*/
package jalview.gui;
+import jalview.analysis.Conservation;
import jalview.api.FeatureColourI;
import jalview.api.ViewStyleI;
import jalview.api.structures.JalviewStructureDisplayI;
}
return sq;
}
+
/**
* @return true if the forward reference was fully resolved
*/
public void resolveFrefedSequences()
{
- Iterator<SeqFref> nextFref=frefedSequence.iterator();
- int toresolve=frefedSequence.size();
- int unresolved=0,failedtoresolve=0;
- while (nextFref.hasNext()) {
+ 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 {
+ try
+ {
if (ref.resolve())
{
nextFref.remove();
- } else {
+ }
+ else
+ {
failedtoresolve++;
}
- } catch (Exception x) {
- System.err.println("IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "+ref.getSref());
+ } catch (Exception x)
+ {
+ System.err
+ .println("IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "
+ + ref.getSref());
x.printStackTrace();
failedtoresolve++;
- }
- } else {
+ }
+ }
+ else
+ {
unresolved++;
}
}
- if (unresolved>0)
+ if (unresolved > 0)
{
System.err.println("Jalview Project Import: There were " + unresolved
+ " forward references left unresolved on the stack.");
}
- if (failedtoresolve>0)
+ if (failedtoresolve > 0)
{
System.err.println("SERIOUS! " + failedtoresolve
+ " resolvable forward references failed to resolve.");
JSeq jseq;
Set<String> calcIdSet = new HashSet<String>();
// record the set of vamsas sequence XML POJO we create.
- HashMap<String,Sequence> vamsasSetIds = new HashMap<String,Sequence>();
+ HashMap<String, Sequence> vamsasSetIds = new HashMap<String, Sequence>();
// SAVE SEQUENCES
for (final SequenceI jds : rjal.getSequences())
{
if (av.isHiddenRepSequence(jds))
{
jalview.datamodel.SequenceI[] reps = av
- .getRepresentedSequences(jds)
- .getSequencesInOrder(rjal);
+ .getRepresentedSequences(jds).getSequencesInOrder(rjal);
for (int h = 0; h < reps.length; h++)
{
for (String featureType : renderOrder)
{
FeatureColourI fcol = ap.getSeqPanel().seqCanvas
- .getFeatureRenderer()
- .getFeatureStyle(featureType);
+ .getFeatureRenderer().getFeatureStyle(featureType);
Setting setting = new Setting();
setting.setType(featureType);
if (!fcol.isSimpleColour())
setting.setAutoScale(fcol.isAutoScaled());
setting.setThreshold(fcol.getThreshold());
// -1 = No threshold, 0 = Below, 1 = Above
- setting.setThreshstate(fcol.isAboveThreshold() ? 1
- : (fcol.isBelowThreshold() ? 0 : -1));
+ setting.setThreshstate(fcol.isAboveThreshold() ? 1 : (fcol
+ .isBelowThreshold() ? 0 : -1));
}
else
{
// is groups actually supposed to be a map here ?
Iterator<String> en = ap.getSeqPanel().seqCanvas
- .getFeatureRenderer()
- .getFeatureGroups().iterator();
+ .getFeatureRenderer().getFeatureGroups().iterator();
Vector<String> groupsAdded = new Vector<String>();
while (en.hasNext())
{
SplitFrame sf = createSplitFrame(dnaFrame, af);
addedToSplitFrames.add(dnaFrame);
addedToSplitFrames.add(af);
+ dnaFrame.setMenusForViewport();
+ af.setMenusForViewport();
if (af.viewport.isGatherViewsHere())
{
gatherTo.add(sf);
Viewport view = candidate.getKey();
Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
view.getHeight());
+ af.setMenusForViewport();
System.err.println("Failed to restore view " + view.getTitle()
+ " to split frame");
}
* @param pdbId
* @return
*/
- String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
+ String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
+ String origFile)
{
if (alreadyLoadedPDB.containsKey(pdbId))
{
return alreadyLoadedPDB.get(pdbId).toString();
}
- String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb");
+ String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
+ origFile);
if (tempFile != null)
{
alreadyLoadedPDB.put(pdbId, tempFile);
* @param prefix
* a prefix for the temporary file name, must be at least three
* characters long
+ * @param origFile
+ * null or original file - so new file can be given the same suffix
+ * as the old one
* @return
*/
protected String copyJarEntry(jarInputStreamProvider jprovider,
- String jarEntryName, String prefix)
+ String jarEntryName, String prefix, String origFile)
{
BufferedReader in = null;
PrintWriter out = null;
-
+ String suffix = ".tmp";
+ if (origFile == null)
+ {
+ origFile = jarEntryName;
+ }
+ int sfpos = origFile.lastIndexOf(".");
+ if (sfpos > -1 && sfpos < (origFile.length() - 3))
+ {
+ suffix = "." + origFile.substring(sfpos + 1);
+ }
try
{
JarInputStream jin = jprovider.getJarInputStream();
if (entry != null)
{
in = new BufferedReader(new InputStreamReader(jin, UTF_8));
- File outFile = File.createTempFile(prefix, ".tmp");
+ File outFile = File.createTempFile(prefix, suffix);
outFile.deleteOnExit();
out = new PrintWriter(new FileOutputStream(outFile));
String data;
List<SequenceI> hiddenSeqs = null;
-
List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
boolean multipleView = false;
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())
- {
+ 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() + " to " + jseqs[i]);
}
- } else {
+ }
+ else
+ {
incompleteSeqs.remove(seqId);
}
if (vamsasSeq.length > vi && vamsasSeq[vi].getId().equals(seqId))
entry.setId(ids[p].getId());
if (ids[p].getType() != null)
{
- if (ids[p].getType().equalsIgnoreCase("PDB"))
+ if (PDBEntry.Type.getType(ids[p].getType()) != null)
{
- entry.setType(PDBEntry.Type.PDB);
+ entry.setType(PDBEntry.Type.getType(ids[p].getType()));
}
else
{
entry.setType(PDBEntry.Type.FILE);
}
}
- if (ids[p].getFile() != null)
+ // jprovider is null when executing 'New View'
+ if (ids[p].getFile() != null && jprovider != null)
{
if (!pdbloaded.containsKey(ids[p].getFile()))
{
- entry.setFile(loadPDBFile(jprovider, ids[p].getId()));
+ entry.setFile(loadPDBFile(jprovider, ids[p].getId(),
+ ids[p].getFile()));
}
else
{
entry.setFile(pdbloaded.get(ids[p].getId()).toString());
}
}
+ if (ids[p].getPdbentryItem() != null)
+ {
+ entry.setProperty(new Hashtable());
+ for (PdbentryItem item : ids[p].getPdbentryItem())
+ {
+ for (Property pr : item.getProperty())
+ {
+ entry.getProperty().put(pr.getName(), pr.getValue());
+ }
+ }
+ }
StructureSelectionManager.getStructureSelectionManager(
Desktop.instance).registerPDBEntry(entry);
// adds PDBEntry to datasequence's set (since Jalview 2.10)
}
if (jGroup.getConsThreshold() != 0)
{
- jalview.analysis.Conservation c = new jalview.analysis.Conservation(
- "All", ResidueProperties.propHash, 3,
+ Conservation c = new Conservation("All", 3,
sg.getSequences(null), 0, sg.getWidth() - 1);
c.calculate();
c.verdict(false, 25);
String rnaTitle = ss.getTitle();
String sessionState = ss.getViewerState();
String tempStateFile = copyJarEntry(jprovider, sessionState,
- "varna");
+ "varna", null);
RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
appVarna.addModelSession(rna, rnaTitle, tempStateFile);
}
// Originally : ids[p].getFile()
// : TODO: verify external PDB file recovery still works in normal
// jalview project load
- jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
+ jpdb.setFile(loadPDBFile(jprovider, ids[p].getId(),
+ ids[p].getFile()));
jpdb.setId(ids[p].getId());
int x = structureState.getXpos();
// Probably don't need to do this anymore...
// Desktop.desktop.getComponentAt(x, y);
// TODO: NOW: check that this recovers the PDB file correctly.
- String pdbFile = loadPDBFile(jprovider, ids[p].getId());
+ String pdbFile = loadPDBFile(jprovider, ids[p].getId(),
+ ids[p].getFile());
jalview.datamodel.SequenceI seq = seqRefIds.get(jseqs[i]
.getId() + "");
if (sviewid == null)
*/
String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
- "chimera");
+ "chimera", null);
Set<Entry<File, StructureData>> fileData = data.getFileData()
.entrySet();
// filename
// translation differently.
StructureData filedat = oldFiles.get(new File(oldfilenam));
+ if (filedat == null)
+ {
+ String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
+ filedat = oldFiles.get(new File(reformatedOldFilename));
+ }
newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
pdbfilenames.add(filedat.getFilePath());
pdbids.add(filedat.getPdbId());
git://source.jalview.org / jalview.git / blobdiff