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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 12:46:57 UTC
[30/50] [abbrv] incubator-taverna-plugin-bioinformatics git commit:
taverna-biomoby-activity-ui/
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/DatatypeMenuItem.java
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diff --git a/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/DatatypeMenuItem.java b/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/DatatypeMenuItem.java
deleted file mode 100644
index c5a7468..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/DatatypeMenuItem.java
+++ /dev/null
@@ -1,196 +0,0 @@
-/*
- * This file is a component of the Taverna project,
- * and is licensed under the GNU LGPL.
- * Copyright Edward Kawas, The BioMoby Project
- */
-package net.sf.taverna.t2.activities.biomoby.ui;
-
-import java.awt.BorderLayout;
-import java.awt.Component;
-import java.awt.Frame;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-
-import javax.swing.BorderFactory;
-import javax.swing.ImageIcon;
-import javax.swing.JDialog;
-import javax.swing.JLabel;
-import javax.swing.JMenuItem;
-import javax.swing.JPanel;
-import javax.swing.JProgressBar;
-
-import net.sf.taverna.t2.activities.biomoby.actions.MobyPanel;
-import net.sf.taverna.t2.activities.biomoby.query.BiomobyObjectActivityItem;
-import net.sf.taverna.t2.workbench.MainWindow;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.helper.HelpEnabledDialog;
-
-import org.apache.log4j.Logger;
-import org.biomoby.client.CentralImpl;
-import org.biomoby.shared.MobyException;
-
-import com.sun.java.help.impl.SwingWorker;
-
-/**
- * DatatypeMenuItem is a JMenuItem that onClick produces a biomoby datatype tree
- * that workbench users can utilize to add datatypes to any workflow.
- *
- * @author Edward Kawas
- *
- */
-public class DatatypeMenuItem extends JMenuItem {
-
- private static Logger logger = Logger.getLogger(DatatypeMenuItem.class);
- private static final long serialVersionUID = -1010828167358361441L;
-
- private String endpoint;
- private String namespace;
-
- private final EditManager editManager;
- private final FileManager fileManager;
-
- /**
- * Default constructor; Creates a menu item for the default registry
- */
- public DatatypeMenuItem(EditManager editManager, FileManager fileManager) {
- this(CentralImpl.DEFAULT_ENDPOINT, CentralImpl.DEFAULT_NAMESPACE, editManager, fileManager);
- }
-
- /**
- * Create a Datatype menu item for a biomoby registry given a specific
- * endpoint and namespace
- *
- * @param endpoint
- * the registry endpoint
- * @param namespace
- * the registry namespace
- */
- public DatatypeMenuItem(String endpoint, String namespace, EditManager editManager, FileManager fileManager) {
- this(endpoint, namespace, endpoint, editManager, fileManager);
- }
-
- /*
- * A private constructor. Every constructor ends up here
- */
- private DatatypeMenuItem(String endpoint, String namespace, String label, EditManager editManager, FileManager fileManager) {
- // set up some specifics
- this.endpoint = endpoint;
- this.namespace = namespace;
- this.editManager = editManager;
- this.fileManager = fileManager;
- // set up the name, label and icon for this menu item
- setName(label);
- setText(label);
- setIcon(new ImageIcon(BiomobyObjectActivityItem.class
- .getResource("/biomoby_object.png")));
- // enable the item
- setEnabled(true);
- // create an action listener to catch clicks
- addActionListener(new ActionListener() {
- public void actionPerformed(ActionEvent e) {
- if (e.getSource() instanceof DatatypeMenuItem) {
- final DatatypeMenuItem item = (DatatypeMenuItem) e
- .getSource();
- // create a swing worker that creates our tree
- SwingWorker worker = new SwingWorker() {
- @Override
- public Object construct() {
- // create a progress bar ...
- JProgressBar bar = new JProgressBar();
- bar.setIndeterminate(true);
- bar.setString("Creating datatype tree ...");
- bar.setStringPainted(true);
- // a dialog frame hold the bar
- String title = "Datatype Tree Builder";
- JDialog frame = new HelpEnabledDialog(MainWindow.getMainWindow(), title, false, null);
- JLabel label = new JLabel(
- "Constructing tree for:\n\t"
- + item.getEndpoint());
- JPanel panel = new JPanel();
- panel.add(bar);
- // the panel that holds the label and bar
- JPanel panel1 = new JPanel();
- panel1.setLayout(new BorderLayout());
- panel1.add(panel, BorderLayout.NORTH);
- panel1.add(label, BorderLayout.CENTER);
- panel1.setBorder(BorderFactory.createEmptyBorder(
- 20, 20, 20, 20));
- frame.setContentPane(panel1);
- frame.setResizable(false);
- frame.pack();
- frame.setVisible(true);
- // do our task
- getTreeForRegistry(item.getEndpoint(), item
- .getNamespace());
- // hide the progress bar ...
- frame.setVisible(false);
- frame.removeAll();
- frame = null;
- return null;
- }
- };
- worker.start();
- }
- }
- });
- }
-
- /**
- * Set the registry namespace
- *
- * @param namespace
- * the registry namespace that this menu item will use
- */
- public void setNamespace(String namespace) {
- this.namespace = namespace;
- }
-
- /**
- * Set the registry endpoint
- *
- * @param endpoint
- * the registry endpoint that this menu item will use
- */
- public void setEndpoint(String endpoint) {
- this.endpoint = endpoint;
- }
-
- /**
- * Get the registry endpoint
- *
- * @return the registry endpoint that this menu item is using
- */
- public String getEndpoint() {
- return endpoint;
- }
-
- /**
- * Get the registry namespace
- *
- * @return the registry namespace that this menu item is using
- */
- public String getNamespace() {
- return namespace;
- }
-
- /*
- * Creates a tree for a given registry
- */
- private void getTreeForRegistry(String endpoint, String namespace) {
- Frame f = MobyPanel.CreateFrame("Datatype Viewer for " + endpoint);
- try {
- Component c = new BiomobyObjectTree(endpoint, namespace, editManager, fileManager)
- .getDatatypeTree();
- f.add(c);
- f.setPreferredSize(c.getPreferredSize());
- f.setMinimumSize(c.getPreferredSize());
- f.pack();
- } catch (MobyException e) {
- logger.error(
- "Error encountered while constructing datatype viewer:\n",
- e);
- }
- f.setVisible(true);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualView.java
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diff --git a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualView.java b/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualView.java
deleted file mode 100644
index 4911721..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualView.java
+++ /dev/null
@@ -1,106 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby.view;
-
-import java.awt.BorderLayout;
-import java.awt.FlowLayout;
-import java.awt.Frame;
-import java.util.Map.Entry;
-
-import javax.swing.Action;
-import javax.swing.JButton;
-import javax.swing.JComponent;
-import javax.swing.JPanel;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean;
-import net.sf.taverna.t2.activities.biomoby.actions.BiomobyActivityConfigurationAction;
-import net.sf.taverna.t2.activities.biomoby.actions.MobyParserAction;
-import net.sf.taverna.t2.activities.biomoby.actions.MobyServiceDetailsAction;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.ui.actions.activity.HTMLBasedActivityContextualView;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-
-@SuppressWarnings("serial")
-public class BiomobyActivityContextualView extends
- HTMLBasedActivityContextualView<BiomobyActivityConfigurationBean> {
-
- private EditManager editManager;
- private final FileManager fileManager;
- private final ActivityIconManager activityIconManager;
-
- @Override
- public Action getConfigureAction(Frame owner) {
- BiomobyActivity activity = (BiomobyActivity) getActivity();
- if (activity.getMobyService() != null && activity.containsSecondaries()) {
- return new BiomobyActivityConfigurationAction((BiomobyActivity) getActivity(), owner,
- editManager, fileManager, activityIconManager);
- } else {
- return null;
- }
- }
-
- public BiomobyActivityContextualView(Activity<?> activity, EditManager editManager,
- FileManager fileManager, ActivityIconManager activityIconManager,
- ColourManager colourManager) {
- super(activity, colourManager);
- this.editManager = editManager;
- this.editManager = editManager;
- this.fileManager = fileManager;
- this.activityIconManager = activityIconManager;
- }
-
- @Override
- protected String getRawTableRowsHtml() {
- String html = "<tr><td>Endpoint</td><td>" + getConfigBean().getMobyEndpoint()
- + "</td></tr>";
- html += "<tr><td>Authority</td><td>" + getConfigBean().getAuthorityName() + "</td></tr>";
- html += "<tr><td>Service</td><td>" + getConfigBean().getServiceName() + "</td></tr>";
- if (getConfigBean().getSecondaries().size() > 0) {
- html += "<tr><th colspan='2' align='left'>Secondaries</th></tr>";
- for (Entry<String, String> entry : getConfigBean().getSecondaries().entrySet()) {
- html += "<tr><td>" + entry.getKey() + "</td><td>" + entry.getValue() + "</td></tr>";
- }
- }
- return html;
- }
-
- @Override
- public String getViewTitle() {
- return "Biomoby service";
- }
-
- /**
- * Gets the component from the {@link HTMLBasedActivityContextualView} and adds buttons to it
- * allowing Moby service details
- */
- @Override
- public JComponent getMainFrame() {
- final JComponent mainFrame = super.getMainFrame();
- JPanel flowPanel = new JPanel(new FlowLayout());
-
- BiomobyActivity activity = (BiomobyActivity) getActivity();
-
- JButton button = new JButton(new MobyServiceDetailsAction(activity, null, editManager,
- fileManager));
- flowPanel.add(button);
- if (activity.getMobyService() != null) {
- JButton button2 = new JButton(new MobyParserAction(activity, null, editManager,
- fileManager));
- flowPanel.add(button2);
- }
- mainFrame.add(flowPanel, BorderLayout.SOUTH);
- return mainFrame;
- }
-
- @Override
- public int getPreferredPosition() {
- return 100;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualViewFactory.java
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diff --git a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualViewFactory.java b/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualViewFactory.java
deleted file mode 100644
index 942e52c..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualViewFactory.java
+++ /dev/null
@@ -1,50 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby.view;
-
-import java.util.Arrays;
-import java.util.List;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
-
-public class BiomobyActivityContextualViewFactory implements ContextualViewFactory<BiomobyActivity> {
-
- private EditManager editManager;
- private FileManager fileManager;
- private ActivityIconManager activityIconManager;
- private ColourManager colourManager;
-
- public boolean canHandle(Object activity) {
- return activity instanceof BiomobyActivity;
- }
-
- public List<ContextualView> getViews(BiomobyActivity activity) {
- return Arrays.asList(new ContextualView[] { new BiomobyActivityContextualView(activity,
- editManager, fileManager, activityIconManager, colourManager) });
- }
-
- public void setEditManager(EditManager editManager) {
- this.editManager = editManager;
- }
-
- public void setFileManager(FileManager fileManager) {
- this.fileManager = fileManager;
- }
-
- public void setActivityIconManager(ActivityIconManager activityIconManager) {
- this.activityIconManager = activityIconManager;
- }
-
- public void setColourManager(ColourManager colourManager) {
- this.colourManager = colourManager;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyConfigView.java
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diff --git a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyConfigView.java b/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyConfigView.java
deleted file mode 100644
index 0e08e0b..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyConfigView.java
+++ /dev/null
@@ -1,108 +0,0 @@
-/**
- *
- */
-package net.sf.taverna.t2.activities.biomoby.view;
-
-import java.awt.BorderLayout;
-import java.util.Map;
-
-import javax.swing.JComponent;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationPanel;
-
-import org.apache.log4j.Logger;
-import org.biomoby.service.dashboard.data.ParametersTable;
-
-/**
- * @author alanrw
- *
- */
-public class BiomobyConfigView extends ActivityConfigurationPanel<BiomobyActivity, BiomobyActivityConfigurationBean> {
-
- private BiomobyActivity activity;
- private BiomobyActivityConfigurationBean configuration;
- private boolean changed = false;
-
- private static Logger logger = Logger
- .getLogger(BiomobyConfigView.class);
- private ParametersTable parameterTable;
-
- public BiomobyConfigView(BiomobyActivity activity) {
- this.activity = activity;
- initialise();
- }
-
- private void initialise() {
- configuration = activity.getConfiguration();
- this.setLayout(new BorderLayout());
- parameterTable = activity.getParameterTable();
- JComponent component = parameterTable.scrollable();
- this.add(component, BorderLayout.NORTH);
- validate();
- }
-
- /* (non-Javadoc)
- * @see net.sf.taverna.t2.workbench.ui.views.contextualviews.ActivityConfigurationPanel#getConfiguration()
- */
- @Override
- public BiomobyActivityConfigurationBean getConfiguration() {
- return configuration;
- }
-
- /* (non-Javadoc)
- * @see net.sf.taverna.t2.workbench.ui.views.contextualviews.ActivityConfigurationPanel#isConfigurationChanged()
- */
- @Override
- public boolean isConfigurationChanged() {
- Map<String,String> secondaries = configuration.getSecondaries();
- int rows = parameterTable.getModel().getRowCount();
- for (int i = 0; i < rows; i++) {
- String key = (String)parameterTable.getModel().getValueAt(i,0);
- String newValue = parameterTable.getModel().getValueAt(i,1).toString();
- String currentValue = secondaries.get(key);
- if (!currentValue.equals(newValue)) {
- return true;
- }
- }
- return false;
- }
-
- /* (non-Javadoc)
- * @see net.sf.taverna.t2.workbench.ui.views.contextualviews.ActivityConfigurationPanel#noteConfiguration()
- */
- @Override
- public void noteConfiguration() {
- BiomobyActivityConfigurationBean newConfiguration =
- (BiomobyActivityConfigurationBean) cloneBean(configuration);
- Map<String,String> secondaries = newConfiguration.getSecondaries();
- int rows = parameterTable.getModel().getRowCount();
- for (int i = 0; i < rows; i++) {
- String key = (String)parameterTable.getModel().getValueAt(i,0);
- String value = parameterTable.getModel().getValueAt(i,1).toString();
- secondaries.put(key, value);
- }
-// logger.info(convertBeanToString(configuration));
-// logger.info("COnfiguration was " + configuration.hashCode());
-// logger.info(convertBeanToString(newConfiguration));
-// logger.info("New configuration is " + newConfiguration.hashCode());
- configuration = newConfiguration;
- }
-
- @Override
- public void refreshConfiguration() {
- logger.info(convertBeanToString(activity.getConfiguration()));
- removeAll();
- initialise();
- }
-
- @Override
- public boolean checkValues() {
- // TODO Not yet implemented
- return true;
- }
-
-
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualView.java
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diff --git a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualView.java b/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualView.java
deleted file mode 100644
index 4ceed9b..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualView.java
+++ /dev/null
@@ -1,95 +0,0 @@
-/**
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- */
-package net.sf.taverna.t2.activities.biomoby.view;
-
-import java.awt.BorderLayout;
-import java.awt.FlowLayout;
-
-import javax.swing.JButton;
-import javax.swing.JComponent;
-import javax.swing.JPanel;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity;
-import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityConfigurationBean;
-import net.sf.taverna.t2.activities.biomoby.actions.MobyObjectDetailsAction;
-import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.ui.actions.activity.HTMLBasedActivityContextualView;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-
-/**
- * @author Stuart Owen
- *
- */
-@SuppressWarnings("serial")
-public class BiomobyObjectActivityContextualView extends
- HTMLBasedActivityContextualView<BiomobyObjectActivityConfigurationBean> {
-
- private EditManager editManager;
- private final FileManager fileManager;
-
- public BiomobyObjectActivityContextualView(Activity<?> activity, EditManager editManager,
- FileManager fileManager, ColourManager colourManager) {
- super(activity, colourManager);
- this.editManager = editManager;
- this.fileManager = fileManager;
- }
-
- @Override
- protected String getRawTableRowsHtml() {
- String html = "<tr><td>Endpoint</td><td>" + getConfigBean().getMobyEndpoint()
- + "</td></tr>";
- html += "<tr><td>Authority</td><td>" + getConfigBean().getAuthorityName() + "</td></tr>";
- html += "<tr><td>Datatype</td><td>" + getConfigBean().getServiceName() + "</td></tr>";
- return html;
- }
-
- @Override
- public String getViewTitle() {
- return "Biomoby Object service";
- }
-
- /**
- * Gets the component from the {@link HTMLBasedActivityContextualView} and adds buttons to it
- * allowing Moby object details
- */
- @Override
- public JComponent getMainFrame() {
- final JComponent mainFrame = super.getMainFrame();
- BiomobyObjectActivity activity = (BiomobyObjectActivity) getActivity();
- if (activity.getMobyObject() != null) {
- JPanel flowPanel = new JPanel(new FlowLayout());
- JButton button = new JButton(new MobyObjectDetailsAction(activity, null, editManager,
- fileManager));
- flowPanel.add(button);
- mainFrame.add(flowPanel, BorderLayout.SOUTH);
- }
- return mainFrame;
- }
-
- @Override
- public int getPreferredPosition() {
- return 100;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualViewFactory.java
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diff --git a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualViewFactory.java b/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualViewFactory.java
deleted file mode 100644
index 0e6ea55..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualViewFactory.java
+++ /dev/null
@@ -1,67 +0,0 @@
-/**
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- */
-package net.sf.taverna.t2.activities.biomoby.view;
-
-import java.util.Arrays;
-import java.util.List;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity;
-import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
-
-/**
- * @author Stuart Owen
- *
- */
-public class BiomobyObjectActivityContextualViewFactory implements
- ContextualViewFactory<BiomobyObjectActivity> {
-
- private EditManager editManager;
- private FileManager fileManager;
- private ColourManager colourManager;
-
- public boolean canHandle(Object activity) {
- return activity instanceof BiomobyObjectActivity;
- }
-
- public List<ContextualView> getViews(BiomobyObjectActivity activity) {
- return Arrays.asList(new ContextualView[] { new BiomobyObjectActivityContextualView(
- activity, editManager, fileManager, colourManager) });
- }
-
- public void setEditManager(EditManager editManager) {
- this.editManager = editManager;
- }
-
- public void setFileManager(FileManager fileManager) {
- this.fileManager = fileManager;
- }
-
- public void setColourManager(ColourManager colourManager) {
- this.colourManager = colourManager;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualView.java
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diff --git a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualView.java b/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualView.java
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index 91d4cd6..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualView.java
+++ /dev/null
@@ -1,62 +0,0 @@
-/**
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- */
-package net.sf.taverna.t2.activities.biomoby.view;
-
-import net.sf.taverna.t2.activities.biomoby.MobyParseDatatypeActivityConfigurationBean;
-import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
-import net.sf.taverna.t2.workbench.ui.actions.activity.HTMLBasedActivityContextualView;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-
-/**
- * @author Stuart Owen
- *
- */
-@SuppressWarnings("serial")
-public class MobyParseDatatypeContextualView extends
- HTMLBasedActivityContextualView<MobyParseDatatypeActivityConfigurationBean> {
-
- public MobyParseDatatypeContextualView(Activity<?> activity, ColourManager colourManager) {
- super(activity, colourManager);
- }
-
- @Override
- protected String getRawTableRowsHtml() {
- String html = "<tr><td>Article name used by service</td><td>"
- + getConfigBean().getArticleNameUsedByService() + "</td></tr>";
- html += "<tr><td>Datatype</td><td>" + getConfigBean().getDatatypeName() + "</td></tr>";
- html += "<tr><td>Registry endpoint</td><td>" + getConfigBean().getRegistryEndpoint()
- + "</td></tr>";
- return html;
- }
-
- @Override
- public String getViewTitle() {
- return "Moby parse datatype service";
- }
-
- @Override
- public int getPreferredPosition() {
- return 100;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualViewFactory.java
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diff --git a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualViewFactory.java b/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualViewFactory.java
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--- a/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualViewFactory.java
+++ /dev/null
@@ -1,69 +0,0 @@
-/**
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- */
-package net.sf.taverna.t2.activities.biomoby.view;
-
-import java.util.Arrays;
-import java.util.List;
-
-import net.sf.taverna.t2.activities.biomoby.MobyParseDatatypeActivity;
-import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
-
-/**
- * @author Stuart Owen
- *
- */
-public class MobyParseDatatypeContextualViewFactory implements
- ContextualViewFactory<MobyParseDatatypeActivity> {
-
- private ColourManager colourManager;
-
- /*
- * (non-Javadoc)
- *
- * @see
- * net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory#canHandle
- * (java.lang.Object)
- */
- public boolean canHandle(Object activity) {
- return activity instanceof MobyParseDatatypeActivity;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory#getView
- * (java.lang.Object)
- */
- public List<ContextualView> getViews(MobyParseDatatypeActivity activity) {
- return Arrays.asList(new ContextualView[] { new MobyParseDatatypeContextualView(activity,
- colourManager) });
- }
-
- public void setColourManager(ColourManager colourManager) {
- this.colourManager = colourManager;
- }
-
-}
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-net.sf.taverna.t2.activities.biomoby.partition.BiomobyPartitionAlgorithmSetSPI
\ No newline at end of file
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\ No newline at end of file
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-net.sf.taverna.t2.activities.biomoby.servicedescriptions.BiomobyServiceProvider
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-net.sf.taverna.t2.activities.biomoby.menu.BiomobyActivityDetailsMenuAction
-net.sf.taverna.t2.activities.biomoby.menu.BiomobyActivityParserMenuAction
-#net.sf.taverna.t2.activities.biomoby.actions.BiomobyAdvancedMenuAction
-net.sf.taverna.t2.activities.biomoby.menu.ConfigureBiomobyMenuAction
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
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-net.sf.taverna.t2.activities.biomoby.query.BiomobyActivityIcon
-net.sf.taverna.t2.activities.biomoby.query.BiomobyObjectActivityIcon
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-net.sf.taverna.t2.activities.biomoby.view.BiomobyActivityContextualViewFactory
-net.sf.taverna.t2.activities.biomoby.view.BiomobyObjectActivityContextualViewFactory
-net.sf.taverna.t2.activities.biomoby.view.MobyParseDatatypeContextualViewFactory
\ No newline at end of file
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-<?xml version="1.0" encoding="UTF-8"?>
-<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:beans="http://www.springframework.org/schema/beans"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd
- http://www.springframework.org/schema/osgi
- http://www.springframework.org/schema/osgi/spring-osgi.xsd">
-
- <service ref="BiomobyActivityIcon" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI" />
- <service ref="BiomobyObjectActivityIcon" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI" />
-
- <service ref="BiomobyServiceProvider" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider" />
-
- <service ref="BiomobyActivityDetailsMenuAction" auto-export="interfaces" />
- <service ref="BiomobyActivityParserMenuAction" auto-export="interfaces" />
- <service ref="ConfigureBiomobyMenuAction" auto-export="interfaces" />
-
- <service ref="BiomobyActivityContextualViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
- <service ref="BiomobyObjectActivityContextualViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
- <service ref="MobyParseDatatypeContextualViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
-
- <reference id="editManager" interface="net.sf.taverna.t2.workbench.edits.EditManager" />
- <reference id="fileManager" interface="net.sf.taverna.t2.workbench.file.FileManager" />
- <reference id="activityIconManager" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconManager" />
- <reference id="colourManager" interface="net.sf.taverna.t2.workbench.configuration.colour.ColourManager" />
- <reference id="serviceDescriptionRegistry" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry" />
-
-</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/src/main/resources/META-INF/spring/biomoby-activity-ui-context.xml
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-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd">
-
- <bean id="BiomobyActivityIcon" class="net.sf.taverna.t2.activities.biomoby.query.BiomobyActivityIcon" />
- <bean id="BiomobyObjectActivityIcon" class="net.sf.taverna.t2.activities.biomoby.query.BiomobyObjectActivityIcon" />
-
- <bean id="BiomobyServiceProvider" class="net.sf.taverna.t2.activities.biomoby.servicedescriptions.BiomobyServiceProvider">
- <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
- </bean>
-
- <bean id="BiomobyActivityDetailsMenuAction" class="net.sf.taverna.t2.activities.biomoby.menu.BiomobyActivityDetailsMenuAction">
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- </bean>
- <bean id="BiomobyActivityParserMenuAction" class="net.sf.taverna.t2.activities.biomoby.menu.BiomobyActivityParserMenuAction">
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- </bean>
- <bean id="ConfigureBiomobyMenuAction" class="net.sf.taverna.t2.activities.biomoby.menu.ConfigureBiomobyMenuAction">
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- <property name="activityIconManager" ref="activityIconManager" />
- </bean>
-
- <bean id="BiomobyActivityContextualViewFactory" class="net.sf.taverna.t2.activities.biomoby.view.BiomobyActivityContextualViewFactory">
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- <property name="activityIconManager" ref="activityIconManager" />
- <property name="colourManager" ref="colourManager" />
- </bean>
- <bean id="BiomobyObjectActivityContextualViewFactory" class="net.sf.taverna.t2.activities.biomoby.view.BiomobyObjectActivityContextualViewFactory">
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- <property name="colourManager" ref="colourManager" />
- </bean>
- <bean id="MobyParseDatatypeContextualViewFactory" class="net.sf.taverna.t2.activities.biomoby.view.MobyParseDatatypeContextualViewFactory">
- <property name="colourManager" ref="colourManager" />
- </bean>
-
-</beans>
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-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby.view;
-
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.util.List;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactoryRegistry;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException;
-
-import org.junit.Before;
-import org.junit.Test;
-
-public class BiomobyContextualViewFactoryTest {
- BiomobyActivity activity;
- @Before
- public void setup() throws ActivityConfigurationException {
- activity=new BiomobyActivity() { //need to prevent the activity trying to configure itself, but store a copy of the config bean
-
- @Override
- public void configure(
- BiomobyActivityConfigurationBean configurationBean)
- throws ActivityConfigurationException {
- this.configurationBean=configurationBean;
- }
-
- };
- BiomobyActivityConfigurationBean b = new BiomobyActivityConfigurationBean();
- b.setAuthorityName("a");
- b.setMobyEndpoint("e");
- b.setServiceName("s");
- activity.configure(b);
- }
-
- @Test
- public void testGetConfigureAction() throws Exception {
- ContextualView view = new BiomobyActivityContextualView(activity, null, null, null, null);
- //will be null because its not a valid activity so therefore has no secondaries
- assertNull("The action should be null",view.getConfigureAction(null));
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/taverna-biomoby-activity-ui/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/pom.xml b/taverna-biomoby-activity-ui/pom.xml
new file mode 100644
index 0000000..8f92c83
--- /dev/null
+++ b/taverna-biomoby-activity-ui/pom.xml
@@ -0,0 +1,86 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>net.sf.taverna</groupId>
+ <artifactId>taverna-parent</artifactId>
+ <version>3.0.1-SNAPSHOT</version>
+ </parent>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>biomoby-activity-ui</artifactId>
+ <version>2.0.1-SNAPSHOT</version>
+ <name>Taverna 2 Biomoby Activity UI</name>
+ <dependencies>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>activity-icons-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>activity-palette-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-impl</groupId>
+ <artifactId>activity-palette-impl</artifactId>
+ <version>${t2.ui.impl.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>biomoby-activity</artifactId>
+ <version>${t2.activities.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-impl</groupId>
+ <artifactId>contextual-views-impl</artifactId>
+ <version>${t2.ui.impl.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>contextual-views-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>activity-tools</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+
+ <!-- testing dependencies -->
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>${junit.version}</version>
+ <scope>test</scope>
+ </dependency>
+<!-- <dependency>
+ <groupId>net.sf.taverna.t2.ui-impl</groupId>
+ <artifactId>activity-palette-impl</artifactId>
+ <version>${t2.ui.impl.version}</version>
+ <scope>test</scope>
+ </dependency> -->
+ </dependencies>
+ <repositories>
+ <repository>
+ <releases />
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <id>mygrid-repository</id>
+ <name>myGrid Repository</name>
+ <url>http://www.mygrid.org.uk/maven/repository
+ </url>
+ </repository>
+ <repository>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <snapshots />
+ <id>mygrid-snapshot-repository</id>
+ <name>myGrid Snapshot Repository</name>
+ <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
+ </repository>
+ </repositories>
+</project>
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/AddParserActionHelper.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/AddParserActionHelper.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/AddParserActionHelper.java
new file mode 100644
index 0000000..b03b98c
--- /dev/null
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/AddParserActionHelper.java
@@ -0,0 +1,280 @@
+/*
+ * This file is a component of the Taverna project, and is licensed under the
+ * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
+ */
+package net.sf.taverna.t2.activities.biomoby.actions;
+
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+
+import javax.swing.ImageIcon;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.JScrollPane;
+import javax.swing.JSeparator;
+import javax.swing.JTree;
+import javax.swing.ToolTipManager;
+import javax.swing.tree.DefaultMutableTreeNode;
+import javax.swing.tree.TreePath;
+import javax.swing.tree.TreeSelectionModel;
+
+import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
+import net.sf.taverna.t2.activities.biomoby.edits.AddMobyParseDatatypeEdit;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workflowmodel.Dataflow;
+import net.sf.taverna.t2.workflowmodel.Edit;
+
+import org.apache.log4j.Logger;
+import org.biomoby.shared.MobyData;
+import org.biomoby.shared.MobyNamespace;
+import org.biomoby.shared.MobyPrimaryDataSet;
+import org.biomoby.shared.MobyPrimaryDataSimple;
+
+/**
+ * An action to add a parser from within the Workflow editor
+ *
+ * @author Eddie Kawas
+ * @author Stuart Owen - adapted for Taverna 2
+ */
+public class AddParserActionHelper {
+ private static Logger logger = Logger.getLogger(AddParserActionHelper.class);
+
+ private EditManager editManager;
+
+ private final FileManager fileManager;
+
+ public AddParserActionHelper(EditManager editManager, FileManager fileManager) {
+ this.editManager = editManager;
+ this.fileManager = fileManager;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.embl.ebi.escience.scuflui.processoractions.AbstractProcessorAction#getComponent(org.embl.ebi.escience.scufl.Processor)
+ */
+ public JComponent getComponent(final BiomobyActivity activity) {
+
+
+ // set up the root node
+ String serviceName = activity.getMobyService().getName();
+ String description = activity.getMobyService().getDescription();
+ MobyServiceTreeNode service = new MobyServiceTreeNode(serviceName,
+ description);
+ DefaultMutableTreeNode rootNode = new DefaultMutableTreeNode(service);
+
+ // now add the child nodes containing useful information about the
+ // service
+ DefaultMutableTreeNode output = new DefaultMutableTreeNode("Parse:");
+ rootNode.add(output);
+ // process outputs
+ MobyData[] outputs = activity.getMobyService().getPrimaryOutputs();
+ for (int i = 0; i < outputs.length; i++) {
+ if (outputs[i] instanceof MobyPrimaryDataSimple) {
+ MobyPrimaryDataSimple simple = (MobyPrimaryDataSimple) outputs[i];
+ StringBuffer sb = new StringBuffer(
+ "Namespaces used by this object: ");
+ MobyNamespace[] namespaces = simple.getNamespaces();
+ for (int j = 0; j < namespaces.length; j++) {
+ sb.append(namespaces[j].getName() + " ");
+ }
+ if (namespaces.length == 0)
+ sb.append(" ANY ");
+ MobyObjectTreeNode mobyObjectTreeNode = new MobyObjectTreeNode(
+ simple.getDataType().getName() + "('"
+ + simple.getName() + "')", sb.toString());
+ mobyObjectTreeNode.setNamespaces(simple.getNamespaces());
+ output.insert(new DefaultMutableTreeNode(mobyObjectTreeNode),
+ output.getChildCount());
+ } else {
+ // we have a collection
+ MobyPrimaryDataSet collection = (MobyPrimaryDataSet) outputs[i];
+ DefaultMutableTreeNode collectionNode = new DefaultMutableTreeNode(
+ "Collection('" + collection.getName() + "')");
+ output.insert(collectionNode, output.getChildCount());
+ MobyPrimaryDataSimple[] simples = collection.getElements();
+ for (int j = 0; j < simples.length; j++) {
+ MobyPrimaryDataSimple simple = simples[j];
+ StringBuffer sb = new StringBuffer(
+ "Namespaces used by this object: ");
+ MobyNamespace[] namespaces = simple.getNamespaces();
+ for (int k = 0; k < namespaces.length; k++) {
+ sb.append(namespaces[k].getName() + " ");
+ }
+ if (namespaces.length == 0)
+ sb.append("ANY ");
+ MobyObjectTreeNode mobyObjectTreeNode = new MobyObjectTreeNode(
+ simple.getDataType().getName() + "('"
+ + simple.getName() + "')", sb.toString());
+ mobyObjectTreeNode.setNamespaces(simple.getNamespaces());
+ collectionNode
+ .insert(new DefaultMutableTreeNode(
+ mobyObjectTreeNode), collectionNode
+ .getChildCount());
+ }
+
+ }
+ }
+ if (outputs.length == 0) {
+ output.add(new DefaultMutableTreeNode(" None "));
+ }
+
+ // finally return a tree describing the object
+ final JTree tree = new JTree(rootNode);
+ tree.setCellRenderer(new BioMobyServiceTreeCustomRenderer());
+ ToolTipManager.sharedInstance().registerComponent(tree);
+ tree.addMouseListener(new MouseListener() {
+ public void mouseClicked(MouseEvent me) {
+ }
+
+ public void mousePressed(MouseEvent me) {
+ mouseReleased(me);
+ }
+
+ public void mouseReleased(MouseEvent me) {
+ if (me.isPopupTrigger()) // right click, show popup menu
+ {
+ TreePath path = tree.getPathForLocation(me.getX(), me
+ .getY());
+ if (path == null)
+ return;
+ if (path.getPathCount() >= 3) {
+ if (path.getParentPath().toString().indexOf("Parse:") >= 0
+ && path.getLastPathComponent().toString()
+ .indexOf(" None ") == -1) {
+ DefaultMutableTreeNode node = (DefaultMutableTreeNode) tree
+ .getLastSelectedPathComponent();
+ if (node == null)
+ return;
+ final String selectedObject = node.toString();
+ if (!selectedObject.equals(path
+ .getLastPathComponent().toString()))
+ return;
+
+ logger.debug("TreePath " + path.toString());
+ if (
+ // path has a collection in it
+ (path.getPathCount() == 4
+ && path.getParentPath()
+ .getLastPathComponent().toString()
+ .startsWith("Collection(") && (path
+ .getParentPath().toString())
+ .indexOf("Parse:") > 0)
+ // or path is just a simple
+ || (path.toString().indexOf("Collection(") < 0)) {
+
+ final JPopupMenu menu = new JPopupMenu();
+
+ final String potentialCollectionString = path
+ .getParentPath().getLastPathComponent()
+ .toString();
+ final boolean isCollection = potentialCollectionString
+ .indexOf("Collection('") >= 0;
+ JMenuItem item3 = new JMenuItem(
+ "Add parser for " + selectedObject
+ + " to the workflow");
+ item3
+ .setIcon(getIcon("/Cut24.gif"));
+ item3.addActionListener(new ActionListener() {
+
+ public void actionPerformed(ActionEvent ae) {
+ // you would like to search for
+ // selectedObject
+ try {
+ try {
+ Dataflow currentDataflow = fileManager.getCurrentDataflow();
+ Edit<?> edit = new AddMobyParseDatatypeEdit(
+ currentDataflow, activity,
+ selectedObject,isCollection, potentialCollectionString, editManager.getEdits());
+ editManager.doDataflowEdit(
+ currentDataflow, edit);
+
+ } catch (Exception e) {
+ logger.error("", e);
+ }
+
+ } catch (Exception e) {
+ logger.error("", e);
+ }
+
+ }
+ });
+
+ menu.add(new JSeparator());
+ menu.add(new JLabel("Parse Moby Data ... ",
+ JLabel.CENTER));
+ menu.add(new JSeparator());
+ menu.add(item3);
+ menu.show(me.getComponent(), me.getX(), me
+ .getY());
+ } else {
+ logger
+ .debug("unexpected situation occured; '"
+ + selectedObject
+ + "' was the object selected and the path is: "
+ + path.toString());
+ }
+ }
+ }
+ }
+ }
+
+ public void mouseEntered(MouseEvent me) {
+ }
+
+ public void mouseExited(MouseEvent me) {
+ }
+ });
+
+ tree.getSelectionModel().setSelectionMode(
+ TreeSelectionModel.SINGLE_TREE_SELECTION);
+ JScrollPane jsp = new JScrollPane(tree);
+ JPanel thePanel = new JPanel(new BorderLayout());
+ thePanel.add(jsp, BorderLayout.CENTER);
+ return thePanel;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.embl.ebi.escience.scuflui.processoractions.ProcessorActionSPI#getDescription()
+ */
+ public String getDescription() {
+ return "Add BioMOBY Parser ...";
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.embl.ebi.escience.scuflui.processoractions.ProcessorActionSPI#getIcon()
+ */
+ public ImageIcon getIcon() {
+ return MobyPanel.getIcon("/Cut24.gif");
+ }
+
+ /**
+ * returns the frame size as a dimension for the content pane housing
+ * this action
+ */
+ public Dimension getFrameSize() {
+ return new Dimension(450, 450);
+ }
+
+ /**
+ * Return an Icon to represent this action
+ *
+ * @param loc
+ * the location of the image to use as an icon
+ */
+ private ImageIcon getIcon(String loc) {
+ return MobyPanel.getIcon(loc);
+ }
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyObjectTreeCustomRenderer.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyObjectTreeCustomRenderer.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyObjectTreeCustomRenderer.java
new file mode 100644
index 0000000..46b4d5a
--- /dev/null
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyObjectTreeCustomRenderer.java
@@ -0,0 +1,97 @@
+/*
+ * This file is a component of the Taverna project,
+ * and is licensed under the GNU LGPL.
+ * Copyright Edward Kawas, The BioMoby Project
+ */
+package net.sf.taverna.t2.activities.biomoby.actions;
+
+import java.awt.Color;
+import java.awt.Component;
+
+import javax.swing.JComponent;
+import javax.swing.JTree;
+import javax.swing.tree.DefaultMutableTreeNode;
+import javax.swing.tree.DefaultTreeCellRenderer;
+
+public class BioMobyObjectTreeCustomRenderer extends DefaultTreeCellRenderer {
+
+ private static final long serialVersionUID = 1L;
+
+ private Color leafForeground = Color.blue;
+
+ private Color rootColor = Color.black;
+
+ @SuppressWarnings("unused")
+ private Color feedsIntoColor = Color.gray;
+
+ @SuppressWarnings("unused")
+ private Color producedColor = Color.lightGray;
+
+ @SuppressWarnings("unused")
+ private Color authorityColor = Color.orange;
+
+ private Color serviceColor = Color.magenta;
+
+ private Color objectColor = Color.green;
+
+ public Component getTreeCellRendererComponent(JTree tree, Object value,
+ boolean selected, boolean expanded, boolean leaf, int row,
+ boolean hasFocus) {
+ // Allow the original renderer to set up the label
+ Component c = super.getTreeCellRendererComponent(tree, value, selected,
+ expanded, leaf, row, hasFocus);
+
+ if (value instanceof DefaultMutableTreeNode) {
+ DefaultMutableTreeNode node = (DefaultMutableTreeNode) value;
+ if (node.getUserObject() instanceof MobyServiceTreeNode) {
+ // service node
+ c.setForeground(serviceColor);
+ ((JComponent) c).setToolTipText(((MobyServiceTreeNode) node
+ .getUserObject()).getDescription());
+ setIcon(MobyPanel.getIcon("/service.png"));
+ } else if (node.getUserObject() instanceof MobyObjectTreeNode) {
+ // object node
+ c.setForeground(objectColor);
+ ((JComponent) c).setToolTipText(((MobyObjectTreeNode) node
+ .getUserObject()).getDescription());
+ } else if (node.isRoot()) {
+ // root node
+ setIcon(MobyPanel.getIcon("/moby.png"));
+ ((JComponent) c).setToolTipText(" Description of "
+ + node.getUserObject());
+ c.setForeground(rootColor);
+ } else if (node.getUserObject() instanceof String) {
+ // check for feeds into and produced by nodes
+ String string = (String) node.getUserObject();
+ if (string.equalsIgnoreCase("feeds into")) {
+ setIcon(MobyPanel.getIcon("/input.png"));
+ ((JComponent) c).setToolTipText(null);
+ } else if (string.equalsIgnoreCase("produced by")) {
+ setIcon(MobyPanel.getIcon("/output.png"));
+ ((JComponent) c).setToolTipText(null);
+ } else if (string.equalsIgnoreCase("produces")) {
+ ((JComponent) c).setToolTipText(null);
+ } else {
+
+ ((JComponent) c).setToolTipText(null);
+
+ if (!leaf) {
+ if (string.startsWith("Collection('")) {
+ setIcon(MobyPanel.getIcon("/collection.png"));
+ } else {
+ setIcon(MobyPanel.getIcon("/authority.png"));
+ }
+ }
+ }
+
+ } else {
+ ((JComponent) c).setToolTipText("nothing node");
+ }
+ }
+ if (selected)
+ c.setBackground(Color.lightGray);
+ if (leaf)
+ c.setForeground(this.leafForeground);
+ return c;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/fd2e9765/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyServiceTreeCustomRenderer.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyServiceTreeCustomRenderer.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyServiceTreeCustomRenderer.java
new file mode 100644
index 0000000..ecce3ca
--- /dev/null
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyServiceTreeCustomRenderer.java
@@ -0,0 +1,86 @@
+/*
+ * This file is a component of the Taverna project,
+ * and is licensed under the GNU LGPL.
+ * Copyright Edward Kawas, The BioMoby Project
+ */
+package net.sf.taverna.t2.activities.biomoby.actions;
+
+import java.awt.Color;
+import java.awt.Component;
+
+import javax.swing.JComponent;
+import javax.swing.JTree;
+import javax.swing.tree.DefaultMutableTreeNode;
+import javax.swing.tree.DefaultTreeCellRenderer;
+
+public class BioMobyServiceTreeCustomRenderer extends DefaultTreeCellRenderer {
+
+ private static final long serialVersionUID = 1L;
+
+ private Color leafForeground = Color.blue;
+
+ @SuppressWarnings("unused")
+ private Color rootColor = Color.black;
+
+ @SuppressWarnings("unused")
+ private Color feedsIntoColor = Color.gray;
+
+ @SuppressWarnings("unused")
+ private Color producedColor = Color.lightGray;
+
+ @SuppressWarnings("unused")
+ private Color authorityColor = Color.orange;
+
+ private Color serviceColor = Color.magenta;
+
+ private Color objectColor = Color.green;
+
+ public Component getTreeCellRendererComponent(JTree tree, Object value,
+ boolean selected, boolean expanded, boolean leaf, int row,
+ boolean hasFocus) {
+ // Allow the original renderer to set up the label
+ Component c = super.getTreeCellRendererComponent(tree, value, selected,
+ expanded, leaf, row, hasFocus);
+
+ if (value instanceof DefaultMutableTreeNode) {
+ DefaultMutableTreeNode node = (DefaultMutableTreeNode) value;
+ if (node.getUserObject() instanceof MobyServiceTreeNode) {
+ // service node
+ c.setForeground(serviceColor);
+ ((JComponent) c).setToolTipText(((MobyServiceTreeNode) node
+ .getUserObject()).getDescription());
+ setIcon(MobyPanel.getIcon("/service.png"));
+ } else if (node.getUserObject() instanceof MobyObjectTreeNode) {
+ // object node
+ c.setForeground(objectColor);
+ ((JComponent) c).setToolTipText(((MobyObjectTreeNode) node
+ .getUserObject()).getDescription());
+ } else if (node.getUserObject() instanceof String) {
+ // check for feeds into and produced by nodes
+ String string = (String) node.getUserObject();
+ if (string.equalsIgnoreCase("inputs")) {
+ setIcon(MobyPanel.getIcon("/input.png"));
+ ((JComponent) c).setToolTipText(null);
+ } else if (string.equalsIgnoreCase("outputs")) {
+ setIcon(MobyPanel.getIcon("/output.png"));
+ ((JComponent) c).setToolTipText(null);
+ } else {
+
+ ((JComponent) c).setToolTipText(null);
+
+ if (!leaf) {
+ if (string.startsWith("Collection('")) {
+ setIcon(MobyPanel.getIcon("/collection.png"));
+ }
+ }
+ }
+
+ } else {
+ ((JComponent) c).setToolTipText("nothing node");
+ }
+ }
+ if (leaf)
+ c.setForeground(this.leafForeground);
+ return c;
+ }
+}