From 72b3f05a1157da32ada5aea139139996dddea219 Mon Sep 17 00:00:00 2001 From: "j.procter@dundee.ac.uk" Date: Fri, 8 Aug 2014 18:11:21 +0100 Subject: [PATCH] JAL-1482 feature renderer and manipulation code refactored to renderer and abstract model --- src/jalview/appletgui/APopupMenu.java | 2 +- src/jalview/appletgui/AlignFrame.java | 48 +- src/jalview/appletgui/FeatureColourChooser.java | 18 +- src/jalview/appletgui/FeatureRenderer.java | 859 +--------------- src/jalview/appletgui/FeatureSettings.java | 164 +-- src/jalview/appletgui/OverviewPanel.java | 4 +- src/jalview/appletgui/SeqPanel.java | 12 +- src/jalview/gui/AlignFrame.java | 2 +- src/jalview/gui/AlignmentPanel.java | 2 +- src/jalview/gui/AnnotationExporter.java | 38 +- src/jalview/gui/FeatureColourChooser.java | 8 +- src/jalview/gui/FeatureRenderer.java | 1088 +------------------- src/jalview/gui/FeatureSettings.java | 218 +--- src/jalview/gui/IdPanel.java | 2 +- src/jalview/gui/Jalview2XML.java | 62 +- src/jalview/gui/Jalview2XML_V1.java | 12 +- src/jalview/gui/OverviewPanel.java | 2 +- src/jalview/gui/PopupMenu.java | 2 +- src/jalview/gui/SeqPanel.java | 62 +- src/jalview/io/FeaturesFile.java | 14 +- src/jalview/io/HTMLOutput.java | 2 +- src/jalview/io/SequenceAnnotationReport.java | 53 +- .../renderer/seqfeatures/FeatureRenderer.java | 435 ++++++++ .../seqfeatures/FeatureRendererModel.java | 2 +- src/jalview/ws/AWSThread.java | 2 +- 25 files changed, 700 insertions(+), 2413 deletions(-) create mode 100644 src/jalview/renderer/seqfeatures/FeatureRenderer.java diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index 7a77935..51ecd88 100644 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -707,7 +707,7 @@ public class APopupMenu extends java.awt.PopupMenu implements true, true, false, - (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax + (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.getMinMax() : null); contents.append("

"); } diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index e0dad58..8d1255c 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -25,6 +25,7 @@ import jalview.analysis.Conservation; import jalview.api.AlignViewControllerGuiI; import jalview.api.AlignViewControllerI; import jalview.api.SequenceStructureBinding; +import jalview.api.FeatureRenderer; import jalview.bin.JalviewLite; import jalview.commands.CommandI; import jalview.commands.EditCommand; @@ -90,9 +91,12 @@ import java.awt.event.WindowEvent; import java.io.IOException; import java.net.URL; import java.net.URLEncoder; +import java.util.Arrays; import java.util.Enumeration; import java.util.Hashtable; +import java.util.Iterator; import java.util.List; +import java.util.Map; import java.util.StringTokenizer; import java.util.Vector; @@ -286,7 +290,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { featuresFile = new jalview.io.FeaturesFile(file, type) .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas - .getFeatureRenderer().featureColours, featureLinks, + .getFeatureRenderer().getFeatureColours(), featureLinks, true, viewport.applet.getDefaultParameter( "relaxedidmatch", false)); } catch (Exception ex) @@ -305,6 +309,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.setShowSequenceFeatures(true); sequenceFeatures.setState(true); } + if (alignPanel.seqPanel.seqCanvas.fr != null) + { + // update the min/max ranges where necessary + alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true); + } if (viewport.featureSettings != null) { viewport.featureSettings.refreshTable(); @@ -1201,20 +1210,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, return annotation; } - private Hashtable getDisplayedFeatureCols() + private Map getDisplayedFeatureCols() { if (alignPanel.getFeatureRenderer() != null - && viewport.featuresDisplayed != null) + && viewport.getFeaturesDisplayed()!= null) { - FeatureRenderer fr = alignPanel.getFeatureRenderer(); - Hashtable fcols = new Hashtable(); - Enumeration en = viewport.featuresDisplayed.keys(); - while (en.hasMoreElements()) - { - Object col = en.nextElement(); - fcols.put(col, fr.featureColours.get(col)); - } - return fcols; + return alignPanel.getFeatureRenderer().getDisplayedFeatureCols(); + } return null; } @@ -1418,6 +1420,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, /** * TODO: JAL-1104 */ + @Override public void addHistoryItem(CommandI command) { if (command.getSize() > 0) @@ -2240,7 +2243,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (alignPanel != null && (fr = alignPanel.getFeatureRenderer()) != null) { - return fr.getGroups(); + List gps = fr.getFeatureGroups(); + int p=0; + String[] _gps = new String[gps.size()]; + for (Object gp:gps) + { + _gps[p++] = gp.toString(); + } + return _gps; } return null; } @@ -2258,7 +2268,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (alignPanel != null && (fr = alignPanel.getFeatureRenderer()) != null) { - return fr.getGroups(visible); + List gps = fr.getGroups(visible); + int p=0; + String[] _gps = new String[gps.size()]; + for (Object gp:gps) + { + _gps[p++] = gp.toString(); + } + return _gps; } return null; } @@ -2279,7 +2296,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (alignPanel != null && (fr = alignPanel.getFeatureRenderer()) != null) { - fr.setGroupState(groups, state); + + fr.setGroupVisibility((List)Arrays.asList(groups), state); alignPanel.seqPanel.seqCanvas.repaint(); if (alignPanel.overviewPanel != null) { diff --git a/src/jalview/appletgui/FeatureColourChooser.java b/src/jalview/appletgui/FeatureColourChooser.java index 32ffdbf..c87803c 100644 --- a/src/jalview/appletgui/FeatureColourChooser.java +++ b/src/jalview/appletgui/FeatureColourChooser.java @@ -73,10 +73,10 @@ public class FeatureColourChooser extends Panel implements ActionListener, { this.type = type; fr = frenderer; - float mm[] = ((float[][]) fr.minmax.get(type))[0]; + float mm[] = ((float[][]) fr.getMinMax().get(type))[0]; min = mm[0]; max = mm[1]; - oldcs = fr.featureColours.get(type); + oldcs = fr.getFeatureColours().get(type); if (oldcs instanceof GraduatedColor) { cs = new GraduatedColor((GraduatedColor) oldcs, min, max); @@ -130,7 +130,7 @@ public class FeatureColourChooser extends Panel implements ActionListener, { // cancel reset(); - PaintRefresher.Refresh(this, fr.av.getSequenceSetId()); + PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId()); frame.setVisible(false); } } @@ -289,7 +289,7 @@ public class FeatureColourChooser extends Panel implements ActionListener, threshline.value = (float) slider.getValue() / 1000f; cs.setThresh(threshline.value); changeColour(); - PaintRefresher.Refresh(this, fr.av.getSequenceSetId()); + PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId()); // ap.paintAlignment(false); } @@ -402,16 +402,16 @@ public class FeatureColourChooser extends Panel implements ActionListener, } } - fr.featureColours.put(type, acg); + fr.setColour(type, acg); cs = acg; - PaintRefresher.Refresh(this, fr.av.getSequenceSetId()); + PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId()); // ap.paintAlignment(false); } void reset() { - fr.featureColours.put(type, oldcs); - PaintRefresher.Refresh(this, fr.av.getSequenceSetId()); + fr.setColour(type, oldcs); + PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId()); // ap.paintAlignment(true); } @@ -433,7 +433,7 @@ public class FeatureColourChooser extends Panel implements ActionListener, } else { - PaintRefresher.Refresh(this, fr.av.getSequenceSetId()); + PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId()); } // ap.paintAlignment(true); } diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java index 14338fa..ac1f58c 100644 --- a/src/jalview/appletgui/FeatureRenderer.java +++ b/src/jalview/appletgui/FeatureRenderer.java @@ -21,15 +21,14 @@ package jalview.appletgui; import java.util.*; - import java.awt.*; - import java.awt.event.*; import jalview.datamodel.*; import jalview.schemes.AnnotationColourGradient; import jalview.schemes.GraduatedColor; import jalview.util.MessageManager; +import jalview.viewmodel.seqfeatures.FeaturesDisplayed; /** * DOCUMENT ME! @@ -37,34 +36,13 @@ import jalview.util.MessageManager; * @author $author$ * @version $Revision$ */ -public class FeatureRenderer implements jalview.api.FeatureRenderer +public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRenderer { - AlignViewport av; - - Hashtable featureColours = new Hashtable(); - - // A higher level for grouping features of a - // particular type - Hashtable featureGroups = null; // Holds web links for feature groups and feature types // in the form label|link Hashtable featureLinks = null; - // This is actually an Integer held in the hashtable, - // Retrieved using the key feature type - Object currentColour; - - String[] renderOrder; - - FontMetrics fm; - - int charOffset; - - float transparency = 1f; - - TransparencySetter transparencySetter = null; - /** * Creates a new FeatureRenderer object. * @@ -73,49 +51,10 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer */ public FeatureRenderer(AlignViewport av) { + super(); this.av = av; - if (!System.getProperty("java.version").startsWith("1.1")) - { - transparencySetter = new TransparencySetter(); - } - } - - public void transferSettings(jalview.api.FeatureRenderer _fr) - { - if (_fr instanceof FeatureRenderer) - { - FeatureRenderer fr = (FeatureRenderer) _fr; - renderOrder = fr.renderOrder; - featureGroups = fr.featureGroups; - featureColours = fr.featureColours; - transparency = fr.transparency; - if (av != null && fr.av != null && fr.av != av) - { - if (fr.av.featuresDisplayed != null) - { - if (av.featuresDisplayed == null) - { - av.featuresDisplayed = new Hashtable(); - } - else - { - av.featuresDisplayed.clear(); - } - Enumeration en = fr.av.featuresDisplayed.keys(); - while (en.hasMoreElements()) - { - av.featuresDisplayed.put(en.nextElement(), Boolean.TRUE); - } - } - } - } - else - { - throw new Error( - "Implementation error: cannot port feature settings from implementation of type " - + _fr.getClass() + " to " + getClass()); - } + setTransparencyAvailable(!System.getProperty("java.version").startsWith("1.1")); } static String lastFeatureAdded; @@ -462,6 +401,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer } ffile.parseDescriptionHTML(sf, false); + setVisible(lastFeatureAdded); // if user edited name then make sure new type is visible } if (deleteFeature) { @@ -482,36 +422,17 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer ffile.parseDescriptionHTML(features[i], false); } - if (av.featuresDisplayed == null) - { - av.featuresDisplayed = new Hashtable(); - } - - if (featureGroups == null) - { - featureGroups = new Hashtable(); - } - col = colourPanel.getBackground(); // setColour(lastFeatureAdded, fcol); if (lastFeatureGroupAdded != null) { - featureGroups.put(lastFeatureGroupAdded, new Boolean(true)); - } - if (fcol instanceof Color) - { - setColour(lastFeatureAdded, fcol); + setGroupVisibility(lastFeatureGroupAdded, true); } - av.featuresDisplayed.put(lastFeatureAdded, - getFeatureStyle(lastFeatureAdded)); - - findAllFeatures(); - - String[] tro = new String[renderOrder.length]; - tro[0] = renderOrder[renderOrder.length - 1]; - System.arraycopy(renderOrder, 0, tro, 1, renderOrder.length - 1); - renderOrder = tro; + setColour(lastFeatureAdded, fcol); + setVisible(lastFeatureAdded); + findAllFeatures(false); // different to original applet behaviour ? + // findAllFeatures(); } else { @@ -520,9 +441,9 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer } } // refresh the alignment and the feature settings dialog - if (av.featureSettings != null) + if (((jalview.appletgui.AlignViewport) av).featureSettings != null) { - av.featureSettings.refreshTable(); + ((jalview.appletgui.AlignViewport) av).featureSettings.refreshTable(); } // findAllFeatures(); @@ -530,760 +451,4 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer return true; } - - public Color findFeatureColour(Color initialCol, SequenceI seq, int i) - { - overview = true; - if (!av.showSequenceFeatures) - { - return initialCol; - } - - lastSeq = seq; - sequenceFeatures = lastSeq.getSequenceFeatures(); - if (sequenceFeatures == null) - { - return initialCol; - } - - sfSize = sequenceFeatures.length; - - if (jalview.util.Comparison.isGap(lastSeq.getCharAt(i))) - { - return Color.white; - } - - currentColour = null; - - drawSequence(null, lastSeq, lastSeq.findPosition(i), -1, -1); - - if (currentColour == null) - { - return initialCol; - } - - return new Color(((Integer) currentColour).intValue()); - } - - /** - * This is used by the Molecule Viewer to get the accurate colour of the - * rendered sequence - */ - boolean overview = false; - - /** - * DOCUMENT ME! - * - * @param g - * DOCUMENT ME! - * @param seq - * DOCUMENT ME! - * @param sg - * DOCUMENT ME! - * @param start - * DOCUMENT ME! - * @param end - * DOCUMENT ME! - * @param x1 - * DOCUMENT ME! - * @param y1 - * DOCUMENT ME! - * @param width - * DOCUMENT ME! - * @param height - * DOCUMENT ME! - */ - // String type; - // SequenceFeature sf; - SequenceI lastSeq; - - SequenceFeature[] sequenceFeatures; - - int sfSize, sfindex, spos, epos; - - synchronized public void drawSequence(Graphics g, SequenceI seq, - int start, int end, int y1) - { - if (seq.getSequenceFeatures() == null - || seq.getSequenceFeatures().length == 0) - { - return; - } - - if (transparencySetter != null && g != null) - { - transparencySetter.setTransparency(g, transparency); - } - - if (lastSeq == null || seq != lastSeq - || sequenceFeatures != seq.getSequenceFeatures()) - { - lastSeq = seq; - sequenceFeatures = seq.getSequenceFeatures(); - sfSize = sequenceFeatures.length; - } - - if (av.featuresDisplayed == null || renderOrder == null) - { - findAllFeatures(); - if (av.featuresDisplayed.size() < 1) - { - return; - } - - sequenceFeatures = seq.getSequenceFeatures(); - sfSize = sequenceFeatures.length; - } - if (!overview) - { - spos = lastSeq.findPosition(start); - epos = lastSeq.findPosition(end); - if (g != null) - { - fm = g.getFontMetrics(); - } - } - String type; - for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++) - { - type = renderOrder[renderIndex]; - if (!av.featuresDisplayed.containsKey(type)) - { - continue; - } - - // loop through all features in sequence to find - // current feature to render - for (sfindex = 0; sfindex < sfSize; sfindex++) - { - if (!sequenceFeatures[sfindex].type.equals(type)) - { - continue; - } - - if (featureGroups != null - && sequenceFeatures[sfindex].featureGroup != null - && featureGroups - .containsKey(sequenceFeatures[sfindex].featureGroup) - && !((Boolean) featureGroups - .get(sequenceFeatures[sfindex].featureGroup)) - .booleanValue()) - { - continue; - } - - if (!overview - && (sequenceFeatures[sfindex].getBegin() > epos || sequenceFeatures[sfindex] - .getEnd() < spos)) - { - continue; - } - - if (overview) - { - if (sequenceFeatures[sfindex].begin <= start - && sequenceFeatures[sfindex].end >= start) - { - currentColour = new Integer( - getColour(sequenceFeatures[sfindex]).getRGB());// av.featuresDisplayed - // .get(sequenceFeatures[sfindex].type); - } - - } - else if (sequenceFeatures[sfindex].type.equals("disulfide bond")) - { - - renderFeature(g, seq, - seq.findIndex(sequenceFeatures[sfindex].begin) - 1, - seq.findIndex(sequenceFeatures[sfindex].begin) - 1, - getColour(sequenceFeatures[sfindex]) - // new Color(((Integer) av.featuresDisplayed - // .get(sequenceFeatures[sfindex].type)).intValue()) - , start, end, y1); - renderFeature(g, seq, - seq.findIndex(sequenceFeatures[sfindex].end) - 1, - seq.findIndex(sequenceFeatures[sfindex].end) - 1, - getColour(sequenceFeatures[sfindex]) - // new Color(((Integer) av.featuresDisplayed - // .get(sequenceFeatures[sfindex].type)).intValue()) - , start, end, y1); - - } - else - { - if (showFeature(sequenceFeatures[sfindex])) - { - renderFeature(g, seq, - seq.findIndex(sequenceFeatures[sfindex].begin) - 1, - seq.findIndex(sequenceFeatures[sfindex].end) - 1, - getColour(sequenceFeatures[sfindex]), start, end, y1); - } - } - - } - } - - if (transparencySetter != null && g != null) - { - transparencySetter.setTransparency(g, 1.0f); - } - } - - char s; - - int i; - - void renderFeature(Graphics g, SequenceI seq, int fstart, int fend, - Color featureColour, int start, int end, int y1) - { - - if (((fstart <= end) && (fend >= start))) - { - if (fstart < start) - { // fix for if the feature we have starts before the sequence start, - fstart = start; // but the feature end is still valid!! - } - - if (fend >= end) - { - fend = end; - } - - for (i = fstart; i <= fend; i++) - { - s = seq.getCharAt(i); - - if (jalview.util.Comparison.isGap(s)) - { - continue; - } - - g.setColor(featureColour); - - g.fillRect((i - start) * av.charWidth, y1, av.charWidth, - av.charHeight); - - if (!av.validCharWidth) - { - continue; - } - - g.setColor(Color.white); - charOffset = (av.charWidth - fm.charWidth(s)) / 2; - g.drawString(String.valueOf(s), charOffset - + (av.charWidth * (i - start)), (y1 + av.charHeight) - - av.charHeight / 5); // pady = height / 5; - - } - } - } - - Hashtable minmax = null; - - /** - * Called when alignment in associated view has new/modified features to - * discover and display. - * - */ - public void featuresAdded() - { - lastSeq = null; - findAllFeatures(); - } - - /** - * find all features on the alignment - */ - void findAllFeatures() - { - jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(); - - av.featuresDisplayed = new Hashtable(); - Vector allfeatures = new Vector(); - minmax = new Hashtable(); - AlignmentI alignment = av.getAlignment(); - for (int i = 0; i < alignment.getHeight(); i++) - { - SequenceFeature[] features = alignment.getSequenceAt(i) - .getSequenceFeatures(); - - if (features == null) - { - continue; - } - - int index = 0; - while (index < features.length) - { - if (features[index].begin == 0 && features[index].end == 0) - { - index++; - continue; - } - if (!av.featuresDisplayed.containsKey(features[index].getType())) - { - if (getColour(features[index].getType()) == null) - { - featureColours.put(features[index].getType(), - ucs.createColourFromName(features[index].getType())); - } - - av.featuresDisplayed.put(features[index].getType(), new Integer( - getColour(features[index].getType()).getRGB())); - allfeatures.addElement(features[index].getType()); - } - if (features[index].score != Float.NaN) - { - int nonpos = features[index].getBegin() >= 1 ? 0 : 1; - float[][] mm = (float[][]) minmax.get(features[index].getType()); - if (mm == null) - { - mm = new float[][] - { null, null }; - minmax.put(features[index].getType(), mm); - } - if (mm[nonpos] == null) - { - mm[nonpos] = new float[] - { features[index].score, features[index].score }; - - } - else - { - if (mm[nonpos][0] > features[index].score) - { - mm[nonpos][0] = features[index].score; - } - if (mm[nonpos][1] < features[index].score) - { - mm[nonpos][1] = features[index].score; - } - } - } - - index++; - } - } - - renderOrder = new String[allfeatures.size()]; - Enumeration en = allfeatures.elements(); - int i = allfeatures.size() - 1; - while (en.hasMoreElements()) - { - renderOrder[i] = en.nextElement().toString(); - i--; - } - } - - /** - * get a feature style object for the given type string. Creates a - * java.awt.Color for a featureType with no existing colourscheme. TODO: - * replace return type with object implementing standard abstract colour/style - * interface - * - * @param featureType - * @return java.awt.Color or GraduatedColor - */ - public Object getFeatureStyle(String featureType) - { - Object fc = featureColours.get(featureType); - if (fc == null) - { - jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(); - Color col = ucs.createColourFromName(featureType); - featureColours.put(featureType, fc = col); - } - return fc; - } - - public Color getColour(String featureType) - { - Object fc = getFeatureStyle(featureType); - - if (fc instanceof Color) - { - return (Color) fc; - } - else - { - if (fc instanceof GraduatedColor) - { - return ((GraduatedColor) fc).getMaxColor(); - } - } - throw new Error("Implementation Error: Unrecognised render object " - + fc.getClass() + " for features of type " + featureType); - } - - /** - * - * @param sequenceFeature - * @return true if feature is visible. - */ - private boolean showFeature(SequenceFeature sequenceFeature) - { - Object fc = getFeatureStyle(sequenceFeature.type); - if (fc instanceof GraduatedColor) - { - return ((GraduatedColor) fc).isColored(sequenceFeature); - } - else - { - return true; - } - } - - /** - * implement graduated colouring for features with scores - * - * @param feature - * @return render colour for the given feature - */ - public Color getColour(SequenceFeature feature) - { - Object fc = getFeatureStyle(feature.getType()); - if (fc instanceof Color) - { - return (Color) fc; - } - else - { - if (fc instanceof GraduatedColor) - { - return ((GraduatedColor) fc).findColor(feature); - } - } - throw new Error("Implementation Error: Unrecognised render object " - + fc.getClass() + " for features of type " + feature.getType()); - } - - public void setColour(String featureType, Object col) - { - // overwrite - // Color _col = (col instanceof Color) ? ((Color) col) : (col instanceof - // GraduatedColor) ? ((GraduatedColor) col).getMaxColor() : null; - // Object c = featureColours.get(featureType); - // if (c == null || c instanceof Color || (c instanceof GraduatedColor && - // !((GraduatedColor)c).getMaxColor().equals(_col))) - { - featureColours.put(featureType, col); - } - } - - public void setFeaturePriority(Object[][] data) - { - // The feature table will display high priority - // features at the top, but theses are the ones - // we need to render last, so invert the data - if (av.featuresDisplayed != null) - { - av.featuresDisplayed.clear(); - } - - /* - * if (visibleNew) { if (av.featuresDisplayed != null) { - * av.featuresDisplayed.clear(); } else { av.featuresDisplayed = new - * Hashtable(); } } if (data == null) { return; } - */ - - renderOrder = new String[data.length]; - - if (data.length > 0) - { - for (int i = 0; i < data.length; i++) - { - String type = data[i][0].toString(); - setColour(type, data[i][1]); - if (((Boolean) data[i][2]).booleanValue()) - { - av.featuresDisplayed.put(type, new Integer(getColour(type) - .getRGB())); - } - - renderOrder[data.length - i - 1] = type; - } - } - } - - /** - * @return a simple list of feature group names or null - */ - public String[] getGroups() - { - buildGroupHash(); - if (featureGroups != null) - { - String[] gps = new String[featureGroups.size()]; - Enumeration gn = featureGroups.keys(); - int i = 0; - while (gn.hasMoreElements()) - { - gps[i++] = (String) gn.nextElement(); - } - return gps; - } - return null; - } - - /** - * get visible or invisible groups - * - * @param visible - * true to return visible groups, false to return hidden ones. - * @return list of groups - */ - public String[] getGroups(boolean visible) - { - buildGroupHash(); - if (featureGroups != null) - { - Vector gp = new Vector(); - - Enumeration gn = featureGroups.keys(); - while (gn.hasMoreElements()) - { - String nm = (String) gn.nextElement(); - Boolean state = (Boolean) featureGroups.get(nm); - if (state.booleanValue() == visible) - { - gp.addElement(nm); - } - } - String[] gps = new String[gp.size()]; - gp.copyInto(gps); - - int i = 0; - while (gn.hasMoreElements()) - { - gps[i++] = (String) gn.nextElement(); - } - return gps; - } - return null; - } - - /** - * set all feature groups in toset to be visible or invisible - * - * @param toset - * group names - * @param visible - * the state of the named groups to set - */ - public void setGroupState(String[] toset, boolean visible) - { - buildGroupHash(); - if (toset != null && toset.length > 0 && featureGroups != null) - { - boolean rdrw = false; - for (int i = 0; i < toset.length; i++) - { - Object st = featureGroups.get(toset[i]); - featureGroups.put(toset[i], new Boolean(visible)); - if (st != null) - { - rdrw = rdrw || (visible != ((Boolean) st).booleanValue()); - } - } - if (rdrw) - { - if (this.av != null) - if (this.av.featureSettings != null) - { - av.featureSettings.rebuildGroups(); - this.av.featureSettings.resetTable(true); - } - else - { - buildFeatureHash(); - } - if (av != null) - { - av.alignmentChanged(null); - } - } - } - } - - ArrayList hiddenGroups = new ArrayList(); - - /** - * analyse alignment for groups and hash tables (used to be embedded in - * FeatureSettings.setTableData) - * - * @return true if features are on the alignment - */ - public boolean buildGroupHash() - { - boolean alignmentHasFeatures = false; - if (featureGroups == null) - { - featureGroups = new Hashtable(); - } - hiddenGroups = new ArrayList(); - hiddenGroups.addAll(featureGroups.keySet()); - ArrayList allFeatures = new ArrayList(); - ArrayList allGroups = new ArrayList(); - SequenceFeature[] tmpfeatures; - String group; - AlignmentI alignment = av.getAlignment(); - for (int i = 0; i < alignment.getHeight(); i++) - { - if (alignment.getSequenceAt(i).getSequenceFeatures() == null) - { - continue; - } - - alignmentHasFeatures = true; - - tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures(); - int index = 0; - while (index < tmpfeatures.length) - { - if (tmpfeatures[index].getFeatureGroup() != null) - { - group = tmpfeatures[index].featureGroup; - // Remove group from the hiddenGroup list - hiddenGroups.remove(group); - if (!allGroups.contains(group)) - { - allGroups.add(group); - - boolean visible = true; - if (featureGroups.containsKey(group)) - { - visible = ((Boolean) featureGroups.get(group)).booleanValue(); - } - else - { - featureGroups.put(group, new Boolean(visible)); - } - } - } - - if (!allFeatures.contains(tmpfeatures[index].getType())) - { - allFeatures.add(tmpfeatures[index].getType()); - } - index++; - } - } - - return alignmentHasFeatures; - } - - /** - * rebuild the featuresDisplayed and renderorder list based on the - * featureGroups hash and any existing display state and force a repaint if - * necessary - * - * @return true if alignment has visible features - */ - public boolean buildFeatureHash() - { - boolean alignmentHasFeatures = false; - if (featureGroups == null) - { - alignmentHasFeatures = buildGroupHash(); - } - if (!alignmentHasFeatures) - return false; - Hashtable fdisp = av.featuresDisplayed; - Vector allFeatures = new Vector(); - SequenceFeature[] tmpfeatures; - String group; - AlignmentI alignment = av.getAlignment(); - for (int i = 0; i < alignment.getHeight(); i++) - { - if (alignment.getSequenceAt(i).getSequenceFeatures() == null) - { - continue; - } - - alignmentHasFeatures = true; - - tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures(); - int index = 0; - while (index < tmpfeatures.length) - { - boolean visible = true; - if (tmpfeatures[index].getFeatureGroup() != null) - { - group = tmpfeatures[index].featureGroup; - if (featureGroups.containsKey(group)) - { - visible = ((Boolean) featureGroups.get(group)).booleanValue(); - } - } - - if (visible && !allFeatures.contains(tmpfeatures[index].getType())) - { - allFeatures.addElement(tmpfeatures[index].getType()); - } - index++; - } - } - if (allFeatures.size() > 0) - { - String[] neworder = new String[allFeatures.size()]; - int p = neworder.length - 1; - for (int i = renderOrder.length - 1; i >= 0; i--) - { - if (allFeatures.contains(renderOrder[i])) - { - neworder[p--] = renderOrder[i]; - allFeatures.removeElement(renderOrder[i]); - } - else - { - av.featuresDisplayed.remove(renderOrder[i]); - } - } - for (int i = allFeatures.size() - 1; i > 0; i++) - { - Object e = allFeatures.elementAt(i); - if (e != null) - { - neworder[p--] = (String) e; - av.featuresDisplayed.put(e, getColour((String) e)); - } - } - renderOrder = neworder; - return true; - } - - return alignmentHasFeatures; - } - - /** - * - * @return the displayed feature type as an array of strings - */ - protected String[] getDisplayedFeatureTypes() - { - String[] typ = null; - synchronized (renderOrder) - { - typ = new String[renderOrder.length]; - System.arraycopy(renderOrder, 0, typ, 0, typ.length); - for (int i = 0; i < typ.length; i++) - { - if (av.featuresDisplayed.get(typ[i]) == null) - { - typ[i] = null; - } - } - } - return typ; - } -} - -class TransparencySetter -{ - void setTransparency(Graphics g, float value) - { - Graphics2D g2 = (Graphics2D) g; - g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, - value)); - } } diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java index f6e7772..bde68cc 100755 --- a/src/jalview/appletgui/FeatureSettings.java +++ b/src/jalview/appletgui/FeatureSettings.java @@ -21,7 +21,7 @@ package jalview.appletgui; import java.util.*; - +import java.util.List; import java.awt.*; import java.awt.event.*; @@ -50,8 +50,6 @@ public class FeatureSettings extends Panel implements ItemListener, ScrollPane scrollPane; - boolean alignmentHasFeatures = false; - Image linkImage; Scrollbar transparency; @@ -64,9 +62,9 @@ public class FeatureSettings extends Panel implements ItemListener, fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); transparency = new Scrollbar(Scrollbar.HORIZONTAL, - 100 - (int) (fr.transparency * 100), 1, 1, 100); + 100 - (int) (fr.getTransparency() * 100), 1, 1, 100); - if (fr.transparencySetter != null) + if (fr.isTransparencyAvailable()) { transparency.addAdjustmentListener(this); } @@ -81,9 +79,9 @@ public class FeatureSettings extends Panel implements ItemListener, linkImage = java.awt.Toolkit.getDefaultToolkit().getImage(url); } - if (av.featuresDisplayed == null) + if (av.isShowSequenceFeatures() || !fr.hasRenderOrder()) { - fr.findAllFeatures(); + fr.findAllFeatures(true); // was default - now true to make all visible } setTableData(); @@ -91,7 +89,7 @@ public class FeatureSettings extends Panel implements ItemListener, this.setLayout(new BorderLayout()); scrollPane = new ScrollPane(); scrollPane.add(featurePanel); - if (alignmentHasFeatures) + if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0) { add(scrollPane, BorderLayout.CENTER); } @@ -104,7 +102,7 @@ public class FeatureSettings extends Panel implements ItemListener, Panel tPanel = new Panel(new BorderLayout()); - if (fr.transparencySetter != null) + if (fr.isTransparencyAvailable()) { tPanel.add(transparency, BorderLayout.CENTER); tPanel.add(new Label("Transparency"), BorderLayout.EAST); @@ -124,8 +122,8 @@ public class FeatureSettings extends Panel implements ItemListener, { groupPanel .setLayout(new GridLayout( - (fr.featureGroups.size() - fr.hiddenGroups.size()) / 4 + 1, - 4)); + (fr.getFeatureGroupsSize()) / 4 + 1, + 4)); // JBPNote - this was scaled on number of visible groups. seems broken groupPanel.validate(); add(groupPanel, BorderLayout.NORTH); @@ -185,7 +183,7 @@ public class FeatureSettings extends Panel implements ItemListener, public void actionPerformed(ActionEvent e) { - me.sortByScore(new String[] + me.ap.alignFrame.avc.sortAlignmentByFeatureScore(new String[] { type }); } @@ -197,7 +195,7 @@ public class FeatureSettings extends Panel implements ItemListener, public void actionPerformed(ActionEvent e) { - me.sortByDens(new String[] + me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(new String[] { type }); } @@ -253,8 +251,7 @@ public class FeatureSettings extends Panel implements ItemListener, public void setTableData() { - alignmentHasFeatures = fr.buildGroupHash(); - if (alignmentHasFeatures) + if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0) { rebuildGroups(); @@ -279,18 +276,17 @@ public class FeatureSettings extends Panel implements ItemListener, } // TODO: JAL-964 - smoothly incorporate new group entries if panel already // displayed and new groups present - Enumeration gps = fr.featureGroups.keys(); - while (gps.hasMoreElements()) + for (String group:(List)fr.getFeatureGroups()) { - String group = (String) gps.nextElement(); - Boolean vis = (Boolean) fr.featureGroups.get(group); - Checkbox check = new MyCheckbox(group, vis.booleanValue(), + boolean vis = fr.checkGroupVisibility(group, false); + Checkbox check = new MyCheckbox(group, vis, (fr.featureLinks != null && fr.featureLinks .containsKey(group))); check.addMouseListener(this); check.setFont(new Font("Serif", Font.BOLD, 12)); - check.addItemListener(this); - check.setVisible(fr.hiddenGroups.contains(group)); + check.addItemListener(groupItemListener); + // note - visibility seems to correlate with displayed. ???wtf ?? + check.setVisible(vis); groupPanel.add(check); } if (rdrw) @@ -298,7 +294,6 @@ public class FeatureSettings extends Panel implements ItemListener, groupPanel.validate(); } } - // This routine adds and removes checkboxes depending on // Group selection states void resetTable(boolean groupsChanged) @@ -320,8 +315,7 @@ public class FeatureSettings extends Panel implements ItemListener, { group = tmpfeatures[index].featureGroup; - if (group == null || fr.featureGroups.get(group) == null - || ((Boolean) fr.featureGroups.get(group)).booleanValue()) + if (group == null || fr.checkGroupVisibility(group, true)) { type = tmpfeatures[index].getType(); if (!visibleChecks.contains(type)) @@ -350,13 +344,14 @@ public class FeatureSettings extends Panel implements ItemListener, } } - if (fr.renderOrder != null) + if (fr.getRenderOrder() != null) { // First add the checks in the previous render order, // in case the window has been closed and reopened - for (int ro = fr.renderOrder.length - 1; ro > -1; ro--) + List rol = fr.getRenderOrder(); + for (int ro = rol.size() - 1; ro > -1; ro--) { - String item = fr.renderOrder[ro]; + String item = rol.get(ro); if (!visibleChecks.contains(item)) { @@ -418,7 +413,7 @@ public class FeatureSettings extends Panel implements ItemListener, if (addCheck) { boolean selected = false; - if (groupsChanged || av.featuresDisplayed.containsKey(type)) + if (groupsChanged || av.getFeaturesDisplayed().isVisible(type)) { selected = true; } @@ -455,26 +450,22 @@ public class FeatureSettings extends Panel implements ItemListener, selectionChanged(); } - public void itemStateChanged(ItemEvent evt) - { - if (evt != null) - { - // Is the source a top level featureGroup? + private ItemListener groupItemListener = new ItemListener() { + public void itemStateChanged(ItemEvent evt) { Checkbox source = (Checkbox) evt.getSource(); - if (fr.featureGroups.containsKey(source.getLabel())) + fr.setGroupVisibility(source.getLabel(), + source.getState()); + ap.seqPanel.seqCanvas.repaint(); + if (ap.overviewPanel != null) { - fr.featureGroups.put(source.getLabel(), - new Boolean(source.getState())); - ap.seqPanel.seqCanvas.repaint(); - if (ap.overviewPanel != null) - { - ap.overviewPanel.updateOverviewImage(); - } - - resetTable(true); - return; + ap.overviewPanel.updateOverviewImage(); } - } + resetTable(true); + return; + }; + }; + public void itemStateChanged(ItemEvent evt) + { selectionChanged(); } @@ -618,7 +609,7 @@ public class FeatureSettings extends Panel implements ItemListener, MyCheckbox check = (MyCheckbox) evt.getSource(); if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) != 0) { - this.popupSort(check, fr.minmax, evt.getX(), evt.getY()); + this.popupSort(check, fr.getMinMax(), evt.getX(), evt.getY()); } if (fr.featureLinks != null && fr.featureLinks.containsKey(check.type)) { @@ -658,7 +649,7 @@ public class FeatureSettings extends Panel implements ItemListener, public void adjustmentValueChanged(AdjustmentEvent evt) { - fr.transparency = ((float) (100 - transparency.getValue()) / 100f); + fr.setTransparency((float) (100 - transparency.getValue()) / 100f); ap.seqPanel.seqCanvas.repaint(); } @@ -772,81 +763,4 @@ public class FeatureSettings extends Panel implements ItemListener, } } - protected void sortByDens(String[] typ) - { - sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY); - } - - private String[] getDisplayedFeatureTypes() - { - String[] typ = null; - if (fr != null) - { - synchronized (fr.renderOrder) - { - typ = new String[fr.renderOrder.length]; - System.arraycopy(fr.renderOrder, 0, typ, 0, typ.length); - for (int i = 0; i < typ.length; i++) - { - if (av.featuresDisplayed.get(typ[i]) == null) - { - typ[i] = null; - } - } - } - } - return typ; - } - - protected void sortBy(String[] typ, String methodText, final String method) - { - if (typ == null) - { - typ = getDisplayedFeatureTypes(); - } - String gps[] = null; - gps = fr.getGroups(true); - if (typ != null) - { - for (int i = 0; i < typ.length; i++) - { - System.err.println("Sorting on Types:" + typ[i]); - } - } - if (gps != null) - { - - for (int i = 0; i < gps.length; i++) - { - System.err.println("Sorting on groups:" + gps[i]); - } - } - AlignmentPanel alignPanel = ap; - AlignmentI al = alignPanel.av.getAlignment(); - - int start, stop; - SequenceGroup sg = alignPanel.av.getSelectionGroup(); - if (sg != null) - { - start = sg.getStartRes(); - stop = sg.getEndRes(); - } - else - { - start = 0; - stop = al.getWidth(); - } - SequenceI[] oldOrder = al.getSequencesArray(); - AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method); - this.ap.alignFrame.addHistoryItem(new OrderCommand(methodText, - oldOrder, alignPanel.av.getAlignment())); - alignPanel.paintAlignment(true); - - } - - protected void sortByScore(String[] typ) - { - sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE); - } - } diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java index e646051..8486fe0 100755 --- a/src/jalview/appletgui/OverviewPanel.java +++ b/src/jalview/appletgui/OverviewPanel.java @@ -69,7 +69,6 @@ public class OverviewPanel extends Panel implements Runnable, sr.renderGaps = false; sr.forOverview = true; fr = new FeatureRenderer(av); - fr.overview = true; // scale the initial size of overviewpanel to shape of alignment float initialScale = (float) av.getAlignment().getWidth() @@ -231,8 +230,7 @@ public class OverviewPanel extends Panel implements Runnable, if (av.isShowSequenceFeatures()) { - fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups; - fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours; + fr.transferSettings(ap.seqPanel.seqCanvas.fr); } resizing = true; diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java index 5ba22b6..baf27f1 100644 --- a/src/jalview/appletgui/SeqPanel.java +++ b/src/jalview/appletgui/SeqPanel.java @@ -800,19 +800,17 @@ public class SeqPanel extends Panel implements MouseMotionListener, { for (int i = 0; i < features.length; i++) { - if (av.featuresDisplayed == null - || !av.featuresDisplayed.containsKey(features[i].getType())) + if (av.getFeaturesDisplayed() == null + || !av.getFeaturesDisplayed().isVisible(features[i].getType())) { continue; } if (features[i].featureGroup != null - && seqCanvas.fr.featureGroups != null - && seqCanvas.fr.featureGroups - .containsKey(features[i].featureGroup) - && !((Boolean) seqCanvas.fr.featureGroups - .get(features[i].featureGroup)).booleanValue()) + && !seqCanvas.fr.checkGroupVisibility(features[i].featureGroup,false)) + { continue; + } if ((features[i].getBegin() <= res) && (features[i].getEnd() >= res)) diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index b958f90..f364f74 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -4786,7 +4786,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { featuresFile = new FeaturesFile(file, type).parse(viewport .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas - .getFeatureRenderer().featureColours, false, + .getFeatureRenderer().getFeatureColours(), false, jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false)); } catch (Exception ex) { diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 8c18a15..1bc4ba7 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1519,7 +1519,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { return seqPanel.seqCanvas.getFeatureRenderer(); } - public void updateFeatureRenderer(FeatureRenderer fr) + public void updateFeatureRenderer(jalview.renderer.seqfeatures.FeatureRenderer fr) { fr.transferSettings(seqPanel.seqCanvas.getFeatureRenderer()); } diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java index 0975d24..61c5ee1 100644 --- a/src/jalview/gui/AnnotationExporter.java +++ b/src/jalview/gui/AnnotationExporter.java @@ -112,14 +112,16 @@ public class AnnotationExporter extends JPanel if (GFFFormat.isSelected()) { text = new FeaturesFile().printGFFFormat(ap.av.getAlignment() - .getDataset().getSequencesArray(), - getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());// ap.av.featuresDisplayed//); + .getDataset().getSequencesArray(), ap + .getFeatureRenderer().getDisplayedFeatureCols(), true, + ap.av.isShowNpFeats());// ap.av.featuresDisplayed//); } else { text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment() - .getDataset().getSequencesArray(), - getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); // ap.av.featuresDisplayed); + .getDataset().getSequencesArray(), ap + .getFeatureRenderer().getDisplayedFeatureCols(), true, + ap.av.isShowNpFeats()); // ap.av.featuresDisplayed); } } else @@ -159,14 +161,14 @@ public class AnnotationExporter extends JPanel if (GFFFormat.isSelected()) { text = new FeaturesFile().printGFFFormat(ap.av.getAlignment() - .getDataset().getSequencesArray(), - getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); + .getDataset().getSequencesArray(), ap.getFeatureRenderer() + .getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); } else { text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment() - .getDataset().getSequencesArray(), - getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); + .getDataset().getSequencesArray(), ap.getFeatureRenderer() + .getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); } } else if (!features) @@ -207,26 +209,6 @@ public class AnnotationExporter extends JPanel close_actionPerformed(null); } - private Hashtable getDisplayedFeatureCols() - { - Hashtable fcols = new Hashtable(); - if (ap.av.featuresDisplayed == null) - { - return fcols; - } - Enumeration en = ap.av.featuresDisplayed.keys(); - FeatureRenderer fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); // consider - // higher - // level - // method ? - while (en.hasMoreElements()) - { - Object col = en.nextElement(); - fcols.put(col, fr.featureColours.get(col)); - } - return fcols; - } - public void close_actionPerformed(ActionEvent e) { try diff --git a/src/jalview/gui/FeatureColourChooser.java b/src/jalview/gui/FeatureColourChooser.java index 8ab7c85..d1d1b6d 100644 --- a/src/jalview/gui/FeatureColourChooser.java +++ b/src/jalview/gui/FeatureColourChooser.java @@ -109,10 +109,10 @@ public class FeatureColourChooser extends JalviewDialog } }); - float mm[] = ((float[][]) fr.minmax.get(type))[0]; + float mm[] = ((float[][]) fr.getMinMax().get(type))[0]; min = mm[0]; max = mm[1]; - oldcs = fr.featureColours.get(type); + oldcs = fr.getFeatureColours().get(type); if (oldcs instanceof GraduatedColor) { if (((GraduatedColor) oldcs).isAutoScale()) @@ -470,7 +470,7 @@ public class FeatureColourChooser extends JalviewDialog maxColour.setForeground(oldmaxColour); minColour.setForeground(oldminColour); } - fr.featureColours.put(type, acg); + fr.setColour(type, acg); cs = acg; ap.paintAlignment(false); } @@ -495,7 +495,7 @@ public class FeatureColourChooser extends JalviewDialog void reset() { - fr.featureColours.put(type, oldcs); + fr.setColour(type, oldcs); ap.paintAlignment(false); cs = null; } diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index d36105a..ccb8ad1 100644 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -21,13 +21,10 @@ package jalview.gui; import java.util.*; -import java.util.concurrent.ConcurrentHashMap; - import java.awt.*; import java.awt.event.*; import java.awt.image.*; import java.beans.PropertyChangeListener; -import java.beans.PropertyChangeSupport; import javax.swing.*; @@ -41,38 +38,11 @@ import jalview.util.MessageManager; * @author $author$ * @version $Revision$ */ -public class FeatureRenderer extends jalview.viewmodel.FeatureRenderer implements jalview.api.FeatureRenderer +public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRenderer implements jalview.api.FeatureRenderer { - AlignmentPanel ap; - - AlignViewport av; - Color resBoxColour; - /** - * global transparency for feature - */ - float transparency = 1.0f; - - FontMetrics fm; - - int charOffset; - - Map featureColours = new ConcurrentHashMap(); - - // A higher level for grouping features of a - // particular type - Map featureGroups = new ConcurrentHashMap(); - - // This is actually an Integer held in the hashtable, - // Retrieved using the key feature type - Object currentColour; - - String[] renderOrder; - - PropertyChangeSupport changeSupport = new PropertyChangeSupport(this); - - Vector allfeatures; + AlignmentPanel ap; /** * Creates a new FeatureRenderer object. @@ -82,6 +52,7 @@ public class FeatureRenderer extends jalview.viewmodel.FeatureRenderer implement */ public FeatureRenderer(AlignmentPanel ap) { + super(); this.ap = ap; this.av = ap.av; if (ap != null && ap.seqPanel != null && ap.seqPanel.seqCanvas != null @@ -91,898 +62,6 @@ public class FeatureRenderer extends jalview.viewmodel.FeatureRenderer implement } } - public class FeatureRendererSettings implements Cloneable - { - String[] renderOrder; - - Map featureGroups; - - Map featureColours; - - float transparency; - - Map featureOrder; - - public FeatureRendererSettings(String[] renderOrder, - Hashtable featureGroups, Hashtable featureColours, - float transparency, Hashtable featureOrder) - { - super(); - this.renderOrder = renderOrder; - this.featureGroups = featureGroups; - this.featureColours = featureColours; - this.transparency = transparency; - this.featureOrder = featureOrder; - } - - /** - * create an independent instance of the feature renderer settings - * - * @param fr - */ - public FeatureRendererSettings(FeatureRenderer fr) - { - renderOrder = null; - featureGroups = new ConcurrentHashMap(); - featureColours = new ConcurrentHashMap(); - featureOrder = new ConcurrentHashMap(); - if (fr.renderOrder != null) - { - this.renderOrder = new String[fr.renderOrder.length]; - System.arraycopy(fr.renderOrder, 0, renderOrder, 0, - fr.renderOrder.length); - } - if (fr.featureGroups != null) - { - this.featureGroups = new ConcurrentHashMap(fr.featureGroups); - } - if (fr.featureColours != null) - { - this.featureColours = new ConcurrentHashMap(fr.featureColours); - } - Iterator en = fr.featureColours.keySet().iterator(); - while (en.hasNext()) - { - Object next = en.next(); - Object val = featureColours.get(next); - if (val instanceof GraduatedColor) - { - featureColours - .put(next, new GraduatedColor((GraduatedColor) val)); - } - } - this.transparency = fr.transparency; - if (fr.featureOrder != null) - { - this.featureOrder = new ConcurrentHashMap(fr.featureOrder); - } - } - } - - public FeatureRendererSettings getSettings() - { - return new FeatureRendererSettings(this); - } - - public void transferSettings(FeatureRendererSettings fr) - { - this.renderOrder = fr.renderOrder; - this.featureGroups = fr.featureGroups; - this.featureColours = fr.featureColours; - this.transparency = fr.transparency; - this.featureOrder = fr.featureOrder; - } - - /** - * update from another feature renderer - * - * @param fr - * settings to copy - */ - public void transferSettings(jalview.api.FeatureRenderer _fr) - { - FeatureRenderer fr = (FeatureRenderer) _fr; - FeatureRendererSettings frs = new FeatureRendererSettings(fr); - this.renderOrder = frs.renderOrder; - this.featureGroups = frs.featureGroups; - this.featureColours = frs.featureColours; - this.transparency = frs.transparency; - this.featureOrder = frs.featureOrder; - if (av != null && av != fr.av) - { - // copy over the displayed feature settings - if (fr.av != null) - { - if (fr.av.featuresDisplayed != null) - { - // update display settings - if (av.featuresDisplayed == null) - { - av.featuresDisplayed = new Hashtable(fr.av.featuresDisplayed); - } - else - { - av.featuresDisplayed.clear(); - Enumeration en = fr.av.featuresDisplayed.keys(); - while (en.hasMoreElements()) - { - av.featuresDisplayed.put(en.nextElement(), Boolean.TRUE); - } - - } - } - } - } - } - - BufferedImage offscreenImage; - - boolean offscreenRender = false; - - public Color findFeatureColour(Color initialCol, SequenceI seq, int res) - { - return new Color(findFeatureColour(initialCol.getRGB(), seq, res)); - } - - /** - * This is used by the Molecule Viewer and Overview to get the accurate - * colourof the rendered sequence - */ - public synchronized int findFeatureColour(int initialCol, SequenceI seq, - int column) - { - if (!av.showSequenceFeatures) - { - return initialCol; - } - - if (seq != lastSeq) - { - lastSeq = seq; - sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures(); - if (sequenceFeatures != null) - { - sfSize = sequenceFeatures.length; - } - } - - if (sequenceFeatures != lastSeq.getDatasetSequence() - .getSequenceFeatures()) - { - sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures(); - if (sequenceFeatures != null) - { - sfSize = sequenceFeatures.length; - } - } - - if (sequenceFeatures == null || sfSize == 0) - { - return initialCol; - } - - if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column))) - { - return Color.white.getRGB(); - } - - // Only bother making an offscreen image if transparency is applied - if (transparency != 1.0f && offscreenImage == null) - { - offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB); - } - - currentColour = null; - // TODO: non-threadsafe - each rendering thread needs its own instance of - // the feature renderer - or this should be synchronized. - offscreenRender = true; - - if (offscreenImage != null) - { - offscreenImage.setRGB(0, 0, initialCol); - drawSequence(offscreenImage.getGraphics(), lastSeq, column, column, 0); - - return offscreenImage.getRGB(0, 0); - } - else - { - drawSequence(null, lastSeq, lastSeq.findPosition(column), -1, -1); - - if (currentColour == null) - { - return initialCol; - } - else - { - return ((Integer) currentColour).intValue(); - } - } - - } - - /** - * DOCUMENT ME! - * - * @param g - * DOCUMENT ME! - * @param seq - * DOCUMENT ME! - * @param sg - * DOCUMENT ME! - * @param start - * DOCUMENT ME! - * @param end - * DOCUMENT ME! - * @param x1 - * DOCUMENT ME! - * @param y1 - * DOCUMENT ME! - * @param width - * DOCUMENT ME! - * @param height - * DOCUMENT ME! - */ - // String type; - // SequenceFeature sf; - SequenceI lastSeq; - - SequenceFeature[] sequenceFeatures; - - int sfSize, sfindex, spos, epos; - - /** - * show scores as heights - */ - protected boolean varyHeight = false; - - synchronized public void drawSequence(Graphics g, SequenceI seq, - int start, int end, int y1) - { - - if (seq.getDatasetSequence().getSequenceFeatures() == null - || seq.getDatasetSequence().getSequenceFeatures().length == 0) - { - return; - } - - if (g != null) - { - fm = g.getFontMetrics(); - } - - if (av.featuresDisplayed == null || renderOrder == null - || newFeatureAdded) - { - findAllFeatures(); - if (av.featuresDisplayed.size() < 1) - { - return; - } - - sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures(); - } - - if (lastSeq == null - || seq != lastSeq - || seq.getDatasetSequence().getSequenceFeatures() != sequenceFeatures) - { - lastSeq = seq; - sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures(); - } - - if (transparency != 1 && g != null) - { - Graphics2D g2 = (Graphics2D) g; - g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, - transparency)); - } - - if (!offscreenRender) - { - spos = lastSeq.findPosition(start); - epos = lastSeq.findPosition(end); - } - - sfSize = sequenceFeatures.length; - String type; - for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++) - { - type = renderOrder[renderIndex]; - - if (type == null || !av.featuresDisplayed.containsKey(type)) - { - continue; - } - - // loop through all features in sequence to find - // current feature to render - for (sfindex = 0; sfindex < sfSize; sfindex++) - { - if (!sequenceFeatures[sfindex].type.equals(type)) - { - continue; - } - - if (featureGroups != null - && sequenceFeatures[sfindex].featureGroup != null - && sequenceFeatures[sfindex].featureGroup.length() != 0 - && featureGroups - .containsKey(sequenceFeatures[sfindex].featureGroup) - && !((Boolean) featureGroups - .get(sequenceFeatures[sfindex].featureGroup)) - .booleanValue()) - { - continue; - } - - if (!offscreenRender - && (sequenceFeatures[sfindex].getBegin() > epos || sequenceFeatures[sfindex] - .getEnd() < spos)) - { - continue; - } - - if (offscreenRender && offscreenImage == null) - { - if (sequenceFeatures[sfindex].begin <= start - && sequenceFeatures[sfindex].end >= start) - { - // this is passed out to the overview and other sequence renderers - // (e.g. molecule viewer) to get displayed colour for rendered - // sequence - currentColour = new Integer( - getColour(sequenceFeatures[sfindex]).getRGB()); - // used to be retreived from av.featuresDisplayed - // currentColour = av.featuresDisplayed - // .get(sequenceFeatures[sfindex].type); - - } - } - else if (sequenceFeatures[sfindex].type.equals("disulfide bond")) - { - - renderFeature(g, seq, - seq.findIndex(sequenceFeatures[sfindex].begin) - 1, - seq.findIndex(sequenceFeatures[sfindex].begin) - 1, - getColour(sequenceFeatures[sfindex]) - // new Color(((Integer) av.featuresDisplayed - // .get(sequenceFeatures[sfindex].type)).intValue()) - , start, end, y1); - renderFeature(g, seq, - seq.findIndex(sequenceFeatures[sfindex].end) - 1, - seq.findIndex(sequenceFeatures[sfindex].end) - 1, - getColour(sequenceFeatures[sfindex]) - // new Color(((Integer) av.featuresDisplayed - // .get(sequenceFeatures[sfindex].type)).intValue()) - , start, end, y1); - - } - else if (showFeature(sequenceFeatures[sfindex])) - { - if (av.showSeqFeaturesHeight - && sequenceFeatures[sfindex].score != Float.NaN) - { - renderScoreFeature(g, seq, - seq.findIndex(sequenceFeatures[sfindex].begin) - 1, - seq.findIndex(sequenceFeatures[sfindex].end) - 1, - getColour(sequenceFeatures[sfindex]), start, end, y1, - normaliseScore(sequenceFeatures[sfindex])); - } - else - { - renderFeature(g, seq, - seq.findIndex(sequenceFeatures[sfindex].begin) - 1, - seq.findIndex(sequenceFeatures[sfindex].end) - 1, - getColour(sequenceFeatures[sfindex]), start, end, y1); - } - } - - } - - } - - if (transparency != 1.0f && g != null) - { - Graphics2D g2 = (Graphics2D) g; - g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, - 1.0f)); - } - } - - Hashtable minmax = new Hashtable(); - - /** - * normalise a score against the max/min bounds for the feature type. - * - * @param sequenceFeature - * @return byte[] { signed, normalised signed (-127 to 127) or unsigned - * (0-255) value. - */ - private final byte[] normaliseScore(SequenceFeature sequenceFeature) - { - float[] mm = ((float[][]) minmax.get(sequenceFeature.type))[0]; - final byte[] r = new byte[] - { 0, (byte) 255 }; - if (mm != null) - { - if (r[0] != 0 || mm[0] < 0.0) - { - r[0] = 1; - r[1] = (byte) ((int) 128.0 + 127.0 * (sequenceFeature.score / mm[1])); - } - else - { - r[1] = (byte) ((int) 255.0 * (sequenceFeature.score / mm[1])); - } - } - return r; - } - - char s; - - int i; - - void renderFeature(Graphics g, SequenceI seq, int fstart, int fend, - Color featureColour, int start, int end, int y1) - { - - if (((fstart <= end) && (fend >= start))) - { - if (fstart < start) - { // fix for if the feature we have starts before the sequence start, - fstart = start; // but the feature end is still valid!! - } - - if (fend >= end) - { - fend = end; - } - int pady = (y1 + av.charHeight) - av.charHeight / 5; - for (i = fstart; i <= fend; i++) - { - s = seq.getCharAt(i); - - if (jalview.util.Comparison.isGap(s)) - { - continue; - } - - g.setColor(featureColour); - - g.fillRect((i - start) * av.charWidth, y1, av.charWidth, - av.charHeight); - - if (offscreenRender || !av.validCharWidth) - { - continue; - } - - g.setColor(Color.white); - charOffset = (av.charWidth - fm.charWidth(s)) / 2; - g.drawString(String.valueOf(s), charOffset - + (av.charWidth * (i - start)), pady); - - } - } - } - - void renderScoreFeature(Graphics g, SequenceI seq, int fstart, int fend, - Color featureColour, int start, int end, int y1, byte[] bs) - { - - if (((fstart <= end) && (fend >= start))) - { - if (fstart < start) - { // fix for if the feature we have starts before the sequence start, - fstart = start; // but the feature end is still valid!! - } - - if (fend >= end) - { - fend = end; - } - int pady = (y1 + av.charHeight) - av.charHeight / 5; - int ystrt = 0, yend = av.charHeight; - if (bs[0] != 0) - { - // signed - zero is always middle of residue line. - if (bs[1] < 128) - { - yend = av.charHeight * (128 - bs[1]) / 512; - ystrt = av.charHeight - yend / 2; - } - else - { - ystrt = av.charHeight / 2; - yend = av.charHeight * (bs[1] - 128) / 512; - } - } - else - { - yend = av.charHeight * bs[1] / 255; - ystrt = av.charHeight - yend; - - } - for (i = fstart; i <= fend; i++) - { - s = seq.getCharAt(i); - - if (jalview.util.Comparison.isGap(s)) - { - continue; - } - - g.setColor(featureColour); - int x = (i - start) * av.charWidth; - g.drawRect(x, y1, av.charWidth, av.charHeight); - g.fillRect(x, y1 + ystrt, av.charWidth, yend); - - if (offscreenRender || !av.validCharWidth) - { - continue; - } - - g.setColor(Color.black); - charOffset = (av.charWidth - fm.charWidth(s)) / 2; - g.drawString(String.valueOf(s), charOffset - + (av.charWidth * (i - start)), pady); - - } - } - } - - boolean newFeatureAdded = false; - - /** - * Called when alignment in associated view has new/modified features to - * discover and display. - * - */ - public void featuresAdded() - { - lastSeq = null; - findAllFeatures(); - } - - boolean findingFeatures = false; - - /** - * search the alignment for all new features, give them a colour and display - * them. Then fires a PropertyChangeEvent on the changeSupport object. - * - */ - void findAllFeatures() - { - synchronized (firing) - { - if (firing.equals(Boolean.FALSE)) - { - firing = Boolean.TRUE; - findAllFeatures(true); // add all new features as visible - changeSupport.firePropertyChange("changeSupport", null, null); - firing = Boolean.FALSE; - } - } - } - - /** - * Searches alignment for all features and updates colours - * - * @param newMadeVisible - * if true newly added feature types will be rendered immediatly - */ - synchronized void findAllFeatures(boolean newMadeVisible) - { - newFeatureAdded = false; - - if (findingFeatures) - { - newFeatureAdded = true; - return; - } - - findingFeatures = true; - - if (av.featuresDisplayed == null) - { - av.featuresDisplayed = new Hashtable(); - } - - allfeatures = new Vector(); - Vector oldfeatures = new Vector(); - if (renderOrder != null) - { - for (int i = 0; i < renderOrder.length; i++) - { - if (renderOrder[i] != null) - { - oldfeatures.addElement(renderOrder[i]); - } - } - } - if (minmax == null) - { - minmax = new Hashtable(); - } - AlignmentI alignment = av.getAlignment(); - for (int i = 0; i < alignment.getHeight(); i++) - { - SequenceFeature[] features = alignment.getSequenceAt(i) - .getDatasetSequence().getSequenceFeatures(); - - if (features == null) - { - continue; - } - - int index = 0; - while (index < features.length) - { - if (!av.featuresDisplayed.containsKey(features[index].getType())) - { - - if (featureGroups.containsKey(features[index].getType())) - { - boolean visible = ((Boolean) featureGroups - .get(features[index].featureGroup)).booleanValue(); - - if (!visible) - { - index++; - continue; - } - } - - if (!(features[index].begin == 0 && features[index].end == 0)) - { - // If beginning and end are 0, the feature is for the whole sequence - // and we don't want to render the feature in the normal way - - if (newMadeVisible - && !oldfeatures.contains(features[index].getType())) - { - // this is a new feature type on the alignment. Mark it for - // display. - av.featuresDisplayed.put(features[index].getType(), - new Integer(getColour(features[index].getType()) - .getRGB())); - setOrder(features[index].getType(), 0); - } - } - } - if (!allfeatures.contains(features[index].getType())) - { - allfeatures.addElement(features[index].getType()); - } - if (features[index].score != Float.NaN) - { - int nonpos = features[index].getBegin() >= 1 ? 0 : 1; - float[][] mm = (float[][]) minmax.get(features[index].getType()); - if (mm == null) - { - mm = new float[][] - { null, null }; - minmax.put(features[index].getType(), mm); - } - if (mm[nonpos] == null) - { - mm[nonpos] = new float[] - { features[index].score, features[index].score }; - - } - else - { - if (mm[nonpos][0] > features[index].score) - { - mm[nonpos][0] = features[index].score; - } - if (mm[nonpos][1] < features[index].score) - { - mm[nonpos][1] = features[index].score; - } - } - } - index++; - } - } - updateRenderOrder(allfeatures); - findingFeatures = false; - } - - protected Boolean firing = Boolean.FALSE; - - /** - * replaces the current renderOrder with the unordered features in - * allfeatures. The ordering of any types in both renderOrder and allfeatures - * is preserved, and all new feature types are rendered on top of the existing - * types, in the order given by getOrder or the order given in allFeatures. - * Note. this operates directly on the featureOrder hash for efficiency. TODO: - * eliminate the float storage for computing/recalling the persistent ordering - * New Cability: updates min/max for colourscheme range if its dynamic - * - * @param allFeatures - */ - private void updateRenderOrder(Vector allFeatures) - { - Vector allfeatures = new Vector(allFeatures); - String[] oldRender = renderOrder; - renderOrder = new String[allfeatures.size()]; - Object mmrange, fc = null; - boolean initOrders = (featureOrder == null); - int opos = 0; - if (oldRender != null && oldRender.length > 0) - { - for (int j = 0; j < oldRender.length; j++) - { - if (oldRender[j] != null) - { - if (initOrders) - { - setOrder(oldRender[j], (1 - (1 + (float) j) - / (float) oldRender.length)); - } - if (allfeatures.contains(oldRender[j])) - { - renderOrder[opos++] = oldRender[j]; // existing features always - // appear below new features - allfeatures.removeElement(oldRender[j]); - if (minmax != null) - { - mmrange = minmax.get(oldRender[j]); - if (mmrange != null) - { - fc = featureColours.get(oldRender[j]); - if (fc != null && fc instanceof GraduatedColor - && ((GraduatedColor) fc).isAutoScale()) - { - ((GraduatedColor) fc).updateBounds( - ((float[][]) mmrange)[0][0], - ((float[][]) mmrange)[0][1]); - } - } - } - } - } - } - } - if (allfeatures.size() == 0) - { - // no new features - leave order unchanged. - return; - } - int i = allfeatures.size() - 1; - int iSize = i; - boolean sort = false; - String[] newf = new String[allfeatures.size()]; - float[] sortOrder = new float[allfeatures.size()]; - Enumeration en = allfeatures.elements(); - // sort remaining elements - while (en.hasMoreElements()) - { - newf[i] = en.nextElement().toString(); - if (minmax != null) - { - // update from new features minmax if necessary - mmrange = minmax.get(newf[i]); - if (mmrange != null) - { - fc = featureColours.get(newf[i]); - if (fc != null && fc instanceof GraduatedColor - && ((GraduatedColor) fc).isAutoScale()) - { - ((GraduatedColor) fc).updateBounds(((float[][]) mmrange)[0][0], - ((float[][]) mmrange)[0][1]); - } - } - } - if (initOrders || !featureOrder.containsKey(newf[i])) - { - int denom = initOrders ? allfeatures.size() : featureOrder.size(); - // new unordered feature - compute persistent ordering at head of - // existing features. - setOrder(newf[i], i / (float) denom); - } - // set order from newly found feature from persisted ordering. - sortOrder[i] = 2 - ((Float) featureOrder.get(newf[i])).floatValue(); - if (i < iSize) - { - // only sort if we need to - sort = sort || sortOrder[i] > sortOrder[i + 1]; - } - i--; - } - if (iSize > 1 && sort) - { - jalview.util.QuickSort.sort(sortOrder, newf); - } - sortOrder = null; - System.arraycopy(newf, 0, renderOrder, opos, newf.length); - } - - /** - * get a feature style object for the given type string. Creates a - * java.awt.Color for a featureType with no existing colourscheme. TODO: - * replace return type with object implementing standard abstract colour/style - * interface - * - * @param featureType - * @return java.awt.Color or GraduatedColor - */ - public Object getFeatureStyle(String featureType) - { - Object fc = featureColours.get(featureType); - if (fc == null) - { - jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(); - Color col = ucs.createColourFromName(featureType); - featureColours.put(featureType, fc = col); - } - return fc; - } - - /** - * return a nominal colour for this feature - * - * @param featureType - * @return standard color, or maximum colour for graduated colourscheme - */ - public Color getColour(String featureType) - { - Object fc = getFeatureStyle(featureType); - - if (fc instanceof Color) - { - return (Color) fc; - } - else - { - if (fc instanceof GraduatedColor) - { - return ((GraduatedColor) fc).getMaxColor(); - } - } - throw new Error("Implementation Error: Unrecognised render object " - + fc.getClass() + " for features of type " + featureType); - } - - /** - * calculate the render colour for a specific feature using current feature - * settings. - * - * @param feature - * @return render colour for the given feature - */ - public Color getColour(SequenceFeature feature) - { - Object fc = getFeatureStyle(feature.getType()); - if (fc instanceof Color) - { - return (Color) fc; - } - else - { - if (fc instanceof GraduatedColor) - { - return ((GraduatedColor) fc).findColor(feature); - } - } - throw new Error("Implementation Error: Unrecognised render object " - + fc.getClass() + " for features of type " + feature.getType()); - } - - private boolean showFeature(SequenceFeature sequenceFeature) - { - Object fc = getFeatureStyle(sequenceFeature.type); - if (fc instanceof GraduatedColor) - { - return ((GraduatedColor) fc).isColored(sequenceFeature); - } - else - { - return true; - } - } - // // ///////////// // // Feature Editing Dialog // // Will be refactored in next release. @@ -1256,7 +335,7 @@ public class FeatureRenderer extends jalview.viewmodel.FeatureRenderer implement sf.description = lastDescriptionAdded; setColour(sf.type, fcol); - av.featuresDisplayed.put(sf.type, getColour(sf.type)); + getFeaturesDisplayed().setVisible(sf.type); try { @@ -1277,27 +356,20 @@ public class FeatureRenderer extends jalview.viewmodel.FeatureRenderer implement for (int i = 0; i < sequences.length; i++) { features[i].type = lastFeatureAdded; - if (lastFeatureGroupAdded != null) - features[i].featureGroup = lastFeatureGroupAdded; + // fix for JAL-1538 - always set feature group here + features[i].featureGroup = lastFeatureGroupAdded; features[i].description = lastDescriptionAdded; sequences[i].addSequenceFeature(features[i]); ffile.parseDescriptionHTML(features[i], false); } - if (av.featuresDisplayed == null) - { - av.featuresDisplayed = new Hashtable(); - } - + if (lastFeatureGroupAdded != null) { - if (featureGroups == null) - featureGroups = new Hashtable(); - featureGroups.put(lastFeatureGroupAdded, new Boolean(true)); + setGroupVisibility(lastFeatureGroupAdded, true); } setColour(lastFeatureAdded, fcol); - av.featuresDisplayed.put(lastFeatureAdded, - getColour(lastFeatureAdded)); + setVisible(lastFeatureAdded); findAllFeatures(false); @@ -1316,6 +388,7 @@ public class FeatureRenderer extends jalview.viewmodel.FeatureRenderer implement return true; } + /** * update the amend feature button dependent on the given style * @@ -1343,145 +416,4 @@ public class FeatureRenderer extends jalview.viewmodel.FeatureRenderer implement // colour.setForeground(colour.getBackground()); } } - - public void setColour(String featureType, Object col) - { - // overwrite - // Color _col = (col instanceof Color) ? ((Color) col) : (col instanceof - // GraduatedColor) ? ((GraduatedColor) col).getMaxColor() : null; - // Object c = featureColours.get(featureType); - // if (c == null || c instanceof Color || (c instanceof GraduatedColor && - // !((GraduatedColor)c).getMaxColor().equals(_col))) - { - featureColours.put(featureType, col); - } - } - - public void setTransparency(float value) - { - transparency = value; - } - - public float getTransparency() - { - return transparency; - } - - /** - * Replace current ordering with new ordering - * - * @param data - * { String(Type), Colour(Type), Boolean(Displayed) } - */ - public void setFeaturePriority(Object[][] data) - { - setFeaturePriority(data, true); - } - - /** - * - * @param data - * { String(Type), Colour(Type), Boolean(Displayed) } - * @param visibleNew - * when true current featureDisplay list will be cleared - */ - public void setFeaturePriority(Object[][] data, boolean visibleNew) - { - if (visibleNew) - { - if (av.featuresDisplayed != null) - { - av.featuresDisplayed.clear(); - } - else - { - av.featuresDisplayed = new Hashtable(); - } - } - if (data == null) - { - return; - } - - // The feature table will display high priority - // features at the top, but theses are the ones - // we need to render last, so invert the data - renderOrder = new String[data.length]; - - if (data.length > 0) - { - for (int i = 0; i < data.length; i++) - { - String type = data[i][0].toString(); - setColour(type, data[i][1]); // todo : typesafety - feature color - // interface object - if (((Boolean) data[i][2]).booleanValue()) - { - av.featuresDisplayed.put(type, new Integer(getColour(type) - .getRGB())); - } - - renderOrder[data.length - i - 1] = type; - } - } - - } - - Map featureOrder = null; - - /** - * analogous to colour - store a normalized ordering for all feature types in - * this rendering context. - * - * @param type - * Feature type string - * @param position - * normalized priority - 0 means always appears on top, 1 means - * always last. - */ - public float setOrder(String type, float position) - { - if (featureOrder == null) - { - featureOrder = new Hashtable(); - } - featureOrder.put(type, new Float(position)); - return position; - } - - /** - * get the global priority (0 (top) to 1 (bottom)) - * - * @param type - * @return [0,1] or -1 for a type without a priority - */ - public float getOrder(String type) - { - if (featureOrder != null) - { - if (featureOrder.containsKey(type)) - { - return ((Float) featureOrder.get(type)).floatValue(); - } - } - return -1; - } - - /** - * @param listener - * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener) - */ - public void addPropertyChangeListener(PropertyChangeListener listener) - { - changeSupport.addPropertyChangeListener(listener); - } - - /** - * @param listener - * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener) - */ - public void removePropertyChangeListener(PropertyChangeListener listener) - { - changeSupport.removePropertyChangeListener(listener); - } } diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 3dae4e5..d30f5a0 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -33,6 +33,7 @@ import javax.swing.event.*; import javax.swing.table.*; import jalview.analysis.AlignmentSorter; +import jalview.api.FeaturesDisplayedI; import jalview.bin.Cache; import jalview.commands.OrderCommand; import jalview.datamodel.*; @@ -58,6 +59,8 @@ public class FeatureSettings extends JPanel Object[][] originalData; + private float originalTransparency; + final JInternalFrame frame; JScrollPane scrollPane = new JScrollPane(); @@ -74,8 +77,8 @@ public class FeatureSettings extends JPanel { this.af = af; fr = af.getFeatureRenderer(); - - transparency.setMaximum(100 - (int) (fr.transparency * 100)); + // allow transparency to be recovered + transparency.setMaximum(100 - (int) ((originalTransparency=fr.getTransparency()) * 100)); try { @@ -104,8 +107,8 @@ public class FeatureSettings extends JPanel if (evt.isPopupTrigger()) { popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0), - table.getValueAt(selectedRow, 1), fr.minmax, evt.getX(), - evt.getY()); + table.getValueAt(selectedRow, 1), fr.getMinMax(), + evt.getX(), evt.getY()); } else if (evt.getClickCount() == 2) { @@ -150,8 +153,7 @@ public class FeatureSettings extends JPanel dassourceBrowser = new DasSourceBrowser(this); dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER); - if (af.getViewport().featuresDisplayed == null - || fr.renderOrder == null) + if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder()) { fr.findAllFeatures(true); // display everything! } @@ -216,7 +218,7 @@ public class FeatureSettings extends JPanel public void actionPerformed(ActionEvent e) { - me.sortByScore(new String[] + me.af.avc.sortAlignmentByFeatureScore(new String[] { type }); } @@ -228,7 +230,7 @@ public class FeatureSettings extends JPanel public void actionPerformed(ActionEvent e) { - me.sortByDens(new String[] + me.af.avc.sortAlignmentByFeatureDensity(new String[] { type }); } @@ -352,10 +354,6 @@ public class FeatureSettings extends JPanel synchronized public void setTableData() { - if (fr.featureGroups == null) - { - fr.featureGroups = new Hashtable(); - } Vector allFeatures = new Vector(); Vector allGroups = new Vector(); SequenceFeature[] tmpfeatures; @@ -386,10 +384,7 @@ public class FeatureSettings extends JPanel if (!allGroups.contains(group)) { allGroups.addElement(group); - if (group != null) - { - checkGroupState(group); - } + checkGroupState(group); } } @@ -407,21 +402,14 @@ public class FeatureSettings extends JPanel } /** + * Synchronise gui group list and check visibility of group * * @param group - * @return true if group has been seen before and is already added to set. + * @return true if group is visible */ private boolean checkGroupState(String group) { - boolean visible; - if (fr.featureGroups.containsKey(group)) - { - visible = ((Boolean) fr.featureGroups.get(group)).booleanValue(); - } - else - { - visible = true; // new group is always made visible - } + boolean visible = fr.checkGroupVisibility(group, true); if (groupPanel == null) { @@ -442,10 +430,8 @@ public class FeatureSettings extends JPanel if (alreadyAdded) { - return true; + return visible; } - - fr.featureGroups.put(group, new Boolean(visible)); final String grp = group; final JCheckBox check = new JCheckBox(group, visible); check.setFont(new Font("Serif", Font.BOLD, 12)); @@ -453,8 +439,7 @@ public class FeatureSettings extends JPanel { public void itemStateChanged(ItemEvent evt) { - fr.featureGroups.put(check.getText(), - new Boolean(check.isSelected())); + fr.setGroupVisibility(check.getText(), check.isSelected()); af.alignPanel.seqPanel.seqCanvas.repaint(); if (af.alignPanel.overviewPanel != null) { @@ -466,7 +451,7 @@ public class FeatureSettings extends JPanel } }); groupPanel.add(check); - return false; + return visible; } boolean resettingTable = false; @@ -510,11 +495,8 @@ public class FeatureSettings extends JPanel continue; } - if (group == null || fr.featureGroups.get(group) == null - || ((Boolean) fr.featureGroups.get(group)).booleanValue()) + if (group == null || checkGroupState(group)) { - if (group != null) - checkGroupState(group); type = tmpfeatures[index].getType(); if (!visibleChecks.contains(type)) { @@ -549,17 +531,20 @@ public class FeatureSettings extends JPanel Object[][] data = new Object[fSize][3]; int dataIndex = 0; - if (fr.renderOrder != null) + if (fr.hasRenderOrder()) { if (!handlingUpdate) + { fr.findAllFeatures(groupChanged != null); // prod to update - // colourschemes. but don't - // affect display - // First add the checks in the previous render order, - // in case the window has been closed and reopened - for (int ro = fr.renderOrder.length - 1; ro > -1; ro--) + // colourschemes. but don't + // affect display + // First add the checks in the previous render order, + // in case the window has been closed and reopened + } + List frl = fr.getRenderOrder(); + for (int ro = frl.size() - 1; ro > -1; ro--) { - type = fr.renderOrder[ro]; + type = frl.get(ro); if (!visibleChecks.contains(type)) { @@ -568,8 +553,8 @@ public class FeatureSettings extends JPanel data[dataIndex][0] = type; data[dataIndex][1] = fr.getFeatureStyle(type); - data[dataIndex][2] = new Boolean( - af.getViewport().featuresDisplayed.containsKey(type)); + data[dataIndex][2] = new Boolean(af.getViewport() + .getFeaturesDisplayed().isVisible(type)); dataIndex++; visibleChecks.removeElement(type); } @@ -587,7 +572,7 @@ public class FeatureSettings extends JPanel if (data[dataIndex][1] == null) { // "Colour has been updated in another view!!" - fr.renderOrder = null; + fr.clearRenderOrder(); return; } @@ -609,8 +594,8 @@ public class FeatureSettings extends JPanel if (groupPanel != null) { - groupPanel.setLayout(new GridLayout(fr.featureGroups.size() / 4 + 1, - 4)); + groupPanel.setLayout(new GridLayout( + fr.getFeatureGroupsSize() / 4 + 1, 4)); groupPanel.validate(); bigPanel.add(groupPanel, BorderLayout.NORTH); @@ -761,9 +746,10 @@ public class FeatureSettings extends JPanel PrintWriter out = new PrintWriter(new OutputStreamWriter( new FileOutputStream(choice), "UTF-8")); - Iterator e = fr.featureColours.keySet().iterator(); - float[] sortOrder = new float[fr.featureColours.size()]; - String[] sortTypes = new String[fr.featureColours.size()]; + Set fr_colours = fr.getAllFeatureColours(); + Iterator e = fr_colours.iterator(); + float[] sortOrder = new float[fr_colours.size()]; + String[] sortTypes = new String[fr_colours.size()]; int i = 0; while (e.hasNext()) { @@ -976,7 +962,7 @@ public class FeatureSettings extends JPanel { public void actionPerformed(ActionEvent e) { - sortByScore(null); + af.avc.sortAlignmentByFeatureScore(null); } }); sortByDens.setFont(JvSwingUtils.getLabelFont()); @@ -986,7 +972,7 @@ public class FeatureSettings extends JPanel { public void actionPerformed(ActionEvent e) { - sortByDens(null); + af.avc.sortAlignmentByFeatureDensity(null); } }); cancel.setFont(JvSwingUtils.getLabelFont()); @@ -995,6 +981,7 @@ public class FeatureSettings extends JPanel { public void actionPerformed(ActionEvent e) { + fr.setTransparency(originalTransparency); updateFeatureRenderer(originalData); close(); } @@ -1086,131 +1073,6 @@ public class FeatureSettings extends JPanel settingsPane.add(buttonPanel, java.awt.BorderLayout.SOUTH); } - protected void sortByDens(String[] typ) - { - sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY); - } - - protected void sortBy(String[] typ, String methodText, final String method) - { - if (typ == null) - { - typ = getDisplayedFeatureTypes(); - } - String gps[] = null; - gps = getDisplayedFeatureGroups(); - if (typ != null) - { - ArrayList types = new ArrayList(); - for (int i = 0; i < typ.length; i++) - { - if (typ[i] != null) - { - types.add(typ[i]); - } - typ = new String[types.size()]; - types.toArray(typ); - } - } - if (gps != null) - { - ArrayList grps = new ArrayList(); - - for (int i = 0; i < gps.length; i++) - { - if (gps[i] != null) - { - grps.add(gps[i]); - } - } - gps = new String[grps.size()]; - grps.toArray(gps); - } - AlignmentPanel alignPanel = af.alignPanel; - AlignmentI al = alignPanel.av.getAlignment(); - - int start, stop; - SequenceGroup sg = alignPanel.av.getSelectionGroup(); - if (sg != null) - { - start = sg.getStartRes(); - stop = sg.getEndRes(); - } - else - { - start = 0; - stop = al.getWidth(); - } - SequenceI[] oldOrder = al.getSequencesArray(); - AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method); - af.addHistoryItem(new OrderCommand(methodText, oldOrder, alignPanel.av - .getAlignment())); - alignPanel.paintAlignment(true); - - } - - protected void sortByScore(String[] typ) - { - sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE); - } - - private String[] getDisplayedFeatureTypes() - { - String[] typ = null; - if (fr != null) - { - synchronized (fr.renderOrder) - { - typ = new String[fr.renderOrder.length]; - System.arraycopy(fr.renderOrder, 0, typ, 0, typ.length); - for (int i = 0; i < typ.length; i++) - { - if (af.viewport.featuresDisplayed.get(typ[i]) == null) - { - typ[i] = null; - } - } - } - } - return typ; - } - - private String[] getDisplayedFeatureGroups() - { - String[] gps = null; - ArrayList _gps = new ArrayList(); - if (fr != null) - { - - if (fr.featureGroups != null) - { - Iterator en = fr.featureGroups.keySet().iterator(); - int g = 0; - boolean valid = false; - while (en.hasNext()) - { - String gp = (String) en.next(); - Boolean on = (Boolean) fr.featureGroups.get(gp); - if (on != null && on.booleanValue()) - { - valid = true; - _gps.add(gp); - } - } - if (!valid) - { - return null; - } - else - { - gps = new String[_gps.size()]; - _gps.toArray(gps); - } - } - } - return gps; - } - public void fetchDAS_actionPerformed(ActionEvent e) { fetchDAS.setEnabled(false); diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index ee779f7..30a8a5e 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -100,7 +100,7 @@ public class IdPanel extends JPanel implements MouseListener, seqAnnotReport .createSequenceAnnotationReport(tip, sequence, av.isShowDbRefs(), av.isShowNpFeats(), - sp.seqCanvas.fr.minmax); + sp.seqCanvas.fr.getMinMax()); setToolTipText("" + sequence.getDisplayId(true) + " " + tip.toString() + ""); } diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 3ab5a8d..d7453c8 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -42,6 +42,8 @@ import jalview.schemes.*; import jalview.util.Platform; import jalview.util.jarInputStreamProvider; import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.seqfeatures.FeatureRendererSettings; +import jalview.viewmodel.seqfeatures.FeaturesDisplayed; import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.dm.AAConSettings; import jalview.ws.jws2.jabaws2.Jws2Instance; @@ -1081,11 +1083,12 @@ public class Jalview2XML view.setFollowHighlight(av.followHighlight); view.setFollowSelection(av.followSelection); view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus()); - if (av.featuresDisplayed != null) + if (av.getFeaturesDisplayed() != null) { jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings(); - String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder; + String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer() + .getRenderOrder().toArray(new String[0]); Vector settingsAdded = new Vector(); Object gstyle = null; @@ -1116,8 +1119,8 @@ public class Jalview2XML .getColour(renderOrder[ro]).getRGB()); } - setting.setDisplay(av.featuresDisplayed - .containsKey(renderOrder[ro])); + setting.setDisplay(av.getFeaturesDisplayed().isVisible( + renderOrder[ro])); float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer() .getOrder(renderOrder[ro]); if (rorder > -1) @@ -1130,8 +1133,8 @@ public class Jalview2XML } // Make sure we save none displayed feature settings - Iterator en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours - .keySet().iterator(); + Iterator en = ap.seqPanel.seqCanvas.getFeatureRenderer() + .getFeatureColours().keySet().iterator(); while (en.hasNext()) { String key = en.next().toString(); @@ -1155,8 +1158,9 @@ public class Jalview2XML fs.addSetting(setting); settingsAdded.addElement(key); } - en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups - .keySet().iterator(); + // is groups actually supposed to be a map here ? + en = ap.seqPanel.seqCanvas.getFeatureRenderer().getFeatureGroups() + .iterator(); Vector groupsAdded = new Vector(); while (en.hasNext()) { @@ -1168,7 +1172,7 @@ public class Jalview2XML Group g = new Group(); g.setName(grp); g.setDisplay(((Boolean) ap.seqPanel.seqCanvas - .getFeatureRenderer().featureGroups.get(grp)) + .getFeatureRenderer().checkGroupVisibility(grp, false)) .booleanValue()); fs.addGroup(g); groupsAdded.addElement(grp); @@ -3500,9 +3504,14 @@ public class Jalview2XML // recover featre settings if (jms.getFeatureSettings() != null) { - af.viewport.featuresDisplayed = new Hashtable(); + FeaturesDisplayed fdi; + af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed()); String[] renderOrder = new String[jms.getFeatureSettings() .getSettingCount()]; + Hashtable featureGroups = new Hashtable(); + Hashtable featureColours = new Hashtable(); + Hashtable featureOrder = new Hashtable(); + for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++) { Setting setting = jms.getFeatureSettings().getSetting(fs); @@ -3529,37 +3538,42 @@ public class Jalview2XML gc.setColourByLabel(setting.getColourByLabel()); } // and put in the feature colour table. - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour( - setting.getType(), gc); + featureColours.put(setting.getType(), gc); } else { - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour( - setting.getType(), + featureColours.put(setting.getType(), new java.awt.Color(setting.getColour())); } renderOrder[fs] = setting.getType(); if (setting.hasOrder()) - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder( - setting.getType(), setting.getOrder()); + { + featureOrder.put(setting.getType(), setting.getOrder()); + } else - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder( - setting.getType(), - fs / jms.getFeatureSettings().getSettingCount()); + { + featureOrder.put(setting.getType(), new Float(fs + / jms.getFeatureSettings().getSettingCount())); + } if (setting.getDisplay()) { - af.viewport.featuresDisplayed.put(setting.getType(), new Integer( - setting.getColour())); + fdi.setVisible(setting.getType()); } } - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder; - Hashtable fgtable; - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable(); + Hashtable 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); + af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer() + .transferSettings(frs); + } if (view.getHiddenColumnsCount() > 0) diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java index 718677c..f246fd3 100755 --- a/src/jalview/gui/Jalview2XML_V1.java +++ b/src/jalview/gui/Jalview2XML_V1.java @@ -27,10 +27,12 @@ import java.util.jar.*; import javax.swing.*; import org.exolab.castor.xml.*; + import jalview.binding.*; import jalview.schemes.*; import jalview.util.MessageManager; import jalview.util.jarInputStreamProvider; +import jalview.viewmodel.seqfeatures.FeatureRendererSettings; /** * DOCUMENT ME! @@ -394,25 +396,27 @@ public class Jalview2XML_V1 if (jms.getFeatureSettings() != null) { - af.viewport.featuresDisplayed = new Hashtable(); + Hashtable featuresDisplayed = new Hashtable(); + Hashtable featureColours = new Hashtable(); String[] renderOrder = new String[jms.getFeatureSettings() .getSettingCount()]; for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++) { Setting setting = jms.getFeatureSettings().getSetting(fs); - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour( + featureColours.put( setting.getType(), new java.awt.Color(setting.getColour())); renderOrder[fs] = setting.getType(); if (setting.getDisplay()) { - af.viewport.featuresDisplayed.put(setting.getType(), new Integer( + featuresDisplayed.put(setting.getType(), new Integer( setting.getColour())); } } - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder; + FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, new Hashtable(), featureColours, 1.0f, null); + af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(frs); } af.setMenusFromViewport(af.viewport); diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java index 5edf218..8829692 100755 --- a/src/jalview/gui/OverviewPanel.java +++ b/src/jalview/gui/OverviewPanel.java @@ -67,7 +67,7 @@ public class OverviewPanel extends JPanel implements Runnable // main visible SeqCanvas SequenceRenderer sr; - FeatureRenderer fr; + jalview.renderer.seqfeatures.FeatureRenderer fr; /** * Creates a new OverviewPanel object. diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 3cf4fe0..6b5040e 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1470,7 +1470,7 @@ public class PopupMenu extends JPopupMenu true, true, false, - (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax + (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.getMinMax() : null); contents.append("

"); } diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 4c2cff2..a13d5f6 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -225,42 +225,6 @@ public class SeqPanel extends JPanel implements MouseListener, return seq; } - SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res) - { - Vector tmp = new Vector(); - SequenceFeature[] features = sequence.getSequenceFeatures(); - if (features != null) - { - for (int i = 0; i < features.length; i++) - { - if (av.featuresDisplayed == null - || !av.featuresDisplayed.containsKey(features[i].getType())) - { - continue; - } - - if (features[i].featureGroup != null - && seqCanvas.fr.featureGroups != null - && seqCanvas.fr.featureGroups - .containsKey(features[i].featureGroup) - && !((Boolean) seqCanvas.fr.featureGroups - .get(features[i].featureGroup)).booleanValue()) - continue; - - if ((features[i].getBegin() <= res) - && (features[i].getEnd() >= res)) - { - tmp.addElement(features[i]); - } - } - } - - features = new SequenceFeature[tmp.size()]; - tmp.copyInto(features); - - return features; - } - void endEditing() { if (editCommand != null && editCommand.getSize() > 0) @@ -729,11 +693,11 @@ public class SeqPanel extends JPanel implements MouseListener, if (av.isShowSequenceFeatures()) { int rpos; - SequenceFeature[] features = findFeaturesAtRes( + List features = ap.getFeatureRenderer().findFeaturesAtRes( sequence.getDatasetSequence(), rpos = sequence.findPosition(res)); seqARep.appendFeatures(tooltipText, rpos, features, - this.ap.seqPanel.seqCanvas.fr.minmax); + this.ap.seqPanel.seqCanvas.fr.getMinMax()); } if (tooltipText.length() == 6) // { @@ -1370,21 +1334,21 @@ public class SeqPanel extends JPanel implements MouseListener, av.setSelectionGroup(null); } - SequenceFeature[] features = findFeaturesAtRes( + List features = seqCanvas.getFeatureRenderer().findFeaturesAtRes( sequence.getDatasetSequence(), sequence.findPosition(findRes(evt))); - if (features != null && features.length > 0) + if (features != null && features.size()> 0) { SearchResults highlight = new SearchResults(); - highlight.addResult(sequence, features[0].getBegin(), - features[0].getEnd()); + highlight.addResult(sequence, features.get(0).getBegin(), + features.get(0).getEnd()); seqCanvas.highlightSearchResults(highlight); } - if (features != null && features.length > 0) + if (features != null && features.size()> 0) { seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[] - { sequence }, features, false, ap); + { sequence }, features.toArray(new SequenceFeature[features.size()]), false, ap); seqCanvas.highlightSearchResults(null); } @@ -1499,16 +1463,16 @@ public class SeqPanel extends JPanel implements MouseListener, if (javax.swing.SwingUtilities.isRightMouseButton(evt)) { - SequenceFeature[] allFeatures = findFeaturesAtRes( + List allFeatures = ap.getFeatureRenderer().findFeaturesAtRes( sequence.getDatasetSequence(), sequence.findPosition(res)); Vector links = new Vector(); - for (int i = 0; i < allFeatures.length; i++) + for (SequenceFeature sf:allFeatures) { - if (allFeatures[i].links != null) + if (sf.links != null) { - for (int j = 0; j < allFeatures[i].links.size(); j++) + for (int j = 0; j < sf.links.size(); j++) { - links.addElement(allFeatures[i].links.elementAt(j)); + links.addElement(sf.links.elementAt(j)); } } } diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java index 87b829f..5b621e7 100755 --- a/src/jalview/io/FeaturesFile.java +++ b/src/jalview/io/FeaturesFile.java @@ -678,7 +678,7 @@ public class FeaturesFile extends AlignFile * hash of feature types and colours * @return features file contents */ - public String printJalviewFormat(SequenceI[] seqs, Hashtable visible) + public String printJalviewFormat(SequenceI[] seqs, Map visible) { return printJalviewFormat(seqs, visible, true, true); } @@ -697,7 +697,7 @@ public class FeaturesFile extends AlignFile * of group or type) * @return features file contents */ - public String printJalviewFormat(SequenceI[] seqs, Hashtable visible, + public String printJalviewFormat(SequenceI[] seqs, Map visible, boolean visOnly, boolean nonpos) { StringBuffer out = new StringBuffer(); @@ -714,11 +714,11 @@ public class FeaturesFile extends AlignFile // write feature colours only if we're given them and we are generating // viewed features // TODO: decide if feature links should also be written here ? - Enumeration en = visible.keys(); + Iterator en = visible.keySet().iterator(); String type, color; - while (en.hasMoreElements()) + while (en.hasNext()) { - type = en.nextElement().toString(); + type = en.next().toString(); if (visible.get(type) instanceof GraduatedColor) { @@ -926,12 +926,12 @@ public class FeaturesFile extends AlignFile * @param visible * @return */ - public String printGFFFormat(SequenceI[] seqs, Hashtable visible) + public String printGFFFormat(SequenceI[] seqs, Map visible) { return printGFFFormat(seqs, visible, true, true); } - public String printGFFFormat(SequenceI[] seqs, Hashtable visible, + public String printGFFFormat(SequenceI[] seqs, Map visible, boolean visOnly, boolean nonpos) { StringBuffer out = new StringBuffer(); diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java index ac7f5b3..af5fc03 100755 --- a/src/jalview/io/HTMLOutput.java +++ b/src/jalview/io/HTMLOutput.java @@ -34,7 +34,7 @@ public class HTMLOutput SequenceRenderer sr; - FeatureRenderer fr; + jalview.renderer.seqfeatures.FeatureRenderer fr; Color color; diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java index 6fba9c6..1757239 100644 --- a/src/jalview/io/SequenceAnnotationReport.java +++ b/src/jalview/io/SequenceAnnotationReport.java @@ -22,6 +22,7 @@ package jalview.io; import java.util.ArrayList; import java.util.Hashtable; +import java.util.List; import java.util.Vector; import jalview.datamodel.DBRefEntry; @@ -54,30 +55,30 @@ public class SequenceAnnotationReport * TODO refactor to Jalview 'utilities' somehow. */ public void appendFeatures(final StringBuffer tooltipText2, int rpos, - SequenceFeature[] features) + List features) { appendFeatures(tooltipText2, rpos, features, null); } public void appendFeatures(final StringBuffer tooltipText2, int rpos, - SequenceFeature[] features, Hashtable minmax) + List features, Hashtable minmax) { String tmpString; if (features != null) { - for (int i = 0; i < features.length; i++) + for (SequenceFeature feature:features) { - if (features[i].getType().equals("disulfide bond")) + if (feature.getType().equals("disulfide bond")) { - if (features[i].getBegin() == rpos - || features[i].getEnd() == rpos) + if (feature.getBegin() == rpos + || feature.getEnd() == rpos) { if (tooltipText2.length() > 6) { tooltipText2.append("
"); } - tooltipText2.append("disulfide bond " + features[i].getBegin() - + ":" + features[i].getEnd()); + tooltipText2.append("disulfide bond " + feature.getBegin() + + ":" + feature.getEnd()); } } else @@ -87,25 +88,25 @@ public class SequenceAnnotationReport tooltipText2.append("
"); } // TODO: remove this hack to display link only features - boolean linkOnly = features[i].getValue("linkonly") != null; + boolean linkOnly = feature.getValue("linkonly") != null; if (!linkOnly) { - tooltipText2.append(features[i].getType() + " "); + tooltipText2.append(feature.getType() + " "); if (rpos != 0) { // we are marking a positional feature - tooltipText2.append(features[i].begin); + tooltipText2.append(feature.begin); } - if (features[i].begin != features[i].end) + if (feature.begin != feature.end) { - tooltipText2.append(" " + features[i].end); + tooltipText2.append(" " + feature.end); } - if (features[i].getDescription() != null - && !features[i].description.equals(features[i] + if (feature.getDescription() != null + && !feature.description.equals(feature .getType())) { - tmpString = features[i].getDescription(); + tmpString = feature.getDescription(); String tmp2up = tmpString.toUpperCase(); int startTag = tmp2up.indexOf(""); if (startTag > -1) @@ -150,27 +151,27 @@ public class SequenceAnnotationReport } } // check score should be shown - if (features[i].getScore() != Float.NaN) + if (feature.getScore() != Float.NaN) { float[][] rng = (minmax == null) ? null : ((float[][]) minmax - .get(features[i].getType())); + .get(feature.getType())); if (rng != null && rng[0] != null && rng[0][0] != rng[0][1]) { - tooltipText2.append(" Score=" + features[i].getScore()); + tooltipText2.append(" Score=" + feature.getScore()); } } - if (features[i].getValue("status") != null) + if (feature.getValue("status") != null) { - String status = features[i].getValue("status").toString(); + String status = feature.getValue("status").toString(); if (status.length() > 0) { - tooltipText2.append("; (" + features[i].getValue("status") + tooltipText2.append("; (" + feature.getValue("status") + ")"); } } } } - if (features[i].links != null) + if (feature.links != null) { if (linkImageURL != null) { @@ -178,7 +179,7 @@ public class SequenceAnnotationReport } else { - for (String urlstring : (Vector) features[i].links) + for (String urlstring : (Vector) feature.links) { try { @@ -364,7 +365,6 @@ public class SequenceAnnotationReport // ADD NON POSITIONAL SEQUENCE INFO SequenceFeature[] features = ds.getSequenceFeatures(); - SequenceFeature[] tfeat = new SequenceFeature[1]; if (showNpFeats && features != null) { for (int i = 0; i < features.length; i++) @@ -372,7 +372,8 @@ public class SequenceAnnotationReport if (features[i].begin == 0 && features[i].end == 0) { int sz = -tip.length(); - tfeat[0] = features[i]; + List tfeat = new ArrayList(); + tfeat.add(features[i]); appendFeatures(tip, 0, tfeat, minmax); sz += tip.length(); maxWidth = Math.max(maxWidth, sz); diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java new file mode 100644 index 0000000..909ee10 --- /dev/null +++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java @@ -0,0 +1,435 @@ +package jalview.renderer.seqfeatures; + +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; + +import java.awt.AlphaComposite; +import java.awt.Color; +import java.awt.FontMetrics; +import java.awt.Graphics; +import java.awt.Graphics2D; +import java.awt.image.BufferedImage; + +public class FeatureRenderer extends + jalview.viewmodel.seqfeatures.FeatureRendererModel +{ + + FontMetrics fm; + + int charOffset; + + boolean offscreenRender = false; + + /** + * DOCUMENT ME! + * + * @param g + * DOCUMENT ME! + * @param seq + * DOCUMENT ME! + * @param sg + * DOCUMENT ME! + * @param start + * DOCUMENT ME! + * @param end + * DOCUMENT ME! + * @param x1 + * DOCUMENT ME! + * @param y1 + * DOCUMENT ME! + * @param width + * DOCUMENT ME! + * @param height + * DOCUMENT ME! + */ + protected SequenceI lastSeq; + + char s; + + int i; + + int av_charHeight, av_charWidth; + + boolean av_validCharWidth, av_isShowSeqFeatureHeight; + + protected void updateAvConfig() + { + av_charHeight = av.getCharHeight(); + av_charWidth = av.getCharWidth(); + av_validCharWidth = av.isValidCharWidth(); + av_isShowSeqFeatureHeight = av.isShowSequenceFeaturesHeight(); + } + + void renderFeature(Graphics g, SequenceI seq, int fstart, int fend, + Color featureColour, int start, int end, int y1) + { + updateAvConfig(); + if (((fstart <= end) && (fend >= start))) + { + if (fstart < start) + { // fix for if the feature we have starts before the sequence start, + fstart = start; // but the feature end is still valid!! + } + + if (fend >= end) + { + fend = end; + } + int pady = (y1 + av_charHeight) - av_charHeight / 5; + for (i = fstart; i <= fend; i++) + { + s = seq.getCharAt(i); + + if (jalview.util.Comparison.isGap(s)) + { + continue; + } + + g.setColor(featureColour); + + g.fillRect((i - start) * av_charWidth, y1, av_charWidth, + av_charHeight); + + if (offscreenRender || !av_validCharWidth) + { + continue; + } + + g.setColor(Color.white); + charOffset = (av_charWidth - fm.charWidth(s)) / 2; + g.drawString(String.valueOf(s), charOffset + + (av_charWidth * (i - start)), pady); + + } + } + } + + void renderScoreFeature(Graphics g, SequenceI seq, int fstart, int fend, + Color featureColour, int start, int end, int y1, byte[] bs) + { + updateAvConfig(); + if (((fstart <= end) && (fend >= start))) + { + if (fstart < start) + { // fix for if the feature we have starts before the sequence start, + fstart = start; // but the feature end is still valid!! + } + + if (fend >= end) + { + fend = end; + } + int pady = (y1 + av_charHeight) - av_charHeight / 5; + int ystrt = 0, yend = av_charHeight; + if (bs[0] != 0) + { + // signed - zero is always middle of residue line. + if (bs[1] < 128) + { + yend = av_charHeight * (128 - bs[1]) / 512; + ystrt = av_charHeight - yend / 2; + } + else + { + ystrt = av_charHeight / 2; + yend = av_charHeight * (bs[1] - 128) / 512; + } + } + else + { + yend = av_charHeight * bs[1] / 255; + ystrt = av_charHeight - yend; + + } + for (i = fstart; i <= fend; i++) + { + s = seq.getCharAt(i); + + if (jalview.util.Comparison.isGap(s)) + { + continue; + } + + g.setColor(featureColour); + int x = (i - start) * av_charWidth; + g.drawRect(x, y1, av_charWidth, av_charHeight); + g.fillRect(x, y1 + ystrt, av_charWidth, yend); + + if (offscreenRender || !av_validCharWidth) + { + continue; + } + + g.setColor(Color.black); + charOffset = (av_charWidth - fm.charWidth(s)) / 2; + g.drawString(String.valueOf(s), charOffset + + (av_charWidth * (i - start)), pady); + + } + } + } + + BufferedImage offscreenImage; + + public Color findFeatureColour(Color initialCol, SequenceI seq, int res) + { + return new Color(findFeatureColour(initialCol.getRGB(), seq, res)); + } + + /** + * This is used by the Molecule Viewer and Overview to get the accurate + * colourof the rendered sequence + */ + public synchronized int findFeatureColour(int initialCol, final SequenceI seq, + int column) + { + if (!av.isShowSequenceFeatures()) + { + return initialCol; + } + + final SequenceI aseq = (seq.getDatasetSequence() != null) ? seq + .getDatasetSequence() : seq; + if (seq != lastSeq) + { + lastSeq = seq; + sequenceFeatures = aseq.getSequenceFeatures(); + if (sequenceFeatures != null) + { + sfSize = sequenceFeatures.length; + } + } + else + { + if (sequenceFeatures != lastSeq.getSequenceFeatures()) + { + sequenceFeatures = lastSeq.getSequenceFeatures(); + if (sequenceFeatures != null) + { + sfSize = sequenceFeatures.length; + } + } + } + + if (sequenceFeatures == null || sfSize == 0) + { + return initialCol; + } + + if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column))) + { + return Color.white.getRGB(); + } + + // Only bother making an offscreen image if transparency is applied + if (transparency != 1.0f && offscreenImage == null) + { + offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB); + } + + currentColour = null; + // TODO: non-threadsafe - each rendering thread needs its own instance of + // the feature renderer - or this should be synchronized. + offscreenRender = true; + + if (offscreenImage != null) + { + offscreenImage.setRGB(0, 0, initialCol); + drawSequence(offscreenImage.getGraphics(), lastSeq, column, column, 0); + + return offscreenImage.getRGB(0, 0); + } + else + { + drawSequence(null, lastSeq, lastSeq.findPosition(column), -1, -1); + + if (currentColour == null) + { + return initialCol; + } + else + { + return ((Integer) currentColour).intValue(); + } + } + + } + + private volatile SequenceFeature[] sequenceFeatures; + + int sfSize; + + int sfindex; + + int spos; + + int epos; + + public synchronized void drawSequence(Graphics g, final SequenceI seq, + int start, int end, int y1) + { + final SequenceI aseq = (seq.getDatasetSequence() != null) ? seq + .getDatasetSequence() : seq; + if (aseq.getSequenceFeatures() == null + || aseq.getSequenceFeatures().length == 0) + { + return; + } + + if (g != null) + { + fm = g.getFontMetrics(); + } + + updateFeatures(); + + if (lastSeq == null || seq != lastSeq + || aseq.getSequenceFeatures() != sequenceFeatures) + { + lastSeq = seq; + sequenceFeatures = aseq.getSequenceFeatures(); + } + + if (transparency != 1 && g != null) + { + Graphics2D g2 = (Graphics2D) g; + g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, + transparency)); + } + + if (!offscreenRender) + { + spos = lastSeq.findPosition(start); + epos = lastSeq.findPosition(end); + } + + sfSize = sequenceFeatures.length; + String type; + for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++) + { + type = renderOrder[renderIndex]; + + if (type == null || !showFeatureOfType(type)) + { + continue; + } + + // loop through all features in sequence to find + // current feature to render + for (sfindex = 0; sfindex < sfSize; sfindex++) + { + if (!sequenceFeatures[sfindex].type.equals(type)) + { + continue; + } + + if (featureGroups != null + && sequenceFeatures[sfindex].featureGroup != null + && sequenceFeatures[sfindex].featureGroup.length() != 0 + && featureGroups + .containsKey(sequenceFeatures[sfindex].featureGroup) + && !((Boolean) featureGroups + .get(sequenceFeatures[sfindex].featureGroup)) + .booleanValue()) + { + continue; + } + + if (!offscreenRender + && (sequenceFeatures[sfindex].getBegin() > epos || sequenceFeatures[sfindex] + .getEnd() < spos)) + { + continue; + } + + if (offscreenRender && offscreenImage == null) + { + if (sequenceFeatures[sfindex].begin <= start + && sequenceFeatures[sfindex].end >= start) + { + // this is passed out to the overview and other sequence renderers + // (e.g. molecule viewer) to get displayed colour for rendered + // sequence + currentColour = new Integer( + getColour(sequenceFeatures[sfindex]).getRGB()); + // used to be retreived from av.featuresDisplayed + // currentColour = av.featuresDisplayed + // .get(sequenceFeatures[sfindex].type); + + } + } + else if (sequenceFeatures[sfindex].type.equals("disulfide bond")) + { + + renderFeature(g, seq, + seq.findIndex(sequenceFeatures[sfindex].begin) - 1, + seq.findIndex(sequenceFeatures[sfindex].begin) - 1, + getColour(sequenceFeatures[sfindex]) + // new Color(((Integer) av.featuresDisplayed + // .get(sequenceFeatures[sfindex].type)).intValue()) + , start, end, y1); + renderFeature(g, seq, + seq.findIndex(sequenceFeatures[sfindex].end) - 1, + seq.findIndex(sequenceFeatures[sfindex].end) - 1, + getColour(sequenceFeatures[sfindex]) + // new Color(((Integer) av.featuresDisplayed + // .get(sequenceFeatures[sfindex].type)).intValue()) + , start, end, y1); + + } + else if (showFeature(sequenceFeatures[sfindex])) + { + if (av_isShowSeqFeatureHeight + && sequenceFeatures[sfindex].score != Float.NaN) + { + renderScoreFeature(g, seq, + seq.findIndex(sequenceFeatures[sfindex].begin) - 1, + seq.findIndex(sequenceFeatures[sfindex].end) - 1, + getColour(sequenceFeatures[sfindex]), start, end, y1, + normaliseScore(sequenceFeatures[sfindex])); + } + else + { + renderFeature(g, seq, + seq.findIndex(sequenceFeatures[sfindex].begin) - 1, + seq.findIndex(sequenceFeatures[sfindex].end) - 1, + getColour(sequenceFeatures[sfindex]), start, end, y1); + } + } + + } + + } + + if (transparency != 1.0f && g != null && transparencyAvailable) + { + Graphics2D g2 = (Graphics2D) g; + g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, + 1.0f)); + } + } + + boolean transparencyAvailable = true; + + protected void setTransparencyAvailable(boolean isTransparencyAvailable) + { + transparencyAvailable = isTransparencyAvailable; + } + + @Override + public boolean isTransparencyAvailable() + { + return transparencyAvailable; + } + + /** + * Called when alignment in associated view has new/modified features to + * discover and display. + * + */ + public void featuresAdded() + { + lastSeq = null; + findAllFeatures(); + } +} diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java index a53004d..c3b6c1e 100644 --- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java +++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java @@ -252,7 +252,7 @@ public abstract class FeatureRendererModel implements { for (int i = 0; i < features.length; i++) { - if (av.areFeaturesDisplayed() + if (!av.areFeaturesDisplayed() || !av.getFeaturesDisplayed().isVisible( features[i].getType())) { diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java index 7ab1781..1fa4663 100644 --- a/src/jalview/ws/AWSThread.java +++ b/src/jalview/ws/AWSThread.java @@ -28,7 +28,7 @@ import jalview.datamodel.AlignmentView; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; import jalview.gui.WebserviceInfo; -import jalview.gui.FeatureRenderer.FeatureRendererSettings; +import jalview.viewmodel.seqfeatures.FeatureRendererSettings; public abstract class AWSThread extends Thread { -- 1.7.10.2