Merge branch 'develop' into improvement/JAL-4124_dont_duplacate_PAE_data_acrossviews

[jalview.git] / test / jalview / gui / SeqCanvasTest.java

diff --git a/test/jalview/gui/SeqCanvasTest.java b/test/jalview/gui/SeqCanvasTest.java
index 213a1c9..aa50301 100644 (file)
--- a/test/jalview/gui/SeqCanvasTest.java
+++ b/test/jalview/gui/SeqCanvasTest.java
@@ -20,27 +20,31 @@
  */
 package jalview.gui;
 
+import java.awt.Font;
+import java.awt.FontMetrics;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertNotNull;
 import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertTrue;
 
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
 import jalview.io.DataSourceType;
+import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
 
-import java.awt.Font;
-import java.awt.FontMetrics;
-
-import org.testng.annotations.Test;
-
 import junit.extensions.PA;
 
 public class SeqCanvasTest
 {
+  private AlignFrame af;
+
   /**
    * Test the method that computes wrapped width in residues, height of wrapped
    * widths in pixels, and the number of widths visible
@@ -48,8 +52,6 @@ public class SeqCanvasTest
   @Test(groups = "Functional")
   public void testCalculateWrappedGeometry_noAnnotations()
   {
-    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
-            "examples/uniref50.fa", DataSourceType.FILE);
     AlignViewport av = af.getViewport();
     AlignmentI al = av.getAlignment();
     assertEquals(al.getWidth(), 157);
@@ -83,13 +85,15 @@ public class SeqCanvasTest
     int canvasWidth = 400;
     int canvasHeight = 300;
     int residueColumns = (canvasWidth - 2 * labelWidth) / charWidth;
-    int wrappedWidth = testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
+    int wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
+            canvasHeight);
     assertEquals(wrappedWidth, residueColumns);
     assertEquals(PA.getValue(testee, "labelWidthWest"), labelWidth);
     assertEquals(PA.getValue(testee, "labelWidthEast"), labelWidth);
     assertEquals(PA.getValue(testee, "wrappedSpaceAboveAlignment"),
             2 * charHeight);
-    int repeatingHeight = (int) PA.getValue(testee, "wrappedRepeatHeightPx");
+    int repeatingHeight = (int) PA.getValue(testee,
+            "wrappedRepeatHeightPx");
     assertEquals(repeatingHeight, charHeight * (2 + al.getHeight()));
     assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 1);
 
@@ -218,13 +222,11 @@ public class SeqCanvasTest
   @Test(groups = "Functional")
   public void testCalculateWrappedGeometry_withAnnotations()
   {
-    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
-            "examples/uniref50.fa", DataSourceType.FILE);
     AlignViewport av = af.getViewport();
     AlignmentI al = av.getAlignment();
     assertEquals(al.getWidth(), 157);
     assertEquals(al.getHeight(), 15);
-  
+
     av.setWrapAlignment(true);
     av.getRanges().setStartEndSeq(0, 14);
     av.setFont(new Font("SansSerif", Font.PLAIN, 14), true);
@@ -232,9 +234,9 @@ public class SeqCanvasTest
     int charWidth = av.getCharWidth();
     assertEquals(charHeight, 17);
     assertEquals(charWidth, 12);
-  
+
     SeqCanvas testee = af.alignPanel.getSeqPanel().seqCanvas;
-  
+
     /*
      * first with scales above, left, right
      */
@@ -254,17 +256,19 @@ public class SeqCanvasTest
     int canvasWidth = 400;
     int canvasHeight = 300;
     int residueColumns = (canvasWidth - 2 * labelWidth) / charWidth;
-    int wrappedWidth = testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
+    int wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
+            canvasHeight);
     assertEquals(wrappedWidth, residueColumns);
     assertEquals(PA.getValue(testee, "labelWidthWest"), labelWidth);
     assertEquals(PA.getValue(testee, "labelWidthEast"), labelWidth);
     assertEquals(PA.getValue(testee, "wrappedSpaceAboveAlignment"),
             2 * charHeight);
-    int repeatingHeight = (int) PA.getValue(testee, "wrappedRepeatHeightPx");
+    int repeatingHeight = (int) PA.getValue(testee,
+            "wrappedRepeatHeightPx");
     assertEquals(repeatingHeight, charHeight * (2 + al.getHeight())
             + SeqCanvas.SEQS_ANNOTATION_GAP + annotationHeight);
     assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 1);
-  
+
     /*
      * repeat height is 17 * (2 + 15) = 289 + 3 + annotationHeight = 510
      * make canvas height 2 of these plus 3 charHeights 
@@ -274,7 +278,7 @@ public class SeqCanvasTest
             + 2 * (annotationHeight + SeqCanvas.SEQS_ANNOTATION_GAP);
     testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
     assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 3);
-  
+
     /*
      * reduce canvas height by 1 pixel - should not be enough height
      * to draw 3 widths
@@ -282,14 +286,14 @@ public class SeqCanvasTest
     canvasHeight -= 1;
     testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
     assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 2);
-  
+
     /*
      * turn off scale above - can now fit in 2 and a bit widths
      */
     av.setScaleAboveWrapped(false);
     testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
     assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 3);
-  
+
     /*
      * reduce height to enough for 2 widths and not quite a third
      * i.e. two repeating heights + spacer + sequence - 1 pixel
@@ -313,23 +317,21 @@ public class SeqCanvasTest
    * endSeq should be unchanged, but the vertical repeat height should include
    * all sequences.
    */
-  @Test(groups = "Functional")
+  @Test(groups = "Functional_Failing")
   public void testCalculateWrappedGeometry_fromScrolled()
   {
-    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
-            "examples/uniref50.fa", DataSourceType.FILE);
     AlignViewport av = af.getViewport();
     AlignmentI al = av.getAlignment();
     assertEquals(al.getWidth(), 157);
     assertEquals(al.getHeight(), 15);
     av.getRanges().setStartEndSeq(0, 3);
+    av.setFont(new Font("SansSerif", Font.PLAIN, 14), true);
+    av.setWrapAlignment(true);
     av.setShowAnnotation(false);
     av.setScaleAboveWrapped(true);
 
     SeqCanvas testee = af.alignPanel.getSeqPanel().seqCanvas;
 
-    av.setWrapAlignment(true);
-    av.setFont(new Font("SansSerif", Font.PLAIN, 14), true);
     int charHeight = av.getCharHeight();
     int charWidth = av.getCharWidth();
     assertEquals(charHeight, 17);
@@ -345,11 +347,32 @@ public class SeqCanvasTest
     assertEquals(repeatingHeight, charHeight * (2 + al.getHeight()));
   }
 
+  @BeforeMethod(alwaysRun = true)
+  public void setUp()
+  {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+            Boolean.TRUE.toString());
+    af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
+            DataSourceType.FILE);
+
+    /*
+     * wait for Consensus thread to complete
+     */
+    do
+    {
+      try
+      {
+        Thread.sleep(50);
+      } catch (InterruptedException x)
+      {
+      }
+    } while (af.getViewport().getCalcManager().isWorking());
+  }
+
   @Test(groups = "Functional")
   public void testClear_HighlightAndSelection()
   {
-    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
-            "examples/uniref50.fa", DataSourceType.FILE);
     AlignViewport av = af.getViewport();
     SearchResultsI highlight = new SearchResults();
     highlight.addResult(