X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=ac56590446bbb586fd553c8bc3a512c32cffe75d;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=c59ec1d34de071d39f97795e610146f7e63dfeb7;hpb=4f1f764c09427cd63c3e355fa729da86735a8194;p=jalview.git diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java old mode 100755 new mode 100644 index c59ec1d..ac56590 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -1,856 +1,486 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 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 + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * 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. - * - * 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 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 + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; -import java.awt.image.*; -import java.beans.PropertyChangeListener; -import java.beans.PropertyChangeSupport; - -import javax.swing.*; - -import jalview.datamodel.*; +import jalview.api.FeatureColourI; +import jalview.datamodel.SearchResults; +import jalview.datamodel.SearchResultsI; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.io.FeaturesFile; +import jalview.schemes.FeatureColour; +import jalview.util.ColorUtils; +import jalview.util.MessageManager; + +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.GridLayout; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; +import java.util.Arrays; +import java.util.Comparator; +import java.util.List; + +import javax.swing.JColorChooser; +import javax.swing.JComboBox; +import javax.swing.JLabel; +import javax.swing.JPanel; +import javax.swing.JScrollPane; +import javax.swing.JSpinner; +import javax.swing.JTextArea; +import javax.swing.JTextField; +import javax.swing.SwingConstants; +import javax.swing.event.DocumentEvent; +import javax.swing.event.DocumentListener; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ -public class FeatureRenderer +public class FeatureRenderer extends + jalview.renderer.seqfeatures.FeatureRenderer { - AlignViewport av; - Color resBoxColour; - 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; + /* + * defaults for creating a new feature are the last created + * feature type and group + */ + static String lastFeatureAdded = "feature_1"; - // This is actually an Integer held in the hashtable, - // Retrieved using the key feature type - Object currentColour; + static String lastFeatureGroupAdded = "Jalview"; - String[] renderOrder; - PropertyChangeSupport changeSupport=new PropertyChangeSupport(this); + Color resBoxColour; - Vector allfeatures; + AlignmentPanel ap; /** - * Creates a new FeatureRenderer object. - * - * @param av - * DOCUMENT ME! + * Creates a new FeatureRenderer object + * + * @param alignPanel */ - public FeatureRenderer(AlignViewport av) + public FeatureRenderer(AlignmentPanel alignPanel) { - this.av = av; + super(alignPanel.av); + this.ap = alignPanel; + if (alignPanel.getSeqPanel() != null + && alignPanel.getSeqPanel().seqCanvas != null + && alignPanel.getSeqPanel().seqCanvas.fr != null) + { + transferSettings(alignPanel.getSeqPanel().seqCanvas.fr); + } } - public void transferSettings(FeatureRenderer fr) - { - renderOrder = fr.renderOrder; - featureGroups = fr.featureGroups; - featureColours = fr.featureColours; - transparency = fr.transparency; - featureOrder = fr.featureOrder; - } + FeatureColourI oldcol, fcol; - BufferedImage offscreenImage; - boolean offscreenRender = false; - public Color findFeatureColour(Color initialCol, SequenceI seq, int res) - { - return new Color(findFeatureColour(initialCol.getRGB(), - seq, res)); - } + int featureIndex = 0; /** - * This is used by the Molecule Viewer and Overview to get the accurate - * colourof the rendered sequence + * Presents a dialog allowing the user to add new features, or amend or delete + * existing features. Currently this can be on + * + * If the supplied feature type is null, show (and update on confirm) the type + * and group of the last new feature created (with initial defaults of + * "feature_1" and "Jalview"). + * + * @param sequences + * the sequences features are to be created on (if creating + * features), or a single sequence (if amending features) + * @param features + * the current features at the position (if amending), or template + * new feature(s) with start/end position set (if creating) + * @param create + * true to create features, false to amend or delete + * @param alignPanel + * @return */ - public int findFeatureColour(int initialCol, SequenceI seq, int column) + protected boolean amendFeatures(final List sequences, + final List features, boolean create, + final AlignmentPanel alignPanel) { - if (!av.showSequenceFeatures) - { - return initialCol; - } + featureIndex = 0; + + final JPanel mainPanel = new JPanel(new BorderLayout()); - if (seq != lastSeq) + final JTextField name = new JTextField(25); + name.getDocument().addDocumentListener(new DocumentListener() { - lastSeq = seq; - sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures(); - if (sequenceFeatures!=null) + @Override + public void insertUpdate(DocumentEvent e) { - sfSize = sequenceFeatures.length; + warnIfTypeHidden(mainPanel, name.getText()); } - } - if (sequenceFeatures!=lastSeq.getDatasetSequence().getSequenceFeatures()) { - sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures(); - if (sequenceFeatures != null) + @Override + public void removeUpdate(DocumentEvent e) { - sfSize = sequenceFeatures.length; + warnIfTypeHidden(mainPanel, name.getText()); } - } - - if (sequenceFeatures == null) - { - 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; - - 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 + @Override + public void changedUpdate(DocumentEvent e) { - return ( (Integer) currentColour).intValue(); + warnIfTypeHidden(mainPanel, name.getText()); } - } - - } - - /** - * 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; - - 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) + final JTextField group = new JTextField(25); + group.getDocument().addDocumentListener(new DocumentListener() { - findAllFeatures(); - if (av.featuresDisplayed.size() < 1) + @Override + public void insertUpdate(DocumentEvent e) { - return; + warnIfGroupHidden(mainPanel, group.getText()); } - sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures(); - sfSize = sequenceFeatures.length; - } - - 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)); - } - - if (!offscreenRender) - { - spos = lastSeq.findPosition(start); - epos = lastSeq.findPosition(end); - } - - String type; - for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++) - { - type = renderOrder[renderIndex]; - - if (type == null || !av.featuresDisplayed.containsKey(type)) + @Override + public void removeUpdate(DocumentEvent e) { - continue; + warnIfGroupHidden(mainPanel, group.getText()); } - // loop through all features in sequence to find - // current feature to render - for (sfindex = 0; sfindex < sfSize; sfindex++) + @Override + public void changedUpdate(DocumentEvent e) { - if (sequenceFeatures.length <= sfindex) - { - continue; - } - 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 (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos - || sequenceFeatures[sfindex].getEnd() < spos)) - { - continue; - } - - if (offscreenRender && offscreenImage == null) - { - if (sequenceFeatures[sfindex].begin <= start && - sequenceFeatures[sfindex].end >= start) - { - 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); - - } - else - { - renderFeature(g, seq, - seq.findIndex(sequenceFeatures[sfindex].begin) - 1, - seq.findIndex(sequenceFeatures[sfindex].end) - 1, - getColour(sequenceFeatures[sfindex].type), - start, end, y1); - } - + warnIfGroupHidden(mainPanel, group.getText()); } + }); - } - - if (transparency != 1.0f && g != null) - { - Graphics2D g2 = (Graphics2D) g; - g2.setComposite( - AlphaComposite.getInstance( - AlphaComposite.SRC_OVER, 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))) + final JTextArea description = new JTextArea(3, 25); + final JSpinner start = new JSpinner(); + final JSpinner end = new JSpinner(); + start.setPreferredSize(new Dimension(80, 20)); + end.setPreferredSize(new Dimension(80, 20)); + final FeatureRenderer me = this; + final JLabel colour = new JLabel(); + colour.setOpaque(true); + // colour.setBorder(BorderFactory.createEtchedBorder()); + colour.setMaximumSize(new Dimension(30, 16)); + colour.addMouseListener(new MouseAdapter() { - if (fstart < start) - { // fix for if the feature we have starts before the sequence start, - fstart = start; // but the feature end is still valid!! - } + FeatureColourChooser fcc = null; - if (fend >= end) - { - fend = end; - } - int pady = (y1 + av.charHeight) - av.charHeight / 5; - for (i = fstart; i <= fend; i++) + @Override + public void mousePressed(MouseEvent evt) { - s = seq.getCharAt(i); - - if (jalview.util.Comparison.isGap(s)) + if (fcol.isSimpleColour()) { - continue; + Color col = JColorChooser.showDialog(Desktop.desktop, + MessageManager.getString("label.select_feature_colour"), + fcol.getColour()); + if (col != null) + { + fcol = new FeatureColour(col); + updateColourButton(mainPanel, colour, fcol); + } } - - g.setColor(featureColour); - - g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight); - - if (offscreenRender || !av.validCharWidth) + else { - continue; - } - - g.setColor(Color.white); - 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. - * - */ - synchronized void findAllFeatures() - { - findAllFeatures(true); // add all new features as visible - if (!firing) { - firing=true; - changeSupport.firePropertyChange("changeSupport",null,null); - firing=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; - } + if (fcc == null) + { + final String ft = features.get(featureIndex).getType(); + final String type = ft == null ? lastFeatureAdded : ft; + fcc = new FeatureColourChooser(me, type); + fcc.setRequestFocusEnabled(true); + fcc.requestFocus(); - findingFeatures = true; + fcc.addActionListener(new ActionListener() + { - if (av.featuresDisplayed == null) - { - av.featuresDisplayed = new Hashtable(); - } + @Override + public void actionPerformed(ActionEvent e) + { + fcol = fcc.getLastColour(); + fcc = null; + setColour(type, fcol); + updateColourButton(mainPanel, colour, fcol); + } + }); - allfeatures = new Vector(); - Vector oldfeatures = new Vector(); - if (renderOrder!=null) - { - for (int i=0; i 1) + { + /* + * more than one feature at selected position - add a drop-down + * to choose the feature to amend + */ + gridPanel = new JPanel(new GridLayout(4, 1)); + JPanel choosePanel = new JPanel(); + choosePanel.add(new JLabel(MessageManager + .getString("label.select_feature") + + ":")); + final JComboBox overlaps = new JComboBox(); + for (SequenceFeature sf : features) { - continue; + String text = sf.getType() + "/" + sf.getBegin() + "-" + + sf.getEnd() + " (" + sf.getFeatureGroup() + ")"; + overlaps.addItem(text); } + choosePanel.add(overlaps); - int index = 0; - while (index < features.length) + overlaps.addItemListener(new ItemListener() { - if (!av.featuresDisplayed.containsKey(features[index].getType())) + @Override + public void itemStateChanged(ItemEvent e) { - if (! (features[index].begin == 0 && features[index].end == 0)) + int index = overlaps.getSelectedIndex(); + if (index != -1) { - // 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()); - } - index++; - } - } - updateRenderOrder(allfeatures); - findingFeatures = false; - } - protected boolean firing=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 - * - * @param 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) - { - for (int j=0; jsortOrder[i+1]; - } - i--; - } - if (iSize>1 && sort) - jalview.util.QuickSort.sort(sortOrder, newf); - sortOrder=null; - System.arraycopy(newf, 0, renderOrder, opos, newf.length); - } - public Color getColour(String featureType) - { - if (featureColours.get(featureType) == null) - { - jalview.schemes.UserColourScheme ucs = new - jalview.schemes.UserColourScheme(); - Color col = ucs.createColourFromName(featureType); - featureColours.put(featureType, col); - return col; - } - else - return (Color) featureColours.get(featureType); - } + featureIndex = index; + SequenceFeature sf = features.get(index); + name.setText(sf.getType()); + description.setText(sf.getDescription()); + group.setText(sf.getFeatureGroup()); + start.setValue(new Integer(sf.getBegin())); + end.setValue(new Integer(sf.getEnd())); - static String lastFeatureAdded; - static String lastFeatureGroupAdded; - static String lastDescriptionAdded; + SearchResultsI highlight = new SearchResults(); + highlight.addResult(sequences.get(0), sf.getBegin(), + sf.getEnd()); - public boolean createNewFeatures(SequenceI[] sequences, - SequenceFeature[] features) - { - return amendFeatures(sequences, features, true, null); - } - - int featureIndex = 0; - boolean amendFeatures(final SequenceI[] sequences, - final SequenceFeature[] features, - boolean newFeatures, - final AlignmentPanel ap) - { - findAllFeatures(); + alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(highlight); - featureIndex = 0; + } + FeatureColourI col = getFeatureStyle(name.getText()); + if (col == null) + { + col = new FeatureColour(ColorUtils + .createColourFromName(name.getText())); + } + oldcol = fcol = col; + updateColourButton(mainPanel, colour, col); + } + }); - JPanel bigPanel = new JPanel(new BorderLayout()); - final JComboBox overlaps; - final JTextField name = new JTextField(25); - final JTextField source = new JTextField(25); - final JTextArea description = new JTextArea(3, 25); - final JSpinner start = new JSpinner(); - final JSpinner end = new JSpinner(); - start.setPreferredSize(new Dimension(80, 20)); - end.setPreferredSize(new Dimension(80, 20)); + gridPanel.add(choosePanel); + } - final JPanel colour = new JPanel(); - colour.setBorder(BorderFactory.createEtchedBorder()); - colour.setMaximumSize(new Dimension(40, 10)); - colour.addMouseListener(new MouseAdapter() - { - public void mousePressed(MouseEvent evt) - { - colour.setBackground( - JColorChooser.showDialog(Desktop.desktop, - "Select Feature Colour", - colour.getBackground())); - } - }); + JPanel namePanel = new JPanel(); + gridPanel.add(namePanel); + namePanel.add(new JLabel(MessageManager.getString("label.name:"), + JLabel.RIGHT)); + namePanel.add(name); - JPanel tmp = new JPanel(); - JPanel panel = new JPanel(new GridLayout(3, 1)); + JPanel groupPanel = new JPanel(); + gridPanel.add(groupPanel); + groupPanel.add(new JLabel(MessageManager.getString("label.group:"), + JLabel.RIGHT)); + groupPanel.add(group); - /////////////////////////////////////// - ///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; i0) + final String enteredType = name.getText().trim(); + final String enteredGroup = group.getText().trim(); + final String enteredDescription = description.getText().replaceAll("\n", " "); + + if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0) { - // This ensures that the last sequence - // is refreshed and new features are rendered - lastSeq = null; - lastFeatureAdded = name.getText().trim(); - lastFeatureGroupAdded = source.getText().trim(); - lastDescriptionAdded = description.getText().replaceAll("\n", " "); - - if(lastFeatureGroupAdded.length()<1) - lastFeatureGroupAdded = null; + /* + * update default values only if creating using default values + */ + if (useLastDefaults) + { + lastFeatureAdded = enteredType; + lastFeatureGroupAdded = enteredGroup; + // TODO: determine if the null feature group is valid + if (lastFeatureGroupAdded.length() < 1) + { + lastFeatureGroupAdded = null; + } + } } - if (!newFeatures) + if (!create) { - SequenceFeature sf = features[featureIndex]; + SequenceFeature sf = features.get(featureIndex); - if (reply == JOptionPane.NO_OPTION) + if (reply == JvOptionPane.NO_OPTION) { - sequences[0].getDatasetSequence().deleteFeature(sf); + /* + * NO_OPTION corresponds to the Delete button + */ + sequences.get(0).getDatasetSequence().deleteFeature(sf); + // update Feature Settings for removal of feature / group + featuresAdded(); } - else if (reply == JOptionPane.YES_OPTION) + else if (reply == JvOptionPane.YES_OPTION) { - sf.type = lastFeatureAdded; - sf.featureGroup = lastFeatureGroupAdded; - sf.description = lastDescriptionAdded; - setColour(sf.type, colour.getBackground()); + /* + * YES_OPTION corresponds to the Amend button + * need to refresh Feature Settings if type, group or colour changed; + * note we don't force the feature to be visible - the user has been + * warned if a hidden feature type or group was entered + */ + boolean refreshSettings = (!featureType.equals(enteredType) || !featureGroup + .equals(enteredGroup)); + refreshSettings |= (fcol != oldcol); + setColour(enteredType, fcol); + int newBegin = sf.begin; + int newEnd = sf.end; try { - sf.begin = ( (Integer) start.getValue()).intValue(); - sf.end = ( (Integer) end.getValue()).intValue(); + newBegin = ((Integer) start.getValue()).intValue(); + newEnd = ((Integer) end.getValue()).intValue(); + } catch (NumberFormatException ex) + { + // JSpinner doesn't accept invalid format data :-) } - catch (NumberFormatException ex) - {} - ffile.parseDescriptionHTML(sf, false); + /* + * replace the feature by deleting it and adding a new one + * (to ensure integrity of SequenceFeatures data store) + */ + sequences.get(0).deleteFeature(sf); + SequenceFeature newSf = new SequenceFeature(sf, newBegin, newEnd, + enteredGroup, sf.getScore()); + sf.setDescription(enteredDescription); + ffile.parseDescriptionHTML(newSf, false); + // amend features dialog only updates one sequence at a time + sequences.get(0).addSequenceFeature(newSf); + + if (refreshSettings) + { + featuresAdded(); + } } } else + // NEW FEATURES ADDED { - if (reply == JOptionPane.OK_OPTION - && name.getText() != null - && source.getText() != null) + if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0) { - for (int i = 0; i < sequences.length; i++) + for (int i = 0; i < sequences.size(); i++) { - features[i].type = lastFeatureAdded; - features[i].featureGroup = lastFeatureGroupAdded; - features[i].description = lastDescriptionAdded; - sequences[i].addSequenceFeature(features[i]); - ffile.parseDescriptionHTML(features[i], false); + SequenceFeature sf = features.get(i); + SequenceFeature sf2 = new SequenceFeature(enteredType, + enteredDescription, sf.getBegin(), sf.getEnd(), + enteredGroup); + ffile.parseDescriptionHTML(sf2, false); + sequences.get(i).addSequenceFeature(sf2); } - if (av.featuresDisplayed == null) - { - av.featuresDisplayed = new Hashtable(); - } - - if (featureGroups == null) - { - featureGroups = new Hashtable(); - } + setColour(enteredType, fcol); + featuresAdded(); - Color col = colour.getBackground(); - setColour(lastFeatureAdded, colour.getBackground()); - - if(lastFeatureGroupAdded!=null) - { - featureGroups.put(lastFeatureGroupAdded, new Boolean(true)); - av.featuresDisplayed.put(lastFeatureGroupAdded, - new Integer(col.getRGB())); - } - findAllFeatures(); + alignPanel.paintAlignment(true); return true; } @@ -860,129 +490,82 @@ public class FeatureRenderer } } - findAllFeatures(); + alignPanel.paintAlignment(true); return true; } - public void setColour(String featureType, Color 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 + * Show a warning message if the entered type is one that is currently hidden + * + * @param panel + * @param type */ - public void setFeaturePriority(Object[][] data, boolean visibleNew) + protected void warnIfTypeHidden(JPanel panel, String type) { - if (visibleNew) - { - if (av.featuresDisplayed != null) - { - av.featuresDisplayed.clear(); - } - else - { - av.featuresDisplayed = new Hashtable(); - } - } - if (data==null) + if (getRenderOrder().contains(type)) { - 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++) + if (!showFeatureOfType(type)) { - String type = data[i][0].toString(); - setColour(type, (Color) data[i][1]); - if ( ( (Boolean) data[i][2]).booleanValue()) - { - av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB())); - } - - renderOrder[data.length - i - 1] = type; + String msg = MessageManager.formatMessage("label.warning_hidden", + MessageManager.getString("label.feature_type"), type); + JvOptionPane.showMessageDialog(panel, msg, "", + JvOptionPane.OK_OPTION); } } - } - Hashtable 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. + * Show a warning message if the entered group is one that is currently hidden + * + * @param panel + * @param group */ - public float setOrder(String type, float position) + protected void warnIfGroupHidden(JPanel panel, String group) { - 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 (featureGroups.containsKey(group) && !featureGroups.get(group)) { - if (featureOrder.containsKey(type)) - { - return ((Float)featureOrder.get(type)).floatValue(); - } + String msg = MessageManager.formatMessage("label.warning_hidden", + MessageManager.getString("label.group"), group); + JvOptionPane.showMessageDialog(panel, msg, "", JvOptionPane.OK_OPTION); } - return -1; } /** - * @param listener - * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener) + * update the amend feature button dependent on the given style + * + * @param bigPanel + * @param col + * @param col */ - public void addPropertyChangeListener(PropertyChangeListener listener) + protected void updateColourButton(JPanel bigPanel, JLabel colour, + FeatureColourI col) { - changeSupport.addPropertyChangeListener(listener); + colour.removeAll(); + colour.setIcon(null); + colour.setToolTipText(null); + colour.setText(""); + + if (col.isSimpleColour()) + { + colour.setBackground(col.getColour()); + } + else + { + colour.setBackground(bigPanel.getBackground()); + colour.setForeground(Color.black); + FeatureSettings.renderGraduatedColor(colour, col); + } } /** - * @param listener - * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener) + * Orders features in render precedence (last in order is last to render, so + * displayed on top of other features) + * + * @param order */ - public void removePropertyChangeListener(PropertyChangeListener listener) + public void orderFeatures(Comparator order) { - changeSupport.removePropertyChangeListener(listener); + Arrays.sort(renderOrder, order); } }