--- /dev/null
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+
+import org.junit.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+public class ImportHomologyModelTest
+{
+
+ public static String base = "examples/testdata/phyre2/";
+
+ public static String profile_msa = base + "query.jal",
+ profile_annot = base + "query.jal.ann";
+
+ public static String templaten[] = new String[] { "c1o1nA_", "c3pt8B_",
+ "d1scta_" };
+
+ AlignmentI al;
+ AlignFrame af;
+
+ /**
+ * Ensure 'process secondary structure from PDB and add annotations' are set
+ * in preferences, and load PDB example file 1gaq
+ *
+ * @throws Exception
+ */
+ @BeforeMethod(alwaysRun = true)
+ public void setup() throws Exception
+ {
+ Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+ Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty("ADD_SS_ANN",
+ Boolean.TRUE.toString());
+ FileLoader loader = new FileLoader(false);
+ af = loader.LoadFileWaitTillLoaded(profile_msa,
+ FormatAdapter.FILE);
+ Desktop.addInternalFrame(af, "homology models", 800, 500);
+ al = af.getViewport().getAlignment();
+ af.loadJalviewDataFile(profile_annot, FormatAdapter.FILE, null, null);
+ // if file was loaded, the view should have a reference sequence set
+ Assert.assertTrue(al.hasSeqrep());
+ }
+
+
+ @Test(groups = { "Functional" })
+ public void testModelsAssociated()
+ {
+ for (String template : templaten)
+ {
+ SequenceI templseq = al.findName(template);
+ Assert.assertNotNull("Couldn't find template sequence for "
+ + template, templseq);
+ PDBEntry querymdl = al.getSeqrep().getPDBEntry(template);
+ PDBEntry templmdl = templseq.getPDBEntry(template);
+ Assert.assertEquals(querymdl.getFile(), templmdl.getFile());
+ }
+ }
+
+ /**
+ * @throws java.lang.Exception
+ */
+ @BeforeClass(alwaysRun = true)
+ public static void setUpBeforeClass() throws Exception
+ {
+ jalview.bin.Jalview.main(new String[] { "-props",
+ "test/jalview/io/testProps.jvprops" });
+ }
+
+ /**
+ * @throws java.lang.Exception
+ */
+ @AfterClass(alwaysRun = true)
+ public static void tearDownAfterClass() throws Exception
+ {
+ jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+ }
+
+
+}