Author: pwang
Date: 2011-11-14 14:16:30 -0800 (Mon, 14 Nov 2011)
New Revision: 27463
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/bookmarks/BookmarkReader.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/cysession/CysessionReader.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReader.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CyAttributesReader.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/expression/ExpressionReader.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/gml/GMLNetworkReader.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/properties/PropertiesReader.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/SessionReaderImpl.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkReader.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/vizmap/VizmapPropertiesReader.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/vizmap/VizmapXMLReader.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkReader.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/cysession/CysessionWriterImpl.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/datatable/csv/CSVCyWriter.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/BitmapWriter.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/PDFWriter.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/PSWriter.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/SVGWriter.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/session/SessionWriterImpl.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/sif/SifWriter.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/vizmap/VizmapWriterImpl.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
Log:
Set progress monitor
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/bookmarks/BookmarkReader.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/bookmarks/BookmarkReader.java
2011-11-14 19:25:03 UTC (rev 27462)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/bookmarks/BookmarkReader.java
2011-11-14 22:16:30 UTC (rev 27463)
@@ -18,9 +18,12 @@
}
public void run(TaskMonitor tm) throws Exception {
+ tm.setProgress(0.0);
final JAXBContext jaxbContext =
JAXBContext.newInstance(BOOKMARK_PACKAGE, getClass().getClassLoader());
+ tm.setProgress(0.1);
final Unmarshaller unmarshaller =
jaxbContext.createUnmarshaller();
-
+ tm.setProgress(0.5);
propertyObject = (Bookmarks)
unmarshaller.unmarshal(inputStream);
+ tm.setProgress(1.0);
}
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/cysession/CysessionReader.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/cysession/CysessionReader.java
2011-11-14 19:25:03 UTC (rev 27462)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/cysession/CysessionReader.java
2011-11-14 22:16:30 UTC (rev 27463)
@@ -19,15 +19,19 @@
public void run(TaskMonitor tm) throws Exception {
+ tm.setProgress(0.0);
// No idea why, but ObjectFactory doesn't get picked up in the
default
// Thread.currentThread().getContextClassLoader() classloader,
whereas
// that approach works fine for bookmarks. Anyway, just force
the issue
// by getting this classloader.
final JAXBContext jaxbContext =
JAXBContext.newInstance(CYSESSION_PACKAGE,
getClass().getClassLoader());
+ tm.setProgress(0.2);
final Unmarshaller unmarshaller =
jaxbContext.createUnmarshaller();
+ tm.setProgress(0.4);
propertyObject = (Cysession)
unmarshaller.unmarshal(inputStream);
+ tm.setProgress(1.0);
}
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReader.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReader.java
2011-11-14 19:25:03 UTC (rev 27462)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CSVCyReader.java
2011-11-14 22:16:30 UTC (rev 27463)
@@ -56,10 +56,17 @@
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
+ taskMonitor.setProgress(0.0);
+
CSVReader reader = new CSVReader(new InputStreamReader(stream));
+ taskMonitor.setProgress(0.2);
+
TableInfo info = readHeader(reader);
table = createTable(reader, info);
+ taskMonitor.setProgress(0.6);
+
tableManager.addTable(table);
+ taskMonitor.setProgress(1.0);
}
CyTable createTable(CSVReader reader, TableInfo info) throws
IOException, SecurityException {
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CyAttributesReader.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CyAttributesReader.java
2011-11-14 19:25:03 UTC (rev 27462)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/datatable/CyAttributesReader.java
2011-11-14 22:16:30 UTC (rev 27463)
@@ -98,13 +98,16 @@
@Override
public void run(TaskMonitor tm) throws IOException {
+ tm.setProgress(0.0);
+
final CyTable table = tableFactory.createTable(
"Table " + Integer.toString(nextTableNumber++),
CyTableEntry.NAME,
String.class, true, true);
cyTables = new CyTable[] { table };
-
+ tm.setProgress(0.1);
try {
loadAttributesInternal(table);
+ tm.setProgress(0.3);
tableManager.addTable(table);
} finally {
if (inputStream != null) {
@@ -112,12 +115,13 @@
inputStream = null;
}
}
-
+ tm.setProgress(0.7);
Class<? extends CyTableEntry> type = getMappingClass();
if (netMgr.getNetworkSet().size() > 0 && type != null)
super.insertTasksAfterCurrentTask(new
MapNetworkAttrTask(type,
table, netMgr, appMgr));
+ tm.setProgress(1.0);
}
private Class<? extends CyTableEntry> getMappingClass() {
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/expression/ExpressionReader.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/expression/ExpressionReader.java
2011-11-14 19:25:03 UTC (rev 27462)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/expression/ExpressionReader.java
2011-11-14 22:16:30 UTC (rev 27463)
@@ -233,6 +233,7 @@
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
+ taskMonitor.setProgress(0.0);
final BufferedReader input = new BufferedReader(new
InputStreamReader(inputStream));
try {
@@ -251,7 +252,8 @@
taskMonitor.setStatusMessage("Missing header in
input file!");
return;
}
-
+ taskMonitor.setProgress(0.1);
+
if (isHeaderLineMTXHeader(headerLine)) {
// for sure we know that the file contains
lambdas
significanceType = LAMBDA;
@@ -265,7 +267,9 @@
final boolean hasCOMMON =
doesHeaderLineHasCOMMON(headerLine);
final boolean expectPvals =
doesHeaderLineHaveDuplicates(headerLine, hasCOMMON);
-
+
+ taskMonitor.setProgress(0.2);
+
if ((significanceType != LAMBDA) && !expectPvals) {
// we know that we don't have a lambda header
and we don't
// have significance values
@@ -329,7 +333,7 @@
if (hasCOMMON) {
headerTok.nextToken();
}
-
+
/* the next numConds tokens are the condition names */
Vector<String> cNames = new
Vector<String>(numberOfConditions);
@@ -353,6 +357,8 @@
}
}
+ taskMonitor.setProgress(0.25);
+
/*
* OK, we have a reasonable header; clobber all old
information
*/
@@ -381,8 +387,9 @@
if (isCancelled)
return;
}
- taskMonitor.setProgress(100.0);
-
+ //taskMonitor.setProgress(100.0);
+ taskMonitor.setProgress(0.9);
+
/* save numGenes and build hash of gene names to
indices */
numGenes = geneNames.size();
@@ -400,6 +407,7 @@
} finally {
input.close();
}
+ taskMonitor.setProgress(1.0);
}
private Map<String,List<String>> getAttributeToIdList(String
keyAttributeName) throws IOException {
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/gml/GMLNetworkReader.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/gml/GMLNetworkReader.java
2011-11-14 19:25:03 UTC (rev 27462)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/gml/GMLNetworkReader.java
2011-11-14 22:16:30 UTC (rev 27463)
@@ -180,21 +180,23 @@
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
+ taskMonitor.setProgress(0.0);
try {
keyVals = (new GMLParser(inputStream)).parseList();
} catch (Exception io) {
io.printStackTrace();
throw new RuntimeException(io.getMessage());
}
-
+ taskMonitor.setProgress(0.05);
initializeStructures();
-
+ taskMonitor.setProgress(0.1);
readGML(keyVals, taskMonitor); // read the GML file
-
+ taskMonitor.setProgress(0.3);
network = cyNetworkFactory.getInstance();
createGraph(taskMonitor);
-
+ taskMonitor.setProgress(0.8);
this.cyNetworks = new CyNetwork[] { network };
+ taskMonitor.setProgress(1.0);
}
@Override
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/properties/PropertiesReader.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/properties/PropertiesReader.java
2011-11-14 19:25:03 UTC (rev 27462)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/properties/PropertiesReader.java
2011-11-14 22:16:30 UTC (rev 27463)
@@ -13,8 +13,11 @@
}
public void run(TaskMonitor tm) throws Exception {
+ tm.setProgress(0.0);
Properties props = new Properties();
+ tm.setProgress(0.1);
props.load(inputStream);
propertyObject = props;
+ tm.setProgress(1.0);
}
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/SessionReaderImpl.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/SessionReaderImpl.java
2011-11-14 19:25:03 UTC (rev 27462)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/SessionReaderImpl.java
2011-11-14 22:16:30 UTC (rev 27463)
@@ -175,11 +175,16 @@
*/
public void run(TaskMonitor tm) throws Exception {
taskMonitor = tm;
-
+ tm.setProgress(0.0);
+
extractEntries();
+ tm.setProgress(0.2);
processNetworks();
+ tm.setProgress(0.6);
mergeNetworkTables();
+ tm.setProgress(0.8);
restoreVirtualColumns();
+ tm.setProgress(1.0);
}
public CySession getCySession() {
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkReader.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkReader.java
2011-11-14 19:25:03 UTC (rev 27462)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkReader.java
2011-11-14 22:16:30 UTC (rev 27463)
@@ -93,7 +93,7 @@
private void readInput(TaskMonitor tm) throws IOException {
this.parentTaskMonitor = tm;
-// tm.setProgress(0.0);
+ tm.setProgress(0.0);
String line;
final BufferedReader br =
@@ -104,6 +104,8 @@
final CyTable nodeTable = network.getDefaultNodeTable();
final CyTable edgeTable = network.getDefaultEdgeTable();
+ tm.setProgress(0.1);
+
// Generate bundled event to avoid too many events problem.
final String firstLine = br.readLine();
@@ -111,6 +113,8 @@
delimiter = TAB;
createEdge(new Interaction(firstLine.trim(), delimiter),
network, nMap);
+ tm.setProgress(0.15);
+ tm.setStatusMessage("Processing the interactions...");
while ((line = br.readLine()) != null) {
if (cancelled) {
// Cancel called. Clean up the garbage.
@@ -141,7 +145,7 @@
this.cyNetworks = new CyNetwork[] {network};
-// tm.setProgress(1.0);
+ tm.setProgress(1.0);
logger.debug("SIF file loaded: ID = " + network.getSUID());
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/vizmap/VizmapPropertiesReader.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/vizmap/VizmapPropertiesReader.java
2011-11-14 19:25:03 UTC (rev 27462)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/vizmap/VizmapPropertiesReader.java
2011-11-14 22:16:30 UTC (rev 27463)
@@ -41,10 +41,12 @@
}
public void run(TaskMonitor tm) throws Exception {
+ tm.setProgress(0.0);
Properties props = new Properties();
props.load(inputStream);
-
+ tm.setProgress(0.3);
// Convert properties to list of visual visualStyles:
this.visualStyles = visualStyleSerializer.createVisualStyles(props);
+ tm.setProgress(1.0);
}
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/vizmap/VizmapXMLReader.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/vizmap/VizmapXMLReader.java
2011-11-14 19:25:03 UTC (rev 27462)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/vizmap/VizmapXMLReader.java
2011-11-14 22:16:30 UTC (rev 27463)
@@ -46,15 +46,18 @@
}
public void run(TaskMonitor tm) throws Exception {
+ tm.setProgress(0.0);
// No idea why, but ObjectFactory doesn't get picked up in the default
// Thread.currentThread().getContextClassLoader() classloader, whereas
// that approach works fine for bookmarks. Anyway, just force the
issue
// by getting this classloader.
final JAXBContext jaxbContext =
JAXBContext.newInstance(VIZMAP_PACKAGE, getClass().getClassLoader());
+ tm.setProgress(0.1);
final Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
-
+ tm.setProgress(0.2);
Vizmap vizmap = (Vizmap) unmarshaller.unmarshal(inputStream);
-
+ tm.setProgress(0.7);
this.visualStyles = visualStyleSerializer.createVisualStyles(vizmap);
+ tm.setProgress(1.0);
}
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkReader.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkReader.java
2011-11-14 19:25:03 UTC (rev 27462)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkReader.java
2011-11-14 22:16:30 UTC (rev 27463)
@@ -114,9 +114,10 @@
readDataMgr.initAllData();
readDataMgr.setSessionFormat(sessionFormat);
readDataMgr.setNetwork(cyNetworkFactory.getInstance());
-
+ tm.setProgress(0.1);
try {
readXGMML();
+ tm.setProgress(0.3);
this.cyNetworks = new CyNetwork[] {
readDataMgr.getNetwork() };
} catch (SAXException e) {
throw new IOException("Could not parse XGMML file: ");
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/cysession/CysessionWriterImpl.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/cysession/CysessionWriterImpl.java
2011-11-14 19:25:03 UTC (rev 27462)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/cysession/CysessionWriterImpl.java
2011-11-14 22:16:30 UTC (rev 27463)
@@ -64,14 +64,17 @@
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
-
+ taskMonitor.setProgress(0.0);
final JAXBContext jc =
JAXBContext.newInstance(Cysession.class.getPackage().getName(),
this.getClass().getClassLoader());
+ taskMonitor.setProgress(0.2);
Marshaller m = jc.createMarshaller();
+ taskMonitor.setProgress(0.4);
m.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
// TODO wtf?
//m.setProperty("com.sun.xml.bind.namespacePrefixMapper",
// new NamespacePrefixMapperForCysession());
-
+ taskMonitor.setProgress(0.6);
m.marshal(cysession, outputStream);
+ taskMonitor.setProgress(1.0);
}
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/datatable/csv/CSVCyWriter.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/datatable/csv/CSVCyWriter.java
2011-11-14 19:25:03 UTC (rev 27462)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/datatable/csv/CSVCyWriter.java
2011-11-14 22:16:30 UTC (rev 27463)
@@ -42,6 +42,7 @@
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
+ taskMonitor.setProgress(0.0);
CSVWriter writer = new CSVWriter(new
OutputStreamWriter(outputStream), ',', '"', "\r\n");
try {
List<CyColumn> columns = new ArrayList<CyColumn>();
@@ -51,6 +52,7 @@
}
columns.add(column);
}
+ taskMonitor.setProgress(0.2);
Collections.sort(columns, new Comparator<CyColumn>() {
@Override
public int compare(CyColumn o1, CyColumn o2) {
@@ -64,14 +66,17 @@
return
o1.getName().compareToIgnoreCase(o2.getName());
}
});
+ taskMonitor.setProgress(0.4);
writeHeader(writer, columns);
if (writeSchema) {
writeSchema(writer, columns);
}
+ taskMonitor.setProgress(0.6);
writeValues(writer, columns);
} finally {
writer.flush();
}
+ taskMonitor.setProgress(1.0);
}
private void writeSchema(CSVWriter writer, List<CyColumn> columns) {
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/BitmapWriter.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/BitmapWriter.java
2011-11-14 19:25:03 UTC (rev 27462)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/BitmapWriter.java
2011-11-14 22:16:30 UTC (rev 27463)
@@ -93,6 +93,7 @@
@Override
public void run(TaskMonitor tm) throws Exception {
+ tm.setProgress(0.0);
logger.debug("Bitmap image rendering start.");
// Extract size
@@ -103,11 +104,13 @@
final double scale =exportBitmapOptionsPanel.getZoom();
final int finalW = exportBitmapOptionsPanel.getWidthPixels();
final int finalH = exportBitmapOptionsPanel.getHeightPixels();
-
+ tm.setProgress(0.1);
final BufferedImage image = new BufferedImage(finalW, finalH,
BufferedImage.TYPE_INT_RGB);
Graphics2D g = (Graphics2D) image.getGraphics();
g.scale(scale, scale);
+ tm.setProgress(0.2);
re.printCanvas(g);
+ tm.setProgress(0.4);
g.dispose();
try {
@@ -117,5 +120,6 @@
}
logger.debug("Bitmap image rendering finished.");
+ tm.setProgress(1.0);
}
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/PDFWriter.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/PDFWriter.java
2011-11-14 19:25:03 UTC (rev 27462)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/PDFWriter.java
2011-11-14 22:16:30 UTC (rev 27463)
@@ -79,6 +79,8 @@
final PdfWriter writer = PdfWriter.getInstance(document,
stream);
document.open();
+ taskMonitor.setProgress(0.1);
+
final PdfContentByte canvas = writer.getDirectContent();
logger.debug("CB0 created: " + canvas.getClass());
@@ -93,12 +95,16 @@
engine.getProperties().setProperty("exportTextAsShape", new
Boolean(!exportTextAsFont).toString());
+ taskMonitor.setProgress(0.2);
+
if (exportTextAsFont) {
g = canvas.createGraphics(pageWidth, pageHeight, new
DefaultFontMapper());
} else {
g = canvas.createGraphicsShapes(pageWidth, pageHeight);
}
-
+
+ taskMonitor.setProgress(0.4);
+
logger.debug("##### G2D created: " + g);
double imageScale = Math.min(pageSize.getWidth() / width,
pageSize.getHeight() / height);
@@ -108,6 +114,8 @@
engine.printCanvas(g);
logger.debug("##### Canvas Rendering Done: ");
+ taskMonitor.setProgress(0.8);
+
g.dispose();
document.close();
writer.close();
@@ -115,6 +123,7 @@
stream.close();
logger.debug("PDF rendering finished.");
+ taskMonitor.setProgress(1.0);
}
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/PSWriter.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/PSWriter.java
2011-11-14 19:25:03 UTC (rev 27462)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/PSWriter.java
2011-11-14 22:16:30 UTC (rev 27463)
@@ -44,6 +44,8 @@
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
+ taskMonitor.setProgress(0.0);
+ taskMonitor.setStatusMessage("PS image rendering start...");
logger.debug("PS image rendering start.");
// TODO should be accomplished with presentation properties
@@ -53,14 +55,19 @@
p.setProperty(PSGraphics2D.PAGE_SIZE, "Letter");
p.setProperty("org.freehep.graphicsio.AbstractVectorGraphicsIO.TEXT_AS_SHAPES",
Boolean.toString(!exportTextAsFont));
-
+ taskMonitor.setProgress(0.1);
PSGraphics2D g = new PSGraphics2D(stream, new
Dimension(width.intValue(), height.intValue()));
g.setMultiPage(false); // true for PS file
g.setProperties(p);
+
+ taskMonitor.setProgress(0.2);
+
g.startExport();
engine.printCanvas(g);
g.endExport();
logger.debug("PS image created.");
+ taskMonitor.setStatusMessage("PS image created.");
+ taskMonitor.setProgress(1.0);
}
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/SVGWriter.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/SVGWriter.java
2011-11-14 19:25:03 UTC (rev 27462)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/graphics/SVGWriter.java
2011-11-14 22:16:30 UTC (rev 27463)
@@ -44,7 +44,8 @@
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
-
+ taskMonitor.setProgress(0.0);
+ taskMonitor.setStatusMessage("SVG Rendering Start...");
logger.debug("SVG Rendering Start.");
final SVGGraphics2D g = new SVGGraphics2D(stream, new
Dimension(width.intValue(), height.intValue()));
@@ -54,13 +55,14 @@
p.setProperty("org.freehep.graphicsio.AbstractVectorGraphicsIO.TEXT_AS_SHAPES",
Boolean.toString(!exportTextAsFont));
g.setProperties(p);
-
+ taskMonitor.setProgress(0.2);
g.startExport();
engine.printCanvas(g);
g.endExport();
logger.debug("SVG Rendering DONE!");
-
+ taskMonitor.setStatusMessage("SVG Rendering DONE!");
+ taskMonitor.setProgress(1.0);
}
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/session/SessionWriterImpl.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/session/SessionWriterImpl.java
2011-11-14 19:25:03 UTC (rev 27462)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/session/SessionWriterImpl.java
2011-11-14 22:16:30 UTC (rev 27463)
@@ -167,20 +167,38 @@
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
this.taskMonitor = taskMonitor;
+ taskMonitor.setProgress(0.0);
zos = new ZipOutputStream(outputStream);
for (CyNetworkView netView : session.getNetworkViews())
zipNetwork(netView);
+
+ taskMonitor.setProgress(0.1);
+ taskMonitor.setStatusMessage("Zip tables...");
zipTables();
+ taskMonitor.setProgress(0.2);
+ taskMonitor.setStatusMessage("Zip virtual columnz...");
zipVirtualColumns();
+ taskMonitor.setProgress(0.3);
+ taskMonitor.setStatusMessage("Zip CySession...");
zipCySession();
+ taskMonitor.setProgress(0.4);
+ taskMonitor.setStatusMessage("Zip Vizmap...");
zipVizmap();
+ taskMonitor.setProgress(0.5);
+ taskMonitor.setStatusMessage("Zip Cytosape properties...");
zipCytoscapeProps();
+ taskMonitor.setProgress(0.6);
+ taskMonitor.setStatusMessage("Zip bookmarks...");
zipBookmarks();
+ taskMonitor.setProgress(0.7);
+ taskMonitor.setStatusMessage("Zip File list...");
zipFileListMap();
-
+ taskMonitor.setProgress(0.8);
zos.close();
+ taskMonitor.setStatusMessage("Done!");
+ taskMonitor.setProgress(1.0);
}
private void zipVirtualColumns() throws IOException {
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/sif/SifWriter.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/sif/SifWriter.java
2011-11-14 19:25:03 UTC (rev 27462)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/sif/SifWriter.java
2011-11-14 22:16:30 UTC (rev 27463)
@@ -28,6 +28,8 @@
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
+ taskMonitor.setProgress(0.0);
+
final Writer writer = new OutputStreamWriter(outputStream);
try {
final String lineSep =
System.getProperty("line.separator");
@@ -37,7 +39,7 @@
for ( CyNode node : nodeList ) {
if (taskMonitor != null) {
// Report on Progress
- double percent = ((double) i++ /
nodeList.size()) * 100.0;
+ double percent = ((double) i++ /
nodeList.size());
taskMonitor.setProgress(percent);
}
@@ -71,6 +73,7 @@
} finally {
writer.close();
}
+ taskMonitor.setProgress(1.0);
}
@Override
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/vizmap/VizmapWriterImpl.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/vizmap/VizmapWriterImpl.java
2011-11-14 19:25:03 UTC (rev 27462)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/vizmap/VizmapWriterImpl.java
2011-11-14 22:16:30 UTC (rev 27463)
@@ -71,19 +71,26 @@
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
+ taskMonitor.setProgress(0.0);
final JAXBContext jc =
JAXBContext.newInstance(Vizmap.class.getPackage().getName(), this.getClass()
.getClassLoader());
Marshaller m = jc.createMarshaller();
+ taskMonitor.setProgress(0.2);
m.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
final DateFormat df = new SimpleDateFormat("yyyy_MM_dd-HH_mm");
String now = df.format(new Date());
String vizmapDocId = "VizMap-" + now;
+ taskMonitor.setProgress(0.2);
+
Vizmap vizmap =
visualStyleSerializer.createVizmap(visualStyles);
vizmap.setId(vizmapDocId);
vizmap.setDocumentVersion(VIZMAP_VERSION);
+ taskMonitor.setProgress(0.4);
+
m.marshal(vizmap, outputStream);
+ taskMonitor.setProgress(1.0);
}
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
2011-11-14 19:25:03 UTC (rev 27462)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
2011-11-14 22:16:30 UTC (rev 27463)
@@ -157,31 +157,33 @@
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
+ taskMonitor.setProgress(0.0);
writer = new OutputStreamWriter(outputStream);
// write out the XGMML preamble
writePreamble();
depth++;
-
+ taskMonitor.setProgress(0.2);
// write out our metadata
writeMetadata();
-
+ taskMonitor.setProgress(0.3);
// write out network attributes
writeNetworkAttributes();
-
+ taskMonitor.setProgress(0.4);
// Output our nodes
writeNodes();
// TODO obviously, fix this
// writeGroups();
-
+ taskMonitor.setProgress(0.6);
// Create edge objects
writeEdges();
-
+ taskMonitor.setProgress(0.8);
depth--;
// Wwrite final tag
writeElement("</graph>\n");
writer.flush();
+ taskMonitor.setProgress(1.0);
}
/**
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