From: gmungoc Date: Mon, 14 Jan 2019 14:05:22 +0000 (+0000) Subject: Merge branch 'develop' into bug/JAL-3184restoreGroupVisibility X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2Fbug%2FJAL-3184restoreGroupVisibility;hp=b3fd7c6e37dae89dbd96f45e78e4d04aa2de0374;p=jalview.git Merge branch 'develop' into bug/JAL-3184restoreGroupVisibility --- diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 1358c8f..c310c47 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -62,6 +62,7 @@ import java.io.FileOutputStream; import java.io.InputStreamReader; import java.io.OutputStreamWriter; import java.io.PrintWriter; +import java.util.ArrayList; import java.util.Arrays; import java.util.Comparator; import java.util.HashMap; @@ -135,6 +136,10 @@ public class FeatureSettings extends JPanel private Map originalFilters; + private List originalVisibleGroups; + + private List originalHiddenGroups; + final JInternalFrame frame; JScrollPane scrollPane = new JScrollPane(); @@ -187,6 +192,10 @@ public class FeatureSettings extends JPanel originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy + originalVisibleGroups = new ArrayList<>(fr.getGroups(true)); + + originalHiddenGroups = new ArrayList<>(fr.getGroups(false)); + try { jbInit(); @@ -1236,10 +1245,7 @@ public class FeatureSettings extends JPanel @Override public void actionPerformed(ActionEvent e) { - fr.setTransparency(originalTransparency); - fr.setFeatureFilters(originalFilters); - updateFeatureRenderer(originalData); - close(); + cancel(); } }); @@ -1321,6 +1327,22 @@ public class FeatureSettings extends JPanel this.add(settingsPane); } + /** + * Restores feature type and group visibility, and any filters and + * transparency setting, to the values when this dialog was opened. Note this + * won't affect any feature types or groups which were added while the dialog + * was open. + */ + void cancel() + { + fr.setTransparency(originalTransparency); + fr.setFeatureFilters(originalFilters); + fr.setGroupVisibility(originalVisibleGroups, true); + fr.setGroupVisibility(originalHiddenGroups, false); + updateFeatureRenderer(originalData); + close(); + } + // /////////////////////////////////////////////////////////////////////// // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html // /////////////////////////////////////////////////////////////////////// diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 9285754..c8e887b 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -52,7 +52,6 @@ import jalview.schemabinding.version2.Annotation; import jalview.schemabinding.version2.AnnotationColours; import jalview.schemabinding.version2.AnnotationElement; import jalview.schemabinding.version2.CalcIdParam; -import jalview.schemabinding.version2.Colour; import jalview.schemabinding.version2.CompoundMatcher; import jalview.schemabinding.version2.DBRef; import jalview.schemabinding.version2.Features; @@ -4639,125 +4638,9 @@ public class Jalview2XML af.viewport.setShowGroupConservation(false); } - // recover feature settings if (jms.getFeatureSettings() != null) { - FeatureRenderer fr = af.alignPanel.getSeqPanel().seqCanvas - .getFeatureRenderer(); - FeaturesDisplayed fdi; - af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed()); - String[] renderOrder = new String[jms.getFeatureSettings() - .getSettingCount()]; - Map featureColours = new Hashtable<>(); - Map featureOrder = new Hashtable<>(); - - for (int fs = 0; fs < jms.getFeatureSettings() - .getSettingCount(); fs++) - { - Setting setting = jms.getFeatureSettings().getSetting(fs); - String featureType = setting.getType(); - - /* - * restore feature filters (if any) - */ - MatcherSet filters = setting.getMatcherSet(); - if (filters != null) - { - FeatureMatcherSetI filter = Jalview2XML - .unmarshalFilter(featureType, filters); - if (!filter.isEmpty()) - { - fr.setFeatureFilter(featureType, filter); - } - } - - /* - * restore feature colour scheme - */ - Color maxColour = new Color(setting.getColour()); - if (setting.hasMincolour()) - { - /* - * minColour is always set unless a simple colour - * (including for colour by label though it doesn't use it) - */ - Color minColour = new Color(setting.getMincolour()); - Color noValueColour = minColour; - NoValueColour noColour = setting.getNoValueColour(); - if (noColour == NoValueColour.NONE) - { - noValueColour = null; - } - else if (noColour == NoValueColour.MAX) - { - noValueColour = maxColour; - } - float min = setting.hasMin() ? setting.getMin() : 0f; - float max = setting.hasMin() ? setting.getMax() : 1f; - FeatureColourI gc = new FeatureColour(minColour, maxColour, - noValueColour, min, max); - if (setting.getAttributeNameCount() > 0) - { - gc.setAttributeName(setting.getAttributeName()); - } - if (setting.hasThreshold()) - { - gc.setThreshold(setting.getThreshold()); - int threshstate = setting.getThreshstate(); - // -1 = None, 0 = Below, 1 = Above threshold - if (threshstate == 0) - { - gc.setBelowThreshold(true); - } - else if (threshstate == 1) - { - gc.setAboveThreshold(true); - } - } - gc.setAutoScaled(true); // default - if (setting.hasAutoScale()) - { - gc.setAutoScaled(setting.getAutoScale()); - } - if (setting.hasColourByLabel()) - { - gc.setColourByLabel(setting.getColourByLabel()); - } - // and put in the feature colour table. - featureColours.put(featureType, gc); - } - else - { - featureColours.put(featureType, - new FeatureColour(maxColour)); - } - renderOrder[fs] = featureType; - if (setting.hasOrder()) - { - featureOrder.put(featureType, setting.getOrder()); - } - else - { - featureOrder.put(featureType, new Float( - fs / jms.getFeatureSettings().getSettingCount())); - } - if (setting.getDisplay()) - { - fdi.setVisible(featureType); - } - } - Map fgtable = new Hashtable<>(); - for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++) - { - Group grp = jms.getFeatureSettings().getGroup(gs); - fgtable.put(grp.getName(), new Boolean(grp.getDisplay())); - } - // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, - // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ? - // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder); - FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, - fgtable, featureColours, 1.0f, featureOrder); - fr.transferSettings(frs); + loadFeatureSettings(jms, af); } if (view.getHiddenColumnsCount() > 0) @@ -4812,6 +4695,160 @@ public class Jalview2XML } /** + * Loads feature settings data from project XML and stores + *
    + *
  • feature type visibility in the Viewport
    • + *
  • other data in the FeatureRenderer: + *
      + *
    • feature type render order
      • + *
    • feature type colours
      • + *
    • feature type filters
      • + *
    • feature groups and their visibility
      • + *
    + *
    • + *
+ * + * @param jms + * @param af + */ + static void loadFeatureSettings(JalviewModelSequence jms, AlignFrame af) + { + FeatureRenderer fr = af.getFeatureRenderer(); + FeaturesDisplayed fdi = new FeaturesDisplayed(); + af.viewport.setFeaturesDisplayed(fdi); + String[] renderOrder = new String[jms.getFeatureSettings() + .getSettingCount()]; + Map featureColours = new Hashtable<>(); + Map featureOrder = new Hashtable<>(); + Map filters = new HashMap<>(); + + for (int fs = 0; fs < jms.getFeatureSettings() + .getSettingCount(); fs++) + { + Setting setting = jms.getFeatureSettings().getSetting(fs); + String featureType = setting.getType(); + + /* + * restore feature filters (if any) + */ + MatcherSet matchers = setting.getMatcherSet(); + if (matchers != null) + { + FeatureMatcherSetI filter = Jalview2XML + .unmarshalFilter(featureType, matchers); + if (!filter.isEmpty()) + { + filters.put(featureType, filter); + } + } + + /* + * restore feature colour scheme + */ + FeatureColourI featureColour = loadFeatureColour(setting); + featureColours.put(featureType, featureColour); + + renderOrder[fs] = featureType; + if (setting.hasOrder()) + { + featureOrder.put(featureType, setting.getOrder()); + } + else + { + featureOrder.put(featureType, new Float( + fs / jms.getFeatureSettings().getSettingCount())); + } + if (setting.getDisplay()) + { + fdi.setVisible(featureType); + } + } + Map fgtable = new Hashtable<>(); + for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++) + { + Group grp = jms.getFeatureSettings().getGroup(gs); + fgtable.put(grp.getName(), new Boolean(grp.getDisplay())); + } + + /* + * todo: save transparency in project (JAL-1147) + */ + float transparency = 1.0f; + FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, + fgtable, featureColours, transparency, featureOrder, filters); + fr.transferSettings(frs); + } + + /** + * Constructs a FeatureColour from the data saved for one FeatureSetting + * setting element + * + * @param setting + * @return + */ + static FeatureColourI loadFeatureColour(Setting setting) + { + FeatureColourI featureColour; + Color maxColour = new Color(setting.getColour()); + if (setting.hasMincolour()) + { + /* + * minColour is always set unless a simple colour + * (including for colour by label though it doesn't use it) + */ + Color minColour = new Color(setting.getMincolour()); + Color noValueColour = minColour; + NoValueColour noColour = setting.getNoValueColour(); + if (noColour == NoValueColour.NONE) + { + noValueColour = null; + } + else if (noColour == NoValueColour.MAX) + { + noValueColour = maxColour; + } + float min = setting.hasMin() ? setting.getMin() : 0f; + float max = setting.hasMin() ? setting.getMax() : 1f; + FeatureColourI gc = new FeatureColour(minColour, maxColour, + noValueColour, min, max); + if (setting.getAttributeNameCount() > 0) + { + gc.setAttributeName(setting.getAttributeName()); + } + if (setting.hasThreshold()) + { + gc.setThreshold(setting.getThreshold()); + int threshstate = setting.getThreshstate(); + // -1 = None, 0 = Below, 1 = Above threshold + if (threshstate == 0) + { + gc.setBelowThreshold(true); + } + else if (threshstate == 1) + { + gc.setAboveThreshold(true); + } + } + gc.setAutoScaled(true); // default + if (setting.hasAutoScale()) + { + gc.setAutoScaled(setting.getAutoScale()); + } + if (setting.hasColourByLabel()) + { + gc.setColourByLabel(setting.getColourByLabel()); + } + featureColour = gc; + } + else + { + featureColour = new FeatureColour(maxColour); + } + + return featureColour; + } + + /** * Reads saved data to restore Colour by Annotation settings * * @param viewAnnColour diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java index 331e738..d2ba95b 100755 --- a/src/jalview/gui/Jalview2XML_V1.java +++ b/src/jalview/gui/Jalview2XML_V1.java @@ -21,6 +21,7 @@ package jalview.gui; import jalview.analysis.Conservation; +import jalview.api.FeatureColourI; import jalview.binding.Annotation; import jalview.binding.AnnotationElement; import jalview.binding.Features; @@ -40,6 +41,7 @@ import jalview.datamodel.SequenceFeature; import jalview.io.FileFormat; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; +import jalview.schemes.FeatureColour; import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; import jalview.util.jarInputStreamProvider; @@ -428,8 +430,8 @@ public class Jalview2XML_V1 if (jms.getFeatureSettings() != null) { - Hashtable featuresDisplayed = new Hashtable(); - Hashtable featureColours = new Hashtable(); + Hashtable featuresDisplayed = new Hashtable<>(); + Hashtable featureColours = new Hashtable<>(); String[] renderOrder = new String[jms.getFeatureSettings() .getSettingCount()]; for (int fs = 0; fs < jms.getFeatureSettings() @@ -438,7 +440,7 @@ public class Jalview2XML_V1 Setting setting = jms.getFeatureSettings().getSetting(fs); featureColours.put(setting.getType(), - new java.awt.Color(setting.getColour())); + new FeatureColour(new java.awt.Color(setting.getColour()))); renderOrder[fs] = setting.getType(); @@ -449,7 +451,8 @@ public class Jalview2XML_V1 } } FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, - new Hashtable(), featureColours, 1.0f, null); + new Hashtable(), featureColours, 1.0f, null, + null); af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() .transferSettings(frs); } diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java index 553f813..ce65f9f 100644 --- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java +++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java @@ -43,6 +43,7 @@ import java.util.Hashtable; import java.util.Iterator; import java.util.List; import java.util.Map; +import java.util.Map.Entry; import java.util.Set; import java.util.concurrent.ConcurrentHashMap; @@ -119,6 +120,7 @@ public abstract class FeatureRendererModel this.featureColours = fr.featureColours; this.transparency = fr.transparency; this.featureOrder = fr.featureOrder; + this.featureFilters = fr.featureFilters; } /** @@ -859,30 +861,27 @@ public abstract class FeatureRendererModel } /** - * get visible or invisible groups + * Answers a (possibly empty) list of visible or invisible feature groups * * @param visible - * true to return visible groups, false to return hidden ones. - * @return list of groups + * true to return visible groups, false to return hidden ones + * @return */ @Override public List getGroups(boolean visible) { + List groups = new ArrayList<>(); if (featureGroups != null) { - List gp = new ArrayList<>(); - - for (String grp : featureGroups.keySet()) + for (Entry grp : featureGroups.entrySet()) { - Boolean state = featureGroups.get(grp); - if (state.booleanValue() == visible) + if (grp.getValue() == visible) { - gp.add(grp); + groups.add(grp.getKey()); } } - return gp; } - return null; + return groups; } @Override diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererSettings.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererSettings.java index f594453..cd6f51b 100644 --- a/src/jalview/viewmodel/seqfeatures/FeatureRendererSettings.java +++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererSettings.java @@ -30,7 +30,18 @@ import java.util.Iterator; import java.util.Map; import java.util.concurrent.ConcurrentHashMap; -public class FeatureRendererSettings implements Cloneable +/** + * A data bean that holds + *
    + *
  • feature types and their render order
    • + *
  • feature groups and their visibility
    • + *
  • colour for each feature type
    • + *
  • filters (if any) for each feature type
    • + *
  • feature colour transparency
    • + *
+ * Note that feature type visibility settings are not held here. + */ +public class FeatureRendererSettings { String[] renderOrder; @@ -53,19 +64,31 @@ public class FeatureRendererSettings implements Cloneable Map featureOrder; + /** + * Constructor + * + * @param renderOrder + * @param featureGroups + * @param featureColours + * @param transparency + * @param featureOrder + * @param filters + */ public FeatureRendererSettings(String[] renderOrder, Map featureGroups, Map featureColours, float transparency, - Map featureOrder) + Map featureOrder, + Map filters) { super(); this.renderOrder = Arrays.copyOf(renderOrder, renderOrder.length); - this.featureGroups = new ConcurrentHashMap( + this.featureGroups = new ConcurrentHashMap<>( featureGroups); - this.featureColours = new ConcurrentHashMap( + this.featureColours = new ConcurrentHashMap<>( featureColours); this.transparency = transparency; - this.featureOrder = new ConcurrentHashMap(featureOrder); + this.featureOrder = new ConcurrentHashMap<>(featureOrder); + featureFilters = filters; } /** @@ -77,10 +100,10 @@ public class FeatureRendererSettings implements Cloneable jalview.viewmodel.seqfeatures.FeatureRendererModel fr) { renderOrder = null; - featureGroups = new ConcurrentHashMap(); - featureColours = new ConcurrentHashMap(); + featureGroups = new ConcurrentHashMap<>(); + featureColours = new ConcurrentHashMap<>(); featureFilters = new HashMap<>(); - featureOrder = new ConcurrentHashMap(); + featureOrder = new ConcurrentHashMap<>(); if (fr.renderOrder != null) { @@ -90,12 +113,12 @@ public class FeatureRendererSettings implements Cloneable } if (fr.featureGroups != null) { - this.featureGroups = new ConcurrentHashMap( + this.featureGroups = new ConcurrentHashMap<>( fr.featureGroups); } if (fr.featureColours != null) { - this.featureColours = new ConcurrentHashMap( + this.featureColours = new ConcurrentHashMap<>( fr.featureColours); } Iterator en = fr.featureColours.keySet().iterator(); @@ -118,7 +141,7 @@ public class FeatureRendererSettings implements Cloneable this.transparency = fr.transparency; if (fr.featureOrder != null) { - this.featureOrder = new ConcurrentHashMap( + this.featureOrder = new ConcurrentHashMap<>( fr.featureOrder); } } diff --git a/test/jalview/gui/FeatureSettingsTest.java b/test/jalview/gui/FeatureSettingsTest.java index 6ddebf8..228d924 100644 --- a/test/jalview/gui/FeatureSettingsTest.java +++ b/test/jalview/gui/FeatureSettingsTest.java @@ -1,6 +1,11 @@ package jalview.gui; +import static jalview.gui.FeatureSettings.COLOUR_COLUMN; +import static jalview.gui.FeatureSettings.FILTER_COLUMN; +import static jalview.gui.FeatureSettings.SHOW_COLUMN; +import static jalview.gui.FeatureSettings.TYPE_COLUMN; import static org.testng.Assert.assertEquals; +import static org.testng.Assert.assertFalse; import static org.testng.Assert.assertNull; import static org.testng.Assert.assertTrue; @@ -11,6 +16,7 @@ import jalview.datamodel.features.FeatureMatcher; import jalview.datamodel.features.FeatureMatcherSet; import jalview.datamodel.features.FeatureMatcherSetI; import jalview.io.DataSourceType; +import jalview.io.FileFormat; import jalview.io.FileLoader; import jalview.schemes.FeatureColour; import jalview.util.matcher.Condition; @@ -33,7 +39,7 @@ public class FeatureSettingsTest public void testSaveLoad() throws IOException { AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( - ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE); + ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE, FileFormat.Fasta); SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0); /* @@ -188,4 +194,186 @@ public class FeatureSettingsTest }); seq.addSequenceFeature(sf); } + + /** + * Test of the behaviour of the Show / Hide checkbox + */ + @Test(groups = "Functional") + public void testHideShow() + { + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE, FileFormat.Fasta); + SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0); + seq1.addSequenceFeature( + new SequenceFeature("type1", "", 1, 4, "group1")); + + FeatureRenderer fr = af.getFeatureRenderer(); + fr.setColour("type1", new FeatureColour(Color.red)); + + af.showSeqFeatures_actionPerformed(null); + FeatureSettings dialog = new FeatureSettings(af); + + assertTrue(fr.getDisplayedFeatureTypes().contains("type1")); + + /* + * check the table has one row, for type1, visible, no filter, red + */ + assertEquals(dialog.table.getRowCount(), 1); + assertEquals(dialog.table.getColumnCount(), 4); + assertEquals(dialog.table.getModel().getValueAt(0, TYPE_COLUMN), + "type1"); + FeatureColourI colour = (FeatureColourI) dialog.table.getModel() + .getValueAt(0, COLOUR_COLUMN); + assertTrue(colour.isSimpleColour()); + assertEquals(colour.getColour(), Color.red); + FeatureMatcherSetI filter = (FeatureMatcherSetI) dialog.table.getModel() + .getValueAt(0, FILTER_COLUMN); + assertTrue(filter.isEmpty()); + assertEquals(dialog.table.getModel().getValueAt(0, SHOW_COLUMN), + Boolean.TRUE); + + /* + * set feature type to hidden by clicking the checkbox in column 4, + * and verify that now no feature types are displayed + */ + dialog.table.setValueAt(Boolean.FALSE, 0, SHOW_COLUMN); + assertTrue(fr.getDisplayedFeatureTypes().isEmpty()); + + /* + * set feature type back to visible by clicking the checkbox in column 4, + * and verify that now the feature type is displayed + */ + dialog.table.setValueAt(Boolean.TRUE, 0, SHOW_COLUMN); + assertTrue(fr.getDisplayedFeatureTypes().contains("type1")); + } + + /** + * Test Cancel resets any changes made + */ + @Test(groups = "Functional") + public void testCancel() + { + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE, FileFormat.Fasta); + SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0); + seq1.addSequenceFeature( + new SequenceFeature("type1", "", 1, 4, "group1")); + seq1.addSequenceFeature( + new SequenceFeature("type2", "", 1, 4, "group2")); + + /* + * set type1: red, filter 'Label Contains metal' + * type2: variable colour red:blue, no filter + */ + FeatureRenderer fr = af.getFeatureRenderer(); + fr.setColour("type1", new FeatureColour(Color.red)); + fr.setColour("type2", new FeatureColour(Color.red, Color.blue, 0f, 1f)); + FeatureMatcherSetI f = new FeatureMatcherSet(); + f.and(FeatureMatcher.byLabel(Condition.Contains, "metal")); + fr.setFeatureFilter("type1", f); + + af.showSeqFeatures_actionPerformed(null); + FeatureSettings dialog = new FeatureSettings(af); + + assertTrue(fr.getDisplayedFeatureTypes().contains("type1")); + assertTrue(fr.getDisplayedFeatureTypes().contains("type2")); + + /* + * check the table has two rows, for type1 and type2 + * note type2 is shown first; the initial ordering is 'random' as driven by + * the Set of feature groups for the sequence + */ + assertEquals(dialog.table.getRowCount(), 2); + assertEquals(dialog.table.getColumnCount(), 4); + + assertEquals(dialog.table.getModel().getValueAt(0, TYPE_COLUMN), + "type2"); + FeatureColourI colour = (FeatureColourI) dialog.table.getModel() + .getValueAt(0, COLOUR_COLUMN); + assertFalse(colour.isSimpleColour()); + assertEquals(colour.getMinColour(), Color.red); + assertEquals(colour.getMaxColour(), Color.blue); + FeatureMatcherSetI filter = (FeatureMatcherSetI) dialog.table.getModel() + .getValueAt(0, FILTER_COLUMN); + assertTrue(filter.isEmpty()); + assertEquals(dialog.table.getModel().getValueAt(0, SHOW_COLUMN), + Boolean.TRUE); + + assertEquals(dialog.table.getModel().getValueAt(1, TYPE_COLUMN), + "type1"); + colour = (FeatureColourI) dialog.table.getModel().getValueAt(1, + COLOUR_COLUMN); + assertTrue(colour.isSimpleColour()); + assertEquals(colour.getColour(), Color.red); + filter = (FeatureMatcherSetI) dialog.table.getModel().getValueAt(1, + FILTER_COLUMN); + assertFalse(filter.isEmpty()); + assertEquals(dialog.table.getModel().getValueAt(1, SHOW_COLUMN), + Boolean.TRUE); + + /* + * Make some changes: + * - set type1 to hidden by clicking the checkbox in column 4 + * - change type2 to plain colour green + * We can do these by setting values in the table model - + * updateFeatureRenderer then updates visibility and colour + */ + dialog.table.setValueAt(Boolean.FALSE, 1, SHOW_COLUMN); + dialog.table.setValueAt(new FeatureColour(Color.green), 0, + COLOUR_COLUMN); + + /* + * - remove the filter on type1 + * - set a filter on type2 + * We have to do this directly on FeatureRendererModel (as done in the + * application from FeatureTypeSettings) + */ + fr.setFeatureFilter("type1", null); + fr.setFeatureFilter("type2", + FeatureMatcherSet.fromString("Label matches Metal")); + + /* + * verify the changes reached the FeatureRender + */ + assertFalse(fr.getDisplayedFeatureTypes().contains("type1")); + assertNull(fr.getFeatureFilter("type1")); + colour = fr.getFeatureColours().get("type2"); + assertTrue(colour.isSimpleColour()); + assertEquals(colour.getColour(), Color.green); + filter = fr.getFeatureFilter("type2"); + assertFalse(filter.isEmpty()); + assertEquals(filter.toStableString(), "Label Matches Metal"); + + /* + * add a new feature type and 'notify' FeatureRenderer + * it should appear in the first row of FeatureSettings table + */ + seq1.addSequenceFeature( + new SequenceFeature("type3", "desc", 4, 5, null)); + fr.featuresAdded(); + assertEquals(dialog.table.getRowCount(), 3); + assertEquals(dialog.table.getModel().getValueAt(0, TYPE_COLUMN), + "type3"); + assertEquals(dialog.table.getModel().getValueAt(0, SHOW_COLUMN), + Boolean.TRUE); + assertTrue(fr.getDisplayedFeatureTypes().contains("type3")); + + /* + * cancel the dialog, and verify FeatureRenderer data has been reset + */ + dialog.cancel(); + // type1 has been reset to visible: + assertTrue(fr.getDisplayedFeatureTypes().contains("type1")); + // type3 has been reset to not visible: + assertTrue(fr.getDisplayedFeatureTypes().contains("type3")); + // type2 colour has been reset to graduated: + colour = fr.getFeatureColours().get("type2"); + assertFalse(colour.isSimpleColour()); + assertEquals(colour.getMaxColour(), Color.blue); + // type2 filter has been reset to none (held as null): + assertNull(fr.getFeatureFilter("type2")); + // type1 filter has been reset: + filter = fr.getFeatureFilter("type1"); + assertEquals(filter.toStableString(), "Label Contains metal"); + } }