Coverage Report
File AlignAnalysisUIText.java
Coverage histogram
37% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| AlignAnalysisUIText | 29 | 31 | 19 |
Contributing tests
This file is covered by 71 tests.
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Source view
| 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.uimodel; | |
| 22 | ||
| 23 | /** | |
| 24 | * configures annotation worker style web service clients | |
| 25 | * | |
| 26 | * @author jprocter | |
| 27 | * | |
| 28 | */ | |
| 29 | public class AlignAnalysisUIText | |
| 30 | { | |
| 31 | ||
| 32 | private String serviceType; | |
| 33 | ||
| 34 | 0 |  public String getServiceType() |
| 35 | { | |
| 36 | 0 | return serviceType; |
| 37 | } | |
| 38 | ||
| 39 | private Class client; | |
| 40 | ||
| 41 | private String calcId; | |
| 42 | ||
| 43 | 0 | public String getCalcId() |
| 44 | { | |
| 45 | 0 | return calcId; |
| 46 | } | |
| 47 | ||
| 48 | private String AAconToggle, AAconToggleTooltip, AAeditSettings, | |
| 49 | AAeditSettingsTooltip; | |
| 50 | ||
| 51 | private boolean isNa; | |
| 52 | ||
| 53 | 0 | public boolean isNa() |
| 54 | { | |
| 55 | 0 | return isNa; |
| 56 | } | |
| 57 | ||
| 58 | 0 | public boolean isPr() |
| 59 | { | |
| 60 | 0 | return isPr; |
| 61 | } | |
| 62 | ||
| 63 | /** | |
| 64 | * @return true if service can accept sequences with gaps | |
| 65 | */ | |
| 66 | 3036 | public boolean isAA() |
| 67 | { | |
| 68 | 3036 | return isAA; |
| 69 | } | |
| 70 | ||
| 71 | private boolean isPr; | |
| 72 | ||
| 73 | private boolean isAA; | |
| 74 | ||
| 75 | private boolean filterSymbols; | |
| 76 | ||
| 77 | ||
| 78 | private boolean needsAlignedSeqs; | |
| 79 | ||
| 80 | private int min_valid_seqs; | |
| 81 | ||
| 82 | ||
| 83 | 6 | 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, | |
| 87 | String toggleTooltip, | |
| 88 | String settings, String settingsTooltip) | |
| 89 | { | |
| 90 | 6 | this.serviceType = serviceType; |
| 91 | 6 | this.calcId = calcId; |
| 92 | 6 | isNa = acceptNucl; |
| 93 | 6 | isPr = acceptProt; |
| 94 | 6 | isAA = acceptGaps; |
| 95 | 6 | this.needsAlignedSeqs = alignedSeq; |
| 96 | 6 | this.filterSymbols = filterNonStandardSymbols; |
| 97 | 6 | this.client = client; |
| 98 | 6 | this.AAconToggle = toggle; |
| 99 | 6 | this.AAconToggleTooltip = toggleTooltip; |
| 100 | 6 | this.AAeditSettings = settings; |
| 101 | 6 | this.AAeditSettingsTooltip = settingsTooltip; |
| 102 | 6 | this.min_valid_seqs = minSeq; |
| 103 | } | |
| 104 | ||
| 105 | /** | |
| 106 | * | |
| 107 | * @return true if non-standard nucleotides and amino acids should be replaced | |
| 108 | * or omitted | |
| 109 | * | |
| 110 | */ | |
| 111 | 0 | public boolean isFilterSymbols() |
| 112 | { | |
| 113 | 0 | return filterSymbols; |
| 114 | } | |
| 115 | ||
| 116 | /** | |
| 117 | * | |
| 118 | * @return true if service needs sequences all the same length (ie padded with | |
| 119 | * gaps if necessary) | |
| 120 | */ | |
| 121 | 0 | public boolean isNeedsAlignedSeqs() |
| 122 | { | |
| 123 | 0 | return needsAlignedSeqs; |
| 124 | } | |
| 125 | ||
| 126 | 3000 | public Class getClient() |
| 127 | { | |
| 128 | 3000 | return client; |
| 129 | } | |
| 130 | ||
| 131 | 0 | public void setClient(Class client) |
| 132 | { | |
| 133 | 0 | this.client = client; |
| 134 | } | |
| 135 | ||
| 136 | 3036 | public String getAAconToggle() |
| 137 | { | |
| 138 | 3036 | return AAconToggle; |
| 139 | } | |
| 140 | ||
| 141 | 0 | public void setAAconToggle(String aAconToggle) |
| 142 | { | |
| 143 | 0 | AAconToggle = aAconToggle; |
| 144 | } | |
| 145 | ||
| 146 | 3036 | public String getAAconToggleTooltip() |
| 147 | { | |
| 148 | 3036 | return AAconToggleTooltip; |
| 149 | } | |
| 150 | ||
| 151 | 0 | public void setAAconToggleTooltip(String aAconToggleTooltip) |
| 152 | { | |
| 153 | 0 | AAconToggleTooltip = aAconToggleTooltip; |
| 154 | } | |
| 155 | ||
| 156 | 3036 | public String getAAeditSettings() |
| 157 | { | |
| 158 | 3036 | return AAeditSettings; |
| 159 | } | |
| 160 | ||
| 161 | 0 | public void setAAeditSettings(String aAeditSettings) |
| 162 | { | |
| 163 | 0 | AAeditSettings = aAeditSettings; |
| 164 | } | |
| 165 | ||
| 166 | 3036 | public String getAAeditSettingsTooltip() |
| 167 | { | |
| 168 | 3036 | return AAeditSettingsTooltip; |
| 169 | } | |
| 170 | ||
| 171 | 0 | public void setAAeditSettingsTooltip(String aAeditSettingsTooltip) |
| 172 | { | |
| 173 | 0 | AAeditSettingsTooltip = aAeditSettingsTooltip; |
| 174 | } | |
| 175 | ||
| 176 | 0 | public int getMinimumSequences() |
| 177 | { | |
| 178 | 0 | return min_valid_seqs; |
| 179 | } | |
| 180 | ||
| 181 | } |