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redo #106
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@AlexanderPico
AlexanderPico committed Mar 19, 2022
1 parent 6b28eba commit 6539595
Showing 1 changed file with 67 additions and 66 deletions.
133 changes: 67 additions & 66 deletions src/main/java/org/wikipathways/cytoscapeapp/impl/GpmlToPathway.java
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Original file line number Diff line number Diff line change
Expand Up @@ -737,29 +737,30 @@ void store(final CyTable cyTable, final CyIdentifiable cyNetObj, final PathwayEl
* Takes a PathVisio element value and stores
* the equivalent Cytoscape visual bypass value in a {@code DelayedVizProp}.
*/
static interface VizPropStore {
DelayedVizProp[] store(final CyIdentifiable cyNetObj, final PathwayElement pvElem);
}

static class BasicVizPropStore implements VizPropStore {
public static final VizPropStore NODE_X = new BasicVizPropStore(BasicExtracter.X, BasicVisualLexicon.NODE_X_LOCATION);
public static final VizPropStore NODE_Y = new BasicVizPropStore(BasicExtracter.Y, BasicVisualLexicon.NODE_Y_LOCATION);
public static final VizPropStore NODE_Z = new BasicVizPropStore(BasicExtracter.Z, BasicVisualLexicon.NODE_Z_LOCATION);
public static final VizPropStore NODE_LABEL = new BasicVizPropStore(BasicExtracter.TEXT_LABEL, BasicVisualLexicon.NODE_LABEL);
public static final VizPropStore NODE_WIDTH = new BasicVizPropStore(BasicExtracter.WIDTH, BasicVisualLexicon.NODE_WIDTH);
public static final VizPropStore NODE_HEIGHT = new BasicVizPropStore(BasicExtracter.HEIGHT, BasicVisualLexicon.NODE_HEIGHT);
public static final VizPropStore NODE_FILL_COLOR = new BasicVizPropStore(BasicExtracter.FILL_COLOR, BasicVisualLexicon.NODE_FILL_COLOR);
public static final VizPropStore NODE_COLOR = new BasicVizPropStore(BasicExtracter.COLOR, BasicVisualLexicon.NODE_LABEL_COLOR, BasicVisualLexicon.NODE_BORDER_PAINT);
public static final VizPropStore NODE_LABEL_FONT = new BasicVizPropStore(BasicExtracter.FONT, BasicVisualLexicon.NODE_LABEL_FONT_FACE);
public static final VizPropStore NODE_LABEL_SIZE = new BasicVizPropStore(BasicExtracter.FONT_SIZE, BasicVisualLexicon.NODE_LABEL_FONT_SIZE);
public static final VizPropStore NODE_TRANSPARENT = new BasicVizPropStore(BasicExtracter.TRANSPARENT, PV_TRANSPARENT_MAP, BasicVisualLexicon.NODE_TRANSPARENCY);
public static final VizPropStore NODE_ALWAYS_TRANSPARENT = new BasicVizPropStore(new DefaultExtracter(0), BasicVisualLexicon.NODE_TRANSPARENCY);
public static final VizPropStore NODE_ALWAYS_SEMI_TRANSPARENT = new BasicVizPropStore(new DefaultExtracter(25), BasicVisualLexicon.NODE_TRANSPARENCY);
// public static final VizPropStore NODE_BORDER_STYLE = new BasicVizPropStore(BasicExtracter.LINE_STYLE_NAME, PV_LINE_STYLE_MAP, BasicVisualLexicon.NODE_BORDER_LINE_TYPE);
public static final VizPropStore NODE_BORDER_THICKNESS = new BasicVizPropStore(BasicExtracter.NODE_LINE_THICKNESS, BasicVisualLexicon.NODE_BORDER_WIDTH);
public static final VizPropStore NODE_SHAPE = new BasicVizPropStore(BasicExtracter.SHAPE, PV_SHAPE_MAP, BasicVisualLexicon.NODE_SHAPE);
public static final VizPropStore NODE_TYPE = new BasicVizPropStore(BasicExtracter.NODE_TYPE, BasicVisualLexicon.NODE_WIDTH); // HACK

//static interface VizPropStore {
// DelayedVizProp[] store(final CyIdentifiable cyNetObj, final PathwayElement pvElem);
//}
//static class BasicVizPropStore implements VizPropStore {
public final BasicVizPropStore NODE_X = new BasicVizPropStore(BasicExtracter.X, BasicVisualLexicon.NODE_X_LOCATION);
public final BasicVizPropStore NODE_Y = new BasicVizPropStore(BasicExtracter.Y, BasicVisualLexicon.NODE_Y_LOCATION);
public final BasicVizPropStore NODE_Z = new BasicVizPropStore(BasicExtracter.Z, BasicVisualLexicon.NODE_Z_LOCATION);
public final BasicVizPropStore NODE_LABEL = new BasicVizPropStore(BasicExtracter.TEXT_LABEL, BasicVisualLexicon.NODE_LABEL);
public final BasicVizPropStore NODE_WIDTH = new BasicVizPropStore(BasicExtracter.WIDTH, BasicVisualLexicon.NODE_WIDTH);
public final BasicVizPropStore NODE_HEIGHT = new BasicVizPropStore(BasicExtracter.HEIGHT, BasicVisualLexicon.NODE_HEIGHT);
public final BasicVizPropStore NODE_FILL_COLOR = new BasicVizPropStore(BasicExtracter.FILL_COLOR, BasicVisualLexicon.NODE_FILL_COLOR);
public final BasicVizPropStore NODE_COLOR = new BasicVizPropStore(BasicExtracter.COLOR, BasicVisualLexicon.NODE_LABEL_COLOR, BasicVisualLexicon.NODE_BORDER_PAINT);
public final BasicVizPropStore NODE_LABEL_FONT = new BasicVizPropStore(BasicExtracter.FONT, BasicVisualLexicon.NODE_LABEL_FONT_FACE);
public final BasicVizPropStore NODE_LABEL_SIZE = new BasicVizPropStore(BasicExtracter.FONT_SIZE, BasicVisualLexicon.NODE_LABEL_FONT_SIZE);
public final BasicVizPropStore NODE_TRANSPARENT = new BasicVizPropStore(BasicExtracter.TRANSPARENT, PV_TRANSPARENT_MAP, BasicVisualLexicon.NODE_TRANSPARENCY);
public final BasicVizPropStore NODE_ALWAYS_TRANSPARENT = new BasicVizPropStore(new DefaultExtracter(0), BasicVisualLexicon.NODE_TRANSPARENCY);
public final BasicVizPropStore NODE_ALWAYS_SEMI_TRANSPARENT = new BasicVizPropStore(new DefaultExtracter(25), BasicVisualLexicon.NODE_TRANSPARENCY);
// public final BasicVizPropStore NODE_BORDER_STYLE = new BasicVizPropStore(BasicExtracter.LINE_STYLE_NAME, PV_LINE_STYLE_MAP, BasicVisualLexicon.NODE_BORDER_LINE_TYPE);
public final BasicVizPropStore NODE_BORDER_THICKNESS = new BasicVizPropStore(BasicExtracter.NODE_LINE_THICKNESS, BasicVisualLexicon.NODE_BORDER_WIDTH);
public final BasicVizPropStore NODE_SHAPE = new BasicVizPropStore(BasicExtracter.SHAPE, PV_SHAPE_MAP, BasicVisualLexicon.NODE_SHAPE);
public final BasicVizPropStore NODE_TYPE = new BasicVizPropStore(BasicExtracter.NODE_TYPE, BasicVisualLexicon.NODE_WIDTH); // HACK

public class BasicVizPropStore
{
final VisualProperty<?>[] cyVizProps;
final Extracter extracter;
final Map<?,?> map;
Expand Down Expand Up @@ -789,8 +790,8 @@ public DelayedVizProp[] store(final CyIdentifiable cyNetObj, final PathwayElemen
}
}

void store(final CyIdentifiable cyNetObj, final PathwayElement pvElem, final VizPropStore ... vizPropStores) {
for (final VizPropStore vizPropStore : vizPropStores)
void store(final CyIdentifiable cyNetObj, final PathwayElement pvElem, final BasicVizPropStore ... vizPropStores) {
for (final BasicVizPropStore vizPropStore : vizPropStores)
{
final DelayedVizProp[] props = vizPropStore.store(cyNetObj, pvElem);
for (DelayedVizProp prop : props)
Expand Down Expand Up @@ -857,7 +858,7 @@ private void convertDataNode(final PathwayElement pvDataNode) {
// BasicVizTableStore.NODE_BORDER_STYLE,
BasicVizTableStore.NODE_BORDER_THICKNESS,
BasicVizTableStore.NODE_SHAPE);
store(cyNode, pvDataNode, BasicVizPropStore.NODE_X, BasicVizPropStore.NODE_Y, BasicVizPropStore.NODE_Z);
store(cyNode, pvDataNode, NODE_X, NODE_Y, NODE_Z);
}

/*
Expand Down Expand Up @@ -886,16 +887,16 @@ private void convertShape(final PathwayElement pvShape) {
// }
store(cyNodeTbl, cyNode, pvShape, BasicTableStore.GRAPH_ID, BasicTableStore.TEXT_LABEL, IS_GPML_SHAPE);
store(cyNode, pvShape,
BasicVizPropStore.NODE_X, BasicVizPropStore.NODE_Y, BasicVizPropStore.NODE_Z,
NODE_X, NODE_Y, NODE_Z,
// BasicTableStore.NODE_TYPE,
BasicVizPropStore.NODE_WIDTH,
BasicVizPropStore.NODE_HEIGHT,
BasicVizPropStore.NODE_FILL_COLOR, BasicVizPropStore.NODE_COLOR,
BasicVizPropStore.NODE_LABEL_FONT, BasicVizPropStore.NODE_LABEL_SIZE,
BasicVizPropStore.NODE_ALWAYS_TRANSPARENT,
// BasicVizPropStore.NODE_BORDER_STYLE,
BasicVizPropStore.NODE_BORDER_THICKNESS,
BasicVizPropStore.NODE_SHAPE,
NODE_WIDTH,
NODE_HEIGHT,
NODE_FILL_COLOR, NODE_COLOR,
NODE_LABEL_FONT, NODE_LABEL_SIZE,
NODE_ALWAYS_TRANSPARENT,
// NODE_BORDER_STYLE,
NODE_BORDER_THICKNESS,
NODE_SHAPE,
SELECTED_COLOR
);
double rotation = pvShape.getRotation();
Expand Down Expand Up @@ -924,8 +925,8 @@ public Object extract(final PathwayElement pvState) {
}
};

final VizPropStore STATE_X_STORE = new BasicVizPropStore(STATE_X_EXTRACTER, BasicVisualLexicon.NODE_X_LOCATION);
final VizPropStore STATE_Y_STORE = new BasicVizPropStore(STATE_Y_EXTRACTER, BasicVisualLexicon.NODE_Y_LOCATION);
final BasicVizPropStore STATE_X_STORE = new BasicVizPropStore(STATE_X_EXTRACTER, BasicVisualLexicon.NODE_X_LOCATION);
final BasicVizPropStore STATE_Y_STORE = new BasicVizPropStore(STATE_Y_EXTRACTER, BasicVisualLexicon.NODE_Y_LOCATION);

private void convertStates() {
DelayedVizProp.clearStateList();
Expand All @@ -945,17 +946,17 @@ private void convertState(final PathwayElement pvState) {
// System.out.println("stored: " + row0.get("name", String.class));

store(cyNode, pvState,
// BasicVizPropStore.NODE_X,
// BasicVizPropStore.NODE_Y,
// NODE_X,
// NODE_Y,
STATE_X_STORE, STATE_Y_STORE,
BasicVizPropStore.NODE_Z,
BasicVizPropStore.NODE_WIDTH, BasicVizPropStore.NODE_HEIGHT,
BasicVizPropStore.NODE_FILL_COLOR, BasicVizPropStore.NODE_COLOR,
BasicVizPropStore.NODE_LABEL, BasicVizPropStore.NODE_LABEL_FONT, BasicVizPropStore.NODE_LABEL_SIZE,
BasicVizPropStore.NODE_TRANSPARENT,
BasicVizPropStore.NODE_BORDER_THICKNESS, BasicVizPropStore.NODE_SHAPE
// BasicVizPropStore.NODE_BORDER_STYLE,
// BasicVizPropStore.NODE_TYPE,
NODE_Z,
NODE_WIDTH, NODE_HEIGHT,
NODE_FILL_COLOR, NODE_COLOR,
NODE_LABEL, NODE_LABEL_FONT, NODE_LABEL_SIZE,
NODE_TRANSPARENT,
NODE_BORDER_THICKNESS, NODE_SHAPE
// NODE_BORDER_STYLE,
// NODE_TYPE,
);
// DelayedVizProp fillColorProp = new DelayedVizProp(cyNode,
// BasicVisualLexicon.NODE_FILL_COLOR, new Color(250, 0, 0), true);
Expand Down Expand Up @@ -1078,16 +1079,16 @@ public Object toCyValue(Object[] pvValues) {

static final Extracter GROUP_BORDER_THICKNESS_EXTRACTER = new BasicExtracter(GROUP_BORDER_THICKNESS_CONVERTER, StaticProperty.GROUPSTYLE);

static final VizPropStore GROUP_X = new BasicVizPropStore(GROUP_X_EXTRACTER, BasicVisualLexicon.NODE_X_LOCATION);
static final VizPropStore GROUP_Y = new BasicVizPropStore(GROUP_Y_EXTRACTER, BasicVisualLexicon.NODE_Y_LOCATION);
static final VizPropStore SELECTED_COLOR = new BasicVizPropStore(new DefaultExtracter(new Color(255, 255, 204, 127)), BasicVisualLexicon.NODE_SELECTED_PAINT);
static final VizPropStore GROUP_WIDTH = new BasicVizPropStore(GROUP_W_EXTRACTER, BasicVisualLexicon.NODE_WIDTH);
static final VizPropStore GROUP_HEIGHT = new BasicVizPropStore(GROUP_H_EXTRACTER, BasicVisualLexicon.NODE_HEIGHT);
static final VizPropStore GROUP_FILL_COLOR = new BasicVizPropStore(GROUP_FILL_COLOR_EXTRACTER, BasicVisualLexicon.NODE_FILL_COLOR);
static final VizPropStore GROUP_COLOR = new BasicVizPropStore(new DefaultExtracter(new Color(0xaaaaaa)), BasicVisualLexicon.NODE_LABEL_COLOR, BasicVisualLexicon.NODE_BORDER_PAINT);
static final VizPropStore GROUP_BORDER_THICKNESS = new BasicVizPropStore(GROUP_BORDER_THICKNESS_EXTRACTER, BasicVisualLexicon.NODE_BORDER_WIDTH);
static final VizPropStore GROUP_BORDER_STYLE = new BasicVizPropStore(GROUP_BORDER_STYLE_EXTRACTER, BasicVisualLexicon.NODE_BORDER_LINE_TYPE);
static final VizPropStore GROUP_SHAPE = new BasicVizPropStore(GROUP_SHAPE_EXTRACTER, BasicVisualLexicon.NODE_SHAPE);
final BasicVizPropStore GROUP_X = new BasicVizPropStore(GROUP_X_EXTRACTER, BasicVisualLexicon.NODE_X_LOCATION);
final BasicVizPropStore GROUP_Y = new BasicVizPropStore(GROUP_Y_EXTRACTER, BasicVisualLexicon.NODE_Y_LOCATION);
final BasicVizPropStore SELECTED_COLOR = new BasicVizPropStore(new DefaultExtracter(new Color(255, 255, 204, 127)), BasicVisualLexicon.NODE_SELECTED_PAINT);
final BasicVizPropStore GROUP_WIDTH = new BasicVizPropStore(GROUP_W_EXTRACTER, BasicVisualLexicon.NODE_WIDTH);
final BasicVizPropStore GROUP_HEIGHT = new BasicVizPropStore(GROUP_H_EXTRACTER, BasicVisualLexicon.NODE_HEIGHT);
final BasicVizPropStore GROUP_FILL_COLOR = new BasicVizPropStore(GROUP_FILL_COLOR_EXTRACTER, BasicVisualLexicon.NODE_FILL_COLOR);
final BasicVizPropStore GROUP_COLOR = new BasicVizPropStore(new DefaultExtracter(new Color(0xaaaaaa)), BasicVisualLexicon.NODE_LABEL_COLOR, BasicVisualLexicon.NODE_BORDER_PAINT);
final BasicVizPropStore GROUP_BORDER_THICKNESS = new BasicVizPropStore(GROUP_BORDER_THICKNESS_EXTRACTER, BasicVisualLexicon.NODE_BORDER_WIDTH);
final BasicVizPropStore GROUP_BORDER_STYLE = new BasicVizPropStore(GROUP_BORDER_STYLE_EXTRACTER, BasicVisualLexicon.NODE_BORDER_LINE_TYPE);
final BasicVizPropStore GROUP_SHAPE = new BasicVizPropStore(GROUP_SHAPE_EXTRACTER, BasicVisualLexicon.NODE_SHAPE);

private void convertGroups() {
for (final PathwayElement pvElem : pvPathway.getDataObjects()) {
Expand All @@ -1104,12 +1105,12 @@ private void convertGroup(final PathwayElement pvGroup) {
// if (verbose) System.out.println("convertGroup: " + pvGroup.getGroupStyle());
// cyGroupNode.pvGroup.getGroupStyle();
store(cyGroupNode, pvGroup,
GROUP_X, GROUP_Y, BasicVizPropStore.NODE_Z,
GROUP_X, GROUP_Y, NODE_Z,
SELECTED_COLOR,
GROUP_WIDTH, GROUP_HEIGHT,
GROUP_COLOR, GROUP_FILL_COLOR,
GROUP_BORDER_THICKNESS, GROUP_BORDER_STYLE,
BasicVizPropStore.NODE_ALWAYS_SEMI_TRANSPARENT, GROUP_SHAPE
NODE_ALWAYS_SEMI_TRANSPARENT, GROUP_SHAPE
);
}
/*
Expand All @@ -1130,13 +1131,13 @@ private void convertLabel(final PathwayElement pvLabel) {
pvToCyNodes.put(pvLabel, cyNode);
store(cyNodeTbl, cyNode, pvLabel, BasicTableStore.TEXT_LABEL);
store(cyNode, pvLabel,
BasicVizPropStore.NODE_X, BasicVizPropStore.NODE_Y, BasicVizPropStore.NODE_Z,
BasicVizPropStore.NODE_WIDTH, BasicVizPropStore.NODE_HEIGHT,
// BasicVizPropStore.NODE_BORDER_STYLE,
BasicVizPropStore.NODE_BORDER_THICKNESS,
BasicVizPropStore.NODE_COLOR, BasicVizPropStore.NODE_SHAPE,
BasicVizPropStore.NODE_LABEL_FONT, BasicVizPropStore.NODE_LABEL_SIZE,
BasicVizPropStore.NODE_TRANSPARENT, SELECTED_COLOR
NODE_X, NODE_Y, NODE_Z,
NODE_WIDTH, NODE_HEIGHT,
// NODE_BORDER_STYLE,
NODE_BORDER_THICKNESS,
NODE_COLOR, NODE_SHAPE,
NODE_LABEL_FONT, NODE_LABEL_SIZE,
NODE_TRANSPARENT, SELECTED_COLOR
);
}

Expand Down

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