X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fext%2Fedu%2Fucsf%2Frbvi%2Fstrucviz2%2FStructureManager.java;h=09a971365e03d73bd9faea1742dfb0efd06ac7c3;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=12086382b08a108da35911045dff6c821b9b0fa7;hpb=739296345a62ffba3edcd23c1213d60db89e7c7e;p=jalview.git

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
index 1208638..09a9713 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.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.bin.Cache;
@@ -24,15 +56,15 @@ import org.slf4j.LoggerFactory;
 
 public class StructureManager
 {
-  static final String[] defaultStructureKeys =
-  { "Structure", "pdb", "pdbFileName", "PDB ID", "structure",
-      "biopax.xref.PDB", "pdb_ids", "ModelName", "ModelNumber" };
+  static final String[] defaultStructureKeys = { "Structure", "pdb",
+      "pdbFileName", "PDB ID", "structure", "biopax.xref.PDB", "pdb_ids",
+      "ModelName", "ModelNumber" };
 
-  static final String[] defaultChemStructKeys =
-  { "Smiles", "smiles", "SMILES" };
+  static final String[] defaultChemStructKeys = { "Smiles", "smiles",
+      "SMILES" };
 
-  static final String[] defaultResidueKeys =
-  { "FunctionalResidues", "ResidueList", "Residues" };
+  static final String[] defaultResidueKeys = { "FunctionalResidues",
+      "ResidueList", "Residues" };
 
   public enum ModelType
   {
@@ -65,7 +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();
   }
 
@@ -78,7 +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();
@@ -814,7 +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)
@@ -855,7 +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;
@@ -864,22 +896,24 @@ public class StructureManager
   StructureSettings defaultSettings = null;
 
   // TODO: [Optional] Change priority of Chimera paths
-  public List<String> getChimeraPaths()
+  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
     // path to chimera
-    if (defaultSettings != null)
-    {
-      String defaultPath = defaultSettings.getChimeraPath();
-      if (defaultPath != null && !defaultPath.equals(""))
-      {
-        pathList.add(defaultPath);
-        return pathList;
-      }
-    }
+    //
+    // For Jalview, Preferences/Cache plays this role instead
+    // if (defaultSettings != null)
+    // {
+    // String defaultPath = defaultSettings.getChimeraPath();
+    // if (defaultPath != null && !defaultPath.equals(""))
+    // {
+    // pathList.add(defaultPath);
+    // return pathList;
+    // }
+    // }
 
     /*
      * Jalview addition: check if path set in user preferences.
@@ -887,7 +921,7 @@ public class StructureManager
     String userPath = Cache.getDefault(Preferences.CHIMERA_PATH, null);
     if (userPath != null)
     {
-      pathList.add(userPath);
+      pathList.add(0, userPath);
     }
 
     // Add default installation paths
@@ -900,8 +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", "1.12.1", "1.12.2", "1.13" })
+        {
+          pathList.add(root + "\\Chimera " + version + "\\bin\\chimera");
+          pathList.add(
+                  root + "\\Chimera " + version + "\\bin\\chimera.exe");
+        }
+      }
     }
     else if (os.startsWith("Mac"))
     {