Author: mes
Date: 2010-10-05 13:52:43 -0700 (Tue, 05 Oct 2010)
New Revision: 22149
Added:
core3/property-impl/trunk/
core3/property-impl/trunk/osgi.bnd
core3/property-impl/trunk/pom.xml
core3/property-impl/trunk/src/
core3/property-impl/trunk/src/main/
core3/property-impl/trunk/src/main/java/
core3/property-impl/trunk/src/main/java/org/
core3/property-impl/trunk/src/main/java/org/cytoscape/
core3/property-impl/trunk/src/main/java/org/cytoscape/property/
core3/property-impl/trunk/src/main/java/org/cytoscape/property/internal/
core3/property-impl/trunk/src/main/java/org/cytoscape/property/internal/PropsReader.java
core3/property-impl/trunk/src/main/java/org/cytoscape/property/internal/bookmark/
core3/property-impl/trunk/src/main/java/org/cytoscape/property/internal/bookmark/BookmarkReader.java
core3/property-impl/trunk/src/main/java/org/cytoscape/property/internal/bookmark/BookmarksUtilImpl.java
core3/property-impl/trunk/src/main/resources/
core3/property-impl/trunk/src/main/resources/META-INF/
core3/property-impl/trunk/src/main/resources/META-INF/spring/
core3/property-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
core3/property-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
core3/property-impl/trunk/src/main/resources/bookmarks.xml
core3/property-impl/trunk/src/main/resources/cytoscape.props
Log:
initial import
Added: core3/property-impl/trunk/osgi.bnd
===================================================================
--- core3/property-impl/trunk/osgi.bnd (rev 0)
+++ core3/property-impl/trunk/osgi.bnd 2010-10-05 20:52:43 UTC (rev 22149)
@@ -0,0 +1,7 @@
+#-----------------------------------------------------------------
+# Use this file to add customized Bnd instructions for the bundle
+#-----------------------------------------------------------------
+
+Import-Package: *
+Private-Package: ${bundle.namespace}, ${bundle.namespace}.*
+
Added: core3/property-impl/trunk/pom.xml
===================================================================
--- core3/property-impl/trunk/pom.xml (rev 0)
+++ core3/property-impl/trunk/pom.xml 2010-10-05 20:52:43 UTC (rev 22149)
@@ -0,0 +1,73 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
+ xmlns="http://maven.apache.org/POM/4.0.0";
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/maven-v4_0_0.xsd";>
+
+ <parent>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>parent</artifactId>
+ <version>1.0-SNAPSHOT</version>
+ </parent>
+
+ <properties>
+
<bundle.symbolicName>org.cytoscape.property.internal</bundle.symbolicName>
+
<bundle.namespace>org.cytoscape.property.internal</bundle.namespace>
+ </properties>
+
+ <modelVersion>4.0.0</modelVersion>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>property-impl</artifactId>
+ <version>1.0-SNAPSHOT</version>
+
+ <name>${bundle.symbolicName}</name>
+
+ <packaging>bundle</packaging>
+
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.ops4j</groupId>
+ <artifactId>maven-pax-plugin</artifactId>
+ <version>1.4</version>
+ <!--
+ | enable improved OSGi compilation
support for the bundle
+ life-cycle. | to switch back to the
standard bundle life-cycle,
+ move this setting | down to the
maven-bundle-plugin section
+ -->
+ <extensions>true</extensions>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.felix</groupId>
+ <artifactId>maven-bundle-plugin</artifactId>
+ <version>1.4.3</version>
+ <!--
+ | the following instructions build a
simple set of public/private
+ classes into an OSGi bundle
+ -->
+ <configuration>
+ <instructions>
+
<Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName>
+
<Bundle-Version>${pom.version}</Bundle-Version>
+ <_include>-osgi.bnd</_include>
+ </instructions>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+ <dependencies>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>property-api</artifactId>
+ <version>1.0-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>${junit.version}</version>
+ <scope>test</scope>
+ </dependency>
+ </dependencies>
+
+</project>
+
Added:
core3/property-impl/trunk/src/main/java/org/cytoscape/property/internal/PropsReader.java
===================================================================
---
core3/property-impl/trunk/src/main/java/org/cytoscape/property/internal/PropsReader.java
(rev 0)
+++
core3/property-impl/trunk/src/main/java/org/cytoscape/property/internal/PropsReader.java
2010-10-05 20:52:43 UTC (rev 22149)
@@ -0,0 +1,48 @@
+package org.cytoscape.property.internal;
+
+import java.io.InputStream;
+import java.io.IOException;
+import java.util.Properties;
+
+import org.cytoscape.property.CyProperty;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class PropsReader implements CyProperty<Properties> {
+
+ private static final Logger logger =
LoggerFactory.getLogger(PropsReader.class);
+
+ private Properties props;
+
+ /**
+ * Creates a new BookmarkReader object.
+ */
+ public PropsReader(String resourceLocation) {
+
+ InputStream is = null;
+
+ try {
+ if ( resourceLocation == null )
+ throw new
NullPointerException("resourceLocation is null");
+
+ is =
this.getClass().getClassLoader().getResourceAsStream(resourceLocation);
+
+ props = new Properties();
+ props.load(is);
+
+ } catch (Exception e) {
+ logger.warn("Could not read properties file - using
empty intance.", e);
+ props = new Properties();
+ } finally {
+ if (is != null) {
+ try { is.close(); } catch (IOException ioe) {}
+ is = null;
+ }
+ }
+ }
+
+ public Properties getProperties() {
+ return props;
+ }
+}
Added:
core3/property-impl/trunk/src/main/java/org/cytoscape/property/internal/bookmark/BookmarkReader.java
===================================================================
---
core3/property-impl/trunk/src/main/java/org/cytoscape/property/internal/bookmark/BookmarkReader.java
(rev 0)
+++
core3/property-impl/trunk/src/main/java/org/cytoscape/property/internal/bookmark/BookmarkReader.java
2010-10-05 20:52:43 UTC (rev 22149)
@@ -0,0 +1,58 @@
+package org.cytoscape.property.internal.bookmark;
+
+import java.io.InputStream;
+import java.io.IOException;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Unmarshaller;
+
+import org.cytoscape.property.CyProperty;
+import org.cytoscape.property.bookmark.Bookmarks;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class BookmarkReader implements CyProperty<Bookmarks> {
+
+ private static final String BOOKMARK_PACKAGE =
Bookmarks.class.getPackage().getName();
+ private static final Logger logger =
LoggerFactory.getLogger(BookmarkReader.class);
+
+ private Bookmarks bookmarks;
+
+ /**
+ * Creates a new BookmarkReader object.
+ */
+ public BookmarkReader(String resourceLocation) {
+
+ InputStream is = null;
+
+ try {
+ if ( resourceLocation == null )
+ throw new
NullPointerException("resourceLocation is null");
+
+ is =
this.getClass().getClassLoader().getResourceAsStream(resourceLocation);
+
+ if (is == null)
+ throw new IllegalArgumentException("Failed to
open resource: " + resourceLocation);
+
+ final JAXBContext jaxbContext =
JAXBContext.newInstance(BOOKMARK_PACKAGE);
+
+ final Unmarshaller unmarshaller =
jaxbContext.createUnmarshaller();
+
+ bookmarks = (Bookmarks) unmarshaller.unmarshal(is);
+ } catch (Exception e) {
+ logger.warn("Could not read bookmark file - using empty
bookmarks.", e);
+ bookmarks = new Bookmarks();
+ } finally {
+ if (is != null) {
+ try { is.close(); } catch (IOException ioe) {}
+ is = null;
+ }
+ }
+ }
+
+ public Bookmarks getProperties() {
+ return bookmarks;
+ }
+}
Added:
core3/property-impl/trunk/src/main/java/org/cytoscape/property/internal/bookmark/BookmarksUtilImpl.java
===================================================================
---
core3/property-impl/trunk/src/main/java/org/cytoscape/property/internal/bookmark/BookmarksUtilImpl.java
(rev 0)
+++
core3/property-impl/trunk/src/main/java/org/cytoscape/property/internal/bookmark/BookmarksUtilImpl.java
2010-10-05 20:52:43 UTC (rev 22149)
@@ -0,0 +1,249 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library 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
+ any later version.
+
+ This library 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. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. 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 library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package org.cytoscape.property.internal.bookmark;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.cytoscape.property.bookmark.Attribute;
+import org.cytoscape.property.bookmark.Bookmarks;
+import org.cytoscape.property.bookmark.BookmarksUtil;
+import org.cytoscape.property.bookmark.Category;
+import org.cytoscape.property.bookmark.DataSource;
+
+/**
+ * Utility methods for getting entries in the bookmark object.
+ *
+ * @author kono
+ *
+ */
+public class BookmarksUtilImpl implements BookmarksUtil {
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ *
org.cytoscape.property.internal.bookmark.BookmarksUtil#getDataSourceList
+ * (java.lang.String, java.util.List)
+ */
+ public List<DataSource> getDataSourceList(String categoryName,
+ List<Category> categoryList) {
+ final Category targetCat = getCategory(categoryName,
categoryList);
+
+ if (targetCat != null) {
+ return extractDataSources(targetCat);
+ } else {
+ return null;
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ *
org.cytoscape.property.internal.bookmark.BookmarksUtil#getCategory(java
+ * .lang.String, java.util.List)
+ */
+ public Category getCategory(String categoryName, List<Category>
categoryList) {
+ Category result = null;
+
+ for (Category cat : categoryList) {
+ if (cat.getName().equals(categoryName)) {
+ result = cat;
+
+ break;
+ } else {
+ List<Category> subCategories =
extractCategory(cat);
+
+ if ((subCategories.size() != 0) && (result ==
null)) {
+ result = getCategory(categoryName,
subCategories);
+ }
+ }
+
+ if (result != null) {
+ break;
+ }
+ }
+
+ return result;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ *
org.cytoscape.property.internal.bookmark.BookmarksUtil#getAttribute(org
+ * .cytoscape.properties.bookmark.DataSource, java.lang.String)
+ */
+ public String getAttribute(DataSource source, String attrName) {
+ List<Attribute> attrs = source.getAttribute();
+
+ for (Attribute attr : attrs) {
+ if (attrName.equals(attr.getName())) {
+ return attr.getContent();
+ }
+ }
+
+ return null;
+ }
+
+ private List<DataSource> extractDataSources(Category cat) {
+ final List<Object> entries = cat.getCategoryOrDataSource();
+ final List<DataSource> datasourceList = new
ArrayList<DataSource>();
+
+ for (Object obj : entries) {
+ if (obj.getClass() == DataSource.class) {
+ datasourceList.add((DataSource) obj);
+ }
+ }
+
+ return datasourceList;
+ }
+
+ private List<Category> extractCategory(Category cat) {
+ final List<Object> entries = cat.getCategoryOrDataSource();
+ final List<Category> categoryList = new ArrayList<Category>();
+
+ for (Object obj : entries) {
+ if (obj.getClass() == Category.class) {
+ categoryList.add((Category) obj);
+ }
+ }
+
+ return categoryList;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ *
org.cytoscape.property.internal.bookmark.BookmarksUtil#saveBookmark(org
+ * .cytoscape.properties.bookmark.Bookmarks, java.lang.String,
+ * org.cytoscape.properties.bookmark.DataSource)
+ */
+ public void saveBookmark(Bookmarks pBookmarks, String pCategoryName,
+ DataSource pDataSource) {
+ if (pBookmarks == null) {
+ pBookmarks = new Bookmarks();
+ }
+
+ List<Category> theCategoryList = pBookmarks.getCategory();
+
+ // if the category does not exist, create it
+ if (theCategoryList.size() == 0) {
+ Category theCategory = new Category();
+ theCategory.setName(pCategoryName);
+ theCategoryList.add(theCategory);
+ }
+
+ Category theCategory = getCategory(pCategoryName,
theCategoryList);
+
+ if (theCategory == null) {
+ Category newCategory = new Category();
+ newCategory.setName(pCategoryName);
+ theCategoryList.add(newCategory);
+ theCategory = newCategory;
+ }
+
+ List<Object> theObjList = theCategory.getCategoryOrDataSource();
+
+ theObjList.add(pDataSource);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * org.cytoscape.property.internal.bookmark.BookmarksUtil#deleteBookmark
+ * (org.cytoscape.properties.bookmark.Bookmarks, java.lang.String,
+ * org.cytoscape.properties.bookmark.DataSource)
+ */
+ public boolean deleteBookmark(Bookmarks pBookmarks, String
pCategoryName,
+ DataSource pDataSource) {
+ if (!isInBookmarks(pBookmarks, pCategoryName, pDataSource)) {
+ return false;
+ }
+
+ List<Category> theCategoryList = pBookmarks.getCategory();
+ Category theCategory = getCategory(pCategoryName,
theCategoryList);
+
+ List<Object> theObjList = theCategory.getCategoryOrDataSource();
+
+ for (int i = 0; i < theObjList.size(); i++) {
+ Object obj = theObjList.get(i);
+
+ if (obj instanceof DataSource) {
+ DataSource theDataSource = (DataSource) obj;
+
+ if (theDataSource.getName().equalsIgnoreCase(
+ pDataSource.getName())) {
+ theObjList.remove(i);
+ }
+ }
+ }
+
+ return true;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * org.cytoscape.property.internal.bookmark.BookmarksUtil#isInBookmarks(
+ * org.cytoscape.properties.bookmark.Bookmarks, java.lang.String,
+ * org.cytoscape.properties.bookmark.DataSource)
+ */
+ public boolean isInBookmarks(Bookmarks pBookmarks, String pCategoryName,
+ DataSource pDataSource) {
+ if (pBookmarks == null) {
+ return false;
+ }
+
+ List<DataSource> theDataSources =
getDataSourceList(pCategoryName,
+ pBookmarks.getCategory());
+
+ if ((theDataSources == null) || (theDataSources.size() == 0)) {
+ return false;
+ }
+
+ for (DataSource theDataSource : theDataSources) {
+ if
(theDataSource.getName().equalsIgnoreCase(pDataSource.getName())) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+}
Added:
core3/property-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
core3/property-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
(rev 0)
+++
core3/property-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2010-10-05 20:52:43 UTC (rev 22149)
@@ -0,0 +1,39 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans";
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xmlns:osgi="http://www.springframework.org/schema/osgi";
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
+ http://www.springframework.org/schema/osgi
http://www.springframework.org/schema/osgi/spring-osgi-1.0.xsd";>
+
+ <!--
+ definitions using elements of the osgi namespace can be
included in
+ this file. There is no requirement to keep these definitions in
a
+ separate file if you do not want to. The rationale for keeping
these
+ definitions separate is to facilitate integration testing of the
+ bundle outside of an OSGi container
+ -->
+
+ <osgi:service id="coreCyPropertyService" ref="corePropsReader"
+ interface="org.cytoscape.property.CyProperty">
+ <osgi:service-properties>
+ <entry key="serviceType" value="property" />
+ <entry key="cyPropertyName" value="coreSettings" />
+ </osgi:service-properties>
+ </osgi:service>
+
+ <osgi:service id="bookmarkCyPropertyService" ref="bookmarksReader"
+ interface="org.cytoscape.property.CyProperty">
+ <osgi:service-properties>
+ <entry key="serviceType" value="property" />
+ <entry key="cyPropertyName" value="bookmarks" />
+ </osgi:service-properties>
+
+ </osgi:service>
+
+ <osgi:service id="bookmarksUtilService" ref="bookmarksUtil"
+ interface="org.cytoscape.property.bookmark.BookmarksUtil">
+ <osgi:service-properties>
+ <entry key="serviceType" value="property.util" />
+ </osgi:service-properties>
+ </osgi:service>
+
+</beans>
Added:
core3/property-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
---
core3/property-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
(rev 0)
+++
core3/property-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2010-10-05 20:52:43 UTC (rev 22149)
@@ -0,0 +1,33 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans";
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xmlns:aop="http://www.springframework.org/schema/aop";
+ xmlns:context="http://www.springframework.org/schema/context";
+ xmlns:lang="http://www.springframework.org/schema/lang";
xmlns:osgi="http://www.springframework.org/schema/osgi";
+ xmlns:util="http://www.springframework.org/schema/util";
+ xsi:schemaLocation="
+ http://www.springframework.org/schema/beans
+
http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
+ http://www.springframework.org/schema/aop
+
http://www.springframework.org/schema/aop/spring-aop-2.5.xsd
+ http://www.springframework.org/schema/context
+
http://www.springframework.org/schema/context/spring-context-2.5.xsd
+ http://www.springframework.org/schema/util
+
http://www.springframework.org/schema/util/spring-util-2.5.xsd
+ http://www.springframework.org/schema/lang
+
http://www.springframework.org/schema/lang/spring-lang-2.5.xsd
+ http://www.springframework.org/schema/osgi
+
http://www.springframework.org/schema/osgi/spring-osgi-1.0.xsd";
+ default-lazy-init="false">
+
+
+ <bean id="corePropsReader"
class="org.cytoscape.property.internal.PropsReader">
+ <constructor-arg value="cytoscape.props" />
+ </bean>
+
+ <bean id="bookmarksReader"
class="org.cytoscape.property.internal.bookmark.BookmarkReader">
+ <constructor-arg value="bookmarks.xml" />
+ </bean>
+
+ <bean id="bookmarksUtil"
class="org.cytoscape.property.internal.bookmark.BookmarksUtilImpl" />
+
+</beans>
Added: core3/property-impl/trunk/src/main/resources/bookmarks.xml
===================================================================
--- core3/property-impl/trunk/src/main/resources/bookmarks.xml
(rev 0)
+++ core3/property-impl/trunk/src/main/resources/bookmarks.xml 2010-10-05
20:52:43 UTC (rev 22149)
@@ -0,0 +1,368 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+ Cytoscape bookmark file.
+
+ - General purpose bookmark file to specify data source locations.
+
+ Keiichiro Ono ([email protected])
+-->
+<bookmarks xmlns:xlink="http://www.w3.org/1999/xlink"; version="0.5">
+ <description>
+ Bookmark file for Cytoscape 2.4 and later.
+ </description>
+ <category name="ontology">
+ <dataSource name="Gene Ontology Full"
+
xlink:href="http://www.geneontology.org/ontology/gene_ontology_edit.obo";
+ format="obo">
+ <attribute name="description">
+ The Gene Ontology (GO) project provides a
controlled vocabulary to describe gene and gene product attributes in any
organism. This data source contains full size GO dag, which contains all GO
terms. This OBO file is written in version 1.2 format.
+ </attribute>
+ <attribute name="ontologyType">GO</attribute>
+ </dataSource>
+ <dataSource name="Generic GO slim"
+
xlink:href="http://www.geneontology.org/GO_slims/goslim_generic.obo";
+ format="obo">
+ <attribute name="description">
+ Subset of general GO Terms.
+ </attribute>
+ <attribute name="ontologyType">GO</attribute>
+ </dataSource>
+ <dataSource name="Yeast GO slim"
+
xlink:href="http://www.geneontology.org/GO_slims/goslim_yeast.obo";
+ format="obo">
+ <attribute name="description">
+ Subset of GO Terms for annotating Yeast data
sets. Maintained by SGD.
+ </attribute>
+ <attribute name="ontologyType">GO</attribute>
+ </dataSource>
+ <dataSource name="Molecule role (INOH Protein name/family name
ontology)"
+
xlink:href="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/molecule_role.obo";
+ format="obo">
+ <attribute name="description">
+ A structured controlled vocabulary of concrete
protein names and generic (abstract) protein names. This ontology is a INOH
pathway annotation ontology, one of a set of ontologies intended to be used in
pathway data annotation to ease data integration. This ontology is used to
annotate protein names, protein family names, generic/concrete protein names in
the INOH pathway data.
+ INOH is part of the BioPAX working group.
+ </attribute>
+ </dataSource>
+ <dataSource name="Event (INOH pathway ontology)"
+
xlink:href="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/event.obo";
+ format="obo">
+ <attribute name="description">
+ A structured controlled vocabulary of pathway
centric biological processes. This ontology is a INOH pathway annotation
ontology, one of a set of ontologies intended to be used in pathway data
annotation to ease data integration. This ontology is used to annotate
biological processes, pathways, sub-pathways in the INOH pathway data.
+ INOH is part of the BioPAX working group.
+ </attribute>
+ </dataSource>
+ <dataSource name="Protein-protein interaction"
+
xlink:href="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/protein/psi-mi.obo";
+ format="obo">
+ <attribute name="description">
+ A structured controlled vocabulary for the
annotation of experiments concerned with protein-protein interactions.
+ </attribute>
+ </dataSource>
+ <dataSource name="Pathway Ontology"
+
xlink:href="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/pathway.obo";
+ format="obo">
+ <attribute name="description">
+ The Pathway Ontology is a controlled vocabulary
for pathways that provides standard terms for the annotation of geneproducts.
+ </attribute>
+ </dataSource>
+ <dataSource name="PATO"
+
xlink:href="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo";
+ format="obo">
+ <attribute name="description">
+ PATO is an ontology of phenotypic qualities,
intended for use in a number of applications, primarily phenotype annotation.
For more information, please visit PATO wiki
(http://www.bioontology.org/wiki/index.php/PATO:Main_Page).
+ </attribute>
+ </dataSource>
+ <dataSource name="Mouse pathology"
+
xlink:href="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/mouse_pathology/mouse_pathology.obo";
+ format="obo">
+ <attribute name="description">
+ Mouse Pathology Ontology (MPATH) is an ontology
for mutant mouse pathology. This is Version 1.
+ </attribute>
+ </dataSource>
+ <dataSource name="Human disease"
+
xlink:href="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/human_disease.obo";
+ format="obo">
+ <attribute name="description">
+ This ontology is a comprehensive hierarchical
controlled vocabulary for human disease representation. For more information,
please visit Disease Ontology website (http://diseaseontology.sourceforge.net/).
+ </attribute>
+ </dataSource>
+ <!-- List of Gene Association files-->
+ <category name="annotation">
+ <dataSource format="Gene Association"
+ name="Gene Association file for Saccharomyces
cerevisiae"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.sgd.gz";>
+ <attribute name="curator">SGD</attribute>
+ <attribute name="species">
+ Saccharomyces cerevisiae
+ </attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Drosophila
melanogaster"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.fb.gz";>
+ <attribute name="curator">FlyBase</attribute>
+ <attribute name="species">
+ Drosophila melanogaster
+ </attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Mus musculus"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.mgi.gz";>
+ <attribute name="curator">MGI</attribute>
+ <attribute name="species">Mus
musculus</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Arabidopsis
thaliana"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.tair.gz";>
+ <attribute name="curator">TAIR/TIGR</attribute>
+ <attribute name="species">
+ Arabidopsis thaliana
+ </attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Caenorhabditis
elegans"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.wb.gz";>
+ <attribute name="curator">WormBase</attribute>
+ <attribute name="species">
+ Caenorhabditis elegans
+ </attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Rattus
norvegicus"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.rgd.gz";>
+ <attribute name="curator">RGD</attribute>
+ <attribute name="species">Rattus
norvegicus</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Oryza sativa"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.gramene_oryza.gz";>
+ <attribute name="curator">Gramene</attribute>
+ <attribute name="species">Oryza
sativa</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Danio rerio"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.zfin.gz";>
+ <attribute name="curator">ZFIN</attribute>
+ <attribute name="species">Danio
rerio</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Dictyostelium
discoideum"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.ddb.gz";>
+ <attribute name="curator">DictyBase</attribute>
+ <attribute name="species">
+ Dictyostelium discoideum
+ </attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Candida
albicans"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.cgd.gz";>
+ <attribute name="curator">CGD</attribute>
+ <attribute name="species">Candida
albicans</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Pseudomonas
aeruginosa PAO1"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.pseudocap.gz";>
+ <attribute name="curator">PseudoCAP</attribute>
+ <attribute name="species">
+ Pseudomonas aeruginosa PAO1
+ </attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Bacillus
anthracis Ames"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.tigr_Banthracis.gz";>
+ <attribute name="curator">TIGR</attribute>
+ <attribute name="species">
+ Bacillus anthracis Ames
+ </attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Coxiella
burnetii RSA 493"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.tigr_Cburnetii.gz";>
+ <attribute name="curator">TIGR</attribute>
+ <attribute name="species">
+ Coxiella burnetii RSA 493
+ </attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Campylobacter
jejuni RM1221"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.tigr_Cjejuni.gz";>
+ <attribute name="curator">TIGR</attribute>
+ <attribute name="species">
+ Campylobacter jejuni RM1221
+ </attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Dehalococcoides
ethenogenes 195"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.tigr_Dethenogenes.gz";>
+ <attribute name="curator">TIGR</attribute>
+ <attribute name="species">
+ Dehalococcoides ethenogenes 195
+ </attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Geobacter
sulfurreducens PCA"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.tigr_Gsulfurreducens.gz";>
+ <attribute name="curator">TIGR</attribute>
+ <attribute name="species">
+ Geobacter sulfurreducens PCA
+ </attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Listeria
monocytogenes 4b F2365"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.tigr_Lmonocytogenes.gz";>
+ <attribute name="curator">TIGR</attribute>
+ <attribute name="species">
+ Listeria monocytogenes 4b F2365
+ </attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Methylococcus
capsulatus Bath"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.tigr_Mcapsulatus.gz";>
+ <attribute name="curator">TIGR</attribute>
+ <attribute name="species">
+ Methylococcus capsulatus Bath
+ </attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Pseudomonas
syringae DC3000"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.tigr_Psyringae.gz";>
+ <attribute name="curator">TIGR</attribute>
+ <attribute name="species">
+ Pseudomonas syringae DC3000
+ </attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Shewanella
oneidensis MR-1"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.tigr_Soneidensis.gz";>
+ <attribute name="curator">TIGR</attribute>
+ <attribute name="species">
+ Shewanella oneidensis MR-1
+ </attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Silicibacter
pomeroyi DSS-3"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.tigr_Spomeroyi.gz";>
+ <attribute name="curator">TIGR</attribute>
+ <attribute name="species">
+ Silicibacter pomeroyi DSS-3
+ </attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Trypanosoma
brucei chr 2"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.tigr_Tbrucei_chr2.gz";>
+ <attribute name="curator">TIGR</attribute>
+ <attribute name="species">
+ Trypanosoma brucei chr 2
+ </attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Vibrio cholerae"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.tigr_Vcholerae.gz";>
+ <attribute name="curator">TIGR</attribute>
+ <attribute name="species">Vibrio
cholerae</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Gallus gallus"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.goa_chicken.gz";>
+ <attribute name="curator">
+ GO Annotations @ EBI
+ </attribute>
+ <attribute name="species">Gallus
gallus</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Bos taurus"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.goa_cow.gz";>
+ <attribute name="curator">
+ GO Annotations @ EBI
+ </attribute>
+ <attribute name="species">Bos taurus</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Homo sapiens"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.goa_human.gz";>
+ <attribute name="curator">
+ GO Annotations @ EBI
+ </attribute>
+ <attribute name="species">Homo
sapiens</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for PDB"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.goa_pdb.gz";>
+ <attribute name="curator">
+ GO Annotations @ EBI
+ </attribute>
+ <attribute name="species">PDB</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for UniProt"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.goa_uniprot.gz";>
+ <attribute name="curator">
+ GO Annotations @ EBI
+ </attribute>
+ <attribute name="species">UniProt</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Leishmania
major"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.GeneDB_Lmajor.gz";>
+ <attribute name="curator">Sanger
GeneDB</attribute>
+ <attribute name="species">Leishmania
major</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Plasmodium
falciparum"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.GeneDB_Pfalciparum.gz";>
+ <attribute name="curator">Sanger
GeneDB</attribute>
+ <attribute name="species">
+ Plasmodium falciparum
+ </attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for
Schizosaccharomyces pombe"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.GeneDB_Spombe.gz";>
+ <attribute name="curator">Sanger
GeneDB</attribute>
+ <attribute name="species">
+ Schizosaccharomyces pombe
+ </attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Trypanosoma
brucei"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.GeneDB_Tbrucei.gz";>
+ <attribute name="curator">Sanger
GeneDB</attribute>
+ <attribute name="species">Trypanosoma
brucei</attribute>
+ </dataSource>
+ <dataSource format="Gene Association"
+ name="Gene Association file for Glossina
morsitans"
+
xlink:href="http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.GeneDB_tsetse.gz";>
+ <attribute name="curator">Sanger
GeneDB</attribute>
+ <attribute name="species">Glossina
morsitans</attribute>
+ </dataSource>
+ </category>
+ </category>
+ <category name="network">
+ <dataSource name="Yeast Protein-Protein: Ideker, T. et al.
(galFiltered.sif)"
+
xlink:href="http://chianti.ucsd.edu/kono/data/galFiltered.sif";
+ format="sif" />
+ <dataSource name="Human Protein-Protein: HPRD Literature
Curated Interactions"
+ xlink:href="http://cytoscape.org/datasets/HPRD.sif";
+ format="sif" />
+ <dataSource name="Human Protein-Protein: Rual et al. Toward a
proteome-scale map of the human protein-protein interaction network. Nature
2005."
+ xlink:href="http://cytoscape.org/datasets/rual.sif";
+ format="sif" />
+ <dataSource name="Human Protein-Protein: Rual et al.
(Subnetwork for tutorial)"
+
xlink:href="http://www.cytoscape.org/tut/getting.started/RUAL.subset.sif";
+ format="sif" />
+ <dataSource name="Human Protein-Protein: Stelzl et al. A human
protein-protein interaction network: a resource for annotating the proteome.
Cell 2005."
+ xlink:href="http://cytoscape.org/datasets/stelzl.sif";
+ format="sif" />
+ <dataSource name="Yeast Protein-Protein: Ptacek et al. Global
analysis of protein phosphorylation in yeast. Nature 2005"
+ xlink:href="http://cytoscape.org/datasets/ptacek.sif";
+ format="sif" />
+ </category>
+
+ <category name="plugins">
+ <dataSource name="Cytoscape"
+ xlink:href="http://cytoscape.org/plugins/plugins.xml"/>
+
+ <dataSource name="Test"
+
xlink:href="http://db.systemsbiology.net/cytoscape/skillcoyne/plugins.xml"/>
+ </category>
+
+</bookmarks>
Property changes on: core3/property-impl/trunk/src/main/resources/bookmarks.xml
___________________________________________________________________
Added: svn:executable
+
Added: core3/property-impl/trunk/src/main/resources/cytoscape.props
===================================================================
--- core3/property-impl/trunk/src/main/resources/cytoscape.props
(rev 0)
+++ core3/property-impl/trunk/src/main/resources/cytoscape.props
2010-10-05 20:52:43 UTC (rev 22149)
@@ -0,0 +1,22 @@
+#Cytoscape Property File
+#Wed Apr 06 15:28:22 PDT 2005
+secondaryViewThreshold=30000
+defaultSpeciesName=Saccharomyces cerevisiae
+bioDataServer=PleaseSpecify
+viewThreshold=10000
+defaultVisualStyle=default
+canonicalizeNames=true
+render.coarseDetailThreshold=2000
+render.nodeBorderThreshold=200
+render.nodeLabelThreshold=100
+render.edgeArrowThreshold=300
+render.edgeLabelThreshold=120
+maximizeViewOnCreate=false
+proxy.server=
+proxy.server.port=
+proxy.server.type=
+cytoscape.version.number=2.7
+exportTextAsShape=true
+vizmapper.cntMapperUpperLimit=2000
+undo.limit=10
+defaultPluginDownloadUrl=http://cytoscape.org/plugins/plugins.xml
Property changes on:
core3/property-impl/trunk/src/main/resources/cytoscape.props
___________________________________________________________________
Added: svn:executable
+
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