[med-svn] [mauve] 04/07: Drop goose.jar (and the Java file using it) according to upstream advise
Andreas Tille
tille at debian.org
Thu Apr 30 11:22:24 UTC 2015
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 <tille at debian.org>
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
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