JAL-3013 resolve symlink to hmmer binaries folder

[jalview.git] / src / jalview / hmmer / HmmerCommand.java

diff --git a/src/jalview/hmmer/HmmerCommand.java b/src/jalview/hmmer/HmmerCommand.java
index dfd5395..b5c1b25 100644 (file)
--- a/src/jalview/hmmer/HmmerCommand.java
+++ b/src/jalview/hmmer/HmmerCommand.java
@@ -24,6 +24,7 @@ import java.io.File;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.io.PrintWriter;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
@@ -247,15 +248,18 @@ public abstract class HmmerCommand implements Runnable
    * @param cmd
    *          command short name e.g. hmmalign
    * @return
+   * @throws IOException
    */
-  protected String getCommandPath(String cmd)
+  protected String getCommandPath(String cmd) throws IOException
   {
     String binariesFolder = Cache.getProperty(Preferences.HMMER_PATH);
+    // ensure any symlink to the directory is resolved:
+    binariesFolder = Paths.get(binariesFolder).toRealPath().toString();
     File file = FileUtils.getExecutable(cmd, binariesFolder);
     if (file == null && af != null)
     {
-        JvOptionPane.showInternalMessageDialog(af,
-                MessageManager.getString("warn.hmm_command_failed"));
+      JvOptionPane.showInternalMessageDialog(af, MessageManager
+              .formatMessage("label.executable_not_found", cmd));
     }
 
     return file == null ? null : getFilePath(file);
@@ -281,6 +285,31 @@ public abstract class HmmerCommand implements Runnable
   }
 
   /**
+   * Answers the HMM profile for the profile sequence the user selected (default
+   * is just the first HMM sequence in the alignment)
+   * 
+   * @return
+   */
+  protected HiddenMarkovModel getHmmProfile()
+  {
+    String alignToParamName = MessageManager.getString("label.use_hmm");
+    for (ArgumentI arg : params)
+    {
+      String name = arg.getName();
+      if (name.equals(alignToParamName))
+      {
+        String seqName = arg.getValue();
+        SequenceI hmmSeq = alignment.findName(seqName);
+        if (hmmSeq.hasHMMProfile())
+        {
+          return hmmSeq.getHMM();
+        }
+      }
+    }
+    return null;
+  }
+
+  /**
    * Answers an absolute path to the given file, in a format suitable for
    * processing by a hmmer command. On a Windows platform, the native Windows file
    * path is converted to Cygwin format, by replacing '\'with '/' and drive letter