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SpringSaLaD graphic editor fixes #1638

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Merged
danv61 merged 2 commits into from
Feb 10, 2026
+114 −31
Merged

SpringSaLaD graphic editor fixes #1638

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ba40195
fixed site size bug
danv61 Feb 9, 2026
fe37be2
Better representation of molecule in the graphic editor
danv61 Feb 10, 2026
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23 changes: 21 additions & 2 deletions vcell-client/src/main/java/cbit/vcell/mapping/gui/MolecularStructuresPropertiesPanel.java
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,7 @@ public class MolecularStructuresPropertiesPanel extends DocumentEditorSubPanel {

private MolecularComponentPattern mcpSelected = null;
private MolecularInternalLinkSpec milsSelected = null;
private Object lastSelectedObject = null; // may be either MolecularComponentPattern or MolecularInternalLinkSpec

private JButton zoomLargerButton = null;
private JButton zoomSmallerButton = null;
Expand Down Expand Up @@ -80,16 +81,32 @@ public void propertyChange(PropertyChangeEvent evt) {
Object o = evt.getNewValue();
if(o instanceof MolecularComponentPattern mcp) {
mcpSelected = mcp;
lastSelectedObject = mcpSelected;
} else {
mcpSelected = null;
if(milsSelected != null) {
// if we had a link selected before, it becomes the last (and only) selected
lastSelectedObject = milsSelected;
} else {
// nothing is selected anymore
lastSelectedObject = null;
}
}
updateShape();
} else if(evt.getSource() instanceof SpeciesContextSpec && evt.getPropertyName().equals(SpeciesContextSpec.PROPERTY_NAME_LINK_SELECTED_IN_TABLE)) {
Object o = evt.getNewValue();
if(o instanceof MolecularInternalLinkSpec mils) {
milsSelected = mils;
lastSelectedObject = milsSelected;
} else {
milsSelected = null;
if(mcpSelected != null) {
// if we had a site selected before, it becomes the last (and only) selected
lastSelectedObject = mcpSelected;
} else {
// nothing is selected anymore
lastSelectedObject = null;
}
}
updateShape();
}
Expand Down Expand Up @@ -121,7 +138,7 @@ public void paintComponent(Graphics g) {
return;
}
scsls = new SpeciesContextSpecLargeShape(speciesContextSpec, shapePanel, speciesContextSpec,
mcpSelected, milsSelected, issueManager);
mcpSelected, milsSelected, lastSelectedObject, issueManager);
scsls.paintSelf(g);
}
@Override
Expand Down Expand Up @@ -188,12 +205,14 @@ public void mouseClicked(MouseEvent e) {
Object overObject = scsls.contains(overWhat); // check if we clicked inside a site oval or link line
if(overObject instanceof MolecularInternalLinkSpec mils) {
milsSelected = mils;
lastSelectedObject = milsSelected;
// redraw the whole shape to highlight the selected site oval
updateShape();
// we tell the table in the upper panel to update the selected row
speciesContextSpec.firePropertyChange(PROPERTY_NAME_LINK_SELECTED_IN_SHAPE, null, milsSelected);
} else if(overObject instanceof SiteAttributesSpec sas) {
mcpSelected = sas.getMolecularComponentPattern();
lastSelectedObject = mcpSelected;
// redraw the whole shape to highlight the selected link line
updateShape();
// we tell the table in the upper panel to update the selected row
Expand Down Expand Up @@ -282,7 +301,7 @@ private void updateShape() {
return;
}
scsls = new SpeciesContextSpecLargeShape(speciesContextSpec, shapePanel, speciesContextSpec,
mcpSelected, milsSelected, issueManager);
mcpSelected, milsSelected, lastSelectedObject, issueManager);

// shapePanel.setPreferredSize(scsls.getMaxSize());

Expand Down
122 changes: 93 additions & 29 deletions vcell-core/src/main/java/cbit/vcell/graph/SpeciesContextSpecLargeShape.java
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,6 @@
import java.awt.geom.Ellipse2D;
import java.awt.geom.Line2D;
import java.util.*;
import java.util.List;

public class SpeciesContextSpecLargeShape extends AbstractComponentShape implements HighlightableShapeInterface {

Expand All @@ -33,9 +32,9 @@ public boolean contains(double x, double y) {
}
}

private static final double NmToPixelRatio = 25;
private static final double DEFAULT_UPPER_CORNER = 3; // default screen coordinates where we want to display the first site
private static final double DEFAULT_LEFT_CORNER = 10; // in nm
private static final double NmToPixelRatio = 18;
private static final double DEFAULT_UPPER_CORNER = 5.3; // default screen coordinates where we want to display the first site
private static final double DEFAULT_LEFT_CORNER = 13; // in nm

// x, y positions where we want to begin drawing the shape (nm from top and left of painting area)
private double x_offset = DEFAULT_LEFT_CORNER;
Expand Down Expand Up @@ -73,13 +72,17 @@ public boolean contains(double x, double y) {

Map<Ellipse2D, SiteAttributesSpec> ellipseToSasMap = new LinkedHashMap<>(); // site oval to site attributes map
Map<CustomLine2D, MolecularInternalLinkSpec> lineToMilsMap = new LinkedHashMap<>(); // link line to link spec
// we need also the inverse association
Map<SiteAttributesSpec, Ellipse2D> sasToEllipseMap = new LinkedHashMap<>();
Map<MolecularInternalLinkSpec, CustomLine2D> milsToLineMap = new LinkedHashMap<>();

private MolecularComponentPattern mcpSelected = null; // any or both of these may be selected in their tables
private MolecularComponentPattern mcpSelected = null; // any or both of these may be selected in their tables, they are highlighted on the shape
private MolecularInternalLinkSpec milsSelected = null;
private Object lastSelectedObject = null; // this is the last selected object, we show it on top of everything else

public SpeciesContextSpecLargeShape(SpeciesContextSpec scs, LargeShapeCanvas shapePanel, Displayable owner,
MolecularComponentPattern mcpSelected, MolecularInternalLinkSpec milsSelected,
IssueListProvider issueListProvider) {
Object lastSelectedObject, IssueListProvider issueListProvider) {
super(issueListProvider);

this.owner = owner;
Expand All @@ -88,6 +91,7 @@ public SpeciesContextSpecLargeShape(SpeciesContextSpec scs, LargeShapeCanvas sha

this.mcpSelected = mcpSelected;
this.milsSelected = milsSelected;
this.lastSelectedObject = lastSelectedObject;

if(scs != null) {
this.sc = scs.getSpeciesContext();
Expand Down Expand Up @@ -204,36 +208,30 @@ private void paintCompartments(Graphics g) {
Stroke strokeOld = g2.getStroke();

Font font;
int z = shapePanel.getZoomFactor();
nmToPixelRatio = NmToPixelRatio + z;
int zoomFactor = shapePanel.getZoomFactor();
nmToPixelRatio = NmToPixelRatio + zoomFactor;
g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);

String name = structure.getName();
if(z > -3) {
if(zoomFactor > -3) {
font = fontOld.deriveFont(Font.BOLD);
g.setFont(font);

} else {
font = fontOld;
g.setFont(font);
}

g.setColor(Color.black);
double VerticalTextOffset = 1.0; // vertical means y coord
if(!hasMembraneSite) {
double x = minX+x_offset;
double y = 1;
g2.drawString(name, (int)(nmToPixelRatio * x), (int)(nmToPixelRatio * y));
double y = VerticalTextOffset;
g2.drawString(name, (int)(nmToPixelRatio * x), (int)(NmToPixelRatio * y));
} else {
double x = membraneX+x_offset-5;
double y = 1;
g2.drawString("Extracellular", (int)(nmToPixelRatio * x), (int)(nmToPixelRatio * y));

x = membraneX+x_offset;
y = 1;
g2.drawString("Membrane Intracellular",
(int)(nmToPixelRatio * x),
// (int)(nmToPixelRatio * (x-membraneRadius)), // move it slightly to the left
(int)(nmToPixelRatio * y));
double x = membraneX+x_offset; // position of membrane bar
double y = VerticalTextOffset;
g2.drawString("Extracellular", (int)(nmToPixelRatio * (x-7)), (int)(NmToPixelRatio * y));
g2.drawString("Intracellular", (int)(nmToPixelRatio * (x+3)), (int)(NmToPixelRatio * y));

g2.setColor(NamedColor.darker(Color.orange, 0.8));
float thickness = 4.0f;
Expand Down Expand Up @@ -343,14 +341,14 @@ public Ellipse2D drawCenteredCircle(Graphics g, NamedColor namedColor, double xd
nmToPixelRatio = NmToPixelRatio + z;
g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);

xd = xd-(rd/2);
yd = yd-(rd/2);
xd = xd-rd;
yd = yd-rd;

int x = (int)(nmToPixelRatio * xd);
int y = (int)(nmToPixelRatio * yd);
int r = (int)(nmToPixelRatio * rd);

Ellipse2D oval = new Ellipse2D.Double(x, y, r, r);
Ellipse2D oval = new Ellipse2D.Double(x, y, 2*r, 2*r);
g2.setColor(namedColor.getColor());
g2.fill(oval);

Expand Down Expand Up @@ -416,6 +414,9 @@ public void paintSelf(Graphics g, boolean bPaintContour) {
}
Map<MolecularComponentPattern, SiteAttributesSpec> sasMap = scs.getSiteAttributesMap();
Set<MolecularInternalLinkSpec> internalLinkSet = scs.getInternalLinkSet();

// we draw all objects as unselected first, and then we redraw the selected objects on top of everything else,
// so that they look highlighted and are not hidden behind other objects
for(MolecularInternalLinkSpec mils : internalLinkSet) {
Pair<MolecularComponentPattern, MolecularComponentPattern> link = mils.getLink();
SiteAttributesSpec sas1 = sasMap.get(link.one);
Expand All @@ -424,9 +425,9 @@ public void paintSelf(Graphics g, boolean bPaintContour) {
double x2 = x_offset + sas2.getCoordinate().getZ();
double y1 = y_offset + sas1.getCoordinate().getY();
double y2 = y_offset + sas2.getCoordinate().getY();
boolean isSelected = mils == milsSelected ? true : false;
CustomLine2D line = drawLink(g, x1, y1, x2, y2, isSelected);
CustomLine2D line = drawLink(g, x1, y1, x2, y2, false);
lineToMilsMap.put(line, mils);
milsToLineMap.put(mils, line);
}
for(MolecularComponentPattern mcp : mtp.getComponentPatternList()) {
SiteAttributesSpec sas = sasMap.get(mcp);
Expand All @@ -435,9 +436,72 @@ public void paintSelf(Graphics g, boolean bPaintContour) {
NamedColor color = sas.getColor();
double x = x_offset + coord.getZ();
double y = y_offset + coord.getY();
boolean isSelected = mcp == mcpSelected ? true : false;
Ellipse2D oval = drawCenteredCircle(g, color, x, y, radius, isSelected);
Ellipse2D oval = drawCenteredCircle(g, color, x, y, radius, false);
ellipseToSasMap.put(oval, sas);
sasToEllipseMap.put(sas, oval);
}

// we redraw the selected objects on top of all unselected objects
if(mcpSelected != null) {
SiteAttributesSpec sas = sasMap.get(mcpSelected);
Coordinate coord = sas.getCoordinate();
double radius = sas.getRadius();
NamedColor color = sas.getColor();
double x = x_offset + coord.getZ();
double y = y_offset + coord.getY();
Ellipse2D newOval = drawCenteredCircle(g, color, x, y, radius, true);
Ellipse2D oldOval = sasToEllipseMap.get(sas);
sasToEllipseMap.put(sas, newOval);
ellipseToSasMap.remove(oldOval);
ellipseToSasMap.put(newOval, sas);
}
if(milsSelected != null) {
Pair<MolecularComponentPattern, MolecularComponentPattern> link = milsSelected.getLink();
SiteAttributesSpec sas1 = sasMap.get(link.one);
SiteAttributesSpec sas2 = sasMap.get(link.two);
double x1 = x_offset + sas1.getCoordinate().getZ();
double x2 = x_offset + sas2.getCoordinate().getZ();
double y1 = y_offset + sas1.getCoordinate().getY();
double y2 = y_offset + sas2.getCoordinate().getY();
CustomLine2D newLine = drawLink(g, x1, y1, x2, y2, true);
// we need to extract the mils from the lineToMilsMap, because the line we just drew is not the same
// as the one we drew in the first loop (and that is the one in the map)
CustomLine2D oldLine = milsToLineMap.get(milsSelected);
milsToLineMap.put(milsSelected, newLine);
lineToMilsMap.remove(oldLine);
lineToMilsMap.put(newLine, milsSelected);
}

// we now redraw the last selected object on top of everything else
if(lastSelectedObject != null) {
if(lastSelectedObject instanceof MolecularComponentPattern) {
MolecularComponentPattern mcp = (MolecularComponentPattern)lastSelectedObject;
SiteAttributesSpec sas = sasMap.get(mcp);
Coordinate coord = sas.getCoordinate();
double radius = sas.getRadius();
NamedColor color = sas.getColor();
double x = x_offset + coord.getZ();
double y = y_offset + coord.getY();
Ellipse2D newOval = drawCenteredCircle(g, color, x, y, radius, true);
Ellipse2D oldOval = sasToEllipseMap.get(sas);
sasToEllipseMap.put(sas, newOval);
ellipseToSasMap.remove(oldOval);
ellipseToSasMap.put(newOval, sas);
} else if(lastSelectedObject instanceof MolecularInternalLinkSpec) {
MolecularInternalLinkSpec mils = (MolecularInternalLinkSpec)lastSelectedObject;
Pair<MolecularComponentPattern, MolecularComponentPattern> link = mils.getLink();
SiteAttributesSpec sas1 = sasMap.get(link.one);
SiteAttributesSpec sas2 = sasMap.get(link.two);
double x1 = x_offset + sas1.getCoordinate().getZ();
double x2 = x_offset + sas2.getCoordinate().getZ();
double y1 = y_offset + sas1.getCoordinate().getY();
double y2 = y_offset + sas2.getCoordinate().getY();
CustomLine2D newLine = drawLink(g, x1, y1, x2, y2, true);
CustomLine2D oldLine = milsToLineMap.get(mils);
milsToLineMap.put(mils, newLine);
lineToMilsMap.remove(oldLine);
lineToMilsMap.put(newLine, mils);
}
}
}

Expand Down
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