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Searched refs:graphGroup (Results 1 – 17 of 17) sorted by relevance

/dports/biology/jalview/jalview/test/jalview/analysis/
H A DAlignmentAnnotationUtilsTest.java279 anns[3].graphGroup = GROUP_5; in testGetShownHiddenTypes_withGraphGroups()
301 anns[1].graphGroup = GROUP_6; in testGetShownHiddenTypes_withGraphGroups()
305 anns[5].graphGroup = GROUP_6; in testGetShownHiddenTypes_withGraphGroups()
316 anns[4].graphGroup = GROUP_4; in testGetShownHiddenTypes_withGraphGroups()
322 anns[0].graphGroup = GROUP_4; in testGetShownHiddenTypes_withGraphGroups()
333 anns[6].graphGroup = GROUP_4; in testGetShownHiddenTypes_withGraphGroups()
387 anns[0].graphGroup = 1; in testGetVisibleGraphGroups()
394 anns[1].graphGroup = 5; in testGetVisibleGraphGroups()
397 anns[2].graphGroup = 5; in testGetVisibleGraphGroups()
404 anns[3].graphGroup = 3; in testGetVisibleGraphGroups()
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/dports/biology/jalview/jalview/src/jalview/analysis/
H A DAlignmentAnnotationUtils.java106 && aa.graphGroup > -1) in getShownHiddenTypes()
114 if (groupLabelsForCalcId.containsKey(aa.graphGroup)) in getShownHiddenTypes()
116 if (!groupLabelsForCalcId.get(aa.graphGroup) in getShownHiddenTypes()
119 groupLabelsForCalcId.get(aa.graphGroup).add(displayLabel); in getShownHiddenTypes()
124 groupLabelsForCalcId.put(aa.graphGroup, labelAsList); in getShownHiddenTypes()
219 int gg = ann.graphGroup; in getVisibleLineGraphGroups()
H A DDna.java343 aa.graphGroup = annotation.graphGroup; in translateAlignedAnnotations()
/dports/biology/jalview/jalview/src/jalview/ws/jws2/
H A DAADisorderClient.java181 int graphGroup = 1; in updateResultAnnotation() local
187 if (ala.graphGroup > graphGroup) in updateResultAnnotation()
189 graphGroup = ala.graphGroup; in updateResultAnnotation()
294 graphGroup++; in updateResultAnnotation()
298 annot.graphGroup = graphGroup; in updateResultAnnotation()
332 ourAnnot.get(lastAnnot).graphGroup = -1; in updateResultAnnotation()
/dports/biology/jalview/jalview/src/jalview/io/
H A DAnnotationFile.java274 if (row.graphGroup > -1) in printAnnotations()
278 if (graphGroup.containsKey(key)) in printAnnotations()
280 graphGroup.put(key, graphGroup.get(key) + "\t" + row.label); in printAnnotations()
411 if (graphGroup.size() > 0) in printAnnotations()
1360 int graphGroup = 0; in combineAnnotations() local
1367 if (aa.graphGroup > graphGroup) in combineAnnotations()
1370 graphGroup = aa.graphGroup + 1; in combineAnnotations()
1375 if (aa.graphGroup > -1) in combineAnnotations()
1377 graphGroup = aa.graphGroup; in combineAnnotations()
1385 aa.graphGroup = graphGroup; in combineAnnotations()
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H A DVamsasAppDatastore.java618 an.setGroup(Integer.toString(aa[i].graphGroup)); // // JBPNote in storeVAMSAS()
681 an.setGroup(Integer.toString(aa[i].graphGroup)); in storeVAMSAS()
1025 an.setGroup(Integer.toString(alan.graphGroup)); in initRangeAnnotationType()
1092 an.setGroup(Integer.toString(alan.graphGroup)); // // JBPNote - in saveDatasetSequenceAnnotation()
2436 jan.graphGroup = Integer.parseInt(annotation.getGroup()); // TODO: in getjAlignmentAnnotation()
/dports/biology/jalview/jalview/src/jalview/xml/binding/jalview/
H A DAnnotation.java108 protected Integer graphGroup; field in Annotation
383 return graphGroup; in getGraphGroup()
395 this.graphGroup = value; in setGraphGroup()
/dports/biology/jalview/jalview/test/jalview/gui/
H A DAnnotationLabelsTest.java129 aa.graphGroup = 1; in testGetStatusMessage()
140 aa2.graphGroup = 1; in testGetStatusMessage()
/dports/biology/jalview/jalview/src/jalview/gui/
H A DAnnotationLabels.java711 if (aa.graphGroup == -1) in getStatusMessage()
720 if (anns[i].graphGroup == aa.graphGroup) in getStatusMessage()
1144 if (aa[i].graphGroup > -1) in drawComponent()
1151 if (aa[gg].graphGroup == aa[i].graphGroup) in drawComponent()
1185 if (aa[gg].graphGroup == aa[i].graphGroup) in drawComponent()
H A DAlignFrame.java2121 if (alan.graphGroup > fgroup) in paste()
2123 fgroup = alan.graphGroup; in paste()
2138 if (newann.graphGroup > -1) in paste()
2140 if (newGraphGroups.size() <= newann.graphGroup in paste()
2148 newGraphGroups.set(newann.graphGroup, in paste()
2151 newann.graphGroup = newGraphGroups.get(newann.graphGroup) in paste()
2183 if (newann.graphGroup > -1) in paste()
2185 if (newann.graphGroup > -1) in paste()
2187 if (newGraphGroups.size() <= newann.graphGroup in paste()
2195 newGraphGroups.set(newann.graphGroup, in paste()
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H A DAnnotationPanel.java853 if (ann.graphGroup > -1) in buildToolTip()
859 if (anns[i].graphGroup == ann.graphGroup in buildToolTip()
/dports/biology/jalview/jalview/src/jalview/renderer/
H A DAnnotationRenderer.java540 if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup)) in drawComponent()
1010 if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup)) in drawComponent()
1017 if (aa[gg].graphGroup != row.graphGroup) in drawComponent()
1038 if (aa[gg].graphGroup == row.graphGroup) in drawComponent()
1045 graphGroupDrawn.set(row.graphGroup); in drawComponent()
/dports/graphics/quickqanava/QuickQanava-ab88d77ec62175b9fd499a154ffaf92f7bf23989/GTpo/src/gtpo/
H A Dgraph.hpp353 … [=](const weak_group_t& graphGroup ){ return ( compare_weak_ptr<>( group, graphGroup ) ); } ); in has_group() argument
/dports/biology/jalview/jalview/src/jalview/datamodel/
H A DAlignmentAnnotation.java266 public int graphGroup = -1; field in AlignmentAnnotation
718 this.graphGroup = annotation.graphGroup; in AlignmentAnnotation()
/dports/biology/jalview/jalview/test/jalview/io/
H A DStockholmFileTest.java306 Integer o_ggrp = Integer.valueOf(aa_original[i].graphGroup + 2); in testAlignmentEquivalence()
307 Integer n_ggrp = Integer.valueOf(aa_new[i].graphGroup + 2); in testAlignmentEquivalence()
/dports/biology/jalview/jalview/src/jalview/viewmodel/
H A DAlignmentViewport.java2116 if (aa.graphGroup > -1) in calcPanelHeight()
2118 if (graphgrp.get(aa.graphGroup)) in calcPanelHeight()
2124 graphgrp.set(aa.graphGroup); in calcPanelHeight()
/dports/biology/jalview/jalview/src/jalview/project/
H A DJalview2XML.java2213 an.setGraphGroup(annotation.graphGroup); in storeAlignmentAnnotation()
3741 jaa.graphGroup = safeInt(annotation.getGraphGroup());