreshGUI();
-
-  @Override
-  public void setLoadingFromArchive(boolean loadingFromArchive)
-  {
-    this.loadingFromArchive = loadingFromArchive;
-  }
-
-  /**
-   * 
-   * @return true if Chimeral is still restoring state or loading is still going
-   *         on (see setFinsihedLoadingFromArchive)
-   */
-  @Override
-  public boolean isLoadingFromArchive()
-  {
-    return loadingFromArchive && !loadingFinished;
-  }
-
-  /**
-   * modify flag which controls if sequence colouring events are honoured by the
-   * binding. Should be true for normal operation
-   * 
-   * @param finishedLoading
-   */
-  @Override
-  public void setFinishedLoadingFromArchive(boolean finishedLoading)
-  {
-    loadingFinished = finishedLoading;
-  }
-
   /**
    * Ask Chimera to save its session to the given file. Returns true if
    * successful, else false.