JAL-2422 pull up refactoring in preparation for ChimeraX subclasses

[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 d0fa5ef..fc9b445 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -87,7 +87,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   /*
    * Object through which we talk to Chimera
    */
-  private ChimeraManager viewer;
+  private ChimeraManager chimeraManager;
 
   /*
    * Object which listens to Chimera notifications
@@ -138,7 +138,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     try
     {
       List<ChimeraModel> modelsToMap = new ArrayList<>();
-      List<ChimeraModel> oldList = viewer.getModelList();
+      List<ChimeraModel> oldList = chimeraManager.getModelList();
       boolean alreadyOpen = false;
 
       /*
@@ -159,8 +159,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
        */
       if (!alreadyOpen)
       {
-        viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL);
-        if (viewer.isChimeraX())
+        chimeraManager.openModel(file, pe.getId(), ModelType.PDB_MODEL);
+        if (chimeraManager.isChimeraX())
         {
           /*
            * ChimeraX hack: force chimera model name to pdbId
@@ -178,7 +178,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
            * Chimera: query for actual models and find the one with
            * matching model name - set in viewer.openModel()
            */
-          List<ChimeraModel> newList = viewer.getModelList();
+          List<ChimeraModel> newList = chimeraManager.getModelList();
           // JAL-1728 newList.removeAll(oldList) does not work
           for (ChimeraModel cm : newList)
           {
@@ -219,9 +219,9 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
           DataSourceType protocol)
   {
     super(ssm, pdbentry, sequenceIs, protocol);
-    viewer = new ChimeraManager(new StructureManager(true));
+    chimeraManager = new ChimeraManager(new StructureManager(true));
     String viewerType = Cache.getProperty(Preferences.STRUCTURE_DISPLAY);
-    viewer.setChimeraX(ViewerType.CHIMERAX.name().equals(viewerType));
+    chimeraManager.setChimeraX(ViewerType.CHIMERAX.name().equals(viewerType));
 
   }
 
@@ -232,7 +232,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   protected void startChimeraProcessMonitor()
   {
-    final Process p = viewer.getChimeraProcess();
+    final Process p = chimeraManager.getChimeraProcess();
     chimeraMonitor = new Thread(new Runnable()
     {
 
@@ -265,7 +265,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     try
     {
       chimeraListener = new ChimeraListener(this);
-      viewer.startListening(chimeraListener.getUri());
+      chimeraManager.startListening(chimeraListener.getUri());
     } catch (BindException e)
     {
       System.err.println(
@@ -319,14 +319,14 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     getSsm().removeStructureViewerListener(this, this.getStructureFiles());
     if (closeChimera)
     {
-      viewer.exitChimera();
+      chimeraManager.exitChimera();
     }
     if (this.chimeraListener != null)
     {
       chimeraListener.shutdown();
       chimeraListener = null;
     }
-    viewer = null;
+    chimeraManager = null;
 
     if (chimeraMonitor != null)
     {
@@ -355,7 +355,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   public void colourByCharge()
   {
     colourBySequence = false;
-    String command = viewer.isChimeraX()
+    String command = chimeraManager.isChimeraX()
             ? "color white;color :ASP,GLU red;color :LYS,ARG blue;color :CYS yellow"
             : "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS";
     sendAsynchronousCommand(command, COLOURING_CHIMERA);
@@ -378,7 +378,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 
     refreshPdbEntries();
     StringBuilder selectioncom = new StringBuilder(256);
-    boolean chimeraX = viewer.isChimeraX();
+    boolean chimeraX = chimeraManager.isChimeraX();
     for (int a = 0; a < _alignment.length; a++)
     {
       int refStructure = _refStructure[a];
@@ -676,13 +676,13 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   public boolean launchChimera()
   {
-    if (viewer.isChimeraLaunched())
+    if (chimeraManager.isChimeraLaunched())
     {
       return true;
     }
 
-    boolean launched = viewer.launchChimera(
-            StructureManager.getChimeraPaths(viewer.isChimeraX()));
+    boolean launched = chimeraManager.launchChimera(
+            StructureManager.getChimeraPaths(chimeraManager.isChimeraX()));
     if (launched)
     {
       startChimeraProcessMonitor();
@@ -702,7 +702,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   public boolean isChimeraRunning()
   {
-    return viewer.isChimeraLaunched();
+    return chimeraManager.isChimeraLaunched();
   }
 
   /**
@@ -717,7 +717,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   public List<String> sendChimeraCommand(final String command,
           boolean getResponse)
   {
-    if (viewer == null)
+    if (chimeraManager == null)
     {
       // ? thread running after viewer shut down
       return null;
@@ -727,7 +727,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     if (true /*lastCommand == null || !lastCommand.equals(command)*/)
     {
       // trim command or it may never find a match in the replyLog!!
-      List<String> lastReply = viewer.sendChimeraCommand(command.trim(),
+      List<String> lastReply = chimeraManager.sendChimeraCommand(command.trim(),
               getResponse);
       if (getResponse)
       {
@@ -783,7 +783,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
           String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
   {
     return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
-            getSequence(), sr, viewPanel, viewer.isChimeraX());
+            getSequence(), sr, viewPanel, chimeraManager.isChimeraX());
   }
 
   /**
@@ -798,7 +798,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 
   private void waitForChimera()
   {
-    while (viewer != null && viewer.isBusy())
+    while (chimeraManager != null && chimeraManager.isBusy())
     {
       try
       {
@@ -831,7 +831,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   @Override
   public synchronized String[] getStructureFiles()
   {
-    if (viewer == null)
+    if (chimeraManager == null)
     {
       return new String[0];
     }
@@ -852,7 +852,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       return;
     }
 
-    boolean forChimeraX = viewer.isChimeraX();
+    boolean forChimeraX = chimeraManager.isChimeraX();
     StringBuilder cmd = new StringBuilder(128);
     boolean first = true;
     boolean found = false;
@@ -906,11 +906,11 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
      */
     if (lastHighlightCommand != null)
     {
-      viewer.sendChimeraCommand("~" + lastHighlightCommand, false);
+      chimeraManager.sendChimeraCommand("~" + lastHighlightCommand, false);
     }
     if (found)
     {
-      viewer.sendChimeraCommand(command, false);
+      chimeraManager.sendChimeraCommand(command, false);
     }
     this.lastHighlightCommand = command;
   }
@@ -923,7 +923,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     /*
      * Ask Chimera for its current selection
      */
-    List<String> selection = viewer.getSelectedResidueSpecs();
+    List<String> selection = chimeraManager.getSelectedResidueSpecs();
 
     /*
      * Parse model number, residue and chain for each selected position,
@@ -949,7 +949,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   protected List<AtomSpec> convertStructureResiduesToAlignment(
           List<String> structureSelection)
   {
-    boolean chimeraX = viewer.isChimeraX();
+    boolean chimeraX = chimeraManager.isChimeraX();
     List<AtomSpec> atomSpecs = new ArrayList<>();
     for (String atomSpec : structureSelection)
     {
@@ -1028,7 +1028,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
      * Chimera format:  color colorCode ::VAL
      * ChimeraX format: color :VAL colourCode
      */
-    boolean chimeraX = viewer.isChimeraX();
+    boolean chimeraX = chimeraManager.isChimeraX();
     for (String resName : residueSet)
     {
       char res = resName.length() == 3
@@ -1101,7 +1101,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   {
     viewerCommandHistory(false);
     String command = "set bgColor " + ColorUtils.toTkCode(col);
-    viewer.sendChimeraCommand(command, false);
+    chimeraManager.sendChimeraCommand(command, false);
     viewerCommandHistory(true);
   }
 
@@ -1121,7 +1121,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
        * ChimeraX: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html
        */
       String command = isChimeraX() ? "save session " : "save ";
-      List<String> reply = viewer.sendChimeraCommand(command + filepath,
+      List<String> reply = chimeraManager.sendChimeraCommand(command + filepath,
               true);
       if (reply.contains("Session written"))
       {
@@ -1172,7 +1172,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   public void focusView()
   {
-    sendChimeraCommand(viewer.isChimeraX() ? "view" : "focus", false);
+    sendChimeraCommand(chimeraManager.isChimeraX() ? "view" : "focus", false);
   }
 
   /**
@@ -1223,7 +1223,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 
     StructureMappingcommandSet commandSet = ChimeraCommands
             .getSetAttributeCommandsForFeatures(getSsm(), files,
-                    getSequence(), avp, viewer.isChimeraX());
+                    getSequence(), avp, chimeraManager.isChimeraX());
     String[] commands = commandSet.commands;
     if (commands.length > 10)
     {
@@ -1248,7 +1248,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   protected void sendCommandsByFile(String[] commands)
   {
-    boolean toChimeraX = viewer.isChimeraX();
+    boolean toChimeraX = chimeraManager.isChimeraX();
     try
     {
       File tmp = File.createTempFile("chim", toChimeraX ? ".cxc" : ".com");
@@ -1320,7 +1320,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   {
     boolean featureAdded = false;
     String featureGroup = getViewerFeatureGroup();
-    boolean chimeraX = viewer.isChimeraX();
+    boolean chimeraX = chimeraManager.isChimeraX();
 
     for (String residue : residues)
     {
@@ -1433,7 +1433,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   public List<String> getChimeraAttributes()
   {
-    List<String> atts = viewer.getAttrList();
+    List<String> atts = chimeraManager.getAttrList();
     Iterator<String> it = atts.iterator();
     while (it.hasNext())
     {
@@ -1450,6 +1450,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 
   public boolean isChimeraX()
   {
-    return viewer.isChimeraX();
+    return chimeraManager.isChimeraX();
   }
 }