X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fhmmer%2FHMMSearch.java;h=57786e592f2be26be37f21d9a051f23d7f2a6178;hb=24514ffaa8ef17fa371dcdd64a4693282d0e93d6;hp=1883fef3dac2a97b48fc5e50fd5f8a842f3cb791;hpb=b4fcf4e6d26742a2dfeadc0e7b13bbca189c363e;p=jalview.git

diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index 1883fef..57786e5 100644
--- a/src/jalview/hmmer/HMMSearch.java
+++ b/src/jalview/hmmer/HMMSearch.java
@@ -181,9 +181,9 @@ public class HMMSearch extends HmmerCommand
           File hitsAlignmentFile, File hmmFile) throws IOException
   {
     args.add("-o");
-    args.add(getFilePath(searchOutputFile));
+    args.add(getFilePath(searchOutputFile, true));
     args.add("-A");
-    args.add(getFilePath(hitsAlignmentFile));
+    args.add(getFilePath(hitsAlignmentFile, true));
 
     boolean dbFound = false;
     String dbPath = "";
@@ -314,8 +314,8 @@ public class HMMSearch extends HmmerCommand
       exportStockholm(copy.getSequencesArray(), databaseFile, null);
     }
 
-    args.add(getFilePath(hmmFile));
-    args.add(getFilePath(databaseFile));
+    args.add(getFilePath(hmmFile, true));
+    args.add(getFilePath(databaseFile, true));
   }
 
   /**
@@ -470,10 +470,11 @@ public class HMMSearch extends HmmerCommand
     {
       line = br.readLine();
     }
-    for (int i = 0; i < 5; i++)
+    while (!line.contains("-------"))
     {
       line = br.readLine();
     }
+    line = br.readLine();
 
     int index = 0;
     while (!"  ------ inclusion threshold ------".equals(line)