From b320470d1ddb95476d3678477b72f6f791a51404 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 24 Nov 2017 14:50:45 +0000 Subject: [PATCH] JAL-2808 update spike to latest --- src/jalview/datamodel/features/FeatureMatcher.java | 37 ++++- .../datamodel/features/FeatureMatcherI.java | 19 ++- .../datamodel/features/FeatureMatcherSet.java | 10 +- src/jalview/gui/FeatureSettings.java | 42 ++--- src/jalview/gui/FeatureTypeSettings.java | 175 ++++++++++++++------ src/jalview/util/matcher/Condition.java | 16 +- src/jalview/util/matcher/Matcher.java | 44 +++-- .../datamodel/features/FeatureMatcherSetTest.java | 13 +- .../datamodel/features/FeatureMatcherTest.java | 57 ++++++- test/jalview/util/matcher/MatcherTest.java | 15 +- 10 files changed, 302 insertions(+), 126 deletions(-) diff --git a/src/jalview/datamodel/features/FeatureMatcher.java b/src/jalview/datamodel/features/FeatureMatcher.java index 1fc0e0f..b86468d 100644 --- a/src/jalview/datamodel/features/FeatureMatcher.java +++ b/src/jalview/datamodel/features/FeatureMatcher.java @@ -1,6 +1,7 @@ package jalview.datamodel.features; import jalview.datamodel.SequenceFeature; +import jalview.util.MessageManager; import jalview.util.matcher.Condition; import jalview.util.matcher.Matcher; import jalview.util.matcher.MatcherI; @@ -22,6 +23,12 @@ import jalview.util.matcher.MatcherI; */ public class FeatureMatcher implements FeatureMatcherI { + /* + * a dummy matcher that comes in useful for the 'add a filter' gui row + */ + public static final FeatureMatcherI NULL_MATCHER = FeatureMatcher + .byLabel(Condition.values()[0], ""); + private static final String COLON = ":"; /* @@ -103,7 +110,7 @@ public class FeatureMatcher implements FeatureMatcherI } @Override - public String[] getKey() + public String[] getAttribute() { return key; } @@ -122,9 +129,21 @@ public class FeatureMatcher implements FeatureMatcherI public String toString() { StringBuilder sb = new StringBuilder(); - sb.append(String.join(COLON, key)).append(" ") - .append(matcher.getCondition().toString()); + if (byLabel) + { + sb.append(MessageManager.getString("label.label")); + } + else if (byScore) + { + sb.append(MessageManager.getString("label.score")); + } + else + { + sb.append(String.join(COLON, key)); + } + Condition condition = matcher.getCondition(); + sb.append(" ").append(condition.toString().toLowerCase()); if (condition.isNumeric()) { sb.append(" ").append(matcher.getPattern()); @@ -136,4 +155,16 @@ public class FeatureMatcher implements FeatureMatcherI return sb.toString(); } + + @Override + public boolean isByLabel() + { + return byLabel; + } + + @Override + public boolean isByScore() + { + return byScore; + } } diff --git a/src/jalview/datamodel/features/FeatureMatcherI.java b/src/jalview/datamodel/features/FeatureMatcherI.java index 078f4a4..07b060c 100644 --- a/src/jalview/datamodel/features/FeatureMatcherI.java +++ b/src/jalview/datamodel/features/FeatureMatcherI.java @@ -21,11 +21,26 @@ public interface FeatureMatcherI boolean matches(SequenceFeature feature); /** - * Answers the value key this matcher operates on + * Answers the attribute key this matcher operates on (or null if match is by + * Label or Score) * * @return */ - String[] getKey(); + String[] getAttribute(); + + /** + * Answers true if match is against feature label (description), else false + * + * @return + */ + boolean isByLabel(); + + /** + * Answers true if match is against feature score, else false + * + * @return + */ + boolean isByScore(); /** * Answers the match condition that is applied diff --git a/src/jalview/datamodel/features/FeatureMatcherSet.java b/src/jalview/datamodel/features/FeatureMatcherSet.java index 64ae61b..eb55387 100644 --- a/src/jalview/datamodel/features/FeatureMatcherSet.java +++ b/src/jalview/datamodel/features/FeatureMatcherSet.java @@ -1,12 +1,19 @@ package jalview.datamodel.features; import jalview.datamodel.SequenceFeature; +import jalview.util.MessageManager; import java.util.ArrayList; import java.util.List; public class FeatureMatcherSet implements FeatureMatcherSetI { + private static final String OR_I18N = MessageManager + .getString("label.or"); + + private static final String AND_18N = MessageManager + .getString("label.and"); + List matchConditions; boolean andConditions; @@ -105,7 +112,8 @@ public class FeatureMatcherSet implements FeatureMatcherSetI { if (!first) { - sb.append(andConditions ? " AND " : " OR "); + String joiner = andConditions ? AND_18N : OR_I18N; + sb.append(" ").append(joiner.toLowerCase()).append(" "); } first = false; sb.append("(").append(matcher.toString()).append(")"); diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 0c4cd56..4b4f363 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -20,11 +20,6 @@ */ package jalview.gui; -import static jalview.gui.FeatureSettings.FeatureTableModel.COLOUR_COLUMN; -import static jalview.gui.FeatureSettings.FeatureTableModel.FILTER_COLUMN; -import static jalview.gui.FeatureSettings.FeatureTableModel.SHOW_COLUMN; -import static jalview.gui.FeatureSettings.FeatureTableModel.TYPE_COLUMN; - import jalview.api.FeatureColourI; import jalview.api.FeatureSettingsControllerI; import jalview.bin.Cache; @@ -110,6 +105,17 @@ import javax.swing.table.TableColumn; public class FeatureSettings extends JPanel implements FeatureSettingsControllerI { + /* + * column indices of fields in Feature Settings table + */ + static final int TYPE_COLUMN = 0; + + static final int COLOUR_COLUMN = 1; + + static final int FILTER_COLUMN = 2; + + static final int SHOW_COLUMN = 3; + private static final int COLUMN_COUNT = 4; private static final int MIN_WIDTH = 400; @@ -648,8 +654,7 @@ public class FeatureSettings extends JPanel } } - int columnCount = COLUMN_COUNT; - Object[][] data = new Object[displayableTypes.size()][columnCount]; + Object[][] data = new Object[displayableTypes.size()][COLUMN_COUNT]; int dataIndex = 0; if (fr.hasRenderOrder()) @@ -712,11 +717,10 @@ public class FeatureSettings extends JPanel if (originalData == null) { - int size = data[0].length; - originalData = new Object[data.length][size]; + originalData = new Object[data.length][COLUMN_COUNT]; for (int i = 0; i < data.length; i++) { - System.arraycopy(data[i], 0, originalData[i], 0, size); + System.arraycopy(data[i], 0, originalData[i], 0, COLUMN_COUNT); } } else @@ -787,11 +791,12 @@ public class FeatureSettings extends JPanel /* * new feature detected - add to original data (on top) */ - int size = currentData[0].length; - Object[][] newData = new Object[originalData.length + 1][size]; + Object[][] newData = new Object[originalData.length + + 1][COLUMN_COUNT]; for (int i = 0; i < originalData.length; i++) { - System.arraycopy(originalData[i], 0, newData[i + 1], 0, size); + System.arraycopy(originalData[i], 0, newData[i + 1], 0, + COLUMN_COUNT); } newData[0] = row; originalData = newData; @@ -1509,17 +1514,6 @@ public class FeatureSettings extends JPanel // /////////////////////////////////////////////////////////////////////// class FeatureTableModel extends AbstractTableModel { - /* - * column indices of fields in Feature Settings table - */ - static final int TYPE_COLUMN = 0; - - static final int COLOUR_COLUMN = 1; - - static final int FILTER_COLUMN = 2; - - static final int SHOW_COLUMN = 3; - private String[] columnNames = { MessageManager.getString("label.feature_type"), MessageManager.getString("action.colour"), diff --git a/src/jalview/gui/FeatureTypeSettings.java b/src/jalview/gui/FeatureTypeSettings.java index 835f1fc..c356731 100644 --- a/src/jalview/gui/FeatureTypeSettings.java +++ b/src/jalview/gui/FeatureTypeSettings.java @@ -38,7 +38,7 @@ import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; import java.awt.FlowLayout; -import java.awt.LayoutManager; +import java.awt.GridLayout; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.FocusAdapter; @@ -79,6 +79,12 @@ import javax.swing.plaf.basic.BasicArrowButton; */ public class FeatureTypeSettings extends JalviewDialog { + private final static String LABEL_18N = MessageManager + .getString("label.label"); + + private final static String SCORE_18N = MessageManager + .getString("label.score"); + private static final int RADIO_WIDTH = 130; private static final String COLON = ":"; @@ -294,8 +300,7 @@ public class FeatureTypeSettings extends JalviewDialog } else { - colourByTextCombo - .setSelectedItem(MessageManager.getString("label.label")); + colourByTextCombo.setSelectedItem(LABEL_18N); } } else @@ -336,8 +341,7 @@ public class FeatureTypeSettings extends JalviewDialog } else { - colourByRangeCombo - .setSelectedItem(MessageManager.getString("label.score")); + colourByRangeCombo.setSelectedItem(SCORE_18N); } Color noColour = fc.getNoColour(); if (noColour == null) @@ -444,8 +448,7 @@ public class FeatureTypeSettings extends JalviewDialog } String colourBy = (String) colourByRangeCombo.getSelectedItem(); - String[] attNames = fromAttributeDisplayName(colourBy); - float[] minMax = getMinMax(attNames); + float[] minMax = getMinMax(colourBy); if (minMax != null) { @@ -461,13 +464,13 @@ public class FeatureTypeSettings extends JalviewDialog *
  • else of the selected attribute
    • * * - * @param attNames + * @param attName * @return */ - private float[] getMinMax(String[] attNames) + private float[] getMinMax(String attName) { float[] minMax = null; - if (MessageManager.getString("label.score").equals(attNames[0])) + if (SCORE_18N.equals(attName)) { minMax = fr.getMinMax().get(featureType)[0]; } @@ -475,7 +478,7 @@ public class FeatureTypeSettings extends JalviewDialog { // colour by attribute range minMax = FeatureAttributes.getInstance().getMinMax(featureType, - attNames); + fromAttributeDisplayName(attName)); } return minMax; } @@ -902,7 +905,7 @@ public class FeatureTypeSettings extends JalviewDialog FeatureColourI fc = new FeatureColour(c, c, null, 0f, 0f); fc.setColourByLabel(true); String byWhat = (String) colourByTextCombo.getSelectedItem(); - if (!MessageManager.getString("label.label").equals(byWhat)) + if (!LABEL_18N.equals(byWhat)) { fc.setAttributeName(fromAttributeDisplayName(byWhat)); } @@ -959,7 +962,7 @@ public class FeatureTypeSettings extends JalviewDialog * set attribute to colour by if selected */ String byWhat = (String) colourByRangeCombo.getSelectedItem(); - if (!MessageManager.getString("label.score").equals(byWhat)) + if (!SCORE_18N.equals(byWhat)) { fc.setAttributeName(fromAttributeDisplayName(byWhat)); } @@ -1134,7 +1137,7 @@ public class FeatureTypeSettings extends JalviewDialog if (withText) { - displayAtts.add(MessageManager.getString("label.label")); + displayAtts.add(LABEL_18N); tooltips.add(MessageManager.getString("label.description")); } if (withRange) @@ -1142,8 +1145,8 @@ public class FeatureTypeSettings extends JalviewDialog float[][] minMax = fr.getMinMax().get(featureType); if (minMax != null && minMax[0][0] != minMax[0][1]) { - displayAtts.add(MessageManager.getString("label.score")); - tooltips.add(MessageManager.getString("label.score")); + displayAtts.add(SCORE_18N); + tooltips.add(SCORE_18N); } } @@ -1188,11 +1191,11 @@ public class FeatureTypeSettings extends JalviewDialog filtersPanel.add(andOrPanel); /* - * panel with filters - populated by refreshFiltersDisplay + * panel with filters - populated by refreshFiltersDisplay, + * which also sets the layout manager */ chooseFiltersPanel = new JPanel(); - LayoutManager box = new BoxLayout(chooseFiltersPanel, BoxLayout.Y_AXIS); - chooseFiltersPanel.setLayout(box); + chooseFiltersPanel.setBackground(Color.white); filtersPanel.add(chooseFiltersPanel); return filtersPanel; @@ -1267,9 +1270,21 @@ public class FeatureTypeSettings extends JalviewDialog /* * and an empty filter for the user to populate (add) */ - FeatureMatcherI noFilter = FeatureMatcher.byLabel(Condition.values()[0], - ""); - filters.add(noFilter); + filters.add(FeatureMatcher.NULL_MATCHER); + + /* + * use GridLayout to 'justify' rows to the top of the panel, until + * there are too many to fit in, then fall back on BoxLayout + */ + if (filters.size() <= 5) + { + chooseFiltersPanel.setLayout(new GridLayout(5, 1)); + } + else + { + chooseFiltersPanel.setLayout( + new BoxLayout(chooseFiltersPanel, BoxLayout.Y_AXIS)); + } /* * render the conditions in rows, each in its own JPanel @@ -1277,11 +1292,7 @@ public class FeatureTypeSettings extends JalviewDialog int filterIndex = 0; for (FeatureMatcherI filter : filters) { - String[] attName = filter.getKey(); - Condition condition = filter.getMatcher().getCondition(); - String pattern = filter.getMatcher().getPattern(); - JPanel row = addFilter(attName, attNames, condition, pattern, - filterIndex); + JPanel row = addFilter(filter, attNames, filterIndex); row.setBorder(BorderFactory.createLineBorder(debugBorderColour)); chooseFiltersPanel.add(row); filterIndex++; @@ -1294,25 +1305,36 @@ public class FeatureTypeSettings extends JalviewDialog /** * A helper method that constructs a row (panel) with one filter condition: * - * If attribute, condition or pattern are not null, they are set as defaults for - * the input fields. The 'remove' button is added unless the pattern is null or - * empty (incomplete filter condition). + * The filter values are set as defaults for the input fields. The 'remove' + * button is added unless the pattern is empty (incomplete filter condition). + *

    + * Action handlers on these fields provide for + *

    * - * @param attName + * @param filter * @param attNames - * @param cond - * @param pattern * @param filterIndex * @return */ - protected JPanel addFilter(String[] attName, List attNames, - Condition cond, String pattern, int filterIndex) + protected JPanel addFilter(FeatureMatcherI filter, + List attNames, int filterIndex) { + String[] attName = filter.getAttribute(); + Condition cond = filter.getMatcher().getCondition(); + String pattern = filter.getMatcher().getPattern(); + JPanel filterRow = new JPanel(new FlowLayout(FlowLayout.LEFT)); filterRow.setBackground(Color.white); @@ -1322,8 +1344,12 @@ public class FeatureTypeSettings extends JalviewDialog */ final JComboBox attCombo = populateAttributesDropdown(attNames, true, true); + String filterBy = setSelectedAttribute(attCombo, filter); + JComboBox condCombo = new JComboBox<>(); + JTextField patternField = new JTextField(8); + patternField.setText(pattern); /* * action handlers that validate and (if valid) apply changes @@ -1351,7 +1377,7 @@ public class FeatureTypeSettings extends JalviewDialog } }; - if (attName == null) // the 'add a condition' row + if (filter == FeatureMatcher.NULL_MATCHER) // the 'add a condition' row { attCombo.setSelectedIndex(0); } @@ -1369,7 +1395,8 @@ public class FeatureTypeSettings extends JalviewDialog * ensure it is appropriate for the attribute datatype */ populateConditions((String) attCombo.getSelectedItem(), - (Condition) condCombo.getSelectedItem(), condCombo); + (Condition) condCombo.getSelectedItem(), condCombo, + patternField); actionListener.actionPerformed(null); } }); @@ -1379,8 +1406,7 @@ public class FeatureTypeSettings extends JalviewDialog /* * drop-down choice of test condition */ - populateConditions((String) attCombo.getSelectedItem(), cond, - condCombo); + populateConditions(filterBy, cond, condCombo, patternField); condCombo.setPreferredSize(new Dimension(150, 20)); condCombo.addItemListener(itemListener); filterRow.add(condCombo); @@ -1388,7 +1414,6 @@ public class FeatureTypeSettings extends JalviewDialog /* * pattern to match against */ - patternField.setText(pattern); patternField.addActionListener(actionListener); patternField.addFocusListener(new FocusAdapter() { @@ -1413,7 +1438,7 @@ public class FeatureTypeSettings extends JalviewDialog * if a numeric condition is selected, show the value range * as a tooltip on the value input field */ - updatePatternTooltip(attName, selectedCondition, patternField); + setPatternTooltip(filterBy, selectedCondition, patternField); /* * add remove button if filter is populated (non-empty pattern) @@ -1441,6 +1466,33 @@ public class FeatureTypeSettings extends JalviewDialog } /** + * Sets the selected item in the Label/Score/Attribute drop-down to match the + * filter + * + * @param attCombo + * @param filter + */ + private String setSelectedAttribute(JComboBox attCombo, + FeatureMatcherI filter) + { + String item = null; + if (filter.isByScore()) + { + item = SCORE_18N; + } + else if (filter.isByLabel()) + { + item = LABEL_18N; + } + else + { + item = toAttributeDisplayName(filter.getAttribute()); + } + attCombo.setSelectedItem(item); + return item; + } + + /** * 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 * @@ -1448,7 +1500,7 @@ public class FeatureTypeSettings extends JalviewDialog * @param selectedCondition * @param patternField */ - private void updatePatternTooltip(String[] attName, + private void setPatternTooltip(String attName, Condition selectedCondition, JTextField patternField) { patternField.setToolTipText(""); @@ -1469,22 +1521,24 @@ public class FeatureTypeSettings extends JalviewDialog * Populates the drop-down list of comparison conditions for the given attribute * name. The conditions added depend on the datatype of the attribute values. * The supplied condition is set as the selected item in the list, provided it - * is in the list. + * is in the list. If the pattern is now invalid (non-numeric pattern for a + * numeric condition), it is cleared. * * @param attName * @param cond * @param condCombo + * @param patternField */ private void populateConditions(String attName, Condition cond, - JComboBox condCombo) + JComboBox condCombo, JTextField patternField) { Datatype type = FeatureAttributes.getInstance().getDatatype(featureType, fromAttributeDisplayName(attName)); - if (MessageManager.getString("label.label").equals(attName)) + if (LABEL_18N.equals(attName)) { type = Datatype.Character; } - else if (MessageManager.getString("label.score").equals(attName)) + else if (SCORE_18N.equals(attName)) { type = Datatype.Number; } @@ -1522,6 +1576,24 @@ public class FeatureTypeSettings extends JalviewDialog } condCombo.addItemListener(listener); + + /* + * clear pattern if it is now invalid for condition + */ + if (((Condition) condCombo.getSelectedItem()).isNumeric()) + { + try + { + String pattern = patternField.getText().trim(); + if (pattern.length() > 0) + { + Float.valueOf(pattern); + } + } catch (NumberFormatException e) + { + patternField.setText(""); + } + } } /** @@ -1544,7 +1616,7 @@ public class FeatureTypeSettings extends JalviewDialog } Condition cond = (Condition) condCombo.getSelectedItem(); - if (cond.needsAPattern()) + if (!cond.needsAPattern()) { return true; } @@ -1598,8 +1670,7 @@ public class FeatureTypeSettings extends JalviewDialog Condition cond = (Condition) condCombo.getSelectedItem(); String pattern = valueField.getText().trim(); - updatePatternTooltip(fromAttributeDisplayName(attName), cond, - valueField); + setPatternTooltip(attName, cond, valueField); if (pattern.length() == 0 && cond.needsAPattern()) { @@ -1611,11 +1682,11 @@ public class FeatureTypeSettings extends JalviewDialog * or named attribute */ FeatureMatcherI km = null; - if (MessageManager.getString("label.label").equals(attName)) + if (LABEL_18N.equals(attName)) { km = FeatureMatcher.byLabel(cond, pattern); } - else if (MessageManager.getString("label.score").equals(attName)) + else if (SCORE_18N.equals(attName)) { km = FeatureMatcher.byScore(cond, pattern); } diff --git a/src/jalview/util/matcher/Condition.java b/src/jalview/util/matcher/Condition.java index 3401ae8..3047802 100644 --- a/src/jalview/util/matcher/Condition.java +++ b/src/jalview/util/matcher/Condition.java @@ -2,9 +2,6 @@ package jalview.util.matcher; import jalview.util.MessageManager; -import java.util.HashMap; -import java.util.Map; - /** * An enumeration for binary conditions that a user might choose from when * setting filter or match conditions for values @@ -15,8 +12,6 @@ public enum Condition NotMatches(false, true), Present(false, false), NotPresent(false, false), EQ(true, true), NE(true, true), LT(true, true), LE(true, true), GT(true, true), GE(true, true); - - private static Map displayNames = new HashMap<>(); private boolean numeric; @@ -60,14 +55,7 @@ public enum Condition @Override public String toString() { - String name = displayNames.get(this); - if (name != null) - { - return name; - } - name = MessageManager - .getStringOrReturn("label.matchCondition_", name()); - displayNames.put(this, name); - return name; + return MessageManager.getStringOrReturn("label.matchCondition_", + name()); } } diff --git a/src/jalview/util/matcher/Matcher.java b/src/jalview/util/matcher/Matcher.java index 14a8585..353df83 100644 --- a/src/jalview/util/matcher/Matcher.java +++ b/src/jalview/util/matcher/Matcher.java @@ -14,12 +14,17 @@ public class Matcher implements MatcherI Condition condition; /* - * the string value (upper-cased), or the regex, to compare to + * the string pattern as entered, or the regex, to compare to * also holds the string form of float value if a numeric condition */ String pattern; /* + * the pattern in upper case, for non-case-sensitive matching + */ + String uppercasePattern; + + /* * the compiled regex if using a pattern match condition * (reserved for possible future enhancement) */ @@ -44,16 +49,21 @@ public class Matcher implements MatcherI */ public Matcher(Condition cond, String compareTo) { + Objects.requireNonNull(cond); condition = cond; if (cond.isNumeric()) { value = Float.valueOf(compareTo); pattern = String.valueOf(value); + uppercasePattern = pattern; } else { - // pattern matches will be non-case-sensitive - pattern = compareTo == null ? null : compareTo.toUpperCase(); + pattern = compareTo; + if (pattern != null) + { + uppercasePattern = pattern.toUpperCase(); + } } // if we add regex conditions (e.g. matchesPattern), then @@ -71,10 +81,7 @@ public class Matcher implements MatcherI */ public Matcher(Condition cond, float compareTo) { - Objects.requireNonNull(cond); - condition = cond; - value = compareTo; - pattern = String.valueOf(compareTo).toUpperCase(); + this(cond, String.valueOf(compareTo)); } /** @@ -113,16 +120,16 @@ public class Matcher implements MatcherI boolean matched = false; switch(condition) { case Matches: - matched = upper.equals(pattern); + matched = upper.equals(uppercasePattern); break; case NotMatches: - matched = !upper.equals(pattern); + matched = !upper.equals(uppercasePattern); break; case Contains: - matched = upper.indexOf(pattern) > -1; + matched = upper.indexOf(uppercasePattern) > -1; break; case NotContains: - matched = upper.indexOf(pattern) == -1; + matched = upper.indexOf(uppercasePattern) == -1; break; case Present: matched = true; @@ -186,7 +193,7 @@ public class Matcher implements MatcherI /** * equals is overridden so that we can safely remove Matcher objects from - * collections (e.g. delete an attribut match condition for a feature colour) + * collections (e.g. delete an attribute match condition for a feature colour) */ @Override public boolean equals(Object obj) @@ -196,8 +203,15 @@ public class Matcher implements MatcherI return false; } Matcher m = (Matcher) obj; - return condition == m.condition && value == m.value - && pattern.equals(m.pattern); + if (condition != m.condition || value != m.value) + { + return false; + } + if (pattern == null) + { + return m.pattern == null; + } + return uppercasePattern.equals(m.uppercasePattern); } @Override @@ -222,7 +236,7 @@ public class Matcher implements MatcherI public String toString() { StringBuilder sb = new StringBuilder(); - sb.append(condition.name()).append(" "); + sb.append(condition.toString()).append(" "); if (condition.isNumeric()) { sb.append(pattern); diff --git a/test/jalview/datamodel/features/FeatureMatcherSetTest.java b/test/jalview/datamodel/features/FeatureMatcherSetTest.java index a98013b..56644fd 100644 --- a/test/jalview/datamodel/features/FeatureMatcherSetTest.java +++ b/test/jalview/datamodel/features/FeatureMatcherSetTest.java @@ -11,6 +11,7 @@ import jalview.util.matcher.Condition; import java.util.HashMap; import java.util.Iterator; +import java.util.Locale; import java.util.Map; import org.testng.annotations.Test; @@ -111,14 +112,14 @@ public class FeatureMatcherSetTest @Test(groups = "Functional") public void testToString() { + Locale.setDefault(Locale.ENGLISH); FeatureMatcherI fm1 = FeatureMatcher.byAttribute(Condition.LT, "1.2", "AF"); assertEquals(fm1.toString(), "AF < 1.2"); FeatureMatcher fm2 = FeatureMatcher.byAttribute(Condition.NotContains, - "path", - "CLIN_SIG"); - assertEquals(fm2.toString(), "CLIN_SIG Does not contain 'PATH'"); + "path", "CLIN_SIG"); + assertEquals(fm2.toString(), "CLIN_SIG does not contain 'path'"); /* * AND them @@ -129,7 +130,7 @@ public class FeatureMatcherSetTest assertEquals(fms.toString(), "(AF < 1.2)"); fms.and(fm2); assertEquals(fms.toString(), - "(AF < 1.2) AND (CLIN_SIG Does not contain 'PATH')"); + "(AF < 1.2) and (CLIN_SIG does not contain 'path')"); /* * OR them @@ -140,7 +141,7 @@ public class FeatureMatcherSetTest assertEquals(fms.toString(), "(AF < 1.2)"); fms.or(fm2); assertEquals(fms.toString(), - "(AF < 1.2) OR (CLIN_SIG Does not contain 'PATH')"); + "(AF < 1.2) or (CLIN_SIG does not contain 'path')"); try { @@ -265,7 +266,7 @@ public class FeatureMatcherSetTest assertFalse(fms.matches(sf)); csq.put("Consequence", "junk"); assertFalse(fms.matches(sf)); - + /* * a string pattern matcher */ diff --git a/test/jalview/datamodel/features/FeatureMatcherTest.java b/test/jalview/datamodel/features/FeatureMatcherTest.java index f4e9351..62b03a3 100644 --- a/test/jalview/datamodel/features/FeatureMatcherTest.java +++ b/test/jalview/datamodel/features/FeatureMatcherTest.java @@ -2,11 +2,15 @@ package jalview.datamodel.features; import static org.testng.Assert.assertEquals; import static org.testng.Assert.assertFalse; +import static org.testng.Assert.assertNull; import static org.testng.Assert.assertTrue; import jalview.datamodel.SequenceFeature; +import jalview.util.MessageManager; import jalview.util.matcher.Condition; +import java.util.Locale; + import org.testng.annotations.Test; public class FeatureMatcherTest @@ -126,6 +130,8 @@ public class FeatureMatcherTest @Test public void testToString() { + Locale.setDefault(Locale.ENGLISH); + /* * toString uses the i18n translation of the enum conditions */ @@ -137,24 +143,65 @@ public class FeatureMatcherTest * Present / NotPresent omit the value pattern */ fm = FeatureMatcher.byAttribute(Condition.Present, "", "AF"); - assertEquals(fm.toString(), "AF Is present"); + assertEquals(fm.toString(), "AF is present"); fm = FeatureMatcher.byAttribute(Condition.NotPresent, "", "AF"); - assertEquals(fm.toString(), "AF Is not present"); + assertEquals(fm.toString(), "AF is not present"); + + /* + * by Label + */ + fm = FeatureMatcher.byLabel(Condition.Matches, "foobar"); + assertEquals(fm.toString(), + MessageManager.getString("label.label") + " matches 'foobar'"); + + /* + * by Score + */ + fm = FeatureMatcher.byScore(Condition.GE, "12.2"); + assertEquals(fm.toString(), + MessageManager.getString("label.score") + " >= 12.2"); } @Test - public void testGetKey() + public void testGetAttribute() { FeatureMatcherI fm = FeatureMatcher.byAttribute(Condition.GE, "-2", "AF"); - assertEquals(fm.getKey(), new String[] { "AF" }); + assertEquals(fm.getAttribute(), new String[] { "AF" }); /* * compound key (attribute / subattribute) */ fm = FeatureMatcher.byAttribute(Condition.GE, "-2F", "CSQ", "Consequence"); - assertEquals(fm.getKey(), new String[] { "CSQ", "Consequence" }); + assertEquals(fm.getAttribute(), new String[] { "CSQ", "Consequence" }); + + /* + * answers null if match is by Label or by Score + */ + assertNull(FeatureMatcher.byLabel(Condition.NotContains, "foo") + .getAttribute()); + assertNull(FeatureMatcher.byScore(Condition.LE, "-1").getAttribute()); + } + + @Test + public void testIsByLabel() + { + assertTrue(FeatureMatcher.byLabel(Condition.NotContains, "foo") + .isByLabel()); + assertFalse(FeatureMatcher.byScore(Condition.LE, "-1").isByLabel()); + assertFalse(FeatureMatcher.byAttribute(Condition.LE, "-1", "AC") + .isByLabel()); + } + + @Test + public void testIsByScore() + { + assertFalse(FeatureMatcher.byLabel(Condition.NotContains, "foo") + .isByScore()); + assertTrue(FeatureMatcher.byScore(Condition.LE, "-1").isByScore()); + assertFalse(FeatureMatcher.byAttribute(Condition.LE, "-1", "AC") + .isByScore()); } @Test diff --git a/test/jalview/util/matcher/MatcherTest.java b/test/jalview/util/matcher/MatcherTest.java index f4c8181..a47fb60 100644 --- a/test/jalview/util/matcher/MatcherTest.java +++ b/test/jalview/util/matcher/MatcherTest.java @@ -6,8 +6,12 @@ import static org.testng.Assert.assertNotEquals; import static org.testng.Assert.assertTrue; import static org.testng.Assert.fail; +import java.util.Locale; + import org.testng.annotations.Test; +import junit.extensions.PA; + public class MatcherTest { @Test(groups = "Functional") @@ -15,7 +19,8 @@ public class MatcherTest { MatcherI m = new Matcher(Condition.Contains, "foo"); assertEquals(m.getCondition(), Condition.Contains); - assertEquals(m.getPattern(), "FOO"); // all comparisons upper-cased + assertEquals(m.getPattern(), "foo"); + assertEquals(PA.getValue(m, "uppercasePattern"), "FOO"); assertEquals(m.getFloatValue(), 0f); m = new Matcher(Condition.GT, -2.1f); @@ -25,7 +30,7 @@ public class MatcherTest m = new Matcher(Condition.NotContains, "-1.2f"); assertEquals(m.getCondition(), Condition.NotContains); - assertEquals(m.getPattern(), "-1.2F"); + assertEquals(m.getPattern(), "-1.2f"); assertEquals(m.getFloatValue(), 0f); m = new Matcher(Condition.GE, "-1.2f"); @@ -208,11 +213,13 @@ public class MatcherTest @Test(groups = "Functional") public void testToString() { + Locale.setDefault(Locale.ENGLISH); + MatcherI m = new Matcher(Condition.LT, 1.2e-6f); - assertEquals(m.toString(), "LT 1.2E-6"); + assertEquals(m.toString(), "< 1.2E-6"); m = new Matcher(Condition.NotMatches, "ABC"); - assertEquals(m.toString(), "NotMatches 'ABC'"); + assertEquals(m.toString(), "Does not match 'ABC'"); m = new Matcher(Condition.Contains, -1.2f); assertEquals(m.toString(), "Contains '-1.2'"); -- 1.7.10.2