JAL-2001 - note about possible side effect on JalviewLite.selectIn due to refactored...

[jalview.git] / src / jalview / bin / JalviewLite.java

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 3d59a12..095cfd3 100644 (file)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -459,6 +459,9 @@ public class JalviewLite extends Applet implements
         if (csel != null)
         {
           List<Integer> cs = csel.getSelected();
+          // note - the following actually clears cs as well, since
+          // csel.getSelected returns a reference. Need to check if we need to
+          // have a concurrentModification exception thrown here
           csel.clear();
           for (Integer selectedCol : cs)
           {
@@ -850,7 +853,7 @@ public class JalviewLite extends Applet implements
   {
     AlignmentI al = null;
 
-    String format = new IdentifyFile().Identify(text,
+    String format = new IdentifyFile().identify(text,
             AppletFormatAdapter.PASTE);
     try
     {
@@ -1967,7 +1970,7 @@ public class JalviewLite extends Applet implements
         return null;
       }
       String resolvedFile = resolveFileProtocol(fileParam);
-      String format = new IdentifyFile().Identify(resolvedFile, protocol);
+      String format = new IdentifyFile().identify(resolvedFile, protocol);
       dbgMsg("File identified as '" + format + "'");
       AlignmentI al = null;
       try
@@ -2404,8 +2407,7 @@ public class JalviewLite extends Applet implements
         return rtn;
       } catch (Exception ex)
       {
-        System.out.println("Exception checking resources: " + f + " "
-                + ex);
+        System.out.println("Exception checking resources: " + f + " " + ex);
         return false;
       }
     }
@@ -2860,6 +2862,15 @@ public class JalviewLite extends Applet implements
           URL localref)
   {
     String resolvedPath = "";
+    if (targetPath.startsWith("/"))
+    {
+      String codebase = localref.toString();
+      String localfile = localref.getFile();
+      resolvedPath = codebase.substring(0,
+              codebase.length() - localfile.length())
+              + targetPath;
+      return resolvedPath;
+    }
 
     /*
      * get URL path and strip off any trailing file e.g.