From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 1 Mar 2017 15:19:09 +0000 (+0000)
Subject: JAL-1264 smarter way to skip autocalc'd annotations in asserts
X-Git-Tag: Release_2_10_2~3^2~172
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=29ee0c7591b0ce7b07abc34a219f532f9b914ac0;p=jalview.git

JAL-1264 smarter way to skip autocalc'd annotations in asserts
---

diff --git a/test/jalview/gui/AnnotationChooserTest.java b/test/jalview/gui/AnnotationChooserTest.java
index cf97711..fbdda09 100644
--- a/test/jalview/gui/AnnotationChooserTest.java
+++ b/test/jalview/gui/AnnotationChooserTest.java
@@ -60,11 +60,6 @@ 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()
@@ -363,8 +358,9 @@ public class AnnotationChooserTest
     AlignmentAnnotation[] anns = parentPanel.getAlignment()
             .getAlignmentAnnotation();
 
-    assertTrue(anns[AUTOCALCD + 2].visible); // JMol for seq3
-    assertTrue(anns[AUTOCALCD + 4].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
@@ -402,7 +398,8 @@ public class AnnotationChooserTest
     AlignmentAnnotation[] anns = parentPanel.getAlignment()
             .getAlignmentAnnotation();
 
-    assertTrue(anns[AUTOCALCD + 4].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
@@ -443,20 +440,35 @@ public class AnnotationChooserTest
 
     // select JMol - all hidden
     setSelected(typeCheckbox, true);
-    assertFalse(anns[AUTOCALCD + 2].visible); // JMol for seq3
-    assertFalse(anns[AUTOCALCD + 4].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); // 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
+    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;
   }
 
   /**
@@ -519,19 +531,15 @@ public class AnnotationChooserTest
     setSelected(allSequencesCheckbox, true);
     setSelected(hideCheckbox, true);
     setSelected(getTypeCheckbox("JMol"), true);
-    assertFalse(anns[AUTOCALCD + 2].visible); // JMol for seq3
-    assertFalse(anns[AUTOCALCD + 4].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); // 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
+    for (AlignmentAnnotation ann : anns)
+    {
+      assertTrue(ann.visible);
+    }
   }
 
   /**
@@ -561,20 +569,16 @@ public class AnnotationChooserTest
     setSelected(hideCheckbox, true);
     setSelected(getTypeCheckbox("JMol"), true);
 
-    assertTrue(anns[AUTOCALCD + 2].visible); // JMol for seq3
-    assertFalse(anns[AUTOCALCD + 4].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); // 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
+    for (AlignmentAnnotation ann : anns)
+    {
+      assertTrue(ann.visible);
+    }
   }
 
   /**
@@ -603,8 +607,9 @@ public class AnnotationChooserTest
     final Checkbox typeCheckbox = getTypeCheckbox("JMol");
     // select JMol - all shown
     setSelected(typeCheckbox, true);
-    assertTrue(anns[AUTOCALCD + 2].visible); // JMol for seq3
-    assertTrue(anns[AUTOCALCD + 4].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);
@@ -645,8 +650,9 @@ public class AnnotationChooserTest
 
     // select JMol - should remain visible
     setSelected(getTypeCheckbox("JMol"), true);
-    assertTrue(anns[AUTOCALCD + 2].visible); // JMol for seq3
-    assertTrue(anns[AUTOCALCD + 4].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);
@@ -734,11 +740,12 @@ public class AnnotationChooserTest
 
     AlignmentAnnotation[] anns = parentPanel.getAlignment()
             .getAlignmentAnnotation();
-    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]));
+    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]));
   }
 
   /**
@@ -759,11 +766,12 @@ public class AnnotationChooserTest
 
     AlignmentAnnotation[] anns = parentPanel.getAlignment()
             .getAlignmentAnnotation();
-    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]));
+    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]));
   }
 
   /**