From: gmungoc Date: Mon, 6 Nov 2017 16:41:54 +0000 (+0000) Subject: JAL-2820 include attribute value used for feature colour in tooltip X-Git-Tag: Release_2_11_0~152 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=81c8008cff0d9a265e0fbe979b17b173e9e4fc0a;p=jalview.git JAL-2820 include attribute value used for feature colour in tooltip --- diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index 46bd4fd..76f2705 100644 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -901,10 +901,7 @@ public class APopupMenu extends java.awt.PopupMenu .formatMessage("label.annotation_for_displayid", new Object[] { seq.getDisplayId(true) })); new SequenceAnnotationReport(null).createSequenceAnnotationReport( - contents, seq, true, true, - (ap.seqPanel.seqCanvas.fr != null) - ? ap.seqPanel.seqCanvas.fr.getMinMax() - : null); + contents, seq, true, true, ap.seqPanel.seqCanvas.fr); contents.append("

"); } Frame frame = new Frame(); diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index a4f79c2..a1726f1 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -108,8 +108,7 @@ public class IdPanel extends JPanel SequenceI sequence = av.getAlignment().getSequenceAt(seq); StringBuilder tip = new StringBuilder(64); seqAnnotReport.createTooltipAnnotationReport(tip, sequence, - av.isShowDBRefs(), av.isShowNPFeats(), - sp.seqCanvas.fr.getMinMax()); + av.isShowDBRefs(), av.isShowNPFeats(), sp.seqCanvas.fr); setToolTipText(JvSwingUtils.wrapTooltip(true, sequence.getDisplayId(true) + " " + tip.toString())); } diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 6da7d4f..97d051b 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1635,10 +1635,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener new Object[] { seq.getDisplayId(true) }) + "

"); new SequenceAnnotationReport(null).createSequenceAnnotationReport( - contents, seq, true, true, - (ap.getSeqPanel().seqCanvas.fr != null) - ? ap.getSeqPanel().seqCanvas.fr.getMinMax() - : null); + contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr); contents.append("

"); } cap.setText("" + contents.toString() + ""); diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 6148a2e..b718783 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -147,35 +147,33 @@ public class SeqPanel extends JPanel SearchResultsI lastSearchResults; /** - * Creates a new SeqPanel object. + * Creates a new SeqPanel object * - * @param avp - * DOCUMENT ME! - * @param p - * DOCUMENT ME! + * @param viewport + * @param alignPanel */ - public SeqPanel(AlignViewport av, AlignmentPanel ap) + public SeqPanel(AlignViewport viewport, AlignmentPanel alignPanel) { linkImageURL = getClass().getResource("/images/link.gif"); seqARep = new SequenceAnnotationReport(linkImageURL.toString()); ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); - this.av = av; + this.av = viewport; setBackground(Color.white); - seqCanvas = new SeqCanvas(ap); + seqCanvas = new SeqCanvas(alignPanel); setLayout(new BorderLayout()); add(seqCanvas, BorderLayout.CENTER); - this.ap = ap; + this.ap = alignPanel; - if (!av.isDataset()) + if (!viewport.isDataset()) { addMouseMotionListener(this); addMouseListener(this); addMouseWheelListener(this); - ssm = av.getStructureSelectionManager(); + ssm = viewport.getStructureSelectionManager(); ssm.addStructureViewerListener(this); ssm.addSelectionListener(this); } @@ -804,7 +802,7 @@ public class SeqPanel extends JPanel List features = ap.getFeatureRenderer() .findFeaturesAtColumn(sequence, column + 1); seqARep.appendFeatures(tooltipText, pos, features, - this.ap.getSeqPanel().seqCanvas.fr.getMinMax()); + this.ap.getSeqPanel().seqCanvas.fr); } if (tooltipText.length() == 6) // { diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java index 6d819d3..1f92428 100644 --- a/src/jalview/io/SequenceAnnotationReport.java +++ b/src/jalview/io/SequenceAnnotationReport.java @@ -20,14 +20,15 @@ */ package jalview.io; +import jalview.api.FeatureColourI; import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; -import jalview.io.gff.GffConstants; import jalview.util.MessageManager; import jalview.util.StringUtils; import jalview.util.UrlLink; +import jalview.viewmodel.seqfeatures.FeatureRendererModel; import java.util.Arrays; import java.util.Collection; @@ -87,14 +88,14 @@ public class SequenceAnnotationReport { return 1; } - int comp = s1 == null ? -1 - : (s2 == null ? 1 : s1.compareToIgnoreCase(s2)); + int comp = s1 == null ? -1 : (s2 == null ? 1 : s1 + .compareToIgnoreCase(s2)); if (comp == 0) { String a1 = ref1.getAccessionId(); String a2 = ref2.getAccessionId(); - comp = a1 == null ? -1 - : (a2 == null ? 1 : a1.compareToIgnoreCase(a2)); + comp = a1 == null ? -1 : (a2 == null ? 1 : a1 + .compareToIgnoreCase(a2)); } return comp; } @@ -115,9 +116,9 @@ public class SequenceAnnotationReport } }; - public SequenceAnnotationReport(String linkImageURL) + public SequenceAnnotationReport(String linkURL) { - this.linkImageURL = linkImageURL; + this.linkImageURL = linkURL; } /** @@ -129,13 +130,13 @@ public class SequenceAnnotationReport * @param minmax */ public void appendFeatures(final StringBuilder sb, int rpos, - List features, Map minmax) + List features, FeatureRendererModel fr) { if (features != null) { for (SequenceFeature feature : features) { - appendFeature(sb, rpos, minmax, feature); + appendFeature(sb, rpos, fr, feature); } } } @@ -149,7 +150,7 @@ public class SequenceAnnotationReport * @param feature */ void appendFeature(final StringBuilder sb, int rpos, - Map minmax, SequenceFeature feature) + FeatureRendererModel fr, SequenceFeature feature) { if (feature.isContactFeature()) { @@ -162,60 +163,91 @@ public class SequenceAnnotationReport sb.append(feature.getType()).append(" ").append(feature.getBegin()) .append(":").append(feature.getEnd()); } + return; } - else + + if (sb.length() > 6) + { + sb.append("
"); + } + // TODO: remove this hack to display link only features + boolean linkOnly = feature.getValue("linkonly") != null; + if (!linkOnly) { - if (sb.length() > 6) + sb.append(feature.getType()).append(" "); + if (rpos != 0) { - sb.append("
"); + // we are marking a positional feature + sb.append(feature.begin); } - // TODO: remove this hack to display link only features - boolean linkOnly = feature.getValue("linkonly") != null; - if (!linkOnly) + if (feature.begin != feature.end) { - sb.append(feature.getType()).append(" "); - if (rpos != 0) - { - // we are marking a positional feature - sb.append(feature.begin); - } - if (feature.begin != feature.end) - { - sb.append(" ").append(feature.end); - } + sb.append(" ").append(feature.end); + } - String description = feature.getDescription(); - if (description != null && !description.equals(feature.getType())) - { - description = StringUtils.stripHtmlTags(description); - sb.append("; ").append(description); - } - // check score should be shown - if (!Float.isNaN(feature.getScore())) + String description = feature.getDescription(); + if (description != null && !description.equals(feature.getType())) + { + description = StringUtils.stripHtmlTags(description); + sb.append("; ").append(description); + } + + if (showScore(feature, fr)) + { + sb.append(" Score=").append(String.valueOf(feature.getScore())); + } + String status = (String) feature.getValue("status"); + if (status != null && status.length() > 0) + { + sb.append("; (").append(status).append(")"); + } + + /* + * add attribute value if coloured by attribute + */ + if (fr != null) + { + FeatureColourI fc = fr.getFeatureColours().get(feature.getType()); + if (fc != null && fc.isColourByAttribute()) { - float[][] rng = (minmax == null) ? null - : minmax.get(feature.getType()); - if (rng != null && rng[0] != null && rng[0][0] != rng[0][1]) + String attName = fc.getAttributeName(); + String attVal = feature.getValueAsString(attName); + if (attVal != null) { - sb.append(" Score=").append(String.valueOf(feature.getScore())); + sb.append("; ").append(attName).append("=").append(attVal); } } - String status = (String) feature.getValue("status"); - if (status != null && status.length() > 0) - { - sb.append("; (").append(status).append(")"); - } - String clinSig = (String) feature - .getValue(GffConstants.CLINICAL_SIGNIFICANCE); - if (clinSig != null) - { - sb.append("; ").append(clinSig); - } } } } /** + * Answers true if score should be shown, else false. Score is shown if it is + * not NaN, and the feature type has a non-trivial min-max score range + */ + boolean showScore(SequenceFeature feature, FeatureRendererModel fr) + { + if (Float.isNaN(feature.getScore())) + { + return false; + } + if (fr == null) + { + return true; + } + float[][] minMax = fr.getMinMax().get(feature.getType()); + + /* + * minMax[0] is the [min, max] score range for positional features + */ + if (minMax == null || minMax[0] == null || minMax[0][0] == minMax[0][1]) + { + return false; + } + return true; + } + + /** * Format and appends any hyperlinks for the sequence feature to the string * buffer * @@ -238,19 +270,20 @@ public class SequenceAnnotationReport { for (List urllink : createLinksFrom(null, urlstring)) { - sb.append("
" + sb.append("
" + (urllink.get(0).toLowerCase() - .equals(urllink.get(1).toLowerCase()) - ? urllink.get(0) - : (urllink.get(0) + ":" - + urllink.get(1))) - + "
"); + .equals(urllink.get(1).toLowerCase()) ? urllink + .get(0) : (urllink.get(0) + ":" + urllink + .get(1))) + "
"); } } catch (Exception x) { - System.err.println( - "problem when creating links from " + urlstring); + System.err.println("problem when creating links from " + + urlstring); x.printStackTrace(); } } @@ -283,10 +316,10 @@ public class SequenceAnnotationReport public void createSequenceAnnotationReport(final StringBuilder tip, SequenceI sequence, boolean showDbRefs, boolean showNpFeats, - Map minmax) + FeatureRendererModel fr) { createSequenceAnnotationReport(tip, sequence, showDbRefs, showNpFeats, - minmax, false); + fr, false); } /** @@ -301,13 +334,13 @@ public class SequenceAnnotationReport * whether to include database references for the sequence * @param showNpFeats * whether to include non-positional sequence features - * @param minmax + * @param fr * @param summary * @return */ int createSequenceAnnotationReport(final StringBuilder sb, SequenceI sequence, boolean showDbRefs, boolean showNpFeats, - Map minmax, boolean summary) + FeatureRendererModel fr, boolean summary) { String tmp; sb.append(""); @@ -324,7 +357,7 @@ public class SequenceAnnotationReport { ds = ds.getDatasetSequence(); } - + if (showDbRefs) { maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary)); @@ -339,7 +372,7 @@ public class SequenceAnnotationReport .getNonPositionalFeatures()) { int sz = -sb.length(); - appendFeature(sb, 0, minmax, sf); + appendFeature(sb, 0, fr, sf); sz += sb.length(); maxWidth = Math.max(maxWidth, sz); } @@ -428,8 +461,7 @@ public class SequenceAnnotationReport } if (moreSources) { - sb.append("
").append(source) - .append(COMMA).append(ELLIPSIS); + sb.append("
").append(source).append(COMMA).append(ELLIPSIS); } if (ellipsis) { @@ -443,10 +475,10 @@ public class SequenceAnnotationReport public void createTooltipAnnotationReport(final StringBuilder tip, SequenceI sequence, boolean showDbRefs, boolean showNpFeats, - Map minmax) + FeatureRendererModel fr) { - int maxWidth = createSequenceAnnotationReport(tip, sequence, showDbRefs, - showNpFeats, minmax, true); + int maxWidth = createSequenceAnnotationReport(tip, sequence, + showDbRefs, showNpFeats, fr, true); if (maxWidth > 60) { diff --git a/test/jalview/io/SequenceAnnotationReportTest.java b/test/jalview/io/SequenceAnnotationReportTest.java index 9e61bec..87e35c7 100644 --- a/test/jalview/io/SequenceAnnotationReportTest.java +++ b/test/jalview/io/SequenceAnnotationReportTest.java @@ -23,15 +23,18 @@ package jalview.io; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertTrue; +import jalview.api.FeatureColourI; import jalview.datamodel.DBRefEntry; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.gui.JvOptionPane; import jalview.io.gff.GffConstants; +import jalview.renderer.seqfeatures.FeatureRenderer; +import jalview.schemes.FeatureColour; +import jalview.viewmodel.seqfeatures.FeatureRendererModel; -import java.util.HashMap; -import java.util.Hashtable; +import java.awt.Color; import java.util.Map; import junit.extensions.PA; @@ -95,8 +98,9 @@ public class SequenceAnnotationReportTest SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3, 1.3f, "group"); - Map minmax = new Hashtable(); - sar.appendFeature(sb, 1, minmax, sf); + FeatureRendererModel fr = new FeatureRenderer(null); + Map minmax = fr.getMinMax(); + sar.appendFeature(sb, 1, fr, sf); /* * map has no entry for this feature type - score is not shown: */ @@ -106,7 +110,7 @@ public class SequenceAnnotationReportTest * map has entry for this feature type - score is shown: */ minmax.put("METAL", new float[][] { { 0f, 1f }, null }); - sar.appendFeature(sb, 1, minmax, sf); + sar.appendFeature(sb, 1, fr, sf); //
is appended to a buffer > 6 in length assertEquals("METAL 1 3; Fe2-S
METAL 1 3; Fe2-S Score=1.3", sb.toString()); @@ -116,7 +120,7 @@ public class SequenceAnnotationReportTest */ minmax.put("METAL", new float[][] { { 2f, 2f }, null }); sb.setLength(0); - sar.appendFeature(sb, 1, minmax, sf); + sar.appendFeature(sb, 1, fr, sf); assertEquals("METAL 1 3; Fe2-S", sb.toString()); } @@ -132,8 +136,11 @@ public class SequenceAnnotationReportTest assertEquals("METAL 1 3; Fe2-S", sb.toString()); } + /** + * A specific attribute value is included if it is used to colour the feature + */ @Test(groups = "Functional") - public void testAppendFeature_clinicalSignificance() + public void testAppendFeature_colouredByAttribute() { SequenceAnnotationReport sar = new SequenceAnnotationReport(null); StringBuilder sb = new StringBuilder(); @@ -141,12 +148,35 @@ public class SequenceAnnotationReportTest Float.NaN, "group"); sf.setValue("clinical_significance", "Benign"); - sar.appendFeature(sb, 1, null, sf); - assertEquals("METAL 1 3; Fe2-S; Benign", sb.toString()); + /* + * first with no colour by attribute + */ + FeatureRendererModel fr = new FeatureRenderer(null); + sar.appendFeature(sb, 1, fr, sf); + assertEquals("METAL 1 3; Fe2-S", sb.toString()); + + /* + * then with colour by an attribute the feature lacks + */ + FeatureColourI fc = new FeatureColour(Color.white, Color.black, 5, 10); + fc.setAttributeName("Pfam"); + fr.setColour("METAL", fc); + sb.setLength(0); + sar.appendFeature(sb, 1, fr, sf); + assertEquals("METAL 1 3; Fe2-S", sb.toString()); // no change + + /* + * then with colour by an attribute the feature has + */ + fc.setAttributeName("clinical_significance"); + sb.setLength(0); + sar.appendFeature(sb, 1, fr, sf); + assertEquals("METAL 1 3; Fe2-S; clinical_significance=Benign", + sb.toString()); } @Test(groups = "Functional") - public void testAppendFeature_withScoreStatusClinicalSignificance() + public void testAppendFeature_withScoreStatusAttribute() { SequenceAnnotationReport sar = new SequenceAnnotationReport(null); StringBuilder sb = new StringBuilder(); @@ -154,11 +184,17 @@ public class SequenceAnnotationReportTest "group"); sf.setStatus("Confirmed"); sf.setValue("clinical_significance", "Benign"); - Map minmax = new Hashtable(); + + FeatureRendererModel fr = new FeatureRenderer(null); + Map minmax = fr.getMinMax(); + FeatureColourI fc = new FeatureColour(Color.white, Color.blue, 12, 22); + fc.setAttributeName("clinical_significance"); + fr.setColour("METAL", fc); minmax.put("METAL", new float[][] { { 0f, 1f }, null }); - sar.appendFeature(sb, 1, minmax, sf); + sar.appendFeature(sb, 1, fr, sf); - assertEquals("METAL 1 3; Fe2-S Score=1.3; (Confirmed); Benign", + assertEquals( + "METAL 1 3; Fe2-S Score=1.3; (Confirmed); clinical_significance=Benign", sb.toString()); } @@ -226,7 +262,7 @@ public class SequenceAnnotationReportTest null)); sb.setLength(0); sar.createSequenceAnnotationReport(sb, seq, true, true, null); - String expected = "
SeqDesc
Type1 ; Nonpos"; + String expected = "
SeqDesc
Type1 ; Nonpos Score=1.0"; assertEquals(expected, sb.toString()); /* @@ -244,10 +280,13 @@ public class SequenceAnnotationReportTest */ seq.addSequenceFeature(new SequenceFeature("Metal", "Desc", 0, 0, 5f, null)); - Map minmax = new HashMap(); + + FeatureRendererModel fr = new FeatureRenderer(null); + Map minmax = fr.getMinMax(); minmax.put("Metal", new float[][] { null, new float[] { 2f, 5f } }); + sb.setLength(0); - sar.createSequenceAnnotationReport(sb, seq, true, true, minmax); + sar.createSequenceAnnotationReport(sb, seq, true, true, fr); expected = "
SeqDesc
Metal ; Desc
Type1 ; Nonpos"; assertEquals(expected, sb.toString()); @@ -260,19 +299,20 @@ public class SequenceAnnotationReportTest sf.setValue("linkonly", Boolean.TRUE); seq.addSequenceFeature(sf); sb.setLength(0); - sar.createSequenceAnnotationReport(sb, seq, true, true, minmax); + sar.createSequenceAnnotationReport(sb, seq, true, true, fr); assertEquals(expected, sb.toString()); // unchanged! /* - * 'clinical_significance' currently being specially included + * 'clinical_significance' attribute only included when + * used for feature colouring */ SequenceFeature sf2 = new SequenceFeature("Variant", "Havana", 0, 0, 5f, null); sf2.setValue(GffConstants.CLINICAL_SIGNIFICANCE, "benign"); seq.addSequenceFeature(sf2); sb.setLength(0); - sar.createSequenceAnnotationReport(sb, seq, true, true, minmax); - expected = "
SeqDesc
Metal ; Desc
Type1 ; Nonpos
Variant ; Havana; benign"; + sar.createSequenceAnnotationReport(sb, seq, true, true, fr); + expected = "
SeqDesc
Metal ; Desc
Type1 ; Nonpos
Variant ; Havana"; assertEquals(expected, sb.toString()); /* @@ -280,18 +320,24 @@ public class SequenceAnnotationReportTest */ seq.addDBRef(new DBRefEntry("PDB", "0", "3iu1")); seq.addDBRef(new DBRefEntry("Uniprot", "1", "P30419")); + // with showDbRefs = false sb.setLength(0); - sar.createSequenceAnnotationReport(sb, seq, false, true, minmax); + sar.createSequenceAnnotationReport(sb, seq, false, true, fr); assertEquals(expected, sb.toString()); // unchanged - // with showDbRefs = true + + // with showDbRefs = true, colour Variant features by clinical_significance sb.setLength(0); - sar.createSequenceAnnotationReport(sb, seq, true, true, minmax); - expected = "
SeqDesc
UNIPROT P30419
PDB 3iu1
Metal ; Desc
Type1 ; Nonpos
Variant ; Havana; benign"; + FeatureColourI fc = new FeatureColour(Color.green, Color.pink, 2, 3); + fc.setAttributeName("clinical_significance"); + fr.setColour("Variant", fc); + sar.createSequenceAnnotationReport(sb, seq, true, true, fr); + expected = "
SeqDesc
UNIPROT P30419
PDB 3iu1
Metal ; Desc
" + + "Type1 ; Nonpos
Variant ; Havana; clinical_significance=benign"; assertEquals(expected, sb.toString()); // with showNonPositionalFeatures = false sb.setLength(0); - sar.createSequenceAnnotationReport(sb, seq, true, false, minmax); + sar.createSequenceAnnotationReport(sb, seq, true, false, fr); expected = "
SeqDesc
UNIPROT P30419
PDB 3iu1"; assertEquals(expected, sb.toString());