X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=4c042b3a379ebedc76e986834a66b1079474d8c8;hb=9b57bab507b537d42d62e9a4c5f387d75d31cd8a;hp=d5b5fae372b1c6fae0159857497cdb0fb3ec03f2;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index d5b5fae..4c042b3 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -1,18 +1,18 @@ /* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle - * + * * This file is part of Jalview. - * + * * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License + * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. - * + * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.gui; @@ -29,7 +29,6 @@ import javax.swing.*; import org.exolab.castor.xml.*; -import uk.ac.vamsas.objects.utils.MapList; import jalview.bin.Cache; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; @@ -37,16 +36,23 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; import jalview.schemabinding.version2.*; import jalview.schemes.*; -import jalview.structure.StructureSelectionManager; +import jalview.util.Platform; import jalview.util.jarInputStreamProvider; +import jalview.ws.jws2.AAConsClient; +import jalview.ws.jws2.Jws2Discoverer; +import jalview.ws.jws2.dm.AAConsSettings; +import jalview.ws.jws2.jabaws2.Jws2Instance; +import jalview.ws.params.ArgumentI; +import jalview.ws.params.AutoCalcSetting; +import jalview.ws.params.WsParamSetI; /** * Write out the current jalview desktop state as a Jalview XML stream. - * + * * Note: the vamsas objects referred to here are primitive versions of the * VAMSAS project schema elements - they are not the same and most likely never * will be :) - * + * * @author $author$ * @version $Revision: 1.134 $ */ @@ -54,7 +60,7 @@ public class Jalview2XML { /** * create/return unique hash string for sq - * + * * @param sq * @return new or existing unique string for sq */ @@ -260,7 +266,7 @@ public class Jalview2XML /** * Writes a jalview project archive to the given Jar output stream. - * + * * @param jout */ public void SaveState(JarOutputStream jout) @@ -401,7 +407,7 @@ public class Jalview2XML /** * create a JalviewModel from an algnment view and marshall it to a * JarOutputStream - * + * * @param ap * panel to create jalview model for * @param fileName @@ -426,9 +432,9 @@ 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(); } @@ -458,6 +464,7 @@ public class Jalview2XML } JSeq jseq; + Set calcIdSet=new HashSet(); // SAVE SEQUENCES String id = ""; @@ -497,15 +504,13 @@ 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++) { @@ -612,7 +617,8 @@ public class Jalview2XML for (int smap = 0; smap < jmol.jmb.sequence[peid].length; smap++) { - if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1) +// if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1) + if (jds==jmol.jmb.sequence[peid][smap]) { StructureState state = new StructureState(); state.setVisible(true); @@ -706,9 +712,9 @@ 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) @@ -764,7 +770,7 @@ 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()); @@ -792,7 +798,6 @@ public class Jalview2XML } } } - // SAVE ANNOTATIONS /** * store forward refs from an annotationRow to any groups @@ -842,6 +847,7 @@ public class Jalview2XML an.setCentreColLabels(aa[i].centreColLabels); an.setScaleColLabels(aa[i].scaleColLabel); an.setShowAllColLabels(aa[i].showAllColLabels); + an.setBelowAlignment(aa[i].belowAlignment); if (aa[i].graph > 0) { @@ -864,8 +870,8 @@ 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); @@ -874,6 +880,13 @@ public class Jalview2XML { an.setScore(aa[i].getScore()); } + + if (aa[i].getCalcId()!=null) + { + calcIdSet.add(aa[i].getCalcId()); + an.setCalcId(aa[i].getCalcId()); + } + AnnotationElement ae; if (aa[i].annotations != null) { @@ -927,13 +940,11 @@ public class Jalview2XML if (jal.getGroups() != null) { JGroup[] groups = new JGroup[jal.getGroups().size()]; - - for (int i = 0; i < groups.length; i++) + int i = -1; + for (jalview.datamodel.SequenceGroup sg:jal.getGroups()) { - groups[i] = new JGroup(); + groups[++i] = new JGroup(); - jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal - .getGroups().elementAt(i); groups[i].setStart(sg.getStartRes()); groups[i].setEnd(sg.getEndRes()); groups[i].setName(sg.getName()); @@ -1159,11 +1170,11 @@ public class Jalview2XML } // Make sure we save none displayed feature settings - Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours - .keys(); - while (en.hasMoreElements()) + Iterator en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours + .keySet().iterator(); + while (en.hasNext()) { - String key = en.nextElement().toString(); + String key = en.next().toString(); if (settingsAdded.contains(key)) { continue; @@ -1184,11 +1195,11 @@ public class Jalview2XML fs.addSetting(setting); settingsAdded.addElement(key); } - en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys(); + en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keySet().iterator(); Vector groupsAdded = new Vector(); - while (en.hasMoreElements()) + while (en.hasNext()) { - String grp = en.nextElement().toString(); + String grp = en.next().toString(); if (groupsAdded.contains(grp)) { continue; @@ -1204,7 +1215,7 @@ public class Jalview2XML } - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { if (av.getColumnSelection() == null || av.getColumnSelection().getHiddenColumns() == null) @@ -1225,6 +1236,15 @@ public class Jalview2XML } } } + if (calcIdSet.size()>0) + { + for (String calcId:calcIdSet) + { + if (calcId.trim().length()>0) { + view.addCalcIdParam(createCalcIdParam(calcId, av)); + } + } + } jms.addViewport(view); @@ -1256,6 +1276,84 @@ public class Jalview2XML return object; } + private CalcIdParam createCalcIdParam(String calcId, AlignViewport av) + { + AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId); + if (settings != null) + { + CalcIdParam vCalcIdParam = new CalcIdParam(); + vCalcIdParam.setCalcId(calcId); + vCalcIdParam.addServiceURL(settings.getServiceURI()); + // generic URI allowing a third party to resolve another instance of the + // service used for this calculation + for (String urls:settings.getServiceURLs()) + { + vCalcIdParam.addServiceURL(urls); + } + vCalcIdParam.setVersion("1.0"); + if (settings.getPreset() != null) + { + WsParamSetI setting = settings.getPreset(); + vCalcIdParam.setName(setting.getName()); + vCalcIdParam.setDescription(setting.getDescription()); + } + else + { + vCalcIdParam.setName(""); + vCalcIdParam.setDescription("Last used parameters"); + } + // need to be able to recover 1) settings 2) user-defined presets or + // recreate settings from preset 3) predefined settings provided by + // service - or settings that can be transferred (or discarded) + vCalcIdParam.setParameters(settings + .getWsParamFile().replace("\n", "|\\n|")); + vCalcIdParam.setAutoUpdate(settings.isAutoUpdate()); + // todo - decide if updateImmediately is needed for any projects. + + return vCalcIdParam; + } + return null; + } + + private boolean recoverCalcIdParam(CalcIdParam calcIdParam, + AlignViewport av) + { + if (calcIdParam.getVersion().equals("1.0")) + { + Jws2Instance service=Jws2Discoverer.getDiscoverer().getPreferredServiceFor(calcIdParam.getServiceURL()); + if (service!=null) + { + WsParamSetI parmSet=null; + try { + parmSet = service.getParamStore().parseServiceParameterFile(calcIdParam.getName(), calcIdParam.getDescription(), calcIdParam.getServiceURL(), calcIdParam.getParameters().replace("|\\n|", "\n")); + } catch (IOException x) + { + warn("Couldn't parse parameter data for "+calcIdParam.getCalcId(), x); + return false; + } + List argList=null; + if (calcIdParam.getName().length()>0) { + parmSet = service.getParamStore().getPreset(calcIdParam.getName()); + if (parmSet!=null) + { + // TODO : check we have a good match with settings in AACons - otherwise we'll need to create a new preset + } + } + else { + argList = parmSet.getArguments(); + parmSet=null; + } + AAConsSettings settings = new AAConsSettings(calcIdParam.isAutoUpdate(), service, parmSet, argList); + av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings, calcIdParam.isNeedsUpdate()); + return true; + } else { + warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server."); + return false; + } + } + throw new Error("Unsupported Version for calcIdparam " + + calcIdParam.toString()); + } /** * External mapping between jalview objects and objects yielding a valid and * unique object ID string. This is null for normal Jalview project IO, but @@ -1267,7 +1365,7 @@ public class Jalview2XML /** * Construct a unique ID for jvobj using either existing bindings or if none * exist, the result of the hashcode call for the object. - * + * * @param jvobj * jalview data object * @return unique ID for referring to jvobj @@ -1298,7 +1396,7 @@ public class Jalview2XML /** * return local jalview object mapped to ID, if it exists - * + * * @param idcode * (may be null) * @return null or object bound to idcode @@ -1534,7 +1632,7 @@ public class Jalview2XML /** * Load a jalview project archive from a jar file - * + * * @param file * - HTTP URL or filename */ @@ -1578,6 +1676,7 @@ public class Jalview2XML return new jarInputStreamProvider() { + @Override public JarInputStream getJarInputStream() throws IOException { if (_url != null) @@ -1590,6 +1689,7 @@ public class Jalview2XML } } + @Override public String getFilename() { return file; @@ -1602,7 +1702,7 @@ public class Jalview2XML * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence * themselves. Any null fields will be initialised with default values, * non-null fields are left alone. - * + * * @param jprovider * @return */ @@ -1754,6 +1854,7 @@ public class Jalview2XML { javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { JOptionPane.showInternalMessageDialog(Desktop.desktop, @@ -1778,7 +1879,7 @@ public class Jalview2XML * Currently (28th Sep 2008) things will go horribly wrong in vamsas document * sync if this is set to true. */ - private boolean updateLocalViews = false; + private final boolean updateLocalViews = false; String loadPDBFile(jarInputStreamProvider jprovider, String pdbId) { @@ -1822,9 +1923,9 @@ public class Jalview2XML } ; out.close(); - - alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath()); - return outFile.getAbsolutePath(); + String t=outFile.getAbsolutePath(); + alreadyLoadedPDB.put(pdbId, t); + return t; } else { @@ -1859,7 +1960,7 @@ public class Jalview2XML /** * Load alignment frame from jalview XML DOM object - * + * * @param object * DOM * @param file @@ -1897,7 +1998,7 @@ public class Jalview2XML if (seqRefIds.get(seqId) != null) { - tmpseqs.add((jalview.datamodel.Sequence) seqRefIds.get(seqId)); + tmpseqs.add(seqRefIds.get(seqId)); multipleView = true; } else @@ -1920,7 +2021,7 @@ public class Jalview2XML hiddenSeqs = new Vector(); } - hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds + hiddenSeqs.addElement(seqRefIds .get(seqId)); } @@ -2263,6 +2364,12 @@ public class Jalview2XML { jaa.graphHeight = an[i].getGraphHeight(); } + if (an[i].hasBelowAlignment()) + { + jaa.belowAlignment=an[i].isBelowAlignment(); + } + jaa.setCalcId(an[i].getCalcId()); + if (jaa.autoCalculated) { autoAlan.add(new JvAnnotRow(i, jaa)); @@ -2603,7 +2710,7 @@ public class Jalview2XML // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, { // seqs_file 2}, boolean[] { // linkAlignPanel,superposeWithAlignpanel}} from hash - Object[] jmoldat = (Object[]) jmolViewIds.get(sviewid); + Object[] jmoldat = jmolViewIds.get(sviewid); ((boolean[]) jmoldat[3])[0] |= ids[p].getStructureState(s) .hasAlignwithAlignPanel() ? ids[p].getStructureState( s).getAlignwithAlignPanel() : false; @@ -2626,12 +2733,13 @@ public class Jalview2XML } if (ids[p].getFile() != null) { + File mapkey=new File(ids[p].getFile()); Object[] seqstrmaps = (Object[]) ((Hashtable) jmoldat[2]) - .get(ids[p].getFile()); + .get(mapkey); if (seqstrmaps == null) { ((Hashtable) jmoldat[2]).put( - new File(ids[p].getFile()).toString(), + mapkey, seqstrmaps = new Object[] { pdbFile, ids[p].getId(), new Vector(), new Vector() }); @@ -2664,7 +2772,7 @@ public class Jalview2XML Object[] svattrib = entry.getValue(); int[] geom = (int[]) svattrib[0]; String state = (String) svattrib[1]; - Hashtable oldFiles = (Hashtable) svattrib[2]; + Hashtable oldFiles = (Hashtable) svattrib[2]; final boolean useinJmolsuperpos = ((boolean[]) svattrib[3])[0], usetoColourbyseq = ((boolean[]) svattrib[3])[1], jmolColouring = ((boolean[]) svattrib[3])[2]; int x = geom[0], y = geom[1], width = geom[2], height = geom[3]; // collate the pdbfile -> sequence mappings from this view @@ -2728,6 +2836,8 @@ public class Jalview2XML { newFileLoc = new StringBuffer(); } + do { + // look for next filename in load statement newFileLoc.append(state.substring(cp, ncp = (state.indexOf("\"", ncp + 1) + 1))); String oldfilenam = state.substring(ncp, @@ -2735,16 +2845,16 @@ public class Jalview2XML // recover the new mapping data for this old filename // have to normalize filename - since Jmol and jalview do filename // translation differently. - Object[] filedat = oldFiles.get(new File(oldfilenam) - .toString()); - newFileLoc.append(((String) filedat[0])); + Object[] filedat = oldFiles.get(new File(oldfilenam)); + newFileLoc.append(Platform.escapeString((String) filedat[0])); pdbfilenames.addElement((String) filedat[0]); pdbids.addElement((String) filedat[1]); - seqmaps.addElement((SequenceI[]) ((Vector) filedat[2]) + seqmaps.addElement(((Vector) filedat[2]) .toArray(new SequenceI[0])); newFileLoc.append("\""); cp = ecp + 1; // advance beyond last \" and set cursor so we can // look for next file statement. + } while ((ncp=state.indexOf("/*file*/",cp))>-1); } if (cp > 0) { @@ -2757,7 +2867,7 @@ public class Jalview2XML .print("Ignoring incomplete Jmol state for PDB ids: "); newFileLoc = new StringBuffer(state); newFileLoc.append("; load append "); - for (String id : oldFiles.keySet()) + for (File id : oldFiles.keySet()) { // add this and any other pdb files that should be present in // the viewer @@ -2766,7 +2876,7 @@ public class Jalview2XML newFileLoc.append(((String) filedat[0])); pdbfilenames.addElement((String) filedat[0]); pdbids.addElement((String) filedat[1]); - seqmaps.addElement((SequenceI[]) ((Vector) filedat[2]) + seqmaps.addElement(((Vector) filedat[2]) .toArray(new SequenceI[0])); newFileLoc.append(" \""); newFileLoc.append((String) filedat[0]); @@ -2802,10 +2912,10 @@ public class Jalview2XML // TODO: assemble String[] { pdb files }, String[] { id for each // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, { // seqs_file 2}} from hash - final String[] pdbf = (String[]) pdbfilenames - .toArray(new String[pdbfilenames.size()]), id = (String[]) pdbids + final String[] pdbf = pdbfilenames + .toArray(new String[pdbfilenames.size()]), id = pdbids .toArray(new String[pdbids.size()]); - final SequenceI[][] sq = (SequenceI[][]) seqmaps + final SequenceI[][] sq = seqmaps .toArray(new SequenceI[seqmaps.size()][]); final String fileloc = newFileLoc.toString(), vid = sviewid; final AlignFrame alf = af; @@ -2815,6 +2925,7 @@ public class Jalview2XML { javax.swing.SwingUtilities.invokeAndWait(new Runnable() { + @Override public void run() { AppJmol sview = null; @@ -2855,36 +2966,36 @@ public class Jalview2XML // add mapping for sequences in this view to an already open Jmol // instance - for (String id : oldFiles.keySet()) + for (File id : oldFiles.keySet()) { // add this and any other pdb files that should be present in the // viewer Object[] filedat = oldFiles.get(id); String pdbFile = (String) filedat[0]; - SequenceI[] seq = (SequenceI[]) ((Vector) filedat[2]) + SequenceI[] seq = ((Vector) filedat[2]) .toArray(new SequenceI[0]); - ((AppJmol) comp).jmb.ssm.setMapping(seq, null, pdbFile, + comp.jmb.ssm.setMapping(seq, null, pdbFile, jalview.io.AppletFormatAdapter.FILE); - ((AppJmol) comp).jmb.addSequenceForStructFile(pdbFile, seq); + comp.jmb.addSequenceForStructFile(pdbFile, seq); } // and add the AlignmentPanel's reference to the Jmol view - ((AppJmol) comp).addAlignmentPanel(ap); + comp.addAlignmentPanel(ap); if (useinJmolsuperpos) { - ((AppJmol) comp).useAlignmentPanelForSuperposition(ap); + comp.useAlignmentPanelForSuperposition(ap); } else { - ((AppJmol) comp).excludeAlignmentPanelForSuperposition(ap); + comp.excludeAlignmentPanelForSuperposition(ap); } if (usetoColourbyseq) { - ((AppJmol) comp).useAlignmentPanelForColourbyseq(ap, + comp.useAlignmentPanelForColourbyseq(ap, !jmolColouring); } else { - ((AppJmol) comp).excludeAlignmentPanelForColourbyseq(ap); + comp.excludeAlignmentPanelForColourbyseq(ap); } } } @@ -2907,7 +3018,7 @@ 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())); } @@ -2918,7 +3029,7 @@ 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 @@ -3008,18 +3119,18 @@ 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) @@ -3031,7 +3142,7 @@ 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()), @@ -3041,7 +3152,7 @@ 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()); @@ -3049,7 +3160,7 @@ 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()); @@ -3060,8 +3171,8 @@ public class Jalview2XML { for (int g = 0; g < al.getGroups().size(); g++) { - jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al - .getGroups().elementAt(g); + jalview.datamodel.SequenceGroup sg = al + .getGroups().get(g); if (sg.cs == null) { @@ -3072,7 +3183,7 @@ 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(). @@ -3081,7 +3192,7 @@ public class Jalview2XML */ { sg.cs = new AnnotationColourGradient( - af.viewport.alignment.getAlignmentAnnotation()[i], + af.viewport.getAlignment().getAlignmentAnnotation()[i], sg.cs, view.getAnnotationColours() .getAboveThreshold()); } @@ -3103,7 +3214,7 @@ public class Jalview2XML if (cs != null) { cs.setThreshold(view.getPidThreshold(), true); - cs.setConsensus(af.viewport.hconsensus); + cs.setConsensus(af.viewport.getSequenceConsensusHash()); } } @@ -3129,8 +3240,8 @@ public class Jalview2XML } if (view.hasIgnoreGapsinConsensus()) { - af.viewport.ignoreGapsInConsensusCalculation = view - .getIgnoreGapsinConsensus(); + af.viewport.setIgnoreGapsConsensus(view + .getIgnoreGapsinConsensus(), null); } if (view.hasFollowHighlight()) { @@ -3151,11 +3262,11 @@ 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()) { @@ -3344,7 +3455,7 @@ public class Jalview2XML /** * TODO remove this method - * + * * @param view * @return AlignFrame bound to sequenceSetId from view, if one exists. private * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) { @@ -3355,7 +3466,7 @@ public class Jalview2XML /** * Check if the Jalview view contained in object should be skipped or not. - * + * * @param object * @return true if view's sequenceSetId is a key in skipList */ @@ -3428,7 +3539,7 @@ public class Jalview2XML } /** - * + * * @param vamsasSeq * sequence definition to create/merge dataset sequence for * @param ds @@ -3446,7 +3557,7 @@ public class Jalview2XML jalview.datamodel.SequenceI dsq = null; if (sq != null && sq.getDatasetSequence() != null) { - dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence(); + dsq = sq.getDatasetSequence(); } String sqid = vamsasSeq.getDsseqid(); @@ -3552,7 +3663,7 @@ public class Jalview2XML /** * make a new dataset ID for this jalview dataset alignment - * + * * @param dataset * @return */ @@ -3719,11 +3830,11 @@ public class Jalview2XML af.closeMenuItem_actionPerformed(true); /* - * if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0; - * i