From e7e676ca075c5b2832be98b4544364e5d6adc4c1 Mon Sep 17 00:00:00 2001
From: Mateusz Warowny <mmzwarowny@dundee.ac.uk>
Date: Thu, 7 Oct 2021 12:34:13 +0200
Subject: [PATCH] JAL-3899 Replace prints with logger messages.

---
 src/jalview/analysis/SeqsetUtils.java |   27 +++++++++++++++++----------
 1 file changed, 17 insertions(+), 10 deletions(-)

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 6683e3b..e2ed9b4 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -20,6 +20,7 @@
  */
 package jalview.analysis;
 
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.PDBEntry;
@@ -37,6 +38,7 @@ import java.util.Map;
 import java.util.Objects;
 import java.util.Optional;
 import java.util.Vector;
+import static java.lang.String.format;
 
 public class SeqsetUtils
 {
@@ -117,9 +119,12 @@ public class SeqsetUtils
       sq.setDescription(sqinfo.description.get());
     if (sqinfo.dataset.isPresent())
     {
-      assert sqinfo.features.isEmpty() :
-        "Setting dataset sequence for a sequence which has sequence features. " +
-          "Dataset sequence features will not be visible.";
+      if (sqinfo.features.isPresent())
+      {
+        Cache.log.warn("Setting dataset sequence for a sequence which has " +
+            "sequence features. Dataset sequence features will not be visible.");
+        assert false;
+      }
       sq.setDatasetSequence(sqinfo.dataset.get());
     }
     if (sqinfo.hmm.isPresent())
@@ -240,25 +245,27 @@ public class SeqsetUtils
         {
           if (!quiet)
           {
-            System.err.println("Can't find '" + ((String) key)
-                    + "' in uniquified alignment");
+            Cache.log.warn(format("Can't find '%s' in uniquified alignment",
+                key));
           }
         }
       } catch (ClassCastException ccastex) {
         if (!quiet)
         {
-          System.err.println("Unexpected object in SeqSet map : "+key.getClass());
+          Cache.log.error("Unexpected object in SeqSet map : "+ key.getClass());
         }
       }
     }
     if (unmatched.size() > 0 && !quiet)
     {
-      System.err.println("Did not find matches for :");
-      for (Enumeration<SequenceI> i = unmatched.elements();
-          i.hasMoreElements();)
+      StringBuilder sb = new StringBuilder("Did not find match for sequences: ");
+      Enumeration<SequenceI> i = unmatched.elements();
+      sb.append(i.nextElement().getName());
+      for (; i.hasMoreElements();)
       {
-        System.out.println(((SequenceI) i.nextElement()).getName());
+        sb.append(", " + i.nextElement().getName());
       }
+      Cache.log.warn(sb.toString());
       return false;
     }
 
-- 
1.7.10.2