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1 | 1 | package tudelft.ti2806.pl3.metafilter;
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2 | 2 |
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3 | 3 | import org.apache.commons.lang.math.IntRange;
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| 4 | +import tudelft.ti2806.pl3.Constants; |
4 | 5 | import tudelft.ti2806.pl3.ControllerContainer;
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5 | 6 | import tudelft.ti2806.pl3.data.Gender;
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6 | 7 | import tudelft.ti2806.pl3.data.Genome;
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10 | 11 | import tudelft.ti2806.pl3.ui.util.DialogUtil;
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11 | 12 | import tudelft.ti2806.pl3.visualization.GraphController;
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12 | 13 |
|
13 |
| -import javax.swing.JOptionPane; |
14 | 14 | import java.util.ArrayList;
|
15 | 15 | import java.util.List;
|
16 | 16 | import java.util.stream.Collectors;
|
17 | 17 |
|
18 | 18 | /**
|
| 19 | + * MetaFilterController controls the {@link MetaFilterView} and |
| 20 | + * handles the selected chooses from the user. |
19 | 21 | * Created by Tom Brouws on 16-06-15.
|
20 | 22 | */
|
21 | 23 | public class MetaFilterController {
|
22 | 24 |
|
23 |
| - private final AbstractGraphData graphData; |
24 |
| - private final ControllerContainer cc; |
25 |
| - private MetaFilterView metaFilterView; |
26 |
| - |
27 |
| - /** |
28 |
| - * Construct the controller and instantiate the view. |
29 |
| - * |
30 |
| - * @param cc |
31 |
| - * Reference to all controllers |
32 |
| - * @param graphData |
33 |
| - * Contains the gene data |
34 |
| - */ |
35 |
| - public MetaFilterController(ControllerContainer cc, GraphDataRepository graphData) { |
36 |
| - this.cc = cc; |
37 |
| - this.graphData = graphData; |
38 |
| - metaFilterView = new MetaFilterView(); |
39 |
| - } |
40 |
| - |
41 |
| - /** |
42 |
| - * Compute the gender from input. |
43 |
| - * |
44 |
| - * @param input |
45 |
| - * the input |
46 |
| - * @return the gender |
47 |
| - */ |
48 |
| - private Gender computeGender(String input) { |
49 |
| - if (input.equals("Female")) { |
50 |
| - return Gender.FEMALE; |
51 |
| - } else if (input.equals("Male")) { |
52 |
| - return Gender.MALE; |
53 |
| - } else { |
54 |
| - return null; |
55 |
| - } |
56 |
| - } |
57 |
| - |
58 |
| - /** |
59 |
| - * Compute the HIV status from input. |
60 |
| - * |
61 |
| - * @param input |
62 |
| - * the input |
63 |
| - * @return the HIV status |
64 |
| - */ |
65 |
| - private boolean computeHivStatus(String input) { |
66 |
| - if (input.equals("Positive")) { |
67 |
| - return true; |
68 |
| - } else { |
69 |
| - return false; |
70 |
| - } |
71 |
| - } |
72 |
| - |
73 |
| - /** |
74 |
| - * Compute the age range from input. |
75 |
| - * |
76 |
| - * @param input |
77 |
| - * the input |
78 |
| - * @return the age range |
79 |
| - */ |
80 |
| - private IntRange computeAge(String input) { |
81 |
| - String[] tokens = input.split("-"); |
82 |
| - try { |
83 |
| - int rangeStart = Integer.parseInt(tokens[0]); |
84 |
| - int rangeEnd = Integer.parseInt(tokens[1]); |
85 |
| - return new IntRange(rangeStart, rangeEnd); |
86 |
| - } catch (ArrayIndexOutOfBoundsException e) { |
87 |
| - return new IntRange(0, Integer.parseInt(tokens[0])); |
88 |
| - } catch (NumberFormatException e) { |
89 |
| - return new IntRange(0, 0); |
90 |
| - } |
91 |
| - } |
92 |
| - |
93 |
| - /** |
94 |
| - * Opens the dialog which lets the user select a gene.<br> |
95 |
| - * After a gene is selected, it will do a call to the {@link GraphController} to navigate to the start of that |
96 |
| - * gene. |
97 |
| - */ |
98 |
| - public void openDialog() { |
99 |
| - JOptionPane |
100 |
| - .showMessageDialog(null, metaFilterView, "Select options to filter on:", JOptionPane.QUESTION_MESSAGE); |
101 |
| - |
102 |
| - List<Genome> firstGenomeList = new ArrayList<>(); |
103 |
| - Gender selectedGender = computeGender(metaFilterView.getGender()); |
104 |
| - String selectedLocation = metaFilterView.getStrainLocation(); |
105 |
| - String selectedIsolationDate = metaFilterView.getIsolationDate(); |
106 |
| - |
107 |
| - final boolean selectedHivStatus; |
108 |
| - final boolean checkHiv; |
109 |
| - if (metaFilterView.getHivStatus().equals("- None -")) { |
110 |
| - checkHiv = false; |
111 |
| - selectedHivStatus = false; |
112 |
| - } else { |
113 |
| - selectedHivStatus = computeHivStatus(metaFilterView.getHivStatus()); |
114 |
| - checkHiv = true; |
115 |
| - } |
116 |
| - |
117 |
| - firstGenomeList.addAll(graphData.getGenomes().stream().filter( |
118 |
| - genome -> (selectedGender == null || genome.getGender().equals(selectedGender)) |
119 |
| - && (selectedLocation.equals("") || genome.getLocation().equals(selectedLocation)) |
120 |
| - && (selectedIsolationDate.equals("") || genome.getIsolationDate().equals(selectedIsolationDate)) |
121 |
| - && (!checkHiv || genome.getHivStatus() == selectedHivStatus)).collect( |
122 |
| - Collectors.toList())); |
123 |
| - |
124 |
| - |
125 |
| - filterGraph(filterOnAge(computeAge(metaFilterView.getAge()), firstGenomeList)); |
126 |
| - } |
127 |
| - |
128 |
| - /** |
129 |
| - * Filter the genome set on age or age range after other filters are applied. |
130 |
| - * |
131 |
| - * @param selectedAge |
132 |
| - * the selected age range |
133 |
| - * @param genomes |
134 |
| - * the result set of earlier filters |
135 |
| - * @return the final result set |
136 |
| - */ |
137 |
| - private List<String> filterOnAge(IntRange selectedAge, List<Genome> genomes) { |
138 |
| - List<String> genomeList = new ArrayList<>(); |
139 |
| - if (selectedAge.getMaximumInteger() == 0) { |
140 |
| - genomeList = genomes.stream().map(Genome::getIdentifier).collect(Collectors.toList()); |
141 |
| - } else if (selectedAge.getMinimumInteger() == 0) { |
142 |
| - genomeList.addAll(genomes.stream().filter( |
143 |
| - genome -> selectedAge.getMaximumInteger() == genome.getAge()).map(Genome::getIdentifier).collect( |
144 |
| - Collectors.toList())); |
145 |
| - } else { |
146 |
| - genomeList.addAll(genomes.stream().filter( |
147 |
| - genome -> selectedAge.containsInteger(genome.getAge())).map(Genome::getIdentifier).collect( |
148 |
| - Collectors.toList())); |
149 |
| - } |
150 |
| - return genomeList; |
151 |
| - } |
152 |
| - |
153 |
| - /** |
154 |
| - * Filter the graph on the result set from the query. |
155 |
| - * |
156 |
| - * @param genomeList |
157 |
| - * the result set |
158 |
| - */ |
159 |
| - private void filterGraph(List<String> genomeList) { |
160 |
| - if (genomeList.size() > 1) { |
161 |
| - cc.getGraphController().addFilter(GenomeFilter.NAME, new GenomeFilter(genomeList)); |
162 |
| - } else if (genomeList.size() == 1) { |
163 |
| - DialogUtil.displayMessage("One genome found", |
164 |
| - "Just one genome has been found for the selected metadata, TKK_REF has been added to the filter " + |
165 |
| - "set."); |
166 |
| - genomeList.add("TKK_REF"); |
167 |
| - cc.getGraphController().addFilter(GenomeFilter.NAME, new GenomeFilter(genomeList)); |
168 |
| - } else { |
169 |
| - if (DialogUtil.confirm("No genomes found", |
170 |
| - "No genomes are found for the selected metadata, want to enter new data?")) { |
171 |
| - openDialog(); |
172 |
| - } |
173 |
| - } |
174 |
| - } |
| 25 | + private final AbstractGraphData graphData; |
| 26 | + private final ControllerContainer cc; |
| 27 | + private MetaFilterView metaFilterView; |
| 28 | + |
| 29 | + /** |
| 30 | + * Construct the controller and instantiate the view. |
| 31 | + * |
| 32 | + * @param cc |
| 33 | + * Reference to all controllers |
| 34 | + * @param graphData |
| 35 | + * Contains the gene data |
| 36 | + */ |
| 37 | + public MetaFilterController(ControllerContainer cc, GraphDataRepository graphData) { |
| 38 | + this.cc = cc; |
| 39 | + this.graphData = graphData; |
| 40 | + metaFilterView = new MetaFilterView(); |
| 41 | + } |
| 42 | + |
| 43 | + /** |
| 44 | + * Compute the gender from input. |
| 45 | + * |
| 46 | + * @param input |
| 47 | + * the input |
| 48 | + * @return the gender |
| 49 | + */ |
| 50 | + private Gender computeGender(String input) { |
| 51 | + if (input.equals("Female")) { |
| 52 | + return Gender.FEMALE; |
| 53 | + } else if (input.equals("Male")) { |
| 54 | + return Gender.MALE; |
| 55 | + } else { |
| 56 | + return null; |
| 57 | + } |
| 58 | + } |
| 59 | + |
| 60 | + /** |
| 61 | + * Compute the HIV status from input. |
| 62 | + * |
| 63 | + * @param input |
| 64 | + * the input |
| 65 | + * @return the HIV status |
| 66 | + */ |
| 67 | + private boolean computeHivStatus(String input) { |
| 68 | + if (input.equals("Positive")) { |
| 69 | + return true; |
| 70 | + } else { |
| 71 | + return false; |
| 72 | + } |
| 73 | + } |
| 74 | + |
| 75 | + /** |
| 76 | + * Compute the age range from input. |
| 77 | + * |
| 78 | + * @param input |
| 79 | + * the input |
| 80 | + * @return the age range |
| 81 | + */ |
| 82 | + private IntRange computeAge(String input) { |
| 83 | + String[] tokens = input.split("-"); |
| 84 | + try { |
| 85 | + int rangeStart = Integer.parseInt(tokens[0]); |
| 86 | + int rangeEnd = Integer.parseInt(tokens[1]); |
| 87 | + return new IntRange(rangeStart, rangeEnd); |
| 88 | + } catch (ArrayIndexOutOfBoundsException e) { |
| 89 | + return new IntRange(0, Integer.parseInt(tokens[0])); |
| 90 | + } catch (NumberFormatException e) { |
| 91 | + return new IntRange(0, 0); |
| 92 | + } |
| 93 | + } |
| 94 | + |
| 95 | + /** |
| 96 | + * Opens the dialog which lets the user select a gene.<br> |
| 97 | + * After a gene is selected, it will do a call to the {@link GraphController} to navigate to the start of that |
| 98 | + * gene. |
| 99 | + */ |
| 100 | + public void openDialog() { |
| 101 | + DialogUtil.displayMessageWithView(metaFilterView, Constants.META_VIEW_TITLE); |
| 102 | + List<Genome> firstGenomeList = new ArrayList<>(); |
| 103 | + Gender selectedGender = computeGender(metaFilterView.getGender()); |
| 104 | + String selectedLocation = metaFilterView.getStrainLocation(); |
| 105 | + String selectedIsolationDate = metaFilterView.getIsolationDate(); |
| 106 | + |
| 107 | + final boolean selectedHivStatus; |
| 108 | + final boolean checkHiv; |
| 109 | + if (metaFilterView.getHivStatus().equals("- None -")) { |
| 110 | + checkHiv = false; |
| 111 | + selectedHivStatus = false; |
| 112 | + } else { |
| 113 | + selectedHivStatus = computeHivStatus(metaFilterView.getHivStatus()); |
| 114 | + checkHiv = true; |
| 115 | + } |
| 116 | + |
| 117 | + firstGenomeList.addAll(graphData.getGenomes().stream().filter( |
| 118 | + genome -> (selectedGender == null || genome.getGender().equals(selectedGender)) |
| 119 | + && (selectedLocation.equals("") || genome.getLocation().equals(selectedLocation)) |
| 120 | + && (selectedIsolationDate.equals("") |
| 121 | + || genome.getIsolationDate().equals(selectedIsolationDate)) |
| 122 | + && (!checkHiv || genome.getHivStatus() == selectedHivStatus)).collect( |
| 123 | + Collectors.toList())); |
| 124 | + |
| 125 | + |
| 126 | + filterGraph(filterOnAge(computeAge(metaFilterView.getAge()), firstGenomeList)); |
| 127 | + } |
| 128 | + |
| 129 | + /** |
| 130 | + * Filter the genome set on age or age range after other filters are applied. |
| 131 | + * |
| 132 | + * @param selectedAge |
| 133 | + * the selected age range |
| 134 | + * @param genomes |
| 135 | + * the result set of earlier filters |
| 136 | + * @return the final result set |
| 137 | + */ |
| 138 | + private List<String> filterOnAge(IntRange selectedAge, List<Genome> genomes) { |
| 139 | + List<String> genomeList = new ArrayList<>(); |
| 140 | + if (selectedAge.getMaximumInteger() == 0) { |
| 141 | + genomeList = genomes.stream().map(Genome::getIdentifier).collect(Collectors.toList()); |
| 142 | + } else if (selectedAge.getMinimumInteger() == 0) { |
| 143 | + genomeList.addAll(genomes.stream().filter( |
| 144 | + genome -> selectedAge.getMaximumInteger() == genome.getAge()).map(Genome::getIdentifier).collect( |
| 145 | + Collectors.toList())); |
| 146 | + } else { |
| 147 | + genomeList.addAll(genomes.stream().filter( |
| 148 | + genome -> selectedAge.containsInteger(genome.getAge())).map(Genome::getIdentifier).collect( |
| 149 | + Collectors.toList())); |
| 150 | + } |
| 151 | + return genomeList; |
| 152 | + } |
| 153 | + |
| 154 | + /** |
| 155 | + * Filter the graph on the result set from the query. |
| 156 | + * |
| 157 | + * @param genomeList |
| 158 | + * the result set |
| 159 | + */ |
| 160 | + private void filterGraph(List<String> genomeList) { |
| 161 | + if (genomeList.size() > 1) { |
| 162 | + cc.getGraphController().addFilter(GenomeFilter.NAME, new GenomeFilter(genomeList)); |
| 163 | + } else if (genomeList.size() == 1) { |
| 164 | + DialogUtil.displayMessage("One genome found", |
| 165 | + "Just one genome has been found for the selected metadata, TKK_REF has been added to the filter " |
| 166 | + + "set."); |
| 167 | + genomeList.add("TKK_REF"); |
| 168 | + cc.getGraphController().addFilter(GenomeFilter.NAME, new GenomeFilter(genomeList)); |
| 169 | + } else { |
| 170 | + if (DialogUtil.confirm("No genomes found", |
| 171 | + "No genomes are found for the selected metadata, want to enter new data?")) { |
| 172 | + openDialog(); |
| 173 | + } |
| 174 | + } |
| 175 | + } |
175 | 176 | }
|
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