JAL-32423 tidying

diff --git a/src/jalview/io/cache/JvCacheableInputBox.java b/src/jalview/io/cache/JvCacheableInputBox.java
index e02a396..3f17172 100644 (file)
--- a/src/jalview/io/cache/JvCacheableInputBox.java
+++ b/src/jalview/io/cache/JvCacheableInputBox.java
@@ -243,13 +243,14 @@ public class JvCacheableInputBox<E>
   }
 
   /**
-   * For TestNG
-   * 
-   * @author Bob Hanson 2019.08.28
+   * Updates the cached values to include the last user input as the most
+   * recently added (without duplication), and rebuilds the dropdown list with
+   * this as the first entry. If the maximum configured cache size would be
+   * exceeded, the oldest entry is removed.
    */
-  public void updateCacheNow()
+  void updateCacheNow()
   {
-    int cacheLimit = Integer.parseInt(appCache.getCacheLimit(cacheKey));
+    int cacheLimit = Integer.valueOf(appCache.getCacheLimit(cacheKey));
     String userInput = getUserInput();
     if (userInput != null && !userInput.isEmpty())
     {

diff --git a/src/jalview/ws/seqfetcher/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
index e205e76..97babfd 100644 (file)
--- a/src/jalview/ws/seqfetcher/ASequenceFetcher.java
+++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
@@ -355,7 +355,6 @@ public class ASequenceFetcher
     {
       try
       {
-        System.err.println("ASeqFetch " + className);
         return (DbSourceProxy) Class.forName(className).newInstance();
       } catch (Exception e)
       {

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index 3ba93bc..891a203 100644 (file)
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -274,7 +274,7 @@ public class AlignViewportTest
    * Test for JAL-1306 - conservation thread should run even when only Quality
    * (and not Conservation) is enabled in Preferences
    */
-  @Test(groups = { "Functional" }, timeOut = 2000) // BH removed timeOut=2000
+  @Test(groups = { "Functional" }, timeOut = 2000)
   public void testUpdateConservation_qualityOnly()
   {
     Cache.setPropertyNoSave("SHOW_ANNOTATIONS",
@@ -296,8 +296,8 @@ public class AlignViewportTest
     AlignViewport viewport = af.getViewport();
     synchronized (this)
     {
-      System.out.println("AVT consv: "
-              + viewport.getAlignmentConservationAnnotation());
+      // System.out.println("AVT consv: "
+      // + viewport.getAlignmentConservationAnnotation());
       try
       {
         wait(250); // BH increased from 50 -- was getting Quality in column 1
@@ -305,8 +305,8 @@ public class AlignViewportTest
       } catch (InterruptedException e)
       {
       }
-      System.out.println("AVT consv: "
-              + viewport.getAlignmentConservationAnnotation());
+      // System.out.println("AVT consv: "
+      // + viewport.getAlignmentConservationAnnotation());
       while (viewport.getAlignmentConservationAnnotation() != null)
       {
         try
@@ -488,7 +488,7 @@ public class AlignViewportTest
     // af.paintImmediately(af.getBounds());
     AlignViewport testme = af.getViewport();
     SequenceI cons = testme.getConsensusSeq();
-    System.out.println("AVT " + cons.getSequenceAsString());
+    // System.out.println("AVT " + cons.getSequenceAsString());
     assertEquals("A-C", cons.getSequenceAsString());
   }
 

diff --git a/test/jalview/gui/AlignmentPanelTest.java b/test/jalview/gui/AlignmentPanelTest.java
index 4d1a730..80dc939 100644 (file)
--- a/test/jalview/gui/AlignmentPanelTest.java
+++ b/test/jalview/gui/AlignmentPanelTest.java
@@ -168,7 +168,7 @@ public class AlignmentPanelTest
    * or without hidden columns
    */
   @Test(groups = "Functional")
-  public void TestSetScrollValues()
+  public void testSetScrollValues()
   {
     ViewportRanges ranges = af.getViewport().getRanges();
     af.alignPanel.setScrollValues(0, 0);
@@ -233,19 +233,19 @@ public class AlignmentPanelTest
    * when switching from wrapped back to unwrapped mode (JAL-2739)
    */
   @Test(groups = "Functional")
-  public void TestUpdateLayout_endRes()
+  public void testUpdateLayout_endRes()
   {
     // get details of original alignment dimensions
     ViewportRanges ranges = af.getViewport().getRanges();
     int endres = ranges.getEndRes();
 
-    System.out.println("APT range end0 " + ranges.getEndRes());
+    // System.out.println("APT range end0 " + ranges.getEndRes());
     // wrap
     af.alignPanel.getAlignViewport().setWrapAlignment(true);
     af.alignPanel.updateLayout();
     af.paintImmediately(af.getBounds());
     waitSome();
-    System.out.println("APT range end1 " + ranges.getEndRes());
+    // System.out.println("APT range end1 " + ranges.getEndRes());
     // endRes has changed
     assertNotEquals(ranges.getEndRes(), endres);
 
@@ -255,7 +255,7 @@ public class AlignmentPanelTest
     waitSome();
     af.paintImmediately(af.getBounds());
 
-    System.out.println("APT range end3 " + ranges.getEndRes());
+    // System.out.println("APT range end3 " + ranges.getEndRes());
 
     // endRes back to original value
     assertEquals(ranges.getEndRes(), endres);

diff --git a/test/jalview/gui/SeqCanvasTest.java b/test/jalview/gui/SeqCanvasTest.java
index 25c4862..801c778 100644 (file)
--- a/test/jalview/gui/SeqCanvasTest.java
+++ b/test/jalview/gui/SeqCanvasTest.java
@@ -48,7 +48,7 @@ public class SeqCanvasTest
    * Test the method that computes wrapped width in residues, height of wrapped
    * widths in pixels, and the number of widths visible
    */
-  @Test(groups = "BHTEST")
+  @Test(groups = "Functional")
   public void testCalculateWrappedGeometry_noAnnotations()
   {
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
@@ -219,7 +219,7 @@ public class SeqCanvasTest
    * Test the method that computes wrapped width in residues, height of wrapped
    * widths in pixels, and the number of widths visible
    */
-  @Test(groups = "BHTEST")
+  @Test(groups = "Functional")
   public void testCalculateWrappedGeometry_withAnnotations()
   {
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
@@ -321,7 +321,7 @@ public class SeqCanvasTest
    * endSeq should be unchanged, but the vertical repeat height should include
    * all sequences.
    */
-  @Test(groups = "BHTEST")
+  @Test(groups = "Functional")
   public void testCalculateWrappedGeometry_fromScrolled()
   {
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
@@ -331,24 +331,12 @@ public class SeqCanvasTest
     assertEquals(al.getWidth(), 157);
     assertEquals(al.getHeight(), 15);
     av.getRanges().setStartEndSeq(0, 3);
-    System.out.println("SCT1 " + av.getRanges().getEndSeq());
     av.setShowAnnotation(false);
     av.setScaleAboveWrapped(true);
 
-    System.out.println("SCT2 " + av.getRanges().getEndSeq());
-
     SeqCanvas testee = af.alignPanel.getSeqPanel().seqCanvas;
-
-    System.out.println("SCT3 " + av.getRanges().getEndSeq());
-
     av.setWrapAlignment(true);
-
-    System.out.println("SCT4 " + av.getRanges().getEndSeq());
-
     av.setFont(new Font("SansSerif", Font.PLAIN, 14), true);
-
-    System.out.println("SCT5 " + av.getRanges().getEndSeq());
-
     int charHeight = av.getCharHeight();
     int charWidth = av.getCharWidth();
     // Windows h=19, w=11.
@@ -359,8 +347,6 @@ public class SeqCanvasTest
     int canvasHeight = 300;
     testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
 
-    System.out.println("SCT6 " + av.getRanges().getEndSeq());
-
     assertEquals(av.getRanges().getEndSeq(), 3); // unchanged
     int repeatingHeight = (int) PA.getValue(testee,
             "wrappedRepeatHeightPx");

diff --git a/test/jalview/gui/SeqPanelTest.java b/test/jalview/gui/SeqPanelTest.java
index c148039..fd611fc 100644 (file)
--- a/test/jalview/gui/SeqPanelTest.java
+++ b/test/jalview/gui/SeqPanelTest.java
@@ -724,9 +724,6 @@ public class SeqPanelTest
     final int charWidth = alignFrame.getViewport().getCharWidth();
     assertTrue(charWidth > 0); // sanity check
     assertEquals(alignFrame.getViewport().getRanges().getStartRes(), 0);
-
-    System.out.println("SPT endres "
-            + alignFrame.getViewport().getRanges().getEndRes());
     /*
      * mouse at top left of unwrapped panel
      */
@@ -767,16 +764,6 @@ public class SeqPanelTest
     SeqCanvas seqCanvas = alignFrame.alignPanel.getSeqPanel().seqCanvas;
     int w = seqCanvas.getWidth();
     // limited to number of whole columns, base 0
-    // BH there are only 61 residues, but this calculation gives 65
-    // from SeqPanel return for findColumn:
-
-    // /*
-    // * make sure we calculate relative to visible alignment,
-    // * rather than right-hand gutter
-    // */
-    // x = Math.min(x, seqCanvas.getX() + seqCanvas.getWidth());
-    // res = (x / charWidth) + startRes;
-    // res = Math.min(res, av.getRanges().getEndRes());
 
     int expected = w / charWidth;
     expected = Math.min(

diff --git a/test/jalview/io/cache/JvCacheableInputBoxTest.java b/test/jalview/io/cache/JvCacheableInputBoxTest.java
index 73aae61..7a2f8b4 100644 (file)
--- a/test/jalview/io/cache/JvCacheableInputBoxTest.java
+++ b/test/jalview/io/cache/JvCacheableInputBoxTest.java
@@ -31,18 +31,7 @@ public class JvCacheableInputBoxTest
     String testInput = "TestInput";
     cacheBox.addItem(testInput);
     cacheBox.setSelectedItem(testInput);
-    cacheBox.updateCacheNow();
-
-    // try
-    // {
-    // // This delay is essential to prevent the
-    // // assertion below from executing before
-    // // swing thread finishes updating the combo-box
-    // Thread.sleep(100);
-    // } catch (InterruptedException e)
-    // {
-    // e.printStackTrace();
-    // }
+    cacheBox.updateCacheNow(); // synchronous update
     userInput = cacheBox.getUserInput();
     Assert.assertEquals(testInput, userInput);
   }
@@ -54,19 +43,6 @@ public class JvCacheableInputBoxTest
     cacheBox.addItem(testInput);
     cacheBox.setSelectedItem(testInput);
     cacheBox.updateCacheNow();
-    // synchronized (this)
-    // {
-    // try
-    // {
-    // wait(100);
-    // // This delay is to let
-    // // cacheBox.updateCache() finish updating the cache
-    // Thread.sleep(200);
-    // } catch (InterruptedException e)
-    // {
-    // e.printStackTrace();
-    // }
-    // }
     LinkedHashSet<String> foundCache = appCache
             .getAllCachedItemsFor(TEST_CACHE_KEY);
     Assert.assertTrue(foundCache.contains(testInput));

diff --git a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
index 43382f8..eab8805 100644 (file)
--- a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
@@ -75,8 +75,13 @@ public class FeatureColourFinderTest
   @BeforeMethod(alwaysRun = true)
   public void setUpBeforeTest()
   {
-    //required for Windows, only when in batch mode?
-         setUp();
+    /*
+     * fudge for failure in test suite on Windows;
+     * without this call added, av.getAlignment() is null;
+     * root cause not known - AlignViewport.dispose() called??
+     */
+    setUp();
+
     List<SequenceFeature> sfs = seq.getSequenceFeatures();
     for (SequenceFeature sf : sfs)
     {