private void prepareToDraw() {
if (forwardSlot0 != null) {
forwardSlot0.setCgview(p);
forwardSlot0.setFeatureThickness(featureThickness);
}
if (forwardSlot1 != null) {
forwardSlot1.setCgview(p);
forwardSlot1.setFeatureThickness(featureThickness);
}
if (forwardSlot2 != null) {
forwardSlot2.setCgview(p);
forwardSlot2.setFeatureThickness(featureThickness);
}
if (forwardSlot3 != null) {
forwardSlot3.setCgview(p);
forwardSlot3.setFeatureThickness(featureThickness);
}
if (forwardSlot4 != null) {
forwardSlot4.setCgview(p);
forwardSlot4.setFeatureThickness(featureThickness);
}
if (forwardSlot5 != null) {
forwardSlot5.setCgview(p);
forwardSlot5.setFeatureThickness(featureThickness);
}
if (forwardSlot6 != null) {
forwardSlot6.setCgview(p);
forwardSlot6.setFeatureThickness(featureThickness);
}
if (forwardSlot7 != null) {
forwardSlot7.setCgview(p);
forwardSlot7.setFeatureThickness(featureThickness);
}
if (reverseSlot0 != null) {
reverseSlot0.setCgview(p);
reverseSlot0.setFeatureThickness(featureThickness);
}
if (reverseSlot1 != null) {
reverseSlot1.setCgview(p);
reverseSlot1.setFeatureThickness(featureThickness);
}
if (reverseSlot2 != null) {
reverseSlot2.setCgview(p);
reverseSlot2.setFeatureThickness(featureThickness);
}
if (reverseSlot3 != null) {
reverseSlot3.setCgview(p);
reverseSlot3.setFeatureThickness(featureThickness);
}
if (reverseSlot4 != null) {
reverseSlot4.setCgview(p);
reverseSlot4.setFeatureThickness(featureThickness);
}
if (reverseSlot5 != null) {
reverseSlot5.setCgview(p);
reverseSlot5.setFeatureThickness(featureThickness);
}
if (reverseSlot6 != null) {
reverseSlot6.setCgview(p);
reverseSlot6.setFeatureThickness(featureThickness);
}
if (reverseSlot7 != null) {
reverseSlot7.setCgview(p);
reverseSlot7.setFeatureThickness(featureThickness);
}
if (restrictionSlot != null) {
restrictionSlot.setCgview(p);
restrictionSlot.setFeatureThickness(featureThickness);
}
// send settings to p
if (showTitle) {
p.setTitle(title);
}
p.setWidth(imageWidth);
p.setHeight(imageHeight);
p.setLabelsToKeep(MAXLABELS);
p.setDrawTickMarks(drawTickMarks);
p.setTitleFont(titleFont);
p.setLabelFont(labelFont);
p.setFeatureThickness(featureThickness);
p.setBackboneThickness(backboneThickness);
p.setFeatureSlotSpacing(featureSpacing);
p.setLegendFont(legendFont);
p.setTickLength(tickLength);
p.setLabelLineLength(labelLineLength);
p.setLabelPlacementQuality(labelPlacementQuality);
p.setUseColoredLabelBackgrounds(useColoredLabelBackground);
p.setShowBorder(showBorder);
p.setShowShading(showShading);
p.setShadingProportion(shadingProportion);
p.setUseInnerLabels(useInnerLabels);
p.setMoveInnerLabelsToOuter(moveInnerLabelsToOuter);
p.setWarningFont(rulerFont);
p.setRulerFont(rulerFont);
// if not drawing labels, don't show message.
if (!(showLabels)) {
p.setShowWarning(false);
}
// set backboneRadius based on smallest image dimension
int smallestDimension = Math.min(imageWidth, imageHeight);
if (smallestDimension <= 750) {
p.setBackboneRadius(0.50d * (double) smallestDimension / 2.0d);
} else {
p.setBackboneRadius(0.50d * 750.0d / 2.0d);
}
// check coloredLabels
if (!(useColoredLabels)) {
if (colorScheme == REGULAR) {
p.setGlobalLabelColor((Color) MAP_ITEM_COLORS.get("titleFont"));
} else if (colorScheme == INVERSE) {
p.setGlobalLabelColor((Color) MAP_ITEM_COLORS_INVERSE.get("titleFont"));
}
}
// set map item colors
if (colorScheme == REGULAR) {
p.setLongTickColor((Color) MAP_ITEM_COLORS.get("tick"));
p.setShortTickColor((Color) MAP_ITEM_COLORS.get("partialTick"));
p.setZeroTickColor((Color) MAP_ITEM_COLORS.get("zeroLine"));
p.setRulerFontColor((Color) MAP_ITEM_COLORS.get("rulerFont"));
p.setBackboneColor((Color) MAP_ITEM_COLORS.get("backbone"));
p.setTitleFontColor((Color) MAP_ITEM_COLORS.get("titleFont"));
p.setWarningFontColor((Color) MAP_ITEM_COLORS.get("titleFont"));
p.setBackgroundColor((Color) MAP_ITEM_COLORS.get("background"));
} else if (colorScheme == INVERSE) {
p.setLongTickColor((Color) MAP_ITEM_COLORS_INVERSE.get("tick"));
p.setShortTickColor((Color) MAP_ITEM_COLORS_INVERSE.get("partialTick"));
p.setZeroTickColor((Color) MAP_ITEM_COLORS_INVERSE.get("zeroLine"));
p.setRulerFontColor((Color) MAP_ITEM_COLORS_INVERSE.get("rulerFont"));
p.setBackboneColor((Color) MAP_ITEM_COLORS_INVERSE.get("backbone"));
p.setTitleFontColor((Color) MAP_ITEM_COLORS_INVERSE.get("titleFont"));
p.setWarningFontColor((Color) MAP_ITEM_COLORS_INVERSE.get("titleFont"));
p.setBackgroundColor((Color) MAP_ITEM_COLORS_INVERSE.get("background"));
}
// build legend
if ((showLegend) && (DRAW_LEGEND_ITEMS.size() > 0)) {
// create legend
legend = new Legend(p);
legend.setAllowLabelClash(allowLabelClashLegend);
legend.setBackgroundOpacity(0.5f);
legend.setFont(legendFont);
legend.setPosition(legendPosition);
if (colorScheme == REGULAR) {
legend.setBackgroundColor((Color) MAP_ITEM_COLORS.get("background"));
legend.setFontColor((Color) MAP_ITEM_COLORS.get("titleFont"));
} else if (colorScheme == INVERSE) {
legend.setBackgroundColor((Color) MAP_ITEM_COLORS_INVERSE.get("background"));
legend.setFontColor((Color) MAP_ITEM_COLORS_INVERSE.get("titleFont"));
}
LegendItem legendItem;
Enumeration legendEntries = DRAW_LEGEND_ITEMS.keys();
ArrayList list = new ArrayList();
while (legendEntries.hasMoreElements()) {
list.add(legendEntries.nextElement());
}
Collections.sort(list);
Iterator i = list.iterator();
while (i.hasNext()) {
String key = (String) i.next();
legendItem = new LegendItem(legend);
legendItem.setDrawSwatch(SWATCH_SHOW);
legendItem.setLabel((String) LEGEND_ITEM_NAMES.get(key));
if (colorScheme == REGULAR) {
legendItem.setSwatchColor((Color) FEATURE_COLORS.get(key));
} else if (colorScheme == INVERSE) {
legendItem.setSwatchColor((Color) FEATURE_COLORS_INVERSE.get(key));
}
}
}
// set message
if (showMessage) {
legend = new Legend(p);
legend.setAllowLabelClash(false);
legend.setBackgroundOpacity(0.5f);
legend.setFont(messageFont);
legend.setPosition(LEGEND_LOWER_RIGHT);
LegendItem legendItem;
if (colorScheme == REGULAR) {
legend.setBackgroundColor((Color) MAP_ITEM_COLORS.get("background"));
legend.setFontColor((Color) MAP_ITEM_COLORS.get("titleFont"));
legendItem = new LegendItem(legend);
legendItem.setLabel(message);
legendItem.setDrawSwatch(SWATCH_NO_SHOW);
} else if (colorScheme == INVERSE) {
legend.setBackgroundColor((Color) MAP_ITEM_COLORS_INVERSE.get("background"));
legend.setFontColor((Color) MAP_ITEM_COLORS_INVERSE.get("titleFont"));
legendItem = new LegendItem(legend);
legendItem.setLabel(message);
legendItem.setDrawSwatch(SWATCH_NO_SHOW);
}
}
}
/**
* Add a feature to this map. Note that the start of the feature should be a smaller number than
* the stop of the feature, regardless of the strand. The only case where start is larger than the
* stop is when the feature runs across the start/stop boundary, for example 6899-10 on a 7000bp
* plasmid.
*
* @param type one of the following: origin_of_replication, promoter, terminator,
* selectable_marker, regulatory_sequence, tag, other_gene, reporter_gene,
* unique_restriction_site, restriction_site.
* @param name the name of the feature, such as EcoRI.
* @param start the start position of the feature. Must be between 1 and the length of the
* plasmid.
* @param stop the end position of the feature. Must be between 1 and the length of the plasmid.
* @param strand the strand of the feature. Can be Plasmid.FORWARD, Plasmid.REVERSE, or
* Plasmid.NO_DIRECTION.
*/
public void addFeature(String type, String name, int start, int stop, int strand) {
// add the feature to the plasmid.
int decoration;
int label;
Color color;
// String slot;
if (start > size) {
start = size;
}
if (start < 1) {
start = 1;
}
if (stop > size) {
stop = size;
}
if (stop < 1) {
stop = 1;
}
try {
color = getFeatureColor(type);
decoration = getFeatureDecoration(type, strand);
label = getLabelType();
addItemToLegend(type, strand);
} catch (NullPointerException e) {
color = new Color(0, 0, 128); // navy
if (colorScheme == REGULAR) {
color = new Color(0, 0, 128); // navy
} else if (colorScheme == INVERSE) {
color = new Color(0, 128, 128); // teal
}
decoration = DECORATION_STANDARD;
label = LABEL;
}
// create a feature and a feature range
// then figure out which feature slot to put the feature in.
Feature feature = new Feature(showShading);
FeatureRange featureRange = new FeatureRange(feature, start, stop);
featureRange.setDecoration(decoration);
featureRange.setColor(color);
featureRange.setOpacity(opacity);
featureRange.setShowLabel(label);
if ((showPositions)
&& ((type.equalsIgnoreCase("restriction_site"))
|| (type.equalsIgnoreCase("unique_restriction_site")))) {
featureRange.setLabel(name + " " + start);
} else {
if (addCategoryInfo) {
try {
featureRange.setLabel(name + (String) FEATURE_CATEGORIES.get(type));
} catch (NullPointerException e) {
featureRange.setLabel(name);
}
} else {
featureRange.setLabel(name);
}
}
if ((type.equalsIgnoreCase("restriction_site"))
|| (type.equalsIgnoreCase("unique_restriction_site"))) {
if (restrictionSlot == null) {
restrictionSlot = new FeatureSlot(DIRECT_STRAND, showShading);
restrictionSlot.setFeatureThickness(1f);
}
feature.setFeatureSlot(restrictionSlot);
} else if ((strand == NO_DIRECTION) || (strand == FORWARD)) {
if (forwardSlot0 == null) {
forwardSlot0 = new FeatureSlot(DIRECT_STRAND, showShading);
feature.setFeatureSlot(forwardSlot0);
} else if (forwardSlot0.isRoom(feature)) {
feature.setFeatureSlot(forwardSlot0);
} else if (forwardSlot1 == null) {
forwardSlot1 = new FeatureSlot(DIRECT_STRAND, showShading);
feature.setFeatureSlot(forwardSlot1);
} else if (forwardSlot1.isRoom(feature)) {
feature.setFeatureSlot(forwardSlot1);
} else if (forwardSlot2 == null) {
forwardSlot2 = new FeatureSlot(DIRECT_STRAND, showShading);
feature.setFeatureSlot(forwardSlot2);
} else if (forwardSlot2.isRoom(feature)) {
feature.setFeatureSlot(forwardSlot2);
} else if (forwardSlot3 == null) {
forwardSlot3 = new FeatureSlot(DIRECT_STRAND, showShading);
feature.setFeatureSlot(forwardSlot3);
} else if (forwardSlot3.isRoom(feature)) {
feature.setFeatureSlot(forwardSlot3);
} else if (forwardSlot4 == null) {
forwardSlot4 = new FeatureSlot(DIRECT_STRAND, showShading);
feature.setFeatureSlot(forwardSlot4);
} else if (forwardSlot4.isRoom(feature)) {
feature.setFeatureSlot(forwardSlot4);
} else if (forwardSlot5 == null) {
forwardSlot5 = new FeatureSlot(DIRECT_STRAND, showShading);
feature.setFeatureSlot(forwardSlot5);
} else if (forwardSlot5.isRoom(feature)) {
feature.setFeatureSlot(forwardSlot5);
} else if (forwardSlot6 == null) {
forwardSlot6 = new FeatureSlot(DIRECT_STRAND, showShading);
feature.setFeatureSlot(forwardSlot6);
} else if (forwardSlot6.isRoom(feature)) {
feature.setFeatureSlot(forwardSlot6);
} else if (forwardSlot7 == null) {
forwardSlot7 = new FeatureSlot(DIRECT_STRAND, showShading);
feature.setFeatureSlot(forwardSlot7);
} else {
feature.setFeatureSlot(forwardSlot7);
}
} else if (strand == REVERSE) {
if (reverseSlot0 == null) {
reverseSlot0 = new FeatureSlot(REVERSE_STRAND, showShading);
feature.setFeatureSlot(reverseSlot0);
} else if (reverseSlot0.isRoom(feature)) {
feature.setFeatureSlot(reverseSlot0);
} else if (reverseSlot1 == null) {
reverseSlot1 = new FeatureSlot(REVERSE_STRAND, showShading);
feature.setFeatureSlot(reverseSlot1);
} else if (reverseSlot1.isRoom(feature)) {
feature.setFeatureSlot(reverseSlot1);
} else if (reverseSlot2 == null) {
reverseSlot2 = new FeatureSlot(REVERSE_STRAND, showShading);
feature.setFeatureSlot(reverseSlot2);
} else if (reverseSlot2.isRoom(feature)) {
feature.setFeatureSlot(reverseSlot2);
} else if (reverseSlot3 == null) {
reverseSlot3 = new FeatureSlot(REVERSE_STRAND, showShading);
feature.setFeatureSlot(reverseSlot3);
} else if (reverseSlot3.isRoom(feature)) {
feature.setFeatureSlot(reverseSlot3);
} else if (reverseSlot4 == null) {
reverseSlot4 = new FeatureSlot(REVERSE_STRAND, showShading);
feature.setFeatureSlot(reverseSlot4);
} else if (reverseSlot4.isRoom(feature)) {
feature.setFeatureSlot(reverseSlot4);
} else if (reverseSlot5 == null) {
reverseSlot5 = new FeatureSlot(REVERSE_STRAND, showShading);
feature.setFeatureSlot(reverseSlot5);
} else if (reverseSlot5.isRoom(feature)) {
feature.setFeatureSlot(reverseSlot5);
} else if (reverseSlot6 == null) {
reverseSlot6 = new FeatureSlot(REVERSE_STRAND, showShading);
feature.setFeatureSlot(reverseSlot6);
} else if (reverseSlot6.isRoom(feature)) {
feature.setFeatureSlot(reverseSlot6);
} else if (reverseSlot7 == null) {
reverseSlot7 = new FeatureSlot(REVERSE_STRAND, showShading);
feature.setFeatureSlot(reverseSlot7);
} else {
feature.setFeatureSlot(reverseSlot7);
}
}
}