X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAnnotationChooserTest.java;fp=test%2Fjalview%2Fgui%2FAnnotationChooserTest.java;h=fbdda0901945fc7a3db67965499eb4ae3eae6f3b;hb=2595e9d4ee0dbbd3406a98c4e49a61ccde806479;hp=6621a9434beb848f1bcd3c5bc45e5a965955658b;hpb=e20075ba805d744d7cc4976e2b8d5e5840fb0a8d;p=jalview.git

diff --git a/test/jalview/gui/AnnotationChooserTest.java b/test/jalview/gui/AnnotationChooserTest.java
index 6621a94..fbdda09 100644
--- a/test/jalview/gui/AnnotationChooserTest.java
+++ b/test/jalview/gui/AnnotationChooserTest.java
@@ -31,7 +31,9 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -46,6 +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;
 
@@ -57,6 +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"
@@ -86,8 +97,8 @@ public class AnnotationChooserTest
     Cache.applicationProperties.setProperty("SHOW_CONSERVATION", TRUE);
     Cache.applicationProperties.setProperty("SHOW_IDENTITY", TRUE);
 
-    AlignmentI al = new jalview.io.FormatAdapter().readFile(TEST_DATA,
-            AppletFormatAdapter.PASTE, "FASTA");
+    AlignmentI al = new FormatAdapter().readFile(TEST_DATA,
+            DataSourceType.PASTE, FileFormat.Fasta);
     af = new AlignFrame(al, 700, 500);
     parentPanel = new AlignmentPanel(af, af.getViewport());
     addAnnotations();
@@ -315,7 +326,7 @@ 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"));
@@ -323,6 +334,7 @@ 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"));
   }
 
   /**
@@ -346,18 +358,20 @@ public class AnnotationChooserTest
     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
   }
 
   /**
@@ -384,17 +398,19 @@ 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
   }
 
   /**
@@ -424,19 +440,35 @@ 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;
   }
 
   /**
@@ -499,18 +531,15 @@ 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);
+    }
   }
 
   /**
@@ -540,19 +569,16 @@ 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);
+    }
   }
 
   /**
@@ -581,19 +607,21 @@ 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
   }
 
   /**
@@ -622,19 +650,21 @@ 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
   }
 
   /**
@@ -710,12 +740,12 @@ 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]));
   }
 
   /**
@@ -736,12 +766,12 @@ 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]));
   }
 
   /**
@@ -776,11 +806,12 @@ 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();