X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fext%2Fedu%2Fucsf%2Frbvi%2Fstrucviz2%2FChimeraManager.java;h=668039bb55da8d604f53f7225218657b0c563984;hb=HEAD;hp=812bfea63fe5ed739cde0e2ff7730ea628abccc5;hpb=882a6c7044693a72c20f336f26e87a5fcf30fe5b;p=jalview.git

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
index 812bfea..668039b 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
@@ -366,7 +366,7 @@ public class ChimeraManager
    * Select something in Chimera
    * 
    * @param command
-   *                  the selection command to pass to Chimera
+   *          the selection command to pass to Chimera
    */
   public void select(String command)
   {
@@ -512,8 +512,8 @@ public class ChimeraManager
 
   /**
    * Return the list of depiction presets available from within Chimera. Chimera
-   * will return the list as a series of lines with the format: Preset type number
-   * "description"
+   * will return the list as a series of lines with the format: Preset type
+   * number "description"
    * 
    * @return list of presets
    */
@@ -554,9 +554,9 @@ public class ChimeraManager
   }
 
   /**
-   * Launch Chimera, unless an instance linked to this object is already running.
-   * Returns true if chimera is successfully launched, or already running, else
-   * false.
+   * Launch Chimera, unless an instance linked to this object is already
+   * running. Returns true if chimera is successfully launched, or already
+   * running, else false.
    * 
    * @param chimeraPaths
    * @return
@@ -699,7 +699,7 @@ public class ChimeraManager
    * Determine the color that Chimera is using for this model.
    * 
    * @param model
-   *                the ChimeraModel we want to get the Color for
+   *          the ChimeraModel we want to get the Color for
    * @return the default model Color for this model in Chimera
    */
   public Color getModelColor(ChimeraModel model)
@@ -716,11 +716,11 @@ public class ChimeraManager
   /**
    * 
    * Get information about the residues associated with a model. This uses the
-   * Chimera listr command. We don't return the resulting residues, but we add the
-   * residues to the model.
+   * Chimera listr command. We don't return the resulting residues, but we add
+   * the residues to the model.
    * 
    * @param model
-   *                the ChimeraModel to get residue information for
+   *          the ChimeraModel to get residue information for
    * 
    */
   public void addResidues(ChimeraModel model)
@@ -812,10 +812,10 @@ public class ChimeraManager
    * Send a command to Chimera.
    * 
    * @param command
-   *                  Command string to be send.
+   *          Command string to be send.
    * @param reply
-   *                  Flag indicating whether the method should return the reply
-   *                  from Chimera or not.
+   *          Flag indicating whether the method should return the reply from
+   *          Chimera or not.
    * @return List of Strings corresponding to the lines in the Chimera reply or
    *         <code>null</code>.
    */
@@ -881,8 +881,7 @@ public class ChimeraManager
     {
       try
       {
-        command = URLEncoder.encode(command,
-                StandardCharsets.UTF_8.toString());
+        command = URLEncoder.encode(command, StandardCharsets.UTF_8.name());
       } catch (UnsupportedEncodingException e)
       {
         command = command.replace(" ", "+").replace("#", "%23")