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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 12:46:43 UTC
[16/50] [abbrv] incubator-taverna-plugin-bioinformatics git commit:
taverna-biomart-martservice/
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/9e08cac0/src/main/java/org/biomart/martservice/config/QueryConfigUtils.java
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diff --git a/src/main/java/org/biomart/martservice/config/QueryConfigUtils.java b/src/main/java/org/biomart/martservice/config/QueryConfigUtils.java
deleted file mode 100644
index 2bc7d71..0000000
--- a/src/main/java/org/biomart/martservice/config/QueryConfigUtils.java
+++ /dev/null
@@ -1,598 +0,0 @@
-/*
- * 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;
-import java.awt.Font;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
-
-import javax.swing.JMenu;
-import javax.swing.JMenuBar;
-import javax.swing.JMenuItem;
-import javax.swing.border.EtchedBorder;
-
-import org.biomart.martservice.MartDataset;
-import org.biomart.martservice.MartService;
-import org.biomart.martservice.MartServiceException;
-import org.biomart.martservice.config.ui.QueryComponent;
-import org.ensembl.mart.lib.config.AttributeDescription;
-import org.ensembl.mart.lib.config.AttributePage;
-import org.ensembl.mart.lib.config.BaseNamedConfigurationObject;
-import org.ensembl.mart.lib.config.DatasetConfig;
-import org.ensembl.mart.lib.config.FilterDescription;
-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);
- }
-
- public static String splitSentence(String sentence, int limit) {
- StringBuffer sb = new StringBuffer();
- sb.append("<html>");
-
- int width = 0;
- String[] split = sentence.split(" ");
- for (int i = 0; i < split.length; i++) {
- if (width == 0) {
- sb.append(split[i]);
- width += split[i].length();
- } else if (width + split[i].length() + 1 > limit) {
- sb.append("<br>");
- sb.append(split[i]);
- width = split[i].length();
- } else {
- sb.append(" ");
- sb.append(split[i]);
- width += split[i].length() + 1;
- }
- }
-
- return sb.toString();
- }
-
- /**
- * Returns name truncated to DISPLAY_WIDTH.
- *
- * @param name
- * @return
- */
- public static String truncateName(String name) {
- if (name.length() > DISPLAY_WIDTH) {
- return name.substring(0, DISPLAY_WIDTH);
- } else {
- return name;
- }
- }
-
- 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
- */
- public static boolean isList(FilterDescription filterDescription) {
- return filterDescription.getOptions().length > 0;
- }
-
- /**
- * 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
- */
- public static boolean isNestedList(FilterDescription filterDescription) {
- Option[] options = filterDescription.getOptions();
- for (int i = 0; i < options.length; i++) {
- if (options[i].getOptions().length > 0) {
- return true;
- }
- }
- return false;
- }
-
- /**
- * 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"
- */
- public static boolean isBooleanList(FilterDescription filterDescription) {
- Option[] options = filterDescription.getOptions();
- if (options.length > 0) {
- if ("boolean".equals(options[0].getType())) {
- return true;
- }
- }
- return false;
- }
-
- /**
- * 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
- */
- public static boolean isIdList(FilterDescription filterDescription) {
- Option[] options = filterDescription.getOptions();
- if (options.length > 0) {
- if (options[0].getValue() == null) {
- return true;
- }
- }
- return false;
- }
-
- public static Option[] fixOptionLength(Option[] options, int length) {
- if (options.length > length) {
- Option[] firstOptions = new Option[length];
- Option[] otherOptions = new Option[options.length - (length - 1)];
- for (int i = 0; i < length - 1; i++) {
- firstOptions[i] = options[i];
- fixOptionLength(options[i].getOptions(), length);
- }
- for (int i = length - 1; i < options.length; i++) {
- otherOptions[i - (length - 1)] = options[i];
- }
- Option newOption = new Option();
- newOption.setInternalName("more");
- newOption.setDisplayName("more");
- newOption.addOptions(fixOptionLength(otherOptions, length));
- firstOptions[length - 1] = newOption;
- return firstOptions;
- } else {
- return options;
- }
- }
-
- public static Component getOptionButton(
- FilterDescription filterDescription, QueryComponent queryComponent) {
- JMenuBar menuBar = new JMenuBar();
- menuBar.setBorder(new EtchedBorder());
- JMenu menu = new JMenu("browse");
- menu.setFont(menu.getFont().deriveFont(Font.PLAIN));
- menuBar.add(menu);
- Option[] options = fixOptionLength(filterDescription.getOptions(), 20);
- for (int i = 0; i < options.length; i++) {
- menu.add(getMenuItem(options[i], queryComponent));
- }
- return menuBar;
- }
-
- public static JMenuItem getMenuItem(final Option option,
- final QueryComponent queryComponent) {
- JMenuItem menuItem;
-
- Option[] options = option.getOptions();
- if (options.length > 0) {
- JMenu menu = new JMenu(option.getDisplayName());
- menu.setFont(menu.getFont().deriveFont(Font.PLAIN));
- for (int i = 0; i < options.length; i++) {
- menu.add(getMenuItem(options[i], queryComponent));
- }
- menuItem = menu;
- } else {
- menuItem = new JMenuItem(option.getDisplayName());
- menuItem.setFont(menuItem.getFont().deriveFont(Font.PLAIN));
- menuItem.addActionListener(new ActionListener() {
-
- public void actionPerformed(ActionEvent e) {
- queryComponent.setValue(option.getValue());
- }
-
- });
- }
-
- return menuItem;
- }
-
- /**
- * 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
- * the datset containing the configuration object
- * @param bnco
- * the configuration object
- * @return the dataset referenced by a configuration object or null if the
- * configuration object does not reference a dataset.
- * @throws MartServiceException
- * if and exception occurs while fetching the dataset
- */
- public static MartDataset getReferencedDataset(MartService martService,
- MartDataset referencedFromDataset,
- BaseNamedConfigurationObject bnco, String softwareVersion)
- throws MartServiceException {
- if ("0.5".equals(softwareVersion)) {
- String pointerDataset = bnco.getAttribute("pointerDataset");
- if (pointerDataset != null) {
- return martService.getDataset(referencedFromDataset
- .getVirtualSchema(), pointerDataset);
- } else {
- return null;
- }
- } else {
- String[] splitName = bnco.getInternalName().split("\\.");
- if (splitName.length > 1) {
- return martService.getDataset(referencedFromDataset
- .getVirtualSchema(), splitName[0]);
- } else {
- return null;
- }
- }
- }
-
- /**
- * Returns the filter description referenced by the filter description.
- *
- * @param martService
- * the MartService to fetch the referenced filter description
- * from
- * @param dataset
- * the datset containing the referenced filter description
- * @param filterDescription
- * the filter description
- * @return the filter description referenced by the filter description
- * @throws MartServiceException
- * if and exception occurs while fetching the filter description
- */
- public static FilterDescription getReferencedFilterDescription(
- MartService martService, MartDataset dataset,
- FilterDescription filterDescription, String softwareVersion)
- throws MartServiceException {
- if ("0.5".equals(softwareVersion)) {
- String pointerFilter = filterDescription
- .getAttribute("pointerFilter");
- if (pointerFilter != null) {
- return getReferencedFilterDescription(martService, dataset,
- pointerFilter);
- } else {
- return null;
- }
- } else {
- String[] splitName = filterDescription.getInternalName().split(
- "\\.");
- FilterDescription ref = getReferencedFilterDescription(martService,
- dataset, splitName[1]);
- return ref;
- }
- }
-
- /**
- * Returns the filter description referenced by the attribute description.
- *
- * @param martService
- * the MartService to fetch the referenced filter description
- * from
- * @param dataset
- * the datset containing the referenced filter description
- * @param attributeDescription
- * the attribute description
- * @return the filter description referenced by the attribute description
- * @throws MartServiceException
- * if and exception occurs while fetching the filter description
- */
- public static FilterDescription getReferencedFilterDescription(
- MartService martService, MartDataset dataset,
- AttributeDescription attributeDescription, String softwareVersion)
- throws MartServiceException {
- if ("0.5".equals(softwareVersion)) {
- String pointerFilter = attributeDescription
- .getAttribute("pointerFilter");
- if (pointerFilter != null) {
- return getReferencedFilterDescription(martService, dataset,
- pointerFilter);
- } else {
- return null;
- }
- } else {
- String[] splitName = attributeDescription.getInternalName().split(
- "\\.");
- return getReferencedFilterDescription(martService, dataset,
- splitName[2]);
- }
- }
-
- public static FilterDescription getReferencedFilterDescription(
- MartService martService, MartDataset dataset, String filterName)
- throws MartServiceException {
- FilterDescription referencedFilter = null;
- DatasetConfig datasetConfig = martService.getDatasetConfig(dataset);
- List<FilterDescription> filterDescriptions = datasetConfig.getAllFilterDescriptions();
- for (FilterDescription filterDescription : filterDescriptions) {
- if (filterName.equals(filterDescription.getInternalName())) {
- if (!"true".equals(filterDescription.getHidden())) {
- referencedFilter = filterDescription;
- break;
- }
- }
- }
- return referencedFilter;
- }
-
- public static FilterDescription getReferencedFilterDescription(
- AttributeDescription attributeDescription, String softwareVersion) {
- FilterDescription filterDescription = new FilterDescription();
- if ("0.5".equals(softwareVersion)) {
- filterDescription.setInternalName(attributeDescription
- .getInternalName());
- filterDescription.setAttribute(attributeDescription
- .getAttribute("pointerDataset"));
- filterDescription.setAttribute(attributeDescription
- .getAttribute("pointerFilter"));
- filterDescription.setAttribute(attributeDescription
- .getAttribute("pointerInterface"));
- } else {
- String[] splitName = attributeDescription.getInternalName().split(
- "\\.");
- filterDescription
- .setInternalName(splitName[0] + "." + splitName[2]);
- }
- return filterDescription;
- }
-
- public static AttributeDescription getReferencedAttributeDescription(
- MartService martService, MartDataset dataset,
- AttributeDescription attributeDescription, String softwareVersion)
- throws MartServiceException {
- AttributeDescription referencedAttributeDescription = null;
- String attributeName = null;
- if ("0.5".equals(softwareVersion)) {
- attributeName = attributeDescription
- .getAttribute("pointerAttribute");
- } else {
- String internalName = attributeDescription.getInternalName();
- String[] splitName = internalName.split("\\.");
- if (splitName.length == 2) {
- attributeName = splitName[1];
- }
- }
- if (attributeName != null) {
- DatasetConfig datasetConfig = martService.getDatasetConfig(dataset);
- if (datasetConfig.containsAttributeDescription(attributeName)) {
- referencedAttributeDescription = datasetConfig
- .getAttributeDescriptionByInternalName(attributeName);
- }
- }
- return referencedAttributeDescription;
- }
-
- /**
- * 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
- * '.' character
- */
- public static boolean isReference(BaseNamedConfigurationObject bnco,
- String softwareVersion) {
- if ("0.5".equals(softwareVersion)) {
- return bnco.getAttribute("pointerDataset") != null
- && (bnco.getAttribute("pointerAttribute") != null || bnco.getAttribute("pointerFilter") != null);
- } else {
- return bnco.getInternalName().indexOf(".") != -1;
- }
- }
-
- /**
- * 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]"
- */
- public static boolean isAttributeReference(
- AttributeDescription attributeDescription, String softwareVersion) {
- if ("0.5".equals(softwareVersion)) {
- return attributeDescription.getAttribute("pointerAttribute") != null;
- } else {
- return attributeDescription.getInternalName().split("\\.").length == 2;
- }
- }
-
- /**
- * 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]"
- */
- public static boolean isFilterReference(
- AttributeDescription attributeDescription, String softwareVersion) {
- if ("0.5".equals(softwareVersion)) {
- return attributeDescription.getAttribute("pointerFilter") != null;
- } else {
- return attributeDescription.getInternalName().split("\\.").length == 3;
- }
- }
-
-// /**
-// * 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
-// * format "[datasetName].[attributeName]"
-// */
-// public static String getQualifiedName(MartDataset dataset,
-// AttributeDescription attributeDescription, String softwareVersion) {
-// if ("0.5".equals(softwareVersion)) {
-// if (isAttributeReference(attributeDescription, softwareVersion)) {
-// return attributeDescription.getAttribute("pointerDataset")
-// + "."
-// + attributeDescription.getAttribute("pointerAttribute");
-// } else if (isFilterReference(attributeDescription, softwareVersion)) {
-// return attributeDescription.getAttribute("pointerDataset")
-// + "."
-// + attributeDescription.getAttribute("pointerFilter");
-// } else {
-// return dataset.getName()
-// + attributeDescription.getInternalName();
-// }
-// } else {
-// if (isAttributeReference(attributeDescription, softwareVersion)) {
-// return attributeDescription.getInternalName();
-// } else if (isFilterReference(attributeDescription, softwareVersion)) {
-// String[] splitName = attributeDescription.getInternalName()
-// .split("\\.");
-// return splitName[0] + "." + splitName[2];
-// } else {
-// return dataset.getName()
-// + attributeDescription.getInternalName();
-// }
-// }
-// }
-
- public static String csvToValuePerLine(String csv) {
- StringBuffer list = new StringBuffer();
-
- String[] splitString = csv.split(",");
- for (int i = 0; i < splitString.length; i++) {
- if (i > 0) {
- list.append(LINE_END);
- }
- list.append(splitString[i].trim());
- }
-
- return list.toString();
- }
-
- public static String valuePerLineToCsv(String list) {
- return list.trim().replaceAll("\\s", ",");
- }
-
- public static List<String> csvToList(String csv) {
- List<String> list = new ArrayList<String>();
-
- String[] splitString = csv.split(",");
- for (int i = 0; i < splitString.length; i++) {
- list.add(splitString[i].trim());
- }
-
- return list;
- }
-
- /**
- * 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
- */
- public static String listToCsv(List<?> list) {
- StringBuffer sb = new StringBuffer();
- for (Iterator<?> iter = list.iterator(); iter.hasNext();) {
- sb.append(iter.next().toString());
- if (iter.hasNext()) {
- sb.append(',');
- }
- }
- return sb.toString();
- }
-
- /**
- * 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
- * is "true"
- */
- public static boolean display(BaseNamedConfigurationObject bnco) {
- boolean display = true;
- String hideDisplay = bnco.getDisplay();
- if (hideDisplay != null) {
- if (hideDisplay.equals("true")) {
- display = false;
- }
- } else {
- String hidden = bnco.getHidden();
- if (hidden != null) {
- if (hidden.equals("true")) {
- display = false;
- }
- }
- }
- return display;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/9e08cac0/src/main/java/org/biomart/martservice/config/event/QueryComponentAdapter.java
----------------------------------------------------------------------
diff --git a/src/main/java/org/biomart/martservice/config/event/QueryComponentAdapter.java b/src/main/java/org/biomart/martservice/config/event/QueryComponentAdapter.java
deleted file mode 100644
index 201cc1d..0000000
--- a/src/main/java/org/biomart/martservice/config/event/QueryComponentAdapter.java
+++ /dev/null
@@ -1,109 +0,0 @@
-/*
- * 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) {
- }
-
- /*
- * (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) {
- }
-
- /*
- * (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) {
- }
-
- /*
- * (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) {
- }
-
- /*
- * (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) {
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.biomart.martservice.config.event.QueryComponentListener#linkAdded(org.biomart.martservice.config.event.QueryComponentEvent)
- */
- public void linkAdded(QueryComponentEvent event) {
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.biomart.martservice.config.event.QueryComponentListener#linkRemoved(org.biomart.martservice.config.event.QueryComponentEvent)
- */
- public void linkRemoved(QueryComponentEvent event) {
- }
-
- /*
- * (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/9e08cac0/src/main/java/org/biomart/martservice/config/event/QueryComponentEvent.java
----------------------------------------------------------------------
diff --git a/src/main/java/org/biomart/martservice/config/event/QueryComponentEvent.java b/src/main/java/org/biomart/martservice/config/event/QueryComponentEvent.java
deleted file mode 100644
index 6fc5d18..0000000
--- a/src/main/java/org/biomart/martservice/config/event/QueryComponentEvent.java
+++ /dev/null
@@ -1,120 +0,0 @@
-/*
- * 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;
-
-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 {
- private static final long serialVersionUID = -7576317475836030298L;
-
- private String name;
-
- private MartDataset dataset;
-
- private String value;
-
- /**
- * Constructs a new <code>QueryComponentEvent</code> instance.
- *
- * @param source
- * the source of the event
- * @param name
- * the name of the attribute or filter affected by this event
- * @param dataset
- * the dataset containing the attribute or filter affected by
- * this event
- */
- public QueryComponentEvent(Object source, String name, MartDataset dataset) {
- this(source, name, dataset, null);
- }
-
- /**
- * Constructs a new <code>QueryComponentEvent</code> instance.
- *
- * @param source
- * the source of the event
- * @param name
- * the name of the attribute or filter affected by this event
- * @param dataset
- * the dataset containing the attribute or filter affected by
- * this event
- * @param value
- * the value of the filter affected by this event
- */
- public QueryComponentEvent(Object source, String name, MartDataset dataset,
- String value) {
- super(source);
- this.name = name;
- this.dataset = dataset;
- this.value = value;
- }
-
- /**
- * 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() {
- return name;
- }
-
- /**
- * Returns the dataset containing the attribute or filter affected by this
- * event.
- *
- * @return the dataset containing the attribute or filter affected by this
- * event.
- */
- public MartDataset getDataset() {
- return dataset;
- }
-
- /**
- * Returns the value of the filter affected by this event.
- *
- * @return the value of the filter affected by this event.
- */
- public String getValue() {
- return value;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/9e08cac0/src/main/java/org/biomart/martservice/config/event/QueryComponentListener.java
----------------------------------------------------------------------
diff --git a/src/main/java/org/biomart/martservice/config/event/QueryComponentListener.java b/src/main/java/org/biomart/martservice/config/event/QueryComponentListener.java
deleted file mode 100644
index af63326..0000000
--- a/src/main/java/org/biomart/martservice/config/event/QueryComponentListener.java
+++ /dev/null
@@ -1,104 +0,0 @@
-/*
- * 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 {
-
- /**
- * Invoked when a <code>QueryComponent</code> for an attribute is
- * selected.
- *
- * @param event the query component event
- */
- public void attributeAdded(QueryComponentEvent event);
-
- /**
- * 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);
-
- /**
- * 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/9e08cac0/src/main/java/org/biomart/martservice/config/ui/ConfigDisplayObject.java
----------------------------------------------------------------------
diff --git a/src/main/java/org/biomart/martservice/config/ui/ConfigDisplayObject.java b/src/main/java/org/biomart/martservice/config/ui/ConfigDisplayObject.java
deleted file mode 100644
index 89820d3..0000000
--- a/src/main/java/org/biomart/martservice/config/ui/ConfigDisplayObject.java
+++ /dev/null
@@ -1,125 +0,0 @@
-/*
- * 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;
-
-import org.ensembl.mart.lib.config.BaseNamedConfigurationObject;
-
-/**
- * An object containing a configuration object and it's graphical component.
- *
- * @author David Withers
- */
-public class ConfigDisplayObject {
- private BaseNamedConfigurationObject configObject;
-
- private Component component;
-
- /**
- * 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>
- */
- public ConfigDisplayObject(BaseNamedConfigurationObject configObject) {
- this(configObject, null);
- }
-
- /**
- * 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
- * the component
- */
- public ConfigDisplayObject(BaseNamedConfigurationObject configObject,
- Component component) {
- if (configObject == null) {
- throw new IllegalArgumentException(
- "Parameter 'configObject' must not be null");
- }
- this.configObject = configObject;
- this.component = component;
- }
-
- /**
- * Returns the display name.
- *
- * @return the display name
- */
- public String getDisplayName() {
- return configObject.getDisplayName();
- }
-
- /**
- * Returns the internal name.
- *
- * @return the internal name
- */
- public String getInternalName() {
- return configObject.getInternalName();
- }
-
- /**
- * Returns the display name.
- *
- * @return the display name
- */
- public String toString() {
- return getDisplayName();
- }
-
- /**
- * Returns the configuration object.
- *
- * @return the configuration object
- */
- public BaseNamedConfigurationObject getConfigObject() {
- return configObject;
- }
-
- /**
- * Returns the component.
- *
- * @return the component.
- */
- public Component getComponent() {
- return component;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/9e08cac0/src/main/java/org/biomart/martservice/config/ui/ExpandableBox.java
----------------------------------------------------------------------
diff --git a/src/main/java/org/biomart/martservice/config/ui/ExpandableBox.java b/src/main/java/org/biomart/martservice/config/ui/ExpandableBox.java
deleted file mode 100644
index d5ff0dd..0000000
--- a/src/main/java/org/biomart/martservice/config/ui/ExpandableBox.java
+++ /dev/null
@@ -1,204 +0,0 @@
-/*
- * 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;
-import java.awt.Component;
-import java.awt.Dimension;
-import java.awt.Insets;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-
-import javax.swing.Box;
-import javax.swing.BoxLayout;
-import javax.swing.JButton;
-import javax.swing.JPanel;
-import javax.swing.Timer;
-import javax.swing.border.CompoundBorder;
-import javax.swing.border.EmptyBorder;
-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;
-
- private JButton expandButton;
-
- private JPanel labelBox;
-
- private boolean expanded = true;
-
- private boolean animated = false;
-
- private Timer timer = new Timer(1, null);
-
- private Dimension minSize;
-
- private Dimension maxSize;
-
- private int height;
-
- private final int increment = 10;
-
- private ActionListener openAction = new ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- if (height <= maxSize.height) {
- setPreferredSize(new Dimension(maxSize.width, height));
- revalidate();
- repaint();
- height += increment;
- } else {
- timer.removeActionListener(this);
- timer.stop();
- setPreferredSize(new Dimension(maxSize.width, maxSize.height));
- revalidate();
- repaint();
- }
- }
- };
-
- private ActionListener closeAction = new ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- if (height >= minSize.height) {
- setPreferredSize(new Dimension(minSize.width, height));
- revalidate();
- repaint();
- height -= increment;
- } else {
- timer.removeActionListener(this);
- timer.stop();
- height = minSize.height;
- setPreferredSize(new Dimension(minSize.width, height));
- revalidate();
- repaint();
- }
- }
- };
-
- public ExpandableBox(Component titleComponent, Color backgroundColor,
- Color borderColor) {
- this(titleComponent, backgroundColor, borderColor, new Insets(10, 10,
- 10, 10), false);
- }
-
- public ExpandableBox(Component titleComponent, Color backgroundColor,
- Color borderColor, Insets borderInsets) {
- this(titleComponent, backgroundColor, borderColor, borderInsets, false);
- }
-
- public ExpandableBox(Component titleComponent, Color backgroundColor,
- Color borderColor, boolean animated) {
- this(titleComponent, backgroundColor, borderColor, new Insets(10, 10,
- 10, 10), animated);
- }
-
- public ExpandableBox(Component titleComponent, Color backgroundColor,
- Color borderColor, Insets borderInsets, boolean animated) {
- this.animated = animated;
- setLayout(new BoxLayout(this, BoxLayout.Y_AXIS));
- setBackground(backgroundColor);
- setBorder(new CompoundBorder(new LineBorder(borderColor, 1),
- new EmptyBorder(borderInsets)));
-
- labelBox = new JPanel();
- labelBox.setLayout(new BoxLayout(labelBox, BoxLayout.X_AXIS));
- labelBox.setBackground(backgroundColor);
-
- expandButton = new JButton(MartServiceIcons.getIcon("contract"));
- expandButton.setActionCommand("contract");
- expandButton.setBackground(backgroundColor);
- expandButton.setBorder(new EmptyBorder(0, 0, 0, 0));
- expandButton.addActionListener(new ActionListener() {
-
- public void actionPerformed(ActionEvent e) {
- if ("contract".equals(e.getActionCommand())) {
- setExpanded(false);
- } else {
- setExpanded(true);
- }
- }
-
- });
- labelBox.add(expandButton);
- labelBox.add(Box.createHorizontalStrut(5));
- labelBox.add(titleComponent);
- labelBox.add(Box.createHorizontalGlue());
- add(labelBox);
- minSize = getPreferredSize();
- }
-
- public void setExpanded(boolean expanded) {
- if (maxSize == null || maxSize.height <= minSize.height) {
- maxSize = getLayout().preferredLayoutSize(this);
- }
- if (this.expanded != expanded) {
- this.expanded = expanded;
- if (expanded) {
- expandButton.setIcon(MartServiceIcons.getIcon("contract"));
- expandButton.setActionCommand("contract");
- if (animated) {
- timer.stop();
- timer.removeActionListener(closeAction);
- timer.addActionListener(openAction);
- timer.start();
- } else {
- setPreferredSize(new Dimension(maxSize.width,
- maxSize.height));
- }
- } else {
- expandButton.setIcon(MartServiceIcons.getIcon("expand"));
- expandButton.setActionCommand("expand");
- if (animated) {
- timer.stop();
- timer.removeActionListener(openAction);
- timer.addActionListener(closeAction);
- timer.start();
- } else {
- setPreferredSize(new Dimension(minSize.width,
- minSize.height));
- }
- }
- revalidate();
- repaint();
- }
- expandButton.setSelected(expanded);
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/9e08cac0/src/main/java/org/biomart/martservice/config/ui/MartServiceIcons.java
----------------------------------------------------------------------
diff --git a/src/main/java/org/biomart/martservice/config/ui/MartServiceIcons.java b/src/main/java/org/biomart/martservice/config/ui/MartServiceIcons.java
deleted file mode 100644
index 15f294a..0000000
--- a/src/main/java/org/biomart/martservice/config/ui/MartServiceIcons.java
+++ /dev/null
@@ -1,104 +0,0 @@
-/*
- * 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;
-import java.util.Map;
-
-import javax.swing.Icon;
-import javax.swing.ImageIcon;
-
-/**
- *
- * @author witherd5
- */
-public class MartServiceIcons {
- private static Map<String, Icon> nameToIcon = new HashMap<String, Icon>();
-
- private static final String imageLocation = "org/biomart/martservice/config/ui/";
-
- static {
- ClassLoader loader = MartServiceQueryConfigUIFactory.class
- .getClassLoader();
- if (loader == null) {
- loader = Thread.currentThread().getContextClassLoader();
- }
-
- nameToIcon.put("gene_schematic", new ImageIcon(loader
- .getResource(imageLocation + "gene_schematic.gif")));
- nameToIcon.put("gene_schematic_3utr", new ImageIcon(loader
- .getResource(imageLocation + "gene_schematic_3utr.gif")));
- nameToIcon.put("gene_schematic_5utr", new ImageIcon(loader
- .getResource(imageLocation + "gene_schematic_5utr.gif")));
- nameToIcon.put("gene_schematic_cdna", new ImageIcon(loader
- .getResource(imageLocation + "gene_schematic_cdna.gif")));
- nameToIcon.put("gene_schematic_coding_gene_flank", new ImageIcon(loader
- .getResource(imageLocation
- + "gene_schematic_coding_gene_flank.gif")));
- nameToIcon.put("gene_schematic_coding_transcript_flank", new ImageIcon(
- loader.getResource(imageLocation
- + "gene_schematic_coding_transcript_flank.gif")));
- nameToIcon.put("gene_schematic_coding", new ImageIcon(loader
- .getResource(imageLocation + "gene_schematic_coding.gif")));
- nameToIcon.put("gene_schematic_gene_exon_intron", new ImageIcon(loader
- .getResource(imageLocation
- + "gene_schematic_gene_exon_intron.gif")));
- nameToIcon.put("gene_schematic_gene_exon", new ImageIcon(loader
- .getResource(imageLocation + "gene_schematic_gene_exon.gif")));
- nameToIcon.put("gene_schematic_gene_flank", new ImageIcon(loader
- .getResource(imageLocation + "gene_schematic_gene_flank.gif")));
- nameToIcon.put("gene_schematic_peptide", new ImageIcon(loader
- .getResource(imageLocation + "gene_schematic_peptide.gif")));
- nameToIcon.put("gene_schematic_transcript_exon_intron", new ImageIcon(
- loader.getResource(imageLocation
- + "gene_schematic_transcript_exon_intron.gif")));
- nameToIcon.put("gene_schematic_transcript_exon", new ImageIcon(
- loader.getResource(imageLocation
- + "gene_schematic_transcript_exon.gif")));
- nameToIcon.put("gene_schematic_transcript_flank", new ImageIcon(loader
- .getResource(imageLocation
- + "gene_schematic_transcript_flank.gif")));
- nameToIcon.put("contract", new ImageIcon(loader
- .getResource(imageLocation
- + "contract.gif")));
- nameToIcon.put("expand", new ImageIcon(loader
- .getResource(imageLocation
- + "expand.gif")));
- }
-
- public static Icon getIcon(String name) {
- return (Icon) nameToIcon.get(name);
- }
-
-}