JAL-4485 Initially look for all installations of Chimera/X and add to the pathlist...

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
index 85d0def..b83333c 100644 (file)
--- a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
@@ -38,6 +38,7 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Locale;
 import java.util.Map;
@@ -49,6 +50,8 @@ import org.slf4j.LoggerFactory;
 
 import jalview.bin.Cache;
 import jalview.gui.Preferences;
+import jalview.util.FileUtils;
+import jalview.util.Platform;
 
 /**
  * This object maintains the relationship between Chimera objects and Cytoscape
@@ -75,11 +78,16 @@ public class StructureManager
       "1.13.1", "1.13", "1.12.2", "1.12.1", "1.12", "1.11.2", "1.11.2",
       "1.11.1", "1.11" };
 
+  private static String[] CHIMERA_VERSIONS_BLACKLIST = new String[] {};
+
   // Missing 1.1 as this has known bug see JAL-2422
   private static String[] CHIMERAX_VERSIONS = new String[] { "1.7", "1.6.1",
       "1.6", "1.5", "1.4", "1.3", "1.2.5", "1.0", "0.93", "0.92", "0.91",
       "0.9" };
 
+  private static String[] CHIMERAX_VERSIONS_BLACKLIST = new String[] {
+      "1.1" };
+
   static final String[] defaultStructureKeys = { "Structure", "pdb",
       "pdbFileName", "PDB ID", "structure", "biopax.xref.PDB", "pdb_ids",
       "ModelName", "ModelNumber" };
@@ -939,7 +947,6 @@ public class StructureManager
     // }
     // }
 
-    String os = System.getProperty("os.name");
     String userPath = Cache
             .getDefault(isChimeraX ? Preferences.CHIMERAX_PATH
                     : Preferences.CHIMERA_PATH, null);
@@ -953,6 +960,8 @@ public class StructureManager
      */
     String chimera = isChimeraX ? "ChimeraX" : "Chimera";
     String chimeraExe = isChimeraX ? "ChimeraX" : "chimera";
+    String[] versionsBlacklist = isChimeraX ? CHIMERAX_VERSIONS_BLACKLIST
+            : CHIMERA_VERSIONS_BLACKLIST;
 
     /*
      * Jalview addition: check if path set in user preferences
@@ -961,7 +970,7 @@ public class StructureManager
     {
       // in macos, deal with the user selecting the .app folder
       boolean adjusted = false;
-      if (os.startsWith("Mac") && userPath.endsWith((".app")))
+      if (Platform.isMac() && userPath.endsWith((".app")))
       {
         String possiblePath = String.format("%s/Contents/MacOS/%s",
                 userPath, chimeraExe);
@@ -978,7 +987,7 @@ public class StructureManager
     }
 
     // Add default installation paths
-    if (os.startsWith("Linux"))
+    if (Platform.isLinux())
     {
       // ChimeraX .deb and .rpm packages put symbolic link from
       // /usr/bin/chimerax
@@ -1015,13 +1024,51 @@ public class StructureManager
       pathList.add(String.format("%s/local/bin/%s",
               System.getProperty("user.home"), chimeraExe));
     }
-    else if (os.startsWith("Windows"))
+    else if (Platform.isWin())
     {
-      for (String root : new String[] { "\\Program Files",
+      Set<File> installedChimera = new HashSet<>();
+      String[] templates = new String[] { "%s\\%s %s\\bin\\%s" };
+      String[] roots = new String[] { "\\Program Files",
           "C:\\Program Files", "\\Program Files (x86)",
           "C:\\Program Files (x86)", String.format("%s\\AppData\\Local",
-                  System.getProperty("user.home")) })
+                  System.getProperty("user.home")) };
+      for (String root : roots)
       {
+        for (String template : templates)
+        {
+          String globMatch = String.format(template, root, chimera, "*",
+                  chimeraExe);
+          List<File> foundInstalls = FileUtils.getFilesFromGlob(globMatch,
+                  false);
+          for (File found : foundInstalls)
+          {
+            boolean add = true;
+            for (String notVersion : versionsBlacklist)
+            {
+              if (String.format(template, root, chimera, notVersion,
+                      chimeraExe).equals(found.getPath()))
+              {
+                add = false;
+                break;
+              }
+            }
+            if (add)
+            {
+              installedChimera.add(found);
+            }
+          }
+        }
+        // try without a version number too
+        String nonVersioned = String.format("%s\\%s\\bin\\%s", root,
+                chimera, chimeraExe);
+        installedChimera
+                .addAll(FileUtils.getFilesFromGlob(nonVersioned, false));
+
+        for (File file : installedChimera)
+        {
+          pathList.add(file.getPath());
+        }
+
         String[] candidates = isChimeraX ? CHIMERAX_VERSIONS
                 : CHIMERA_VERSIONS;
         for (String version : candidates)
@@ -1039,25 +1086,65 @@ public class StructureManager
         pathList.add(path + ".exe");
       }
     }
-    else if (os.startsWith("Mac"))
+    else if (Platform.isMac())
     {
-      // check for installations with version numbers first
-      String[] candidates = isChimeraX ? CHIMERAX_VERSIONS
-              : CHIMERA_VERSIONS;
-      for (String version : candidates)
+      Set<File> installedChimera = new HashSet<>();
+      String[] templates = new String[] {
+          "%s/%s-%s.app/Contents/MacOS/%s" };
+      String[] roots = new String[] { "/Application", String
+              .format("%s/Application", System.getProperty("user.home")) };
+      for (String root : roots)
       {
-        pathList.add(
-                String.format("/Applications/%s-%s.app/Contents/MacOS/%s",
-                        chimera, version, chimeraExe));
-        pathList.add(
-                String.format("%s/Applications/%s-%s.app/Contents/MacOS/%s",
-                        System.getProperty("user.home"), chimera, version,
-                        chimeraExe));
+        for (String template : templates)
+        {
+          String globMatch = String.format(template, root, chimera, "*",
+                  chimeraExe);
+          List<File> foundInstalls = FileUtils.getFilesFromGlob(globMatch,
+                  false);
+          for (File found : foundInstalls)
+          {
+            boolean add = true;
+            for (String notVersion : versionsBlacklist)
+            {
+              if (String.format(template, root, chimera, notVersion,
+                      chimeraExe).equals(found.getPath()))
+              {
+                add = false;
+                break;
+              }
+            }
+            if (add)
+            {
+              installedChimera.add(found);
+            }
+          }
+        }
+        // try without a version number too
+        String nonVersioned = String.format("%s/%s.app/Contents/MacOS/%s",
+                root, chimera, chimeraExe);
+        installedChimera
+                .addAll(FileUtils.getFilesFromGlob(nonVersioned, false));
+
+        for (File file : installedChimera)
+        {
+          pathList.add(file.getPath());
+        }
+
+        // check for installations with version numbers first
+        String[] candidates = isChimeraX ? CHIMERAX_VERSIONS
+                : CHIMERA_VERSIONS;
+        for (String version : candidates)
+        {
+
+          for (String template : templates)
+          {
+            pathList.add(String.format(template, root, chimera, version,
+                    chimeraExe));
+          }
+        }
+        pathList.add(String.format("%s/%s.app/Contents/MacOS/%s", root,
+                chimera, chimeraExe));
       }
-      pathList.add(String.format("/Applications/%s.app/Contents/MacOS/%s",
-              chimera, chimeraExe));
-      pathList.add(String.format("%s/Applications/%s.app/Contents/MacOS/%s",
-              System.getProperty("user.home"), chimera, chimeraExe));
     }
     return pathList;
   }

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 883d270..84dff9c 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -1046,6 +1046,7 @@ public class Preferences extends GPreferences
     Cache.enableSessionProperties();
   }
 
+  @Override
   public void saveProxySettings()
   {
     Cache.disableSessionProperties();
@@ -1467,11 +1468,17 @@ public class Preferences extends GPreferences
     Cache.enableSessionProperties();
     structureViewerPath.setText(viewerPath);
 
+    jalview.bin.Console.debug("Found " + paths.size()
+            + " paths to look for " + selectedItem.toString());
     paths.add(0, structureViewerPath.getText());
     for (String path : paths)
     {
+      jalview.bin.Console.debug("Looking for " + selectedItem.toString()
+              + " in " + path.trim());
       if (new File(path.trim()).canExecute())
       {
+        jalview.bin.Console.debug(
+                "Found " + selectedItem.toString() + " in " + path.trim());
         found = true;
         break;
       }