| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/sequence/ |
| H A D | MarkerRange.java | 136 public Range getRawRange () { in getRawRange() method in MarkerRange
268 new uk.ac.sanger.artemis.io.Location (getRawRange ()); in createLocation()
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| H A D | Strand.java | 563 range.getStrand ().getBases ().deleteRange (range.getRawRange ()); in deleteRange()
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| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/test/evosuite-tests/uk/ac/sanger/artemis/sequence/ |
| H A D | MarkerRange_ESTest.java | 87 Range range0 = markerRange0.getRawRange(); in test03()
100 Range range0 = markerRange0.getRawRange(); in test04()
209 markerRange0.getRawRange(); in test12()
630 Range range0 = markerRange0.getRawRange(); in test38()
642 Range range0 = markerRange0.getRawRange(); in test39()
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| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/genebuilder/ |
| H A D | BasicGeneViewerPanel.java | 212 status_line.setText(selected_range.getRawRange().getStart() + ".." in BasicGeneViewerPanel()
213 + selected_range.getRawRange().getEnd()); in BasicGeneViewerPanel()
656 Range segment_range = segment.getRawRange(); in getFeatureAt()
786 Range segment_range = this_segment.getRawRange(); in maybeShowPopup()
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| H A D | GeneViewerPanel.java | 219 status_line.setText(selected_range.getRawRange().getStart() + ".." in GeneViewerPanel()
220 + selected_range.getRawRange().getEnd()); in GeneViewerPanel()
864 Range segment_range = segment.getRawRange(); in getFeatureAt()
1036 if(range.equals(segment.getRawRange()) in drawTranscriptOnLine()
1681 Range segment_range = this_segment.getRawRange(); in maybeShowPopup()
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| H A D | ButtonPanel.java | 331 final Range selected_range = selected_marker_range.getRawRange(); in removeSelectedRange()
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| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/ |
| H A D | FeatureBaseViewer.java | 148 hdr.append(i == 0 ? " " : ",").append(segment.getRawRange().toString()); in redisplay()
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| H A D | MarkerRangeRequesterEvent.java | 190 public Range getRawRange() in getRawRange() method in MarkerRangeRequesterEvent
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| H A D | SelectMenu.java | 904 final Range range = event.getRawRange (); in selectFeatureAARange()
996 final Range raw_range = selected_marker_range.getRawRange (); in selectOverlappingFeatures()
1034 selected_marker_range.getRawRange()); in selectContainedFeatures()
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| H A D | Navigator.java | 690 match_range.getRawRange().toString()+") outside selection."); in doGotoBasePattern()
741 match_range.getRawRange().toString()+") outside selection."); in doGotoAAPattern()
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| H A D | SelectionInfoDisplay.java | 366 final Range raw_range = marker_range.getRawRange (); in markerRangeText()
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| H A D | EditMenu.java | 1254 final Range this_range = this_segment.getRawRange(); in mergeFeatures()
1304 this_range.combineRanges(next_range, false).getRawRange(); in mergeFeatures()
1501 ranges.add(this_segment.getRawRange()); in gffMergeFeatures()
3040 final Range raw_range = marker_range.getRawRange (); in deleteSelectedBases()
3085 final Range this_segment_range = this_segment.getRawRange (); in deleteSelectedBases()
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| H A D | AddMenu.java | 654 range.isForwardMarker(), range.getRawRange()); in createFeatureFromBaseRange()
1521 if (test_feature_range.overlaps (this_segment.getRawRange ())) { in overlapsAnActiveSegment()
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| H A D | FeatureEdit.java | 1296 final Range selected_range = selected_marker_range.getRawRange(); in removeSelectedRange()
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| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/alignment/ |
| H A D | BamUtils.java | 83 Range r = segs.elementAt(i).getRawRange(); in getFeatureLength()
375 start = f.getSegments().elementAt(seg).getRawRange().getEnd(); in calculateMappedReads()
376 end = f.getSegments().elementAt(nextSeg).getRawRange().getStart(); in calculateMappedReads()
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| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/ |
| H A D | Selection.java | 465 return_ranges.add (this_segment.getRawRange ()); in getSelectionRanges()
471 return_ranges.add (marker_range.getRawRange ()); in getSelectionRanges()
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| H A D | Feature.java | 313 final Range this_segment_range = this_segment.getRawRange(); in sequenceChanged()
2694 if(old_segment.getRawRange().equals(new_range)) in reexamineSegments()
2717 if(old_segment.getRawRange().getStart() == in reexamineSegments()
2719 old_segment.getRawRange().getEnd() == in reexamineSegments()
2938 ranges.addElement(segments.elementAt (i).getRawRange ()); in updateEMBLFeatureLocation()
3281 old_location.removeRange(segment.getRawRange()); in removeSegment()
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| H A D | FeatureSegment.java | 209 public Range getRawRange () { in getRawRange() method in FeatureSegment
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| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/variant/ |
| H A D | IOUtils.java | 555 Range range = marker.getRawRange(); in exportFastaByRange()
731 int sbeg = seg.getRawRange().getStart(); in exportFasta()
732 int send = seg.getRawRange().getEnd(); in exportFasta()
1075 int sbeg = seg.getRawRange().getStart(); in countVariants()
1076 int send = seg.getRawRange().getEnd(); in countVariants()
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| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/io/ |
| H A D | DatabaseInferredFeature.java | 300 Range exonRange = segments.elementAt(j).getRawRange(); in setLocation()
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| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/chado/ |
| H A D | ChadoTransactionManager.java | 489 Range range = segment.getRawRange(); in entryChanged()
615 final Range range = segment.getRawRange(); in segmentNumberChanged()
946 featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); in insertFeatureSegment()
947 featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); in insertFeatureSegment()
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