From 23857aedb7848e47e5cb6336a5f4acf269b6e13a Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 21 Sep 2018 14:52:20 +0100 Subject: [PATCH] JAL-3063 wrappers with check for null getting optional Integer, Float, Boolean XML attributes --- src/jalview/project/Jalview2XML.java | 360 +++++++++++++++------------------- 1 file changed, 160 insertions(+), 200 deletions(-) diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index c4ad897..3a9060e 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -60,6 +60,7 @@ import jalview.gui.StructureViewerBase; import jalview.gui.TreePanel; import jalview.io.DataSourceType; import jalview.io.FileFormat; +import jalview.io.NewickFile; import jalview.renderer.ResidueShaderI; import jalview.schemes.AnnotationColourGradient; import jalview.schemes.ColourSchemeI; @@ -226,6 +227,45 @@ public class Jalview2XML private Map rnaSessions = new HashMap<>(); /** + * A helper method for safely using the value of an optional attribute that + * may be null if not present in the XML. Answers the boolean value, or false + * if null. + * + * @param b + * @return + */ + public static boolean safeBoolean(Boolean b) + { + return b == null ? false : b.booleanValue(); + } + + /** + * A helper method for safely using the value of an optional attribute that + * may be null if not present in the XML. Answers the integer value, or zero + * if null. + * + * @param i + * @return + */ + public static int safeInt(Integer i) + { + return i == null ? 0 : i.intValue(); + } + + /** + * A helper method for safely using the value of an optional attribute that + * may be null if not present in the XML. Answers the float value, or zero if + * null. + * + * @param f + * @return + */ + public static float safeFloat(Float f) + { + return f == null ? 0f : f.floatValue(); + } + + /** * create/return unique hash string for sq * * @param sq @@ -2732,8 +2772,8 @@ public class Jalview2XML if (!addedToSplitFrames.contains(af)) { Viewport view = candidate.getKey(); - Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), - view.getHeight()); + Desktop.addInternalFrame(af, view.getTitle(), + safeInt(view.getWidth()), safeInt(view.getHeight())); af.setMenusForViewport(); System.err.println("Failed to restore view " + view.getTitle() + " to split frame"); @@ -3057,8 +3097,9 @@ public class Jalview2XML vi++; } - if (jseq.isViewreference() != null - && jseq.isViewreference().booleanValue()) + if (safeBoolean(jseq.isViewreference())) + // if (jseq.isViewreference() != null + // && jseq.isViewreference().booleanValue()) { referenceseqForView = tmpseqs.get(tmpseqs.size() - 1); } @@ -3150,7 +3191,7 @@ public class Jalview2XML Feature feat = features.get(f); SequenceFeature sf = new SequenceFeature(feat.getType(), feat.getDescription(), feat.getBegin(), feat.getEnd(), - feat.getScore(), feat.getFeatureGroup()); + safeFloat(feat.getScore()), feat.getFeatureGroup()); sf.setStatus(feat.getStatus()); /* @@ -3352,14 +3393,14 @@ public class Jalview2XML annotation.setId(null); } - // set visiblity for other annotation in this view + // set visibility for other annotation in this view String annotationId = annotation.getId(); if (annotationId != null && annotationIds.containsKey(annotationId)) { AlignmentAnnotation jda = annotationIds.get(annotationId); // in principle Visible should always be true for annotation displayed // in multiple views - if (annotation.isVisible() != null) // annotation.hasVisible()) + if (annotation.isVisible() != null) { jda.visible = annotation.isVisible(); } @@ -3386,8 +3427,7 @@ public class Jalview2XML continue; } - float value = annElement.getValue() == null ? 0f - : annElement.getValue().floatValue(); + float value = safeFloat(annElement.getValue()); anot[anpos] = new jalview.datamodel.Annotation( annElement.getDisplayCharacter(), annElement.getDescription(), @@ -3399,16 +3439,7 @@ public class Jalview2XML .getSecondaryStructure() .charAt(0), value); - // JBPNote: Consider verifying dataflow for IO of secondary - // structure annotation read from Stockholm files - // this was added to try to ensure that - // if (anot[ annElement.getPosition()].secondaryStructure>' ') - // { - // anot[ annElement.getPosition()].displayCharacter = ""; - // } - final int colourValue = annElement.getColour() == null ? 0 - : annElement.getColour().intValue(); - anot[anpos].colour = new java.awt.Color(colourValue); + anot[anpos].colour = new Color(safeInt(annElement.getColour())); if (firstColour == null) { firstColour = anot[anpos].colour; @@ -3425,18 +3456,17 @@ public class Jalview2XML // } jaa = new jalview.datamodel.AlignmentAnnotation( annotation.getLabel(), annotation.getDescription(), anot, - llim, hlim, annotation.getGraphType()); + llim, hlim, safeInt(annotation.getGraphType())); - jaa.graphGroup = annotation.getGraphGroup(); + jaa.graphGroup = safeInt(annotation.getGraphGroup()); jaa._linecolour = firstColour; if (annotation.getThresholdLine() != null) { jaa.setThreshold(new jalview.datamodel.GraphLine( - annotation.getThresholdLine().getValue(), + safeFloat(annotation.getThresholdLine().getValue()), annotation.getThresholdLine().getLabel(), - new java.awt.Color( - annotation.getThresholdLine().getColour()))); - + new java.awt.Color(safeInt( + annotation.getThresholdLine().getColour())))); } if (autoForView || annotation.isAutoCalculated()) { @@ -3490,7 +3520,7 @@ public class Jalview2XML if (annotation.getScore() != null) { - jaa.setScore(annotation.getScore()); + jaa.setScore(annotation.getScore().doubleValue()); } if (annotation.isVisible() != null) { @@ -3507,8 +3537,7 @@ public class Jalview2XML { jaa.scaleColLabel = annotation.isScaleColLabels().booleanValue(); } - if (/*annotation.hasAutoCalculated() && */annotation - .isAutoCalculated()) + if (annotation.isAutoCalculated()) { // newer files have an 'autoCalculated' flag and store calculation // state in viewport properties @@ -3519,11 +3548,7 @@ public class Jalview2XML { jaa.graphHeight = annotation.getGraphHeight().intValue(); } - // if (annotation.hasBelowAlignment()) - // { - // schema specifies default for optional attribute - jaa.belowAlignment = annotation.isBelowAlignment(); - // } + jaa.belowAlignment = annotation.isBelowAlignment(); jaa.setCalcId(annotation.getCalcId()); if (annotation.getProperty().size() > 0) { @@ -3574,8 +3599,7 @@ public class Jalview2XML jGroup.getColour()); } } - int pidThreshold = jGroup.getPidThreshold() == null ? 0 - : jGroup.getPidThreshold().intValue(); + int pidThreshold = safeInt(jGroup.getPidThreshold()); Vector seqs = new Vector<>(); @@ -3596,40 +3620,24 @@ public class Jalview2XML } SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs, - jGroup.isDisplayBoxes(), jGroup.isDisplayText(), - jGroup.isColourText(), jGroup.getStart(), jGroup.getEnd()); + safeBoolean(jGroup.isDisplayBoxes()), + safeBoolean(jGroup.isDisplayText()), + safeBoolean(jGroup.isColourText()), + safeInt(jGroup.getStart()), safeInt(jGroup.getEnd())); sg.getGroupColourScheme().setThreshold(pidThreshold, true); sg.getGroupColourScheme() - .setConservationInc(jGroup.getConsThreshold() == null ? 0 - : jGroup.getConsThreshold().intValue()); - sg.setOutlineColour( - new java.awt.Color(jGroup.getOutlineColour() == null ? 0 - : jGroup.getOutlineColour().intValue())); - - sg.textColour = new java.awt.Color(jGroup.getTextCol1()); - sg.textColour2 = new java.awt.Color(jGroup.getTextCol2()); - sg.setShowNonconserved( - jGroup.isShowUnconserved() != null - ? jGroup.isShowUnconserved().booleanValue() - : false); - sg.thresholdTextColour = jGroup.getTextColThreshold(); + .setConservationInc(safeInt(jGroup.getConsThreshold())); + sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour()))); + + sg.textColour = new Color(safeInt(jGroup.getTextCol1())); + sg.textColour2 = new Color(safeInt(jGroup.getTextCol2())); + sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved())); + sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold()); // attributes with a default in the schema are never null - // if (jGroup.hasShowConsensusHistogram()) - // { sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram()); - // } - // if (jGroup.hasShowSequenceLogo()) - // { sg.setshowSequenceLogo(jGroup.isShowSequenceLogo()); - // } - // if (jGroup.hasNormaliseSequenceLogo()) - // { sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo()); - // } - // if (jGroup.hasIgnoreGapsinConsensus()) - // { sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus()); - // } if (jGroup.getConsThreshold() != null && jGroup.getConsThreshold().intValue() != 0) { @@ -3819,7 +3827,7 @@ public class Jalview2XML * add the structure to the Varna display (with session state copied * from the jar to a temporary file) */ - boolean gapped = ss.isGapped(); + boolean gapped = safeBoolean(ss.isGapped()); String rnaTitle = ss.getTitle(); String sessionState = ss.getViewerState(); String tempStateFile = copyJarEntry(jprovider, sessionState, @@ -3827,7 +3835,7 @@ public class Jalview2XML RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped); appVarna.addModelSession(rna, rnaTitle, tempStateFile); } - appVarna.setInitialSelection(viewer.getSelectedRna()); + appVarna.setInitialSelection(safeInt(viewer.getSelectedRna())); } } } @@ -3868,8 +3876,9 @@ public class Jalview2XML * viewer not found - make it */ RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(), - viewer.getXpos(), viewer.getYpos(), viewer.getWidth(), - viewer.getHeight(), viewer.getDividerLocation()); + safeInt(viewer.getXpos()), safeInt(viewer.getYpos()), + safeInt(viewer.getWidth()), safeInt(viewer.getHeight()), + safeInt(viewer.getDividerLocation())); AppVarna varna = new AppVarna(model, ap); return varna; @@ -3898,10 +3907,10 @@ public class Jalview2XML TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId()); if (tp == null) { - tp = af.showNewickTree( - new jalview.io.NewickFile(tree.getNewick()), - tree.getTitle(), tree.getWidth(), tree.getHeight(), - tree.getXpos(), tree.getYpos()); + tp = af.showNewickTree(new NewickFile(tree.getNewick()), + tree.getTitle(), safeInt(tree.getWidth()), + safeInt(tree.getHeight()), safeInt(tree.getXpos()), + safeInt(tree.getYpos())); if (tree.getId() != null) { // perhaps bind the tree id to something ? @@ -3913,11 +3922,11 @@ public class Jalview2XML // TODO: should check if tp has been manipulated by user - if so its // settings shouldn't be modified tp.setTitle(tree.getTitle()); - tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), - tree.getWidth(), tree.getHeight())); - tp.setViewport(av); // af.viewport; // TODO: verify 'associate with all - // views' - // works still + tp.setBounds(new Rectangle(safeInt(tree.getXpos()), + safeInt(tree.getYpos()), safeInt(tree.getWidth()), + safeInt(tree.getHeight()))); + tp.setViewport(av); // af.viewport; + // TODO: verify 'associate with all views' works still tp.getTreeCanvas().setViewport(av); // af.viewport; tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel; @@ -3929,27 +3938,29 @@ public class Jalview2XML continue; } - tp.fitToWindow.setState(tree.isFitToWindow()); + tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow())); tp.fitToWindow_actionPerformed(null); if (tree.getFontName() != null) { - tp.setTreeFont(new java.awt.Font(tree.getFontName(), - tree.getFontStyle(), tree.getFontSize())); + tp.setTreeFont( + new Font(tree.getFontName(), safeInt(tree.getFontStyle()), + safeInt(tree.getFontSize()))); } else { - tp.setTreeFont(new java.awt.Font(view.getFontName(), - view.getFontStyle(), tree.getFontSize())); + tp.setTreeFont( + new Font(view.getFontName(), safeInt(view.getFontStyle()), + safeInt(view.getFontSize()))); } - tp.showPlaceholders(tree.isMarkUnlinked()); - tp.showBootstrap(tree.isShowBootstrap()); - tp.showDistances(tree.isShowDistances()); + tp.showPlaceholders(safeBoolean(tree.isMarkUnlinked())); + tp.showBootstrap(safeBoolean(tree.isShowBootstrap())); + tp.showDistances(safeBoolean(tree.isShowDistances())); - tp.getTreeCanvas().setThreshold(tree.getThreshold()); + tp.getTreeCanvas().setThreshold(safeFloat(tree.getThreshold())); - if (tree.isCurrentTree()) + if (safeBoolean(tree.isCurrentTree())) { af.getViewport().setCurrentTree(tp.getTree()); } @@ -4003,10 +4014,10 @@ public class Jalview2XML loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile())); jpdb.setId(pdbid.getId()); - int x = structureState.getXpos(); - int y = structureState.getYpos(); - int width = structureState.getWidth(); - int height = structureState.getHeight(); + int x = safeInt(structureState.getXpos()); + int y = safeInt(structureState.getYpos()); + int width = safeInt(structureState.getWidth()); + int height = safeInt(structureState.getHeight()); // Probably don't need to do this anymore... // Desktop.desktop.getComponentAt(x, y); @@ -4569,17 +4580,17 @@ public class Jalview2XML String viewId, List autoAlan) { AlignFrame af = null; - af = new AlignFrame(al, view.getWidth(), view.getHeight(), - uniqueSeqSetId, viewId); + af = new AlignFrame(al, safeInt(view.getWidth()), + safeInt(view.getHeight()), uniqueSeqSetId, viewId); af.setFileName(file, FileFormat.Jalview); final AlignViewport viewport = af.getViewport(); for (int i = 0; i < JSEQ.size(); i++) { - viewport.setSequenceColour( - viewport.getAlignment().getSequenceAt(i), - new java.awt.Color(JSEQ.get(i).getColour())); + int colour = safeInt(JSEQ.get(i).getColour()); + viewport.setSequenceColour(viewport.getAlignment().getSequenceAt(i), + new Color(colour)); } if (al.hasSeqrep()) @@ -4588,7 +4599,7 @@ public class Jalview2XML viewport.setDisplayReferenceSeq(true); } - viewport.setGatherViewsHere(view.isGatheredViews()); + viewport.setGatherViewsHere(safeBoolean(view.isGatheredViews())); if (view.getSequenceSetId() != null) { @@ -4640,49 +4651,48 @@ public class Jalview2XML } // recover view properties and display parameters - viewport.setShowAnnotation(view.isShowAnnotation()); - viewport.setAbovePIDThreshold(view.isPidSelected()); - final int pidThreshold = view.getPidThreshold() == null ? 0 - : view.getPidThreshold().intValue(); + viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation())); + viewport.setAbovePIDThreshold(safeBoolean(view.isPidSelected())); + final int pidThreshold = safeInt(view.getPidThreshold()); viewport.setThreshold(pidThreshold); - viewport.setColourText(view.isShowColourText()); + viewport.setColourText(safeBoolean(view.isShowColourText())); viewport - .setConservationSelected(view.isConservationSelected()); - viewport.setIncrement(view.getConsThreshold() == null ? 0 - : view.getConsThreshold().intValue()); - viewport.setShowJVSuffix(view.isShowFullId()); - viewport.setRightAlignIds(view.isRightAlignIds()); - viewport.setFont(new java.awt.Font(view.getFontName(), - view.getFontStyle(), view.getFontSize()), true); + .setConservationSelected( + safeBoolean(view.isConservationSelected())); + viewport.setIncrement(safeInt(view.getConsThreshold())); + viewport.setShowJVSuffix(safeBoolean(view.isShowFullId())); + viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds())); + viewport.setFont(new Font(view.getFontName(), + safeInt(view.getFontStyle()), safeInt(view.getFontSize())), + true); ViewStyleI vs = viewport.getViewStyle(); vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna()); viewport.setViewStyle(vs); // TODO: allow custom charWidth/Heights to be restored by updating them // after setting font - which means set above to false - viewport.setRenderGaps(view.isRenderGaps()); - viewport.setWrapAlignment(view.isWrapAlignment()); - viewport.setShowAnnotation(view.isShowAnnotation()); + viewport.setRenderGaps(safeBoolean(view.isRenderGaps())); + viewport.setWrapAlignment(safeBoolean(view.isWrapAlignment())); + viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation())); - viewport.setShowBoxes(view.isShowBoxes()); + viewport.setShowBoxes(safeBoolean(view.isShowBoxes())); - viewport.setShowText(view.isShowText()); + viewport.setShowText(safeBoolean(view.isShowText())); - viewport.setTextColour(new java.awt.Color(view.getTextCol1())); - viewport.setTextColour2(new java.awt.Color(view.getTextCol2())); - viewport.setThresholdTextColour(view.getTextColThreshold()); - viewport.setShowUnconserved( - view.isShowUnconserved() ? view.isShowUnconserved() : false); - viewport.getRanges().setStartRes(view.getStartRes()); + viewport.setTextColour(new Color(safeInt(view.getTextCol1()))); + viewport.setTextColour2(new Color(safeInt(view.getTextCol2()))); + viewport.setThresholdTextColour(safeInt(view.getTextColThreshold())); + viewport.setShowUnconserved(view.isShowUnconserved()); + viewport.getRanges().setStartRes(safeInt(view.getStartRes())); if (view.getViewName() != null) { viewport.setViewName(view.getViewName()); af.setInitialTabVisible(); } - af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), - view.getHeight()); + af.setBounds(safeInt(view.getXpos()), safeInt(view.getYpos()), + safeInt(view.getWidth()), safeInt(view.getHeight())); // startSeq set in af.alignPanel.updateLayout below af.alignPanel.updateLayout(); ColourSchemeI cs = null; @@ -4714,10 +4724,10 @@ public class Jalview2XML .setConsensus(viewport.getSequenceConsensusHash()); viewport.setColourAppliesToAllGroups(false); - if (view.isConservationSelected() && cs != null) + if (safeBoolean(view.isConservationSelected()) && cs != null) { viewport.getResidueShading() - .setConservationInc(view.getConsThreshold()); + .setConservationInc(safeInt(view.getConsThreshold())); } af.changeColour(cs); @@ -4725,69 +4735,20 @@ public class Jalview2XML viewport.setColourAppliesToAllGroups(true); viewport - .setShowSequenceFeatures(view.isShowSequenceFeatures()); + .setShowSequenceFeatures( + safeBoolean(view.isShowSequenceFeatures())); - // if (view.hasCentreColumnLabels()) - // { viewport.setCentreColumnLabels(view.isCentreColumnLabels()); - // } - // if (view.hasIgnoreGapsinConsensus()) - // { viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null); - // } - // if (view.hasFollowHighlight()) - // { - viewport.setFollowHighlight(view.isFollowHighlight()); - // } - // if (view.hasFollowSelection()) - // { viewport.followSelection = view.isFollowSelection(); - // } - // if (view.hasShowConsensusHistogram()) - // { viewport.setShowConsensusHistogram(view.isShowConsensusHistogram()); - // } - // else - // { - // viewport.setShowConsensusHistogram(true); - // } - // if (view.hasShowSequenceLogo()) - // { viewport.setShowSequenceLogo(view.isShowSequenceLogo()); - // } - // else - // { - // viewport.setShowSequenceLogo(false); - // } - // if (view.hasNormaliseSequenceLogo()) - // { viewport.setNormaliseSequenceLogo(view.isNormaliseSequenceLogo()); - // } - if (view.isShowDbRefTooltip() != null) - { - viewport.setShowDBRefs(view.isShowDbRefTooltip()); - } - if (view.isShowNPfeatureTooltip() != null) - { - viewport.setShowNPFeats(view.isShowNPfeatureTooltip()); - } - // if (view.hasShowGroupConsensus()) - // { + viewport.setShowDBRefs(safeBoolean(view.isShowDbRefTooltip())); + viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip())); viewport.setShowGroupConsensus(view.isShowGroupConsensus()); - // } - // else - // { - // viewport.setShowGroupConsensus(false); - // } - // if (view.hasShowGroupConservation()) - // { viewport.setShowGroupConservation(view.isShowGroupConservation()); - // } - // else - // { - // viewport.setShowGroupConservation(false); - // } // recover feature settings if (jm.getFeatureSettings() != null) @@ -4843,12 +4804,9 @@ public class Jalview2XML { noValueColour = maxColour; } - float min = setting.getMin() != null - ? setting.getMin().floatValue() - : 0f; - float max = setting.getMin() != null - ? setting.getMax().floatValue() - : 1f; + float min = safeFloat(safeFloat(setting.getMin())); + float max = setting.getMax() == null ? 1f + : setting.getMax().floatValue(); FeatureColourI gc = new FeatureColour(minColour, maxColour, noValueColour, min, max); if (setting.getAttributeName().size() > 0) @@ -4859,7 +4817,7 @@ public class Jalview2XML if (setting.getThreshold() != null) { gc.setThreshold(setting.getThreshold().floatValue()); - int threshstate = setting.getThreshstate().intValue(); + int threshstate = safeInt(setting.getThreshstate()); // -1 = None, 0 = Below, 1 = Above threshold if (threshstate == 0) { @@ -4897,7 +4855,7 @@ public class Jalview2XML featureOrder.put(featureType, new Float( fs / jm.getFeatureSettings().getSetting().size())); } - if (setting.isDisplay()) + if (safeBoolean(setting.isDisplay())) { fdi.setVisible(featureType); } @@ -4920,9 +4878,9 @@ public class Jalview2XML { for (int c = 0; c < view.getHiddenColumns().size(); c++) { - viewport.hideColumns(view.getHiddenColumns().get(c).getStart(), - view.getHiddenColumns().get(c).getEnd() // +1 - ); + final HiddenColumns hc = view.getHiddenColumns().get(c); + viewport.hideColumns(safeInt(hc.getStart()), + safeInt(hc.getEnd()) /* +1 */); } } if (view.getCalcIdParam() != null) @@ -4953,8 +4911,8 @@ public class Jalview2XML String complementaryViewId = view.getComplementId(); if (complementaryViewId == null) { - Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), - view.getHeight()); + Desktop.addInternalFrame(af, view.getTitle(), + safeInt(view.getWidth()), safeInt(view.getHeight())); // recompute any autoannotation af.alignPanel.updateAnnotation(false, true); reorderAutoannotation(af, al, autoAlan); @@ -5029,34 +4987,36 @@ public class Jalview2XML } if (matchedAnnotation.getThreshold() == null) { - matchedAnnotation.setThreshold(new GraphLine( - viewAnnColour.getThreshold(), "Threshold", Color.black)); + matchedAnnotation.setThreshold( + new GraphLine(safeFloat(viewAnnColour.getThreshold()), + "Threshold", Color.black)); } AnnotationColourGradient cs = null; if (viewAnnColour.getColourScheme().equals("None")) { cs = new AnnotationColourGradient(matchedAnnotation, - new Color(viewAnnColour.getMinColour()), - new Color(viewAnnColour.getMaxColour()), - viewAnnColour.getAboveThreshold()); + new Color(safeInt(viewAnnColour.getMinColour())), + new Color(safeInt(viewAnnColour.getMaxColour())), + safeInt(viewAnnColour.getAboveThreshold())); } else if (viewAnnColour.getColourScheme().startsWith("ucs")) { cs = new AnnotationColourGradient(matchedAnnotation, getUserColourScheme(model, viewAnnColour.getColourScheme()), - viewAnnColour.getAboveThreshold()); + safeInt(viewAnnColour.getAboveThreshold())); } else { cs = new AnnotationColourGradient(matchedAnnotation, ColourSchemeProperty.getColourScheme(al, viewAnnColour.getColourScheme()), - viewAnnColour.getAboveThreshold()); + safeInt(viewAnnColour.getAboveThreshold())); } - boolean perSequenceOnly = viewAnnColour.isPerSequence(); - boolean useOriginalColours = viewAnnColour.isPredefinedColours(); + boolean perSequenceOnly = safeBoolean(viewAnnColour.isPerSequence()); + boolean useOriginalColours = safeBoolean( + viewAnnColour.isPredefinedColours()); cs.setSeqAssociated(perSequenceOnly); cs.setPredefinedColours(useOriginalColours); @@ -5073,7 +5033,7 @@ public class Jalview2XML AnnotationColourGradient groupScheme = new AnnotationColourGradient( matchedAnnotation, sg.getColourScheme(), - viewAnnColour.getAboveThreshold()); + safeInt(viewAnnColour.getAboveThreshold())); sg.setColourScheme(groupScheme); groupScheme.setSeqAssociated(perSequenceOnly); groupScheme.setPredefinedColours(useOriginalColours); @@ -6130,8 +6090,8 @@ public class Jalview2XML } colour = new FeatureColour(mincol, maxcol, noValueColour, - colourModel.getMin(), - colourModel.getMax()); + safeFloat(colourModel.getMin()), + safeFloat(colourModel.getMax())); final List attributeName = colourModel.getAttributeName(); String[] attributes = attributeName .toArray(new String[attributeName.size()]); -- 1.7.10.2