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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 12:46:41 UTC
[14/50] [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/ui/MinimalLayout.java
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diff --git a/src/main/java/org/biomart/martservice/config/ui/MinimalLayout.java b/src/main/java/org/biomart/martservice/config/ui/MinimalLayout.java
deleted file mode 100644
index 153b982..0000000
--- a/src/main/java/org/biomart/martservice/config/ui/MinimalLayout.java
+++ /dev/null
@@ -1,158 +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: 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;
-import java.awt.Container;
-import java.awt.Dimension;
-import java.awt.Insets;
-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 {
- public static final int HORIZONTAL = 0;
-
- public static final int VERTICAL = 1;
-
- private static final int gap = 5;
-
- private int type;
-
- public MinimalLayout() {
- type = HORIZONTAL;
- }
-
- public MinimalLayout(int type) {
- this.type = type;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see java.awt.LayoutManager#removeLayoutComponent(java.awt.Component)
- */
- public void removeLayoutComponent(Component comp) {
- }
-
- /*
- * (non-Javadoc)
- *
- * @see java.awt.LayoutManager#layoutContainer(java.awt.Container)
- */
- public void layoutContainer(Container parent) {
- Insets insets = parent.getInsets();
- int x = insets.left;
- int y = insets.top;
- if (type == HORIZONTAL) {
- Component[] components = parent.getComponents();
- for (int i = 0; i < components.length; i++) {
- components[i].setLocation(x, y);
- components[i].setSize(getSize(components[i]));
- x = x + gap + components[i].getWidth();
- }
- } else {
- Component[] components = parent.getComponents();
- for (int i = 0; i < components.length; i++) {
- components[i].setLocation(x, y);
- components[i].setSize(getSize(components[i]));
- y = y + gap + components[i].getHeight();
- }
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see java.awt.LayoutManager#addLayoutComponent(java.lang.String,
- * java.awt.Component)
- */
- public void addLayoutComponent(String name, Component comp) {
- }
-
- /*
- * (non-Javadoc)
- *
- * @see java.awt.LayoutManager#minimumLayoutSize(java.awt.Container)
- */
- public Dimension minimumLayoutSize(Container parent) {
- Insets insets = parent.getInsets();
- Dimension minimumSize = new Dimension(insets.left, insets.top);
- if (type == HORIZONTAL) {
- int x = insets.left;
- Component[] components = parent.getComponents();
- for (int i = 0; i < components.length; i++) {
- Dimension size = getSize(components[i]);
- if (insets.top + size.height > minimumSize.height) {
- minimumSize.height = insets.top + size.height;
- }
- minimumSize.width = x + size.width;
- x = x + size.width + gap;
- }
- } else {
- int y = insets.top;
- Component[] components = parent.getComponents();
- for (int i = 0; i < components.length; i++) {
- Dimension size = getSize(components[i]);
- if (insets.left + size.width > minimumSize.width) {
- minimumSize.width = insets.left + size.width;
- }
- minimumSize.height = y + size.height;
- y = y + size.height + gap;
- }
- }
- minimumSize.width = minimumSize.width + insets.right;
- minimumSize.height = minimumSize.height + insets.bottom;
-
- return (minimumSize);
- }
-
- /*
- * (non-Javadoc)
- *
- * @see java.awt.LayoutManager#preferredLayoutSize(java.awt.Container)
- */
- public Dimension preferredLayoutSize(Container parent) {
- return minimumLayoutSize(parent);
- }
-
- private Dimension getSize(Component component) {
- return component.getPreferredSize();
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/9e08cac0/src/main/java/org/biomart/martservice/config/ui/QueryComponent.java
----------------------------------------------------------------------
diff --git a/src/main/java/org/biomart/martservice/config/ui/QueryComponent.java b/src/main/java/org/biomart/martservice/config/ui/QueryComponent.java
deleted file mode 100644
index b976684..0000000
--- a/src/main/java/org/biomart/martservice/config/ui/QueryComponent.java
+++ /dev/null
@@ -1,342 +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: 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;
-import java.awt.event.ItemListener;
-import java.util.Vector;
-
-import javax.swing.AbstractButton;
-import javax.swing.JPanel;
-
-import org.biomart.martservice.MartDataset;
-import org.biomart.martservice.config.event.QueryComponentEvent;
-import org.biomart.martservice.config.event.QueryComponentListener;
-import org.ensembl.mart.lib.config.BaseNamedConfigurationObject;
-
-/**
- * Abstract class for creating query configuration UI components.
- *
- * @author David Withers
- */
-public abstract class QueryComponent extends JPanel {
- public static final int ATTRIBUTE = 0;
-
- public static final int FILTER = 1;
-
- public static final int LINK = 2;
-
- private Vector<QueryComponentListener> queryComponentListeners = new Vector<QueryComponentListener>();
-
- private MartDataset dataset;
-
- private String pointerDataset;
-
- private String name;
-
- private String value;
-
- private BaseNamedConfigurationObject configObject;
-
- protected AbstractButton selectorButton;
-
- public abstract int getType();
-
- /**
- * Returns the dataset.
- *
- * @return the dataset.
- */
- public MartDataset getDataset() {
- return dataset;
- }
-
- /**
- * Sets the dataset.
- *
- * @param dataset
- * the dataset to set.
- */
- public void setDataset(MartDataset dataset) {
- this.dataset = dataset;
- }
-
- /**
- * Returns the pointerDataset.
- *
- * @return the pointerDataset
- */
- public String getPointerDataset() {
- return pointerDataset;
- }
-
- /**
- * Sets the pointerDataset.
- *
- * @param pointerDataset the new pointerDataset
- */
- public void setPointerDataset(String pointerDataset) {
- this.pointerDataset = pointerDataset;
- }
-
- /**
- * Returns the name.
- *
- * @return the name.
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set.
- */
- public void setName(String name) {
- this.name = name;
- }
-
- public String getQualifiedName() {
- return getDataset().getName() + "." + getName();
- }
-
- public String getOldQualifiedName() {
- if (pointerDataset == null) {
- return getDataset().getName() + "." + getName();
- } else {
- return pointerDataset + "." + getName();
- }
- }
-
- /**
- * Returns the value.
- *
- * @return the value.
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value.
- *
- * @param value
- * the value to set.
- */
- public void setValue(String value) {
- this.value = value;
- }
-
- /**
- * Returns the configObject.
- *
- * @return the configObject
- */
- public BaseNamedConfigurationObject getConfigObject() {
- return configObject;
- }
-
- /**
- * Sets the configObject.
- *
- * @param configObject
- * the configObject to set.
- */
- public void setConfigObject(BaseNamedConfigurationObject configObject) {
- this.configObject = configObject;
- }
-
- /**
- * Sets the selected state of this component.
- *
- * @param selected
- * <code>true</code> if this component is selected,
- * <code>false</code> otherwise
- */
- public void setSelected(boolean selected) {
- if (selectorButton != null) {
- selectorButton.setSelected(selected);
- }
- }
-
- /**
- * 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.
- */
- public void setSelectorButton(AbstractButton button) {
- selectorButton = button;
- button.addItemListener(new ItemListener() {
- public void itemStateChanged(ItemEvent e) {
- if (e.getStateChange() == ItemEvent.SELECTED) {
- if (getType() == ATTRIBUTE) {
- fireAttributeAdded(new QueryComponentEvent(
- QueryComponent.this, getName(), getDataset()));
- } else {
- fireFilterAdded(new QueryComponentEvent(
- QueryComponent.this, getName(), getDataset()));
- }
- } else if (e.getStateChange() == ItemEvent.DESELECTED) {
- if (getType() == ATTRIBUTE) {
- fireAttributeRemoved(new QueryComponentEvent(
- QueryComponent.this, getName(), getDataset()));
- } else {
- fireFilterRemoved(new QueryComponentEvent(
- QueryComponent.this, getName(), getDataset()));
- }
- }
- }
- });
- }
-
- /**
- * 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
- */
- public void addQueryComponentListener(QueryComponentListener listener) {
- queryComponentListeners.add(listener);
- }
-
- /**
- * Removes the specified query component listener so that it no longer
- * receives component query events. This method performs no function, nor
- * 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
- */
- public void removeQueryComponentListener(QueryComponentListener listener) {
- queryComponentListeners.remove(listener);
- }
-
- /**
- * Fires an attribute added event.
- *
- * @param event the event to be fired
- */
- protected void fireAttributeAdded(QueryComponentEvent event) {
- for (QueryComponentListener listener : queryComponentListeners) {
- listener.attributeAdded(event);
- }
- }
-
- /**
- * Fires an attribute removed event.
- *
- * @param event the event to be fired
- */
- protected void fireAttributeRemoved(QueryComponentEvent event) {
- for (QueryComponentListener listener : queryComponentListeners) {
- listener.attributeRemoved(event);
- }
- }
-
- /**
- * Fires an filter added event.
- *
- * @param event the event to be fired
- */
- protected void fireFilterAdded(QueryComponentEvent event) {
- for (QueryComponentListener listener : queryComponentListeners) {
- listener.filterAdded(event);
- }
- }
-
- /**
- * Fires an filter removed event.
- *
- * @param event the event to be fired
- */
- protected void fireFilterRemoved(QueryComponentEvent event) {
- for (QueryComponentListener listener : queryComponentListeners) {
- listener.filterRemoved(event);
- }
- }
-
- /**
- * Fires an filter changed event.
- *
- * @param event the event to be fired
- */
- protected void fireFilterChanged(QueryComponentEvent event) {
- for (QueryComponentListener listener : queryComponentListeners) {
- listener.filterChanged(event);
- }
- }
-
- /**
- * Fires an link added event.
- *
- * @param event the event to be fired
- */
- protected void fireLinkAdded(QueryComponentEvent event) {
- for (QueryComponentListener listener : queryComponentListeners) {
- listener.linkAdded(event);
- }
- }
-
- /**
- * Fires an link removed event.
- *
- * @param event the event to be fired
- */
- protected void fireLinkRemoved(QueryComponentEvent event) {
- for (QueryComponentListener listener : queryComponentListeners) {
- listener.linkRemoved(event);
- }
- }
-
- /**
- * Fires an link changed event.
- *
- * @param event the event to be fired
- */
- protected void fireLinkChanged(QueryComponentEvent event) {
- for (QueryComponentListener listener : queryComponentListeners) {
- listener.linkChanged(event);
- }
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/9e08cac0/src/main/java/org/biomart/martservice/config/ui/QueryConfigUIFactory.java
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diff --git a/src/main/java/org/biomart/martservice/config/ui/QueryConfigUIFactory.java b/src/main/java/org/biomart/martservice/config/ui/QueryConfigUIFactory.java
deleted file mode 100644
index d0a740a..0000000
--- a/src/main/java/org/biomart/martservice/config/ui/QueryConfigUIFactory.java
+++ /dev/null
@@ -1,345 +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: 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;
-
-import org.biomart.martservice.MartServiceException;
-import org.ensembl.mart.lib.config.AttributeCollection;
-import org.ensembl.mart.lib.config.AttributeDescription;
-import org.ensembl.mart.lib.config.AttributeGroup;
-import org.ensembl.mart.lib.config.AttributeList;
-import org.ensembl.mart.lib.config.AttributePage;
-import org.ensembl.mart.lib.config.FilterCollection;
-import org.ensembl.mart.lib.config.FilterDescription;
-import org.ensembl.mart.lib.config.FilterGroup;
-import org.ensembl.mart.lib.config.FilterPage;
-
-/**
- * Interface for generating graphical components from <code>DatasetConfig</code>
- * objects.
- *
- * @author David Withers
- */
-public interface QueryConfigUIFactory {
-
- public final static String SINGLE_SELECTION = "SINGLE";
-
- public final static String MULTIPLE_SELECTION = "MULTIPLE";
-
- public final static String LIST_SELECTION = "LIST";
-
- /**
- * 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
- */
- public Component getDatasetConfigUI() throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an array of
- * <code>AttributePage</code>.
- *
- * @param attributePages
- * an array of <code>AttributePage</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getAttributePagesUI(AttributePage[] attributePages,
- Object data) throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an <code>AttributePage</code>.
- *
- * @param attributePage
- * an <code>AttributePage</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getAttributePageUI(AttributePage attributePage, Object data)
- throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an array of
- * <code>AttributeGroup</code>.
- *
- * @param attributeGroups
- * an array of <code>AttributeGroup</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getAttributeGroupsUI(AttributeGroup[] attributeGroups,
- Object data) throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an <code>AttributeGroup</code>.
- *
- * @param attributeGroup
- * an <code>AttributeGroup</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getAttributeGroupUI(AttributeGroup attributeGroup,
- Object data) throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an array of
- * <code>AttributeCollection</code>.
- *
- * @param attributeCollections
- * an array of <code>AttributeCollection</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getAttributeCollectionsUI(
- AttributeCollection[] attributeCollections, Object data)
- throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an
- * <code>AttributeCollection</code>.
- *
- * @param attributeCollection
- * an <code>AttributeCollection</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getAttributeCollectionUI(
- AttributeCollection attributeCollection, Object data)
- throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an array of
- * <code>AttributeDescription</code>.
- *
- * @param attributeDescriptions
- * an array of <code>AttributeDescription</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getAttributeDescriptionsUI(
- AttributeDescription[] attributeDescriptions, Object data)
- throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an
- * <code>AttributeDescription</code>.
- *
- * @param attributeDescription
- * an <code>AttributeDescription</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getAttributeDescriptionUI(
- AttributeDescription attributeDescription, Object data)
- throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an array of
- * <code>AttributeList</code>.
- *
- * @param attributeLists
- * an array of <code>AttributeList</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getAttributeListsUI(
- AttributeList[] attributeLists, Object data)
- throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an
- * <code>AttributeList</code>.
- *
- * @param attributeList
- * an <code>AttributeList</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getAttributeListUI(
- AttributeList attributeList, Object data)
- throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an array of
- * <code>FilterPage</code>.
- *
- * @param filterPages
- * an array of <code>FilterPage</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getFilterPagesUI(FilterPage[] filterPages, Object data)
- throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for a <code>FilterPage</code>.
- *
- * @param filterPage
- * a <code>FilterPage</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getFilterPageUI(FilterPage filterPage, Object data)
- throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an array of
- * <code>FilterGroup</code>.
- *
- * @param filterGroups
- * an array of <code>FilterGroup</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getFilterGroupsUI(FilterGroup[] filterGroups, Object data)
- throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for a <code>FilterGroup</code>.
- *
- * @param filterGroup
- * a <code>FilterGroup</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getFilterGroupUI(FilterGroup filterGroup, Object data)
- throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an array of
- * <code>FilterCollection</code>.
- *
- * @param filterCollections
- * an array of <code>FilterCollection</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getFilterCollectionsUI(
- FilterCollection[] filterCollections, Object data)
- throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for a <code>FilterCollection</code>.
- *
- * @param filterCollection
- * a <code>FilterCollection</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getFilterCollectionUI(FilterCollection filterCollection,
- Object data) throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an array of
- * <code>FilterDescription</code>.
- *
- * @param filterDescriptions
- * an array of <code>FilterDescription</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getFilterDescriptionsUI(
- FilterDescription[] filterDescriptions, Object data)
- throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for a <code>FilterDescription</code>.
- *
- * @param filterDescription
- * a <code>FilterDescription</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getFilterDescriptionUI(
- FilterDescription filterDescription, Object data)
- throws MartServiceException;
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/9e08cac0/src/main/java/org/biomart/martservice/query/Attribute.java
----------------------------------------------------------------------
diff --git a/src/main/java/org/biomart/martservice/query/Attribute.java b/src/main/java/org/biomart/martservice/query/Attribute.java
deleted file mode 100644
index 7ec9932..0000000
--- a/src/main/java/org/biomart/martservice/query/Attribute.java
+++ /dev/null
@@ -1,198 +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: 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;
-
-/**
- * Class for creating attribute elements of mart queries.
- *
- * @author David Withers
- */
-public class Attribute {
- private String name;
-
- private String attributes;
-
- private int attributesCount;
-
- private Dataset containingDataset;
-
- /**
- * Constructs an instance of an <code>Attribute</code> with the specified name.
- *
- * @param name
- * the name of the <code>Attribute</code>; must not be <code>null</code>
- */
- public Attribute(String name) {
- if (name == null) {
- throw new IllegalArgumentException("Parameter 'name' must not be null");
- }
- this.name = name;
- }
-
- /**
- * Constructs an instance of an <code>Attribute</code> which is a copy of
- * another <code>Attribute</code>.
- *
- * @param attribute
- * the <code>Attribute</code> to copy; must not be <code>null</code>
- */
- public Attribute(Attribute attribute) {
- if (attribute == null) {
- throw new IllegalArgumentException("Parameter 'attribute' must not be null");
- }
- setName(attribute.getName());
- setAttributes(attribute.getAttributes());
- }
-
- /**
- * Returns the name of the Attribute.
- *
- * @return the name of the Attribute
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the name of the Attribute.
- *
- * @param name
- * the name of the Attribute; must not be <code>null</code>
- */
- public void setName(String name) {
- if (name == null) {
- throw new IllegalArgumentException("Parameter 'name' must not be null");
- }
- this.name = name;
- }
-
- /**
- * Returns the qualified name of this <code>Attribute</code>.
- *
- * The qualified name is <code>containingDatasetName.attributeName</code>
- * or just <code>attributeName</code> if the <code>Attribute</code> is
- * not in a <code>Dataset</code>.
- *
- * @return the qualified name of this <code>Attribute</code>
- */
- public String getQualifiedName() {
- if (containingDataset == null) {
- return name;
- } else {
- return containingDataset.getName() + "." + getName();
- }
- }
-
- /**
- * Returns the component attributes as a comma separated list.
- *
- * @return the attributes as a comma separated list or null if there are no component attributes
- */
- public String getAttributes() {
- return attributes;
- }
-
- /**
- * Sets the attributes.
- *
- * @param attributes the new attributes
- */
- public void setAttributes(String attributes) {
- this.attributes = attributes;
- if (attributes == null) {
- attributesCount = 0;
- } else {
- attributesCount = attributes.split(",").length;
- }
- }
-
- /**
- * Returns the number of component attributes.
- *
- * @return the number of component attributes
- */
- public int getAttributesCount() {
- return attributesCount;
- }
-
- /**
- * Returns the Dataset containing this Attribute or null if it is not in a
- * Dataset.
- *
- * @return the Dataset containing this Attribute or null if it is not in a
- * Dataset
- */
- public Dataset getContainingDataset() {
- return containingDataset;
- }
-
- /**
- * Sets the containing Dataset.
- *
- * @param dataset
- * the containing Dataset
- */
- void setContainingDataset(Dataset dataset) {
- this.containingDataset = dataset;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see java.lang.Object#equals(java.lang.Object)
- */
- public boolean equals(Object obj) {
- boolean result = false;
- if (obj != null) {
- Attribute attribute = (Attribute) obj;
- String qualifiedName = getQualifiedName();
- if (qualifiedName == null) {
- result = attribute.getQualifiedName() == null;
- } else {
- result = qualifiedName.equals(attribute.getQualifiedName());
- }
- }
- return result;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see java.lang.Object#hashCode()
- */
- public int hashCode() {
- return getQualifiedName().hashCode();
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/9e08cac0/src/main/java/org/biomart/martservice/query/Dataset.java
----------------------------------------------------------------------
diff --git a/src/main/java/org/biomart/martservice/query/Dataset.java b/src/main/java/org/biomart/martservice/query/Dataset.java
deleted file mode 100644
index 20ea68f..0000000
--- a/src/main/java/org/biomart/martservice/query/Dataset.java
+++ /dev/null
@@ -1,309 +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: 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;
-import java.util.List;
-
-/**
- * Class for creating dataset elements of mart queries.
- *
- * @author David Withers
- */
-public class Dataset {
- private String name;
-
- private List<Attribute> attributes = new ArrayList<Attribute>();
-
- private List<Filter> filters = new ArrayList<Filter>();
-
- private Query containingQuery;
-
- /**
- * Constructs an instance of a <code>Dataset</code> with the specified
- * name.
- *
- * @param name
- * the name of the <code>Dataset</code>
- */
- public Dataset(String name) {
- setName(name);
- }
-
- /**
- * 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
- */
- public Dataset(Dataset dataset) {
- setName(dataset.getName());
- for (Attribute attribute : dataset.getAttributes()) {
- addAttribute(new Attribute(attribute));
- }
- for (Filter filter : dataset.getFilters()) {
- addFilter(new Filter(filter));
- }
- }
-
- /**
- * Returns the name of the Dataset.
- *
- * @return the name of the Dataset.
- */
- public String getName() {
- return name;
- }
-
- /**
- * Set the name of the Dataset.
- *
- * @param name
- * the new name for this Dataset.
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * Returns a List of the Attributes in this dataset.
- *
- * @return a List of the Attributes in this dataset
- */
- public List<Attribute> getAttributes() {
- return new ArrayList<Attribute>(attributes);
- }
-
- /**
- * 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
- */
- public boolean addAttribute(Attribute attribute) {
- if (!attributes.contains(attribute)) {
- attributes.add(attribute);
- attribute.setContainingDataset(this);
- if (containingQuery != null) {
- containingQuery.fireAttributeAdded(attribute, this);
- }
- return true;
- } else {
- return false;
- }
- }
-
- /**
- * Adds an array of Attributes to the dataset.
- *
- * @param attributeArray
- * the array of Attributes to add
- */
- public void addAttributes(Attribute[] attributeArray) {
- for (int i = 0; i < attributeArray.length; i++) {
- addAttribute(attributeArray[i]);
- }
- }
-
- /**
- * Returns true if attribute is in the dataset.
- *
- * @param attribute
- * @return true if attribute is in the dataset.
- */
- public boolean hasAttribute(Attribute attribute) {
- return attributes.contains(attribute);
- }
-
- /**
- * Returns true if the dataset contains any Attributes.
- *
- * @return true if the dataset contains any Attributes
- */
- public boolean hasAttributes() {
- return attributes.size() > 0;
- }
-
- /**
- * 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
- */
- public boolean removeAttribute(Attribute attribute) {
- if (attributes.remove(attribute)) {
- attribute.setContainingDataset(null);
- if (containingQuery != null) {
- containingQuery.fireAttributeRemoved(attribute, this);
- }
- return true;
- } else {
- return false;
- }
- }
-
- /**
- * Removes all the Attributes from this dataset.
- */
- public void removeAllAttributes() {
- for (Attribute attribute : getAttributes()) {
- removeAttribute(attribute);
- }
- }
-
- /**
- * Returns a List of the Filters in this dataset.
- *
- * @return a List of the Filters in this dataset
- */
- public List<Filter> getFilters() {
- return new ArrayList<Filter>(filters);
- }
-
- /**
- * 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
- */
- public boolean addFilter(Filter filter) {
- if (!filters.contains(filter)) {
- filters.add(filter);
- filter.setContainingDataset(this);
- if (containingQuery != null) {
- containingQuery.fireFilterAdded(filter, this);
- }
- return true;
- } else {
- return false;
- }
- }
-
- /**
- * Adds an array of Filters to the dataset.
- *
- * @param filterArray
- * the array of Filters to add
- */
- public void addFilters(Filter[] filterArray) {
- for (int i = 0; i < filterArray.length; i++) {
- addFilter(filterArray[i]);
- }
- }
-
- /**
- * Returns true if filter is in the dataset.
- *
- * @param filter
- * @return true if filter is in the dataset
- */
- public boolean hasFilter(Filter filter) {
- return filters.contains(filter);
- }
-
- /**
- * Returns true if the dataset contains any filters.
- *
- * @return true if the dataset contains any filters
- */
- public boolean hasFilters() {
- return filters.size() > 0;
- }
-
- /**
- * 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
- */
- public boolean removeFilter(Filter filter) {
- if (filters.remove(filter)) {
- filter.setContainingDataset(null);
- if (containingQuery != null) {
- containingQuery.fireFilterRemoved(filter, this);
- }
- return true;
- } else {
- return false;
- }
- }
-
- /**
- * Removes all the filters from the dataset.
- */
- public void removeAllFilters() {
- for (Filter filter : getFilters()) {
- removeFilter(filter);
- }
- }
-
- /**
- * Returns the containingQuery.
- *
- * @return the containingQuery.
- */
- public Query getContainingQuery() {
- return containingQuery;
- }
-
- /**
- * Sets the containingQuery.
- *
- * @param containingQuery
- * the containingQuery to set.
- */
- void setContainingQuery(Query containingQuery) {
- this.containingQuery = containingQuery;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/9e08cac0/src/main/java/org/biomart/martservice/query/Filter.java
----------------------------------------------------------------------
diff --git a/src/main/java/org/biomart/martservice/query/Filter.java b/src/main/java/org/biomart/martservice/query/Filter.java
deleted file mode 100644
index 1c088d0..0000000
--- a/src/main/java/org/biomart/martservice/query/Filter.java
+++ /dev/null
@@ -1,243 +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: 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 {
- private String name;
-
- private String value;
-
- private boolean booleanFilter;
-
- private boolean listFilter;
-
- private Dataset containingDataset;
-
- /**
- * 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>
- */
- public Filter(String name) {
- this(name, null);
- }
-
- /**
- * 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
- * the value of the <code>Filter</code>
- */
- public Filter(String name, String value) {
- this(name, value, false);
- }
-
- /**
- * 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
- * the value of the <code>Filter</code>
- * @param booleanFilter
- */
- public Filter(String name, String value, boolean booleanFilter) {
- if (name == null) {
- throw new IllegalArgumentException("Parameter 'name' must not be null");
- }
- this.name = name;
- this.value = value;
- this.booleanFilter = booleanFilter;
- }
-
- /**
- * 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>
- */
- public Filter(Filter filter) {
- if (filter == null) {
- throw new IllegalArgumentException("Parameter 'filter' must not be null");
- }
- this.name = filter.name;
- this.value = filter.value;
- this.booleanFilter = filter.booleanFilter;
- }
-
- /**
- * Returns the name of the Filter.
- *
- * @return the name of the Filter
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the name of the Filter.
- *
- * @param name
- * the name of the Filter; must not be <code>null</code>
- */
- public void setName(String name) {
- if (name == null) {
- throw new IllegalArgumentException("Parameter 'name' must not be null");
- }
- this.name = name;
- }
-
- /**
- * 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() {
- if (containingDataset == null) {
- return name;
- } else {
- return containingDataset.getName() + "." + getName();
- }
- }
-
- /**
- * 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>
- */
- public Dataset getContainingDataset() {
- return containingDataset;
- }
-
- /**
- * Sets the containing <code>Dataset</code>.
- *
- * @param dataset
- * the containing <code>Dataset</code>
- */
- void setContainingDataset(Dataset dataset) {
- this.containingDataset = dataset;
- }
-
- /**
- * Returns the value.
- *
- * @return the value.
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value.
- *
- * @param value
- * the value to set.
- */
- public void setValue(String value) {
- boolean valueChanged = false;
- if (this.value == null) {
- if (value != null) {
- this.value = value;
- valueChanged = true;
- }
- } else if (!this.value.equals(value)) {
- this.value = value;
- valueChanged = true;
- }
- if (valueChanged) {
- if (containingDataset != null) {
- if (containingDataset.getContainingQuery() != null) {
- containingDataset.getContainingQuery().fireFilterChanged(
- this, containingDataset);
- }
- }
- }
- }
-
- /**
- * Returns <code>true</code> if this is a boolean filter.
- *
- * @return <code>true</code> if this is a boolean filter.
- */
- public boolean isBoolean() {
- return booleanFilter;
- }
-
- /**
- * Sets the booleanFilter flag.
- *
- * @param booleanFilter
- */
- public void setBoolean(boolean booleanFilter) {
- this.booleanFilter = booleanFilter;
- }
-
- /**
- * Returns <code>true</code> if this is a list filter.
- *
- * @return <code>true</code> if this is a list filter.
- */
- public boolean isList() {
- return listFilter;
- }
-
- /**
- * Sets the listFilter flag.
- *
- * @param listFilter
- */
- public void setList(boolean listFilter) {
- this.listFilter = listFilter;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/9e08cac0/src/main/java/org/biomart/martservice/query/Link.java
----------------------------------------------------------------------
diff --git a/src/main/java/org/biomart/martservice/query/Link.java b/src/main/java/org/biomart/martservice/query/Link.java
deleted file mode 100644
index 721428c..0000000
--- a/src/main/java/org/biomart/martservice/query/Link.java
+++ /dev/null
@@ -1,181 +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: 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 {
- private String source;
-
- private String target;
-
- private String defaultLink;
-
- private Query containingQuery;
-
- /**
- * Constructs an instance of a <code>Link</code>.
- *
- * @param source
- * the source dataset of the <code>Link</code>
- * @param target
- * the target dataset of the <code>Link</code>
- * @param defaultLink
- * the ID the links the datasets
- */
- public Link(String source, String target, String defaultLink) {
- this.source = source;
- this.target = target;
- this.defaultLink = defaultLink;
- }
-
- /**
- * 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
- */
- public Link(Link link) {
- this.source = link.source;
- this.target = link.target;
- this.defaultLink = link.defaultLink;
- }
-
- /**
- * Returns the defaultLink.
- *
- * @return the defaultLink.
- */
- public String getDefaultLink() {
- return defaultLink;
- }
-
- /**
- * @param defaultLink
- * the defaultLink to set.
- */
- public void setDefaultLink(String defaultLink) {
- this.defaultLink = defaultLink;
- }
-
- /**
- * Returns the source dataset.
- *
- * @return the source dataset.
- */
- public String getSource() {
- return source;
- }
-
- /**
- * Sets the source dataset.
- *
- * @param source
- * the source dataset to set.
- */
- public void setSource(String source) {
- this.source = source;
- }
-
- /**
- * Returns the target dataset.
- *
- * @return the target dataset.
- */
- public String getTarget() {
- return target;
- }
-
- /**
- * Sets the target dataset.
- *
- * @param target
- * the target dataset to set.
- */
- public void setTarget(String target) {
- this.target = target;
- }
-
- /**
- * Returns the containingQuery.
- *
- * @return the containingQuery.
- */
- public Query getContainingQuery() {
- return containingQuery;
- }
-
- /**
- * Sets the containingQuery.
- *
- * @param containingQuery
- * the containingQuery to set.
- */
- void setContainingQuery(Query containingQuery) {
- this.containingQuery = containingQuery;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see java.lang.Object#equals(java.lang.Object)
- */
- public boolean equals(Object obj) {
- boolean result = false;
- if (obj != null) {
- Link link = (Link) obj;
- result = ((source == null && link.source == null) || source
- .equals(link.source))
- && ((target == null && link.target == null) || target
- .equals(link.target))
- && ((defaultLink == null && link.defaultLink == null) || defaultLink
- .equals(link.defaultLink));
- }
- return result;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see java.lang.Object#hashCode()
- */
- public int hashCode() {
- return source.hashCode() + target.hashCode() + defaultLink.hashCode();
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/9e08cac0/src/main/java/org/biomart/martservice/query/Query.java
----------------------------------------------------------------------
diff --git a/src/main/java/org/biomart/martservice/query/Query.java b/src/main/java/org/biomart/martservice/query/Query.java
deleted file mode 100644
index c7c9f20..0000000
--- a/src/main/java/org/biomart/martservice/query/Query.java
+++ /dev/null
@@ -1,555 +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: 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;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.biomart.martservice.MartServiceException;
-
-/**
- * Class for creating mart queries.
- *
- * @author David Withers
- */
-public class Query {
- private String virtualSchemaName;
-
- private int count;
-
- private int uniqueRows;
-
- private String softwareVersion;
-
- private String formatter;
-
- private String requestId;
-
- private List<Dataset> datasets = new ArrayList<Dataset>();
-
- private Map<String, Dataset> datasetMap = new HashMap<String, Dataset>();
-
- private Set<Link> links = new HashSet<Link>();
-
- private Map<String, Link> linkSourceMap = new HashMap<String, Link>();
-
- private List<QueryListener> listeners = new ArrayList<QueryListener>();
-
- /**
- * 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) {
- this(virtualSchemaName, 0);
- }
-
- /**
- * Constructs an instance of a <code>Query</code> with the specified
- * <code>virtualSchemaName</code> and <code>count</code>.
- *
- * @param virtualSchemaName
- * @param count
- */
- public Query(String virtualSchemaName, int count) {
- setVirtualSchemaName(virtualSchemaName);
- setCount(count);
- }
-
- /**
- * 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
- */
- public Query(String virtualSchemaName, String softwareVersion,
- String requestId) {
- this(virtualSchemaName, 0, softwareVersion, requestId);
- }
-
- /**
- * 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
- */
- public Query(String virtualSchemaName, int count, String softwareVersion) {
- this(virtualSchemaName, count, softwareVersion, null);
- }
-
- /**
- * 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
- * @param requestId
- */
- public Query(String virtualSchemaName, int count, String softwareVersion,
- String requestId) {
- setVirtualSchemaName(virtualSchemaName);
- setCount(count);
- setSoftwareVersion(softwareVersion);
- setRequestId(requestId);
- }
-
- /**
- * 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
- */
- public Query(Query query) {
- setVirtualSchemaName(query.virtualSchemaName);
- setCount(query.count);
- setUniqueRows(query.uniqueRows);
- setSoftwareVersion(query.softwareVersion);
- setFormatter(query.formatter);
- setRequestId(query.requestId);
- for (Dataset dataset : query.getDatasets()) {
- addDataset(new Dataset(dataset));
- }
- for (Link link : query.getLinks()) {
- addLink(new Link(link));
- }
- }
-
- /**
- * Returns the virtualSchema.
- *
- * @return the virtualSchema.
- */
- public String getVirtualSchemaName() {
- return virtualSchemaName;
- }
-
- /**
- * Sets the virtualSchema.
- *
- * @param virtualSchemaName
- * the virtualSchema to set.
- */
- public void setVirtualSchemaName(String virtualSchemaName) {
- this.virtualSchemaName = virtualSchemaName;
- }
-
- /**
- * Returns the count.
- *
- * @return the count.
- */
- public int getCount() {
- return count;
- }
-
- /**
- * Sets the count.
- *
- * @param count
- * the count to set.
- */
- public void setCount(int count) {
- this.count = count;
- }
-
- /**
- * Returns the uniqueRows query attribute
- *
- * @return the uniqueRows query attribute
- */
- public int getUniqueRows() {
- return uniqueRows;
- }
-
- /**
- * Sets the uniqueRows query attribute.
- *
- * Valid values are 0 or 1.
- *
- * @param uniqueRows value for the uniqueRows query attribute
- */
- public void setUniqueRows(int uniqueRows) {
- this.uniqueRows = uniqueRows;
- }
-
- /**
- * Returns the softwareVersion.
- *
- * @return the softwareVersion
- */
- public String getSoftwareVersion() {
- return softwareVersion;
- }
-
- /**
- * Sets the softwareVersion.
- *
- * @param softwareVersion
- * the new softwareVersion
- */
- public void setSoftwareVersion(String softwareVersion) {
- this.softwareVersion = softwareVersion;
- }
-
- /**
- * Returns the formatter.
- *
- * @return the formatter
- */
- public String getFormatter() {
- return formatter;
- }
-
- /**
- * Sets the formatter.
- *
- * @param formatter the new formatter
- */
- public void setFormatter(String formatter) {
- if (this.formatter == null) {
- if (formatter != null) {
- this.formatter = formatter;
- fireFormatterAdded(formatter);
- }
- } else if (!this.formatter.equals(formatter)) {
- if (formatter == null) {
- String removedFormatter = this.formatter;
- this.formatter = formatter;
- fireFormatterRemoved(removedFormatter);
- } else {
- this.formatter = formatter;
- fireFormatterChanged(formatter);
- }
- }
- }
-
- /**
- * Returns the requestId.
- *
- * @return the requestId
- */
- public String getRequestId() {
- return requestId;
- }
-
- /**
- * Sets the requestId.
- *
- * @param requestId
- * the new requestId
- */
- public void setRequestId(String requestId) {
- this.requestId = requestId;
- }
-
- /**
- * Adds a Dataset to the Query.
- *
- * The Dataset is added at the end of the list of Datasets.
- *
- * @param dataset
- * the Dataset to add
- */
- public void addDataset(Dataset dataset) {
- addDataset(datasets.size(), dataset);
- }
-
- /**
- * Adds a Dataset to the Query at the specified position.
- *
- * @param index
- * the position to add the Dataset
- * @param dataset
- * the Dataset to add
- */
- public void addDataset(int index, Dataset dataset) {
- datasets.add(index, dataset);
- datasetMap.put(dataset.getName(), dataset);
- if (dataset.getContainingQuery() != null) {
- dataset.getContainingQuery().removeDataset(dataset);
- }
- dataset.setContainingQuery(this);
- }
-
- /**
- * Removes a Dataset from the Query.
- *
- * @param dataset
- * the Dataset to remove
- */
- public void removeDataset(Dataset dataset) {
- datasets.remove(dataset);
- datasetMap.remove(dataset.getName());
- dataset.setContainingQuery(null);
- }
-
- /**
- * Removes all the Datasets from the Query.
- */
- public void removeAllDatasets() {
- for (Dataset dataset : datasets) {
- dataset.setContainingQuery(null);
- }
- datasets.clear();
- datasetMap.clear();
- }
-
- /**
- * Returns the Datasets that this Query contains.
- *
- * @return the Datasets that this Query contains.
- */
- public List<Dataset> getDatasets() {
- return new ArrayList<Dataset>(datasets);
- }
-
- /**
- * 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
- */
- public Dataset getDataset(String datasetName) {
- return (Dataset) datasetMap.get(datasetName);
- }
-
- /**
- * 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>.
- */
- public boolean containsDataset(String datasetName) {
- return datasetMap.containsKey(datasetName);
- }
-
- /**
- * Adds a Link to the Query.
- *
- * @param link
- * the Link to add
- */
- public void addLink(Link link) {
- links.add(link);
- linkSourceMap.put(link.getSource(), link);
- if (link.getContainingQuery() != null) {
- link.getContainingQuery().removeLink(link);
- }
- link.setContainingQuery(this);
- }
-
- /**
- * Removes a link from the Query
- *
- * @param link
- * the Link to remove
- */
- public void removeLink(Link link) {
- links.remove(link);
- linkSourceMap.remove(link.getSource());
- link.setContainingQuery(null);
- }
-
- /**
- * Returns the Links that this Query contains.
- *
- * @return the Links that this Query contains.
- */
- public Set<Link> getLinks() {
- return new HashSet<Link>(links);
- }
-
- /**
- * 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
- */
- public Link getLink(String source) {
- return (Link) linkSourceMap.get(source);
- }
-
- /**
- * 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.
- */
- public boolean containsLink(String source) {
- return linkSourceMap.containsKey(source);
- }
-
- /**
- * 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
- */
- public Set<Link> getLinks(String target) {
- Set<Link> result = new HashSet<Link>();
- Set<Link> links = getLinks();
- for (Link link: links) {
- if (link.getTarget().equals(target)) {
- result.add(link);
- }
- }
- return result;
- }
-
- /**
- * 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() {
- List<Attribute> attributes = new ArrayList<Attribute>();
- for (Dataset dataset : datasets) {
- attributes.addAll(dataset.getAttributes());
- }
- return attributes;
- }
-
- /**
- * 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() {
- List<Filter> filters = new ArrayList<Filter>();
- for (Dataset dataset : datasets) {
- filters.addAll(dataset.getFilters());
- }
- return filters;
- }
-
- /**
- * 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
- */
- public void addQueryListener(QueryListener listener) {
- if (listener != null) {
- listeners.add(listener);
- }
- }
-
- /**
- * Removes the specified query listener so that it no longer receives query
- * events. This method performs no function, nor 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 listener
- */
- public void removeQueryListener(QueryListener listener) {
- listeners.remove(listener);
- }
-
- void fireAttributeAdded(Attribute attribute, Dataset dataset) {
- for (QueryListener listener : listeners) {
- listener.attributeAdded(attribute, dataset);
- }
- }
-
- void fireAttributeRemoved(Attribute attribute, Dataset dataset) {
- for (QueryListener listener : listeners) {
- listener.attributeRemoved(attribute, dataset);
- }
- }
-
- void fireFilterAdded(Filter filter, Dataset dataset) {
- for (QueryListener listener : listeners) {
- listener.filterAdded(filter, dataset);
- }
- }
-
- void fireFilterRemoved(Filter filter, Dataset dataset) {
- for (QueryListener listener : listeners) {
- listener.filterRemoved(filter, dataset);
- }
- }
-
- void fireFilterChanged(Filter filter, Dataset dataset) {
- for (QueryListener listener : listeners) {
- listener.filterChanged(filter, dataset);
- }
- }
-
- void fireFormatterAdded(String formatter) {
- for (QueryListener listener : listeners) {
- listener.formatterAdded(formatter);
- }
- }
-
- void fireFormatterRemoved(String formatter) {
- for (QueryListener listener : listeners) {
- listener.formatterRemoved(formatter);
- }
- }
-
- void fireFormatterChanged(String formatter) {
- for (QueryListener listener : listeners) {
- listener.formatterChanged(formatter);
- }
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/9e08cac0/src/main/java/org/biomart/martservice/query/QueryListener.java
----------------------------------------------------------------------
diff --git a/src/main/java/org/biomart/martservice/query/QueryListener.java b/src/main/java/org/biomart/martservice/query/QueryListener.java
deleted file mode 100644
index 9f10f45..0000000
--- a/src/main/java/org/biomart/martservice/query/QueryListener.java
+++ /dev/null
@@ -1,108 +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: 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.
- */
- public void attributeAdded(Attribute attribute, Dataset dataset);
-
- /**
- * Invoked when an <code>Attribute</code> is removed from a
- * <code>Query</code>.
- *
- * @param attribute
- * the <code>Attribute</code> removed.
- */
- public void attributeRemoved(Attribute attribute, Dataset dataset);
-
- /**
- * Invoked when a <code>Filter</code> is added to a <code>Query</code>.
- *
- * @param filter
- * the <code>Filter</code> added.
- */
- public void filterAdded(Filter filter, Dataset dataset);
-
- /**
- * Invoked when a <code>Filter</code> is removed from a <code>Query</code>.
- *
- * @param filter
- * the <code>Filter</code> removed.
- */
- public void filterRemoved(Filter filter, Dataset dataset);
-
- /**
- * Invoked when the value of a <code>Filter</code> is changed.
- *
- * @param filter
- * the <code>Filter</code> whose value has changed.
- */
- public void filterChanged(Filter filter, Dataset dataset);
-
- /**
- * Invoked when a formatter is added to a <code>Query</code>.
- *
- * @param formatter
- * the formatter added.
- */
- public void formatterAdded(String formatter);
-
- /**
- * Invoked when a formatter is removed from a <code>Query</code>.
- *
- * @param formatter
- * the formatter removed.
- */
- public void formatterRemoved(String formatter);
-
- /**
- * Invoked when the value of the formatter is changed.
- *
- * @param filter
- * the new value of the formatter.
- */
- public void formatterChanged(String formatter);
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/9e08cac0/src/main/java/org/biomart/martservice/query/QueryXMLHandler.java
----------------------------------------------------------------------
diff --git a/src/main/java/org/biomart/martservice/query/QueryXMLHandler.java b/src/main/java/org/biomart/martservice/query/QueryXMLHandler.java
deleted file mode 100644
index 13c7791..0000000
--- a/src/main/java/org/biomart/martservice/query/QueryXMLHandler.java
+++ /dev/null
@@ -1,332 +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: QueryXMLHandler.java,v $
- * Revision $Revision: 1.6 $
- * Release status $State: Exp $
- * Last modified on $Date: 2008/03/04 16:45:18 $
- * by $Author: davidwithers $
- * Created on 28-Apr-2006
- *****************************************************************/
-package org.biomart.martservice.query;
-
-import java.util.List;
-
-import org.jdom.Element;
-import org.jdom.Namespace;
-
-/**
- * Utility class for serializing <code>Query</code> classes to XML.
- *
- * @author David Withers
- */
-public class QueryXMLHandler {
- public static final String QUERY_ELEMENT = "Query";
-
- public static final String DATASET_ELEMENT = "Dataset";
-
- public static final String ATTRIBUTE_ELEMENT = "Attribute";
-
- public static final String FILTER_ELEMENT = "Filter";
-
- public static final String LINK_ELEMENT = "Links";
-
- public static final String ATTRIBUTES_ATTRIBUTE = "attributes";
-
- public static final String NAME_ATTRIBUTE = "name";
-
- public static final String COUNT_ATTRIBUTE = "count";
-
- public static final String UNIQUE_ROWS_ATTRIBUTE = "uniqueRows";
-
- public static final String VERSION_ATTRIBUTE = "softwareVersion";
-
- public static final String FORMATTER_ATTRIBUTE = "formatter";
-
- public static final String HEADER_ATTRIBUTE = "header";
-
- public static final String REQUEST_ID_ATTRIBUTE = "requestId";
-
- public static final String SCHEMA_ATTRIBUTE = "virtualSchemaName";
-
- /**
- * Converts a <code>Query</code> to an XML element.
- *
- * @param query
- * the <code>Query</code> to serialize
- * @param namespace
- * the <code>Namespace</code> to use when constructing the
- * <code>Element</code>
- * @return an XML serialization of the <code>Query</code>
- */
- public static Element queryToElement(Query query, Namespace namespace) {
- Element queryElement = new Element(QUERY_ELEMENT, namespace);
- String virtualSchemaName = query.getVirtualSchemaName();
- if (virtualSchemaName == null) {
- queryElement.setAttribute(SCHEMA_ATTRIBUTE, "default");
- } else {
- queryElement.setAttribute(SCHEMA_ATTRIBUTE, virtualSchemaName);
- }
- queryElement.setAttribute(COUNT_ATTRIBUTE, String.valueOf(query.getCount()));
- queryElement.setAttribute(UNIQUE_ROWS_ATTRIBUTE, String.valueOf(query.getUniqueRows()));
- String softwareVersion = query.getSoftwareVersion();
- if (softwareVersion != null) {
- queryElement.setAttribute(VERSION_ATTRIBUTE, softwareVersion);
- }
- String formatter = query.getFormatter();
- if (formatter != null) {
- queryElement.setAttribute(FORMATTER_ATTRIBUTE, formatter);
- queryElement.setAttribute(HEADER_ATTRIBUTE, "1");
- }
- String requestId = query.getRequestId();
- if (requestId != null) {
- queryElement.setAttribute(REQUEST_ID_ATTRIBUTE, requestId);
- }
- for (Dataset dataset : query.getDatasets()) {
- queryElement.addContent(datasetToElement(dataset, namespace));
- }
- for (Link link : query.getLinks()) {
- queryElement.addContent(linkToElement(link, namespace));
- }
-
- return queryElement;
- }
-
- /**
- * Converts a <code>Dataset</code> to an XML element.
- *
- * @param dataset
- * the <code>Dataset</code> to serialize
- * @param namespace
- * the <code>Namespace</code> to use when constructing the
- * <code>Element</code>
- * @return an XML serialization of the <code>Dataset</code>
- */
- public static Element datasetToElement(Dataset dataset, Namespace namespace) {
- Element datasetElement = new Element(DATASET_ELEMENT, namespace);
- datasetElement.setAttribute(NAME_ATTRIBUTE, dataset.getName());
-
- for (Attribute attribute : dataset.getAttributes()) {
- datasetElement.addContent(attributeToElement(attribute, namespace));
- }
-
- for (Filter filter : dataset.getFilters()) {
- datasetElement.addContent(filterToElement(filter, namespace));
- }
-
- return datasetElement;
- }
-
- /**
- * Converts a <code>Link</code> to an XML element.
- *
- * @param link
- * the <code>Link</code> to serialize
- * @param namespace
- * the <code>Namespace</code> to use when constructing the
- * <code>Element</code>
- * @return an XML serialization of the <code>Link</code>
- */
- public static Element linkToElement(Link link, Namespace namespace) {
- Element linkElement = new Element(LINK_ELEMENT, namespace);
- linkElement.setAttribute("source", link.getSource());
- linkElement.setAttribute("target", link.getTarget());
- linkElement.setAttribute("defaultLink", link.getDefaultLink());
- return linkElement;
- }
-
- /**
- * Converts an <code>Attribute</code> to an XML element.
- *
- * @param attribute
- * the <code>Attribute</code> to serialize
- * @param namespace
- * the <code>Namespace</code> to use when constructing the
- * <code>Element</code>
- * @return an XML serialization of the <code>Attribute</code>
- */
- public static Element attributeToElement(Attribute attribute,
- Namespace namespace) {
- Element attributeElement = new Element(ATTRIBUTE_ELEMENT, namespace);
- attributeElement.setAttribute(NAME_ATTRIBUTE, attribute.getName());
- String attributes = attribute.getAttributes();
- if (attributes != null) {
- attributeElement.setAttribute(ATTRIBUTES_ATTRIBUTE, attributes);
- }
- return attributeElement;
- }
-
- /**
- * Converts a <code>Filter</code> to an XML element.
- *
- * @param filter
- * the <code>Filter</code> to serialize
- * @param namespace
- * the <code>Namespace</code> to use when constructing the
- * <code>Element</code>
- * @return an XML serialization of the <code>Filter</code>
- */
- public static Element filterToElement(Filter filter, Namespace namespace) {
- Element filterElement = new Element(FILTER_ELEMENT, namespace);
- filterElement.setAttribute(NAME_ATTRIBUTE, filter.getName());
- String value = filter.getValue();
- if (filter.isBoolean()) {
- if ("excluded".equalsIgnoreCase(value)) {
- filterElement.setAttribute("excluded", "1");
- } else {
- filterElement.setAttribute("excluded", "0");
- }
- } else {
- if (value == null) {
- filterElement.setAttribute("value", "");
- } else {
- filterElement.setAttribute("value", value);
- }
- }
- if (filter.isList()) {
- filterElement.setAttribute("list", "true");
- }
- return filterElement;
- }
-
- /**
- * Creates a <code>Query</code> from an XML element.
- *
- * @param element
- * the <code>Element</code> to deserialize
- * @param namespace
- * the <code>Namespace</code> containing the
- * <code>Element</code>
- * @return a deserialized <code>Query</code>
- */
- public static Query elementToQuery(Element element, Namespace namespace) {
- String virtualSchema = element.getAttributeValue(SCHEMA_ATTRIBUTE);
- int count = Integer.parseInt(element.getAttributeValue(COUNT_ATTRIBUTE));
- String version = element.getAttributeValue(VERSION_ATTRIBUTE);
- String formatter = element.getAttributeValue(FORMATTER_ATTRIBUTE);
- String requestId = element.getAttributeValue(REQUEST_ID_ATTRIBUTE);
- Query query = new Query(virtualSchema, count, version, requestId);
- query.setFormatter(formatter);
- String uniqueRows = element.getAttributeValue(UNIQUE_ROWS_ATTRIBUTE);
- if (uniqueRows != null) {
- query.setUniqueRows(Integer.parseInt(uniqueRows));
- }
- List<Element> datasets = element.getChildren(DATASET_ELEMENT, namespace);
- for (Element datasetElement : datasets) {
- query.addDataset(elementToDataset(datasetElement, namespace));
- }
- List<Element> links = element.getChildren(LINK_ELEMENT, namespace);
- for (Element linkElement : links) {
- query.addLink(elementToLink(linkElement));
- }
- return query;
- }
-
- /**
- * Creates a <code>Dataset</code> from an XML element.
- *
- * @param element
- * the <code>Element</code> to deserialize
- * @param namespace
- * the <code>Namespace</code> containing the
- * <code>Element</code>
- * @return a deserialized <code>Dataset</code>
- */
- public static Dataset elementToDataset(Element element, Namespace namespace) {
- Dataset dataset = new Dataset(element.getAttributeValue(NAME_ATTRIBUTE));
-
- List<Element> attributes = element.getChildren(ATTRIBUTE_ELEMENT, namespace);
- for (Element attributeElement : attributes) {
- dataset.addAttribute(elementToAttribute(attributeElement));
- }
-
- List<Element> filters = element.getChildren(FILTER_ELEMENT, namespace);
- for (Element filterElement : filters) {
- dataset.addFilter(elementToFilter(filterElement));
- }
- return dataset;
- }
-
- /**
- * Creates a <code>Filter</code> from an XML element.
- *
- * @param element
- * the <code>Element</code> to deserialize
- * @return a deserialized <code>Filter</code>
- */
- public static Filter elementToFilter(Element element) {
- Filter filter;
- String filterName = element.getAttributeValue(NAME_ATTRIBUTE);
- String filterValue = element.getAttributeValue("value");
- if (filterValue != null) {
- filter = new Filter(filterName, filterValue);
- } else {
- filterValue = element.getAttributeValue("excluded");
- if ("1".equals(filterValue)) {
- filter = new Filter(filterName, "excluded", true);
- } else {
- filter = new Filter(filterName, "only", true);
- }
- }
- String listValue = element.getAttributeValue("list");
- if ("true".equals(listValue)) {
- filter.setList(true);
- }
- return filter;
- }
-
- /**
- * Creates an <code>Attribute</code> from an XML element.
- *
- * @param element
- * the <code>Element</code> to deserialize
- * @return a deserialized <code>Attribute</code>
- */
- public static Attribute elementToAttribute(Element element) {
- String attributeName = element.getAttributeValue(NAME_ATTRIBUTE);
- Attribute attribute = new Attribute(attributeName);
- String attributes = element.getAttributeValue(ATTRIBUTES_ATTRIBUTE);
- if (attributes != null) {
- attribute.setAttributes(attributes);
- }
- return attribute;
- }
-
- /**
- * Creates an <code>Link</code> from an XML element.
- *
- * @param element
- * the <code>Element</code> to deserialize
- * @return a deserialized <code>Link</code>
- * @deprecated MartJ 0.5 won't require links to be specified
- */
- public static Link elementToLink(Element element) {
- return new Link(element.getAttributeValue("source"), element
- .getAttributeValue("target"), element
- .getAttributeValue("defaultLink"));
- }
-
-}
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