Author: clopes
Date: 2012-11-07 12:59:13 -0800 (Wed, 07 Nov 2012)
New Revision: 30755
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEAboutAction.java
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEVisualStyleAction.java
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODEAlgorithm.java
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODECluster.java
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/util/MCODEUtil.java
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODEAboutDialog.java
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODELoader.java
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODEResultsPanel.java
csplugins/trunk/toronto/clopes/mcode/src/test/java/org/cytoscape/mcode/internal/model/MCODEAlgorithmTest.java
Log:
Fixed a bug that could cause an infinite loop when changing the size threshold
of an MCODE cluster.
Some minor refactoring.
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEAboutAction.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEAboutAction.java
2012-11-07 20:10:08 UTC (rev 30754)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEAboutAction.java
2012-11-07 20:59:13 UTC (rev 30755)
@@ -55,6 +55,7 @@
private final OpenBrowser openBrowser;
private final MCODEUtil mcodeUtil;
+ private MCODEAboutDialog aboutDialog;
public MCODEAboutAction(final String name,
final
CyApplicationManager applicationManager,
@@ -71,7 +72,17 @@
@Override
public void actionPerformed(ActionEvent e) {
//display about box
- MCODEAboutDialog aboutDialog = new
MCODEAboutDialog(swingApplication, openBrowser, mcodeUtil);
- aboutDialog.setVisible(true);
+ synchronized (this) {
+ if (aboutDialog == null) {
+ aboutDialog = new
MCODEAboutDialog(swingApplication, openBrowser, mcodeUtil);
+ }
+
+ if (!aboutDialog.isVisible()) {
+ aboutDialog.setLocationRelativeTo(null);
+ aboutDialog.setVisible(true);
+ }
+ }
+
+ aboutDialog.toFront();
}
}
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEVisualStyleAction.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEVisualStyleAction.java
2012-11-07 20:10:08 UTC (rev 30754)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEVisualStyleAction.java
2012-11-07 20:59:13 UTC (rev 30755)
@@ -97,13 +97,14 @@
double maxScore =
resultsPanel.setNodeAttributesAndGetMaxScore();
// We also need the selected row if one is selected at
all
resultsPanel.selectCluster(null);
- int selectedRow =
resultsPanel.getClusterBrowserTable().getSelectedRow();
- resultsPanel.getClusterBrowserTable().clearSelection();
-
- if (selectedRow >= 0) {
-
resultsPanel.getClusterBrowserTable().setRowSelectionInterval(selectedRow,
selectedRow);
- }
-
+// TODO: delete/fix
+// int selectedRow = resultsPanel.getSelectedRow();
+// resultsPanel.getClusterBrowserTable().clearSelection();
+//
+// if (selectedRow >= 0) {
+//
resultsPanel.getClusterBrowserTable().setRowSelectionInterval(selectedRow,
selectedRow);
+// }
+
// Get the updated app's style
VisualStyle appStyle = mcodeUtil.getAppStyle(maxScore);
// Register the app's style but don't make it active by
default
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODEAlgorithm.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODEAlgorithm.java
2012-11-07 20:10:08 UTC (rev 30754)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODEAlgorithm.java
2012-11-07 20:59:13 UTC (rev 30755)
@@ -335,7 +335,7 @@
currentNode = alNodesWithSameScore.get(j);
if (!nodeSeenHashMap.containsKey(currentNode)) {
- // We store the current node seen hash
map for later exploration purposes
+ // Store the list of all the nodes that
have already been seen and incorporated in other clusters
Map<Long, Boolean>
nodeSeenHashMapSnapShot = new HashMap<Long, Boolean>(nodeSeenHashMap);
// Here we use the original node score
cutoff
@@ -361,15 +361,11 @@
fluffClusterBoundary(alCluster, nodeSeenHashMap, nodeInfoHashMap);
clusterNet =
createClusterNetwork(alCluster, inputNetwork);
+ final double score =
scoreCluster(clusterNet);
- MCODECluster
currentCluster = new MCODECluster();
-
currentCluster.setALCluster(alCluster);
-
currentCluster.setSeedNode(currentNode);//store the current node as the seed
node
-
currentCluster.setNetwork(clusterNet);
-
currentCluster.setClusterScore(scoreCluster(currentCluster));
-
currentCluster.setNodeSeenHashMap(nodeSeenHashMapSnapShot);//store the list of
all the nodes that have already been seen and incorporated in other clusters
-
currentCluster.setResultId(resultId);
- //store detected
cluster for later
+ MCODECluster
currentCluster = new MCODECluster(resultId, currentNode, clusterNet, score,
+
alCluster, nodeSeenHashMapSnapShot);
+
alClusters.add(currentCluster);
}
}
@@ -446,22 +442,21 @@
final int resultId) {
// This method is similar to the finding method with the
exception of the filtering so that the decrease of the cluster size
// can produce a single node, also the use of the node seen
hash map is differentially applied...
- Map<Long, NodeInfo> nodeInfoHashMap =
nodeInfoResultsMap.get(resultId);
- MCODEParameterSet params =
mcodeUtil.getCurrentParameters().getResultParams(cluster.getResultId());
+ final Map<Long, NodeInfo> nodeInfoHashMap =
nodeInfoResultsMap.get(resultId);
+ final MCODEParameterSet params =
mcodeUtil.getCurrentParameters().getResultParams(cluster.getResultId());
final Map<Long, Boolean> nodeSeenHashMap;
// If the size slider is below the set node score cutoff we use
the node seen hash map so that clusters
// with higher scoring seeds have priority, however when the
slider moves higher than the node score cutoff
// we allow the cluster to accrue nodes from all around without
the priority restriction
- if (nodeScoreCutoff <= params.getNodeScoreCutoff()) {
+ if (nodeScoreCutoff <= params.getNodeScoreCutoff())
nodeSeenHashMap = new HashMap<Long,
Boolean>(cluster.getNodeSeenHashMap());
- } else {
+ else
nodeSeenHashMap = new HashMap<Long, Boolean>();
- }
- Long seedNode = cluster.getSeedNode();
+ final Long seedNode = cluster.getSeedNode();
- List<Long> alCluster = getClusterCore(seedNode,
nodeSeenHashMap, nodeScoreCutoff, params
+ final List<Long> alCluster = getClusterCore(seedNode,
nodeSeenHashMap, nodeScoreCutoff, params
.getMaxDepthFromStart(), nodeInfoHashMap);
// Make sure seed node is part of cluster, if not already in
there
@@ -478,12 +473,13 @@
fluffClusterBoundary(alCluster, nodeSeenHashMap,
nodeInfoHashMap);
clusterNet = createClusterNetwork(alCluster, inputNet);
+ final double score = scoreCluster(clusterNet);
- cluster.setNetwork(clusterNet);
- cluster.setALCluster(alCluster);
- cluster.setClusterScore(scoreCluster(cluster));
+ final MCODECluster newCluster = new MCODECluster(resultId,
seedNode, clusterNet, score, alCluster,
+ nodeSeenHashMap);
+ newCluster.setRank(cluster.getRank());
- return cluster;
+ return newCluster;
}
private CySubNetwork createClusterNetwork(final List<Long> alCluster,
final CyNetwork inputNet) {
@@ -521,15 +517,15 @@
* Score a cluster. Currently this ranks larger, denser clusters
higher, although
* in the future other scoring functions could be created
*
- * @param cluster
+ * @param clusterNet
* @return The score of the cluster
*/
- public double scoreCluster(MCODECluster cluster) {
+ public double scoreCluster(final CySubNetwork clusterNet) {
int numNodes = 0;
double density = 0.0, score = 0.0;
- numNodes = cluster.getNetwork().getNodeCount();
- density = calcDensity(cluster.getNetwork(),
params.isIncludeLoops());
+ numNodes = clusterNet.getNodeCount();
+ density = calcDensity(clusterNet, params.isIncludeLoops());
score = density * numNodes;
return score;
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODECluster.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODECluster.java
2012-11-07 20:10:08 UTC (rev 30754)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/model/MCODECluster.java
2012-11-07 20:59:13 UTC (rev 30755)
@@ -52,104 +52,110 @@
private CySubNetwork network;
private Long seedNode;
private Map<Long, Boolean> nodeSeenHashMap; // stores the nodes that
have already been included in higher ranking clusters
- private double clusterScore;
- private String clusterName; // pretty much unused so far, but could
store name by user's input
+ private double score;
+ private String name; // pretty much unused so far, but could store name
by user's input
private int rank;
private int resultId;
+ private boolean disposed;
- public MCODECluster() {
+ public MCODECluster(final int resultId,
+ final Long seedNode,
+ final CySubNetwork network,
+ final double score,
+ final List<Long> alCluster,
+ final Map<Long, Boolean>
nodeSeenHashMap) {
+ assert seedNode != null;
+ assert network != null;
+ assert alCluster != null;
+ assert nodeSeenHashMap != null;
+
+ this.resultId = resultId;
+ this.seedNode = seedNode;
+ this.network = network;
+ this.score = score;
+ this.alCluster = alCluster;
+ this.nodeSeenHashMap = nodeSeenHashMap;
}
public int getResultId() {
return resultId;
}
- public void setResultId(int resultId) {
- this.resultId = resultId;
+ public String getName() {
+ return name;
}
- public String getClusterName() {
- return clusterName;
+ public void setName(final String name) {
+ throwExceptionIfDisposed();
+ this.name = name;
}
- public void setClusterName(final String clusterName) {
- this.clusterName = clusterName;
- }
-
- public CyNetworkView getView() {
+ public synchronized CyNetworkView getView() {
return view;
}
- public void setView(final CyNetworkView view) {
+ public synchronized void setView(final CyNetworkView view) {
+ throwExceptionIfDisposed();
+
if (this.view != null)
this.view.dispose();
this.view = view;
}
- public CySubNetwork getNetwork() {
+ public synchronized CySubNetwork getNetwork() {
return network;
}
- public void setNetwork(final CySubNetwork network) {
- if (view != null && view.getModel().equals(this.network))
- view.dispose();
-
- dispose(this.network);
- this.network = network;
+ public double getScore() {
+ return score;
}
- public double getClusterScore() {
- return clusterScore;
- }
-
- public void setClusterScore(final double clusterScore) {
- this.clusterScore = clusterScore;
- }
-
public List<Long> getALCluster() {
return alCluster;
}
- public void setALCluster(final List<Long> alCluster) {
- this.alCluster = alCluster;
- }
-
public Long getSeedNode() {
return seedNode;
}
- public void setSeedNode(Long seedNode) {
- this.seedNode = seedNode;
- }
-
public Map<Long, Boolean> getNodeSeenHashMap() {
return nodeSeenHashMap;
}
- public void setNodeSeenHashMap(Map<Long, Boolean> nodeSeenHashMap) {
- this.nodeSeenHashMap = nodeSeenHashMap;
- }
-
public int getRank() {
return rank;
}
public void setRank(int rank) {
this.rank = rank;
- this.clusterName = "Cluster " + (rank + 1);
+ this.name = "Cluster " + (rank + 1);
}
- public void dispose() {
+ public synchronized boolean isDisposed() {
+ return disposed;
+ }
+
+ public synchronized void dispose() {
+ if (isDisposed()) return;
+
if (view != null)
view.dispose();
- dispose(network);
+
+ network.getRootNetwork().removeSubNetwork(network);
+ network.dispose();
+
+ disposed = true;
}
-
- private static void dispose(final CySubNetwork net) {
- if (net != null) {
- net.getRootNetwork().removeSubNetwork(net);
- net.dispose();
- }
+
+ @Override
+ public String toString() {
+ return "MCODECluster [clusterName=" + name + ", clusterScore="
+ score +
+ ", rank=" + rank + ", resultId=" + resultId +
", disposed=" + disposed + "]";
}
+
+ private void throwExceptionIfDisposed() {
+ if (isDisposed())
+ throw new RuntimeException("MCODECluster has been
disposed and cannot be used anymore: ");
+ }
}
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/util/MCODEUtil.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/util/MCODEUtil.java
2012-11-07 20:10:08 UTC (rev 30754)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/util/MCODEUtil.java
2012-11-07 20:59:13 UTC (rev 30755)
@@ -333,6 +333,8 @@
SpringEmbeddedLayouter layouter,
boolean
layoutNecessary,
final
MCODELoader loader) {
+ final CyNetwork net = cluster.getNetwork();
+
// Progress reporters.
// There are three basic tasks, the progress of each is
calculated and then combined
// using the respective weighting to get an overall progress
global progress
@@ -349,14 +351,14 @@
double progress = 0;
final VisualStyle vs = getClusterStyle();
- final CyNetworkView clusterView =
createNetworkView(cluster.getNetwork(), vs);
+ final CyNetworkView clusterView = createNetworkView(net, vs);
clusterView.setVisualProperty(NETWORK_WIDTH, new Double(width));
clusterView.setVisualProperty(NETWORK_HEIGHT, new
Double(height));
for (View<CyNode> nv : clusterView.getNodeViews()) {
if (interrupted) {
- logger.error("Interrupted: Node Setup");
+ logger.debug("Interrupted: Node Setup");
// before we short-circuit the method we reset
the interruption so that the method can run without
// problems the next time around
if (layouter != null) layouter.resetDoLayout();
@@ -446,7 +448,6 @@
final Graphics2D g = (Graphics2D) image.getGraphics();
SwingUtilities.invokeLater(new Runnable() {
-
@Override
public void run() {
try {
@@ -476,7 +477,8 @@
if (clusterView.getNodeViews().size() >
0) {
cluster.setView(clusterView);
- }
+ } else {
+System.out.println("\t>> no node views--nodes: " +
clusterView.getModel().getNodeCount() + " | " + net.getNodeCount());}// TODO:
delete
} catch (Exception ex) {
throw new RuntimeException(ex);
}
@@ -485,7 +487,7 @@
layouter.resetDoLayout();
resetLoading();
-
+
return image;
}
@@ -525,6 +527,7 @@
if (vs == null) vs = visualMappingMgr.getDefaultVisualStyle();
visualMappingMgr.setVisualStyle(vs, view);
vs.apply(view);
+ view.updateView();
return view;
}
@@ -711,8 +714,8 @@
//sorting clusters by decreasing score
public int compare(MCODECluster c1, MCODECluster c2) {
- double d1 = c1.getClusterScore();
- double d2 = c2.getClusterScore();
+ double d1 = c1.getScore();
+ double d2 = c2.getScore();
if (d1 == d2) {
return 0;
} else if (d1 < d2) {
@@ -795,7 +798,7 @@
fout.write((i + 1) + "\t"); //rank
NumberFormat nf =
NumberFormat.getInstance();
nf.setMaximumFractionDigits(3);
-
fout.write(nf.format(clusters[i].getClusterScore()) + "\t");
+
fout.write(nf.format(clusters[i].getScore()) + "\t");
// cluster size - format: (# prot, #
intx)
fout.write(clusterNetwork.getNodeCount() + "\t");
fout.write(clusterNetwork.getEdgeCount() + "\t");
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODEAboutDialog.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODEAboutDialog.java
2012-11-07 20:10:08 UTC (rev 30754)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODEAboutDialog.java
2012-11-07 20:59:13 UTC (rev 30755)
@@ -1,7 +1,6 @@
package org.cytoscape.mcode.internal.view;
import java.awt.BorderLayout;
-import java.awt.Component;
import java.awt.Insets;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
@@ -66,7 +65,6 @@
private static final long serialVersionUID = 635333288924094273L;
- private final CySwingApplication swingApplication;
private final OpenBrowser openBrowser;
private final String version;
private final String buildDate;
@@ -79,8 +77,7 @@
public MCODEAboutDialog(final CySwingApplication swingApplication,
final OpenBrowser
openBrowser,
final MCODEUtil
mcodeUtil) {
- super(swingApplication.getJFrame(), "About MCODE", true);
- this.swingApplication = swingApplication;
+ super(swingApplication.getJFrame(), "About MCODE", false);
this.openBrowser = openBrowser;
version = mcodeUtil.getProperty("project.version");
buildDate = mcodeUtil.getProperty("buildDate");
@@ -89,7 +86,6 @@
getContentPane().add(getMainContainer(), BorderLayout.CENTER);
getContentPane().add(getButtonPanel(), BorderLayout.SOUTH);
pack();
- setLocationRelativeTo(getApplicationParent());
}
private JEditorPane getMainContainer() {
@@ -177,13 +173,4 @@
}
}
}
-
- private Component getApplicationParent() {
- Component c = swingApplication.getJFrame();
-
- while (c.getParent() != null)
- c = c.getParent();
-
- return c;
- }
}
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODELoader.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODELoader.java
2012-11-07 20:10:08 UTC (rev 30754)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODELoader.java
2012-11-07 20:59:13 UTC (rev 30755)
@@ -52,35 +52,36 @@
private static final long serialVersionUID = 3709336791661338561L;
- JTable table; //cluster browser table reference
- int selectedRow; //row of cluster
- ImageIcon graphImage; //picture of the graph as is before loading
- BufferedImage onScreenLoader; //picture of loader
- BufferedImage offScreenLoader;
- Graphics2D onScreenG2; //graphics context of loader
- Graphics2D offScreenG2;
- Color bgColor; //background of selected cluster browser table cell
- Color fgColor; //color of foreground in the selected cluster browser table
cell
- double fadeInAlpha; //global variable that allows the loader to fade in
when it's first displayed
- int degreesForDisk; //global variable keeping track of the loading disk
rotation
- int fontSize;
+ private JTable table; //cluster browser table reference
+ private int selectedRow; //row of cluster
+ private ImageIcon graphImage; //picture of the graph as is before
loading
+ private BufferedImage onScreenLoader; //picture of loader
+ private BufferedImage offScreenLoader;
+ private Graphics2D onScreenG2; //graphics context of loader
+ private Graphics2D offScreenG2;
+ private Color bgColor; //background of selected cluster browser table
cell
+ private Color fgColor; //color of foreground in the selected cluster
browser table cell
+ private double fadeInAlpha; //global variable that allows the loader to
fade in when it's first displayed
+ private int degreesForDisk; //global variable keeping track of the
loading disk rotation
+ private int fontSize;
- int progress; //progress bar progress value
- String process; //current process being computed
+ private int progress; //progress bar progress value
+ private String process; //current process being computed
- Thread t;
- boolean loading; // run switch
- boolean loaderDisplayed; //allows mcode to display a continous loading
animation during continous exploration
+ private Thread t;
+ private boolean loading; // run switch
+ private boolean loaderDisplayed; //allows mcode to display a continuous
loading animation during continuous exploration
/**
- * Constructer for the loader.
+ * Constructor for the loader.
*
* @param table Reference to the cluster browser table
* @param width cell width
* @param height cell height
*/
- MCODELoader (JTable table, int width, int height) {
- this.table = table;
+ MCODELoader (final int selectedRow, final JTable table, int width, int
height) {
+ this.selectedRow = selectedRow;
+ this.table = table;
//First we get the tables colors and set the font
bgColor = table.getSelectionBackground();
fgColor = table.getSelectionForeground();
@@ -99,78 +100,69 @@
//the on screen image is the one that this ImageIcon will display
this.setImage(onScreenLoader);
-
- loading = false;
-
- t = new Thread(this);
-
}
- /**
- * Sets the row and network image on top of which the loader will be drawn
as well as
- * progress to 0 and process to "Starting".
- *
- * @param selectedRow the row in a table where the loader is to be drawn
- * @param table an image of the cluster before the loader is drawn on top
- */
- public void setLoader(int selectedRow, JTable table) {
- this.selectedRow = selectedRow;
+ public void start() {
graphImage = (ImageIcon) table.getValueAt(selectedRow, 0);
fadeInAlpha = 0.0;
degreesForDisk = 0;
progress = 0;
process = "Starting";
-
loaderDisplayed = false;
loading = true;
+
+ t = new Thread(this);
+ t.start();
}
+ /**
+ * Sets the run switch to false to stop the drawing process
+ */
+ public void stop() {
+ loading = false;
+ loaderDisplayed = false;
+ t = null;
+ }
+
@Override
public void run() {
try {
- while (true) {
+ final Thread curentThread = Thread.currentThread();
+
+ while (t == curentThread) {
+ //First we make sure that if the loader is being displayed for
the first time in this exploration
+ //session, then we wait half a second to make sure it isn't
displayed for process that are really quick
+ if (loading && !loaderDisplayed)
+ Thread.sleep(500);
+
+ //Then we compute the loading picture if loading is still
taking place
if (loading) {
- //First we make sure that if the loader is being displayed
for the first time in this exploration
- //session, then we wait half a second to make sure it
isn't displayed for process that are really
- //quick
+ drawLoader();
+
+ //If the loader has not been displayed yet and loading is
still taking place, we put it in the table
if (loading && !loaderDisplayed) {
- Thread.sleep(500);
+ table.setValueAt(this, selectedRow, 0);
+ loaderDisplayed = true;
}
- //Then we compute the loading picture if loading is still
taking place
- if (loading) {
- drawLoader();
- //If the loader has not been displayed yet and loading
is still taking place,
- //we put it in the table
- if (loading && !loaderDisplayed) {
- table.setValueAt(this, selectedRow, 0);
- loaderDisplayed = true;
- }
- //Since the table consolidates paint updates, the
animation would not show up unless
- //we implicitly force it to repaint
- //This paintImmediately function causes problems in
windows (paints on every component sometimes)
- //Rectangle bounds = table.getCellRect(selectedRow, 0,
false);
- //if (loading) table.paintImmediately(bounds);
- //This fireTableCellUpdated function seems to
consolidate some painting too so it is not very responsive in windows
- if (loading) ((AbstractTableModel)
table.getModel()).fireTableCellUpdated(selectedRow, 0);
- //Both work on the mac just fine
- }
+ //Since the table consolidates paint updates, the
animation would not show up unless
+ //we implicitly force it to repaint.
+ //This paintImmediately function causes problems in
windows (paints on every component sometimes)
+ //Rectangle bounds = table.getCellRect(selectedRow, 0,
false);
+ //if (loading) table.paintImmediately(bounds);
+ //This fireTableCellUpdated function seems to consolidate
some painting too so it is not very responsive in windows
+ if (loading)
+ ((AbstractTableModel)
table.getModel()).fireTableCellUpdated(selectedRow, 0);
+ //Both work on the mac just fine
}
- //This sleep time generates a ~30 fps animation
- Thread.sleep(30);
}
+
+ //This sleep time generates a ~30 fps animation
+ Thread.sleep(30);
} catch (Exception e) {}
}
/**
- * Sets the run switch to false to stop the drawing process
- */
- public void loaded() {
- loading = false;
- loaderDisplayed = false;
- }
-
- /**
* Initially, fades the graph into the background color, draws the Loading
string and an animated disk to indicate
* responsiveness as well as a progress bar and process status.
*/
@@ -212,7 +204,7 @@
int r = 20;//radius of the disk
//To draw the animated rotating disk, we must create the Mask, or
drawable area, in which we will
//rotate a triangular polygon around a common center
- //the inner circle is subracted from the outter to create the disk area
+ //the inner circle is subtracted from the outer to create the disk area
Ellipse2D circOutter = new Ellipse2D.Double((loader.getWidth() / 2) -
r, (loader.getHeight() / 2) - r, 2 * r, 2 * r);
Ellipse2D circInner = new Ellipse2D.Double((loader.getWidth() / 2) -
(r / 2), (loader.getHeight() / 2) - (r / 2), r, r);
@@ -240,10 +232,10 @@
//In order for the leading portion of the rotating disk to be one
color and the trailing portion another we use
//this weighting variable to slowly change the weighting of the two
colors in finding the average between the two
double markerLeadColorWeighting = 1.0;
- //this is the transparency of the initial polygon which is
exponantially decremented to fade away the polygons
+ //this is the transparency of the initial polygon which is
exponentially decremented to fade away the polygons
double markerAlpha = 255 * fadeInAlpha;
- //In order for the polygons to cover the disk entirely, the outter
polygon points must circle in an orbit that is further
+ //In order for the polygons to cover the disk entirely, the outer
polygon points must circle in an orbit that is further
//than the disk itself, otherwise we would get a flat line between the
two points and the resulting circle would not be smooth
r = r + 10;
//We will only draw the polygons as long as they are visible
@@ -356,8 +348,4 @@
this.progress = progress;
this.process = process;
}
-
- public void start() {
- t.start();
- }
}
Modified:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODEResultsPanel.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODEResultsPanel.java
2012-11-07 20:10:08 UTC (rev 30754)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODEResultsPanel.java
2012-11-07 20:59:13 UTC (rev 30755)
@@ -28,6 +28,10 @@
import java.util.List;
import java.util.Map;
import java.util.Set;
+import java.util.concurrent.Executors;
+import java.util.concurrent.ScheduledExecutorService;
+import java.util.concurrent.ScheduledFuture;
+import java.util.concurrent.TimeUnit;
import javax.swing.AbstractAction;
import javax.swing.BorderFactory;
@@ -74,6 +78,8 @@
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
import org.cytoscape.view.vizmap.VisualStyle;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
/**
* * Copyright (c) 2004 Memorial Sloan-Kettering Cancer Center
@@ -126,8 +132,7 @@
private int resultId;
private MCODEAlgorithm alg;
private MCODECluster[] clusters;
- private JTable table;
- private MCODEResultsPanel.MCODEClusterBrowserTableModel modelBrowser;
+
// Actual cluster data
private CyNetwork network; // Keep a record of the original input
record for use in
// the table row selection listener
@@ -141,10 +146,12 @@
private int enumerationSelection = 0;
// Graphical classes
- private MCODELoader loader;
+ private MCODEClusterBrowserPanel clusterBrowserPanel;
private final MCODEUtil mcodeUtil;
private final MCODEDiscardResultAction discardResultAction;
+
+ private static final Logger logger =
LoggerFactory.getLogger(MCODEResultsPanel.class);
/**
* Constructor for the Results Panel which displays the clusters in a
@@ -153,7 +160,7 @@
* @param clusters Found clusters from the MCODEAnalyzeTask
* @param alg A reference to the alg for this particular network
* @param network Network were these clusters were found
- * @param imageList A list of images of the found clusters
+ * @param clusterImages A list of images of the found clusters
* @param resultId Title of this result as determined by
MCODESCoreAndFindAction
*/
public MCODEResultsPanel(MCODECluster[] clusters,
@@ -161,7 +168,7 @@
MCODEUtil mcodeUtil,
CyNetwork network,
CyNetworkView
networkView,
- Image[] imageList,
+ Image[] clusterImages,
int resultId,
final
MCODEDiscardResultAction discardResultAction) {
setLayout(new BorderLayout());
@@ -174,18 +181,12 @@
// The view may not exist, but we only test for that when we
need to (in the TableRowSelectionHandler below)
this.networkView = networkView;
this.discardResultAction = discardResultAction;
-
- currentParamsCopy =
mcodeUtil.getCurrentParameters().getResultParams(resultId);
-
- JPanel clusterBrowserPanel =
createClusterBrowserPanel(imageList);
- JPanel bottomPanel = createBottomPanel();
-
+ this.currentParamsCopy =
mcodeUtil.getCurrentParameters().getResultParams(resultId);
+
+ this.clusterBrowserPanel = new
MCODEClusterBrowserPanel(clusterImages);
add(clusterBrowserPanel, BorderLayout.CENTER);
- add(bottomPanel, BorderLayout.SOUTH);
+ add(createBottomPanel(), BorderLayout.SOUTH);
- loader = new MCODELoader(table, graphPicSize, graphPicSize);
- loader.start();
-
this.setSize(this.getMinimumSize());
}
@@ -217,6 +218,10 @@
public CyNetworkView getNetworkView() {
return networkView;
}
+
+ public int getSelectedClusterRow() {
+ return clusterBrowserPanel.getSelectedRow();
+ }
public void discard(final boolean requestUserConfirmation) {
SwingUtilities.invokeLater(new Runnable() {
@@ -236,39 +241,6 @@
}
/**
- * Creates a panel that contains the browser table with a scroll bar.
- *
- * @param imageList
- * images of cluster graphs
- * @return panel
- */
- private JPanel createClusterBrowserPanel(Image[] imageList) {
- JPanel panel = new JPanel();
- panel.setLayout(new BorderLayout());
- panel.setBorder(BorderFactory.createTitledBorder("Cluster
Browser"));
-
- // main data table
- modelBrowser = new
MCODEResultsPanel.MCODEClusterBrowserTableModel(imageList);
-
- table = new JTable(modelBrowser);
- table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
- table.setDefaultRenderer(StringBuffer.class, new
MCODEResultsPanel.JTextAreaRenderer(defaultRowHeight));
- table.setIntercellSpacing(new Dimension(0, 4)); // gives a
little vertical room between clusters
- table.setFocusable(false); // removes an outline that appears
when the user clicks on the images
-
- // Ask to be notified of selection changes.
- ListSelectionModel rowSM = table.getSelectionModel();
- rowSM.addListSelectionListener(new
MCODEResultsPanel.TableRowSelectionHandler());
-
- JScrollPane tableScrollPane = new JScrollPane(table);
- tableScrollPane.getViewport().setBackground(Color.WHITE);
-
- panel.add(tableScrollPane, BorderLayout.CENTER);
-
- return panel;
- }
-
- /**
* Creates a panel containing the explore collapsable panel and result
set
* specific buttons
*
@@ -447,7 +419,7 @@
if (nodeRow.isSet(CLUSTER_ATTR))
clusterNameSet.addAll(nodeRow.getList(CLUSTER_ATTR, String.class));
-
clusterNameSet.add(cluster.getClusterName());
+ clusterNameSet.add(cluster.getName());
nodeRow.set(CLUSTER_ATTR, new
ArrayList<String>(clusterNameSet));
if (cluster.getSeedNode() == rgi)
@@ -460,7 +432,30 @@
return alg.getMaxScore(resultId);
}
+
+ private static StringBuffer getClusterDetails(final MCODECluster
cluster) {
+ StringBuffer details = new StringBuffer();
+ details.append("Rank: ");
+ details.append(String.valueOf(cluster.getRank() + 1));
+
+ details.append("\n");
+ details.append("Score: ");
+ NumberFormat nf = NumberFormat.getInstance();
+ nf.setMaximumFractionDigits(3);
+ details.append(nf.format(cluster.getScore()));
+
+ details.append("\n");
+ details.append("Nodes: ");
+ details.append(cluster.getNetwork().getNodeCount());
+
+ details.append("\n");
+ details.append("Edges: ");
+ details.append(cluster.getNetwork().getEdgeCount());
+
+ return details;
+ }
+
/**
* Handles the create child network press in the cluster exploration
panel
*/
@@ -480,8 +475,8 @@
nf.setMaximumFractionDigits(3);
final MCODECluster cluster = clusters[selectedRow];
final CyNetwork clusterNetwork = cluster.getNetwork();
- final String title = trigger.getResultId() + ": " +
cluster.getClusterName() + " (Score: " +
-
nf.format(cluster.getClusterScore()) + ")";
+ final String title = trigger.getResultId() + ": " +
cluster.getName() + " (Score: " +
+
nf.format(cluster.getScore()) + ")";
// Create the child network and view
final SwingWorker<CyNetworkView, ?> worker = new
SwingWorker<CyNetworkView, Object>() {
@@ -549,13 +544,62 @@
}
/**
+ * Panel that contains the browser table with a scroll bar.
+ */
+ private class MCODEClusterBrowserPanel extends JPanel {
+
+ private final MCODEResultsPanel.MCODEClusterBrowserTableModel
browserModel;
+ private final JTable table;
+
+ public MCODEClusterBrowserPanel(final Image[] images) {
+ super();
+ setLayout(new BorderLayout());
+ setBorder(BorderFactory.createTitledBorder("Cluster
Browser"));
+
+ // main data table
+ browserModel = new
MCODEResultsPanel.MCODEClusterBrowserTableModel(images);
+
+ table = new JTable(browserModel);
+
table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+ table.setDefaultRenderer(StringBuffer.class, new
MCODEResultsPanel.JTextAreaRenderer(defaultRowHeight));
+ table.setIntercellSpacing(new Dimension(0, 4)); //
gives a little vertical room between clusters
+ table.setFocusable(false); // removes an outline that
appears when the user clicks on the images
+
+ // Ask to be notified of selection changes.
+ ListSelectionModel rowSM = table.getSelectionModel();
+ rowSM.addListSelectionListener(new
MCODEResultsPanel.TableRowSelectionHandler());
+
+ JScrollPane tableScrollPane = new JScrollPane(table);
+
tableScrollPane.getViewport().setBackground(Color.WHITE);
+
+ add(tableScrollPane, BorderLayout.CENTER);
+ }
+
+ public int getSelectedRow() {
+ return table.getSelectedRow();
+ }
+
+ public void update(final ImageIcon image, final int row) {
+ table.setValueAt(image, row, 0);
+ }
+
+ public void update(final MCODECluster cluster, final int row) {
+ final StringBuffer details = getClusterDetails(cluster);
+ table.setValueAt(details, row, 1);
+ }
+
+ JTable getTable() { // TODO: delete it: do not expose the JTable
+ return table;
+ }
+ }
+
+ /**
* Handles the data to be displayed in the cluster browser table
*/
private class MCODEClusterBrowserTableModel extends AbstractTableModel {
- // Create column headings
- String[] columnNames = { "Network", "Details" };
- Object[][] data; // the actual table data
+ private final String[] columnNames = { "Network", "Details" };
+ private final Object[][] data; // the actual table data
public MCODEClusterBrowserTableModel(Image[] imageList) {
exploreContent = new JPanel[clusters.length];
@@ -563,7 +607,7 @@
for (int i = 0; i < clusters.length; i++) {
clusters[i].setRank(i);
- StringBuffer details = new
StringBuffer(getClusterDetails(clusters[i]));
+ StringBuffer details =
getClusterDetails(clusters[i]);
data[i][1] = new StringBuffer(details);
// get an image for each cluster - make it a
nice layout of the cluster
@@ -572,63 +616,39 @@
}
}
+ @Override
public String getColumnName(int col) {
return columnNames[col];
}
+ @Override
public int getColumnCount() {
return columnNames.length;
}
+ @Override
public int getRowCount() {
return data.length;
}
+ @Override
public Object getValueAt(int row, int col) {
return data[row][col];
}
+ @Override
public void setValueAt(Object object, int row, int col) {
data[row][col] = object;
fireTableCellUpdated(row, col);
}
+ @Override
public Class<?> getColumnClass(int c) {
return getValueAt(0, c).getClass();
}
}
/**
- * Generates a string buffer with the cluster's details
- *
- * @param cluster
- * The cluster
- * @return details String buffer containing the details
- */
- private StringBuffer getClusterDetails(MCODECluster cluster) {
- StringBuffer details = new StringBuffer();
-
- details.append("Rank: ");
- details.append(String.valueOf(cluster.getRank() + 1));
-
- details.append("\n");
- details.append("Score: ");
- NumberFormat nf = NumberFormat.getInstance();
- nf.setMaximumFractionDigits(3);
- details.append(nf.format(cluster.getClusterScore()));
-
- details.append("\n");
- details.append("Nodes: ");
- details.append(cluster.getNetwork().getNodeCount());
-
- details.append("\n");
- details.append("Edges: ");
- details.append(cluster.getNetwork().getEdgeCount());
-
- return details;
- }
-
- /**
* Handles the data to be displayed in the node attribute enumeration
table
*/
private class MCODEResultsEnumeratorTableModel extends
AbstractTableModel {
@@ -873,8 +893,8 @@
// event to display the new content with the
name of the cluster, if it exists
String title = "Explore: ";
- if (clusters[selectedRow].getClusterName() !=
null) {
- title = title +
clusters[selectedRow].getClusterName();
+ if (clusters[selectedRow].getName() != null) {
+ title = title +
clusters[selectedRow].getName();
} else {
title = title + "Cluster " +
(selectedRow + 1);
}
@@ -992,96 +1012,88 @@
}
/**
- * Getter for the browser table used in MCODEVisualStyleAction to
reselect
- * the selected cluster whenever the user focuses on this result set
- */
- public JTable getClusterBrowserTable() {
- return table;
- }
-
- /**
* Handles the dynamic cluster size manipulation via the JSlider
*/
private class SizeAction implements ChangeListener {
+ private final ScheduledExecutorService scheduler =
Executors.newScheduledThreadPool(3);
+ private ScheduledFuture<?> futureLoader;
+
private int selectedRow;
- public boolean loaderSet = false;
private JComboBox nodeAttributesComboBox;
- private GraphDrawer drawer;
private boolean drawPlaceHolder;
-
+ private final GraphDrawer drawer;
+ private final MCODELoader loader;
+
/**
- * Constructor
- *
- * @param selectedRow
- * The selected cluster
- * @param nodeAttributesComboBox
- * Reference to the attribute enumeration picker
+ * @param selectedRow The selected cluster
+ * @param nodeAttributesComboBox Reference to the attribute
enumeration picker
*/
- SizeAction(int selectedRow, JComboBox nodeAttributesComboBox) {
+ SizeAction(final int selectedRow, final JComboBox
nodeAttributesComboBox) {
this.selectedRow = selectedRow;
this.nodeAttributesComboBox = nodeAttributesComboBox;
- drawer = new GraphDrawer();
- loaderSet = false;
+ loader = new MCODELoader(selectedRow,
clusterBrowserPanel.getTable(), graphPicSize, graphPicSize);
+ drawer = new GraphDrawer(loader);
}
- public void stateChanged(ChangeEvent e) {
+ public void stateChanged(final ChangeEvent e) {
// This method as been written so that the slider is
responsive to the user's input at all times, despite
// the computationally challenging drawing, layout out,
and selection of large clusters. As such, we only
// perform real work if the slider produces a different
cluster, and furthermore we only perform the quick
// processes here, while the heavy weights are handled
by the drawer's thread.
- JSlider source = (JSlider) e.getSource();
- double nodeScoreCutoff = (((double) source.getValue())
/ 1000);
-
+ final JSlider source = (JSlider) e.getSource();
+ final double nodeScoreCutoff = (((double)
source.getValue()) / 1000);
+ final int clusterRow = selectedRow;
// Store current cluster content for comparison
- List<Long> oldCluster =
clusters[selectedRow].getALCluster();
-
- // Find the new cluster given the node score cutoff
- MCODECluster cluster =
alg.exploreCluster(clusters[selectedRow], nodeScoreCutoff, network, resultId);
-
- // We only want to do the following work if the newly
found cluster
- // is actually different
- // So we get the new cluster content
- List<Long> newCluster = cluster.getALCluster();
-
- // If the new cluster is too large to draw within a
reasonable time
- // and won't look understandable in the table cell then
we draw a place holder
- drawPlaceHolder = newCluster.size() > 300;
-
- // And compare the old and new
- if (!newCluster.equals(oldCluster)) {
- // If the cluster has changed, then we conduct
all
- // non-rate-limiting steps:
- // Interrupt the drawing
- drawer.interruptDrawing();
- // Update the cluster array
- clusters[selectedRow] = cluster;
- // Update the details
- StringBuffer details =
getClusterDetails(cluster);
- table.setValueAt(details, selectedRow, 1);
- // Fire the enumeration action
-
nodeAttributesComboBox.setSelectedIndex(nodeAttributesComboBox.getSelectedIndex());
-
- // Ensure that a loader is set with the
selected row and table object
- // Also, we want to set the loader only once
during continuous exploration
- // It is only set again when a graph is fully
loaded and placed in the table
- if (!loaderSet && !drawPlaceHolder) {
- // internally, the loader is only drawn
into the appropriate
- // cell after a short sleep period
- // to ensure that quick loads are not
displayed unecessarily
- loader.setLoader(selectedRow, table);
- loaderSet = true;
- }
-
- // There is a small difference between
expanding and retracting the cluster size.
- // When expanding, new nodes need random
position and thus must go through the layout.
- // When retracting, we simply use the layout
that was generated and stored.
- // This speeds up the drawing process greatly.
- boolean layoutNecessary = newCluster.size() >
oldCluster.size();
- // Draw Graph and select the cluster in the
view in a separate thread so that it can be
- // interrupted by the slider movement
- drawer.drawGraph(cluster, layoutNecessary,
this, drawPlaceHolder);
+ final MCODECluster oldCluster = clusters[clusterRow];
+
+ if (futureLoader != null && !futureLoader.isDone()) {
+ drawer.stop();
+ futureLoader.cancel(false);
}
+
+ final Runnable command = new Runnable() {
+ @Override
+ public void run() {
+ final List<Long> oldALCluster =
oldCluster.getALCluster();
+ // Find the new cluster given the node
score cutoff
+ final MCODECluster newCluster =
alg.exploreCluster(oldCluster, nodeScoreCutoff, network, resultId);
+
+ // We only want to do the following
work if the newly found cluster is actually different
+ // So we get the new cluster content
+ List<Long> newALCluster =
newCluster.getALCluster();
+
+ // If the new cluster is too large to
draw within a reasonable time
+ // and won't look understandable in the
table cell, then we draw a place holder
+ drawPlaceHolder = newALCluster.size() >
300;
+
+ // And compare the old and new
+ if (!newALCluster.equals(oldALCluster))
{
+ // If the cluster has changed,
then we conduct all non-rate-limiting steps:
+ // Update the cluster array
+ clusters[clusterRow] =
newCluster;
+ // Update the cluster details
+
clusterBrowserPanel.update(newCluster, clusterRow);
+ // Fire the enumeration action
+
nodeAttributesComboBox.setSelectedIndex(nodeAttributesComboBox.getSelectedIndex());
+
+ // There is a small difference
between expanding and retracting the cluster size.
+ // When expanding, new nodes
need random position and thus must go through the layout.
+ // When retracting, we simply
use the layout that was generated and stored.
+ // This speeds up the drawing
process greatly.
+ boolean layoutNecessary =
newALCluster.size() > oldALCluster.size();
+ // Draw Graph and select the
cluster in the view in a separate thread so that it can be
+ // interrupted by the slider
movement
+ if (!newCluster.isDisposed())
+
drawer.drawGraph(newCluster, layoutNecessary, drawPlaceHolder);
+
+ // Prevent memory leaks
+ oldCluster.dispose();
+ }
+ }
+ };
+
+ futureLoader = scheduler.schedule(command, 100,
TimeUnit.MILLISECONDS);
}
}
@@ -1091,22 +1103,19 @@
*/
private class GraphDrawer implements Runnable {
- private Thread t;
private boolean drawGraph; // run switch
private boolean placeHolderDrawn;
private boolean drawPlaceHolder;
MCODECluster cluster;
SpringEmbeddedLayouter layouter;
- MCODEResultsPanel.SizeAction trigger;
boolean layoutNecessary;
boolean clusterSelected;
+ private Thread t;
+ private final MCODELoader loader;
- GraphDrawer() {
- drawGraph = false;
- drawPlaceHolder = false;
+ GraphDrawer(final MCODELoader loader) {
+ this.loader = loader;
layouter = new SpringEmbeddedLayouter();
- t = new Thread(this);
- t.start();
}
/**
@@ -1120,10 +1129,8 @@
*/
public void drawGraph(MCODECluster cluster,
boolean
layoutNecessary,
-
MCODEResultsPanel.SizeAction trigger,
boolean
drawPlaceHolder) {
this.cluster = cluster;
- this.trigger = trigger;
this.layoutNecessary = layoutNecessary;
// Graph drawing will only occur if the cluster is not
too large,
@@ -1131,11 +1138,23 @@
drawGraph = !drawPlaceHolder;
this.drawPlaceHolder = drawPlaceHolder;
clusterSelected = false;
+ t = new Thread(this);
+ t.start();
}
public void run() {
try {
- while (true) {
+ // We want to set the loader only once during
continuous exploration
+ // It is only set again when a graph is fully
loaded and placed in the table
+ if (!drawPlaceHolder) {
+ // internally, the loader is only drawn
into the appropriate cell after a short sleep period
+ // to ensure that quick loads are not
displayed unnecessarily
+ loader.start();
+ }
+
+ final Thread currentThread =
Thread.currentThread();
+
+ while (t == currentThread) {
// This ensures that the drawing of
this cluster is only attempted once
// if it is unsuccessful it is because
the setup or layout
// process was interrupted by the
slider movement
@@ -1157,12 +1176,7 @@
selectCluster(cluster.getNetwork());
clusterSelected = true;
// Update the table
- table.setValueAt(new
ImageIcon(image), cluster.getRank(), 0);
- // Loader is no longer
showing, so we let the SizeAction know that
- trigger.loaderSet =
false;
- // stop loader from
animating and taking up computer processing power
- loader.loaded();
-
+
clusterBrowserPanel.update(new ImageIcon(image), cluster.getRank());
drawGraph = false;
}
@@ -1172,13 +1186,9 @@
// draw place holder, only once
though (as per the if statement)
Image image =
mcodeUtil.getPlaceHolderImage(graphPicSize, graphPicSize);
// Update the table
- table.setValueAt(new
ImageIcon(image), cluster.getRank(), 0);
+ clusterBrowserPanel.update(new
ImageIcon(image), cluster.getRank());
// select the cluster
selectCluster(cluster.getNetwork());
- // Loader is no longer showing,
so we let the SizeAction know that
- trigger.loaderSet = false;
- // stop loader from animating
and taking up computer processing power
- loader.loaded();
drawGraph = false;
// Make sure this block is not
run again unless if we need to reload the image
placeHolderDrawn = true;
@@ -1187,17 +1197,24 @@
clusterSelected = true;
}
+ if ((!drawGraph && !drawPlaceHolder) ||
placeHolderDrawn)
+ stop();
+
// This sleep time produces the drawing
response time of 1 20th of a second
Thread.sleep(100);
}
} catch (Exception e) {
+ logger.error("Error while drawing cluster
image", e);
}
}
- public void interruptDrawing() {
- drawGraph = false;
+ void stop() {
+ // stop loader from animating and taking up computer
processing power
+ loader.stop();
layouter.interruptDoLayout();
mcodeUtil.interruptLoading();
+ drawGraph = false;
+ t = null;
}
}
}
Modified:
csplugins/trunk/toronto/clopes/mcode/src/test/java/org/cytoscape/mcode/internal/model/MCODEAlgorithmTest.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/test/java/org/cytoscape/mcode/internal/model/MCODEAlgorithmTest.java
2012-11-07 20:10:08 UTC (rev 30754)
+++
csplugins/trunk/toronto/clopes/mcode/src/test/java/org/cytoscape/mcode/internal/model/MCODEAlgorithmTest.java
2012-11-07 20:59:13 UTC (rev 30755)
@@ -125,7 +125,7 @@
assertNotNull(cn);
assertEquals(resultId, c.getResultId());
- assertEquals(16, c.getClusterScore(), 0.0);
+ assertEquals(16, c.getScore(), 0.0);
assertEquals(16, cn.getNodeCount());
assertEquals(120, cn.getEdgeCount());
assertNotNull(c.getSeedNode());
@@ -152,7 +152,7 @@
assertNotNull(cn);
assertEquals(resultId, c.getResultId());
- assertEquals(14.118, c.getClusterScore(), 0.0009);
+ assertEquals(14.118, c.getScore(), 0.0009);
assertEquals(16, cn.getNodeCount());
assertEquals(120, cn.getEdgeCount());
assertNotNull(c.getSeedNode());
--
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