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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.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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| 51% |
Uncovered Elements: 117 (239) |
Complexity: 65 |
Complexity Density: 0.45 |
|
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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 |
|
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public AlignViewController(AlignViewControllerGuiI alignFrame,... |
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AlignViewportI vp, AlignmentViewPanel ap) |
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{ |
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this.avcg = alignFrame; |
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this.viewport = vp; |
60 |
435 |
this.alignPanel = ap; |
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} |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
63 |
91 |
@Override... |
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public void setViewportAndAlignmentPanel(AlignViewportI vp, |
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AlignmentViewPanel ap) |
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{ |
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this.alignPanel = ap; |
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this.viewport = vp; |
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} |
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| 0% |
Uncovered Elements: 30 (30) |
Complexity: 8 |
Complexity Density: 0.4 |
|
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0 |
@Override... |
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public boolean makeGroupsFromSelection() |
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{ |
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SequenceGroup sg = viewport.getSelectionGroup(); |
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ColumnSelection cs = viewport.getColumnSelection(); |
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SequenceGroup[] gps = null; |
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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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{ |
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if (cs != null) |
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{ |
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gps = jalview.analysis.Grouping.makeGroupsFromCols( |
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(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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} |
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if (gps != null) |
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{ |
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viewport.getAlignment().deleteAllGroups(); |
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viewport.clearSequenceColours(); |
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viewport.setSelectionGroup(null); |
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|
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for (int g = 0; g < gps.length; g++) |
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{ |
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gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo()); |
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viewport.getAlignment().addGroup(gps[g]); |
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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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col = col.brighter(); |
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for (SequenceI sq : gps[g].getSequences(null)) |
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{ |
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viewport.setSequenceColour(sq, col); |
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} |
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} |
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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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SequenceGroup sg = viewport.getSelectionGroup(); |
124 |
0 |
if (sg != null) |
125 |
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{ |
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viewport.getAlignment().addGroup(sg); |
127 |
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return true; |
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} |
129 |
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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 unGroup() |
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{ |
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SequenceGroup sg = viewport.getSelectionGroup(); |
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0 |
if (sg != null) |
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{ |
138 |
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viewport.getAlignment().deleteGroup(sg); |
139 |
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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: 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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{ |
147 |
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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(); |
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viewport.setSelectionGroup(null); |
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return true; |
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} |
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return false; |
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} |
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| 85.7% |
Uncovered Elements: 5 (35) |
Complexity: 11 |
Complexity Density: 0.58 |
|
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8 |
@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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SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null |
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|| extendCurrent) ? viewport.getAlignment() |
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: viewport.getSelectionGroup(); |
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int nseq = findColumnsWithFeature(featureType, sqcol, bs); |
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ColumnSelection cs = viewport.getColumnSelection(); |
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if (cs == null) |
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{ |
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cs = new ColumnSelection(); |
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} |
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8 |
if (bs.cardinality() > 0 || invert) |
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{ |
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boolean changed = cs.markColumns(bs, sqcol.getStartRes(), |
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sqcol.getEndRes(), invert, extendCurrent, toggle); |
181 |
6 |
if (changed) |
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{ |
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viewport.setColumnSelection(cs); |
184 |
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alignPanel.paintAlignment(false, false); |
185 |
5 |
int columnCount = invert |
186 |
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? (sqcol.getEndRes() - sqcol.getStartRes() + 1) |
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- bs.cardinality() |
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: bs.cardinality(); |
189 |
5 |
avcg.setStatus(MessageManager.formatMessage( |
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"label.view_controller_toggled_marked", new String[] |
191 |
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{ toggle ? MessageManager.getString("label.toggled") |
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: MessageManager.getString("label.marked"), |
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String.valueOf(columnCount), |
194 |
5 |
invert ? MessageManager |
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.getString("label.not_containing") |
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: MessageManager.getString("label.containing"), |
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featureType, Integer.valueOf(nseq).toString() })); |
198 |
5 |
return true; |
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} |
200 |
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} |
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else |
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{ |
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2 |
avcg.setStatus(MessageManager |
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.formatMessage("label.no_feature_of_type_found", new String[] |
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{ featureType })); |
206 |
2 |
if (!extendCurrent) |
207 |
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{ |
208 |
2 |
cs.clear(); |
209 |
2 |
alignPanel.paintAlignment(false, false); |
210 |
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} |
211 |
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} |
212 |
3 |
return false; |
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} |
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218 |
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219 |
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@param |
222 |
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@param |
223 |
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@param |
224 |
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@return |
225 |
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| 90% |
Uncovered Elements: 5 (50) |
Complexity: 13 |
Complexity Density: 0.43 |
|
226 |
16 |
int findColumnsWithFeature(String featureType,... |
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SequenceCollectionI sqcol, BitSet bs) |
228 |
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{ |
229 |
16 |
FeatureRenderer fr = alignPanel == null ? null : alignPanel |
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.getFeatureRenderer(); |
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|
232 |
16 |
final int startColumn = sqcol.getStartRes() + 1; |
233 |
16 |
final int endColumn = sqcol.getEndRes() + 1; |
234 |
16 |
List<SequenceI> seqs = sqcol.getSequences(); |
235 |
16 |
int nseq = 0; |
236 |
16 |
for (SequenceI sq : seqs) |
237 |
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{ |
238 |
48 |
if (sq != null) |
239 |
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{ |
240 |
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|
241 |
48 |
List<SequenceFeature> sfs = sq.findFeatures(startColumn, |
242 |
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endColumn, featureType); |
243 |
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244 |
48 |
boolean found = false; |
245 |
48 |
for (SequenceFeature sf : sfs) |
246 |
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{ |
247 |
17 |
if (fr.getColour(sf) == null) |
248 |
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{ |
249 |
3 |
continue; |
250 |
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} |
251 |
14 |
if (!found) |
252 |
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{ |
253 |
14 |
nseq++; |
254 |
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} |
255 |
14 |
found = true; |
256 |
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|
257 |
14 |
int sfStartCol = sq.findIndex(sf.getBegin()); |
258 |
14 |
int sfEndCol = sq.findIndex(sf.getEnd()); |
259 |
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|
260 |
14 |
if (sf.isContactFeature()) |
261 |
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{ |
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263 |
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264 |
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265 |
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|
266 |
1 |
if (sfStartCol >= startColumn && sfStartCol <= endColumn) |
267 |
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{ |
268 |
1 |
bs.set(sfStartCol - 1); |
269 |
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} |
270 |
1 |
if (sfEndCol >= startColumn && sfEndCol <= endColumn) |
271 |
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{ |
272 |
1 |
bs.set(sfEndCol - 1); |
273 |
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} |
274 |
1 |
continue; |
275 |
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} |
276 |
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277 |
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278 |
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279 |
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280 |
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|
281 |
13 |
if (sfStartCol < startColumn) |
282 |
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{ |
283 |
1 |
sfStartCol = startColumn; |
284 |
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} |
285 |
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286 |
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287 |
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288 |
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289 |
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|
290 |
13 |
if (sfEndCol > endColumn) |
291 |
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{ |
292 |
4 |
sfEndCol = endColumn; |
293 |
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} |
294 |
55 |
for (; sfStartCol <= sfEndCol; sfStartCol++) |
295 |
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{ |
296 |
42 |
bs.set(sfStartCol - 1); |
297 |
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} |
298 |
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} |
299 |
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} |
300 |
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} |
301 |
16 |
return nseq; |
302 |
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} |
303 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
304 |
0 |
@Override... |
305 |
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public void sortAlignmentByFeatureDensity(List<String> typ) |
306 |
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{ |
307 |
0 |
sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY); |
308 |
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} |
309 |
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|
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|
| 0% |
Uncovered Elements: 24 (24) |
Complexity: 5 |
Complexity Density: 0.28 |
|
310 |
0 |
protected void sortBy(List<String> typ, String methodText,... |
311 |
|
final String method) |
312 |
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{ |
313 |
0 |
FeatureRenderer fr = alignPanel.getFeatureRenderer(); |
314 |
0 |
if (typ == null && fr != null) |
315 |
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{ |
316 |
0 |
typ = fr.getDisplayedFeatureTypes(); |
317 |
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} |
318 |
0 |
List<String> gps = null; |
319 |
0 |
if (fr != null) |
320 |
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{ |
321 |
0 |
gps = fr.getDisplayedFeatureGroups(); |
322 |
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} |
323 |
0 |
AlignmentI al = viewport.getAlignment(); |
324 |
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|
325 |
0 |
int start, stop; |
326 |
0 |
SequenceGroup sg = viewport.getSelectionGroup(); |
327 |
0 |
if (sg != null) |
328 |
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{ |
329 |
0 |
start = sg.getStartRes(); |
330 |
0 |
stop = sg.getEndRes(); |
331 |
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} |
332 |
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else |
333 |
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{ |
334 |
0 |
start = 0; |
335 |
0 |
stop = al.getWidth(); |
336 |
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} |
337 |
0 |
SequenceI[] oldOrder = al.getSequencesArray(); |
338 |
0 |
AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method); |
339 |
0 |
avcg.addHistoryItem(new OrderCommand(methodText, oldOrder, |
340 |
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viewport.getAlignment())); |
341 |
0 |
alignPanel.paintAlignment(true, false); |
342 |
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|
343 |
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} |
344 |
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|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
345 |
0 |
@Override... |
346 |
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public void sortAlignmentByFeatureScore(List<String> typ) |
347 |
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{ |
348 |
0 |
sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE); |
349 |
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} |
350 |
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|
|
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| 73.7% |
Uncovered Elements: 5 (19) |
Complexity: 5 |
Complexity Density: 0.38 |
|
351 |
2 |
@Override... |
352 |
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public boolean parseFeaturesFile(Object file, DataSourceType protocol, |
353 |
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boolean relaxedIdMatching) |
354 |
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{ |
355 |
2 |
boolean featuresAdded = false; |
356 |
2 |
FeatureRenderer fr = alignPanel.getFeatureRenderer(); |
357 |
2 |
try |
358 |
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{ |
359 |
2 |
featuresAdded = new FeaturesFile(false, file, protocol).parse( |
360 |
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viewport.getAlignment().getDataset(), fr.getFeatureColours(), |
361 |
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fr.getFeatureFilters(), false, relaxedIdMatching); |
362 |
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} catch (Exception ex) |
363 |
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{ |
364 |
0 |
ex.printStackTrace(); |
365 |
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} |
366 |
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|
367 |
2 |
if (featuresAdded) |
368 |
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{ |
369 |
2 |
avcg.refreshFeatureUI(true); |
370 |
2 |
if (fr != null) |
371 |
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{ |
372 |
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|
373 |
2 |
fr.findAllFeatures(true); |
374 |
|
} |
375 |
2 |
if (avcg.getFeatureSettingsUI() != null) |
376 |
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{ |
377 |
0 |
avcg.getFeatureSettingsUI().discoverAllFeatureData(); |
378 |
|
} |
379 |
2 |
alignPanel.paintAlignment(true, true); |
380 |
|
} |
381 |
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|
382 |
2 |
return featuresAdded; |
383 |
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|
384 |
|
} |
385 |
|
|
|
|
| 56.4% |
Uncovered Elements: 17 (39) |
Complexity: 12 |
Complexity Density: 0.57 |
|
386 |
1 |
@Override... |
387 |
|
public boolean markHighlightedColumns(boolean invert, |
388 |
|
boolean extendCurrent, boolean toggle) |
389 |
|
{ |
390 |
1 |
if (!viewport.hasSearchResults()) |
391 |
|
{ |
392 |
|
|
393 |
0 |
return false; |
394 |
|
} |
395 |
|
|
396 |
1 |
BitSet bs = new BitSet(); |
397 |
1 |
SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null |
398 |
|
|| extendCurrent) ? viewport.getAlignment() |
399 |
|
: viewport.getSelectionGroup(); |
400 |
|
|
401 |
|
|
402 |
|
|
403 |
1 |
int nseq = viewport.getSearchResults().markColumns(sqcol, bs); |
404 |
|
|
405 |
1 |
ColumnSelection cs = viewport.getColumnSelection(); |
406 |
1 |
if (cs == null) |
407 |
|
{ |
408 |
0 |
cs = new ColumnSelection(); |
409 |
|
} |
410 |
|
|
411 |
1 |
if (bs.cardinality() > 0 || invert) |
412 |
|
{ |
413 |
1 |
boolean changed = cs.markColumns(bs, sqcol.getStartRes(), |
414 |
|
sqcol.getEndRes(), invert, extendCurrent, toggle); |
415 |
1 |
if (changed) |
416 |
|
{ |
417 |
1 |
viewport.setColumnSelection(cs); |
418 |
1 |
alignPanel.paintAlignment(false, false); |
419 |
1 |
int columnCount = invert |
420 |
|
? (sqcol.getEndRes() - sqcol.getStartRes() + 1) |
421 |
|
- bs.cardinality() |
422 |
|
: bs.cardinality(); |
423 |
1 |
avcg.setStatus(MessageManager.formatMessage( |
424 |
|
"label.view_controller_toggled_marked", new String[] |
425 |
1 |
{ toggle ? MessageManager.getString("label.toggled") |
426 |
|
: MessageManager.getString("label.marked"), |
427 |
|
String.valueOf(columnCount), |
428 |
1 |
invert ? MessageManager |
429 |
|
.getString("label.not_containing") |
430 |
|
: MessageManager.getString("label.containing"), |
431 |
|
"Highlight", Integer.valueOf(nseq).toString() })); |
432 |
1 |
return true; |
433 |
|
} |
434 |
|
} |
435 |
|
else |
436 |
|
{ |
437 |
0 |
avcg.setStatus(MessageManager |
438 |
|
.formatMessage("No highlighted regions marked")); |
439 |
0 |
if (!extendCurrent) |
440 |
|
{ |
441 |
0 |
cs.clear(); |
442 |
0 |
alignPanel.paintAlignment(false, false); |
443 |
|
} |
444 |
|
} |
445 |
0 |
return false; |
446 |
|
} |
447 |
|
|
448 |
|
} |