From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 9 Feb 2017 10:05:21 +0000 (+0000)
Subject: JAL-2371 no test for lower case consensus as not expected or handled
X-Git-Tag: Release_2_10_3b1~349
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=301bcabf2b63d653ab9f5ce7102c1ea8951d6d75;p=jalview.git

JAL-2371 no test for lower case consensus as not expected or handled
---

diff --git a/test/jalview/schemes/Blosum62ColourSchemeTest.java b/test/jalview/schemes/Blosum62ColourSchemeTest.java
index b3dd165..0b5b6bd 100644
--- a/test/jalview/schemes/Blosum62ColourSchemeTest.java
+++ b/test/jalview/schemes/Blosum62ColourSchemeTest.java
@@ -29,11 +29,10 @@ public class Blosum62ColourSchemeTest
 
     /*
      * findColour does not use column, sequence or pid score
+     * we assume consensus residue is computed as upper case
      */
     assertEquals(blosum.findColour('A', 0, null, "A", 0f), darkBlue);
     assertEquals(blosum.findColour('a', 0, null, "A", 0f), darkBlue);
-    assertEquals(blosum.findColour('A', 0, null, "a", 0f), darkBlue);
-    assertEquals(blosum.findColour('a', 0, null, "a", 0f), darkBlue);
 
     /*
      * L has a Blosum score of 
diff --git a/test/jalview/schemes/PIDColourSchemeTest.java b/test/jalview/schemes/PIDColourSchemeTest.java
index 73b270f..fa4b5d9 100644
--- a/test/jalview/schemes/PIDColourSchemeTest.java
+++ b/test/jalview/schemes/PIDColourSchemeTest.java
@@ -42,6 +42,7 @@ public class PIDColourSchemeTest
 
     /*
      * doesn't use column or sequence
+     * we assume consensus residue is computed as upper case
      */
     assertEquals(scheme.findColour('A', 0, null, "A", 0f), white);
     assertEquals(scheme.findColour('A', 0, null, "A", 40f), white);
@@ -54,8 +55,6 @@ public class PIDColourSchemeTest
     assertEquals(scheme.findColour('A', 0, null, "KFV", 100f), white);
 
     assertEquals(scheme.findColour('a', 0, null, "A", 80f), over60);
-    assertEquals(scheme.findColour('A', 0, null, "a", 80f), over60);
-    assertEquals(scheme.findColour('a', 0, null, "a", 80f), over60);
     assertEquals(scheme.findColour('A', 0, null, "AC", 80f), over60);
     assertEquals(scheme.findColour('A', 0, null, "KCA", 80f), over60);
   }
@@ -78,10 +77,26 @@ public class PIDColourSchemeTest
      * first column PID is 50%, or 67% ignoring gaps
      */
     String seqs = ">seq1\nAAAAA\n>seq2\nAAAAA\n>seq3\n-CCCC\n>seq4\nFFFFF\n";
+
+    /*
+     * load data and wait for consensus to be computed
+     */
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqs,
             DataSourceType.PASTE);
     AlignViewport viewport = af.getViewport();
     viewport.setIgnoreGapsConsensus(false, af.alignPanel);
+    while (viewport.getConsensusSeq() == null)
+    {
+      synchronized (this)
+      {
+        try
+        {
+          wait(50);
+        } catch (InterruptedException e)
+        {
+        }
+      }
+    }
     af.changeColour_actionPerformed(JalviewColourScheme.PID.toString());
 
     SequenceI seq = viewport.getAlignment().getSequenceAt(0);