Author: mes
Date: 2011-03-30 15:54:41 -0700 (Wed, 30 Mar 2011)
New Revision: 24628
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderFactory.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractPropertyReaderFactory.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractTableReaderFactory.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/GenericReaderManager.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/session/SessionReaderFactoryImpl.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/session/SessionReaderImpl.java
Log:
added input name argument to all readers
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderFactory.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderFactory.java
2011-03-30 22:54:30 UTC (rev 24627)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderFactory.java
2011-03-30 22:54:41 UTC (rev 24628)
@@ -42,6 +42,7 @@
protected final CyNetworkFactory cyNetworkFactory;
protected InputStream inputStream;
+ protected String inputName;
public AbstractNetworkViewReaderFactory(CyFileFilter filter,
CyNetworkViewFactory
cyNetworkViewFactory,
@@ -51,9 +52,10 @@
this.cyNetworkFactory = cyNetworkFactory;
}
- public void setInputStream(InputStream is) {
+ public void setInputStream(InputStream is, String in) {
if (is == null) throw new NullPointerException("Input stream is null");
inputStream = is;
+ inputName = in;
}
public CyFileFilter getCyFileFilter() {
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractPropertyReaderFactory.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractPropertyReaderFactory.java
2011-03-30 22:54:30 UTC (rev 24627)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractPropertyReaderFactory.java
2011-03-30 22:54:41 UTC (rev 24628)
@@ -39,15 +39,17 @@
private final CyFileFilter filter;
protected InputStream inputStream;
+ protected String inputName;
public AbstractPropertyReaderFactory(CyFileFilter filter) {
this.filter = filter;
}
- public void setInputStream(InputStream is) {
+ public void setInputStream(InputStream is, String in) {
if (is == null)
throw new NullPointerException("Input stream is null");
inputStream = is;
+ inputName = in;
}
public CyFileFilter getCyFileFilter() {
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractTableReaderFactory.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractTableReaderFactory.java
2011-03-30 22:54:30 UTC (rev 24627)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractTableReaderFactory.java
2011-03-30 22:54:41 UTC (rev 24628)
@@ -39,6 +39,7 @@
private final CyFileFilter filter;
protected InputStream inputStream;
+ protected String inputName;
protected final CyTableFactory tableFactory;
public AbstractTableReaderFactory(CyFileFilter filter, CyTableFactory
tableFactory) {
@@ -51,10 +52,11 @@
this.tableFactory = tableFactory;
}
- public void setInputStream(InputStream is) {
+ public void setInputStream(InputStream is, String in) {
if (is == null)
throw new NullPointerException("Input stream is null");
inputStream = is;
+ inputName = in;
}
public CyFileFilter getCyFileFilter() {
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/GenericReaderManager.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/GenericReaderManager.java
2011-03-30 22:54:30 UTC (rev 24627)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/GenericReaderManager.java
2011-03-30 22:54:41 UTC (rev 24628)
@@ -61,7 +61,7 @@
* File name or null if no reader is capable of reading the
file.
* @return GraphReader capable of reading the specified file.
*/
- public R getReader(URI uri) {
+ public R getReader(URI uri, String inputName) {
for (T factory : factories) {
CyFileFilter cff = factory.getCyFileFilter();
@@ -73,7 +73,7 @@
InputStream stream =
uri.toURL().openStream();
if ( !stream.markSupported() )
stream = new MarkSupportedInputStream(stream);
- factory.setInputStream( stream );
+ factory.setInputStream( stream,
inputName );
return
(R)factory.getTaskIterator().next();
} catch (IOException e) {
logger.warn("Error opening stream to
URI: " + uri.toString(), e);
@@ -85,7 +85,7 @@
return null;
}
- public R getReader(InputStream stream) {
+ public R getReader(InputStream stream, String inputName) {
try {
if ( !stream.markSupported() )
@@ -100,7 +100,7 @@
// of the first 2KB rather than the stream
itself.
if
(cff.accepts(CopyInputStream.copyKBytes(stream,2), category)) {
logger.debug("successfully matched
factory " + factory);
- factory.setInputStream(stream);
+ factory.setInputStream(stream,
inputName);
return
(R)factory.getTaskIterator().next();
}
}
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/session/SessionReaderFactoryImpl.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/session/SessionReaderFactoryImpl.java
2011-03-30 22:54:30 UTC (rev 24627)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/session/SessionReaderFactoryImpl.java
2011-03-30 22:54:41 UTC (rev 24628)
@@ -46,6 +46,7 @@
private final CyPropertyReaderManager propertyReaderMgr;
private final CyProperty<Properties> properties;
private InputStream inputStream;
+ private String inputName;
public SessionReaderFactoryImpl(CyFileFilter filter,
CyNetworkViewReaderManager
netviewReaderMgr,
@@ -57,10 +58,11 @@
this.properties = properties;
}
- public void setInputStream(InputStream is) {
+ public void setInputStream(InputStream is, String in) {
if (is == null)
throw new NullPointerException("Input stream is null");
inputStream = is;
+ inputName = in;
}
public CyFileFilter getCyFileFilter() {
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/session/SessionReaderImpl.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/session/SessionReaderImpl.java
2011-03-30 22:54:30 UTC (rev 24627)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/session/SessionReaderImpl.java
2011-03-30 22:54:41 UTC (rev 24628)
@@ -188,18 +188,18 @@
extractPluginEntry(tmpIs, entryName);
} else if (entryName.endsWith(CYSESSION)) {
//System.out.println(" extracting session
file");
- extractSessionState(tmpIs);
+ extractSessionState(tmpIs, entryName);
} else if (entryName.endsWith(VIZMAP_PROPS)) {
//System.out.println(" extracting vizmap
props");
- extractVizmapProps(tmpIs);
+ extractVizmapProps(tmpIs, entryName);
} else if (entryName.endsWith(CY_PROPS)) {
//System.out.println(" extracting cytoscape
props");
- extractCytoscapeProps(tmpIs);
+ extractCytoscapeProps(tmpIs, entryName);
} else if (entryName.endsWith(XGMML_EXT)) {
//System.out.println(" extracting network");
extractNetwork(tmpIs, entryName);
} else if (entryName.endsWith(BOOKMARKS_FILE)) {
- extractBookmarks(tmpIs);
+ extractBookmarks(tmpIs, entryName);
//System.out.println(" extracting bookmarks");
} else {
logger.warn("Unknown entry found in session zip
file!\n" + entryName);
@@ -232,7 +232,7 @@
// force the vsbSwitch off
prop.setProperty("visualStyleBuilder", "off");
- CyNetworkViewReader reader = netviewReaderMgr.getReader(is);
+ CyNetworkViewReader reader = netviewReaderMgr.getReader(is,
entryName);
reader.run(taskMonitor);
networkViews.put(entryName, reader.getNetworkViews());
@@ -287,9 +287,9 @@
}
- private void extractVizmapProps(InputStream is) throws Exception {
+ private void extractVizmapProps(InputStream is, String entryName)
throws Exception {
- CyPropertyReader reader = propertyReaderMgr.getReader(is);
+ CyPropertyReader reader = propertyReaderMgr.getReader(is,
entryName);
if(reader == null){
return;
}
@@ -297,20 +297,20 @@
vizmapProps = (Properties) reader.getProperty();
}
- private void extractCytoscapeProps(InputStream is) throws Exception {
- CyPropertyReader reader = propertyReaderMgr.getReader(is);
+ private void extractCytoscapeProps(InputStream is, String entryName)
throws Exception {
+ CyPropertyReader reader = propertyReaderMgr.getReader(is,
entryName);
reader.run(taskMonitor);
cytoscapeProps = (Properties) reader.getProperty();
}
- private void extractBookmarks(InputStream is) throws Exception {
- CyPropertyReader reader = propertyReaderMgr.getReader(is);
+ private void extractBookmarks(InputStream is, String entryName) throws
Exception {
+ CyPropertyReader reader = propertyReaderMgr.getReader(is,
entryName);
reader.run(taskMonitor);
bookmarks = (Bookmarks) reader.getProperty();
}
- private void extractSessionState(InputStream is) throws Exception {
- CyPropertyReader reader = propertyReaderMgr.getReader(is);
+ private void extractSessionState(InputStream is, String entryName)
throws Exception {
+ CyPropertyReader reader = propertyReaderMgr.getReader(is,
entryName);
reader.run(taskMonitor);
cysession = (Cysession) reader.getProperty();
}
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