-/**
- *
- */
-package uk.ac.vamsas.objects.utils;
-import java.util.Vector;
-
-
-import uk.ac.vamsas.client.ClientHandle;
-import uk.ac.vamsas.client.UserHandle;
-import uk.ac.vamsas.client.simpleclient.VamsasArchive;
-import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
-import uk.ac.vamsas.objects.core.*;
-/**
- * Form, accessors and validation for ApplicationData references in
- * vamsas document.
- * TODO: LATER:extend XML Schema to properly validate against the same forms required by this class
- * TODO: VAMSAS: URNS for appDatas are supposed to be unique, aren't they ?
- */
-public class AppDataReference {
- /**
- * search interface for collecting particular types of AppDatas in a vamsas document
- * @author jimp
- *
- */
- interface IAppDSearch {
- /**
- * process the appData Vobject d
- * @param d
- * @return true if appData should be collected
- */
- public boolean process(AppData d);
- }
- /**
- * collect all appData reference strings in a vamsas document
- * @param doc
- * @return vector of String objects
- */
- static public Vector getAppDataReferences(VamsasDocument doc) {
- if ((doc!=null) && (doc.getApplicationDataCount()>0)) {
- Vector apdrefs = new Vector();
- ApplicationData[] appdatas = doc.getApplicationData();
- for (int q=0; q<appdatas.length; q++) {
- String refstring=appdatas[q].getDataReference();
- if (refstring!=null)
- apdrefs.add(refstring);
- User users[] = appdatas[q].getUser();
-
- if (users!=null)
- for (int u=0; u<users.length; u++) {
- refstring=users[u].getDataReference();
- if (refstring!=null)
- apdrefs.add(new String(refstring)); // avoid referencing.
- }
- }
- if (apdrefs.size()>0)
- return apdrefs;
- }
- return null;
- }
- /**
- * General search through the set of AppData objects for a particular profile of Client and User handle.
- * @param doc
- * @param test interface implemented by the filter selecting particular AppDatas.
- * @param cascade if true only User objects for ApplicationData objects that test.process returned true will be tested.
- * @return set of uk.ac.vamsas.objects.core.AppData objects for which test.process returned true
- */
- static public Vector searchAppDatas(VamsasDocument doc, IAppDSearch test, boolean cascade) {
- if ((doc!=null) && (doc.getApplicationDataCount()>0)) {
- Vector apdrefs = new Vector();
- ApplicationData[] appdatas = doc.getApplicationData();
- for (int q=0; q<appdatas.length; q++) {
- boolean t;
- if (t=test.process(appdatas[q]))
- apdrefs.add(appdatas[q]);
- if (t || cascade) {
- User users[] = appdatas[q].getUser();
- if (users!=null)
- for (int u=0; u<users.length; u++)
- if (test.process(users[u]))
- apdrefs.add(users[u]);
- }
- }
- if (apdrefs.size()>0)
- return apdrefs;
- }
- return null;
- }
- static public boolean equals(User p, UserHandle u) {
- if (p.getFullname().equals(u.getFullName())
- && p.getOrganization().equals(u.getOrganization()))
- return true;
- return false;
- }
- /**
- * returns true if Name matches in c and p, and Urn's match (or c.getUrn()==null) and Version's match (or c.getVersion()==null)
- * @param p
- * @param c
- * @return match of p on template c.
- */
- static public boolean equals(ApplicationData p, ClientHandle c) {
- if (
- //((c.getClientUrn()==null) || p.getUrn().equals(c.getClientUrn()))
- //&&
- (p.getName().equals(c.getClientName()))
- &&
- ((c.getVersion()==null) || (p.getVersion().equals(c.getVersion())))
- )
- return true;
- return false;
- }
- /**
- * Searches document appData structure for particular combinations of client and user data
- * @param doc the data
- * @param user template user data to match against
- * @see AppDataReference.equals(uk.ac.vamsas.objects.core.User, uk.ac.vamsas.client.UserHandle)
- * @param app
- * @see AppDataReference.equals(uk.ac.vamsas.objects.core.ApplicationData, uk.ac.vamsas.client.ClientHandle)
- * @return set of matching client app datas for this client and user combination
- */
- static public Vector getUserandApplicationsData(VamsasDocument doc, UserHandle user, ClientHandle app) {
- if (doc==null) {
- return null;
- }
- final UserHandle u = user;
- final ClientHandle c = app;
-
- IAppDSearch match = new IAppDSearch() {
- public boolean process(AppData p) {
- if (p instanceof User) {
- if (AppDataReference.equals((User) p, u))
- return true;
- } else
- if (p instanceof ApplicationData) {
- if (AppDataReference.equals((ApplicationData) p, c))
- return true;
- }
- return false;
- }
- };
-
- return searchAppDatas(doc, match, true); // only return AppDatas belonging to appdata app.
- }
- /**
- * safely creates a new appData reference
- * @param dest destination document Vobject
- * @param entry base application reference to make unique
- */
- public static String uniqueAppDataReference(VamsasDocument dest,String base) {
- String urn = base.replace('/','_').replace('\\','_').replace(':', '_').replace('.', '_');
- int v = 1;
- for (int i=0, j=dest.getApplicationDataCount(); i<j; i++) {
- ApplicationData o = dest.getApplicationData()[i];
- // ensure new urn is really unique
- while (o.getDataReference()!=null && o.getDataReference().equals(urn)) {
- urn = base+"_"+v++;
- }
- }
- return urn;
- }
-}
+/*\r
+ * This file is part of the Vamsas Client version 0.1. \r
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite, \r
+ * Andrew Waterhouse and Dominik Lindner.\r
+ * \r
+ * Earlier versions have also been incorporated into Jalview version 2.4 \r
+ * since 2008, and TOPALi version 2 since 2007.\r
+ * \r
+ * The Vamsas Client is free software: you can redistribute it and/or modify\r
+ * it under the terms of the GNU Lesser General Public License as published by\r
+ * the Free Software Foundation, either version 3 of the License, or\r
+ * (at your option) any later version.\r
+ * \r
+ * The Vamsas Client is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU Lesser General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU Lesser General Public License\r
+ * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
+package uk.ac.vamsas.objects.utils;\r
+\r
+import java.util.Vector;\r
+\r
+import uk.ac.vamsas.client.ClientHandle;\r
+import uk.ac.vamsas.client.UserHandle;\r
+import uk.ac.vamsas.client.simpleclient.VamsasArchive;\r
+import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;\r
+import uk.ac.vamsas.objects.core.*;\r
+\r
+/**\r
+ * Form, accessors and validation for ApplicationData references in vamsas\r
+ * document. TODO: LATER:extend XML Schema to properly validate against the same\r
+ * forms required by this class TODO: VAMSAS: URNS for appDatas are supposed to\r
+ * be unique, aren't they ?\r
+ */\r
+public class AppDataReference {\r
+ /**\r
+ * search interface for collecting particular types of AppDatas in a vamsas\r
+ * document\r
+ * \r
+ * @author jimp\r
+ * \r
+ */\r
+ interface IAppDSearch {\r
+ /**\r
+ * process the appData Vobject d\r
+ * \r
+ * @param d\r
+ * @return true if appData should be collected\r
+ */\r
+ public boolean process(AppData d);\r
+ }\r
+\r
+ /**\r
+ * collect all appData reference strings in a vamsas document\r
+ * \r
+ * @param doc\r
+ * @return vector of String objects\r
+ */\r
+ static public Vector getAppDataReferences(VamsasDocument doc) {\r
+ if ((doc != null) && (doc.getApplicationDataCount() > 0)) {\r
+ Vector apdrefs = new Vector();\r
+ ApplicationData[] appdatas = doc.getApplicationData();\r
+ for (int q = 0; q < appdatas.length; q++) {\r
+ String refstring = appdatas[q].getDataReference();\r
+ if (refstring != null)\r
+ apdrefs.add(refstring);\r
+ User users[] = appdatas[q].getUser();\r
+\r
+ if (users != null)\r
+ for (int u = 0; u < users.length; u++) {\r
+ refstring = users[u].getDataReference();\r
+ if (refstring != null)\r
+ apdrefs.add(new String(refstring)); // avoid referencing.\r
+ }\r
+ }\r
+ if (apdrefs.size() > 0)\r
+ return apdrefs;\r
+ }\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * General search through the set of AppData objects for a particular profile\r
+ * of Client and User handle.\r
+ * \r
+ * @param doc\r
+ * @param test\r
+ * interface implemented by the filter selecting particular AppDatas.\r
+ * @param cascade\r
+ * if true only User objects for ApplicationData objects that\r
+ * test.process returned true will be tested.\r
+ * @return set of uk.ac.vamsas.objects.core.AppData objects for which\r
+ * test.process returned true\r
+ */\r
+ static public Vector searchAppDatas(VamsasDocument doc, IAppDSearch test,\r
+ boolean cascade) {\r
+ if ((doc != null) && (doc.getApplicationDataCount() > 0)) {\r
+ Vector apdrefs = new Vector();\r
+ ApplicationData[] appdatas = doc.getApplicationData();\r
+ for (int q = 0; q < appdatas.length; q++) {\r
+ boolean t;\r
+ if (t = test.process(appdatas[q]))\r
+ apdrefs.add(appdatas[q]);\r
+ if (t || cascade) {\r
+ User users[] = appdatas[q].getUser();\r
+ if (users != null)\r
+ for (int u = 0; u < users.length; u++)\r
+ if (test.process(users[u]))\r
+ apdrefs.add(users[u]);\r
+ }\r
+ }\r
+ if (apdrefs.size() > 0)\r
+ return apdrefs;\r
+ }\r
+ return null;\r
+ }\r
+\r
+ static public boolean equals(User p, UserHandle u) {\r
+ if (p.getFullname().equals(u.getFullName())\r
+ && p.getOrganization().equals(u.getOrganization()))\r
+ return true;\r
+ return false;\r
+ }\r
+\r
+ /**\r
+ * returns true if Name matches in c and p, and Urn's match (or\r
+ * c.getUrn()==null) and Version's match (or c.getVersion()==null)\r
+ * \r
+ * @param p\r
+ * @param c\r
+ * @return match of p on template c.\r
+ */\r
+ static public boolean equals(ApplicationData p, ClientHandle c) {\r
+ if (\r
+ // ((c.getClientUrn()==null) || p.getUrn().equals(c.getClientUrn()))\r
+ // &&\r
+ (p.getName().equals(c.getClientName()))\r
+ && ((c.getVersion() == null) || (p.getVersion().equals(c.getVersion()))))\r
+ return true;\r
+ return false;\r
+ }\r
+\r
+ /**\r
+ * Searches document appData structure for particular combinations of client\r
+ * and user data\r
+ * \r
+ * @param doc\r
+ * the data\r
+ * @param user\r
+ * template user data to match against\r
+ * @see AppDataReference.equals(uk.ac.vamsas.objects.core.User,\r
+ * uk.ac.vamsas.client.UserHandle)\r
+ * @param app\r
+ * @see AppDataReference.equals(uk.ac.vamsas.objects.core.ApplicationData,\r
+ * uk.ac.vamsas.client.ClientHandle)\r
+ * @return set of matching client app datas for this client and user\r
+ * combination\r
+ */\r
+ static public Vector getUserandApplicationsData(VamsasDocument doc,\r
+ UserHandle user, ClientHandle app) {\r
+ if (doc == null) {\r
+ return null;\r
+ }\r
+ final UserHandle u = user;\r
+ final ClientHandle c = app;\r
+\r
+ IAppDSearch match = new IAppDSearch() {\r
+ public boolean process(AppData p) {\r
+ if (p instanceof User) {\r
+ if (AppDataReference.equals((User) p, u))\r
+ return true;\r
+ } else if (p instanceof ApplicationData) {\r
+ if (AppDataReference.equals((ApplicationData) p, c))\r
+ return true;\r
+ }\r
+ return false;\r
+ }\r
+ };\r
+\r
+ return searchAppDatas(doc, match, true); // only return AppDatas belonging\r
+ // to appdata app.\r
+ }\r
+\r
+ /**\r
+ * safely creates a new appData reference\r
+ * \r
+ * @param dest\r
+ * destination document Vobject\r
+ * @param entry\r
+ * base application reference to make unique\r
+ */\r
+ public static String uniqueAppDataReference(VamsasDocument dest, String base) {\r
+ String urn = base.replace('/', '_').replace('\\', '_').replace(':', '_')\r
+ .replace('.', '_');\r
+ int v = 1;\r
+ for (int i = 0, j = dest.getApplicationDataCount(); i < j; i++) {\r
+ ApplicationData o = dest.getApplicationData()[i];\r
+ // ensure new urn is really unique\r
+ while (o.getDataReference() != null && o.getDataReference().equals(urn)) {\r
+ urn = base + "_" + v++;\r
+ }\r
+ }\r
+ return urn;\r
+ }\r
+}\r
git://source.jalview.org / vamsas.git / blobdiff