import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SeqCigar;
import jalview.datamodel.SequenceI;
import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
-import jalview.hmmer.HMMAlignThread;
-import jalview.hmmer.HMMBuildThread;
+import jalview.hmmer.HMMAlign;
+import jalview.hmmer.HMMBuild;
import jalview.hmmer.HMMERParamStore;
import jalview.hmmer.HMMERPreset;
-import jalview.hmmer.HMMSearchThread;
+import jalview.hmmer.HMMSearch;
+import jalview.hmmer.HmmerCommand;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
import jalview.io.BioJsHTMLOutput;
import jalview.io.NewickFile;
import jalview.io.ScoreMatrixFile;
import jalview.io.TCoffeeScoreFile;
+import jalview.io.vcf.VCFLoader;
import jalview.jbgui.GAlignFrame;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemes;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Deque;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.Hashtable;
+import java.util.HashSet;
import java.util.List;
-import java.util.Map;
+import java.util.Set;
import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JEditorPane;
-import javax.swing.JFrame;
+import javax.swing.JFileChooser;
import javax.swing.JInternalFrame;
import javax.swing.JLayeredPane;
import javax.swing.JMenu;
public class AlignFrame extends GAlignFrame implements DropTargetListener,
IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
{
-
- Map<String, Float> distribution = new HashMap<>(); // temporary
-
public static final int DEFAULT_WIDTH = 700;
public static final int DEFAULT_HEIGHT = 500;
- boolean autoAlignNewSequences;
-
-
/*
* The currently displayed panel (selected tabbed view if more than one)
*/
AlignViewport viewport;
- ViewportRanges vpRanges;
-
public AlignViewControllerI avc;
- /*
- * The selected HMM for this align frame
- */
- SequenceI selectedHMMSequence;
List<AlignmentPanel> alignPanels = new ArrayList<>();
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
}
- vpRanges = viewport.getRanges();
avc = new jalview.controller.AlignViewController(this, viewport,
alignPanel);
if (viewport.getAlignmentConservationAnnotation() == null)
}
});
buildColourMenu();
- buildHMMERMenu();
if (Desktop.desktop != null)
{
}
/**
- * Adds all menu items to the HMMER menu
- */
- private void buildHMMERMenu()
- {
- hmmerMenu.removeAll();
-
- hmmerMenu.add(hmmAlign);
- hmmerMenu.add(hmmBuild);
- hmmerMenu.add(hmmSearch);
- }
-
- /**
* Change the filename and format for the alignment, and enable the 'reload'
* button functionality.
*
{ (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
- alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
+ ViewportRanges ranges = viewport.getRanges();
+ alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
.getStartRes();
- alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
+ alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
.getStartSeq();
}
alignPanel.getSeqPanel().seqCanvas.repaint();
break;
}
case KeyEvent.VK_PAGE_UP:
- vpRanges.pageUp();
+ viewport.getRanges().pageUp();
break;
case KeyEvent.VK_PAGE_DOWN:
- vpRanges.pageDown();
+ viewport.getRanges().pageDown();
break;
}
}
ap.av.updateConservation(ap);
ap.av.updateConsensus(ap);
ap.av.updateStrucConsensus(ap);
- ap.av.updateInformation(ap);
+ ap.av.initInformationWorker(ap);
}
}
AlignmentI al = getViewport().getAlignment();
boolean nucleotide = al.isNucleotide();
+ loadVcf.setVisible(nucleotide);
showTranslation.setVisible(nucleotide);
showReverse.setVisible(nucleotide);
showReverseComplement.setVisible(nucleotide);
}
@Override
- public void hmmBuildSettings_actionPerformed(ActionEvent e)
- throws IOException, InterruptedException
+ public void hmmBuild_actionPerformed(boolean withDefaults)
{
- if (!(alignmentIsSufficient(1)))
+ if (!alignmentIsSufficient(1))
{
return;
}
- WsParamSetI set = new HMMERPreset();
- List<ArgumentI> args = new ArrayList<>();
- ParamDatastoreI store = new HMMERParamStore("hmmalign");
- WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
- args);
- params.showRunDialog();
- new Thread(new HMMBuildThread(this, params.getJobParams())).start();
- alignPanel.repaint();
- }
+ /*
+ * get default parameters, and optionally show a dialog
+ * to allow them to be modified
+ */
+ ParamDatastoreI store = HMMERParamStore.forBuild(viewport);
+ List<ArgumentI> args = store.getServiceParameters();
- @Override
- public void hmmAlignSettings_actionPerformed(ActionEvent e)
- throws IOException, InterruptedException
- {
- if (!(checkForHMM() && alignmentIsSufficient(2)))
+ if (!withDefaults)
{
- return;
+ WsParamSetI set = new HMMERPreset();
+ WsJobParameters params = new WsJobParameters(store, set, args);
+ if (params.showRunDialog())
+ {
+ args = params.getJobParams();
+ }
+ else
+ {
+ return; // user cancelled
+ }
}
- WsParamSetI set = new HMMERPreset();
- List<ArgumentI> args = new ArrayList<>();
- ParamDatastoreI store = new HMMERParamStore("hmmalign");
- WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
- args);
- params.showRunDialog();
- new Thread(new HMMAlignThread(this, true, params.getJobParams()))
- .start();
- alignPanel.repaint();
+ new Thread(new HMMBuild(this, args)).start();
}
@Override
- public void hmmSearchSettings_actionPerformed(ActionEvent e)
+ public void hmmAlign_actionPerformed(boolean withDefaults)
{
- if (!checkForHMM())
+ if (!(checkForHMM() && alignmentIsSufficient(2)))
{
return;
}
- WsParamSetI set = new HMMERPreset();
- List<ArgumentI> args = new ArrayList<>();
- ParamDatastoreI store = new HMMERParamStore("hmmsearch");
- WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
- args);
- params.showRunDialog();
- new Thread(new HMMSearchThread(this, true, params.getJobParams()))
- .start();
- alignPanel.repaint();
- }
- @Override
- public void hmmBuildRun_actionPerformed(ActionEvent e)
- throws IOException, InterruptedException
- {
- if (!alignmentIsSufficient(1))
+ /*
+ * get default parameters, and optionally show a dialog
+ * to allow them to be modified
+ */
+ ParamDatastoreI store = HMMERParamStore.forAlign(viewport);
+ List<ArgumentI> args = store.getServiceParameters();
+
+ if (!withDefaults)
{
- return;
+ WsParamSetI set = new HMMERPreset();
+ WsJobParameters params = new WsJobParameters(store, set, args);
+ if (params.showRunDialog())
+ {
+ args = params.getJobParams();
+ }
+ else
+ {
+ return; // user cancelled
+ }
}
- new Thread(new HMMBuildThread(this, null)).start();
- alignPanel.repaint();
-
+ new Thread(new HMMAlign(this, args)).start();
}
@Override
- public void hmmAlignRun_actionPerformed(ActionEvent e)
- throws IOException, InterruptedException
+ public void hmmSearch_actionPerformed(boolean withDefaults)
{
- if (!(checkForHMM() && alignmentIsSufficient(2)))
+ if (!checkForHMM())
{
return;
}
- new Thread(new HMMAlignThread(this, true, null))
- .start();
- alignPanel.repaint();
- }
- @Override
- public void hmmSearchRun_actionPerformed(ActionEvent e)
- {
- if (!checkForHMM())
+ /*
+ * get default parameters, and (if requested) show
+ * dialog to allow modification
+ */
+ ParamDatastoreI store = HMMERParamStore.forSearch(viewport);
+ List<ArgumentI> args = store.getServiceParameters();
+
+ if (!withDefaults)
{
- return;
+ WsParamSetI set = new HMMERPreset();
+ WsJobParameters params = new WsJobParameters(store, set, args);
+ if (params.showRunDialog())
+ {
+ args = params.getJobParams();
+ }
+ else
+ {
+ return; // user cancelled
+ }
}
- new Thread(new HMMSearchThread(this, true, null))
- .start();
+ new Thread(new HMMSearch(this, args)).start();
alignPanel.repaint();
}
/**
- * Checks if the frame has a selected hidden Markov model
+ * Checks if the alignment has at least one hidden Markov model, if not shows
+ * a dialog advising to run hmmbuild or load an HMM profile
*
* @return
*/
private boolean checkForHMM()
{
- if (getSelectedHMM() == null)
+ if (viewport.getAlignment().getHmmSequences().isEmpty())
{
JOptionPane.showMessageDialog(this,
- MessageManager.getString("warn.no_selected_hmm"));
+ MessageManager.getString("warn.no_hmm"));
return false;
}
return true;
if (getViewport().getAlignment().getSequences().size() < required)
{
JOptionPane.showMessageDialog(this,
- MessageManager.getString("warn.not_enough_sequences"));
+ MessageManager.getString("label.not_enough_sequences"));
return false;
}
return true;
}
+ /**
+ * Opens a file browser and adds the selected file, if in Fasta, Stockholm or
+ * Pfam format, to the list held under preference key "HMMSEARCH_DBS" (as a
+ * comma-separated list)
+ */
+ @Override
+ public void addDatabase_actionPerformed() throws IOException
+ {
+ if (Cache.getProperty(Preferences.HMMSEARCH_DBS) == null)
+ {
+ Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
+ }
+
+ String path = openFileChooser(false);
+ if (path != null && new File(path).exists())
+ {
+ IdentifyFile identifier = new IdentifyFile();
+ FileFormatI format = identifier.identify(path, DataSourceType.FILE);
+ if (format == FileFormat.Fasta || format == FileFormat.Stockholm
+ || format == FileFormat.Pfam)
+ {
+ String currentDbPaths = Cache
+ .getProperty(Preferences.HMMSEARCH_DBS);
+ currentDbPaths += Preferences.COMMA + path;
+ Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths);
+ }
+ else
+ {
+ JOptionPane.showMessageDialog(this,
+ MessageManager.getString("warn.invalid_format"));
+ }
+ }
+ }
+
+ /**
+ * Opens a file chooser, optionally restricted to selecting folders
+ * (directories) only. Answers the path to the selected file or folder, or
+ * null if none is chosen.
+ *
+ * @param
+ * @return
+ */
+ protected String openFileChooser(boolean forFolder)
+ {
+ // TODO duplicates GPreferences method - relocate to JalviewFileChooser?
+ String choice = null;
+ JFileChooser chooser = new JFileChooser();
+ if (forFolder)
+ {
+ chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+ }
+ chooser.setDialogTitle(
+ MessageManager.getString("label.open_local_file"));
+ chooser.setToolTipText(MessageManager.getString("action.open"));
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JFileChooser.APPROVE_OPTION)
+ {
+ choice = chooser.getSelectedFile().getPath();
+ }
+ return choice;
+ }
+
@Override
public void reload_actionPerformed(ActionEvent e)
{
@Override
public void exportFeatures_actionPerformed(ActionEvent e)
{
- new AnnotationExporter().exportFeatures(alignPanel);
+ new AnnotationExporter(alignPanel).exportFeatures();
}
@Override
public void exportAnnotations_actionPerformed(ActionEvent e)
{
- new AnnotationExporter().exportAnnotations(alignPanel);
+ new AnnotationExporter(alignPanel).exportAnnotations();
}
@Override
}
viewport.getAlignment().moveSelectedSequencesByOne(sg,
viewport.getHiddenRepSequences(), up);
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
synchronized void slideSequences(boolean right, int size)
@Override
protected void copy_actionPerformed(ActionEvent e)
{
- System.gc();
if (viewport.getSelectionGroup() == null)
{
return;
return;
}
- ArrayList<int[]> hiddenColumns = null;
+ HiddenColumns hiddenColumns = null;
if (viewport.hasHiddenColumns())
{
- hiddenColumns = new ArrayList<>();
-
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
- ArrayList<int[]> hiddenRegions = viewport.getAlignment()
- .getHiddenColumns().getHiddenColumnsCopy();
- for (int[] region : hiddenRegions)
- {
- if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
- {
- hiddenColumns
- .add(new int[]
- { region[0] - hiddenOffset, region[1] - hiddenOffset });
- }
- }
+ // create new HiddenColumns object with copy of hidden regions
+ // between startRes and endRes, offset by startRes
+ hiddenColumns = new HiddenColumns(
+ viewport.getAlignment().getHiddenColumns(), hiddenOffset,
+ hiddenCutoff, hiddenOffset);
}
Desktop.jalviewClipboard = new Object[] { seqs,
{
// propagate alignment changed.
- vpRanges.setEndSeq(alignment.getHeight());
+ viewport.getRanges().setEndSeq(alignment.getHeight());
if (annotationAdded)
{
// Duplicate sequence annotation in all views.
if (Desktop.jalviewClipboard != null
&& Desktop.jalviewClipboard[2] != null)
{
- List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
- for (int[] region : hc)
- {
- af.viewport.hideColumns(region[0], region[1]);
- }
+ HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
+ af.viewport.setHiddenColumns(hc);
}
// >>>This is a fix for the moment, until a better solution is
if (Desktop.jalviewClipboard != null
&& Desktop.jalviewClipboard[2] != null)
{
- List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
- for (int region[] : hc)
- {
- af.viewport.hideColumns(region[0], region[1]);
- }
+ HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
+ af.viewport.setHiddenColumns(hc);
}
// >>>This is a fix for the moment, until a better solution is
{
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.setSelectionGroup(null);
viewport.getColumnSelection().clear();
viewport.setSelectionGroup(null);
- alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
alignPanel.getIdPanel().getIdCanvas().searchResults = null;
// 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();
}
// alignPanel to decide if overview needs
// updating.
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
public void invertColSel_actionPerformed(ActionEvent e)
{
viewport.invertColumnSelection();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
viewport.sendSelection();
}
{
trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
column, viewport.getAlignment());
- vpRanges.setStartRes(0);
+ viewport.getRanges().setStartRes(0);
}
else
{
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
- int startRes = seq.findPosition(vpRanges.getStartRes());
+ ViewportRanges ranges = viewport.getRanges();
+ int startRes = seq.findPosition(ranges.getStartRes());
// ShiftList shifts;
// viewport.getAlignment().removeGaps(shifts=new ShiftList());
// edit.alColumnChanges=shifts.getInverse();
// if (viewport.hasHiddenColumns)
// viewport.getColumnSelection().compensateForEdits(shifts);
- vpRanges.setStartRes(seq.findIndex(startRes) - 1);
+ ranges.setStartRes(seq.findIndex(startRes) - 1);
viewport.firePropertyChange("alignment", null,
viewport.getAlignment().getSequences());
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
- int startRes = seq.findPosition(vpRanges.getStartRes());
+ int startRes = seq.findPosition(viewport.getRanges().getStartRes());
addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
viewport.getAlignment()));
- vpRanges.setStartRes(seq.findIndex(startRes) - 1);
+ viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
viewport.firePropertyChange("alignment", null,
viewport.getAlignment().getSequences());
/*
* Create a new AlignmentPanel (with its own, new Viewport)
*/
- AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
- true);
+ AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
if (!copyAnnotation)
{
/*
alignPanel.getIdPanel().getIdCanvas()
.setPreferredSize(alignPanel.calculateIdWidth());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
@Override
public void idRightAlign_actionPerformed(ActionEvent e)
{
viewport.setRightAlignIds(idRightAlign.isSelected());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
@Override
public void centreColumnLabels_actionPerformed(ActionEvent e)
{
viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
/*
protected void colourTextMenuItem_actionPerformed(ActionEvent e)
{
viewport.setColourText(colourTextMenuItem.isSelected());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
/**
public void showAllColumns_actionPerformed(ActionEvent e)
{
viewport.showAllHiddenColumns();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
viewport.expandColSelection(sg, false);
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
{
viewport.showAllHiddenColumns();
viewport.showAllHiddenSeqs();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
public void hideSelColumns_actionPerformed(ActionEvent e)
{
viewport.hideSelectedColumns();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
protected void scaleAbove_actionPerformed(ActionEvent e)
{
viewport.setScaleAboveWrapped(scaleAbove.isSelected());
- alignPanel.paintAlignment(true);
+ // TODO: do we actually need to update overview for scale above change ?
+ alignPanel.paintAlignment(true, false);
}
/**
protected void scaleLeft_actionPerformed(ActionEvent e)
{
viewport.setScaleLeftWrapped(scaleLeft.isSelected());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
/**
protected void scaleRight_actionPerformed(ActionEvent e)
{
viewport.setScaleRightWrapped(scaleRight.isSelected());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
/**
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
/**
public void viewTextMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowText(viewTextMenuItem.isSelected());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
/**
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
{
viewport.setRenderGaps(renderGapsMenuItem.isSelected());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
public FeatureSettings featureSettings;
public void showSeqFeatures_actionPerformed(ActionEvent evt)
{
viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
}
/**
viewport.setGlobalColourScheme(cs);
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
}
/**
viewport.getAlignment().getSequenceAt(0));
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
/**
AlignmentSorter.sortByID(viewport.getAlignment());
addHistoryItem(
new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
/**
AlignmentSorter.sortByLength(viewport.getAlignment());
addHistoryItem(new OrderCommand("Length Sort", oldOrder,
viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
/**
addHistoryItem(new OrderCommand("Group Sort", oldOrder,
viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
/**
addHistoryItem(new OrderCommand(order.getName(), oldOrder,
viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
});
}
viewport.getAlignment());// ,viewport.getSelectionGroup());
addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
});
}
}
if (viewport.getAlignment().getAlignmentAnnotation()
- .hashCode() != _annotationScoreVectorHash)
+ .hashCode() == _annotationScoreVectorHash)
{
- sortByAnnotScore.removeAll();
- // almost certainly a quicker way to do this - but we keep it simple
- Hashtable scoreSorts = new Hashtable();
- AlignmentAnnotation aann[];
- for (SequenceI sqa : viewport.getAlignment().getSequences())
+ return;
+ }
+
+ sortByAnnotScore.removeAll();
+ Set<String> scoreSorts = new HashSet<>();
+ for (SequenceI sqa : viewport.getAlignment().getSequences())
+ {
+ AlignmentAnnotation[] anns = sqa.getAnnotation();
+ for (int i = 0; anns != null && i < anns.length; i++)
{
- aann = sqa.getAnnotation();
- for (int i = 0; aann != null && i < aann.length; i++)
+ AlignmentAnnotation aa = anns[i];
+ if (aa != null && aa.hasScore() && aa.sequenceRef != null)
{
- if (aann[i].hasScore() && aann[i].sequenceRef != null)
- {
- scoreSorts.put(aann[i].label, aann[i].label);
- }
+ scoreSorts.add(aa.label);
}
}
- Enumeration labels = scoreSorts.keys();
- while (labels.hasMoreElements())
- {
- addSortByAnnotScoreMenuItem(sortByAnnotScore,
- (String) labels.nextElement());
- }
- sortByAnnotScore.setVisible(scoreSorts.size() > 0);
- scoreSorts.clear();
-
- _annotationScoreVectorHash = viewport.getAlignment()
- .getAlignmentAnnotation().hashCode();
}
+ for (String label : scoreSorts)
+ {
+ addSortByAnnotScoreMenuItem(sortByAnnotScore, label);
+ }
+ sortByAnnotScore.setVisible(!scoreSorts.isEmpty());
+
+ _annotationScoreVectorHash = viewport.getAlignment()
+ .getAlignmentAnnotation().hashCode();
}
/**
addHistoryItem(new OrderCommand(undoname, oldOrder,
viewport.getAlignment()));
}
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
return true;
}
protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
final String source)
{
- new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
+ new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
.start();
}
// Java's Transferable for native dnd
evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
Transferable t = evt.getTransferable();
- List<String> files = new ArrayList<>();
+ final AlignFrame thisaf = this;
+ final List<String> files = new ArrayList<>();
List<DataSourceType> protocols = new ArrayList<>();
try
}
if (files != null)
{
- try
+ new Thread(new Runnable()
{
- // check to see if any of these files have names matching sequences in
- // the alignment
- SequenceIdMatcher idm = new SequenceIdMatcher(
- viewport.getAlignment().getSequencesArray());
- /**
- * Object[] { String,SequenceI}
- */
- ArrayList<Object[]> filesmatched = new ArrayList<>();
- ArrayList<String> filesnotmatched = new ArrayList<>();
- for (int i = 0; i < files.size(); i++)
+ @Override
+ public void run()
{
- String file = files.get(i).toString();
- String pdbfn = "";
- DataSourceType protocol = FormatAdapter.checkProtocol(file);
- if (protocol == DataSourceType.FILE)
- {
- File fl = new File(file);
- pdbfn = fl.getName();
- }
- else if (protocol == DataSourceType.URL)
- {
- URL url = new URL(file);
- pdbfn = url.getFile();
- }
- if (pdbfn.length() > 0)
+ try
{
- // attempt to find a match in the alignment
- SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
- int l = 0, c = pdbfn.indexOf(".");
- while (mtch == null && c != -1)
+ // check to see if any of these files have names matching sequences
+ // in
+ // the alignment
+ SequenceIdMatcher idm = new SequenceIdMatcher(
+ viewport.getAlignment().getSequencesArray());
+ /**
+ * Object[] { String,SequenceI}
+ */
+ ArrayList<Object[]> filesmatched = new ArrayList<>();
+ ArrayList<String> filesnotmatched = new ArrayList<>();
+ for (int i = 0; i < files.size(); i++)
{
- do
+ String file = files.get(i).toString();
+ String pdbfn = "";
+ DataSourceType protocol = FormatAdapter.checkProtocol(file);
+ if (protocol == DataSourceType.FILE)
{
- l = c;
- } while ((c = pdbfn.indexOf(".", l)) > l);
- if (l > -1)
- {
- pdbfn = pdbfn.substring(0, l);
+ File fl = new File(file);
+ pdbfn = fl.getName();
}
- mtch = idm.findAllIdMatches(pdbfn);
- }
- if (mtch != null)
- {
- FileFormatI type = null;
- try
+ else if (protocol == DataSourceType.URL)
{
- type = new IdentifyFile().identify(file, protocol);
- } catch (Exception ex)
- {
- type = null;
+ URL url = new URL(file);
+ pdbfn = url.getFile();
}
- if (type != null && type.isStructureFile())
+ if (pdbfn.length() > 0)
{
- filesmatched.add(new Object[] { file, protocol, mtch });
- continue;
+ // attempt to find a match in the alignment
+ SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
+ int l = 0, c = pdbfn.indexOf(".");
+ while (mtch == null && c != -1)
+ {
+ do
+ {
+ l = c;
+ } while ((c = pdbfn.indexOf(".", l)) > l);
+ if (l > -1)
+ {
+ pdbfn = pdbfn.substring(0, l);
+ }
+ mtch = idm.findAllIdMatches(pdbfn);
+ }
+ if (mtch != null)
+ {
+ FileFormatI type = null;
+ try
+ {
+ type = new IdentifyFile().identify(file, protocol);
+ } catch (Exception ex)
+ {
+ type = null;
+ }
+ if (type != null && type.isStructureFile())
+ {
+ filesmatched.add(new Object[] { file, protocol, mtch });
+ continue;
+ }
+ }
+ // File wasn't named like one of the sequences or wasn't a PDB
+ // file.
+ filesnotmatched.add(file);
}
}
- // File wasn't named like one of the sequences or wasn't a PDB file.
- filesnotmatched.add(file);
- }
- }
- int assocfiles = 0;
- if (filesmatched.size() > 0)
- {
- if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
- || JvOptionPane.showConfirmDialog(this,
- MessageManager.formatMessage(
- "label.automatically_associate_structure_files_with_sequences_same_name",
- new Object[]
- { Integer.valueOf(filesmatched.size())
- .toString() }),
- MessageManager.getString(
- "label.automatically_associate_structure_files_by_name"),
- JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
-
- {
- for (Object[] fm : filesmatched)
+ int assocfiles = 0;
+ if (filesmatched.size() > 0)
{
- // try and associate
- // TODO: may want to set a standard ID naming formalism for
- // associating PDB files which have no IDs.
- for (SequenceI toassoc : (SequenceI[]) fm[2])
+ if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
+ || JvOptionPane.showConfirmDialog(thisaf,
+ MessageManager.formatMessage(
+ "label.automatically_associate_structure_files_with_sequences_same_name",
+ new Object[]
+ { Integer.valueOf(filesmatched.size())
+ .toString() }),
+ MessageManager.getString(
+ "label.automatically_associate_structure_files_by_name"),
+ JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
+
{
- PDBEntry pe = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq((String) fm[0],
- (DataSourceType) fm[1], toassoc, false,
- Desktop.instance);
- if (pe != null)
+ for (Object[] fm : filesmatched)
{
- System.err.println("Associated file : " + ((String) fm[0])
- + " with " + toassoc.getDisplayId(true));
- assocfiles++;
+ // try and associate
+ // TODO: may want to set a standard ID naming formalism for
+ // associating PDB files which have no IDs.
+ for (SequenceI toassoc : (SequenceI[]) fm[2])
+ {
+ PDBEntry pe = new AssociatePdbFileWithSeq()
+ .associatePdbWithSeq((String) fm[0],
+ (DataSourceType) fm[1], toassoc, false,
+ Desktop.instance);
+ if (pe != null)
+ {
+ System.err.println("Associated file : "
+ + ((String) fm[0]) + " with "
+ + toassoc.getDisplayId(true));
+ assocfiles++;
+ }
+ }
+ // TODO: do we need to update overview ? only if features are
+ // shown I guess
+ alignPanel.paintAlignment(true, false);
}
}
- alignPanel.paintAlignment(true);
}
- }
- }
- if (filesnotmatched.size() > 0)
- {
- if (assocfiles > 0 && (Cache.getDefault(
- "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
- || JvOptionPane.showConfirmDialog(this,
- "<html>" + MessageManager.formatMessage(
- "label.ignore_unmatched_dropped_files_info",
- new Object[]
- { Integer.valueOf(filesnotmatched.size())
- .toString() })
- + "</html>",
- MessageManager.getString(
- "label.ignore_unmatched_dropped_files"),
- JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
- {
- return;
- }
- for (String fn : filesnotmatched)
+ if (filesnotmatched.size() > 0)
+ {
+ if (assocfiles > 0 && (Cache.getDefault(
+ "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
+ || JvOptionPane.showConfirmDialog(thisaf,
+ "<html>" + MessageManager.formatMessage(
+ "label.ignore_unmatched_dropped_files_info",
+ new Object[]
+ { Integer.valueOf(
+ filesnotmatched.size())
+ .toString() })
+ + "</html>",
+ MessageManager.getString(
+ "label.ignore_unmatched_dropped_files"),
+ JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
+ {
+ return;
+ }
+ for (String fn : filesnotmatched)
+ {
+ loadJalviewDataFile(fn, null, null, null);
+ }
+
+ }
+ } catch (Exception ex)
{
- loadJalviewDataFile(fn, null, null, null);
+ ex.printStackTrace();
}
-
}
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
+ }).start();
}
}
new JnetAnnotationMaker();
JnetAnnotationMaker.add_annotation(predictions,
viewport.getAlignment(), 0, false);
- SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
- viewport.getAlignment().setSeqrep(repseq);
- HiddenColumns cs = new HiddenColumns();
- cs.hideInsertionsFor(repseq);
- viewport.getAlignment().setHiddenColumns(cs);
+ viewport.getAlignment().setupJPredAlignment();
isAnnotation = true;
}
// else if (IdentifyFile.FeaturesFile.equals(format))
{
if (parseFeaturesFile(file, sourceType))
{
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
}
}
else
alignPanel.adjustAnnotationHeight();
viewport.updateSequenceIdColours();
buildSortByAnnotationScoresMenu();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
}
} catch (Exception ex)
{
MessageManager.getString("option.trim_retrieved_seqs"));
trimrs.setToolTipText(
MessageManager.getString("label.trim_retrieved_sequences"));
- trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
+ trimrs.setSelected(
+ Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
trimrs.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
trimrs.setSelected(trimrs.isSelected());
- Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
+ Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
Boolean.valueOf(trimrs.isSelected()).toString());
};
});
protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowUnconserved(showNonconservedMenuItem.getState());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
/*
}
@Override
- protected void showInformationHistogram_actionPerformed(ActionEvent e)
- {
- viewport.setShowInformationHistogram(
- showInformationHistogram.getState());
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
- }
-
- @Override
- protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
- {
- viewport.setShowHMMSequenceLogo(showHMMSequenceLogo.getState());
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
- }
-
- @Override
- protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
- {
- showHMMSequenceLogo.setState(true);
- viewport.setShowHMMSequenceLogo(true);
- viewport.setNormaliseHMMSequenceLogo(normaliseSequenceLogo.getState());
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
- }
-
- @Override
protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
{
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
{
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
}
}
viewport.getAlignment().setSeqrep(null);
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
}
}
this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
this.alignPanel.av
.setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
/**
/**
* Sets the status of the HMMER menu
- *
- * @param status
*/
- public void updateHMMERStatus(boolean status)
+ public void updateHMMERStatus()
{
- hmmerMenu.setEnabled(status);
- }
-
- /**
- * Returns the selected hidden Markov model.
- *
- * @return
- */
- public HiddenMarkovModel getSelectedHMM()
- {
- if (selectedHMMSequence == null)
- {
- return null;
- }
- return selectedHMMSequence.getHMM();
- }
-
- /**
- * Returns the selected hidden Markov model.
- *
- * @return
- */
- public SequenceI getSelectedHMMSequence()
- {
- return selectedHMMSequence;
- }
-
- /**
- * Sets the selected hidden Markov model
- *
- * @param selectedHMM
- */
- public void setSelectedHMMSequence(SequenceI selectedHMM)
- {
- this.selectedHMMSequence = selectedHMM;
- hmmAlign.setText(MessageManager.getString("label.hmmalign") + " to "
- + selectedHMM.getHMM().getName() + "_HMM");
- hmmSearch.setText(MessageManager.getString("label.hmmsearch") + " with "
- + selectedHMM.getHMM().getName() + "_HMM");
+ hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
}
@Override
}
}
+ @Override
+ protected void loadVcf_actionPerformed()
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ Cache.getProperty("LAST_DIRECTORY"));
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
+ chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
+
+ int value = chooser.showOpenDialog(null);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ Cache.setProperty("LAST_DIRECTORY", choice);
+ SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
+ new VCFLoader(choice).loadVCF(seqs, this);
+ }
+
+ }
}
class PrintThread extends Thread
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