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package jalview.controller; |
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import jalview.analysis.AlignmentSorter; |
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import jalview.api.AlignViewControllerGuiI; |
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import jalview.api.AlignViewControllerI; |
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import jalview.api.AlignViewportI; |
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import jalview.api.AlignmentViewPanel; |
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import jalview.api.FeatureRenderer; |
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import jalview.commands.OrderCommand; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.ColumnSelection; |
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import jalview.datamodel.SequenceCollectionI; |
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import jalview.datamodel.SequenceFeature; |
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import jalview.datamodel.SequenceGroup; |
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import jalview.datamodel.SequenceI; |
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import jalview.io.DataSourceType; |
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import jalview.io.FeaturesFile; |
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import jalview.schemes.ColourSchemeI; |
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import jalview.util.MessageManager; |
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import java.awt.Color; |
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import java.util.BitSet; |
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import java.util.List; |
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| 49.6% |
Uncovered Elements: 128 (254) |
Complexity: 67 |
Complexity Density: 0.44 |
|
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public class AlignViewController implements AlignViewControllerI |
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{ |
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AlignViewportI viewport = null; |
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AlignmentViewPanel alignPanel = null; |
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private AlignViewControllerGuiI avcg; |
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| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
56 |
526 |
public AlignViewController(AlignViewControllerGuiI alignFrame,... |
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AlignViewportI vp, AlignmentViewPanel ap) |
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{ |
59 |
526 |
this.avcg = alignFrame; |
60 |
526 |
this.viewport = vp; |
61 |
526 |
this.alignPanel = ap; |
62 |
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} |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
64 |
89 |
@Override... |
65 |
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public void setViewportAndAlignmentPanel(AlignViewportI vp, |
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AlignmentViewPanel ap) |
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{ |
68 |
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this.alignPanel = ap; |
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89 |
this.viewport = vp; |
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} |
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| 0% |
Uncovered Elements: 35 (35) |
Complexity: 9 |
Complexity Density: 0.39 |
|
72 |
0 |
@Override... |
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public boolean makeGroupsFromSelection() |
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{ |
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0 |
SequenceGroup sg = viewport.getSelectionGroup(); |
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0 |
ColumnSelection cs = viewport.getColumnSelection(); |
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0 |
SequenceGroup[] gps = null; |
78 |
0 |
if (sg != null && (cs == null || cs.isEmpty())) |
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{ |
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gps = jalview.analysis.Grouping.makeGroupsFrom( |
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viewport.getSequenceSelection(), |
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viewport.getAlignmentView(true) |
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.getSequenceStrings(viewport.getGapCharacter()), |
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viewport.getAlignment().getGroups()); |
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} |
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else |
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{ |
88 |
0 |
if (cs != null) |
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{ |
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0 |
gps = jalview.analysis.Grouping.makeGroupsFromCols( |
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0 |
(sg == null) ? viewport.getAlignment().getSequencesArray() |
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: sg.getSequences().toArray(new SequenceI[0]), |
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cs, viewport.getAlignment().getGroups()); |
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} |
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} |
96 |
0 |
if (gps != null) |
97 |
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{ |
98 |
0 |
viewport.getAlignment().deleteAllGroups(); |
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0 |
viewport.clearSequenceColours(); |
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0 |
viewport.setSelectionGroup(null); |
101 |
0 |
ColourSchemeI colours = viewport.getGlobalColourScheme(); |
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|
103 |
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for (int g = 0; g < gps.length; g++) |
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{ |
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|
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0 |
gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo()); |
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0 |
viewport.getAlignment().addGroup(gps[g]); |
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if (colours != null) |
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{ |
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gps[g].setColourScheme(colours.getInstance(viewport, gps[g])); |
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} |
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Color col = new Color((int) (Math.random() * 255), |
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(int) (Math.random() * 255), (int) (Math.random() * 255)); |
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gps[g].idColour = col; |
115 |
0 |
viewport.setUpdateStructures(true); |
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viewport.addSequenceGroup(gps[g]); |
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} |
118 |
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return true; |
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} |
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return false; |
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} |
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| 0% |
Uncovered Elements: 7 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
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0 |
@Override... |
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public boolean createGroup() |
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{ |
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127 |
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SequenceGroup sg = viewport.getSelectionGroup(); |
128 |
0 |
if (sg != null) |
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{ |
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viewport.getAlignment().addGroup(sg); |
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0 |
return true; |
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} |
133 |
0 |
return false; |
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} |
135 |
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| 0% |
Uncovered Elements: 7 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
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0 |
@Override... |
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public boolean unGroup() |
138 |
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{ |
139 |
0 |
SequenceGroup sg = viewport.getSelectionGroup(); |
140 |
0 |
if (sg != null) |
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{ |
142 |
0 |
viewport.getAlignment().deleteGroup(sg); |
143 |
0 |
return true; |
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} |
145 |
0 |
return false; |
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} |
147 |
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| 0% |
Uncovered Elements: 8 (8) |
Complexity: 3 |
Complexity Density: 0.5 |
|
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0 |
@Override... |
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public boolean deleteGroups() |
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{ |
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if (viewport.getAlignment().getGroups() != null |
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&& viewport.getAlignment().getGroups().size() > 0) |
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{ |
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viewport.getAlignment().deleteAllGroups(); |
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viewport.clearSequenceColours(); |
156 |
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viewport.setSelectionGroup(null); |
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return true; |
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} |
159 |
0 |
return false; |
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} |
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| 84.6% |
Uncovered Elements: 6 (39) |
Complexity: 11 |
Complexity Density: 0.52 |
|
162 |
12 |
@Override... |
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public boolean markColumnsContainingFeatures(boolean invert, |
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boolean extendCurrent, boolean toggle, String featureType) |
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{ |
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BitSet bs = new BitSet(); |
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boolean searchSelection = viewport.getSelectionGroup() != null |
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&& !extendCurrent; |
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SequenceCollectionI sqcol = searchSelection ? viewport |
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.getSelectionGroup() : viewport.getAlignment(); |
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|
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int nseq = findColumnsWithFeature(featureType, sqcol, bs); |
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|
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12 |
ColumnSelection cs = viewport.getColumnSelection(); |
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12 |
if (cs == null) |
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{ |
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cs = new ColumnSelection(); |
180 |
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} |
181 |
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182 |
12 |
if (bs.cardinality() > 0 || invert) |
183 |
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{ |
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10 |
boolean changed = cs.markColumns(bs, sqcol.getStartRes(), |
185 |
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sqcol.getEndRes(), invert, extendCurrent, toggle); |
186 |
10 |
if (changed) |
187 |
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{ |
188 |
9 |
viewport.setColumnSelection(cs); |
189 |
9 |
alignPanel.paintAlignment(false, false); |
190 |
9 |
int columnCount = invert |
191 |
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? (sqcol.getEndRes() - sqcol.getStartRes() + 1) |
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- bs.cardinality() |
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: bs.cardinality(); |
194 |
9 |
avcg.setStatus(MessageManager.formatMessage( |
195 |
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"label.view_controller_toggled_marked", new String[] |
196 |
9 |
{ toggle ? MessageManager.getString("label.toggled") |
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: MessageManager.getString("label.marked"), |
198 |
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String.valueOf(columnCount), |
199 |
9 |
invert ? MessageManager |
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.getString("label.not_containing") |
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: MessageManager.getString("label.containing"), |
202 |
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featureType, Integer.valueOf(nseq).toString() })); |
203 |
9 |
return true; |
204 |
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} |
205 |
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} |
206 |
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else |
207 |
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{ |
208 |
2 |
String key = searchSelection ? "label.no_feature_found_selection" |
209 |
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: "label.no_feature_of_type_found"; |
210 |
2 |
avcg.setStatus(MessageManager.formatMessage(key, |
211 |
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new String[] { featureType })); |
212 |
2 |
if (!extendCurrent) |
213 |
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{ |
214 |
2 |
cs.clear(); |
215 |
2 |
alignPanel.paintAlignment(false, false); |
216 |
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} |
217 |
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} |
218 |
3 |
return false; |
219 |
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} |
220 |
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221 |
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223 |
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224 |
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225 |
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226 |
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227 |
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@param |
228 |
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@param |
229 |
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@param |
230 |
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@return |
231 |
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| 92% |
Uncovered Elements: 4 (50) |
Complexity: 13 |
Complexity Density: 0.43 |
|
232 |
20 |
int findColumnsWithFeature(String featureType,... |
233 |
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SequenceCollectionI sqcol, BitSet bs) |
234 |
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{ |
235 |
20 |
FeatureRenderer fr = alignPanel == null ? null : alignPanel |
236 |
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.getFeatureRenderer(); |
237 |
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|
238 |
20 |
final int startColumn = sqcol.getStartRes() + 1; |
239 |
20 |
final int endColumn = sqcol.getEndRes() + 1; |
240 |
20 |
List<SequenceI> seqs = sqcol.getSequences(); |
241 |
20 |
int nseq = 0; |
242 |
20 |
for (SequenceI sq : seqs) |
243 |
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{ |
244 |
92 |
if (sq != null) |
245 |
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{ |
246 |
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|
247 |
92 |
List<SequenceFeature> sfs = sq.findFeatures(startColumn, |
248 |
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endColumn, featureType); |
249 |
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|
250 |
92 |
boolean found = false; |
251 |
92 |
for (SequenceFeature sf : sfs) |
252 |
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{ |
253 |
545 |
if (fr.getColour(sf) == null) |
254 |
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{ |
255 |
3 |
continue; |
256 |
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} |
257 |
542 |
if (!found) |
258 |
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{ |
259 |
58 |
nseq++; |
260 |
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} |
261 |
542 |
found = true; |
262 |
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|
263 |
542 |
int sfStartCol = sq.findIndex(sf.getBegin()); |
264 |
542 |
int sfEndCol = sq.findIndex(sf.getEnd()); |
265 |
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|
266 |
542 |
if (sf.isContactFeature()) |
267 |
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{ |
268 |
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269 |
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|
270 |
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|
271 |
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|
272 |
1 |
if (sfStartCol >= startColumn && sfStartCol <= endColumn) |
273 |
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{ |
274 |
1 |
bs.set(sfStartCol - 1); |
275 |
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} |
276 |
1 |
if (sfEndCol >= startColumn && sfEndCol <= endColumn) |
277 |
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{ |
278 |
1 |
bs.set(sfEndCol - 1); |
279 |
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} |
280 |
1 |
continue; |
281 |
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} |
282 |
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283 |
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284 |
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285 |
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|
286 |
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|
287 |
541 |
if (sfStartCol < startColumn) |
288 |
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{ |
289 |
1 |
sfStartCol = startColumn; |
290 |
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} |
291 |
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292 |
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|
293 |
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|
294 |
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|
295 |
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|
296 |
541 |
if (sfEndCol > endColumn) |
297 |
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{ |
298 |
4 |
sfEndCol = endColumn; |
299 |
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} |
300 |
25219 |
for (; sfStartCol <= sfEndCol; sfStartCol++) |
301 |
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{ |
302 |
24678 |
bs.set(sfStartCol - 1); |
303 |
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} |
304 |
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} |
305 |
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} |
306 |
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} |
307 |
20 |
return nseq; |
308 |
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} |
309 |
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|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
310 |
0 |
@Override... |
311 |
|
public void sortAlignmentByFeatureDensity(List<String> typ) |
312 |
|
{ |
313 |
0 |
String methodText = MessageManager.getString("label.sort_by_density"); |
314 |
0 |
sortByFeatures(typ, methodText, AlignmentSorter.FEATURE_DENSITY); |
315 |
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} |
316 |
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317 |
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318 |
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319 |
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320 |
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321 |
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322 |
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323 |
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@param |
324 |
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@param |
325 |
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|
326 |
|
@param |
327 |
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|
328 |
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|
329 |
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|
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|
| 0% |
Uncovered Elements: 28 (28) |
Complexity: 6 |
Complexity Density: 0.3 |
|
330 |
0 |
protected void sortByFeatures(List<String> types, String methodText,... |
331 |
|
final String method) |
332 |
|
{ |
333 |
0 |
FeatureRenderer fr = alignPanel.getFeatureRenderer(); |
334 |
0 |
if (types == null && fr != null) |
335 |
|
{ |
336 |
0 |
types = fr.getDisplayedFeatureTypes(); |
337 |
|
} |
338 |
0 |
if (types.isEmpty()) |
339 |
|
{ |
340 |
0 |
return; |
341 |
|
} |
342 |
0 |
List<String> gps = null; |
343 |
0 |
if (fr != null) |
344 |
|
{ |
345 |
0 |
gps = fr.getDisplayedFeatureGroups(); |
346 |
|
} |
347 |
0 |
AlignmentI al = viewport.getAlignment(); |
348 |
|
|
349 |
0 |
int start, stop; |
350 |
0 |
SequenceGroup sg = viewport.getSelectionGroup(); |
351 |
0 |
if (sg != null) |
352 |
|
{ |
353 |
0 |
start = sg.getStartRes(); |
354 |
0 |
stop = sg.getEndRes(); |
355 |
|
} |
356 |
|
else |
357 |
|
{ |
358 |
0 |
start = 0; |
359 |
0 |
stop = al.getWidth(); |
360 |
|
} |
361 |
0 |
SequenceI[] oldOrder = al.getSequencesArray(); |
362 |
0 |
AlignmentSorter.sortByFeature(types, gps, start, stop, al, method); |
363 |
0 |
avcg.addHistoryItem(new OrderCommand(methodText, oldOrder, |
364 |
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viewport.getAlignment())); |
365 |
0 |
alignPanel.paintAlignment(true, false); |
366 |
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|
367 |
|
} |
368 |
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|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
369 |
0 |
@Override... |
370 |
|
public void sortAlignmentByFeatureScore(List<String> typ) |
371 |
|
{ |
372 |
0 |
String methodText = MessageManager.getString("label.sort_by_score"); |
373 |
0 |
sortByFeatures(typ, methodText, AlignmentSorter.FEATURE_SCORE); |
374 |
|
} |
375 |
|
|
|
|
| 73.7% |
Uncovered Elements: 5 (19) |
Complexity: 5 |
Complexity Density: 0.38 |
|
376 |
3 |
@Override... |
377 |
|
public boolean parseFeaturesFile(Object file, DataSourceType protocol, |
378 |
|
boolean relaxedIdMatching) |
379 |
|
{ |
380 |
3 |
boolean featuresAdded = false; |
381 |
3 |
FeatureRenderer fr = alignPanel.getFeatureRenderer(); |
382 |
3 |
try |
383 |
|
{ |
384 |
3 |
featuresAdded = new FeaturesFile(false, file, protocol).parse( |
385 |
|
viewport.getAlignment().getDataset(), fr.getFeatureColours(), |
386 |
|
fr.getFeatureFilters(), false, relaxedIdMatching); |
387 |
|
} catch (Exception ex) |
388 |
|
{ |
389 |
0 |
ex.printStackTrace(); |
390 |
|
} |
391 |
|
|
392 |
3 |
if (featuresAdded) |
393 |
|
{ |
394 |
3 |
avcg.refreshFeatureUI(true); |
395 |
3 |
if (fr != null) |
396 |
|
{ |
397 |
|
|
398 |
3 |
fr.findAllFeatures(true); |
399 |
|
} |
400 |
3 |
if (avcg.getFeatureSettingsUI() != null) |
401 |
|
{ |
402 |
0 |
avcg.getFeatureSettingsUI().discoverAllFeatureData(); |
403 |
|
} |
404 |
3 |
alignPanel.paintAlignment(true, true); |
405 |
|
} |
406 |
|
|
407 |
3 |
return featuresAdded; |
408 |
|
|
409 |
|
} |
410 |
|
|
|
|
| 56.4% |
Uncovered Elements: 17 (39) |
Complexity: 12 |
Complexity Density: 0.57 |
|
411 |
2 |
@Override... |
412 |
|
public boolean markHighlightedColumns(boolean invert, |
413 |
|
boolean extendCurrent, boolean toggle) |
414 |
|
{ |
415 |
2 |
if (!viewport.hasSearchResults()) |
416 |
|
{ |
417 |
|
|
418 |
0 |
return false; |
419 |
|
} |
420 |
|
|
421 |
2 |
BitSet bs = new BitSet(); |
422 |
2 |
SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null |
423 |
|
|| extendCurrent) ? viewport.getAlignment() |
424 |
|
: viewport.getSelectionGroup(); |
425 |
|
|
426 |
|
|
427 |
|
|
428 |
2 |
int nseq = viewport.getSearchResults().markColumns(sqcol, bs); |
429 |
|
|
430 |
2 |
ColumnSelection cs = viewport.getColumnSelection(); |
431 |
2 |
if (cs == null) |
432 |
|
{ |
433 |
0 |
cs = new ColumnSelection(); |
434 |
|
} |
435 |
|
|
436 |
2 |
if (bs.cardinality() > 0 || invert) |
437 |
|
{ |
438 |
2 |
boolean changed = cs.markColumns(bs, sqcol.getStartRes(), |
439 |
|
sqcol.getEndRes(), invert, extendCurrent, toggle); |
440 |
2 |
if (changed) |
441 |
|
{ |
442 |
2 |
viewport.setColumnSelection(cs); |
443 |
2 |
alignPanel.paintAlignment(false, false); |
444 |
2 |
int columnCount = invert |
445 |
|
? (sqcol.getEndRes() - sqcol.getStartRes() + 1) |
446 |
|
- bs.cardinality() |
447 |
|
: bs.cardinality(); |
448 |
2 |
avcg.setStatus(MessageManager.formatMessage( |
449 |
|
"label.view_controller_toggled_marked", new String[] |
450 |
2 |
{ toggle ? MessageManager.getString("label.toggled") |
451 |
|
: MessageManager.getString("label.marked"), |
452 |
|
String.valueOf(columnCount), |
453 |
2 |
invert ? MessageManager |
454 |
|
.getString("label.not_containing") |
455 |
|
: MessageManager.getString("label.containing"), |
456 |
|
"Highlight", Integer.valueOf(nseq).toString() })); |
457 |
2 |
return true; |
458 |
|
} |
459 |
|
} |
460 |
|
else |
461 |
|
{ |
462 |
0 |
avcg.setStatus(MessageManager.getString("label.no_highlighted_regions_marked")); |
463 |
0 |
if (!extendCurrent) |
464 |
|
{ |
465 |
0 |
cs.clear(); |
466 |
0 |
alignPanel.paintAlignment(false, false); |
467 |
|
} |
468 |
|
} |
469 |
0 |
return false; |
470 |
|
} |
471 |
|
|
472 |
|
} |