Author: pwang
Date: 2011-12-09 17:28:11 -0800 (Fri, 09 Dec 2011)
New Revision: 27763
Modified:
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/CyActivator.java
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/FilterIO.java
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/FilterPlugin.java
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/util/FilterUtil.java
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/view/FilterMainPanel.java
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/view/InteractionFilterPanel.java
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/view/TopoFilterPanel.java
Log:
use CyProperty to get the filter properties
Modified:
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/CyActivator.java
2011-12-10 01:27:03 UTC (rev 27762)
+++
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/CyActivator.java
2011-12-10 01:28:11 UTC (rev 27763)
@@ -3,6 +3,7 @@
import org.cytoscape.work.TaskManager;
import org.cytoscape.model.CyNetworkManager;
+import org.cytoscape.property.CyProperty;
import org.cytoscape.application.CytoscapeVersion;
import org.cytoscape.application.CyApplicationConfiguration;
import org.cytoscape.view.model.CyNetworkViewManager;
@@ -22,15 +23,14 @@
import
org.cytoscape.application.swing.events.CytoPanelComponentSelectedListener;
import org.cytoscape.application.swing.CyAction;
-
import org.osgi.framework.BundleContext;
-
import org.cytoscape.service.util.AbstractCyActivator;
+import org.cytoscape.session.events.SessionLoadedListener;
import java.util.Properties;
+import org.cytoscape.filter.internal.read.filter.FilterReader;
+import org.cytoscape.filter.internal.ServicesUtil;
-
-
public class CyActivator extends AbstractCyActivator {
public CyActivator() {
super();
@@ -48,15 +48,28 @@
TaskManager taskManagerServiceRef =
getService(bc,TaskManager.class);
CyApplicationConfiguration cyApplicationConfigurationServiceRef
= getService(bc,CyApplicationConfiguration.class);
CytoscapeVersion cytoscapeVersionService =
getService(bc,CytoscapeVersion.class);
+
+ //
+ ServicesUtil.cySwingApplicationServiceRef =
cySwingApplicationServiceRef;
+ ServicesUtil.cyApplicationManagerServiceRef =
cyApplicationManagerServiceRef;
+ ServicesUtil.cyNetworkViewManagerServiceRef =
cyNetworkViewManagerServiceRef;
+ ServicesUtil.cyNetworkManagerServiceRef =
cyNetworkManagerServiceRef;
+ ServicesUtil.cyServiceRegistrarServiceRef =
cyServiceRegistrarServiceRef;
+ ServicesUtil.cyEventHelperServiceRef = cyEventHelperServiceRef;
+ ServicesUtil.taskManagerServiceRef = taskManagerServiceRef;
+ //
+
+ FilterReader filterReader = new FilterReader("props.filters");
+ ServicesUtil.filterReader = filterReader;
- FilterPlugin filterPlugin = new
FilterPlugin(cyApplicationManagerServiceRef,cySwingApplicationServiceRef,
- cyApplicationConfigurationServiceRef,
cytoscapeVersionService);
+ FilterPlugin filterPlugin = new FilterPlugin();
QuickFindApp quickFindApp = new
QuickFindApp(cyApplicationManagerServiceRef,cyNetworkViewManagerServiceRef,cySwingApplicationServiceRef,cyNetworkManagerServiceRef);
FilterMainPanel filterMainPanel = new
FilterMainPanel(cyApplicationManagerServiceRef,filterPlugin,cyNetworkManagerServiceRef,cyServiceRegistrarServiceRef,cyEventHelperServiceRef,taskManagerServiceRef);
FilterCytoPanelComponent filterCytoPanelComponent = new
FilterCytoPanelComponent(filterMainPanel);
FilterPanelSelectedListener filterPanelSelectedListener = new
FilterPanelSelectedListener(filterMainPanel);
FilterMenuItemAction filterAction = new
FilterMenuItemAction(cyApplicationManagerServiceRef,cySwingApplicationServiceRef,filterMainPanel);
-
+ //FiltersProperty filtersProps = new
FiltersProperty(cyApplicationConfigurationServiceRef);
+
registerService(bc,filterCytoPanelComponent,CytoPanelComponent.class, new
Properties());
registerAllServices(bc,filterMainPanel, new Properties());
registerService(bc,filterPanelSelectedListener,CytoPanelComponentSelectedListener.class,
new Properties());
@@ -64,6 +77,13 @@
registerAllServices(bc,quickFindApp, new Properties());
registerAllServices(bc,filterPlugin, new Properties());
+ //registerAllServices(bc,filtersProps, new Properties());
+ Properties filterReaderProps = new Properties();
+ filterReaderProps.setProperty("cyPropertyName","filters");
+ filterReaderProps.setProperty("serviceType","property");
+
+ registerAllServices(bc,filterReader, filterReaderProps);
+
}
}
Modified:
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/FilterIO.java
===================================================================
---
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/FilterIO.java
2011-12-10 01:27:03 UTC (rev 27762)
+++
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/FilterIO.java
2011-12-10 01:28:11 UTC (rev 27763)
@@ -49,6 +49,7 @@
import java.util.Vector;
import org.cytoscape.application.CyApplicationManager;
+import org.cytoscape.filter.internal.ServicesUtil;
import org.cytoscape.filter.internal.filters.util.FilterUtil;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -69,13 +70,10 @@
/**
* Construct the filter objects based on the string representation of
each filter.
*/
- public int[] getFilterVectFromPropFile(final InputStreamReader reader) {
- int addCount = 0;
- int totalCount = 0;
- int retValue[] = new int[2];
- retValue[0] = totalCount;
- retValue[1] = addCount;
+ public static Vector<CompositeFilter> getFilterVectFromPropFile(final
InputStreamReader reader) {
+ Vector<CompositeFilter> retFilterVect = new
Vector<CompositeFilter>();
+
try {
BufferedReader in = new BufferedReader(reader);
@@ -83,7 +81,7 @@
String oneLine = in.readLine();
if (oneLine == null) {
- return retValue;
+ return null;
}
double filterVersion = 0.0;
if (oneLine.trim().startsWith("FilterVersion"))
{
@@ -93,10 +91,9 @@
// Ignore filters from the old version
if (filterVersion <0.2) {
- return retValue;
+ return null;
}
-
- Vector<CompositeFilter> allFilterVect =
filterPlugin.getAllFilterVect();
+
while (oneLine != null) {
// ignore comment, empty line or the
version line
if (oneLine.startsWith("#") ||
oneLine.trim().equals("")||oneLine.startsWith("FilterVersion")) {
@@ -117,12 +114,9 @@
filterStrVect.add(oneLine);
} // inner while loop
- totalCount++;
-
CompositeFilter aFilter =
getFilterFromStrVect(filterStrVect);
- if (aFilter != null &&
!FilterUtil.isFilterNameDuplicated(filterPlugin, aFilter.getName())) {
-
allFilterVect.add(aFilter);
- addCount++;
+ if (aFilter != null &&
!FilterUtil.isFilterNameDuplicated(retFilterVect, aFilter.getName())) {
+
retFilterVect.add(aFilter);
}
}
@@ -135,29 +129,28 @@
}
}
} catch (Exception ex) {
- logger.error("Filter Read error", ex);
+ //logger.error("Filter Read error", ex);
+ ex.printStackTrace();
}
-
- retValue[0] = totalCount;
- retValue[1] = addCount;
- return retValue;
+
+ return retFilterVect;
}
/**
* Construct the filter objects based on the string representation of
each filter.
*/
- public int[] getFilterVectFromPropFile(final File input) {
+ public static Vector<CompositeFilter> getFilterVectFromPropFile(final
File input) {
try {
return getFilterVectFromPropFile(new FileReader(input));
}
catch (final FileNotFoundException e) {
- logger.error("Filter Read error", e);
+ //logger.error("Filter Read error", e);
final int[] retval = { 0, 0 };
- return retval;
+ return null;
}
}
- private AdvancedSetting getAdvancedSettingFromStrVect(List<String>
pAdvSettingStrVect) {
+ private static AdvancedSetting
getAdvancedSettingFromStrVect(List<String> pAdvSettingStrVect) {
AdvancedSetting advSetting = new AdvancedSetting();
String line = null;
for (int i=0; i<pAdvSettingStrVect.size(); i++ ) {
@@ -210,7 +203,7 @@
}
- private CompositeFilter getFilterFromStrVect(List<String>
pFilterStrVect){
+ private static CompositeFilter getFilterFromStrVect(List<String>
pFilterStrVect){
boolean isTopologyFilter = false;
boolean isInteractionFilter = false;
@@ -244,11 +237,11 @@
filterStrVect.addAll(pFilterStrVect.subList(1, startIndex));
filterStrVect.addAll(pFilterStrVect.subList(endIndex+1,
pFilterStrVect.size()));
- CompositeFilter retFilter = new
CompositeFilter(applicationManager);
+ CompositeFilter retFilter = new
CompositeFilter(ServicesUtil.cyApplicationManagerServiceRef);
retFilter.setAdvancedSetting(getAdvancedSettingFromStrVect(advSettingStrVect));
if (isTopologyFilter) {
- retFilter = new TopologyFilter(applicationManager);
+ retFilter = new
TopologyFilter(ServicesUtil.cyApplicationManagerServiceRef);
retFilter.setAdvancedSetting(getAdvancedSettingFromStrVect(advSettingStrVect));
getTopologyFilterFromStrVect((TopologyFilter)retFilter,
filterStrVect);
return retFilter;
@@ -257,10 +250,10 @@
if (isInteractionFilter) {
AdvancedSetting advSetting =
getAdvancedSettingFromStrVect(advSettingStrVect);
if (advSetting.isNodeChecked()) {
- retFilter = new
NodeInteractionFilter(applicationManager);
+ retFilter = new
NodeInteractionFilter(ServicesUtil.cyApplicationManagerServiceRef);
}
else {//advSetting.isEdgeChecked() == true
- retFilter = new
EdgeInteractionFilter(applicationManager);
+ retFilter = new
EdgeInteractionFilter(ServicesUtil.cyApplicationManagerServiceRef);
}
retFilter.setAdvancedSetting(advSetting);
@@ -269,7 +262,8 @@
}
- Vector<CompositeFilter> allFilterVect =
filterPlugin.getAllFilterVect();
+ Vector<CompositeFilter> allFilterVect = new
Vector<CompositeFilter>(); //ServicesUtil.filterReader.getProperties();
+
for (int i=0; i<filterStrVect.size(); i++ ) {
line = filterStrVect.get(i) ;
@@ -395,10 +389,10 @@
}
- private void getTopologyFilterFromStrVect(TopologyFilter pFilter,
List<String> pFilterStrVect){
+ private static void getTopologyFilterFromStrVect(TopologyFilter
pFilter, List<String> pFilterStrVect){
//logger.debug("\nFilterIO.getTopologyFilterFromStrVect()
...\n");
- Vector<CompositeFilter> allFilterVect =
filterPlugin.getAllFilterVect();
+ Vector<CompositeFilter> allFilterVect =
ServicesUtil.filterReader.getProperties();
String line = null;
for (int i=0; i<pFilterStrVect.size(); i++ ) {
line = pFilterStrVect.get(i) ;
@@ -445,9 +439,9 @@
}
- private void getInteractionFilterFromStrVect(InteractionFilter pFilter,
List<String> pFilterStrVect){
+ private static void getInteractionFilterFromStrVect(InteractionFilter
pFilter, List<String> pFilterStrVect){
- Vector<CompositeFilter> allFilterVect =
filterPlugin.getAllFilterVect();
+ Vector<CompositeFilter> allFilterVect =
ServicesUtil.filterReader.getProperties();
String line = null;
for (int i=0; i<pFilterStrVect.size(); i++ ) {
line = pFilterStrVect.get(i) ;
@@ -489,36 +483,36 @@
public void saveGlobalPropFile(File pPropFile) {
- // Because one filter may depend on the other, CompositeFilters
must
- // be sorted in the order of depthLevel before save
- Vector<CompositeFilter> allFilterVect =
filterPlugin.getAllFilterVect();
- Object [] sortedFilters =
getSortedCompositeFilter(allFilterVect);
- Object[] globalFilters = getFiltersByScope(sortedFilters,
"global");
-
- try {
- BufferedWriter writer = new BufferedWriter(new
FileWriter(pPropFile));
-
- try {
- // Need to allow writing of header only so that when the last
- // global filter is deleted, the props file is updated to
reflect this
- writer.write("FilterVersion=0.2\n");
-
- if (globalFilters != null) {
- for (int i = 0; i < globalFilters.length; i++) {
- CompositeFilter theFilter = (CompositeFilter)
globalFilters[i];
- writer.write(theFilter.toSerializedForm());
- writer.newLine();
- }
- }
- }
- finally {
- if (writer != null) {
- writer.close();
- }
- }
- } catch (Exception ex) {
- logger.error("Global filter Write error",ex);
- }
+// // Because one filter may depend on the other, CompositeFilters
must
+// // be sorted in the order of depthLevel before save
+// Vector<CompositeFilter> allFilterVect =
filterPlugin.getAllFilterVect();
+// Object [] sortedFilters =
getSortedCompositeFilter(allFilterVect);
+// Object[] globalFilters = getFiltersByScope(sortedFilters,
"global");
+//
+// try {
+// BufferedWriter writer = new BufferedWriter(new
FileWriter(pPropFile));
+//
+// try {
+// // Need to allow writing of header only so that when the last
+// // global filter is deleted, the props file is updated to
reflect this
+// writer.write("FilterVersion=0.2\n");
+//
+// if (globalFilters != null) {
+// for (int i = 0; i < globalFilters.length; i++) {
+// CompositeFilter theFilter = (CompositeFilter)
globalFilters[i];
+// writer.write(theFilter.toSerializedForm());
+// writer.newLine();
+// }
+// }
+// }
+// finally {
+// if (writer != null) {
+// writer.close();
+// }
+// }
+// } catch (Exception ex) {
+// logger.error("Global filter Write error",ex);
+// }
}
@@ -547,47 +541,47 @@
public void saveSessionStateFiles(List<File> pFileList){
- // Because one filter may depend on the other, CompositeFilters
must
- // be sorted in the order of depthLevel before save
- Vector<CompositeFilter> allFilterVect =
filterPlugin.getAllFilterVect();
- Object [] sortedFilters =
getSortedCompositeFilter(allFilterVect);
- Object[] sessionFilters = getFiltersByScope(sortedFilters,
"session");
-
- if (sessionFilters == null || sessionFilters.length == 0) {
- return;
- }
-
- // Create an empty file on system temp directory
- String tmpDir = System.getProperty("java.io.tmpdir");
- // logger.debug("java.io.tmpdir: [" + tmpDir + "]");
-
- File session_filter_file = new File(tmpDir,
"session_filters.props");
-
- //
- try {
- BufferedWriter writer = new BufferedWriter(new
FileWriter(session_filter_file));
-
- try {
- writer.write("FilterVersion=0.2\n");
-
- for (int i = 0; i < sessionFilters.length; i++) {
- CompositeFilter theFilter = (CompositeFilter)
sessionFilters[i];
- writer.write(theFilter.toSerializedForm());
- writer.newLine();
- }
- }
- finally {
- if ( writer != null) {
- writer.close();
- }
- }
- } catch (Exception ex) {
- logger.error("Session filter Write error",ex);
- }
-
- if ((session_filter_file != null) && (session_filter_file.exists())) {
- pFileList.add(session_filter_file);
- }
+// // Because one filter may depend on the other, CompositeFilters
must
+// // be sorted in the order of depthLevel before save
+// Vector<CompositeFilter> allFilterVect =
filterPlugin.getAllFilterVect();
+// Object [] sortedFilters =
getSortedCompositeFilter(allFilterVect);
+// Object[] sessionFilters = getFiltersByScope(sortedFilters,
"session");
+//
+// if (sessionFilters == null || sessionFilters.length == 0) {
+// return;
+// }
+//
+// // Create an empty file on system temp directory
+// String tmpDir = System.getProperty("java.io.tmpdir");
+// // logger.debug("java.io.tmpdir: [" + tmpDir + "]");
+//
+// File session_filter_file = new File(tmpDir,
"session_filters.props");
+//
+// //
+// try {
+// BufferedWriter writer = new BufferedWriter(new
FileWriter(session_filter_file));
+//
+// try {
+// writer.write("FilterVersion=0.2\n");
+//
+// for (int i = 0; i < sessionFilters.length; i++) {
+// CompositeFilter theFilter = (CompositeFilter)
sessionFilters[i];
+// writer.write(theFilter.toSerializedForm());
+// writer.newLine();
+// }
+// }
+// finally {
+// if ( writer != null) {
+// writer.close();
+// }
+// }
+// } catch (Exception ex) {
+// logger.error("Session filter Write error",ex);
+// }
+//
+// if ((session_filter_file != null) && (session_filter_file.exists()))
{
+// pFileList.add(session_filter_file);
+// }
}
@@ -600,9 +594,10 @@
try {
File session_filter_file = pStateFileList.get(0);
- int[] loadCounts =
getFilterVectFromPropFile(session_filter_file);
- logger.info("\tLoad " + loadCounts[1] + " session
filters");
- logger.info("\t\t" + (loadCounts[0]-loadCounts[1]) + "
duplicated filters are not loaded");
+ //int[] loadCounts =
+ getFilterVectFromPropFile(session_filter_file);
+ //logger.info("\tLoad " + loadCounts[1] + " session
filters");
+ //logger.info("\t\t" + (loadCounts[0]-loadCounts[1]) +
" duplicated filters are not loaded");
} catch (Throwable ee) {
logger.error("Failed to restore Filters from session!");
}
Modified:
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/FilterPlugin.java
===================================================================
---
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/FilterPlugin.java
2011-12-10 01:27:03 UTC (rev 27762)
+++
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/FilterPlugin.java
2011-12-10 01:28:11 UTC (rev 27763)
@@ -44,6 +44,7 @@
import org.cytoscape.application.swing.CySwingApplication;
import org.cytoscape.application.CyApplicationConfiguration;
import org.cytoscape.application.CytoscapeVersion;
+import org.cytoscape.filter.internal.read.filter.FilterReader;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.InputStream;
@@ -53,10 +54,10 @@
/**
*
*/
-public class FilterPlugin implements CytoscapeShutdownListener{
+public class FilterPlugin { //implements CytoscapeShutdownListener {
private Vector<CompositeFilter> allFilterVect = null;
- private final FilterIO filterIO;
+ //private final FilterIO filterIO;
private final Logger logger;
public static final String DYNAMIC_FILTER_THRESHOLD =
"dynamicFilterThreshold";
@@ -66,13 +67,15 @@
public static boolean shouldFireFilterEvent = false;
public static String cyConfigVerDir;
+ private FilterReader filterReader;
+
// Other plugin can get a handler to all the filters defined
- public Vector<CompositeFilter> getAllFilterVect() {
- if (allFilterVect == null) {
- allFilterVect = new Vector<CompositeFilter>();
- }
- return allFilterVect;
- }
+// public Vector<CompositeFilter> getAllFilterVect() {
+// if (allFilterVect == null) {
+// allFilterVect = new Vector<CompositeFilter>();
+// }
+// return allFilterVect;
+// }
/**
* Creates a new FilterPlugin object.
@@ -82,72 +85,77 @@
* @param csfilter
* DOCUMENT ME!
*/
- public FilterPlugin(CyApplicationManager applicationManager,
CySwingApplication application, final CyApplicationConfiguration config,
CytoscapeVersion version) {
- filterIO = new FilterIO(applicationManager, this);
+ public FilterPlugin() {
- if (allFilterVect == null) {
- allFilterVect = new Vector<CompositeFilter>();
- }
-
+ //this.filterReader = filterReader;
+
+ //System.out.println("\n\nFilterPlugin constructor:
\n\tthis.filterReader.getProperties().size() =
"+this.filterReader.getProperties().size());
+
+// filterIO = new FilterIO(applicationManager, this);
+//
+// if (allFilterVect == null) {
+// allFilterVect = new Vector<CompositeFilter>();
+// }
+//
logger = LoggerFactory.getLogger(FilterPlugin.class);
-
- cyConfigVerDir = new File(config.getSettingLocation(),
File.separator + version.getMajorVersion()+ "." +
version.getMinorVersion()).getAbsolutePath();
-
- restoreInitState();
+//
+// cyConfigVerDir = new File(config.getSettingLocation(),
File.separator + version.getMajorVersion()+ "." +
version.getMinorVersion()).getAbsolutePath();
+//
+// restoreInitState();
}
- @Override
- public void handleEvent(CytoscapeShutdownEvent e) {
- //onCytoscapeExit
-
- final File globalFilterFile = new File(cyConfigVerDir +
File.separator + "filters.props");
- filterIO.saveGlobalPropFile(globalFilterFile);
- }
+// @Override
+// public void handleEvent(CytoscapeShutdownEvent e) {
+// //onCytoscapeExit
+//
+// //final File globalFilterFile = new File(cyConfigVerDir +
File.separator + "filters.props");
+// //filterIO.saveGlobalPropFile(globalFilterFile);
+// }
public void restoreInitState() {
- final File globalFilterFile = new File(cyConfigVerDir +
File.separator + "filters.props");
-
- if (!globalFilterFile.isFile()){
- // filers.props does not exist, so load the default one
- loadDefaultFilter();
- return;
- }
-
- int[] loadCount =
filterIO.getFilterVectFromPropFile(globalFilterFile);
- logger.debug("FilterPlugin: load " + loadCount[1] + " of " +
loadCount[0] + " filters from filters.prop");
-
- if (loadCount[1] == 0) {
- final String DEFAULT_FILTERS_FILENAME =
"/default_filters.props";
- final InputStream inputStream =
FilterPlugin.class.getResourceAsStream(DEFAULT_FILTERS_FILENAME);
-
- if (inputStream == null) {
- System.err.println("FilterPlugin: Failed to
read default filters from \""
- + DEFAULT_FILTERS_FILENAME +
"\" in the plugin's jar file!");
- return;
- }
-
- final InputStreamReader inputStreamReader = new
InputStreamReader(inputStream);
- loadCount =
filterIO.getFilterVectFromPropFile(inputStreamReader);
-
- logger.debug("FilterPlugin: load " + loadCount[1] + "
of " + loadCount[0]
- + " filters from " +
DEFAULT_FILTERS_FILENAME);
- }
+// final File globalFilterFile = new File(cyConfigVerDir +
File.separator + "filters.props");
+//
+// if (!globalFilterFile.isFile()){
+// // filers.props does not exist, so load the default one
+// loadDefaultFilter();
+// return;
+// }
+//
+// int[] loadCount =
filterIO.getFilterVectFromPropFile(globalFilterFile);
+// logger.debug("FilterPlugin: load " + loadCount[1] + " of " +
loadCount[0] + " filters from filters.prop");
+//
+// if (loadCount[1] == 0) {
+// final String DEFAULT_FILTERS_FILENAME =
"/default_filters.props";
+// final InputStream inputStream =
FilterPlugin.class.getResourceAsStream(DEFAULT_FILTERS_FILENAME);
+//
+// if (inputStream == null) {
+// System.err.println("FilterPlugin: Failed to
read default filters from \""
+// + DEFAULT_FILTERS_FILENAME +
"\" in the plugin's jar file!");
+// return;
+// }
+//
+// final InputStreamReader inputStreamReader = new
InputStreamReader(inputStream);
+// loadCount =
filterIO.getFilterVectFromPropFile(inputStreamReader);
+//
+// logger.debug("FilterPlugin: load " + loadCount[1] + "
of " + loadCount[0]
+// + " filters from " +
DEFAULT_FILTERS_FILENAME);
+// }
}
private void loadDefaultFilter(){
- final String DEFAULT_FILTERS_FILENAME =
"/default_filters.props";
- final InputStream inputStream =
FilterPlugin.class.getResourceAsStream(DEFAULT_FILTERS_FILENAME);
-
- if (inputStream == null) {
- System.err.println("FilterPlugin: Failed to read
default filters from \""
- + DEFAULT_FILTERS_FILENAME + "\" in
the plugin's jar file!");
- return;
- }
-
- final InputStreamReader inputStreamReader = new
InputStreamReader(inputStream);
- filterIO.getFilterVectFromPropFile(inputStreamReader);
+// final String DEFAULT_FILTERS_FILENAME =
"/default_filters.props";
+// final InputStream inputStream =
FilterPlugin.class.getResourceAsStream(DEFAULT_FILTERS_FILENAME);
+//
+// if (inputStream == null) {
+// System.err.println("FilterPlugin: Failed to read
default filters from \""
+// + DEFAULT_FILTERS_FILENAME + "\" in
the plugin's jar file!");
+// return;
+// }
+//
+// final InputStreamReader inputStreamReader = new
InputStreamReader(inputStream);
+// filterIO.getFilterVectFromPropFile(inputStreamReader);
}
// override the following two methods to save state.
@@ -158,7 +166,7 @@
* DOCUMENT ME!
*/
public void restoreSessionState(List<File> pStateFileList) {
- filterIO.restoreSessionState(pStateFileList);
+ //filterIO.restoreSessionState(pStateFileList);
}
/**
@@ -168,6 +176,6 @@
* DOCUMENT ME!
*/
public void saveSessionStateFiles(List<File> pFileList) {
- filterIO.saveSessionStateFiles(pFileList);
+ //filterIO.saveSessionStateFiles(pFileList);
}
}
Modified:
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/util/FilterUtil.java
===================================================================
---
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/util/FilterUtil.java
2011-12-10 01:27:03 UTC (rev 27762)
+++
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/util/FilterUtil.java
2011-12-10 01:28:11 UTC (rev 27763)
@@ -6,6 +6,7 @@
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.filter.internal.ServicesUtil;
import org.cytoscape.filter.internal.filters.CompositeFilter;
import org.cytoscape.filter.internal.filters.FilterPlugin;
import org.cytoscape.filter.internal.quickfind.util.QuickFind;
@@ -88,8 +89,9 @@
}
- public static boolean isFilterNameDuplicated(FilterPlugin filterPlugin,
String pFilterName) {
- Vector<CompositeFilter> allFilterVect =
filterPlugin.getAllFilterVect();
+ public static boolean isFilterNameDuplicated(Vector<CompositeFilter>
allFilterVect, String pFilterName) {
+ // TODO
+ //Vector<CompositeFilter> allFilterVect =
ServicesUtil.filterReader.getProperties();
if (allFilterVect == null || allFilterVect.size() == 0)
return false;
Modified:
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/view/FilterMainPanel.java
===================================================================
---
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/view/FilterMainPanel.java
2011-12-10 01:27:03 UTC (rev 27762)
+++
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/view/FilterMainPanel.java
2011-12-10 01:28:11 UTC (rev 27763)
@@ -72,6 +72,7 @@
import org.cytoscape.application.events.SetCurrentNetworkViewEvent;
import org.cytoscape.application.events.SetCurrentNetworkViewListener;
import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.filter.internal.ServicesUtil;
import org.cytoscape.filter.internal.filters.CompositeFilter;
import org.cytoscape.filter.internal.filters.EdgeInteractionFilter;
import org.cytoscape.filter.internal.filters.FilterPlugin;
@@ -111,6 +112,7 @@
import org.cytoscape.view.presentation.RenderingEngine;
import org.cytoscape.work.Task;
import org.cytoscape.work.TaskManager;
+import org.cytoscape.filter.internal.*;
public class FilterMainPanel extends JPanel implements ActionListener,
@@ -519,7 +521,7 @@
}
public void initCMBSelectFilter(){
- Vector<CompositeFilter> allFilterVect =
filterPlugin.getAllFilterVect();
+ Vector<CompositeFilter> allFilterVect =
ServicesUtil.filterReader.getProperties();//filterPlugin.getAllFilterVect();
ComboBoxModel theModel = new
FilterSelectWidestStringComboBoxModel(allFilterVect);
cmbSelectFilter.setModel(theModel);
cmbSelectFilter.setRenderer(new FilterRenderer());
@@ -595,7 +597,7 @@
}
cbm.addElement(filtersSeperator);
- Vector<CompositeFilter> allFilterVect =
filterPlugin.getAllFilterVect();
+ Vector<CompositeFilter> allFilterVect =
ServicesUtil.filterReader.getProperties(); //filterPlugin.getAllFilterVect();
if (allFilterVect != null) {
for (int i = 0; i < allFilterVect.size(); i++) {
Object fi;
@@ -1016,7 +1018,7 @@
}
if
(org.cytoscape.filter.internal.filters.util.FilterUtil
-
.isFilterNameDuplicated(filterPlugin, newFilterName)) {
+
.isFilterNameDuplicated(ServicesUtil.filterReader.getProperties(),
newFilterName)) {
Object[] options = { "OK" };
JOptionPane.showOptionDialog(this,
"Filter name already existed!", "Warning",
@@ -1099,7 +1101,7 @@
}
private void updateInteractionMenuItemStatus() {
- Vector<CompositeFilter> allFilterVect =
filterPlugin.getAllFilterVect();
+ Vector<CompositeFilter> allFilterVect =
ServicesUtil.filterReader.getProperties(); //filterPlugin.getAllFilterVect();
//Disable interactionMenuItem if there is no other filters to
depend on
if (allFilterVect == null || allFilterVect.size() == 0) {
newNodeInteractionFilterMenuItem.setEnabled(false);
@@ -1182,7 +1184,7 @@
}
if
(org.cytoscape.filter.internal.filters.util.FilterUtil
- .isFilterNameDuplicated(filterPlugin,
newFilterName)) {
+
.isFilterNameDuplicated(ServicesUtil.filterReader.getProperties(),newFilterName))
{
Object[] options = { "OK" };
JOptionPane.showOptionDialog(this,
"Filter name
already existed!", "Warning",
@@ -1198,7 +1200,7 @@
CompositeFilter newFilter = (CompositeFilter)
theFilter.clone();
newFilter.setName(newFilterName);
- Vector<CompositeFilter> allFilterVect =
filterPlugin.getAllFilterVect();
+ Vector<CompositeFilter> allFilterVect =
ServicesUtil.filterReader.getProperties(); //filterPlugin.getAllFilterVect();
allFilterVect.add(newFilter);
FilterSettingPanel newFilterSettingPanel = new
FilterSettingPanel(this, newFilter, applicationManager, filterPlugin,
eventHelper);
filter2SettingPanelMap.put(newFilter, newFilterSettingPanel);
@@ -1229,7 +1231,7 @@
}
if
(org.cytoscape.filter.internal.filters.util.FilterUtil
- .isFilterNameDuplicated(filterPlugin,
newFilterName)) {
+
.isFilterNameDuplicated(ServicesUtil.filterReader.getProperties(),newFilterName))
{
Object[] options = { "OK" };
JOptionPane.showOptionDialog(this,
"Filter name
already existed!", "Warning",
@@ -1253,7 +1255,7 @@
filter2SettingPanelMap.remove(pFilter);
cmbSelectFilter.removeItem(pFilter);
- Vector<CompositeFilter> allFilterVect =
filterPlugin.getAllFilterVect();
+ Vector<CompositeFilter> allFilterVect =
ServicesUtil.filterReader.getProperties(); //filterPlugin.getAllFilterVect();
if (allFilterVect == null || allFilterVect.size() == 0) {
replaceFilterSettingPanel(null);
}
@@ -1287,7 +1289,7 @@
newFilter.setNetwork(applicationManager.getCurrentNetwork());
- Vector<CompositeFilter> allFilterVect =
filterPlugin.getAllFilterVect();
+ Vector<CompositeFilter> allFilterVect =
ServicesUtil.filterReader.getProperties(); //filterPlugin.getAllFilterVect();
allFilterVect.add(newFilter);
FilterSettingPanel newFilterSettingPanel = new
FilterSettingPanel(this, newFilter, applicationManager, filterPlugin,
eventHelper);
filter2SettingPanelMap.put(newFilter, newFilterSettingPanel);
Modified:
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/view/InteractionFilterPanel.java
===================================================================
---
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/view/InteractionFilterPanel.java
2011-12-10 01:27:03 UTC (rev 27762)
+++
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/view/InteractionFilterPanel.java
2011-12-10 01:28:11 UTC (rev 27763)
@@ -51,6 +51,7 @@
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.filter.internal.ServicesUtil;
import org.cytoscape.filter.internal.filters.CompositeFilter;
import org.cytoscape.filter.internal.filters.EdgeInteractionFilter;
import org.cytoscape.filter.internal.filters.FilterPlugin;
@@ -168,7 +169,7 @@
Vector<CompositeFilter> tmpVect = new Vector<CompositeFilter>();
//tmpVect.add(emptyFilter);
- Vector<CompositeFilter> allFilterVect =
filterPlugin.getAllFilterVect();
+ Vector<CompositeFilter> allFilterVect =
ServicesUtil.filterReader.getProperties();//filterPlugin.getAllFilterVect();
tmpVect.addAll(allFilterVect);
PassFilterWidestStringComboBoxModel pfwscbm = new
PassFilterWidestStringComboBoxModel(tmpVect);
Modified:
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/view/TopoFilterPanel.java
===================================================================
---
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/view/TopoFilterPanel.java
2011-12-10 01:27:03 UTC (rev 27762)
+++
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/filters/view/TopoFilterPanel.java
2011-12-10 01:28:11 UTC (rev 27763)
@@ -55,6 +55,7 @@
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.filter.internal.ServicesUtil;
import org.cytoscape.filter.internal.filters.CompositeFilter;
import org.cytoscape.filter.internal.filters.FilterPlugin;
import org.cytoscape.filter.internal.filters.TopologyFilter;
@@ -153,7 +154,7 @@
Vector<CompositeFilter> tmpVect = new Vector<CompositeFilter>();
tmpVect.add(emptyFilter);
- Vector<CompositeFilter> allFilterVect =
filterPlugin.getAllFilterVect();
+ Vector<CompositeFilter> allFilterVect =
ServicesUtil.filterReader.getProperties() ;//filterPlugin.getAllFilterVect();
tmpVect.addAll(allFilterVect);
PassFilterWidestStringComboBoxModel pfwscbm = new
PassFilterWidestStringComboBoxModel(tmpVect);
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