import jalview.analysis.AlignmentUtils;
import jalview.analysis.CrossRef;
import jalview.analysis.Dna;
+import jalview.analysis.GeneticCodeI;
import jalview.analysis.ParseProperties;
import jalview.analysis.SequenceIdMatcher;
import jalview.api.AlignExportSettingI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureSettingsControllerI;
+import jalview.api.FeatureSettingsModelI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
import jalview.api.analysis.SimilarityParamsI;
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.hmmer.HMMERPreset;
import jalview.hmmer.HMMSearch;
import jalview.hmmer.HmmerCommand;
+import jalview.hmmer.JackHMMER;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
+import jalview.io.BackupFiles;
import jalview.io.BioJsHTMLOutput;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.schemes.ResidueColourScheme;
import jalview.schemes.TCoffeeColourScheme;
import jalview.util.MessageManager;
-import jalview.util.StringUtils;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.ViewportRanges;
import jalview.ws.DBRefFetcher;
import jalview.ws.params.ParamDatastoreI;
import jalview.ws.params.WsParamSetI;
import jalview.ws.seqfetcher.DbSourceProxy;
+import jalview.ws.slivkaws.SlivkaWSDiscoverer;
import java.awt.BorderLayout;
import java.awt.Component;
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.Scanner;
+import java.util.Set;
import java.util.Vector;
+import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JEditorPane;
import javax.swing.JFileChooser;
-import javax.swing.JFrame;
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;
AlignViewport viewport;
public AlignViewControllerI avc;
- /*
- * The selected HMM for this align frame
- */
- SequenceI selectedHMMSequence;
List<AlignmentPanel> alignPanels = new ArrayList<>();
int aSize = alignPanels.size();
- tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
+ tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
- if (aSize == 1 && ap.av.viewName == null)
+ if (aSize == 1 && ap.av.getViewName() == null)
{
this.getContentPane().add(ap, BorderLayout.CENTER);
}
expandViews.setEnabled(true);
gatherViews.setEnabled(true);
- tabbedPane.addTab(ap.av.viewName, ap);
+ tabbedPane.addTab(ap.av.getViewName(), ap);
ap.setVisible(false);
}
gatherViews.setEnabled(true);
tabbedPane.setVisible(true);
AlignmentPanel first = alignPanels.get(0);
- tabbedPane.addTab(first.av.viewName, first);
+ tabbedPane.addTab(first.av.getViewName(), first);
this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
}
* @param av
* AlignViewport
*/
- void setMenusFromViewport(AlignViewport av)
+ public void setMenusFromViewport(AlignViewport av)
{
padGapsMenuitem.setSelected(av.isPadGaps());
colourTextMenuItem.setSelected(av.isShowColourText());
return progressBar.operationInProgress();
}
+ /**
+ * Sets the text of the status bar. Note that setting a null or empty value
+ * will cause the status bar to be hidden, with possibly undesirable flicker
+ * of the screen layout.
+ */
@Override
public void setStatus(String text)
{
- statusBar.setText(text);
+ statusBar.setText(text == null || text.isEmpty() ? " " : text);
}
/*
}
@Override
- public void hmmBuildSettings_actionPerformed()
+ 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("hmmbuild");
- WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
- args);
- if (params.showRunDialog())
+
+ /*
+ * get default parameters, and optionally show a dialog
+ * to allow them to be modified
+ */
+ ParamDatastoreI store = HMMERParamStore.forBuild(viewport);
+ List<ArgumentI> args = store.getServiceParameters();
+
+ if (!withDefaults)
{
- new Thread(new HMMBuild(this, params.getJobParams())).start();
+ WsParamSetI set = new HMMERPreset();
+ WsJobParameters params = new WsJobParameters(store, set, args);
+ if (params.showRunDialog())
+ {
+ args = params.getJobParams();
+ }
+ else
+ {
+ return; // user cancelled
+ }
}
- alignPanel.repaint();
-
+ new Thread(new HMMBuild(this, args)).start();
}
@Override
- public void hmmAlignSettings_actionPerformed()
+ public void hmmAlign_actionPerformed(boolean withDefaults)
{
if (!(checkForHMM() && alignmentIsSufficient(2)))
{
return;
}
- WsParamSetI set = new HMMERPreset();
- List<ArgumentI> args = new ArrayList<>();
- ParamDatastoreI store = new HMMERParamStore("hmmalign");
- WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
- args);
- if (params.showRunDialog())
+
+ /*
+ * 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)
{
- new Thread(new HMMAlign(this, params.getJobParams()))
- .start();
+ WsParamSetI set = new HMMERPreset();
+ WsJobParameters params = new WsJobParameters(store, set, args);
+ if (params.showRunDialog())
+ {
+ args = params.getJobParams();
+ }
+ else
+ {
+ return; // user cancelled
+ }
}
- alignPanel.repaint();
+ new Thread(new HMMAlign(this, args)).start();
}
@Override
- public void hmmSearchSettings_actionPerformed()
+ public void hmmSearch_actionPerformed(boolean withDefaults)
{
if (!checkForHMM())
{
return;
}
- WsParamSetI set = new HMMERPreset();
- List<ArgumentI> args = new ArrayList<>();
- ParamDatastoreI store = new HMMERParamStore("hmmsearch");
- WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
- args);
- if (params.showRunDialog())
- {
- new Thread(new HMMSearch(this, params.getJobParams()))
- .start();
- }
- alignPanel.repaint();
- }
- @Override
- public void hmmBuildRun_actionPerformed()
- {
- if (!alignmentIsSufficient(1))
- {
- return;
- }
- new Thread(new HMMBuild(this, null))
- .start();
- }
+ /*
+ * get default parameters, and (if requested) show
+ * dialog to allow modification
+ */
+ ParamDatastoreI store = HMMERParamStore.forSearch(viewport);
+ List<ArgumentI> args = store.getServiceParameters();
- @Override
- public void hmmAlignRun_actionPerformed()
- {
- 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
+ }
}
- new Thread(new HMMAlign(this, null)).start();
+ new Thread(new HMMSearch(this, args)).start();
+ alignPanel.repaint();
}
-
+
@Override
- public void hmmSearchRun_actionPerformed()
+ public void jackhmmer_actionPerformed(boolean withDefaults)
{
- if (!checkForHMM())
+
+ /*
+ * get default parameters, and (if requested) show
+ * dialog to allow modification
+ */
+
+ ParamDatastoreI store = HMMERParamStore.forJackhmmer(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 HMMSearch(this, null)).start();
+ new Thread(new JackHMMER(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;
}
+
+ @Override
+ protected void filterByEValue_actionPerformed()
+ {
+ viewport.filterByEvalue(inputDouble("Enter E-Value Cutoff"));
+ }
+
+ @Override
+ protected void filterByScore_actionPerformed()
+ {
+ viewport.filterByScore(inputDouble("Enter Bit Score Threshold"));
+ }
+
+ private double inputDouble(String message)
+ {
+ String str = null;
+ Double d = null;
+ while(d == null || d <= 0)
+ {
+ str = JOptionPane.showInputDialog(this.alignPanel, message);
+ try
+ {
+ d = Double.valueOf(str);
+ }
+ catch (NumberFormatException e)
+ {
+ }
+ }
+ return d;
+ }
/**
* Checks if the alignment contains the required number of sequences.
*/
public boolean alignmentIsSufficient(int required)
{
- if (getViewport().getAlignment().getSequences().size() < required)
- {
- JOptionPane.showMessageDialog(this,
- MessageManager.getString("warn.not_enough_sequences"));
- return false;
- }
- return true;
+ if (getViewport().getSequenceSelection().length < required)
+ {
+ JOptionPane.showMessageDialog(this,
+ 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_DB_PATHS) == null)
+ if (Cache.getProperty(Preferences.HMMSEARCH_DBS) == null)
{
Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
- Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
}
String path = openFileChooser(false);
- if (new File(path).exists())
+ 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 currentDbs = Cache.getProperty(Preferences.HMMSEARCH_DBS);
String currentDbPaths = Cache
- .getProperty(Preferences.HMMSEARCH_DB_PATHS);
- currentDbPaths += " " + path;
-
- String fileName = StringUtils.getLastToken(path, File.separator);
- Scanner scanner = new Scanner(fileName).useDelimiter(".");
- String name = scanner.next();
- scanner.close();
- currentDbs += " " + path; // TODO remove path from file name
- scanner.close();
-
- Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, currentDbPaths);
+ .getProperty(Preferences.HMMSEARCH_DBS);
+ currentDbPaths += Preferences.COMMA + path;
Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths);
}
else
MessageManager.getString("warn.invalid_format"));
}
}
- else
- {
- JOptionPane.showMessageDialog(this,
- MessageManager.getString("warn.not_enough_sequences"));
- }
}
/**
- * Opens a file chooser
+ * 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 forFolder
+ * @param
* @return
*/
protected String openFileChooser(boolean forFolder)
{
+ // TODO duplicates GPreferences method - relocate to JalviewFileChooser?
String choice = null;
JFileChooser chooser = new JFileChooser();
if (forFolder)
shortName.lastIndexOf(java.io.File.separatorChar) + 1);
}
- success = new Jalview2XML().saveAlignment(this, file, shortName);
+ success = new jalview.project.Jalview2XML().saveAlignment(this, file,
+ shortName);
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
}
else
{
+ // create backupfiles object and get new temp filename destination
+ BackupFiles backupfiles = new BackupFiles(file);
+
try
{
- PrintWriter out = new PrintWriter(new FileWriter(file));
+ PrintWriter out = new PrintWriter(
+ new FileWriter(backupfiles.getTempFilePath()));
out.print(output);
out.close();
success = false;
ex.printStackTrace();
}
+
+ backupfiles.setWriteSuccess(success);
+ // do the backup file roll and rename the temp file to actual file
+ success = backupfiles.rollBackupsAndRenameTempFile();
+
}
}
newGraphGroups.add(q, null);
}
newGraphGroups.set(newann.graphGroup,
- new Integer(++fgroup));
+ Integer.valueOf(++fgroup));
}
newann.graphGroup = newGraphGroups.get(newann.graphGroup)
.intValue();
newGraphGroups.add(q, null);
}
newGraphGroups.set(newann.graphGroup,
- new Integer(++fgroup));
+ Integer.valueOf(++fgroup));
}
newann.graphGroup = newGraphGroups.get(newann.graphGroup)
.intValue();
@Override
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
- SequenceGroup sg = new SequenceGroup();
-
- for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
- {
- sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
- }
+ SequenceGroup sg = new SequenceGroup(
+ viewport.getAlignment().getSequences());
sg.setEndRes(viewport.getAlignment().getWidth() - 1);
viewport.setSelectionGroup(sg);
+ viewport.isSelectionGroupChanged(true);
viewport.sendSelection();
// JAL-2034 - should delegate to
// alignPanel to decide if overview needs
/*
* Create a new AlignmentPanel (with its own, new Viewport)
*/
- AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
+ AlignmentPanel newap = new jalview.project.Jalview2XML()
+ .copyAlignPanel(alignPanel);
if (!copyAnnotation)
{
/*
newap.av.setGatherViewsHere(false);
- if (viewport.viewName == null)
+ if (viewport.getViewName() == null)
{
- viewport.viewName = MessageManager
- .getString("label.view_name_original");
+ viewport.setViewName(MessageManager
+ .getString("label.view_name_original"));
}
/*
newap.av.setRedoList(viewport.getRedoList());
/*
+ * copy any visualisation settings that are not saved in the project
+ */
+ newap.av.setColourAppliesToAllGroups(
+ viewport.getColourAppliesToAllGroups());
+
+ /*
* Views share the same mappings; need to deregister any new mappings
* created by copyAlignPanel, and register the new reference to the shared
* mappings
newap.refresh(true); // adjust layout of annotations
}
- newap.av.viewName = getNewViewName(viewTitle);
+ newap.av.setViewName(getNewViewName(viewTitle));
addAlignmentPanel(newap, true);
newap.alignmentChanged();
if (comp instanceof AlignmentPanel)
{
AlignmentPanel ap = (AlignmentPanel) comp;
- if (!existingNames.contains(ap.av.viewName))
+ if (!existingNames.contains(ap.av.getViewName()))
{
- existingNames.add(ap.av.viewName);
+ existingNames.add(ap.av.getViewName());
}
}
}
viewport.setFollowHighlight(state);
if (state)
{
- alignPanel.scrollToPosition(viewport.getSearchResults(), false);
+ alignPanel.scrollToPosition(viewport.getSearchResults());
}
}
viewport.expandColSelection(sg, false);
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
public void hideSelColumns_actionPerformed(ActionEvent e)
{
viewport.hideSelectedColumns();
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
protected void scaleAbove_actionPerformed(ActionEvent e)
{
viewport.setScaleAboveWrapped(scaleAbove.isSelected());
- // TODO: do we actually need to update overview for scale above change ?
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, false);
}
protected void scaleLeft_actionPerformed(ActionEvent e)
{
viewport.setScaleLeftWrapped(scaleLeft.isSelected());
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, false);
}
protected void scaleRight_actionPerformed(ActionEvent e)
{
viewport.setScaleRightWrapped(scaleRight.isSelected());
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, false);
}
alignPanel.setOverviewPanel(null);
};
});
+ if (getKeyListeners().length > 0)
+ {
+ frame.addKeyListener(getKeyListeners()[0]);
+ }
alignPanel.setOverviewPanel(overview);
}
* otherwise set the chosen colour scheme (or null for 'None')
*/
ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
+ viewport,
viewport.getAlignment(), viewport.getHiddenRepSequences());
changeColour(cs);
}
alignPanel.paintAlignment(true, false);
}
+ @Override
+ public void sortEValueMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByEValue(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true, false);
+
+ }
+
+ @Override
+ public void sortBitScoreMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByBitScore(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true, false);
+
+ }
+
/**
* DOCUMENT ME!
*
frameTitle += " from ";
- if (viewport.viewName != null)
+ if (viewport.getViewName() != null)
{
- frameTitle += viewport.viewName + " of ";
+ frameTitle += viewport.getViewName() + " of ";
}
frameTitle += this.title;
}
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();
}
/**
jws2servs.attachWSMenuEntry(webService, me);
for (Jws2Instance sv : jws2servs.getServices())
{
- if (sv.description.toLowerCase().contains("jpred"))
+ if (sv.getName().toLowerCase().contains("jpred"))
{
for (JMenuItem jmi : legacyItems)
{
}
}
build_urlServiceMenu(me.webService);
+
+
+ // TODO Mateusz - follow pattern for adding web service
+ // JMenuItems for slivka-based services
+
+ SlivkaWSDiscoverer slivkaDiscoverer = SlivkaWSDiscoverer.getInstance();
+ slivkaDiscoverer.attachWSMenuEntry(webService, me);
+
+
build_fetchdbmenu(webService);
for (JMenu item : wsmenu)
{
* frame's DNA sequences to their aligned protein (amino acid) equivalents.
*/
@Override
- public void showTranslation_actionPerformed(ActionEvent e)
+ public void showTranslation_actionPerformed(GeneticCodeI codeTable)
{
AlignmentI al = null;
try
{
Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
- al = dna.translateCdna();
+ al = dna.translateCdna(codeTable);
} catch (Exception ex)
{
jalview.bin.Cache.log.error(
af.setFileFormat(this.currentFileFormat);
final String newTitle = MessageManager
.formatMessage("label.translation_of_params", new Object[]
- { this.getTitle() });
+ { this.getTitle(), codeTable.getId() });
af.setTitle(newTitle);
if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
{
int assocfiles = 0;
if (filesmatched.size() > 0)
{
- 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)
-
+ boolean autoAssociate = Cache
+ .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
+ if (!autoAssociate)
+ {
+ String msg = MessageManager.formatMessage(
+ "label.automatically_associate_structure_files_with_sequences_same_name",
+ new Object[]
+ { Integer.valueOf(filesmatched.size())
+ .toString() });
+ String ttl = MessageManager.getString(
+ "label.automatically_associate_structure_files_by_name");
+ int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
+ ttl, JvOptionPane.YES_NO_OPTION);
+ autoAssociate = choice == JvOptionPane.YES_OPTION;
+ }
+ if (autoAssociate)
{
for (Object[] fm : filesmatched)
{
alignPanel.paintAlignment(true, false);
}
}
+ else
+ {
+ /*
+ * add declined structures as sequences
+ */
+ for (Object[] o : filesmatched)
+ {
+ filesnotmatched.add((String) o[0]);
+ }
+ }
}
if (filesnotmatched.size() > 0)
{
if (reply != null)
{
- viewport.viewName = reply;
+ viewport.setViewName(reply);
// TODO warn if reply is in getExistingViewNames()?
tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
}
@Override
public void finished()
{
+
+ for (FeatureSettingsModelI srcSettings : dbRefFetcher
+ .getFeatureSettingsModels())
+ {
+
+ alignPanel.av.mergeFeaturesStyle(srcSettings);
+ }
AlignFrame.this.setMenusForViewport();
}
});
@Override
public void finished()
{
+ FeatureSettingsModelI srcSettings = dassource[0]
+ .getFeatureColourScheme();
+ alignPanel.av.mergeFeaturesStyle(
+ srcSettings);
AlignFrame.this.setMenusForViewport();
}
});
{
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
- alignPanel.paintAlignment(true, true);
+ alignPanel.paintAlignment(true,
+ viewport.needToUpdateStructureViews());
}
}
{
if (avc.createGroup())
{
+ if (applyAutoAnnotationSettings.isSelected())
+ {
+ alignPanel.updateAnnotation(true, false);
+ }
alignPanel.alignmentChanged();
}
}
*/
public List<? extends AlignmentViewPanel> getAlignPanels()
{
- return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+ // alignPanels is never null
+ // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+ return alignPanels;
}
/**
colourMenu.add(textColour);
colourMenu.addSeparator();
- ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
- false);
+ ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
+ viewport.getAlignment(), false);
+ colourMenu.add(annotationColour);
+ bg.add(annotationColour);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
colourMenu.add(modifyConservation);
colourMenu.add(abovePIDThreshold);
colourMenu.add(modifyPID);
- colourMenu.add(annotationColour);
ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
}
- /**
- * 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());
- hmmSearch.setText(MessageManager.getString("label.hmmsearch") + " with "
- + selectedHMM.getHMM().getName());
- }
-
- @Override
- public void hmmerMenu_actionPerformed(ActionEvent e)
- {
- SequenceGroup grp = getViewport().getSelectionGroup();
- if (grp != null)
- {
- hmmBuild.setText(MessageManager.getString("label.hmmbuild") + " from "
- + grp.getName());
- }
- else
- {
- hmmBuild.setText(MessageManager.getString("label.hmmbuild")
- + " from Alignment");
- }
- }
-
@Override
protected void loadVcf_actionPerformed()
{
git://source.jalview.org / jalview.git / blobdiff