}
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++)
{
}
}
- if (entry.getProperty() != null && !entry.getProperty().isEmpty())
+ Enumeration<String> props = entry.getProperties();
+ if (props.hasMoreElements())
{
PdbentryItem item = new PdbentryItem();
- Hashtable properties = entry.getProperty();
- Enumeration en2 = properties.keys();
- while (en2.hasMoreElements())
+ while (props.hasMoreElements())
{
Property prop = new Property();
- String key = en2.nextElement().toString();
+ String key = props.nextElement();
prop.setName(key);
- prop.setValue(properties.get(key).toString());
+ prop.setValue(entry.getProperty(key).toString());
item.addProperty(prop);
}
pdb.addPdbentryItem(item);
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");
}
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.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()))
{
}
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());
+ entry.setProperty(pr.getName(), pr.getValue());
}
}
}
// filename
// translation differently.
StructureData filedat = oldFiles.get(new File(oldfilenam));
- if (filedat == null)
- {
- String reformatedOldFilename = oldfilenam.replaceAll("/",
- "\\\\");
- filedat = oldFiles.get(new File(reformatedOldFilename));
+ if (filedat == null)
+ {
+ String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
+ filedat = oldFiles.get(new File(reformatedOldFilename));
}
newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
pdbfilenames.add(filedat.getFilePath());