Author: scooter
Date: 2012-09-07 14:48:46 -0700 (Fri, 07 Sep 2012)
New Revision: 30337
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/GroupUtil.java
Log:
Improve handling of Cy2 groups
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/GroupUtil.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/GroupUtil.java
2012-09-07 21:48:13 UTC (rev 30336)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/GroupUtil.java
2012-09-07 21:48:46 UTC (rev 30337)
@@ -26,14 +26,16 @@
// 3.x group attributes
private final String EXTERNAL_EDGE_ATTRIBUTE="__externalEdges.SUID";
private final String GROUP_COLLAPSED_ATTRIBUTE="__groupCollapsed.SUID";
+ private final String GROUP_NETWORKS_ATTRIBUTE="__groupNetworks.SUID";
private final String GROUP_ATTRIBUTE="__isGroup";
+ private final String ISMETA_EDGE_ATTR="__isMetaEdge";
+ private final String X_LOCATION_ATTR="__xLocation";
+ private final String Y_LOCATION_ATTR="__yLocation";
// 2.x group attributes
private final String GROUP_STATE_ATTRIBUTE="__groupState";
private final String GROUP_ISLOCAL_ATTRIBUTE="__groupIsLocal";
private final String GROUP_NODEX_ATTRIBUTE="__metanodeHintX";
private final String GROUP_NODEY_ATTRIBUTE="__metanodeHintY";
- private final String X_LOCATION_ATTR="__xLocation";
- private final String Y_LOCATION_ATTR="__yLocation";
private final String X_OFFSET_ATTR="__xOffset";
private final String Y_OFFSET_ATTR="__yOffset";
@@ -167,6 +169,17 @@
}
}
+ /*
+ System.out.print("Node "+n+": is ");
+ if (!collapsed) System.out.print("not ");
+ System.out.print("collapsed and is ");
+ if (cy2group)
+ System.out.println("a cy2 group");
+ else
+ System.out.println("a cy3 group");
+ */
+
+
// If we're not collapsed, remove the group node from
the network before
// we create the group
if (!collapsed) {
@@ -187,6 +200,7 @@
}
hnTable.getRow(n.getSUID()).set(GROUP_STATE_ATTRIBUTE, 1);
}
+
}
// Create the group
@@ -200,28 +214,27 @@
for (Long suid: externalIDs) {
CyEdge newEdge = rootNet.getEdge(suid);
- if (newEdge != null)
+ if (newEdge != null) {
+ // Don't add the edge if it
already exists
externalEdges.add(newEdge);
+ }
}
+ if (cy2group && collapsed) {
+ updateMetaEdges(net, n);
+ }
+
group.addEdges(externalEdges);
}
- /*
- // Disable nested network
- final boolean nestedNetVisible =
dnRow.get("nested_network_is_visible", Boolean.class, Boolean.FALSE);
- if
(dnRow.getTable().getColumn("nested_network_is_visible") == null) {
-
dnRow.getTable().createColumn("nested_network_is_visible", Boolean.class,
false);
- }
- dnRow.set("nested_network_is_visible", Boolean.FALSE);
- */
-
// TODO: restore group's settings
// Some special handling for cy2 groups. We need to
restore the X,Y coordinates of the nodes
// if we're collapsed.
if (cy2group) {
- // Copy all of the tables for the group
- copyTables(netPointer, net, n);
+ if (collapsed) {
+ // Update the locations of child nodes
+ updateChildOffsets(netPointer, net, n);
+ }
// TODO add groups to a cached map: xgmmlreader has to access all groups and
update their node locations when creating new views
// If the group is collapsed, we need to
provide the location information so we can expand it
if (viewSet != null) {
@@ -229,6 +242,7 @@
for (CyNetworkView view :
viewSet) {
if
(view.getModel().equals(net))
updateGroupNodeLocation(view, n);
+
disableNestedNetworkIcon(view, n);
}
}
}
@@ -316,53 +330,68 @@
hiddenTable.getRow(node.getSUID()).set(GROUP_ATTRIBUTE,
Boolean.TRUE);
}
- private void copyTables(CyNetwork netPointer, CyNetwork net, CyNode
groupNode) {
- // Copy the tables from the subnetwork
- CyTable subTable = netPointer.getDefaultNodeTable();
- CyTable nodeTable = net.getDefaultNodeTable();
-
+ private void updateChildOffsets(CyNetwork netPointer, CyNetwork net,
CyNode groupNode) {
CyTable hiddenSubTable = netPointer.getTable(CyNode.class,
CyNetwork.HIDDEN_ATTRS);
- CyTable hiddenTable = net.getTable(CyNode.class,
CyNetwork.HIDDEN_ATTRS);
- // The group code stores location information in the root table
- CyRootNetwork rootNetwork =
((CySubNetwork)net).getRootNetwork();
- CyTable hiddenRootTable = rootNetwork.getTable(CyNode.class,
CyNetwork.HIDDEN_ATTRS);
+ // Create our columns, if we need to
+ createListColumn(hiddenSubTable, X_LOCATION_ATTR, Double.class);
+ createListColumn(hiddenSubTable, Y_LOCATION_ATTR, Double.class);
+ createListColumn(hiddenSubTable, GROUP_NETWORKS_ATTRIBUTE,
Long.class);
+
for (CyNode child: netPointer.getNodeList()) {
- CyRow row = netPointer.getRow(child);
- CyRow nodeRow = nodeTable.getRow(child.getSUID());
-
- for (CyColumn col: subTable.getColumns()) {
- String name = col.getName();
- if (nodeTable.getColumn(name) != null &&
-
!nodeTable.getColumn(name).getVirtualColumnInfo().isVirtual()) {
- nodeRow.set(col.getName(),
row.get(name, col.getType()));
- }
+ CyRow row = hiddenSubTable.getRow(child.getSUID());
+
+ // Load the existing information in, if any
+ List<Long> networks = new ArrayList<Long>();
+ List<Double> xLocation = new ArrayList<Double>();
+ List<Double> yLocation = new ArrayList<Double>();
+
+ if (row.isSet(GROUP_NETWORKS_ATTRIBUTE))
+ networks =
row.getList(GROUP_NETWORKS_ATTRIBUTE, Long.class);
+ if (row.isSet(X_LOCATION_ATTR))
+ xLocation = row.getList(X_LOCATION_ATTR,
Double.class);
+ if (row.isSet(Y_LOCATION_ATTR))
+ yLocation = row.getList(Y_LOCATION_ATTR,
Double.class);
+
+ networks.add(net.getSUID());
+
+ // Look for child node location information
+ if ((hiddenSubTable.getColumn(GROUP_NODEX_ATTRIBUTE) !=
null)
+ && (row.isSet(GROUP_NODEX_ATTRIBUTE))) {
+ xLocation.add(row.get(GROUP_NODEX_ATTRIBUTE,
Double.class));
+ } else {
+ xLocation.add(0.0d);
}
- CyRow hiddenRow = hiddenTable.getRow(child.getSUID());
- CyRow hiddenSubRow =
hiddenSubTable.getRow(child.getSUID());
- CyRow hiddenRootRow =
hiddenRootTable.getRow(child.getSUID());
-
- for (CyColumn col: hiddenSubTable.getColumns()) {
- String name = col.getName();
-
- // Look for child node location information
- if (name.equals(GROUP_NODEX_ATTRIBUTE)) {
- Double offset = hiddenSubRow.get(name,
Double.class);
- createColumn(hiddenRootRow,
X_OFFSET_ATTR, Double.class);
- hiddenRootRow.set(X_OFFSET_ATTR,
offset);
- } else if (name.equals(GROUP_NODEY_ATTRIBUTE)) {
- Double offset = hiddenSubRow.get(name,
Double.class);
- createColumn(hiddenRootRow,
Y_OFFSET_ATTR, Double.class);
- hiddenRootRow.set(Y_OFFSET_ATTR,
offset);
- } else if (hiddenTable.getColumn(name) != null
&&
-
!hiddenTable.getColumn(name).getVirtualColumnInfo().isVirtual()) {
- hiddenSubRow.set(col.getName(),
hiddenRow.get(name, col.getType()));
- }
+ if ((hiddenSubTable.getColumn(GROUP_NODEY_ATTRIBUTE) !=
null)
+ && (row.isSet(GROUP_NODEY_ATTRIBUTE))) {
+ yLocation.add(row.get(GROUP_NODEY_ATTRIBUTE,
Double.class));
+ } else {
+ yLocation.add(0.0d);
}
+
+ row.set(GROUP_NETWORKS_ATTRIBUTE, networks);
+ row.set(X_LOCATION_ATTR, xLocation);
+ row.set(Y_LOCATION_ATTR, yLocation);
}
}
+
+ private void updateMetaEdges(final CyNetwork net, final CyNode
groupNode) {
+ CyRootNetwork rootNetwork =
((CySubNetwork)net).getRootNetwork();
+
+ // Find all of the edges from the group node and if they are
+ // meta-edges, mark them as such
+ List<CyEdge> edgeList = net.getAdjacentEdgeList(groupNode,
CyEdge.Type.ANY);
+ for (CyEdge edge: edgeList) {
+ String interaction =
net.getRow(edge).get(CyEdge.INTERACTION, String.class);
+ if (interaction.startsWith("meta-")) {
+ createColumn(rootNetwork.getTable(CyEdge.class,
CyNetwork.HIDDEN_ATTRS),
+ ISMETA_EDGE_ATTR, Boolean.class);
+ rootNetwork.getRow(edge,
CyNetwork.HIDDEN_ATTRS).set(ISMETA_EDGE_ATTR, Boolean.TRUE);
+ }
+ }
+ }
private void updateGroupNodeLocation(final CyNetworkView view, final
CyNode groupNode) {
if (view == null) return;
@@ -375,16 +404,25 @@
// Save it
// TODO these attributes will not work with multiple views per
network!
CyRow hRow = rootNetwork.getRow(groupNode,
CyNetwork.HIDDEN_ATTRS);
- createColumn(hRow, X_LOCATION_ATTR, Double.class);
- createColumn(hRow, Y_LOCATION_ATTR, Double.class);
+ createColumn(hRow.getTable(), X_LOCATION_ATTR, Double.class);
+ createColumn(hRow.getTable(), Y_LOCATION_ATTR, Double.class);
hRow.set(X_LOCATION_ATTR, new Double(x));
hRow.set(Y_LOCATION_ATTR, new Double(y));
}
+
+ public void disableNestedNetworkIcon(final CyNetworkView view, CyNode
n) {
+ View<CyNode> nView = view.getNodeView(n);
+
nView.setLockedValue(BasicVisualLexicon.NODE_NESTED_NETWORK_IMAGE_VISIBLE,
+ Boolean.FALSE);
+ }
- private void createColumn(CyRow row, String column, Class<?> type) {
- CyTable table = row.getTable();
-
+ private void createColumn(CyTable table, String column, Class<?> type) {
if (table.getColumn(column) == null)
table.createColumn(column, type, false);
}
+
+ private void createListColumn(CyTable table, String column, Class<?>
type) {
+ if (table.getColumn(column) == null)
+ table.createListColumn(column, type, false);
+ }
}
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