From: gmungoc Date: Mon, 6 Jul 2015 11:03:19 +0000 (+0100) Subject: JAL-1782 refactored test to ensure it passes in TestNG X-Git-Tag: Release_2_10_0~587 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6c9641bac3b88be7bc98788a0cd1fb1c969c380f;p=jalview.git JAL-1782 refactored test to ensure it passes in TestNG --- diff --git a/test/jalview/analysis/AnnotationSorterTest.java b/test/jalview/analysis/AnnotationSorterTest.java index 8c3489b..6149048 100644 --- a/test/jalview/analysis/AnnotationSorterTest.java +++ b/test/jalview/analysis/AnnotationSorterTest.java @@ -242,23 +242,23 @@ public class AnnotationSorterTest */ private void testTiming_presorted(final int numSeqs, final int numAnns) { - al = buildAlignment(numSeqs); - anns = buildAnnotations(numAnns); + Alignment alignment = buildAlignment(numSeqs); + AlignmentAnnotation[] annotations = buildAnnotations(numAnns); /* * Set the annotations presorted by label */ Random r = new Random(); - final SequenceI[] sequences = al.getSequencesArray(); - for (int i = 0; i < anns.length; i++) + final SequenceI[] sequences = alignment.getSequencesArray(); + for (int i = 0; i < annotations.length; i++) { SequenceI randomSequenceRef = sequences[r.nextInt(sequences.length)]; - anns[i].sequenceRef = randomSequenceRef; - anns[i].label = "label" + i; + annotations[i].sequenceRef = randomSequenceRef; + annotations[i].label = "label" + i; } long startTime = System.currentTimeMillis(); - AnnotationSorter testee = new AnnotationSorter(al, false); - testee.sort(anns, SequenceAnnotationOrder.LABEL_AND_SEQUENCE); + AnnotationSorter testee = new AnnotationSorter(alignment, false); + testee.sort(annotations, SequenceAnnotationOrder.LABEL_AND_SEQUENCE); long endTime = System.currentTimeMillis(); final long elapsed = endTime - startTime; System.out.println("Timing test for presorted " + numSeqs @@ -286,23 +286,23 @@ public class AnnotationSorterTest */ private void testTiming_unsorted(final int numSeqs, final int numAnns) { - al = buildAlignment(numSeqs); - anns = buildAnnotations(numAnns); + Alignment alignment = buildAlignment(numSeqs); + AlignmentAnnotation[] annotations = buildAnnotations(numAnns); /* * Set the annotations in random order with respect to the sequences */ Random r = new Random(); - final SequenceI[] sequences = al.getSequencesArray(); - for (int i = 0; i < anns.length; i++) + final SequenceI[] sequences = alignment.getSequencesArray(); + for (int i = 0; i < annotations.length; i++) { SequenceI randomSequenceRef = sequences[r.nextInt(sequences.length)]; - anns[i].sequenceRef = randomSequenceRef; - anns[i].label = "label" + i; + annotations[i].sequenceRef = randomSequenceRef; + annotations[i].label = "label" + i; } long startTime = System.currentTimeMillis(); - AnnotationSorter testee = new AnnotationSorter(al, false); - testee.sort(anns, SequenceAnnotationOrder.SEQUENCE_AND_LABEL); + AnnotationSorter testee = new AnnotationSorter(alignment, false); + testee.sort(annotations, SequenceAnnotationOrder.SEQUENCE_AND_LABEL); long endTime = System.currentTimeMillis(); final long elapsed = endTime - startTime; System.out.println("Timing test for unsorted " + numSeqs @@ -336,8 +336,8 @@ public class AnnotationSorterTest */ private void testTiming_semiSorted(final int numSeqs, final int numAnns) { - al = buildAlignment(numSeqs); - anns = buildAnnotations(numAnns); + Alignment alignment = buildAlignment(numSeqs); + AlignmentAnnotation[] annotations = buildAnnotations(numAnns); String[] labels = new String[] { "label1", "label2", "label3", "label4", "label5", "label6" }; @@ -346,16 +346,16 @@ public class AnnotationSorterTest * Set the annotations in sequence order with randomly assigned labels. */ Random r = new Random(); - final SequenceI[] sequences = al.getSequencesArray(); - for (int i = 0; i < anns.length; i++) + final SequenceI[] sequences = alignment.getSequencesArray(); + for (int i = 0; i < annotations.length; i++) { SequenceI sequenceRef = sequences[i % sequences.length]; - anns[i].sequenceRef = sequenceRef; - anns[i].label = labels[r.nextInt(labels.length)]; + annotations[i].sequenceRef = sequenceRef; + annotations[i].label = labels[r.nextInt(labels.length)]; } long startTime = System.currentTimeMillis(); - AnnotationSorter testee = new AnnotationSorter(al, false); - testee.sort(anns, SequenceAnnotationOrder.LABEL_AND_SEQUENCE); + AnnotationSorter testee = new AnnotationSorter(alignment, false); + testee.sort(annotations, SequenceAnnotationOrder.LABEL_AND_SEQUENCE); long endTime = System.currentTimeMillis(); long elapsed = endTime - startTime; System.out.println("Sort by label for semisorted " + numSeqs @@ -364,7 +364,7 @@ public class AnnotationSorterTest // now resort by sequence startTime = System.currentTimeMillis(); - testee.sort(anns, SequenceAnnotationOrder.SEQUENCE_AND_LABEL); + testee.sort(annotations, SequenceAnnotationOrder.SEQUENCE_AND_LABEL); endTime = System.currentTimeMillis(); elapsed = endTime - startTime; System.out.println("Resort by sequence for semisorted " + numSeqs @@ -373,7 +373,7 @@ public class AnnotationSorterTest // now resort by label startTime = System.currentTimeMillis(); - testee.sort(anns, SequenceAnnotationOrder.LABEL_AND_SEQUENCE); + testee.sort(annotations, SequenceAnnotationOrder.LABEL_AND_SEQUENCE); endTime = System.currentTimeMillis(); elapsed = endTime - startTime; System.out.println("Resort by label for semisorted " + numSeqs