2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.ws.uimodel;
24 * configures annotation worker style web service clients
29 public class AlignAnalysisUIText
32 private String serviceType;
34 public String getServiceType()
41 private String calcId;
43 public String getCalcId()
48 private String AAconToggle, AAconToggleTooltip, AAeditSettings,
49 AAeditSettingsTooltip;
64 * @return true if service can accept sequences with gaps
75 private boolean filterSymbols;
78 private boolean needsAlignedSeqs;
80 private int min_valid_seqs;
83 public AlignAnalysisUIText(String serviceType, Class<?> client,
84 String calcId, boolean acceptNucl, boolean acceptProt,
85 boolean acceptGaps, boolean alignedSeq,
86 boolean filterNonStandardSymbols, int minSeq, String toggle,
88 String settings, String settingsTooltip)
90 this.serviceType = serviceType;
95 this.needsAlignedSeqs = alignedSeq;
96 this.filterSymbols = filterNonStandardSymbols;
98 this.AAconToggle = toggle;
99 this.AAconToggleTooltip = toggleTooltip;
100 this.AAeditSettings = settings;
101 this.AAeditSettingsTooltip = settingsTooltip;
102 this.min_valid_seqs = minSeq;
107 * @return true if non-standard nucleotides and amino acids should be replaced
111 public boolean isFilterSymbols()
113 return filterSymbols;
118 * @return true if service needs sequences all the same length (ie padded with
121 public boolean isNeedsAlignedSeqs()
123 return needsAlignedSeqs;
126 public Class getClient()
131 public void setClient(Class client)
133 this.client = client;
136 public String getAAconToggle()
141 public void setAAconToggle(String aAconToggle)
143 AAconToggle = aAconToggle;
146 public String getAAconToggleTooltip()
148 return AAconToggleTooltip;
151 public void setAAconToggleTooltip(String aAconToggleTooltip)
153 AAconToggleTooltip = aAconToggleTooltip;
156 public String getAAeditSettings()
158 return AAeditSettings;
161 public void setAAeditSettings(String aAeditSettings)
163 AAeditSettings = aAeditSettings;
166 public String getAAeditSettingsTooltip()
168 return AAeditSettingsTooltip;
171 public void setAAeditSettingsTooltip(String aAeditSettingsTooltip)
173 AAeditSettingsTooltip = aAeditSettingsTooltip;
176 public int getMinimumSequences()
178 return min_valid_seqs;