Package org.broad.igv.track

Examples of org.broad.igv.track.TrackGroup$AttributeComparator

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            groupExtents.clear();

            //Rectangle clipRect = g.getClipBounds();

            for (Iterator<TrackGroup> groupIter = groups.iterator(); groupIter.hasNext(); ) {
                TrackGroup group = groupIter.next();

                if (regionY > visibleRect.getMaxY()) {
                    break;
                }

                if (group.isVisible()) {
                    if (isGrouped) {
                        if (regionY + UIConstants.groupGap >= visibleRect.y && regionY < visibleRect.getMaxY()) {
                            greyGraphics.fillRect(0, regionY + 1, getWidth(), UIConstants.groupGap - 1);
                        }
                        regionY += UIConstants.groupGap;
                    }

                    if (group.isDrawBorder() && regionY + UIConstants.groupGap >= visibleRect.y &&
                            regionY < visibleRect.getMaxY()) {
                        g.drawLine(0, regionY - 1, getWidth(), regionY - 1);
                    }

                    int h = group.getHeight();
                    Rectangle groupRect = new Rectangle(visibleRect.x, regionY, visibleRect.width, h);
                    Rectangle displayableRect = getDisplayableRect(groupRect, visibleRect);
                    regionY = printTrackNames(group, displayableRect, visibleRect, graphics2D, 0, regionY);

                    if (isGrouped) {
                        groupExtents.add(new GroupExtent(group, groupRect.y, groupRect.y + groupRect.height));
                        if (showGroupNames) {
                            //Rectangle displayableRect = getDisplayableRect(groupRect, visibleRect);
                            group.renderName(graphics2D, displayableRect, group == selectedGroup);
                        }
                    }

                    if (group.isDrawBorder()) {
                        g.drawLine(0, regionY, getWidth(), regionY);
                    }
                }

            }
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            boolean isGrouped = isGrouped();

            if (e.isPopupTrigger()) {
                if (isGrouped) {
                    clearTrackSelections();
                    TrackGroup g = getGroup(e.getY());
                    if (null == g || g == selectedGroup) {
                        selectedGroup = null;
                    } else {
                        selectGroup(g);
                    }
                } else if (!isTrackSelected(e)) {
                    clearTrackSelections();
                    selectTracks(e);
                }
                TrackClickEvent te = new TrackClickEvent(e, null);
                openPopupMenu(te);
            } // meta (mac) or control,  toggle selection]
            else if (e.getButton() == MouseEvent.BUTTON1) {

                if (isGrouped) {
                    clearTrackSelections();
                    TrackGroup g = getGroup(e.getY());
                    if (g == selectedGroup) {
                        selectedGroup = null;
                    } else {
                        selectGroup(getGroup(e.getY()));
                    }
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        int trackX = 0;
        int trackY = 0;

        for (Iterator<TrackGroup> groupIter = groups.iterator(); groupIter.hasNext(); ) {
            TrackGroup group = groupIter.next();

            if (visibleRect != null && (trackY > visibleRect.y + visibleRect.height)) {
                break;
            }

            if (group.isVisible()) {
                if (groups.size() > 1) {
                    final Graphics2D greyGraphics = context.getGraphic2DForColor(UIConstants.LIGHT_GREY);
                    greyGraphics.fillRect(0, trackY + 1, width, UIConstants.groupGap - 1);
                    trackY += UIConstants.groupGap;
                }

                // Draw a line just above group.
                if (group.isDrawBorder()) {
                    Graphics2D graphics2D = context.getGraphic2DForColor(Color.black);
                    graphics2D.drawLine(0, trackY - 1, width, trackY - 1);
                }

                List<Track> trackList = group.getTracks();
                synchronized (trackList) {
                    for (Track track : trackList) {
                        if (track == null) continue;
                        int trackHeight = track.getHeight();
                        if (visibleRect != null) {
                            if (trackY > visibleRect.y + visibleRect.height) {
                                break;
                            } else if (trackY + trackHeight < visibleRect.y) {
                                if (track.isVisible()) {
                                    trackY += trackHeight;
                                }
                                continue;
                            }
                        }


                        if (track.isVisible()) {
                            Rectangle rect = new Rectangle(trackX, trackY, width, trackHeight);
                            draw(track, rect, context);
                            trackY += trackHeight;
                        }
                    }
                }

                // Draw a line just below group.
                if (group.isDrawBorder()) {
                    Graphics2D graphics2D = context.getGraphic2DForColor(Color.black);
                    graphics2D.drawLine(0, trackY, width, trackY);
                }
            }
        }
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    private List<Track> getVisibleTracks(final Collection<TrackGroup> groups) {
        // Find the tracks that need loaded, we go to this bother to avoid loading tracks scrolled out of view
        final List<Track> visibleTracks = new ArrayList<Track>();
        for (Iterator<TrackGroup> groupIter = groups.iterator(); groupIter.hasNext(); ) {
            TrackGroup group = groupIter.next();
            List<Track> trackList = new ArrayList(group.getTracks());
            for (Track track : trackList) {
                if (track != null && track.isVisible()) {
                    visibleTracks.add(track);
                }
            }
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     * @param name
     */
    public TrackPanel(String name, MainPanel mainPanel) {
        super(mainPanel);
        this.name = name;
        TrackGroup nullGroup = new TrackGroup();
        nullGroup.setDrawBorder(false);
        trackGroups = Collections.synchronizedList(new LinkedList<TrackGroup>());
        trackGroups.add(nullGroup);
        init();
    }
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                foundGroup = true;
                break;
            }
        }
        if (!foundGroup) {
            TrackGroup newGroup = new TrackGroup(groupName);
            newGroup.add(track);
            if (groupAttribute == null) {
                newGroup.setDrawBorder(false);
            }
            trackGroups.add(newGroup);
        }
        log.debug("Done adding track to TrackPanel");
        trackCountEstimate++;
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        this.groupAttribute = attribute;
        List<Track> tracks = getTracks();
        trackGroups.clear();

        if (attribute == null || attribute.length() == 0) {
            TrackGroup nullGroup = new TrackGroup();
            nullGroup.addAll(tracks);
            nullGroup.setDrawBorder(false);
            trackGroups.add(nullGroup);
        } else {
            Map<String, TrackGroup> groupMap = new HashMap();
            for (Track track : tracks) {
                String attributeValue = track.getAttributeValue(attribute);

                if (attributeValue == null) {
                    attributeValue = "";
                }

                TrackGroup group = groupMap.get(attributeValue);

                if (group == null) {
                    group = new TrackGroup(attributeValue);
                    groupMap.put(attributeValue, group);
                    trackGroups.add(group);
                }
                group.add(track);
            }
        }
    }
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        }

        synchronized (groups) {

            for (Iterator<TrackGroup> groupIter = groups.iterator(); groupIter.hasNext(); ) {
                TrackGroup group = groupIter.next();
                if (group != null && group.isVisible()) {
                    if (groups.size() > 1) {
                        height += UIConstants.groupGap;
                    }
                    height += group.getHeight();
                }
            }
        }

        return Math.max(20, height);
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                final int left = AttributeHeaderPanel.COLUMN_BORDER_WIDTH;
                int regionY = 0;
                final int bottom = rect.y + rect.height;

                for (Iterator<TrackGroup> groupIter = groups.iterator(); groupIter.hasNext(); ) {
                    TrackGroup group = groupIter.next();

                    // Out of view?
                    if (regionY > bottom) {
                        break;
                    }

                    if (group.isVisible()) {
                        if (groups.size() > 1) {
                            greyGraphics.fillRect(0, regionY + 1, getWidth(), UIConstants.groupGap - 1);
                            regionY += UIConstants.groupGap;
                        }


                        if (group.isDrawBorder()) {
                            g.drawLine(0, regionY - 1, getWidth(), regionY - 1);
                        }

                        for (Track track : group.getTracks()) {
                            if (track == null) continue;
                            int trackHeight = track.getHeight();
                            if (regionY > bottom) {
                                break;
                            }

                            if (track.isVisible()) {
                                int border = trackHeight < 5 ? 0 : 1;
                                if (regionY + trackHeight >= rect.y) {
                                    Rectangle trackRectangle = new Rectangle(left, regionY+border, getWidth(), trackHeight-border);
                                    track.renderAttributes(graphics2D, trackRectangle, rect, names, mouseRegions);
                                    //regionY = draw(names, track, regionX, regionY, attributeColumnWidth, track.getHeight(), graphics2D);
                                }
                                regionY += trackHeight;
                            }
                        }

                        if (group.isDrawBorder()) {
                            g.drawLine(0, regionY, getWidth(), regionY);
                        }
                    }
                }
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