Example usage for java.awt Graphics2D setColor

List of usage examples for java.awt Graphics2D setColor

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Introduction

In this page you can find the example usage for java.awt Graphics2D setColor.

Prototype

public abstract void setColor(Color c);

Source Link

Document

Sets this graphics context's current color to the specified color.

Usage

From source file:org.forester.archaeopteryx.TreePanel.java

final private void paintGainedAndLostCharacters(final Graphics2D g, final PhylogenyNode node,
        final String gained, final String lost) {
    if (node.getParent() != null) {
        final double parent_x = node.getParent().getXcoord();
        final double x = node.getXcoord();
        g.setFont(getTreeFontSet().getLargeFont());
        g.setColor(getTreeColorSet().getGainedCharactersColor());
        if (Constants.SPECIAL_CUSTOM) {
            g.setColor(Color.BLUE);
        }/* w  ww  .j  a v  a  2s . c o  m*/
        TreePanel.drawString(gained,
                parent_x + ((x - parent_x - getTreeFontSet()._fm_large.stringWidth(gained)) / 2),
                (node.getYcoord() - getTreeFontSet()._fm_large.getMaxDescent()) - 1, g);
        g.setColor(getTreeColorSet().getLostCharactersColor());
        TreePanel.drawString(lost,
                parent_x + ((x - parent_x - getTreeFontSet()._fm_large.stringWidth(lost)) / 2),
                (node.getYcoord() + getTreeFontSet()._fm_large.getMaxAscent()) + 1, g);
    }
}

From source file:org.forester.archaeopteryx.TreePanel.java

final private void paintNodeLite(final Graphics2D g, final PhylogenyNode node) {
    if (node.isCollapse()) {
        if ((!node.isRoot() && !node.getParent().isCollapse()) || node.isRoot()) {
            paintCollapsedNode(g, node, false, false, false);
        }/*from  w  w  w . ja v  a  2  s  . c  om*/
        return;
    }
    if (isInFoundNodes(node)) {
        g.setColor(getTreeColorSet().getFoundColor());
        drawRectFilled(node.getXSecondary() - 1, node.getYSecondary() - 1, 3, 3, g);
    }
    float new_x = 0;
    if (!node.isExternal() && !node.isCollapse()) {
        boolean first_child = true;
        float y2 = 0.0f;
        final int parent_max_branch_to_leaf = getMaxBranchesToLeaf(node);
        for (int i = 0; i < node.getNumberOfDescendants(); ++i) {
            final PhylogenyNode child_node = node.getChildNode(i);
            int factor_x;
            if (!isUniformBranchLengthsForCladogram()) {
                factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
            } else {
                factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf(child_node);
            }
            if (first_child) {
                first_child = false;
                y2 = node.getYSecondary() - (getOvYDistance()
                        * (node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes()));
            } else {
                y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
            }
            final float x2 = calculateOvBranchLengthToParent(child_node, factor_x);
            new_x = x2 + node.getXSecondary();
            final float diff_y = node.getYSecondary() - y2;
            final float diff_x = node.getXSecondary() - new_x;
            if ((diff_y > 2) || (diff_y < -2) || (diff_x > 2) || (diff_x < -2)) {
                paintBranchLite(g, node.getXSecondary(), new_x, node.getYSecondary(), y2, child_node);
            }
            child_node.setXSecondary(new_x);
            child_node.setYSecondary(y2);
            y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
        }
    }
}

From source file:org.forester.archaeopteryx.TreePanel.java

/**
 * Draw a box at the indicated node./*from   ww  w.ja va 2 s  .  c o m*/
 * 
 * @param x
 * @param y
 * @param node
 * @param g
 */
final private void paintNodeBox(final double x, final double y, final PhylogenyNode node, final Graphics2D g,
        final boolean to_pdf, final boolean to_graphics_file, final boolean is_in_found_nodes) {
    if (node.isCollapse()) {
        return;
    }
    // if this node should be highlighted, do so
    if ((_highlight_node == node) && !to_pdf && !to_graphics_file) {
        g.setColor(getTreeColorSet().getFoundColor());

        drawOval(x - 8, y - 8, 16, 16, g);
        drawOval(x - 9, y - 8, 17, 17, g);
        drawOval(x - 9, y - 9, 18, 18, g);

        //            drawOval( x - 20, y - 8, 16, 16, g );
        //            drawOval( x - 21, y - 8, 17, 17, g );
        //            drawOval( x - 21, y - 9, 18, 18, g );

    }
    if (is_in_found_nodes) {
        paintFoundNode(ForesterUtil.roundToInt(x), ForesterUtil.roundToInt(y), g);
    } else {
        if ((to_pdf || to_graphics_file) && getOptions().isPrintBlackAndWhite()) {
            g.setColor(Color.BLACK);
        } else if (getControlPanel().isEvents() && Util.isHasAssignedEvent(node)) {
            final Event event = node.getNodeData().getEvent();
            if (event.isDuplication()) {
                g.setColor(getTreeColorSet().getDuplicationBoxColor());
            } else if (event.isSpeciation()) {
                g.setColor(getTreeColorSet().getSpecBoxColor());
            } else if (event.isSpeciationOrDuplication()) {
                g.setColor(getTreeColorSet().getDuplicationOrSpeciationColor());
            }
        } else {
            assignGraphicsForNodeBoxWithColorForParentBranch(node, g);
        }
        if ((getOptions().isShowNodeBoxes() && !to_pdf && !to_graphics_file)
                || (getControlPanel().isEvents() && node.isHasAssignedEvent())) {
            if (to_pdf || to_graphics_file) {
                if (node.isDuplication() || !getOptions().isPrintBlackAndWhite()) {
                    drawOvalFilled(x - HALF_BOX_SIZE, y - HALF_BOX_SIZE, BOX_SIZE, BOX_SIZE, g);
                }
            } else {
                // if the option show boxes is activated then draw boxes corresponding to the inserted reads below.
                if (node.getNodeData().isHasSequence()) {

                    double max_box_size = 20.0;
                    double most_inserts = Double
                            .valueOf(((Annotation) node.getNodeData().getSequences().get(0).getAnnotation(0))
                                    .getDesc().split(",")[0]);
                    List<PhylogenyNode> descendants = node.getAllExternalDescendants();
                    double inserts = 0.0;
                    for (int i = 1; i < descendants.size(); i++) { // first node does not get into account, because we want to only the branches after the node to count
                        inserts = inserts + ((double) descendants.get(i).getNodeData().getSequences().size())
                                - 1.0; //first sequence tag is always the histogram   
                    }

                    final double NODE_SIZE = 3.0 + max_box_size * inserts / most_inserts;
                    final double HALF_NODE_SIZE = NODE_SIZE / 2.0;
                    drawRectFilled(x - HALF_NODE_SIZE, y - HALF_NODE_SIZE, NODE_SIZE, NODE_SIZE, g);
                } else {
                    final double NODE_SIZE = 3.0;
                    final double HALF_NODE_SIZE = 1.5;
                    drawRectFilled(x - HALF_NODE_SIZE, y - HALF_NODE_SIZE, NODE_SIZE, NODE_SIZE, g);
                }
                //drawRectFilled( x - HALF_BOX_SIZE, y - HALF_BOX_SIZE, BOX_SIZE, BOX_SIZE, g );
            }
        }
    }
}

From source file:org.forester.archaeopteryx.TreePanel.java

final private int paintTaxonomy(final Graphics2D g, final PhylogenyNode node, final boolean is_in_found_nodes,
        final boolean to_pdf, final boolean to_graphics_file) {
    final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
    g.setFont(getTreeFontSet().getLargeItalicFont());
    if ((to_pdf || to_graphics_file) && getOptions().isPrintBlackAndWhite()) {
        g.setColor(Color.BLACK);
    } else if (is_in_found_nodes) {
        g.setFont(getTreeFontSet().getLargeItalicFont().deriveFont(TreeFontSet.BOLD_AND_ITALIC));
        g.setColor(getTreeColorSet().getFoundColor());
    } else if (getControlPanel().isColorAccordingToTaxonomy()) {
        g.setColor(getTaxonomyBasedColor(node));
    } else {/*from  w w w  .  ja v  a  2s  .  c  om*/
        g.setColor(getTreeColorSet().getTaxonomyColor());
    }
    final double start_x = node.getXcoord() + 3 + TreePanel.HALF_BOX_SIZE;
    final double start_y = node.getYcoord()
            + (getTreeFontSet()._fm_large.getAscent() / (node.getNumberOfDescendants() == 1 ? 1 : 3.0));
    _sb.setLength(0);
    if (_control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty(taxonomy.getTaxonomyCode())) {
        _sb.append(taxonomy.getTaxonomyCode());
        _sb.append(" ");
    }
    if (_control_panel.isShowTaxonomyNames()) {
        if (!ForesterUtil.isEmpty(taxonomy.getScientificName())
                && !ForesterUtil.isEmpty(taxonomy.getCommonName())) {
            _sb.append(taxonomy.getScientificName());
            _sb.append(" (");
            _sb.append(taxonomy.getCommonName());
            _sb.append(") ");
        } else if (!ForesterUtil.isEmpty(taxonomy.getScientificName())) {
            _sb.append(taxonomy.getScientificName());
            _sb.append(" ");
        } else if (!ForesterUtil.isEmpty(taxonomy.getCommonName())) {
            _sb.append(taxonomy.getCommonName());
            _sb.append(" ");
        }
    }
    final String label = _sb.toString();
    /* GUILHEM_BEG */
    if ((label.length() > 0) && (node.getNodeData().isHasSequence())
            && node.getNodeData().getSequence().equals(_query_sequence)) {
        // invert font color and background color to show that this is the query sequence
        final Rectangle2D nodeTextBounds = new TextLayout(label, g.getFont(),
                new FontRenderContext(null, false, false)).getBounds();
        g.fillRect((int) start_x - 1, (int) start_y - 8, (int) nodeTextBounds.getWidth() + 4, 11);
        g.setColor(getTreeColorSet().getBackgroundColor());
    }
    /* GUILHEM_END */
    TreePanel.drawString(label, start_x, start_y, g);
    if (is_in_found_nodes) {
        return getTreeFontSet()._fm_large_italic_bold.stringWidth(label);
    } else {
        return getTreeFontSet()._fm_large_italic.stringWidth(label);
    }
}

From source file:de.tor.tribes.ui.panels.MinimapPanel.java

private boolean redraw() {
    Village[][] mVisibleVillages = DataHolder.getSingleton().getVillages();

    if (mVisibleVillages == null || mBuffer == null) {
        return false;
    }//from w ww.  ja  v  a2 s  .  c o  m

    Graphics2D g2d = (Graphics2D) mBuffer.getGraphics();
    Composite tempC = g2d.getComposite();
    //clear
    g2d.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR));
    g2d.fillRect(0, 0, mBuffer.getWidth(), mBuffer.getHeight());

    //reset composite
    g2d.setComposite(tempC);

    boolean markPlayer = GlobalOptions.getProperties().getBoolean("mark.villages.on.minimap");
    if (ServerSettings.getSingleton().getMapDimension() == null) {
        //could not draw minimap if dimensions are not loaded yet
        return false;
    }
    boolean showBarbarian = GlobalOptions.getProperties().getBoolean("show.barbarian");

    Color DEFAULT = Constants.DS_DEFAULT_MARKER;
    try {
        int mark = Integer.parseInt(GlobalOptions.getProperty("default.mark"));
        if (mark == 0) {
            DEFAULT = Constants.DS_DEFAULT_MARKER;
        } else if (mark == 1) {
            DEFAULT = Color.RED;
        } else if (mark == 2) {
            DEFAULT = Color.WHITE;
        }
    } catch (Exception e) {
        DEFAULT = Constants.DS_DEFAULT_MARKER;
    }

    Rectangle mapDim = ServerSettings.getSingleton().getMapDimension();
    double wField = mapDim.getWidth() / (double) visiblePart.width;
    double hField = mapDim.getHeight() / (double) visiblePart.height;

    UserProfile profile = GlobalOptions.getSelectedProfile();
    Tribe currentTribe = InvalidTribe.getSingleton();
    if (profile != null) {
        currentTribe = profile.getTribe();
    }

    for (int i = visiblePart.x; i < (visiblePart.width + visiblePart.x); i++) {
        for (int j = visiblePart.y; j < (visiblePart.height + visiblePart.y); j++) {
            Village v = mVisibleVillages[i][j];
            if (v != null) {
                Color markerColor = null;
                boolean isLeft = false;
                if (v.getTribe() == Barbarians.getSingleton()) {
                    isLeft = true;
                } else {
                    if ((currentTribe != null) && (v.getTribe().getId() == currentTribe.getId())) {
                        //village is owned by current player. mark it dependent on settings
                        if (markPlayer) {
                            markerColor = Color.YELLOW;
                        }
                    } else {
                        try {
                            Marker marker = MarkerManager.getSingleton().getMarker(v.getTribe());
                            if (marker != null && !marker.isShownOnMap()) {
                                marker = null;
                                markerColor = DEFAULT;
                            }

                            if (marker == null) {
                                marker = MarkerManager.getSingleton().getMarker(v.getTribe().getAlly());
                                if (marker != null && marker.isShownOnMap()) {
                                    markerColor = marker.getMarkerColor();
                                }
                            } else {
                                if (marker.isShownOnMap()) {
                                    markerColor = marker.getMarkerColor();
                                }
                            }
                        } catch (Exception e) {
                            markerColor = null;
                        }
                    }
                }

                if (!isLeft) {
                    if (markerColor != null) {
                        g2d.setColor(markerColor);
                    } else {
                        g2d.setColor(DEFAULT);
                    }
                    g2d.fillRect((int) Math.round((i - visiblePart.x) * wField),
                            (int) Math.round((j - visiblePart.y) * hField), (int) Math.floor(wField),
                            (int) Math.floor(hField));
                } else {
                    if (showBarbarian) {
                        g2d.setColor(Color.LIGHT_GRAY);
                        g2d.fillRect((int) Math.round((i - visiblePart.x) * wField),
                                (int) Math.round((j - visiblePart.y) * hField), (int) Math.floor(wField),
                                (int) Math.floor(hField));
                    }
                }
            }
        }
    }

    try {
        if (GlobalOptions.getProperties().getBoolean("map.showcontinents")) {
            g2d.setColor(Color.BLACK);
            Composite c = g2d.getComposite();
            Composite a = AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.4f);
            Font f = g2d.getFont();
            Font t = new Font("Serif", Font.BOLD, (int) Math.round(30 * hField));
            g2d.setFont(t);
            int fact = 10;
            int mid = (int) Math.round(50 * wField);

            for (int i = 0; i < 10; i++) {
                for (int j = 0; j < 10; j++) {
                    g2d.setComposite(a);

                    String conti = "K" + (j * 10 + i);
                    Rectangle2D bounds = g2d.getFontMetrics(t).getStringBounds(conti, g2d);
                    int cx = i * fact * 10 - visiblePart.x;
                    int cy = j * fact * 10 - visiblePart.y;
                    cx = (int) Math.round(cx * wField);
                    cy = (int) Math.round(cy * hField);
                    g2d.drawString(conti, (int) Math.rint(cx + mid - bounds.getWidth() / 2),
                            (int) Math.rint(cy + mid + bounds.getHeight() / 2));
                    g2d.setComposite(c);
                    int wk = 100;
                    int hk = 100;

                    if (i == 9) {
                        wk -= 1;
                    }
                    if (j == 9) {
                        hk -= 1;
                    }

                    g2d.drawRect(cx, cy, (int) Math.round(wk * wField), (int) Math.round(hk * hField));
                }
            }
            g2d.setFont(f);
        }
    } catch (Exception e) {
        logger.error("Creation of Minimap failed", e);
    }
    g2d.dispose();
    return true;
}

From source file:org.forester.archaeopteryx.TreePanel.java

final void paintBranchCircularLite(final PhylogenyNode p, final PhylogenyNode c, final Graphics2D g) {
    final double angle = _urt_nodeid_angle_map.get(c.getNodeId());
    final double root_x = _root.getXSecondary();
    final double root_y = _root.getYSecondary();
    final double dx = root_x - p.getXSecondary();
    final double dy = root_y - p.getYSecondary();
    final double arc = (_urt_nodeid_angle_map.get(p.getNodeId())) - angle;
    final double parent_radius = Math.sqrt(dx * dx + dy * dy);
    g.setColor(getTreeColorSet().getOvColor());
    if ((c.isFirstChildNode() || c.isLastChildNode()) && (Math.abs(arc) > 0.02)) {
        final double r2 = 2.0 * parent_radius;
        drawArc(root_x - parent_radius, root_y - parent_radius, r2, r2, (-angle - arc), arc, g);
    }/*w w  w  . jav  a2  s .c  om*/
    drawLine(c.getXSecondary(), c.getYSecondary(), root_x + (Math.cos(angle) * parent_radius),
            root_y + (Math.sin(angle) * parent_radius), g);
    if (isInFoundNodes(c)) {
        g.setColor(getTreeColorSet().getFoundColor());
        drawRectFilled(c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, g);
    }
}

From source file:org.forester.archaeopteryx.TreePanel.java

final private void paintNodeDataUnrootedCirc(final Graphics2D g, final PhylogenyNode node, final boolean to_pdf,
        final boolean to_graphics_file, final boolean radial_labels, final double ur_angle,
        final boolean is_in_found_nodes) {
    if (isNodeDataInvisibleUnrootedCirc(node) && !to_graphics_file && !to_pdf) {
        return;//from   w w  w .j  av a  2 s  .c  om
    }
    if ((to_pdf || to_graphics_file) && getOptions().isPrintBlackAndWhite()) {
        g.setColor(Color.BLACK);
    } else if (is_in_found_nodes) {
        g.setColor(getTreeColorSet().getFoundColor());
    } else if (getControlPanel().isColorAccordingToTaxonomy()) {
        g.setColor(getTaxonomyBasedColor(node));
    } else {
        g.setColor(getTreeColorSet().getSequenceColor());
    }
    _sb.setLength(0);
    _sb.append(" ");
    if (node.getNodeData().isHasTaxonomy()
            && (getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyNames())) {
        final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
        if (_control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty(taxonomy.getTaxonomyCode())) {
            _sb.append(taxonomy.getTaxonomyCode());
            _sb.append(" ");
        }
        if (_control_panel.isShowTaxonomyNames()) {
            if (!ForesterUtil.isEmpty(taxonomy.getScientificName())
                    && !ForesterUtil.isEmpty(taxonomy.getCommonName())) {
                _sb.append(taxonomy.getScientificName());
                _sb.append(" (");
                _sb.append(taxonomy.getCommonName());
                _sb.append(") ");
            } else if (!ForesterUtil.isEmpty(taxonomy.getScientificName())) {
                _sb.append(taxonomy.getScientificName());
                _sb.append(" ");
            } else if (!ForesterUtil.isEmpty(taxonomy.getCommonName())) {
                _sb.append(taxonomy.getCommonName());
                _sb.append(" ");
            }
        }
    }
    if (node.isCollapse() && ((!node.isRoot() && !node.getParent().isCollapse()) || node.isRoot())) {
        _sb.append(" [");
        _sb.append(node.getAllExternalDescendants().size());
        _sb.append("]");
    }
    if (getControlPanel().isShowNodeNames() && (node.getNodeName().length() > 0)) {
        if (_sb.length() > 0) {
            _sb.append(" ");
        }
        _sb.append(node.getNodeName());
    }
    if (node.getNodeData().isHasSequence()) {
        if (getControlPanel().isShowSequenceAcc()
                && (node.getNodeData().getSequence().getAccession() != null)) {
            if (_sb.length() > 0) {
                _sb.append(" ");
            }
            if (!ForesterUtil.isEmpty(node.getNodeData().getSequence().getAccession().getSource())) {
                _sb.append(node.getNodeData().getSequence().getAccession().getSource());
                _sb.append(":");
            }
            _sb.append(node.getNodeData().getSequence().getAccession().getValue());
        }
        if (getControlPanel().isShowGeneNames() && (node.getNodeData().getSequence().getName().length() > 0)) {
            //                if ( _sb.length() > 0 ) {
            //                    _sb.append( " " );
            //                }
            //                _sb.append( node.getNodeData().getSequence().getName() );
            PhylogenyNode parent = node.getParent();
            double x1 = parent.getXcoord();
            double y1 = parent.getYcoord();
            double x2 = node.getXcoord();
            double y2 = node.getYcoord();
            double above_the_line = 1.0;

            if (getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED) {
                double center_of_branch_x = Math.abs(x1 + x2) / 2.0;
                double center_of_branch_y = Math.abs(y1 + y2) / 2.0;
                TreePanel.drawString(node.getNodeData().getSequence().getName(), center_of_branch_x,
                        center_of_branch_y - above_the_line, g);
            }
        }
    }
    g.setFont(getTreeFontSet().getLargeFont());
    if (is_in_found_nodes) {
        g.setFont(getTreeFontSet().getLargeFont().deriveFont(Font.BOLD));
    }
    if (_sb.length() > 1) {
        final String sb_str = _sb.toString();
        double m = 0;
        if (_graphics_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR) {
            m = _urt_nodeid_angle_map.get(node.getNodeId()) % TWO_PI;
        } else {
            m = (float) (ur_angle % TWO_PI);
        }
        _at = g.getTransform();
        boolean need_to_reset = false;
        final float x_coord = node.getXcoord();
        final float y_coord = node.getYcoord() + (getTreeFontSet()._fm_large.getAscent() / 3.0f);
        if (radial_labels) {
            need_to_reset = true;
            boolean left = false;
            if ((m > HALF_PI) && (m < ONEHALF_PI)) {
                m -= PI;
                left = true;
            }
            g.rotate(m, x_coord, node.getYcoord());
            if (left) {
                g.translate(-(getTreeFontSet()._fm_large.getStringBounds(sb_str, g).getWidth()), 0);
            }
        } else {
            if ((m > HALF_PI) && (m < ONEHALF_PI)) {
                need_to_reset = true;
                g.translate(-getTreeFontSet()._fm_large.getStringBounds(sb_str, g).getWidth(), 0);
            }
        }
        TreePanel.drawString(sb_str, x_coord, y_coord, g);
        if (need_to_reset) {
            g.setTransform(_at);
        }
    }
}

From source file:org.forester.archaeopteryx.TreePanel.java

final private void paintScale(final Graphics2D g, int x1, int y1, final boolean to_pdf,
        final boolean to_graphics_file) {
    if (!getControlPanel().isDrawPhylogram() || (getScaleDistance() <= 0.0)) {
        return;//from w ww.jav  a  2  s . co  m
    }
    x1 += MOVE;
    final double x2 = x1 + (getScaleDistance() * getXcorrectionFactor());
    y1 -= 12;
    final int y2 = y1 - 8;
    final int y3 = y1 - 4;
    g.setFont(getTreeFontSet().getSmallFont());
    if ((to_pdf || to_graphics_file) && getOptions().isPrintBlackAndWhite()) {
        g.setColor(Color.BLACK);
    } else {
        g.setColor(getTreeColorSet().getBranchLengthColor());
    }
    drawLine(x1, y1, x1, y2, g);
    drawLine(x2, y1, x2, y2, g);
    drawLine(x1, y3, x2, y3, g);
    if (getScaleLabel() != null) {
        g.drawString(getScaleLabel(), (x1 + 2), y3 - 2);
    }
}

From source file:org.forester.archaeopteryx.TreePanel.java

final private void paintOvRectangle(final Graphics2D g) {
    final float w_ratio = (float) getWidth() / getVisibleRect().width;
    final float h_ratio = (float) getHeight() / getVisibleRect().height;
    final float x_ratio = (float) getWidth() / getVisibleRect().x;
    final float y_ratio = (float) getHeight() / getVisibleRect().y;
    final float width = getOvMaxWidth() / w_ratio;
    final float height = getOvMaxHeight() / h_ratio;
    final float x = getVisibleRect().x + getOvXPosition() + getOvMaxWidth() / x_ratio;
    final float y = getVisibleRect().y + getOvYPosition() + getOvMaxHeight() / y_ratio;
    g.setColor(getTreeColorSet().getFoundColor());
    getOvRectangle().setRect(x, y, width, height);
    if ((width < 6) && (height < 6)) {
        drawRectFilled(x, y, 6, 6, g);// ww w  .j  a  va2s . c o m
        getOvVirtualRectangle().setRect(x, y, 6, 6);
    } else if (width < 6) {
        drawRectFilled(x, y, 6, height, g);
        getOvVirtualRectangle().setRect(x, y, 6, height);
    } else if (height < 6) {
        drawRectFilled(x, y, width, 6, g);
        getOvVirtualRectangle().setRect(x, y, width, 6);
    } else {
        drawRect(x, y, width, height, g);
        if (isInOvRect()) {
            drawRect(x + 1, y + 1, width - 2, height - 2, g);
        }
        getOvVirtualRectangle().setRect(x, y, width, height);
    }
}

From source file:org.forester.archaeopteryx.TreePanel.java

final void paintPhylogeny(final Graphics2D g, final boolean to_pdf, final boolean to_graphics_file,
        final int graphics_file_width, final int graphics_file_height, final int graphics_file_x,
        final int graphics_file_y) {
    /* GUILHEM_BEG */
    _query_sequence = _control_panel.getSelectedQuerySequence();
    /* GUILHEM_END */
    // Color the background
    if (!to_pdf) {
        final Rectangle r = getVisibleRect();
        if (!getOptions().isBackgroundColorGradient() || getOptions().isPrintBlackAndWhite()) {
            g.setColor(getTreeColorSet().getBackgroundColor());
            if (!to_graphics_file) {
                g.fill(r);/*from   w ww .j av  a 2 s  .  c o  m*/
            } else {
                if (getOptions().isPrintBlackAndWhite()) {
                    g.setColor(Color.WHITE);
                }
                g.fillRect(graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height);
            }
        } else {
            if (!to_graphics_file) {
                g.setPaint(new GradientPaint(r.x, r.y, getTreeColorSet().getBackgroundColor(), r.x,
                        r.y + r.height, getTreeColorSet().getBackgroundColorGradientBottom()));
                g.fill(r);
            } else {
                g.setPaint(new GradientPaint(graphics_file_x, graphics_file_y,
                        getTreeColorSet().getBackgroundColor(), graphics_file_x,
                        graphics_file_y + graphics_file_height,
                        getTreeColorSet().getBackgroundColorGradientBottom()));
                g.fillRect(graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height);
            }
        }
        g.setStroke(new BasicStroke(1));
    } else {
        g.setStroke(new BasicStroke(getOptions().getPrintLineWidth()));
    }
    if ((getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED)
            && (getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR)) {
        _external_node_index = 0;
        // Position starting X of tree
        if (!_phylogeny.isRooted()) {
            _phylogeny.getRoot().setXcoord(TreePanel.MOVE);
        } else if ((_phylogeny.getRoot().getDistanceToParent() > 0.0) && getControlPanel().isDrawPhylogram()) {
            _phylogeny.getRoot().setXcoord((float) (TreePanel.MOVE
                    + (_phylogeny.getRoot().getDistanceToParent() * getXcorrectionFactor())));
        } else {
            _phylogeny.getRoot().setXcoord(TreePanel.MOVE + getXdistance());
        }
        // Position starting Y of tree
        _phylogeny.getRoot().setYcoord(
                (getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes()) + (TreePanel.MOVE / 2.0f));
        final int dynamic_hiding_factor = (int) (getTreeFontSet()._fm_large.getHeight()
                / (1.5 * getYdistance()));
        if (getControlPanel().isDynamicallyHideData()) {
            if (dynamic_hiding_factor > 1) {
                getControlPanel().setDynamicHidingIsOn(true);
            } else {
                getControlPanel().setDynamicHidingIsOn(false);
            }
        }
        final PhylogenyNodeIterator it;
        for (it = _phylogeny.iteratorPreorder(); it.hasNext();) {
            paintNodeRectangular(g, it.next(), to_pdf,
                    getControlPanel().isDynamicallyHideData() && (dynamic_hiding_factor > 1),
                    dynamic_hiding_factor, to_graphics_file);
        }
        if (getOptions().isShowScale()) {
            if (!(to_graphics_file || to_pdf)) {
                paintScale(g, getVisibleRect().x, getVisibleRect().y + getVisibleRect().height, to_pdf,
                        to_graphics_file);
            } else {
                paintScale(g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf,
                        to_graphics_file);
            }
        }
        if (getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf) {
            paintPhylogenyLite(g);
        }
    } else if (getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED) {
        if (getControlPanel().getDynamicallyHideData() != null) {
            getControlPanel().setDynamicHidingIsOn(false);
        }
        final double angle = getStartingAngle();
        final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
        _dynamic_hiding_factor = 0;
        if (getControlPanel().isDynamicallyHideData()) {
            _dynamic_hiding_factor = (int) ((getTreeFontSet()._fm_large.getHeight() * 1.5
                    * getPhylogeny().getNumberOfExternalNodes()) / (TWO_PI * 10));
        }
        if (getControlPanel().getDynamicallyHideData() != null) {
            if (_dynamic_hiding_factor > 1) {
                getControlPanel().setDynamicHidingIsOn(true);
            } else {
                getControlPanel().setDynamicHidingIsOn(false);
            }
        }
        paintUnrooted(_phylogeny.getRoot(), angle, (float) (angle + 2 * Math.PI), radial_labels, g, to_pdf,
                to_graphics_file);
        if (getOptions().isShowScale()) {
            if (!(to_graphics_file || to_pdf)) {
                paintScale(g, getVisibleRect().x, getVisibleRect().y + getVisibleRect().height, to_pdf,
                        to_graphics_file);
            } else {
                paintScale(g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf,
                        to_graphics_file);
            }
        }
        if (getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf) {
            g.setColor(getTreeColorSet().getOvColor());
            paintUnrootedLite(_phylogeny.getRoot(), angle, angle + 2 * Math.PI, g,
                    (getUrtFactorOv() / (getVisibleRect().width / getOvMaxWidth())));
            paintOvRectangle(g);
        }
    } else if (getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR) {
        final int radius = (int) ((Math.min(getPreferredSize().getWidth(), getPreferredSize().getHeight()) / 2)
                - (MOVE + getLongestExtNodeInfo()));
        final int d = radius + MOVE + getLongestExtNodeInfo();
        _dynamic_hiding_factor = 0;
        if (getControlPanel().isDynamicallyHideData() && (radius > 0)) {
            _dynamic_hiding_factor = (int) ((getTreeFontSet()._fm_large.getHeight() * 1.5
                    * getPhylogeny().getNumberOfExternalNodes()) / (TWO_PI * radius));
        }
        if (getControlPanel().getDynamicallyHideData() != null) {
            if (_dynamic_hiding_factor > 1) {
                getControlPanel().setDynamicHidingIsOn(true);
            } else {
                getControlPanel().setDynamicHidingIsOn(false);
            }
        }
        paintCircular(_phylogeny, getStartingAngle(), d, d, radius > 0 ? radius : 0, g, to_pdf,
                to_graphics_file);
        if (getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf) {
            final int radius_ov = (int) (getOvMaxHeight() < getOvMaxWidth() ? getOvMaxHeight() / 2
                    : getOvMaxWidth() / 2);
            double x_scale = 1.0;
            double y_scale = 1.0;
            int x_pos = getVisibleRect().x + getOvXPosition();
            int y_pos = getVisibleRect().y + getOvYPosition();
            if (getWidth() > getHeight()) {
                x_scale = (double) getHeight() / getWidth();
                x_pos = ForesterUtil.roundToInt(x_pos / x_scale);
            } else {
                y_scale = (double) getWidth() / getHeight();
                y_pos = ForesterUtil.roundToInt(y_pos / y_scale);
            }
            _at = g.getTransform();
            g.scale(x_scale, y_scale);
            paintCircularLite(_phylogeny, getStartingAngle(), x_pos + radius_ov, y_pos + radius_ov,
                    (int) (radius_ov - (getLongestExtNodeInfo()
                            / (getVisibleRect().width / getOvRectangle().getWidth()))),
                    g);
            g.setTransform(_at);
            paintOvRectangle(g);
        }
    }
}