X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=244b650a13306cf81f8fe34282fdd638f9bce1e7;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=08b09704372fecffb4638433255b895f84f80105;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java index 08b0970..244b650 100755 --- a/src/jalview/appletgui/FeatureRenderer.java +++ b/src/jalview/appletgui/FeatureRenderer.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.appletgui; @@ -26,6 +25,7 @@ import java.awt.event.*; import jalview.appletgui.FeatureSettings.MyCheckbox; import jalview.datamodel.*; +import jalview.schemes.AnnotationColourGradient; import jalview.schemes.GraduatedColor; /** @@ -34,7 +34,7 @@ import jalview.schemes.GraduatedColor; * @author $author$ * @version $Revision$ */ -public class FeatureRenderer +public class FeatureRenderer implements jalview.api.FeatureRenderer { AlignViewport av; @@ -66,7 +66,7 @@ public class FeatureRenderer * Creates a new FeatureRenderer object. * * @param av - * DOCUMENT ME! + * DOCUMENT ME! */ public FeatureRenderer(AlignViewport av) { @@ -84,6 +84,23 @@ public class FeatureRenderer 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); + } + } + } } static String lastFeatureAdded; @@ -96,7 +113,98 @@ public class FeatureRenderer boolean deleteFeature = false; - Panel colourPanel; + FeatureColourPanel colourPanel; + + class FeatureColourPanel extends Panel + { + String label = ""; + + private Color maxCol; + + private boolean isColourByLabel, isGcol; + + /** + * render a feature style in the amend feature dialog box + */ + public void updateColor(Object newcol) + { + + Color bg, col = null; + GraduatedColor gcol = null; + String vlabel = ""; + if (newcol instanceof Color) + { + isGcol = false; + col = (Color) newcol; + gcol = null; + } + else if (newcol instanceof GraduatedColor) + { + isGcol = true; + gcol = (GraduatedColor) newcol; + col = null; + } + else + { + throw new Error("Invalid color for MyCheckBox"); + } + if (col != null) + { + setBackground(bg = col); + } + else + { + if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD) + { + vlabel += " " + + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)" + : "(<)"); + } + if (isColourByLabel = gcol.isColourByLabel()) + { + setBackground(bg = Color.white); + vlabel += " (by Label)"; + } + else + { + setBackground(bg = gcol.getMinColor()); + maxCol = gcol.getMaxColor(); + } + } + label = vlabel; + setBackground(bg); + repaint(); + } + + FeatureColourPanel() + { + super(null); + } + + public void paint(Graphics g) + { + Dimension d = getSize(); + if (isGcol) + { + if (isColourByLabel) + { + g.setColor(Color.white); + g.fillRect(d.width / 2, 0, d.width / 2, d.height); + g.setColor(Color.black); + Font f = new Font("Verdana", Font.PLAIN, 10); + g.setFont(f); + g.drawString("Label", 0, 0); + } + else + { + g.setColor(maxCol); + g.fillRect(d.width / 2, 0, d.width / 2, d.height); + + } + } + } + + } boolean amendFeatures(final SequenceI[] sequences, final SequenceFeature[] features, boolean newFeatures, @@ -112,12 +220,13 @@ public class FeatureRenderer Button deleteButton = new Button("Delete"); deleteFeature = false; - colourPanel = new Panel(null); + colourPanel = new FeatureColourPanel(); colourPanel.setSize(110, 15); final FeatureRenderer fr = this; Panel panel = new Panel(new GridLayout(3, 1)); + featureIndex = 0; // feature to be amended. Panel tmp; // ///////////////////////////////////// @@ -162,14 +271,14 @@ public class FeatureRenderer ap.seqPanel.seqCanvas.highlightSearchResults(highlight); } - Color col = getColour(name.getText()); + Object col = getFeatureStyle(name.getText()); if (col == null) { col = new jalview.schemes.UserColourScheme() .createColourFromName(name.getText()); } - colourPanel.setBackground(col); + colourPanel.updateColor(col); } }); @@ -271,26 +380,33 @@ public class FeatureRenderer start.setText(features[0].getBegin() + ""); end.setText(features[0].getEnd() + ""); description.setText(features[0].getDescription()); - Color col = getColour(name.getText()); if (col == null) { col = new jalview.schemes.UserColourScheme() .createColourFromName(name.getText()); } - - colourPanel.setBackground(col); - + Object fcol = getFeatureStyle(name.getText()); + // simply display the feature color in a box + colourPanel.updateColor(fcol); dialog.setResizable(true); - + // TODO: render the graduated color in the box. colourPanel.addMouseListener(new java.awt.event.MouseAdapter() { public void mousePressed(java.awt.event.MouseEvent evt) { - new UserDefinedColours(fr, ap.alignFrame); + if (!colourPanel.isGcol) + { + new UserDefinedColours(fr, ap.alignFrame); + } + else + { + FeatureColourChooser fcc = new FeatureColourChooser( + ap.alignFrame, name.getText()); + dialog.transferFocus(); + } } }); - dialog.setVisible(true); jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile(); @@ -310,14 +426,18 @@ public class FeatureRenderer if (!newFeatures) { - SequenceFeature sf = features[featureIndex]; + SequenceFeature sf = features[featureIndex]; if (dialog.accept) { sf.type = lastFeatureAdded; sf.featureGroup = lastFeatureGroupAdded; sf.description = lastDescriptionAdded; - setColour(sf.type, colourPanel.getBackground()); + if (!colourPanel.isGcol) + { + // update colour - otherwise its already done. + setColour(sf.type, colourPanel.getBackground()); + } try { sf.begin = Integer.parseInt(start.getText()); @@ -358,32 +478,38 @@ public class FeatureRenderer } col = colourPanel.getBackground(); - setColour(lastFeatureAdded, col); + // setColour(lastFeatureAdded, fcol); if (lastFeatureGroupAdded != null) { featureGroups.put(lastFeatureGroupAdded, new Boolean(true)); - av.featuresDisplayed.put(lastFeatureGroupAdded, new Integer(col - .getRGB())); } + if (fcol instanceof Color) + { + setColour(lastFeatureAdded, fcol); + } + 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; - - ap.paintAlignment(true); - - return true; } else { + // no update to the alignment return false; } } - - findAllFeatures(); + // refresh the alignment and the feature settings dialog + if (av.featureSettings != null) + { + av.featureSettings.refreshTable(); + } + // findAllFeatures(); ap.paintAlignment(true); @@ -434,23 +560,23 @@ public class FeatureRenderer * DOCUMENT ME! * * @param g - * DOCUMENT ME! + * DOCUMENT ME! * @param seq - * DOCUMENT ME! + * DOCUMENT ME! * @param sg - * DOCUMENT ME! + * DOCUMENT ME! * @param start - * DOCUMENT ME! + * DOCUMENT ME! * @param end - * DOCUMENT ME! + * DOCUMENT ME! * @param x1 - * DOCUMENT ME! + * DOCUMENT ME! * @param y1 - * DOCUMENT ME! + * DOCUMENT ME! * @param width - * DOCUMENT ME! + * DOCUMENT ME! * @param height - * DOCUMENT ME! + * DOCUMENT ME! */ // String type; // SequenceFeature sf; @@ -543,38 +669,40 @@ public class FeatureRenderer if (sequenceFeatures[sfindex].begin <= start && sequenceFeatures[sfindex].end >= start) { - currentColour = new Integer(getColour(sequenceFeatures[sfindex]).getRGB());//av.featuresDisplayed - //.get(sequenceFeatures[sfindex].type); + currentColour = new Integer( + getColour(sequenceFeatures[sfindex]).getRGB());// av.featuresDisplayed + // .get(sequenceFeatures[sfindex].type); } } else if (sequenceFeatures[sfindex].type.equals("disulfide bond")) { - renderFeature( - g, - seq, + renderFeature(g, seq, seq.findIndex(sequenceFeatures[sfindex].begin) - 1, seq.findIndex(sequenceFeatures[sfindex].begin) - 1, - new Color(((Integer) av.featuresDisplayed - .get(sequenceFeatures[sfindex].type)).intValue()), - start, end, y1); - renderFeature( - g, - seq, + 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, - new Color(((Integer) av.featuresDisplayed - .get(sequenceFeatures[sfindex].type)).intValue()), - start, end, y1); + getColour(sequenceFeatures[sfindex]) + // new Color(((Integer) av.featuresDisplayed + // .get(sequenceFeatures[sfindex].type)).intValue()) + , start, end, y1); } else { - renderFeature(g, seq, seq - .findIndex(sequenceFeatures[sfindex].begin) - 1, seq - .findIndex(sequenceFeatures[sfindex].end) - 1, - getColour(sequenceFeatures[sfindex]), start, end, y1); + 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); + } } } @@ -634,7 +762,23 @@ public class FeatureRenderer } } } - Hashtable minmax=null; + + 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(); @@ -642,7 +786,7 @@ public class FeatureRenderer av.featuresDisplayed = new Hashtable(); Vector allfeatures = new Vector(); minmax = new Hashtable(); - + for (int i = 0; i < av.alignment.getHeight(); i++) { SequenceFeature[] features = av.alignment.getSequenceAt(i) @@ -656,7 +800,8 @@ public class FeatureRenderer int index = 0; while (index < features.length) { - if (features[index].begin==0 && features[index].end==0) { + if (features[index].begin == 0 && features[index].end == 0) + { index++; continue; } @@ -664,27 +809,29 @@ public class FeatureRenderer { if (getColour(features[index].getType()) == null) { - featureColours.put(features[index].getType(), ucs - .createColourFromName(features[index].getType())); + 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) + if (features[index].score != Float.NaN) { - int nonpos= features[index].getBegin()>=1 ? 0 : 1; + int nonpos = features[index].getBegin() >= 1 ? 0 : 1; float[][] mm = (float[][]) minmax.get(features[index].getType()); if (mm == null) { - mm = new float[][] {null, 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 }; - + if (mm[nonpos] == null) + { + mm[nonpos] = new float[] + { features[index].score, features[index].score }; + } else { @@ -698,7 +845,7 @@ public class FeatureRenderer } } } - + index++; } } @@ -713,17 +860,32 @@ public class FeatureRenderer } } - public Color getColour(String featureType) + /** + * 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, col); - return col; + featureColours.put(featureType, fc = col); } - else if (fc instanceof Color) + return fc; + } + + public Color getColour(String featureType) + { + Object fc = getFeatureStyle(featureType); + + if (fc instanceof Color) { return (Color) fc; } @@ -733,10 +895,29 @@ public class FeatureRenderer { return ((GraduatedColor) fc).getMaxColor(); } - // TODO: raise an implementation error here. - return null; // Color.white; + } + 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 * @@ -745,15 +926,8 @@ public class FeatureRenderer */ public Color getColour(SequenceFeature feature) { - Object fc = featureColours.get(feature.type); - if (fc == null) - { - jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(); - Color col = ucs.createColourFromName(feature.type); - featureColours.put(feature.type, col); - return col; - } - else if (fc instanceof Color) + Object fc = getFeatureStyle(feature.getType()); + if (fc instanceof Color) { return (Color) fc; } @@ -763,14 +937,22 @@ public class FeatureRenderer { return ((GraduatedColor) fc).findColor(feature); } - // TODO: raise an implementation error here. - return null; // Color.white; } + throw new Error("Implementation Error: Unrecognised render object " + + fc.getClass() + " for features of type " + feature.getType()); } - public void setColour(String featureType, Color col) + public void setColour(String featureType, Object col) { - featureColours.put(featureType, 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) @@ -796,7 +978,7 @@ public class FeatureRenderer for (int i = 0; i < data.length; i++) { String type = data[i][0].toString(); - setColour(type, (Color) data[i][1]); + setColour(type, data[i][1]); if (((Boolean) data[i][2]).booleanValue()) { av.featuresDisplayed.put(type, new Integer(getColour(type) @@ -832,7 +1014,7 @@ public class FeatureRenderer * get visible or invisible groups * * @param visible - * true to return visible groups, false to return hidden ones. + * true to return visible groups, false to return hidden ones. * @return list of groups */ public String[] getGroups(boolean visible) @@ -869,9 +1051,9 @@ public class FeatureRenderer * set all feature groups in toset to be visible or invisible * * @param toset - * group names + * group names * @param visible - * the state of the named groups to set + * the state of the named groups to set */ public void setGroupState(String[] toset, boolean visible) { @@ -1049,6 +1231,7 @@ public class FeatureRenderer return alignmentHasFeatures; } + /** * * @return the displayed feature type as an array of strings @@ -1065,9 +1248,9 @@ public class FeatureRenderer if (av.featuresDisplayed.get(typ[i]) == null) { typ[i] = null; - } - } + } } + } return typ; } }