Author: mes
Date: 2012-04-06 14:14:41 -0700 (Fri, 06 Apr 2012)
New Revision: 28755
Removed:
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/SBMLVisualStyleFactory.java.hold
Log:
not being used
Deleted:
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/SBMLVisualStyleFactory.java.hold
===================================================================
---
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/SBMLVisualStyleFactory.java.hold
2012-04-06 21:01:19 UTC (rev 28754)
+++
csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/SBMLVisualStyleFactory.java.hold
2012-04-06 21:14:41 UTC (rev 28755)
@@ -1,165 +0,0 @@
-
-/*
- Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
-
- The Cytoscape Consortium is:
- - Institute for Systems Biology
- - University of California San Diego
- - Memorial Sloan-Kettering Cancer Center
- - Institut Pasteur
- - Agilent Technologies
-
- 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 sbmlreader;
-
-import cytoscape.*;
-
-import cytoscape.data.Semantics;
-
-import cytoscape.view.CytoscapeDesktop;
-
-import cytoscape.visual.*;
-
-import cytoscape.visual.calculators.*;
-
-import cytoscape.visual.mappings.*;
-
-import cytoscape.visual.ui.*;
-
-import giny.view.EdgeView;
-
-import java.awt.Color;
-
-
-/**
- * VisualStyleFactory.java
- * This class defines the visualstyle in Cytoscape for the SBMLReader plugin.
- *
- * @author W.P.A. Ligtenberg, Eindhoven University of Technology
- */
-public class SBMLVisualStyleFactory {
- /**
- *
- */
- public static final String SBMLReader_VS = "SBMLReader Style";
-
- /**
- *
- */
- public static final String NODE_TYPE_ATT = "sbml type";
-
- /**
- *
- */
- public static final String EDGE_TYPE_ATT = "interaction";
-
- /**
- * DOCUMENT ME!
- *
- * @param network DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public static VisualStyle createVisualStyle(CyNetwork network) {
- VisualMappingManager vmManager =
Cytoscape.getVisualMappingManager();
- NodeAppearanceCalculator nodeAppCalc = new
NodeAppearanceCalculator();
- EdgeAppearanceCalculator edgeAppCalc = new
EdgeAppearanceCalculator();
- CalculatorCatalog calculatorCatalog =
vmManager.getCalculatorCatalog();
-
- // ------------------------------ Set node shapes
---------------------------//
- DiscreteMapping disMapping = new DiscreteMapping(NodeShape.RECT,
-
ObjectMapping.NODE_MAPPING);
- disMapping.setControllingAttributeName(NODE_TYPE_ATT, network,
false);
- disMapping.putMapValue("species", NodeShape.DIAMOND);
- disMapping.putMapValue("reaction", NodeShape.ELLIPSE);
-
- Calculator shapeCalculator = new BasicCalculator("SBMLReader
Shape Calculator",
-
disMapping,
-
VisualPropertyType.NODE_SHAPE);
- nodeAppCalc.setCalculator(shapeCalculator);
-
- // ------------------------------ Set the label
------------------------------//
- // Display the value for geneName as a label
- String cName = "sbml name";
- Calculator nlc =
calculatorCatalog.getCalculator(VisualPropertyType.NODE_LABEL, cName);
-
- if (nlc == null) {
- PassThroughMapping m = new PassThroughMapping(new
String(), cName);
- nlc = new BasicCalculator(cName, m,
VisualPropertyType.NODE_LABEL);
- }
-
- nodeAppCalc.setCalculator(nlc);
-
- //--------------------- Set the size of the nodes
--------------------------//
- //Discrete mapping on nodeType
- Double speciesNodeSize = new Double(30);
- Double reactionNodeSize = new Double(30);
- DiscreteMapping sizeMapping = new
DiscreteMapping(reactionNodeSize,
-
ObjectMapping.NODE_MAPPING);
- sizeMapping.setControllingAttributeName(NODE_TYPE_ATT, network,
false);
- sizeMapping.putMapValue("species", speciesNodeSize);
- sizeMapping.putMapValue("reaction", reactionNodeSize);
-
- Calculator sizeCalculator = new BasicCalculator("SBMLReader
Size Calculator",
-
sizeMapping,
-
VisualPropertyType.NODE_SIZE);
- nodeAppCalc.setCalculator(sizeCalculator);
- nodeAppCalc.setNodeSizeLocked(true);
-
- // ------------------------------ Set edge arrow shape
---------------------------//
- DiscreteMapping arrowMapping = new
DiscreteMapping(ArrowShape.DELTA,
-
ObjectMapping.NODE_MAPPING);
- arrowMapping.setControllingAttributeName(EDGE_TYPE_ATT,
network, false);
- arrowMapping.putMapValue("reaction-product", ArrowShape.ARROW);
- arrowMapping.putMapValue("reaction-reactant", ArrowShape.NONE);
- arrowMapping.putMapValue("reaction-modifier",
ArrowShape.CIRCLE);
-
- Calculator edgeArrowCalculator = new
BasicCalculator("SBMLReader Edge Arrow Calculator",
- arrowMapping,
-
VisualPropertyType.EDGE_SRCARROW_SHAPE);
- edgeAppCalc.setCalculator(edgeArrowCalculator);
-
- // ------------------------------ Set edge colour
---------------------------//
- DiscreteMapping edgeColorMapping = new
DiscreteMapping(Color.BLACK,
-
ObjectMapping.NODE_MAPPING);
- edgeColorMapping.setControllingAttributeName(EDGE_TYPE_ATT,
network, false);
- edgeColorMapping.putMapValue("reaction-product", Color.GREEN);
- edgeColorMapping.putMapValue("reaction-reactant", Color.RED);
- edgeColorMapping.putMapValue("reaction-modifier", Color.BLACK);
-
- Calculator edgeColorCalculator = new
BasicCalculator("SBMLReader Edge Color Calculator",
-
edgeColorMapping,
-
VisualPropertyType.EDGE_COLOR);
- edgeAppCalc.setCalculator(edgeColorCalculator);
-
- //------------------------- Create a visual style
-------------------------------//
- GlobalAppearanceCalculator gac =
vmManager.getVisualStyle().getGlobalAppearanceCalculator();
- VisualStyle visualStyle = new VisualStyle(SBMLReader_VS,
nodeAppCalc, edgeAppCalc, gac);
-
- return visualStyle;
- }
-}
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