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;
*/
Map<String, SequenceI> seqRefIds = null;
- Vector<Object[]> frefedSequence = null;
+ Map<String, SequenceI> incompleteSeqs = null;
+
+ List<SeqFref> frefedSequence = null;
boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
{
seqsToIds.clear();
}
+ if (incompleteSeqs != null)
+ {
+ incompleteSeqs.clear();
+ }
// seqRefIds = null;
// seqsToIds = null;
}
{
seqRefIds = new HashMap<String, SequenceI>();
}
+ if (incompleteSeqs == null)
+ {
+ incompleteSeqs = new HashMap<String, SequenceI>();
+ }
+ if (frefedSequence == null)
+ {
+ frefedSequence = new ArrayList<SeqFref>();
+ }
}
public Jalview2XML()
this.raiseGUI = raiseGUI;
}
- public void resolveFrefedSequences()
+ /**
+ * base class for resolving forward references to sequences by their ID
+ *
+ * @author jprocter
+ *
+ */
+ abstract class SeqFref
{
- if (frefedSequence.size() > 0)
+ String sref;
+
+ public SeqFref(String _sref)
+ {
+ sref = _sref;
+ }
+
+ public String getSref()
{
- int r = 0, rSize = frefedSequence.size();
- while (r < rSize)
+ return sref;
+ }
+
+ public SequenceI getSrefSeq()
+ {
+ return seqRefIds.get(sref);
+ }
+
+ public boolean isResolvable()
+ {
+ return seqRefIds.get(sref) != null;
+ }
+
+ public SequenceI getSrefDatasetSeq()
+ {
+ SequenceI sq = seqRefIds.get(sref);
+ if (sq != null)
{
- Object[] ref = frefedSequence.elementAt(r);
- if (ref != null)
+ while (sq.getDatasetSequence() != null)
{
- String sref = (String) ref[0];
- if (seqRefIds.containsKey(sref))
- {
- if (ref[1] instanceof jalview.datamodel.Mapping)
- {
- SequenceI seq = seqRefIds.get(sref);
- while (seq.getDatasetSequence() != null)
- {
- seq = seq.getDatasetSequence();
- }
- ((jalview.datamodel.Mapping) ref[1]).setTo(seq);
- }
- else
- {
- if (ref[1] instanceof jalview.datamodel.AlignedCodonFrame)
- {
- SequenceI seq = seqRefIds.get(sref);
- while (seq.getDatasetSequence() != null)
- {
- seq = seq.getDatasetSequence();
- }
- if (ref[2] != null
- && ref[2] instanceof jalview.datamodel.Mapping)
- {
- jalview.datamodel.Mapping mp = (jalview.datamodel.Mapping) ref[2];
- ((jalview.datamodel.AlignedCodonFrame) ref[1]).addMap(
- seq, mp.getTo(), mp.getMap());
- }
- else
- {
- System.err
- .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for AlcodonFrames involving "
- + ref[2].getClass() + " type objects.");
- }
- }
- else
- {
- System.err
- .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for "
- + ref[1].getClass() + " type objects.");
- }
- }
- frefedSequence.remove(r);
- rSize--;
- }
- else
+ sq = sq.getDatasetSequence();
+ }
+ }
+ return sq;
+ }
+ /**
+ * @return true if the forward reference was fully resolved
+ */
+ abstract boolean resolve();
+ }
+
+ /**
+ * create forward reference for a mapping
+ *
+ * @param sref
+ * @param _jmap
+ * @return
+ */
+ public SeqFref newMappingRef(final String sref,
+ final jalview.datamodel.Mapping _jmap)
+ {
+ SeqFref fref = new SeqFref(sref)
+ {
+ public jalview.datamodel.Mapping jmap = _jmap;
+
+ @Override
+ boolean resolve()
+ {
+ SequenceI seq = getSrefDatasetSeq();
+ if (seq == null)
+ {
+ return false;
+ }
+ jmap.setTo(seq);
+ return true;
+ }
+ };
+ return fref;
+ }
+
+ public SeqFref newAlcodMapRef(final String sref,
+ final AlignedCodonFrame _cf, final jalview.datamodel.Mapping _jmap)
+ {
+
+ SeqFref fref = new SeqFref(sref)
+ {
+ AlignedCodonFrame cf = _cf;
+
+ public jalview.datamodel.Mapping mp = _jmap;
+
+ @Override
+ boolean resolve()
+ {
+ SequenceI seq = getSrefDatasetSeq();
+ if (seq == null)
+ {
+ return false;
+ }
+ cf.addMap(seq, mp.getTo(), mp.getMap());
+ return true;
+ }
+ };
+ return fref;
+ }
+
+ public void resolveFrefedSequences()
+ {
+ Iterator<SeqFref> nextFref=frefedSequence.iterator();
+ int toresolve=frefedSequence.size();
+ int unresolved=0,failedtoresolve=0;
+ while (nextFref.hasNext()) {
+ SeqFref ref = nextFref.next();
+ if (ref.isResolvable())
+ {
+ try {
+ if (ref.resolve())
{
- System.err
- .println("IMPLEMENTATION WARNING: Unresolved forward reference for hash string "
- + ref[0]
- + " with objecttype "
- + ref[1].getClass());
- r++;
+ nextFref.remove();
+ } else {
+ failedtoresolve++;
}
- }
- else
+ } catch (Exception x) {
+ System.err.println("IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "+ref.getSref());
+ x.printStackTrace();
+ failedtoresolve++;
+ }
+ } else {
+ unresolved++;
+ }
+ }
+ if (unresolved>0)
+ {
+ System.err.println("Jalview Project Import: There were " + unresolved
+ + " forward references left unresolved on the stack.");
+ }
+ if (failedtoresolve>0)
+ {
+ System.err.println("SERIOUS! " + failedtoresolve
+ + " resolvable forward references failed to resolve.");
+ }
+ if (incompleteSeqs != null && incompleteSeqs.size() > 0)
+ {
+ System.err.println("Jalview Project Import: There are "
+ + incompleteSeqs.size()
+ + " sequences which may have incomplete metadata.");
+ if (incompleteSeqs.size() < 10)
+ {
+ for (SequenceI s : incompleteSeqs.values())
{
- // empty reference
- frefedSequence.remove(r);
- rSize--;
+ System.err.println(s.toString());
}
}
+ else
+ {
+ System.err
+ .println("Too many to report. Skipping output of incomplete sequences.");
+ }
}
}
{
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<AlignFrame> frames, JarOutputStream jout)
+ {
Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
/*
List<String> viewIds = new ArrayList<String>();
// 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
{
try
{
- int ap = 0;
- int apSize = af.alignPanels.size();
FileOutputStream fos = new FileOutputStream(jarFile);
JarOutputStream jout = new JarOutputStream(fos);
- Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
- List<String> viewIds = new ArrayList<String>();
+ List<AlignFrame> frames = new ArrayList<AlignFrame>();
- 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();
}
if (seqRefIds == null)
{
- seqRefIds = new HashMap<String, SequenceI>();
- }
- if (frefedSequence == null)
- {
- frefedSequence = new Vector<Object[]>();
+ initSeqRefs();
}
-
AlignFrame af = null, _af = null;
Map<String, AlignFrame> gatherToThisFrame = new HashMap<String, AlignFrame>();
final String file = jprovider.getFilename();
SequenceI tmpSeq = seqRefIds.get(seqId);
if (tmpSeq != null)
{
+ if (!incompleteSeqs.containsKey(seqId))
+ {
+ // may not need this check, but keep it for at least 2.9,1 release
+ if (tmpSeq.getStart()!=jseqs[i].getStart() || tmpSeq.getEnd()!=jseqs[i].getEnd())
+ {
+ System.err
+ .println("Warning JAL-2154 regression: updating start/end for sequence "
+ + tmpSeq.toString());
+ }
+ } else {
+ incompleteSeqs.remove(seqId);
+ }
tmpSeq.setStart(jseqs[i].getStart());
tmpSeq.setEnd(jseqs[i].getEnd());
tmpseqs.add(tmpSeq);
else
{
// defer to later
- frefedSequence.add(new Object[] { maps[m].getDnasq(), cf,
- mapping });
+ frefedSequence.add(newAlcodMapRef(maps[m].getDnasq(), cf,
+ mapping));
}
}
al.addCodonFrame(cf);
}
}
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
}
else
{
- frefedSequence.add(new Object[] { dsfor, jmap });
+ frefedSequence.add(newMappingRef(dsfor, jmap));
}
}
else
djs.setEnd(jmap.getMap().getToHighest());
djs.setVamsasId(uniqueSetSuffix + sqid);
jmap.setTo(djs);
+ incompleteSeqs.put(sqid, djs);
seqRefIds.put(sqid, djs);
}
git://source.jalview.org / jalview.git / blobdiff