X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=c952ea02619a8df1412ed29fb593690785c67fa4;hb=10211ab17c9941d56c0aa703d49b59ca8c04b5af;hp=4d883c4740b6f4aee634024a44bbcc5991af572a;hpb=4b48ff7b994c2eb30d06a19e68a1eecfcc9b82b5;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 4d883c4..c952ea0 100755 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -762,6 +762,10 @@ public class Jalview2XML } // SAVE ANNOTATIONS + /** + * store forward refs from an annotationRow to any groups + */ + IdentityHashMap groupRefs = new IdentityHashMap(); if (jal.getAlignmentAnnotation() != null) { jalview.datamodel.AlignmentAnnotation[] aa = jal @@ -778,15 +782,7 @@ public class Jalview2XML an.setId(aa[i].annotationId); - if (aa[i] == av.quality || aa[i] == av.conservation - || aa[i] == av.consensus) - { - an.setLabel(aa[i].label); - an.setGraph(true); - vamsasSet.addAnnotation(an); - continue; - } - + an.setVisible(aa[i].visible); an.setDescription(aa[i].description); @@ -797,6 +793,27 @@ public class Jalview2XML // sequence rather than its display name an.setSequenceRef(aa[i].sequenceRef.getName()); } + if (aa[i].groupRef!=null) + { + Object groupIdr = groupRefs.get(aa[i].groupRef); + if (groupIdr==null) + { + // make a locally unique String + groupRefs.put(aa[i].groupRef, groupIdr = (""+System.currentTimeMillis()+aa[i].groupRef.getName()+groupRefs.size())); + } + an.setGroupRef(groupIdr.toString()); + } + if (aa[i] == av.quality || aa[i] == av.conservation + || aa[i] == av.consensus || aa[i].autoCalculated) + { + // new way of indicating autocalculated annotation - + an.setAutoCalculated(aa[i].autoCalculated); + // write a stub for this annotation - indicate presence of autocalc rows + an.setLabel(aa[i].label); + an.setGraph(true); + vamsasSet.addAnnotation(an); + continue; + } if (aa[i].graph > 0) { @@ -865,7 +882,6 @@ public class Jalview2XML vamsasSet.addAnnotation(an); } } - // SAVE GROUPS if (jal.getGroups() != null) { @@ -879,9 +895,11 @@ public class Jalview2XML .getGroups().elementAt(i); groups[i].setStart(sg.getStartRes()); groups[i].setEnd(sg.getEndRes()); - groups[i].setName(sg.getName()); // TODO later sequence group should - // specify IDs of sequences, not just - // names + groups[i].setName(sg.getName()); + if (groupRefs.containsKey(sg)) { + // group has references so set it's ID field + groups[i].setId(groupRefs.get(sg).toString()); + } if (sg.cs != null) { if (sg.cs.conservationApplied()) @@ -927,6 +945,9 @@ public class Jalview2XML groups[i].setTextCol2(sg.textColour2.getRGB()); groups[i].setTextColThreshold(sg.thresholdTextColour); groups[i].setShowUnconserved(sg.getShowunconserved()); + groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus()); + groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram()); + groups[i].setShowSequenceLogo(sg.isShowSequenceLogo()); for (int s = 0; s < sg.getSize(); s++) { jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg @@ -1038,7 +1059,15 @@ public class Jalview2XML view.setTextCol1(av.textColour.getRGB()); view.setTextCol2(av.textColour2.getRGB()); view.setTextColThreshold(av.thresholdTextColour); - + view.setShowConsensusHistogram(av.isShowConsensusHistogram()); + view.setShowSequenceLogo(av.isShowSequenceLogo()); + view.setShowGroupConsensus(av.isShowGroupConsensus()); + view.setShowGroupConservation(av.isShowGroupConservation()); + view.setShowNPfeatureTooltip(av.isShowNpFeats()); + view.setShowDbRefTooltip(av.isShowDbRefs()); + view.setFollowHighlight(av.followHighlight); + view.setFollowSelection(av.followSelection); + view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus()); if (av.featuresDisplayed != null) { jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings(); @@ -1046,13 +1075,27 @@ public class Jalview2XML String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder; Vector settingsAdded = new Vector(); + Object gstyle=null; + GraduatedColor gcol = null; for (int ro = 0; ro < renderOrder.length; ro++) { + gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer().getFeatureStyle(renderOrder[ro]); Setting setting = new Setting(); setting.setType(renderOrder[ro]); - setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer() - .getColour(renderOrder[ro]).getRGB()); - + if (gstyle instanceof GraduatedColor) { + gcol = (GraduatedColor) gstyle; + setting.setColour(gcol.getMaxColor().getRGB()); + setting.setMincolour(gcol.getMinColor().getRGB()); + setting.setMin(gcol.getMin()); + setting.setMax(gcol.getMax()); + setting.setColourByLabel(gcol.isColourByLabel()); + setting.setAutoScale(gcol.isAutoScale()); + setting.setThreshold(gcol.getThresh()); + setting.setThreshstate(gcol.getThreshType()); + } else { + setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer() .getColour(renderOrder[ro]).getRGB()); + } + setting.setDisplay(av.featuresDisplayed .containsKey(renderOrder[ro])); float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder( @@ -1348,11 +1391,15 @@ public class Jalview2XML { String id = null; jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs; - + boolean newucs=false; if (!userColours.contains(ucs)) { userColours.add(ucs); - + newucs=true; + } + id = "ucs" + userColours.indexOf(ucs); + if (newucs) { + // actually create the scheme's entry in the XML model java.awt.Color[] colours = ucs.getColours(); jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours(); jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme(); @@ -1376,7 +1423,6 @@ public class Jalview2XML } } - id = "ucs" + userColours.indexOf(ucs); uc.setId(id); uc.setUserColourScheme(jbucs); jms.addUserColours(uc); @@ -1976,6 +2022,10 @@ public class Jalview2XML // //////////////////////////////// // LOAD ANNOTATIONS boolean hideQuality = true, hideConservation = true, hideConsensus = true; + /** + * store any annotations which forward reference a group's ID + */ + Hashtable groupAnnotRefs = new Hashtable(); if (vamsasSet.getAnnotationCount() > 0) { @@ -1998,7 +2048,7 @@ public class Jalview2XML { hideConsensus = false; continue; - } + } // set visiblity for other annotation in this view if (an[i].getId() != null && annotationIds.containsKey(an[i].getId())) @@ -2086,14 +2136,31 @@ public class Jalview2XML al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa); } } + // and make a note of any group association + if (an[i].getGroupRef()!=null && an[i].getGroupRef().length()>0) + { + groupAnnotRefs.put(an[i].getGroupRef(),jaa); + } + if (an[i].hasScore()) { jaa.setScore(an[i].getScore()); } - if (an[i].hasVisible()) jaa.visible = an[i].getVisible(); - + + if (an[i].hasCentreColLabels()) + jaa.centreColLabels = an[i].getCentreColLabels(); + + if (an[i].hasScaleColLabels()) + { + jaa.scaleColLabel = an[i].getScaleColLabels(); + } + if (an[i].hasAutoCalculated() && an[i].isAutoCalculated()) + { + // newer files have an 'autoCalculated' flag and store calculation state in viewport properties + jaa.autoCalculated = true; // means annotation will be marked for update at end of load. + } al.addAnnotation(jaa); } } @@ -2159,7 +2226,16 @@ public class Jalview2XML sg.setShowunconserved(groups[i].hasShowUnconserved() ? groups[i] .isShowUnconserved() : false); sg.thresholdTextColour = groups[i].getTextColThreshold(); - + if (groups[i].hasShowConsensusHistogram()) { + sg.setShowConsensusHistogram(groups[i].isShowConsensusHistogram()); + }; + if (groups[i].hasShowSequenceLogo()) { + sg.setIncludeAllConsSymbols(groups[i].isShowSequenceLogo()); + } + if (groups[i].hasIgnoreGapsinConsensus()) + { + sg.setIgnoreGapsConsensus(groups[i].getIgnoreGapsinConsensus()); + } if (groups[i].getConsThreshold() != 0) { jalview.analysis.Conservation c = new jalview.analysis.Conservation( @@ -2169,8 +2245,19 @@ public class Jalview2XML c.verdict(false, 25); sg.cs.setConservation(c); } - + + if (groups[i].getId()!=null + && groupAnnotRefs.size()>0) + { + // re-instate unique group/annotation row reference + jalview.datamodel.AlignmentAnnotation jaa = (jalview.datamodel.AlignmentAnnotation) groupAnnotRefs.get(groups[i].getId()); + if (jaa!=null) + { + jaa.groupRef = sg; + } + } al.addGroup(sg); + } } @@ -2705,6 +2792,55 @@ public class Jalview2XML { af.viewport.showSequenceFeatures = true; } + if (view.hasCentreColumnLabels()) + { + af.viewport.setCentreColumnLabels(view.getCentreColumnLabels()); + } + if (view.hasIgnoreGapsinConsensus()) + { + af.viewport.ignoreGapsInConsensusCalculation=view.getIgnoreGapsinConsensus(); + } + if (view.hasFollowHighlight()) + { + af.viewport.followHighlight = view.getFollowHighlight(); + } + if (view.hasFollowSelection()) + { + af.viewport.followSelection = view.getFollowSelection(); + } + if (view.hasShowConsensusHistogram()) + { + af.viewport.setShowConsensusHistogram(view.getShowConsensusHistogram()); + } else { + af.viewport.setShowConsensusHistogram(true); + } + if (view.hasShowSequenceLogo()) + { + af.viewport.setShowSequenceLogo(view.getShowSequenceLogo()); + } else { + af.viewport.setShowSequenceLogo(false); + } + if (view.hasShowDbRefTooltip()) + { + af.viewport.setShowDbRefs(view.getShowDbRefTooltip()); + } + if (view.hasShowNPfeatureTooltip()) + { + af.viewport.setShowNpFeats(view.hasShowNPfeatureTooltip()); + } + if (view.hasShowGroupConsensus()) + { + af.viewport.setShowGroupConsensus(view.getShowGroupConsensus()); + } else { + af.viewport.setShowGroupConsensus(false); + } + if (view.hasShowGroupConservation()) + { + af.viewport.setShowGroupConservation(view.getShowGroupConservation()); + } else { + af.viewport.setShowGroupConservation(false); + } + // recover featre settings if (jms.getFeatureSettings() != null) { @@ -2716,16 +2852,28 @@ public class Jalview2XML Setting setting = jms.getFeatureSettings().getSetting(fs); if (setting.hasMincolour()) { - // TODO: determine how to set data independent bounds for a graduated - // colour scheme's range. - GraduatedColor gc = new GraduatedColor(new java.awt.Color(setting + GraduatedColor gc = setting.hasMin() ? new GraduatedColor(new java.awt.Color(setting + .getMincolour()), + new java.awt.Color(setting.getColour()), setting.getMin(), setting.getMax()) + : new GraduatedColor(new java.awt.Color(setting .getMincolour()), - new java.awt.Color(setting.getColour()), 0, 1); + new java.awt.Color(setting.getColour()), 0,1); if (setting.hasThreshold()) { gc.setThresh(setting.getThreshold()); gc.setThreshType(setting.getThreshstate()); } + gc.setAutoScaled(true); // default + if (setting.hasAutoScale()) + { + gc.setAutoScaled(setting.getAutoScale()); + } + if (setting.hasColourByLabel()) + { + gc.setColourByLabel(setting.getColourByLabel()); + } + // and put in the feature colour table. + af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),gc); } else { @@ -2768,6 +2916,7 @@ public class Jalview2XML } af.setMenusFromViewport(af.viewport); + af.alignPanel.updateAnnotation(false); // recompute any autoannotation // TODO: we don't need to do this if the viewport is aready visible. Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view .getHeight());