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Merged
danv61 merged 16 commits into from
May 11, 2026
Merged

Dan ss structural sites #1685

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754f263
Generalized use of LinkNode.
danv61 Apr 21, 2026
2525624
Generalized use of LinkNode, creation, deletion, visualization, edit
danv61 Apr 23, 2026
a114b6e
Generalized use of LinkNode: consistency, bug fixing, testing
danv61 Apr 24, 2026
11f17a4
Generalized use of LinkNode: mouse coordinates capture
danv61 Apr 27, 2026
8d6a2a3
Test fixed, issue upgraded from WARNING to ERROR due to causing consi…
danv61 Apr 28, 2026
e29e9df
Bug fixed, lastSelectedObject could be stale
danv61 Apr 28, 2026
d6a31f5
Cursor tracking, crosshair, snap to grid
danv61 Apr 29, 2026
0a31fb8
Structural sites. Added to the LangevinMathMapping
danv61 Apr 30, 2026
47f4d55
Structural sites: solver input file creation
danv61 May 1, 2026
76ae1b9
Structural sites: import / export from / to ssld file.
danv61 May 4, 2026
87f666d
Structural sites: XmlReader, XMLProducer
danv61 May 6, 2026
0d2ec6a
Structural sites: read from, write to the DB
danv61 May 6, 2026
213304c
Structural sites: read from, write to the DB
danv61 May 7, 2026
43b0ac0
Structural sites: database write / read roundtrip test
danv61 May 7, 2026
ea36c43
Structural sites: database write / read roundtrip test
danv61 May 8, 2026
6e36db5
Structural sites: database write / read roundtrip test
danv61 May 8, 2026
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12 changes: 5 additions & 7 deletions vcell-client/src/main/java/cbit/vcell/mapping/gui/LinkSpecsTableModel.java
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Original file line number Diff line number Diff line change
Expand Up @@ -94,8 +94,6 @@ public void setValueAt(Object aValue, int row, int col) {
ColumnType columnType = columns.get(col);
SpeciesContextSpec scs = getSpeciesContextSpec();

MolecularComponentPattern mcpOne = mils.getMolecularComponentPatternOne();
MolecularComponentPattern mcpTwo = mils. getMolecularComponentPatternTwo();
SiteAttributesSpec sasOne = mils. getSite1();
SiteAttributesSpec sasTwo = mils. getSite2();

Expand Down Expand Up @@ -267,11 +265,11 @@ public int compare(MolecularInternalLinkSpec mils1, MolecularInternalLinkSpec mi
if(fieldSpeciesContextSpec != scs) {
throw new RuntimeException("SpeciesContextSpec inconsistent.");
}
MolecularComponentPattern mcp1 = mils1.getLink().one;
MolecularComponentPattern mcp2 = mils2.getLink().one;
Map<MolecularComponentPattern, SiteAttributesSpec> siteAttributesMap = getSpeciesContextSpec().getSiteAttributesMap();
SiteAttributesSpec sas1 = siteAttributesMap.get(mcp1);
SiteAttributesSpec sas2 = siteAttributesMap.get(mcp2);
LinkNode node1 = mils1.getLink().one;
LinkNode node2 = mils2.getLink().one;
Map<LinkNode, SiteAttributesSpec> merged = getSpeciesContextSpec().getAllSiteAttributes();
SiteAttributesSpec sas1 = merged.get(node1);
SiteAttributesSpec sas2 = merged.get(node2);
Double z1 = sas1.getCoordinate().getZ();
Double z2 = sas2.getCoordinate().getZ();
return z1.compareTo(z2);
Expand Down
119 changes: 67 additions & 52 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 @@ -2,32 +2,24 @@

import cbit.vcell.biomodel.BioModel;
import cbit.vcell.client.desktop.biomodel.DocumentEditorSubPanel;
import cbit.vcell.graph.PointLocationInShapeContext;
import cbit.vcell.graph.ReactionCartoon;
import cbit.vcell.graph.SpeciesContextSpecLargeShape;
import cbit.vcell.graph.SpeciesPatternLargeShape;
import cbit.vcell.graph.gui.LargeShapePanel;
import cbit.vcell.graph.gui.SsldLargeShapePanel;
import cbit.vcell.graph.gui.ZoomShapeIcon;
import cbit.vcell.mapping.MolecularInternalLinkSpec;
import cbit.vcell.mapping.SiteAttributesSpec;
import cbit.vcell.mapping.SpeciesContextSpec;
import cbit.vcell.model.GroupingCriteria;
import cbit.vcell.model.Model;
import cbit.vcell.model.RuleParticipantSignature;
import cbit.vcell.model.SpeciesContext;
import cbit.vcell.parser.ExpressionException;
import org.vcell.model.rbm.LinkNode;
import org.vcell.model.rbm.MolecularComponentPattern;
import org.vcell.model.rbm.MolecularTypePattern;
import org.vcell.model.rbm.SpeciesPattern;

import javax.swing.*;
import java.awt.*;
import java.awt.event.ActionListener;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.awt.event.MouseMotionAdapter;
import java.awt.geom.Ellipse2D;
import java.awt.event.*;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;

Expand All @@ -44,16 +36,20 @@ public class MolecularStructuresPropertiesPanel extends DocumentEditorSubPanel {
private LargeShapePanel shapePanel = null;
private SpeciesContextSpecLargeShape scsls; // the real thing

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

private JButton zoomLargerButton = null;
private JButton zoomSmallerButton = null;

// tracking mouse coordinates
// will use for drag and drop (not implemented yet, but we need to track the mouse movements for that)
private boolean mouseInsidePanel = false; // whether mouse is inside the panel client area (we use this to decide whether to show the coordinates or not, we hide them when the mouse is outside the panel)
private Integer mousePixelX = null; // we also track the mouse in pixel coordinates, which we transform in nm units in the shape
private Integer mousePixelY = null;

private class EventHandler implements ActionListener, PropertyChangeListener {

@Override
public void actionPerformed(java.awt.event.ActionEvent e) {
if (e.getSource() == getZoomLargerButton()) {
Expand All @@ -79,11 +75,11 @@ public void propertyChange(PropertyChangeEvent evt) {
updateShape();
} else if(evt.getSource() instanceof SpeciesContextSpec && evt.getPropertyName().equals(SpeciesContextSpec.PROPERTY_NAME_SITE_SELECTED_IN_TABLE)) {
Object o = evt.getNewValue();
if(o instanceof MolecularComponentPattern mcp) {
mcpSelected = mcp;
lastSelectedObject = mcpSelected;
if(o instanceof LinkNode ln) {
lnSelected = ln;
lastSelectedObject = lnSelected;
} else {
mcpSelected = null;
lnSelected = null;
if(milsSelected != null) {
// if we had a link selected before, it becomes the last (and only) selected
lastSelectedObject = milsSelected;
Expand All @@ -100,9 +96,9 @@ public void propertyChange(PropertyChangeEvent evt) {
lastSelectedObject = milsSelected;
} else {
milsSelected = null;
if(mcpSelected != null) {
if(lnSelected != null) {
// if we had a site selected before, it becomes the last (and only) selected
lastSelectedObject = mcpSelected;
lastSelectedObject = lnSelected;
} else {
// nothing is selected anymore
lastSelectedObject = null;
Expand Down Expand Up @@ -137,9 +133,10 @@ public void paintComponent(Graphics g) {
if (speciesContextSpec == null || speciesContextSpec.getSpeciesContext() == null) {
return;
}
Rectangle visibleViewport = getVisibleRect();
scsls = new SpeciesContextSpecLargeShape(speciesContextSpec, shapePanel, speciesContextSpec,
mcpSelected, milsSelected, lastSelectedObject, issueManager);
scsls.paintSelf(g);
lnSelected, milsSelected, lastSelectedObject, issueManager);
scsls.paintSelf(g, mousePixelX, mousePixelY, mouseInsidePanel, visibleViewport);
}
@Override
public DisplayMode getDisplayMode() {
Expand Down Expand Up @@ -185,13 +182,15 @@ public boolean isViewSingleRow() {
shapePanel.addMouseMotionListener(new MouseMotionAdapter() {
@Override
public void mouseMoved(MouseEvent e) {
// this will fire if the mouse moves over the panel, we may need it for drag and drop
super.mouseMoved(e);
// Point overWhat = e.getPoint();
// Object overObject = scsls.contains(overWhat);
// if(overObject != null) {
// System.out.println("MouseMotionAdapter: over something");
// }
mousePixelX = e.getX();
mousePixelY = e.getY();
shapePanel.repaint();
}
@Override
public void mouseDragged(MouseEvent e) {
mousePixelX = e.getX();
mousePixelY = e.getY();
shapePanel.repaint();
}
});
shapePanel.addMouseListener(new MouseAdapter() {
Expand All @@ -211,15 +210,48 @@ public void mouseClicked(MouseEvent e) {
// 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;
lnSelected = sas.getLinkNode();
lastSelectedObject = lnSelected;
// redraw the whole shape to highlight the selected link line
updateShape();
// we tell the table in the upper panel to update the selected row
speciesContextSpec.firePropertyChange(PROPERTY_NAME_SITE_SELECTED_IN_SHAPE, null, mcpSelected);
speciesContextSpec.firePropertyChange(PROPERTY_NAME_SITE_SELECTED_IN_SHAPE, null, lnSelected);
}
}
@Override
public void mouseReleased(MouseEvent e) {
mousePixelX = e.getX();
mousePixelY = e.getY();
shapePanel.repaint();
}
@Override
public void mouseEntered(MouseEvent e) {
mouseInsidePanel = true;
}
@Override
public void mouseExited(MouseEvent e) {
mouseInsidePanel = false;
mousePixelX = null;
mousePixelY = null;
shapePanel.repaint();
}
});
shapePanel.addMouseWheelListener(new MouseWheelListener() {
@Override
public void mouseWheelMoved(MouseWheelEvent e) {
if (!mouseInsidePanel) {
return;
}
Point mouseScreen = MouseInfo.getPointerInfo().getLocation(); // get current mouse location on screen
Point mousePanel = new Point(mouseScreen); // convert to shapePanel coordinate system
SwingUtilities.convertPointFromScreen(mousePanel, shapePanel);
mousePixelX = mousePanel.x; // update stored pixel coordinates
mousePixelY = mousePanel.y;
shapePanel.repaint();
shapePanel.getParent().dispatchEvent(e); // we dispatch the event to the parent scroll pane, which will handle the actual scrolling
}
});

shapePanel.setPreferredSize(new Dimension(2000, 800));
shapePanel.setBackground(new Color(0xe0e0e0));
shapePanel.setZoomFactor(-2);
Expand Down Expand Up @@ -251,20 +283,6 @@ public void mouseClicked(MouseEvent e) {
gbc.anchor = GridBagConstraints.WEST;
optionsPanel.add(getZoomSmallerButton(), gbc);

// gbc = new GridBagConstraints();
// gbc.gridx = 0;
// gbc.gridy = 2;
// gbc.anchor = GridBagConstraints.WEST;
// gbc.insets = new Insets(4, 4, 4, 10);
// optionsPanel.add(new JLabel("Reaction Radius"), gbc);
//
// gbc = new GridBagConstraints();
// gbc.gridx = 1;
// gbc.gridy = 2;
// gbc.anchor = GridBagConstraints.WEST;
// gbc.insets = new Insets(4, 4, 4, 10);
// optionsPanel.add(new JLabel("2 nm"), gbc);

gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = 2; // make this 3 if we show reaction radius here
Expand Down Expand Up @@ -295,16 +313,12 @@ private void updateInterface() {
}
updateShape();
}

private void updateShape() {
if(speciesContextSpec == null || speciesContextSpec.getSpeciesContext() == null) {
return;
}
scsls = new SpeciesContextSpecLargeShape(speciesContextSpec, shapePanel, speciesContextSpec,
mcpSelected, milsSelected, lastSelectedObject, issueManager);

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

lnSelected, milsSelected, lastSelectedObject, issueManager);
shapePanel.repaint();
}

Expand All @@ -319,12 +333,12 @@ public void setSpeciesContextSpec(SpeciesContextSpec scSpec) {
this.speciesContextSpec = scSpec;
scSpec.addPropertyChangeListener(eventHandler);
}
// getSpeciesContextSpecParameterTableModel().setSpeciesContextSpec(scSpec);

mcpSelected = null;
lnSelected = null;
milsSelected = null;
lastSelectedObject = null;
updateInterface();
}

public void setBioModel(BioModel newValue) {
if (bioModel == newValue) {
return;
Expand Down Expand Up @@ -374,4 +388,5 @@ private JButton getZoomSmallerButton() {
}
return zoomSmallerButton;
}

}
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