/*...............................................................................................................*/
int numSites(int it) {
CharacterState cs = null;
if (observedStates == null) return 0;
int count = 0;
for (int ic = 0; ic < observedStates.getNumChars(); ic++) {
cs = observedStates.getCharacterState(cs, ic, it);
if (cs == null) return 0;
if (!cs.isInapplicable() && !cs.isUnassigned()) count++;
}
return count;
} /*...............................................................................................................*/
boolean hasData(int it) {
CharacterState cs = null;
try {
for (int ic = 0; ic < observedStates.getNumChars(); ic++) {
cs = observedStates.getCharacterState(cs, ic, it);
if (cs == null) return false;
if (!cs.isInapplicable() && !cs.isUnassigned()) return true;
}
} catch (NullPointerException e) {
}
return false;
}
/**
* 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;
}
}
/*...............................................................................................................*/
int sequenceLength(int it) {
CharacterState cs = null;
if (observedStates == null) return 0;
int count = 0;
for (int ic = 0; ic < observedStates.getNumChars(); ic++) {
cs = observedStates.getCharacterState(cs, ic, it);
if (cs == null) return 0;
if (cs instanceof MolecularState) {
if (!cs.isInapplicable()) // if Molecular, then count missing & with state
count++;
} else if (!cs.isInapplicable()
&& !cs.isUnassigned()) // if Molecular, then count missing & with state
count++;
}
return count;
}
public String getExplanationForRow(int ic) {
if (observedStates != null && observedStates.getParentData() != null) {
captureCharacterDataFromObservedStates();
Associable tInfo = data.getTaxaInfo(false);
if (tInfo == null) return null;
return "Notes: " + tInfo.toString(ic);
}
return null;
}
public void calculateNumber(Taxon taxon, MesquiteNumber result, MesquiteString resultString) {
if (result == null) return;
clearResultAndLastResult(result);
Taxa taxa = taxon.getTaxa();
int it = taxa.whichTaxonNumber(taxon);
if (taxa != currentTaxa || observedStates == null) {
observedStates = matrixSourceTask.getCurrentMatrix(taxa);
currentTaxa = taxa;
}
if (observedStates == null || !(observedStates.getParentData() instanceof DNAData)) return;
DNAData data = (DNAData) observedStates.getParentData();
int count = data.getAminoAcidNumbers(it, ProteinData.TER, countEvenIfOthers.getValue());
if (result != null) result.setValue(count);
if (resultString != null)
resultString.setValue(
"Number of stop codons in taxon " + observedStates.getName() + ": " + count);
saveLastResult(result);
saveLastResultString(resultString);
}
/*.................................................................................................................*/
public String getTitle() {
if (observedStates == null) doCalcs();
if (observedStates != null && getProject().getNumberCharMatricesVisible() > 1) {
CharacterData d = observedStates.getParentData();
if (d != null && d.getName() != null) {
String n = d.getName();
if (n.length() > 12) n = n.substring(0, 12);
return "Has Data (" + n + ")";
}
}
return "Has Data in Matrix";
}
void captureCharacterDataFromObservedStates() {
if (observedStates == null) {
if (data != null) data.removeListener(this);
data = null;
} else {
CharacterData temp = observedStates.getParentData();
if (temp != data) {
if (data != null) data.removeListener(this);
if (temp != null) temp.addListenerHighPriority(this);
data = temp;
}
}
}
/*.................................................................................................................*/
public boolean arrowTouchInRow(
Graphics g, int ic, int x, int y, boolean doubleClick, int modifiers) {
if (MesquiteEvent.rightClick(modifiers)) {
MesquitePopup popup = new MesquitePopup(table.getMatrixPanel());
String copyMenuText = "Copy ";
if (observedStates != null) {
CharacterData data = observedStates.getParentData();
if (data != null) {
copyMenuText += data.getName() + " Data";
copyMenuText += " [from " + data.getTaxa().getTaxonName(ic) + "]";
}
}
MesquiteCommand mcCopy = makeCommand("copyData", this);
mcCopy.setDefaultArguments("" + ic);
MesquiteCheckMenuItem mCopyItem =
new MesquiteCheckMenuItem(copyMenuText, this, mcCopy, null, null);
popup.add(mCopyItem);
String pasteMenuText = "Paste ";
if (StringUtil.notEmpty(localCopyDataClipboard) && localCopyData != null) {
pasteMenuText += localCopyData.getName() + " Data";
if (StringUtil.notEmpty(localCopyDataTaxon)) {
pasteMenuText += " [from " + localCopyDataTaxon + "] ";
}
}
MesquiteCommand mcPaste = makeCommand("pasteData", this); // only if something in clipboard
mcPaste.setDefaultArguments("" + ic);
MesquiteCheckMenuItem mPasteItem =
new MesquiteCheckMenuItem(pasteMenuText, this, mcPaste, null, null);
mPasteItem.setEnabled(StringUtil.notEmpty(localCopyDataClipboard));
popup.add(mPasteItem);
MesquiteCommand mcDelete = makeCommand("deleteDataTouched", this);
mcDelete.setDefaultArguments("" + ic);
MesquiteCheckMenuItem mDeleteItem =
new MesquiteCheckMenuItem("Delete Data", this, mcDelete, null, null);
popup.add(mDeleteItem);
popup.showPopup(x, y + 18);
return true;
}
return false;
}
/*.................................................................................................................*/
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);
}