X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;h=7df7cb2a614dd33639846c45f5db329c680aca7c;hb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;hp=82282395155218814d5df433e13c33d03947d858;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java index 8228239..7df7cb2 100644 --- a/src/jalview/io/VamsasAppDatastore.java +++ b/src/jalview/io/VamsasAppDatastore.java @@ -1,30 +1,29 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * 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 - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * 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 * 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 . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.io; import jalview.bin.Cache; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.AlignmentView; -import jalview.datamodel.DBRefEntry; import jalview.datamodel.GraphLine; -import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; import jalview.gui.AlignViewport; @@ -34,7 +33,8 @@ import jalview.io.vamsas.Datasetsequence; import jalview.io.vamsas.DatastoreItem; import jalview.io.vamsas.DatastoreRegistry; import jalview.io.vamsas.Rangetype; -import jalview.util.UrlLink; +import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; import java.io.IOException; import java.util.Enumeration; @@ -42,23 +42,47 @@ import java.util.HashMap; import java.util.Hashtable; import java.util.IdentityHashMap; import java.util.Iterator; +import java.util.List; +import java.util.Set; import java.util.Vector; import java.util.jar.JarInputStream; import java.util.jar.JarOutputStream; -import uk.ac.vamsas.client.*; -import uk.ac.vamsas.objects.core.*; +import uk.ac.vamsas.client.IClientAppdata; +import uk.ac.vamsas.client.IClientDocument; +import uk.ac.vamsas.client.Vobject; +import uk.ac.vamsas.client.VorbaId; +import uk.ac.vamsas.objects.core.Alignment; +import uk.ac.vamsas.objects.core.AlignmentSequence; +import uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation; +import uk.ac.vamsas.objects.core.AnnotationElement; +import uk.ac.vamsas.objects.core.DataSet; +import uk.ac.vamsas.objects.core.DataSetAnnotations; +import uk.ac.vamsas.objects.core.DbRef; +import uk.ac.vamsas.objects.core.Entry; +import uk.ac.vamsas.objects.core.Glyph; +import uk.ac.vamsas.objects.core.Local; +import uk.ac.vamsas.objects.core.MapType; +import uk.ac.vamsas.objects.core.Mapped; +import uk.ac.vamsas.objects.core.Property; +import uk.ac.vamsas.objects.core.Provenance; +import uk.ac.vamsas.objects.core.RangeAnnotation; +import uk.ac.vamsas.objects.core.RangeType; +import uk.ac.vamsas.objects.core.Seg; +import uk.ac.vamsas.objects.core.Sequence; +import uk.ac.vamsas.objects.core.SequenceType; +import uk.ac.vamsas.objects.core.VAMSAS; import uk.ac.vamsas.objects.utils.Properties; /* - * + * * static { * org.exolab.castor.util.LocalConfiguration.getInstance().getProperties().setProperty( * "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer"); } - * + * */ /* - * TODO: check/verify consistency for vamsas sync with group associated alignment annotation + * TODO: check/verify consistency for vamsas sync with group associated alignment annotation */ public class VamsasAppDatastore { @@ -127,7 +151,7 @@ public class VamsasAppDatastore private void buildSkipList() { skipList = new Hashtable(); - AlignFrame[] al = Desktop.getAlignframes(); + AlignFrame[] al = Desktop.getAlignFrames(); for (int f = 0; al != null && f < al.length; f++) { skipList.put(al[f].getViewport().getSequenceSetId(), al[f]); @@ -224,8 +248,7 @@ public class VamsasAppDatastore { Cache.log.debug( "Warning? Overwriting existing vamsas id binding for " - + vobj.getVorbaId(), new Exception( - "Overwriting vamsas id binding.")); + + vobj.getVorbaId(), new Exception(MessageManager.getString("exception.overwriting_vamsas_id_binding"))); } else if (jv2vobj.containsKey(jvobj) && !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId())) @@ -312,8 +335,7 @@ public class VamsasAppDatastore if (vbound.getV_parent() != null && dataset != vbound.getV_parent()) { - throw new Error( - "IMPLEMENTATION ERROR: Cannot map an alignment of sequences from different datasets into a single alignment in the vamsas document."); + throw new Error(MessageManager.getString("error.implementation_error_cannot_map_alignment_sequences")); // This occurs because the dataset for the alignment we are // trying to } @@ -546,12 +568,8 @@ public class VamsasAppDatastore else { // first find the alignment sequence to associate this with. - SequenceI jvalsq = null; - Enumeration jval = av.getAlignment().getSequences() - .elements(); - while (jval.hasMoreElements()) + for (SequenceI jvalsq : av.getAlignment().getSequences()) { - jvalsq = (SequenceI) jval.nextElement(); // saveDatasetSequenceAnnotation(AlSeqMaps,(uk.ac.vamsas.objects.core.Sequence) // sref, aa[i]); if (jvalsq.getDatasetSequence() == aa[i].sequenceRef) @@ -734,12 +752,12 @@ public class VamsasAppDatastore * @return true if alignment associated with this view will be stored in * document. */ - public boolean alignmentWillBeSkipped(AlignViewport av) + public boolean alignmentWillBeSkipped(AlignmentViewport av) { return (!av.getAlignment().isAligned()); } - private void addToSkipList(AlignViewport av) + private void addToSkipList(AlignmentViewport av) { if (skipList == null) { @@ -884,7 +902,7 @@ public class VamsasAppDatastore * creates/syncs the jvalsq from the alignment sequence */ private boolean syncFromAlignmentSequence(AlignmentSequence valseq, - char valGapchar, char gapChar, Vector dsseqs) + char valGapchar, char gapChar, List dsseqs) { boolean modal = false; @@ -1074,8 +1092,10 @@ public class VamsasAppDatastore an.addProperty(Properties.newProperty(THRESHOLD, Properties.FLOATTYPE, "" + alan.getThreshold().value)); if (alan.getThreshold().label != null) + { an.addProperty(Properties.newProperty(THRESHOLD + "Name", Properties.STRINGTYPE, "" + alan.getThreshold().label)); + } } ((DataSet) sref.getV_parent()).addDataSetAnnotations(an); bindjvvobj(alan, an); @@ -1260,7 +1280,7 @@ public class VamsasAppDatastore /** * list of alignment views created when updating Jalview from document. */ - private Vector newAlignmentViews = new Vector(); + private final Vector newAlignmentViews = new Vector(); /** * update local jalview view settings from the stored appdata (if any) @@ -1292,6 +1312,7 @@ public class VamsasAppDatastore jalview.util.jarInputStreamProvider jprovider = new jalview.util.jarInputStreamProvider() { + @Override public String getFilename() { @@ -1299,6 +1320,7 @@ public class VamsasAppDatastore return "Jalview Vamsas Document Client Data"; } + @Override public JarInputStream getJarInputStream() throws IOException { jalview.bin.Cache.log @@ -1308,7 +1330,7 @@ public class VamsasAppDatastore }; if (dojvsync) { - fromxml.LoadJalviewAlign(jprovider); + fromxml.loadJalviewAlign(jprovider); } } catch (Exception e) { @@ -1338,6 +1360,7 @@ public class VamsasAppDatastore jalview.util.jarInputStreamProvider jarstream = new jalview.util.jarInputStreamProvider() { + @Override public String getFilename() { @@ -1345,6 +1368,7 @@ public class VamsasAppDatastore return "Jalview Vamsas Document User Data"; } + @Override public JarInputStream getJarInputStream() throws IOException { jalview.bin.Cache.log @@ -1354,7 +1378,7 @@ public class VamsasAppDatastore }; if (dojvsync) { - fromxml.LoadJalviewAlign(jarstream); + fromxml.loadJalviewAlign(jarstream); } } catch (Exception e) { @@ -1383,12 +1407,12 @@ public class VamsasAppDatastore // sync, // and if any contain more than one view, then remove the one generated by // document update. - AlignViewport views[], av = null; + AlignmentViewport views[], av = null; AlignFrame af = null; Iterator newviews = newAlignmentViews.iterator(); while (newviews.hasNext()) { - av = (AlignViewport) newviews.next(); + av = (AlignmentViewport) newviews.next(); af = Desktop.getAlignFrameFor(av); // TODO implement this : af.getNumberOfViews String seqsetidobj = av.getSequenceSetId(); @@ -1405,7 +1429,8 @@ public class VamsasAppDatastore // to the align frames. boolean gathered = false; String newviewid = null; - AlignedCodonFrame[] mappings = av.getAlignment().getCodonFrames(); + Set mappings = av.getAlignment() + .getCodonFrames(); for (int i = 0; i < views.length; i++) { if (views[i] != av) @@ -1440,10 +1465,11 @@ public class VamsasAppDatastore { // ensure sequence mappings from vamsas document view still // active - if (mappings != null && mappings.length > 0) + if (mappings != null) { jalview.structure.StructureSelectionManager - .getStructureSelectionManager(Desktop.instance).addMappings(mappings); + .getStructureSelectionManager(Desktop.instance) + .addMappings(mappings); } } } @@ -1472,9 +1498,9 @@ public class VamsasAppDatastore Object vobject = jv2vobj.remove(oldjvobject); if (vobject == null) { - throw new Error( - "IMPLEMENTATION ERROR: old jalview object is not bound ! (" - + oldjvobject + ")"); + // NOTE: this happens if user deletes object in one session then updates + // from another client + throw new Error(MessageManager.formatMessage("error.implementation_error_old_jalview_object_not_bound", new String[]{oldjvobject.toString()})); } if (newjvobject != null) { @@ -1499,7 +1525,7 @@ public class VamsasAppDatastore jxml.setSkipList(skipList); if (dojvsync) { - jxml.SaveState(new JarOutputStream(cappdata + jxml.saveState(new JarOutputStream(cappdata .getClientOutputStream())); } @@ -1573,7 +1599,7 @@ public class VamsasAppDatastore // ///LOAD DATASET DataSet dataset = root.getDataSet(_ds); int i, iSize = dataset.getSequenceCount(); - Vector dsseqs; + List dsseqs; jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment) getvObj2jv(dataset); int jremain = 0; if (jdataset == null) @@ -1620,8 +1646,8 @@ public class VamsasAppDatastore SequenceI[] seqs = new SequenceI[dsseqs.size()]; for (i = 0, iSize = dsseqs.size(); i < iSize; i++) { - seqs[i] = (SequenceI) dsseqs.elementAt(i); - dsseqs.setElementAt(null, i); + seqs[i] = dsseqs.get(i); + dsseqs.set(i, null); } jdataset = new jalview.datamodel.Alignment(seqs); Cache.log.debug("New vamsas dataset imported into jalview."); @@ -1683,7 +1709,7 @@ public class VamsasAppDatastore uk.ac.vamsas.objects.core.Alignment alignment = dataset .getAlignment(al); // TODO check this handles multiple views properly - AlignViewport av = findViewport(alignment); + AlignmentViewport av = findViewport(alignment); jalview.datamodel.AlignmentI jal = null; if (av != null) @@ -1782,8 +1808,8 @@ public class VamsasAppDatastore SequenceI[] seqs = new SequenceI[dsseqs.size()]; for (i = 0, iSize = dsseqs.size(); i < iSize; i++) { - seqs[i] = (SequenceI) dsseqs.elementAt(i); - dsseqs.setElementAt(null, i); + seqs[i] = dsseqs.get(i); + dsseqs.set(i, null); } jal = new jalview.datamodel.Alignment(seqs); Cache.log.debug("New vamsas alignment imported into jalview " @@ -1957,10 +1983,10 @@ public class VamsasAppDatastore return newAlignmentViews.size(); } - public AlignViewport findViewport(Alignment alignment) + public AlignmentViewport findViewport(Alignment alignment) { - AlignViewport av = null; - AlignViewport[] avs = Desktop + AlignmentViewport av = null; + AlignmentViewport[] avs = Desktop .getViewports((String) getvObj2jv(alignment)); if (avs != null) { @@ -2208,6 +2234,7 @@ public class VamsasAppDatastore Cache.log.warn("Failed to parse threshold property"); } if (val != null) + { if (gl == null) { gl = new GraphLine(val.floatValue(), "", java.awt.Color.black); @@ -2216,11 +2243,14 @@ public class VamsasAppDatastore { gl.value = val.floatValue(); } + } } else if (props[p].getName().equalsIgnoreCase(THRESHOLD + "Name")) { if (gl == null) + { gl = new GraphLine(0, "", java.awt.Color.black); + } gl.label = props[p].getContent(); } } @@ -2416,8 +2446,7 @@ public class VamsasAppDatastore int[] se = null; if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0) { - throw new Error( - "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!"); + throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists")); } if (dseta.getSegCount() > 0) { @@ -2475,8 +2504,7 @@ public class VamsasAppDatastore int[] se = null; if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0) { - throw new Error( - "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!"); + throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists")); } if (dseta.getSegCount() > 0) { @@ -2542,15 +2570,15 @@ public class VamsasAppDatastore * initialise a range type object from a set of start/end inclusive intervals * * @param mrt - * @param range + * @param ranges */ - private void initRangeType(RangeType mrt, int[] range) + private void initRangeType(RangeType mrt, List ranges) { - for (int i = 0; i < range.length; i += 2) + for (int[] range : ranges) { Seg vSeg = new Seg(); - vSeg.setStart(range[i]); - vSeg.setEnd(range[i + 1]); + vSeg.setStart(range[0]); + vSeg.setEnd(range[1]); mrt.addSeg(vSeg); } } @@ -2673,10 +2701,10 @@ public class VamsasAppDatastore return vobj2jv; } - public void storeSequenceMappings(AlignViewport viewport, String title) + public void storeSequenceMappings(AlignmentViewport viewport, String title) throws Exception { - AlignViewport av = viewport; + AlignmentViewport av = viewport; try { jalview.datamodel.AlignmentI jal = av.getAlignment(); @@ -2698,18 +2726,15 @@ public class VamsasAppDatastore } // Store any sequence mappings. - if (av.getAlignment().getCodonFrames() != null - && av.getAlignment().getCodonFrames().length > 0) + Set cframes = av.getAlignment().getCodonFrames(); + if (cframes != null) { - jalview.datamodel.AlignedCodonFrame[] cframes = av.getAlignment() - .getCodonFrames(); - for (int cf = 0; cf < cframes.length; cf++) + for (AlignedCodonFrame acf : cframes) { - if (cframes[cf].getdnaSeqs() != null - && cframes[cf].getdnaSeqs().length > 0) + if (acf.getdnaSeqs() != null && acf.getdnaSeqs().length > 0) { - jalview.datamodel.SequenceI[] dmps = cframes[cf].getdnaSeqs(); - jalview.datamodel.Mapping[] mps = cframes[cf].getProtMappings(); + jalview.datamodel.SequenceI[] dmps = acf.getdnaSeqs(); + jalview.datamodel.Mapping[] mps = acf.getProtMappings(); for (int smp = 0; smp < mps.length; smp++) { uk.ac.vamsas.objects.core.SequenceType mfrom = (SequenceType) getjv2vObj(dmps[smp]); @@ -2732,8 +2757,7 @@ public class VamsasAppDatastore } } catch (Exception e) { - throw new Exception("Couldn't store sequence mappings for " + title, - e); + throw new Exception(MessageManager.formatMessage("exception.couldnt_store_sequence_mappings", new String[]{title}),e); } }