X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2FMCview%2FPDBChainTest.java;h=defcdbc1dac7099af48cf0f166fb2fe8528d8333;hb=02d91bab6246aa621844864b2351bbe1ed3905f6;hp=b84ca2848789b8e2e9508de862e838e4af6cb425;hpb=5247711ab4a6453614e2a9fb9307e6bae6a7b4a9;p=jalview.git
diff --git a/test/MCview/PDBChainTest.java b/test/MCview/PDBChainTest.java
index b84ca28..defcdbc 100644
--- a/test/MCview/PDBChainTest.java
+++ b/test/MCview/PDBChainTest.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 MCview;
import static org.testng.AssertJUnit.assertEquals;
@@ -10,17 +30,29 @@ import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.TaylorColourScheme;
+import jalview.structure.StructureImportSettings;
import java.awt.Color;
+import java.util.List;
import java.util.Vector;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class PDBChainTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
PDBChain c;
final Atom a1 = new Atom(1f, 2f, 3f);
@@ -35,10 +67,11 @@ public class PDBChainTest
public void setUp()
{
System.out.println("setup");
+ StructureImportSettings.setShowSeqFeatures(true);
c = new PDBChain("1GAQ", "A");
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testGetNewlineString()
{
assertEquals(System.lineSeparator(), c.getNewlineString());
@@ -46,7 +79,7 @@ public class PDBChainTest
assertEquals("gaga", c.getNewlineString());
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testPrint()
{
c.offset = 7;
@@ -74,7 +107,7 @@ public class PDBChainTest
* Test the method that constructs a Bond between two atoms and adds it to the
* chain's list of bonds
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testMakeBond()
{
/*
@@ -109,7 +142,7 @@ public class PDBChainTest
assertEquals(3f, b2.end[2], 0.0001f);
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testSetChainColours_colour()
{
c.makeBond(a1, a2);
@@ -126,7 +159,7 @@ public class PDBChainTest
* Test setting bond start/end colours based on a colour scheme i.e. colour by
* residue
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testSetChainColours_colourScheme()
{
Color alaColour = new Color(204, 255, 0);
@@ -154,7 +187,7 @@ public class PDBChainTest
assertEquals(Color.gray, b.endCol);
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testGetChargeColour()
{
assertEquals(Color.red, PDBChain.getChargeColour("ASP"));
@@ -169,7 +202,7 @@ public class PDBChainTest
/**
* Test the method that sets bond start/end colours by residue charge property
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testSetChargeColours()
{
a1.resName = "ASP"; // red
@@ -198,7 +231,7 @@ public class PDBChainTest
/**
* Test the method that converts the raw list of atoms to a list of residues
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testMakeResidueList_noAnnotation()
{
Vector atoms = new Vector();
@@ -226,19 +259,19 @@ public class PDBChainTest
/*
* check sequence features
*/
- SequenceFeature[] sfs = c.sequence.getSequenceFeatures();
- assertEquals(3, sfs.length);
- assertEquals("RESNUM", sfs[0].type);
- assertEquals("MET:4 1gaqA", sfs[0].description);
- assertEquals(4, sfs[0].begin);
- assertEquals(4, sfs[0].end);
- assertEquals("RESNUM", sfs[0].type);
- assertEquals("LYS:5 1gaqA", sfs[1].description);
- assertEquals(5, sfs[1].begin);
- assertEquals(5, sfs[1].end);
- assertEquals("LEU:6 1gaqA", sfs[2].description);
- assertEquals(6, sfs[2].begin);
- assertEquals(6, sfs[2].end);
+ List sfs = c.sequence.getSequenceFeatures();
+ assertEquals(3, sfs.size());
+ assertEquals("RESNUM", sfs.get(0).type);
+ assertEquals("MET:4 1gaqA", sfs.get(0).description);
+ assertEquals(4, sfs.get(0).begin);
+ assertEquals(4, sfs.get(0).end);
+ assertEquals("RESNUM", sfs.get(0).type);
+ assertEquals("LYS:5 1gaqA", sfs.get(1).description);
+ assertEquals(5, sfs.get(1).begin);
+ assertEquals(5, sfs.get(1).end);
+ assertEquals("LEU:6 1gaqA", sfs.get(2).description);
+ assertEquals(6, sfs.get(2).begin);
+ assertEquals(6, sfs.get(2).end);
}
private Atom makeAtom(int resnum, String name, String resname)
@@ -256,35 +289,35 @@ public class PDBChainTest
* Test the method that converts the raw list of atoms to a list of residues,
* including parsing of tempFactor to an alignment annotation
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testMakeResidueList_withTempFactor()
{
Vector atoms = new Vector();
c.atoms = atoms;
atoms.add(makeAtom(4, "N", "MET"));
- atoms.get(atoms.size()-1).tfactor = 1f;
+ atoms.get(atoms.size() - 1).tfactor = 1f;
atoms.add(makeAtom(4, "CA", "MET"));
- atoms.get(atoms.size()-1).tfactor = 2f;
+ atoms.get(atoms.size() - 1).tfactor = 2f;
atoms.add(makeAtom(4, "C", "MET"));
- atoms.get(atoms.size()-1).tfactor = 3f;
+ atoms.get(atoms.size() - 1).tfactor = 3f;
atoms.add(makeAtom(5, "O", "LYS"));
- atoms.get(atoms.size()-1).tfactor = 7f;
+ atoms.get(atoms.size() - 1).tfactor = 7f;
atoms.add(makeAtom(5, "N", "LYS"));
- atoms.get(atoms.size()-1).tfactor = 8f;
+ atoms.get(atoms.size() - 1).tfactor = 8f;
atoms.add(makeAtom(5, "CA", "LYS"));
- atoms.get(atoms.size()-1).tfactor = 9f;
+ atoms.get(atoms.size() - 1).tfactor = 9f;
atoms.add(makeAtom(6, "O", "LEU"));
- atoms.get(atoms.size()-1).tfactor = 4f;
+ atoms.get(atoms.size() - 1).tfactor = 4f;
atoms.add(makeAtom(6, "N", "LEU"));
- atoms.get(atoms.size()-1).tfactor = 5f;
+ atoms.get(atoms.size() - 1).tfactor = 5f;
atoms.add(makeAtom(6, "CA", "LEU"));
- atoms.get(atoms.size()-1).tfactor = 6f;
-
+ atoms.get(atoms.size() - 1).tfactor = 6f;
+
/*
* make residues including temp factor annotation
*/
c.makeResidueList(true);
-
+
/*
* Verify annotations; note the tempFactor is read from the first atom in
* each residue i.e. we expect values 1, 7, 4 for the residues
@@ -307,7 +340,7 @@ public class PDBChainTest
* Test the method that constructs bonds between successive residues' CA or P
* atoms
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testMakeCaBondList()
{
c.isNa = true;
@@ -338,7 +371,7 @@ public class PDBChainTest
assertTrue(c.isNa);
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testMakeCaBondList_nucleotide()
{
c.isNa = false;
@@ -370,7 +403,7 @@ public class PDBChainTest
/**
* Test the method that updates atoms with their alignment positions
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testMakeExactMapping()
{
Vector atoms = new Vector();