X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;h=2c35547a69358651052cc9f4253172463d285c21;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=2ec7fdebdcdddcd34b60f3dba6afbdae4e52d9c2;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java index 2ec7fde..2c35547 100644 --- a/src/jalview/io/VamsasAppDatastore.java +++ b/src/jalview/io/VamsasAppDatastore.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -34,6 +34,7 @@ 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; @@ -46,8 +47,30 @@ 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; /* @@ -127,7 +150,7 @@ 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]); @@ -222,9 +245,12 @@ public class VamsasAppDatastore if (vobj2jv.containsKey(vobj.getVorbaId()) && !((VorbaId) vobj2jv.get(vobj.getVorbaId())).equals(jvobj)) { - Cache.log.debug( - "Warning? Overwriting existing vamsas id binding for " - + vobj.getVorbaId(), new Exception(MessageManager.getString("exception.overwriting_vamsas_id_binding"))); + Cache.log + .debug("Warning? Overwriting existing vamsas id binding for " + + vobj.getVorbaId(), + new Exception( + MessageManager + .getString("exception.overwriting_vamsas_id_binding"))); } else if (jv2vobj.containsKey(jvobj) && !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId())) @@ -311,7 +337,9 @@ public class VamsasAppDatastore if (vbound.getV_parent() != null && dataset != vbound.getV_parent()) { - throw new Error(MessageManager.getString("error.implementation_error_cannot_map_alignment_sequences")); + throw new Error( + MessageManager + .getString("error.implementation_error_cannot_map_alignment_sequences")); // This occurs because the dataset for the alignment we are // trying to } @@ -728,12 +756,12 @@ 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) { @@ -1068,8 +1096,10 @@ 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); @@ -1232,8 +1262,7 @@ public class VamsasAppDatastore end = start; start = t; } - return new int[] - { start, end, pol < 0 ? 1 : 0 }; + return new int[] { start, end, pol < 0 ? 1 : 0 }; } /** @@ -1304,7 +1333,7 @@ public class VamsasAppDatastore }; if (dojvsync) { - fromxml.LoadJalviewAlign(jprovider); + fromxml.loadJalviewAlign(jprovider); } } catch (Exception e) { @@ -1352,7 +1381,7 @@ public class VamsasAppDatastore }; if (dojvsync) { - fromxml.LoadJalviewAlign(jarstream); + fromxml.loadJalviewAlign(jarstream); } } catch (Exception e) { @@ -1381,12 +1410,12 @@ 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(); @@ -1403,7 +1432,8 @@ public class VamsasAppDatastore // to the align frames. boolean gathered = false; String newviewid = null; - AlignedCodonFrame[] mappings = av.getAlignment().getCodonFrames(); + List mappings = av.getAlignment() + .getCodonFrames(); for (int i = 0; i < views.length; i++) { if (views[i] != av) @@ -1438,11 +1468,11 @@ 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); + .registerMappings(mappings); } } } @@ -1473,7 +1503,9 @@ public class VamsasAppDatastore { // 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()})); + throw new Error(MessageManager.formatMessage( + "error.implementation_error_old_jalview_object_not_bound", + new String[] { oldjvobject.toString() })); } if (newjvobject != null) { @@ -1498,7 +1530,7 @@ public class VamsasAppDatastore jxml.setSkipList(skipList); if (dojvsync) { - jxml.SaveState(new JarOutputStream(cappdata + jxml.saveState(new JarOutputStream(cappdata .getClientOutputStream())); } @@ -1682,7 +1714,7 @@ 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) @@ -1956,10 +1988,10 @@ 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) { @@ -2002,8 +2034,7 @@ public class VamsasAppDatastore // may not quite cope with this (without binding an array of annotations to // a vamsas alignment annotation) // summary flags saying what we found over the set of annotation rows. - boolean[] AeContent = new boolean[] - { false, false, false, false, false }; + boolean[] AeContent = new boolean[] { false, false, false, false, false }; int[] rangeMap = getMapping(annotation); jalview.datamodel.Annotation[][] anot = new jalview.datamodel.Annotation[][] { new jalview.datamodel.Annotation[rangeMap.length], @@ -2138,15 +2169,13 @@ public class VamsasAppDatastore anot[1][i].description = anot[1][i].description + " (after)"; } } - return new Object[] - { AeContent, rangeMap, anot[0], anot[1] }; + return new Object[] { AeContent, rangeMap, anot[0], anot[1] }; } else { // no annotations to parse. Just return an empty annotationElement[] // array. - return new Object[] - { AeContent, rangeMap, anot[0], anot[1] }; + return new Object[] { AeContent, rangeMap, anot[0], anot[1] }; } // return null; } @@ -2207,6 +2236,7 @@ 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); @@ -2215,11 +2245,14 @@ 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(); } } @@ -2415,7 +2448,9 @@ public class VamsasAppDatastore int[] se = null; if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0) { - throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists")); + throw new Error( + MessageManager + .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists")); } if (dseta.getSegCount() > 0) { @@ -2438,8 +2473,7 @@ public class VamsasAppDatastore // could do a polarity for pos range too. and pass back indication of // discontinuities. int pos = dseta.getPos(0).getI(); - se = new int[] - { pos, pos }; + se = new int[] { pos, pos }; for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++) { pos = dseta.getPos(p).getI(); @@ -2473,7 +2507,9 @@ public class VamsasAppDatastore int[] se = null; if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0) { - throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists")); + throw new Error( + MessageManager + .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists")); } if (dseta.getSegCount() > 0) { @@ -2539,15 +2575,15 @@ 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); } } @@ -2670,10 +2706,10 @@ 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(); @@ -2695,18 +2731,15 @@ public class VamsasAppDatastore } // Store any sequence mappings. - if (av.getAlignment().getCodonFrames() != null - && av.getAlignment().getCodonFrames().length > 0) + List 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]); @@ -2729,7 +2762,9 @@ public class VamsasAppDatastore } } catch (Exception e) { - throw new Exception(MessageManager.formatMessage("exception.couldnt_store_sequence_mappings", new String[]{title}),e); + throw new Exception(MessageManager.formatMessage( + "exception.couldnt_store_sequence_mappings", + new String[] { title }), e); } }