[MOBY-guts] biomoby commit
Martin Senger
senger at pub.open-bio.org
Thu May 19 15:57:25 UTC 2005
senger
Thu May 19 11:57:25 EDT 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory pub.open-bio.org:/tmp/cvs-serv3891/src/main/org/biomoby/client
Modified Files:
CentralDigestCachedImpl.java GraphsServlet.java Graphviz.java
RDF.java SimpleCache.java SimpleFileCache.java Taverna.java
package.html
Log Message:
moby-live/Java/src/main/org/biomoby/client CentralDigestCachedImpl.java,1.3,1.4 GraphsServlet.java,1.9,1.10 Graphviz.java,1.6,1.7 RDF.java,1.2,1.3 SimpleCache.java,1.3,1.4 SimpleFileCache.java,1.2,1.3 Taverna.java,1.2,1.3 package.html,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2005/04/07 16:37:02 1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedImpl.java 2005/05/19 15:57:25 1.4
@@ -359,9 +359,9 @@
if (list == null)
throw new MobyException ("Surprisingly, '" + servicesCache.getAbsolutePath() + "' is not a directory. Strange...");
for (int i = 0; i < list.length; i++) {
- MobyService[] services = extractServices (load (list[i]));
- for (int j = 0; j < services.length; j++)
- v.addElement (services[j]);
+ MobyService[] servs = extractServices (load (list[i]));
+ for (int j = 0; j < servs.length; j++)
+ v.addElement (servs[j]);
}
MobyService[] result = new MobyService [v.size()];
v.copyInto (result);
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/GraphsServlet.java,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/GraphsServlet.java 2005/04/07 22:55:06 1.9
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/GraphsServlet.java 2005/05/19 15:57:25 1.10
@@ -1639,13 +1639,13 @@
static final int BUF_SIZE = 8192;
public void run() {
- byte[] buf = new byte [BUF_SIZE];
+ byte[] myBuf = new byte [BUF_SIZE];
int readBytes;
try {
- while ((readBytes = stream.read (buf)) != -1) {
+ while ((readBytes = stream.read (myBuf)) != -1) {
byte[] tmp = new byte [result.length + readBytes];
System.arraycopy (result, 0, tmp, 0, result.length);
- System.arraycopy (buf, 0, tmp, result.length, readBytes);
+ System.arraycopy (myBuf, 0, tmp, result.length, readBytes);
result = new byte [tmp.length];
System.arraycopy (tmp, 0, result, 0, tmp.length);
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Graphviz.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Graphviz.java 2005/04/07 16:37:02 1.6
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Graphviz.java 2005/05/19 15:57:25 1.7
@@ -17,7 +17,7 @@
/**
* A utility class that understands how to create
- * {@link http://www.research.att.com/sw/tools/graphviz/ graphviz} graphs from a set of
+ * <a href="http://www.research.att.com/sw/tools/graphviz/">graphviz</a> graphs from a set of
* {@link org.biomoby.client.ServicesEdge ServiceEdges}, or from other
* data structures.
*
@@ -293,7 +293,7 @@
* Creates a graph connecting 'serviceTypes' using their ISA
* relationship. <p>
*
- * @param servicesTypes represent nodes in the created graph
+ * @param serviceTypes represent nodes in the created graph
* @param props are some properties that can influence how the
* graph will look like; see the property names elswhere in this
* API what properties are understood
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/RDF.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/RDF.java 2005/04/07 16:37:02 1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/RDF.java 2005/05/19 15:57:25 1.3
@@ -19,7 +19,7 @@
/**
* A utility class that understands how to create
- * {@link http://www.research.att.com/sw/tools/graphviz/ graphviz} graphs from a set of
+ * <a href="http://www.research.att.com/sw/tools/graphviz/">graphviz</a> graphs from a set of
* {@link org.biomoby.client.ServicesEdge ServiceEdges}, or from other
* data structures.
*
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/SimpleCache.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/SimpleCache.java 2005/04/07 16:37:02 1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/SimpleCache.java 2005/05/19 15:57:25 1.4
@@ -65,7 +65,7 @@
* @param id a unique ID of the object being returned
* @return data previously stored under 'id'; or null if such data
* do not exist
- * @thow IOExcepiton if the retrieving failed
+ * @throws IOExcepiton if the retrieving failed
**************************************************************************/
java.lang.Object getContents (String id)
throws IOException;
@@ -75,7 +75,7 @@
*
* @param id a unique ID of the object being stored
* @param data are being stored
- * @thow IOExcepiton if the storing failed
+ * @throws IOExcepiton if the storing failed
**************************************************************************/
void setContents (String id, java.lang.Object data)
throws IOException;
@@ -85,7 +85,7 @@
* <p>
*
* @param id a unique ID
- * @throw IOException if the object exists but cannot be removed
+ * @throws IOException if the object exists but cannot be removed
* (meaning that it <b>does not</b> raise any exception if the
* object is not anymore in the cache)
**************************************************************************/
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/SimpleFileCache.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/SimpleFileCache.java 2005/04/07 16:37:02 1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/SimpleFileCache.java 2005/05/19 15:57:25 1.3
@@ -32,7 +32,7 @@
*
* @param id a unique ID of the cached (or possibly cached) object
* @return a filename with the full path representing an object 'id'
- * @throw IOException if creating the parent directories caused problem
+ * @throws IOException if creating the parent directories caused problem
**************************************************************************/
String getFilename (String id)
throws IOException;
@@ -42,7 +42,7 @@
*
* @param id a unique ID of the object being stored
* @param data are being stored
- * @thow IOExcepiton if the storing failed
+ * @throws IOExcepiton if the storing failed
**************************************************************************/
void setContents (String id, byte[] data)
throws IOException;
@@ -62,7 +62,7 @@
*
* @param millis how many milliseconds must be an object stored to
* be remopved by calling this method
- * @throw IOException if any object that exists in the cache and
+ * @throws IOException if any object that exists in the cache and
* is targeted to be removed but cannot be removed
**************************************************************************/
void removeOlderThen (long millis)
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Taverna.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Taverna.java 2005/04/07 16:37:02 1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Taverna.java 2005/05/19 15:57:25 1.3
@@ -24,7 +24,7 @@
/**
* A utility class that understands how to create workflow definitions
- * for {@link http://taverna.sf.net/ Taverna}. <p>
+ * for <a href="http://taverna.sf.net/">Taverna</a>. <p>
*
* @see MobyGraphs
* @author <A HREF="mailto:senger at ebi.ac.uk">Martin Senger</A>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/package.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/package.html 2003/09/24 14:33:37 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/package.html 2005/05/19 15:57:25 1.2
@@ -3,17 +3,13 @@
</head>
<body>
-The components used for developing Moby clients.
-<p>
-The most important class is {@link org.biomoby.client.CentralImpl}
-implementing interface {@link org.biomoby.shared.Central} and by doing so
-hiding all Moby complexity (and changes) under the hood.
+The components used for developing Moby clients. The Moby clients can
+be both clients of the Moby registry and clients of the Moby services.
<p>
-Note that this package does not contain ready and complete Moby clients
-but only pieces, tools and helpers to build such clients. The ready/full
-clients are in the <tt>Clients</tt> sub-directory (they are not in any
-named package) - {@link MobyCmdLineClient} and {@link TestingCentral}.
+The most important class is {@link org.biomoby.client.CentralImpl}
+implementing interface {@link org.biomoby.shared.Central} and by doing
+so hiding all Moby complexity (and changes) under the hood. <p>
</body> </html>
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