Author: ghuck
Date: 2010-07-28 16:26:56 -0700 (Wed, 28 Jul 2010)
New Revision: 21065
Modified:
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/LayoutLabelNodeImpl.java
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/LayoutLabelPartition.java
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/LayoutPartition.java
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/GroupAttributesLayout.java
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/bioLayout/BioLayoutAlgorithm.java
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/force/ForceDirectedLayout.java
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/graphPartition/AbstractGraphPartition.java
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/graphPartition/AttributeCircleLayout.java
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
Log:
Modified:
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/LayoutLabelNodeImpl.java
===================================================================
---
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/LayoutLabelNodeImpl.java
2010-07-28 22:29:50 UTC (rev 21064)
+++
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/LayoutLabelNodeImpl.java
2010-07-28 23:26:56 UTC (rev 21065)
@@ -85,16 +85,37 @@
lp = parser.parseStringValue(labelPosition);
// logger.info("ObjectPosition succesfully parsed!");
}
-
-// logger.info("Parent node: " + parentNodeView.getNode().getIdentifier());
-// logger.info("Offset = " + lp.getOffsetX() + ", " + lp.getOffsetY() );
- this.setX(lp.getOffsetX() + parentNodeView.getXPosition());
- this.setY(lp.getOffsetY() + parentNodeView.getYPosition());
- this.neighbors = new ArrayList<LayoutNode>();
- this.index = index;
+ try {
+ // logger.info("Parent node: " +
parentNodeView.getNode().getIdentifier());
+ // logger.info("Offset = " + lp.getOffsetX() + ", " +
lp.getOffsetY() );
+
+ this.setX(lp.getOffsetX() + parentNodeView.getXPosition());
+ this.setY(lp.getOffsetY() + parentNodeView.getYPosition());
+ this.neighbors = new ArrayList<LayoutNode>();
+ this.index = index;
- // logger.info("Created " + this.getIdentifier() + "placed in: " +
this.getX() + ", " + this.getY() );
+ // logger.info("Created " + this.getIdentifier() + "placed in: " +
this.getX() + ", " + this.getY() );
+ }
+ catch(Exception e) {
+ // Log error
+ logger.warning("Error detected while creating LayoutLabelNodeImp: "
+ e.toString() );
+
+ // Reset this attribute by eliminating it
+
+ if (nodeAtts.hasAttribute(parentNodeView.getNode().getIdentifier(),
"node.labelPosition")) {
+
nodeAtts.deleteAttribute(parentNodeView.getNode().getIdentifier(),
"node.labelPosition");
+ logger.warning("Deleted 'node.labelPosition' attribute");
+ }
+
+ lp = new ObjectPositionImpl();
+ logger.warning("Created new ObjectPosition!");
+
+ this.setX( parentNodeView.getXPosition() );
+ this.setY( parentNodeView.getYPosition() );
+ this.neighbors = new ArrayList<LayoutNode>();
+ this.index = index;
+ }
}
/**
@@ -123,7 +144,8 @@
nodeAtts.setAttribute(parentNodeView.getNode().getIdentifier(),
"node.labelPosition", lp.shortString());
- // logger.info("Label node was moved!");
+// logger.info("Label node was moved!, short string: " +
lp.shortString());
+// logger.info("full label string: " + lp.toString() );
}
}
Modified:
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/LayoutLabelPartition.java
===================================================================
---
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/LayoutLabelPartition.java
2010-07-28 22:29:50 UTC (rev 21064)
+++
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/LayoutLabelPartition.java
2010-07-28 23:26:56 UTC (rev 21065)
@@ -87,8 +87,7 @@
public LayoutLabelPartition(LayoutPartition part,
double weightCoefficient,
boolean moveNodes,
- boolean selectedOnly,
- boolean isWeighted) {
+ boolean selectedOnly) {
super(part.size(), part.getEdgeList().size());
@@ -197,32 +196,28 @@
Double weight = null;
// -- First set labelEdges weights --
- if (this.isWeighted) {
- // Calculate maximum preexisting weight
- Double maxWeight = new Double(Double.MIN_VALUE);
- ListIterator<LayoutEdge>iter = edgeList.listIterator();
+ // Calculate maximum preexisting weight
+ Double maxWeight = new Double(Double.MIN_VALUE);
- while (iter.hasNext()) {
- LayoutEdge edge = iter.next();
-
- // Only consider non label edges
- if (labelToParentMap.keySet().contains(edge.getSource()) ||
- labelToParentMap.keySet().contains(edge.getTarget()) ) {
- continue;
- }
+ ListIterator<LayoutEdge>iter = edgeList.listIterator();
- if ( edge.getWeight() > maxWeight ) {
- maxWeight = edge.getWeight();
- }
+ while (iter.hasNext()) {
+ LayoutEdge edge = iter.next();
+
+ // Only consider non label edges
+ if (labelToParentMap.keySet().contains(edge.getSource()) ||
+ labelToParentMap.keySet().contains(edge.getTarget()) ) {
+ continue;
}
- // Value which will be used as weight for all label edges
- weight = maxWeight * weightCoefficient;
- }
- else { // if (!this.isWeighted)
- weight = weightCoefficient;
+ if ( edge.getWeight() > maxWeight ) {
+ maxWeight = edge.getWeight();
+ }
}
+
+ // Value which will be used as weight for all label edges
+ weight = maxWeight * weightCoefficient;
// Set all labelEdge weights
ListIterator<LayoutEdge>iter2 = edgeList.listIterator();
@@ -234,11 +229,7 @@
labelToParentMap.keySet().contains(edge.getTarget()) ) {
// set label edges weights
edge.setWeight(weight);
- } else{ // non label edge (normal one)
- if (!this.isWeighted){
- edge.setWeight(1.0);
- }
- }
+ }
}
Modified:
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/LayoutPartition.java
===================================================================
---
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/LayoutPartition.java
2010-07-28 22:29:50 UTC (rev 21064)
+++
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/LayoutPartition.java
2010-07-28 23:26:56 UTC (rev 21065)
@@ -313,7 +313,7 @@
iter.remove();
//logger.debug("Edge "+edge.getEdge().getIdentifier()+" now has
weight "+edge.getWeight());
- logger.info( edge.toString() + " now has weight "+edge.getWeight());
+ // logger.info( edge.toString() + " now has weight
"+edge.getWeight());
}
}
Modified:
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/GroupAttributesLayout.java
===================================================================
---
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/GroupAttributesLayout.java
2010-07-28 22:29:50 UTC (rev 21064)
+++
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/GroupAttributesLayout.java
2010-07-28 23:26:56 UTC (rev 21065)
@@ -286,7 +286,7 @@
/**
* DOCUMENT ME!
*/
- public void layoutPartion(LayoutPartition partition) {
+ public void layoutPartition(LayoutPartition partition) {
if (canceled) return;
taskMonitor.setStatus("Initializing");
Modified:
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/bioLayout/BioLayoutAlgorithm.java
===================================================================
---
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/bioLayout/BioLayoutAlgorithm.java
2010-07-28 22:29:50 UTC (rev 21064)
+++
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/bioLayout/BioLayoutAlgorithm.java
2010-07-28 23:26:56 UTC (rev 21065)
@@ -313,7 +313,7 @@
/**
* Main function that must be implemented by the child class.
*/
- public abstract void layoutPartion(LayoutPartition partition);
+ public abstract void layoutPartition(LayoutPartition partition);
protected void initialize_local() {
}
Modified:
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
===================================================================
---
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
2010-07-28 22:29:50 UTC (rev 21064)
+++
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
2010-07-28 23:26:56 UTC (rev 21065)
@@ -509,7 +509,7 @@
/**
* Perform a layout
*/
- public void layoutPartion(LayoutPartition partition) {
+ public void layoutPartition(LayoutPartition partition) {
this.partition = partition;
Dimension initialLocation = null;
Modified:
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
===================================================================
---
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
2010-07-28 22:29:50 UTC (rev 21064)
+++
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
2010-07-28 23:26:56 UTC (rev 21065)
@@ -432,7 +432,7 @@
/**
* Perform a layout
*/
- public void layoutPartion(LayoutPartition partition) {
+ public void layoutPartition(LayoutPartition partition) {
Iterator iter = null;
Dimension initialLocation = null;
this.partition = partition;
Modified:
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
===================================================================
---
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
2010-07-28 22:29:50 UTC (rev 21064)
+++
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
2010-07-28 23:26:56 UTC (rev 21065)
@@ -132,7 +132,7 @@
*
* @param partition DOCUMENT ME!
*/
- public void layoutPartion(LayoutPartition partition) {
+ public void layoutPartition(LayoutPartition partition) {
if (canceled)
return;
Modified:
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/force/ForceDirectedLayout.java
===================================================================
---
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/force/ForceDirectedLayout.java
2010-07-28 22:29:50 UTC (rev 21064)
+++
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/force/ForceDirectedLayout.java
2010-07-28 23:26:56 UTC (rev 21065)
@@ -121,12 +121,12 @@
}
- public void layoutPartion(LayoutPartition part) {
+ public void layoutPartition(LayoutPartition part) {
Dimension initialLocation = null;
- // logger.debug("layoutPartion: "+part.getEdgeList().size()+"
edges");
+ // logger.debug("layoutPartition: "+part.getEdgeList().size()+"
edges");
// Calculate our edge weights
part.calculateEdgeWeights();
- // logger.debug("layoutPartion: "+part.getEdgeList().size()+"
edges after calculateEdgeWeights");
+ // logger.debug("layoutPartition: "+part.getEdgeList().size()+"
edges after calculateEdgeWeights");
m_fsim.clear();
Modified:
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/graphPartition/AbstractGraphPartition.java
===================================================================
---
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/graphPartition/AbstractGraphPartition.java
2010-07-28 22:29:50 UTC (rev 21064)
+++
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/graphPartition/AbstractGraphPartition.java
2010-07-28 23:26:56 UTC (rev 21065)
@@ -6,7 +6,9 @@
import cern.colt.map.*;
import csplugins.layout.LayoutNode;
+import csplugins.layout.LayoutLabelNodeImpl;
import csplugins.layout.LayoutPartition;
+import csplugins.layout.LayoutLabelPartition;
import csplugins.layout.EdgeWeighter;
import cytoscape.CyNetwork;
@@ -14,6 +16,11 @@
import cytoscape.CyNode;
import cytoscape.layout.AbstractLayout;
+import cytoscape.layout.LayoutProperties;
+import cytoscape.layout.Tunable;
+
+import cytoscape.data.CyAttributes;
+
import cytoscape.logger.CyLogger;
import cytoscape.task.*;
@@ -28,203 +35,414 @@
import javax.swing.JOptionPane;
+import java.awt.Dimension;
+
/**
* An abstract class that handles the partitioning of graphs so that
* the partitions will be laid out individually.
*/
public abstract class AbstractGraphPartition extends AbstractLayout {
- double incr = 100;
- protected List <LayoutPartition> partitionList = null;
- protected EdgeWeighter edgeWeighter = null;
- protected boolean singlePartition = false;
- protected CyLogger logger = null;
+ double incr = 100;
+ protected List <LayoutPartition> partitionList = null;
+ protected EdgeWeighter edgeWeighter = null;
+ protected boolean singlePartition = false;
+ protected CyLogger logger = null;
- // Information for taskMonitor
- double current_start = 0; // Starting node number
- double current_size = 0; // Partition size
- double total_nodes = 0; // Total number of nodes
+ /**
+ * Whether Labels should be repositioned in their default positions
+ */
+ protected boolean resetPosition = false;
+
+ /**
+ * Whether network nodes will be moved or not
+ */
+ protected boolean moveNodes = false;
- /**
- * Creates a new AbstractGraphPartition object.
- */
- public AbstractGraphPartition() {
- super();
- }
+ /**
+ * Coefficient to determine label edge weights
+ */
+ protected double weightCoefficient = 10.0;
- /**
- * Override this method and layout the LayoutPartion just
- * like you would a NetworkView.
- *
- * @param partition The LayoutPartion to be laid out.
- */
- public abstract void layoutPartion(LayoutPartition partition);
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean supportsSelectedOnly() {
- return true;
- }
- /**
- * Sets the singlePartition flag, which disables partitioning. This
- * can be used by users who do not want to partition their graph for
- * some reason.
- *
- * @param flag if false, no paritioning will be done
- */
- public void setPartition(boolean flag) {
- if (flag)
- this.singlePartition = false;
- else
- this.singlePartition = true;
+ // Information for taskMonitor
+ double current_start = 0; // Starting node number
+ double current_size = 0; // Partition size
+ double total_nodes = 0; // Total number of nodes
+
+ /**
+ * Creates a new AbstractGraphPartition object.
+ */
+ public AbstractGraphPartition() {
+ super();
+ }
+
+ /**
+ * Override this method and layout the LayoutPartion just
+ * like you would a NetworkView.
+ *
+ * @param partition The LayoutPartion to be laid out.
+ */
+ public abstract void layoutPartition(LayoutPartition partition);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean supportsSelectedOnly() {
+ return true;
+ }
+
+ /**
+ * If overridden by a subclass to return true, before calling to
+ * layoutPartition mathod, fake nodes will be created to represent label
+ * positions, and labels will be placed acordingly.
+ *
+ * It is an easy way of creating label layout algorithms.
+ *
+ * For this to work fine with labels, weights should be supported.
+ *
+ * @return Whether the layout algorithm supports label layout.
+ */
+ public boolean supportsLabelLayout() {
+ return false;
+ }
+
+
+ /**
+ * Sets the singlePartition flag, which disables partitioning. This
+ * can be used by users who do not want to partition their graph for
+ * some reason.
+ *
+ * @param flag if false, no paritioning will be done
+ */
+ public void setPartition(boolean flag) {
+ if (flag)
+ this.singlePartition = false;
+ else
+ this.singlePartition = true;
+ }
+
+ /**
+ * Sets the singlePartition flag, which disables partitioning. This
+ * can be used by users who do not want to partition their graph for
+ * some reason.
+ *
+ * @param value if "false", no paritioning will be done
+ */
+ public void setPartition(String value) {
+ Boolean val = new Boolean(value);
+ setPartition(val.booleanValue());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param percent The percentage of completion for this partition
+ */
+ protected void setTaskStatus(int percent) {
+ if (taskMonitor != null) {
+ // Calculate the nodes done for this partition
+ double nodesDone = current_size*(double)percent/100.;
+ // Calculate the percent done overall
+ double pDone = ((nodesDone+current_start)/total_nodes)*100.;
+ taskMonitor.setPercentCompleted((int)pDone);
+ taskMonitor.setStatus("Completed " + (int)pDone + "%");
}
+ }
- /**
- * Sets the singlePartition flag, which disables partitioning. This
- * can be used by users who do not want to partition their graph for
- * some reason.
- *
- * @param value if "false", no paritioning will be done
- */
- public void setPartition(String value) {
- Boolean val = new Boolean(value);
- setPartition(val.booleanValue());
+ /**
+ * AbstractGraphPartitionLayout implements the construct method
+ * and calls layoutPartition for each partition.
+ */
+ public void construct() {
+ initialize();
+
+ // Reset label positions if necessary
+ if (resetPosition) {
+ resetLabelPositions();
+ return;
}
- /**
- * DOCUMENT ME!
- *
- * @param percent The percentage of completion for this partition
- */
- protected void setTaskStatus(int percent) {
- if (taskMonitor != null) {
- // Calculate the nodes done for this partition
- double nodesDone = current_size*(double)percent/100.;
- // Calculate the percent done overall
- double pDone =
((nodesDone+current_start)/total_nodes)*100.;
- taskMonitor.setPercentCompleted((int)pDone);
- taskMonitor.setStatus("Completed " + (int)pDone + "%");
+ if (edgeWeighter != null)
+ edgeWeighter.reset();
+
+ // Depending on whether we are partitioned or not,
+ // we use different initialization. Note that if the user only wants
+ // to lay out selected nodes, partitioning becomes a very bad idea!
+ if (selectedOnly || singlePartition) {
+ // We still use the partition abstraction, even if we're
+ // not partitioning. This makes the code further down
+ // much cleaner
+ LayoutPartition partition = new LayoutPartition(network,
networkView, selectedOnly, edgeWeighter);
+ partitionList = new ArrayList(1);
+ partitionList.add(partition);
+ } else if (staticNodes != null && staticNodes.size() > 0) {
+ // Someone has programmatically locked a set of nodes -- construct
+ // the list of unlocked nodes
+ List<CyNode> unlockedNodes = new ArrayList();
+ for (CyNode node: (List<CyNode>)network.nodesList()) {
+ if
(!isLocked(networkView.getNodeView(node.getRootGraphIndex()))) {
+ unlockedNodes.add(node);
}
+ }
+ LayoutPartition partition = new LayoutPartition(network,
networkView, unlockedNodes, edgeWeighter);
+ partitionList = new ArrayList(1);
+ partitionList.add(partition);
+ } else {
+ partitionList = LayoutPartition.partition(network, networkView,
false, edgeWeighter);
}
- /**
- * AbstractGraphPartitionLayout implements the constuct method
- * and calls layoutPartion for each partition.
- */
- public void construct() {
- initialize();
+ total_nodes = network.getNodeCount();
+ current_start = 0;
- if (edgeWeighter != null)
- edgeWeighter.reset();
+ // Set up offsets -- we start with the overall min and max
+ double xStart = (partitionList.get(0)).getMinX();
+ double yStart = (partitionList.get(0)).getMinY();
- // Depending on whether we are partitioned or not,
- // we use different initialization. Note that if the user only
wants
- // to lay out selected nodes, partitioning becomes a very bad
idea!
- if (selectedOnly || singlePartition) {
- // We still use the partition abstraction, even if we're
- // not partitioning. This makes the code further down
- // much cleaner
- LayoutPartition partition = new
LayoutPartition(network, networkView, selectedOnly, edgeWeighter);
- partitionList = new ArrayList(1);
- partitionList.add(partition);
- } else if (staticNodes != null && staticNodes.size() > 0) {
- // Someone has programmatically locked a set of nodes
-- construct
- // the list of unlocked nodes
- List<CyNode> unlockedNodes = new ArrayList();
- for (CyNode node: (List<CyNode>)network.nodesList()) {
- if
(!isLocked(networkView.getNodeView(node.getRootGraphIndex()))) {
- unlockedNodes.add(node);
- }
- }
- LayoutPartition partition = new
LayoutPartition(network, networkView, unlockedNodes, edgeWeighter);
- partitionList = new ArrayList(1);
- partitionList.add(partition);
- } else {
- partitionList = LayoutPartition.partition(network,
networkView, false, edgeWeighter);
+ for (LayoutPartition part: partitionList) {
+ xStart = Math.min(xStart, part.getMinX());
+ yStart = Math.min(yStart, part.getMinY());
+ }
+
+ double next_x_start = xStart;
+ double next_y_start = yStart;
+ double current_max_y = 0;
+
+ double max_dimensions = Math.sqrt((double) network.getNodeCount());
+ // give each node room
+ max_dimensions *= incr;
+ max_dimensions += xStart;
+
+ for (LayoutPartition partition: partitionList) {
+ if (canceled) break;
+ // get the partition
+ current_size = (double)partition.size();
+ // logger.debug("Partition #"+partition.getPartitionNumber()+" has
"+current_size+" nodes");
+ setTaskStatus(1);
+
+ // Partitions Requiring Layout
+ if (partition.nodeCount() > 1) { // TODO: add case when nodeCount =
1
+ try {
+ layoutSinglePartition(partition);
+ } catch (OutOfMemoryError _e) {
+ System.gc();
+ logger.error("Layout algorithm failed: Out of memory");
+ return;
+ } catch (Exception _e) {
+ logger.error("Layout algorithm failed: ", (Throwable)_e);
+ return;
}
- total_nodes = network.getNodeCount();
- current_start = 0;
+ if (!selectedOnly && !singlePartition) {
+ // logger.debug("Offsetting partition
#"+partition.getPartitionNumber()+" to "+next_x_start+", "+next_y_start);
+ // OFFSET
+ partition.offset(next_x_start, next_y_start);
+ }
- // Set up offsets -- we start with the overall min and max
- double xStart = (partitionList.get(0)).getMinX();
- double yStart = (partitionList.get(0)).getMinY();
+ // single nodes
+ } else if ( partition.nodeCount() == 1 ) {
+ // Reset our bounds
+ partition.resetNodes();
- for (LayoutPartition part: partitionList) {
- xStart = Math.min(xStart, part.getMinX());
- yStart = Math.min(yStart, part.getMinY());
+ // Single node -- get it
+ LayoutNode node = (LayoutNode) partition.getNodeList().get(0);
+ node.setLocation(next_x_start, next_y_start);
+ partition.moveNodeToLocation(node);
+ } else {
+ continue;
+ }
+
+ double last_max_x = partition.getMaxX();
+ double last_max_y = partition.getMaxY();
+
+ if (last_max_y > current_max_y) {
+ current_max_y = last_max_y;
+ }
+
+ if (last_max_x > max_dimensions) {
+ next_x_start = xStart;
+ next_y_start = current_max_y;
+ next_y_start += incr;
+ } else {
+ next_x_start = last_max_x;
+ next_x_start += incr;
+ }
+
+ setTaskStatus( 100 );
+ current_start += current_size;
+ }
+ }
+
+
+ /**
+ *
+ */
+ protected void layoutSinglePartition(LayoutPartition partition){
+
+ if(supportsLabelLayout()) {
+
+ Dimension initialLocation = null;
+
+ if (canceled)
+ return;
+
+ // Create new Label partition
+ LayoutLabelPartition newPartition = new
LayoutLabelPartition(partition,
+
weightCoefficient,
+
moveNodes,
+
selectedOnly);
+
+ // logger.info("New partition succesfully created!");
+
+ // Figure out our starting point - This will be used when:
+ // 1- Laying out labels off all nodes
+ // - and-
+ // 2- (normal) Nodes are not allowed to move
+ if (selectedOnly && moveNodes) {
+ newPartition.recalculateStatistics();
+ initialLocation = newPartition.getAverageLocation();
+ }
+
+ if (canceled)
+ return;
+
+ // Layout the new partition using the parent class layout algorithm
+ layoutPartition(newPartition);
+
+ if (canceled)
+ return;
+
+ // Not quite done, yet. We may need to migrate labels back to their
starting position
+ // This will be necessary if:
+ // 1- Laying out only selected nodes
+ // - and -
+ // 2- (normal) Nodes are allowed to move
+
+ taskMonitor.setStatus("Making final arrangements to partition...");
+
+ if (selectedOnly && moveNodes) {
+ // logger.info("moving back labels (and possibly nodes) to
their location");
+
+ newPartition.recalculateStatistics();
+ Dimension finalLocation = newPartition.getAverageLocation();
+ double xDelta = 0.0;
+ double yDelta = 0.0;
+
+ xDelta = finalLocation.getWidth() - initialLocation.getWidth();
+ yDelta = finalLocation.getHeight() -
initialLocation.getHeight();
+
+ for (LayoutNode v: newPartition.getNodeList()) {
+ if (!v.isLocked()) {
+ v.decrement(xDelta, yDelta);
+ newPartition.moveNodeToLocation(v);
+ }
}
+ }
- double next_x_start = xStart;
- double next_y_start = yStart;
- double current_max_y = 0;
- double max_dimensions = Math.sqrt((double)
network.getNodeCount());
- // give each node room
- max_dimensions *= incr;
- max_dimensions += xStart;
+ // make sure nodes are where they should be
+ for(LayoutNode node: newPartition.getLabelToParentMap().values() ) {
- for (LayoutPartition partition: partitionList) {
- if (canceled) break;
- // get the partition
- current_size = (double)partition.size();
- // logger.debug("Partition
#"+partition.getPartitionNumber()+" has "+current_size+" nodes");
- setTaskStatus(1);
+ if (canceled)
+ return;
- // Partitions Requiring Layout
- if (partition.nodeCount() > 1) {
- try {
- layoutPartion(partition);
- } catch (OutOfMemoryError _e) {
- System.gc();
- logger.error("Layout algorithm failed:
Out of memory");
- return;
- } catch (Exception _e) {
- logger.error("Layout algorithm failed:
", (Throwable)_e);
- return;
- }
+ node.moveToLocation();
+ logger.info( node.toString() );
+ }
- if (!selectedOnly && !singlePartition) {
- // logger.debug("Offsetting partition
#"+partition.getPartitionNumber()+" to "+next_x_start+", "+next_y_start);
- // OFFSET
- partition.offset(next_x_start,
next_y_start);
- }
+ // make sure that all labels are where they should be
+ for(LayoutLabelNodeImpl node: newPartition.getLabelNodes() ) {
- // single nodes
- } else if ( partition.nodeCount() == 1 ) {
- // Reset our bounds
- partition.resetNodes();
+ if (canceled)
+ return;
- // Single node -- get it
- LayoutNode node = (LayoutNode)
partition.getNodeList().get(0);
- node.setLocation(next_x_start, next_y_start);
- partition.moveNodeToLocation(node);
- } else {
- continue;
- }
+ node.moveToLocation();
+ logger.info( node.toString() );
+ }
- double last_max_x = partition.getMaxX();
- double last_max_y = partition.getMaxY();
+ taskMonitor.setStatus("Updating Display...");
- if (last_max_y > current_max_y) {
- current_max_y = last_max_y;
- }
+ // redraw the network so that the new label positions are visible
+ networkView.updateView();
+ networkView.redrawGraph(true, true);
- if (last_max_x > max_dimensions) {
- next_x_start = xStart;
- next_y_start = current_max_y;
- next_y_start += incr;
- } else {
- next_x_start = last_max_x;
- next_x_start += incr;
- }
- setTaskStatus( 100 );
- current_start += current_size;
- }
+
+ } else {
+ layoutPartition(partition);
}
+
+ }
+
+ /**
+ * Adds the necessary tunables to control the label layout.
+ */
+ public void getLabelTunables(LayoutProperties layoutProperties) {
+
+ layoutProperties.add(new Tunable("labels_settings",
+ "Label specific settings",
+ Tunable.GROUP, new Integer(3)));
+
+ layoutProperties.add(new Tunable("resetPosition",
+ "Reset label positions",
+ Tunable.BOOLEAN, new
Boolean(resetPosition)));
+
+ layoutProperties.add(new Tunable("moveNodes",
+ "Allow nodes to move",
+ Tunable.BOOLEAN, new
Boolean(moveNodes)));
+
+ layoutProperties.add(new Tunable("weightCoefficient",
+ "weightCoefficient",
+ Tunable.DOUBLE, new
Double(weightCoefficient)));
+ }
+
+ /**
+ * Update our tunable settings
+ *
+ * @param layoutProperties the LayoutProperties handler for this layout
+ * @param force whether or not to force the update
+ */
+ public void updateSettings(LayoutProperties layoutProperties, boolean
force) {
+
+ Tunable t = layoutProperties.get("resetPosition");
+ if ((t != null) && (t.valueChanged() || force))
+ resetPosition = ((Boolean) t.getValue()).booleanValue();
+
+ t = layoutProperties.get("moveNodes");
+ if ((t != null) && (t.valueChanged() || force))
+ moveNodes = ((Boolean) t.getValue()).booleanValue();
+
+ t = layoutProperties.get("weightCoefficient");
+ if ((t != null) && (t.valueChanged() || force))
+ weightCoefficient = ((Double) t.getValue()).doubleValue();
+ }
+
+
+ /**
+ * Moves labels to the same position in which their parent nodes are
+ */
+ protected void resetLabelPositions() {
+
+ logger.info("Reseting labels position");
+
+ CyAttributes nodeAtts = Cytoscape.getNodeAttributes();
+
+ // Go through all nodes deleting the label position attribute
+ for (CyNode node: (List<CyNode>)network.nodesList()) {
+ if (!selectedOnly ||
!isLocked(networkView.getNodeView(node.getRootGraphIndex()))) {
+ if (nodeAtts.hasAttribute(node.getIdentifier(),
"node.labelPosition")) {
+ nodeAtts.deleteAttribute(node.getIdentifier(),
"node.labelPosition");
+ }
+ }
+ }
+
+ // redraw the network so that the new label positions are visible
+ networkView.updateView();
+ networkView.redrawGraph(true, true);
+ }
+
+
}
Modified:
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/graphPartition/AttributeCircleLayout.java
===================================================================
---
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/graphPartition/AttributeCircleLayout.java
2010-07-28 22:29:50 UTC (rev 21064)
+++
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/graphPartition/AttributeCircleLayout.java
2010-07-28 23:26:56 UTC (rev 21065)
@@ -242,7 +242,7 @@
*
* @param partition DOCUMENT ME!
*/
- public void layoutPartion(LayoutPartition partition) {
+ public void layoutPartition(LayoutPartition partition) {
data = Cytoscape.getNodeAttributes();
// just add the unlocked nodes
Modified:
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
===================================================================
---
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
2010-07-28 22:29:50 UTC (rev 21064)
+++
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
2010-07-28 23:26:56 UTC (rev 21065)
@@ -57,7 +57,7 @@
*
* @param partition DOCUMENT ME!
*/
- public void layoutPartion(LayoutPartition partition) {
+ public void layoutPartition(LayoutPartition partition) {
// just add the unlocked nodes
List<LayoutNode> nodes = new ArrayList<LayoutNode>();
Modified:
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
===================================================================
---
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
2010-07-28 22:29:50 UTC (rev 21064)
+++
coreplugins/branches/labelLayout/AutomaticLayout/src/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
2010-07-28 23:26:56 UTC (rev 21065)
@@ -218,7 +218,7 @@
*
* @param partition DOCUMENT ME!
*/
- public void layoutPartion(LayoutPartition partition) {
+ public void layoutPartition(LayoutPartition partition) {
this.partition = partition;
int nodeCount = partition.nodeCount();
--
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.
