X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=68245b6be5925b13d885e3c32a5def8370bd484d;hb=0f40a8334651302a74a223ecd3e583451302bb42;hp=9b2b04a332073f688171f6df933fda58b986a1e1;hpb=213312e8ad1e085a1075be810473d359b795bf2e;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 9b2b04a..68245b6 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -108,6 +108,7 @@ import java.lang.reflect.InvocationTargetException; import java.net.MalformedURLException; import java.net.URL; import java.util.ArrayList; +import java.util.Arrays; import java.util.Enumeration; import java.util.HashMap; import java.util.HashSet; @@ -277,9 +278,12 @@ public class Jalview2XML { String sref; - public SeqFref(String _sref) + String type; + + public SeqFref(String _sref, String type) { sref = _sref; + this.type = type; } public String getSref() @@ -313,6 +317,12 @@ public class Jalview2XML * @return true if the forward reference was fully resolved */ abstract boolean resolve(); + + @Override + public String toString() + { + return type + " reference to " + sref; + } } /** @@ -325,7 +335,7 @@ public class Jalview2XML public SeqFref newMappingRef(final String sref, final jalview.datamodel.Mapping _jmap) { - SeqFref fref = new SeqFref(sref) + SeqFref fref = new SeqFref(sref, "Mapping") { public jalview.datamodel.Mapping jmap = _jmap; @@ -348,7 +358,7 @@ public class Jalview2XML final AlignedCodonFrame _cf, final jalview.datamodel.Mapping _jmap) { - SeqFref fref = new SeqFref(sref) + SeqFref fref = new SeqFref(sref, "Codon Frame") { AlignedCodonFrame cf = _cf; @@ -396,7 +406,8 @@ public class Jalview2XML } if (unresolved>0) { - System.err.println("There were "+unresolved+" forward references left unresolved on the stack."); + System.err.println("Jalview Project Import: There were " + unresolved + + " forward references left unresolved on the stack."); } if (failedtoresolve>0) { @@ -491,7 +502,20 @@ public class Jalview2XML { return; } + saveAllFrames(Arrays.asList(frames), jout); + } + /** + * core method for storing state for a set of AlignFrames. + * + * @param frames + * - frames involving all data to be exported (including containing + * splitframes) + * @param jout + * - project output stream + */ + private void saveAllFrames(List frames, JarOutputStream jout) + { Hashtable dsses = new Hashtable(); /* @@ -511,9 +535,9 @@ public class Jalview2XML List viewIds = new ArrayList(); // REVERSE ORDER - for (int i = frames.length - 1; i > -1; i--) + for (int i = frames.size() - 1; i > -1; i--) { - AlignFrame af = frames[i]; + AlignFrame af = frames.get(i); // skip ? if (skipList != null && skipList @@ -616,30 +640,20 @@ public class Jalview2XML { try { - int ap = 0; - int apSize = af.alignPanels.size(); FileOutputStream fos = new FileOutputStream(jarFile); JarOutputStream jout = new JarOutputStream(fos); - Hashtable dsses = new Hashtable(); - List viewIds = new ArrayList(); + List frames = new ArrayList(); - for (AlignmentPanel apanel : af.alignPanels) + // resolve splitframes + if (af.getViewport().getCodingComplement() != null) { - String jfileName = apSize == 1 ? fileName : fileName + ap; - ap++; - if (!jfileName.endsWith(".xml")) - { - jfileName = jfileName + ".xml"; - } - saveState(apanel, jfileName, jout, viewIds); - String dssid = getDatasetIdRef(af.getViewport().getAlignment() - .getDataset()); - if (!dsses.containsKey(dssid)) - { - dsses.put(dssid, af); - } + frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames(); + } + else + { + frames.add(af); } - writeDatasetFor(dsses, fileName, jout); + saveAllFrames(frames, jout); try { jout.flush(); @@ -987,7 +1001,8 @@ public class Jalview2XML jal = av.getAlignment(); } // SAVE MAPPINGS - if (jal.getCodonFrames() != null) + // FOR DATASET + if (storeDS && jal.getCodonFrames() != null) { List jac = jal.getCodonFrames(); for (AlignedCodonFrame acf : jac) @@ -2035,16 +2050,17 @@ public class Jalview2XML if (jds.getDatasetSequence() != null) { vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence())); - if (jds.getDatasetSequence().getDBRefs() != null) - { - dbrefs = jds.getDatasetSequence().getDBRefs(); - } } else { - vamsasSeq.setDsseqid(id); // so we can tell which sequences really are + // seqId==dsseqid so we can tell which sequences really are // dataset sequences only + vamsasSeq.setDsseqid(id); dbrefs = jds.getDBRefs(); + if (parentseq == null) + { + parentseq = jds; + } } if (dbrefs != null) { @@ -2096,38 +2112,32 @@ public class Jalview2XML if (jmp.getTo() != null) { MappingChoice mpc = new MappingChoice(); - if (recurse - && (parentseq != jmp.getTo() || parentseq - .getDatasetSequence() != jmp.getTo())) + + // check/create ID for the sequence referenced by getTo() + + String jmpid = ""; + SequenceI ps = null; + if (parentseq != jmp.getTo() + && parentseq.getDatasetSequence() != jmp.getTo()) { - mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()), - jmp.getTo(), jds)); + // chaining dbref rather than a handshaking one + jmpid = seqHash(ps = jmp.getTo()); } else { - String jmpid = ""; - SequenceI ps = null; - if (parentseq != jmp.getTo() - && parentseq.getDatasetSequence() != jmp.getTo()) - { - // chaining dbref rather than a handshaking one - jmpid = seqHash(ps = jmp.getTo()); - } - else - { - jmpid = seqHash(ps = parentseq); - } - mpc.setDseqFor(jmpid); - if (!seqRefIds.containsKey(mpc.getDseqFor())) - { - jalview.bin.Cache.log.debug("creatign new DseqFor ID"); - seqRefIds.put(mpc.getDseqFor(), ps); - } - else - { - jalview.bin.Cache.log.debug("reusing DseqFor ID"); - } + jmpid = seqHash(ps = parentseq); + } + mpc.setDseqFor(jmpid); + if (!seqRefIds.containsKey(mpc.getDseqFor())) + { + jalview.bin.Cache.log.debug("creatign new DseqFor ID"); + seqRefIds.put(mpc.getDseqFor(), ps); + } + else + { + jalview.bin.Cache.log.debug("reusing DseqFor ID"); } + mp.setMappingChoice(mpc); } } @@ -2339,6 +2349,7 @@ public class Jalview2XML initSeqRefs(); } AlignFrame af = null, _af = null; + IdentityHashMap importedDatasets = new IdentityHashMap(); Map gatherToThisFrame = new HashMap(); final String file = jprovider.getFilename(); try @@ -2366,13 +2377,24 @@ public class Jalview2XML if (true) // !skipViewport(object)) { _af = loadFromObject(object, file, true, jprovider); - if (object.getJalviewModelSequence().getViewportCount() > 0) + if (_af != null + && object.getJalviewModelSequence().getViewportCount() > 0) { - af = _af; - if (af.viewport.isGatherViewsHere()) + if (af == null) + { + // store a reference to the first view + af = _af; + } + if (_af.viewport.isGatherViewsHere()) { - gatherToThisFrame.put(af.viewport.getSequenceSetId(), af); + // if this is a gathered view, keep its reference since + // after gathering views, only this frame will remain + af = _af; + gatherToThisFrame.put(_af.viewport.getSequenceSetId(), _af); } + // Save dataset to register mappings once all resolved + importedDatasets.put(af.viewport.getAlignment().getDataset(), + af.viewport.getAlignment().getDataset()); } } entryCount++; @@ -2428,11 +2450,6 @@ public class Jalview2XML e.printStackTrace(); } - if (Desktop.instance != null) - { - Desktop.instance.stopLoading(); - } - /* * Regather multiple views (with the same sequence set id) to the frame (if * any) that is flagged as the one to gather to, i.e. convert them to tabbed @@ -2446,11 +2463,24 @@ public class Jalview2XML } restoreSplitFrames(); - + for (AlignmentI ds : importedDatasets.keySet()) + { + if (ds.getCodonFrames() != null) + { + StructureSelectionManager.getStructureSelectionManager( + Desktop.instance).registerMappings(ds.getCodonFrames()); + } + } if (errorMessage != null) { reportErrors(); } + + if (Desktop.instance != null) + { + Desktop.instance.stopLoading(); + } + return af; } @@ -2823,7 +2853,39 @@ public class Jalview2XML SequenceI[] orderedSeqs = tmpseqs .toArray(new SequenceI[tmpseqs.size()]); - AlignmentI al = new Alignment(orderedSeqs); + AlignmentI al = null; + // so we must create or recover the dataset alignment before going further + // /////////////////////////////// + if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "") + { + // older jalview projects do not have a dataset - so creat alignment and + // dataset + al = new Alignment(orderedSeqs); + al.setDataset(null); + } + else + { + boolean isdsal = object.getJalviewModelSequence().getViewportCount() == 0; + if (isdsal) + { + // we are importing a dataset record, so + // recover reference to an alignment already materialsed as dataset + al = getDatasetFor(vamsasSet.getDatasetId()); + } + if (al == null) + { + // materialse the alignment + al = new Alignment(orderedSeqs); + } + if (isdsal) + { + addDatasetRef(vamsasSet.getDatasetId(), al); + } + + // finally, verify all data in vamsasSet is actually present in al + // passing on flag indicating if it is actually a stored dataset + recoverDatasetFor(vamsasSet, al, isdsal); + } if (referenceseqForView != null) { @@ -2836,22 +2898,6 @@ public class Jalview2XML al.setProperty(ssp.getKey(), ssp.getValue()); } - // / - // SequenceFeatures are added to the DatasetSequence, - // so we must create or recover the dataset before loading features - // /////////////////////////////// - if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "") - { - // older jalview projects do not have a dataset id. - al.setDataset(null); - } - else - { - // recover dataset - passing on flag indicating if this a 'viewless' - // sequence set (a.k.a. a stored dataset for the project) - recoverDatasetFor(vamsasSet, al, object.getJalviewModelSequence() - .getViewportCount() == 0); - } // /////////////////////////////// Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this?? @@ -4534,7 +4580,7 @@ public class Jalview2XML } } af.setMenusFromViewport(af.viewport); - + af.setTitle(view.getTitle()); // TODO: we don't need to do this if the viewport is aready visible. /* * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it