X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAnnotationChooserTest.java;h=f3c0dee6eecac20ceada348ae1d031a44ac82d02;hb=dc5a5883cfe90255079e41538e56bc433bd1e4a5;hp=1a61c3e8e809f0f4a8e843cac611ceaa8d3ef404;hpb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;p=jalview.git

diff --git a/test/jalview/gui/AnnotationChooserTest.java b/test/jalview/gui/AnnotationChooserTest.java
index 1a61c3e..f3c0dee 100644
--- a/test/jalview/gui/AnnotationChooserTest.java
+++ b/test/jalview/gui/AnnotationChooserTest.java
@@ -48,6 +48,7 @@ import java.util.List;
 import javax.swing.JButton;
 import javax.swing.JPanel;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
@@ -59,6 +60,14 @@ import org.testng.annotations.Test;
  */
 public class AnnotationChooserTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   // 4 sequences x 13 positions
   final static String TEST_DATA = ">FER_CAPAA Ferredoxin\n"
           + "TIETHKEAELVG-\n"
@@ -77,12 +86,13 @@ public class AnnotationChooserTest
   @BeforeMethod(alwaysRun = true)
   public void setUp() throws IOException
   {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
     // pin down annotation sort order for test
     Cache.applicationProperties.setProperty(Preferences.SORT_ANNOTATIONS,
             SequenceAnnotationOrder.NONE.name());
     final String TRUE = Boolean.TRUE.toString();
-    Cache.applicationProperties.setProperty(
-            Preferences.SHOW_AUTOCALC_ABOVE, TRUE);
+    Cache.applicationProperties.setProperty(Preferences.SHOW_AUTOCALC_ABOVE,
+            TRUE);
     Cache.applicationProperties.setProperty("SHOW_QUALITY", TRUE);
     Cache.applicationProperties.setProperty("SHOW_CONSERVATION", TRUE);
     Cache.applicationProperties.setProperty("SHOW_IDENTITY", TRUE);
@@ -98,11 +108,9 @@ public class AnnotationChooserTest
    * Add 4 annotations, 3 of them sequence-specific.
    * 
    * <PRE>
-   * ann1 - for sequence 0 - label 'IUPRED' 
-   * ann2 - not sequence related - label 'Beauty' 
-   * ann3 - for sequence 3 - label 'JMol'
-   * ann4 - for sequence 2 - label 'IUPRED'
-   * ann5 - for sequence 1 - label 'JMol'
+   * ann1 - for sequence 0 - label 'IUPRED' ann2 - not sequence related - label
+   * 'Beauty' ann3 - for sequence 3 - label 'JMol' ann4 - for sequence 2 - label
+   * 'IUPRED' ann5 - for sequence 1 - label 'JMol'
    */
   private void addAnnotations()
   {
@@ -174,8 +182,8 @@ public class AnnotationChooserTest
     assertTrue("Not enabled", cb1.isEnabled());
     assertTrue("Not enabled", cb2.isEnabled());
     assertTrue("Not enabled", cb3.isEnabled());
-    assertEquals("Option not selected", cb2, cb2.getCheckboxGroup()
-            .getSelectedCheckbox());
+    assertEquals("Option not selected", cb2,
+            cb2.getCheckboxGroup().getSelectedCheckbox());
 
     // check state variables match checkbox selection
     assertTrue(testee.isApplyToSelectedSequences());
@@ -225,15 +233,16 @@ public class AnnotationChooserTest
     assertTrue("Not enabled", cb1.isEnabled());
     assertFalse("Enabled", cb2.isEnabled());
     assertFalse("Enabled", cb3.isEnabled());
-    assertEquals("Not selected", cb1, cb1.getCheckboxGroup()
-            .getSelectedCheckbox());
+    assertEquals("Not selected", cb1,
+            cb1.getCheckboxGroup().getSelectedCheckbox());
 
     // check state variables match checkbox selection
     assertTrue(testee.isApplyToSelectedSequences());
     assertTrue(testee.isApplyToUnselectedSequences());
 
     assertEquals("Wrong text",
-            MessageManager.getString("label.all_sequences"), cb1.getLabel());
+            MessageManager.getString("label.all_sequences"),
+            cb1.getLabel());
     assertEquals("Wrong text",
             MessageManager.getString("label.selected_sequences"),
             cb2.getLabel());
@@ -267,8 +276,8 @@ public class AnnotationChooserTest
     assertTrue("Hide not enabled", cb2.isEnabled());
 
     // Hide (button 2) selected; note this may change to none (null)
-    assertEquals("Not selected", cb2, cb2.getCheckboxGroup()
-            .getSelectedCheckbox());
+    assertEquals("Not selected", cb2,
+            cb2.getCheckboxGroup().getSelectedCheckbox());
 
     assertTrue("Show is flagged", !testee.isShowSelected());
 
@@ -308,15 +317,15 @@ public class AnnotationChooserTest
     // selection group should make no difference to the result
     // as all annotation types for the alignment are considered
 
-    List<String> types = AnnotationChooser.getAnnotationTypes(
-            parentPanel.getAlignment(), true);
+    List<String> types = AnnotationChooser
+            .getAnnotationTypes(parentPanel.getAlignment(), true);
     assertEquals("Not two annotation types", 2, types.size());
     assertTrue("IUPRED missing", types.contains("IUPRED"));
     assertTrue("JMol missing", types.contains("JMol"));
 
-    types = AnnotationChooser.getAnnotationTypes(
-            parentPanel.getAlignment(), false);
-    assertEquals("Not six annotation types", 6, types.size());
+    types = AnnotationChooser.getAnnotationTypes(parentPanel.getAlignment(),
+            false);
+    assertEquals("Not six annotation types", 7, types.size());
     assertTrue("IUPRED missing", types.contains("IUPRED"));
     assertTrue("JMol missing", types.contains("JMol"));
     assertTrue("Beauty missing", types.contains("Beauty"));
@@ -324,6 +333,7 @@ public class AnnotationChooserTest
     assertTrue("Consensus missing", types.contains("Consensus"));
     assertTrue("Quality missing", types.contains("Quality"));
     assertTrue("Conservation missing", types.contains("Conservation"));
+    assertTrue("Occupancy missing", types.contains("Occupancy"));
   }
 
   /**
@@ -340,25 +350,27 @@ public class AnnotationChooserTest
     final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1);
     setSelected(hideCheckbox, true);
 
-    final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee,
-            1, 1, 0);
+    final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee, 1,
+            1, 0);
     setSelected(allSequencesCheckbox, true);
 
     AlignmentAnnotation[] anns = parentPanel.getAlignment()
             .getAlignmentAnnotation();
 
-    assertTrue(anns[5].visible); // JMol for seq3
-    assertTrue(anns[7].visible); // JMol for seq1
+    int autocalc = countAutocalc(anns);
+    assertTrue(anns[autocalc + 2].visible); // JMol for seq3
+    assertTrue(anns[autocalc + 4].visible); // JMol for seq1
 
     setSelected(getTypeCheckbox("JMol"), true);
     assertTrue(anns[0].visible); // Conservation
     assertTrue(anns[1].visible); // Quality
     assertTrue(anns[2].visible); // Consensus
-    assertTrue(anns[3].visible); // IUPred for seq0
-    assertTrue(anns[4].visible); // Beauty
-    assertFalse(anns[5].visible); // JMol for seq3 - not selected but hidden
-    assertTrue(anns[6].visible); // IUPRED for seq2
-    assertFalse(anns[7].visible); // JMol for seq1 - selected and hidden
+    assertTrue(anns[3].visible); // Occupancy
+    assertTrue(anns[4].visible); // IUPred for seq0
+    assertTrue(anns[5].visible); // Beauty
+    assertFalse(anns[6].visible); // JMol for seq3 - not selected but hidden
+    assertTrue(anns[7].visible); // IUPRED for seq2
+    assertFalse(anns[8].visible); // JMol for seq1 - selected and hidden
   }
 
   /**
@@ -385,17 +397,19 @@ public class AnnotationChooserTest
     AlignmentAnnotation[] anns = parentPanel.getAlignment()
             .getAlignmentAnnotation();
 
-    assertTrue(anns[7].visible); // JMol for seq1
+    int autocalc = countAutocalc(anns);
+    assertTrue(anns[autocalc + 4].visible); // JMol for seq1
 
     setSelected(getTypeCheckbox("JMol"), true);
     assertTrue(anns[0].visible); // Conservation
     assertTrue(anns[1].visible); // Quality
     assertTrue(anns[2].visible); // Consensus
-    assertTrue(anns[3].visible); // IUPred for seq0
-    assertTrue(anns[4].visible); // Beauty
-    assertTrue(anns[5].visible); // JMol for seq3 not in selection group
-    assertTrue(anns[6].visible); // IUPRED for seq2
-    assertFalse(anns[7].visible); // JMol for seq1 in selection group
+    assertTrue(anns[3].visible); // Occupancy
+    assertTrue(anns[4].visible); // IUPred for seq0
+    assertTrue(anns[5].visible); // Beauty
+    assertTrue(anns[6].visible); // JMol for seq3 not in selection group
+    assertTrue(anns[7].visible); // IUPRED for seq2
+    assertFalse(anns[8].visible); // JMol for seq1 in selection group
   }
 
   /**
@@ -414,8 +428,8 @@ public class AnnotationChooserTest
     final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1);
     setSelected(hideCheckbox, true);
 
-    final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee,
-            1, 1, 0);
+    final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee, 1,
+            1, 0);
     setSelected(allSequencesCheckbox, true);
 
     AlignmentAnnotation[] anns = parentPanel.getAlignment()
@@ -425,19 +439,35 @@ public class AnnotationChooserTest
 
     // select JMol - all hidden
     setSelected(typeCheckbox, true);
-    assertFalse(anns[5].visible); // JMol for seq3
-    assertFalse(anns[7].visible); // JMol for seq1
+    int autocalc = countAutocalc(anns);
+    assertFalse(anns[autocalc + 2].visible); // JMol for seq3
+    assertFalse(anns[autocalc + 4].visible); // JMol for seq1
 
     // deselect JMol - all unhidden
     setSelected(typeCheckbox, false);
-    assertTrue(anns[0].visible); // Conservation
-    assertTrue(anns[1].visible); // Quality
-    assertTrue(anns[2].visible); // Consensus
-    assertTrue(anns[3].visible); // IUPred for seq0
-    assertTrue(anns[4].visible); // Beauty
-    assertTrue(anns[5].visible); // JMol for seq3
-    assertTrue(anns[6].visible); // IUPRED for seq2
-    assertTrue(anns[7].visible); // JMol for seq1
+    for (AlignmentAnnotation ann : anns)
+    {
+      assertTrue(ann.visible);
+    }
+  }
+
+  /**
+   * Returns a count of autocalculated annotations in the set provided
+   * 
+   * @param anns
+   * @return
+   */
+  private int countAutocalc(AlignmentAnnotation[] anns)
+  {
+    int count = 0;
+    for (AlignmentAnnotation ann : anns)
+    {
+      if (ann.autoCalculated)
+      {
+        count++;
+      }
+    }
+    return count;
   }
 
   /**
@@ -490,8 +520,8 @@ public class AnnotationChooserTest
     final Checkbox showCheckbox = (Checkbox) getComponent(testee, 1, 0, 0);
     final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1);
 
-    final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee,
-            1, 1, 0);
+    final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee, 1,
+            1, 0);
 
     AlignmentAnnotation[] anns = parentPanel.getAlignment()
             .getAlignmentAnnotation();
@@ -500,18 +530,15 @@ public class AnnotationChooserTest
     setSelected(allSequencesCheckbox, true);
     setSelected(hideCheckbox, true);
     setSelected(getTypeCheckbox("JMol"), true);
-    assertFalse(anns[5].visible); // JMol for seq3
-    assertFalse(anns[7].visible); // JMol for seq1
+    int autocalc = countAutocalc(anns);
+    assertFalse(anns[autocalc + 2].visible); // JMol for seq3
+    assertFalse(anns[autocalc + 4].visible); // JMol for seq1
     // ...now show them...
     setSelected(showCheckbox, true);
-    assertTrue(anns[0].visible); // Conservation
-    assertTrue(anns[1].visible); // Quality
-    assertTrue(anns[2].visible); // Consensus
-    assertTrue(anns[3].visible); // IUPred for seq0
-    assertTrue(anns[4].visible); // Beauty
-    assertTrue(anns[5].visible); // JMol for seq3
-    assertTrue(anns[6].visible); // IUPRED for seq2
-    assertTrue(anns[7].visible); // JMol for seq1
+    for (AlignmentAnnotation ann : anns)
+    {
+      assertTrue(ann.visible);
+    }
   }
 
   /**
@@ -541,19 +568,16 @@ public class AnnotationChooserTest
     setSelected(hideCheckbox, true);
     setSelected(getTypeCheckbox("JMol"), true);
 
-    assertTrue(anns[5].visible); // JMol for seq3
-    assertFalse(anns[7].visible); // JMol for seq1
+    int autocalc = countAutocalc(anns);
+    assertTrue(anns[autocalc + 2].visible); // JMol for seq3
+    assertFalse(anns[autocalc + 4].visible); // JMol for seq1
     // ...now show them...
     setSelected(showCheckbox, true);
 
-    assertTrue(anns[0].visible); // Conservation
-    assertTrue(anns[1].visible); // Quality
-    assertTrue(anns[2].visible); // Consensus
-    assertTrue(anns[3].visible); // IUPred for seq0
-    assertTrue(anns[4].visible); // Beauty
-    assertTrue(anns[5].visible); // JMol for seq3
-    assertTrue(anns[6].visible); // IUPRED for seq2
-    assertTrue(anns[7].visible); // JMol for seq1
+    for (AlignmentAnnotation ann : anns)
+    {
+      assertTrue(ann.visible);
+    }
   }
 
   /**
@@ -572,8 +596,8 @@ public class AnnotationChooserTest
     final Checkbox showCheckbox = (Checkbox) getComponent(testee, 1, 0, 0);
     setSelected(showCheckbox, true);
 
-    final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee,
-            1, 1, 0);
+    final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee, 1,
+            1, 0);
     setSelected(allSequencesCheckbox, true);
 
     AlignmentAnnotation[] anns = parentPanel.getAlignment()
@@ -582,19 +606,21 @@ public class AnnotationChooserTest
     final Checkbox typeCheckbox = getTypeCheckbox("JMol");
     // select JMol - all shown
     setSelected(typeCheckbox, true);
-    assertTrue(anns[5].visible); // JMol for seq3
-    assertTrue(anns[7].visible); // JMol for seq1
+    int autocalc = countAutocalc(anns);
+    assertTrue(anns[autocalc + 2].visible); // JMol for seq3
+    assertTrue(anns[autocalc + 4].visible); // JMol for seq1
 
     // deselect JMol - all hidden
     setSelected(typeCheckbox, false);
     assertTrue(anns[0].visible); // Conservation
     assertTrue(anns[1].visible); // Quality
     assertTrue(anns[2].visible); // Consensus
-    assertTrue(anns[3].visible); // IUPred for seq0
-    assertTrue(anns[4].visible); // Beauty
-    assertFalse(anns[5].visible); // JMol for seq3
-    assertTrue(anns[6].visible); // IUPRED for seq2
-    assertFalse(anns[7].visible); // JMol for seq1
+    assertTrue(anns[3].visible); // Occupancy
+    assertTrue(anns[4].visible); // IUPred for seq0
+    assertTrue(anns[5].visible); // Beauty
+    assertFalse(anns[6].visible); // JMol for seq3
+    assertTrue(anns[7].visible); // IUPRED for seq2
+    assertFalse(anns[8].visible); // JMol for seq1
   }
 
   /**
@@ -623,19 +649,21 @@ public class AnnotationChooserTest
 
     // select JMol - should remain visible
     setSelected(getTypeCheckbox("JMol"), true);
-    assertTrue(anns[5].visible); // JMol for seq3
-    assertTrue(anns[7].visible); // JMol for seq1
+    int autocalc = countAutocalc(anns);
+    assertTrue(anns[autocalc + 2].visible); // JMol for seq3
+    assertTrue(anns[autocalc + 4].visible); // JMol for seq1
 
     // deselect JMol - should be hidden for selected sequences only
     setSelected(getTypeCheckbox("JMol"), false);
     assertTrue(anns[0].visible); // Conservation
     assertTrue(anns[1].visible); // Quality
     assertTrue(anns[2].visible); // Consensus
-    assertTrue(anns[3].visible); // IUPred for seq0
-    assertTrue(anns[4].visible); // Beauty
-    assertTrue(anns[5].visible); // JMol for seq3 not in selection group
-    assertTrue(anns[6].visible); // IUPRED for seq2
-    assertFalse(anns[7].visible); // JMol for seq1 in selection group
+    assertTrue(anns[3].visible); // Occupancy
+    assertTrue(anns[4].visible); // IUPred for seq0
+    assertTrue(anns[5].visible); // Beauty
+    assertTrue(anns[6].visible); // JMol for seq3 not in selection group
+    assertTrue(anns[7].visible); // IUPRED for seq2
+    assertFalse(anns[8].visible); // JMol for seq1 in selection group
   }
 
   /**
@@ -668,9 +696,9 @@ public class AnnotationChooserTest
     // TODO refactor to a test utility class
     cb.setState(select);
     // have to manually fire the action listener
-    cb.getItemListeners()[0].itemStateChanged(new ItemEvent(cb,
-            ItemEvent.ITEM_STATE_CHANGED, cb, select ? ItemEvent.SELECTED
-                    : ItemEvent.DESELECTED));
+    cb.getItemListeners()[0].itemStateChanged(
+            new ItemEvent(cb, ItemEvent.ITEM_STATE_CHANGED, cb,
+                    select ? ItemEvent.SELECTED : ItemEvent.DESELECTED));
   }
 
   /**
@@ -711,12 +739,12 @@ public class AnnotationChooserTest
 
     AlignmentAnnotation[] anns = parentPanel.getAlignment()
             .getAlignmentAnnotation();
-    // remember 3 annotations to skip (Conservation/Quality/Consensus)
-    assertFalse(testee.isInActionScope(anns[3]));
-    assertFalse(testee.isInActionScope(anns[4]));
-    assertFalse(testee.isInActionScope(anns[5]));
-    assertTrue(testee.isInActionScope(anns[6]));
-    assertTrue(testee.isInActionScope(anns[7]));
+    int autocalc = countAutocalc(anns);
+    assertFalse(testee.isInActionScope(anns[autocalc]));
+    assertFalse(testee.isInActionScope(anns[autocalc + 1]));
+    assertFalse(testee.isInActionScope(anns[autocalc + 2]));
+    assertTrue(testee.isInActionScope(anns[autocalc + 3]));
+    assertTrue(testee.isInActionScope(anns[autocalc + 4]));
   }
 
   /**
@@ -737,12 +765,12 @@ public class AnnotationChooserTest
 
     AlignmentAnnotation[] anns = parentPanel.getAlignment()
             .getAlignmentAnnotation();
-    // remember 3 annotations to skip (Conservation/Quality/Consensus)
-    assertTrue(testee.isInActionScope(anns[3]));
-    assertTrue(testee.isInActionScope(anns[4]));
-    assertTrue(testee.isInActionScope(anns[5]));
-    assertFalse(testee.isInActionScope(anns[6]));
-    assertFalse(testee.isInActionScope(anns[7]));
+    int autocalc = countAutocalc(anns);
+    assertTrue(testee.isInActionScope(anns[autocalc]));
+    assertTrue(testee.isInActionScope(anns[autocalc + 1]));
+    assertTrue(testee.isInActionScope(anns[autocalc + 2]));
+    assertFalse(testee.isInActionScope(anns[autocalc + 3]));
+    assertFalse(testee.isInActionScope(anns[autocalc + 4]));
   }
 
   /**
@@ -767,8 +795,8 @@ public class AnnotationChooserTest
     final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1);
     setSelected(hideCheckbox, true);
 
-    final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee,
-            1, 1, 0);
+    final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee, 1,
+            1, 0);
     setSelected(allSequencesCheckbox, true);
 
     setSelected(getTypeCheckbox("JMol"), true);
@@ -777,11 +805,12 @@ public class AnnotationChooserTest
     assertTrue(anns[0].visible); // Conservation
     assertTrue(anns[1].visible); // Quality
     assertTrue(anns[2].visible); // Consensus
-    assertFalse(anns[3].visible); // IUPRED
-    assertTrue(anns[4].visible); // Beauty (not seq-related)
-    assertFalse(anns[5].visible); // JMol
-    assertFalse(anns[6].visible); // IUPRED
-    assertFalse(anns[7].visible); // JMol
+    assertTrue(anns[3].visible); // Occupancy
+    assertFalse(anns[4].visible); // IUPRED
+    assertTrue(anns[5].visible); // Beauty (not seq-related)
+    assertFalse(anns[6].visible); // JMol
+    assertFalse(anns[7].visible); // IUPRED
+    assertFalse(anns[8].visible); // JMol
 
     // reset - should all be visible
     testee.resetOriginalState();