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Revert "Refs Murali-group#33: Create sub packages for different classes"
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This reverts commit aff4a13.
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@LHuang2019
LHuang2019 committed Oct 22, 2017
1 parent aff4a13 commit 8e20037
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Showing 13 changed files with 26 additions and 46 deletions.
2 changes: 1 addition & 1 deletion .gitignore
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target/
.repo
.uuid
.gitignore/bin/
.gitignore
2 changes: 1 addition & 1 deletion ...path_linker/internal/util/Algorithms.java → ...nker/path_linker/internal/Algorithms.java
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package com.dpgil.pathlinker.path_linker.internal.util;
package com.dpgil.pathlinker.path_linker.internal;

import java.util.Comparator;
import java.util.Collections;
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5 changes: 0 additions & 5 deletions src/main/java/com/dpgil/pathlinker/path_linker/internal/CyActivator.java
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import org.cytoscape.service.util.CyServiceRegistrar;
import org.osgi.framework.BundleContext;

import com.dpgil.pathlinker.path_linker.internal.event.PathLinkerColumnUpdateListener;
import com.dpgil.pathlinker.path_linker.internal.event.PathLinkerNetworkEventListener;
import com.dpgil.pathlinker.path_linker.internal.event.PathLinkerNodeSelectionListener;
import com.dpgil.pathlinker.path_linker.internal.view.PathLinkerControlPanel;

/**
* // -------------------------------------------------------------------------
* /** CyActivator class for the PathLinker Cytoscape Plugin. Runs when
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2 changes: 1 addition & 1 deletion ...nker/internal/util/EdgeWeightSetting.java → ...th_linker/internal/EdgeWeightSetting.java
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package com.dpgil.pathlinker.path_linker.internal.util;
package com.dpgil.pathlinker.path_linker.internal;

/**
* Setting of the edge weight selected by the user
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2 changes: 1 addition & 1 deletion ...ernal/view/PathLinkerAboutMenuDialog.java → ...r/internal/PathLinkerAboutMenuDialog.java
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package com.dpgil.pathlinker.path_linker.internal.view;
package com.dpgil.pathlinker.path_linker.internal;

import java.awt.BorderLayout;
import java.awt.Desktop;
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4 changes: 1 addition & 3 deletions ...event/PathLinkerColumnUpdateListener.java → ...ernal/PathLinkerColumnUpdateListener.java
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package com.dpgil.pathlinker.path_linker.internal.event;
package com.dpgil.pathlinker.path_linker.internal;

import org.cytoscape.model.events.ColumnCreatedEvent;
import org.cytoscape.model.events.ColumnCreatedListener;
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import org.cytoscape.model.events.ColumnNameChangedEvent;
import org.cytoscape.model.events.ColumnNameChangedListener;

import com.dpgil.pathlinker.path_linker.internal.view.PathLinkerControlPanel;

/**
* Listener class for _edgeWeightColumnBox in PathLinkerPanel class
* Updates the _suidToPathIndexMap and _pathIndexToSuidMap
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27 changes: 12 additions & 15 deletions ...internal/view/PathLinkerControlPanel.java → ...nker/internal/PathLinkerControlPanel.java
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package com.dpgil.pathlinker.path_linker.internal.view;
package com.dpgil.pathlinker.path_linker.internal;

import com.dpgil.pathlinker.path_linker.internal.event.PathLinkerNodeSelectionListener;
import com.dpgil.pathlinker.path_linker.internal.model.PathLinkerModel;
import com.dpgil.pathlinker.path_linker.internal.util.EdgeWeightSetting;
import com.dpgil.pathlinker.path_linker.internal.util.Algorithms.Path;
import com.dpgil.pathlinker.path_linker.internal.Algorithms.Path;

import java.awt.BorderLayout;
import java.awt.Color;
Expand Down Expand Up @@ -83,28 +80,28 @@ public class PathLinkerControlPanel extends JPanel implements CytoPanelComponent

private JButton _helpBtn;
private JButton _aboutBtn;
public static JButton _loadNodeToSourceButton;
public static JButton _loadNodeToTargetButton;
protected static JButton _loadNodeToSourceButton;
protected static JButton _loadNodeToTargetButton;
private JButton _clearSourceTargetPanelButton;
private JButton _submitButton;
private JButton _closeButton;

public static JComboBox<String> _networkCmb;
protected static JComboBox<String> _networkCmb;
protected static JComboBox<String> _edgeWeightColumnBox;
private static ButtonGroup _weightedOptionGroup;
private static JRadioButton _unweighted;
private static JRadioButton _weightedAdditive;
private static JRadioButton _weightedProbabilities;

private JCheckBox _allowSourcesTargetsInPathsOption;
public static JCheckBox _targetsSameAsSourcesOption;
protected static JCheckBox _targetsSameAsSourcesOption;
private JCheckBox _includePathScoreTiesOption;

private CyServiceRegistrar _serviceRegistrar;

/** Cytoscape class for network and view management */
private CySwingApplication _cySwingApp;
public static CyApplicationManager _applicationManager;
protected static CyApplicationManager _applicationManager;
private static CyNetworkManager _networkManager;
private CyAppAdapter _adapter;

Expand Down Expand Up @@ -142,11 +139,11 @@ public class PathLinkerControlPanel extends JPanel implements CytoPanelComponent
/** The map stores the index-SUID pair of each network inside the networkCmb */
protected static Map<Integer, Long> _indexToSUIDMap;
/** The map stores the SUID-index pair of each network inside the networkCmb */
public static Map<Long, Integer> _suidToIndexMap;
protected static Map<Long, Integer> _suidToIndexMap;
/** The map stores the SUID to path index column name pair of each network */
public static Map<Long, String> _suidToPathIndexMap;
protected static Map<Long, String> _suidToPathIndexMap;
/** The map stores path index column name to SUID pair of each network */
public static Map<String, Long> _pathIndexToSuidMap;
protected static Map<String, Long> _pathIndexToSuidMap;
/** Global sync index number to sync network, Path Index, and result names upon creation */
protected static int nameIndex;

Expand Down Expand Up @@ -435,7 +432,7 @@ public void actionPerformed(ActionEvent e) {
* construct/update the combo box items for selecting edge weight
* Called by PathLinkerNetworkEventListener and PathLinkerColumnUpdateListener class if event triggered
*/
public static void updateEdgeWeightColumn() {
protected static void updateEdgeWeightColumn() {

_edgeWeightColumnBox.removeAllItems(); //remove all items for update

Expand All @@ -461,7 +458,7 @@ public static void updateEdgeWeightColumn() {
* Use when the PathLinker starts
* when network name is changed
*/
public static void initializeNetworkCmb() {
protected static void initializeNetworkCmb() {

//make sure combo box and related maps is empty when initializing
_networkCmb.removeAllItems();
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4 changes: 1 addition & 3 deletions src/main/java/com/dpgil/pathlinker/path_linker/internal/PathLinkerMenuAction.java
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package com.dpgil.pathlinker.path_linker.internal;

import com.dpgil.pathlinker.path_linker.internal.PathLinkerControlPanel.PanelState;
import java.awt.event.ActionEvent;
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.application.swing.AbstractCyAction;

import com.dpgil.pathlinker.path_linker.internal.view.PathLinkerControlPanel;
import com.dpgil.pathlinker.path_linker.internal.view.PathLinkerControlPanel.PanelState;

/**
* // -------------------------------------------------------------------------
* /** Menu option to open the PathLinker plugin
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6 changes: 2 additions & 4 deletions ...inker/internal/model/PathLinkerModel.java → ...path_linker/internal/PathLinkerModel.java
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package com.dpgil.pathlinker.path_linker.internal.model;
package com.dpgil.pathlinker.path_linker.internal;

import java.util.ArrayList;
import java.util.Arrays;
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import org.cytoscape.model.subnetwork.CyRootNetwork;
import org.cytoscape.model.subnetwork.CySubNetwork;

import com.dpgil.pathlinker.path_linker.internal.util.Algorithms;
import com.dpgil.pathlinker.path_linker.internal.util.EdgeWeightSetting;
import com.dpgil.pathlinker.path_linker.internal.util.Algorithms.Path;
import com.dpgil.pathlinker.path_linker.internal.Algorithms.Path;

/** Back end model for the PathLinker plugin */
public class PathLinkerModel {
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4 changes: 1 addition & 3 deletions ...event/PathLinkerNetworkEventListener.java → ...ernal/PathLinkerNetworkEventListener.java
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package com.dpgil.pathlinker.path_linker.internal.event;
package com.dpgil.pathlinker.path_linker.internal;

import org.cytoscape.application.events.SetCurrentNetworkEvent;
import org.cytoscape.application.events.SetCurrentNetworkListener;
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import org.cytoscape.model.events.NetworkDestroyedEvent;
import org.cytoscape.model.events.NetworkDestroyedListener;

import com.dpgil.pathlinker.path_linker.internal.view.PathLinkerControlPanel;

/**
* Listener class for _edgeWeightColumnBox
* _networkCmb
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4 changes: 1 addition & 3 deletions ...vent/PathLinkerNodeSelectionListener.java → ...rnal/PathLinkerNodeSelectionListener.java
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package com.dpgil.pathlinker.path_linker.internal.event;
package com.dpgil.pathlinker.path_linker.internal;

import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.events.RowSetRecord;
import org.cytoscape.model.events.RowsSetEvent;
import org.cytoscape.model.events.RowsSetListener;

import com.dpgil.pathlinker.path_linker.internal.view.PathLinkerControlPanel;

/** Listener class for _loadNodeToSourceButton and _loadNodeToTargetButton in PathLinkerPanel class */
public class PathLinkerNodeSelectionListener implements RowsSetListener {

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6 changes: 3 additions & 3 deletions .../internal/view/PathLinkerResultPanel.java → ...inker/internal/PathLinkerResultPanel.java
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package com.dpgil.pathlinker.path_linker.internal.view;
package com.dpgil.pathlinker.path_linker.internal;

import com.dpgil.pathlinker.path_linker.internal.Algorithms.Path;

import java.awt.Component;
import java.awt.Container;
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import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyTableUtil;

import com.dpgil.pathlinker.path_linker.internal.util.Algorithms.Path;

/**
* // -------------------------------------------------------------------------
* /** Panel that displays the results for the PathLinker CytoScape plugin
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4 changes: 1 addition & 3 deletions src/test/java/com/dpgil/pathlinker/path_linker/internal/PathLinkerModelTest.java
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import org.junit.Before;
import org.junit.Test;

import com.dpgil.pathlinker.path_linker.internal.model.PathLinkerModel;
import com.dpgil.pathlinker.path_linker.internal.util.EdgeWeightSetting;
import com.dpgil.pathlinker.path_linker.internal.util.Algorithms.Path;
import com.dpgil.pathlinker.path_linker.internal.Algorithms.Path;

/** JUnit Test class for the PathLinker */
public class PathLinkerModelTest {
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