/**
* Gets background color for cell for row ic. Override it if you want to change the color from the
* default.
*/
public Color getBackgroundColorOfCell(int it, boolean selected) {
if (observedStates == null) {
doCalcs();
if (observedStates == null) return null;
}
if (observedStates.getParentData() != null) {
captureCharacterDataFromObservedStates();
Associable tInfo = data.getTaxaInfo(false);
NameReference genBankColor = NameReference.getNameReference("genbankcolor");
Object obj = tInfo.getAssociatedObject(genBankColor, it); // not saved to file
if (obj instanceof Color) return (Color) obj;
}
if (bits == null || it < 0 || it > bits.getSize()) return null;
String note = getNote(it);
if (selected) {
if (bits.isBitOn(it)) return ColorDistribution.darkGreen;
else return ColorDistribution.darkRed;
} else if (bits.isBitOn(it)) {
if (StringUtil.blank(note)) return ColorDistribution.veryLightGreen;
if (!(note.equalsIgnoreCase("x"))) return ColorDistribution.lightGreenYellowish;
return ColorDistribution.lightGreenYellow;
} else {
if (StringUtil.blank(note)) return ColorDistribution.brown;
if (!(note.equalsIgnoreCase("x"))) {
return Color.red;
}
return ColorDistribution.lightRed;
}
}
/* ======================================================================== */
public class ColorTaxon extends TaxaListAssistantI {
Taxa taxa;
MesquiteTable table;
TableTool tool;
long currentColor = ColorDistribution.numberOfRed;
String colorString = "Color Red";
long savedColor = currentColor;
MesquiteBoolean removeColor;
NameReference colorNameRef = NameReference.getNameReference("color");
public String getName() {
return "Color Taxa";
}
public String getExplanation() {
return "Provides paintbrush to color taxon names.";
}
/*.................................................................................................................*/
public int getVersionOfFirstRelease() {
return 260;
}
/*.................................................................................................................*/
public boolean startJob(String arguments, Object condition, boolean hiredByName) {
MesquiteSubmenuSpec mss =
addSubmenu(
null,
"Cell paint color",
makeCommand("setColor", this),
ColorDistribution.standardColorNames);
removeColor = new MesquiteBoolean(false);
addCheckMenuItem(null, "Remove color", makeCommand("removeColor", this), removeColor);
addMenuItem(null, "Remove all color", makeCommand("removeAllColor", this));
MesquiteSubmenuSpec mss2 =
addSubmenu(
null,
"Set Color of Selected",
makeCommand("setColorSelected", this),
ColorDistribution.standardColorNames);
// addMenuItem(null, "-", null);
// addMenuItem(null, "Color Selected", makeCommand("colorSelected", this));
setUseMenubar(false); // menu available by touching button
return true;
}
private void removeColor(int it, boolean notify) {
setColor(it, MesquiteLong.unassigned);
if (notify) table.redrawCell(-1, it);
}
private void removeAllColor(boolean notify) {
for (int it = 0; it < taxa.getNumTaxa(); it++) setColor(it, MesquiteLong.unassigned);
if (notify) table.repaintAll();
}
private void setColor(int it, long c) {
if (it < 0) return;
taxa.setAssociatedLong(colorNameRef, it, c);
table.redrawCell(-1, it);
}
/*.................................................................................................................*/
public Snapshot getSnapshot(MesquiteFile file) {
Snapshot temp = new Snapshot();
temp.addLine(
"setColor "
+ ColorDistribution.getStandardColorName(
ColorDistribution.getStandardColor((int) currentColor)));
temp.addLine("removeColor " + removeColor.toOffOnString());
return temp;
}
/*.................................................................................................................*/
/**
* A request for the MesquiteModule to perform a command. It is passed two strings, the name of
* the command and the arguments. This should be overridden by any module that wants to respond to
* a command.
*/
public Object doCommand(String commandName, String arguments, CommandChecker checker) {
if (checker.compare(MesquiteModule.class, null, null, commandName, "paint")) {
MesquiteInteger io = new MesquiteInteger(0);
int column = MesquiteInteger.fromString(arguments, io);
int row = MesquiteInteger.fromString(arguments, io);
if (MesquiteInteger.isCombinable(row)) {
if (!MesquiteLong.isCombinable(currentColor)) removeColor(row, true);
else setColor(row, (int) currentColor);
}
} else if (checker.compare(
this.getClass(),
"Sets the color to be used to paint cells",
"[name of color]",
commandName,
"setColor")) {
int bc = ColorDistribution.standardColorNames.indexOf(parser.getFirstToken(arguments));
if (bc >= 0 && MesquiteLong.isCombinable(bc)) {
removeColor.setValue(false);
currentColor = bc;
savedColor = bc;
colorString = "Color " + ColorDistribution.standardColorNames.getValue(bc);
}
} else if (checker.compare(
this.getClass(),
"Sets the color of selected taxa",
"[name of color]",
commandName,
"setColorSelected")) {
int bc = ColorDistribution.standardColorNames.indexOf(parser.getFirstToken(arguments));
if (bc >= 0 && MesquiteLong.isCombinable(bc)) {
for (int it = 0; it < taxa.getNumTaxa(); it++) if (taxa.getSelected(it)) setColor(it, bc);
}
} else if (checker.compare(
this.getClass(), "Removes color from all the cells", null, commandName, "removeAllColor")) {
removeAllColor(true);
} else if (checker.compare(
this.getClass(),
"Sets the paint brush so that it removes colors from any cells touched",
null,
commandName,
"removeColor")) {
if (StringUtil.blank(arguments)) removeColor.setValue(!removeColor.getValue());
else removeColor.toggleValue(parser.getFirstToken(arguments));
if (removeColor.getValue()) {
colorString = "Remove color";
currentColor = MesquiteLong.unassigned;
} else {
colorString = "Color " + ColorDistribution.standardColorNames.getValue((int) currentColor);
currentColor = savedColor;
}
} else return super.doCommand(commandName, arguments, checker);
return null;
}
/*.................................................................................................................*/
public boolean isSubstantive() {
return false;
}
/*.................................................................................................................*/
public void setTableAndTaxa(MesquiteTable table, Taxa taxa) {
this.table = table;
this.taxa = taxa;
if (containerOfModule() instanceof ListWindow && tool == null) {
String sortExplanation = "Assigns colors to taxa. ";
tool =
new TableTool(
this,
"sort",
getPath(),
"color.gif",
0,
0,
"Color taxon",
sortExplanation,
MesquiteModule.makeCommand("paint", this),
null,
null);
tool.setWorksOnRowNames(true);
((ListWindow) containerOfModule()).addTool(tool);
tool.setPopUpOwner(this);
}
}
}