Skip to content

Commit

Permalink
bug fixes
Browse files Browse the repository at this point in the history
  • Loading branch information
@jrobinso
jrobinso committed Nov 28, 2023
1 parent 62d311c commit 752375e
Show file tree
Hide file tree
Showing 7 changed files with 84 additions and 113 deletions.
5 changes: 4 additions & 1 deletion src/main/java/org/broad/igv/feature/genome/GenomeManager.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,7 @@
import org.broad.igv.ui.PanelName;
import org.broad.igv.ui.commandbar.GenomeListManager;
import org.broad.igv.ui.panel.FrameManager;
import org.broad.igv.ui.panel.ReferenceFrame;
import org.broad.igv.ui.util.MessageUtils;
import org.broad.igv.ui.util.ProgressBar;
import org.broad.igv.ui.util.ProgressMonitor;
Expand All @@ -72,6 +73,7 @@
import java.net.SocketException;
import java.net.URL;
import java.net.URLDecoder;
import java.sql.Ref;
import java.util.*;
import java.util.List;

Expand Down Expand Up @@ -231,8 +233,9 @@ public Genome loadGenome(String genomePath, ProgressMonitor monitor) throws IOEx

// hasInstance() test needed for unit tests
if (IGV.hasInstance()) {
IGV.getInstance().goToLocus(newGenome.getDefaultPos());
IGV.getInstance().goToLocus(newGenome.getHomeChromosome()); // newGenome.getDefaultPos());
loadGenomeAnnotations(newGenome);
IGV.getInstance().resetFrames();
}

if (PreferencesManager.getPreferences().getAsBoolean(Constants.CIRC_VIEW_ENABLED) && CircularViewUtilities.ping()) {
Expand Down
25 changes: 11 additions & 14 deletions src/main/java/org/broad/igv/ui/IGV.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -259,7 +259,7 @@ public void windowGainedFocus(WindowEvent windowEvent) {
subscribeToEvents();

// Start running periodic autosaves (unless the user has specified not to retain timed autosaves)
if(PreferencesManager.getPreferences().getAsInt(Constants.AUTOSAVES_TO_KEEP) > 0) {
if (PreferencesManager.getPreferences().getAsInt(Constants.AUTOSAVES_TO_KEEP) > 0) {
int timerDelay = PreferencesManager.getPreferences().getAsInt(AUTOSAVE_FREQUENCY) * 60000; // Convert timer delay to ms
sessionAutosaveTimer.scheduleAtFixedRate(new AutosaveTimerTask(this), timerDelay, timerDelay);
}
Expand Down Expand Up @@ -515,11 +515,10 @@ final public void saveStateForExit() {
this.stopTimedAutosave();

// Autosave current session if configured to do so
if(PreferencesManager.getPreferences().getAsBoolean(AUTOSAVE_ON_EXIT)) {
if (PreferencesManager.getPreferences().getAsBoolean(AUTOSAVE_ON_EXIT)) {
try {
SessionAutosaveManager.saveExitSessionAutosaveFile(session);
}
catch(Exception e) {
} catch (Exception e) {
log.error("Error autosaving session", e);
}
}
Expand Down Expand Up @@ -885,9 +884,9 @@ public boolean scrollToTrack(String trackName) {
if (tp.getScrollPane().getNamePanel().scrollTo(trackName)) {
found = true;
}
}
return found;
}
return found;
}


/**
Expand Down Expand Up @@ -1238,7 +1237,7 @@ public List<Track> load(ResourceLocator locator) throws DataLoadException {
track.setAttributeValue(Globals.TRACK_DATA_TYPE_ATTRIBUTE, track.getTrackType().toString());

TrackProperties properties = locator.getTrackProperties();
if(properties != null) {
if (properties != null) {
track.setProperties(properties);
}
}
Expand Down Expand Up @@ -1287,7 +1286,7 @@ public TrackPanel getPanelFor(Track track) {
}
}

if(track.getClass() == FeatureTrack.class && !PreferencesManager.getPreferences().getAsBoolean(SHOW_SINGLE_TRACK_PANE_KEY))
if (track.getClass() == FeatureTrack.class && !PreferencesManager.getPreferences().getAsBoolean(SHOW_SINGLE_TRACK_PANE_KEY))
return getTrackPanel(FEATURE_PANEL_NAME);
else {
return getTrackPanel(DATA_PANEL_NAME);
Expand Down Expand Up @@ -1365,7 +1364,7 @@ public void sortAlignmentTracks(SortOption option, String tag, final boolean inv
public void sortAlignmentTracks(SortOption option, Double location, String tag, boolean invertSort, Set<String> priorityRecords) {
List<AlignmentTrack> alignmentTracks = getAllTracks().stream()
.filter(track -> track instanceof AlignmentTrack)
.map(track -> (AlignmentTrack)track)
.map(track -> (AlignmentTrack) track)
.peek(track -> track.sortRows(option, location, tag, invertSort, priorityRecords))
.collect(Collectors.toList());
this.repaint(alignmentTracks);
Expand Down Expand Up @@ -1900,8 +1899,7 @@ public void run() {
boolean autosavePresent = false;
try {
autosavePresent = SessionAutosaveManager.getMostRecentAutosaveFile().isPresent();
}
catch(Exception e) {
} catch (Exception e) {
log.error("Failure trying to get most recent autosave file", e);
}
boolean loadAutosave = autosavePresent && PreferencesManager.getPreferences().getAsBoolean(AUTOLOAD_LAST_AUTOSAVE);
Expand All @@ -1918,7 +1916,7 @@ public void run() {
}
}
// If we're not loading a session file, attempt to load a default genome file
if(igvArgs.getSessionFile() == null && !loadAutosave && !genomeLoaded) {
if (igvArgs.getSessionFile() == null && !loadAutosave && !genomeLoaded) {
String genomeId = preferences.getDefaultGenome();
try {
GenomeManager.getInstance().loadGenomeById(genomeId);
Expand Down Expand Up @@ -2041,8 +2039,7 @@ public void run() {
// Get the last autosave and attempt to load
File sessionAutosave = SessionAutosaveManager.getMostRecentAutosaveFile().get();
success = loadSession(sessionAutosave.getAbsolutePath(), null);
}
catch(Exception e) {
} catch (Exception e) {
log.error("Failure trying to load most recent autosave file", e);
}

Expand Down
137 changes: 54 additions & 83 deletions src/main/java/org/broad/igv/ui/action/SearchCommand.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -70,36 +70,10 @@ public class SearchCommand implements Runnable {
Genome genome;


private static HashMap<ResultType, String> tokenMatchers;
private static HashMap<String, ResultType> tokenMatchers;

static {

//Regexp for a number with commas in it (no periods)
String num_withcommas = "(((\\d)+,?)+)";

//chromosome can include anything except whitespace
String chromo_string = "(\\S)+";

String chromo = chromo_string;
//This will match chr1:1-100, chr1:1, chr1 1, chr1 1 100
String chromo_range = chromo_string + "(:|(\\s)+)" + num_withcommas + "(-|(\\s)+)?" + num_withcommas + "?(\\s)*";

//Simple feature
String feature = chromo_string;
//Amino acid mutation notation. e.g. KRAS:G12C. * is stop codon
String featureMutAA = chromo_string + ":[A-Z,a-z,*]" + num_withcommas + "[A-Z,a-z,*]";

//Nucleotide mutation notation. e.g. KRAS:123A>T
String nts = "[A,C,G,T,a,c,g,t]";
String featureMutNT = chromo_string + ":" + num_withcommas + nts + "\\>" + nts;

tokenMatchers = new HashMap<ResultType, String>();
tokenMatchers.put(ResultType.CHROMOSOME, chromo);
tokenMatchers.put(ResultType.FEATURE, feature);
tokenMatchers.put(ResultType.LOCUS, chromo_range);
tokenMatchers.put(ResultType.FEATURE_MUT_AA, featureMutAA);
tokenMatchers.put(ResultType.FEATURE_MUT_NT, featureMutNT);
}
static String featureMutAA = "(\\S)+" + ":[A-Z,a-z,*]" + "(((\\d)+,?)+)" + "[A-Z,a-z,*]";
static String featureMutNT = "(\\S)+" + ":" + "(\\S)+" + "[A,C,G,T,a,c,g,t]" + "\\>" + "[A,C,G,T,a,c,g,t]";


public SearchCommand(ReferenceFrame referenceFrame, String searchString) {
Expand Down Expand Up @@ -166,10 +140,10 @@ public List<SearchResult> runSearch(String searchString) {
}
if (mightBeLocus) {
Chromosome c1 = genome.getChromosome(tokens[0]);
if(c1 != null) {
if (c1 != null) {
Chromosome c2 = genome.getChromosome(tokens[1]);
if(c2 == null) {
results.add (calcChromoLocus(searchString));
if (c2 == null) {
results.add(calcChromoLocus(searchString));
return results;
}
}
Expand All @@ -184,8 +158,6 @@ public List<SearchResult> runSearch(String searchString) {
}




// If this is a liftover search map the results
// if (liftover != null) {
// List<SearchResult> mappedResults = new ArrayList<>();
Expand Down Expand Up @@ -232,23 +204,23 @@ public void showSearchResult(List<SearchResult> results) {
showFlankedRegion(result.chr, result.start, result.end);
break;
case LOCUS:

Chromosome chromosome = GenomeManager.getInstance().getCurrentGenome().getChromosome(result.chr);
if (chromosome == null) {
message = "Unknow chromosome: " + result.chr;
success = false;
showMessage = true;
} else if (result.start > chromosome.getLength()) {
message = "Range " + result.locus + " is beyond the end of the chromosome";
success = false;
showMessage = true;
if (result.chr.equalsIgnoreCase(Globals.CHR_ALL)) {
referenceFrame.changeChromosome(Globals.CHR_ALL, false);
} else {
referenceFrame.jumpTo(result.chr, result.start, result.end);
Chromosome chromosome = GenomeManager.getInstance().getCurrentGenome().getChromosome(result.chr);
if (chromosome == null) {
message = "Unknow chromosome: " + result.chr;
success = false;
showMessage = true;
} else if (result.start > chromosome.getLength()) {
message = "Range " + result.locus + " is beyond the end of the chromosome";
success = false;
showMessage = true;
} else {
referenceFrame.jumpTo(result.chr, result.start, result.end);
}
}
break;
case CHROMOSOME:
referenceFrame.changeChromosome(result.chr, true);
break;
case ERROR:
default: {
message = "Cannot find feature or locus: " + searchString;
Expand Down Expand Up @@ -321,9 +293,9 @@ public static Object[] getSelectionList(List<SearchResult> results, boolean long
Set<ResultType> checkTokenType(String token) {
token = token.trim();
Set<ResultType> possibles = new HashSet<>();
for (ResultType type : tokenMatchers.keySet()) {
if (token.matches(tokenMatchers.get(type))) { //note: entire string must match
possibles.add(type);
for (String key : tokenMatchers.keySet()) {
if (token.matches(key)) {
possibles.add(tokenMatchers.get(key));
}
}
return possibles;
Expand All @@ -343,32 +315,26 @@ private SearchResult parseToken(String token) {
return new SearchResult(feat);
}

//Guess at token type via regex.
//We don't assume success
Set<ResultType> types = checkTokenType(token);

if (types.contains(ResultType.LOCUS) || types.contains(ResultType.CHROMOSOME)) {
//Check if a full or partial locus string
SearchResult result = calcChromoLocus(token);
if (result != null) {
return result;
}
//Check if a full or partial locus string
SearchResult result = calcChromoLocus(token);
if (result != null) {
return result;
}


if (types.contains(ResultType.FEATURE)) {
//Check if we have an exact match for the feature name
List<Track> searchableTracks = IGV.getInstance().getAllTracks().stream().filter(Track::isSearchable).toList();
for (Track t : searchableTracks) {
NamedFeature match = t.search(token);
if (match != null) {
return new SearchResult(match);
}
//Check if we have an exact match for the feature name
List<Track> searchableTracks = IGV.getInstance().getAllTracks().stream().filter(Track::isSearchable).toList();
for (Track t : searchableTracks) {
NamedFeature match = t.search(token);
if (match != null) {
return new SearchResult(match);
}
}

//2 possible mutation notations, either amino acid (A123B) or nucleotide (123G>C)
if (types.contains(ResultType.FEATURE_MUT_AA) || types.contains(ResultType.FEATURE_MUT_NT)) {
boolean mutAA = token.matches(featureMutAA);
boolean mutNT = token.matches(featureMutNT);
if (mutAA || mutNT) {
//We know it has the right form, but may
//not be valid feature name or mutation
//which exists.
Expand All @@ -380,15 +346,15 @@ private SearchResult parseToken(String token) {
Map<Integer, BasicFeature> genomePosList;

//Should never match both mutation notations
if (types.contains(ResultType.FEATURE_MUT_AA)) {
if (mutAA) {
String refSymbol = coords.substring(0, 1);
String mutSymbol = coords.substring(coordLength - 1);

String strLoc = coords.substring(1, coordLength - 1);
int location = Integer.parseInt(strLoc) - 1;

genomePosList = FeatureDB.getMutationAA(name, location + 1, refSymbol, mutSymbol, genome);
} else if (types.contains(ResultType.FEATURE_MUT_NT)) {
} else if (mutNT) {
//Exclude the "A>T" at end
String strLoc = coords.substring(0, coordLength - 3);
String refSymbol = coords.substring(coordLength - 3, coordLength - 2);
Expand Down Expand Up @@ -470,18 +436,24 @@ private SearchResult calcChromoLocus(String searchString) {
int colonIdx = searchString.lastIndexOf(":");
if (colonIdx > 0) {
chr = searchString.substring(0, colonIdx);
String posString = searchString.substring(colonIdx).replace(":", "");
startEnd = getStartEnd(posString);
//This MAY for case of chromoname having semicolon in it
if (startEnd == null) {
chr = searchString;
Chromosome chromosome = genome.getChromosome(chr);
if (chromosome == null) {
// try entire search string, chr name may have embedded colon
if (genome.getChromosome(searchString) != null) {
chr = searchString;
startEnd = null;
}
} else {
String posString = searchString.substring(colonIdx).replace(":", "");
startEnd = getStartEnd(posString);

}
}
}

// Show the "All chromosomes" view if the search string is "*"
if (chr.equals("*") || chr.toLowerCase().equals("all")) {
return new SearchResult(ResultType.CHROMOSOME, Globals.CHR_ALL, 0, 1);
return new SearchResult(ResultType.LOCUS, Globals.CHR_ALL, 0, Integer.MAX_VALUE);
}

//startEnd will have coordinates if found.
Expand All @@ -498,12 +470,14 @@ private SearchResult calcChromoLocus(String searchString) {
}

if (chromosome != null && !searchString.equals(Globals.CHR_ALL)) {
if (startEnd != null) {
chr = chromosome.getName();
if (startEnd == null) {
return new SearchResult(ResultType.LOCUS, chr, 0, chromosome.getLength());
} else {
int start = Math.min(startEnd[0], startEnd[1]);
int end = Math.max(startEnd[0], startEnd[1]);
return new SearchResult(ResultType.LOCUS, chr, start, end);
}
return new SearchResult(ResultType.CHROMOSOME, chr, 0, chromosome.getLength() - 1);
}
return null;
}
Expand Down Expand Up @@ -562,10 +536,7 @@ private static int[] getStartEnd(String posString) {

public enum ResultType {
FEATURE,
FEATURE_MUT_AA,
FEATURE_MUT_NT,
LOCUS,
CHROMOSOME,
ERROR,
LIFTOVER
}
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/org/broad/igv/ui/commandbar/IGVCommandBar.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -328,7 +328,7 @@ public void searchByLocus(final String searchText) {

if ((searchText != null) && (searchText.length() > 0)) {
String homeChr = GenomeManager.getInstance().getCurrentGenome().getHomeChromosome();
if (searchText.equalsIgnoreCase("home") || searchText.equalsIgnoreCase(homeChr)) {
if (searchText.equalsIgnoreCase("home")) {
homeButtonActionPerformed(null);
} else {
searchTextField.setText(searchText);
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/org/broad/igv/ui/panel/HeaderPanel.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -94,7 +94,7 @@ private void init() {
geneListPanel.setPreferredSize(new java.awt.Dimension(0, 0));
geneListPanel.setLayout(new java.awt.BorderLayout());

label = new JLabel(frame.getName());
label = new JLabel(frame.getFormattedLocusString());
label.setForeground(Color.blue);
label.setToolTipText("Go to " + frame.getName());
label.addMouseListener(new MouseAdapter() {
Expand Down
8 changes: 4 additions & 4 deletions src/main/java/org/broad/igv/ui/panel/ReferenceFrame.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -635,13 +635,13 @@ public int getMidpoint() {
*/
public String getFormattedLocusString() {

if (zoom == 0) {
return getGenome().getChromosomeDisplayName(getChrName());
} else {
// if (zoom == 0) {
// return getGenome().getChromosomeDisplayName(getChrName());
// } else {
Range range = getCurrentRange();
String c = getGenome().getChromosomeDisplayName(range.getChr());
return Locus.getFormattedLocusString(c, range.getStart(), range.getEnd());
}
// }
}

public Range getCurrentRange() {
Expand Down
Loading

0 comments on commit 752375e

Please sign in to comment.