mev-4.0.01/source/org/tigr/microarray/mev/action/ActionManager.java

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2 26 Feb 07 jari 1 /*
2 26 Feb 07 jari 2 Copyright @ 1999-2004, The Institute for Genomic Research (TIGR).
2 26 Feb 07 jari 3 All rights reserved.
2 26 Feb 07 jari 4  */
2 26 Feb 07 jari 5 /*
2 26 Feb 07 jari 6  * $RCSfile: ActionManager.java,v $
2 26 Feb 07 jari 7  * $Revision: 1.17 $
2 26 Feb 07 jari 8  * $Date: 2006/05/15 21:15:33 $
2 26 Feb 07 jari 9  * $Author: eleanorahowe $
2 26 Feb 07 jari 10  * $State: Exp $
2 26 Feb 07 jari 11  */
2 26 Feb 07 jari 12 package org.tigr.microarray.mev.action;
2 26 Feb 07 jari 13
2 26 Feb 07 jari 14 import java.awt.event.ActionEvent;
2 26 Feb 07 jari 15 import java.awt.event.ActionListener;
2 26 Feb 07 jari 16 import java.net.URL;
2 26 Feb 07 jari 17 import java.util.HashMap;
2 26 Feb 07 jari 18
2 26 Feb 07 jari 19 import javax.swing.Action;
2 26 Feb 07 jari 20 import javax.swing.ImageIcon;
2 26 Feb 07 jari 21 import org.tigr.microarray.mev.TMEV;
2 26 Feb 07 jari 22 import org.tigr.microarray.mev.cluster.gui.AnalysisDescription;
2 26 Feb 07 jari 23 import org.tigr.microarray.mev.cluster.gui.IGUIFactory;
2 26 Feb 07 jari 24
2 26 Feb 07 jari 25 public class ActionManager implements java.io.Serializable {
2 26 Feb 07 jari 26     public static final long serialVersionUID = 100010201010001L;
2 26 Feb 07 jari 27     
2 26 Feb 07 jari 28     public static final String PARAMETER = "command-parameter";
2 26 Feb 07 jari 29     public static final String LARGE_ICON = "LargeIcon";
2 26 Feb 07 jari 30     public static final String CATEGORY="category";
2 26 Feb 07 jari 31     private HashMap actions = new HashMap();
2 26 Feb 07 jari 32     private ActionListener listener;
2 26 Feb 07 jari 33     
2 26 Feb 07 jari 34     /**
2 26 Feb 07 jari 35      * Constructs an <code>ActionManager</code> with specified
2 26 Feb 07 jari 36      * action listener, array of labels and gui factory.
2 26 Feb 07 jari 37      */
2 26 Feb 07 jari 38     public ActionManager(ActionListener listener, String[] labels, IGUIFactory factory) {
2 26 Feb 07 jari 39         this.listener = listener;
2 26 Feb 07 jari 40         initActions();
2 26 Feb 07 jari 41         initLabelActions(labels);
2 26 Feb 07 jari 42         initAnalysisActions(factory);
2 26 Feb 07 jari 43     }
2 26 Feb 07 jari 44     
2 26 Feb 07 jari 45     /**
2 26 Feb 07 jari 46      * Returns a wrapped action listaner.
2 26 Feb 07 jari 47      */
2 26 Feb 07 jari 48     public ActionListener getListener() {
2 26 Feb 07 jari 49         return listener;
2 26 Feb 07 jari 50     }
2 26 Feb 07 jari 51     
2 26 Feb 07 jari 52     /**
2 26 Feb 07 jari 53      * Rturns an action by its name.
2 26 Feb 07 jari 54      */
2 26 Feb 07 jari 55     public Action getAction(String name) {
2 26 Feb 07 jari 56         return(Action)actions.get(name);
2 26 Feb 07 jari 57     }
2 26 Feb 07 jari 58     
2 26 Feb 07 jari 59     /**
2 26 Feb 07 jari 60      * Delegates this invokation to a wrapped action listener.
2 26 Feb 07 jari 61      */
2 26 Feb 07 jari 62     public void forwardAction(ActionEvent event) {
2 26 Feb 07 jari 63         listener.actionPerformed(event);
2 26 Feb 07 jari 64     }
2 26 Feb 07 jari 65     
2 26 Feb 07 jari 66     /**
2 26 Feb 07 jari 67      * Initializes main menu and toolbar actions.
2 26 Feb 07 jari 68      */
2 26 Feb 07 jari 69     private void initActions() {
2 26 Feb 07 jari 70       actions.put(NEW_MULTIPLEARRAYVIEWER, new DefaultAction(this, NEW_MAV_NAME, NEW_MAV_COMMAND, getIcon(NEW_MAV_SMALLICON), getIcon(NEW_MAV_LARGEICON)));
2 26 Feb 07 jari 71         actions.put(LOAD_ACTION, new DefaultAction(this, LOAD_NAME, LOAD_COMMAND, getIcon(LOAD_FILE_SMALLICON), getIcon(LOAD_FILE_LARGEICON)));
2 26 Feb 07 jari 72         actions.put(LOAD_ANALYSIS_ACTION, new DefaultAction(this, LOAD_ANALYSIS_NAME, LOAD_ANALYSIS_COMMAND, getIcon(LOAD_ANALYSIS_SMALLICON), getIcon(LOAD_ANALYSIS_LARGEICON)));
2 26 Feb 07 jari 73         actions.put(SAVE_ANALYSIS_ACTION, new DefaultAction(this, SAVE_ANALYSIS_NAME, SAVE_ANALYSIS_COMMAND, getIcon(SAVE_ANALYSIS_SMALLICON), getIcon(SAVE_ANALYSIS_LARGEICON)));
2 26 Feb 07 jari 74         actions.put(SAVE_ANALYSIS_AS_ACTION, new DefaultAction(this, SAVE_ANALYSIS_AS_NAME, SAVE_ANALYSIS_AS_COMMAND, getIcon(SAVE_ANALYSIS_AS_SMALLICON), getIcon(SAVE_ANALYSIS_AS_LARGEICON)));
2 26 Feb 07 jari 75         actions.put(NEW_SCRIPT_ACTION, new DefaultAction(this, NEW_SCRIPT_NAME, NEW_SCRIPT_COMMAND, getIcon(NEW_SCRIPT_SMALLICON), getIcon(NEW_SCRIPT_LARGEICON)));
2 26 Feb 07 jari 76         actions.put(LOAD_SCRIPT_ACTION, new DefaultAction(this, LOAD_SCRIPT_NAME, LOAD_SCRIPT_COMMAND, getIcon(LOAD_SCRIPT_SMALLICON), getIcon(LOAD_SCRIPT_LARGEICON)));
2 26 Feb 07 jari 77         
2 26 Feb 07 jari 78         
2 26 Feb 07 jari 79         actions.put(LOAD_DIRECTORY_ACTION, new DefaultAction(this, LOAD_DIRECTORY_NAME, LOAD_DIRECTORY_COMMAND, getIcon(LOAD_DIRECTORY_SMALLICON), getIcon(LOAD_DIRECTORY_LARGEICON)));
2 26 Feb 07 jari 80         actions.put(LOAD_FILE_ACTION, new DefaultAction(this, LOAD_FILE_NAME, LOAD_FILE_COMMAND, getIcon(LOAD_FILE_SMALLICON), getIcon(LOAD_FILE_LARGEICON)));
2 26 Feb 07 jari 81         actions.put(LOAD_EXPRESSION_ACTION, new DefaultAction(this, LOAD_EXPRESSION_NAME, LOAD_EXPRESSION_COMMAND, getIcon(LOAD_EXPRESSION_SMALLICON), getIcon(LOAD_EXPRESSION_LARGEICON)));
2 26 Feb 07 jari 82         actions.put(LOAD_DB_ACTION, new DefaultAction(this, LOAD_DB_NAME, LOAD_DB_COMMAND, getIcon(LOAD_DB_SMALLICON), getIcon(LOAD_DB_LARGEICON)));
2 26 Feb 07 jari 83         actions.put(LOAD_STANFORD_ACTION, new DefaultAction(this, LOAD_STANFORD_NAME, LOAD_STANFORD_COMMAND, getIcon(LOAD_STANFORD_ICON)));
2 26 Feb 07 jari 84         actions.put(LOAD_CLUSTER_ACTION, new DefaultAction(this, LOAD_CLUSTER_NAME, LOAD_CLUSTER_COMMAND, getIcon(LOAD_CLUSTER_ICON)));
2 26 Feb 07 jari 85         actions.put(SAVE_MATRIX_ACTION, new DefaultAction(this, SAVE_MATRIX_NAME, SAVE_MATRIX_COMMAND, getIcon(SAVE_MATRIX_ICON)));
2 26 Feb 07 jari 86         actions.put(SAVE_IMAGE_ACTION, new DefaultAction(this, SAVE_IMAGE_NAME, SAVE_IMAGE_COMMAND, getIcon(SAVE_IMAGE_SMALLICON), getIcon(SAVE_IMAGE_LARGEICON)));
2 26 Feb 07 jari 87         actions.put(PRINT_IMAGE_ACTION, new DefaultAction(this, PRINT_IMAGE_NAME, PRINT_IMAGE_COMMAND, getIcon(PRINT_IMAGE_SMALLICON), getIcon(PRINT_IMAGE_LARGEICON)));
2 26 Feb 07 jari 88         actions.put(CLOSE_ACTION, new DefaultAction(this, CLOSE_NAME, CLOSE_COMMAND, getIcon(CLOSE_ICON)));
2 26 Feb 07 jari 89         actions.put(DELETE_ALL_ACTION, new DefaultAction(this, DELETE_ALL_NAME, DELETE_ALL_COMMAND, getIcon(DELETE_ALL_ICON)));
2 26 Feb 07 jari 90         actions.put(DELETE_ALL_EXPERIMENT_CLUSTERS_ACTION, new DefaultAction(this, DELETE_ALL_EXPERIMENT_CLUSTERS_NAME, DELETE_ALL_EXPERIMENT_CLUSTERS_COMMAND, getIcon(DELETE_ALL_ICON)));
2 26 Feb 07 jari 91         actions.put(SEARCH_ACTION, new DefaultAction(this, SEARCH_NAME, SEARCH_COMMAND, getIcon(SEARCH_ICON)));
2 26 Feb 07 jari 92         actions.put(IMPORT_GENE_LIST_ACTION, new DefaultAction(this, IMPORT_GENE_LIST_NAME, IMPORT_GENE_LIST_COMMAND, getIcon(IMPORT_GENE_LIST_ICON)));
2 26 Feb 07 jari 93         actions.put(IMPORT_SAMPLE_LIST_ACTION, new DefaultAction(this, IMPORT_SAMPLE_LIST_NAME, IMPORT_SAMPLE_LIST_COMMAND, getIcon(IMPORT_SAMPLE_LIST_ICON)));
2 26 Feb 07 jari 94
2 26 Feb 07 jari 95         actions.put(APPEND_SAMPLE_ANNOTATION_ACTION, new DefaultAction(this, APPEND_SAMPLE_ANNOTATION_NAME, APPEND_SAMPLE_ANNOTATION_COMMAND, getIcon(APPEND_SAMPLE_ANNOTATION_ICON)));            
2 26 Feb 07 jari 96         actions.put(APPEND_GENE_ANNOTATION_ACTION, new DefaultAction(this, APPEND_GENE_ANNOTATION_NAME, APPEND_GENE_ANNOTATION_COMMAND, getIcon(APPEND_GENE_ANNOTATION_ICON)));            
2 26 Feb 07 jari 97         actions.put(CDNA_LOW_INTENSITY_ACTION, new DefaultAction(this, CDNA_LOW_INTENSITY_NAME, CDNA_LOW_INTENSITY_CMD, getIcon(CDNA_LOW_INTENSITY_ICON)));
2 26 Feb 07 jari 98         actions.put(OLIGEN_LOW_INTENSITY_ACTION, new DefaultAction(this, OLIGEN_LOW_INTENSITY_NAME, OLIGEN_LOW_INTENSITY_CMD, getIcon(OLIGEN_LOW_INTENSITY_ICON)));
2 26 Feb 07 jari 99
2 26 Feb 07 jari 100         /*
2 26 Feb 07 jari 101          * Raktim Sept 29, 05
2 26 Feb 07 jari 102          * CGH Actions
2 26 Feb 07 jari 103          */
2 26 Feb 07 jari 104         actions.put(LOAD_SAMPLE_LIST_ACTION, new DefaultAction(this, LOAD_SAMPLE_LIST_NAME, LOAD_SAMPLE_LIST_ACTION, getIcon("TreeInfoLeaf.gif")));
2 26 Feb 07 jari 105         actions.put(LOAD_WSL_ACTION, new DefaultAction(this, LOAD_WSL_NAME, LOAD_WSL_ACTION, getIcon(LOAD_WSL_SMALLICON)));
2 26 Feb 07 jari 106         actions.put(LOAD_CLONE_DISTRIBUTIONS_ACTION, new DefaultAction(this, LOAD_CLONE_DISTRIBUTIONS_NAME, LOAD_CLONE_DISTRIBUTIONS_ACTION, getIcon("p.gif")));
2 26 Feb 07 jari 107         actions.put(LOAD_CLONE_DISTRIBUTIONS_FROM_FILE_ACTION, new DefaultAction(this, LOAD_CLONE_DISTRIBUTIONS_FROM_FILE_NAME, LOAD_CLONE_DISTRIBUTIONS_FROM_FILE_ACTION, getIcon("p.gif")));
2 26 Feb 07 jari 108     }
2 26 Feb 07 jari 109
2 26 Feb 07 jari 110     
2 26 Feb 07 jari 111     /**
2 26 Feb 07 jari 112      * Initializes 'display/label' menu actions.
2 26 Feb 07 jari 113      */
2 26 Feb 07 jari 114     public void initLabelActions(String[] labels) {
2 26 Feb 07 jari 115         DefaultAction action = new DefaultAction(this, "No Label", DISPLAY_LABEL_CMD);
2 26 Feb 07 jari 116         action.putValue(PARAMETER, String.valueOf(-1));
2 26 Feb 07 jari 117         actions.put(DISPLAY_LABEL_ACTION+String.valueOf(-1), action);
2 26 Feb 07 jari 118         
2 26 Feb 07 jari 119         if(labels == null)
2 26 Feb 07 jari 120             return;
2 26 Feb 07 jari 121         
2 26 Feb 07 jari 122         for (int i=0; i<labels.length; i++) {
2 26 Feb 07 jari 123             action = new DefaultAction(this, "Label by "+labels[i], DISPLAY_LABEL_CMD);
2 26 Feb 07 jari 124             action.putValue(PARAMETER, String.valueOf(i));
2 26 Feb 07 jari 125             actions.put(DISPLAY_LABEL_ACTION+String.valueOf(i), action);
2 26 Feb 07 jari 126         }
2 26 Feb 07 jari 127     }
2 26 Feb 07 jari 128     
2 26 Feb 07 jari 129     /**
2 26 Feb 07 jari 130      * Initializes analysis actions, using specified <code>IGUIFactory</code>.
2 26 Feb 07 jari 131      * @see IGUIFactory
2 26 Feb 07 jari 132      */
2 26 Feb 07 jari 133     private void initAnalysisActions(IGUIFactory factory) {
2 26 Feb 07 jari 134         if (factory == null) {
2 26 Feb 07 jari 135             return;
2 26 Feb 07 jari 136         }
2 26 Feb 07 jari 137         AnalysisDescription[] descs = factory.getAnalysisDescriptions();
2 26 Feb 07 jari 138         if (descs == null) {
2 26 Feb 07 jari 139             return;
2 26 Feb 07 jari 140         }
2 26 Feb 07 jari 141         int counter = 0;
2 26 Feb 07 jari 142         for (int i=0; i<descs.length; i++) {
2 26 Feb 07 jari 143             if (isValidDescription(descs[i])) {
2 26 Feb 07 jari 144               actions.put(ANALYSIS_ACTION+String.valueOf(i), new AnalysisAction(this, descs[i]));
2 26 Feb 07 jari 145               counter++;
2 26 Feb 07 jari 146             }
2 26 Feb 07 jari 147         }
2 26 Feb 07 jari 148     }
2 26 Feb 07 jari 149     /**
2 26 Feb 07 jari 150      * Raktim
2 26 Feb 07 jari 151      * Initializes The CGH Copy Number based analysis actions;
2 26 Feb 07 jari 152      * @param factory
2 26 Feb 07 jari 153      */
2 26 Feb 07 jari 154     public void initCghAnalysiActions(IGUIFactory factory){
2 26 Feb 07 jari 155           if (factory == null) {
2 26 Feb 07 jari 156         return;
2 26 Feb 07 jari 157     }
2 26 Feb 07 jari 158     AnalysisDescription[] descs = factory.getAnalysisDescriptions();
2 26 Feb 07 jari 159     if (descs == null) {
2 26 Feb 07 jari 160         return;
2 26 Feb 07 jari 161     }
2 26 Feb 07 jari 162     int counter = 0;
2 26 Feb 07 jari 163     for (int i=0; i<descs.length; i++) {
2 26 Feb 07 jari 164         if (isValidDescription(descs[i])) {
2 26 Feb 07 jari 165       actions.put(CGH_ANALYSIS_ACTION+String.valueOf(i), new AnalysisAction(this, descs[i]));
2 26 Feb 07 jari 166       counter++;
2 26 Feb 07 jari 167         }
2 26 Feb 07 jari 168     }
2 26 Feb 07 jari 169     }
2 26 Feb 07 jari 170     
2 26 Feb 07 jari 171     /**
2 26 Feb 07 jari 172      * Checkes if specified <code>AnalysisDescription</code> is valid.
2 26 Feb 07 jari 173      */
2 26 Feb 07 jari 174     private boolean isValidDescription(AnalysisDescription desc) {
2 26 Feb 07 jari 175         return desc != null && desc.getName() != null && desc.getClassName() != null;
2 26 Feb 07 jari 176     }
2 26 Feb 07 jari 177     
2 26 Feb 07 jari 178
2 26 Feb 07 jari 179     /**
2 26 Feb 07 jari 180      * Creates an image by specified name.
2 26 Feb 07 jari 181      */
2 26 Feb 07 jari 182     private ImageIcon getIcon(String name) {
2 26 Feb 07 jari 183         URL url = getClass().getResource("/org/tigr/images/"+name);
2 26 Feb 07 jari 184         if (url == null)
2 26 Feb 07 jari 185             return null;
2 26 Feb 07 jari 186         return new ImageIcon(url);
2 26 Feb 07 jari 187     }
2 26 Feb 07 jari 188     
2 26 Feb 07 jari 189     // analysis action(s)
2 26 Feb 07 jari 190     public static final String ANALYSIS_ACTION = "analysis-action";
2 26 Feb 07 jari 191     public static final String ANALYSIS_COMMAND = "analysis-command";
2 26 Feb 07 jari 192     
2 26 Feb 07 jari 193     //launch a new customized MAV
2 26 Feb 07 jari 194     public static final String NEW_MULTIPLEARRAYVIEWER  = "new-mav-load";
2 26 Feb 07 jari 195     public static final String  NEW_MAV_COMMAND = "newmav-command-load";
2 26 Feb 07 jari 196     public static final String  NEW_MAV_NAME    = "Customize Toolbar";
2 26 Feb 07 jari 197     private static final String NEW_MAV_SMALLICON = "addmultiple16.gif";
2 26 Feb 07 jari 198     private static final String NEW_MAV_LARGEICON = "addmultiple.gif";
2 26 Feb 07 jari 199     //load data action
2 26 Feb 07 jari 200     public static final String  LOAD_ACTION  = "action-load";
2 26 Feb 07 jari 201     public static final String  LOAD_COMMAND = "command-load";
2 26 Feb 07 jari 202     public static final String  LOAD_NAME    = "Load Data";
2 26 Feb 07 jari 203     private static final String LOAD_SMALLICON = "addmultiple16.gif";
2 26 Feb 07 jari 204     private static final String LOAD_LARGEICON = "addmultiple.gif";
2 26 Feb 07 jari 205     
2 26 Feb 07 jari 206     //load analysis action
2 26 Feb 07 jari 207     public static final String  LOAD_ANALYSIS_ACTION  = "action-load-analysis";
2 26 Feb 07 jari 208     public static final String  LOAD_ANALYSIS_COMMAND = "command-load-analysis";
2 26 Feb 07 jari 209     public static final String  LOAD_ANALYSIS_NAME    = "Open Analysis...";
2 26 Feb 07 jari 210     private static final String LOAD_ANALYSIS_SMALLICON = "addmultiple16.gif";
2 26 Feb 07 jari 211     private static final String LOAD_ANALYSIS_LARGEICON = "addmultiple.gif";
2 26 Feb 07 jari 212     
2 26 Feb 07 jari 213     //save analysis action
2 26 Feb 07 jari 214     public static final String  SAVE_ANALYSIS_ACTION  = "action-save-analysis";
2 26 Feb 07 jari 215     public static final String  SAVE_ANALYSIS_COMMAND = "command-save-analysis";
2 26 Feb 07 jari 216     public static final String  SAVE_ANALYSIS_NAME    = "Save Analysis";
2 26 Feb 07 jari 217     private static final String SAVE_ANALYSIS_SMALLICON = "save16.gif";
2 26 Feb 07 jari 218     private static final String SAVE_ANALYSIS_LARGEICON = "save16.gif";
2 26 Feb 07 jari 219     
2 26 Feb 07 jari 220     //save analysis action
2 26 Feb 07 jari 221     public static final String  SAVE_ANALYSIS_AS_ACTION  = "action-save-analysis-as";
2 26 Feb 07 jari 222     public static final String  SAVE_ANALYSIS_AS_COMMAND = "command-save-analysis-as";
2 26 Feb 07 jari 223     public static final String  SAVE_ANALYSIS_AS_NAME    = "Save Analysis As...";
2 26 Feb 07 jari 224     private static final String SAVE_ANALYSIS_AS_SMALLICON = "save16.gif";
2 26 Feb 07 jari 225     private static final String SAVE_ANALYSIS_AS_LARGEICON = "save16.gif";
2 26 Feb 07 jari 226     
2 26 Feb 07 jari 227     
2 26 Feb 07 jari 228     public static final String  NEW_SCRIPT_ACTION  = "action-new-script";
2 26 Feb 07 jari 229     public static final String  NEW_SCRIPT_COMMAND = "command-new-script";
2 26 Feb 07 jari 230     public static final String  NEW_SCRIPT_NAME    = "New Script";
2 26 Feb 07 jari 231     private static final String NEW_SCRIPT_SMALLICON = "newScript16.gif";
2 26 Feb 07 jari 232     private static final String NEW_SCRIPT_LARGEICON = "newScript16.gif";
2 26 Feb 07 jari 233     
2 26 Feb 07 jari 234     
2 26 Feb 07 jari 235     public static final String  LOAD_SCRIPT_ACTION  = "action-load-script";
2 26 Feb 07 jari 236     public static final String  LOAD_SCRIPT_COMMAND = "command-load-script";
2 26 Feb 07 jari 237     public static final String  LOAD_SCRIPT_NAME    = "Load Script";
2 26 Feb 07 jari 238     private static final String LOAD_SCRIPT_SMALLICON = "loadScript16.gif";
2 26 Feb 07 jari 239     private static final String LOAD_SCRIPT_LARGEICON = "loadScript16.gif";
2 26 Feb 07 jari 240     
2 26 Feb 07 jari 241     
2 26 Feb 07 jari 242     // load directory action
2 26 Feb 07 jari 243     public static final String  LOAD_DIRECTORY_ACTION  = "action-load-directory";
2 26 Feb 07 jari 244     public static final String  LOAD_DIRECTORY_COMMAND = "command-load-directory";
2 26 Feb 07 jari 245     public static final String  LOAD_DIRECTORY_NAME    = "Add Samples from Directory";
2 26 Feb 07 jari 246     private static final String LOAD_DIRECTORY_SMALLICON = "addmultiple16.gif";
2 26 Feb 07 jari 247     private static final String LOAD_DIRECTORY_LARGEICON = "addmultiple.gif";
2 26 Feb 07 jari 248     // load file action
2 26 Feb 07 jari 249     public static final String  LOAD_FILE_ACTION  = "action-load-file";
2 26 Feb 07 jari 250     public static final String  LOAD_FILE_COMMAND = "command-load-file";
2 26 Feb 07 jari 251     public static final String  LOAD_FILE_NAME    = "Add Sample from File";
2 26 Feb 07 jari 252     private static final String LOAD_FILE_SMALLICON    = "addfromfile16.gif";
2 26 Feb 07 jari 253     private static final String LOAD_FILE_LARGEICON    = "addfromfile.gif";
2 26 Feb 07 jari 254     
2 26 Feb 07 jari 255     // pcahan
2 26 Feb 07 jari 256     
2 26 Feb 07 jari 257     // load affy directory action
2 26 Feb 07 jari 258     public static final String  LOAD_AFFY_DIRECTORY_ACTION  = "action-affy-load-directory";
2 26 Feb 07 jari 259     public static final String  LOAD_AFFY_DIRECTORY_COMMAND = "command-affy-load-directory";
2 26 Feb 07 jari 260     public static final String  LOAD_AFFY_DIRECTORY_NAME    = "Add Affymetrix Chips from Directory";
2 26 Feb 07 jari 261     private static final String LOAD_AFFY_DIRECTORY_SMALLICON = "addmultiple16.gif";
2 26 Feb 07 jari 262     private static final String LOAD_AFFY_DIRECTORY_LARGEICON = "addmultiple.gif";
2 26 Feb 07 jari 263     
2 26 Feb 07 jari 264     // load Affy action
2 26 Feb 07 jari 265     public static final String  LOAD_AFFY_ACTION  = "action-load-affy";
2 26 Feb 07 jari 266     public static final String  LOAD_AFFY_COMMAND = "command-load-affy";
2 26 Feb 07 jari 267     public static final String  LOAD_AFFY_NAME    = "Add Sample from Affymetrix datafile";
2 26 Feb 07 jari 268     private static final String LOAD_AFFY_SMALLICON    = "addfromfile16.gif";
2 26 Feb 07 jari 269     private static final String LOAD_AFFY_LARGEICON    = "addfromfile.gif";
2 26 Feb 07 jari 270     
2 26 Feb 07 jari 271     
2 26 Feb 07 jari 272     // load expression action
2 26 Feb 07 jari 273     public static final String  LOAD_EXPRESSION_ACTION  = "action-load-expression";
2 26 Feb 07 jari 274     public static final String  LOAD_EXPRESSION_COMMAND = "command-load-expression";
2 26 Feb 07 jari 275     public static final String  LOAD_EXPRESSION_NAME    = "Add Sample from Expression File";
2 26 Feb 07 jari 276     private static final String LOAD_EXPRESSION_SMALLICON    = "addfromfile16.gif";
2 26 Feb 07 jari 277     private static final String LOAD_EXPRESSION_LARGEICON    = "addfromfile.gif";
2 26 Feb 07 jari 278     // load db action
2 26 Feb 07 jari 279     public static final String  LOAD_DB_ACTION  = "action-load-db";
2 26 Feb 07 jari 280     public static final String  LOAD_DB_COMMAND = "command-load-db";
2 26 Feb 07 jari 281     public static final String  LOAD_DB_NAME    = "Add Samples from DB";
2 26 Feb 07 jari 282     private static final String LOAD_DB_SMALLICON    = "addfromdb16.gif";
2 26 Feb 07 jari 283     private static final String LOAD_DB_LARGEICON    = "addfromdb.gif";
2 26 Feb 07 jari 284     // load stanford action
2 26 Feb 07 jari 285     public static final String  LOAD_STANFORD_ACTION  = "action-load-stanford";
2 26 Feb 07 jari 286     public static final String  LOAD_STANFORD_COMMAND = "command-load-stanford";
2 26 Feb 07 jari 287     private static final String LOAD_STANFORD_NAME    = "Add Samples from Stanford File";
2 26 Feb 07 jari 288     private static final String LOAD_STANFORD_ICON    = "addmultiple16.gif";
2 26 Feb 07 jari 289     // load cluster action
2 26 Feb 07 jari 290     public static final String  LOAD_CLUSTER_ACTION  = "action-load-cluster";
2 26 Feb 07 jari 291     public static final String  LOAD_CLUSTER_COMMAND = "command-load-cluster";
2 26 Feb 07 jari 292     private static final String LOAD_CLUSTER_NAME    = "Load Cluster";
2 26 Feb 07 jari 293     private static final String LOAD_CLUSTER_ICON    = "addfromfile16.gif";
2 26 Feb 07 jari 294     // save matrix action
2 26 Feb 07 jari 295     public static final String  SAVE_MATRIX_ACTION  = "action-save-matrix";
2 26 Feb 07 jari 296     public static final String  SAVE_MATRIX_COMMAND = "command-save-matrix";
2 26 Feb 07 jari 297     private static final String SAVE_MATRIX_NAME    = "Save Matrix";
2 26 Feb 07 jari 298     private static final String SAVE_MATRIX_ICON    = "expression.gif";
2 26 Feb 07 jari 299     // save image action
2 26 Feb 07 jari 300     public static final String  SAVE_IMAGE_ACTION  = "action-save-image";
2 26 Feb 07 jari 301     public static final String  SAVE_IMAGE_COMMAND = "command-save-image";
2 26 Feb 07 jari 302     public static final String  SAVE_IMAGE_NAME    = "Save Image";
2 26 Feb 07 jari 303     private static final String SAVE_IMAGE_SMALLICON    = "saveimage16.gif";
2 26 Feb 07 jari 304     private static final String SAVE_IMAGE_LARGEICON    = "saveimage.gif";
2 26 Feb 07 jari 305     // print image action
2 26 Feb 07 jari 306     public static final String  PRINT_IMAGE_ACTION  = "action-print-image";
2 26 Feb 07 jari 307     public static final String  PRINT_IMAGE_COMMAND = "command-print-image";
2 26 Feb 07 jari 308     private static final String PRINT_IMAGE_NAME    = "Print Image";
2 26 Feb 07 jari 309     private static final String PRINT_IMAGE_SMALLICON = "printimage16.gif";
2 26 Feb 07 jari 310     private static final String PRINT_IMAGE_LARGEICON = "printimage.gif";
2 26 Feb 07 jari 311     // close action
2 26 Feb 07 jari 312     public static final String  CLOSE_ACTION  = "action-close";
2 26 Feb 07 jari 313     public static final String  CLOSE_COMMAND = "command-close";
2 26 Feb 07 jari 314     private static final String CLOSE_NAME    = "Close";
2 26 Feb 07 jari 315     private static final String CLOSE_ICON    = "close16.gif";
2 26 Feb 07 jari 316
2 26 Feb 07 jari 317   // delete all gene clusters action
2 26 Feb 07 jari 318     public static final String  DELETE_ALL_ACTION  = "delete-all-action";
2 26 Feb 07 jari 319     public static final String  DELETE_ALL_COMMAND = "delete-all-cmd";
2 26 Feb 07 jari 320     private static final String DELETE_ALL_NAME    = "Delete All Gene Clusters";
2 26 Feb 07 jari 321     private static final String DELETE_ALL_ICON    = "Delete16.gif";
2 26 Feb 07 jari 322     // delete all experiment clusters action
2 26 Feb 07 jari 323     public static final String  DELETE_ALL_EXPERIMENT_CLUSTERS_ACTION  = "delete-all-experiments-action";
2 26 Feb 07 jari 324     public static final String  DELETE_ALL_EXPERIMENT_CLUSTERS_COMMAND = "delete-all-experiments-cmd";
2 26 Feb 07 jari 325     private static final String DELETE_ALL_EXPERIMENT_CLUSTERS_NAME    = "Delete All Sample Clusters";
2 26 Feb 07 jari 326     // abbr. expt. names toggle
2 26 Feb 07 jari 327     public static final String TOGGLE_ABBR_EXPT_NAMES_ACTION = "toggle-abbr-expt-names-action";
2 26 Feb 07 jari 328     public static final String TOGGLE_ABBR_EXPT_NAMES_CMD = "toggle-abbr-expt-names-cmd";
2 26 Feb 07 jari 329     public static final String TOGGLE_ABBR_EXPT_NAMES_NAME = "Abbr. Sample Names";
2 26 Feb 07 jari 330     // display label actions
2 26 Feb 07 jari 331     public static final String DISPLAY_LABEL_ACTION = "display--label-action";
2 26 Feb 07 jari 332     public static final String DISPLAY_LABEL_CMD    = "display-label-cmd";
2 26 Feb 07 jari 333     // display experiment label actions
2 26 Feb 07 jari 334     public static final String ADD_NEW_EXPERIMENT_LABEL_ACTION = "add-new-experiment-action";
2 26 Feb 07 jari 335     public static final String ADD_NEW_EXPERIMENT_LABEL_CMD = "add-new-experiment-label";
2 26 Feb 07 jari 336     public static final String DISPLAY_EXPERIMENT_LABEL_ACTION = "display-experiment_label-action";
2 26 Feb 07 jari 337     public static final String DISPLAY_EXPERIMENT_LABEL_CMD    = "display-experiment-label-cmd";
2 26 Feb 07 jari 338     // sort label actions
2 26 Feb 07 jari 339     public static final String SORT_LABEL_ACTION = "sort-label-action";
2 26 Feb 07 jari 340     public static final String SORT_LABEL_CMD    = "sort-label-cmd";
2 26 Feb 07 jari 341    
2 26 Feb 07 jari 342     //wwang add for low intensity filter(cdna and oligne)
2 26 Feb 07 jari 343     public static final String CDNA_LOW_INTENSITY_ACTION="cdna-low-intensity-action";
2 26 Feb 07 jari 344     public static final String CDNA_LOW_INTENSITY_NAME = "two color microarray";
2 26 Feb 07 jari 345     public static final String CDNA_LOW_INTENSITY_ICON = "empty16.gif";
2 26 Feb 07 jari 346     public static final String CDNA_LOW_INTENSITY_CMD="cdna-low-intensity-cmd";
2 26 Feb 07 jari 347     
2 26 Feb 07 jari 348     public static final String OLIGEN_LOW_INTENSITY_ACTION="oligen-low-intensity-action";
2 26 Feb 07 jari 349     public static final String OLIGEN_LOW_INTENSITY_NAME = "one color microarray";
2 26 Feb 07 jari 350     public static final String OLIGEN_LOW_INTENSITY_ICON = "empty16.gif";
2 26 Feb 07 jari 351     public static final String OLIGEN_LOW_INTENSITY_CMD="oligen-low-intensity-cmd";
2 26 Feb 07 jari 352     // pcahan
2 26 Feb 07 jari 353     public static final String SET_DETECTION_FILTER_CMD = "set-detection-filter-cmd";
2 26 Feb 07 jari 354     public static final String USE_DETECTION_FILTER_CMD = "use-detection-filter-cmd";
2 26 Feb 07 jari 355     
2 26 Feb 07 jari 356     public static final String SET_FOLD_FILTER_CMD = "set-fold-filter-cmd";
2 26 Feb 07 jari 357     public static final String USE_FOLD_FILTER_CMD = "use-fold-filter-cmd";
2 26 Feb 07 jari 358     
2 26 Feb 07 jari 359     // adjust data commands
2 26 Feb 07 jari 360     public static final String LOG2_TRANSFORM_CMD  = "log2-transform-cmd";
2 26 Feb 07 jari 361     //wwang
2 26 Feb 07 jari 362     public static final String UNLOG2_TRANSFORM_CMD  = "unlog2-transform-cmd";
2 26 Feb 07 jari 363     public static final String NORMALIZE_SPOTS_CMD = "normalize-spots-cmd";
2 26 Feb 07 jari 364     public static final String DIVIDE_SPOTS_RMS_CMD = "divide-spots-rms-cmd";
2 26 Feb 07 jari 365     public static final String DIVIDE_SPOTS_SD_CMD = "divide-spots-sd-cmd";
2 26 Feb 07 jari 366     public static final String MEAN_CENTER_SPOTS_CMD = "mean-center-spots-cmd";
2 26 Feb 07 jari 367     public static final String MEDIAN_CENTER_SPOTS_CMD = "median-center-spots-cmd";
2 26 Feb 07 jari 368     public static final String DIGITAL_SPOTS_CMD = "digital-spots-cmd";
2 26 Feb 07 jari 369     public static final String NORMALIZE_EXPERIMENTS_CMD = "normalize-experiments-cmd";
2 26 Feb 07 jari 370     public static final String DIVIDE_EXPERIMENTS_RMS_CMD = "divide-experiments-rms-cmd";
2 26 Feb 07 jari 371     public static final String DIVIDE_EXPERIMENTS_SD_CMD = "divide-experiments-sd-cmd";
2 26 Feb 07 jari 372     public static final String MEAN_CENTER_EXPERIMENTS_CMD = "mean-center-experiments-cmd";
2 26 Feb 07 jari 373     public static final String MEDIAN_CENTER_EXPERIMENTS_CMD = "median-center-experiments-cmd";
2 26 Feb 07 jari 374     public static final String DIGITAL_EXPERIMENTS_CMD = "digital-experiments-cmd";
2 26 Feb 07 jari 375     public static final String LOG10_TO_LOG2_CMD = "log10-to-log2-cmd";
2 26 Feb 07 jari 376     public static final String LOG2_TO_LOG10_CMD = "log2-to-log10-cmd";
2 26 Feb 07 jari 377     public static final String USE_LOWER_CUTOFFS_CMD = "use-lower-cutoffs-cmd";
2 26 Feb 07 jari 378     //add for mas5
2 26 Feb 07 jari 379     public static final String USE_PRESENT_CALL_CMD = "use-present-call-cmd";
2 26 Feb 07 jari 380     //add for GCOS
2 26 Feb 07 jari 381     public static final String USE_GCOS_PERCENTAGE_CUTOFF_CMD = "use-gcos-percentage-cutoff-cmd";
2 26 Feb 07 jari 382     //add for pvalue filter
2 26 Feb 07 jari 383     public static final String USE_PVALUE_CUTOFF_CMD = "use-pvalue-percentage-cutoff-cmd";
2 26 Feb 07 jari 384     //add for Genepix flags filter
2 26 Feb 07 jari 385     public static final String USE_GENEPIXFLAGS_CMD = "use-genepixflags-cmd";
2 26 Feb 07 jari 386     public static final String USE_PERCENTAGE_CUTOFFS_CMD = "use-percentage-cutoffs-cmd";
2 26 Feb 07 jari 387     public static final String USE_VARIANCE_FILTER_CMD = "use-variance-filter-cmd";
2 26 Feb 07 jari 388     public static final String ADJUST_INTENSITIES_0_CMD = "adjust-intensities-0-cmd";
2 26 Feb 07 jari 389     //vu 7.22.05
2 26 Feb 07 jari 390   public static final String RAMA_CMD = "rama-cmd";
2 26 Feb 07 jari 391   public static final String RAMA_DOC_CMD = "rama-doc-cmd";
2 26 Feb 07 jari 392
2 26 Feb 07 jari 393     // pcahan
2 26 Feb 07 jari 394     public static final String DIVIDE_GENES_MEDIAN_CMD = "divide-genes-median-cmd";
2 26 Feb 07 jari 395     public static final String UNDIVIDE_GENES_MEDIAN_CMD = "undivide-genes-median-cmd";
2 26 Feb 07 jari 396     
2 26 Feb 07 jari 397     public static final String DIVIDE_GENES_MEAN_CMD = "divide-genes-mean-cmd";
2 26 Feb 07 jari 398     public static final String UNDIVIDE_GENES_MEAN_CMD = "undivide-genes-mean-cmd";
2 26 Feb 07 jari 399     
2 26 Feb 07 jari 400     
2 26 Feb 07 jari 401     // normalization commands
2 26 Feb 07 jari 402     public static final String TOTAL_INTENSITY_CMD        = "total-intensity-cmd";
2 26 Feb 07 jari 403     public static final String LINEAR_REGRESSION_CMD      = "linear-regression-cmd";
2 26 Feb 07 jari 404     public static final String RATIO_STATISTICS_CMD       = "ratio-statistics-cmd";
2 26 Feb 07 jari 405     public static final String ITERATIVE_LOG_CMD          = "iterative-log-cmd";
2 26 Feb 07 jari 406     public static final String TOTAL_INTENSITY_LIST_CMD   = "total-intensity-list-cmd";
2 26 Feb 07 jari 407     public static final String LINEAR_REGRESSION_LIST_CMD = "linear-regression-list-cmd";
2 26 Feb 07 jari 408     public static final String RATIO_STATISTICS_LIST_CMD  = "ratio-statistics-list-cmd";
2 26 Feb 07 jari 409     public static final String ITERATIVE_LOG_LIST_CMD     = "iterative-log-list-cmd";
2 26 Feb 07 jari 410     public static final String NO_NORMALIZATION_CMD       = "no-normalization-cmd";
2 26 Feb 07 jari 411     // distance commands
2 26 Feb 07 jari 412     public static final String DEFAULT_DISTANCE_CMD = "default-distance-cmd";
2 26 Feb 07 jari 413     public static final String PEARSON_CORRELATION_CMD = "pearson-correlation-cmd";
2 26 Feb 07 jari 414     public static final String PEARSON_UNCENTERED_CMD = "pearson-uncentered-cmd";
2 26 Feb 07 jari 415     public static final String PEARSON_SQUARED_CMD = "pearson-squared-cmd";
2 26 Feb 07 jari 416     public static final String COSINE_CORRELATION_CMD = "cosine-correlation-cmd";
2 26 Feb 07 jari 417     public static final String COVARIANCE_VALUE_CMD = "covariance-value-cmd";
2 26 Feb 07 jari 418     public static final String EUCLIDEAN_DISTANCE_CMD = "euclidean-distance-cmd";
2 26 Feb 07 jari 419     public static final String AVERAGE_DOT_PRODUCT_CMD = "average-dot-product-cmd";
2 26 Feb 07 jari 420     public static final String MANHATTAN_DISTANCE_CMD = "manhattan-distance-cmd";
2 26 Feb 07 jari 421     public static final String MUTUAL_INFORMATION_CMD = "mutual-information-cmd";
2 26 Feb 07 jari 422     public static final String SPEARMAN_RANK_CORRELATION_CMD = "spearman-rank-correlation-cmd";
2 26 Feb 07 jari 423     public static final String KENDALLS_TAU_CMD = "kendalls-tau-cmd";
2 26 Feb 07 jari 424     public static final String ABSOLUTE_DISTANCE_CMD = "absolute-distance-cmd";
2 26 Feb 07 jari 425     // display commands
2 26 Feb 07 jari 426     public static final String GREEN_RED_COLOR_SCHEME_CMD = "display-green-red-scheme-cmd";
2 26 Feb 07 jari 427     public static final String BLUE_YELLOW_COLOR_SCHEME_CMD = "display-blue-yellow-scheme-cmd";
2 26 Feb 07 jari 428     public static final String RAINBOW_COLOR_SCHEME_CMD = "display-rainbow-scheme-cmd";
2 26 Feb 07 jari 429     public static final String CUSTOM_COLOR_SCHEME_CMD = "display-custom-color-scheme-cmd";
2 26 Feb 07 jari 430     public static final String COLOR_GRADIENT_CMD = "display-color-gradient-cmd";
2 26 Feb 07 jari 431     public static final String DISPLAY_DRAW_BORDERS_CMD = "display-draw-borders-cmd";
2 26 Feb 07 jari 432     public static final String DISPLAY_SET_RATIO_SCALE_CMD = "display-set-ratio-scale-cmd";
2 26 Feb 07 jari 433     public static final String DISPLAY_5X2_CMD = "display-5x2-cmd";
2 26 Feb 07 jari 434     public static final String DISPLAY_10X10_CMD = "display-10x10-cmd";
2 26 Feb 07 jari 435     public static final String DISPLAY_20X5_CMD = "display-20x5-cmd";
2 26 Feb 07 jari 436     public static final String DISPLAY_50X10_CMD = "display-50x10-cmd";
2 26 Feb 07 jari 437     public static final String DISPLAY_OTHER_CMD = "display-other-cmd";
2 26 Feb 07 jari 438     public static final String SYSTEM_INFO_CMD = "system-info-cmd";
2 26 Feb 07 jari 439     public static final String DEFAULT_DISTANCES_CMD = "default-distances-cmd";
2 26 Feb 07 jari 440     // popup commands
2 26 Feb 07 jari 441     public static final String DELETE_NODE_CMD = "delete-node-cmd";
2 26 Feb 07 jari 442
2 26 Feb 07 jari 443     public static final String  SEARCH_ACTION  = "search-action";
2 26 Feb 07 jari 444     public static final String  SEARCH_COMMAND = "search-cmd";
2 26 Feb 07 jari 445     private static final String SEARCH_NAME    = "Search";
2 26 Feb 07 jari 446     private static final String SEARCH_ICON    = "search_16.gif";
2 26 Feb 07 jari 447     
2 26 Feb 07 jari 448     public static final String IMPORT_GENE_LIST_COMMAND = "import-gene-list-command";
2 26 Feb 07 jari 449     public static final String IMPORT_GENE_LIST_ACTION = "import-gene-list-action";
2 26 Feb 07 jari 450     public static final String IMPORT_GENE_LIST_NAME = "Import Gene List";
2 26 Feb 07 jari 451     public static final String IMPORT_GENE_LIST_ICON = "import_list.gif";
2 26 Feb 07 jari 452     
2 26 Feb 07 jari 453     public static final String IMPORT_SAMPLE_LIST_COMMAND = "import-sample-list-command";
2 26 Feb 07 jari 454     public static final String IMPORT_SAMPLE_LIST_ACTION = "import-sample-list-action";
2 26 Feb 07 jari 455     public static final String IMPORT_SAMPLE_LIST_NAME = "Import Sample List";
2 26 Feb 07 jari 456     public static final String IMPORT_SAMPLE_LIST_ICON = "import_list.gif";
2 26 Feb 07 jari 457     
2 26 Feb 07 jari 458     public static final String SET_DATA_SOURCE_COMMAND = "set-data-source-command";
2 26 Feb 07 jari 459     
2 26 Feb 07 jari 460     public static final String APPEND_SAMPLE_ANNOTATION_COMMAND = "append-sample-annotation-command";
2 26 Feb 07 jari 461     public static final String APPEND_SAMPLE_ANNOTATION_ACTION = "append-sample-annotation-action";
2 26 Feb 07 jari 462     public static final String APPEND_SAMPLE_ANNOTATION_NAME = "Append Sample Annotation";
2 26 Feb 07 jari 463     public static final String APPEND_SAMPLE_ANNOTATION_ICON = "append_sample_annotation.gif";    
2 26 Feb 07 jari 464
2 26 Feb 07 jari 465     public static final String APPEND_GENE_ANNOTATION_COMMAND = "append-gene-annotation-command";
2 26 Feb 07 jari 466     public static final String APPEND_GENE_ANNOTATION_ACTION = "append-gene-annotation-action";
2 26 Feb 07 jari 467     public static final String APPEND_GENE_ANNOTATION_NAME = "Append Gene Annotation";
2 26 Feb 07 jari 468     public static final String APPEND_GENE_ANNOTATION_ICON = "append_gene_annotation.gif";
2 26 Feb 07 jari 469     /**
2 26 Feb 07 jari 470      * Raktim Spet 29, 05
2 26 Feb 07 jari 471      * Adding CGH Commands
2 26 Feb 07 jari 472      * CGH display commands
2 26 Feb 07 jari 473      */
2 26 Feb 07 jari 474     public static final String SHOW_FLANKING_REGIONS = "show-flanking-regions";
2 26 Feb 07 jari 475     // popup commands
2 26 Feb 07 jari 476     //public static final String DELETE_NODE_CMD = "delete-node-cmd";
2 26 Feb 07 jari 477     public static final String RENAME_NODE_CMD = "rename-node-cmd";
2 26 Feb 07 jari 478     // help commands
2 26 Feb 07 jari 479     public static final String SHOW_SUPPORTTREE_LEGEND_COMMAND = "show-supporttree-legend-command";
2 26 Feb 07 jari 480     public static final String CGH_ELEMENT_LENGTH_5  = "cgh-element-length-5";
2 26 Feb 07 jari 481     public static final String CGH_ELEMENT_LENGTH_10  = "cgh-element-length-10";
2 26 Feb 07 jari 482     public static final String CGH_ELEMENT_LENGTH_20 = "cgh-element-length-20";
2 26 Feb 07 jari 483     public static final String CGH_ELEMENT_LENGTH_50  = "cgh-element-length-50";
2 26 Feb 07 jari 484     public static final String CGH_ELEMENT_LENGTH_100  = "cgh-element-length-100";
2 26 Feb 07 jari 485     public static final String CGH_ELEMENT_LENGTH_OTHER  = "cgh-element-length-other";
2 26 Feb 07 jari 486     public static final String CGH_ELEMENT_LENGTH_FIT = "cgh-element-length-fit";
2 26 Feb 07 jari 487     public static final String CGH_ELEMENT_WIDTH_5  = "cgh-element-width-5";
2 26 Feb 07 jari 488     public static final String CGH_ELEMENT_WIDTH_10  = "cgh-element-width-10";
2 26 Feb 07 jari 489     public static final String CGH_ELEMENT_WIDTH_20 = "cgh-element-width-20";
2 26 Feb 07 jari 490     public static final String CGH_ELEMENT_WIDTH_50  = "cgh-element-width-50";
2 26 Feb 07 jari 491     public static final String CGH_ELEMENT_WIDTH_100  = "cgh-element-width-100";
2 26 Feb 07 jari 492     public static final String CGH_ELEMENT_WIDTH_OTHER  = "cgh-element-width-other";
2 26 Feb 07 jari 493     public static final String CGH_ELEMENT_WIDTH_FIT = "cgh-element-width-fit";
2 26 Feb 07 jari 494     public static final String CGH_DISPLAY_TYPE_COMBINED = "cgh-display-type-combined";
2 26 Feb 07 jari 495     public static final String CGH_DISPLAY_TYPE_SEPARATED = "cgh-display-type-separated";
2 26 Feb 07 jari 496     public static final String CGH_DISPLAY_ORDER = "cgh-display-order";
2 26 Feb 07 jari 497     public static final String CGH_DELETE_SAMPLE = "cgh-delete-sample";
2 26 Feb 07 jari 498     public static final String CGH_DISPLAY_LABEL_WSL_ID = "cgh-display-label-wsl-id";
2 26 Feb 07 jari 499     public static final String CGH_DISPLAY_LABEL_ALIAS = "cgh-display-label-alias";
2 26 Feb 07 jari 500     public static final String CGH_DISPLAY_LABEL_ID1 = "cgh-display-label-id1";
2 26 Feb 07 jari 501     public static final String DELETED_BACS = "deleted-bacs";
2 26 Feb 07 jari 502     public static final String LOAD_SAMPLE_LIST_ACTION = "action-load-sample-list";
2 26 Feb 07 jari 503     public static final String LOAD_SAMPLE_LIST_NAME = "Load From Sample List";
2 26 Feb 07 jari 504     public static final String LOAD_WSL_ACTION = "action-load-wsl";
2 26 Feb 07 jari 505     public static final String LOAD_WSL_NAME = "Add Experiment from WSL";
2 26 Feb 07 jari 506     private static final String LOAD_WSL_SMALLICON    = "addfromdb16.gif";
2 26 Feb 07 jari 507     public static final String LOAD_CLONE_DISTRIBUTIONS_ACTION = "load-clone-distributions";
2 26 Feb 07 jari 508     public static final String LOAD_CLONE_DISTRIBUTIONS_NAME = "Load Clone Distributions";
2 26 Feb 07 jari 509     public static final String LOAD_CLONE_DISTRIBUTIONS_FROM_FILE_ACTION = "load-clone-distributions-from-file";
2 26 Feb 07 jari 510     public static final String LOAD_CLONE_DISTRIBUTIONS_FROM_FILE_NAME = "Load Clone Distributions From File";
2 26 Feb 07 jari 511     public static final String CGH_SET_THRESHOLDS = "cgh-set-thresholds";
2 26 Feb 07 jari 512     public static final String CGH_SET_MMSDs = "cgh-set-mmsds";
2 26 Feb 07 jari 513     public static final String CGH_COPY_NUMBER_BY_MMSDs = "cgh-copy-number-by-mmsds";
2 26 Feb 07 jari 514     public static final String CGH_COPY_NUMBER_BY_THRESHOLDS = "cgh-copy-number-by-thresholds";
2 26 Feb 07 jari 515     public static final String CGH_CLEAR_ANNOTATIONS = "cgh-clear-annotations";
2 26 Feb 07 jari 516     public static final String CGH_ANALYSIS_ACTION = "cgh-analysis-action";
2 26 Feb 07 jari 517     public static final String CGH_ANALYSIS_COMMAND = "cgh-analysis-command";
2 26 Feb 07 jari 518     public static final String CIRCLE_VIEWER_BACKGROUND = "circle-viewer-background";
2 26 Feb 07 jari 519     public static final String CLONE_VALUE_DISCRETE_DETERMINATION = "clone-ratio-discrete-determination";
2 26 Feb 07 jari 520     public static final String CLONE_VALUE_LOG_AVERAGE_INVERTED = "clone-ratio-log-invert-average";
2 26 Feb 07 jari 521     public static final String CLONE_VALUE_LOG_CLONE_DISTRIBUTION = "clone-ratio-log-clone-distribution";
2 26 Feb 07 jari 522     public static final String CLONE_VALUE_THRESHOLD_OR_CLONE_DISTRIBUTION = "clone-value-threshold-or-clone-distribution";
2 26 Feb 07 jari 523     public static final String SHOW_HEADER = "show-header";
2 26 Feb 07 jari 524     public static final String CLONE_P_THRESH = "clone-p-thresh";
2 26 Feb 07 jari 525     public static final String FLANKING_REGIONS_BY_THRESHOLD = "flanking-regions-by-threshold";
2 26 Feb 07 jari 526     public static final String FLANKING_REGIONS_BY_LOG_CLONE_DISTRIBUTION = "flanking-regions-by-log-clone-distribution";
2 26 Feb 07 jari 527     public static final String FLANKING_REGIONS_BY_THRESHOLD_OR_CLONE_DISTRIBUTION = "flanking-regions-by-threshold-or-clone-distribution";
2 26 Feb 07 jari 528     public static final String FIND_GENE = "find-gene";
2 26 Feb 07 jari 529     public static final String COMPARE_EXPERIMENTS = "compare-experiments";
2 26 Feb 07 jari 530     /* End CGH Commands */
2 26 Feb 07 jari 531     
2 26 Feb 07 jari 532 }

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