/**
* 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);
}
}
}
