This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository mauve.
commit e5410c1dc43d728a119461074983b4e5bf18b414 Author: Andreas Tille <[email protected]> Date: Thu Apr 30 13:16:44 2015 +0200 Drop goose.jar (and the Java file using it) according to upstream advise --- debian/patches/do_not_use_goose_jar.patch | 719 ++++++++++++++++++++++++++++++ debian/patches/series | 1 + 2 files changed, 720 insertions(+) diff --git a/debian/patches/do_not_use_goose_jar.patch b/debian/patches/do_not_use_goose_jar.patch new file mode 100644 index 0000000..9e7b022 --- /dev/null +++ b/debian/patches/do_not_use_goose_jar.patch @@ -0,0 +1,719 @@ +--- a/.classpath ++++ b/.classpath +@@ -9,7 +9,6 @@ + <classpathentry kind="lib" path="/usr/share/java/zeus-jscl.jar"/> + <classpathentry kind="lib" path="/usr/share/java/dbus.jar"/> + <classpathentry kind="lib" path="/usr/share/java/unix.jar"/> +- <classpathentry kind="lib" path="ext/goose.jar"/> + <classpathentry kind="lib" path="/usr/share/icedtea-web/netx.jar"/> + <classpathentry kind="lib" path="/usr/share/java/biojava.jar"/> + <classpathentry kind="output" path="bin"/> +--- a/build.xml ++++ b/build.xml +@@ -82,7 +82,6 @@ + ${deblib}/commons-cli.jar; + ${support}/junit.jar; + ${deblib}/zeus-jscl.jar; +- ${ext}/goose.jar; + ${deblib}/ant.jar; + ${deblib}/dbus.jar; + ${deblib}/unix.jar" +--- a/src/org/gel/mauve/gaggle/SampleGoose.java ++++ /dev/null +@@ -1,696 +0,0 @@ +-package org.gel.mauve.gaggle; +-// SampleGoose.java +-//------------------------------------------------------------------------------ +-// $Revision: 503 $ +-// $Date: 2005/04/03 19:15:04 $ +-//------------------------------------------------------------------------------------- +-/* +- * Copyright (C) 2006 by Institute for Systems Biology, +- * Seattle, Washington, USA. All rights reserved. +- * +- * This source code is distributed under the GNU Lesser +- * General Public License, the text of which is available at: +- * http://www.gnu.org/copyleft/lesser.html +- */ +- +-// todo - this is the canonical goose - remove warnings +- +- +-import java.rmi.*; +- +-import org.systemsbiology.gaggle.core.datatypes.DataMatrix; +-import org.systemsbiology.gaggle.core.Boss; +-import org.systemsbiology.gaggle.core.Goose; +-import org.systemsbiology.gaggle.core.datatypes.*; +-import org.systemsbiology.gaggle.core.datatypes.Interaction; +-import org.systemsbiology.gaggle.util.MiscUtil; +-import org.systemsbiology.gaggle.geese.common.RmiGaggleConnector; +-import org.systemsbiology.gaggle.geese.common.GooseShutdownHook; +-import org.systemsbiology.gaggle.geese.common.GaggleConnectionListener; +- +-import javax.swing.*; +-import javax.swing.border.*; +-import java.awt.*; +-import java.awt.event.*; +-import java.net.URL; +-import java.net.MalformedURLException; +- +-/** +- * A goose useful for testing and diagnostics and learning how to write a goose +- * that uses the new (2007-04) API. +- */ +-public class SampleGoose extends JFrame implements Goose, GaggleConnectionListener, +- WindowListener { +- String myGaggleName = "Sample"; +- String[] activeGooseNames; +- Boss boss; +- RmiGaggleConnector connector = new RmiGaggleConnector(this); +- protected JScrollPane scrollPane; +- protected JTextArea textArea; +- JComboBox gooseChooser; +- String targetGoose = "Boss"; +- +- JButton connectButton; +- JButton disconnectButton; +- +- //------------------------------------------------------------------------------------- +- public SampleGoose() { +- super("Sample"); +- addWindowListener(this); +- new GooseShutdownHook(connector); +- +- +- +- try { +- connectToGaggle(); +- } +- catch (Exception ex0) { +- System.err.println("SampleGoose failed to connect to gaggle: " + ex0.getMessage()); +- } +- add(createGui()); +- +- connector.addListener(this); +- +- setSize(500, 500); +- MiscUtil.placeInCenter(this); +- setVisible(true); +- +- } +- +- //------------------------------------------------------------------------------------- +- JPanel createGui() { +- ToolTipManager.sharedInstance().setInitialDelay(0); +- setLayout(new BorderLayout()); +- JPanel mainPanel = new JPanel(); +- mainPanel.setLayout(new BorderLayout()); +- JPanel controlPanel = new JPanel(); +- JToolBar toolbar = new JToolBar(); +- controlPanel.add(toolbar); +- toolbar.setFloatable(false); +- +- mainPanel.add(controlPanel, BorderLayout.NORTH); +- MiscUtil.setApplicationIcon(this); +- +- +- +- gooseChooser = new JComboBox(new String[]{"Boss"}); +- gooseChooser.setPrototypeDisplayValue("a very very long goose name"); +- gooseChooser.setToolTipText("Specify goose for broadcast"); +- toolbar.add(gooseChooser); +- +- +- gooseChooser.addActionListener(new ActionListener() { +- public void actionPerformed(ActionEvent e) { +- JComboBox cb = (JComboBox) e.getSource(); +- int gooseChooserIndex = cb.getSelectedIndex(); +- System.out.println("choose goose index: " + gooseChooserIndex); +- targetGoose = (String) cb.getSelectedItem(); +- System.out.println("target: " + targetGoose); +- } +- }); +- +- JButton showGooseButton = new JButton("S"); +- JButton hideGooseButton = new JButton("H"); +- +- // broadcast small & simple versions of each data type +- JButton broadcastListButton = new JButton("B"); +- JButton broadcastMatrixButton = new JButton("M"); +- JButton broadcastNetworkButton = new JButton("N"); +- JButton broadcastHashButton = new JButton("T"); +- JButton broadcastClusterButton = new JButton("C"); +- +- showGooseButton.setToolTipText("Show selected goose"); +- hideGooseButton.setToolTipText("Hide selected goose"); +- broadcastListButton.setToolTipText("Broadcast sample name list"); +- broadcastMatrixButton.setToolTipText("Broadcast sample matrix"); +- broadcastNetworkButton.setToolTipText("Broadcast sample network"); +- broadcastHashButton.setToolTipText("Broadcast sample Tuple (lists of data and metadata)"); +- broadcastClusterButton.setToolTipText("Broadcast cluster: selected row and column names"); +- +- showGooseButton.addActionListener(new ActionListener() { +- public void actionPerformed(ActionEvent e) { +- try { +- boss.show(targetGoose); +- } +- catch (Exception ex2) { +- ex2.printStackTrace(); +- } +- } +- }); +- +- hideGooseButton.addActionListener(new ActionListener() { +- public void actionPerformed(ActionEvent e) { +- try { +- boss.hide(targetGoose); +- } +- catch (Exception ex2) { +- ex2.printStackTrace(); +- } +- } +- }); +- +- broadcastListButton.addActionListener(new ActionListener() { +- public void actionPerformed(ActionEvent e) { +- try { +- broadcastSampleList(); +- } +- catch (Exception ex2) { +- ex2.printStackTrace(); +- } +- } +- }); +- +- broadcastMatrixButton.addActionListener(new ActionListener() { +- public void actionPerformed(ActionEvent e) { +- broadcastSampleMatrix(); +- } +- }); +- +- broadcastNetworkButton.addActionListener(new ActionListener() { +- public void actionPerformed(ActionEvent e) { +- try { +- broadcastSampleNetwork(); +- } +- catch (Exception ex2) { +- ex2.printStackTrace(); +- } +- } +- }); +- +- broadcastHashButton.addActionListener(new ActionListener() { +- public void actionPerformed(ActionEvent e) { +- try { +- broadcastSampleTuple(); +- } +- catch (Exception ex2) { +- ex2.printStackTrace(); +- } +- } +- }); +- +- broadcastClusterButton.addActionListener(new ActionListener() { +- public void actionPerformed(ActionEvent e) { +- try { +- broadcastSampleCluster(); +- } +- catch (Exception ex2) { +- ex2.printStackTrace(); +- } +- } +- }); +- +- toolbar.add(showGooseButton); +- toolbar.add(hideGooseButton); +- toolbar.add(broadcastListButton); +- toolbar.add(broadcastMatrixButton); +- toolbar.add(broadcastNetworkButton); +- toolbar.add(broadcastHashButton); +- toolbar.add(broadcastClusterButton); +- +- JPanel searchPanel = new JPanel(); +- textArea = new JTextArea(); +- JScrollPane scrollPane = new JScrollPane(textArea); +- mainPanel.setBorder(createBorder()); +- mainPanel.add(scrollPane, BorderLayout.CENTER); +- +- JPanel buttonPanel = new JPanel(); +- +- connectButton = new JButton("Connect"); +- connectButton.setToolTipText("Connect to Boss"); +- connectButton.setEnabled(!connector.isConnected()); +- connectButton.addActionListener(new ActionListener() { +- +- public void actionPerformed(ActionEvent actionEvent) { +- try { +- connector.connectToGaggle(); +- connectButton.setEnabled(false); +- disconnectButton.setEnabled(true); +- } catch (Exception e) { +- JOptionPane.showMessageDialog(SampleGoose.this, +- "Couldn't connect to boss, is the boss running?"); +- e.printStackTrace(); +- } +- } +- }); +- +- +- disconnectButton = new JButton("Disconnect"); +- disconnectButton.setToolTipText("Disconnect from Boss"); +- disconnectButton.setEnabled(connector.isConnected()); +- disconnectButton.addActionListener(new ActionListener() { +- +- public void actionPerformed(ActionEvent actionEvent) { +- connector.disconnectFromGaggle(false); +- connectButton.setEnabled(true); +- disconnectButton.setEnabled(false); +- } +- }); +- +- +- JButton clearButton = new JButton("Clear"); +- clearButton.addActionListener(new ActionListener() { +- public void actionPerformed(ActionEvent e) { +- textArea.setText(""); +- } +- }); +- +- +- JButton exitButton = new JButton("Quit"); +- exitButton.addActionListener(new ActionListener() { +- public void actionPerformed(ActionEvent e) { +- doExit(); +- } +- }); +- +- buttonPanel.add(connectButton); +- buttonPanel.add(disconnectButton); +- buttonPanel.add(clearButton); +- buttonPanel.add(exitButton); +- +- mainPanel.add(buttonPanel, BorderLayout.SOUTH); +- MiscUtil.updateGooseChooser(gooseChooser, myGaggleName, activeGooseNames); +- +- return mainPanel; +- +- } // createGui +- +- +- //----------------------------------------------------------------------------------- +- private Border createBorder() { +- int right = 10; +- int left = 10; +- int top = 10; +- int bottom = 10; +- return new EmptyBorder(top, left, bottom, right); +- } +- +- //------------------------------------------------------------------------------- +- public void connectToGaggle() { +- try { +- connector.connectToGaggle(); +- } +- catch (Exception ex0) { +- System.err.println("failed to connect to gaggle: " + ex0.getMessage()); +- ex0.printStackTrace(); +- } +- boss = connector.getBoss(); +- } +- +- //---------------------------------------------------------------------------------------- +- public void handleNameList(String source, Namelist nameList) { +- StringBuffer sb = new StringBuffer(); +- sb.append(" >>> handleNameList, name = " + nameList.getName() + +- ", length " + nameList.getNames().length + ", source = " + source + "\n"); +- sb.append(" species: " + nameList.getSpecies() + "\n"); +- +- int max = 5; +- if (nameList.getNames().length < max) +- max = nameList.getNames().length; +- for (int i = 0; i < max; i++) +- sb.append(" " + nameList.getNames()[i] + "\n"); +- +- sb.append("\n\n"); +- textArea.append(sb.toString()); +- textArea.setCaretPosition(textArea.getText().length()); +- } +- +- //---------------------------------------------------------------------------------------- +- public void handleMatrix(String source, DataMatrix matrix) { +- StringBuffer sb = new StringBuffer(); +- sb.append(" >>> handleMatrix: " + matrix.getRowCount() + " x " + matrix.getColumnCount() + "\n"); +- sb.append(" species: " + matrix.getSpecies() + "\n"); +- sb.append("matrix name = " + matrix.getName() + ", source = " + source + "\n"); +- sb.append("\n\n"); +- textArea.append(sb.toString()); +- textArea.setCaretPosition(textArea.getText().length()); +- +- } +-//---------------------------------------------------------------------------------------- +- +- public void handleTuple(String source, GaggleTuple gaggleTuple) { // todo - extract this to common code for other diag/sample geese +- // todo - figure out a better way to show a small subset of a gaggleTuple +- // (right now we just show the whole thing) +- System.out.println("in SampleGoose.handleTuple()"); +- StringBuilder sb = new StringBuilder(); +- sb.append(" >>> handleTuple: " + gaggleTuple.getName() + "\n"); +- sb.append(" species: " + gaggleTuple.getSpecies() + "\n"); +- sb.append(" source: " + source + "\n\n"); +- +- int datalength = (gaggleTuple.getData().getSingleList().size() > 5) ? 5 +- : gaggleTuple.getData().getSingleList().size(); +- +- int metadatalength = (gaggleTuple.getMetadata().getSingleList().size() > 5) ? 5 +- : gaggleTuple.getMetadata().getSingleList().size(); +- +- sb.append("First few rows of metadata: \n"); +- sb.append(gaggleTuple.getMetadata().toString()); +- sb.append("\n"); +- +- /* +- if (gaggleTuple.getMetadata().getSingleList().size() == 0) { +- sb.append(gaggleTuple.getMetadata().toString()); +- sb.append("\n"); +- } else { +- String[] msegs = gaggleTuple.getMetadata().toString().split("\n"); +- for (int i = 0; i < metadatalength; i++) { +- sb.append(msegs[i]); +- sb.append("\n"); +- } +- +- } +- */ +- +- +- sb.append("\n\nFirst few rows of data: \n"); +- sb.append(gaggleTuple.getData().toString()); +- sb.append("\n"); +- /* +- if (gaggleTuple.getData().getSingleList().size() == 0) { +- sb.append(gaggleTuple.getData().toString()); +- sb.append("\n"); +- } else { +- String[] dsegs = gaggleTuple.getData().toString().split("\n"); +- for (int i = 0; i < datalength; i++) { +- //Tuple tuple = (Tuple)gaggleTuple.getData().getSingleAt(i).getValue(); +- //sb.append(tuple.toString()); +- sb.append(dsegs[i]); +- sb.append("\n"); +- } +- +- } +- */ +- +- sb.append("\n\n"); +- textArea.append(sb.toString()); +- textArea.setCaretPosition(textArea.getText().length()); +- } +- +- //---------------------------------------------------------------------------------------- +- public void handleCluster( +- String source, Cluster cluster) { +- StringBuffer sb = new StringBuffer(); +- sb.append(" >>> handleCluster: name =" + cluster.getName() + "\n"); +- sb.append(" species: " + cluster.getSpecies() + "\n"); +- sb.append(" source: " + source + "\n"); +- sb.append(" rows: " + cluster.getRowNames().length + "\n"); +- sb.append(" cols: " + cluster.getColumnNames().length + "\n"); +- +- sb.append("\n\n"); +- textArea.append(sb.toString()); +- textArea.setCaretPosition(textArea.getText().length()); +- +- } +- +- //---------------------------------------------------------------------------------------- +- public void handleNetwork(String source, Network network) { +- StringBuffer sb = new StringBuffer(); +- sb.append(" >>> handleNetwork, name = " + network.getName() + "\n"); +- sb.append(" source: " + source + "\n"); +- sb.append(" species: " + network.getSpecies() + "\n"); +- sb.append(" nodes: " + network.nodeCount() + "\n"); +- sb.append(" edges: " + network.edgeCount() + "\n"); +- if (network.getMetadata() == null) { +- sb.append(" no metadata"); +- } else { +- sb.append(" metadata found, # of singles: "); +- sb.append(network.getMetadata().getSingleList().size()); +- } +- +- sb.append("\n\n"); +- textArea.append(sb.toString()); +- textArea.setCaretPosition(textArea.getText().length()); +- } +- +- //---------------------------------------------------------------------------------------- +- protected void broadcastSampleList() { +- String[] nameList = {"YFL036W", "YFL037W", "YLR212C", "YLR213C", +- "YML085C", "YML086C", "YML123C", "YML124C"}; +- +- String species = "Saccharomyces cerevisiae"; +- Namelist gaggleNameList = new Namelist(); +- gaggleNameList.setSpecies(species); +- gaggleNameList.setNames(nameList); +- try { +- boss.broadcastNamelist(myGaggleName, targetGoose, gaggleNameList); +- } +- catch (RemoteException rex) { +- System.err.println("SampleGoose: " + "rmi error calling boss.broadcast (nameList)"); +- rex.printStackTrace(); +- } +- +- } // broadcastSampleList +- +- //---------------------------------------------------------------------------------------- +- protected void broadcastSampleCluster() { +- String[] rowNames = {"YFL036W", "YLR212C", "YML085C", "YML123C"}; +- String[] columnNames = {"T000", "T120", "T240"}; +- +- String species = "Saccharomyces cerevisiae"; +- String clusterName = "Sample Cluster"; +- +- try { +- boss.broadcastCluster(myGaggleName, targetGoose, new Cluster(clusterName, species, rowNames, columnNames)); +- } +- catch (RemoteException rex) { +- System.err.println("SampleGoose: " + "rmi error calling boss.broadcast (cluster)"); +- rex.printStackTrace(); +- } +- +- } // broadcastSampleCluster +- +- //---------------------------------------------------------------------------------------- +- protected void broadcastSampleMatrix() { +- org.systemsbiology.gaggle.core.datatypes.DataMatrix matrix = new org.systemsbiology.gaggle.core.datatypes.DataMatrix(); +- +- matrix.setFullName("Demo Yeast created on the fly, meaningless data"); +- matrix.setShortName("Demo Yeast"); +- +- String[] columnTitles = {"T000", "T060", "T120", "T240"}; +- String[] rowTitles = {"YFL036W", "YFL037W", "YLR212C", "YLR213C", +- "YML085C", "YML086C", "YML123C", "YML124C"}; +- int dataRows = rowTitles.length; +- int dataColumns = columnTitles.length; +- matrix.setSize(dataRows, dataColumns); +- +- matrix.setSpecies("Saccharomyces cerevisiae"); +- matrix.setRowTitlesTitle("GENE"); +- matrix.setColumnTitles(columnTitles); +- matrix.setRowTitles(rowTitles); +- +- for (int r = 0; r < dataRows; r++) +- for (int c = 0; c < dataColumns; c++) +- matrix.set(r, c, (r * 0.38) + c * 0.09); +- +- matrix.setName("a sample matrix"); +- try { +- boss.broadcastMatrix(myGaggleName, targetGoose, matrix); +- } +- catch (RemoteException rex) { +- System.err.println("SampleGoose: " + "rmi error calling boss.broadcast (matrix)"); +- rex.printStackTrace(); +- } +- +- } // broadcastSampleMatrix +- +- //---------------------------------------------------------------------------------------- +- protected void broadcastSampleNetwork() { +- Interaction i0 = new Interaction("YFL036W", "YFL037W", "GeneCluster"); +- Interaction i1 = new Interaction("YFL037W", "YLR212C", "GeneFusion"); +- Interaction i2 = new Interaction("YFL037W", "YML085C", "GeneFusion"); +- Interaction i3 = new Interaction("YFL037W", "YML124C", "GeneFusion"); +- Interaction i4 = new Interaction("YLR212C", "YLR213C", "GeneCluster"); +- Interaction i5 = new Interaction("YLR212C", "YML085C", "GeneFusion"); +- Interaction i6 = new Interaction("YLR212C", "YML124C", "GeneFusion"); +- Interaction i7 = new Interaction("YML123C", "YML124C", "GeneCluster"); +- Interaction i8 = new Interaction("YML085C", "YML086C", "GeneCluster"); +- Interaction i9 = new Interaction("YML085C", "YML124C", "GeneFusion"); +- +- org.systemsbiology.gaggle.core.datatypes.Network network = new org.systemsbiology.gaggle.core.datatypes.Network(); +- +- network.add(i0); +- network.add(i1); +- network.add(i2); +- network.add(i3); +- network.add(i4); +- network.add(i5); +- network.add(i6); +- network.add(i7); +- network.add(i8); +- network.add(i9); +- +- String species = "Saccharomyces cerevisiae"; +- String[] nodeNames = {"YFL036W", "YFL037W", "YLR212C", "YLR213C", +- "YML085C", "YML086C", "YML123C", "YML124C"}; +- for (int i = 0; i < nodeNames.length; i++) { +- network.addNodeAttribute(nodeNames[i], "moleculeType", "DNA"); +- network.addNodeAttribute(nodeNames[i], "species", species); +- } +- +- network.addEdgeAttribute("YFL036W (GeneCluster) YFL037W", "score", new Double(0.5)); +- network.addEdgeAttribute("YFL037W (GeneFusion) YLR212C", "score", new Double(0.4)); +- network.addEdgeAttribute("YFL037W (GeneFusion) YML085C", "score", new Double(0.3)); +- network.addEdgeAttribute("YFL037W (GeneFusion) YML124C", "score", new Double(0.2)); +- network.addEdgeAttribute("YLR212C (GeneCluster) YLR213C", "score", new Double(0.1)); +- network.addEdgeAttribute("YLR212C (GeneFusion) YML085C", "score", new Double(0.8)); +- network.addEdgeAttribute("YLR212C (GeneFusion) YML124C", "score", new Double(0.75)); +- network.addEdgeAttribute("YML123C (GeneCluster) YML124C", "score", new Double(0.55)); +- network.addEdgeAttribute("YML085C (GeneCluster) YML086C", "score", new Double(0.45)); +- network.addEdgeAttribute("YML085C (GeneFusion) YML124C", "score", new Double(0.35)); +- network.setSpecies(species); +- network.setName("a sample network"); +- +- try { +- boss.broadcastNetwork(myGaggleName, targetGoose, network); +- } +- catch (RemoteException rex) { +- System.err.println("SampleGoose: " + "rmi error calling boss.broadcast (network)"); +- rex.printStackTrace(); +- } +- +- } // broadcastSimpleNetwork +- +- //---------------------------------------------------------------------------------------- +- protected void broadcastSampleTuple() { +- // todo change this to broadcast vng names (and change species accordingly) +- System.out.println("in SampleGoose.broadcastSampleTuple()"); +- +- double[] values = {0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8}; +- String[] rowNames = {"YFL036W", "YFL037W", "YLR212C", "YLR213C", +- "YML085C", "YML086C", "YML123C", "YML124C"}; +- +- GaggleTuple gaggleTuple = new GaggleTuple(); +- gaggleTuple.setName("a tuple list holding a frame of a movie"); +- gaggleTuple.setSpecies("escargot"); +- +- // todo - think of convenience methods that would allow doing this in one line: +- Single condition = new Single("condition", "a condition name"); +- gaggleTuple.getMetadata().addSingle(condition); +- // +- +- for (int i = 0; i < rowNames.length; i++) { +- Tuple tuple = new Tuple(); +- tuple.addSingle(new Single(null, rowNames[i])); +- tuple.addSingle(new Single(null, "log10 ratios")); +- tuple.addSingle(new Single(null, values[i])); +- gaggleTuple.getData().addSingle(new Single(tuple)); +- } +- +- +- +- try { +- boss.broadcastTuple(myGaggleName, targetGoose, gaggleTuple); +- } +- catch (RemoteException rex) { +- System.err.println("SampleGoose: " + "rmi error calling boss.broadcastTuple"); +- rex.printStackTrace(); +- } +- +- } +- +- //---------------------------------------------------------------------------------------- +- public void clearSelections() { +- System.out.println("clearSelections"); +- } +- +- //---------------------------------------------------------------------------------------- +- public int getSelectionCount() { +- return 0; +- } +- +- //---------------------------------------------------------------------------------------- +- public String getName() { +- return myGaggleName; +- } +- +- //---------------------------------------------------------------------------------------- +- public void setName(String newName) { +- myGaggleName = newName; +- setTitle(myGaggleName); +- } +- +- //---------------------------------------------------------------------------------------- +- public void setGeometry(int x, int y, int width, int height) { +- System.out.println("setGeometry"); +- } +- +- //---------------------------------------------------------------------------------------- +- public void doBroadcastList() { +- +- } +- +- //---------------------------------------------------------------------------------------- +- public void doHide() { +- setVisible(false); +- } +- +- //---------------------------------------------------------------------------------------- +- public void doShow() { +- setAlwaysOnTop(true); +- setVisible(true); +- setAlwaysOnTop(false); +- +- } +- +- //---------------------------------------------------------------------------------------- +- public void doExit() { +- connector.disconnectFromGaggle(true); +- System.exit(0); +- } +- +- public void update(String[] activeGooseNames) { +- this.activeGooseNames = activeGooseNames; +- +- MiscUtil.updateGooseChooser(gooseChooser, myGaggleName, activeGooseNames); +- +- if (textArea != null) { +- StringBuffer sb = new StringBuffer(); +- sb.append(" >>> GOT AN UPDATE EVENT. New goose names are: \n"); +- for (String gooseName : activeGooseNames) { +- sb.append(gooseName); +- sb.append("\n"); +- } +- +- sb.append("\n\n"); +- textArea.append(sb.toString()); +- textArea.setCaretPosition(textArea.getText().length()); +- } +- } +- +- +- public void setConnected(boolean connected, Boss boss) { +- this.boss = boss; +- System.out.println("SampleGoose: received connection status: " + connected); +- if (connectButton != null) +- connectButton.setEnabled(!connected); +- if (disconnectButton != null) +- disconnectButton.setEnabled(connected); +- } +- +- +- public void windowOpened(WindowEvent e) { +- } +- +- public void windowClosing(WindowEvent e) { +- doExit(); +- } +- +- public void windowClosed(WindowEvent e) { +- } +- +- public void windowIconified(WindowEvent e) { +- } +- +- public void windowDeiconified(WindowEvent e) { +- } +- +- public void windowActivated(WindowEvent e) { +- } +- +- public void windowDeactivated(WindowEvent e) { +- } +- +- public static void main(String[] args) throws Exception { +- new SampleGoose(); +- } // main +-//------------------------------------------------------------------------------------- +-} // SampleGoose diff --git a/debian/patches/series b/debian/patches/series index 3eef136..4e25b6c 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,3 +1,4 @@ build_xml.patch debian_classes.patch use_JConsole_of_zeus-jscl_properly.patch +do_not_use_goose_jar.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/mauve.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
