From 6f2610ec4d7a79dde17f9b3d02225c62aa52cfd8 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 15 Sep 2015 12:26:34 +0100
Subject: [PATCH] JAL-1859 refactoring / debugging added

---
 src/jalview/bin/JalviewLite.java                   |   10 +-
 .../javascript/MouseOverStructureListener.java     |  101 +++++++++++++-------
 2 files changed, 74 insertions(+), 37 deletions(-)

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 7112381..e736009 100644
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -2400,10 +2400,11 @@ public class JalviewLite extends Applet implements
        * Try relative to document base
        */
       URL documentBase = getDocumentBase();
+      System.err.println("Trying documentbase: " + documentBase);
       String url = applet.resolveUrlForLocalOrAbsolute(f, documentBase);
       if (urlExists(url))
       {
-        if (debug)
+        if (true/* debug */)
         {
           System.err.println("Prepended document base '" + documentBase
                   + "' to make: '" + url + "'");
@@ -2415,10 +2416,11 @@ public class JalviewLite extends Applet implements
        * Try relative to codebase
        */
       URL codeBase = getCodeBase();
+      System.err.println("Trying codebase: " + codeBase);
       url = applet.resolveUrlForLocalOrAbsolute(f, codeBase);
       if (urlExists(url))
       {
-        if (debug)
+        if (true/* debug */)
         {
           System.err.println("Prepended codebase '" + codeBase
                   + "' to make: '" + url + "'");
@@ -2924,13 +2926,13 @@ public class JalviewLite extends Applet implements
     {
       url = localref + url;
     }
-    if (debug)
+    if (true/* debug */)
     {
       System.err.println("URL: " + localref.toString());
       System.err.println("URL.getFile: " + localref.getFile());
       System.err.println("URL.getPath: " + localref.getPath());
       System.err.println("URL.getQuery: " + localref.getQuery());
-      System.err.println("returning " + url);
+      System.err.println("resolveUrlForLocalOrAbsolute returning " + url);
     }
     return url;
   }
diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index 2ef957e..88fba02 100644
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -33,6 +33,9 @@ import jalview.structure.StructureMapping;
 import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
 
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URL;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -87,45 +90,77 @@ public class MouseOverStructureListener extends JSFunctionExec implements
     {
       for (int i = 0; i < modelSet.length; i++)
       {
-        // resolve a real filename
-        try
-        {
-          if (new java.net.URL(modelSet[i]).openConnection() != null)
-          {
-            continue;
-          }
-        } catch (Exception x)
-        {
-        }
-        ;
-        try
-        {
-          String db = jvlite.getDocumentBase().toString();
-          db = db.substring(0, db.lastIndexOf("/"));
-          if (new java.net.URL(db + "/" + modelSet[i]).openConnection() != null)
-          {
-            modelSet[i] = db + "/" + modelSet[i];
-            continue;
-          }
-        } catch (Exception x)
-        {
-        }
-        ;
+        modelSet[i] = resolveModelFile(modelSet[i]);
+      }
+    }
+  }
+
+  /**
+   * Returns the first of file, file prefixed by document base, file prefixed by
+   * codebase which can be resolved to a valid URL. If none can, returns the
+   * input parameter value.
+   * 
+   * @param file
+   */
+  public String resolveModelFile(String file)
+  {
+    if (isValidUrl(file))
+    {
+      return file;
+    }
+
+    String db = jvlite.getDocumentBase().toString();
+    db = db.substring(0, db.lastIndexOf("/"));
+    String docBaseFile = db + "/" + file;
+    if (isValidUrl(docBaseFile))
+    {
+      return docBaseFile;
+    }
+
+    String cb = jvlite.getCodeBase() + file;
+    if (isValidUrl(cb))
+    {
+      return cb;
+    }
+
+    return file;
+  }
+
+  /**
+   * Returns true if it is possible to open an input stream at the given URL,
+   * else false. The input stream is closed.
+   * 
+   * @param file
+   * @return
+   */
+  private boolean isValidUrl(String file)
+  {
+    InputStream is = null;
+    try
+    {
+      is = new URL(file).openStream();
+      if (is != null)
+      {
+        return true;
+      }
+    } catch (IOException x)
+    {
+      // MalformedURLException, FileNotFoundException
+      return false;
+    } finally
+    {
+      if (is != null)
+      {
         try
         {
-          if (new java.net.URL(jvlite.getCodeBase() + modelSet[i])
-                  .openConnection() != null)
-          {
-            modelSet[i] = jvlite.getCodeBase() + modelSet[i];
-            continue;
-          }
-        } catch (Exception x)
+          is.close();
+        } catch (IOException e)
         {
+          // ignore
         }
-        ;
-
       }
     }
+    return false;
   }
 
   @Override
-- 
1.7.10.2