From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 31 May 2018 16:35:35 +0000 (+0100)
Subject: JAL-1950 JAL-2629 insert gaps into HMM used to search DB - AVOIDS NEED TO RUN HMMALIG... 
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=b4fcf4e6d26742a2dfeadc0e7b13bbca189c363e

JAL-1950 JAL-2629 insert gaps into HMM used to search DB - AVOIDS NEED TO RUN HMMALIGN AFTERWARDS !
---

diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index 409ef80..1883fef 100644
--- a/src/jalview/hmmer/HMMSearch.java
+++ b/src/jalview/hmmer/HMMSearch.java
@@ -365,7 +365,31 @@ public class HMMSearch extends HmmerCommand
       hmmSeq = hmmSeq.deriveSequence(); // otherwise all bad things happen
       hmmAndSeqs[0] = hmmSeq;
       System.arraycopy(seqs, 0, hmmAndSeqs, 1, seqCount);
-
+      if (modelpos != null)
+      {
+        // TODO need - get ungapped sequence method
+        hmmSeq.setSequence(
+                hmmSeq.getDatasetSequence().getSequenceAsString());
+        Annotation[] refpos = modelpos.annotations;
+        // insert gaps to match with refseq positions
+        int gc = 0, lcol = 0;
+        for (int c = 0; c < refpos.length; c++)
+        {
+          if (refpos[c] != null && ("x".equals(refpos[c].displayCharacter)))
+          {
+            if (gc > 0)
+            {
+              hmmSeq.insertCharAt(lcol + 1, gc, '-');
+            }
+            gc = 0;
+            lcol = c;
+          }
+          else
+          {
+            gc++;
+          }
+        }
+      }
       if (realign)
       {
         realignResults(hmmAndSeqs);