Merge branch 'develop' (JAL-4102 2.11.2.6 patch release) into features/r2_11_2_alphaf...

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

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index 6d4caa2..829f092 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@ -20,19 +20,17 @@
  */
 package jalview.ext.rbvi.chimera;
 
-import java.util.Locale;
-
 import java.awt.Color;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 
 import jalview.structure.AtomSpecModel;
 import jalview.structure.StructureCommand;
 import jalview.structure.StructureCommandI;
 import jalview.structure.StructureCommandsBase;
-import jalview.structure.StructureCommandsI.AtomSpecType;
 import jalview.util.ColorUtils;
 
 /**
@@ -44,21 +42,27 @@ import jalview.util.ColorUtils;
 public class ChimeraCommands extends StructureCommandsBase
 {
   // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/focus.html
-  private static final StructureCommand FOCUS_VIEW = new StructureCommand("focus");
+  private static final StructureCommand FOCUS_VIEW = new StructureCommand(
+          "focus");
 
   // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listresattr
-  private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand("list resattr");
+  private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand(
+          "list resattr");
 
   // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/stop.html
-  private static final StructureCommand CLOSE_CHIMERA = new StructureCommand("stop really");
+  private static final StructureCommand CLOSE_CHIMERA = new StructureCommand(
+          "stop really");
 
   // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
-  private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand("listen stop selection");
+  private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand(
+          "listen stop selection");
 
-  private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand("listen stop models");
+  private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand(
+          "listen stop models");
 
   // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listselection
-  private static final StructureCommand GET_SELECTION = new StructureCommand("list selection level residue");
+  private static final StructureCommand GET_SELECTION = new StructureCommand(
+          "list selection level residue");
 
   private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
           "~display all;~ribbon;chain @CA|P");
@@ -156,8 +160,7 @@ public class ChimeraCommands extends StructureCommandsBase
    * @return
    */
   protected StructureCommandI setAttribute(String attributeName,
-          String attributeValue,
-          AtomSpecModel atomSpecModel)
+          String attributeValue, AtomSpecModel atomSpecModel)
   {
     StringBuilder sb = new StringBuilder(128);
     sb.append("setattr res ").append(attributeName).append(" '")
@@ -273,7 +276,8 @@ public class ChimeraCommands extends StructureCommandsBase
     StringBuilder cmd = new StringBuilder();
     String atomSpecAlphaOnly = getAtomSpec(spec, backbone);
     String refSpecAlphaOnly = getAtomSpec(ref, backbone);
-    cmd.append("match ").append(atomSpecAlphaOnly).append(" ").append(refSpecAlphaOnly);
+    cmd.append("match ").append(atomSpecAlphaOnly).append(" ")
+            .append(refSpecAlphaOnly);
 
     /*
      * show superposed residues as ribbon
@@ -414,7 +418,8 @@ public class ChimeraCommands extends StructureCommandsBase
     // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
     List<StructureCommandI> cmds = new ArrayList<>();
     cmds.add(new StructureCommand("listen start models url " + uri));
-    cmds.add(new StructureCommand("listen start select prefix SelectionChanged url " + uri));
+    cmds.add(new StructureCommand(
+            "listen start select prefix SelectionChanged url " + uri));
     return cmds;
   }
 
@@ -449,4 +454,11 @@ public class ChimeraCommands extends StructureCommandsBase
     return new StructureCommand("list residues attr '" + attName + "'");
   }
 
+  @Override
+  public List<StructureCommandI> centerViewOn(List<AtomSpecModel> residues)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
 }