X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=75ce63acee4ad33ddebddde613bbdcd9c4169fc8;hb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;hp=04324ac428b51193bb187fb9486d428f92541626;hpb=cbfa4d2bc1282662ad88756f1b0b2d8b3b82bd11;p=jalview.git diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index 04324ac..75ce63a 100755 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -1,17 +1,17 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * + * 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 + * * 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 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. - * + * * 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 @@ -29,42 +29,52 @@ import java.beans.PropertyChangeSupport; import javax.swing.*; import jalview.datamodel.*; +import jalview.schemes.GraduatedColor; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ public class FeatureRenderer { AlignmentPanel ap; + AlignViewport av; + Color resBoxColour; + + /** + * global transparency for feature + */ float transparency = 1.0f; + FontMetrics fm; + int charOffset; Hashtable featureColours = new Hashtable(); // A higher level for grouping features of a // particular type - Hashtable featureGroups = null; + Hashtable featureGroups = new Hashtable(); // This is actually an Integer held in the hashtable, // Retrieved using the key feature type Object currentColour; String[] renderOrder; - PropertyChangeSupport changeSupport=new PropertyChangeSupport(this); + + PropertyChangeSupport changeSupport = new PropertyChangeSupport(this); Vector allfeatures; /** * Creates a new FeatureRenderer object. - * + * * @param av - * DOCUMENT ME! + * DOCUMENT ME! */ public FeatureRenderer(AlignmentPanel ap) { @@ -72,6 +82,53 @@ public class FeatureRenderer this.av = ap.av; } + public class FeatureRendererSettings implements Cloneable + { + String[] renderOrder; + + Hashtable featureGroups; + + Hashtable featureColours; + + float transparency; + + Hashtable 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; + } + + public FeatureRendererSettings(FeatureRenderer fr) + { + this.renderOrder = fr.renderOrder; + this.featureGroups = fr.featureGroups; + this.featureColours = fr.featureColours; + this.transparency = fr.transparency; + this.featureOrder = 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; + } public void transferSettings(FeatureRenderer fr) { @@ -83,11 +140,12 @@ public class FeatureRenderer } BufferedImage offscreenImage; + boolean offscreenRender = false; + public Color findFeatureColour(Color initialCol, SequenceI seq, int res) { - return new Color(findFeatureColour(initialCol.getRGB(), - seq, res)); + return new Color(findFeatureColour(initialCol.getRGB(), seq, res)); } /** @@ -105,13 +163,15 @@ public class FeatureRenderer { lastSeq = seq; sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures(); - if (sequenceFeatures!=null) + if (sequenceFeatures != null) { sfSize = sequenceFeatures.length; } } - if (sequenceFeatures!=lastSeq.getDatasetSequence().getSequenceFeatures()) { + if (sequenceFeatures != lastSeq.getDatasetSequence() + .getSequenceFeatures()) + { sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures(); if (sequenceFeatures != null) { @@ -119,12 +179,11 @@ public class FeatureRenderer } } - if (sequenceFeatures == null) + if (sequenceFeatures == null || sfSize == 0) { return initialCol; } - if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column))) { return Color.white.getRGB(); @@ -143,18 +202,13 @@ public class FeatureRenderer if (offscreenImage != null) { offscreenImage.setRGB(0, 0, initialCol); - drawSequence(offscreenImage.getGraphics(), - lastSeq, - column, column, 0); + drawSequence(offscreenImage.getGraphics(), lastSeq, column, column, 0); return offscreenImage.getRGB(0, 0); } else { - drawSequence(null, - lastSeq, - lastSeq.findPosition(column), - -1, -1); + drawSequence(null, lastSeq, lastSeq.findPosition(column), -1, -1); if (currentColour == null) { @@ -162,7 +216,7 @@ public class FeatureRenderer } else { - return ( (Integer) currentColour).intValue(); + return ((Integer) currentColour).intValue(); } } @@ -170,37 +224,45 @@ 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; SequenceI lastSeq; + SequenceFeature[] sequenceFeatures; + int sfSize, sfindex, spos, epos; - public void drawSequence(Graphics g, SequenceI seq, - int start, int end, int y1) + /** + * 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) + || seq.getDatasetSequence().getSequenceFeatures().length == 0) { return; } @@ -210,9 +272,8 @@ public class FeatureRenderer fm = g.getFontMetrics(); } - if (av.featuresDisplayed == null - || renderOrder == null - || newFeatureAdded) + if (av.featuresDisplayed == null || renderOrder == null + || newFeatureAdded) { findAllFeatures(); if (av.featuresDisplayed.size() < 1) @@ -221,23 +282,21 @@ public class FeatureRenderer } sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures(); - sfSize = sequenceFeatures.length; } - if (lastSeq == null || seq != lastSeq - || seq.getDatasetSequence().getSequenceFeatures()!=sequenceFeatures) + if (lastSeq == null + || seq != lastSeq + || seq.getDatasetSequence().getSequenceFeatures() != sequenceFeatures) { lastSeq = seq; sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures(); - sfSize = sequenceFeatures.length; } if (transparency != 1 && g != null) { Graphics2D g2 = (Graphics2D) g; - g2.setComposite( - AlphaComposite.getInstance( - AlphaComposite.SRC_OVER, transparency)); + g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, + transparency)); } if (!offscreenRender) @@ -246,6 +305,7 @@ public class FeatureRenderer epos = lastSeq.findPosition(end); } + sfSize = sequenceFeatures.length; String type; for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++) { @@ -260,68 +320,90 @@ public class FeatureRenderer // current feature to render for (sfindex = 0; sfindex < sfSize; sfindex++) { - if (sequenceFeatures.length <= sfindex) - { - continue; - } 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()) + && 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)) + if (!offscreenRender + && (sequenceFeatures[sfindex].getBegin() > epos || sequenceFeatures[sfindex] + .getEnd() < spos)) { continue; } if (offscreenRender && offscreenImage == null) { - if (sequenceFeatures[sfindex].begin <= start && - sequenceFeatures[sfindex].end >= start) + if (sequenceFeatures[sfindex].begin <= start + && sequenceFeatures[sfindex].end >= start) { - currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex]. - type); + // 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, - 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); + 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 - { - renderFeature(g, seq, - seq.findIndex(sequenceFeatures[sfindex].begin) - 1, + 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].type), - start, end, y1); - } + 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); + } + } } @@ -330,20 +412,49 @@ public class FeatureRenderer if (transparency != 1.0f && g != null) { Graphics2D g2 = (Graphics2D) g; - g2.setComposite( - AlphaComposite.getInstance( - AlphaComposite.SRC_OVER, 1.0f)); + 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) + + 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 <= end) && (fend >= start))) { if (fstart < start) { // fix for if the feature we have starts before the sequence start, @@ -366,7 +477,8 @@ public class FeatureRenderer g.setColor(featureColour); - g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight); + g.fillRect((i - start) * av.charWidth, y1, av.charWidth, + av.charHeight); if (offscreenRender || !av.validCharWidth) { @@ -375,48 +487,121 @@ public class FeatureRenderer g.setColor(Color.white); charOffset = (av.charWidth - fm.charWidth(s)) / 2; - g.drawString(String.valueOf(s), - charOffset + (av.charWidth * (i - start)), - pady); + 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. - * + * Called when alignment in associated view has new/modified features to + * discover and display. + * */ public void featuresAdded() { - lastSeq=null; + 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. - * + * */ - synchronized void findAllFeatures() + void findAllFeatures() { - findAllFeatures(true); // add all new features as visible - if (!firing) { - firing=true; - changeSupport.firePropertyChange("changeSupport",null,null); - firing=false; + 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 + * if true newly added feature types will be rendered + * immediatly */ - synchronized void findAllFeatures(boolean newMadeVisible) { + synchronized void findAllFeatures(boolean newMadeVisible) + { newFeatureAdded = false; if (findingFeatures) @@ -434,20 +619,24 @@ public class FeatureRenderer allfeatures = new Vector(); Vector oldfeatures = new Vector(); - if (renderOrder!=null) + if (renderOrder != null) { - for (int i=0; i=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=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. + * 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) { + private void updateRenderOrder(Vector allFeatures) + { Vector allfeatures = new Vector(allFeatures); String[] oldRender = renderOrder; renderOrder = new String[allfeatures.size()]; - boolean initOrders=(featureOrder==null); - int opos=0; - if (oldRender!=null && oldRender.length>0) + Object mmrange,fc=null; + boolean initOrders = (featureOrder == null); + int opos = 0; + if (oldRender != null && oldRender.length > 0) { - for (int j=0; jsortOrder[i+1]; + sort = sort || sortOrder[i] > sortOrder[i + 1]; } i--; } - if (iSize>1 && sort) + if (iSize > 1 && sort) + { jalview.util.QuickSort.sort(sortOrder, newf); - sortOrder=null; + } + sortOrder = null; System.arraycopy(newf, 0, renderOrder, opos, newf.length); } + public Color getColour(String featureType) { - if (!featureColours.containsKey(featureType)) + Object fc = featureColours.get(featureType); + if (fc == null) { - jalview.schemes.UserColourScheme ucs = new - jalview.schemes.UserColourScheme(); + jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(); Color col = ucs.createColourFromName(featureType); featureColours.put(featureType, col); return col; } + else if (fc instanceof Color) + { + return (Color) fc; + } + else + { + if (fc instanceof GraduatedColor) + { + return ((GraduatedColor) fc).getMaxColor(); + } + // TODO: raise an implementation error here. + return null; // Color.white; + } + } + + /** + * implement graduated colouring for features with scores + * + * @param feature + * @return render colour for the given feature + */ + 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) + { + return (Color) fc; + } else - return (Color) featureColours.get(featureType); + { + if (fc instanceof GraduatedColor) + { + return ((GraduatedColor) fc).findColor(feature); + } + // TODO: raise an implementation error here. + return null; // Color.white; + } + } + private boolean showFeature(SequenceFeature sequenceFeature) + { + Object fc = featureColours.get(sequenceFeature.type); + if (fc instanceof GraduatedColor) + { + return ((GraduatedColor) fc).isColored(sequenceFeature); + } else { return true; } } + static String lastFeatureAdded; + static String lastFeatureGroupAdded; + static String lastDescriptionAdded; int featureIndex = 0; + boolean amendFeatures(final SequenceI[] sequences, - final SequenceFeature[] features, - boolean newFeatures, - final AlignmentPanel ap) + final SequenceFeature[] features, boolean newFeatures, + final AlignmentPanel ap) { featureIndex = 0; @@ -613,9 +916,9 @@ public class FeatureRenderer { public void mousePressed(MouseEvent evt) { + // TODO: use featurecolourchooser here Color col = JColorChooser.showDialog(Desktop.desktop, - "Select Feature Colour", - colour.getBackground()); + "Select Feature Colour", colour.getBackground()); if (col != null) colour.setBackground(col); @@ -625,62 +928,59 @@ public class FeatureRenderer JPanel tmp = new JPanel(); JPanel panel = new JPanel(new GridLayout(3, 1)); - /////////////////////////////////////// - ///MULTIPLE FEATURES AT SELECTED RESIDUE - if(!newFeatures && features.length>1) - { - panel = new JPanel(new GridLayout(4, 1)); - tmp = new JPanel(); - tmp.add(new JLabel("Select Feature: ")); - overlaps = new JComboBox(); - for(int i=0; i 1) + { + panel = new JPanel(new GridLayout(4, 1)); + tmp = new JPanel(); + tmp.add(new JLabel("Select Feature: ")); + overlaps = new JComboBox(); + for (int i = 0; i < features.length; i++) + { + overlaps.addItem(features[i].getType() + "/" + + features[i].getBegin() + "-" + features[i].getEnd() + + " (" + features[i].getFeatureGroup() + ")"); + } + + tmp.add(overlaps); + + overlaps.addItemListener(new ItemListener() + { + public void itemStateChanged(ItemEvent e) + { + int index = overlaps.getSelectedIndex(); + if (index != -1) + { + featureIndex = index; + name.setText(features[index].getType()); + description.setText(features[index].getDescription()); + source.setText(features[index].getFeatureGroup()); + start.setValue(new Integer(features[index].getBegin())); + end.setValue(new Integer(features[index].getEnd())); + + SearchResults highlight = new SearchResults(); + highlight.addResult(sequences[0], features[index].getBegin(), + features[index].getEnd()); + + ap.seqPanel.seqCanvas.highlightSearchResults(highlight); + + } + Color col = getColour(name.getText()); + if (col == null) + { + col = new jalview.schemes.UserColourScheme() + .createColourFromName(name.getText()); + } + + colour.setBackground(col); + } + }); + + panel.add(tmp); + } + // //////// + // //////////////////////////////////// tmp = new JPanel(); panel.add(tmp); @@ -746,7 +1046,7 @@ public class FeatureRenderer } } - if(newFeatures) + if (newFeatures) { name.setText(lastFeatureAdded); source.setText(lastFeatureGroupAdded); @@ -762,36 +1062,28 @@ public class FeatureRenderer description.setText(features[0].getDescription()); colour.setBackground(getColour(name.getText())); - Object[] options; if (!newFeatures) { options = new Object[] - { - "Amend", "Delete", "Cancel"}; + { "Amend", "Delete", "Cancel" }; } else { options = new Object[] - { - "OK", "Cancel"}; + { "OK", "Cancel" }; } - String title = newFeatures ? "Create New Sequence Feature(s)" : - "Amend/Delete Features for " - + sequences[0].getName(); + String title = newFeatures ? "Create New Sequence Feature(s)" + : "Amend/Delete Features for " + sequences[0].getName(); int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop, - bigPanel, - title, - JOptionPane.YES_NO_CANCEL_OPTION, - JOptionPane.QUESTION_MESSAGE, - null, - options, "OK"); + bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION, + JOptionPane.QUESTION_MESSAGE, null, options, "OK"); jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile(); - if (reply == JOptionPane.OK_OPTION && name.getText().length()>0) + if (reply == JOptionPane.OK_OPTION && name.getText().length() > 0) { // This ensures that the last sequence // is refreshed and new features are rendered @@ -800,7 +1092,7 @@ public class FeatureRenderer lastFeatureGroupAdded = source.getText().trim(); lastDescriptionAdded = description.getText().replaceAll("\n", " "); - if(lastFeatureGroupAdded.length()<1) + if (lastFeatureGroupAdded.length() < 1) lastFeatureGroupAdded = null; } @@ -819,29 +1111,29 @@ public class FeatureRenderer sf.description = lastDescriptionAdded; setColour(sf.type, colour.getBackground()); - av.featuresDisplayed.put(sf.type, - new Integer(colour.getBackground().getRGB())); + av.featuresDisplayed.put(sf.type, new Integer(colour + .getBackground().getRGB())); try { - sf.begin = ( (Integer) start.getValue()).intValue(); - sf.end = ( (Integer) end.getValue()).intValue(); + sf.begin = ((Integer) start.getValue()).intValue(); + sf.end = ((Integer) end.getValue()).intValue(); + } catch (NumberFormatException ex) + { } - catch (NumberFormatException ex) - {} ffile.parseDescriptionHTML(sf, false); } } - else //NEW FEATURES ADDED + else + // NEW FEATURES ADDED { - if (reply == JOptionPane.OK_OPTION - && lastFeatureAdded.length()>0) + if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0) { for (int i = 0; i < sequences.length; i++) { features[i].type = lastFeatureAdded; - if (lastFeatureGroupAdded!=null) + if (lastFeatureGroupAdded != null) features[i].featureGroup = lastFeatureGroupAdded; features[i].description = lastDescriptionAdded; sequences[i].addSequenceFeature(features[i]); @@ -863,13 +1155,12 @@ public class FeatureRenderer Color col = colour.getBackground(); setColour(lastFeatureAdded, colour.getBackground()); av.featuresDisplayed.put(lastFeatureAdded, - new Integer(col.getRGB())); + new Integer(col.getRGB())); findAllFeatures(false); ap.paintAlignment(true); - return true; } else @@ -885,7 +1176,11 @@ public class FeatureRenderer public void setColour(String featureType, Color col) { - featureColours.put(featureType, col); + 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) @@ -897,23 +1192,29 @@ public class FeatureRenderer { return transparency; } + /** * Replace current ordering with new ordering - * @param data { String(Type), Colour(Type), Boolean(Displayed) } + * + * @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 + * + * @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(); @@ -923,7 +1224,7 @@ public class FeatureRenderer av.featuresDisplayed = new Hashtable(); } } - if (data==null) + if (data == null) { return; } @@ -939,9 +1240,10 @@ public class FeatureRenderer { String type = data[i][0].toString(); setColour(type, (Color) data[i][1]); - if ( ( (Boolean) data[i][2]).booleanValue()) + if (((Boolean) data[i][2]).booleanValue()) { - av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB())); + av.featuresDisplayed.put(type, new Integer(getColour(type) + .getRGB())); } renderOrder[data.length - i - 1] = type; @@ -949,38 +1251,42 @@ public class FeatureRenderer } } - Hashtable featureOrder=null; + + Hashtable featureOrder = null; + /** * analogous to colour - store a normalized ordering for all feature types in * this rendering context. - * + * * @param type - * Feature type string + * Feature type string * @param position - * normalized priority - 0 means always appears on top, 1 means - * always last. + * normalized priority - 0 means always appears on top, 1 means + * always last. */ public float setOrder(String type, float position) { - if (featureOrder==null) + 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) + public float getOrder(String type) + { + if (featureOrder != null) { if (featureOrder.containsKey(type)) { - return ((Float)featureOrder.get(type)).floatValue(); + return ((Float) featureOrder.get(type)).floatValue(); } } return -1;