X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;h=7df7cb2a614dd33639846c45f5db329c680aca7c;hb=4bba61a3c701f83bdcb6707c4d9f17a1f5faaa04;hp=735f415206a55d692ab1c67532b4a21172b850c7;hpb=f1cf002d98f35e6d471ebf1af95b37c63cf86d1c;p=jalview.git diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java index 735f415..7df7cb2 100644 --- a/src/jalview/io/VamsasAppDatastore.java +++ b/src/jalview/io/VamsasAppDatastore.java @@ -1,19 +1,22 @@ /* - * 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 - * + * 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. - * - * 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 + * 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 * 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; @@ -30,6 +33,9 @@ import jalview.io.vamsas.Datasetsequence; import jalview.io.vamsas.DatastoreItem; import jalview.io.vamsas.DatastoreRegistry; import jalview.io.vamsas.Rangetype; +import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; + import java.io.IOException; import java.util.Enumeration; import java.util.HashMap; @@ -37,12 +43,35 @@ 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; /* @@ -122,7 +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]); @@ -178,7 +207,7 @@ public class VamsasAppDatastore } /** - * + * * @param vobj * @return Jalview datamodel object bound to the vamsas document object */ @@ -219,8 +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())) @@ -245,7 +273,7 @@ public class VamsasAppDatastore /** * put the alignment viewed by AlignViewport into cdoc. - * + * * @param av * alignViewport to be stored * @param aFtitle @@ -307,8 +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 } @@ -486,14 +513,14 @@ public class VamsasAppDatastore /* * We do not put local Alignment Sequence Features into the vamsas * document yet. - * - * + * + * * jalview.datamodel.SequenceFeature[] features = alseq * .getSequenceFeatures(); for (int f = 0; f < features.length; f++) { * if (features[f] != null) { AlignmentSequenceAnnotation valseqf = ( * AlignmentSequenceAnnotation) getjv2vObj(features[i]); if (valseqf * == null) { - * + * * valseqf = (AlignmentSequenceAnnotation) getDSAnnotationFromJalview( * new AlignmentSequenceAnnotation(), features[i]); * valseqf.setGraph(false); @@ -541,7 +568,8 @@ public class VamsasAppDatastore else { // first find the alignment sequence to associate this with. - for (SequenceI jvalsq:av.getAlignment().getSequences()) { + for (SequenceI jvalsq : av.getAlignment().getSequences()) + { // saveDatasetSequenceAnnotation(AlSeqMaps,(uk.ac.vamsas.objects.core.Sequence) // sref, aa[i]); if (jvalsq.getDatasetSequence() == aa[i].sequenceRef) @@ -719,17 +747,17 @@ public class VamsasAppDatastore * very quick test to see if the viewport would be stored in the vamsas * document. Reasons for not storing include the unaligned flag being false * (for all sequences, including the hidden ones!) - * + * * @param av * @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) { @@ -741,7 +769,7 @@ public class VamsasAppDatastore /** * remove docseqs from the given alignment marking provenance appropriately * and removing any references to the sequences. - * + * * @param alignment * @param docseqs */ @@ -809,7 +837,7 @@ public class VamsasAppDatastore * vamsas alignment sequence for jvalsq and adds it to the alignment if * necessary. unbounddocseq is a duplicate of the vamsas alignment sequences * and these are removed after being processed w.r.t a bound jvalsq - * + * */ private boolean syncToAlignmentSequence(SequenceI jvalsq, Alignment alignment, Vector unbounddocseq) @@ -1064,8 +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); @@ -1158,7 +1188,7 @@ public class VamsasAppDatastore /** * set vamsas annotation object type from jalview annotation - * + * * @param an * @param alan */ @@ -1206,7 +1236,7 @@ public class VamsasAppDatastore /** * get start mappings = av.getAlignment() + .getCodonFrames(); for (int i = 0; i < views.length; i++) { if (views[i] != av) @@ -1434,10 +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); } } } @@ -1456,7 +1488,7 @@ public class VamsasAppDatastore /** * replaces oldjvobject with newjvobject in the Jalview Object <> VorbaID * binding tables - * + * * @param oldjvobject * @param newjvobject * (may be null) @@ -1466,10 +1498,9 @@ public class VamsasAppDatastore Object vobject = jv2vobj.remove(oldjvobject); if (vobject == null) { - // NOTE: this happens if user deletes object in one session then updates from another client - 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) { @@ -1494,7 +1525,7 @@ public class VamsasAppDatastore jxml.setSkipList(skipList); if (dojvsync) { - jxml.SaveState(new JarOutputStream(cappdata + jxml.saveState(new JarOutputStream(cappdata .getClientOutputStream())); } @@ -1515,7 +1546,7 @@ public class VamsasAppDatastore /** * translate the Vobject keys to strings for use in Jalview2XML - * + * * @param jv2vobj2 * @return */ @@ -1533,7 +1564,7 @@ public class VamsasAppDatastore /** * translate the Vobject values to strings for use in Jalview2XML - * + * * @param vobj2jv2 * @return hashtable with string values */ @@ -1551,7 +1582,7 @@ public class VamsasAppDatastore /** * synchronize Jalview from the vamsas document - * + * * @return number of new views from document */ public int updateToJalview() @@ -1678,7 +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) @@ -1778,7 +1809,7 @@ public class VamsasAppDatastore for (i = 0, iSize = dsseqs.size(); i < iSize; i++) { seqs[i] = dsseqs.get(i); - dsseqs.set(i,null); + dsseqs.set(i, null); } jal = new jalview.datamodel.Alignment(seqs); Cache.log.debug("New vamsas alignment imported into jalview " @@ -1952,10 +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) { @@ -1982,7 +2013,7 @@ public class VamsasAppDatastore * jalview.datamodel.Annotation[] rows Two annotation rows are made if there * are distinct annotation for both at 'pos' and 'after pos' at any particular * site. - * + * * @param annotation * @return { boolean[static int constants ], int[ae.length] - map to annotated * object frame, jalview.datamodel.Annotation[], @@ -2203,6 +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); @@ -2211,11 +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(); } } @@ -2400,7 +2435,7 @@ public class VamsasAppDatastore * get real bounds of a RangeType's specification. start and end are an * inclusive range within which all segments and positions lie. TODO: refactor * to vamsas utils - * + * * @param dseta * @return int[] { start, end} */ @@ -2411,8 +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) { @@ -2458,7 +2492,7 @@ public class VamsasAppDatastore /** * map from a rangeType's internal frame to the referenced object's coordinate * frame. - * + * * @param dseta * @return int [] { ref(pos)...} for all pos in rangeType's frame. */ @@ -2470,8 +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) { @@ -2510,7 +2543,7 @@ public class VamsasAppDatastore } /** - * + * * @param maprange * where the from range is the local mapped range, and the to range * is the 'mapped' range in the MapRangeType @@ -2535,24 +2568,24 @@ 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); } } /** * initialise a MapType object from a MapList object. - * + * * @param maprange * @param ml * @param setUnits @@ -2577,12 +2610,12 @@ public class VamsasAppDatastore * App and Action here. Provenance prov = new Provenance(); * org.exolab.castor.types.Date date = new org.exolab.castor.types.Date( new * java.util.Date()); Entry provEntry; - * + * * if (jprov != null) { entries = jprov.getEntries(); for (int i = 0; i < * entries.length; i++) { provEntry = new Entry(); try { date = new * org.exolab.castor.types.Date(entries[i].getDate()); } catch (Exception ex) * { ex.printStackTrace(); - * + * * date = new org.exolab.castor.types.Date(entries[i].getDate()); } * provEntry.setDate(date); provEntry.setUser(entries[i].getUser()); * provEntry.setAction(entries[i].getAction()); prov.addEntry(provEntry); } } @@ -2590,7 +2623,7 @@ public class VamsasAppDatastore * provEntry.setUser(System.getProperty("user.name")); // TODO: ext string * provEntry.setApp("JVAPP"); // TODO: ext string provEntry.setAction(action); * prov.addEntry(provEntry); } - * + * * return prov; } */ jalview.datamodel.Provenance getJalviewProvenance(Provenance prov) @@ -2608,7 +2641,7 @@ public class VamsasAppDatastore } /** - * + * * @return default initial provenance list for a Jalview created vamsas * object. */ @@ -2668,10 +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(); @@ -2693,18 +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]); @@ -2727,8 +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); } }