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Searched refs:MarkerRange (Results 1 – 25 of 65) sorted by relevance

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/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/test/evosuite-tests/uk/ac/sanger/artemis/sequence/
H A DMarkerRange_ESTest.java42 MarkerRange markerRange1 = new MarkerRange(marker0); in test00()
73 MarkerRange markerRange1 = new MarkerRange(strand0, 5, 1); in test02()
132 MarkerRange markerRange0 = new MarkerRange((Marker) null); in test07()
158 MarkerRange markerRange0 = new MarkerRange((Marker) null); in test09()
174 MarkerRange markerRange0 = new MarkerRange((Marker) null); in test10()
190 MarkerRange markerRange0 = new MarkerRange((Marker) null); in test11()
206 MarkerRange markerRange0 = new MarkerRange((Marker) null); in test12()
222 MarkerRange markerRange0 = new MarkerRange((Marker) null); in test13()
238 MarkerRange markerRange0 = new MarkerRange((Marker) null); in test14()
254 MarkerRange markerRange0 = new MarkerRange((Marker) null); in test15()
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H A DMarkerRangeVector_ESTest.java15 import uk.ac.sanger.artemis.sequence.MarkerRange;
24 MarkerRange markerRange0 = new MarkerRange((Marker) null); in test0()
33 markerRangeVector0.add((MarkerRange) null); in test1()
41 MarkerRange markerRange0 = new MarkerRange((Marker) null); in test2()
43 markerRangeVector0.add((MarkerRange) null); in test2()
51 MarkerRange markerRange0 = new MarkerRange((Marker) null); in test3()
53 markerRangeVector0.add((MarkerRange) null); in test3()
54 markerRangeVector0.add((MarkerRange) null); in test3()
55 markerRangeVector0.add((MarkerRange) null); in test3()
70 markerRangeVector0.add((MarkerRange) null); in test5()
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H A DBasePattern_ESTest.java18 import uk.ac.sanger.artemis.sequence.MarkerRange;
37 … MarkerRange markerRange0 = basePattern0.findMatch(bases0, (Marker) null, 862, true, true, false); in test01()
199 … MarkerRange markerRange0 = basePattern0.findMatch(bases0, (Marker) null, 255, false, true, false); in test20()
209 …MarkerRange markerRange0 = basePattern0.findMatch(bases0, (Marker) null, (-2154), false, true, tru… in test21()
366 … MarkerRange markerRange0 = basePattern0.findMatch(bases0, (Marker) null, 255, true, true, true); in test34()
376 …MarkerRange markerRange0 = basePattern0.findMatch(bases0, (Marker) null, (-2154), false, true, tru… in test35()
396 … MarkerRange markerRange0 = basePattern0.findMatch(bases0, (Marker) null, 255, true, true, true); in test37()
406 …MarkerRange markerRange0 = basePattern0.findMatch(bases0, (Marker) null, (-2154), false, false, fa… in test38()
H A DStrand_ESTest.java29 import uk.ac.sanger.artemis.sequence.MarkerRange;
44 MarkerRange markerRange0 = simpleGotoEventSource0.gotoBase(1); in test00()
45 MarkerRange[] markerRangeArray0 = Strand.getOpenReadingFrameRanges(markerRange0, 2, (-5), 0); in test00()
55 MarkerRange markerRange0 = new MarkerRange(marker0); in test01()
388 Strand.getOpenReadingFrameRanges((MarkerRange) null, (-2575), (-2010), 75); in test24()
486 Strand.deleteRange((MarkerRange) null); in test30()
694 MarkerRange markerRange0 = simpleGotoEventSource0.gotoBase(1); in test48()
714 MarkerRange markerRange0 = Strand.getORFAroundMarker(marker0, false); in test49()
782 MarkerRange markerRange0 = simpleGotoEventSource0.gotoBase(1); in test54()
837 MarkerRange markerRange0 = Strand.getORFAroundMarker(marker0, false); in test58()
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/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/sequence/
H A DStrand.java172 public static MarkerRange [] getOpenReadingFrameRanges (final MarkerRange search_range, in getOpenReadingFrameRanges()
178 final MarkerRange [] [] frame_ranges = new MarkerRange [3] []; in getOpenReadingFrameRanges()
209 final MarkerRange [] temp_range_array = new MarkerRange [max_range_count]; in getOpenReadingFrameRanges()
214 final MarkerRange [] frame_range_array = frame_ranges[i]; in getOpenReadingFrameRanges()
234 final MarkerRange [] return_array = in getOpenReadingFrameRanges()
235 new MarkerRange [temp_range_array_index]; in getOpenReadingFrameRanges()
288 return new MarkerRange (search_strand, in getORFAroundMarker()
433 final MarkerRange [] return_array = in getORFsFromStopCodons()
434 new MarkerRange [stop_codons.length + 1]; in getORFsFromStopCodons()
527 return new MarkerRange (this, start_position, end_position); in makeMarkerRangeFromPositions()
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H A DMarkerRange.java40 public class MarkerRange { class
48 public MarkerRange (final Strand strand, final int start, final int end) in MarkerRange() method in MarkerRange
64 public MarkerRange (final Marker marker) { in MarkerRange() method in MarkerRange
167 public boolean overlaps (final MarkerRange arg_range) { in overlaps()
184 public MarkerRange extendRange (final MarkerRange arg_range) { in extendRange()
200 public MarkerRange combineRanges (final MarkerRange arg_range, in combineRanges()
206 final MarkerRange return_range; in combineRanges()
210 new MarkerRange (getStrand (), in combineRanges()
250 public boolean contains (final MarkerRange arg_range) { in contains()
H A DMarkerRangeVector.java48 public void add (final MarkerRange range) { in add()
55 public MarkerRange elementAt (final int index) { in elementAt()
56 return (MarkerRange) vector.elementAt (index); in elementAt()
62 public boolean contains (final MarkerRange range) { in contains()
73 public int indexOf (final MarkerRange range) { in indexOf()
H A DBasePattern.java112 public MarkerRange findMatch (final Bases bases, in findMatch()
228 return new MarkerRange (match_strand, in findMatch()
257 final MarkerRange new_match_position = in findMatches()
/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/
H A DSelection.java118 final MarkerRange marker_range = getMarkerRange (); in getSelectionText()
316 public void setMarkerRange (final MarkerRange marker_range) { in setMarkerRange()
318 final MarkerRange old_marker_range = this.marker_range; in setMarkerRange()
468 final MarkerRange marker_range = getMarkerRange (); in getSelectionRanges()
512 final MarkerRange range = getMarkerRange (); in getLowestBaseOfSelection()
562 final MarkerRange range = getMarkerRange (); in getHighestBaseOfSelection()
631 final MarkerRange range = getMarkerRange (); in getStartBaseOfSelection()
695 final MarkerRange range = getMarkerRange (); in getEndBaseOfSelection()
731 public MarkerRange getMarkerRange () { in getMarkerRange()
864 private MarkerRange marker_range = null;
H A DSimpleGotoEventSource.java89 public MarkerRange gotoBase (final int destination_base) { in gotoBase()
96 return new MarkerRange (destination_marker.getStrand (), in gotoBase()
H A DGotoEventSource.java54 MarkerRange gotoBase (final int destination_base); in gotoBase()
/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/
H A DGotoMenu.java30 import uk.ac.sanger.artemis.sequence.MarkerRange;
340 final MarkerRange range = new MarkerRange (sequence_marker); in gotoFeaturePosition()
344 /*final*/ MarkerRange selection_range; in gotoFeaturePosition()
350 final MarkerRange codon_end_marker_range = in gotoFeaturePosition()
351 new MarkerRange (sequence_marker.moveBy (2)); in gotoFeaturePosition()
H A DSelectMenu.java463 final MarkerRange new_range = in selectAllBases()
810 final MarkerRange range = getSelection ().getMarkerRange (); in selectOrf()
811 final MarkerRange start_orf_range = in selectOrf()
828 final MarkerRange end_orf_range = in selectOrf()
831 MarkerRange new_range = range; in selectOrf()
864 final MarkerRange marker_range = in selectBaseRange()
923 final MarkerRange marker_range = in selectFeatureAARange()
924 new MarkerRange (start_marker.getStrand (), in selectFeatureAARange()
951 final MarkerRange selected_marker_range = in selectOverlappingFeatures()
1009 final MarkerRange selected_marker_range = in selectContainedFeatures()
H A DNavigator.java493 private static MarkerRange findBasePattern (final BasePattern pattern, in findBasePattern()
512 final MarkerRange match_range = in findBasePattern()
540 private static MarkerRange findAminoAcidSequence (final AminoAcidSequence sequence, in findAminoAcidSequence()
643 final MarkerRange destination_range = in doGotoBase()
677 final MarkerRange match_range = in doGotoBasePattern()
728 final MarkerRange match_range = in doGotoAAPattern()
759 final MarkerRange match_range) in overlapsRange()
H A DMarkerRangeRequesterEvent.java139 public MarkerRange getMarkerRange(final Bases bases) in getMarkerRange()
143 final MarkerRange marker_range; in getMarkerRange()
H A DAddMenu.java35 import uk.ac.sanger.artemis.sequence.MarkerRange;
632 final MarkerRange range = selection.getMarkerRange (); in createFeatureFromBaseRange()
1317 final MarkerRange forward_range = in markOpenReadingFrames()
1325 final MarkerRange backward_range = in markOpenReadingFrames()
1339 final MarkerRange forward_range = forward_strand in markOpenReadingFrames()
1348 final MarkerRange backward_range = backward_strand in markOpenReadingFrames()
1396 final MarkerRange selection_range = in markOpenReadingFramesInRange()
1426 final MarkerRange search_range, in markOpenReadingFrames()
1431 final MarkerRange [] forward_orf_ranges = in markOpenReadingFrames()
1445 final MarkerRange this_range = forward_orf_ranges[i]; in markOpenReadingFrames()
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H A DBasePlot.java202 final MarkerRange marker_range = in BasePlot()
483 MarkerRange range = new MarkerRange( in calculateFeatures()
508 MarkerRange range = new MarkerRange( in calculateFeatures()
/dports/www/gitlab-workhorse/gitlab-foss-0a901d60f8ae4a60c04ae82e6e9c3a03e9321417/lib/gitlab/
H A Dstring_range_marker.rb101 range = MarkerRange.new(start, prev, mode: mode)
104 range = MarkerRange.new(start, pos, mode: mode)
109 range = MarkerRange.new(start, prev, mode: mode)
H A Dmarker_range.rb7 class MarkerRange < Range class
/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/alignment/
H A DMappedReads.java35 import uk.ac.sanger.artemis.sequence.MarkerRange;
418 MarkerRange r;
420 MarkerObj(MarkerRange r, int bamIdx) in MarkerObj()
533 MarkerRange mri = mi.r; in createFeatures()
540 MarkerRange mrj = mj.r; in createFeatures()
661 final MarkerRange marker = new MarkerRange( in findFeatures()
688 final MarkerRange marker = new MarkerRange( in findFeatures()
/dports/www/gitlab-workhorse/gitlab-foss-0a901d60f8ae4a60c04ae82e6e9c3a03e9321417/lib/gitlab/diff/
H A Dchar_diff.rb35 …old_diffs << MarkerRange.new(old_pointer, old_pointer + content_size - 1, mode: MarkerRange::DELET…
40 …new_diffs << MarkerRange.new(new_pointer, new_pointer + content_size - 1, mode: MarkerRange::ADDIT…
/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/circular/digest/
H A DUtils.java30 import uk.ac.sanger.artemis.sequence.MarkerRange;
231 final MarkerRange r; in addFeature()
238 r = new MarkerRange(dna.getArtemisEntryGroup().getSequenceEntry() in addFeature()
/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/genebuilder/
H A DBasicGeneViewerPanel.java51 import uk.ac.sanger.artemis.sequence.MarkerRange;
70 private MarkerRange click_range = null;
156 MarkerRange drag_range; in BasicGeneViewerPanel()
159 drag_range = new MarkerRange(strand, select_start, select_start + 1); in BasicGeneViewerPanel()
197 final MarkerRange selected_range = selection.getMarkerRange(); in BasicGeneViewerPanel()
200 MarkerRange drag_range = new MarkerRange(strand, select_start, in BasicGeneViewerPanel()
/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/test/evosuite-tests/uk/ac/sanger/artemis/
H A DGotoEventSource_ESTest.java25 import uk.ac.sanger.artemis.sequence.MarkerRange;
50 MarkerRange markerRange0 = simpleGotoEventSource0.gotoBase((-662)); in test1()
H A DSimpleGotoEventSource_ESTest.java32 import uk.ac.sanger.artemis.sequence.MarkerRange;
58 MarkerRange markerRange0 = simpleGotoEventSource0.gotoBase(1); in test01()
168 MarkerRange markerRange0 = simpleGotoEventSource0.gotoBase(2207); in test10()

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