From: Jim Procter Date: Wed, 18 Jul 2018 14:25:48 +0000 (+0100) Subject: Merge branch 'features/mchmmer' into features/mchmmer_merge_JAL-1950 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2Ffeatures%2Fmchmmer_merge_JAL-1950;hp=061c304150f3db1f126b2e8e274d3f7da4846887;p=jalview.git Merge branch 'features/mchmmer' into features/mchmmer_merge_JAL-1950 --- diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java index 85ae718..a910a5a 100644 --- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java +++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java @@ -40,6 +40,7 @@ import java.io.File; import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; +import java.nio.file.Paths; import java.util.ArrayList; import java.util.Collection; import java.util.HashMap; @@ -83,7 +84,7 @@ public class ChimeraManager this.structureManager = structureManager; chimera = null; chimeraListenerThread = null; - currentModelsMap = new HashMap(); + currentModelsMap = new HashMap<>(); } @@ -98,7 +99,7 @@ public class ChimeraManager public List getChimeraModels(String modelName, ModelType modelType) { - List models = new ArrayList(); + List models = new ArrayList<>(); for (ChimeraModel model : currentModelsMap.values()) { if (modelName.equals(model.getModelName()) @@ -112,7 +113,7 @@ public class ChimeraManager public Map> getChimeraModelsMap() { - Map> models = new HashMap>(); + Map> models = new HashMap<>(); for (ChimeraModel model : currentModelsMap.values()) { String modelName = model.getModelName(); @@ -393,7 +394,7 @@ public class ChimeraManager public Map getSelectedModels() { - Map selectedModelsMap = new HashMap(); + Map selectedModelsMap = new HashMap<>(); List chimeraReply = sendChimeraCommand( "list selection level molecule", true); if (chimeraReply != null) @@ -418,7 +419,7 @@ public class ChimeraManager */ public List getSelectedResidueSpecs() { - List selectedResidues = new ArrayList(); + List selectedResidues = new ArrayList<>(); List chimeraReply = sendChimeraCommand( "list selection level residue", true); if (chimeraReply != null) @@ -471,7 +472,7 @@ public class ChimeraManager // TODO: [Optional] Handle smiles names in a better way in Chimera? public List getModelList() { - List modelList = new ArrayList(); + List modelList = new ArrayList<>(); List list = sendChimeraCommand("list models type molecule", true); if (list != null) @@ -494,7 +495,7 @@ public class ChimeraManager */ public List getPresets() { - ArrayList presetList = new ArrayList(); + ArrayList presetList = new ArrayList<>(); List output = sendChimeraCommand("preset list", true); if (output != null) { @@ -550,17 +551,19 @@ public class ChimeraManager // iterate over possible paths for starting Chimera for (String chimeraPath : chimeraPaths) { - File path = new File(chimeraPath); - // uncomment the next line to simulate Chimera not installed - // path = new File(chimeraPath + "x"); - if (!path.canExecute()) - { - error += "File '" + path + "' does not exist.\n"; - continue; - } try { - List args = new ArrayList(); + // ensure symbolic links are resolved + chimeraPath = Paths.get(chimeraPath).toRealPath().toString(); + File path = new File(chimeraPath); + // uncomment the next line to simulate Chimera not installed + // path = new File(chimeraPath + "x"); + if (!path.canExecute()) + { + error += "File '" + path + "' does not exist.\n"; + continue; + } + List args = new ArrayList<>(); args.add(chimeraPath); // shows Chimera output window but suppresses REST responses: // args.add("--debug"); @@ -573,7 +576,7 @@ public class ChimeraManager break; } catch (Exception e) { - // Chimera could not be started + // Chimera could not be started using this path error += e.getMessage(); } } @@ -699,7 +702,7 @@ public class ChimeraManager public List getAttrList() { - List attributes = new ArrayList(); + List attributes = new ArrayList<>(); final List reply = sendChimeraCommand("list resattr", true); if (reply != null) { @@ -718,7 +721,7 @@ public class ChimeraManager public Map getAttrValues(String aCommand, ChimeraModel model) { - Map values = new HashMap(); + Map values = new HashMap<>(); final List reply = sendChimeraCommand("list residue spec " + model.toSpec() + " attribute " + aCommand, true); if (reply != null) @@ -818,10 +821,10 @@ public class ChimeraManager protected List sendRestCommand(String command) { String restUrl = "http://127.0.0.1:" + this.chimeraRestPort + "/run"; - List commands = new ArrayList(1); + List commands = new ArrayList<>(1); commands.add(new BasicNameValuePair("command", command)); - List reply = new ArrayList(); + List reply = new ArrayList<>(); BufferedReader response = null; try { diff --git a/src/jalview/datamodel/features/FeatureAttributes.java b/src/jalview/datamodel/features/FeatureAttributes.java index e359b62..10249f3 100644 --- a/src/jalview/datamodel/features/FeatureAttributes.java +++ b/src/jalview/datamodel/features/FeatureAttributes.java @@ -87,8 +87,8 @@ public class FeatureAttributes Datatype type; /** - * Note one instance of this attribute, recording unique, non-null names, - * and the min/max of any numerical values + * Note one instance of this attribute, recording unique, non-null + * descriptions, and the min/max of any numerical values * * @param desc * @param value @@ -99,20 +99,35 @@ public class FeatureAttributes if (value != null) { - try - { - float f = Float.valueOf(value); - min = hasValue ? Float.min(min, f) : f; - max = hasValue ? Float.max(max, f) : f; - hasValue = true; - type = (type == null || type == Datatype.Number) ? Datatype.Number - : Datatype.Mixed; - } catch (NumberFormatException e) + value = value.trim(); + + /* + * Parse numeric value unless we have previously + * seen text data for this attribute type + */ + if (type == null || type == Datatype.Number) { - // not a number, ignore for min-max purposes - type = (type == null || type == Datatype.Character) - ? Datatype.Character - : Datatype.Mixed; + try + { + float f = Float.valueOf(value); + min = hasValue ? Float.min(min, f) : f; + max = hasValue ? Float.max(max, f) : f; + hasValue = true; + type = (type == null || type == Datatype.Number) + ? Datatype.Number + : Datatype.Mixed; + } catch (NumberFormatException e) + { + /* + * non-numeric data: treat attribute as Character (or Mixed) + */ + type = (type == null || type == Datatype.Character) + ? Datatype.Character + : Datatype.Mixed; + min = 0f; + max = 0f; + hasValue = false; + } } } } @@ -284,9 +299,8 @@ public class FeatureAttributes /** * Answers the [min, max] value range of the given attribute for the given - * feature type, if known, else null. Attributes which only have text values - * would normally return null, however text values which happen to be numeric - * could result in a 'min-max' range. + * feature type, if known, else null. Attributes with a mixture of text and + * numeric values are considered text (do not return a min-max range). * * @param featureType * @param attName diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java index 9dea886..92972eb 100644 --- a/src/jalview/ext/ensembl/EnsemblRestClient.java +++ b/src/jalview/ext/ensembl/EnsemblRestClient.java @@ -66,17 +66,14 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher * @see https://github.com/Ensembl/ensembl-rest/wiki/Change-log * @see http://rest.ensembl.org/info/rest?content-type=application/json */ - private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "6.0"; + private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "6.3"; - private static final String LATEST_ENSEMBL_REST_VERSION = "6.1"; + private static final String LATEST_ENSEMBL_REST_VERSION = "6.3"; private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log"; private static Map domainData; - // @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats - private static final String PING_URL = "http://rest.ensembl.org/info/ping.json"; - private final static long AVAILABILITY_RETEST_INTERVAL = 10000L; // 10 seconds private final static long VERSION_RETEST_INTERVAL = 1000L * 3600; // 1 hr diff --git a/src/jalview/gui/CutAndPasteHtmlTransfer.java b/src/jalview/gui/CutAndPasteHtmlTransfer.java index 2e51bce..1d7d1c9 100644 --- a/src/jalview/gui/CutAndPasteHtmlTransfer.java +++ b/src/jalview/gui/CutAndPasteHtmlTransfer.java @@ -143,6 +143,7 @@ public class CutAndPasteHtmlTransfer extends GCutAndPasteHtmlTransfer { textarea.setDocument(textarea.getEditorKit().createDefaultDocument()); textarea.setText(text); + textarea.setCaretPosition(0); } @Override diff --git a/src/jalview/gui/FeatureTypeSettings.java b/src/jalview/gui/FeatureTypeSettings.java index 6eb583c..e13f6ee 100644 --- a/src/jalview/gui/FeatureTypeSettings.java +++ b/src/jalview/gui/FeatureTypeSettings.java @@ -1414,7 +1414,7 @@ public class FeatureTypeSettings extends JalviewDialog * if a numeric condition is selected, show the value range * as a tooltip on the value input field */ - setPatternTooltip(filterBy, selectedCondition, patternField); + setNumericHints(filterBy, selectedCondition, patternField); /* * add remove button if filter is populated (non-empty pattern) @@ -1469,14 +1469,19 @@ public class FeatureTypeSettings extends JalviewDialog } /** - * If a numeric comparison condition is selected, retrieve the min-max range for - * the value (score or attribute), and set it as a tooltip on the value file + * If a numeric comparison condition is selected, retrieves the min-max range + * for the value (score or attribute), and sets it as a tooltip on the value + * field. If the field is currently empty, then pre-populates it with + *
    + *
  • the minimum value, if condition is > or >=
    • + *
  • the maximum value, if condition is < or <=
    • + *
* * @param attName * @param selectedCondition * @param patternField */ - private void setPatternTooltip(String attName, + private void setNumericHints(String attName, Condition selectedCondition, JTextField patternField) { patternField.setToolTipText(""); @@ -1486,9 +1491,26 @@ public class FeatureTypeSettings extends JalviewDialog float[] minMax = getMinMax(attName); if (minMax != null) { - String tip = String.format("(%s - %s)", - DECFMT_2_2.format(minMax[0]), DECFMT_2_2.format(minMax[1])); + String minFormatted = DECFMT_2_2.format(minMax[0]); + String maxFormatted = DECFMT_2_2.format(minMax[1]); + String tip = String.format("(%s - %s)", minFormatted, maxFormatted); patternField.setToolTipText(tip); + if (patternField.getText().isEmpty()) + { + if (selectedCondition == Condition.GE + || selectedCondition == Condition.GT) + { + patternField.setText(minFormatted); + } + else + { + if (selectedCondition == Condition.LE + || selectedCondition == Condition.LT) + { + patternField.setText(maxFormatted); + } + } + } } } } @@ -1525,10 +1547,11 @@ public class FeatureTypeSettings extends JalviewDialog ItemListener listener = condCombo.getItemListeners()[0]; condCombo.removeItemListener(listener); boolean condIsValid = false; + condCombo.removeAllItems(); for (Condition c : Condition.values()) { - if ((c.isNumeric() && type != Datatype.Character) + if ((c.isNumeric() && type == Datatype.Number) || (!c.isNumeric() && type != Datatype.Number)) { condCombo.addItem(c); @@ -1551,8 +1574,6 @@ public class FeatureTypeSettings extends JalviewDialog condCombo.setSelectedIndex(0); } - condCombo.addItemListener(listener); - /* * clear pattern if it is now invalid for condition */ @@ -1570,6 +1591,11 @@ public class FeatureTypeSettings extends JalviewDialog patternField.setText(""); } } + + /* + * restore the listener + */ + condCombo.addItemListener(listener); } /** @@ -1646,7 +1672,7 @@ public class FeatureTypeSettings extends JalviewDialog Condition cond = (Condition) condCombo.getSelectedItem(); String pattern = valueField.getText().trim(); - setPatternTooltip(attName, cond, valueField); + setNumericHints(attName, cond, valueField); if (pattern.length() == 0 && cond.needsAPattern()) { diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index aed73d6..9af840a 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -3192,7 +3192,7 @@ public class Jalview2XML * load any HMMER profile */ String hmmJarFile = jseqs[i].getHmmerProfile(); - if (hmmJarFile != null) + if (hmmJarFile != null && jprovider != null) { loadHmmerProfile(jprovider, hmmJarFile, alignmentSeq); } diff --git a/src/jalview/hmmer/HmmerCommand.java b/src/jalview/hmmer/HmmerCommand.java index f8f2cde..b5c1b25 100644 --- a/src/jalview/hmmer/HmmerCommand.java +++ b/src/jalview/hmmer/HmmerCommand.java @@ -24,6 +24,7 @@ import java.io.File; import java.io.IOException; import java.io.InputStreamReader; import java.io.PrintWriter; +import java.nio.file.Paths; import java.util.ArrayList; import java.util.Hashtable; import java.util.List; @@ -247,10 +248,13 @@ public abstract class HmmerCommand implements Runnable * @param cmd * command short name e.g. hmmalign * @return + * @throws IOException */ - protected String getCommandPath(String cmd) + protected String getCommandPath(String cmd) throws IOException { String binariesFolder = Cache.getProperty(Preferences.HMMER_PATH); + // ensure any symlink to the directory is resolved: + binariesFolder = Paths.get(binariesFolder).toRealPath().toString(); File file = FileUtils.getExecutable(cmd, binariesFolder); if (file == null && af != null) { diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java index 6b82671..5ada355 100644 --- a/src/jalview/io/SequenceAnnotationReport.java +++ b/src/jalview/io/SequenceAnnotationReport.java @@ -21,6 +21,7 @@ package jalview.io; import jalview.api.FeatureColourI; +import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; import jalview.datamodel.SequenceFeature; @@ -353,12 +354,27 @@ public class SequenceAnnotationReport sb.append("
").append(tmp); maxWidth = Math.max(maxWidth, tmp.length()); } + SequenceI ds = sequence; while (ds.getDatasetSequence() != null) { ds = ds.getDatasetSequence(); } + /* + * add any annotation scores + */ + AlignmentAnnotation[] anns = ds.getAnnotation(); + for (int i = 0; anns != null && i < anns.length; i++) + { + AlignmentAnnotation aa = anns[i]; + if (aa != null && aa.hasScore() && aa.sequenceRef != null) + { + sb.append("
").append(aa.label).append(": ") + .append(aa.getScore()); + } + } + if (showDbRefs) { maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary)); diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java index 60054f1..39a7120 100644 --- a/src/jalview/util/MapList.java +++ b/src/jalview/util/MapList.java @@ -327,6 +327,13 @@ public class MapList fromHighest = Integer.MIN_VALUE; for (int[] range : fromRange) { + if (range.length != 2) + { + // throw new IllegalArgumentException(range); + System.err.println( + "Invalid format for fromRange " + Arrays.toString(range) + + " may cause errors"); + } fromLowest = Math.min(fromLowest, Math.min(range[0], range[1])); fromHighest = Math.max(fromHighest, Math.max(range[0], range[1])); } @@ -335,6 +342,13 @@ public class MapList toHighest = Integer.MIN_VALUE; for (int[] range : toRange) { + if (range.length != 2) + { + // throw new IllegalArgumentException(range); + System.err.println("Invalid format for toRange " + + Arrays.toString(range) + + " may cause errors"); + } toLowest = Math.min(toLowest, Math.min(range[0], range[1])); toHighest = Math.max(toHighest, Math.max(range[0], range[1])); } @@ -1148,11 +1162,20 @@ public class MapList for (int[] range : getToRanges()) { int[] transferred = map.locateInTo(range[0], range[1]); - if (transferred == null) + if (transferred == null || transferred.length % 2 != 0) { return null; } - toRanges.add(transferred); + + /* + * convert [start1, end1, start2, end2, ...] + * to [[start1, end1], [start2, end2], ...] + */ + for (int i = 0; i < transferred.length;) + { + toRanges.add(new int[] { transferred[i], transferred[i + 1] }); + i += 2; + } } return new MapList(getFromRanges(), toRanges, outFromRatio, outToRatio); diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java index 92bf0ce..a7a7d34 100644 --- a/test/jalview/analysis/AlignmentUtilsTests.java +++ b/test/jalview/analysis/AlignmentUtilsTests.java @@ -2685,14 +2685,14 @@ public class AlignmentUtilsTests assertEquals(2, toMap.getFromRanges().get(0).length); assertEquals(1, toMap.getFromRanges().get(0)[0]); assertEquals(12, toMap.getFromRanges().get(0)[1]); - assertEquals(1, toMap.getToRanges().size()); - assertEquals(4, toMap.getToRanges().get(0).length); + assertEquals(2, toMap.getToRanges().size()); + assertEquals(2, toMap.getToRanges().get(0).length); assertEquals(158, toMap.getToRanges().get(0)[0]); assertEquals(164, toMap.getToRanges().get(0)[1]); - assertEquals(210, toMap.getToRanges().get(0)[2]); - assertEquals(214, toMap.getToRanges().get(0)[3]); + assertEquals(210, toMap.getToRanges().get(1)[0]); + assertEquals(214, toMap.getToRanges().get(1)[1]); // or summarised as (but toString might change in future): - assertEquals("[ [1, 12] ] 1:1 to [ [158, 164, 210, 214] ]", + assertEquals("[ [1, 12] ] 1:1 to [ [158, 164] [210, 214] ]", toMap.toString()); /* @@ -2704,7 +2704,7 @@ public class AlignmentUtilsTests assertEquals("GRCh38", toLoci.getAssemblyId()); assertEquals("7", toLoci.getChromosomeId()); toMap = toLoci.getMap(); - assertEquals("[ [1, 12] ] 1:1 to [ [158, 164, 210, 214] ]", + assertEquals("[ [1, 12] ] 1:1 to [ [158, 164] [210, 214] ]", toMap.toString()); } diff --git a/test/jalview/datamodel/features/FeatureAttributesTest.java b/test/jalview/datamodel/features/FeatureAttributesTest.java index 686cd2f..0846ec2 100644 --- a/test/jalview/datamodel/features/FeatureAttributesTest.java +++ b/test/jalview/datamodel/features/FeatureAttributesTest.java @@ -76,12 +76,14 @@ public class FeatureAttributesTest assertNull(fa.getMinMax("Pfam", "kd")); sf.setValue("domain", "xyz"); assertNull(fa.getMinMax("Pfam", "kd")); - sf.setValue("kd", "some text"); - assertNull(fa.getMinMax("Pfam", "kd")); sf.setValue("kd", "1.3"); assertEquals(fa.getMinMax("Pfam", "kd"), new float[] { 1.3f, 1.3f }); sf.setValue("kd", "-2.6"); assertEquals(fa.getMinMax("Pfam", "kd"), new float[] { -2.6f, 1.3f }); + // setting 'mixed' character and numeric values wipes the min/max value + sf.setValue("kd", "some text"); + assertNull(fa.getMinMax("Pfam", "kd")); + Map csq = new HashMap<>(); csq.put("AF", "-3"); sf.setValue("CSQ", csq); diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java index cd3e124..493545a 100644 --- a/test/jalview/util/MapListTest.java +++ b/test/jalview/util/MapListTest.java @@ -774,22 +774,31 @@ public class MapListTest */ MapList ml1 = new MapList(new int[] { 3, 4, 8, 12 }, new int[] { 5, 8, 11, 13 }, 1, 1); + assertEquals("{[3, 4], [8, 12]}", prettyPrint(ml1.getFromRanges())); + assertEquals("{[5, 8], [11, 13]}", prettyPrint(ml1.getToRanges())); + MapList ml2 = new MapList(new int[] { 1, 50 }, new int[] { 40, 45, 70, 75, 90, 127 }, 1, 1); + assertEquals("{[1, 50]}", prettyPrint(ml2.getFromRanges())); + assertEquals("{[40, 45], [70, 75], [90, 127]}", + prettyPrint(ml2.getToRanges())); + MapList compound = ml1.traverse(ml2); - assertEquals(compound.getFromRatio(), 1); - assertEquals(compound.getToRatio(), 1); + assertEquals(1, compound.getFromRatio()); + assertEquals(1, compound.getToRatio()); List fromRanges = compound.getFromRanges(); - assertEquals(fromRanges.size(), 2); + assertEquals(2, fromRanges.size()); assertArrayEquals(new int[] { 3, 4 }, fromRanges.get(0)); assertArrayEquals(new int[] { 8, 12 }, fromRanges.get(1)); List toRanges = compound.getToRanges(); - assertEquals(toRanges.size(), 2); + assertEquals(4, toRanges.size()); // 5-8 maps to 44-45,70-71 // 11-13 maps to 74-75,90 - assertArrayEquals(new int[] { 44, 45, 70, 71 }, toRanges.get(0)); - assertArrayEquals(new int[] { 74, 75, 90, 90 }, toRanges.get(1)); + assertArrayEquals(new int[] { 44, 45 }, toRanges.get(0)); + assertArrayEquals(new int[] { 70, 71 }, toRanges.get(1)); + assertArrayEquals(new int[] { 74, 75 }, toRanges.get(2)); + assertArrayEquals(new int[] { 90, 90 }, toRanges.get(3)); /* * 1:1 over 1:1 backwards ('reverse strand') @@ -799,14 +808,15 @@ public class MapListTest new int[] { 1000, 901, 600, 201 }, 1, 1); compound = ml1.traverse(ml2); - assertEquals(compound.getFromRatio(), 1); - assertEquals(compound.getToRatio(), 1); + assertEquals(1, compound.getFromRatio()); + assertEquals(1, compound.getToRatio()); fromRanges = compound.getFromRanges(); - assertEquals(fromRanges.size(), 1); + assertEquals(1, fromRanges.size()); assertArrayEquals(new int[] { 1, 50 }, fromRanges.get(0)); toRanges = compound.getToRanges(); - assertEquals(toRanges.size(), 1); - assertArrayEquals(new int[] { 931, 901, 600, 582 }, toRanges.get(0)); + assertEquals(2, toRanges.size()); + assertArrayEquals(new int[] { 931, 901 }, toRanges.get(0)); + assertArrayEquals(new int[] { 600, 582 }, toRanges.get(1)); /* * 1:1 plus 1:3 should result in 1:3 @@ -816,15 +826,16 @@ public class MapListTest 1, 3); compound = ml1.traverse(ml2); - assertEquals(compound.getFromRatio(), 1); - assertEquals(compound.getToRatio(), 3); + assertEquals(1, compound.getFromRatio()); + assertEquals(3, compound.getToRatio()); fromRanges = compound.getFromRanges(); - assertEquals(fromRanges.size(), 1); + assertEquals(1, fromRanges.size()); assertArrayEquals(new int[] { 1, 30 }, fromRanges.get(0)); // 11-40 maps to 31-50,91-160 toRanges = compound.getToRanges(); - assertEquals(toRanges.size(), 1); - assertArrayEquals(new int[] { 31, 50, 91, 160 }, toRanges.get(0)); + assertEquals(2, toRanges.size()); + assertArrayEquals(new int[] { 31, 50 }, toRanges.get(0)); + assertArrayEquals(new int[] { 91, 160 }, toRanges.get(1)); /* * 3:1 plus 1:1 should result in 3:1 @@ -834,15 +845,16 @@ public class MapListTest 1, 1); compound = ml1.traverse(ml2); - assertEquals(compound.getFromRatio(), 3); - assertEquals(compound.getToRatio(), 1); + assertEquals(3, compound.getFromRatio()); + assertEquals(1, compound.getToRatio()); fromRanges = compound.getFromRanges(); - assertEquals(fromRanges.size(), 1); + assertEquals(1, fromRanges.size()); assertArrayEquals(new int[] { 1, 30 }, fromRanges.get(0)); // 11-20 maps to 11-15, 91-95 toRanges = compound.getToRanges(); - assertEquals(toRanges.size(), 1); - assertArrayEquals(new int[] { 11, 15, 91, 95 }, toRanges.get(0)); + assertEquals(2, toRanges.size()); + assertArrayEquals(new int[] { 11, 15 }, toRanges.get(0)); + assertArrayEquals(new int[] { 91, 95 }, toRanges.get(1)); /* * 1:3 plus 3:1 should result in 1:1 @@ -852,15 +864,16 @@ public class MapListTest 3, 1); compound = ml1.traverse(ml2); - assertEquals(compound.getFromRatio(), 1); - assertEquals(compound.getToRatio(), 1); + assertEquals(1, compound.getFromRatio()); + assertEquals(1, compound.getToRatio()); fromRanges = compound.getFromRanges(); - assertEquals(fromRanges.size(), 1); + assertEquals(1, fromRanges.size()); assertArrayEquals(new int[] { 21, 40 }, fromRanges.get(0)); // 13-72 maps 3:1 to 55-70, 121-124 toRanges = compound.getToRanges(); - assertEquals(toRanges.size(), 1); - assertArrayEquals(new int[] { 55, 70, 121, 124 }, toRanges.get(0)); + assertEquals(2, toRanges.size()); + assertArrayEquals(new int[] { 55, 70 }, toRanges.get(0)); + assertArrayEquals(new int[] { 121, 124 }, toRanges.get(1)); /* * 3:1 plus 1:3 should result in 1:1 @@ -870,15 +883,16 @@ public class MapListTest 1, 3); compound = ml1.traverse(ml2); - assertEquals(compound.getFromRatio(), 1); - assertEquals(compound.getToRatio(), 1); + assertEquals(1, compound.getFromRatio()); + assertEquals(1, compound.getToRatio()); fromRanges = compound.getFromRanges(); - assertEquals(fromRanges.size(), 1); + assertEquals(1, fromRanges.size()); assertArrayEquals(new int[] { 31, 90 }, fromRanges.get(0)); // 13-32 maps to 47-50,71-126 toRanges = compound.getToRanges(); - assertEquals(toRanges.size(), 1); - assertArrayEquals(new int[] { 47, 50, 71, 126 }, toRanges.get(0)); + assertEquals(2, toRanges.size()); + assertArrayEquals(new int[] { 47, 50 }, toRanges.get(0)); + assertArrayEquals(new int[] { 71, 126 }, toRanges.get(1)); /* * method returns null if not all regions are mapped through