import jalview.analysis.PCA;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.analysis.scoremodels.SimilarityParams;
-import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
import jalview.api.ViewStyleI;
import jalview.api.analysis.ScoreModelI;
import jalview.schemes.FeatureColour;
import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
+import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.Format;
import jalview.util.MessageManager;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
+import java.lang.reflect.InvocationTargetException;
import java.math.BigInteger;
import java.net.MalformedURLException;
import java.net.URL;
* core method for storing state for a set of AlignFrames.
*
* @param frames
- * - frames involving all data to be exported (including those
- * contained in splitframes, though not the split frames themselves)
+ * - 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<>();
/*
for (int i = frames.size() - 1; i > -1; i--)
{
AlignFrame af = frames.get(i);
- AlignViewport vp = af.getViewport();
// skip ?
if (skipList != null && skipList
- .containsKey(vp.getSequenceSetId()))
+ .containsKey(af.getViewport().getSequenceSetId()))
{
continue;
}
String shortName = makeFilename(af, shortNames);
- AlignmentI alignment = vp.getAlignment();
- List<? extends AlignmentViewPanel> panels = af.getAlignPanels();
- int apSize = panels.size();
+ int apSize = af.getAlignPanels().size();
+
for (int ap = 0; ap < apSize; ap++)
- {
- AlignmentPanel apanel = (AlignmentPanel) panels.get(ap);
+ {
+ AlignmentPanel apanel = (AlignmentPanel) af.getAlignPanels()
+ .get(ap);
String fileName = apSize == 1 ? shortName : ap + shortName;
if (!fileName.endsWith(".xml"))
{
}
saveState(apanel, fileName, jout, viewIds);
- }
- if (apSize > 0)
- {
- // BH moved next bit out of inner loop, not that it really matters.
- // so we are testing to make sure we actually have an alignment,
- // apparently.
- String dssid = getDatasetIdRef(alignment.getDataset());
+
+ String dssid = getDatasetIdRef(
+ af.getViewport().getAlignment().getDataset());
if (!dsses.containsKey(dssid))
{
- // We have not already covered this data by reference from another
- // frame.
dsses.put(dssid, af);
}
}
}
}
- /**
- * Each AlignFrame has a single data set associated with it. Note that none of
- * these frames are split frames, because Desktop.getAlignFrames() collects
- * top and bottom separately here.
- *
- * @param dsses
- * @param fileName
- * @param jout
- */
private void writeDatasetFor(Hashtable<String, AlignFrame> dsses,
String fileName, JarOutputStream jout)
{
- // Note that in saveAllFrames we have associated each specific dataset to
- // ONE of its associated frames.
-
for (String dssids : dsses.keySet())
{
AlignFrame _af = dsses.get(dssids);
* only view *should* be coped with sensibly.
*/
// This must have been loaded, is it still visible?
- JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
String matchedFile = null;
for (int f = frames.length - 1; f > -1; f--)
{
{
// FIND ANY ASSOCIATED TREES
// NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
- if (Desktop.getDesktopPane() != null)
+ if (Desktop.desktop != null)
{
- JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
for (int t = 0; t < frames.length; t++)
{
/*
* save PCA viewers
*/
- if (!storeDS && Desktop.getDesktopPane() != null)
+ if (!storeDS && Desktop.desktop != null)
{
- for (JInternalFrame frame : Desktop.getDesktopPane().getAllFrames())
+ for (JInternalFrame frame : Desktop.desktop.getAllFrames())
{
if (frame instanceof PCAPanel)
{
// using save and then load
try
{
- fileName = fileName.replace('\\', '/');
+ fileName = fileName.replace('\\', '/');
System.out.println("Writing jar entry " + fileName);
JarEntry entry = new JarEntry(fileName);
jout.putNextEntry(entry);
final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
boolean storeDataset)
{
- if (Desktop.getDesktopPane() == null)
+ if (Desktop.desktop == null)
{
return;
}
- JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
for (int f = frames.length - 1; f > -1; f--)
{
if (frames[f] instanceof AppVarna)
if (calcIdParam.getVersion().equals("1.0"))
{
final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
- Jws2Instance service = Jws2Discoverer.getInstance()
+ Jws2Instance service = Jws2Discoverer.getDiscoverer()
.getPreferredServiceFor(calcIds);
if (service != null)
{
{
try
{
- // BH 2019 -- can't wait
- SwingUtilities.invokeLater(new Runnable()
+ SwingUtilities.invokeAndWait(new Runnable()
{
@Override
public void run()
return af;
}
- @SuppressWarnings("unused")
- private jarInputStreamProvider createjarInputStreamProvider(final Object ofile) throws MalformedURLException {
+ @SuppressWarnings("unused")
+ private jarInputStreamProvider createjarInputStreamProvider(final Object ofile) throws MalformedURLException {
- // BH 2018 allow for bytes already attached to File object
- try {
- String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString());
+ // BH 2018 allow for bytes already attached to File object
+ try {
+ String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString());
byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
: null;
- URL url = null;
- errorMessage = null;
- uniqueSetSuffix = null;
- seqRefIds = null;
- viewportsAdded.clear();
- frefedSequence = null;
-
- if (file.startsWith("http://")) {
- url = new URL(file);
- }
- final URL _url = url;
- return new jarInputStreamProvider() {
-
- @Override
- public JarInputStream getJarInputStream() throws IOException {
- if (bytes != null) {
-// System.out.println("Jalview2XML: opening byte jarInputStream for bytes.length=" + bytes.length);
- return new JarInputStream(new ByteArrayInputStream(bytes));
- }
- if (_url != null) {
-// System.out.println("Jalview2XML: opening url jarInputStream for " + _url);
- return new JarInputStream(_url.openStream());
- } else {
-// System.out.println("Jalview2XML: opening file jarInputStream for " + file);
- return new JarInputStream(new FileInputStream(file));
- }
- }
-
- @Override
- public String getFilename() {
- return file;
- }
- };
- } catch (IOException e) {
- e.printStackTrace();
- return null;
- }
- }
+ URL url = null;
+ errorMessage = null;
+ uniqueSetSuffix = null;
+ seqRefIds = null;
+ viewportsAdded.clear();
+ frefedSequence = null;
+
+ if (file.startsWith("http://")) {
+ url = new URL(file);
+ }
+ final URL _url = url;
+ return new jarInputStreamProvider() {
+
+ @Override
+ public JarInputStream getJarInputStream() throws IOException {
+ if (bytes != null) {
+// System.out.println("Jalview2XML: opening byte jarInputStream for bytes.length=" + bytes.length);
+ return new JarInputStream(new ByteArrayInputStream(bytes));
+ }
+ if (_url != null) {
+// System.out.println("Jalview2XML: opening url jarInputStream for " + _url);
+ return new JarInputStream(_url.openStream());
+ } else {
+// System.out.println("Jalview2XML: opening file jarInputStream for " + file);
+ return new JarInputStream(new FileInputStream(file));
+ }
+ }
+
+ @Override
+ public String getFilename() {
+ return file;
+ }
+ };
+ } catch (IOException e) {
+ e.printStackTrace();
+ return null;
+ }
+ }
/**
* Recover jalview session from a jalview project archive. Caller may
IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
final String file = jprovider.getFilename();
-
- List<AlignFrame> alignFrames = new ArrayList<>();
-
try
{
JarInputStream jin = null;
JarEntry jarentry = null;
int entryCount = 1;
-
- // Look for all the entry names ending with ".xml"
- // This includes all panels and at least one frame.
-// Platform.timeCheck(null, Platform.TIME_MARK);
do
{
jin = jprovider.getJarInputStream();
{
jarentry = jin.getNextJarEntry();
}
- String name = (jarentry == null ? null : jarentry.getName());
-// System.out.println("Jalview2XML opening " + name);
- if (name != null && name.endsWith(".xml"))
+ if (jarentry != null && jarentry.getName().endsWith(".xml"))
{
-
- // DataSet for.... is read last.
-
-
- // The question here is what to do with the two
- // .xml files in the jvp file.
- // Some number of them, "...Dataset for...", will be the
- // Only AlignPanels and will have Viewport.
- // One or more will be the source data, with the DBRefs.
- //
- // JVP file writing (above) ensures tha the AlignPanels are written
- // first, then all relevant datasets (which are
- // Jalview.datamodel.Alignment).
- //
-
-// Platform.timeCheck("Jalview2XML JAXB " + name, Platform.TIME_MARK);
JAXBContext jc = JAXBContext
.newInstance("jalview.xml.binding.jalview");
XMLStreamReader streamReader = XMLInputFactory.newInstance()
javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
JAXBElement<JalviewModel> jbe = um
.unmarshal(streamReader, JalviewModel.class);
- JalviewModel model = jbe.getValue();
+ JalviewModel object = jbe.getValue();
if (true) // !skipViewport(object))
{
- // Q: Do we have to load from the model, even if it
- // does not have a viewport, could we discover that early on?
- // Q: Do we need to load this object?
- _af = loadFromObject(model, file, true, jprovider);
-// Platform.timeCheck("Jalview2XML.loadFromObject",
- // Platform.TIME_MARK);
-
- if (_af != null)
- {
- alignFrames.add(_af);
- }
- if (_af != null && model.getViewport().size() > 0)
+ _af = loadFromObject(object, file, true, jprovider);
+ if (_af != null && object.getViewport().size() > 0)
+ // getJalviewModelSequence().getViewportCount() > 0)
{
-
- // That is, this is one of the AlignmentPanel models
if (af == null)
{
// store a reference to the first view
af.getViewport().getAlignment().getDataset());
}
}
-// Platform.timeCheck("JAXB " + name, Platform.TIME_MARK);
entryCount++;
}
else if (jarentry != null)
entryCount++;
}
} while (jarentry != null);
-// Platform.timeCheck("JAXB loop exit", Platform.TIME_MARK);
resolveFrefedSequences();
-// Platform.timeCheck("JAXB resolveFrefed", Platform.TIME_MARK);
-
} catch (IOException ex)
{
ex.printStackTrace();
{
// used to attempt to parse as V1 castor-generated xml
}
- if (Desktop.getInstance() != null)
+ if (Desktop.instance != null)
{
- Desktop.getInstance().stopLoading();
+ Desktop.instance.stopLoading();
}
if (af != null)
{
errorMessage = "Out of memory loading jalview XML file";
System.err.println("Out of memory whilst loading jalview XML file");
e.printStackTrace();
- } finally
- {
- for (AlignFrame alf : alignFrames)
- {
- alf.alignPanel.setHoldRepaint(false);
- }
-
}
/*
*/
for (AlignFrame fr : gatherToThisFrame.values())
{
- Desktop.getInstance().gatherViews(fr);
+ Desktop.instance.gatherViews(fr);
}
restoreSplitFrames();
{
if (ds.getCodonFrames() != null)
{
- Desktop.getInstance().getStructureSelectionManager()
+ StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance)
.registerMappings(ds.getCodonFrames());
}
}
reportErrors();
}
- if (Desktop.getInstance() != null)
+ if (Desktop.instance != null)
{
- Desktop.getInstance().stopLoading();
+ Desktop.instance.stopLoading();
}
return af;
*/
for (SplitFrame sf : gatherTo)
{
- Desktop.getInstance().gatherViews(sf);
+ Desktop.instance.gatherViews(sf);
}
splitFrameCandidates.clear();
@Override
public void run()
{
- JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
finalErrorMessage,
"Error " + (saving ? "saving" : "loading")
+ " Jalview file",
}
/**
- * Load alignment frame from jalview XML DOM object. For a DOM object that
- * includes one or more Viewport elements (one with a title that does NOT
- * contain "Dataset for"), create the frame.
+ * Load alignment frame from jalview XML DOM object
*
* @param jalviewModel
* DOM
AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
{
-
-// Platform.timeCheck("Jalview2XML.loadFromObject0", Platform.TIME_MARK);
-
SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
List<Sequence> vamsasSeqs = vamsasSet.getSequence();
-
// JalviewModelSequence jms = object.getJalviewModelSequence();
// Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
: view.getId() + uniqueSetSuffix);
}
-// Platform.timeCheck("Jalview2XML.loadFromObject1", Platform.TIME_MARK);
// ////////////////////////////////
// LOAD SEQUENCES
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
}
}
-// Platform.timeCheck("Jalview2XML.loadFromObject-seq",
-// Platform.TIME_MARK);
// /
// Create the alignment object from the sequence set
// ///////////////////////////////
recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId);
}
-// Platform.timeCheck("Jalview2XML.loadFromObject-align",
-// Platform.TIME_MARK);
if (referenceseqForView != null)
{
al.setSeqrep(referenceseqForView);
al.setProperty(ssp.getKey(), ssp.getValue());
}
-// Platform.timeCheck("Jalview2XML.loadFromObject-setseqprop",
-// Platform.TIME_MARK);
// ///////////////////////////////
Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
// now, for 2.10 projects, this is also done if the xml doc includes
// dataset sequences not actually present in any particular view.
//
-// Platform.timeCheck("J2XML features0", Platform.TIME_RESET);
for (int i = 0; i < vamsasSeqs.size(); i++)
{
JSeq jseq = jseqs.get(i);
}
// adds feature to datasequence's feature set (since Jalview 2.10)
-// Platform.timeCheck(null, Platform.TIME_SET);
al.getSequenceAt(i).addSequenceFeature(sf);
-// Platform.timeCheck(null, Platform.TIME_MARK);
}
}
if (vamsasSeqs.get(i).getDBRef().size() > 0)
{
entry.setProperty(prop.getName(), prop.getValue());
}
- Desktop.getInstance().getStructureSelectionManager()
+ StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance)
.registerPDBEntry(entry);
// adds PDBEntry to datasequence's set (since Jalview 2.10)
if (al.getSequenceAt(i).getDatasetSequence() != null)
}
}
}
-
}
-
-// Platform.timeCheck("features done", Platform.TIME_GET);
-// Platform.timeCheck("Jalview2XML.loadFromObject-endmultiview",
-// Platform.TIME_MARK);
} // end !multipleview
// ///////////////////////////////
al.addCodonFrame(cf);
}
}
-// Platform.timeCheck("Jalview2XML.loadFromObject-seqmap",
-// Platform.TIME_MARK);
}
// ////////////////////////////////
}
// Construct new annotation from model.
List<AnnotationElement> ae = annotation.getAnnotationElement();
-// System.err.println(
-// "Jalview2XML processing " + ae.size() + " annotations");
-
jalview.datamodel.Annotation[] anot = null;
java.awt.Color firstColour = null;
int anpos;
}
}
}
- // create the new AlignmentAnnotation
jalview.datamodel.AlignmentAnnotation jaa = null;
if (annotation.isGraph())
jaa._linecolour = firstColour;
}
// register new annotation
- // Annotation graphs such as Conservation will not have id.
if (annotation.getId() != null)
{
annotationIds.put(annotation.getId(), jaa);
al.addAnnotation(jaa);
}
}
-// Platform.timeCheck("Jalview2XML.loadFromObject-annot",
-// Platform.TIME_MARK);
}
// ///////////////////////
// LOAD GROUPS
jGroup.getAnnotationColours(), null, al, jalviewModel, false));
}
}
-// Platform.timeCheck("Jalview2XML.loadFromObject-groups",
-// Platform.TIME_MARK);
}
if (view == null)
{
// ///////////////////////////////
// LOAD VIEWPORT
+ AlignFrame af = null;
+ AlignViewport av = null;
// now check to see if we really need to create a new viewport.
if (multipleView && viewportsAdded.size() == 0)
{
}
}
-// Platform.timeCheck("Jalview2XML.loadFromObject-viewport",
-// Platform.TIME_MARK);
}
/**
* indicate that annotation colours are applied across all groups (pre
boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
jalviewModel.getVersion());
- AlignFrame af = null;
AlignmentPanel ap = null;
- AlignViewport av = null;
+ boolean isnewview = true;
if (viewId != null)
{
// Check to see if this alignment already has a view id == viewId
{
for (int v = 0; v < views.length; v++)
{
- ap = views[v];
- av = ap.av;
- if (av.getViewId().equalsIgnoreCase(viewId))
+ if (views[v].av.getViewId().equalsIgnoreCase(viewId))
{
// recover the existing alignpanel, alignframe, viewport
- af = ap.alignFrame;
- break;
+ af = views[v].alignFrame;
+ av = views[v].av;
+ ap = views[v];
// TODO: could even skip resetting view settings if we don't want to
// change the local settings from other jalview processes
+ isnewview = false;
}
}
}
}
- if (af == null)
+ if (isnewview)
{
af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
uniqueSeqSetId, viewId, autoAlan);
av = af.getViewport();
- // note that this only retrieves the most recently accessed
- // tab of an AlignFrame.
ap = af.alignPanel;
}
*
* Not done if flag is false (when this method is used for New View)
*/
- final AlignFrame af0 = af;
- final AlignViewport av0 = av;
- final AlignmentPanel ap0 = ap;
-// Platform.timeCheck("Jalview2XML.loadFromObject-beforetree",
-// Platform.TIME_MARK);
if (loadTreesAndStructures)
{
- if (!jalviewModel.getTree().isEmpty())
- {
- SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
-// Platform.timeCheck(null, Platform.TIME_MARK);
- loadTrees(jalviewModel, view, af0, av0, ap0);
-// Platform.timeCheck("Jalview2XML.loadTrees", Platform.TIME_MARK);
- }
- });
- }
- if (!jalviewModel.getPcaViewer().isEmpty())
- {
- SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
-// Platform.timeCheck(null, Platform.TIME_MARK);
- loadPCAViewers(jalviewModel, ap0);
-// Platform.timeCheck("Jalview2XML.loadPCA", Platform.TIME_MARK);
- }
- });
- }
- SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
-// Platform.timeCheck(null, Platform.TIME_MARK);
- loadPDBStructures(jprovider, jseqs, af0, ap0);
-// Platform.timeCheck("Jalview2XML.loadPDB", Platform.TIME_MARK);
- }
- });
- SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- loadRnaViewers(jprovider, jseqs, ap0);
- }
- });
+ loadTrees(jalviewModel, view, af, av, ap);
+ loadPCAViewers(jalviewModel, ap);
+ loadPDBStructures(jprovider, jseqs, af, ap);
+ loadRnaViewers(jprovider, jseqs, ap);
}
// and finally return.
- // but do not set holdRepaint true just yet, because this could be the
- // initial frame with just its dataset.
return af;
}
* @param jseqs
* @param ap
*/
- protected void loadRnaViewers(jarInputStreamProvider jprovider,
+ private void loadRnaViewers(jarInputStreamProvider jprovider,
List<JSeq> jseqs, AlignmentPanel ap)
{
/*
int height = safeInt(structureState.getHeight());
// Probably don't need to do this anymore...
- // Desktop.getDesktop().getComponentAt(x, y);
+ // Desktop.desktop.getComponentAt(x, y);
// TODO: NOW: check that this recovers the PDB file correctly.
String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
pdbid.getFile());
String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
filedat = oldFiles.get(new File(reformatedOldFilename));
}
- newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
+ newFileLoc.append(Platform.escapeBackslashes(filedat.getFilePath()));
pdbfilenames.add(filedat.getFilePath());
pdbids.add(filedat.getPdbId());
seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
final AlignFrame alf = af;
final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
svattrib.getWidth(), svattrib.getHeight());
- // try
- // {
- javax.swing.SwingUtilities.invokeLater(new Runnable()
+ try
+ {
+ javax.swing.SwingUtilities.invokeAndWait(new Runnable()
{
@Override
public void run()
}
}
});
- // } catch (InvocationTargetException ex)
- // {
- // warn("Unexpected error when opening Jmol view.", ex);
- //
- // } catch (InterruptedException e)
- // {
- // // e.printStackTrace();
- // }
+ } catch (InvocationTargetException ex)
+ {
+ warn("Unexpected error when opening Jmol view.", ex);
+
+ } catch (InterruptedException e)
+ {
+ // e.printStackTrace();
+ }
}
{
try
{
- frames = Desktop.getDesktopPane().getAllFrames();
+ frames = Desktop.desktop.getAllFrames();
} catch (ArrayIndexOutOfBoundsException e)
{
// occasional No such child exceptions are thrown here...
{
AlignFrame af = null;
af = new AlignFrame(al, safeInt(view.getWidth()),
- safeInt(view.getHeight()), uniqueSeqSetId, viewId)
+ safeInt(view.getHeight()), uniqueSeqSetId, viewId)
// {
-//
-// @Override
-// protected void processKeyEvent(java.awt.event.KeyEvent e) {
-// System.out.println("Jalview2XML AF " + e);
-// super.processKeyEvent(e);
-//
-// }
-//
+//
+// @Override
+// protected void processKeyEvent(java.awt.event.KeyEvent e) {
+// System.out.println("Jalview2XML AF " + e);
+// super.processKeyEvent(e);
+//
+// }
+//
// }
;
- af.alignPanel.setHoldRepaint(true);
+
af.setFileName(file, FileFormat.Jalview);
final AlignViewport viewport = af.getViewport();
viewport.setViewName(view.getViewName());
af.setInitialTabVisible();
}
- int x = safeInt(view.getXpos());
- int y = safeInt(view.getYpos());
- int w = safeInt(view.getWidth());
- int h = safeInt(view.getHeight());
- // // BH we cannot let the title bar go off the top
- // if (Platform.isJS())
- // {
- // x = Math.max(50 - w, x);
- // y = Math.max(0, y);
- // }
-
- af.setBounds(x, y, w, h);
+ af.setBounds(safeInt(view.getXpos()), safeInt(view.getYpos()),
+ safeInt(view.getWidth()), safeInt(view.getHeight()));
// startSeq set in af.alignPanel.updateLayout below
af.alignPanel.updateLayout();
ColourSchemeI cs = null;
}
else
{
- featureOrder.put(featureType, new Float(
+ featureOrder.put(featureType, Float.valueOf(
fs / jm.getFeatureSettings().getSetting().size()));
}
if (safeBoolean(setting.isDisplay()))
for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
{
Group grp = jm.getFeatureSettings().getGroup().get(gs);
- fgtable.put(grp.getName(), new Boolean(grp.isDisplay()));
+ fgtable.put(grp.getName(), Boolean.valueOf(grp.isDisplay()));
}
// FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
// fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
SequenceI[] dsseqs = new SequenceI[dseqs.size()];
dseqs.copyInto(dsseqs);
ds = new jalview.datamodel.Alignment(dsseqs);
-// debug("Jalview2XML Created new dataset " + vamsasSet.getDatasetId()
-// + " for alignment " + System.identityHashCode(al));
+ debug("Created new dataset " + vamsasSet.getDatasetId()
+ + " for alignment " + System.identityHashCode(al));
addDatasetRef(vamsasSet.getDatasetId(), ds);
}
// set the dataset for the newly imported alignment.
git://source.jalview.org / jalview.git / blobdiff