public GeneOrthologyEntry(String line) {
String[] a = line.split("\\s");
geneName = a[0];
s288cCoords = parseCoordsString(a[1]);
sigmaCoords = parseCoordsString(a[2]);
try {
identity = Double.parseDouble(a[3]);
} catch (NumberFormatException e) {
identity = null;
}
flags = new HashSet<Flag>();
orfCoords = null;
if (a.length > 4) {
String[] fa = a[4].split(",");
for (int i = 0; i < fa.length; i++) {
try {
if (fa[i].length() > 0) {
flags.add(Flag.valueOf(fa[i]));
} else {
flags.add(Flag.UNKNOWN);
}
} catch (IllegalArgumentException e) {
System.err.println(String.format("Unknown FLAG: \"%s\"", fa[i]));
flags.add(Flag.UNKNOWN);
}
}
if (a.length > 5) {
orfCoords = parseCoordsString(a[5]);
}
}
}
public static boolean isFlagSet(short flags, Flag flag) {
return flag != null && ((flags & flag.value()) == flag.value());
}
/**
* Clears a number of flags in a message
*
* @param flags The flags
* @return A reference to the message
*/
public Message clearFlag(Flag... flags) {
if (flags != null) for (Flag flag : flags) if (flag != null) this.flags &= ~flag.value();
return this;
}
/**
* Sets a number of flags in a message
*
* @param flags The flag or flags
* @return A reference to the message
*/
public Message setFlag(Flag... flags) {
if (flags != null) for (Flag flag : flags) if (flag != null) this.flags |= flag.value();
return this;
}