X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fclient%2Fsimpleclient%2FClientDocument.java;h=f518f718ba92f69958941384b2313f6b12b11671;hb=1eea4b639911330e7cd65e17c5421cc584f0d22e;hp=b9e918e2475d02185fb24944cc492d351381ca9d;hpb=616cdc52fd0e998a95ceb3f7a56a2d4eee20e68f;p=vamsas.git
diff --git a/src/uk/ac/vamsas/client/simpleclient/ClientDocument.java b/src/uk/ac/vamsas/client/simpleclient/ClientDocument.java
index b9e918e..f518f71 100644
--- a/src/uk/ac/vamsas/client/simpleclient/ClientDocument.java
+++ b/src/uk/ac/vamsas/client/simpleclient/ClientDocument.java
@@ -1,5 +1,23 @@
/*
- *
+ * This file is part of the Vamsas Client version 0.2.
+ * Copyright 2010 by Jim Procter, Iain Milne, Pierre Marguerite,
+ * Andrew Waterhouse and Dominik Lindner.
+ *
+ * Earlier versions have also been incorporated into Jalview version 2.4
+ * since 2008, and TOPALi version 2 since 2007.
+ *
+ * The Vamsas Client 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 3 of the License, or
+ * (at your option) any later version.
+ *
+ * The Vamsas Client 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 the Vamsas Client. If not, see .
*/
package uk.ac.vamsas.client.simpleclient;
@@ -23,281 +41,302 @@ import uk.ac.vamsas.objects.utils.AppDataReference;
import uk.ac.vamsas.test.objects.Core;
/**
- * Maintains a collection of vamsas objects, appdatas and states,
- * and provides api for a SimpleClient's client.
- * TODO: test and migrate ArchiveClient.getAppData methods to here and retest in ExampleApplication
- * @author jimp
+ * Maintains a collection of vamsas objects, appdatas and states, and provides
+ * api for a SimpleClient's client. TODO: test and migrate
+ * ArchiveClient.getAppData methods to here and retest in ExampleApplication
+ *
+ * @author jimp
*/
-public class ClientDocument extends uk.ac.vamsas.client.ClientDocument implements IClientDocument {
+public class ClientDocument extends uk.ac.vamsas.client.ClientDocument
+ implements IClientDocument {
private static Log log = LogFactory.getLog(ClientDocument.class);
+
private VamsasDocument doc;
+
protected SimpleClient sclient;
+
protected VamsasArchive iohandler = null;
+
/**
* indicate if new data has been incorporated
*/
private boolean isModified = false;
+
/**
* Public method for internal use by SimpleClient.
+ *
* @return true if document has been modified.
*/
public boolean isModified() {
return isModified;
}
+
/**
- *
- * prepare Application-side dataset from the vamsas Document iohandler
- * @param doc - the dataset
- * @param docHandler - the sessionFile IO handler
- * @param Factory - the source of current and new vorbaIds
- * @param sclient - the simpleclient instance
+ *
+ * prepare Application-side dataset from the vamsas Document iohandler
+ *
+ * @param doc
+ * - the dataset
+ * @param docHandler
+ * - the sessionFile IO handler
+ * @param Factory
+ * - the source of current and new vorbaIds
+ * @param sclient
+ * - the simpleclient instance
*/
- protected ClientDocument(VamsasDocument doc, VamsasArchive docHandler, IdFactory Factory, SimpleClient sclient) {
+ protected ClientDocument(VamsasDocument doc, VamsasArchive docHandler,
+ IdFactory Factory, SimpleClient sclient) {
super(Factory.getVorbaIdHash(), Factory);
-
-
+
/**
* prepare Application-side dataset from the vamsas Document iohandler
*/
this.sclient = sclient;
iohandler = docHandler;
this.doc = doc;
- _VamsasRoots=doc.getVAMSAS();
+ _VamsasRoots = doc.getVAMSAS();
}
-
+
/*
* (non-Javadoc)
*
- * @see uk.ac.vamsas.client.IClientDocument#getObject(uk.ac.vamsas.client.VorbaId)
+ * @see
+ * uk.ac.vamsas.client.IClientDocument#getObject(uk.ac.vamsas.client.VorbaId)
*/
public Vobject getObject(VorbaId id) {
- if (vamsasObjects==null) {
+ if (vamsasObjects == null) {
log.debug("getObject called on null objrefs list.");
return null;
}
if (vamsasObjects.containsKey(id))
return (Vobject) vamsasObjects.get(id);
- log.debug("Returning null Vobject reference for id "+id.getId());
+ log.debug("Returning null Vobject reference for id " + id.getId());
return null;
}
-
+
/*
* (non-Javadoc)
*
- * @see uk.ac.vamsas.client.IClientDocument#getObjects(uk.ac.vamsas.client.VorbaId[])
+ * @see
+ * uk.ac.vamsas.client.IClientDocument#getObjects(uk.ac.vamsas.client.VorbaId
+ * [])
*/
public Vobject[] getObjects(VorbaId[] ids) {
- if (vamsasObjects==null) {
+ if (vamsasObjects == null) {
log.debug("getObject[] called on null vamsasObjects list.");
return null;
}
Vobject[] vo = new Vobject[ids.length];
- for (int i=0,j=ids.length; i-1) {
+ if (k > -1) {
if (isValidUpdate(newr[k], original[i], modflag)) {
- // set by isValidUpdate if the hashcodes were really different from last store
+ // set by isValidUpdate if the hashcodes were really different from
+ // last store
rts.add(newr[k]);
- newr[k]=null;
+ newr[k] = null;
} else {
// LATER: try harder to merge ducument roots.
- log.warn("Couldn't merge new VAMSAS root "+newr[k].getId());
+ log.warn("Couldn't merge new VAMSAS root " + newr[k].getId());
newr[k] = null; // LATER: this means we ignore mangled roots. NOT GOOD
}
} else {
@@ -306,136 +345,153 @@ public class ClientDocument extends uk.ac.vamsas.client.ClientDocument implement
}
}
// add remaining (new) roots
- for (int i=0,j=newr.length; i