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

[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 9b8fb91..b6e6a65 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -59,29 +59,19 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 {
   private String lastMessage;
 
-  boolean allChainsSelected = false;
-
   /*
    * when true, try to search the associated datamodel for sequences that are
    * associated with any unknown structures in the Jmol view.
    */
   private boolean associateNewStructs = false;
 
-  Vector<String> atomsPicked = new Vector<>();
-
-  /*
-   * the default or current model displayed if the model cannot be identified
-   * from the selection message
-   */
-  int frameNo = 0;
-
-  // protected JmolGenericPopup jmolpopup; // not used - remove?
+  private Vector<String> atomsPicked = new Vector<>();
 
-  String lastCommand;
+  private String lastCommand;
 
-  boolean loadedInline;
+  private boolean loadedInline;
 
-  StringBuffer resetLastRes = new StringBuffer();
+  private StringBuffer resetLastRes = new StringBuffer();
 
   public Viewer jmolViewer;
 
@@ -135,7 +125,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   /**
    * superpose the structures associated with sequences in the alignment
    * according to their corresponding positions.
+   * 
+   * @deprecated not used - remove?
    */
+  @Deprecated
   public void superposeStructures(AlignmentI alignment)
   {
     superposeStructures(alignment, -1, null);
@@ -148,7 +141,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    * @param refStructure
    *          - select which pdb file to use as reference (default is -1 - the
    *          first structure in the alignment)
+   * @deprecated not used - remove?
    */
+  @Deprecated
   public void superposeStructures(AlignmentI alignment, int refStructure)
   {
     superposeStructures(alignment, refStructure, null);
@@ -163,7 +158,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    *          first structure in the alignment)
    * @param hiddenCols
    *          TODO
+   * @deprecated not used - remove?
    */
+  @Deprecated
   public void superposeStructures(AlignmentI alignment, int refStructure,
           HiddenColumns hiddenCols)
   {
@@ -465,13 +462,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   /**
-   * 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
-   * 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.
@@ -570,9 +560,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     jmolHistory(false);
 
     StringBuilder cmd = new StringBuilder(64);
-    cmd.append("select " + pdbResNum); // +modelNum
+    cmd.append("select ").append(String.valueOf(pdbResNum)); // +modelNum
 
-    resetLastRes.append("select " + pdbResNum); // +modelNum
+    resetLastRes.append("select ").append(String.valueOf(pdbResNum)); // +modelNum
 
     cmd.append(":");
     resetLastRes.append(":");
@@ -582,8 +572,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       resetLastRes.append(chain);
     }
     {
-      cmd.append(" /" + (mdlNum + 1));
-      resetLastRes.append("/" + (mdlNum + 1));
+      cmd.append(" /").append(String.valueOf(mdlNum + 1));
+      resetLastRes.append("/").append(String.valueOf(mdlNum + 1));
     }
     cmd.append(";wireframe 100;" + cmd.toString() + " and not hetero;");
 
@@ -597,7 +587,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   }
 
-  boolean debug = true;
+  private boolean debug = true;
 
   private void jmolHistory(boolean enable)
   {
@@ -658,8 +648,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       chainId = " ";
     }
 
-    String pdbfilename = modelFileNames[frameNo]; // default is first or current
-    // model
+    String pdbfilename = modelFileNames[0]; // default is first model
     if (mdlSep > -1)
     {
       if (chainSeparator1 == -1)
@@ -1117,13 +1106,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   public abstract void showUrl(String url, String target);
 
   /**
-   * called when the binding thinks the UI needs to be refreshed after a Jmol
-   * state change. this could be because structures were loaded, or because an
-   * error has occured.
-   */
-  public abstract void refreshGUI();
-
-  /**
    * called to show or hide the associated console window container.
    * 
    * @param show