createAlignFrameWindow(embedded);
validate();
alignPanel.adjustAnnotationHeight();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
}
public AlignViewport getAlignViewport()
{
viewport.featureSettings.refreshTable();
}
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
statusBar.setText(MessageManager
.getString("label.successfully_added_features_alignment"));
}
break;
}
- alignPanel.paintAlignment(true);
+ // TODO: repaint flags set only if the keystroke warrants it
+ alignPanel.paintAlignment(true, true);
}
/**
{
applyAutoAnnotationSettings_actionPerformed();
}
- alignPanel.paintAlignment(true);
+ // TODO: repaint flags set only if warranted
+ alignPanel.paintAlignment(true, true);
}
/**
else if (source == invertColSel)
{
viewport.invertColumnSelection();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
viewport.sendSelection();
}
else if (source == remove2LeftMenuItem)
else if (source == showColumns)
{
viewport.showAllHiddenColumns();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
else if (source == showSeqs)
{
viewport.showAllHiddenSeqs();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
// uncomment if we want to slave sequence selections in split frame
// viewport.sendSelection();
}
else if (source == hideColumns)
{
viewport.hideSelectedColumns();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
else if (source == hideSequences
&& viewport.getSelectionGroup() != null)
{
viewport.hideAllSelectedSeqs();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
// uncomment if we want to slave sequence selections in split frame
// viewport.sendSelection();
}
else if (source == hideAllButSelection)
{
toggleHiddenRegions(false, false);
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
else if (source == hideAllSelection)
viewport.expandColSelection(sg, false);
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
else if (source == showAllHidden)
{
viewport.showAllHiddenColumns();
viewport.showAllHiddenSeqs();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
else if (source == showGroupConsensus)
{
System.exit(0);
}
- else
+
+ viewport = null;
+ if (alignPanel != null && alignPanel.overviewPanel != null)
{
+ alignPanel.overviewPanel.dispose();
}
- viewport = null;
alignPanel = null;
this.dispose();
}
}
viewport.getAlignment().moveSelectedSequencesByOne(sg,
up ? null : viewport.getHiddenRepSequences(), up);
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
/*
* Also move cDNA/protein complement sequences
viewport, complement);
complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
up ? null : complement.getHiddenRepSequences(), up);
- getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
+ getSplitFrame().getComplement(this).alignPanel.paintAlignment(true,
+ false);
}
}
{
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
}
}
// JAL-2034 - should delegate to
// alignPanel to decide if overview needs
// updating.
- alignPanel.paintAlignment(false);
+ alignPanel.paintAlignment(false, false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
// JAL-2034 - should delegate to
// alignPanel to decide if overview needs
// updating.
- alignPanel.paintAlignment(false);
+ alignPanel.paintAlignment(false, false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
public void invertColSel_actionPerformed()
{
viewport.invertColumnSelection();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
{
viewport.setShowJVSuffix(seqLimits.getState());
alignPanel.fontChanged();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
protected void colourTextMenuItem_actionPerformed()
{
viewport.setColourText(colourTextMenuItem.getState());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
protected void displayNonconservedMenuItem_actionPerformed()
{
viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
protected void wrapMenuItem_actionPerformed()
scaleAbove.setEnabled(wrapMenuItem.getState());
scaleLeft.setEnabled(wrapMenuItem.getState());
scaleRight.setEnabled(wrapMenuItem.getState());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
public void overviewMenuItem_actionPerformed()
{
viewport.setGlobalColourScheme(cs);
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
}
protected void modifyPID_actionPerformed()
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
public void sortIDMenuItem_actionPerformed()
AlignmentSorter.sortByID(viewport.getAlignment());
addHistoryItem(
new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
public void sortLengthMenuItem_actionPerformed()
AlignmentSorter.sortByLength(viewport.getAlignment());
addHistoryItem(new OrderCommand("Length Sort", oldOrder,
viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
public void sortGroupMenuItem_actionPerformed()
AlignmentSorter.sortByGroup(viewport.getAlignment());
addHistoryItem(new OrderCommand("Group Sort", oldOrder,
viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
current.insertCharAt(Width - 1, viewport.getGapCharacter());
}
}
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
if ((viewport.getSelectionGroup() != null
current.insertCharAt(Width - 1, viewport.getGapCharacter());
}
}
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
addHistoryItem(new OrderCommand(MessageManager
.formatMessage("label.order_by_params", new String[]
{ title }), oldOrder, viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
/**
addHistoryItem(new OrderCommand(undoname, oldOrder,
viewport.getAlignment()));
}
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
return true;
}
{
// register the association(s) and quit, don't create any windows.
if (StructureSelectionManager.getStructureSelectionManager(applet)
- .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
+ .setMapping(seqs, chains, pdb.getFile(), protocol, null) == null)
{
System.err.println("Failed to map " + pdb.getFile() + " ("
+ protocol + ") to any sequences");
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+ import jalview.gui.IProgressIndicator;
import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.schemes.ColourSchemeI;
*/
private boolean associateNewStructs = false;
- Vector<String> atomsPicked = new Vector<String>();
+ Vector<String> atomsPicked = new Vector<>();
private List<String> chainNames;
}
if (modelFileNames == null)
{
- List<String> mset = new ArrayList<String>();
+ List<String> mset = new ArrayList<>();
_modelFileNameMap = new int[viewer.ms.mc];
String m = viewer.ms.getModelFileName(0);
if (m != null)
@Override
public synchronized String[] getStructureFiles()
{
- List<String> mset = new ArrayList<String>();
+ List<String> mset = new ArrayList<>();
if (viewer == null)
{
return new String[0];
notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1],
(String) data[0]);
// also highlight in alignment
+ // deliberate fall through
case HOVER:
notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1],
(String) data[0]);
fileLoadingError = null;
String[] oldmodels = modelFileNames;
modelFileNames = null;
- chainNames = new ArrayList<String>();
- chainFile = new Hashtable<String, String>();
+ chainNames = new ArrayList<>();
+ chainFile = new Hashtable<>();
boolean notifyLoaded = false;
String[] modelfilenames = getStructureFiles();
// first check if we've lost any structures
// see JAL-623 - need method of matching pasted data up
{
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
- pdbfile, DataSourceType.PASTE);
+ pdbfile, DataSourceType.PASTE,
+ getIProgressIndicator());
getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
matches = true;
foundEntry = true;
}
// Explicitly map to the filename used by Jmol ;
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
- fileName, protocol);
+ fileName, protocol, getIProgressIndicator());
// pdbentry[pe].getFile(), protocol);
}
return chainNames;
}
+ protected abstract IProgressIndicator getIProgressIndicator();
+
public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
{
notifyAtomPicked(iatom, strMeasure, null);
public abstract ViewerType getViewerType();
+ protected abstract IProgressIndicator getIProgressIndicator();
+
/**
* add a new structure (with associated sequences and chains) to this viewer,
* retrieving it if necessary first.
* create the mappings
*/
apanel.getStructureSelectionManager().setMapping(seq, chains,
- pdbFilename, DataSourceType.FILE);
+ pdbFilename, DataSourceType.FILE, getIProgressIndicator());
/*
* alert the FeatureRenderer to show new (PDB RESNUM) features
if (apanel.getSeqPanel().seqCanvas.fr != null)
{
apanel.getSeqPanel().seqCanvas.fr.featuresAdded();
- apanel.paintAlignment(true);
+ // note - we don't do a refresh for structure here because we do it
+ // explicitly for all panels later on
+ apanel.paintAlignment(true, false);
}
/*
static IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> instances;
- private List<StructureMapping> mappings = new ArrayList<StructureMapping>();
+ private List<StructureMapping> mappings = new ArrayList<>();
private boolean processSecondaryStructure = false;
private boolean addTempFacAnnot = false;
- private IProgressIndicator progressIndicator;
-
private SiftsClient siftsClient = null;
/*
* Set of any registered mappings between (dataset) sequences.
*/
- private List<AlignedCodonFrame> seqmappings = new ArrayList<AlignedCodonFrame>();
+ private List<AlignedCodonFrame> seqmappings = new ArrayList<>();
- private List<CommandListener> commandListeners = new ArrayList<CommandListener>();
+ private List<CommandListener> commandListeners = new ArrayList<>();
- private List<SelectionListener> sel_listeners = new ArrayList<SelectionListener>();
+ private List<SelectionListener> sel_listeners = new ArrayList<>();
/**
* @return true if will try to use external services for processing secondary
* map between the PDB IDs (or structure identifiers) used by Jalview and the
* absolute filenames for PDB data that corresponds to it
*/
- Map<String, String> pdbIdFileName = new HashMap<String, String>();
+ Map<String, String> pdbIdFileName = new HashMap<>();
- Map<String, String> pdbFileNameId = new HashMap<String, String>();
+ Map<String, String> pdbFileNameId = new HashMap<>();
public void registerPDBFile(String idForFile, String absoluteFile)
{
}
if (instances == null)
{
- instances = new java.util.IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager>();
+ instances = new java.util.IdentityHashMap<>();
}
StructureSelectionManager instance = instances.get(context);
if (instance == null)
* @return null or the structure data parsed as a pdb file
*/
synchronized public StructureFile setMapping(SequenceI[] sequence,
- String[] targetChains, String pdbFile, DataSourceType protocol)
+ String[] targetChains, String pdbFile, DataSourceType protocol,
+ IProgressIndicator progress)
{
- return setMapping(true, sequence, targetChains, pdbFile, protocol);
+ return computeMapping(true, sequence, targetChains, pdbFile, protocol,
+ progress);
}
/**
SequenceI[] sequenceArray, String[] targetChainIds,
String pdbFile, DataSourceType sourceType)
{
+ return computeMapping(forStructureView, sequenceArray, targetChainIds,
+ pdbFile, sourceType, null);
+ }
+
+ synchronized public StructureFile computeMapping(
+ boolean forStructureView, SequenceI[] sequenceArray,
+ String[] targetChainIds, String pdbFile, DataSourceType sourceType,
+ IProgressIndicator progress)
+ {
+ long progressSessionId = System.currentTimeMillis() * 3;
/*
* There will be better ways of doing this in the future, for now we'll use
* the tried and tested MCview pdb mapping
pdbFile = "INLINE" + pdb.getId();
}
- List<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
+ List<StructureMapping> seqToStrucMapping = new ArrayList<>();
if (isMapUsingSIFTs && seq.isProtein())
{
- setProgressBar(null);
- setProgressBar(MessageManager
- .getString("status.obtaining_mapping_with_sifts"));
+ if (progress!=null) {
+ progress.setProgressBar(MessageManager
+ .getString("status.obtaining_mapping_with_sifts"),
+ progressSessionId);
+ }
jalview.datamodel.Mapping sqmpping = maxAlignseq
.getMappingFromS1(false);
if (targetChainId != null && !targetChainId.trim().isEmpty())
}
else
{
- List<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
+ List<StructureMapping> foundSiftsMappings = new ArrayList<>();
for (PDBChain chain : pdb.getChains())
{
try
}
else
{
- setProgressBar(null);
- setProgressBar(MessageManager
- .getString("status.obtaining_mapping_with_nw_alignment"));
+ if (progress != null)
+ {
+ progress.setProgressBar(MessageManager
+ .getString("status.obtaining_mapping_with_nw_alignment"),
+ progressSessionId);
+ }
StructureMapping nwMapping = getNWMappings(seq, pdbFile, maxChainId,
maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
-
}
-
if (forStructureView)
{
mappings.addAll(seqToStrucMapping);
}
+ if (progress != null)
+ {
+ progress.setProgressBar(null, progressSessionId);
+ }
}
return pdb;
}
.getMappingFromS1(false);
maxChain.transferRESNUMFeatures(seq, null);
- HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
+ HashMap<Integer, int[]> mapping = new HashMap<>();
int resNum = -10000;
int index = 0;
char insCode = ' ';
* Remove mappings to the closed listener's PDB files, but first check if
* another listener is still interested
*/
- List<String> pdbs = new ArrayList<String>(Arrays.asList(pdbfiles));
+ List<String> pdbs = new ArrayList<>(Arrays.asList(pdbfiles));
StructureListener sl;
for (int i = 0; i < listeners.size(); i++)
*/
if (pdbs.size() > 0)
{
- List<StructureMapping> tmp = new ArrayList<StructureMapping>();
+ List<StructureMapping> tmp = new ArrayList<>();
for (StructureMapping sm : mappings)
{
if (!pdbs.contains(sm.pdbfile))
&& sm.pdbchain.equals(atom.getChain()))
{
int indexpos = sm.getSeqPos(atom.getPdbResNum());
- if (lastipos != indexpos && lastseq != sm.sequence)
+ if (lastipos != indexpos || lastseq != sm.sequence)
{
results.addResult(sm.sequence, indexpos, indexpos);
lastipos = indexpos;
return;
}
int atomNo;
- List<AtomSpec> atoms = new ArrayList<AtomSpec>();
+ List<AtomSpec> atoms = new ArrayList<>();
for (StructureMapping sm : mappings)
{
if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence()
public StructureMapping[] getMapping(String pdbfile)
{
- List<StructureMapping> tmp = new ArrayList<StructureMapping>();
+ List<StructureMapping> tmp = new ArrayList<>();
for (StructureMapping sm : mappings)
{
if (sm.pdbfile.equals(pdbfile))
}
}
- Vector<AlignmentViewPanelListener> view_listeners = new Vector<AlignmentViewPanelListener>();
+ Vector<AlignmentViewPanelListener> view_listeners = new Vector<>();
public synchronized void sendViewPosition(
jalview.api.AlignmentViewPanel source, int startRes, int endRes,
return null;
}
- public IProgressIndicator getProgressIndicator()
- {
- return progressIndicator;
- }
-
- public void setProgressIndicator(IProgressIndicator progressIndicator)
- {
- this.progressIndicator = progressIndicator;
- }
-
- public long getProgressSessionId()
- {
- return progressSessionId;
- }
-
- public void setProgressSessionId(long progressSessionId)
- {
- this.progressSessionId = progressSessionId;
- }
-
- public void setProgressBar(String message)
- {
- if (progressIndicator == null)
- {
- return;
- }
- progressIndicator.setProgressBar(message, progressSessionId);
- }
-
public List<AlignedCodonFrame> getSequenceMappings()
{
return seqmappings;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.IProgressIndicator;
+ import jalview.gui.IProgressIndicatorHandler;
import jalview.schemes.ResidueProperties;
import jalview.workers.AlignCalcWorker;
import jalview.ws.jws2.dm.AAConSettings;
progressId = System.currentTimeMillis());
}
rslt = submitToService(seqs);
-
+ if (guiProgress != null)
+ {
+ guiProgress.registerHandler(progressId,
+ new IProgressIndicatorHandler()
+ {
+
+ @Override
+ public boolean cancelActivity(long id)
+ {
+ cancelCurrentJob();
+ return true;
+ }
+
+ @Override
+ public boolean canCancel()
+ {
+ return true;
+ }
+ });
+ }
boolean finished = false;
long rpos = 0;
do
{
guiProgress.setProgressBar("", progressId);
}
- ap.paintAlignment(true);
+ // TODO: may not need to paintAlignment again !
+ ap.paintAlignment(false, false);
}
if (msg.length() > 0)
{
protected boolean checkDone()
{
calcMan.notifyStart(this);
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
while (!calcMan.notifyWorking(this))
{
if (calcMan.isWorking(this))
{
if (ap != null)
{
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
}
Thread.sleep(200);
git://source.jalview.org / jalview.git / commitdiff