X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=cd9495e0df7e3ed5ec4718806649286edb6c51b9;hb=refs%2Fheads%2Ffeatures%2FJAL-2094_colourInterface;hp=cb9736e8c832a54d9de912092c54d937cb062798;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java old mode 100755 new mode 100644 index cb9736e..cd9495e --- a/src/jalview/appletgui/FeatureRenderer.java +++ b/src/jalview/appletgui/FeatureRenderer.java @@ -1,31 +1,55 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * - * 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. + * + * 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.appletgui; -import java.util.*; - -import java.awt.*; - -import java.awt.event.*; - -import jalview.appletgui.FeatureSettings.MyCheckbox; -import jalview.datamodel.*; +import jalview.api.FeatureColourI; +import jalview.datamodel.SearchResults; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.io.FeaturesFile; +import jalview.schemes.Colour; +import jalview.schemes.FeatureColour; +import jalview.schemes.UserColourScheme; +import jalview.util.ColorUtils; +import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; + +import java.awt.BorderLayout; +import java.awt.Button; +import java.awt.Choice; +import java.awt.Color; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.Graphics; +import java.awt.GridLayout; +import java.awt.Label; +import java.awt.Panel; +import java.awt.ScrollPane; +import java.awt.TextArea; +import java.awt.TextField; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; +import java.util.Hashtable; /** * DOCUMENT ME! @@ -33,69 +57,112 @@ import jalview.datamodel.*; * @author $author$ * @version $Revision$ */ -public class 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; + static String lastFeatureAdded; - String[] renderOrder; + static String lastFeatureGroupAdded; - FontMetrics fm; + static String lastDescriptionAdded; - int charOffset; + int featureIndex = 0; - float transparency = 1f; + boolean deleteFeature = false; - TransparencySetter transparencySetter = null; + FeatureColourPanel colourPanel; /** * Creates a new FeatureRenderer object. * * @param av - * DOCUMENT ME! */ - public FeatureRenderer(AlignViewport av) + public FeatureRenderer(AlignmentViewport av) { - this.av = av; - - if (!System.getProperty("java.version").startsWith("1.1")) - { - transparencySetter = new TransparencySetter(); - } + super(av); } - public void transferSettings(FeatureRenderer fr) + class FeatureColourPanel extends Panel { - renderOrder = fr.renderOrder; - featureGroups = fr.featureGroups; - featureColours = fr.featureColours; - transparency = fr.transparency; - } + String label = ""; - static String lastFeatureAdded; + private Color maxCol; - static String lastFeatureGroupAdded; + private boolean isColourByLabel, isGcol; - static String lastDescriptionAdded; + /** + * render a feature style in the amend feature dialog box + */ + public void updateColor(FeatureColourI newcol) + { + Color bg = null; + String vlabel = ""; + if (newcol.isSimpleColour()) + { + bg = ColorUtils.getColor(newcol.getColour()); + setBackground(bg); + } + else + { + if (newcol.isAboveThreshold()) + { + vlabel += " (>)"; + } + else if (newcol.isBelowThreshold()) + { + vlabel += " (<)"; + } - int featureIndex = 0; + if (isColourByLabel = newcol.isColourByLabel()) + { + setBackground(bg = Color.white); + vlabel += " (by Label)"; + } + else + { + setBackground(bg = ColorUtils.getColor(newcol.getMinColour())); + maxCol = ColorUtils.getColor(newcol.getMaxColour()); + } + } + label = vlabel; + setBackground(bg); + repaint(); + } - boolean deleteFeature = false; + FeatureColourPanel() + { + super(null); + } - Panel colourPanel; + @Override + 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(MessageManager.getString("label.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, @@ -111,12 +178,13 @@ 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; // ///////////////////////////////////// @@ -133,7 +201,9 @@ public class FeatureRenderer + "-" + features[i].getEnd(); if (features[i].getFeatureGroup() != null) + { item += " (" + features[i].getFeatureGroup() + ")"; + } overlaps.addItem(item); } @@ -142,6 +212,7 @@ public class FeatureRenderer overlaps.addItemListener(new java.awt.event.ItemListener() { + @Override public void itemStateChanged(java.awt.event.ItemEvent e) { int index = overlaps.getSelectedIndex(); @@ -161,14 +232,15 @@ public class FeatureRenderer ap.seqPanel.seqCanvas.highlightSearchResults(highlight); } - Color col = getColour(name.getText()); + FeatureColourI col = getFeatureStyle(name.getText()); if (col == null) { - col = new jalview.schemes.UserColourScheme() + Color generatedColour = UserColourScheme .createColourFromName(name.getText()); + col = new FeatureColour(new Colour(generatedColour)); } - colourPanel.setBackground(col); + colourPanel.updateColor(col); } }); @@ -179,23 +251,24 @@ public class FeatureRenderer tmp = new Panel(); panel.add(tmp); - tmp.add(new Label("Name: ", Label.RIGHT)); + tmp.add(new Label(MessageManager.getString("label.name:"), Label.RIGHT)); tmp.add(name); tmp = new Panel(); panel.add(tmp); - tmp.add(new Label("Group: ", Label.RIGHT)); + tmp.add(new Label(MessageManager.getString("label.group:"), Label.RIGHT)); tmp.add(source); tmp = new Panel(); panel.add(tmp); - tmp.add(new Label("Colour: ", Label.RIGHT)); + tmp.add(new Label(MessageManager.getString("label.colour"), Label.RIGHT)); tmp.add(colourPanel); bigPanel.add(panel, BorderLayout.NORTH); panel = new Panel(); - panel.add(new Label("Description: ", Label.RIGHT)); + panel.add(new Label(MessageManager.getString("label.description:"), + Label.RIGHT)); panel.add(new ScrollPane().add(description)); if (!newFeatures) @@ -203,9 +276,11 @@ public class FeatureRenderer bigPanel.add(panel, BorderLayout.SOUTH); panel = new Panel(); - panel.add(new Label(" Start:", Label.RIGHT)); + panel.add(new Label(MessageManager.getString("label.start"), + Label.RIGHT)); panel.add(start); - panel.add(new Label(" End:", Label.RIGHT)); + panel.add(new Label(MessageManager.getString("label.end"), + Label.RIGHT)); panel.add(end); bigPanel.add(panel, BorderLayout.CENTER); } @@ -238,8 +313,10 @@ public class FeatureRenderer } } - String title = newFeatures ? "Create New Sequence Feature(s)" - : "Amend/Delete Features for " + sequences[0].getName(); + String title = newFeatures ? MessageManager + .getString("label.create_new_sequence_features") + : MessageManager.formatMessage("label.amend_delete_features", + new String[] { sequences[0].getName() }); final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385, 240); @@ -253,10 +330,11 @@ public class FeatureRenderer } else { - dialog.ok.setLabel("Amend"); + dialog.ok.setLabel(MessageManager.getString("label.amend")); dialog.buttonPanel.add(deleteButton, 1); deleteButton.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { deleteFeature = true; @@ -270,29 +348,31 @@ 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); - + // lookup (or generate) the feature colour + FeatureColourI fcol = getFeatureStyle(name.getText()); + // simply display the feature color in a box + colourPanel.updateColor(fcol); dialog.setResizable(true); - - colourPanel.addMouseListener(new java.awt.event.MouseAdapter() + // TODO: render the graduated color in the box. + colourPanel.addMouseListener(new MouseAdapter() { - public void mousePressed(java.awt.event.MouseEvent evt) + @Override + public void mousePressed(MouseEvent evt) { - new UserDefinedColours(fr, ap.alignFrame); + if (!colourPanel.isGcol) + { + new UserDefinedColours(fr, ap.alignFrame); + } + else + { + new FeatureColourChooser(ap.alignFrame, name.getText()); + dialog.transferFocus(); + } } }); - dialog.setVisible(true); - jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile(); + FeaturesFile ffile = new FeaturesFile(); if (dialog.accept) { @@ -305,18 +385,26 @@ public class FeatureRenderer } if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1) + { lastFeatureGroupAdded = null; + } 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, + new FeatureColour(new Colour(colourPanel.getBackground()))); + } try { sf.begin = Integer.parseInt(start.getText()); @@ -326,6 +414,8 @@ public class FeatureRenderer } ffile.parseDescriptionHTML(sf, false); + setVisible(lastFeatureAdded); // if user edited name then make sure new + // type is visible } if (deleteFeature) { @@ -346,641 +436,34 @@ public class 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, col); + Color newColour = colourPanel.getBackground(); + // setColour(lastFeatureAdded, fcol); if (lastFeatureGroupAdded != null) { - featureGroups.put(lastFeatureGroupAdded, new Boolean(true)); - av.featuresDisplayed.put(lastFeatureGroupAdded, new Integer(col - .getRGB())); + setGroupVisibility(lastFeatureGroupAdded, true); } - 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; + setColour(lastFeatureAdded, + new FeatureColour(new Colour(newColour))); // was fcol + setVisible(lastFeatureAdded); + findAllFeatures(false); // different to original applet behaviour ? + // findAllFeatures(); } else { + // no update to the alignment return false; } } - - findAllFeatures(); - - ap.paintAlignment(true); - - 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 = 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); - } - - } - } - - 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; - - } - } - } - - void findAllFeatures() - { - jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(); - - av.featuresDisplayed = new Hashtable(); - Vector allfeatures = new Vector(); - for (int i = 0; i < av.alignment.getHeight(); i++) - { - SequenceFeature[] features = av.alignment.getSequenceAt(i) - .getSequenceFeatures(); - - if (features == null) - { - continue; - } - - int index = 0; - while (index < features.length) - { - 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()); - } - index++; - } - } - - renderOrder = new String[allfeatures.size()]; - Enumeration en = allfeatures.elements(); - int i = allfeatures.size() - 1; - while (en.hasMoreElements()) + // refresh the alignment and the feature settings dialog + if (((jalview.appletgui.AlignViewport) av).featureSettings != null) { - renderOrder[i] = en.nextElement().toString(); - i--; + ((jalview.appletgui.AlignViewport) av).featureSettings.refreshTable(); } - } - - public Color getColour(String featureType) - { - if (!featureColours.containsKey(featureType)) - { - 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); - } + // findAllFeatures(); - public void setColour(String featureType, Color 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, (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; - } - } - } - - /** - * @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]); - if (st != null) - { - featureGroups.put(toset[i], new Boolean(visible)); - 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); - } - } - } - } - - /** - * 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(); - } - Vector allFeatures = new Vector(); - Vector allGroups = new Vector(); - SequenceFeature[] tmpfeatures; - String group; - for (int i = 0; i < av.alignment.getHeight(); i++) - { - if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null) - { - continue; - } - - alignmentHasFeatures = true; - - tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures(); - int index = 0; - while (index < tmpfeatures.length) - { - if (tmpfeatures[index].getFeatureGroup() != null) - { - group = tmpfeatures[index].featureGroup; - if (!allGroups.contains(group)) - { - allGroups.addElement(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.addElement(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; - for (int i = 0; i < av.alignment.getHeight(); i++) - { - if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null) - { - continue; - } - - alignmentHasFeatures = true; - - tmpfeatures = av.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; - } -} + ap.paintAlignment(true); -class TransparencySetter -{ - void setTransparency(Graphics g, float value) - { - Graphics2D g2 = (Graphics2D) g; - g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, - value)); + return true; } }