From: gmungoc Date: Fri, 1 Mar 2019 15:35:54 +0000 (+0000) Subject: Merge branch 'bug/JAL-2791exportFilteredFeature' into merge/JAL-2791 X-Git-Tag: Release_2_11_0~17^2~81 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=09d3b755d9b00f5c3acb44049aedd49361dc0690;hp=d34f80c67881e79d7304eb143e9c907bc16d052b;p=jalview.git Merge branch 'bug/JAL-2791exportFilteredFeature' into merge/JAL-2791 --- diff --git a/src/jalview/api/FeatureColourI.java b/src/jalview/api/FeatureColourI.java index 4dbb1bb..999104c 100644 --- a/src/jalview/api/FeatureColourI.java +++ b/src/jalview/api/FeatureColourI.java @@ -192,4 +192,16 @@ public interface FeatureColourI * @return */ void setAttributeName(String... name); + + /** + * Answers true if colour has a threshold set, and the feature score (or other + * attribute selected for colouring) is outwith the threshold. + *

+ * Answers false if not a graduated colour, or no threshold is set, or value + * is not outwith the threshold, or value is null or non-numeric. + * + * @param sf + * @return + */ + boolean isOutwithThreshold(SequenceFeature sf); } diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java index 868f196..404c497 100644 --- a/src/jalview/api/FeatureRenderer.java +++ b/src/jalview/api/FeatureRenderer.java @@ -265,4 +265,19 @@ public interface FeatureRenderer * @return */ Color getColour(SequenceFeature feature); + + /** + * Answers true if feature would be shown, else false. A feature is shown if + *

+ * + * @param feature + * @return + */ + boolean isVisible(SequenceFeature feature); } diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 5ad212e..85fb03c 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -1447,14 +1447,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { features = formatter.printJalviewFormat( viewport.getAlignment().getSequencesArray(), - getDisplayedFeatureCols(), null, getDisplayedFeatureGroups(), - true); + alignPanel.getFeatureRenderer(), true); } else { features = formatter.printGffFormat(viewport.getAlignment() - .getSequencesArray(), getDisplayedFeatureCols(), - getDisplayedFeatureGroups(), true); + .getSequencesArray(), alignPanel.getFeatureRenderer(), true); } if (displayTextbox) diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java index 6fefbd0..fac531e 100644 --- a/src/jalview/gui/AnnotationExporter.java +++ b/src/jalview/gui/AnnotationExporter.java @@ -20,11 +20,10 @@ */ package jalview.gui; -import jalview.api.FeatureColourI; +import jalview.api.FeatureRenderer; import jalview.bin.Cache; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.SequenceI; -import jalview.datamodel.features.FeatureMatcherSetI; import jalview.io.AnnotationFile; import jalview.io.FeaturesFile; import jalview.io.JalviewFileChooser; @@ -38,8 +37,6 @@ import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.io.FileWriter; import java.io.PrintWriter; -import java.util.List; -import java.util.Map; import javax.swing.BorderFactory; import javax.swing.ButtonGroup; @@ -214,24 +211,18 @@ public class AnnotationExporter extends JPanel { String text; SequenceI[] sequences = ap.av.getAlignment().getSequencesArray(); - Map featureColours = ap.getFeatureRenderer() - .getDisplayedFeatureCols(); - Map featureFilters = ap.getFeatureRenderer() - .getFeatureFilters(); - List featureGroups = ap.getFeatureRenderer() - .getDisplayedFeatureGroups(); boolean includeNonPositional = ap.av.isShowNPFeats(); FeaturesFile formatter = new FeaturesFile(); + final FeatureRenderer fr = ap.getFeatureRenderer(); if (GFFFormat.isSelected()) { - text = formatter.printGffFormat(sequences, featureColours, - featureGroups, includeNonPositional); + text = formatter.printGffFormat(sequences, fr, includeNonPositional); } else { - text = formatter.printJalviewFormat(sequences, featureColours, - featureFilters, featureGroups, includeNonPositional); + text = formatter.printJalviewFormat(sequences, fr, + includeNonPositional); } return text; } diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java index 169da5a..12ad0d4 100755 --- a/src/jalview/io/FeaturesFile.java +++ b/src/jalview/io/FeaturesFile.java @@ -24,6 +24,7 @@ import jalview.analysis.AlignmentUtils; import jalview.analysis.SequenceIdMatcher; import jalview.api.AlignViewportI; import jalview.api.FeatureColourI; +import jalview.api.FeatureRenderer; import jalview.api.FeaturesSourceI; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; @@ -562,28 +563,27 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI } /** - * Returns contents of a Jalview format features file, for visible features, as - * filtered by type and group. Features with a null group are displayed if their - * feature type is visible. Non-positional features may optionally be included - * (with no check on type or group). + * Returns contents of a Jalview format features file, for visible features, + * as filtered by type and group. Features with a null group are displayed if + * their feature type is visible. Non-positional features may optionally be + * included (with no check on type or group). * * @param sequences - * source of features - * @param visible - * map of colour for each visible feature type - * @param featureFilters - * @param visibleFeatureGroups + * @param fr * @param includeNonPositional * if true, include non-positional features (regardless of group or * type) * @return */ public String printJalviewFormat(SequenceI[] sequences, - Map visible, - Map featureFilters, - List visibleFeatureGroups, boolean includeNonPositional) + FeatureRenderer fr, boolean includeNonPositional) { - if (!includeNonPositional && (visible == null || visible.isEmpty())) + Map visibleColours = fr + .getDisplayedFeatureCols(); + Map featureFilters = fr.getFeatureFilters(); + + if (!includeNonPositional + && (visibleColours == null || visibleColours.isEmpty())) { // no point continuing. return "No Features Visible"; @@ -594,9 +594,10 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI */ // TODO: decide if feature links should also be written here ? StringBuilder out = new StringBuilder(256); - if (visible != null) + if (visibleColours != null) { - for (Entry featureColour : visible.entrySet()) + for (Entry featureColour : visibleColours + .entrySet()) { FeatureColourI colour = featureColour.getValue(); out.append(colour.toJalviewFormat(featureColour.getKey())).append( @@ -604,50 +605,22 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI } } - String[] types = visible == null ? new String[0] : visible.keySet() - .toArray(new String[visible.keySet().size()]); + String[] types = visibleColours == null ? new String[0] + : visibleColours.keySet() + .toArray(new String[visibleColours.keySet().size()]); /* * feature filters if any */ - outputFeatureFilters(out, visible, featureFilters); - - /* - * sort groups alphabetically, and ensure that features with a - * null or empty group are output after those in named groups - */ - List sortedGroups = new ArrayList<>(visibleFeatureGroups); - sortedGroups.remove(null); - sortedGroups.remove(""); - Collections.sort(sortedGroups); - sortedGroups.add(null); - sortedGroups.add(""); - - boolean foundSome = false; - - /* - * first output any non-positional features - */ - if (includeNonPositional) - { - for (int i = 0; i < sequences.length; i++) - { - String sequenceName = sequences[i].getName(); - for (SequenceFeature feature : sequences[i].getFeatures() - .getNonPositionalFeatures()) - { - foundSome = true; - out.append(formatJalviewFeature(sequenceName, feature)); - } - } - } + outputFeatureFilters(out, visibleColours, featureFilters); /* - * positional features within groups + * output features within groups */ - foundSome |= outputFeaturesByGroup(out, sortedGroups, types, sequences); + int count = outputFeaturesByGroup(out, fr, types, sequences, + includeNonPositional); - return foundSome ? out.toString() : "No Features Visible"; + return count > 0 ? out.toString() : "No Features Visible"; } /** @@ -685,65 +658,104 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI } if (!first) { - out.append(ENDFILTERS).append(newline).append(newline); + out.append(ENDFILTERS).append(newline); } } /** - * Appends output of sequence features within feature groups to the output - * buffer. Groups other than the null or empty group are sandwiched by - * STARTGROUP and ENDGROUP lines. + * Appends output of visible sequence features within feature groups to the + * output buffer. Groups other than the null or empty group are sandwiched by + * STARTGROUP and ENDGROUP lines. Answers the number of features written. * * @param out - * @param groups + * @param fr * @param featureTypes * @param sequences + * @param includeNonPositional * @return */ - private boolean outputFeaturesByGroup(StringBuilder out, - List groups, String[] featureTypes, SequenceI[] sequences) + private int outputFeaturesByGroup(StringBuilder out, + FeatureRenderer fr, String[] featureTypes, + SequenceI[] sequences, boolean includeNonPositional) { - boolean foundSome = false; - for (String group : groups) + List featureGroups = fr.getFeatureGroups(); + + /* + * sort groups alphabetically, and ensure that features with a + * null or empty group are output after those in named groups + */ + List sortedGroups = new ArrayList<>(featureGroups); + sortedGroups.remove(null); + sortedGroups.remove(""); + Collections.sort(sortedGroups); + sortedGroups.add(null); + sortedGroups.add(""); + + int count = 0; + List visibleGroups = fr.getDisplayedFeatureGroups(); + + /* + * loop over all groups (may be visible or not); + * non-positional features are output even if group is not visible + */ + for (String group : sortedGroups) { - boolean isNamedGroup = (group != null && !"".equals(group)); - if (isNamedGroup) - { - out.append(newline); - out.append(STARTGROUP).append(TAB); - out.append(group); - out.append(newline); - } + boolean firstInGroup = true; + boolean isNullGroup = group == null || "".equals(group); - /* - * output positional features within groups - */ for (int i = 0; i < sequences.length; i++) { String sequenceName = sequences[i].getName(); List features = new ArrayList<>(); - if (featureTypes.length > 0) + + /* + * get any non-positional features in this group, if wanted + * (for any feature type, whether visible or not) + */ + if (includeNonPositional) + { + features.addAll(sequences[i].getFeatures() + .getFeaturesForGroup(false, group)); + } + + /* + * add positional features for visible feature types, but + * (for named groups) only if feature group is visible + */ + if (featureTypes.length > 0 + && (isNullGroup || visibleGroups.contains(group))) { features.addAll(sequences[i].getFeatures().getFeaturesForGroup( true, group, featureTypes)); } - for (SequenceFeature sequenceFeature : features) + for (SequenceFeature sf : features) { - foundSome = true; - out.append(formatJalviewFeature(sequenceName, sequenceFeature)); + if (sf.isNonPositional() || fr.isVisible(sf)) + { + count++; + if (firstInGroup) + { + out.append(newline); + if (!isNullGroup) + { + out.append(STARTGROUP).append(TAB).append(group) + .append(newline); + } + } + firstInGroup = false; + out.append(formatJalviewFeature(sequenceName, sf)); + } } } - if (isNamedGroup) + if (!isNullGroup && !firstInGroup) { - out.append(ENDGROUP).append(TAB); - out.append(group); - out.append(newline); + out.append(ENDGROUP).append(TAB).append(group).append(newline); } } - return foundSome; + return count; } /** @@ -872,23 +884,23 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * @return */ public String printGffFormat(SequenceI[] sequences, - Map visible, - List visibleFeatureGroups, - boolean includeNonPositionalFeatures) + FeatureRenderer fr, boolean includeNonPositionalFeatures) { + Map visibleColours = fr.getDisplayedFeatureCols(); + StringBuilder out = new StringBuilder(256); out.append(String.format("%s %d\n", GFF_VERSION, gffVersion == 0 ? 2 : gffVersion)); if (!includeNonPositionalFeatures - && (visible == null || visible.isEmpty())) + && (visibleColours == null || visibleColours.isEmpty())) { return out.toString(); } - String[] types = visible == null ? new String[0] : visible.keySet() - .toArray( - new String[visible.keySet().size()]); + String[] types = visibleColours == null ? new String[0] + : visibleColours.keySet() + .toArray(new String[visibleColours.keySet().size()]); for (SequenceI seq : sequences) { @@ -897,21 +909,23 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI { features.addAll(seq.getFeatures().getNonPositionalFeatures()); } - if (visible != null && !visible.isEmpty()) + if (visibleColours != null && !visibleColours.isEmpty()) { features.addAll(seq.getFeatures().getPositionalFeatures(types)); } for (SequenceFeature sf : features) { - String source = sf.featureGroup; - if (!sf.isNonPositional() && source != null - && !visibleFeatureGroups.contains(source)) + if (!sf.isNonPositional() && !fr.isVisible(sf)) { - // group is not visible + /* + * feature hidden by group visibility, colour threshold, + * or feature filter condition + */ continue; } + String source = sf.featureGroup; if (source == null) { source = sf.getDescription(); diff --git a/src/jalview/schemes/FeatureColour.java b/src/jalview/schemes/FeatureColour.java index 51e7645..f34478c 100644 --- a/src/jalview/schemes/FeatureColour.java +++ b/src/jalview/schemes/FeatureColour.java @@ -689,9 +689,12 @@ public class FeatureColour implements FeatureColourI /** * Returns the colour for the given instance of the feature. This may be a - * simple colour, a colour generated from the feature description (if - * isColourByLabel()), or a colour derived from the feature score (if - * isGraduatedColour()). + * simple colour, a colour generated from the feature description or other + * attribute (if isColourByLabel()), or a colour derived from the feature + * score or other attribute (if isGraduatedColour()). + *

+ * Answers null if feature score (or attribute) value lies outside a + * configured threshold. * * @param feature * @return @@ -890,4 +893,32 @@ public class FeatureColour implements FeatureColourI attributeName = name; } + @Override + public boolean isOutwithThreshold(SequenceFeature feature) + { + if (!isGraduatedColour()) + { + return false; + } + float scr = feature.getScore(); + if (attributeName != null) + { + try + { + String attVal = feature.getValueAsString(attributeName); + scr = Float.valueOf(attVal); + } catch (Throwable e) + { + scr = Float.NaN; + } + } + if (Float.isNaN(scr)) + { + return false; + } + + return ((isAboveThreshold() && scr <= threshold) + || (isBelowThreshold() && scr >= threshold)); + } + } diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java index 5db8751..4af6fde 100644 --- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java +++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java @@ -1156,4 +1156,32 @@ public abstract class FeatureRendererModel return filter == null ? true : filter.matches(sf); } + @Override + public boolean isVisible(SequenceFeature feature) + { + if (feature == null) + { + return false; + } + if (getFeaturesDisplayed() == null + || !getFeaturesDisplayed().isVisible(feature.getType())) + { + return false; + } + if (featureGroupNotShown(feature)) + { + return false; + } + FeatureColourI fc = featureColours.get(feature.getType()); + if (fc != null && fc.isOutwithThreshold(feature)) + { + return false; + } + if (!featureMatchesFilters(feature)) + { + return false; + } + return true; + } + } diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java index 32ca841..3632cc7 100644 --- a/test/jalview/io/FeaturesFileTest.java +++ b/test/jalview/io/FeaturesFileTest.java @@ -45,12 +45,12 @@ import jalview.gui.JvOptionPane; import jalview.schemes.FeatureColour; import jalview.structure.StructureSelectionManager; import jalview.util.matcher.Condition; +import jalview.viewmodel.seqfeatures.FeatureRendererModel; +import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean; import java.awt.Color; import java.io.File; import java.io.IOException; -import java.util.ArrayList; -import java.util.Arrays; import java.util.HashMap; import java.util.Iterator; import java.util.List; @@ -475,24 +475,22 @@ public class FeaturesFileTest * first with no features displayed, exclude non-positional features */ FeatureRenderer fr = af.alignPanel.getFeatureRenderer(); - Map visible = fr.getDisplayedFeatureCols(); - List visibleGroups = new ArrayList<>( - Arrays.asList(new String[] {})); - String exported = featuresFile.printJalviewFormat( - al.getSequencesArray(), visible, null, visibleGroups, false); + String exported = featuresFile + .printJalviewFormat(al.getSequencesArray(), fr, false); String expected = "No Features Visible"; assertEquals(expected, exported); /* - * include non-positional features + * include non-positional features, but still no positional features */ - visibleGroups.add("uniprot"); - exported = featuresFile.printJalviewFormat(al.getSequencesArray(), - visible, null, visibleGroups, true); - expected = "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n" - + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n" - + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n" // NaN is not output - + "\nSTARTGROUP\tuniprot\nENDGROUP\tuniprot\n"; + fr.setGroupVisibility("uniprot", true); + exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, + true); + expected = "\nSTARTGROUP\tuniprot\n" + + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n" + + "ENDGROUP\tuniprot\n\n" + + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n\n" + + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"; // NaN is not output assertEquals(expected, exported); /* @@ -500,9 +498,8 @@ public class FeaturesFileTest */ fr.setVisible("METAL"); fr.setVisible("GAMMA-TURN"); - visible = fr.getDisplayedFeatureCols(); - exported = featuresFile.printJalviewFormat(al.getSequencesArray(), - visible, null, visibleGroups, false); + exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, + false); expected = "METAL\tcc9900\n" + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n" + "\nSTARTGROUP\tuniprot\n" @@ -515,11 +512,10 @@ public class FeaturesFileTest * now set Pfam visible */ fr.setVisible("Pfam"); - visible = fr.getDisplayedFeatureCols(); - exported = featuresFile.printJalviewFormat(al.getSequencesArray(), - visible, null, visibleGroups, false); + exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, + false); /* - * features are output within group, ordered by sequence and by type + * features are output within group, ordered by sequence and type */ expected = "METAL\tcc9900\n" + "Pfam\tff0000\n" @@ -529,9 +525,36 @@ public class FeaturesFileTest + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n" + "Pfam domainPfam_3_4\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n" + "ENDGROUP\tuniprot\n" - // null / empty group features output after features in named - // groups: + // null / empty group features are output after named groups + + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n" + + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n"; + assertEquals(expected, exported); + + /* + * hide uniprot group + */ + fr.setGroupVisibility("uniprot", false); + expected = "METAL\tcc9900\n" + "Pfam\tff0000\n" + + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n" + + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n" + + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n"; + exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, + false); + assertEquals(expected, exported); + + /* + * include non-positional (overrides group not shown) + */ + exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, + true); + expected = "METAL\tcc9900\n" + "Pfam\tff0000\n" + + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n" + + "\nSTARTGROUP\tuniprot\n" + + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n" + + "ENDGROUP\tuniprot\n" + + "\ndesc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n" + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n" + + "\ndesc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n" + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n"; assertEquals(expected, exported); } @@ -547,16 +570,14 @@ public class FeaturesFileTest * no features */ FeaturesFile featuresFile = new FeaturesFile(); - FeatureRenderer fr = af.alignPanel.getFeatureRenderer(); - Map visible = new HashMap<>(); - List visibleGroups = new ArrayList<>( - Arrays.asList(new String[] {})); + FeatureRendererModel fr = (FeatureRendererModel) af.alignPanel + .getFeatureRenderer(); String exported = featuresFile.printGffFormat(al.getSequencesArray(), - visible, visibleGroups, false); + fr, false); String gffHeader = "##gff-version 2\n"; assertEquals(gffHeader, exported); - exported = featuresFile.printGffFormat(al.getSequencesArray(), visible, - visibleGroups, true); + exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, + true); assertEquals(gffHeader, exported); /* @@ -578,18 +599,31 @@ public class FeaturesFileTest al.getSequenceAt(1).addSequenceFeature(sf); /* + * 'discover' features then hide all feature types + */ + fr.findAllFeatures(true); + FeatureSettingsBean[] data = new FeatureSettingsBean[4]; + FeatureColourI fc = new FeatureColour(Color.PINK); + data[0] = new FeatureSettingsBean("Domain", fc, null, false); + data[1] = new FeatureSettingsBean("METAL", fc, null, false); + data[2] = new FeatureSettingsBean("GAMMA-TURN", fc, null, false); + data[3] = new FeatureSettingsBean("Pfam", fc, null, false); + fr.setFeaturePriority(data); + + /* * with no features displayed, exclude non-positional features */ - exported = featuresFile.printGffFormat(al.getSequencesArray(), visible, - visibleGroups, false); + exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, + false); assertEquals(gffHeader, exported); /* * include non-positional features */ - visibleGroups.add("Uniprot"); - exported = featuresFile.printGffFormat(al.getSequencesArray(), visible, - visibleGroups, true); + fr.setGroupVisibility("Uniprot", true); + fr.setGroupVisibility("s3dm", false); + exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, + true); String expected = gffHeader + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n"; assertEquals(expected, exported); @@ -600,9 +634,8 @@ public class FeaturesFileTest */ fr.setVisible("METAL"); fr.setVisible("GAMMA-TURN"); - visible = fr.getDisplayedFeatureCols(); - exported = featuresFile.printGffFormat(al.getSequencesArray(), visible, - visibleGroups, false); + exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, + false); // METAL feature has null group: description used for column 2 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"; assertEquals(expected, exported); @@ -610,9 +643,9 @@ public class FeaturesFileTest /* * set s3dm group visible */ - visibleGroups.add("s3dm"); - exported = featuresFile.printGffFormat(al.getSequencesArray(), visible, - visibleGroups, false); + fr.setGroupVisibility("s3dm", true); + exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, + false); // METAL feature has null group: description used for column 2 expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n" + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n"; @@ -622,9 +655,8 @@ public class FeaturesFileTest * now set Pfam visible */ fr.setVisible("Pfam"); - visible = fr.getDisplayedFeatureCols(); - exported = featuresFile.printGffFormat(al.getSequencesArray(), visible, - visibleGroups, false); + exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, + false); // Pfam feature columns include strand(+), phase(2), attributes expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n" @@ -704,7 +736,167 @@ public class FeaturesFileTest featureFilters.put("pfam", filter2); visible.put("foobar", new FeatureColour(Color.blue)); ff.outputFeatureFilters(sb, visible, featureFilters); - String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n\n"; + String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n"; assertEquals(expected, sb.toString()); } + + /** + * Output as GFF should not include features which are not visible due to + * colour threshold or feature filter settings + * + * @throws Exception + */ + @Test(groups = { "Functional" }) + public void testPrintGffFormat_withFilters() throws Exception + { + File f = new File("examples/uniref50.fa"); + AlignmentI al = readAlignmentFile(f); + AlignFrame af = new AlignFrame(al, 500, 500); + SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, + null); + sf1.setValue("clin_sig", "Likely Pathogenic"); + sf1.setValue("AF", "24"); + al.getSequenceAt(0).addSequenceFeature(sf1); + SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f, + null); + sf2.setValue("clin_sig", "Benign"); + sf2.setValue("AF", "46"); + al.getSequenceAt(0).addSequenceFeature(sf2); + + FeaturesFile featuresFile = new FeaturesFile(); + FeatureRenderer fr = af.alignPanel.getFeatureRenderer(); + final String gffHeader = "##gff-version 2\n"; + + fr.setVisible("METAL"); + fr.setColour("METAL", new FeatureColour(Color.PINK)); + String exported = featuresFile.printGffFormat(al.getSequencesArray(), + fr, false); + String expected = gffHeader + + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n" + + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n"; + assertEquals(expected, exported); + + /* + * now threshold to Score > 1.1 - should exclude sf2 + */ + FeatureColourI fc = new FeatureColour(Color.white, Color.BLACK, + Color.white, 0f, 2f); + fc.setAboveThreshold(true); + fc.setThreshold(1.1f); + fr.setColour("METAL", fc); + exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, + false); + expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"; + assertEquals(expected, exported); + + /* + * remove threshold and check sf2 is exported + */ + fc.setAboveThreshold(false); + exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, + false); + expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n" + + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n"; + assertEquals(expected, exported); + + /* + * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1 + */ + FeatureMatcherSetI filter = new FeatureMatcherSet(); + filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign", + "clin_sig")); + fr.setFeatureFilter("METAL", filter); + exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, + false); + expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n"; + assertEquals(expected, exported); + } + + /** + * Output as Jalview should not include features which are not visible due to + * colour threshold or feature filter settings + * + * @throws Exception + */ + @Test(groups = { "Functional" }) + public void testPrintJalviewFormat_withFilters() throws Exception + { + File f = new File("examples/uniref50.fa"); + AlignmentI al = readAlignmentFile(f); + AlignFrame af = new AlignFrame(al, 500, 500); + SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, + "grp1"); + sf1.setValue("clin_sig", "Likely Pathogenic"); + sf1.setValue("AF", "24"); + al.getSequenceAt(0).addSequenceFeature(sf1); + SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f, + "grp2"); + sf2.setValue("clin_sig", "Benign"); + sf2.setValue("AF", "46"); + al.getSequenceAt(0).addSequenceFeature(sf2); + + FeaturesFile featuresFile = new FeaturesFile(); + FeatureRenderer fr = af.alignPanel.getFeatureRenderer(); + fr.findAllFeatures(true); + + fr.setVisible("METAL"); + fr.setColour("METAL", new FeatureColour(Color.PINK)); + String exported = featuresFile.printJalviewFormat( + al.getSequencesArray(), + fr, false); + String expected = "METAL\tffafaf\n\nSTARTGROUP\tgrp1\n" + + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n" + + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n" + + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n" + + "ENDGROUP\tgrp2\n"; + assertEquals(expected, exported); + + /* + * now threshold to Score > 1.1 - should exclude sf2 + * (and there should be no empty STARTGROUP/ENDGROUP output) + */ + FeatureColourI fc = new FeatureColour(Color.white, Color.BLACK, + Color.white, 0f, 2f); + fc.setAboveThreshold(true); + fc.setThreshold(1.1f); + fr.setColour("METAL", fc); + exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, + false); + expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|above|1.1\n\n" + + "STARTGROUP\tgrp1\n" + + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n" + + "ENDGROUP\tgrp1\n"; + assertEquals(expected, exported); + + /* + * remove threshold and check sf2 is exported + */ + fc.setAboveThreshold(false); + exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, + false); + expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n" + + "STARTGROUP\tgrp1\n" + + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n" + + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n" + + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n" + + "ENDGROUP\tgrp2\n"; + assertEquals(expected, exported); + + /* + * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1 + */ + FeatureMatcherSetI filter = new FeatureMatcherSet(); + filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign", + "clin_sig")); + fr.setFeatureFilter("METAL", filter); + exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr, + false); + expected = "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n"; + expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n" + + "STARTFILTERS\nMETAL\tclin_sig Contains benign\nENDFILTERS\n\n" + + "STARTGROUP\tgrp2\n" + + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n" + + "ENDGROUP\tgrp2\n"; + assertEquals(expected, exported); + } } diff --git a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java index a9e3754..a0fb498 100644 --- a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java +++ b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java @@ -535,4 +535,71 @@ public class FeatureRendererTest csqData.put("Feature", "ENST01234"); assertEquals(fr.getColour(sf2), expected); } + + @Test(groups = "Functional") + public void testIsVisible() + { + String seqData = ">s1\nMLQGIFPRS\n"; + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData, + DataSourceType.PASTE); + AlignViewportI av = af.getViewport(); + FeatureRenderer fr = new FeatureRenderer(av); + SequenceI seq = av.getAlignment().getSequenceAt(0); + SequenceFeature sf = new SequenceFeature("METAL", "Desc", 10, 10, 1f, + "Group"); + sf.setValue("AC", "11"); + sf.setValue("CLIN_SIG", "Likely Pathogenic"); + seq.addSequenceFeature(sf); + + assertFalse(fr.isVisible(null)); + + /* + * initial state FeatureRenderer hasn't 'found' feature + * and so its feature type has not yet been set visible + */ + assertFalse(fr.getDisplayedFeatureCols().containsKey("METAL")); + assertFalse(fr.isVisible(sf)); + + fr.findAllFeatures(true); + assertTrue(fr.isVisible(sf)); + + /* + * feature group not visible + */ + fr.setGroupVisibility("Group", false); + assertFalse(fr.isVisible(sf)); + fr.setGroupVisibility("Group", true); + assertTrue(fr.isVisible(sf)); + + /* + * feature score outwith colour threshold (score > 2) + */ + FeatureColourI fc = new FeatureColour(Color.white, Color.black, + Color.white, 0, 10); + fc.setAboveThreshold(true); + fc.setThreshold(2f); + fr.setColour("METAL", fc); + assertFalse(fr.isVisible(sf)); // score 1 is not above threshold 2 + fc.setBelowThreshold(true); + assertTrue(fr.isVisible(sf)); // score 1 is below threshold 2 + + /* + * colour with threshold on attribute AC (value is 11) + */ + fc.setAttributeName("AC"); + assertFalse(fr.isVisible(sf)); // value 11 is not below threshold 2 + fc.setAboveThreshold(true); + assertTrue(fr.isVisible(sf)); // value 11 is above threshold 2 + + fc.setAttributeName("AF"); // attribute AF is absent in sf + assertTrue(fr.isVisible(sf)); // feature is not excluded by threshold + + FeatureMatcherSetI filter = new FeatureMatcherSet(); + filter.and(FeatureMatcher.byAttribute(Condition.Contains, "pathogenic", + "CLIN_SIG")); + fr.setFeatureFilter("METAL", filter); + assertTrue(fr.isVisible(sf)); // feature matches filter + filter.and(FeatureMatcher.byScore(Condition.LE, "0.4")); + assertFalse(fr.isVisible(sf)); // feature doesn't match filter + } } diff --git a/test/jalview/schemes/FeatureColourTest.java b/test/jalview/schemes/FeatureColourTest.java index a96caec..6ccce85 100644 --- a/test/jalview/schemes/FeatureColourTest.java +++ b/test/jalview/schemes/FeatureColourTest.java @@ -712,4 +712,44 @@ public class FeatureColourTest Color expected = new Color(70, 120, 170); assertEquals(expected, fc.getColor(sf)); } + + @Test(groups = { "Functional" }) + public void testIsOutwithThreshold() + { + FeatureColourI fc = new FeatureColour(Color.red); + SequenceFeature sf = new SequenceFeature("METAL", "desc", 10, 12, 1.2f, "grp"); + assertFalse(fc.isOutwithThreshold(null)); + assertFalse(fc.isOutwithThreshold(sf)); + + fc = new FeatureColour(Color.white, Color.black, Color.green, 0f, 10f); + assertFalse(fc.isOutwithThreshold(sf)); // no threshold + + fc.setAboveThreshold(true); + fc.setThreshold(1f); + assertFalse(fc.isOutwithThreshold(sf)); // feature score 1.2 is above 1 + + fc.setThreshold(2f); + assertTrue(fc.isOutwithThreshold(sf)); // feature score 1.2 is not above 2 + + fc.setBelowThreshold(true); + assertFalse(fc.isOutwithThreshold(sf)); // feature score 1.2 is below 2 + + fc.setThreshold(1f); + assertTrue(fc.isOutwithThreshold(sf)); // feature score 1.2 is not below 1 + + /* + * with attribute value threshold + */ + fc.setAttributeName("AC"); + assertFalse(fc.isOutwithThreshold(sf)); // missing attribute AC is ignored + + sf.setValue("AC", "-1"); + assertFalse(fc.isOutwithThreshold(sf)); // value -1 is below 1 + + sf.setValue("AC", "1"); + assertTrue(fc.isOutwithThreshold(sf)); // value 1 is not below 1 + + sf.setValue("AC", "junk"); + assertFalse(fc.isOutwithThreshold(sf)); // bad value is ignored + } }