X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=bde3035939a292f6faf92d9f9626f44cc9cc2e78;hb=af563e083b2a94e50f23d317f260fb734c52c266;hp=a9827d4f2826554a08af3b5827450180dabbf3ae;hpb=ff4d98fbde57ca9dea2fc607d36d80a00963746d;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index a9827d4..bde3035 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 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * + * 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 +504,14 @@ 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 +618,8 @@ 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 +713,9 @@ 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 +771,7 @@ 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 +799,6 @@ public class Jalview2XML } } } - // SAVE ANNOTATIONS /** * store forward refs from an annotationRow to any groups @@ -842,6 +848,7 @@ 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 +871,10 @@ 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 +883,13 @@ 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 +943,11 @@ 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 +1173,11 @@ 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 +1198,12 @@ 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 +1219,7 @@ public class Jalview2XML } - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { if (av.getColumnSelection() == null || av.getColumnSelection().getHiddenColumns() == null) @@ -1225,6 +1240,21 @@ public class Jalview2XML } } } + if (calcIdSet.size() > 0) + { + for (String calcId : calcIdSet) + { + if (calcId.trim().length() > 0) + { + CalcIdParam cidp = createCalcIdParam(calcId, av); + // Some calcIds have no parameters. + if (cidp != null) + { + view.addCalcIdParam(cidp); + } + } + } + } jms.addViewport(view); @@ -1256,6 +1286,99 @@ 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 @@ -1578,6 +1701,7 @@ public class Jalview2XML return new jarInputStreamProvider() { + @Override public JarInputStream getJarInputStream() throws IOException { if (_url != null) @@ -1590,6 +1714,7 @@ public class Jalview2XML } } + @Override public String getFilename() { return file; @@ -1754,6 +1879,7 @@ public class Jalview2XML { javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { JOptionPane.showInternalMessageDialog(Desktop.desktop, @@ -1778,7 +1904,7 @@ 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 +1948,9 @@ public class Jalview2XML } ; out.close(); - - alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath()); - return outFile.getAbsolutePath(); + String t = outFile.getAbsolutePath(); + alreadyLoadedPDB.put(pdbId, t); + return t; } else { @@ -1897,7 +2023,7 @@ public class Jalview2XML if (seqRefIds.get(seqId) != null) { - tmpseqs.add((jalview.datamodel.Sequence) seqRefIds.get(seqId)); + tmpseqs.add(seqRefIds.get(seqId)); multipleView = true; } else @@ -1920,8 +2046,7 @@ public class Jalview2XML hiddenSeqs = new Vector(); } - hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds - .get(seqId)); + hiddenSeqs.addElement(seqRefIds.get(seqId)); } } @@ -2142,16 +2267,19 @@ public class Jalview2XML // Construct new annotation from model. AnnotationElement[] ae = an[i].getAnnotationElement(); jalview.datamodel.Annotation[] anot = null; - + java.awt.Color firstColour=null; + int anpos; if (!an[i].getScoreOnly()) { anot = new jalview.datamodel.Annotation[al.getWidth()]; for (int aa = 0; aa < ae.length && aa < anot.length; aa++) { - if (ae[aa].getPosition() >= anot.length) + anpos = ae[aa].getPosition(); + + if (anpos >= anot.length) continue; - anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation( + anot[anpos] = new jalview.datamodel.Annotation( ae[aa].getDisplayCharacter(), ae[aa].getDescription(), (ae[aa].getSecondaryStructure() == null || ae[aa] @@ -2167,8 +2295,12 @@ public class Jalview2XML // { // anot[ae[aa].getPosition()].displayCharacter = ""; // } - anot[ae[aa].getPosition()].colour = new java.awt.Color( + anot[anpos].colour = new java.awt.Color( ae[aa].getColour()); + if (firstColour==null) + { + firstColour=anot[anpos].colour; + } } } jalview.datamodel.AlignmentAnnotation jaa = null; @@ -2184,7 +2316,7 @@ public class Jalview2XML an[i].getGraphType()); jaa.graphGroup = an[i].getGraphGroup(); - + jaa._linecolour=firstColour; if (an[i].getThresholdLine() != null) { jaa.setThreshold(new jalview.datamodel.GraphLine(an[i] @@ -2204,25 +2336,22 @@ public class Jalview2XML { jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), an[i].getDescription(), anot); + jaa._linecolour=firstColour; } - if (autoForView) + // register new annotation + if (an[i].getId() != null) { - // register new annotation - if (an[i].getId() != null) - { - annotationIds.put(an[i].getId(), jaa); - jaa.annotationId = an[i].getId(); - } - // recover sequence association - if (an[i].getSequenceRef() != null) + annotationIds.put(an[i].getId(), jaa); + jaa.annotationId = an[i].getId(); + } + // recover sequence association + if (an[i].getSequenceRef() != null) + { + if (al.findName(an[i].getSequenceRef()) != null) { - if (al.findName(an[i].getSequenceRef()) != null) - { - jaa.createSequenceMapping( - al.findName(an[i].getSequenceRef()), 1, true); - al.findName(an[i].getSequenceRef()).addAlignmentAnnotation( - jaa); - } + jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()), + 1, true); + al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa); } } // and make a note of any group association @@ -2263,6 +2392,12 @@ 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 +2738,7 @@ 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 +2761,12 @@ 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(), + ((Hashtable) jmoldat[2]).put(mapkey, seqstrmaps = new Object[] { pdbFile, ids[p].getId(), new Vector(), new Vector() }); @@ -2664,7 +2799,7 @@ 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 @@ -2728,23 +2863,28 @@ public class Jalview2XML { newFileLoc = new StringBuffer(); } - newFileLoc.append(state.substring(cp, - ncp = (state.indexOf("\"", ncp + 1) + 1))); - String oldfilenam = state.substring(ncp, - ecp = state.indexOf("\"", ncp)); - // 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])); - pdbfilenames.addElement((String) filedat[0]); - pdbids.addElement((String) filedat[1]); - seqmaps.addElement((SequenceI[]) ((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. + do + { + // look for next filename in load statement + newFileLoc.append(state.substring(cp, + ncp = (state.indexOf("\"", ncp + 1) + 1))); + String oldfilenam = state.substring(ncp, + ecp = state.indexOf("\"", ncp)); + // 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)); + newFileLoc.append(Platform + .escapeString((String) filedat[0])); + pdbfilenames.addElement((String) filedat[0]); + pdbids.addElement((String) filedat[1]); + 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 +2897,7 @@ 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 +2906,7 @@ 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 +2942,10 @@ 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 +2955,7 @@ public class Jalview2XML { javax.swing.SwingUtilities.invokeAndWait(new Runnable() { + @Override public void run() { AppJmol sview = null; @@ -2855,36 +2996,35 @@ 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, - !jmolColouring); + comp.useAlignmentPanelForColourbyseq(ap, !jmolColouring); } else { - ((AppJmol) comp).excludeAlignmentPanelForColourbyseq(ap); + comp.excludeAlignmentPanelForColourbyseq(ap); } } } @@ -2907,8 +3047,8 @@ public class Jalview2XML for (int i = 0; i < JSEQ.length; i++) { - af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i), - new java.awt.Color(JSEQ[i].getColour())); + af.viewport.setSequenceColour(af.viewport.getAlignment() + .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour())); } af.viewport.gatherViewsHere = view.getGatheredViews(); @@ -2918,7 +3058,7 @@ 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 +3148,18 @@ 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) @@ -3030,8 +3170,8 @@ public class Jalview2XML if (view.getAnnotationColours().getColourScheme() .equals("None")) { - cs = new AnnotationColourGradient( - af.viewport.alignment.getAlignmentAnnotation()[i], + cs = new AnnotationColourGradient(af.viewport + .getAlignment().getAlignmentAnnotation()[i], new java.awt.Color(view.getAnnotationColours() .getMinColour()), new java.awt.Color(view .getAnnotationColours().getMaxColour()), @@ -3040,16 +3180,16 @@ public class Jalview2XML else if (view.getAnnotationColours().getColourScheme() .startsWith("ucs")) { - cs = new AnnotationColourGradient( - af.viewport.alignment.getAlignmentAnnotation()[i], + cs = new AnnotationColourGradient(af.viewport + .getAlignment().getAlignmentAnnotation()[i], GetUserColourScheme(jms, view .getAnnotationColours().getColourScheme()), view.getAnnotationColours().getAboveThreshold()); } else { - cs = new AnnotationColourGradient( - af.viewport.alignment.getAlignmentAnnotation()[i], + cs = new AnnotationColourGradient(af.viewport + .getAlignment().getAlignmentAnnotation()[i], ColourSchemeProperty.getColour(al, view .getAnnotationColours().getColourScheme()), view.getAnnotationColours().getAboveThreshold()); @@ -3060,8 +3200,8 @@ 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 +3212,7 @@ 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(). @@ -3080,8 +3220,8 @@ public class Jalview2XML * view.getAnnotationColours().getAboveThreshold()); } else */ { - sg.cs = new AnnotationColourGradient( - af.viewport.alignment.getAlignmentAnnotation()[i], + sg.cs = new AnnotationColourGradient(af.viewport + .getAlignment().getAlignmentAnnotation()[i], sg.cs, view.getAnnotationColours() .getAboveThreshold()); } @@ -3103,7 +3243,7 @@ public class Jalview2XML if (cs != null) { cs.setThreshold(view.getPidThreshold(), true); - cs.setConsensus(af.viewport.hconsensus); + cs.setConsensus(af.viewport.getSequenceConsensusHash()); } } @@ -3129,8 +3269,8 @@ public class Jalview2XML } if (view.hasIgnoreGapsinConsensus()) { - af.viewport.ignoreGapsInConsensusCalculation = view - .getIgnoreGapsinConsensus(); + af.viewport.setIgnoreGapsConsensus(view.getIgnoreGapsinConsensus(), + null); } if (view.hasFollowHighlight()) { @@ -3151,11 +3291,11 @@ 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()) { @@ -3256,7 +3396,23 @@ public class Jalview2XML ); } } - + if (view.getCalcIdParam() != null) + { + for (CalcIdParam calcIdParam : view.getCalcIdParam()) + { + if (calcIdParam != null) + { + if (recoverCalcIdParam(calcIdParam, af.viewport)) + { + } + else + { + warn("Couldn't recover parameters for " + + calcIdParam.getCalcId()); + } + } + } + } af.setMenusFromViewport(af.viewport); // TODO: we don't need to do this if the viewport is aready visible. Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), @@ -3286,21 +3442,34 @@ public class Jalview2XML } for (JvAnnotRow auan : autoAlan) { - visan.put(auan.template.label, auan); + visan.put(auan.template.label + + (auan.template.getCalcId() == null ? "" : "\t" + + auan.template.getCalcId()), auan); } int hSize = al.getAlignmentAnnotation().length; ArrayList reorder = new ArrayList(); + // work through any autoCalculated annotation already on the view + // removing it if it should be placed in a different location on the + // annotation panel. + List remains = new ArrayList(visan.keySet()); for (int h = 0; h < hSize; h++) { jalview.datamodel.AlignmentAnnotation jalan = al .getAlignmentAnnotation()[h]; if (jalan.autoCalculated) { - JvAnnotRow valan = visan.get(jalan.label); + String k; + JvAnnotRow valan = visan.get(k = jalan.label); + if (jalan.getCalcId() != null) + { + valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId()); + } + if (valan != null) { // delete the auto calculated row from the alignment - al.deleteAnnotation(al.getAlignmentAnnotation()[h], false); + al.deleteAnnotation(jalan, false); + remains.remove(k); hSize--; h--; if (valan != nullAnnot) @@ -3322,6 +3491,18 @@ public class Jalview2XML } } } + // Add any (possibly stale) autocalculated rows that were not appended to + // the view during construction + for (String other : remains) + { + JvAnnotRow othera = visan.get(other); + if (othera != nullAnnot && othera.template.getCalcId() != null + && othera.template.getCalcId().length() > 0) + { + reorder.add(othera); + } + } + // now put the automatic annotation in its correct place int s = 0, srt[] = new int[reorder.size()]; JvAnnotRow[] rws = new JvAnnotRow[reorder.size()]; for (JvAnnotRow jvar : reorder) @@ -3344,7 +3525,7 @@ 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 +3536,7 @@ 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 +3609,7 @@ public class Jalview2XML } /** - * + * * @param vamsasSeq * sequence definition to create/merge dataset sequence for * @param ds @@ -3446,7 +3627,7 @@ 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 +3733,7 @@ public class Jalview2XML /** * make a new dataset ID for this jalview dataset alignment - * + * * @param dataset * @return */ @@ -3719,11 +3900,11 @@ public class Jalview2XML af.closeMenuItem_actionPerformed(true); /* - * if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0; - * i