Author: abeld
Date: 2009-07-09 11:19:28 -0700 (Thu, 09 Jul 2009)
New Revision: 17288
Added:
core3/automatic.layout/trunk/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java.broken
Removed:
core3/automatic.layout/trunk/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java
Log:
temporarily disable GroupAttributesLayout since I can't get it to compile due
to a generic typing problem
Deleted:
core3/automatic.layout/trunk/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java
===================================================================
---
core3/automatic.layout/trunk/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java
2009-07-09 17:22:45 UTC (rev 17287)
+++
core3/automatic.layout/trunk/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java
2009-07-09 18:19:28 UTC (rev 17288)
@@ -1,308 +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 csplugins.layout.algorithms;
-
-import org.cytoscape.model.CyDataTable;
-import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyRow;
-import org.cytoscape.layout.AbstractLayout;
-import org.cytoscape.view.presentation.property.TwoDVisualLexicon;
-import org.cytoscape.work.Tunable;
-import org.cytoscape.work.UndoSupport;
-
-import javax.swing.*;
-import java.awt.*;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.HashSet;
-import java.util.TreeMap;
-
-
-/*
- This layout partitions the graph according to the selected node attribute's
values.
- The nodes of the graph are broken into discrete partitions, where each
partition has
- the same attribute value. For example, assume there are four nodes, where
each node
- has the "IntAttr" attribute defined. Assume node 1 and 2 have the value
"100" for
- the "IntAttr" attribute, and node 3 and 4 have the value "200." This will
place nodes
- 1 and 2 in the first partition and nodes 3 and 4 in the second partition.
Each
- partition is drawn in a circle.
-*/
-/**
- *
- */
-public class GroupAttributesLayout extends AbstractLayout {
- /*
- Layout parameters:
- - spacingx: Horizontal spacing (on the x-axis) between two
partitions in a row.
- - spacingy: Vertical spacing (on the y-axis) between the largest
partitions of two rows.
- - maxwidth: Maximum width of a row
- - minrad: Minimum radius of a partition.
- - radmult: The scale of the radius of the partition. Increasing
this value
- will increase the size of the partition proportionally.
- */
- @Tunable(description="Horizontal spacing between two partitions in a
row")
- public double spacingx = 400.0;
- @Tunable(description="Vertical spacing between the largest partitions
of two rows")
- public double spacingy = 400.0;
- @Tunable(description="Maximum width of a row")
- public double maxwidth = 5000.0;
- @Tunable(description="Minimum width of a partition")
- public double minrad = 100.0;
- @Tunable(description="Scale of the radius of the partition")
- public double radmult = 50.0;
- @Tunable(description="The attribute to use for the layout")
- public String attributeName;
- @Tunable(description="The namespace of the attribute to use for the
layout")
- public String attributeNamespace;
-
- /**
- * Creates a new GroupAttributesLayout object.
- */
- public GroupAttributesLayout(UndoSupport undoSupport) {
- super(undoSupport);
- }
-
- /**
- * Overrides for CyLayoutAlgorithm support
- */
- public String getName() {
- return "attributes-layout";
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String toString() {
- return "Group Attributes Layout";
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Set<Class<?>> supportsNodeAttributes() {
- Set<Class<?>> ret = new HashSet<Class<?>>();
-
- ret.add(Integer.class);
- ret.add(Double.class);
- ret.add(String.class);
- ret.add(Boolean.class);
-
- return ret;
- }
-
- /**
- * Sets the attribute to use for the weights
- *
- * @param value the name of the attribute
- */
- public void setLayoutAttribute(String value) {
- if (value == null) {
- attributeName = null;
- } else {
- attributeName = value;
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public List<String> getInitialAttributeList() {
- return null;
- }
-
- /*
- Psuedo-procedure:
- 1. Call makeDiscrete(). This will create a map for each value of the
- node attribute to the list of nodes with that attribute value.
- Each of these lists will become a partition in the graph.
- makeDiscrete() will also add nodes to the invalidNodes list
- that do not have a value associated with the attribute.
- 2. Call sort(). This will return a list of partitions that is
- sorted based on the value of the attribute. Add the invalid
- nodes to the end of the sorted list. All the invalid nodes
- will be grouped together in the last partition of the layout.
- 3. Begin plotting each partition.
- a. Call encircle(). This will plot the partition in a circle.
- b. Store the diameter of the last circle plotted.
- c. Update maxheight. This stores the height of the largest circle
- in a row.
- d. Update offsetx. If we've reached the end of the row,
- reset offsetx and maxheight; update offsety so that
- it will store the y-axis location of the next row.
- */
- /**
- * DOCUMENT ME!
- */
- public void construct() {
- taskMonitor.setStatusMessage("Initializing");
- initialize(); // Calls initialize_local
-
- CyDataTable dataTable =
network.getCyDataTables("NODE").get(attributeNamespace);
- Class<?> klass =
dataTable.getColumnTypeMap().get(attributeName);
- if (Comparable.class.isAssignableFrom(klass)){
- Class<Comparable<?>>kasted = (Class<Comparable<?>>)
klass;
- doConstruct(kasted);
- } else {
- /* FIXME Error! */
- }
- }
- /** Needed to allow usage of parametric types */
- private <T extends Comparable<T>> void doConstruct(Class<T> klass){
- Map<T, List<CyNode>> partitionMap = new TreeMap<T,
List<CyNode>>();
- List<CyNode> invalidNodes = new ArrayList<CyNode>();
- makeDiscrete(partitionMap, invalidNodes, klass);
-
- List<List<CyNode>> partitionList = sort(partitionMap);
- partitionList.add(invalidNodes);
-
- double offsetx = 0.0;
- double offsety = 0.0;
- double maxheight = 0.0;
-
- for (List<CyNode> partition : partitionList) {
- if (canceled)
- return;
-
- double radius = encircle(partition, offsetx, offsety);
-
- double diameter = 2.0 * radius;
-
- if (diameter > maxheight)
- maxheight = diameter;
-
- offsetx += diameter;
-
- if (offsetx > maxwidth) {
- offsety += (maxheight + spacingy);
- offsetx = 0.0;
- maxheight = 0.0;
- } else
- offsetx += spacingx;
- }
- }
-
- private <T extends Comparable<T>> void makeDiscrete(Map<T,
List<CyNode>> map, List<CyNode> invalidNodes, Class<T> klass) {
- if (map == null)
- return;
-
- for (CyNode node:network.getNodeList()){
- T key =
node.getCyRow(attributeNamespace).get(attributeName, klass);
-
- if (key == null) {
- if (invalidNodes != null)
- invalidNodes.add(node);
- } else {
- if (!map.containsKey(key))
- map.put(key, new ArrayList<CyNode>());
-
- map.get(key).add(node);
- }
- }
- }
-
- private <T extends Comparable<T>> List<List<CyNode>> sort(final Map<T,
List<CyNode>> map) {
- if (map == null)
- return null;
-
- List<T> keys = new ArrayList<T>(map.keySet());
- Collections.sort(keys);
-
- Comparator<CyNode> comparator = new Comparator<CyNode>() {
- public int compare(CyNode node1, CyNode node2) {
- // FIXME: this code was originally comparing
node1.getIdentifier() to node2.getIdentifier()
- // I'm not sure that comparing the indices of
the nodes gets the same effect
- // on the other hand, nodes don't have a
human-readable uid in 3.0
- Integer a = Integer.valueOf(node1.getIndex());
- Integer b = Integer.valueOf(node2.getIndex());
-
- return a.compareTo(b);
- }
- };
-
- List<List<CyNode>> sortedlist = new
ArrayList<List<CyNode>>(map.keySet().size());
-
- for (T key : keys) {
- List<CyNode> partition = map.get(key);
- Collections.sort(partition, comparator);
- sortedlist.add(partition);
- }
-
- return sortedlist;
- }
-
- private double encircle(List<CyNode> partition, double offsetx, double
offsety) {
- if (partition == null)
- return 0.0;
-
- if (partition.size() == 1) {
- CyNode node = partition.get(0);
-
networkView.getNodeView(node).setVisualProperty(TwoDVisualLexicon.NODE_X_LOCATION,
offsetx);
-
networkView.getNodeView(node).setVisualProperty(TwoDVisualLexicon.NODE_Y_LOCATION,
offsety);
-
- return 0.0;
- }
-
- double radius = radmult * Math.sqrt(partition.size());
-
- if (radius < minrad)
- radius = minrad;
-
- double phidelta = (2.0 * Math.PI) / partition.size();
- double phi = 0.0;
-
- for (CyNode node : partition) {
- double x = offsetx + radius + (radius * Math.cos(phi));
- double y = offsety + radius + (radius * Math.sin(phi));
-
networkView.getNodeView(node).setVisualProperty(TwoDVisualLexicon.NODE_X_LOCATION,
x);
-
networkView.getNodeView(node).setVisualProperty(TwoDVisualLexicon.NODE_Y_LOCATION,
y);
- phi += phidelta;
- }
-
- return radius;
- }
-}
Copied:
core3/automatic.layout/trunk/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java.broken
(from rev 17284,
core3/automatic.layout/trunk/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java)
===================================================================
---
core3/automatic.layout/trunk/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java.broken
(rev 0)
+++
core3/automatic.layout/trunk/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java.broken
2009-07-09 18:19:28 UTC (rev 17288)
@@ -0,0 +1,308 @@
+
+/*
+ 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 csplugins.layout.algorithms;
+
+import org.cytoscape.model.CyDataTable;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyRow;
+import org.cytoscape.layout.AbstractLayout;
+import org.cytoscape.view.presentation.property.TwoDVisualLexicon;
+import org.cytoscape.work.Tunable;
+import org.cytoscape.work.UndoSupport;
+
+import javax.swing.*;
+import java.awt.*;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.HashSet;
+import java.util.TreeMap;
+
+
+/*
+ This layout partitions the graph according to the selected node attribute's
values.
+ The nodes of the graph are broken into discrete partitions, where each
partition has
+ the same attribute value. For example, assume there are four nodes, where
each node
+ has the "IntAttr" attribute defined. Assume node 1 and 2 have the value
"100" for
+ the "IntAttr" attribute, and node 3 and 4 have the value "200." This will
place nodes
+ 1 and 2 in the first partition and nodes 3 and 4 in the second partition.
Each
+ partition is drawn in a circle.
+*/
+/**
+ *
+ */
+public class GroupAttributesLayout extends AbstractLayout {
+ /*
+ Layout parameters:
+ - spacingx: Horizontal spacing (on the x-axis) between two
partitions in a row.
+ - spacingy: Vertical spacing (on the y-axis) between the largest
partitions of two rows.
+ - maxwidth: Maximum width of a row
+ - minrad: Minimum radius of a partition.
+ - radmult: The scale of the radius of the partition. Increasing
this value
+ will increase the size of the partition proportionally.
+ */
+ @Tunable(description="Horizontal spacing between two partitions in a
row")
+ public double spacingx = 400.0;
+ @Tunable(description="Vertical spacing between the largest partitions
of two rows")
+ public double spacingy = 400.0;
+ @Tunable(description="Maximum width of a row")
+ public double maxwidth = 5000.0;
+ @Tunable(description="Minimum width of a partition")
+ public double minrad = 100.0;
+ @Tunable(description="Scale of the radius of the partition")
+ public double radmult = 50.0;
+ @Tunable(description="The attribute to use for the layout")
+ public String attributeName;
+ @Tunable(description="The namespace of the attribute to use for the
layout")
+ public String attributeNamespace;
+
+ /**
+ * Creates a new GroupAttributesLayout object.
+ */
+ public GroupAttributesLayout(UndoSupport undoSupport) {
+ super(undoSupport);
+ }
+
+ /**
+ * Overrides for CyLayoutAlgorithm support
+ */
+ public String getName() {
+ return "attributes-layout";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString() {
+ return "Group Attributes Layout";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Set<Class<?>> supportsNodeAttributes() {
+ Set<Class<?>> ret = new HashSet<Class<?>>();
+
+ ret.add(Integer.class);
+ ret.add(Double.class);
+ ret.add(String.class);
+ ret.add(Boolean.class);
+
+ return ret;
+ }
+
+ /**
+ * Sets the attribute to use for the weights
+ *
+ * @param value the name of the attribute
+ */
+ public void setLayoutAttribute(String value) {
+ if (value == null) {
+ attributeName = null;
+ } else {
+ attributeName = value;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List<String> getInitialAttributeList() {
+ return null;
+ }
+
+ /*
+ Psuedo-procedure:
+ 1. Call makeDiscrete(). This will create a map for each value of the
+ node attribute to the list of nodes with that attribute value.
+ Each of these lists will become a partition in the graph.
+ makeDiscrete() will also add nodes to the invalidNodes list
+ that do not have a value associated with the attribute.
+ 2. Call sort(). This will return a list of partitions that is
+ sorted based on the value of the attribute. Add the invalid
+ nodes to the end of the sorted list. All the invalid nodes
+ will be grouped together in the last partition of the layout.
+ 3. Begin plotting each partition.
+ a. Call encircle(). This will plot the partition in a circle.
+ b. Store the diameter of the last circle plotted.
+ c. Update maxheight. This stores the height of the largest circle
+ in a row.
+ d. Update offsetx. If we've reached the end of the row,
+ reset offsetx and maxheight; update offsety so that
+ it will store the y-axis location of the next row.
+ */
+ /**
+ * DOCUMENT ME!
+ */
+ public void construct() {
+ taskMonitor.setStatusMessage("Initializing");
+ initialize(); // Calls initialize_local
+
+ CyDataTable dataTable =
network.getCyDataTables("NODE").get(attributeNamespace);
+ Class<?> klass =
dataTable.getColumnTypeMap().get(attributeName);
+ if (Comparable.class.isAssignableFrom(klass)){
+ Class<Comparable<?>>kasted = (Class<Comparable<?>>)
klass;
+ doConstruct(kasted);
+ } else {
+ /* FIXME Error! */
+ }
+ }
+ /** Needed to allow usage of parametric types */
+ private <T extends Comparable<T>> void doConstruct(Class<T> klass){
+ Map<T, List<CyNode>> partitionMap = new TreeMap<T,
List<CyNode>>();
+ List<CyNode> invalidNodes = new ArrayList<CyNode>();
+ makeDiscrete(partitionMap, invalidNodes, klass);
+
+ List<List<CyNode>> partitionList = sort(partitionMap);
+ partitionList.add(invalidNodes);
+
+ double offsetx = 0.0;
+ double offsety = 0.0;
+ double maxheight = 0.0;
+
+ for (List<CyNode> partition : partitionList) {
+ if (canceled)
+ return;
+
+ double radius = encircle(partition, offsetx, offsety);
+
+ double diameter = 2.0 * radius;
+
+ if (diameter > maxheight)
+ maxheight = diameter;
+
+ offsetx += diameter;
+
+ if (offsetx > maxwidth) {
+ offsety += (maxheight + spacingy);
+ offsetx = 0.0;
+ maxheight = 0.0;
+ } else
+ offsetx += spacingx;
+ }
+ }
+
+ private <T extends Comparable<T>> void makeDiscrete(Map<T,
List<CyNode>> map, List<CyNode> invalidNodes, Class<T> klass) {
+ if (map == null)
+ return;
+
+ for (CyNode node:network.getNodeList()){
+ T key =
node.getCyRow(attributeNamespace).get(attributeName, klass);
+
+ if (key == null) {
+ if (invalidNodes != null)
+ invalidNodes.add(node);
+ } else {
+ if (!map.containsKey(key))
+ map.put(key, new ArrayList<CyNode>());
+
+ map.get(key).add(node);
+ }
+ }
+ }
+
+ private <T extends Comparable<T>> List<List<CyNode>> sort(final Map<T,
List<CyNode>> map) {
+ if (map == null)
+ return null;
+
+ List<T> keys = new ArrayList<T>(map.keySet());
+ Collections.sort(keys);
+
+ Comparator<CyNode> comparator = new Comparator<CyNode>() {
+ public int compare(CyNode node1, CyNode node2) {
+ // FIXME: this code was originally comparing
node1.getIdentifier() to node2.getIdentifier()
+ // I'm not sure that comparing the indices of
the nodes gets the same effect
+ // on the other hand, nodes don't have a
human-readable uid in 3.0
+ Integer a = Integer.valueOf(node1.getIndex());
+ Integer b = Integer.valueOf(node2.getIndex());
+
+ return a.compareTo(b);
+ }
+ };
+
+ List<List<CyNode>> sortedlist = new
ArrayList<List<CyNode>>(map.keySet().size());
+
+ for (T key : keys) {
+ List<CyNode> partition = map.get(key);
+ Collections.sort(partition, comparator);
+ sortedlist.add(partition);
+ }
+
+ return sortedlist;
+ }
+
+ private double encircle(List<CyNode> partition, double offsetx, double
offsety) {
+ if (partition == null)
+ return 0.0;
+
+ if (partition.size() == 1) {
+ CyNode node = partition.get(0);
+
networkView.getNodeView(node).setVisualProperty(TwoDVisualLexicon.NODE_X_LOCATION,
offsetx);
+
networkView.getNodeView(node).setVisualProperty(TwoDVisualLexicon.NODE_Y_LOCATION,
offsety);
+
+ return 0.0;
+ }
+
+ double radius = radmult * Math.sqrt(partition.size());
+
+ if (radius < minrad)
+ radius = minrad;
+
+ double phidelta = (2.0 * Math.PI) / partition.size();
+ double phi = 0.0;
+
+ for (CyNode node : partition) {
+ double x = offsetx + radius + (radius * Math.cos(phi));
+ double y = offsety + radius + (radius * Math.sin(phi));
+
networkView.getNodeView(node).setVisualProperty(TwoDVisualLexicon.NODE_X_LOCATION,
x);
+
networkView.getNodeView(node).setVisualProperty(TwoDVisualLexicon.NODE_Y_LOCATION,
y);
+ phi += phidelta;
+ }
+
+ return radius;
+ }
+}
Property changes on:
core3/automatic.layout/trunk/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java.broken
___________________________________________________________________
Name: svn:mergeinfo
+
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