public SeqSpan getSpan(BioSeq bs) {
if (bs.equals(this.seq)) {
return this;
} else {
return null;
}
}
public boolean getSpan(BioSeq bs, MutableSeqSpan span) {
if (bs.equals(this.seq)) {
if (forward) {
span.set(txMin, txMax, seq);
} else {
span.set(txMax, txMin, seq);
}
return true;
} else {
return false;
}
}
@Override
public Map<String, Object> cloneProperties() {
HashMap<String, Object> tprops = new HashMap<>();
tprops.put("id", name);
tprops.put("type", type);
tprops.put("gene name", geneName);
tprops.put("seq id", seq.getID());
tprops.put("forward", forward);
if (props != null) {
tprops.putAll(props);
}
return tprops;
}
@Override
public Object getProperty(String key) {
// test for standard gene sym props
if (key.equals("id")) {
return name;
} else if (key.equals("type")) {
return getType();
} else if (key.equals("gene name") || key.equals("gene_name")) {
return geneName;
} else if (key.equals("seq id")) {
return seq.getID();
} else if (key.equals("forward")) {
return forward;
} else if (key.equals("cds min")) {
return cdsMin;
} else if (key.equals("cds max")) {
return cdsMax;
} else if (props != null) {
return props.get(key);
} else {
return null;
}
}