/** condition passed to this module must be subclass of CharacterState */
public boolean startJob(String arguments, Object condition, boolean hiredByName) {
hiringCondition = condition;
String exp, mexp;
if (getExplanationByWhichHired() != null) {
exp = getExplanationByWhichHired();
mexp = exp;
} else {
exp = "Source of Characters (for " + getEmployer().getName() + ")";
mexp = exp;
}
MesquiteModuleInfo mmi =
MesquiteTrunk.mesquiteModulesInfoVector.findModule(
mesquite.charMatrices.StoredCharacters.StoredCharacters.class);
if (mmi != null && !mmi.isCompatible(condition, getProject(), this)) {
if (!MesquiteDialog.useWizards) {
exp +=
"\n\nNOTE: The choice Stored Characters does not appear because there are no appropriate matrices currently defined and stored in the data file or project. ";
}
} else if (CharacterSource.useStoredAsDefault()) {
characterSourceTask =
(CharacterObedSource)
hireNamedEmployee(
CharacterObedSource.class,
"#mesquite.charMatrices.StoredCharacters.StoredCharacters",
condition);
}
if (characterSourceTask == null) {
if (arguments == null) arguments = MesquiteThread.retrieveAndDeleteHint(this);
if (arguments != null)
characterSourceTask =
(CharacterObedSource)
hireNamedEmployee(CharacterObedSource.class, arguments, condition);
if (characterSourceTask == null) {
if (condition != null)
characterSourceTask =
(CharacterObedSource)
hireCompatibleEmployee(CharacterObedSource.class, condition, exp);
else
characterSourceTask = (CharacterObedSource) hireEmployee(CharacterObedSource.class, exp);
}
}
if (characterSourceTask == null)
return sorry(getName() + " couldn't start because no source of characters was obtained.");
charSourceName = new MesquiteString(characterSourceTask.getName());
cstC = makeCommand("setCharacterSource", this);
characterSourceTask.setHiringCommand(cstC);
if (numModulesAvailable(CharacterObedSource.class) > 1) {
mss = addSubmenu(null, mexp, cstC, CharacterObedSource.class);
mss.setNameHolder(this);
if (condition != null) mss.setCompatibilityCheck(hiringCondition);
mss.setSelected(charSourceName);
}
return true;
}
/*.................................................................................................................*/
public boolean queryOptions() {
if (!MesquiteThread.isScripting()) {
duplicateExcludedCharacters =
!AlertDialog.query(
containerOfModule(),
"Remove excluded characters?",
"Remove excluded characters?",
"Yes",
"No");
}
return true;
}
/*.................................................................................................................*/
public boolean startJob(String arguments, Object condition, boolean hiredByName) {
if (!MesquiteThread.isScripting()) {
int s =
MesquiteInteger.queryInteger(
containerOfModule(),
"Number of taxa to exclude",
"Enter the number of randomly chosen taxa to exclude",
numExcluded);
if (MesquiteInteger.isCombinable(s)) numExcluded = s;
else return false;
}
addMenuItem("Number of Taxa Excluded...", makeCommand("setNumberExcluded", this));
return true;
}
/**
* Called to provoke any necessary initialization. This helps prevent the module's intialization
* queries to the user from happening at inopportune times (e.g., while a long chart calculation
* is in mid-progress)
*/
public void initialize(Taxa taxa) {
setPreferredTaxa(taxa);
fillerTask.initialize(taxa);
if (!fillerTask.hasLimitedTrees(taxa)) {
if (!MesquiteThread.isScripting() && !nTreesSet) {
int n =
MesquiteInteger.queryInteger(
containerOfModule(),
"Trees per block?",
"How many trees to include per tree block?",
numTrees);
if (MesquiteInteger.isCombinable(n) && n > 0) numTrees = n;
nTreesSet = true;
}
}
ntreesItem.setEnabled(!fillerTask.hasLimitedTrees(taxa));
MesquiteTrunk.resetMenuItemEnabling();
}
/**
* Called to provoke any necessary initialization. This helps prevent the module's intialization
* queries to the user from happening at inopportune times (e.g., while a long chart calculation
* is in mid-progress)
*/
public void initialize(Taxa taxa) {
setPreferredTaxa(taxa);
fillerTask.initialize(taxa);
if (!fillerTask.hasLimitedTrees(taxa)) {
if (!MesquiteThread.isScripting() && !nTreesSet) {
int n =
MesquiteInteger.queryInteger(
containerOfModule(),
"Trees per block?",
"How many trees to include per tree block?",
numTrees);
if (MesquiteInteger.isCombinable(n) && n > 0) numTrees = n;
nTreesSet = true;
}
}
if (enableNumTreesChoice() && ntreesItem == null)
ntreesItem = addMenuItem("Number of Trees...", makeCommand("setNumberTrees", this));
if (ntreesItem != null && fillerTask != null)
ntreesItem.setEnabled(!fillerTask.hasLimitedTrees(taxa));
MesquiteTrunk.resetMenuItemEnabling();
}
/*.................................................................................................................*/
public boolean startJob(String arguments, Object condition, boolean hiredByName) {
if (arguments == null) {
if (MesquiteThread.isScripting())
fillerTask = (TreeBlockFiller) hireNamedEmployee(TreeBlockFiller.class, "#StoredTrees");
if (fillerTask == null)
fillerTask =
(TreeBlockFiller)
hireEmployee(TreeBlockFiller.class, "Source of trees for tree blocks");
} else {
fillerTask = (TreeBlockFiller) hireNamedEmployee(TreeBlockFiller.class, arguments);
if (fillerTask == null)
fillerTask =
(TreeBlockFiller)
hireEmployee(TreeBlockFiller.class, "Source of trees for tree blocks");
}
if (fillerTask == null)
return sorry(getName() + " couldn't start because no source of trees obtained.");
ntreesItem = addMenuItem("Number of Trees...", makeCommand("setNumberTrees", this));
return true;
}
/*.................................................................................................................*/
public Tree retrieveTreeBlock(TreeVector treeList, MesquiteDouble finalScore) {
logln("Preparing to receive TNT trees.");
boolean success = false;
taxa = treeList.getTaxa();
// TODO finalScore.setValue(finalValue);
suppressProjectPanelReset();
CommandRecord oldCR = MesquiteThread.getCurrentCommandRecord();
CommandRecord scr = new CommandRecord(true);
MesquiteThread.setCurrentCommandRecord(scr);
// define file paths and set tree files as needed.
setFileNames();
String[] outputFilePaths = externalProcRunner.getOutputFilePaths();
String treeFilePath = outputFilePaths[OUT_TREEFILE];
taxonNumberTranslation = getTaxonNumberTranslation(taxa);
namer.setNumberTranslationTable(taxonNumberTranslation);
runFilesAvailable();
// read in the tree files
success = false;
Tree t = null;
MesquiteBoolean readSuccess = new MesquiteBoolean(false);
// TreeVector tv = new TreeVector(taxa);
if (bootstrapOrJackknife()) {
if (resamplingAllConsensusTrees)
t =
ZephyrUtil.readTNTTreeFile(
this,
treeList,
taxa,
treeFilePath,
"TNT " + getResamplingKindName() + " Rep",
0,
readSuccess,
false,
false,
null,
namer); // set first tree number as 0 as will remove the first one later.
else
t =
ZephyrUtil.readTNTTreeFile(
this,
treeList,
taxa,
treeFilePath,
"TNT " + getResamplingKindName() + " Majority Rule Tree",
1,
readSuccess,
false,
false,
freqRef,
namer);
} else
t =
ZephyrUtil.readTNTTreeFile(
this,
treeList,
taxa,
treeFilePath,
"TNTTree",
1,
readSuccess,
false,
harvestOnlyStrictConsensus,
null,
namer);
success = t != null;
if (success && bootstrapOrJackknife() && resamplingAllConsensusTrees) {
t = t.cloneTree();
treeList.removeElementAt(0, false); // get rid of first one as this is the bootstrap tree
}
MesquiteThread.setCurrentCommandRecord(oldCR);
success = readSuccess.getValue();
if (!success) {
logln("Execution of TNT unsuccessful [2]");
if (!beanWritten) postBean("unsuccessful [2]", false);
beanWritten = true;
} else {
if (!beanWritten) postBean("successful", false);
beanWritten = true;
}
desuppressProjectPanelReset();
if (data != null) data.decrementEditInhibition();
// manager.deleteElement(tv); // get rid of temporary tree block
externalProcRunner.finalCleanup();
if (success) return t;
return null;
}
public boolean queryOptions() {
if (!okToInteractWithUser(
CAN_PROCEED_ANYWAY,
"Querying Options")) // Debugg.println needs to check that options set well enough to
// proceed anyway
return true;
boolean closeWizard = false;
if ((MesquiteTrunk.isMacOSXBeforeSnowLeopard()) && MesquiteDialog.currentWizard == null) {
CommandRecord cRec = null;
cRec = MesquiteThread.getCurrentCommandRecordDefIfNull(null);
if (cRec != null) {
cRec.requestEstablishWizard(true);
closeWizard = true;
}
}
MesquiteInteger buttonPressed = new MesquiteInteger(1);
queryOptionsDialog =
new ExtensibleDialog(
containerOfModule(),
"TNT Options & Locations",
buttonPressed); // MesquiteTrunk.mesquiteTrunk.containerOfModule()
// queryOptionsDialog.addLabel("TNT - Options and Locations");
String helpString =
"This module will prepare a matrix for TNT, and ask TNT do to an analysis. A command-line version of TNT must be installed. "
+ "You can ask it to do a bootstrap analysis or not. "
+ "Mesquite will read in the trees found by TNT. ";
queryOptionsDialog.appendToHelpString(helpString);
queryOptionsDialog.setHelpURL(zephyrRunnerEmployer.getProgramURL());
MesquiteTabbedPanel tabbedPanel = queryOptionsDialog.addMesquiteTabbedPanel();
tabbedPanel.addPanel("TNT Program Details", true);
externalProcRunner.addItemsToDialogPanel(queryOptionsDialog);
Checkbox parallelCheckBox =
queryOptionsDialog.addCheckBox("use PVM for parallel processing", parallel);
parallelCheckBox.addItemListener(this);
IntegerField slavesField =
queryOptionsDialog.addIntegerField(
"Number of Slaves", numSlaves, 4, 0, MesquiteInteger.infinite);
IntegerField maxRamField =
queryOptionsDialog.addIntegerField("mxram value", mxram, 4, 0, MesquiteInteger.infinite);
tabbedPanel.addPanel("Search Options", true);
Choice searchStyleChoice = null;
if (bootstrapAllowed)
searchStyleChoice =
queryOptionsDialog.addPopUpMenu(
"Type of search/resampling:",
new String[] {
"Regular Search",
"Bootstrap",
"Jackknife",
"Symmetric Resampled",
"Poisson Bootstrap"
},
searchStyle);
queryOptionsDialog.addLabel("Regular Search Commands");
searchField = queryOptionsDialog.addTextAreaSmallFont(searchArguments, 7, 80);
searchScriptPathField =
queryOptionsDialog.addTextField(
"Path to TNT run file containing search commands", searchScriptPath, 40);
Button browseSearchScriptPathButton =
queryOptionsDialog.addAListenedButton("Browse...", null, this);
browseSearchScriptPathButton.setActionCommand("browseSearchScript");
harvestOnlyStrictConsensusBox =
queryOptionsDialog.addCheckBox("only acquire strict consensus", harvestOnlyStrictConsensus);
queryOptionsDialog.addHorizontalLine(1);
// Checkbox doBootstrapBox = queryOptionsDialog.addCheckBox("do bootstrapping", doBootstrap);
if (bootstrapAllowed) {
bootStrapRepsField =
queryOptionsDialog.addIntegerField(
"Resampling Replicates", bootstrapreps, 8, 0, MesquiteInteger.infinite);
queryOptionsDialog.addLabel("Resampling Search Commands");
bootstrapSearchField =
queryOptionsDialog.addTextAreaSmallFont(bootstrapSearchArguments, 7, 80);
bootSearchScriptPathField =
queryOptionsDialog.addTextField(
"Path to TNT run file containing search commands for resampled",
bootSearchScriptPath,
30);
Button browseBootSearchScriptPathButton =
queryOptionsDialog.addAListenedButton("Browse...", null, this);
browseSearchScriptPathButton.setActionCommand("browseBootSearchScript");
resamplingAllConsensusTreesBox =
queryOptionsDialog.addCheckBox(
"allow TNT to calculate consensus tree", !resamplingAllConsensusTrees);
}
adjustDialogText();
queryOptionsDialog.addHorizontalLine(1);
queryOptionsDialog.addNewDialogPanel();
useDefaultsButton = queryOptionsDialog.addAListenedButton("Set to Defaults", null, this);
useDefaultsButton.setActionCommand("setToDefaults");
tabbedPanel.addPanel("Other Options", true);
convertGapsBox =
queryOptionsDialog.addCheckBox(
"convert gaps to missing (to avoid gap=extra state)", convertGapsToMissing);
queryOptionsDialog.addHorizontalLine(1);
queryOptionsDialog.addLabel("Post-Search TNT Commands");
otherOptionsField = queryOptionsDialog.addTextAreaSmallFont(otherOptions, 7, 80);
queryOptionsDialog.addHorizontalLine(1);
queryOptionsDialog.addNewDialogPanel();
useDefaultsOtherOptionsButton =
queryOptionsDialog.addAListenedButton("Set to Defaults", null, this);
useDefaultsOtherOptionsButton.setActionCommand("setToDefaultsOtherOptions");
tabbedPanel.cleanup();
queryOptionsDialog.nullifyAddPanel();
queryOptionsDialog.completeAndShowDialog("Search", "Cancel", null, null);
if (buttonPressed.getValue() == 0) {
boolean infererOK = (treeInferer == null || treeInferer.optionsChosen());
if (externalProcRunner.optionsChosen() && infererOK) {
if (bootstrapAllowed) {
bootstrapreps = bootStrapRepsField.getValue();
bootstrapSearchArguments = bootstrapSearchField.getText();
bootSearchScriptPath = bootSearchScriptPathField.getText();
harvestOnlyStrictConsensus = harvestOnlyStrictConsensusBox.getState();
resamplingAllConsensusTrees = !resamplingAllConsensusTreesBox.getState();
searchStyle = searchStyleChoice.getSelectedIndex();
}
numSlaves = slavesField.getValue();
otherOptions = otherOptionsField.getText();
convertGapsToMissing = convertGapsBox.getState();
parallel = parallelCheckBox.getState();
// doBootstrap = doBootstrapBox.getState();
searchArguments = searchField.getText();
searchScriptPath = searchScriptPathField.getText();
mxram = maxRamField.getValue();
storeRunnerPreferences();
}
}
queryOptionsDialog.dispose();
if (closeWizard) MesquiteDialog.closeWizard();
return (buttonPressed.getValue() == 0);
}