/**
* 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;
}
/*.................................................................................................................*/
void zapData(CharacterData data, int it) {
Taxa taxa = data.getTaxa();
if (it < 0 || it >= taxa.getNumTaxa()) return;
Associable tInfo = data.getTaxaInfo(false);
int myColumn = -1;
if (getEmployer() instanceof ListModule) {
myColumn = ((ListModule) getEmployer()).getMyColumn(this);
}
if (tInfo != null) tInfo.deassignAssociated(it);
for (int ic = 0; ic < data.getNumChars(); ic++) data.deassign(ic, it);
data.notifyListeners(this, new Notification(MesquiteListener.DATA_CHANGED));
outputInvalid();
parametersChanged();
}
/*...............................................................................................................*/
boolean selected(Taxa taxa, int it, int myColumn) {
if (taxa.getSelected(it)) {
return true;
}
if (table != null && myColumn >= 0) {
if (table.isCellSelectedAnyWay(myColumn, it)) return true;
}
return false;
}
public void doCalcs() {
if (bits != null) bits.clearAllBits();
if (taxa == null) return;
if (bits == null) bits = new Bits(taxa.getNumTaxa());
else bits.resetSize(taxa.getNumTaxa());
if (observedStates == null) {
tInfo = null;
observedStates = matrixSourceTask.getCurrentMatrix(taxa);
if (observedStates != null) {
captureCharacterDataFromObservedStates();
if (data != null) tInfo = data.getTaxaInfo(true);
}
}
if (observedStates == null) return;
for (int it = 0; it < taxa.getNumTaxa(); it++) {
if (hasData(it)) bits.setBit(it);
}
}
private void setColor(int it, long c) {
if (it < 0) return;
taxa.setAssociatedLong(colorNameRef, it, c);
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();
}
/*.................................................................................................................*/
public Object doCommand(String commandName, String arguments, CommandChecker checker) {
if (checker.compare(
this.getClass(), "Returns the matrix source", null, commandName, "getMatrixSource")) {
return matrixSourceTask;
} else if (checker.compare(
this.getClass(), "Copies the data for selected taxon", null, commandName, "copyData")) {
if (observedStates == null) return null;
CharacterData data = observedStates.getParentData();
if (data == null) return null;
int it = MesquiteInteger.fromString(parser.getFirstToken(arguments));
if (MesquiteInteger.isCombinable(it)) {
StringBuffer sb = new StringBuffer();
data.copyDataFromRowIntoBuffer(it, sb);
if (StringUtil.notEmpty(sb.toString())) {
localCopyDataClipboard = sb.toString();
localCopyData = data;
localCopyDataTaxon = data.getTaxa().getTaxonName(it);
} else {
localCopyDataClipboard = null;
localCopyData = null;
localCopyDataTaxon = null;
}
}
return null;
} else if (checker.compare(
this.getClass(), "Pastes the data for selected taxon", null, commandName, "pasteData")) {
if (observedStates == null) return null;
CharacterData data = observedStates.getParentData();
if (data == null) return null;
int it = MesquiteInteger.fromString(parser.getFirstToken(arguments));
if (MesquiteInteger.isCombinable(it) && StringUtil.notEmpty(localCopyDataClipboard)) {
data.pasteDataFromStringIntoTaxon(it, localCopyDataClipboard);
}
return null;
} else if (checker.compare(
this.getClass(),
"Pastes the data for selected taxon",
null,
commandName,
"deleteDataTouched")) {
if (observedStates == null) return null;
CharacterData data = observedStates.getParentData();
if (data == null) return null;
int it = MesquiteInteger.fromString(parser.getFirstToken(arguments));
Debugg.println("prepare to delete row: " + it);
if (MesquiteInteger.isCombinable(it)) {
if (!AlertDialog.query(
containerOfModule(),
"Delete Data?",
"Are you sure you want to delete the data for taxon "
+ data.getTaxa().getTaxonName(it)
+ " in the matrix \""
+ data.getName()
+ "\"",
"No",
"Yes")) {
zapData(data, it);
}
}
return null;
} else if (checker.compare(
this.getClass(), "Deletes the data for selected taxa", null, commandName, "deleteData")) {
if (observedStates == null) return null;
captureCharacterDataFromObservedStates();
if (data == null) return null;
if (!AlertDialog.query(
containerOfModule(),
"Delete Data?",
"Are you sure you want to delete the data for these taxa in the matrix \""
+ data.getName()
+ "\"",
"No",
"Yes")) zapData(data);
return null;
} else if (checker.compare(
this.getClass(),
"deleteds () and anything between",
null,
commandName,
"deletePrepended")) {
if (observedStates == null || taxa == null) return null;
boolean anySelected = taxa.anySelected();
int myColumn = -1;
if (getEmployer() instanceof ListModule) {
myColumn = ((ListModule) getEmployer()).getMyColumn(this);
if (table != null)
anySelected = anySelected || table.anyCellSelectedInColumnAnyWay(myColumn);
}
for (int it = 0; it < taxa.getNumTaxa(); it++) {
if ((!anySelected || selected(taxa, it, myColumn))) {
String note = getNote(it);
while (!StringUtil.blank(note) && note.indexOf("(") >= 0) {
int start = note.indexOf("(");
int end = note.indexOf(")");
String firstBit = "";
if (start > 0) firstBit = note.substring(0, start);
note = firstBit + note.substring(end + 1, note.length());
}
setNote(it, note);
}
}
outputInvalid();
parametersChanged();
return null;
} else if (checker.compare(this.getClass(), "deletes *", null, commandName, "deleteStar")) {
if (observedStates == null || taxa == null) return null;
boolean anySelected = taxa.anySelected();
int myColumn = -1;
if (getEmployer() instanceof ListModule) {
myColumn = ((ListModule) getEmployer()).getMyColumn(this);
if (table != null)
anySelected = anySelected || table.anyCellSelectedInColumnAnyWay(myColumn);
}
for (int it = 0; it < taxa.getNumTaxa(); it++) {
if ((!anySelected || selected(taxa, it, myColumn))) {
String note = getNote(it);
while (!StringUtil.blank(note) && note.indexOf("*") >= 0) {
int start = note.indexOf("*");
String firstBit = "";
if (start > 0) firstBit = note.substring(0, start);
note = firstBit + note.substring(start + 1, note.length());
}
setNote(it, note);
}
}
outputInvalid();
parametersChanged();
return null;
} else if (checker.compare(
this.getClass(),
"Prepends to the note the sequence length (including N\'s and ?\'s) for the selected taxa",
null,
commandName,
"prependLength")) {
if (observedStates == null || taxa == null) return null;
boolean anySelected = taxa.anySelected();
int myColumn = -1;
if (getEmployer() instanceof ListModule) {
myColumn = ((ListModule) getEmployer()).getMyColumn(this);
if (table != null)
anySelected = anySelected || table.anyCellSelectedInColumnAnyWay(myColumn);
}
for (int it = 0; it < taxa.getNumTaxa(); it++) {
if (hasData(it) && (!anySelected || selected(taxa, it, myColumn))) {
String note = getNote(it);
if (StringUtil.blank(note)) note = "(" + sequenceLength(it) + ")";
else note = "(" + sequenceLength(it) + ") " + note;
setNote(it, note);
}
}
outputInvalid();
parametersChanged();
return null;
} else if (checker.compare(
this.getClass(),
"Prepends to the note the number of non-missing sites (not including N\'s and ?\'s) for the selected taxa",
null,
commandName,
"prependNumSites")) {
if (observedStates == null || taxa == null) return null;
boolean anySelected = taxa.anySelected();
int myColumn = -1;
if (getEmployer() instanceof ListModule) {
myColumn = ((ListModule) getEmployer()).getMyColumn(this);
if (table != null)
anySelected = anySelected || table.anyCellSelectedInColumnAnyWay(myColumn);
}
for (int it = 0; it < taxa.getNumTaxa(); it++) {
if (hasData(it) && (!anySelected || selected(taxa, it, myColumn))) {
String note = getNote(it);
if (StringUtil.blank(note)) note = "(" + numSites(it) + ")";
else note = "(" + numSites(it) + ") " + note;
setNote(it, note);
}
}
outputInvalid();
parametersChanged();
return null;
} else if (checker.compare(
this.getClass(),
"Deletes the notes for the selected taxa",
null,
commandName,
"deleteAnnotation")) {
if (observedStates == null || taxa == null) return null;
boolean anySelected = taxa.anySelected();
int myColumn = -1;
if (getEmployer() instanceof ListModule) {
myColumn = ((ListModule) getEmployer()).getMyColumn(this);
if (table != null)
anySelected = anySelected || table.anyCellSelectedInColumnAnyWay(myColumn);
}
for (int it = 0; it < taxa.getNumTaxa(); it++) {
if (hasData(it) && (!anySelected || selected(taxa, it, myColumn))) {
setNote(it, null);
}
}
outputInvalid();
parametersChanged();
return null;
} else return super.doCommand(commandName, arguments, checker);
}