JAL-3005 JAL-2629 file chooser argument for HMM search database

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

diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index a58b949..6cda421 100644 (file)
--- a/src/jalview/hmmer/HMMSearch.java
+++ b/src/jalview/hmmer/HMMSearch.java
@@ -195,6 +195,7 @@ public class HMMSearch extends HmmerCommand
     String seqScoreCutoff = null;
     String domScoreCutoff = null;
     databaseName = "Alignment";
+    boolean searchAlignment = false;
 
     if (params != null)
     {
@@ -206,6 +207,18 @@ public class HMMSearch extends HmmerCommand
         {
           seqsToReturn = Integer.parseInt(arg.getValue());
         }
+        else if (MessageManager.getString("action.search").equals(name))
+        {
+          searchAlignment = arg.getValue().equals(
+                  MessageManager.getString(HMMSearch.THIS_ALIGNMENT_KEY));
+        }
+        else if (MessageManager.getString(DATABASE_KEY).equals(name))
+        {
+          dbPath = arg.getValue();
+          int pos = dbPath.lastIndexOf(File.separator);
+          databaseName = dbPath.substring(pos + 1);
+          databaseFile = new File(dbPath);
+        }
         else if (MessageManager.getString(AUTO_ALIGN_SEQS_KEY)
                 .equals(name))
         {
@@ -280,8 +293,9 @@ public class HMMSearch extends HmmerCommand
       args.add(domScoreCutoff);
     }
 
-    if (!dbFound || MessageManager.getString(THIS_ALIGNMENT_KEY)
-            .equals(dbPath))
+//    if (!dbFound || MessageManager.getString(THIS_ALIGNMENT_KEY)
+//            .equals(dbPath))
+      if (searchAlignment)
     {
       /*
        * no external database specified for search, so