X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fext%2Fedu%2Fucsf%2Frbvi%2Fstrucviz2%2FStructureManager.java;h=22c90987ba76200dc5d2263f2eeea24e63d16e44;hb=87018985bd993952fd848fd6b6a57d1a50aef484;hp=4797b374f609400e201b7cf67231b6e88ae6dcb9;hpb=e8479b912a9f5caf2e86d2dee10f153955522e33;p=jalview.git

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
index 4797b37..22c9098 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();
@@ -89,8 +121,8 @@ public class StructureManager
       for (String chimObjName : names)
       {
         // get or open the corresponding models if they already exist
-        List<ChimeraModel> currentModels = chimeraManager.getChimeraModels(
-                chimObjName, type);
+        List<ChimeraModel> currentModels = chimeraManager
+                .getChimeraModels(chimObjName, type);
         if (currentModels.size() == 0)
         {
           // open and return models
@@ -530,11 +562,11 @@ public class StructureManager
         // Get the corresponding "real" model
         if (chimeraManager.hasChimeraModel(modelNumber, subModelNumber))
         {
-          ChimeraModel dataModel = chimeraManager.getChimeraModel(
-                  modelNumber, subModelNumber);
-          if (dataModel.getResidueCount() == selectedModel
-                  .getResidueCount()
-                  || dataModel.getModelType() == StructureManager.ModelType.SMILES)
+          ChimeraModel dataModel = chimeraManager
+                  .getChimeraModel(modelNumber, subModelNumber);
+          if (dataModel.getResidueCount() == selectedModel.getResidueCount()
+                  || dataModel
+                          .getModelType() == StructureManager.ModelType.SMILES)
           {
             // Select the entire model
             addChimSelection(dataModel);
@@ -544,8 +576,8 @@ public class StructureManager
           {
             for (ChimeraChain selectedChain : selectedModel.getChains())
             {
-              ChimeraChain dataChain = dataModel.getChain(selectedChain
-                      .getChainId());
+              ChimeraChain dataChain = dataModel
+                      .getChain(selectedChain.getChainId());
               if (selectedChain.getResidueCount() == dataChain
                       .getResidueCount())
               {
@@ -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;
@@ -866,7 +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
@@ -899,11 +931,22 @@ public class StructureManager
       pathList.add("/usr/local/chimera/bin/chimera");
       pathList.add("/usr/local/bin/chimera");
       pathList.add("/usr/bin/chimera");
+      pathList.add(System.getProperty("user.home") + "/opt/bin/chimera");
     }
     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"))
     {