X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=6d55c3299db85af1c1e3a7724e22f55715b0bca1;hb=6bd9630607bd38aaf9b42738a0ae90de8fe5c6e8;hp=b1b1f5511f8eb68cab2ff1f69f12176f8f54f4fe;hpb=0f368572e180ae64ad32158e80c46ca5a6acef96;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index b1b1f55..6d55c32 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -427,9 +427,9 @@ public class Jalview2XML object.setCreationDate(new java.util.Date(System.currentTimeMillis())); object.setVersion(jalview.bin.Cache.getProperty("VERSION")); - jalview.datamodel.AlignmentI jal = av.alignment; + jalview.datamodel.AlignmentI jal = av.getAlignment(); - if (av.hasHiddenRows) + if (av.hasHiddenRows()) { jal = jal.getHiddenSequences().getFullAlignment(); } @@ -498,15 +498,13 @@ public class Jalview2XML jseq.setId(id); // jseq id should be a string not a number - if (av.hasHiddenRows) + if (av.hasHiddenRows()) { - jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds)); + jseq.setHidden(av.getAlignment().getHiddenSequences().isHidden(jds)); - if (av.hiddenRepSequences != null - && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i))) + if (av.isHiddenRepSequence(jal.getSequenceAt(i))) { - jalview.datamodel.SequenceI[] reps = ((jalview.datamodel.SequenceGroup) av.hiddenRepSequences - .get(jal.getSequenceAt(i))).getSequencesInOrder(jal); + jalview.datamodel.SequenceI[] reps = av.getRepresentedSequences(jal.getSequenceAt(i)).getSequencesInOrder(jal); for (int h = 0; h < reps.length; h++) { @@ -708,9 +706,9 @@ public class Jalview2XML jms.addJSeq(jseq); } - if (av.hasHiddenRows) + if (av.hasHiddenRows()) { - jal = av.alignment; + jal = av.getAlignment(); } // SAVE MAPPINGS if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0) @@ -766,7 +764,7 @@ public class Jalview2XML { TreePanel tp = (TreePanel) frames[t]; - if (tp.treeCanvas.av.alignment == jal) + if (tp.treeCanvas.av.getAlignment() == jal) { Tree tree = new Tree(); tree.setTitle(tp.getTitle()); @@ -866,8 +864,8 @@ public class Jalview2XML an.setLabel(aa[i].label); - if (aa[i] == av.quality || aa[i] == av.conservation - || aa[i] == av.consensus || aa[i].autoCalculated) + if (aa[i] == av.getAlignmentQualityAnnot() || aa[i] == av.getAlignmentConservationAnnotation() + || aa[i] == av.getAlignmentConsensusAnnotation() || aa[i].autoCalculated) { // new way of indicating autocalculated annotation - an.setAutoCalculated(aa[i].autoCalculated); @@ -1206,7 +1204,7 @@ public class Jalview2XML } - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { if (av.getColumnSelection() == null || av.getColumnSelection().getHiddenColumns() == null) @@ -2912,7 +2910,7 @@ public class Jalview2XML for (int i = 0; i < JSEQ.length; i++) { - af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i), + af.viewport.setSequenceColour(af.viewport.getAlignment().getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour())); } @@ -2923,7 +2921,7 @@ public class Jalview2XML jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded .get(uniqueSeqSetId); - af.viewport.sequenceSetID = uniqueSeqSetId; + af.viewport.setSequenceSetId(uniqueSeqSetId); if (av != null) { // propagate shared settings to this new view @@ -3013,18 +3011,18 @@ public class Jalview2XML else if (view.getBgColour().startsWith("Annotation")) { // int find annotation - if (af.viewport.alignment.getAlignmentAnnotation() != null) + if (af.viewport.getAlignment().getAlignmentAnnotation() != null) { - for (int i = 0; i < af.viewport.alignment + for (int i = 0; i < af.viewport.getAlignment() .getAlignmentAnnotation().length; i++) { - if (af.viewport.alignment.getAlignmentAnnotation()[i].label + if (af.viewport.getAlignment().getAlignmentAnnotation()[i].label .equals(view.getAnnotationColours().getAnnotation())) { - if (af.viewport.alignment.getAlignmentAnnotation()[i] + if (af.viewport.getAlignment().getAlignmentAnnotation()[i] .getThreshold() == null) { - af.viewport.alignment.getAlignmentAnnotation()[i] + af.viewport.getAlignment().getAlignmentAnnotation()[i] .setThreshold(new jalview.datamodel.GraphLine(view .getAnnotationColours().getThreshold(), "Threshold", java.awt.Color.black) @@ -3036,7 +3034,7 @@ public class Jalview2XML .equals("None")) { cs = new AnnotationColourGradient( - af.viewport.alignment.getAlignmentAnnotation()[i], + af.viewport.getAlignment().getAlignmentAnnotation()[i], new java.awt.Color(view.getAnnotationColours() .getMinColour()), new java.awt.Color(view .getAnnotationColours().getMaxColour()), @@ -3046,7 +3044,7 @@ public class Jalview2XML .startsWith("ucs")) { cs = new AnnotationColourGradient( - af.viewport.alignment.getAlignmentAnnotation()[i], + af.viewport.getAlignment().getAlignmentAnnotation()[i], GetUserColourScheme(jms, view .getAnnotationColours().getColourScheme()), view.getAnnotationColours().getAboveThreshold()); @@ -3054,7 +3052,7 @@ public class Jalview2XML else { cs = new AnnotationColourGradient( - af.viewport.alignment.getAlignmentAnnotation()[i], + af.viewport.getAlignment().getAlignmentAnnotation()[i], ColourSchemeProperty.getColour(al, view .getAnnotationColours().getColourScheme()), view.getAnnotationColours().getAboveThreshold()); @@ -3077,7 +3075,7 @@ public class Jalview2XML * if * (view.getAnnotationColours().getColourScheme().equals("None" * )) { sg.cs = new AnnotationColourGradient( - * af.viewport.alignment.getAlignmentAnnotation()[i], new + * af.viewport.getAlignment().getAlignmentAnnotation()[i], new * java.awt.Color(view.getAnnotationColours(). * getMinColour()), new * java.awt.Color(view.getAnnotationColours(). @@ -3086,7 +3084,7 @@ public class Jalview2XML */ { sg.cs = new AnnotationColourGradient( - af.viewport.alignment.getAlignmentAnnotation()[i], + af.viewport.getAlignment().getAlignmentAnnotation()[i], sg.cs, view.getAnnotationColours() .getAboveThreshold()); } @@ -3108,7 +3106,7 @@ public class Jalview2XML if (cs != null) { cs.setThreshold(view.getPidThreshold(), true); - cs.setConsensus(af.viewport.hconsensus); + cs.setConsensus(af.viewport.getSequenceConsensusHash()); } } @@ -3134,8 +3132,8 @@ public class Jalview2XML } if (view.hasIgnoreGapsinConsensus()) { - af.viewport.ignoreGapsInConsensusCalculation = view - .getIgnoreGapsinConsensus(); + af.viewport.setIgnoreGapsConsensus(view + .getIgnoreGapsinConsensus(), null); } if (view.hasFollowHighlight()) { @@ -3156,11 +3154,11 @@ public class Jalview2XML } if (view.hasShowSequenceLogo()) { - af.viewport.showSequenceLogo = view.getShowSequenceLogo(); + af.viewport.setShowSequenceLogo(view.getShowSequenceLogo()); } else { - af.viewport.showSequenceLogo = false; + af.viewport.setShowSequenceLogo(false); } if (view.hasShowDbRefTooltip()) { @@ -3724,11 +3722,11 @@ public class Jalview2XML af.closeMenuItem_actionPerformed(true); /* - * if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0; - * i