Package org.broad.igv

Examples of org.broad.igv.PreferenceManager


        ionTorrent = dataManager.isIonTorrent();

        minimumHeight = 50;
        maximumHeight = Integer.MAX_VALUE;

        PreferenceManager prefs = PreferenceManager.getInstance();

        setShowSpliceJunctions(prefs.getAsBoolean(PreferenceManager.SAM_SHOW_JUNCTION_TRACK));

        float maxRange = prefs.getAsFloat(PreferenceManager.SAM_MAX_VISIBLE_RANGE);
        minVisibleScale = (maxRange * 1000) / 700;

        renderer = AlignmentRenderer.getInstance();

        this.setDisplayMode(DisplayMode.EXPANDED);

        if (prefs.getAsBoolean(PreferenceManager.SAM_SHOW_REF_SEQ)) {
            sequenceTrack = new SequenceTrack("Reference sequence");
            sequenceTrack.setHeight(14);
        }

        if (renderOptions.getColorOption() == ColorOption.BISULFITE) {
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    /**
     * The visibility window has changed.
     */
    private void visibilityWindowChanged() {
        PreferenceManager prefs = PreferenceManager.getInstance();
        float maxRange = prefs.getAsFloat(PreferenceManager.SAM_MAX_VISIBLE_RANGE);
        minVisibleScale = (maxRange * 1000) / 700;
    }
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        }
    }

    public static void sortAlignmentTracks(SortOption option, String tag) {
        IGV.getInstance().sortAlignmentTracks(option, tag);
        final PreferenceManager prefMgr = PreferenceManager.getInstance();
        prefMgr.put(PreferenceManager.SAM_SORT_OPTION, option.toString());
        prefMgr.put(PreferenceManager.SAM_SORT_BY_TAG, tag);
        refresh();
    }
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     * @param track
     * @param context
     * @param rect
     */
    public void renderAxis(Track track, RenderContext context, Rectangle rect) {
        PreferenceManager prefs = PreferenceManager.getInstance();

        // For now disable axes for all chromosome view
        if (context.getChr().equals(Globals.CHR_ALL)) {
            return;
        }
        if (prefs.getAsBoolean(PreferenceManager.CHART_DRAW_Y_AXIS))  {

            Rectangle axisRect = new Rectangle(rect.x, rect.y + 1, AXIS_AREA_WIDTH, rect.height);
            Graphics2D whiteGraphics = context.getGraphic2DForColor(Color.white);

            whiteGraphics.fillRect(axisRect.x, axisRect.y, axisRect.width, axisRect.height);
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        super.renderAxis(track, context, arect);

        Rectangle drawingRect = calculateDrawingRect(arect);

        PreferenceManager prefs = PreferenceManager.getInstance();

        Color labelColor = prefs.getAsBoolean(PreferenceManager.CHART_COLOR_TRACK_NAME) ? track.getColor() : Color.black;
        Graphics2D labelGraphics = context.getGraphic2DForColor(labelColor);

        labelGraphics.setFont(FontManager.getFont(8));

        if (prefs.getAsBoolean(PreferenceManager.CHART_DRAW_TRACK_NAME)) {

            // Only attempt if track height is > 25 pixels
            if (arect.getHeight() > 25) {
                Rectangle labelRect = new Rectangle(arect.x, arect.y + 10, arect.width, 10);
                labelGraphics.setFont(FontManager.getFont(10));
                GraphicUtils.drawCenteredText(track.getName(), labelRect, labelGraphics);
            }
        }

        if (prefs.getAsBoolean(PreferenceManager.CHART_DRAW_Y_AXIS)) {

            Rectangle axisRect = new Rectangle(arect.x, arect.y + 1, AXIS_AREA_WIDTH, arect.height);


            DataRange axisDefinition = track.getDataRange();
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                int baseY = computeYPixelValue(adjustedRect, axisDefinition, baseValue);

                getBaselineGraphics(context).drawLine((int) x, baseY, (int) maxX, baseY);
            }

            PreferenceManager prefs = PreferenceManager.getInstance();

            Color altColor = track.getAltColor();
            Color borderColor = (prefs.getAsBoolean(PreferenceManager.CHART_COLOR_BORDERS) && altColor != null && altColor.equals(track.getColor()) )
                    ? track.getColor() : Color.lightGray;
            Graphics2D borderGraphics = context.getGraphic2DForColor(borderColor);

            // Draw the baseline -- todo, this is a wig track option?
            double zeroValue = axisDefinition.getBaseline();
            int zeroY = computeYPixelValue(adjustedRect, axisDefinition, zeroValue);
            borderGraphics.drawLine(adjustedRect.x, zeroY, adjustedRect.x + adjustedRect.width, zeroY);

            // Optionally draw "Y" line  (UCSC track line option)
            if (track.isDrawYLine()) {
                Graphics2D yLineGraphics = context.getGraphic2DForColor(Color.gray);
                int yLine = computeYPixelValue(adjustedRect, axisDefinition, track.getYLine());
                GraphicUtils.drawDashedLine(borderGraphics, adjustedRect.x, yLine, adjustedRect.x + adjustedRect.width, yLine);
            }


            // If the chart has + and - numbers draw both borders or none. This
            // needs documented somewhere.
            boolean drawBorders = true;

            if (minValue * maxValue < 0) {
                drawBorders = prefs.getAsBoolean(PreferenceManager.CHART_DRAW_BOTTOM_BORDER) &&
                        prefs.getAsBoolean(PreferenceManager.CHART_DRAW_TOP_BORDER);
            }

            if (drawBorders && prefs.getAsBoolean(PreferenceManager.CHART_DRAW_TOP_BORDER)) {
                borderGraphics.drawLine(adjustedRect.x, adjustedRect.y,
                        adjustedRect.x + adjustedRect.width, adjustedRect.y);
            }

            if (drawBorders && prefs.getAsBoolean(PreferenceManager.CHART_DRAW_BOTTOM_BORDER)) {
                borderGraphics.drawLine(adjustedRect.x, adjustedRect.y + adjustedRect.height,
                        adjustedRect.x + adjustedRect.width,
                        adjustedRect.y + adjustedRect.height);
            }
        }
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            }
            fontGraphics.setFont(font);

            //determine whether to show flanking regions
            PreferenceManager prefs = PreferenceManager.getInstance();
            boolean shouldShowFlankingRegions = prefs.getAsBoolean(PreferenceManager.SAM_SHOW_JUNCTION_FLANKINGREGIONS);

            // Track coordinates
            double trackRectangleX = trackRectangle.getX();
            double trackRectangleMaxX = trackRectangle.getMaxX();
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        private boolean flagLargeInsertions;
        private int largeInsertionsThreshold;

        RenderOptions() {
            PreferenceManager prefs = PreferenceManager.getInstance();

            String shadeOptionString = prefs.get(PreferenceManager.SAM_SHADE_BASES);
            if (shadeOptionString.equals("false")) {
                shadeBasesOption = ShadeBasesOption.NONE;
            } else if (shadeOptionString.equals("true")) {
                shadeBasesOption = ShadeBasesOption.QUALITY;
            } else {
                shadeBasesOption = ShadeBasesOption.valueOf(shadeOptionString);
            }
            shadeCenters = prefs.getAsBoolean(PreferenceManager.SAM_SHADE_CENTER);
            flagUnmappedPairs = prefs.getAsBoolean(PreferenceManager.SAM_FLAG_UNMAPPED_PAIR);
            computeIsizes = prefs.getAsBoolean(PreferenceManager.SAM_COMPUTE_ISIZES);
            minInsertSize = prefs.getAsInt(PreferenceManager.SAM_MIN_INSERT_SIZE_THRESHOLD);
            maxInsertSize = prefs.getAsInt(PreferenceManager.SAM_MAX_INSERT_SIZE_THRESHOLD);
            minInsertSizePercentile = prefs.getAsFloat(PreferenceManager.SAM_MIN_INSERT_SIZE_PERCENTILE);
            maxInsertSizePercentile = prefs.getAsFloat(PreferenceManager.SAM_MAX_INSERT_SIZE_PERCENTILE);
            showAllBases = DEFAULT_SHOWALLBASES;
            colorOption = CollUtils.valueOf(ColorOption.class, prefs.get(PreferenceManager.SAM_COLOR_BY), ColorOption.NONE);
            groupByOption = null;
            flagZeroQualityAlignments = prefs.getAsBoolean(PreferenceManager.SAM_FLAG_ZERO_QUALITY);
            bisulfiteContext = DEFAULT_BISULFITE_CONTEXT;


            colorByTag = prefs.get(PreferenceManager.SAM_COLOR_BY_TAG);
            sortByTag = prefs.get(PreferenceManager.SAM_SORT_BY_TAG);
            groupByTag = prefs.get(PreferenceManager.SAM_GROUP_BY_TAG);

            //updateColorScale();

            peStats = new HashMap<String, PEStats>();

            flagLargeInsertions = prefs.getAsBoolean(PreferenceManager.SAM_FLAG_LARGE_INSERTIONS);
            largeInsertionsThreshold = prefs.getAsInt(PreferenceManager.SAM_LARGE_INSERTIONS_THRESHOLD);
        }
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    }

    public static void setNucleotideColors() {

        PreferenceManager prefs = PreferenceManager.getInstance();

        nucleotideColors = new HashMap();

        Color a = ColorUtilities.stringToColor(prefs.get(PreferenceManager.COLOR_A), new Color(0, 150, 0));
        Color c = ColorUtilities.stringToColor(prefs.get(PreferenceManager.COLOR_C), Color.blue);
        Color t = ColorUtilities.stringToColor(prefs.get(PreferenceManager.COLOR_T),  Color.red);
        Color g = ColorUtilities.stringToColor(prefs.get(PreferenceManager.COLOR_G),  Color.gray);
        Color n = ColorUtilities.stringToColor(prefs.get(PreferenceManager.COLOR_N),  Color.gray);

        nucleotideColors.put('A', a);
        nucleotideColors.put('a', a);
        nucleotideColors.put('C', c);
        nucleotideColors.put('c', c);
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    // Storage for the header tokens
    private String[] headerTokens = new String[1000];

    public DescriptionCache() {

        PreferenceManager prefs = PreferenceManager.getInstance();
        this.maxSize = prefs.getAsInt(PreferenceManager.GWAS_DESCRIPTION_CACHE_SIZE);

    }
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