From: Jim Procter <jprocter@dundee.ac.uk>
Date: Thu, 1 May 2014 16:05:20 +0000 (+0100)
Subject: JAL-1397 (probably buggy) test for recovery of background and per group alignment... 
X-Git-Tag: Jalview_2_9~190^2~4
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=be1777c33711ef0c9f1014ad6d47c7c2021b2526;p=jalview.git

JAL-1397 (probably buggy) test for recovery of background and per group alignment annotation shading
---

diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index d553629..e294616 100644
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -2,8 +2,11 @@ package jalview.io;
 
 import static org.junit.Assert.*;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
 
 import java.io.File;
 
@@ -97,4 +100,70 @@ public class Jalview2xmlTests
     assertTrue("Didn't set T-coffee colourscheme for imported project.",af.getViewport().getGlobalColourScheme().getClass().equals(jalview.schemes.TCoffeeColourScheme.class));
     System.out.println("T-Coffee score shading successfully recovered from project.");
   }
+  @Test
+  public void testColourByAnnotScores() throws Exception
+  {
+    String inFile = "examples/uniref50.fa",inAnnot="examples/testdata/uniref50_iupred.jva";
+    String tfile = File.createTempFile("JalviewTest", ".jvp").getAbsolutePath();
+    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(inFile, FormatAdapter.FILE);
+    assertTrue("Didn't read input file "+inFile, af!=null);
+    af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null,null);
+    AlignmentAnnotation[] aa = af.getViewport().getAlignment().getSequenceAt(0).getAnnotation("IUPredWS (Short)");
+    assertTrue("Didn't find any IUPred annotation to use to shade alignment.",aa!=null && aa.length>0);
+    AnnotationColourGradient cs = new jalview.schemes.AnnotationColourGradient(aa[0], null, AnnotationColourGradient.ABOVE_THRESHOLD);
+    AnnotationColourGradient gcs = new jalview.schemes.AnnotationColourGradient(aa[0], null, AnnotationColourGradient.BELOW_THRESHOLD);
+    cs.setSeqAssociated(true);
+    gcs.setSeqAssociated(true);
+    af.changeColour(cs);
+    SequenceGroup sg = new SequenceGroup();
+    sg.setStartRes(57);
+    sg.setEndRes(92);
+    sg.cs = gcs;
+    af.getViewport().getAlignment().addGroup(sg);
+    sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
+    sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
+    af.alignPanel.alignmentChanged();
+    assertTrue("Failed to store as a project.",af.saveAlignment(tfile, "Jalview"));
+    af.closeMenuItem_actionPerformed(true);
+    af=null;
+    af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
+    assertTrue("Failed to import new project", af!=null);
+    
+    // check for group and alignment colourschemes
+    
+    ColourSchemeI _rcs=af.getViewport().getGlobalColourScheme();
+    ColourSchemeI _rgcs=af.getViewport().getAlignment().getGroups().get(0).cs;
+    assertTrue("Didn't recover global colourscheme",_rcs!=null); 
+    assertTrue("Didn't recover annotation colour global scheme",_rcs instanceof AnnotationColourGradient);
+    AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs;
+    assertTrue("Annotation colourscheme wasn't sequence associated",__rcs.isSeqAssociated());
+
+    
+    boolean diffseqcols=false,diffgseqcols=false;
+    SequenceI[] sqs=af.getViewport().getAlignment().getSequencesArray();
+    for (int p=0,pSize=af.getViewport().getAlignment().getWidth();p<pSize && (!diffseqcols || !diffgseqcols);p++)
+    {
+      if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0])!=_rcs.findColour(sqs[5].getCharAt(p), p, sqs[5]))
+      {
+        diffseqcols = true;
+      }
+    }
+    assertTrue("Got Different sequence colours", diffseqcols);
+    System.out.println("Per sequence colourscheme (Background) successfully applied and recovered.");
+    
+    assertTrue("Didn't recover group colourscheme",_rgcs!=null); 
+    assertTrue("Didn't recover annotation colour group colourscheme",_rgcs instanceof AnnotationColourGradient);
+    __rcs = (AnnotationColourGradient) _rgcs;
+    assertTrue("Group Annotation colourscheme wasn't sequence associated",__rcs.isSeqAssociated());
+    
+    for (int p=0,pSize=af.getViewport().getAlignment().getWidth();p<pSize && (!diffseqcols || !diffgseqcols);p++)
+    {
+    if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1])!=_rgcs.findColour(sqs[2].getCharAt(p), p, sqs[2]))
+      {
+        diffgseqcols = true;
+      }
+    }
+    assertTrue("Got Different group sequence colours", diffgseqcols);
+    System.out.println("Per sequence (Group) colourscheme successfully applied and recovered.");
+  }
 }