http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigUtils.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigUtils.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigUtils.java index 2bc7d71..8b93922 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigUtils.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigUtils.java @@ -1,36 +1,3 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: QueryConfigUtils.java,v $ - * Revision $Revision: 1.3 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/12/13 11:38:57 $ - * by $Author: davidwithers $ - * Created on 30-Mar-2006 - *****************************************************************/ package org.biomart.martservice.config; import java.awt.Component; @@ -59,14 +26,14 @@ import org.ensembl.mart.lib.config.Option; /** * Utility class for configuration objects. - * + * * @author David Withers */ public abstract class QueryConfigUtils { public static final String LINE_END = System.getProperty("line.separator"); private static int DISPLAY_WIDTH = 35; - + public static String splitSentence(String sentence) { return splitSentence(sentence, DISPLAY_WIDTH); } @@ -97,7 +64,7 @@ public abstract class QueryConfigUtils { /** * Returns name truncated to DISPLAY_WIDTH. - * + * * @param name * @return */ @@ -111,17 +78,17 @@ public abstract class QueryConfigUtils { public static List<String> getOutputFormats(AttributePage attributePage) { List<String> outputFormats = new ArrayList<String>(); - + String[] formats = attributePage.getOutFormats().split(","); for (int i = 0; i < formats.length; i++) { outputFormats.add(formats[i]); } return outputFormats; } - + /** * Returns true if filterDescription has no options. - * + * * @param filterDescription * @return true if filterDescription has no options */ @@ -132,7 +99,7 @@ public abstract class QueryConfigUtils { /** * Returns true if filterDescription has options and at least one option * also has options. - * + * * @param filterDescription * @return true if filterDescription has options and at least one option * also has options @@ -150,7 +117,7 @@ public abstract class QueryConfigUtils { /** * Returns true if filterDescription has options and the first option has a * type equal to "boolean". - * + * * @param filterDescription * @return true if filterDescription has options and the first option has a * type equal to "boolean" @@ -168,7 +135,7 @@ public abstract class QueryConfigUtils { /** * Returns true if filterDescription has options and the first option has a * value equal to null. - * + * * @param filterDescription * @return true if filterDescription has options and the first option has a * value equal to null @@ -249,7 +216,7 @@ public abstract class QueryConfigUtils { /** * Returns the dataset referenced by a configuration object or null if the * configuration object does not reference a dataset. - * + * * @param martService * the MartService to fetch the referenced dataset from * @param referencedFromDataset @@ -286,7 +253,7 @@ public abstract class QueryConfigUtils { /** * Returns the filter description referenced by the filter description. - * + * * @param martService * the MartService to fetch the referenced filter description * from @@ -322,7 +289,7 @@ public abstract class QueryConfigUtils { /** * Returns the filter description referenced by the attribute description. - * + * * @param martService * the MartService to fetch the referenced filter description * from @@ -422,7 +389,7 @@ public abstract class QueryConfigUtils { /** * Returns true if the internal name of the configuration object contains a * '.' character. - * + * * @param bnco * the configuration object * @return true if the internal name of the configuration object contains a @@ -431,7 +398,7 @@ public abstract class QueryConfigUtils { public static boolean isReference(BaseNamedConfigurationObject bnco, String softwareVersion) { if ("0.5".equals(softwareVersion)) { - return bnco.getAttribute("pointerDataset") != null + return bnco.getAttribute("pointerDataset") != null && (bnco.getAttribute("pointerAttribute") != null || bnco.getAttribute("pointerFilter") != null); } else { return bnco.getInternalName().indexOf(".") != -1; @@ -441,7 +408,7 @@ public abstract class QueryConfigUtils { /** * Returns true if the internal name of the AttributeDescription has the * format "[datasetName].[attributeName]". - * + * * @param attributeDescription * @return true if the internal name of the AttributeDescription has the * format "[datasetName].[attributeName]" @@ -458,7 +425,7 @@ public abstract class QueryConfigUtils { /** * Returns true if the internal name of the AttributeDescription has the * format "[datasetName].filter.[filterName]". - * + * * @param attributeDescription * @return true if the internal name of the AttributeDescription has the * format "[datasetName].filter.[filterName]" @@ -475,7 +442,7 @@ public abstract class QueryConfigUtils { // /** // * Returns the qualified name of the AttributeDescription in the format // * "[datasetName].[attributeName]". -// * +// * // * @param dataset // * @param attributeDescription // * @return true if the qualified name of the AttributeDescription in the @@ -543,16 +510,16 @@ public abstract class QueryConfigUtils { * Converts a List of objects to a comma separated string of the objects' * string representations in the order given by the List's iterator. For * example: - * + * * <blockquote> - * + * * <pre> * List list = Arrays.toList(new String[] {"one", "two", "three"}; * System.out.println(listToCsv(list)); * </pre> - * + * * </blockquote> would return the string "one,two,three". - * + * * @param list * @return a List of objects to a comma separated string of the object's * string representations @@ -571,7 +538,7 @@ public abstract class QueryConfigUtils { /** * Returns true iff the 'display' or 'hidden' value of the configuration * object is not "true". - * + * * @param bnco * the configuration object * @return true iff the 'display' or 'hidden' value of configuration object
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentAdapter.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentAdapter.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentAdapter.java index 201cc1d..c22d3ff 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentAdapter.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentAdapter.java @@ -1,50 +1,17 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: QueryComponentAdapter.java,v $ - * Revision $Revision: 1.1 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/01/31 14:12:06 $ - * by $Author: davidwithers $ - * Created on 04-Apr-2006 - *****************************************************************/ package org.biomart.martservice.config.event; /** * An abstract adapter class for receiving <code>QueryComponent</code> events. * The methods in this class are empty. This class exists as convenience for * creating listener objects. - * + * * @author David Withers */ public class QueryComponentAdapter implements QueryComponentListener { /* * (non-Javadoc) - * + * * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#attributeAdded(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent) */ public void attributeAdded(QueryComponentEvent event) { @@ -52,7 +19,7 @@ public class QueryComponentAdapter implements QueryComponentListener { /* * (non-Javadoc) - * + * * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#attributeRemoved(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent) */ public void attributeRemoved(QueryComponentEvent event) { @@ -60,7 +27,7 @@ public class QueryComponentAdapter implements QueryComponentListener { /* * (non-Javadoc) - * + * * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#filterAdded(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent) */ public void filterAdded(QueryComponentEvent event) { @@ -68,7 +35,7 @@ public class QueryComponentAdapter implements QueryComponentListener { /* * (non-Javadoc) - * + * * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#filterRemoved(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent) */ public void filterRemoved(QueryComponentEvent event) { @@ -76,7 +43,7 @@ public class QueryComponentAdapter implements QueryComponentListener { /* * (non-Javadoc) - * + * * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#filterChanged(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent) */ public void filterChanged(QueryComponentEvent event) { @@ -84,7 +51,7 @@ public class QueryComponentAdapter implements QueryComponentListener { /* * (non-Javadoc) - * + * * @see org.biomart.martservice.config.event.QueryComponentListener#linkAdded(org.biomart.martservice.config.event.QueryComponentEvent) */ public void linkAdded(QueryComponentEvent event) { @@ -92,7 +59,7 @@ public class QueryComponentAdapter implements QueryComponentListener { /* * (non-Javadoc) - * + * * @see org.biomart.martservice.config.event.QueryComponentListener#linkRemoved(org.biomart.martservice.config.event.QueryComponentEvent) */ public void linkRemoved(QueryComponentEvent event) { @@ -100,7 +67,7 @@ public class QueryComponentAdapter implements QueryComponentListener { /* * (non-Javadoc) - * + * * @see org.biomart.martservice.config.QueryComponentListener#linkChanged(org.biomart.martservice.config.QueryComponentEvent) */ public void linkChanged(QueryComponentEvent event) { http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentEvent.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentEvent.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentEvent.java index 6fc5d18..8364233 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentEvent.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentEvent.java @@ -1,36 +1,3 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: QueryComponentEvent.java,v $ - * Revision $Revision: 1.1 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/01/31 14:12:06 $ - * by $Author: davidwithers $ - * Created on 03-Apr-2006 - *****************************************************************/ package org.biomart.martservice.config.event; import java.util.EventObject; @@ -40,7 +7,7 @@ import org.biomart.martservice.MartDataset; /** * An event which indicates that a <code>QueryComponent</code> has been * selected, deselected or its value has been modified. - * + * * @author David Withers */ public class QueryComponentEvent extends EventObject { @@ -54,7 +21,7 @@ public class QueryComponentEvent extends EventObject { /** * Constructs a new <code>QueryComponentEvent</code> instance. - * + * * @param source * the source of the event * @param name @@ -69,7 +36,7 @@ public class QueryComponentEvent extends EventObject { /** * Constructs a new <code>QueryComponentEvent</code> instance. - * + * * @param source * the source of the event * @param name @@ -90,7 +57,7 @@ public class QueryComponentEvent extends EventObject { /** * Returns the name of the attribute or filter affected by this event. - * + * * @return the name of the attribute or filter affected by this event. */ public String getName() { @@ -100,7 +67,7 @@ public class QueryComponentEvent extends EventObject { /** * Returns the dataset containing the attribute or filter affected by this * event. - * + * * @return the dataset containing the attribute or filter affected by this * event. */ @@ -110,7 +77,7 @@ public class QueryComponentEvent extends EventObject { /** * Returns the value of the filter affected by this event. - * + * * @return the value of the filter affected by this event. */ public String getValue() { http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentListener.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentListener.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentListener.java index af63326..6542da8 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentListener.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentListener.java @@ -1,43 +1,10 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: QueryComponentListener.java,v $ - * Revision $Revision: 1.1 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/01/31 14:12:06 $ - * by $Author: davidwithers $ - * Created on 03-Apr-2006 - *****************************************************************/ package org.biomart.martservice.config.event; import java.util.EventListener; /** * The listener interface for receiving QueryComponent events. - * + * * @author David Withers */ public interface QueryComponentListener extends EventListener { @@ -45,7 +12,7 @@ public interface QueryComponentListener extends EventListener { /** * Invoked when a <code>QueryComponent</code> for an attribute is * selected. - * + * * @param event the query component event */ public void attributeAdded(QueryComponentEvent event); @@ -53,42 +20,42 @@ public interface QueryComponentListener extends EventListener { /** * Invoked when a <code>QueryComponent</code> for an attribute is * deselected. - * + * * @param event the query component event */ public void attributeRemoved(QueryComponentEvent event); /** * Invoked when a <code>QueryComponent</code> for a filter is selected. - * + * * @param event the query component event */ public void filterAdded(QueryComponentEvent event); /** * Invoked when a <code>QueryComponent</code> for a filter is deselected. - * + * * @param event the query component event */ public void filterRemoved(QueryComponentEvent event); /** * Invoked when a <code>QueryComponent</code> for a filter is changed. - * + * * @param event the query component event */ public void filterChanged(QueryComponentEvent event); /** * Invoked when a <code>QueryComponent</code> for a link is selected. - * + * * @param event the query component event */ public void linkAdded(QueryComponentEvent event); /** * Invoked when a <code>QueryComponent</code> for a link is deselected. - * + * * @param event the query component event */ public void linkRemoved(QueryComponentEvent event); @@ -96,7 +63,7 @@ public interface QueryComponentListener extends EventListener { /** * Invoked when a <code>QueryComponent</code> for a dataset link id is * changed. - * + * * @param event the query component event */ public void linkChanged(QueryComponentEvent event); http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ConfigDisplayObject.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ConfigDisplayObject.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ConfigDisplayObject.java index 89820d3..0e5b1e1 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ConfigDisplayObject.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ConfigDisplayObject.java @@ -1,36 +1,3 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: ConfigDisplayObject.java,v $ - * Revision $Revision: 1.1 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/01/31 14:12:09 $ - * by $Author: davidwithers $ - * Created on 17-Mar-2006 - *****************************************************************/ package org.biomart.martservice.config.ui; import java.awt.Component; @@ -39,7 +6,7 @@ import org.ensembl.mart.lib.config.BaseNamedConfigurationObject; /** * An object containing a configuration object and it's graphical component. - * + * * @author David Withers */ public class ConfigDisplayObject { @@ -50,7 +17,7 @@ public class ConfigDisplayObject { /** * Constructs an instance of a <code>ConfigDisplayObject</code> with the * specified configuration object and a <code>null</code> component. - * + * * @param configObject * the configuration object; must not be <code>null</code> */ @@ -61,7 +28,7 @@ public class ConfigDisplayObject { /** * Constructs an instance of a <code>ConfigDisplayObject</code> with the * specified configuration object and component. - * + * * @param configObject * the configuration object; must not be <code>null</code> * @param component @@ -79,7 +46,7 @@ public class ConfigDisplayObject { /** * Returns the display name. - * + * * @return the display name */ public String getDisplayName() { @@ -88,7 +55,7 @@ public class ConfigDisplayObject { /** * Returns the internal name. - * + * * @return the internal name */ public String getInternalName() { @@ -97,7 +64,7 @@ public class ConfigDisplayObject { /** * Returns the display name. - * + * * @return the display name */ public String toString() { @@ -106,7 +73,7 @@ public class ConfigDisplayObject { /** * Returns the configuration object. - * + * * @return the configuration object */ public BaseNamedConfigurationObject getConfigObject() { @@ -115,7 +82,7 @@ public class ConfigDisplayObject { /** * Returns the component. - * + * * @return the component. */ public Component getComponent() { http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ExpandableBox.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ExpandableBox.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ExpandableBox.java index d5ff0dd..932ea9d 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ExpandableBox.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ExpandableBox.java @@ -1,36 +1,3 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: ExpandableBox.java,v $ - * Revision $Revision: 1.2 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/12/13 11:38:56 $ - * by $Author: davidwithers $ - * Created on Jun 22, 2007 - *****************************************************************/ package org.biomart.martservice.config.ui; import java.awt.Color; @@ -52,9 +19,9 @@ import javax.swing.border.LineBorder; /** * A component that when collapsed only shows a title and when expanded shows * the title and contained components. - * + * * @author David Withers - * + * */ public class ExpandableBox extends JPanel { private static final long serialVersionUID = -5678399632577606442L; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MartServiceIcons.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MartServiceIcons.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MartServiceIcons.java index 15f294a..33471fa 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MartServiceIcons.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MartServiceIcons.java @@ -1,36 +1,3 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: MartServiceIcons.java,v $ - * Revision $Revision: 1.2 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/12/13 11:38:56 $ - * by $Author: davidwithers $ - * Created on 24-Aug-2006 - *****************************************************************/ package org.biomart.martservice.config.ui; import java.util.HashMap; @@ -40,7 +7,7 @@ import javax.swing.Icon; import javax.swing.ImageIcon; /** - * + * * @author witherd5 */ public class MartServiceIcons { http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MartServiceQueryConfigUIFactory.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MartServiceQueryConfigUIFactory.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MartServiceQueryConfigUIFactory.java index 3531539..2655d7b 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MartServiceQueryConfigUIFactory.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MartServiceQueryConfigUIFactory.java @@ -1,36 +1,3 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: MartServiceQueryConfigUIFactory.java,v $ - * Revision $Revision: 1.6 $ - * Release status $State: Exp $ - * Last modified on $Date: 2008/03/04 16:46:53 $ - * by $Author: davidwithers $ - * Created on 21-Jun-2007 - *****************************************************************/ package org.biomart.martservice.config.ui; import java.awt.BorderLayout; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MinimalLayout.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MinimalLayout.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MinimalLayout.java index 153b982..bf67bdb 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MinimalLayout.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MinimalLayout.java @@ -1,36 +1,3 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: MinimalLayout.java,v $ - * Revision $Revision: 1.1 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/06/27 12:49:48 $ - * by $Author: davidwithers $ - * Created on 26 Jun 2007 - *****************************************************************/ package org.biomart.martservice.config.ui; import java.awt.Component; @@ -42,7 +9,7 @@ import java.awt.LayoutManager; /** * A layout manager that lays out components, either horizontally or vertically, * according to their minimum size. - * + * * @author David Withers */ class MinimalLayout implements LayoutManager { @@ -64,7 +31,7 @@ class MinimalLayout implements LayoutManager { /* * (non-Javadoc) - * + * * @see java.awt.LayoutManager#removeLayoutComponent(java.awt.Component) */ public void removeLayoutComponent(Component comp) { @@ -72,7 +39,7 @@ class MinimalLayout implements LayoutManager { /* * (non-Javadoc) - * + * * @see java.awt.LayoutManager#layoutContainer(java.awt.Container) */ public void layoutContainer(Container parent) { @@ -98,7 +65,7 @@ class MinimalLayout implements LayoutManager { /* * (non-Javadoc) - * + * * @see java.awt.LayoutManager#addLayoutComponent(java.lang.String, * java.awt.Component) */ @@ -107,7 +74,7 @@ class MinimalLayout implements LayoutManager { /* * (non-Javadoc) - * + * * @see java.awt.LayoutManager#minimumLayoutSize(java.awt.Container) */ public Dimension minimumLayoutSize(Container parent) { @@ -144,7 +111,7 @@ class MinimalLayout implements LayoutManager { /* * (non-Javadoc) - * + * * @see java.awt.LayoutManager#preferredLayoutSize(java.awt.Container) */ public Dimension preferredLayoutSize(Container parent) { http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryComponent.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryComponent.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryComponent.java index b976684..fdc92c7 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryComponent.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryComponent.java @@ -1,36 +1,3 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: QueryComponent.java,v $ - * Revision $Revision: 1.2 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/12/13 11:38:56 $ - * by $Author: davidwithers $ - * Created on 03-Apr-2006 - *****************************************************************/ package org.biomart.martservice.config.ui; import java.awt.event.ItemEvent; @@ -47,7 +14,7 @@ import org.ensembl.mart.lib.config.BaseNamedConfigurationObject; /** * Abstract class for creating query configuration UI components. - * + * * @author David Withers */ public abstract class QueryComponent extends JPanel { @@ -75,7 +42,7 @@ public abstract class QueryComponent extends JPanel { /** * Returns the dataset. - * + * * @return the dataset. */ public MartDataset getDataset() { @@ -84,7 +51,7 @@ public abstract class QueryComponent extends JPanel { /** * Sets the dataset. - * + * * @param dataset * the dataset to set. */ @@ -112,7 +79,7 @@ public abstract class QueryComponent extends JPanel { /** * Returns the name. - * + * * @return the name. */ public String getName() { @@ -141,7 +108,7 @@ public abstract class QueryComponent extends JPanel { /** * Returns the value. - * + * * @return the value. */ public String getValue() { @@ -150,7 +117,7 @@ public abstract class QueryComponent extends JPanel { /** * Sets the value. - * + * * @param value * the value to set. */ @@ -160,7 +127,7 @@ public abstract class QueryComponent extends JPanel { /** * Returns the configObject. - * + * * @return the configObject */ public BaseNamedConfigurationObject getConfigObject() { @@ -169,7 +136,7 @@ public abstract class QueryComponent extends JPanel { /** * Sets the configObject. - * + * * @param configObject * the configObject to set. */ @@ -179,7 +146,7 @@ public abstract class QueryComponent extends JPanel { /** * Sets the selected state of this component. - * + * * @param selected * <code>true</code> if this component is selected, * <code>false</code> otherwise @@ -192,11 +159,11 @@ public abstract class QueryComponent extends JPanel { /** * Sets the button used to select/deselect this QueryComponent. - * + * * This function adds an ItemListener to the button and fires the * appropriate QueryComponentEvent when the button is selected or * deselected. - * + * * @param button * the button used to select/deselect this QueryComponent. */ @@ -229,7 +196,7 @@ public abstract class QueryComponent extends JPanel { * Adds the specified query component listener to receive query component * events. If <code>listener</code> is null, no exception is thrown and no * action is performed. - * + * * @param listener * the query component listener */ @@ -243,7 +210,7 @@ public abstract class QueryComponent extends JPanel { * does it throw an exception, if <code>listener</code> was not previously * added to this component. If <code>listener</code> is null, no exception * is thrown and no action is performed. - * + * * @param listener * the query component listener */ @@ -253,7 +220,7 @@ public abstract class QueryComponent extends JPanel { /** * Fires an attribute added event. - * + * * @param event the event to be fired */ protected void fireAttributeAdded(QueryComponentEvent event) { @@ -264,7 +231,7 @@ public abstract class QueryComponent extends JPanel { /** * Fires an attribute removed event. - * + * * @param event the event to be fired */ protected void fireAttributeRemoved(QueryComponentEvent event) { @@ -275,7 +242,7 @@ public abstract class QueryComponent extends JPanel { /** * Fires an filter added event. - * + * * @param event the event to be fired */ protected void fireFilterAdded(QueryComponentEvent event) { @@ -286,7 +253,7 @@ public abstract class QueryComponent extends JPanel { /** * Fires an filter removed event. - * + * * @param event the event to be fired */ protected void fireFilterRemoved(QueryComponentEvent event) { @@ -297,7 +264,7 @@ public abstract class QueryComponent extends JPanel { /** * Fires an filter changed event. - * + * * @param event the event to be fired */ protected void fireFilterChanged(QueryComponentEvent event) { @@ -308,7 +275,7 @@ public abstract class QueryComponent extends JPanel { /** * Fires an link added event. - * + * * @param event the event to be fired */ protected void fireLinkAdded(QueryComponentEvent event) { @@ -319,7 +286,7 @@ public abstract class QueryComponent extends JPanel { /** * Fires an link removed event. - * + * * @param event the event to be fired */ protected void fireLinkRemoved(QueryComponentEvent event) { @@ -330,7 +297,7 @@ public abstract class QueryComponent extends JPanel { /** * Fires an link changed event. - * + * * @param event the event to be fired */ protected void fireLinkChanged(QueryComponentEvent event) { http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryConfigUIFactory.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryConfigUIFactory.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryConfigUIFactory.java index d0a740a..20ca314 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryConfigUIFactory.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryConfigUIFactory.java @@ -1,36 +1,3 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: QueryConfigUIFactory.java,v $ - * Revision $Revision: 1.1 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/01/31 14:12:08 $ - * by $Author: davidwithers $ - * Created on 04-Apr-2006 - *****************************************************************/ package org.biomart.martservice.config.ui; import java.awt.Component; @@ -49,7 +16,7 @@ import org.ensembl.mart.lib.config.FilterPage; /** * Interface for generating graphical components from <code>DatasetConfig</code> * objects. - * + * * @author David Withers */ public interface QueryConfigUIFactory { @@ -62,7 +29,7 @@ public interface QueryConfigUIFactory { /** * Generates a <code>Component</code> for a <code>DatasetConfig</code>. - * + * * @return the generated <code>Component</code> * @throws MartServiceException * if the MartService returns an error or is unavailable @@ -72,7 +39,7 @@ public interface QueryConfigUIFactory { /** * Generates a <code>Component</code> for an array of * <code>AttributePage</code>. - * + * * @param attributePages * an array of <code>AttributePage</code> * @param data @@ -86,7 +53,7 @@ public interface QueryConfigUIFactory { /** * Generates a <code>Component</code> for an <code>AttributePage</code>. - * + * * @param attributePage * an <code>AttributePage</code> * @param data @@ -101,7 +68,7 @@ public interface QueryConfigUIFactory { /** * Generates a <code>Component</code> for an array of * <code>AttributeGroup</code>. - * + * * @param attributeGroups * an array of <code>AttributeGroup</code> * @param data @@ -115,7 +82,7 @@ public interface QueryConfigUIFactory { /** * Generates a <code>Component</code> for an <code>AttributeGroup</code>. - * + * * @param attributeGroup * an <code>AttributeGroup</code> * @param data @@ -130,7 +97,7 @@ public interface QueryConfigUIFactory { /** * Generates a <code>Component</code> for an array of * <code>AttributeCollection</code>. - * + * * @param attributeCollections * an array of <code>AttributeCollection</code> * @param data @@ -146,7 +113,7 @@ public interface QueryConfigUIFactory { /** * Generates a <code>Component</code> for an * <code>AttributeCollection</code>. - * + * * @param attributeCollection * an <code>AttributeCollection</code> * @param data @@ -162,7 +129,7 @@ public interface QueryConfigUIFactory { /** * Generates a <code>Component</code> for an array of * <code>AttributeDescription</code>. - * + * * @param attributeDescriptions * an array of <code>AttributeDescription</code> * @param data @@ -178,7 +145,7 @@ public interface QueryConfigUIFactory { /** * Generates a <code>Component</code> for an * <code>AttributeDescription</code>. - * + * * @param attributeDescription * an <code>AttributeDescription</code> * @param data @@ -194,7 +161,7 @@ public interface QueryConfigUIFactory { /** * Generates a <code>Component</code> for an array of * <code>AttributeList</code>. - * + * * @param attributeLists * an array of <code>AttributeList</code> * @param data @@ -210,7 +177,7 @@ public interface QueryConfigUIFactory { /** * Generates a <code>Component</code> for an * <code>AttributeList</code>. - * + * * @param attributeList * an <code>AttributeList</code> * @param data @@ -226,7 +193,7 @@ public interface QueryConfigUIFactory { /** * Generates a <code>Component</code> for an array of * <code>FilterPage</code>. - * + * * @param filterPages * an array of <code>FilterPage</code> * @param data @@ -240,7 +207,7 @@ public interface QueryConfigUIFactory { /** * Generates a <code>Component</code> for a <code>FilterPage</code>. - * + * * @param filterPage * a <code>FilterPage</code> * @param data @@ -255,7 +222,7 @@ public interface QueryConfigUIFactory { /** * Generates a <code>Component</code> for an array of * <code>FilterGroup</code>. - * + * * @param filterGroups * an array of <code>FilterGroup</code> * @param data @@ -269,7 +236,7 @@ public interface QueryConfigUIFactory { /** * Generates a <code>Component</code> for a <code>FilterGroup</code>. - * + * * @param filterGroup * a <code>FilterGroup</code> * @param data @@ -284,7 +251,7 @@ public interface QueryConfigUIFactory { /** * Generates a <code>Component</code> for an array of * <code>FilterCollection</code>. - * + * * @param filterCollections * an array of <code>FilterCollection</code> * @param data @@ -299,7 +266,7 @@ public interface QueryConfigUIFactory { /** * Generates a <code>Component</code> for a <code>FilterCollection</code>. - * + * * @param filterCollection * a <code>FilterCollection</code> * @param data @@ -314,7 +281,7 @@ public interface QueryConfigUIFactory { /** * Generates a <code>Component</code> for an array of * <code>FilterDescription</code>. - * + * * @param filterDescriptions * an array of <code>FilterDescription</code> * @param data @@ -329,7 +296,7 @@ public interface QueryConfigUIFactory { /** * Generates a <code>Component</code> for a <code>FilterDescription</code>. - * + * * @param filterDescription * a <code>FilterDescription</code> * @param data http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Attribute.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Attribute.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Attribute.java index 7ec9932..45dc0d4 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Attribute.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Attribute.java @@ -1,36 +1,3 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: Attribute.java,v $ - * Revision $Revision: 1.2 $ - * Release status $State: Exp $ - * Last modified on $Date: 2008/03/04 16:43:40 $ - * by $Author: davidwithers $ - * Created on 26-Apr-2006 - *****************************************************************/ package org.biomart.martservice.query; /** http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Dataset.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Dataset.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Dataset.java index 20ea68f..7e24117 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Dataset.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Dataset.java @@ -1,36 +1,3 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: Dataset.java,v $ - * Revision $Revision: 1.2 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/10/03 15:57:30 $ - * by $Author: davidwithers $ - * Created on 21-Apr-2006 - *****************************************************************/ package org.biomart.martservice.query; import java.util.ArrayList; @@ -38,7 +5,7 @@ import java.util.List; /** * Class for creating dataset elements of mart queries. - * + * * @author David Withers */ public class Dataset { @@ -53,7 +20,7 @@ public class Dataset { /** * Constructs an instance of a <code>Dataset</code> with the specified * name. - * + * * @param name * the name of the <code>Dataset</code> */ @@ -64,7 +31,7 @@ public class Dataset { /** * Constructs an instance of a <code>Dataset</code> which is a deep copy * of another <code>Dataset</code>. - * + * * @param dataset * the <code>Dataset</code> to copy */ @@ -80,7 +47,7 @@ public class Dataset { /** * Returns the name of the Dataset. - * + * * @return the name of the Dataset. */ public String getName() { @@ -89,7 +56,7 @@ public class Dataset { /** * Set the name of the Dataset. - * + * * @param name * the new name for this Dataset. */ @@ -99,7 +66,7 @@ public class Dataset { /** * Returns a List of the Attributes in this dataset. - * + * * @return a List of the Attributes in this dataset */ public List<Attribute> getAttributes() { @@ -110,7 +77,7 @@ public class Dataset { * Adds an Attribute to the dataset. The attribute's containing dataset will * be set to this dataset. If this dataset is in a query an attribute added * event will be fired. - * + * * @param attribute * the Attribute to add * @return true if the Attribute is not already in the dataset @@ -130,7 +97,7 @@ public class Dataset { /** * Adds an array of Attributes to the dataset. - * + * * @param attributeArray * the array of Attributes to add */ @@ -142,7 +109,7 @@ public class Dataset { /** * Returns true if attribute is in the dataset. - * + * * @param attribute * @return true if attribute is in the dataset. */ @@ -152,7 +119,7 @@ public class Dataset { /** * Returns true if the dataset contains any Attributes. - * + * * @return true if the dataset contains any Attributes */ public boolean hasAttributes() { @@ -160,13 +127,13 @@ public class Dataset { } /** - * Removes an Attribute from the dataset. - * + * Removes an Attribute from the dataset. + * * If the attribute is contained in this dataset: * <ul> * <li>The attribute's containing dataset will be set to null. * <li>If this dataset is in a query an attribute removed event will be fired. - * + * * @param attribute * the attribute to remove * @return true if the attribute is removed @@ -194,7 +161,7 @@ public class Dataset { /** * Returns a List of the Filters in this dataset. - * + * * @return a List of the Filters in this dataset */ public List<Filter> getFilters() { @@ -205,7 +172,7 @@ public class Dataset { * Adds a Filter to the dataset. The filter's containing dataset will be set * to this dataset. If this dataset is in a query a filter added event will * be fired. - * + * * @param filter * the Filter to add * @return true if the Filter is not already in the dataset @@ -225,7 +192,7 @@ public class Dataset { /** * Adds an array of Filters to the dataset. - * + * * @param filterArray * the array of Filters to add */ @@ -237,7 +204,7 @@ public class Dataset { /** * Returns true if filter is in the dataset. - * + * * @param filter * @return true if filter is in the dataset */ @@ -247,7 +214,7 @@ public class Dataset { /** * Returns true if the dataset contains any filters. - * + * * @return true if the dataset contains any filters */ public boolean hasFilters() { @@ -256,12 +223,12 @@ public class Dataset { /** * Removes an Filter from the dataset. - * + * * If the filter is contained in this dataset: * <ul> * <li>The filter's containing dataset will be set to null. * <li>If this dataset is in a query an attribute removed event will be fired. - * + * * @param filter * the filter to remove * @return true if the filter is removed @@ -289,7 +256,7 @@ public class Dataset { /** * Returns the containingQuery. - * + * * @return the containingQuery. */ public Query getContainingQuery() { @@ -298,7 +265,7 @@ public class Dataset { /** * Sets the containingQuery. - * + * * @param containingQuery * the containingQuery to set. */ http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Filter.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Filter.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Filter.java index 1c088d0..860e38f 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Filter.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Filter.java @@ -1,41 +1,8 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: Filter.java,v $ - * Revision $Revision: 1.1 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/01/31 14:12:09 $ - * by $Author: davidwithers $ - * Created on 26-Apr-2006 - *****************************************************************/ package org.biomart.martservice.query; /** * Class for creating filter elements of mart queries. - * + * * @author David Withers */ public class Filter { @@ -51,7 +18,7 @@ public class Filter { /** * Constructs an instance of a <code>Filter</code> with the specified name. - * + * * @param name * the name of the <code>Filter</code>; must not be <code>null</code> */ @@ -62,7 +29,7 @@ public class Filter { /** * Constructs a instance of a <code>Filter</code> with the specified name * and value. - * + * * @param name * the name of the <code>Filter</code>; must not be <code>null</code> * @param value @@ -76,7 +43,7 @@ public class Filter { * Constructs a instance of a <code>Filter</code> with the specified name * and value, and sets a flag to indicate if this is a boolean * <code>Filter</code>. - * + * * @param name * the name of the <code>Filter</code>; must not be <code>null</code> * @param value @@ -95,7 +62,7 @@ public class Filter { /** * Constructs an instance of a <code>Filter</code> which is a copy of * another <code>Filter</code>. - * + * * @param filter * the <code>Filter</code> to copy; must not be <code>null</code> */ @@ -110,7 +77,7 @@ public class Filter { /** * Returns the name of the Filter. - * + * * @return the name of the Filter */ public String getName() { @@ -119,7 +86,7 @@ public class Filter { /** * Sets the name of the Filter. - * + * * @param name * the name of the Filter; must not be <code>null</code> */ @@ -132,11 +99,11 @@ public class Filter { /** * Returns the qualified name of this <code>Filter</code>. - * + * * The qualified name is <code>containingDatasetName.filterName</code> or * just <code>attributeName</code> if the <code>Filter</code> is not in * a <code>Dataset</code>. - * + * * @return the qualified name of this <code>Filter</code>. */ public String getQualifiedName() { @@ -150,7 +117,7 @@ public class Filter { /** * Returns the <code>Dataset</code> containing this <code>Filter</code> * or null if it is not in a <code>Dataset</code>. - * + * * @return the <code>Dataset</code> containing this <code>Filter</code> * or null if it is not in a <code>Dataset</code> */ @@ -160,7 +127,7 @@ public class Filter { /** * Sets the containing <code>Dataset</code>. - * + * * @param dataset * the containing <code>Dataset</code> */ @@ -170,7 +137,7 @@ public class Filter { /** * Returns the value. - * + * * @return the value. */ public String getValue() { @@ -179,7 +146,7 @@ public class Filter { /** * Sets the value. - * + * * @param value * the value to set. */ @@ -206,7 +173,7 @@ public class Filter { /** * Returns <code>true</code> if this is a boolean filter. - * + * * @return <code>true</code> if this is a boolean filter. */ public boolean isBoolean() { @@ -215,7 +182,7 @@ public class Filter { /** * Sets the booleanFilter flag. - * + * * @param booleanFilter */ public void setBoolean(boolean booleanFilter) { @@ -224,7 +191,7 @@ public class Filter { /** * Returns <code>true</code> if this is a list filter. - * + * * @return <code>true</code> if this is a list filter. */ public boolean isList() { @@ -233,7 +200,7 @@ public class Filter { /** * Sets the listFilter flag. - * + * * @param listFilter */ public void setList(boolean listFilter) { http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Link.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Link.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Link.java index 721428c..834efa1 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Link.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Link.java @@ -1,41 +1,8 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: Link.java,v $ - * Revision $Revision: 1.1 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/01/31 14:12:09 $ - * by $Author: davidwithers $ - * Created on 26-Apr-2006 - *****************************************************************/ package org.biomart.martservice.query; /** * Class for creating link elements of mart queries. - * + * * @author David Withers */ public class Link { @@ -49,7 +16,7 @@ public class Link { /** * Constructs an instance of a <code>Link</code>. - * + * * @param source * the source dataset of the <code>Link</code> * @param target @@ -66,7 +33,7 @@ public class Link { /** * Constructs an instance of a <code>Link</code> which is a copy of * another <code>Link</code>. - * + * * @param filter * the <code>Link</code> to copy */ @@ -78,7 +45,7 @@ public class Link { /** * Returns the defaultLink. - * + * * @return the defaultLink. */ public String getDefaultLink() { @@ -95,7 +62,7 @@ public class Link { /** * Returns the source dataset. - * + * * @return the source dataset. */ public String getSource() { @@ -104,7 +71,7 @@ public class Link { /** * Sets the source dataset. - * + * * @param source * the source dataset to set. */ @@ -114,7 +81,7 @@ public class Link { /** * Returns the target dataset. - * + * * @return the target dataset. */ public String getTarget() { @@ -123,7 +90,7 @@ public class Link { /** * Sets the target dataset. - * + * * @param target * the target dataset to set. */ @@ -133,7 +100,7 @@ public class Link { /** * Returns the containingQuery. - * + * * @return the containingQuery. */ public Query getContainingQuery() { @@ -142,7 +109,7 @@ public class Link { /** * Sets the containingQuery. - * + * * @param containingQuery * the containingQuery to set. */ @@ -152,7 +119,7 @@ public class Link { /* * (non-Javadoc) - * + * * @see java.lang.Object#equals(java.lang.Object) */ public boolean equals(Object obj) { @@ -171,7 +138,7 @@ public class Link { /* * (non-Javadoc) - * + * * @see java.lang.Object#hashCode() */ public int hashCode() { http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Query.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Query.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Query.java index c7c9f20..5261bc4 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Query.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Query.java @@ -1,36 +1,3 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: Query.java,v $ - * Revision $Revision: 1.4 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/10/03 15:57:30 $ - * by $Author: davidwithers $ - * Created on 03-Apr-2006 - *****************************************************************/ package org.biomart.martservice.query; import java.util.ArrayList; @@ -44,7 +11,7 @@ import org.biomart.martservice.MartServiceException; /** * Class for creating mart queries. - * + * * @author David Withers */ public class Query { @@ -55,7 +22,7 @@ public class Query { private int uniqueRows; private String softwareVersion; - + private String formatter; private String requestId; @@ -73,7 +40,7 @@ public class Query { /** * Constructs an instance of a <code>Query</code> with the specified * <code>virtualSchemaName</code> and a <code>count</code> of 0. - * + * * @param virtualSchemaName */ public Query(String virtualSchemaName) { @@ -83,7 +50,7 @@ public class Query { /** * Constructs an instance of a <code>Query</code> with the specified * <code>virtualSchemaName</code> and <code>count</code>. - * + * * @param virtualSchemaName * @param count */ @@ -96,7 +63,7 @@ public class Query { * Constructs an instance of a <code>Query</code> with the specified * <code>virtualSchemaName</code>, <code>softwareVersion</code> and * <code>requestId</code>. - * + * * @param virtualSchemaName * @param softwareVersion * @param requestId @@ -110,7 +77,7 @@ public class Query { * Constructs an instance of a <code>Query</code> with the specified * <code>virtualSchemaName</code>, <code>count</code> and * <code>softwareVersion</code>. - * + * * @param virtualSchemaName * @param count * @param softwareVersion @@ -123,7 +90,7 @@ public class Query { * Constructs an instance of a <code>Query</code> with the specified * <code>virtualSchemaName</code>, <code>count</code>, * <code>softwareVersion</code> and <code>requestId</code>. - * + * * @param virtualSchemaName * @param count * @param softwareVersion @@ -140,7 +107,7 @@ public class Query { /** * Constructs an instance of a <code>Query</code> which is a deep copy of * another <code>Query</code>. - * + * * @param query * the <code>Query</code> to copy * @throws MartServiceException @@ -162,7 +129,7 @@ public class Query { /** * Returns the virtualSchema. - * + * * @return the virtualSchema. */ public String getVirtualSchemaName() { @@ -171,7 +138,7 @@ public class Query { /** * Sets the virtualSchema. - * + * * @param virtualSchemaName * the virtualSchema to set. */ @@ -181,7 +148,7 @@ public class Query { /** * Returns the count. - * + * * @return the count. */ public int getCount() { @@ -190,7 +157,7 @@ public class Query { /** * Sets the count. - * + * * @param count * the count to set. */ @@ -200,7 +167,7 @@ public class Query { /** * Returns the uniqueRows query attribute - * + * * @return the uniqueRows query attribute */ public int getUniqueRows() { @@ -209,9 +176,9 @@ public class Query { /** * Sets the uniqueRows query attribute. - * + * * Valid values are 0 or 1. - * + * * @param uniqueRows value for the uniqueRows query attribute */ public void setUniqueRows(int uniqueRows) { @@ -220,7 +187,7 @@ public class Query { /** * Returns the softwareVersion. - * + * * @return the softwareVersion */ public String getSoftwareVersion() { @@ -229,7 +196,7 @@ public class Query { /** * Sets the softwareVersion. - * + * * @param softwareVersion * the new softwareVersion */ @@ -239,7 +206,7 @@ public class Query { /** * Returns the formatter. - * + * * @return the formatter */ public String getFormatter() { @@ -248,7 +215,7 @@ public class Query { /** * Sets the formatter. - * + * * @param formatter the new formatter */ public void setFormatter(String formatter) { @@ -271,7 +238,7 @@ public class Query { /** * Returns the requestId. - * + * * @return the requestId */ public String getRequestId() { @@ -280,7 +247,7 @@ public class Query { /** * Sets the requestId. - * + * * @param requestId * the new requestId */ @@ -290,9 +257,9 @@ public class Query { /** * Adds a Dataset to the Query. - * + * * The Dataset is added at the end of the list of Datasets. - * + * * @param dataset * the Dataset to add */ @@ -302,7 +269,7 @@ public class Query { /** * Adds a Dataset to the Query at the specified position. - * + * * @param index * the position to add the Dataset * @param dataset @@ -319,7 +286,7 @@ public class Query { /** * Removes a Dataset from the Query. - * + * * @param dataset * the Dataset to remove */ @@ -342,7 +309,7 @@ public class Query { /** * Returns the Datasets that this Query contains. - * + * * @return the Datasets that this Query contains. */ public List<Dataset> getDatasets() { @@ -352,7 +319,7 @@ public class Query { /** * Returns a Dataset with the given datasetName. If the Query has no Dataset * with the given datasetName null is returned. - * + * * @param datasetName * @return a Dataset with the given datasetName */ @@ -363,7 +330,7 @@ public class Query { /** * Returns true if this Query contains a Dataset with the name * <code>datasetName</code>. - * + * * @param datasetName * @return true if this Query contains a Dataset with the name * <code>datasetName</code>. @@ -374,7 +341,7 @@ public class Query { /** * Adds a Link to the Query. - * + * * @param link * the Link to add */ @@ -389,7 +356,7 @@ public class Query { /** * Removes a link from the Query - * + * * @param link * the Link to remove */ @@ -401,7 +368,7 @@ public class Query { /** * Returns the Links that this Query contains. - * + * * @return the Links that this Query contains. */ public Set<Link> getLinks() { @@ -411,7 +378,7 @@ public class Query { /** * Returns a Link with the given source. If the Query has no Link with the * given source null is returned. - * + * * @param source * the source of the link * @return a Link with the given source @@ -422,7 +389,7 @@ public class Query { /** * Returns true if this Query contains a Link with the same source. - * + * * @param source * the source of the link * @return true if this Query contains a Link with the same source. @@ -434,7 +401,7 @@ public class Query { /** * Returns a List of Links with the given target. If the Query has no Link * with the given target an empty List is returned. - * + * * @param target * the target of the link * @return a Link with the given target @@ -452,7 +419,7 @@ public class Query { /** * Returns all the Attributes from all the Datasets in this Query. - * + * * @return all the Attributes from all the Datasets in this Query. */ public List<Attribute> getAttributes() { @@ -465,7 +432,7 @@ public class Query { /** * Returns all the Filters from all the Datasets in this Query. - * + * * @return all the Filters from all the Datasets in this Query. */ public List<Filter> getFilters() { @@ -480,7 +447,7 @@ public class Query { * Adds the specified query listener to receive query events. If * <code>listener</code> is null, no exception is thrown and no action is * performed. - * + * * @param listener * the query listener */ @@ -496,7 +463,7 @@ public class Query { * if <code>listener</code> was not previously added to this component. If * <code>listener</code> is null, no exception is thrown and no action is * performed. - * + * * @param listener * the query listener */ http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryListener.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryListener.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryListener.java index 9f10f45..1752823 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryListener.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryListener.java @@ -1,48 +1,15 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: QueryListener.java,v $ - * Revision $Revision: 1.2 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/10/03 15:57:30 $ - * by $Author: davidwithers $ - * Created on 03-Apr-2006 - *****************************************************************/ package org.biomart.martservice.query; /** * The listener interface for receiving Query events. - * + * * @author David Withers */ public interface QueryListener { /** * Invoked when an <code>Attribute</code> is added to a <code>Query</code>. - * + * * @param attribute * the <code>Attribute</code> added. */ @@ -51,7 +18,7 @@ public interface QueryListener { /** * Invoked when an <code>Attribute</code> is removed from a * <code>Query</code>. - * + * * @param attribute * the <code>Attribute</code> removed. */ @@ -59,7 +26,7 @@ public interface QueryListener { /** * Invoked when a <code>Filter</code> is added to a <code>Query</code>. - * + * * @param filter * the <code>Filter</code> added. */ @@ -67,7 +34,7 @@ public interface QueryListener { /** * Invoked when a <code>Filter</code> is removed from a <code>Query</code>. - * + * * @param filter * the <code>Filter</code> removed. */ @@ -75,7 +42,7 @@ public interface QueryListener { /** * Invoked when the value of a <code>Filter</code> is changed. - * + * * @param filter * the <code>Filter</code> whose value has changed. */ @@ -83,7 +50,7 @@ public interface QueryListener { /** * Invoked when a formatter is added to a <code>Query</code>. - * + * * @param formatter * the formatter added. */ @@ -91,7 +58,7 @@ public interface QueryListener { /** * Invoked when a formatter is removed from a <code>Query</code>. - * + * * @param formatter * the formatter removed. */ @@ -99,7 +66,7 @@ public interface QueryListener { /** * Invoked when the value of the formatter is changed. - * + * * @param filter * the new value of the formatter. */
