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Fix default values, edge parents, and loading
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@Randoom97
Randoom97 committed Jun 15, 2020
1 parent c5c4c94 commit e8c9430
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Showing 5 changed files with 150 additions and 113 deletions.
221 changes: 119 additions & 102 deletions SBOLCanvasBackend/src/utils/Converter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -659,8 +659,7 @@ private Set<ComponentDefinition> createModuleView(SBOLDocument document, mxGraph
mxCell glyphCell = this.getGraphicalLayout(graph, glyphArray[glyphIndex].getIdentity());
if (glyphCell != null) {
glyphCell.setValue(glyphComponent.getDefinition().getIdentity().toString());
//TODO fix the base style name
glyphCell.setStyle(STYLE_SEQUENCE_FEATURE);
glyphCell.setStyle(STYLE_SEQUENCE_FEATURE + ";" + glyphCell.getStyle());
model.add(container, glyphCell, glyphIndex);
} else {
glyphCell = (mxCell) graph.insertVertex(container, null,
Expand Down Expand Up @@ -691,9 +690,9 @@ private Set<ComponentDefinition> createModuleView(SBOLDocument document, mxGraph
Set<Interaction> interactions = modDef.getInteractions();
for (Interaction interaction : interactions) {
Annotation interactionAnn = interaction.getAnnotation(new QName(uriPrefix, "edge", annPrefix));
mxCell edge = null;
if (interactionAnn != null) {
edge = (mxCell) decodeMxGraphObject(interactionAnn.getStringValue());
mxCell edge = this.getGraphicalLayout(graph, interaction.getIdentity());
if (edge != null) {
edge.setStyle(STYLE_INTERACTION + ";"+edge.getStyle());
edge = (mxCell) model.add(rootViewCell, edge, 0);
} else {
edge = (mxCell) graph.insertEdge(rootViewCell, null, null, null, null);
Expand Down Expand Up @@ -797,6 +796,7 @@ private void createComponentView(SBOLDocument document, mxGraph graph, Component

private mxGraph parseGraph(InputStream graphStream) throws IOException {
mxGraph graph = new mxGraph();
((mxGraphModel) graph.getModel()).setMaintainEdgeParent(false);
Document document = mxXmlUtils.parseXml(mxUtils.readInputStream(graphStream));
mxCodec codec = new mxCodec(document);
codec.decode(document.getDocumentElement(), graph.getModel());
Expand Down Expand Up @@ -909,44 +909,37 @@ private void createGraphicalLayout(mxGraph graph, mxCell cell, URI reference)
annList.add(new Annotation(new QName(uriPrefix, "height", annPrefix), cellGeometry.getHeight()));

// styling
String strokeColor = (String) styles.get(mxConstants.STYLE_STROKECOLOR);
if (strokeColor != null)
annList.add(
new Annotation(new QName(uriPrefix, "strokeColor", annPrefix), strokeColor));
if (cell.getStyle().contains(mxConstants.STYLE_STROKECOLOR))
annList.add(new Annotation(new QName(uriPrefix, "strokeColor", annPrefix),
(String) styles.get(mxConstants.STYLE_STROKECOLOR)));

String strokeOpacity = (String) styles.get(mxConstants.STYLE_STROKE_OPACITY);
if (strokeOpacity != null)
if (cell.getStyle().contains(mxConstants.STYLE_STROKE_OPACITY))
annList.add(new Annotation(new QName(uriPrefix, "strokeOpacity", annPrefix),
strokeOpacity));
(String) styles.get(mxConstants.STYLE_STROKE_OPACITY)));

String strokeWidth = (String) styles.get(mxConstants.STYLE_STROKEWIDTH);
if (strokeWidth != null)
annList.add(
new Annotation(new QName(uriPrefix, "strokeWidth", annPrefix), strokeWidth));
if (cell.getStyle().contains(mxConstants.STYLE_STROKEWIDTH))
annList.add(new Annotation(new QName(uriPrefix, "strokeWidth", annPrefix),
(String) styles.get(mxConstants.STYLE_STROKEWIDTH)));

String fillColor = (String) styles.get(mxConstants.STYLE_FILLCOLOR);
if (fillColor != null)
annList.add(new Annotation(new QName(uriPrefix, "fillColor", annPrefix), fillColor));
if (cell.getStyle().contains(mxConstants.STYLE_FILLCOLOR))
annList.add(new Annotation(new QName(uriPrefix, "fillColor", annPrefix),
(String) styles.get(mxConstants.STYLE_FILLCOLOR)));

String fillOpacity = (String) styles.get(mxConstants.STYLE_FILL_OPACITY);
if (fillOpacity != null)
annList.add(
new Annotation(new QName(uriPrefix, "fillOpacity", annPrefix), fillOpacity));
if (cell.getStyle().contains(mxConstants.STYLE_FILL_OPACITY))
annList.add(new Annotation(new QName(uriPrefix, "fillOpacity", annPrefix),
(String) styles.get(mxConstants.STYLE_FILL_OPACITY)));

String fontColor = (String) styles.get(mxConstants.STYLE_FONTCOLOR);
if (fontColor != null)
annList.add(new Annotation(new QName(uriPrefix, "fontColor", annPrefix), fontColor));
if (cell.getStyle().contains(mxConstants.STYLE_FONTCOLOR))
annList.add(new Annotation(new QName(uriPrefix, "fontColor", annPrefix),
(String) styles.get(mxConstants.STYLE_FONTCOLOR)));

String fontSize = (String) styles.get(mxConstants.STYLE_FONTSIZE);
if (fontSize != null)
annList.add(new Annotation(new QName(uriPrefix, "fontSize", annPrefix), fontSize));
if (cell.getStyle().contains(mxConstants.STYLE_FONTSIZE))
annList.add(new Annotation(new QName(uriPrefix, "fontSize", annPrefix),
(String) styles.get(mxConstants.STYLE_FONTSIZE)));

if (cell.getStyle().contains(STYLE_TEXTBOX))
annList.add(new Annotation(new QName(uriPrefix, "text", annPrefix), (String) cell.getValue()));

// annList.add(new Annotation(new QName(uriPrefix, "reference", annPrefix),
// reference));

Annotation nodeGlyph = layout.createAnnotation(new QName(uriPrefix, "NodeGlyph", annPrefix),
new QName(uriPrefix, "attributes", annPrefix), "attributes", annList);
nodeGlyph.setNestedIdentity(reference);
Expand All @@ -956,50 +949,41 @@ private void createGraphicalLayout(mxGraph graph, mxCell cell, URI reference)
List<Annotation> annList = new ArrayList<Annotation>();

// styling
String strokeColor = (String) styles.get(mxConstants.STYLE_STROKECOLOR);
if (strokeColor != null)
annList.add(
new Annotation(new QName(uriPrefix, "strokeColor", annPrefix), strokeColor));
if (cell.getStyle().contains(mxConstants.STYLE_STROKECOLOR))
annList.add(new Annotation(new QName(uriPrefix, "strokeColor", annPrefix),
(String) styles.get(mxConstants.STYLE_STROKECOLOR)));

String strokeOpacity = (String) styles.get(mxConstants.STYLE_STROKE_OPACITY);
if (strokeOpacity != null)
if (cell.getStyle().contains(mxConstants.STYLE_STROKE_OPACITY))
annList.add(new Annotation(new QName(uriPrefix, "strokeOpacity", annPrefix),
strokeOpacity));
(String) styles.get(mxConstants.STYLE_STROKE_OPACITY)));

String strokeWidth = (String) styles.get(mxConstants.STYLE_STROKEWIDTH);
if (strokeWidth != null)
annList.add(
new Annotation(new QName(uriPrefix, "strokeWidth", annPrefix), strokeWidth));
if (cell.getStyle().contains(mxConstants.STYLE_STROKEWIDTH))
annList.add(new Annotation(new QName(uriPrefix, "strokeWidth", annPrefix),
(String) styles.get(mxConstants.STYLE_STROKEWIDTH)));

String arrowSize = (String) styles.get(mxConstants.STYLE_ENDSIZE);
if (arrowSize != null)
annList.add(new Annotation(new QName(uriPrefix, "endSize", annPrefix), arrowSize));
if (cell.getStyle().contains(mxConstants.STYLE_ENDSIZE))
annList.add(new Annotation(new QName(uriPrefix, "endSize", annPrefix),
(String) styles.get(mxConstants.STYLE_ENDSIZE)));

String sourceMargin = (String) styles.get(mxConstants.STYLE_SOURCE_PERIMETER_SPACING);
if (sourceMargin != null)
if (cell.getStyle().contains(mxConstants.STYLE_SOURCE_PERIMETER_SPACING))
annList.add(new Annotation(new QName(uriPrefix, "sourceSpacing", annPrefix),
sourceMargin));
(String) styles.get(mxConstants.STYLE_SOURCE_PERIMETER_SPACING)));

String targetMargin = (String) styles.get(mxConstants.STYLE_TARGET_PERIMETER_SPACING);
if (targetMargin != null)
if (cell.getStyle().contains(mxConstants.STYLE_TARGET_PERIMETER_SPACING))
annList.add(new Annotation(new QName(uriPrefix, "targetSpacing", annPrefix),
targetMargin));
(String) styles.get(mxConstants.STYLE_TARGET_PERIMETER_SPACING)));

String edgeStyle = (String) styles.get(mxConstants.STYLE_EDGE);
if (edgeStyle != null)
annList.add(new Annotation(new QName(uriPrefix, "edge", annPrefix), edgeStyle));
if (cell.getStyle().contains(mxConstants.STYLE_EDGE))
annList.add(new Annotation(new QName(uriPrefix, "edge", annPrefix),
(String) styles.get(mxConstants.STYLE_EDGE)));

String rounded = (String) styles.get(mxConstants.STYLE_ROUNDED);
if (rounded != null)
if (cell.getStyle().contains(mxConstants.STYLE_ROUNDED))
annList.add(new Annotation(new QName(uriPrefix, "rounded", annPrefix),
Integer.parseInt(rounded) == 1));

String curved = (String) styles.get("curved");
if (curved != null)
annList.add(new Annotation(new QName(uriPrefix, "curved", annPrefix), Integer.parseInt(curved) == 1));
Integer.parseInt((String) styles.get(mxConstants.STYLE_ROUNDED)) == 1));

// annList.add(new Annotation(new QName(uriPrefix, "reference", annPrefix),
// reference));
if (cell.getStyle().contains("curved"))
annList.add(new Annotation(new QName(uriPrefix, "curved", annPrefix),
Integer.parseInt((String) styles.get("curved")) == 1));

Annotation edgeGlyphAnn = layout.createAnnotation(new QName(uriPrefix, "EdgeGlyph", annPrefix),
new QName(uriPrefix, "attributes", annPrefix), "attributes", annList);
Expand Down Expand Up @@ -1047,95 +1031,128 @@ private mxCell getGraphicalLayout(mxGraph graph, URI refference) {
break;
}
}
if(ann == null)
if (ann == null)
return null;

mxCell[] cellArr = {cell};
mxCell[] cellArr = { cell };
cell.setGeometry(new mxGeometry());
if (ann.getQName().getLocalPart().equals("NodeGlyph")) {
if (ann.getQName().getLocalPart().equals("NodeGlyph")) {
cell.setVertex(true);
for (Annotation attributeAnn : ann.getAnnotations()) {
String value = attributeAnn.getStringValue();
switch (attributeAnn.getQName().getLocalPart()) {
case "x":
cell.getGeometry().setX(Double.parseDouble(value)); break;
cell.getGeometry().setX(Double.parseDouble(value));
break;
case "y":
cell.getGeometry().setY(Double.parseDouble(value)); break;
cell.getGeometry().setY(Double.parseDouble(value));
break;
case "width":
cell.getGeometry().setWidth(Double.parseDouble(value)); break;
cell.getGeometry().setWidth(Double.parseDouble(value));
break;
case "height":
cell.getGeometry().setHeight(Double.parseDouble(value)); break;
cell.getGeometry().setHeight(Double.parseDouble(value));
break;
case "strokeColor":
graph.setCellStyles(mxConstants.STYLE_STROKECOLOR, value, cellArr); break;
graph.setCellStyles(mxConstants.STYLE_STROKECOLOR, value, cellArr);
break;
case "strokeOpacity":
graph.setCellStyles(mxConstants.STYLE_STROKE_OPACITY, value, cellArr); break;
graph.setCellStyles(mxConstants.STYLE_STROKE_OPACITY, value, cellArr);
break;
case "strokeWidth":
graph.setCellStyles(mxConstants.STYLE_STROKEWIDTH, value, cellArr); break;
graph.setCellStyles(mxConstants.STYLE_STROKEWIDTH, value, cellArr);
break;
case "fillColor":
graph.setCellStyles(mxConstants.STYLE_FILLCOLOR, value, cellArr); break;
graph.setCellStyles(mxConstants.STYLE_FILLCOLOR, value, cellArr);
break;
case "fillOpacity":
graph.setCellStyles(mxConstants.STYLE_FILL_OPACITY, value, cellArr); break;
graph.setCellStyles(mxConstants.STYLE_FILL_OPACITY, value, cellArr);
break;
case "fontColor":
graph.setCellStyles(mxConstants.STYLE_FONTCOLOR, value, cellArr); break;
graph.setCellStyles(mxConstants.STYLE_FONTCOLOR, value, cellArr);
break;
case "fontSize":
graph.setCellStyles(mxConstants.STYLE_FONTSIZE, value, cellArr); break;
graph.setCellStyles(mxConstants.STYLE_FONTSIZE, value, cellArr);
break;
case "text":
cell.setValue(value); break;
cell.setValue(value);
break;
}
}
} else if (ann.getQName().getLocalPart().equals("EdgeGlyph")) {
for(Annotation attributeAnn : ann.getAnnotations()) {
cell.setEdge(true);
for (Annotation attributeAnn : ann.getAnnotations()) {
String value = attributeAnn.getStringValue();
switch(attributeAnn.getQName().getLocalPart()) {
switch (attributeAnn.getQName().getLocalPart()) {
case "strokeColor":
graph.setCellStyles(mxConstants.STYLE_STROKECOLOR, value, cellArr); break;
graph.setCellStyles(mxConstants.STYLE_STROKECOLOR, value, cellArr);
break;
case "strokeOpacity":
graph.setCellStyles(mxConstants.STYLE_STROKE_OPACITY, value, cellArr); break;
graph.setCellStyles(mxConstants.STYLE_STROKE_OPACITY, value, cellArr);
break;
case "strokeWidth":
graph.setCellStyles(mxConstants.STYLE_STROKEWIDTH, value, cellArr); break;
graph.setCellStyles(mxConstants.STYLE_STROKEWIDTH, value, cellArr);
break;
case "endSize":
graph.setCellStyles(mxConstants.STYLE_ENDSIZE, value, cellArr); break;
graph.setCellStyles(mxConstants.STYLE_ENDSIZE, value, cellArr);
break;
case "sourceSpacing":
graph.setCellStyles(mxConstants.STYLE_SOURCE_PERIMETER_SPACING, value, cellArr); break;
graph.setCellStyles(mxConstants.STYLE_SOURCE_PERIMETER_SPACING, value, cellArr);
break;
case "targetSpacing":
graph.setCellStyles(mxConstants.STYLE_TARGET_PERIMETER_SPACING, value, cellArr); break;
graph.setCellStyles(mxConstants.STYLE_TARGET_PERIMETER_SPACING, value, cellArr);
break;
case "edge":
graph.setCellStyles(mxConstants.STYLE_EDGE, value, cellArr); break;
graph.setCellStyles(mxConstants.STYLE_EDGE, value, cellArr);
break;
case "rounded":
graph.setCellStyles(mxConstants.STYLE_ROUNDED, value, cellArr); break;
if(value.equals("true")) {
graph.setCellStyles(mxConstants.STYLE_ROUNDED, "1", cellArr);
}
break;
case "curved":
graph.setCellStyles("curved", value, cellArr); break;
if(value.equals("true")) {
graph.setCellStyles("curved", "1", cellArr);
}
break;
case "sourcePoint":
mxPoint sourcePoint = new mxPoint();
for(Annotation sourceAnn: attributeAnn.getAnnotations()) {
switch(sourceAnn.getQName().getLocalPart()) {
for (Annotation sourceAnn : attributeAnn.getAnnotations()) {
switch (sourceAnn.getQName().getLocalPart()) {
case "x":
sourcePoint.setX(Double.parseDouble(sourceAnn.getStringValue())); break;
sourcePoint.setX(Double.parseDouble(sourceAnn.getStringValue()));
break;
case "y":
sourcePoint.setY(Double.parseDouble(sourceAnn.getStringValue())); break;
sourcePoint.setY(Double.parseDouble(sourceAnn.getStringValue()));
break;
}
}
cell.getGeometry().setSourcePoint(sourcePoint);
break;
case "targetPoint":
mxPoint targetPoint = new mxPoint();
for(Annotation sourceAnn: attributeAnn.getAnnotations()) {
switch(sourceAnn.getQName().getLocalPart()) {
for (Annotation sourceAnn : attributeAnn.getAnnotations()) {
switch (sourceAnn.getQName().getLocalPart()) {
case "x":
targetPoint.setX(Double.parseDouble(sourceAnn.getStringValue())); break;
targetPoint.setX(Double.parseDouble(sourceAnn.getStringValue()));
break;
case "y":
targetPoint.setY(Double.parseDouble(sourceAnn.getStringValue())); break;
targetPoint.setY(Double.parseDouble(sourceAnn.getStringValue()));
break;
}
}
cell.getGeometry().setSourcePoint(targetPoint);
break;
case "point":
mxPoint point = new mxPoint();
for(Annotation sourceAnn: attributeAnn.getAnnotations()) {
switch(sourceAnn.getQName().getLocalPart()) {
for (Annotation sourceAnn : attributeAnn.getAnnotations()) {
switch (sourceAnn.getQName().getLocalPart()) {
case "x":
point.setX(Double.parseDouble(sourceAnn.getStringValue())); break;
point.setX(Double.parseDouble(sourceAnn.getStringValue()));
break;
case "y":
point.setY(Double.parseDouble(sourceAnn.getStringValue())); break;
point.setY(Double.parseDouble(sourceAnn.getStringValue()));
break;
}
}
cell.getGeometry().getPoints().add(point);
Expand Down
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