jalviewX
File Jws2InstanceFactory.java
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Classes
| Class | Line # | Actions | ||||
|---|---|---|---|---|---|---|
| Jws2InstanceFactory | 32 | 12 | 7 | 0 |
Contributing tests
This file is covered by 36 tests.
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| 1 | /* | |
| 2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
| 3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
| 4 | * | |
| 5 | * This file is part of Jalview. | |
| 6 | * | |
| 7 | * Jalview is free software: you can redistribute it and/or | |
| 8 | * modify it under the terms of the GNU General Public License | |
| 9 | * as published by the Free Software Foundation, either version 3 | |
| 10 | * of the License, or (at your option) any later version. | |
| 11 | * | |
| 12 | * Jalview is distributed in the hope that it will be useful, but | |
| 13 | * WITHOUT ANY WARRANTY; without even the implied warranty | |
| 14 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | |
| 15 | * PURPOSE. See the GNU General Public License for more details. | |
| 16 | * | |
| 17 | * You should have received a copy of the GNU General Public License | |
| 18 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | |
| 19 | * The Jalview Authors are detailed in the 'AUTHORS' file. | |
| 20 | */ | |
| 21 | package jalview.ws.jws2.jabaws2; | |
| 22 | ||
| 23 | import jalview.ws.jws2.AAConClient; | |
| 24 | import jalview.ws.jws2.RNAalifoldClient; | |
| 25 | import jalview.ws.uimodel.AlignAnalysisUIText; | |
| 26 | ||
| 27 | import java.util.HashMap; | |
| 28 | import java.util.HashSet; | |
| 29 | ||
| 30 | import compbio.data.msa.JABAService; | |
| 31 | ||
| 32 | public class Jws2InstanceFactory | |
| 33 | { | |
| 34 | private static HashMap<String, AlignAnalysisUIText> aaConGUI; | |
| 35 | ||
| 36 | private static HashSet<String> ignoreGUI; | |
| 37 | ||
| 38 | 132 |  private static String category_rewrite(String cat_name) |
| 39 | { | |
| 40 | 132 | return (cat_name != null && cat_name.equals("Prediction")) |
| 41 | ? "Secondary Structure Prediction" | |
| 42 | : cat_name; | |
| 43 | } | |
| 44 | ||
| 45 | 264 | private static void init() |
| 46 | { | |
| 47 | 264 | if (aaConGUI == null) |
| 48 | { | |
| 49 | 1 | aaConGUI = new HashMap<String, AlignAnalysisUIText>(); |
| 50 | 1 | aaConGUI.put(compbio.ws.client.Services.AAConWS.toString(), |
| 51 | AAConClient.getAlignAnalysisUITest()); | |
| 52 | 1 | aaConGUI.put(compbio.ws.client.Services.RNAalifoldWS.toString(), |
| 53 | RNAalifoldClient.getAlignAnalysisUITest()); | |
| 54 | // ignore list for JABAWS services not supported in jalview ... | |
| 55 | 1 | ignoreGUI = new HashSet<String>(); |
| 56 | } | |
| 57 | } | |
| 58 | ||
| 59 | /** | |
| 60 | * exclusion list to avoid creating GUI elements for services we don't fully | |
| 61 | * support | |
| 62 | * | |
| 63 | * @param serviceType | |
| 64 | * @return | |
| 65 | */ | |
| 66 | 132 | public static boolean ignoreService(String serviceType) |
| 67 | { | |
| 68 | 132 | init(); |
| 69 | 132 | return (ignoreGUI.contains(serviceType.toString())); |
| 70 | } | |
| 71 | ||
| 72 | /** | |
| 73 | * construct a service instance and configure it with any additional | |
| 74 | * properties needed so Jalview can access it correctly | |
| 75 | * | |
| 76 | * @param jwsservers | |
| 77 | * @param serviceType | |
| 78 | * @param name | |
| 79 | * @param description | |
| 80 | * @param service | |
| 81 | * @return | |
| 82 | */ | |
| 83 | 132 | public static Jws2Instance newJws2Instance(String jwsservers, |
| 84 | String serviceType, String name, String description, | |
| 85 | JABAService service) | |
| 86 | { | |
| 87 | 132 | init(); |
| 88 | 132 | Jws2Instance svc = new Jws2Instance(jwsservers, serviceType, |
| 89 | category_rewrite(name), description, service); | |
| 90 | 132 | svc.aaui = aaConGUI.get(serviceType.toString()); |
| 91 | 132 | return svc; |
| 92 | } | |
| 93 | ||
| 94 | } |