X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=6024872fea41920d8dba722dfb299ccc2c2fd639;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=5e654093f98d42efcc0681479cb7928307be7566;hpb=9c8561a294fb638ae78c01a440a863b05db2bdee;p=jalview.git diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java old mode 100755 new mode 100644 index 5e65409..6024872 --- a/src/jalview/appletgui/FeatureRenderer.java +++ b/src/jalview/appletgui/FeatureRenderer.java @@ -1,20 +1,22 @@ /* - * 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 2.8.2b1) + * Copyright (C) 2014 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.appletgui; @@ -24,17 +26,18 @@ import java.awt.*; import java.awt.event.*; - -import jalview.appletgui.FeatureSettings.MyCheckbox; import jalview.datamodel.*; +import jalview.schemes.AnnotationColourGradient; +import jalview.schemes.GraduatedColor; +import jalview.util.MessageManager; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ -public class FeatureRenderer +public class FeatureRenderer implements jalview.api.FeatureRenderer { AlignViewport av; @@ -55,6 +58,7 @@ public class FeatureRenderer String[] renderOrder; FontMetrics fm; + int charOffset; float transparency = 1f; @@ -63,8 +67,9 @@ public class FeatureRenderer /** * Creates a new FeatureRenderer object. - * - * @param av DOCUMENT ME! + * + * @param av + * DOCUMENT ME! */ public FeatureRenderer(AlignViewport av) { @@ -82,20 +87,133 @@ 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; + static String lastFeatureGroupAdded; + static String lastDescriptionAdded; int featureIndex = 0; + 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(MessageManager.getString("error.invalid_colour_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(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, - final AlignmentPanel ap) + final SequenceFeature[] features, boolean newFeatures, + final AlignmentPanel ap) { Panel bigPanel = new Panel(new BorderLayout()); final TextField name = new TextField(16); @@ -107,75 +225,72 @@ public class FeatureRenderer Button deleteButton = new Button("Delete"); deleteFeature = false; - colourPanel = new Panel(null); - colourPanel.setSize(110,15); + 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; - /////////////////////////////////////// - ///MULTIPLE FEATURES AT SELECTED RESIDUE - if(!newFeatures && features.length>1) + // ///////////////////////////////////// + // /MULTIPLE FEATURES AT SELECTED RESIDUE + if (!newFeatures && features.length > 1) { - panel = new Panel(new GridLayout(4, 1)); - tmp = new Panel(); - tmp.add(new Label("Select Feature: ")); - overlaps = new Choice(); - for(int i=0; i0) + if (dialog.accept && name.getText().length() > 0) { for (int i = 0; i < sequences.length; i++) { @@ -364,39 +483,44 @@ public class FeatureRenderer } col = colourPanel.getBackground(); - setColour(lastFeatureAdded, col); + // setColour(lastFeatureAdded, fcol); - if(lastFeatureGroupAdded!=null) + 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); + 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); return true; } - public Color findFeatureColour(Color initialCol, SequenceI seq, int i) { overview = true; @@ -428,41 +552,50 @@ public class FeatureRenderer return initialCol; } - return new Color( ( (Integer) currentColour).intValue()); + return new Color(((Integer) currentColour).intValue()); } /** - * This is used by the Molecule Viewer to get the accurate colour - * of the rendered sequence + * 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! + * + * @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) + int start, int end, int y1) { if (seq.getSequenceFeatures() == null - || seq.getSequenceFeatures().length == 0) + || seq.getSequenceFeatures().length == 0) { return; } @@ -472,7 +605,8 @@ public class FeatureRenderer transparencySetter.setTransparency(g, transparency); } - if (lastSeq == null || seq != lastSeq || sequenceFeatures!=seq.getSequenceFeatures()) + if (lastSeq == null || seq != lastSeq + || sequenceFeatures != seq.getSequenceFeatures()) { lastSeq = seq; sequenceFeatures = seq.getSequenceFeatures(); @@ -518,30 +652,31 @@ public class FeatureRenderer } if (featureGroups != null - && sequenceFeatures[sfindex].featureGroup != null - && - featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup) - && - ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex]. - featureGroup)). - booleanValue()) + && 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)) + if (!overview + && (sequenceFeatures[sfindex].getBegin() > epos || sequenceFeatures[sfindex] + .getEnd() < spos)) { continue; } if (overview) { - 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); + currentColour = new Integer( + getColour(sequenceFeatures[sfindex]).getRGB());// av.featuresDisplayed + // .get(sequenceFeatures[sfindex].type); } } @@ -549,26 +684,30 @@ public class FeatureRenderer { 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); + 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, - new Color( ( (Integer) av.featuresDisplayed.get( - sequenceFeatures[sfindex].type)).intValue()), - start, end, y1); + 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, - seq.findIndex(sequenceFeatures[sfindex].end) - 1, - getColour(sequenceFeatures[sfindex].type), - 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); + } } } @@ -581,13 +720,14 @@ public class FeatureRenderer } 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, @@ -610,7 +750,8 @@ 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 (!av.validCharWidth) { @@ -619,25 +760,42 @@ public class FeatureRenderer 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; + g.drawString(String.valueOf(s), charOffset + + (av.charWidth * (i - start)), (y1 + av.charHeight) + - av.charHeight / 5); // pady = height / 5; } } } + Hashtable minmax = null; + + /** + * Called when alignment in associated view has new/modified features to + * discover and display. + * + */ + public void featuresAdded() + { + lastSeq = null; + findAllFeatures(); + } + + /** + * find all features on the alignment + */ void findAllFeatures() { - jalview.schemes.UserColourScheme ucs = new - jalview.schemes.UserColourScheme(); + 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++) + minmax = new Hashtable(); + AlignmentI alignment = av.getAlignment(); + for (int i = 0; i < alignment.getHeight(); i++) { - SequenceFeature[] features = av.alignment.getSequenceAt(i). - getSequenceFeatures(); + SequenceFeature[] features = alignment.getSequenceAt(i) + .getSequenceFeatures(); if (features == null) { @@ -647,20 +805,52 @@ public class FeatureRenderer int index = 0; while (index < features.length) { + if (features[index].begin == 0 && features[index].end == 0) + { + index++; + continue; + } if (!av.featuresDisplayed.containsKey(features[index].getType())) { if (getColour(features[index].getType()) == null) { featureColours.put(features[index].getType(), - ucs.createColourFromName(features[index]. - getType())); + ucs.createColourFromName(features[index].getType())); } - av.featuresDisplayed.put(features[index].getType(), - new Integer(getColour(features[index]. - getType()).getRGB())); + av.featuresDisplayed.put(features[index].getType(), new Integer( + getColour(features[index].getType()).getRGB())); allfeatures.addElement(features[index].getType()); } + if (features[index].score != Float.NaN) + { + int nonpos = features[index].getBegin() >= 1 ? 0 : 1; + float[][] mm = (float[][]) minmax.get(features[index].getType()); + if (mm == null) + { + mm = new float[][] + { null, null }; + minmax.put(features[index].getType(), mm); + } + if (mm[nonpos] == null) + { + mm[nonpos] = new float[] + { features[index].score, features[index].score }; + + } + else + { + if (mm[nonpos][0] > features[index].score) + { + mm[nonpos][0] = features[index].score; + } + if (mm[nonpos][1] < features[index].score) + { + mm[nonpos][1] = features[index].score; + } + } + } + index++; } } @@ -675,24 +865,98 @@ 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) { - 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; + featureColours.put(featureType, fc = col); + } + return fc; + } + + public Color getColour(String featureType) + { + Object fc = getFeatureStyle(featureType); + + if (fc instanceof Color) + { + return (Color) fc; + } + else + { + if (fc instanceof GraduatedColor) + { + return ((GraduatedColor) fc).getMaxColor(); + } + } + throw new Error(MessageManager.formatMessage("error.implementation_error_unrecognised_render_object_for_features_type", new String[]{fc.getClass().getCanonicalName(),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 (Color) featureColours.get(featureType); + { + return true; + } } + /** + * implement graduated colouring for features with scores + * + * @param feature + * @return render colour for the given feature + */ + public Color getColour(SequenceFeature feature) + { + Object fc = getFeatureStyle(feature.getType()); + if (fc instanceof Color) + { + return (Color) fc; + } + else + { + if (fc instanceof GraduatedColor) + { + return ((GraduatedColor) fc).findColor(feature); + } + } + throw new Error("Implementation Error: Unrecognised render object " + + fc.getClass() + " for features of type " + feature.getType()); + } - public void setColour(String featureType, 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) @@ -705,22 +969,11 @@ public class FeatureRenderer av.featuresDisplayed.clear(); } - /* if (visibleNew) - { - if (av.featuresDisplayed != null) - { - av.featuresDisplayed.clear(); - } - else - { - av.featuresDisplayed = new Hashtable(); - } - } - if (data == null) - { - return; - }*/ - + /* + * if (visibleNew) { if (av.featuresDisplayed != null) { + * av.featuresDisplayed.clear(); } else { av.featuresDisplayed = new + * Hashtable(); } } if (data == null) { return; } + */ renderOrder = new String[data.length]; @@ -729,147 +982,169 @@ public class FeatureRenderer 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()) + setColour(type, data[i][1]); + 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; } } } + /** - * @return a simple list of feature group names or null + * @return a simple list of feature group names or null */ public String[] getGroups() { buildGroupHash(); - if (featureGroups!=null) + if (featureGroups != null) { String[] gps = new String[featureGroups.size()]; Enumeration gn = featureGroups.keys(); - int i=0; + int i = 0; while (gn.hasMoreElements()) { - gps[i++] = (String) gn.nextElement(); + 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. + * + * @param visible + * true to return visible groups, false to return hidden ones. * @return list of groups */ - public String[] getGroups(boolean visible) + public String[] getGroups(boolean visible) { buildGroupHash(); - if (featureGroups!=null) + 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) + if (state.booleanValue() == visible) { gp.addElement(nm); } } String[] gps = new String[gp.size()]; gp.copyInto(gps); - - int i=0; + + int i = 0; while (gn.hasMoreElements()) { - gps[i++] = (String) gn.nextElement(); + 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 + * + * @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) + if (toset != null && toset.length > 0 && featureGroups != null) { boolean rdrw = false; - for (int i=0;i hiddenGroups = new ArrayList(); + /** - * analyse alignment for groups and hash tables - * (used to be embedded in FeatureSettings.setTableData) + * 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; + boolean alignmentHasFeatures = false; if (featureGroups == null) { featureGroups = new Hashtable(); } - Vector allFeatures = new Vector(); - Vector allGroups = new Vector(); + hiddenGroups = new ArrayList(); + hiddenGroups.addAll(featureGroups.keySet()); + ArrayList allFeatures = new ArrayList(); + ArrayList allGroups = new ArrayList(); SequenceFeature[] tmpfeatures; String group; - for (int i = 0; i < av.alignment.getHeight(); i++) + AlignmentI alignment = av.getAlignment(); + for (int i = 0; i < alignment.getHeight(); i++) { - if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null) + if (alignment.getSequenceAt(i).getSequenceFeatures() == null) { continue; } alignmentHasFeatures = true; - tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures(); + tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures(); int index = 0; while (index < tmpfeatures.length) { if (tmpfeatures[index].getFeatureGroup() != null) { group = tmpfeatures[index].featureGroup; + // Remove group from the hiddenGroup list + hiddenGroups.remove(group); if (!allGroups.contains(group)) { - allGroups.addElement(group); + allGroups.add(group); boolean visible = true; if (featureGroups.containsKey(group)) { - visible = ( (Boolean) featureGroups.get(group)).booleanValue(); - } else { + visible = ((Boolean) featureGroups.get(group)).booleanValue(); + } + else + { featureGroups.put(group, new Boolean(visible)); } } @@ -877,22 +1152,26 @@ public class FeatureRenderer if (!allFeatures.contains(tmpfeatures[index].getType())) { - allFeatures.addElement(tmpfeatures[index].getType()); + allFeatures.add(tmpfeatures[index].getType()); } index++; } } - + return alignmentHasFeatures; } + /** - * rebuild the featuresDisplayed and renderorder list based on the featureGroups hash and any existing display state - * and force a repaint if necessary + * 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) + public boolean buildFeatureHash() + { + boolean alignmentHasFeatures = false; + if (featureGroups == null) { alignmentHasFeatures = buildGroupHash(); } @@ -902,16 +1181,17 @@ public class FeatureRenderer Vector allFeatures = new Vector(); SequenceFeature[] tmpfeatures; String group; - for (int i = 0; i < av.alignment.getHeight(); i++) + AlignmentI alignment = av.getAlignment(); + for (int i = 0; i < alignment.getHeight(); i++) { - if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null) + if (alignment.getSequenceAt(i).getSequenceFeatures() == null) { continue; } alignmentHasFeatures = true; - tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures(); + tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures(); int index = 0; while (index < tmpfeatures.length) { @@ -921,10 +1201,10 @@ public class FeatureRenderer group = tmpfeatures[index].featureGroup; if (featureGroups.containsKey(group)) { - visible = ( (Boolean) featureGroups.get(group)).booleanValue(); + visible = ((Boolean) featureGroups.get(group)).booleanValue(); } } - + if (visible && !allFeatures.contains(tmpfeatures[index].getType())) { allFeatures.addElement(tmpfeatures[index].getType()); @@ -932,44 +1212,67 @@ public class FeatureRenderer index++; } } - if (allFeatures.size()>0) + if (allFeatures.size() > 0) { String[] neworder = new String[allFeatures.size()]; - int p=neworder.length-1; - for (int i=renderOrder.length-1; i>=0; i--) + 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 { + } + else + { av.featuresDisplayed.remove(renderOrder[i]); } } - for (int i=allFeatures.size()-1; i>0; i++) + for (int i = allFeatures.size() - 1; i > 0; i++) { Object e = allFeatures.elementAt(i); - if (e!=null) + if (e != null) { neworder[p--] = (String) e; - av.featuresDisplayed.put(e, getColour((String)e)); + av.featuresDisplayed.put(e, getColour((String) e)); } } renderOrder = neworder; return true; } - + return alignmentHasFeatures; } + + /** + * + * @return the displayed feature type as an array of strings + */ + protected String[] getDisplayedFeatureTypes() + { + String[] typ = null; + synchronized (renderOrder) + { + typ = new String[renderOrder.length]; + System.arraycopy(renderOrder, 0, typ, 0, typ.length); + for (int i = 0; i < typ.length; i++) + { + if (av.featuresDisplayed.get(typ[i]) == null) + { + typ[i] = null; + } + } + } + return typ; + } } class TransparencySetter { void setTransparency(Graphics g, float value) { - Graphics2D g2 = (Graphics2D) g; - g2.setComposite( - AlphaComposite.getInstance( - AlphaComposite.SRC_OVER, value)); + Graphics2D g2 = (Graphics2D) g; + g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, + value)); } }