From a4be3ff77b3f97c6dd124a73c89e293f6105709b Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 25 May 2018 09:13:00 +0100
Subject: [PATCH] JAL-2994 temporary patch with paths to Chimera for Windows

---
 .../edu/ucsf/rbvi/strucviz2/StructureManager.java  |   24 ++++++++++++++------
 1 file changed, 17 insertions(+), 7 deletions(-)

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
index effe556..bf58705 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
@@ -97,7 +97,7 @@ public class StructureManager
     this.haveGUI = haveGUI;
     // Create the Chimera interface
     chimeraManager = new ChimeraManager(this);
-    chimSelectionList = new ArrayList<ChimeraStructuralObject>();
+    chimSelectionList = new ArrayList<>();
     pathProps = new Properties();
   }
 
@@ -110,7 +110,7 @@ public class StructureManager
           ModelType type)
   {
     // new models
-    Map<String, List<ChimeraModel>> newModels = new HashMap<String, List<ChimeraModel>>();
+    Map<String, List<ChimeraModel>> newModels = new HashMap<>();
     if (chimObjNames.size() > 0)
     {
       List<String> names = chimObjNames.iterator().next();
@@ -846,7 +846,7 @@ public class StructureManager
     // alDialog.dispose();
     // }
     // System.out.println("launch align dialog");
-    List<ChimeraStructuralObject> chimObjectList = new ArrayList<ChimeraStructuralObject>();
+    List<ChimeraStructuralObject> chimObjectList = new ArrayList<>();
     for (ChimeraModel model : chimeraManager.getChimeraModels())
     {
       if (useChains)
@@ -887,7 +887,7 @@ public class StructureManager
 
   public List<String> getAllChimeraResidueAttributes()
   {
-    List<String> attributes = new ArrayList<String>();
+    List<String> attributes = new ArrayList<>();
     // attributes.addAll(rinManager.getResAttrs());
     attributes.addAll(chimeraManager.getAttrList());
     return attributes;
@@ -898,7 +898,7 @@ public class StructureManager
   // TODO: [Optional] Change priority of Chimera paths
   public static List<String> getChimeraPaths()
   {
-    List<String> pathList = new ArrayList<String>();
+    List<String> pathList = new ArrayList<>();
 
     // if no network is available and the settings have been modified by the
     // user, check for a
@@ -934,8 +934,18 @@ public class StructureManager
     }
     else if (os.startsWith("Windows"))
     {
-      pathList.add("\\Program Files\\Chimera\\bin\\chimera");
-      pathList.add("C:\\Program Files\\Chimera\\bin\\chimera.exe");
+      for (String root : new String[] { "\\Program Files",
+          "C:\\Program Files", "\\Program Files (x86)",
+          "C:\\Program Files (x86)" })
+      {
+        for (String version : new String[] { "1.11", "1.11.1", "1.11.2",
+            "1.12", "1.13" })
+        {
+          pathList.add(root + "\\Chimera " + version + "\\bin\\chimera");
+          pathList.add(
+                  root + "\\Chimera " + version + "\\bin\\chimera.exe");
+        }
+      }
     }
     else if (os.startsWith("Mac"))
     {
-- 
1.7.10.2