X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAnnotationChooserTest.java;fp=test%2Fjalview%2Fgui%2FAnnotationChooserTest.java;h=cf97711a971e16e584f8518eb769ce5aa95331d8;hb=4762b29420ed4df01b55a8afe5ab05467aaf41a9;hp=38c18555ae8d5c11e3cba3fef595fb2e653d1dd0;hpb=29c183b0d0de9f6f9f94d2b528d10e20b1891684;p=jalview.git

diff --git a/test/jalview/gui/AnnotationChooserTest.java b/test/jalview/gui/AnnotationChooserTest.java
index 38c1855..cf97711 100644
--- a/test/jalview/gui/AnnotationChooserTest.java
+++ b/test/jalview/gui/AnnotationChooserTest.java
@@ -60,6 +60,11 @@ import org.testng.annotations.Test;
  */
 public class AnnotationChooserTest
 {
+  /*
+   * number of automatically computed annotation rows
+   * (Conservation, Quality, Consensus, Occupancy)
+   */
+  private static final int AUTOCALCD = 4;
 
   @BeforeClass(alwaysRun = true)
   public void setUpJvOptionPane()
@@ -326,7 +331,7 @@ public class AnnotationChooserTest
 
     types = AnnotationChooser.getAnnotationTypes(
             parentPanel.getAlignment(), false);
-    assertEquals("Not six annotation types", 6, types.size());
+    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"));
@@ -334,6 +339,7 @@ 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"));
   }
 
   /**
@@ -357,18 +363,19 @@ public class AnnotationChooserTest
     AlignmentAnnotation[] anns = parentPanel.getAlignment()
             .getAlignmentAnnotation();
 
-    assertTrue(anns[5].visible); // JMol for seq3
-    assertTrue(anns[7].visible); // JMol for seq1
+    assertTrue(anns[AUTOCALCD + 2].visible); // JMol for seq3
+    assertTrue(anns[AUTOCALCD + 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
   }
 
   /**
@@ -395,17 +402,18 @@ public class AnnotationChooserTest
     AlignmentAnnotation[] anns = parentPanel.getAlignment()
             .getAlignmentAnnotation();
 
-    assertTrue(anns[7].visible); // JMol for seq1
+    assertTrue(anns[AUTOCALCD + 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
   }
 
   /**
@@ -435,19 +443,20 @@ public class AnnotationChooserTest
 
     // select JMol - all hidden
     setSelected(typeCheckbox, true);
-    assertFalse(anns[5].visible); // JMol for seq3
-    assertFalse(anns[7].visible); // JMol for seq1
+    assertFalse(anns[AUTOCALCD + 2].visible); // JMol for seq3
+    assertFalse(anns[AUTOCALCD + 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
+    assertTrue(anns[3].visible); // Occupancy
+    assertTrue(anns[4].visible); // IUPred for seq0
+    assertTrue(anns[5].visible); // Beauty
+    assertTrue(anns[6].visible); // JMol for seq3
+    assertTrue(anns[7].visible); // IUPRED for seq2
+    assertTrue(anns[8].visible); // JMol for seq1
   }
 
   /**
@@ -510,18 +519,19 @@ 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
+    assertFalse(anns[AUTOCALCD + 2].visible); // JMol for seq3
+    assertFalse(anns[AUTOCALCD + 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
+    assertTrue(anns[3].visible); // Occupancy
+    assertTrue(anns[4].visible); // IUPred for seq0
+    assertTrue(anns[5].visible); // Beauty
+    assertTrue(anns[6].visible); // JMol for seq3
+    assertTrue(anns[7].visible); // IUPRED for seq2
+    assertTrue(anns[8].visible); // JMol for seq1
   }
 
   /**
@@ -551,19 +561,20 @@ public class AnnotationChooserTest
     setSelected(hideCheckbox, true);
     setSelected(getTypeCheckbox("JMol"), true);
 
-    assertTrue(anns[5].visible); // JMol for seq3
-    assertFalse(anns[7].visible); // JMol for seq1
+    assertTrue(anns[AUTOCALCD + 2].visible); // JMol for seq3
+    assertFalse(anns[AUTOCALCD + 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
+    assertTrue(anns[3].visible); // Occupancy
+    assertTrue(anns[4].visible); // IUPred for seq0
+    assertTrue(anns[5].visible); // Beauty
+    assertTrue(anns[6].visible); // JMol for seq3
+    assertTrue(anns[7].visible); // IUPRED for seq2
+    assertTrue(anns[8].visible); // JMol for seq1
   }
 
   /**
@@ -592,19 +603,20 @@ 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
+    assertTrue(anns[AUTOCALCD + 2].visible); // JMol for seq3
+    assertTrue(anns[AUTOCALCD + 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
   }
 
   /**
@@ -633,19 +645,20 @@ 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
+    assertTrue(anns[AUTOCALCD + 2].visible); // JMol for seq3
+    assertTrue(anns[AUTOCALCD + 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
   }
 
   /**
@@ -721,12 +734,11 @@ 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]));
+    assertFalse(testee.isInActionScope(anns[AUTOCALCD]));
+    assertFalse(testee.isInActionScope(anns[AUTOCALCD + 1]));
+    assertFalse(testee.isInActionScope(anns[AUTOCALCD + 2]));
+    assertTrue(testee.isInActionScope(anns[AUTOCALCD + 3]));
+    assertTrue(testee.isInActionScope(anns[AUTOCALCD + 4]));
   }
 
   /**
@@ -747,12 +759,11 @@ 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]));
+    assertTrue(testee.isInActionScope(anns[AUTOCALCD]));
+    assertTrue(testee.isInActionScope(anns[AUTOCALCD + 1]));
+    assertTrue(testee.isInActionScope(anns[AUTOCALCD + 2]));
+    assertFalse(testee.isInActionScope(anns[AUTOCALCD + 3]));
+    assertFalse(testee.isInActionScope(anns[AUTOCALCD + 4]));
   }
 
   /**
@@ -787,11 +798,12 @@ 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();