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diff --git a/backend/src/main/java/de/thm/calc/CalcCaller.java b/backend/src/main/java/de/thm/calc/CalcCaller.java
index 5c2c6f84bcfaf943dc01a46380721ce044610256..a0bd23ac94fe060a1d1337d0cedd54b6f50ec85e 100644
--- a/backend/src/main/java/de/thm/calc/CalcCaller.java
+++ b/backend/src/main/java/de/thm/calc/CalcCaller.java
@@ -10,6 +10,7 @@ import de.thm.logo.LogoCreator;
import de.thm.misc.ChromosomSizes;
import de.thm.misc.Genome;
import de.thm.positionData.Sites;
+import de.thm.positionData.UserData;
import de.thm.result.ResultCollector;
import de.thm.stat.IndependenceTest;
import de.thm.stat.TestResult;
@@ -68,12 +69,12 @@ public final class CalcCaller {
//////////// Sequencelogo ////////////////
if(createLogo && measuredPositions.getAssembly().equals(Genome.Assembly.hg19)){
- String first = "Measured sites";//TODO FIX measuredPositions.getFilename();
+ String first = ((UserData) measuredPositions).getFilename();
LogoWrapper logoWrapper = new LogoWrapper(measuredPositions,collector, tracks.get(0).getAssembly(), first);
futures.add(exe.submit(logoWrapper));
//String second = randomPositions.getFilename();
- String second = "Random sites";//TODO FIX measuredPositions.getFilename();
+ String second = "Background";
LogoWrapper logoWrapper2 = new LogoWrapper(randomPositions, collector, tracks.get(0).getAssembly(), second);
futures.add(exe.submit(logoWrapper2));
}
diff --git a/backend/src/main/java/de/thm/calc/TestTrackResult.java b/backend/src/main/java/de/thm/calc/TestTrackResult.java
deleted file mode 100644
index d1188350e6aae7e1e7bb8259dab69f926ee8b0d9..0000000000000000000000000000000000000000
--- a/backend/src/main/java/de/thm/calc/TestTrackResult.java
+++ /dev/null
@@ -1,85 +0,0 @@
-package de.thm.calc;
-
-import de.thm.genomeData.tracks.Track;
-
-import java.util.List;
-import java.util.Map;
-
-/**
- * Results of one intersect run with the count of inside values. And depening on the interval type result names and result scores.
- *
- * Created by Michael Menzel on 8/12/15.
- */
-public final class TestTrackResult {
-
-
- private final Map resultNames;
- private final List resultScores;
- private final Track usedInterval;
- private final int in;
- private final int out;
-
-
- /**
- * Constructor
- */
- public TestTrackResult(Track usedInterval, int in, int out) {
- this.usedInterval = usedInterval;
- this.in = in;
- this.out = out;
- this.resultNames = null;
- this.resultScores = null;
- }
-
- /**
- * Constructor
- */
- public TestTrackResult(Track usedInterval, int in, int out, Map names) {
- this.usedInterval = usedInterval;
- this.in = in;
- this.out = out;
- this.resultNames= names;
- this.resultScores = null;
- }
-
- /**
- * Constructor
- */
- public TestTrackResult(Track usedInterval, int in, int out, List scores) {
- this.usedInterval = usedInterval;
- this.in = in;
- this.out = out;
- this.resultNames = null;
- this.resultScores = scores;
- }
-
-
- public Map getResultNames() {
- return resultNames;
- }
-
-
- public List getResultScores() {
- return resultScores;
- }
-
- @Override
- public String toString() {
- return usedInterval.getName() + "\t" + in + "\t" + out;
- }
-
- public int getIn() {
- return in;
- }
-
- public int getOut() { return this.out; }
-
- public Class getType() {
- return getClass();
- }
-
- public Track getUsedTrack() {
- return usedInterval;
- }
-}
-
diff --git a/backend/src/main/java/de/thm/genomeData/sql/DBConnector.java b/backend/src/main/java/de/thm/genomeData/sql/DBConnector.java
index 18be525df7583285140edc37206efe74e775576a..c2278d92e88b7b1101ee657ba5d37c4a3b3e00bd 100644
--- a/backend/src/main/java/de/thm/genomeData/sql/DBConnector.java
+++ b/backend/src/main/java/de/thm/genomeData/sql/DBConnector.java
@@ -40,7 +40,7 @@ public class DBConnector {
while (rs.next()) {
- String assembly = rs.getString("assembly");
+ String assembly = rs.getString("genome_assembly");
Map map = new HashMap<>();
Statement innerstmt = conn.createStatement();
@@ -80,7 +80,7 @@ public class DBConnector {
TrackEntry entry = new TrackEntry(rs.getString("name"),
rs.getString("description"),
rs.getString("directory") + "/" + rs.getString("bed_filename"),
- (rs.getString("bed_format").contains("SCORE") ? "scored" : "inout"),
+ (rs.getString("category").contains("Scored") ? "scored" : "inout"),
rs.getString("genome_assembly"),
rs.getString("cell_line"),
rs.getInt("lines"),
diff --git a/backend/src/main/java/de/thm/genomeData/tracks/FileLoader.java b/backend/src/main/java/de/thm/genomeData/tracks/FileLoader.java
index a7c796b5cf956d440904df94b12359cb3e377268..0dabf8df87e7517c4dc4275b7741979f311e05c0 100644
--- a/backend/src/main/java/de/thm/genomeData/tracks/FileLoader.java
+++ b/backend/src/main/java/de/thm/genomeData/tracks/FileLoader.java
@@ -152,7 +152,7 @@ class FileLoader implements Callable> {
if (type == TrackFactory.Type.inout)
continue;
- if (type == TrackFactory.Type.named)
+ if (type == TrackFactory.Type.Named)
names.add(parts[3].intern());
if (type == TrackFactory.Type.scored) {
@@ -189,13 +189,13 @@ class FileLoader implements Callable> {
if (ends.stream().anyMatch(Objects::isNull))
logger.warn("List of ends is missing something for " + file.getName());
- if ((type == TrackFactory.Type.named || type == TrackFactory.Type.scored) && names.stream().anyMatch(Objects::isNull))
+ if ((type == TrackFactory.Type.Named || type == TrackFactory.Type.scored) && names.stream().anyMatch(Objects::isNull))
logger.warn("List of names is missing something for " + file.getName());
if (type == TrackFactory.Type.scored && scores.stream().anyMatch(Objects::isNull))
logger.warn("List of scores is missing something for " + file.getName());
- if(type != TrackFactory.Type.scored && type != TrackFactory.Type.named) {
+ if(type != TrackFactory.Type.scored && type != TrackFactory.Type.Named) {
for (int i = 0; i < starts.size() - 1; i++)
if (starts.get(i) > starts.get(i + 1)) {
@@ -230,7 +230,7 @@ class FileLoader implements Callable> {
return Optional.of(new InOutTrack(starts, ends, trackEntry));
case scored:
return Optional.of(PositionPreprocessor.preprocessData(new ScoredTrack(starts, ends, names, scores, trackEntry)));
- case named:
+ case Named:
return Optional.of(PositionPreprocessor.preprocessData(new NamedTrack(starts, ends, names, trackEntry)));
case distance:
return Optional.of(new DistanceTrack(starts, trackEntry));
@@ -261,7 +261,7 @@ class FileLoader implements Callable> {
return Optional.of(new InOutTrack(starts, ends, trackEntry));
case scored:
return Optional.of(PositionPreprocessor.preprocessData(new ScoredTrack(starts, ends, names, scores, trackEntry)));
- case named:
+ case Named:
return Optional.of(PositionPreprocessor.preprocessData(new NamedTrack(starts, ends, names, trackEntry)));
case distance:
return Optional.of(new DistanceTrack(starts, trackEntry));
diff --git a/backend/src/main/java/de/thm/genomeData/tracks/TrackFactory.java b/backend/src/main/java/de/thm/genomeData/tracks/TrackFactory.java
index 758472117d3bf3299c1ca902f6b69ed9df6c9cc6..2085ce5623a9bf7eb110e9ac12e8981596e058a1 100644
--- a/backend/src/main/java/de/thm/genomeData/tracks/TrackFactory.java
+++ b/backend/src/main/java/de/thm/genomeData/tracks/TrackFactory.java
@@ -93,11 +93,14 @@ public final class TrackFactory {
if (System.getenv("HOME").contains("menzel")) {
allTracks = connector.getAllTracks(" WHERE directory like '%genetic%' and genome_assembly = 'hg19' ORDER BY lines ASC ");
- allTracks.addAll(connector.getAllTracks("WHERE name like 'ontigs'"));
- allTracks.addAll(connector.getAllTracks("WHERE cell_line like 'K-562' LIMIT 200"));
- //allTracks.addAll(connector.getAllTracks("WHERE cell_line like 'K-562'"));
+ allTracks.addAll(connector.getAllTracks("WHERE genome_assembly = 'hg19' and directory like '%encode%HeLa%'"));
+ //allTracks = connector.getAllTracks("WHERE bed_filename = 'SRX062365.05.bed'");
+ allTracks.addAll(connector.getAllTracks("WHERE name like '%ontigs'"));
//allTracks = connector.getAllTracks(" WHERE genome_assembly = 'hg19' ORDER BY lines ASC LIMIT 3000");
} else {
+
+ allTracks = connector.getAllTracks("WHERE (cell_line NOT like '%GM%' or cell_line like '%GM12878')");
+ /*
allTracks = connector.getAllTracks(" WHERE directory like '%genetic%' and genome_assembly = 'hg19' ORDER BY lines ASC ");
allTracks.addAll(connector.getAllTracks("WHERE cell_line like 'HeLa%'"));
allTracks.addAll(connector.getAllTracks("WHERE cell_line like 'K-562'"));
@@ -106,6 +109,7 @@ public final class TrackFactory {
allTracks.addAll(connector.getAllTracks("WHERE cell_line like '%GM12878%'"));
allTracks.addAll(connector.getAllTracks("WHERE cell_line like '%Hep-G2%'"));
allTracks.addAll(connector.getAllTracks("WHERE cell_line like '%A-549%'"));
+ */
}
logger.info("Trying to load " + allTracks.size() + " tracks");
@@ -166,7 +170,7 @@ public final class TrackFactory {
exe.shutdown();
try {
- int timeout = (System.getenv("HOME").contains("menzel")) ? 60 : 60 * 5;
+ int timeout = (System.getenv("HOME").contains("menzel")) ? 10 : 60 * 2;
completionService.poll(timeout, TimeUnit.SECONDS);
logger.warn("Still loading track files. Stopping now");
@@ -477,6 +481,6 @@ public final class TrackFactory {
- enum Type {inout, named, distance, strand, scored}
+ enum Type {inout, Named, distance, strand, scored}
}
diff --git a/enhortlib/.idea/misc.xml b/enhortlib/.idea/misc.xml
index 5755a998780a3352b3706bc6c89e9280257b8d39..5b2bcaf2550137a1ec2bd09423339e99a7d7abde 100644
--- a/enhortlib/.idea/misc.xml
+++ b/enhortlib/.idea/misc.xml
@@ -7,7 +7,7 @@