Example 21 with MIRIAMQualifier
use of org.vcell.sybil.models.miriam.MIRIAMQualifier in project vcell by virtualcell.
the class BioModelCellRenderer method getTreeCellRendererComponent.
/**
* Insert the method's description here.
* Creation date: (7/27/2000 6:41:57 PM)
* @return java.awt.Component
*/
public java.awt.Component getTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) {
JLabel component = (JLabel) super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf, row, hasFocus);
//
try {
if (value instanceof DateNode) {
DateNode dateNode = (DateNode) value;
AnnotationQualifier qualifier = dateNode.getDateQualifier();
String colorString = (sel) ? "white" : "black";
component.setText("<html>" + qualifier.getDescription() + " <font color=\"" + colorString + "\">" + dateNode.getDate().getDateString() + "</font></html>");
} else if (value instanceof LinkNode) {
LinkNode ln = (LinkNode) value;
String link = ln.getLink();
String text = ln.getText();
MIRIAMQualifier mQualifier = ln.getMiriamQualifier();
String qualifier = "";
if (mQualifier.equals(MIRIAMQualifier.MODEL_isDescribedBy)) {
String colorString = (sel) ? "white" : "black";
qualifier = "<font color=\"" + colorString + "\">" + mQualifier.getDescription() + "</font>";
} else {
String colorString = (sel) ? "white" : "#8B0000";
qualifier = "<font color=\"" + colorString + "\">" + mQualifier.getDescription() + "</font>";
}
if (link != null) {
String colorString = (sel) ? "white" : "blue";
component.setToolTipText("Double-click to open link");
component.setText("<html>" + qualifier + " <font color=\"" + colorString + "\"><a href=" + link + ">" + text + "</a></font></html>");
} else {
String colorString = (sel) ? "white" : "black";
component.setText("<html>" + qualifier + " <font color=\"" + colorString + "\">" + text + "</font></html>");
}
} else if (value instanceof PublicationInfoNode) {
BioModelNode node = (PublicationInfoNode) value;
PublicationInfo pi = (PublicationInfo) node.getUserObject();
String label = pi.getTitle();
String name = "";
if (pi.getAuthors() != null && pi.getAuthors().length > 0) {
name = pi.getAuthors()[0];
}
if (name.contains(",")) {
name = name.substring(0, name.indexOf(","));
}
int year = Integer.parseInt((new SimpleDateFormat("yyyy")).format(pi.getPubDate()));
String label2 = name + " " + year + " " + label;
int maxLen = MaxPublicationLabelLength + (node.getChildCount() > 1 ? 0 : 4);
if (label2.length() > maxLen) {
label2 = label2.substring(0, maxLen) + "...";
}
if (node.getChildCount() > 1) {
String prefix = sel ? "" : "<span style=\"color:#8B0000\">";
String suffix = sel ? "" : "</span>";
label += prefix + " (" + node.getChildCount() + ")" + suffix;
label2 += prefix + " (" + node.getChildCount() + ")" + suffix;
}
component.setText("<html>" + label2 + "</html>");
component.setToolTipText("<html>" + label + "</html>");
if (pi.getPubDate().compareTo(Calendar.getInstance().getTime()) > 0) {
// sanity check
setIcon(fieldFolderWarningIcon);
} else if (pi.getDoi() == null) {
setIcon(fieldFolderWarningIcon);
} else if (name.contains(" ")) {
setIcon(fieldFolderWarningIcon);
} else {
// publications have their own icon
setIcon(fieldPublishedPublicationIcon);
}
} else if (value instanceof UserNameNode) {
UserNameNode node = (UserNameNode) value;
String label = (String) node.getUserObject();
String qualifier = "";
if (sessionUser != null && sessionUser.getName().contentEquals(label)) {
String colorString = (sel) ? "white" : "#8B0000";
qualifier = "<font color=\"" + colorString + "\"><b>" + label + "</b></font>";
} else {
String colorString = (sel) ? "white" : "black";
qualifier = "<font color=\"" + colorString + "\">" + label + "</font>";
}
component.setToolTipText(label);
component.setText("<html>" + qualifier + " (" + node.getChildCount() + ")" + "</html>");
component.setIcon(fieldFolderUserIcon);
} else if (value instanceof BioModelNode) {
BioModelNode node = (BioModelNode) value;
Object userObject = node.getUserObject();
if (userObject instanceof User) {
String label = null;
if (sessionUser != null && sessionUser.compareEqual((User) userObject)) {
label = "My BioModels (" + ((User) userObject).getName() + ") (" + node.getChildCount() + ")";
} else {
label = ((User) userObject).getName() + "(abcdefghijklmnopq)(000000)";
}
component.setToolTipText(label);
component.setText(label);
} else if (userObject instanceof BioModelInfo) {
BioModelInfo biomodelInfo = (BioModelInfo) userObject;
if (biomodelInfo.getPublicationInfos() != null && biomodelInfo.getPublicationInfos().length > 0) {
if (biomodelInfo.getVersion().getFlag().compareEqual(org.vcell.util.document.VersionFlag.Published)) {
component.setText("(Published) " + component.getText());
} else {
component.setText("(Curated) " + component.getText());
}
} else if (biomodelInfo.getVersion().getFlag().compareEqual(org.vcell.util.document.VersionFlag.Archived)) {
component.setText("(Archived) " + component.getText());
}
String str = component.getToolTipText();
if (str != null && !str.isEmpty()) {
component.setToolTipText(str + " " + biomodelInfo.getVersion().getVersionKey());
}
// we change color of version if it's in the Other folder (Uncurated) and belongs to login user
Object pNode = node.getParent();
if (pNode instanceof BioModelNode) {
pNode = ((BioModelNode) pNode).getParent();
if (pNode instanceof BioModelNode && ((BioModelNode) pNode).getUserObject() instanceof String) {
str = (String) ((BioModelNode) pNode).getUserObject();
if (str.equals(VCDocumentDbTreeModel.ModelBricks) && sessionUser.getName().contentEquals(VCDocumentDbTreeModel.USER_modelBricks)) {
// GRAY
String prefix = sel ? "" : "<span style=\"color:#808080\">";
String suffix = sel ? "" : "</span>";
String str1 = prefix + component.getText() + suffix;
setText("<html>" + str1 + "</html>");
} else {
pNode = ((BioModelNode) pNode).getParent();
if (((BioModelNode) pNode).getUserObject() instanceof String && str.equalsIgnoreCase(sessionUser.getName())) {
str = (String) ((BioModelNode) pNode).getUserObject();
if (str.equals(VCDocumentDbTreeModel.Other_BioModels)) {
// GRAY
String prefix = sel ? "" : "<span style=\"color:#808080\">";
String suffix = sel ? "" : "</span>";
String str1 = prefix + component.getText() + suffix;
setText("<html>" + str1 + "</html>");
}
}
}
}
}
} else if (userObject instanceof Geometry) {
Geometry geo = (Geometry) userObject;
String label = "";
// geomety info, when spatial--shows name+1D/2D/3D
if (geo.getDimension() > 0) {
label = geo.getName() + " (" + geo.getDimension() + "D)";
} else {
label = BioModelChildSummary.COMPARTMENTAL_GEO_STR;
}
component.setToolTipText("Geometry");
component.setText(label);
setIcon(fieldGeometryIcon);
} else if (userObject instanceof String && "AppType".equals(node.getRenderHint("type"))) {
String label = (String) userObject;
component.setToolTipText("Application type");
component.setText(label);
setIcon(VCellIcons.mathTypeIcon);
} else if (userObject instanceof VCDocumentInfoNode) {
VCDocumentInfoNode infonode = (VCDocumentInfoNode) userObject;
User nodeUser = infonode.getVCDocumentInfo().getVersion().getOwner();
String modelName = infonode.getVCDocumentInfo().getVersion().getName();
String username = nodeUser.getName();
if (username.equals(VCDocumentDbTreeModel.USER_tutorial) || // || username.equals(VCDocumentDbTreeModel.USER_Education)
username.equals(VCDocumentDbTreeModel.USER_tutorial610) || username.equals(VCDocumentDbTreeModel.USER_tutorial611)) {
if (node.getParent() instanceof BioModelNode && ((BioModelNode) node.getParent()).getUserObject() instanceof String) {
String pName = (String) ((BioModelNode) node.getParent()).getUserObject();
if (pName.equals(VCDocumentDbTreeModel.Curated_BioModels)) {
// we add the user name to Curated
setText("<html><b>" + nodeUser.getName() + " </b> : " + modelName + "</html>");
} else {
// keep it simple for Education and Tutorial
component.setText(modelName);
}
} else {
component.setText(modelName);
}
} else if (username.equals(VCDocumentDbTreeModel.USER_modelBricks)) {
if (node.getParent() instanceof UserNameNode && sessionUser.getName().contentEquals(VCDocumentDbTreeModel.USER_modelBricks)) {
// login user is ModelBrick, must gray everything in the Other (Uncurated) folder
// ATTANTION: the Uncurated folder is populated with bricks only in the versions of vCell where the ModelBricks
// folder is missing !!!
String toolTip = modelName;
// GRAY
String prefix = sel ? "" : "<span style=\"color:#808080\">";
String suffix = sel ? "" : "</span>";
String str1 = prefix + modelName + suffix;
component.setText("<html>" + str1 + "</html>");
component.setToolTipText(toolTip);
} else if (node.getParent() instanceof BioModelNode && ((BioModelNode) node.getParent()).getUserObject() instanceof String && sessionUser.getName().contentEquals(VCDocumentDbTreeModel.USER_modelBricks) && ((String) ((BioModelNode) node.getParent()).getUserObject()).equals(VCDocumentDbTreeModel.ModelBricks)) {
// login user is ModelBrick, and the model Bricks folder is present -> we must gray everything in it
// do exactly what we did for the "Other" folder, just above
String toolTip = modelName;
// GRAY
String prefix = sel ? "" : "<span style=\"color:#808080\">";
String suffix = sel ? "" : "</span>";
String str1 = prefix + modelName + suffix;
component.setText("<html>" + str1 + "</html>");
component.setToolTipText(toolTip);
} else if (node.getParent() instanceof BioModelNode && ((BioModelNode) node.getParent()).getUserObject() instanceof String) {
String pName = (String) ((BioModelNode) node.getParent()).getUserObject();
String toolTip = modelName;
if (!sessionUser.getName().contentEquals(VCDocumentDbTreeModel.USER_modelBricks) && modelName.contains(VCDocumentDbTreeModel.ModelBricksNameSeparator)) {
modelName = modelName.substring(modelName.indexOf(VCDocumentDbTreeModel.ModelBricksNameSeparator) + VCDocumentDbTreeModel.ModelBricksNameSeparator.length());
String prefix = toolTip.substring(0, toolTip.indexOf(VCDocumentDbTreeModel.ModelBricksNameSeparator));
toolTip = "id: " + prefix + ", name: " + modelName;
}
if (pName.equals(VCDocumentDbTreeModel.Curated_BioModels)) {
// we add the user name to Curated
setText("<html><b>" + nodeUser.getName() + " </b> : " + modelName + "</html>");
component.setToolTipText(toolTip);
} else if (pName.equals(VCDocumentDbTreeModel.ModelBricks)) {
component.setText(modelName);
component.setToolTipText(toolTip);
} else {
String str = modelName;
if (node.getChildCount() > 1) {
String prefix = sel ? "" : "<span style=\"color:#8B0000\">";
String suffix = sel ? "" : "</span>";
str += prefix + " (" + node.getChildCount() + ")" + suffix;
}
component.setText("<html>" + str + "</html>");
component.setToolTipText(toolTip);
}
} else {
component.setText(modelName);
}
} else if (nodeUser.compareEqual(sessionUser)) {
Object pNode = node.getParent();
if (pNode instanceof BioModelNode) {
BioModelNode parent = (BioModelNode) pNode;
// TODO: do this differently
if (parent.getUserObject() instanceof String) {
// the Published, Curated and Other folders are the only
// ones where the user object is a String
String str = (String) parent.getUserObject();
if (str.equals(VCDocumentDbTreeModel.Published_BioModels) || str.equals(VCDocumentDbTreeModel.Curated_BioModels)) /*|| str.equals(VCDocumentDbTreeModel.Other_BioModels)*/
{
String prefix = sel ? "" : "<span style=\"color:#8B0000\">";
String suffix = sel ? "" : "</span>";
setText("<html><b>" + prefix + nodeUser.getName() + suffix + "</b> : " + modelName + "</html>");
} else {
// in the Other folder / owner folder
// GRAY
String prefix = sel ? "" : "<span style=\"color:#808080\">";
String suffix = sel ? "" : "</span>";
String str1 = prefix + modelName + suffix;
if (node.getChildCount() > 1) {
prefix = sel ? "" : "<span style=\"color:#8B0000\">";
suffix = sel ? "" : "</span>";
str1 += prefix + " (" + node.getChildCount() + ")" + suffix;
}
// the name of the model container - which holds the versions
setText("<html>" + str1 + "</html>");
}
} else if (parent.getUserObject() instanceof PublicationInfo) {
String prefix = sel ? "" : "<span style=\"color:#8B0000\">";
String suffix = sel ? "" : "</span>";
setText("<html><b>" + prefix + nodeUser.getName() + suffix + "</b> : " + modelName + "</html>");
} else {
String str = modelName;
if (node.getChildCount() > 1) {
String prefix = sel ? "" : "<span style=\"color:#8B0000\">";
String suffix = sel ? "" : "</span>";
str += prefix + " (" + node.getChildCount() + ")" + suffix;
}
setText("<html>" + str + "</html>");
}
} else {
// unreachable
setText(modelName);
}
} else {
Object pNode = node.getParent();
if (pNode instanceof UserNameNode) {
// if we are inside an UserName folder (like Shared or Uncurated public),
// don't prefix again the model with the user name
String str = modelName;
if (node.getChildCount() > 1) {
String prefix = sel ? "" : "<span style=\"color:#8B0000\">";
String suffix = sel ? "" : "</span>";
str += prefix + " (" + node.getChildCount() + ")" + suffix;
}
setText("<html>" + str + "</html>");
} else {
// content of "Published" folder
setText("<html><b>" + nodeUser.getName() + " </b> : " + modelName + "</html>");
}
}
}
}
} catch (Throwable e) {
e.printStackTrace(System.out);
}
//
if (component.getToolTipText() == null || component.getToolTipText().length() == 0) {
component.setToolTipText(component.getText());
}
return component;
}
Also used :
UserNameNode(cbit.vcell.desktop.BioModelNode.UserNameNode)
DateNode(cbit.vcell.xml.gui.MiriamTreeModel.DateNode)
User(org.vcell.util.document.User)
PublicationInfo(org.vcell.util.document.PublicationInfo)
BioModelInfo(org.vcell.util.document.BioModelInfo)
JLabel(javax.swing.JLabel)
Geometry(cbit.vcell.geometry.Geometry)
AnnotationQualifier(org.vcell.sybil.models.AnnotationQualifier)
LinkNode(cbit.vcell.xml.gui.MiriamTreeModel.LinkNode)
MIRIAMQualifier(org.vcell.sybil.models.miriam.MIRIAMQualifier)
SimpleDateFormat(java.text.SimpleDateFormat)
PublicationInfoNode(cbit.vcell.desktop.BioModelNode.PublicationInfoNode)
Aggregations
MIRIAMQualifier (org.vcell.sybil.models.miriam.MIRIAMQualifier)21
MiriamManager (cbit.vcell.biomodel.meta.MiriamManager)12
MiriamRefGroup (cbit.vcell.biomodel.meta.MiriamManager.MiriamRefGroup)12
Identifiable (org.vcell.util.document.Identifiable)12
MiriamResource (cbit.vcell.biomodel.meta.MiriamManager.MiriamResource)9
Map (java.util.Map)9
TreeMap (java.util.TreeMap)9
URNParseFailureException (org.vcell.sybil.models.miriam.MIRIAMRef.URNParseFailureException)7
HashSet (java.util.HashSet)4
Entry (cbit.vcell.biomodel.meta.registry.Registry.Entry)3
ReactionStep (cbit.vcell.model.ReactionStep)3
Icon (javax.swing.Icon)3
DataType (cbit.vcell.biomodel.meta.MiriamManager.DataType)2
VCID (cbit.vcell.biomodel.meta.VCID)2
VCMetaData (cbit.vcell.biomodel.meta.VCMetaData)2
VCMetaDataMiriamManager (cbit.vcell.biomodel.meta.VCMetaDataMiriamManager)2
Registry (cbit.vcell.biomodel.meta.registry.Registry)2
StructureToolShapeIcon (cbit.vcell.graph.gui.StructureToolShapeIcon)2
SpeciesContext (cbit.vcell.model.SpeciesContext)2
LinkNode (cbit.vcell.xml.gui.MiriamTreeModel.LinkNode)2
