X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fschemes%2FPIDColourSchemeTest.java;h=dff19cd65228c4be92aed3937c7d3a830157ee8e;hb=a7169b1c72607f3c9357195b4999869650a2a891;hp=1518fb354611deb50418fc04a844dd32a30ec4cd;hpb=8e1be43e250107a4d86898bd554cf03098fa5957;p=jalview.git
diff --git a/test/jalview/schemes/PIDColourSchemeTest.java b/test/jalview/schemes/PIDColourSchemeTest.java
index 1518fb3..dff19cd 100644
--- a/test/jalview/schemes/PIDColourSchemeTest.java
+++ b/test/jalview/schemes/PIDColourSchemeTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.schemes;
import static org.testng.Assert.assertEquals;
@@ -6,8 +26,22 @@ import java.awt.Color;
import org.testng.annotations.Test;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+
public class PIDColourSchemeTest
{
+ static final Color white = Color.white;
+
+ static final Color over40 = new Color(204, 204, 255);
+
+ static final Color over60 = new Color(153, 153, 255);
+
+ static final Color over80 = new Color(100, 100, 255);
+
/**
* Test findColour for cases:
*
@@ -21,31 +55,80 @@ public class PIDColourSchemeTest
* - case insensitive matching
*
*/
- @Test
+ @Test(groups = "Functional")
public void testFindColour()
{
ColourSchemeI scheme = new PIDColourScheme();
- Color over40 = new Color(204, 204, 255);
- Color over60 = new Color(153, 153, 255);
- Color over80 = new Color(100, 100, 255);
-
/*
* doesn't use column or sequence
+ * we assume consensus residue is computed as upper case
*/
- assertEquals(scheme.findColour('A', 0, null, "A", 0f), Color.white);
- assertEquals(scheme.findColour('A', 0, null, "A", 40f), Color.white);
+ assertEquals(scheme.findColour('A', 0, null, "A", 0f), white);
+ assertEquals(scheme.findColour('A', 0, null, "A", 40f), white);
assertEquals(scheme.findColour('A', 0, null, "A", 40.1f), over40);
assertEquals(scheme.findColour('A', 0, null, "A", 60f), over40);
assertEquals(scheme.findColour('A', 0, null, "A", 60.1f), over60);
assertEquals(scheme.findColour('A', 0, null, "A", 80f), over60);
assertEquals(scheme.findColour('A', 0, null, "A", 80.1f), over80);
assertEquals(scheme.findColour('A', 0, null, "A", 100f), over80);
+ 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);
}
+
+ /**
+ * Test that changing the 'ignore gaps in consensus' in the viewport (an
+ * option on the annotation label popup menu) results in a change to the
+ * colouring
+ */
+ @Test(groups = "Functional")
+ public void testFindColour_ignoreGaps()
+ {
+ /*
+ * AAAAA
+ * AAAAA
+ * -CCCC
+ * FFFFF
+ *
+ * first column consensus is A
+ * 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);
+ do
+ {
+ try
+ {
+ Thread.sleep(50);
+ } catch (InterruptedException x)
+ {
+ }
+ } while (af.getViewport().getCalcManager().isWorking());
+ af.changeColour_actionPerformed(JalviewColourScheme.PID.toString());
+
+ SequenceI seq = viewport.getAlignment().getSequenceAt(0);
+
+ /*
+ * including gaps, A should be coloured for 50% consensus
+ */
+ Color c = viewport.getResidueShading().findColour('A', 0, seq);
+ assertEquals(c, over40);
+
+ /*
+ * now choose to ignore gaps; colour should be for 67%
+ */
+ viewport.setIgnoreGapsConsensus(true, af.alignPanel);
+ c = viewport.getResidueShading().findColour('A', 0, seq);
+ assertEquals(c, over60);
+ }
}