Author: pwang
Date: 2010-08-17 17:34:22 -0700 (Tue, 17 Aug 2010)
New Revision: 21442
Added:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/gml/GMLWriter.javax
Removed:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/gml/GMLWriter.java
Log:
Rename
Deleted:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/gml/GMLWriter.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/gml/GMLWriter.java
2010-08-18 00:33:45 UTC (rev 21441)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/gml/GMLWriter.java
2010-08-18 00:34:22 UTC (rev 21442)
@@ -1,630 +0,0 @@
-/*
- File: GMLWriter.java
-
- Copyright (c) 2006, 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 org.cytoscape.io.internal.write.gml;
-
-import org.cytoscape.io.internal.read.gml.KeyValue;
-import org.cytoscape.io.internal.read.gml.GMLReader;
-import org.cytoscape.model.CyEdge;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyNode;
-import org.cytoscape.view.model.View;
-import org.cytoscape.view.model.CyNetworkView;
-
-import java.awt.*;
-import java.awt.geom.Point2D;
-import java.util.*;
-import java.util.List;
-
-
-/**
- * The purpse of this class is to translate cytoscape data structures into a
gml
- * object tree, we can then use the gml parser to write this tree out into a
- * file
- */
-public class GMLWriter {
- /**
- * It is possible that nodes have been added to the graph since it was
- * loaded. This set will keep track of nodes and edges that are
currently in
- * the perspective that have no corresponding entry in the object tree
that
- * was loaded with the netowrk
- */
- private Set<Integer> newNodes;
-
- /**
- * It is possible that nodes have been added to the graph since it was
- * loaded. This set will keep track of nodes and edges that are
currently in
- * the perspective that have no corresponding entry in the object tree
that
- * was loaded with the netowrk
- */
- private Set<Integer> newEdges;
-
- /**
- * Given an object tree given in oldList, update it with the information
- * provided in network and optionall view (if view is not null). The GML
- * spec requires that we remember all information provided in the
original
- * gml file. Therefore, we pass in the old object tree as oldList, as
- * execute functions which will update that data structure. We would
also
- * like to save files that may not have been loaded from a gml file.
This
- * list is empty in that case. Those same update functions must be able
to
- * create all relevant key-value pairs as well then.
- */
- @SuppressWarnings("unchecked") // for the casts of KeyValue.value
- public void writeGML(final CyNetwork network, final CyNetworkView view,
final List<KeyValue> oldList) {
- /*
- * Initially all the nodes and edges have not been seen
- */
- newNodes = new HashSet<Integer>(network.getNodeCount());
- newEdges = new HashSet<Integer>(network.getEdgeCount());
-
- for ( CyNode node : network.getNodeList() ) {
- newNodes.add(Integer.valueOf(node.getIndex()));
- }
-
- for ( CyEdge edge : network.getEdgeList() ) {
- newEdges.add(Integer.valueOf(edge.getIndex()));
- }
-
- /*
- * We are going to make sure the keys graph,creator,and version
are
- * present and update them fi they are already present
- */
- KeyValue graph = null;
-
- /*
- * We are going to make sure the keys graph,creator,and version
are
- * present and update them fi they are already present
- */
- KeyValue creator = null;
-
- /*
- * We are going to make sure the keys graph,creator,and version
are
- * present and update them fi they are already present
- */
- KeyValue version = null;
- KeyValue keyVal = null;
-
- for (Iterator<KeyValue> it = oldList.iterator(); it.hasNext();)
{
- keyVal = it.next();
-
- if (keyVal.key.equals(GMLReader.GRAPH)) {
- graph = keyVal;
- } else if (keyVal.key.equals(GMLReader.CREATOR)) {
- creator = keyVal;
- } else if (keyVal.key.equals(GMLReader.VERSION)) {
- version = keyVal;
- }
- }
-
- if (creator == null) {
- creator = new KeyValue(GMLReader.CREATOR, null);
- oldList.add(creator);
- }
-
- if (version == null) {
- version = new KeyValue(GMLReader.VERSION, null);
- oldList.add(version);
- }
-
- if (graph == null) {
- graph = new KeyValue(GMLReader.GRAPH, new Vector());
- oldList.add(graph);
- }
-
- /*
- * Update the list associated with the graph pair
- */
- writeGraph(network, view, (List<KeyValue>) graph.value);
- creator.value = "Cytoscape";
- version.value = new Double(1.0);
-
- /*
- * After update all of the graph objects that were already
present in
- * the object tree check and see if there are any objects in
the current
- * perspective that were not updated For these objects, create
an empty
- * key-value mapping and then update it
- */
- List<KeyValue> graph_list = (List<KeyValue>) graph.value;
-
- while (!newNodes.isEmpty()) {
- KeyValue nodePair = new KeyValue(GMLReader.NODE, new
Vector());
- graph_list.add(nodePair);
- ((List) nodePair.value).add(new
KeyValue(GMLReader.ROOT_INDEX,
-
newNodes.iterator().next()));
- writeGraphNode(network, view, (List) nodePair.value);
- }
-
- while (!newEdges.isEmpty()) {
- KeyValue edgePair = new KeyValue(GMLReader.EDGE, new
Vector());
- graph_list.add(edgePair);
- ((List<KeyValue>) edgePair.value).add(new
KeyValue(GMLReader.ROOT_INDEX,
-
newEdges.iterator().next()));
- writeGraphEdge(network, view, (List) edgePair.value);
- }
- }
-
- /**
- * Update the list associated with a graph key
- */
- @SuppressWarnings("unchecked") // for the casts of KeyValue.value
- private void writeGraph(final CyNetwork network, final CyNetworkView
view, final List<KeyValue> oldList) {
-
-
- // To enhance compatibility with non-cytoscape GML-conformant
- // programs, add directedness flag to graph: allways use
'directed',
- // to match pre-3.0 cytoscape's 'edges are directed' behaviour
- // TODO: could use undirected here if network is undirected
i.e. all edges are undirected.
- oldList.add(new KeyValue("directed", Integer.valueOf(0)));
-
- for (Iterator<KeyValue> it = oldList.iterator();
it.hasNext();) {
- KeyValue keyVal = it.next();
-
- /*
- * For all nodes in the object tree, update the list
that is
- * associated with that key. If this node is no longer
present in
- * the perpsective, then we must remove it from the
ojbect tree.
- * Also do the same thing for the edges.
- */
- if (keyVal.key.equals(GMLReader.NODE)) {
- if (!writeGraphNode(network, view,
(List<KeyValue>) keyVal.value)) {
- it.remove();
- }
- } else if (keyVal.key.equals(GMLReader.EDGE)) {
- if (!writeGraphEdge(network, view,
(List<KeyValue>) keyVal.value)) {
- it.remove();
- }
- }
- }
- }
-
- /**
- * Update the list associated with a node key
- */
- @SuppressWarnings("unchecked") // for the cast of KeyValue.value
- private boolean writeGraphNode(final CyNetwork network, final
CyNetworkView view,
- final List<KeyValue> oldList) {
- /*
- * We expect a list associated with node key to potentially
have a
- * graphic key, id key, and root_index key
- */
- Integer root_index = null;
- KeyValue graphicsPair = null;
- KeyValue labelPair = null;
- KeyValue idPair = null;
-
- for (Iterator it = oldList.iterator(); it.hasNext();) {
- KeyValue keyVal = (KeyValue) it.next();
-
- if (keyVal.key.equals(GMLReader.ROOT_INDEX)) {
- root_index = (Integer) keyVal.value;
- } else if (keyVal.key.equals(GMLReader.GRAPHICS)) {
- graphicsPair = keyVal;
- } else if (keyVal.key.equals(GMLReader.LABEL)) {
- labelPair = keyVal;
- } else if (keyVal.key.equals(GMLReader.ID)) {
- idPair = keyVal;
- }
- }
-
- /*
- * Check to see if this nodes is still in the perspective
- */
- if (root_index == null) {
- return false;
- }
-
- CyNode node = network.getNode(root_index.intValue());
-
- if (node == null || !network.containsNode(node)) {
- return false;
- }
-
- /*
- * Mark this node as seen
- */
- newNodes.remove(root_index);
-
- /*
- * Update or create the id key-value pair for this list
- */
- if (idPair == null) {
- idPair = new KeyValue(GMLReader.ID, null);
- oldList.add(idPair);
- }
-
- idPair.value = root_index;
-
- /*
- * Optionall update/create the graphics key-value pair for this
list if
- * there is currently defined. NOte that if no view is defined,
the
- * previously loaded view information will remain intact
- */
- if (view != null) {
- if (graphicsPair == null) {
- graphicsPair = new KeyValue(GMLReader.GRAPHICS,
new Vector<KeyValue>());
- oldList.add(graphicsPair);
- }
-
- writeGraphNodeGraphics(network, view.getNodeView(node),
(List<KeyValue>) graphicsPair.value);
- }
-
- /*
- * Update/create the label key-value pair. We have co-opted
this field
- * to mean the canoncial name
- */
- if (labelPair == null) {
- labelPair = new KeyValue(GMLReader.LABEL, null);
- oldList.add(labelPair);
- }
-
- labelPair.value = node.attrs().get("name",String.class);
-
- return true;
- }
-
- /**
- * Update the list associated with an edge key
- */
- @SuppressWarnings("unchecked") // for the cast of KeyValue.value
- private boolean writeGraphEdge(final CyNetwork network, final
CyNetworkView view,
- final List<KeyValue> oldList) {
- /*
- * An edge key will definitely have a root_index, labelPair (we
enforce
- * this on loading), source key, and a target key
- */
- Integer root_index = null;
- KeyValue graphicsPair = null;
- KeyValue labelPair = null;
- KeyValue sourcePair = null;
- KeyValue targetPair = null;
- KeyValue isDirected = null;
-
- for (Iterator it = oldList.iterator(); it.hasNext();) {
- KeyValue keyVal = (KeyValue) it.next();
-
- if (keyVal.key.equals(GMLReader.GRAPHICS)) {
- graphicsPair = keyVal;
- } else if (keyVal.key.equals(GMLReader.LABEL)) {
- labelPair = keyVal;
- } else if (keyVal.key.equals(GMLReader.ROOT_INDEX)) {
- root_index = (Integer) keyVal.value;
- } else if (keyVal.key.equals(GMLReader.SOURCE)) {
- sourcePair = keyVal;
- } else if (keyVal.key.equals(GMLReader.TARGET)) {
- targetPair = keyVal;
- } else if (keyVal.key.equals(GMLReader.IS_DIRECTED)) {
- isDirected = keyVal;
- }
- }
-
- /*
- * Make sure the edge is still present in this perspective
- */
- if (root_index == null) {
- return false;
- }
-
- CyEdge edge = network.getEdge(root_index.intValue());
-
- if (edge == null || !network.containsEdge(edge)) {
- return false;
- }
-
- newEdges.remove(root_index);
-
- if (targetPair == null) {
- targetPair = new KeyValue(GMLReader.TARGET, null);
- oldList.add(targetPair);
- }
-
- targetPair.value = Integer.valueOf(edge.getTarget().getIndex());
-
- if (sourcePair == null) {
- sourcePair = new KeyValue(GMLReader.SOURCE, null);
- oldList.add(sourcePair);
- }
-
- sourcePair.value = Integer.valueOf(edge.getSource().getIndex());
-
- if (view != null) {
- if (graphicsPair == null) {
- graphicsPair = new KeyValue(GMLReader.GRAPHICS,
new Vector());
- oldList.add(graphicsPair);
- }
-
- writeGraphEdgeGraphics(network, view.getEdgeView(edge),
(List<KeyValue>) graphicsPair.value);
- }
-
- if (labelPair == null) {
- labelPair = new KeyValue(GMLReader.LABEL, null);
- oldList.add(labelPair);
- }
-
- labelPair.value = edge.attrs().get("interaction",String.class);
-
- if (isDirected == null) {
- isDirected = new KeyValue(GMLReader.IS_DIRECTED, null);
- oldList.add(isDirected);
- }
- if (edge.isDirected()){
- isDirected.value = Integer.valueOf(0);
- } else {
- isDirected.value = Integer.valueOf(1);
- }
-
- return true;
- }
-
- /**
- * This writes all the graphical information for a particular node into
an
- * object tree
- */
- private void writeGraphNodeGraphics(final CyNetwork network, final
View<CyNode> nodeView,
- final List<KeyValue> oldList) {
- // TODO fix for new style view
-/*
- KeyValue x = null;
- KeyValue y = null;
- KeyValue w = null;
- KeyValue h = null;
- KeyValue type = null;
- KeyValue fill = null;
- KeyValue outline = null;
- KeyValue outline_width = null;
-
- for (Iterator it = oldList.iterator(); it.hasNext();) {
- KeyValue keyVal = (KeyValue) it.next();
-
- if (keyVal.key.equals(GMLReader.X)) {
- x = keyVal;
- } else if (keyVal.key.equals(GMLReader.Y)) {
- y = keyVal;
- } else if (keyVal.key.equals(GMLReader.W)) {
- w = keyVal;
- } else if (keyVal.key.equals(GMLReader.H)) {
- h = keyVal;
- } else if (keyVal.key.equals(GMLReader.TYPE)) {
- type = keyVal;
- } else if (keyVal.key.equals(GMLReader.FILL)) {
- fill = keyVal;
- } else if (keyVal.key.equals(GMLReader.OUTLINE)) {
- outline = keyVal;
- } else if (keyVal.key.equals(GMLReader.OUTLINE_WIDTH)) {
- outline_width = keyVal;
- }
- }
-
- if (x == null) {
- x = new KeyValue(GMLReader.X, null);
- oldList.add(x);
- }
-
- if (y == null) {
- y = new KeyValue(GMLReader.Y, null);
- oldList.add(y);
- }
-
- if (w == null) {
- w = new KeyValue(GMLReader.W, null);
- oldList.add(w);
- }
-
- if (h == null) {
- h = new KeyValue(GMLReader.H, null);
- oldList.add(h);
- }
-
- if (fill == null) {
- fill = new KeyValue(GMLReader.FILL, null);
- oldList.add(fill);
- }
-
- if (type == null) {
- type = new KeyValue(GMLReader.TYPE, null);
- oldList.add(type);
- }
-
- if (outline == null) {
- outline = new KeyValue(GMLReader.OUTLINE, null);
- oldList.add(outline);
- }
-
- if (outline_width == null) {
- outline_width = new KeyValue(GMLReader.OUTLINE_WIDTH,
null);
- oldList.add(outline_width);
- }
-
- if (nodeView == null) return; // If no view data, simply don't
save it (instead of crashing)
-
- x.value = new Double(nodeView.getXPosition());
- y.value = new Double(nodeView.getYPosition());
- w.value = new Double(nodeView.getWidth());
- h.value = new Double(nodeView.getHeight());
- fill.value = getColorHexString((Color)
nodeView.getUnselectedPaint());
- outline.value = getColorHexString((Color)
nodeView.getBorderPaint());
- outline_width.value = new Double(nodeView.getBorderWidth());
-
- switch (nodeView.getShape()) {
- case NodeView.RECTANGLE:
- type.value = GMLReader.RECTANGLE;
-
- break;
-
- case NodeView.ELLIPSE:
- type.value = GMLReader.ELLIPSE;
-
- break;
-
- case NodeView.DIAMOND:
- type.value = GMLReader.DIAMOND;
-
- break;
-
- case NodeView.HEXAGON:
- type.value = GMLReader.HEXAGON;
-
- break;
-
- case NodeView.OCTAGON:
- type.value = GMLReader.OCTAGON;
-
- break;
-
- case NodeView.PARALELLOGRAM:
- type.value = GMLReader.PARALELLOGRAM;
-
- break;
-
- case NodeView.TRIANGLE:
- type.value = GMLReader.TRIANGLE;
-
- break;
- }
- */
- }
-
- private void writeGraphEdgeGraphics(final CyNetwork network, final
View<CyEdge> edgeView,
- final List<KeyValue> oldList) {
- // TODO fix for new style view
- /*
- KeyValue width = null;
- KeyValue fill = null;
- KeyValue line = null;
- KeyValue type = null;
- KeyValue source_arrow = null;
- KeyValue target_arrow = null;
-
- for (Iterator it = oldList.iterator(); it.hasNext();) {
- KeyValue keyVal = (KeyValue) it.next();
-
- if (keyVal.key.equals(GMLReader.WIDTH)) {
- width = keyVal;
- } else if (keyVal.key.equals(GMLReader.FILL)) {
- fill = keyVal;
- } else if (keyVal.key.equals(GMLReader.LINE)) {
- line = keyVal;
- } else if (keyVal.key.equals(GMLReader.TYPE)) {
- type = keyVal;
- } else if (keyVal.key.equals(GMLReader.SOURCE_ARROW)) {
- source_arrow = keyVal;
- } else if (keyVal.key.equals(GMLReader.TARGET_ARROW)) {
- target_arrow = keyVal;
- }
- }
-
- if (width == null) {
- width = new KeyValue(GMLReader.WIDTH, null);
- oldList.add(width);
- }
-
- if (edgeView == null) return; // If no view data, simply don't
save it (instead of crashing)
-
- width.value = new Double(edgeView.getStrokeWidth());
-
- if (fill == null) {
- fill = new KeyValue(GMLReader.FILL, null);
- oldList.add(fill);
- }
-
- fill.value = getColorHexString((Color)
edgeView.getUnselectedPaint());
-
- if (type == null) {
- type = new KeyValue(GMLReader.TYPE, null);
- oldList.add(type);
- }
-
- switch (edgeView.getLineType()) {
- case EdgeView.STRAIGHT_LINES:
- type.value = GMLReader.STRAIGHT_LINES;
-
- break;
-
- case EdgeView.CURVED_LINES:
- type.value = GMLReader.CURVED_LINES;
-
- break;
- }
-
- if (line == null) {
- line = new KeyValue(GMLReader.LINE, null);
- oldList.add(line);
- }
-
- Point2D[] pointsArray = edgeView.getBend().getDrawPoints();
- Vector<KeyValue> points = new
Vector<KeyValue>(pointsArray.length);
-
- // CTW funny thing with anchor points, need to trim off the
first and
- // last
- // and reverse the order x
- for (int idx = pointsArray.length - 2; idx > 0; idx--) {
- Vector<KeyValue> coords = new Vector<KeyValue>(2);
- coords.add(new KeyValue(GMLReader.X, new
Double(pointsArray[idx].getX())));
- coords.add(new KeyValue(GMLReader.Y, new
Double(pointsArray[idx].getY())));
- points.add(new KeyValue(GMLReader.POINT, coords));
- }
-
- line.value = points;
-
- if (source_arrow == null) {
- source_arrow = new KeyValue(GMLReader.SOURCE_ARROW,
null);
- oldList.add(source_arrow);
- }
-
- source_arrow.value =
Integer.valueOf(edgeView.getSourceEdgeEnd());
-
- if (target_arrow == null) {
- target_arrow = new KeyValue(GMLReader.TARGET_ARROW,
null);
- oldList.add(target_arrow);
- }
-
- target_arrow.value =
Integer.valueOf(edgeView.getTargetEdgeEnd());
- */
- }
-
- /**
- * Get the String representation of the 6 character hexidecimal RGB
values
- * i.e. #ff000a
- *
- * @param Color
- * The color to be converted
- */
- private static String getColorHexString(final Color c) {
- return ("#" // +Integer.toHexString(c.getRGB());
- + Integer.toHexString(256 + c.getRed()).substring(1)
- + Integer.toHexString(256 + c.getGreen()).substring(1)
- + Integer.toHexString(256 + c.getBlue()).substring(1));
- }
-}
Added:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/gml/GMLWriter.javax
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/gml/GMLWriter.javax
(rev 0)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/gml/GMLWriter.javax
2010-08-18 00:34:22 UTC (rev 21442)
@@ -0,0 +1,630 @@
+/*
+ File: GMLWriter.java
+
+ Copyright (c) 2006, 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 org.cytoscape.io.internal.write.gml;
+
+import org.cytoscape.io.internal.read.gml.KeyValue;
+import org.cytoscape.io.internal.read.gml.GMLReader;
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.view.model.View;
+import org.cytoscape.view.model.CyNetworkView;
+
+import java.awt.*;
+import java.awt.geom.Point2D;
+import java.util.*;
+import java.util.List;
+
+
+/**
+ * The purpse of this class is to translate cytoscape data structures into a
gml
+ * object tree, we can then use the gml parser to write this tree out into a
+ * file
+ */
+public class GMLWriter {
+ /**
+ * It is possible that nodes have been added to the graph since it was
+ * loaded. This set will keep track of nodes and edges that are
currently in
+ * the perspective that have no corresponding entry in the object tree
that
+ * was loaded with the netowrk
+ */
+ private Set<Integer> newNodes;
+
+ /**
+ * It is possible that nodes have been added to the graph since it was
+ * loaded. This set will keep track of nodes and edges that are
currently in
+ * the perspective that have no corresponding entry in the object tree
that
+ * was loaded with the netowrk
+ */
+ private Set<Integer> newEdges;
+
+ /**
+ * Given an object tree given in oldList, update it with the information
+ * provided in network and optionall view (if view is not null). The GML
+ * spec requires that we remember all information provided in the
original
+ * gml file. Therefore, we pass in the old object tree as oldList, as
+ * execute functions which will update that data structure. We would
also
+ * like to save files that may not have been loaded from a gml file.
This
+ * list is empty in that case. Those same update functions must be able
to
+ * create all relevant key-value pairs as well then.
+ */
+ @SuppressWarnings("unchecked") // for the casts of KeyValue.value
+ public void writeGML(final CyNetwork network, final CyNetworkView view,
final List<KeyValue> oldList) {
+ /*
+ * Initially all the nodes and edges have not been seen
+ */
+ newNodes = new HashSet<Integer>(network.getNodeCount());
+ newEdges = new HashSet<Integer>(network.getEdgeCount());
+
+ for ( CyNode node : network.getNodeList() ) {
+ newNodes.add(Integer.valueOf(node.getIndex()));
+ }
+
+ for ( CyEdge edge : network.getEdgeList() ) {
+ newEdges.add(Integer.valueOf(edge.getIndex()));
+ }
+
+ /*
+ * We are going to make sure the keys graph,creator,and version
are
+ * present and update them fi they are already present
+ */
+ KeyValue graph = null;
+
+ /*
+ * We are going to make sure the keys graph,creator,and version
are
+ * present and update them fi they are already present
+ */
+ KeyValue creator = null;
+
+ /*
+ * We are going to make sure the keys graph,creator,and version
are
+ * present and update them fi they are already present
+ */
+ KeyValue version = null;
+ KeyValue keyVal = null;
+
+ for (Iterator<KeyValue> it = oldList.iterator(); it.hasNext();)
{
+ keyVal = it.next();
+
+ if (keyVal.key.equals(GMLReader.GRAPH)) {
+ graph = keyVal;
+ } else if (keyVal.key.equals(GMLReader.CREATOR)) {
+ creator = keyVal;
+ } else if (keyVal.key.equals(GMLReader.VERSION)) {
+ version = keyVal;
+ }
+ }
+
+ if (creator == null) {
+ creator = new KeyValue(GMLReader.CREATOR, null);
+ oldList.add(creator);
+ }
+
+ if (version == null) {
+ version = new KeyValue(GMLReader.VERSION, null);
+ oldList.add(version);
+ }
+
+ if (graph == null) {
+ graph = new KeyValue(GMLReader.GRAPH, new Vector());
+ oldList.add(graph);
+ }
+
+ /*
+ * Update the list associated with the graph pair
+ */
+ writeGraph(network, view, (List<KeyValue>) graph.value);
+ creator.value = "Cytoscape";
+ version.value = new Double(1.0);
+
+ /*
+ * After update all of the graph objects that were already
present in
+ * the object tree check and see if there are any objects in
the current
+ * perspective that were not updated For these objects, create
an empty
+ * key-value mapping and then update it
+ */
+ List<KeyValue> graph_list = (List<KeyValue>) graph.value;
+
+ while (!newNodes.isEmpty()) {
+ KeyValue nodePair = new KeyValue(GMLReader.NODE, new
Vector());
+ graph_list.add(nodePair);
+ ((List) nodePair.value).add(new
KeyValue(GMLReader.ROOT_INDEX,
+
newNodes.iterator().next()));
+ writeGraphNode(network, view, (List) nodePair.value);
+ }
+
+ while (!newEdges.isEmpty()) {
+ KeyValue edgePair = new KeyValue(GMLReader.EDGE, new
Vector());
+ graph_list.add(edgePair);
+ ((List<KeyValue>) edgePair.value).add(new
KeyValue(GMLReader.ROOT_INDEX,
+
newEdges.iterator().next()));
+ writeGraphEdge(network, view, (List) edgePair.value);
+ }
+ }
+
+ /**
+ * Update the list associated with a graph key
+ */
+ @SuppressWarnings("unchecked") // for the casts of KeyValue.value
+ private void writeGraph(final CyNetwork network, final CyNetworkView
view, final List<KeyValue> oldList) {
+
+
+ // To enhance compatibility with non-cytoscape GML-conformant
+ // programs, add directedness flag to graph: allways use
'directed',
+ // to match pre-3.0 cytoscape's 'edges are directed' behaviour
+ // TODO: could use undirected here if network is undirected
i.e. all edges are undirected.
+ oldList.add(new KeyValue("directed", Integer.valueOf(0)));
+
+ for (Iterator<KeyValue> it = oldList.iterator();
it.hasNext();) {
+ KeyValue keyVal = it.next();
+
+ /*
+ * For all nodes in the object tree, update the list
that is
+ * associated with that key. If this node is no longer
present in
+ * the perpsective, then we must remove it from the
ojbect tree.
+ * Also do the same thing for the edges.
+ */
+ if (keyVal.key.equals(GMLReader.NODE)) {
+ if (!writeGraphNode(network, view,
(List<KeyValue>) keyVal.value)) {
+ it.remove();
+ }
+ } else if (keyVal.key.equals(GMLReader.EDGE)) {
+ if (!writeGraphEdge(network, view,
(List<KeyValue>) keyVal.value)) {
+ it.remove();
+ }
+ }
+ }
+ }
+
+ /**
+ * Update the list associated with a node key
+ */
+ @SuppressWarnings("unchecked") // for the cast of KeyValue.value
+ private boolean writeGraphNode(final CyNetwork network, final
CyNetworkView view,
+ final List<KeyValue> oldList) {
+ /*
+ * We expect a list associated with node key to potentially
have a
+ * graphic key, id key, and root_index key
+ */
+ Integer root_index = null;
+ KeyValue graphicsPair = null;
+ KeyValue labelPair = null;
+ KeyValue idPair = null;
+
+ for (Iterator it = oldList.iterator(); it.hasNext();) {
+ KeyValue keyVal = (KeyValue) it.next();
+
+ if (keyVal.key.equals(GMLReader.ROOT_INDEX)) {
+ root_index = (Integer) keyVal.value;
+ } else if (keyVal.key.equals(GMLReader.GRAPHICS)) {
+ graphicsPair = keyVal;
+ } else if (keyVal.key.equals(GMLReader.LABEL)) {
+ labelPair = keyVal;
+ } else if (keyVal.key.equals(GMLReader.ID)) {
+ idPair = keyVal;
+ }
+ }
+
+ /*
+ * Check to see if this nodes is still in the perspective
+ */
+ if (root_index == null) {
+ return false;
+ }
+
+ CyNode node = network.getNode(root_index.intValue());
+
+ if (node == null || !network.containsNode(node)) {
+ return false;
+ }
+
+ /*
+ * Mark this node as seen
+ */
+ newNodes.remove(root_index);
+
+ /*
+ * Update or create the id key-value pair for this list
+ */
+ if (idPair == null) {
+ idPair = new KeyValue(GMLReader.ID, null);
+ oldList.add(idPair);
+ }
+
+ idPair.value = root_index;
+
+ /*
+ * Optionall update/create the graphics key-value pair for this
list if
+ * there is currently defined. NOte that if no view is defined,
the
+ * previously loaded view information will remain intact
+ */
+ if (view != null) {
+ if (graphicsPair == null) {
+ graphicsPair = new KeyValue(GMLReader.GRAPHICS,
new Vector<KeyValue>());
+ oldList.add(graphicsPair);
+ }
+
+ writeGraphNodeGraphics(network, view.getNodeView(node),
(List<KeyValue>) graphicsPair.value);
+ }
+
+ /*
+ * Update/create the label key-value pair. We have co-opted
this field
+ * to mean the canoncial name
+ */
+ if (labelPair == null) {
+ labelPair = new KeyValue(GMLReader.LABEL, null);
+ oldList.add(labelPair);
+ }
+
+ labelPair.value = node.attrs().get("name",String.class);
+
+ return true;
+ }
+
+ /**
+ * Update the list associated with an edge key
+ */
+ @SuppressWarnings("unchecked") // for the cast of KeyValue.value
+ private boolean writeGraphEdge(final CyNetwork network, final
CyNetworkView view,
+ final List<KeyValue> oldList) {
+ /*
+ * An edge key will definitely have a root_index, labelPair (we
enforce
+ * this on loading), source key, and a target key
+ */
+ Integer root_index = null;
+ KeyValue graphicsPair = null;
+ KeyValue labelPair = null;
+ KeyValue sourcePair = null;
+ KeyValue targetPair = null;
+ KeyValue isDirected = null;
+
+ for (Iterator it = oldList.iterator(); it.hasNext();) {
+ KeyValue keyVal = (KeyValue) it.next();
+
+ if (keyVal.key.equals(GMLReader.GRAPHICS)) {
+ graphicsPair = keyVal;
+ } else if (keyVal.key.equals(GMLReader.LABEL)) {
+ labelPair = keyVal;
+ } else if (keyVal.key.equals(GMLReader.ROOT_INDEX)) {
+ root_index = (Integer) keyVal.value;
+ } else if (keyVal.key.equals(GMLReader.SOURCE)) {
+ sourcePair = keyVal;
+ } else if (keyVal.key.equals(GMLReader.TARGET)) {
+ targetPair = keyVal;
+ } else if (keyVal.key.equals(GMLReader.IS_DIRECTED)) {
+ isDirected = keyVal;
+ }
+ }
+
+ /*
+ * Make sure the edge is still present in this perspective
+ */
+ if (root_index == null) {
+ return false;
+ }
+
+ CyEdge edge = network.getEdge(root_index.intValue());
+
+ if (edge == null || !network.containsEdge(edge)) {
+ return false;
+ }
+
+ newEdges.remove(root_index);
+
+ if (targetPair == null) {
+ targetPair = new KeyValue(GMLReader.TARGET, null);
+ oldList.add(targetPair);
+ }
+
+ targetPair.value = Integer.valueOf(edge.getTarget().getIndex());
+
+ if (sourcePair == null) {
+ sourcePair = new KeyValue(GMLReader.SOURCE, null);
+ oldList.add(sourcePair);
+ }
+
+ sourcePair.value = Integer.valueOf(edge.getSource().getIndex());
+
+ if (view != null) {
+ if (graphicsPair == null) {
+ graphicsPair = new KeyValue(GMLReader.GRAPHICS,
new Vector());
+ oldList.add(graphicsPair);
+ }
+
+ writeGraphEdgeGraphics(network, view.getEdgeView(edge),
(List<KeyValue>) graphicsPair.value);
+ }
+
+ if (labelPair == null) {
+ labelPair = new KeyValue(GMLReader.LABEL, null);
+ oldList.add(labelPair);
+ }
+
+ labelPair.value = edge.attrs().get("interaction",String.class);
+
+ if (isDirected == null) {
+ isDirected = new KeyValue(GMLReader.IS_DIRECTED, null);
+ oldList.add(isDirected);
+ }
+ if (edge.isDirected()){
+ isDirected.value = Integer.valueOf(0);
+ } else {
+ isDirected.value = Integer.valueOf(1);
+ }
+
+ return true;
+ }
+
+ /**
+ * This writes all the graphical information for a particular node into
an
+ * object tree
+ */
+ private void writeGraphNodeGraphics(final CyNetwork network, final
View<CyNode> nodeView,
+ final List<KeyValue> oldList) {
+ // TODO fix for new style view
+/*
+ KeyValue x = null;
+ KeyValue y = null;
+ KeyValue w = null;
+ KeyValue h = null;
+ KeyValue type = null;
+ KeyValue fill = null;
+ KeyValue outline = null;
+ KeyValue outline_width = null;
+
+ for (Iterator it = oldList.iterator(); it.hasNext();) {
+ KeyValue keyVal = (KeyValue) it.next();
+
+ if (keyVal.key.equals(GMLReader.X)) {
+ x = keyVal;
+ } else if (keyVal.key.equals(GMLReader.Y)) {
+ y = keyVal;
+ } else if (keyVal.key.equals(GMLReader.W)) {
+ w = keyVal;
+ } else if (keyVal.key.equals(GMLReader.H)) {
+ h = keyVal;
+ } else if (keyVal.key.equals(GMLReader.TYPE)) {
+ type = keyVal;
+ } else if (keyVal.key.equals(GMLReader.FILL)) {
+ fill = keyVal;
+ } else if (keyVal.key.equals(GMLReader.OUTLINE)) {
+ outline = keyVal;
+ } else if (keyVal.key.equals(GMLReader.OUTLINE_WIDTH)) {
+ outline_width = keyVal;
+ }
+ }
+
+ if (x == null) {
+ x = new KeyValue(GMLReader.X, null);
+ oldList.add(x);
+ }
+
+ if (y == null) {
+ y = new KeyValue(GMLReader.Y, null);
+ oldList.add(y);
+ }
+
+ if (w == null) {
+ w = new KeyValue(GMLReader.W, null);
+ oldList.add(w);
+ }
+
+ if (h == null) {
+ h = new KeyValue(GMLReader.H, null);
+ oldList.add(h);
+ }
+
+ if (fill == null) {
+ fill = new KeyValue(GMLReader.FILL, null);
+ oldList.add(fill);
+ }
+
+ if (type == null) {
+ type = new KeyValue(GMLReader.TYPE, null);
+ oldList.add(type);
+ }
+
+ if (outline == null) {
+ outline = new KeyValue(GMLReader.OUTLINE, null);
+ oldList.add(outline);
+ }
+
+ if (outline_width == null) {
+ outline_width = new KeyValue(GMLReader.OUTLINE_WIDTH,
null);
+ oldList.add(outline_width);
+ }
+
+ if (nodeView == null) return; // If no view data, simply don't
save it (instead of crashing)
+
+ x.value = new Double(nodeView.getXPosition());
+ y.value = new Double(nodeView.getYPosition());
+ w.value = new Double(nodeView.getWidth());
+ h.value = new Double(nodeView.getHeight());
+ fill.value = getColorHexString((Color)
nodeView.getUnselectedPaint());
+ outline.value = getColorHexString((Color)
nodeView.getBorderPaint());
+ outline_width.value = new Double(nodeView.getBorderWidth());
+
+ switch (nodeView.getShape()) {
+ case NodeView.RECTANGLE:
+ type.value = GMLReader.RECTANGLE;
+
+ break;
+
+ case NodeView.ELLIPSE:
+ type.value = GMLReader.ELLIPSE;
+
+ break;
+
+ case NodeView.DIAMOND:
+ type.value = GMLReader.DIAMOND;
+
+ break;
+
+ case NodeView.HEXAGON:
+ type.value = GMLReader.HEXAGON;
+
+ break;
+
+ case NodeView.OCTAGON:
+ type.value = GMLReader.OCTAGON;
+
+ break;
+
+ case NodeView.PARALELLOGRAM:
+ type.value = GMLReader.PARALELLOGRAM;
+
+ break;
+
+ case NodeView.TRIANGLE:
+ type.value = GMLReader.TRIANGLE;
+
+ break;
+ }
+ */
+ }
+
+ private void writeGraphEdgeGraphics(final CyNetwork network, final
View<CyEdge> edgeView,
+ final List<KeyValue> oldList) {
+ // TODO fix for new style view
+ /*
+ KeyValue width = null;
+ KeyValue fill = null;
+ KeyValue line = null;
+ KeyValue type = null;
+ KeyValue source_arrow = null;
+ KeyValue target_arrow = null;
+
+ for (Iterator it = oldList.iterator(); it.hasNext();) {
+ KeyValue keyVal = (KeyValue) it.next();
+
+ if (keyVal.key.equals(GMLReader.WIDTH)) {
+ width = keyVal;
+ } else if (keyVal.key.equals(GMLReader.FILL)) {
+ fill = keyVal;
+ } else if (keyVal.key.equals(GMLReader.LINE)) {
+ line = keyVal;
+ } else if (keyVal.key.equals(GMLReader.TYPE)) {
+ type = keyVal;
+ } else if (keyVal.key.equals(GMLReader.SOURCE_ARROW)) {
+ source_arrow = keyVal;
+ } else if (keyVal.key.equals(GMLReader.TARGET_ARROW)) {
+ target_arrow = keyVal;
+ }
+ }
+
+ if (width == null) {
+ width = new KeyValue(GMLReader.WIDTH, null);
+ oldList.add(width);
+ }
+
+ if (edgeView == null) return; // If no view data, simply don't
save it (instead of crashing)
+
+ width.value = new Double(edgeView.getStrokeWidth());
+
+ if (fill == null) {
+ fill = new KeyValue(GMLReader.FILL, null);
+ oldList.add(fill);
+ }
+
+ fill.value = getColorHexString((Color)
edgeView.getUnselectedPaint());
+
+ if (type == null) {
+ type = new KeyValue(GMLReader.TYPE, null);
+ oldList.add(type);
+ }
+
+ switch (edgeView.getLineType()) {
+ case EdgeView.STRAIGHT_LINES:
+ type.value = GMLReader.STRAIGHT_LINES;
+
+ break;
+
+ case EdgeView.CURVED_LINES:
+ type.value = GMLReader.CURVED_LINES;
+
+ break;
+ }
+
+ if (line == null) {
+ line = new KeyValue(GMLReader.LINE, null);
+ oldList.add(line);
+ }
+
+ Point2D[] pointsArray = edgeView.getBend().getDrawPoints();
+ Vector<KeyValue> points = new
Vector<KeyValue>(pointsArray.length);
+
+ // CTW funny thing with anchor points, need to trim off the
first and
+ // last
+ // and reverse the order x
+ for (int idx = pointsArray.length - 2; idx > 0; idx--) {
+ Vector<KeyValue> coords = new Vector<KeyValue>(2);
+ coords.add(new KeyValue(GMLReader.X, new
Double(pointsArray[idx].getX())));
+ coords.add(new KeyValue(GMLReader.Y, new
Double(pointsArray[idx].getY())));
+ points.add(new KeyValue(GMLReader.POINT, coords));
+ }
+
+ line.value = points;
+
+ if (source_arrow == null) {
+ source_arrow = new KeyValue(GMLReader.SOURCE_ARROW,
null);
+ oldList.add(source_arrow);
+ }
+
+ source_arrow.value =
Integer.valueOf(edgeView.getSourceEdgeEnd());
+
+ if (target_arrow == null) {
+ target_arrow = new KeyValue(GMLReader.TARGET_ARROW,
null);
+ oldList.add(target_arrow);
+ }
+
+ target_arrow.value =
Integer.valueOf(edgeView.getTargetEdgeEnd());
+ */
+ }
+
+ /**
+ * Get the String representation of the 6 character hexidecimal RGB
values
+ * i.e. #ff000a
+ *
+ * @param Color
+ * The color to be converted
+ */
+ private static String getColorHexString(final Color c) {
+ return ("#" // +Integer.toHexString(c.getRGB());
+ + Integer.toHexString(256 + c.getRed()).substring(1)
+ + Integer.toHexString(256 + c.getGreen()).substring(1)
+ + Integer.toHexString(256 + c.getBlue()).substring(1));
+ }
+}
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
