Author: scooter
Date: 2012-08-20 15:43:34 -0700 (Mon, 20 Aug 2012)
New Revision: 30234
Modified:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/package-info.java
Log:
Fixed some typos...
Modified:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/package-info.java
===================================================================
---
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/package-info.java
2012-08-20 22:12:19 UTC (rev 30233)
+++
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/package-info.java
2012-08-20 22:43:34 UTC (rev 30234)
@@ -53,13 +53,13 @@
the forest has a "root" ({@link org.cytoscape.model.subnetwork.CyRootNetwork})
and a series of
branches ({@link org.cytoscape.model.subnetwork.CySubNetwork}). This is
generally hidden since most App implementers don't need
to know about the root network, and a {@link
org.cytoscape.model.subnetwork.CySubNetwork} is also a
-{@link org.cytoscape.model.subnetwork.CyNetwork} with a couple of extra
methods. Even though this isn't
+{@link org.cytoscape.model.CyNetwork} with a couple of extra methods. Even
though this isn't
commonly used by App implementers, there are some nice features that this
provides.
Since all nodes and edges will exist in the root network, it means that they
are shared amongst all of the subnetworks. This
allows Cytoscape to set up shared tables so that data values in one subnetwork
(say for a node) are shared with the
same node in another subnetwork. This can be very useful when importing a lot
of data (e.g. large expression data sets).
The other advantage is that it provides a place to "save" nodes and edges that
we might use later. This is used extensively
-in the {@link org.cytoscape.groups.CyGroup} implementation, which builds a
hierarchical structure onto Cytoscape's model.
+in the {@link org.cytoscape.group.CyGroup} implementation, which builds a
hierarchical structure onto Cytoscape's model.
<p>The way all of this works is that when the first network is by the {@link
org.cytoscape.model.CyNetworkFactory}, a new
{@link org.cytoscape.model.subnetwork.CyRootNetwork} is actually created. A
root network always has a "base network" defined,
which is essentially a {@link org.cytoscape.model.subnetwork.CySubNetwork}
that contains everything in the root network. This is
@@ -103,9 +103,9 @@
<dd><code>CyRow edgeRow = network.getRow(edge);</code></dd>
</dl>
Cytoscape provides convenience methods to get the default table for a network
-({@link org.cytoscape.mode.CyNetwork#getDefaultNetworkTable}),
-nodes ({@link org.cytoscape.mode.CyNetwork#getDefaultNodeTable}), and
-edges ({@link org.cytoscape.mode.CyNetwork#getDefaultEdgeTable}).
+({@link org.cytoscape.model.CyNetwork#getDefaultNetworkTable}),
+nodes ({@link org.cytoscape.model.CyNetwork#getDefaultNodeTable}), and
+edges ({@link org.cytoscape.model.CyNetwork#getDefaultEdgeTable}).
<p>One thing to keep in mind -- when working with the {@link
org.cytoscape.model.CyNetwork#getRow} methods, the argument
is the actual {@link org.cytoscape.model.CyNode} and {@link
org.cytoscape.model.CyEdge}. However, when you are using the
{@link org.cytoscape.model.CyTable#getRow} method, the argument is the
<i>ID</i>
@@ -144,7 +144,7 @@
</code></pre></dd>
</dl>
Selection in Cytoscape 3 is actually handled by setting a boolean value in a
{@link org.cytoscape.model.CyTable} --
-in this case, the {@link org.cytoscape.model.CyNetwork.SELECTED} column in the
{@link org.cytoscape.model.CyNetwork.DEFAULT_ATTRS}
+in this case, the {@link org.cytoscape.model.CyNetwork#SELECTED} column in the
{@link org.cytoscape.model.CyNetwork#DEFAULT_ATTRS}
table for the associated node or edge. As a result, the way to listen for
selection is
actually to listen for a change in the appropriate row:
<dl>
@@ -181,12 +181,12 @@
One of the common requirements for Apps is to be able to get the list of
selected nodes or edges. In Cytoscape, the information
about what's selected is stored in the {@link
org.cytoscape.model.CyNetwork#LOCAL_ATTRS} table for nodes and edges, which is
also available through the {@link org.cytoscape.model.CyNetwork#DEFAULT_ATTRS}
table. Because getting the state of nodes and edges
-is such a common equirement, Cytoscape provides some utility methods ({@link
org.cytoscape.model.CyTableUtils}) to help out. For
-selection, there are two: {@link
org.cytoscape.model.CyTableUtils#getEdgesInState} and
-{@link org.cytoscape.model.CyTableUtils#getNodesInState}. These methods can
be easily used to get the list of selected nodes or edges.
+is such a common equirement, Cytoscape provides some utility methods ({@link
org.cytoscape.model.CyTableUtil}) to help out. For
+selection, there are two: {@link
org.cytoscape.model.CyTableUtil#getEdgesInState} and
+{@link org.cytoscape.model.CyTableUtil#getNodesInState}. These methods can be
easily used to get the list of selected nodes or edges.
For example, to get the list of selected nodes:
<dl>
-<dd><code>List<CyNode> selectedNodes =
CyTableUtil.getNodesInState(network, CyNetwork.SELECTED, true);</code></dd>
+<dd><code>List<CyNode> selectedNodes =
CyTableUtil.getNodesInState(network, CyNetwork#SELECTED, true);</code></dd>
</dl>
*/
package org.cytoscape.model;
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