From: gmungoc Date: Fri, 15 May 2015 13:11:40 +0000 (+0100) Subject: JAL-1270 added test for regex actually used; include sequence name in X-Git-Tag: Release_2_10_0~674 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8fe789715bfbea0db5869a55e37252a0dee06ea7;p=jalview.git JAL-1270 added test for regex actually used; include sequence name in sysout of extracted scores --- diff --git a/src/jalview/analysis/ParseProperties.java b/src/jalview/analysis/ParseProperties.java index 38d8371..3347800 100644 --- a/src/jalview/analysis/ParseProperties.java +++ b/src/jalview/analysis/ParseProperties.java @@ -22,7 +22,9 @@ package jalview.analysis; import com.stevesoft.pat.Regex; -import jalview.datamodel.*; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceI; public class ParseProperties { @@ -101,7 +103,9 @@ public class ParseProperties ScoreNames = tnames; String descrbase = ScoreDescriptions[onamelen - 1]; if (descrbase == null) + { descrbase = "Score parsed from (" + regex + ")"; + } tnames = new String[pattern.numSubs() + 1]; System.arraycopy(ScoreDescriptions, 0, tnames, 0, ScoreDescriptions.length); @@ -116,7 +120,9 @@ public class ParseProperties { String descr = seqs[i].getDescription(); if (descr == null) + { continue; + } int pos = 0; boolean added = false; int reps = 0; @@ -140,7 +146,8 @@ public class ParseProperties + ((reps > 0) ? "_" + reps : ""), ScoreDescriptions[cols], null); an.setScore(score); - System.out.println("Score: " + ScoreNames[cols] + "=" + score); // DEBUG + System.out.println(seqs[i].getName() + " score: '" + + ScoreNames[cols] + "' = " + score); // DEBUG an.setSequenceRef(seqs[i]); seqs[i].addAlignmentAnnotation(an); al.addAnnotation(an); diff --git a/test/jalview/analysis/ParsePropertiesTest.java b/test/jalview/analysis/ParsePropertiesTest.java index a679a46..a01d255 100644 --- a/test/jalview/analysis/ParsePropertiesTest.java +++ b/test/jalview/analysis/ParsePropertiesTest.java @@ -3,6 +3,8 @@ package jalview.analysis; import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertNull; +import java.util.List; + import org.junit.Before; import org.junit.Test; @@ -47,9 +49,6 @@ public class ParsePropertiesTest @Test public void testGetScoresFromDescription() { - // TODO - test the regex actually used by Jalview? - // \\W*([-+eE0-9.]+) - // see AlignFrame.extractScores_actionPerformed String regex = ".*([-0-9.+]+)"; final int count = pp.getScoresFromDescription("my Score", "my Score Description", regex, true); @@ -138,4 +137,57 @@ public class ParsePropertiesTest assertEquals("my Score Description (column 1)", anns[1].description); assertEquals("my Score_1", anns[1].label); } + + /** + * Test with a regex that looks for numbers separated by words - as currently + * used in Jalview (May 2015) + * + * @see AlignFrame.extractScores_actionPerformed + */ + @Test + public void testGetScoresFromDescription_wordBoundaries() + { + String regex = "\\W*([-+eE0-9.]+)"; + List seqs = al.getSequences(); + seqs.get(0).setDescription("Ferredoxin"); + seqs.get(1).setDescription(" Ferredoxin-1, chloroplast precursor"); + seqs.get(2).setDescription("GH28E30p"); + seqs.get(3).setDescription("At1g10960/T19D16_12"); + final int count = pp.getScoresFromDescription("description column", + "score in description column ", regex, true); + assertEquals(3, count); + + /* + * No score parsable from seq1 description + */ + AlignmentAnnotation[] anns = al.getSequenceAt(0).getAnnotation(); + assertNull(anns); + + /* + * Seq2 description has a '1' in it + */ + anns = al.getSequenceAt(1).getAnnotation(); + assertEquals(1, anns.length); + assertEquals(1d, anns[0].getScore(), 0.001d); + + /* + * Seq3 description has '28E30' in it + * + * Note: 1.8E308 or larger would result in 'Infinity' + */ + anns = al.getSequenceAt(2).getAnnotation(); + assertEquals(1, anns.length); + assertEquals(2.8E31d, anns[0].getScore(), 0.001d); + + /* + * Seq4 description has several numbers in it + */ + anns = al.getSequenceAt(3).getAnnotation(); + assertEquals(5, anns.length); + assertEquals(1d, anns[0].getScore(), 0.001d); + assertEquals(10960d, anns[1].getScore(), 0.001d); + assertEquals(19d, anns[2].getScore(), 0.001d); + assertEquals(16d, anns[3].getScore(), 0.001d); + assertEquals(12d, anns[4].getScore(), 0.001d); + } }