/**
* Pathway information is added to the pathway element model.
*
* @param title
* @param version
* @param organism
* @param commentList
* @param bioPaxRefs
* @return pwElt
*/
public static PathwayElement createMapInfo(
String title,
String version,
String organism,
List<String> commentList,
List<String> bioPaxRefs) {
// create pathwayElement line
PathwayElement pwElt = PathwayElement.createPathwayElement(ObjectType.MAPPINFO);
if (!(title.equals(""))) pwElt.setMapInfoName(title);
if (!(version.equals(""))) pwElt.setVersion(version);
if (!(organism.equals(""))) pwElt.setOrganism(organism);
if (commentList.size() > 0) {
for (int i = 0; i < commentList.size(); i += 2) {
pwElt.addComment(commentList.get(i), commentList.get(i + 1));
}
}
if (bioPaxRefs.size() > 0) {
for (int i = 0; i < bioPaxRefs.size(); i++) {
pwElt.addBiopaxRef(bioPaxRefs.get(i));
}
}
return pwElt;
}
/**
* Add anchors to the lines
*
* @param pwElt
* @param anchorList
* @return pwElt
*/
private static PathwayElement createAnchor(PathwayElement pwElt, List<String> anchorList) {
// create anchors
for (int i = 0; i < anchorList.size(); i += 2) {
MAnchor anchor = pwElt.addMAnchor(Double.parseDouble(anchorList.get(i)));
anchor.setGraphId(anchorList.get(i + 1));
}
return pwElt;
}
/**
* Updates the bottom part of the {@link RegIntTab} with information about the Xref selected in
* the top part of RIPTab and its interaction
*
* @param xref one of the interaction partners (displayed in the top part of the RIPTAB) of the
* Xref selected in the main pathway
* @param results the results object from updating the top part of the RIPTab by selecting an Xref
* in the main pathway
*/
public void updateBackpagePanel(Xref xref, ResultsObj results) {
backpagePanel.removeAll();
backpagePanel.setLayout(new BoxLayout(backpagePanel, BoxLayout.PAGE_AXIS));
PathwayElement e = PathwayElement.createPathwayElement(ObjectType.DATANODE);
e.setDataSource(xref.getDataSource());
e.setElementID(xref.getId());
BackpageTextProvider bpt = new BackpageTextProvider();
bpt.addBackpageHook(new BackpageInfo(swingEngine.getGdbManager().getCurrentGdb(), results));
// TODO: fix file table, doesn't always show files
bpt.addBackpageHook(new BackpageFileTable(results, plugin));
bpt.addBackpageHook(new BackpagePMID(results));
// TODO: change this to use multiple BridgeDb databases?
bpt.addBackpageHook(
new BackpageTextProvider.BackpageXrefs(swingEngine.getGdbManager().getCurrentGdb()));
bpt.addBackpageHook(new BackpageExpression(plugin.getDesktop().getGexManager()));
bpt.addBackpageHook(new BackpageMiscInfo(results));
BackpagePane bpp = new BackpagePane(bpt, swingEngine.getEngine());
bpp.setInput(e);
bpp.addHyperlinkListener(
new HyperlinkListener() {
@Override
public void hyperlinkUpdate(HyperlinkEvent e) {
if (e.getEventType().equals(HyperlinkEvent.EventType.ACTIVATED)) {
try {
Desktop.getDesktop().browse(e.getURL().toURI());
} catch (IOException e1) {
e1.printStackTrace();
} catch (URISyntaxException e1) {
e1.printStackTrace();
}
}
}
});
backpagePanel.add(bpp);
backpagePanel.revalidate();
backpagePanel.repaint();
}
/**
* Set the type of line (curved, segmented, etc.) and add mPoints on them.
*
* @param pwElt
* @param connectorType
* @param mPointsDoubles
* @return mPoints
*/
private static List<MPoint> addLineType(
PathwayElement pwElt, String connectorType, List<Double> mPointsDoubles) {
List<MPoint> mPoints = new ArrayList<MPoint>();
// type of line
if (connectorType.toLowerCase().equals("curved")) {
pwElt.setConnectorType(ConnectorType.CURVED);
createMPoints(pwElt, mPoints, mPointsDoubles);
// add MPoints
pwElt.setMPoints(mPoints);
} else if (connectorType.toLowerCase().equals("segmented")) {
pwElt.setConnectorType(ConnectorType.SEGMENTED);
createMPoints(pwElt, mPoints, mPointsDoubles);
// add MPoints
pwElt.setMPoints(mPoints);
} else if (connectorType.toLowerCase().equals("elbow")) {
pwElt.setConnectorType(ConnectorType.ELBOW);
createMPoints(pwElt, mPoints, mPointsDoubles);
// add MPoints
pwElt.setMPoints(mPoints);
} else if (connectorType.toLowerCase().equals("straight")) {
pwElt.setConnectorType(ConnectorType.STRAIGHT);
createMPoints(pwElt, mPoints, mPointsDoubles);
// add MPoints
pwElt.setMPoints(mPoints);
} else {
pwElt.setConnectorType(ConnectorType.STRAIGHT);
createMPoints(pwElt, mPoints, mPointsDoubles);
// add MPoints
pwElt.setMPoints(mPoints);
}
return mPoints;
}
/**
* Group values are added to the pathway element model.
*
* @param groupRef
* @param graphRef
* @param type
* @return pwElt
*/
public static PathwayElement createGroup(String groupRef, String graphRef, String type) {
// create group element
MGroup pwElt = (MGroup) PathwayElement.createPathwayElement(ObjectType.GROUP);
// set ids
pwElt.setGroupId(groupRef);
pwElt.setGraphId(graphRef);
// style type
if (type.toLowerCase() == "complex") {
GroupStyle gs = GroupStyle.COMPLEX;
pwElt.setGroupStyle(gs);
} else if (type.toLowerCase() == "group") {
GroupStyle gs = GroupStyle.GROUP;
pwElt.setGroupStyle(gs);
} else {
}
return pwElt;
}
/**
* State values are added to the pathway element model.
*
* @param relX
* @param relY
* @param width
* @param height
* @param color
* @param lineStyle
* @param lnThickness
* @param fillColor
* @param shapeType
* @param zOrder
* @param database
* @param ID
* @param bioPaxRefs
* @param graphId
* @param graphRef
* @param textLabel
* @param stateType
* @return pwElt
*/
public static PathwayElement createState(
double relX,
double relY,
double width,
double height,
Color color,
int lineStyle,
int lnThickness,
Color fillColor,
IShape shapeType,
int zOrder,
DataSource database,
String ID,
List<String> bioPaxRefs,
String graphId,
String graphRef,
String textLabel,
String stateType) {
// create pathwayElement State
PathwayElement pwElt = PathwayElement.createPathwayElement(ObjectType.STATE);
// for better definition of identifier and database
Xref ref = new Xref(ID, database);
pwElt.setRelX(relX);
pwElt.setRelY(relY);
pwElt.setMWidth(width);
pwElt.setMHeight(height);
pwElt.setColor(color);
pwElt.setLineStyle(lineStyle);
pwElt.setLineThickness(lnThickness);
pwElt.setFillColor(fillColor);
pwElt.setShapeType(shapeType);
pwElt.setZOrder(zOrder);
pwElt.setDataSource(ref.getDataSource());
pwElt.setElementID(ref.getId());
pwElt.setGraphId(graphId);
pwElt.setGraphRef(graphRef);
pwElt.setTextLabel(textLabel);
if (stateType == "unknown") {
} else {
}
if (bioPaxRefs.size() > 0) {
for (int i = 0; i < bioPaxRefs.size(); i++) {
pwElt.addBiopaxRef(bioPaxRefs.get(i));
}
}
return pwElt;
}
/**
* Shape values are added to the pathway element model.
*
* @param centerX
* @param centerY
* @param width
* @param height
* @param fontStyle
* @param fontDecoration
* @param fontStrikeThru
* @param fontWeight
* @param fontName
* @param fontSize
* @param align
* @param vAlign
* @param color
* @param lineStyle
* @param lnThickness
* @param fillColor
* @param shapeType
* @param zOrder
* @param rotation
* @return pwElt
*/
public static PathwayElement createShape(
double centerX,
double centerY,
double width,
double height,
boolean fontStyle,
boolean fontDecoration,
boolean fontStrikeThru,
boolean fontWeight,
String fontName,
double fontSize,
AlignType align,
ValignType vAlign,
Color color,
int lineStyle,
double lnThickness,
Color fillColor,
IShape shapeType,
int zOrder,
double rotation) {
// create pathwayElement Shape
PathwayElement pwElt = PathwayElement.createPathwayElement(ObjectType.SHAPE);
pwElt.setMCenterX(centerX);
pwElt.setMCenterY(centerY);
pwElt.setMWidth(width);
pwElt.setMHeight(height);
pwElt.setItalic(fontStyle);
pwElt.setUnderline(fontDecoration);
pwElt.setStrikethru(fontStrikeThru);
pwElt.setBold(fontWeight);
pwElt.setFontName(fontName);
pwElt.setMFontSize(fontSize);
pwElt.setAlign(align);
pwElt.setValign(vAlign);
pwElt.setColor(color);
pwElt.setLineStyle(lineStyle);
pwElt.setLineThickness(lnThickness);
pwElt.setFillColor(fillColor);
pwElt.setShapeType(shapeType);
pwElt.setZOrder(zOrder);
pwElt.setRotation(rotation);
return pwElt;
}
/**
* GraphicalLine values are added to the pathway element model.
*
* @param mPointsDoubles
* @param relX
* @param relY
* @param startGraphRef
* @param endGraphRef
* @param pointGraphId
* @param arrowHead
* @param anchorList
* @param color
* @param lnThickness
* @param lineStyle
* @param connectorType
* @param zOrder
* @param groupRef
* @param bioPaxRefs
* @param graphId
* @param type
* @return pwElt
*/
public static PathwayElement createGraphicalLine(
List<Double> mPointsDoubles,
double relX,
double relY,
String startGraphRef,
String endGraphRef,
String pointGraphId,
String arrowHead,
List<String> anchorList,
Color color,
int lnThickness,
int lineStyle,
String connectorType,
int zOrder,
String groupRef,
List<String> bioPaxRefs,
String graphId,
String type) {
// !!! not done yet
// create pathwayElement line
PathwayElement pwElt = PathwayElement.createPathwayElement(ObjectType.GRAPHLINE);
pwElt.setStartGraphRef(startGraphRef);
pwElt.setEndGraphRef(endGraphRef);
pwElt.setGraphId(graphId);
pwElt.setColor(color);
pwElt.setLineThickness(lnThickness);
pwElt.setLineStyle(lineStyle);
pwElt.setZOrder(zOrder);
pwElt.setGroupRef(groupRef);
pwElt.setGraphId(graphId);
pwElt.setEndLineType(LineType.fromName(arrowHead));
// add MPoints
addLineType(pwElt, connectorType, mPointsDoubles);
// add Anchor
if (anchorList.size() > 0) {
createAnchor(pwElt, anchorList);
}
if (bioPaxRefs.size() > 0) {
for (int i = 0; i < bioPaxRefs.size(); i++) {
pwElt.addBiopaxRef(bioPaxRefs.get(i));
}
}
return null;
}
/**
* Line values are added to the pathway element model.
*
* @param mPointsDoubles
* @param startGraphId
* @param endGraphId
* @param zOrder
* @param lnThickness
* @param connectorType
* @param arrowHead
* @param anchorList
* @param startDataNodeId
* @param endDataNodeId
* @param startRelX
* @param startRelY
* @param endRelX
* @param endRelY
* @return pwElt
*/
public static PathwayElement createLine(
List<Double> mPointsDoubles,
String startGraphId,
String endGraphId,
Integer zOrder,
Double lnThickness,
String connectorType,
String arrowHead,
List<String> anchorList,
GraphIdContainer startDataNodeId,
GraphIdContainer endDataNodeId,
Double startRelX,
Double startRelY,
Double endRelX,
Double endRelY) {
// create pathwayElement line
PathwayElement pwElt = PathwayElement.createPathwayElement(ObjectType.LINE);
// set graph line variables
if (mPointsDoubles.isEmpty()) {
System.out.println("No mPoints for line!!");
throw new EmptyStackException();
}
if (!(startGraphId.equals(""))) pwElt.setStartGraphRef(startGraphId);
else {
System.out.println("No startGraphId for line!!");
throw new EmptyStackException();
}
if (!(endGraphId.equals(""))) pwElt.setEndGraphRef(endGraphId);
else {
System.out.println("No endGraphId for line!!");
throw new EmptyStackException();
}
if (zOrder != -1) pwElt.setZOrder(zOrder);
if (lnThickness != null) pwElt.setLineThickness(lnThickness);
if (arrowHead != null) pwElt.setEndLineType(LineType.fromName(arrowHead));
if (startRelX == null) {
System.out.println("No relX 1 for line!!");
throw new EmptyStackException();
}
if (endRelX == null) {
System.out.println("No relX 2 for line!!");
throw new EmptyStackException();
}
if (startRelY == null) {
System.out.println("No relY 1 for line!!");
throw new EmptyStackException();
}
if (endRelY == null) {
System.out.println("No no relY 2 for line!!");
throw new EmptyStackException();
}
// add MPoints
addLineType(pwElt, connectorType, mPointsDoubles);
// add Anchor
if (anchorList.size() > 0) createAnchor(pwElt, anchorList);
// bind on the correct place
MPoint startLine = pwElt.getMStart();
MPoint endLine = pwElt.getMEnd();
if (startDataNodeId.equals("")) {
startLine.linkTo(startDataNodeId, startRelX, startRelY);
}
if (startDataNodeId.equals("")) {
endLine.linkTo(endDataNodeId, endRelX, endRelY);
}
return pwElt;
}
/**
* Label values are added to the pathway element model.
*
* @param centerX
* @param centerY
* @param width
* @param height
* @param fontName
* @param fontStyle
* @param fontDecoration
* @param fontStrikeThru
* @param fontWeight
* @param fontSize
* @param align
* @param vAlign
* @param color
* @param lnThickness
* @param fillcolor
* @param zOrder
* @param bioPaxRefs
* @param graphId
* @param groupId
* @param textLabel
* @return pwElt
*/
public static PathwayElement createLabel(
Double centerX,
Double centerY,
Double width,
Double height,
String fontName,
Boolean fontStyle,
Boolean fontDecoration,
Boolean fontStrikeThru,
Boolean fontWeight,
Double fontSize,
String align,
String vAlign,
Color color,
Double lnThickness,
Color fillcolor,
Integer zOrder,
List<String> bioPaxRefs,
String graphId,
String groupId,
String textLabel) {
// create pathwayElement label
PathwayElement pwElt = PathwayElement.createPathwayElement(ObjectType.LABEL);
// put variables in element
if (centerX != null) {
pwElt.setMCenterX(centerX);
} else {
System.out.println("No CenterX for label!!");
throw new EmptyStackException();
}
if (centerY != null) {
pwElt.setMCenterY(centerY);
} else {
System.out.println("No centerY for label!!");
throw new EmptyStackException();
}
if (width != null) {
pwElt.setMWidth(width);
} else {
System.out.println("No width for label!!");
throw new EmptyStackException();
}
if (height != null) {
pwElt.setMHeight(height);
} else {
System.out.println("No height for label!!");
throw new EmptyStackException();
}
if (fontSize != null) pwElt.setMFontSize(fontSize);
if (color != null) {
pwElt.setColor(color);
}
if (lnThickness != null) pwElt.setLineThickness(lnThickness);
if (fillcolor != null) pwElt.setFillColor(fillcolor);
if (!(graphId.equals(""))) {
pwElt.setGraphId(graphId);
} else {
System.out.println("No GraphId for label!!");
throw new EmptyStackException();
}
if (!(textLabel.equals(""))) {
pwElt.setTextLabel(textLabel);
} else {
System.out.println("No label name for label!!");
throw new EmptyStackException();
}
if (fontStyle == true) pwElt.setItalic(fontStyle);
if (fontDecoration == true) pwElt.setUnderline(fontDecoration);
if (fontStrikeThru == true) pwElt.setStrikethru(fontStrikeThru);
if (fontWeight == true) pwElt.setBold(fontWeight);
if (!(fontName.equals(""))) pwElt.setFontName(fontName);
if (zOrder != -1) pwElt.setZOrder(zOrder);
if (!(groupId.equals(""))) pwElt.setGraphRef(groupId);
if (align.toLowerCase() == "center") {
pwElt.setAlign(AlignType.CENTER);
} else if (align.toLowerCase() == "left") {
pwElt.setAlign(AlignType.LEFT);
} else if (align.toLowerCase() == "right") {
pwElt.setAlign(AlignType.RIGHT);
} else {
pwElt.setAlign(AlignType.CENTER);
}
if (vAlign.toLowerCase() == "middle") {
pwElt.setValign(ValignType.MIDDLE);
} else if (vAlign.toLowerCase() == "bottom") {
pwElt.setValign(ValignType.BOTTOM);
} else if (vAlign.toLowerCase() == "top") {
pwElt.setValign(ValignType.TOP);
} else {
pwElt.setValign(ValignType.MIDDLE);
}
if (bioPaxRefs.size() > 0) {
for (int i = 0; i < bioPaxRefs.size(); i++) {
pwElt.addBiopaxRef(bioPaxRefs.get(i));
}
}
return pwElt;
}
/**
* DataNode values are added to the pathway element model.
*
* @param centerX
* @param centerY
* @param width
* @param height
* @param textLabel
* @param identifier
* @param source
* @param dnType
* @param graphId
* @param color
* @param fontSize
* @param zOrder
* @param vAlign
* @param groupRef
* @param bioPaxRefs
* @param commentList
* @return pwElt
*/
public static PathwayElement createDataNode(
Double centerX,
Double centerY,
Double width,
Double height,
String textLabel,
String identifier,
DataSource source,
String dnType,
String graphId,
Color color,
Double fontSize,
Integer zOrder,
String vAlign,
String groupRef,
List<String> bioPaxRefs,
List<String> commentList) {
// create pathwayElement data node
PathwayElement pwElt = PathwayElement.createPathwayElement(ObjectType.DATANODE);
// for better definition of identifier and database
Xref ref = new Xref(identifier, source);
// put variables in element
if (centerX != null) {
pwElt.setMCenterX(centerX);
} else {
System.out.println("No CenterX for datanode!!");
throw new EmptyStackException();
}
if (centerY != null) {
pwElt.setMCenterY(centerY);
} else {
System.out.println("No centerY for datanode!!");
throw new EmptyStackException();
}
if (width != null) {
pwElt.setMWidth(width);
} else {
System.out.println("No width for datanode!!");
throw new EmptyStackException();
}
if (height != null) {
pwElt.setMHeight(height);
} else {
System.out.println("No height for datanode!!");
throw new EmptyStackException();
}
if (!(textLabel.equals(""))) pwElt.setTextLabel(textLabel);
else {
System.out.println("No label name for datanode!!");
throw new EmptyStackException();
}
if (!(ref.getId().isEmpty())) pwElt.setElementID(ref.getId());
if (ref.getDataSource() != null) pwElt.setDataSource(ref.getDataSource());
if (dnType != null) pwElt.setDataNodeType(dnType);
if (!(graphId.equals(""))) {
pwElt.setGraphId(graphId);
} else {
System.out.println("No GraphId for datanode!!");
throw new EmptyStackException();
}
if (color != null) {
pwElt.setColor(color);
}
if (fontSize != null) pwElt.setMFontSize(fontSize);
if (zOrder != -1) pwElt.setZOrder(zOrder);
// System.out.println(groupRef);
// if (!(groupRef.equals(""))) pwElt.setGraphRef(groupRef);
if (vAlign.toLowerCase() == "middle") {
pwElt.setValign(ValignType.MIDDLE);
} else if (vAlign.toLowerCase() == "bottom") {
pwElt.setValign(ValignType.BOTTOM);
} else if (vAlign.toLowerCase() == "top") {
pwElt.setValign(ValignType.TOP);
} else {
pwElt.setValign(ValignType.MIDDLE);
}
if (bioPaxRefs.size() > 0) {
for (int i = 0; i < bioPaxRefs.size(); i++) {
pwElt.addBiopaxRef(bioPaxRefs.get(i));
}
}
if (commentList.size() > 0) {
for (int i = 0; i < commentList.size(); i += 2) {
pwElt.addComment(commentList.get(i), commentList.get(i + 1));
}
}
return pwElt;
}
private PathwayElement createPathwayELement(Xref xref) {
PathwayElement pwe = PathwayElement.createPathwayElement(ObjectType.DATANODE);
pwe.setDataSource(xref.getDataSource());
pwe.setElementID(xref.getId());
pwe.setTextLabel(xref.toString());
pwe.setTransparent(false);
pwe.setColor(Color.BLACK);
pwe.setShapeType(ShapeType.RECTANGLE);
pwe.setLineStyle(LineStyle.SOLID);
pwe.setInitialSize();
pwe.setMWidth(120);
pwe.setMCenterX(60);
pwe.setMCenterY((35 * x) + 14);
return pwe;
}
/**
* Updates the top part of the {@link RegIntTab} with a list of interaction partners of the
* selected Xref
*
* @param xref The {@link Xref} from the selected pathway element
*/
public void updatePathwayPanel(PathwayElement elm) {
Xref xref = elm.getXref();
backpagePanel.removeAll();
JLabel loading = new JLabel("<html><br> Loading...</html>", JLabel.LEFT);
loading.setVerticalAlignment(JLabel.TOP);
pathwayPanel.removeAll();
pathwayPanel.setLayout(new BorderLayout());
pathwayPanel.setBackground(Color.WHITE);
pathwayPanel.add(loading, BorderLayout.CENTER);
pathwayPanel.revalidate();
try {
ResultsObj results = plugin.findInteractions(xref);
if (results != null) {
FormLayout layout =
new FormLayout(
"5dlu, 123px, 3dlu, pref, 3dlu, pref, 5dlu",
tab.getRowLayout(results.getRegulatorMap().size(), results.getTargetMap().size()));
PanelBuilder builder = new PanelBuilder(layout);
builder.setDefaultDialogBorder();
CellConstraints cc = new CellConstraints();
builder.addSeparator("", cc.xyw(1, 1, 7));
y = 2;
int y2 = y;
if (results.getRegulatorMap().size() > 0) {
builder.addLabel("Regulators:", cc.xy(2, y));
y = y + 2;
y2 = y;
JScrollPane sourceScroll =
new JScrollPane(
ScrollPaneConstants.VERTICAL_SCROLLBAR_NEVER,
ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
sourceScroll.setMinimumSize(new Dimension(50, 50));
VPathwaySwing vPathwaySwing =
createPathway(sourceScroll, results.getRegulatorMap(), results, builder);
sourceScroll.add(vPathwaySwing);
builder.add(sourceScroll, cc.xywh(2, y2, 1, (2 * results.getRegulatorMap().size())));
}
if (results.getTargetMap().size() > 0) {
y++;
builder.addLabel("Targets:", cc.xy(2, y));
y = y + 2;
y2 = y;
JScrollPane targetScroll =
new JScrollPane(
ScrollPaneConstants.VERTICAL_SCROLLBAR_NEVER,
ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
targetScroll.setMinimumSize(new Dimension(50, 50));
VPathwaySwing vPathwaySwing =
createPathway(targetScroll, results.getTargetMap(), results, builder);
targetScroll.add(vPathwaySwing);
builder.add(targetScroll, cc.xywh(2, y2, 1, (2 * results.getTargetMap().size())));
}
JPanel panel = builder.getPanel();
pathwayPanel.removeAll();
JLabel selectedLabel =
new JLabel(
"<html><br /> <B>Selected: "
+ elm.getTextLabel()
+ " ("
+ xref.getDataSource().getSystemCode()
+ ": "
+ xref.getId()
+ ")</B></html>");
pathwayPanel.setLayout(new BorderLayout());
pathwayPanel.add(selectedLabel, BorderLayout.NORTH);
pathwayPanel.add(panel, BorderLayout.CENTER);
pathwayPanel.setBackground(Color.WHITE);
pathwayPanel.revalidate();
pathwayPanel.repaint();
} else {
setPathwayPanelText("<html><br> No results found.</html>");
}
} catch (Exception e) {
e.printStackTrace();
}
}