JAL-3336 add better method of determining where data table begins

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

diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index 1883fef..57786e5 100644 (file)
--- 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)