/** ************************************************************************* * * Command */
public void doAdd() {
UserTreePathStopCreationDialog scd = new UserTreePathStopCreationDialog(appState_);
scd.setVisible(true);
if (!scd.haveResult()) {
return;
}
String addToPathKey = scd.getChosenPath();
String insertMode = scd.getInsertionMode();
appState_.getPathController().addAStop(addToPathKey, insertMode, dacx_);
appState_.getPathControls().handlePathButtons();
return;
}
/** ************************************************************************* * * Constructor */
protected BTStashResultsDialog(
BTState appState, String titleResource, Dimension size, int columns) {
super(appState.getTopFrame(), appState.getRMan().getString(titleResource), true);
haveResult_ = false;
appState_ = appState;
rMan_ = appState_.getRMan();
setSize(size.width, size.height);
cp_ = (JPanel) getContentPane();
cp_.setBorder(new EmptyBorder(20, 20, 20, 20));
cp_.setLayout(new GridBagLayout());
gbc_ = new GridBagConstraints();
rowNum_ = 0;
ds_ = new DialogSupport(this, appState_, gbc_);
columns_ = columns;
}
/** ************************************************************************* * * Command */
public void doRemove() {
if (appState_.getPathController().pathHasOnlyOneStop()) {
ResourceManager rMan = appState_.getRMan();
int ok =
JOptionPane.showConfirmDialog(
appState_.getTopFrame(),
rMan.getString("treePathDeleteStop.oneStopWarningMessage"),
rMan.getString("treePathDeleteStop.oneStopWarningMessageTitle"),
JOptionPane.YES_NO_OPTION);
if (ok != JOptionPane.YES_OPTION) {
return;
}
}
appState_.getPathController().deleteCurrentStop(dacx_);
appState_.getPathControls().handlePathButtons();
return;
}
/** ************************************************************************* * * Do the step */
private DialogAndInProcessCmd stepToProcess() {
if (doAdd) {
doAdd();
} else {
doRemove();
}
appState_.getPathControls().handlePathButtons();
return (new DialogAndInProcessCmd(DialogAndInProcessCmd.Progress.DONE, this));
}
/**
* ************************************************************************* * * Show the
* expression key
*/
public static void expressionKeyCSV(BTState appState, PrintWriter out, boolean encodeConfidence) {
ResourceManager rMan = appState.getRMan();
out.println("\"\"");
out.println("\"\"");
out.print("\"");
out.print(rMan.getString("csvTcdExport.keyTitle"));
out.println("\"");
out.print("\"");
out.print(rMan.getString((encodeConfidence) ? "csvTcdExport.var" : "csvTcdExport.varNC"));
out.println("\"");
out.print("\"");
out.print(rMan.getString("csvTcdExport.number"));
out.print("\",\"");
out.print(rMan.getString("csvTcdExport.level"));
if (encodeConfidence) {
out.print("\",\"");
out.print(rMan.getString("csvTcdExport.confidence"));
}
out.println("\"");
out.print("0,\"");
out.print(rMan.getString("csvTcdExport." + mapExpression(NO_DATA)));
if (encodeConfidence) {
out.print("\",\"");
out.print(rMan.getString("csvTcdExport.nA"));
}
out.println("\"");
int topConf =
(encodeConfidence) ? (TimeCourseGene.NUM_CONFIDENCE - 1) : TimeCourseGene.NORMAL_CONFIDENCE;
int confLev = 1;
for (int i = 0; i <= topConf; i++) {
String conf = rMan.getString("csvTcdExportConf." + TimeCourseGene.mapConfidence(i));
int expLev = 0;
for (int j = 0; j < NUM_EXPRESSIONS; j++) {
if ((j != NO_DATA) && (j != VARIABLE)) {
String expr = rMan.getString("csvTcdExport." + mapExpression(j));
int totLev = (expLev++) + confLev;
out.print(totLev);
out.print(",\"");
out.print(expr);
if (encodeConfidence) {
out.print("\",\"");
out.print(conf);
}
out.println("\"");
}
}
confLev += expLev;
}
return;
}
/** ************************************************************************* * * Constructor */
public HaloLayoutSetupPanel(
BTState appState,
Genome genome,
String selectedID,
HaloLayout halo,
HaloLayout.HaloLayoutParams params) {
appState_ = appState;
haveResult_ = false;
params_ = (HaloLayout.HaloLayoutParams) params.clone();
params_.selected = selectedID;
ResourceManager rMan = appState_.getRMan();
setLayout(new GridBagLayout());
GridBagConstraints gbc = new GridBagConstraints();
if ((params_.selected != null) && !halo.selectionIsValid(genome, params_.selected)) {
params_.selected = null;
}
JLabel strategyLabel = new JLabel(rMan.getString("haloLayout.strategyType"));
strategyCombo_ =
new JComboBox(HaloLayout.StartSeed.getChoices(appState_, params_.selected != null));
UiUtil.gbcSet(gbc, 0, 0, 1, 1, UiUtil.HOR, 0, 0, 5, 5, 5, 5, UiUtil.CEN, 1.0, 0.0);
add(strategyLabel, gbc);
UiUtil.gbcSet(gbc, 1, 0, 1, 1, UiUtil.HOR, 0, 0, 5, 5, 5, 5, UiUtil.CEN, 1.0, 0.0);
add(strategyCombo_, gbc);
JLabel overlayLabel = new JLabel(rMan.getString("haloLayout.overlayOptions"));
Vector<ChoiceContent> relayoutChoices = NetOverlayProperties.getRelayoutOptions(appState);
overlayOptionCombo_ = new JComboBox(relayoutChoices);
boolean activate = (genome == null) || (genome.getNetworkOverlayCount() > 0);
if (!activate) {
overlayLabel.setEnabled(false);
overlayOptionCombo_.setEnabled(false);
}
UiUtil.gbcSet(gbc, 0, 1, 1, 1, UiUtil.HOR, 0, 0, 5, 5, 5, 5, UiUtil.CEN, 1.0, 0.0);
add(overlayLabel, gbc);
UiUtil.gbcSet(gbc, 1, 1, 1, 1, UiUtil.HOR, 0, 0, 5, 5, 5, 5, UiUtil.CEN, 1.0, 0.0);
add(overlayOptionCombo_, gbc);
}
/**
* ************************************************************************* * * Do the
* relocation
*/
private DialogAndInProcessCmd stepRelocateSource() {
//
// Go and find if we intersect anything.
//
List<Intersection.AugmentedIntersection> augs =
appState_.getGenomePresentation().intersectItem(x, y, rcxT_, true, false);
Intersection.AugmentedIntersection ai =
(new IntersectionChooser(true, rcxT_)).selectionRanker(augs);
Intersection inter = ((ai == null) || (ai.intersect == null)) ? null : ai.intersect;
//
// If we don't intersect anything, we need to bag it.
//
if (inter == null) {
return (new DialogAndInProcessCmd(ServerControlFlowHarness.ClickResult.REJECT, this));
}
Object sub = inter.getSubID();
if (sub == null) {
return (new DialogAndInProcessCmd(ServerControlFlowHarness.ClickResult.REJECT, this));
}
String id = inter.getObjectID();
Node node = rcxT_.getGenome().getNode(id);
if (node == null) {
return (new DialogAndInProcessCmd(ServerControlFlowHarness.ClickResult.REJECT, this));
}
if (!(sub instanceof Intersection.PadVal)) {
return (new DialogAndInProcessCmd(ServerControlFlowHarness.ClickResult.REJECT, this));
}
List<Intersection.PadVal> pads = inter.getPadCand();
if (LinkSupport.changeLinkSource(appState_, intersect, inter, pads, id, rcxT_)) {
return (new DialogAndInProcessCmd(ServerControlFlowHarness.ClickResult.ACCEPT, this));
} else {
return (new DialogAndInProcessCmd(ServerControlFlowHarness.ClickResult.REJECT, this));
}
}
/**
* ************************************************************************* * * Build display
* name
*/
public static String buildMaternalDisplayName(BTState appState, String name) {
String format = appState.getRMan().getString("expressionChannel.maternalSource");
String desc = MessageFormat.format(format, new Object[] {name});
return (desc);
}
/** ************************************************************************* * * Constructor */
public ExpressionEntry(
BTState appState,
String region,
String time,
String expr,
String source,
String confidence,
String strategySource,
String startStrategy,
String endStrategy,
String variable)
throws IOException {
region_ = region;
try {
time_ = Integer.parseInt(time);
} catch (NumberFormatException nfex) {
throw new IOException();
}
TimeAxisDefinition tad = appState.getDB().getTimeAxisDefinition();
if (!tad.timeIsOk(time_)) {
throw new IOException();
}
if (expr == null) {
throw new IOException();
} else {
expr = expr.trim();
try {
expr_ = mapFromExpressionTag(expr);
} catch (IllegalArgumentException iaex) {
throw new IOException();
}
}
if (expr_ == VARIABLE) {
if (variable == null) {
throw new IOException();
}
try {
variable_ = Double.parseDouble(variable);
} catch (NumberFormatException nfex) {
throw new IOException();
}
if ((variable_ < 0.0) || (variable_ > 1.0)) {
throw new IOException();
}
}
if (source == null) {
source_ = NO_SOURCE_SPECIFIED;
} else {
source = source.trim();
try {
source_ = mapFromSourceTag(source);
} catch (IllegalArgumentException iaex) {
throw new IOException();
}
}
if (strategySource == null) {
strategySource_ = NO_SOURCE_SPECIFIED;
} else {
strategySource = strategySource.trim();
try {
strategySource_ = mapFromSourceTag(strategySource);
} catch (IllegalArgumentException iaex) {
throw new IOException();
}
}
if (confidence == null) {
confidence_ = TimeCourseGene.USE_BASE_CONFIDENCE;
} else {
confidence = confidence.trim();
if (confidence.equalsIgnoreCase("normal")) {
confidence_ = TimeCourseGene.NORMAL_CONFIDENCE;
} else if (confidence.equalsIgnoreCase("interpolated")) {
confidence_ = TimeCourseGene.INTERPOLATED;
} else if (confidence.equalsIgnoreCase("assumption")) {
confidence_ = TimeCourseGene.ASSUMPTION;
} else if (confidence.equalsIgnoreCase("inferred")) {
confidence_ = TimeCourseGene.INFERRED;
} else if (confidence.equalsIgnoreCase("questionable")) {
confidence_ = TimeCourseGene.QUESTIONABLE;
} else {
throw new IOException();
}
}
try {
startStrategy_ = calculateStrategy(startStrategy, true);
endStrategy_ = calculateStrategy(endStrategy, false);
} catch (IllegalArgumentException iae) {
throw new IOException();
}
}
/**
* ************************************************************************* * * Finish building
*/
protected void finishConstructionWithMultiExtraLeftButtons(List<JButton> xtraButtonList) {
ds_.buildAndInstallButtonBoxWithMultiExtra(cp_, rowNum_, columns_, false, xtraButtonList, true);
setLocationRelativeTo(appState_.getTopFrame());
return;
}
/**
* ************************************************************************* * * Finish building
*/
protected void finishConstruction() {
ds_.buildAndInstallButtonBox(cp_, rowNum_, columns_, false, true);
setLocationRelativeTo(appState_.getTopFrame());
return;
}
/**
* ************************************************************************* * * Do the
* relocation
*/
private DialogAndInProcessCmd stepRelocateModuleSource() {
String currentOverlay = rcxT_.oso.getCurrentOverlay();
//
// Go and find if we intersect anything.
//
Intersection intersected =
appState_
.getGenomePresentation()
.intersectANetModuleElement(
x, y, rcxT_, GenomePresentation.NetModuleIntersect.NET_MODULE_LINK_PAD);
//
// If we don't intersect anything, or the correct thing, we need to bag it.
//
if (intersected == null) {
return (new DialogAndInProcessCmd(ServerControlFlowHarness.ClickResult.REJECT, this));
}
String id = intersected.getObjectID();
NetOverlayOwner owner =
rcxT_.getGenomeSource().getOverlayOwnerFromGenomeKey(rcxT_.getGenomeID());
NetworkOverlay novr = owner.getNetworkOverlay(currentOverlay);
NetModule nm = novr.getModule(id);
if (nm == null) {
return (new DialogAndInProcessCmd(ServerControlFlowHarness.ClickResult.REJECT, this));
}
NetModuleFree.IntersectionExtraInfo ei =
(NetModuleFree.IntersectionExtraInfo) intersected.getSubID();
if (ei == null) {
return (new DialogAndInProcessCmd(ServerControlFlowHarness.ClickResult.REJECT, this));
}
if (ei.type != NetModuleFree.IntersectionExtraInfo.IS_PAD) {
return (new DialogAndInProcessCmd(ServerControlFlowHarness.ClickResult.REJECT, this));
}
// New point:
Point2D padPt = (Point2D) ei.intersectPt.clone();
UiUtil.forceToGrid(padPt, UiUtil.GRID_SIZE);
Vector2D toSide = ei.padNorm.scaled(-1.0);
String treeID = intersect.getObjectID();
NetModuleLinkageProperties nmlp =
rcxT_
.getLayout()
.getNetOverlayProperties(currentOverlay)
.getNetModuleLinkagePropertiesFromTreeID(treeID);
LinkSegmentID[] linkIDs = intersect.segmentIDsFromIntersect();
Set<String> throughSeg = nmlp.resolveLinkagesThroughSegment(linkIDs[0]);
int totalLinks = nmlp.getLinkageList().size();
if (throughSeg.size() != totalLinks) {
return (new DialogAndInProcessCmd(ServerControlFlowHarness.ClickResult.REJECT, this));
}
String myLinkId = throughSeg.iterator().next();
NetModuleLinkage myLink = novr.getLinkage(myLinkId);
if (!myLink.getSource().equals(id)) {
return (new DialogAndInProcessCmd(ServerControlFlowHarness.ClickResult.REJECT, this));
}
//
// Pretty lax about links in and out of modules. Only restriction is that
// link cannot end on the same pad as it starts (avoids zero-length links!)
//
Iterator<String> tsit = throughSeg.iterator();
while (tsit.hasNext()) {
String linkID = tsit.next();
if (!novr.linkIsFeedback(linkID)) {
continue;
}
Point2D targPt = nmlp.getTargetEnd(linkID, 0.0);
if (padPt.equals(targPt)) {
return (new DialogAndInProcessCmd(ServerControlFlowHarness.ClickResult.REJECT, this));
}
}
//
// Undo/Redo support
//
UndoSupport support = new UndoSupport(appState_, "undo.changeModuleLinkSource");
//
// We reject unless the target we are intersecting matches the
// link we are trying to relocate.
//
Layout.PropChange lpc =
rcxT_.getLayout().changeNetModuleSource(currentOverlay, treeID, padPt, toSide, rcxT_);
if (lpc != null) {
PropChangeCmd mov = new PropChangeCmd(appState_, rcxT_, lpc);
support.addEdit(mov);
support.addEvent(
new LayoutChangeEvent(rcxT_.getLayoutID(), LayoutChangeEvent.UNSPECIFIED_CHANGE));
support.finish();
return (new DialogAndInProcessCmd(ServerControlFlowHarness.ClickResult.ACCEPT, this));
} else {
return (new DialogAndInProcessCmd(ServerControlFlowHarness.ClickResult.REJECT, this));
}
}
/**
* ************************************************************************* * * Gets a valid
* measurement types
*/
public static ObjChoiceContent getProxySignValue(BTState appState, String proxVal) {
return (new ObjChoiceContent(appState.getRMan().getString("proxyTypes." + proxVal), proxVal));
}
