Author: mes
Date: 2012-04-20 16:15:46 -0700 (Fri, 20 Apr 2012)
New Revision: 28931
Modified:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyNetwork.java
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyNetworkFactory.java
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyRow.java
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTable.java
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTableMetadata.java
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/VirtualColumnInfo.java
Log:
updated javadoc
Modified:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyNetwork.java
===================================================================
--- core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyNetwork.java
2012-04-20 23:15:18 UTC (rev 28930)
+++ core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyNetwork.java
2012-04-20 23:15:46 UTC (rev 28931)
@@ -216,7 +216,8 @@
* are no neighbor nodes found.
* This method should never return null.
* Modifying this list (if allowed by the implementation)
- * has no effect on the network.
+ * has no effect on the network. This method only returns immediate
+ * neighbors.
*
* @param node the node whose neighbors we're looking for
* @param edgeType the directionality of the edges we're interested in
@@ -261,8 +262,9 @@
* Get the list of edges that connect two nodes. The {@link
CyEdge.Type} enum is
* used to determine whether the list includes undirected, directed,
* incoming, or outgoing edges. The list will be empty if no connecting
- * edges are found.
- * This method should never return null.
+ * edges are found.
+ * This method should never return null. This method will NOT find the
+ * shortest path between two nodes that are not already immediate
neighbors.
* Modifying this list (if allowed by the implementation)
* has no effect on the network.
*
Modified:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyNetworkFactory.java
===================================================================
---
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyNetworkFactory.java
2012-04-20 23:15:18 UTC (rev 28930)
+++
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyNetworkFactory.java
2012-04-20 23:15:46 UTC (rev 28931)
@@ -43,6 +43,8 @@
/**
* Returns a new, empty {@link CyNetwork} object where the associated
default tables are private.
+ * This method should only be used in special cases where the network
created is not intended to
+ * be used or shared like a normal network within the system.
* @return A new, empty {@link CyNetwork} object.
*/
CyNetwork createNetworkWithPrivateTables();
Modified: core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyRow.java
===================================================================
--- core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyRow.java
2012-04-20 23:15:18 UTC (rev 28930)
+++ core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyRow.java
2012-04-20 23:15:46 UTC (rev 28931)
@@ -113,8 +113,10 @@
Map<String, Object> getAllValues();
/**
- * Note that the returned object may well not be of the type that get()
for this column might
- * return! You should therefore almost always use get() instead!
+ * Returns the Object that contains the value for the specified column.
+ * The returned object may or may not be of the type that get() for
this
+ * column will return, for example it may return an equation object that
+ * has not yet been evaluated!
* @param columnName The name identifying the attribute.
* @return The row Object that represents the value in a column.
*/
Modified:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTable.java
===================================================================
--- core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTable.java
2012-04-20 23:15:18 UTC (rev 28930)
+++ core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTable.java
2012-04-20 23:15:46 UTC (rev 28931)
@@ -239,7 +239,11 @@
int getRowCount();
/**
- * Adds a "virtual" column to the the current table.
+ * Adds a "virtual" column to the the current table.
+ * A virtual column is a column in one table that points to a column in
a different table.
+ * Instead of duplicating the column data found in the other table, a
virtual column allows
+ * us to share that data by reference. A virtual column requires that
columns be matched
+ * according to the primary key of the other table with a column in
this table.
* @param virtualColumn The name of the new virtual column, if this
name already exists,
* new column names with -1, -2 and so appended
to this name on will
* be tried until a non-existing name will be
found.
@@ -258,6 +262,10 @@
String targetJoinKey, boolean isImmutable);
/** Adds all columns in another table as "virtual" columns to the the
current table.
+ * A virtual column is a column in one table that points to a column in
a different table.
+ * Instead of duplicating the column data found in the other table, a
virtual column allows
+ * us to share that data by reference. A virtual column requires that
columns be matched
+ * according to the primary key of the other table with a column in
this table.
* @param sourceTable The table that really contains the column
that we're adding (all
* updates and lookups of this new column will
be redirected to here).
* The table will be joined on the primary key
column of this table.
@@ -281,10 +289,13 @@
*/
void setSavePolicy(SavePolicy policy);
- /** Swaps the contents and properties, like mutability etc. of
"otherTable" with this table.
- * @param otherTable the table that we're being swapped with.
- * Note: the one "property" that is not being swapped is the SUID!
Also, no events are being
- * fired to give any listeners a chance to react to the exchange!
+ /**
+ * Swaps the contents and properties (such as mutability) of
"otherTable" with this table.
+ * This method is used to copy tables for backup, undo, and deletion
and generally shouldn't
+ * be needed for most normal work.
+ * @param otherTable the table that we're being swapped with.
+ * Note: the one "property" that is not being swapped is the SUID!
Also, no events are being
+ * fired to give any listeners a chance to react to the exchange!
*/
void swap(CyTable otherTable);
}
Modified:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTableMetadata.java
===================================================================
---
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTableMetadata.java
2012-04-20 23:15:18 UTC (rev 28930)
+++
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyTableMetadata.java
2012-04-20 23:15:46 UTC (rev 28931)
@@ -2,7 +2,9 @@
/**
* A snapshot of information about a relationship shared between a CyTable
- * instance and an associated CyNetworks.
+ * instance and an associated CyNetworks. The interface is used to capture
+ * table information for serialization and shouldn't be needed for most
+ * normal use of tables.
* @CyAPI.Api.Interface
*/
public interface CyTableMetadata {
Modified:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/VirtualColumnInfo.java
===================================================================
---
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/VirtualColumnInfo.java
2012-04-20 23:15:18 UTC (rev 28930)
+++
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/VirtualColumnInfo.java
2012-04-20 23:15:46 UTC (rev 28931)
@@ -2,7 +2,8 @@
/**
* Information object for columns that stores extra Virtual Column information
- * if applicable.
+ * if applicable. See {@link CyTable#addVirtualColumn} for details on
+ * what virtual columns are.
* @CyAPI.Api.Interface
*/
public interface VirtualColumnInfo {
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