X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fjmol%2FJmolCommandsTest.java;h=353d5ea48b8fc951c03fff3eefebacd244e76c44;hb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;hp=46fa241a69ffff45a9f7af1721d4a4c893289a27;hpb=b03ec66ae6238b44bd20d2403d1157cadc5f0e01;p=jalview.git

diff --git a/test/jalview/ext/jmol/JmolCommandsTest.java b/test/jalview/ext/jmol/JmolCommandsTest.java
index 46fa241..353d5ea 100644
--- a/test/jalview/ext/jmol/JmolCommandsTest.java
+++ b/test/jalview/ext/jmol/JmolCommandsTest.java
@@ -1,19 +1,56 @@
+/*
+ * 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.ext.jmol;
 
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertTrue;
+
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
 import jalview.gui.SequenceRenderer;
+import jalview.schemes.JalviewColourScheme;
+import jalview.structure.StructureMapping;
 import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
 
+import java.util.HashMap;
+
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class JmolCommandsTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   @Test(groups = { "Functional" })
   public void testGetColourBySequenceCommand_noFeatures()
   {
@@ -24,11 +61,84 @@ public class JmolCommandsTest
     SequenceRenderer sr = new SequenceRenderer(af.getViewport());
     SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
     String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
-    StructureSelectionManager ssm = new StructureSelectionManager();
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(null);
 
     // need some mappings!
 
     StructureMappingcommandSet[] commands = JmolCommands
-            .getColourBySequenceCommand(ssm, files, seqs, sr, null, al);
+            .getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetColourBySequenceCommands_hiddenColumns()
+  {
+    /*
+     * load these sequences, coloured by Strand propensity,
+     * with columns 2-4 hidden
+     */
+    SequenceI seq1 = new Sequence("seq1", "MHRSQSSSGG");
+    SequenceI seq2 = new Sequence("seq2", "MVRSNGGSSS");
+    AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
+    AlignFrame af = new AlignFrame(al, 800, 500);
+    af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString());
+    ColumnSelection cs = new ColumnSelection();
+    cs.addElement(2);
+    cs.addElement(3);
+    cs.addElement(4);
+    af.getViewport().setColumnSelection(cs);
+    af.hideSelColumns_actionPerformed(null);
+    SequenceRenderer sr = new SequenceRenderer(af.getViewport());
+    SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
+    String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(null);
+  
+    /*
+     * map residues 1-10 to residues 21-30 (atoms 105-150) in structures
+     */
+    HashMap<Integer, int[]> map = new HashMap<>();
+    for (int pos = 1; pos <= seq1.getLength(); pos++)
+    {
+      map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
+    }
+    StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1",
+            "A", map, null);
+    ssm.addStructureMapping(sm1);
+    StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
+            "B", map, null);
+    ssm.addStructureMapping(sm2);
+  
+    StructureMappingcommandSet[] commands = JmolCommands
+            .getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel);
+    assertEquals(commands.length, 2);
+    assertEquals(commands[0].commands.length, 1);
+
+    String chainACommand = commands[0].commands[0];
+    // M colour is #82827d == (130, 130, 125) (see strand.html help page)
+    assertTrue(chainACommand
+            .contains("select 21:A/1.1;color[130,130,125]")); // first one
+    // H colour is #60609f == (96, 96, 159)
+    assertTrue(chainACommand.contains(";select 22:A/1.1;color[96,96,159]"));
+    // hidden columns are Gray (128, 128, 128)
+    assertTrue(chainACommand
+            .contains(";select 23-25:A/1.1;color[128,128,128]"));
+    // S and G are both coloured #4949b6 == (73, 73, 182)
+    assertTrue(chainACommand
+            .contains(";select 26-30:A/1.1;color[73,73,182]"));
+
+    String chainBCommand = commands[1].commands[0];
+    // M colour is #82827d == (130, 130, 125)
+    assertTrue(chainBCommand
+            .contains("select 21:B/2.1;color[130,130,125]"));
+    // V colour is #ffff00 == (255, 255, 0)
+    assertTrue(chainBCommand
+.contains(";select 22:B/2.1;color[255,255,0]"));
+    // hidden columns are Gray (128, 128, 128)
+    assertTrue(chainBCommand
+            .contains(";select 23-25:B/2.1;color[128,128,128]"));
+    // S and G are both coloured #4949b6 == (73, 73, 182)
+    assertTrue(chainBCommand
+            .contains(";select 26-30:B/2.1;color[73,73,182]"));
   }
 }