Author: pwang
Date: 2012-08-21 15:50:55 -0700 (Tue, 21 Aug 2012)
New Revision: 30244
Modified:
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/actions/BookmarkAction.java
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/dialogs/BookmarkDialogFactoryImpl.java
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/dialogs/BookmarkDialogImpl.java
Log:
Use dataSourceManager instead of bookmarksUtil
Modified:
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java
2012-08-21 21:46:52 UTC (rev 30243)
+++
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java
2012-08-21 22:50:55 UTC (rev 30244)
@@ -99,6 +99,7 @@
import org.cytoscape.internal.view.help.HelpContactHelpDeskTaskFactory;
import org.cytoscape.internal.view.help.HelpContentsTaskFactory;
import org.cytoscape.internal.view.help.HelpReportABugTaskFactory;
+import org.cytoscape.io.datasource.DataSourceManager;
import org.cytoscape.io.read.CySessionReaderManager;
import org.cytoscape.io.util.RecentlyOpenedTracker;
import org.cytoscape.model.CyNetworkManager;
@@ -192,15 +193,17 @@
DynamicTaskFactoryProvisioner
dynamicTaskFactoryProvisionerServiceRef = getService(bc,
DynamicTaskFactoryProvisioner.class);
+ DataSourceManager dsManagerServiceRef = getService(bc,
DataSourceManager.class);
+ //////////////
UndoAction undoAction = new UndoAction(undoSupportServiceRef);
RedoAction redoAction = new RedoAction(undoSupportServiceRef);
ConfigDirPropertyWriter configDirPropertyWriter = new
ConfigDirPropertyWriter(dialogTaskManagerServiceRef,
cyApplicationConfigurationServiceRef);
CyHelpBrokerImpl cyHelpBroker = new CyHelpBrokerImpl();
PreferencesDialogFactoryImpl preferencesDialogFactory = new
PreferencesDialogFactoryImpl(cyEventHelperServiceRef);
- BookmarkDialogFactoryImpl bookmarkDialogFactory = new
BookmarkDialogFactoryImpl(bookmarkServiceRef,
-
bookmarksUtilServiceRef);
+ BookmarkDialogFactoryImpl bookmarkDialogFactory = new
BookmarkDialogFactoryImpl(/*bookmarkServiceRef,
+ bookmarksUtilServiceRef,*/ dsManagerServiceRef);
registerService(bc, bookmarkDialogFactory,
SessionLoadedListener.class, new Properties());
Modified:
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/actions/BookmarkAction.java
===================================================================
---
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/actions/BookmarkAction.java
2012-08-21 21:46:52 UTC (rev 30243)
+++
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/actions/BookmarkAction.java
2012-08-21 22:50:55 UTC (rev 30244)
@@ -36,6 +36,7 @@
import org.cytoscape.application.swing.AbstractCyAction;
import org.cytoscape.internal.dialogs.BookmarkDialogImpl;
import org.cytoscape.internal.dialogs.BookmarkDialogFactoryImpl;
+import org.cytoscape.io.datasource.DataSourceManager;
public class BookmarkAction extends AbstractCyAction {
@@ -43,6 +44,7 @@
private CySwingApplication desktop;
private BookmarkDialogFactoryImpl bookmarkDialogFactory;
+
/**
* Creates a new BookmarkAction object.
*/
Modified:
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/dialogs/BookmarkDialogFactoryImpl.java
===================================================================
---
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/dialogs/BookmarkDialogFactoryImpl.java
2012-08-21 21:46:52 UTC (rev 30243)
+++
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/dialogs/BookmarkDialogFactoryImpl.java
2012-08-21 22:50:55 UTC (rev 30244)
@@ -12,28 +12,33 @@
import javax.swing.SwingUtilities;
import org.cytoscape.io.DataCategory;
+import org.cytoscape.io.datasource.DataSourceManager;
import org.cytoscape.property.CyProperty;
-import org.cytoscape.property.bookmark.Bookmarks;
-import org.cytoscape.property.bookmark.Category;
-import org.cytoscape.property.bookmark.DataSource;
-import org.cytoscape.property.bookmark.BookmarksUtil;
+//import org.cytoscape.property.bookmark.Bookmarks;
+//import org.cytoscape.property.bookmark.Category;
+//import org.cytoscape.property.bookmark.DataSource;
+//import org.cytoscape.property.bookmark.BookmarksUtil;
import org.cytoscape.session.CySession;
import org.cytoscape.session.events.SessionLoadedEvent;
import org.cytoscape.session.events.SessionLoadedListener;
public class BookmarkDialogFactoryImpl implements SessionLoadedListener {
- private CyProperty<Bookmarks> bookmarksProp;
- private BookmarksUtil bkUtil;
+// private CyProperty<Bookmarks> bookmarksProp;
+// private BookmarksUtil bkUtil;
+ private DataSourceManager dsManagerServiceRef;
+
+ private BookmarkDialogImpl bmDialog= null;;
-
- public BookmarkDialogFactoryImpl(CyProperty<Bookmarks> bookmarksProp,
BookmarksUtil bkUtil) {
- this.bookmarksProp = bookmarksProp;
- this.bkUtil = bkUtil;
+ public BookmarkDialogFactoryImpl(/*CyProperty<Bookmarks> bookmarksProp,
BookmarksUtil bkUtil,*/ DataSourceManager dsManagerServiceRef) {
+// this.bookmarksProp = bookmarksProp;
+// this.bkUtil = bkUtil;
+ this.dsManagerServiceRef = dsManagerServiceRef;
}
public BookmarkDialogImpl getBookmarkDialog(Frame parent) {
- return new BookmarkDialogImpl(parent,
bookmarksProp.getProperties(), bkUtil);
+ bmDialog = new BookmarkDialogImpl(parent,
/*bookmarksProp.getProperties(), bkUtil,*/ dsManagerServiceRef);
+ return bmDialog;
}
@Override
@@ -42,49 +47,52 @@
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
- updateBookmarks(e.getLoadedSession());
+ if (BookmarkDialogFactoryImpl.this.bmDialog !=
null){
+
BookmarkDialogFactoryImpl.this.bmDialog.loadBookmarks();
+ }
+// updateBookmarks(e.getLoadedSession());
}
});
}
- private void updateBookmarks(final CySession sess) {
- // Update bookmarks
- List<Category> categoryList = new ArrayList<Category>();
- List<String> sourcesNameList = new ArrayList<String>();
- List<DataSource> theDataSourceList;
-
-
- if (sess != null) {
- //Check if the data source bookmarks are different from
previous session
- //if so they need to be loaded to datasource Manager
- theDataSourceList = new ArrayList<DataSource>();
- categoryList = bookmarksProp.getProperties().getCategory();
- for (Category category : categoryList) {
- theDataSourceList =
bkUtil.getDataSourceList(category.getName(), categoryList);
- for (final DataSource ds : theDataSourceList) {
- sourcesNameList.add( ds.getHref());
- }
- }
- for (CyProperty<?> p : sess.getProperties()) {
- if
(Bookmarks.class.isAssignableFrom(p.getPropertyType())) {
- // There should be only one CyProperty
of type Bookmarks in the session!
- bookmarksProp = (CyProperty<Bookmarks>)
p;
- break;
- }
- }
- categoryList =
bookmarksProp.getProperties().getCategory();
-
- for (Category category : categoryList) {
-
- theDataSourceList =
bkUtil.getDataSourceList(category.getName(), categoryList);
- if (theDataSourceList != null) {
- for (final DataSource ds :
theDataSourceList) {
-
if(!sourcesNameList.contains(ds.getHref())){
-
bkUtil.saveBookmark(bookmarksProp.getProperties(), category.getName(), ds);
- }
- }
- }
- }
- }
- }
+// private void updateBookmarks(final CySession sess) {
+// // Update bookmarks
+// List<Category> categoryList = new ArrayList<Category>();
+// List<String> sourcesNameList = new ArrayList<String>();
+// List<DataSource> theDataSourceList;
+//
+//
+// if (sess != null) {
+// //Check if the data source bookmarks are different from
previous session
+// //if so they need to be loaded to datasource Manager
+// theDataSourceList = new ArrayList<DataSource>();
+// categoryList = bookmarksProp.getProperties().getCategory();
+// for (Category category : categoryList) {
+// theDataSourceList =
bkUtil.getDataSourceList(category.getName(), categoryList);
+// for (final DataSource ds : theDataSourceList) {
+// sourcesNameList.add( ds.getHref());
+// }
+// }
+// for (CyProperty<?> p : sess.getProperties()) {
+// if
(Bookmarks.class.isAssignableFrom(p.getPropertyType())) {
+// // There should be only one CyProperty
of type Bookmarks in the session!
+// bookmarksProp = (CyProperty<Bookmarks>)
p;
+// break;
+// }
+// }
+// categoryList =
bookmarksProp.getProperties().getCategory();
+//
+// for (Category category : categoryList) {
+//
+// theDataSourceList =
bkUtil.getDataSourceList(category.getName(), categoryList);
+// if (theDataSourceList != null) {
+// for (final DataSource ds :
theDataSourceList) {
+//
if(!sourcesNameList.contains(ds.getHref())){
+//
bkUtil.saveBookmark(bookmarksProp.getProperties(), category.getName(), ds);
+// }
+// }
+// }
+// }
+// }
+// }
}
Modified:
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/dialogs/BookmarkDialogImpl.java
===================================================================
---
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/dialogs/BookmarkDialogImpl.java
2012-08-21 21:46:52 UTC (rev 30243)
+++
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/dialogs/BookmarkDialogImpl.java
2012-08-21 22:50:55 UTC (rev 30244)
@@ -55,11 +55,20 @@
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
-import org.cytoscape.property.bookmark.Bookmarks;
-import org.cytoscape.property.bookmark.DataSource;
+//import org.cytoscape.property.bookmark.Bookmarks;
+//import org.cytoscape.property.bookmark.DataSource;
import org.cytoscape.property.bookmark.BookmarksUtil;
-
-
+//import org.cytoscape.io.DataCategory;
+//import org.cytoscape.io.datasource.DataSource;
+import org.cytoscape.io.datasource.DataSourceManager;
+import java.util.Collection;
+import java.util.Iterator;
+import org.cytoscape.io.DataCategory;
+import java.util.Set;
+import java.util.HashSet;
+import org.cytoscape.io.datasource.DefaultDataSource;
+import java.net.URL;
+import java.net.MalformedURLException;
/**
*
*/
@@ -67,17 +76,19 @@
ListSelectionListener, ItemListener {
private String bookmarkCategory;
- private Bookmarks bookmarks;
- private BookmarksUtil bkUtil;
+ //private Bookmarks bookmarks;
+ //private BookmarksUtil bkUtil;
// private Category theCategory = new Category();;
- private String[] bookmarkCategories = { "network", "annotation", "apps"
};
+ private String[] bookmarkCategories = { "network", "table",
"image","properties","session","script","vizmap", "unspecified" };
+ private DataSourceManager dsManagerServiceRef;
private final static long serialVersionUID = 1202339873340615L;
- public BookmarkDialogImpl(Frame pParent, Bookmarks bookmarks,
BookmarksUtil bkUtil) {
+ public BookmarkDialogImpl(Frame pParent, /*Bookmarks bookmarks,
BookmarksUtil bkUtil,*/ DataSourceManager dsManagerServiceRef) {
super(pParent, true);
- this.bookmarks = bookmarks;
- this.bkUtil = bkUtil;
+ //this.bookmarks = bookmarks;
+ //this.bkUtil = bkUtil;
+ this.dsManagerServiceRef = dsManagerServiceRef;
basicInit();
this.setLocationRelativeTo(pParent);
}
@@ -204,10 +215,44 @@
// pack();
} // </editor-fold>
- private void loadBookmarks() {
- List<DataSource> theDataSourceList = bkUtil.getDataSourceList(
- bookmarkCategory, bookmarks.getCategory());
+ public void loadBookmarks() {
+ Collection<org.cytoscape.io.datasource.DataSource>
theDataSourceCollection = new HashSet<org.cytoscape.io.datasource.DataSource>();
+ if (this.cmbCategory.getSelectedItem().equals("network")){
+ theDataSourceCollection =
this.dsManagerServiceRef.getDataSources(org.cytoscape.io.DataCategory.NETWORK);
+ }
+ else if (this.cmbCategory.getSelectedItem().equals("table")){
+ theDataSourceCollection =
this.dsManagerServiceRef.getDataSources(org.cytoscape.io.DataCategory.TABLE);
+ }
+ else if (this.cmbCategory.getSelectedItem().equals("image")){
+ theDataSourceCollection =
this.dsManagerServiceRef.getDataSources(org.cytoscape.io.DataCategory.IMAGE);
+ }
+ else if
(this.cmbCategory.getSelectedItem().equals("properties")){
+ theDataSourceCollection =
this.dsManagerServiceRef.getDataSources(org.cytoscape.io.DataCategory.PROPERTIES);
+ }
+ else if (this.cmbCategory.getSelectedItem().equals("session")){
+ theDataSourceCollection =
this.dsManagerServiceRef.getDataSources(org.cytoscape.io.DataCategory.SESSION);
+ }
+ else if (this.cmbCategory.getSelectedItem().equals("script")){
+ theDataSourceCollection =
this.dsManagerServiceRef.getDataSources(org.cytoscape.io.DataCategory.SCRIPT);
+ }
+ else if (this.cmbCategory.getSelectedItem().equals("vizmap")){
+ theDataSourceCollection =
this.dsManagerServiceRef.getDataSources(org.cytoscape.io.DataCategory.VIZMAP);
+ }
+ else if
(this.cmbCategory.getSelectedItem().equals("unspecified")){
+ theDataSourceCollection =
this.dsManagerServiceRef.getDataSources(org.cytoscape.io.DataCategory.UNSPECIFIED);
+ }
+ else {
+ theDataSourceCollection =
this.dsManagerServiceRef.getDataSources(org.cytoscape.io.DataCategory.UNSPECIFIED);
+ }
+
+ Iterator<org.cytoscape.io.datasource.DataSource> it =
theDataSourceCollection.iterator();
+
+ ArrayList<org.cytoscape.io.datasource.DataSource>
theDataSourceList = new ArrayList(theDataSourceCollection.size());
+ while(it.hasNext()){
+ theDataSourceList.add(it.next());
+ }
+
MyListModel theModel = new MyListModel(theDataSourceList);
listBookmark.setModel(theModel);
}
@@ -230,17 +275,17 @@
this.dispose();
} else if (_btn == btnAddBookmark) {
EditBookmarkDialog theNewDialog = new
EditBookmarkDialog(this,
- true, bookmarks,
bookmarkCategory, "new", null);
+ true, /* bookmarks,*/
bookmarkCategory, "new", null);
theNewDialog.setSize(400, 300);
theNewDialog.setLocationRelativeTo(this);
theNewDialog.setVisible(true);
loadBookmarks(); // reload is required to
update the GUI
} else if (_btn == btnEditBookmark) {
- DataSource theDataSource = (DataSource)
listBookmark
+ org.cytoscape.io.datasource.DataSource
theDataSource = (org.cytoscape.io.datasource.DataSource) listBookmark
.getSelectedValue();
EditBookmarkDialog theEditDialog = new
EditBookmarkDialog(this,
- true, bookmarks,
bookmarkCategory, "edit",
+ true, /*bookmarks,*/
bookmarkCategory, "edit",
theDataSource);
theEditDialog.setSize(400, 300);
theEditDialog.setLocationRelativeTo(this);
@@ -248,14 +293,13 @@
theEditDialog.setVisible(true);
loadBookmarks(); // reload is required to
update the GUI
} else if (_btn == btnDeleteBookmark) {
- DataSource theDataSource = (DataSource)
listBookmark
+ org.cytoscape.io.datasource.DataSource
theDataSource = (org.cytoscape.io.datasource.DataSource) listBookmark
.getSelectedValue();
MyListModel theModel = (MyListModel)
listBookmark.getModel();
theModel.removeElement(listBookmark.getSelectedIndex());
- bkUtil.deleteBookmark(bookmarks,
bookmarkCategory,
- theDataSource);
+
this.dsManagerServiceRef.deleteDataSource(theDataSource);
if (theModel.getSize() == 0) {
btnEditBookmark.setEnabled(false);
@@ -284,9 +328,9 @@
class MyListModel extends javax.swing.AbstractListModel {
private final static long serialVersionUID = 1202339873199984L;
- List<DataSource> theDataSourceList = new
ArrayList<DataSource>(0);
+ List<org.cytoscape.io.datasource.DataSource> theDataSourceList
= new ArrayList<org.cytoscape.io.datasource.DataSource>(0);
- public MyListModel(List<DataSource> pDataSourceList) {
+ public MyListModel(List<org.cytoscape.io.datasource.DataSource>
pDataSourceList) {
theDataSourceList = pDataSourceList;
}
@@ -306,7 +350,7 @@
return theDataSourceList.get(i);
}
- public void addElement(DataSource pDataSource) {
+ public void addElement(org.cytoscape.io.datasource.DataSource
pDataSource) {
theDataSourceList.add(pDataSource);
}
@@ -326,9 +370,9 @@
public Component getListCellRendererComponent(JList list,
Object value,
int index, boolean isSelected, boolean
cellHasFocus) {
- DataSource theDataSource = (DataSource) value;
+ org.cytoscape.io.datasource.DataSource theDataSource =
(org.cytoscape.io.datasource.DataSource) value;
setText(theDataSource.getName());
- setToolTipText(theDataSource.getHref());
+ setToolTipText(theDataSource.getLocation().toString());
setBackground(isSelected ? Color.blue : Color.white);
setForeground(isSelected ? Color.white : Color.black);
@@ -342,18 +386,18 @@
private String URLstr;
private String provider = "";
private JDialog parent;
- private Bookmarks theBookmarks;
+ //private Bookmarks theBookmarks;
private String categoryName;
private String mode = "new"; // new/edit
- private DataSource dataSource = null;
+ private org.cytoscape.io.datasource.DataSource dataSource =
null;
/** Creates new form NewBookmarkDialog */
public EditBookmarkDialog(JDialog parent, boolean modal,
- Bookmarks pBookmarks, String categoryName,
String pMode,
- DataSource pDataSource) {
+ /*Bookmarks pBookmarks,*/ String categoryName,
String pMode,
+ org.cytoscape.io.datasource.DataSource
pDataSource) {
super(parent, modal);
this.parent = parent;
- this.theBookmarks = pBookmarks;
+ //this.theBookmarks = pBookmarks;
this.categoryName = categoryName;
this.mode = pMode;
this.dataSource = pDataSource;
@@ -370,13 +414,8 @@
this.setTitle("Edit bookmark");
tfName.setText(dataSource.getName());
tfName.setEditable(false);
- tfURL.setText(dataSource.getHref());
- if
(BookmarkDialogImpl.this.bkUtil.getProvider(dataSource) != null){
-
tfProvider.setText(bkUtil.getProvider(dataSource));
- }
- else {
- tfProvider.setText("");
- }
+
tfURL.setText(dataSource.getLocation().toString());
+ tfProvider.setText(dataSource.getProvider());
}
}
@@ -401,22 +440,29 @@
return;
}
- DataSource theDataSource = new
DataSource();
- theDataSource.setName(name);
- theDataSource.setHref(URLstr);
+ URL newURL;
+ try {
+ newURL = new URL(URLstr);
+ }
+ catch (MalformedURLException ex){
+
JOptionPane.showMessageDialog(parent, "Invalid URL", "Warning",
+
JOptionPane.INFORMATION_MESSAGE);
+ return;
+ }
- if (bkUtil.containsBookmarks(bookmarks,
categoryName,
- theDataSource)) {
+ org.cytoscape.io.datasource.DataSource
theDataSource = new DefaultDataSource(name,
+ provider, "",
getCategoryByName(this.categoryName), newURL);
+
+
+ if
(BookmarkDialogImpl.this.dsManagerServiceRef.containsDataSource(theDataSource)){
String msg = "Bookmark already
existed.";
// display info dialog
JOptionPane.showMessageDialog(parent, msg, "Warning",
JOptionPane.INFORMATION_MESSAGE);
-
- return;
+ return;
}
-
- bkUtil.saveBookmark(theBookmarks,
categoryName,
- theDataSource,
provider);
+
+
BookmarkDialogImpl.this.dsManagerServiceRef.saveDataSource(theDataSource);
this.dispose();
}
@@ -424,33 +470,69 @@
name = tfName.getText();
URLstr = tfURL.getText();
provider = tfProvider.getText().trim();
-
+ URL newURL;
+
if (URLstr.trim().equals("")) {
String msg = "URL is empty.";
// display info dialog
JOptionPane.showMessageDialog(parent, msg, "Warning",
JOptionPane.INFORMATION_MESSAGE);
+ return;
+ }
+ try {
+ newURL = new URL(URLstr);
+ }
+ catch (MalformedURLException ex){
+
JOptionPane.showMessageDialog(parent, "Invalid URL", "Warning",
+
JOptionPane.INFORMATION_MESSAGE);
return;
}
- DataSource theDataSource = new
DataSource();
- theDataSource.setName(name);
- theDataSource.setHref(URLstr);
+ org.cytoscape.io.datasource.DataSource
theDataSource = new DefaultDataSource(name,
+ provider,
this.dataSource.getDescription(), this.dataSource.getDataCategory(), newURL);
+
+
BookmarkDialogImpl.this.dsManagerServiceRef.deleteDataSource(this.dataSource);
+
BookmarkDialogImpl.this.dsManagerServiceRef.saveDataSource(theDataSource);
- // first dellete the old one, then add
(note: name is key of
- // DataSource)
- bkUtil.deleteBookmark(theBookmarks,
- bookmarkCategory,
theDataSource);
- bkUtil.saveBookmark(theBookmarks,
categoryName,
- theDataSource,
this.provider);
this.dispose();
+
} else if (_btn == btnCancel) {
this.dispose();
}
}
} // End of actionPerformed()
+
+ private DataCategory getCategoryByName(String categoryName){
+
+ if (categoryName.equalsIgnoreCase("network")){
+ return DataCategory.NETWORK;
+ }
+ else if (categoryName.equalsIgnoreCase("table")){
+ return DataCategory.TABLE;
+ }
+ else if (categoryName.equalsIgnoreCase("image")){
+ return DataCategory.IMAGE;
+ }
+ else if (categoryName.equalsIgnoreCase("properties")){
+ return DataCategory.PROPERTIES;
+ }
+ else if (categoryName.equalsIgnoreCase("session")){
+ return DataCategory.SESSION;
+ }
+ else if (categoryName.equalsIgnoreCase("script")){
+ return DataCategory.SCRIPT;
+ }
+ else if (categoryName.equalsIgnoreCase("vizmap")){
+ return DataCategory.VIZMAP;
+ }
+ else if (categoryName.equalsIgnoreCase("unspecified")){
+ return DataCategory.UNSPECIFIED;
+ }
+ return DataCategory.UNSPECIFIED;
+ }
+
/**
* This method is called from within the constructor to
initialize the
* form. WARNING: Do NOT modify this code. The content of this
method is
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