Author: mes
Date: 2012-01-12 15:37:34 -0800 (Thu, 12 Jan 2012)
New Revision: 28006
Added:
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/AbstractEdgeWeightedLayoutAlgorithm.java
Log:
first pass at support for edge weighting
Added:
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/AbstractEdgeWeightedLayoutAlgorithm.java
===================================================================
---
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/AbstractEdgeWeightedLayoutAlgorithm.java
(rev 0)
+++
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/AbstractEdgeWeightedLayoutAlgorithm.java
2012-01-12 23:37:34 UTC (rev 28006)
@@ -0,0 +1,101 @@
+/*
+ File: AbstractEdgeWeightedLayoutAlgorithm.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.view.layout;
+
+
+import org.cytoscape.model.CyTable;
+import org.cytoscape.model.CyColumn;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.work.util.ListSingleSelection;
+import org.cytoscape.work.Tunable;
+import org.cytoscape.work.undo.UndoSupport;
+
+import java.util.SortedSet;
+import java.util.TreeSet;
+import java.util.ArrayList;
+
+/**
+ * The AbstractEdgeWeightedLayoutAlgorithm provides edge weighting Tunables
that
+ * can be used by an implementing layout algorithm.
+ * @CyAPI.Abstract.Class
+ */
+abstract public class AbstractEdgeWeightedLayoutAlgorithm extends
AbstractLayoutAlgorithm {
+
+ private static final String groupName = "Edge Weight Settings";
+
+ /** A tunable for determining the edge attribute that contains the
weights. */
+ @Tunable(description="The edge attribute that contains the
weights",groups=groupName)
+ public ListSingleSelection<String> edgeWeightColumn;
+
+ /** A tunable for determining how to interpret weight values. */
+ @Tunable(description="How to interpret weight values",groups=groupName)
+ public ListSingleSelection<WeightTypes> weightChoices;
+
+ /** A tunable for determining the minimum edge weight to consider. */
+ @Tunable(description="The minimum edge weight to
consider",groups=groupName)
+ public double minWeight = 0;
+
+ /** A tunable for determining the maximum edge weight to consider. */
+ @Tunable(description="The maximum edge weight to
consider",groups=groupName)
+ public double maxWeight = Double.MAX_VALUE;
+
+ /**
+ * The Constructor.
+ * @param undo the UndoSupport object used for allowing undo of layouts.
+ * @param computerName a computer readable name used to construct property
strings.
+ * @param humanName a user visible name of the layout.
+ * @param supportsSelectedOnly indicates whether only selected nodes
should be laid out.
+ */
+ public AbstractEdgeWeightedLayoutAlgorithm(final UndoSupport undo, final
String computerName,
+ final String humanName,
boolean supportsSelectedOnly) {
+ super(undo,computerName,humanName,supportsSelectedOnly);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public void setNetworkView(CyNetworkView view) {
+ super.setNetworkView(view);
+ initSelectionTunables();
+ }
+
+ private void initSelectionTunables() {
+ weightChoices = new ListSingleSelection<WeightTypes>(
WeightTypes.values() );
+
+ CyTable edgeTable = network.getDefaultEdgeTable();
+ SortedSet<String> goodColumns = new TreeSet<String>();
+ for ( CyColumn col : edgeTable.getColumns() ) {
+ if ( col.getType() == Integer.class || col.getType() ==
Double.class )
+ goodColumns.add(col.getName());
+ }
+ edgeWeightColumn = new ListSingleSelection<String>( new
ArrayList<String>( goodColumns ) );
+ }
+}
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