Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

[jalview.git] / src / ext / edu / ucsf / rbvi / strucviz2 / ChimeraManager.java

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
index fdcf34f..85ae718 100644 (file)
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
@@ -1,3 +1,35 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2006 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ *   1. Redistributions of source code must retain the above copyright
+ *      notice, this list of conditions, and the following disclaimer.
+ *   2. Redistributions in binary form must reproduce the above
+ *      copyright notice, this list of conditions, and the following
+ *      disclaimer in the documentation and/or other materials provided
+ *      with the distribution.
+ *   3. Redistributions must acknowledge that this software was
+ *      originally developed by the UCSF Computer Graphics Laboratory
+ *      under support by the NIH National Center for Research Resources,
+ *      grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
 package ext.edu.ucsf.rbvi.strucviz2;
 
 import jalview.ws.HttpClientUtils;
@@ -348,6 +380,8 @@ public class ChimeraManager
       sendChimeraCommand("stop really", false);
       try
       {
+        // TODO is this too violent? could it force close the process
+        // before it has done an orderly shutdown?
         chimera.destroy();
       } catch (Exception ex)
       {
@@ -389,6 +423,11 @@ public class ChimeraManager
             "list selection level residue", true);
     if (chimeraReply != null)
     {
+      /*
+       * expect 0, 1 or more lines of the format
+       * residue id #0:43.A type GLY
+       * where we are only interested in the atomspec #0.43.A
+       */
       for (String inputLine : chimeraReply)
       {
         String[] inputLineParts = inputLine.split("\\s+");
@@ -854,4 +893,9 @@ public class ChimeraManager
   {
     return busy;
   }
+
+  public Process getChimeraProcess()
+  {
+    return chimera;
+  }
 }