X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FJalview2xmlTests.java;h=dc192344d467b59af43910b00c885d97ff59dad8;hb=47168f025aefdaa044802bd5f8f510ffe43a4808;hp=d553629bc89f1551c1be4d211581bac060f2e118;hpb=c4719851fb6199dd1d2fd5efa82f7805f7bb74a1;p=jalview.git
diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index d553629..dc19234 100644
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -1,9 +1,33 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.io;
import static org.junit.Assert.*;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
import java.io.File;
@@ -97,4 +121,79 @@ 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