JAL-2909 mininal merge of bam import demo to Jalview 2.11.2 develop

[jalview.git] / src / jalview / io / IdentifyFile.java

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 5a3d700..0c201e1 100755 (executable)
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -164,14 +164,21 @@ public class IdentifyFile
         {
           // jar files are special - since they contain all sorts of random
           // characters.
-          if (source.inFile != null)
+          if (source.inFile != null || source.getDataName() != null)
           {
-            String fileStr = source.inFile.getName();
+            String fileStr = source.inFile == null ? source.getDataName()
+                    : source.inFile.getName();
             if (fileStr.contains(".jar")
                     || fileStr.contains(".zip") || fileStr.contains(".jvp"))
             {
               // possibly a Jalview archive (but check further)
               reply = FileFormat.Jalview;
+              // TODO shouldn't there be a break here?
+            }
+            else if (fileStr.lastIndexOf(".bam") > -1)
+            {
+              reply = FileFormat.Bam;
+              break;
             }
           }
           if (!lineswereskipped && data.startsWith("PK"))