Apply upstream BEDPE support changes mostly

Author: brainstorm

.travis.yml

@@ -7,7 +7,7 @@ jdk: openjdk11
 install:
 - ./gradlew assemble
 script:
-  - ./gradlew check --debug
+  - ./gradlew check
   - ./gradlew createMacAppDistZip
   - ./gradlew createLinuxDistZip
   - ./gradlew createWinDistZip

build.gradle

@@ -22,6 +22,7 @@
 // THE SOFTWARE.
 
 apply plugin: 'java'
+apply plugin: 'maven'
 apply plugin: 'application'
 
 import org.apache.tools.ant.filters.ReplaceTokens
@@ -190,19 +191,19 @@ tasks.withType(Test) {
     systemProperties['ignore.ioexceptions'] = 'false'
     maxHeapSize = '2g'
     maxParallelForks = Runtime.runtime.availableProcessors().intdiv(2) ?: 1
-    
-    
-    
+
+
+
 }
 
 compileTestJava {
     inputs.property("moduleName", moduleName)
     doFirst {
         options.compilerArgs = [
-            '--module-path',  classpath.asPath, 
+            '--module-path',  classpath.asPath,
             '--add-modules', 'junit',
             '--add-modules', 'fest.swing',
-            '--patch-module', "$moduleName=" + files(sourceSets.test.java.srcDirs).asPath, 
+            '--patch-module', "$moduleName=" + files(sourceSets.test.java.srcDirs).asPath,
         ]
         classpath = files()
     }
@@ -377,7 +378,26 @@ task signWinExeDist(type: Exec, dependsOn: createWinExeDist) {
     }
 }
 
-tasks.build.dependsOn { [createDistZip, createLinuxDistZip, createMacAppDistZip, createWinDistZip] }
+task fullJar(type: Jar, dependsOn: jar) {
+    // Based on https://discuss.gradle.org/t/removing-dependencies-from-a-jar-file-during-jar-task/5521/3
+    from {
+        ((configurations.compile - configurations.default) + "${buildDir}/libs/igv.jar").collect {
+            zipTree(it)
+        }
+    } {
+        exclude "META-INF/**"
+    }
+
+    manifest {
+        attributes(
+                "Permissions": "all-permissions",
+                "Application-Name": "IGV",
+                "Built-By": System.getProperty('user.name'),
+                "Main-Class": mainClassName,
+                "Class-Path": configurations.default.collect { it.getName() }.join(' ')
+        )
+    }
+}
 
 // XXX: META-INF versions support seem to clash with proguard at this point in time:
 // https://sourceforge.net/p/proguard/bugs/665/

docs/AWS.md

@@ -0,0 +1,6 @@
+# Amazon Web Services support for IGV desktop
+
+Please refer to the following step by step tutorial to setup an AWS backend that provides 
+access to S3 for IGV:
+
+https://umccr.org/blog/igv-amazon-backend-setup/

src/main/java/org/broad/igv/Globals.java

@@ -28,7 +28,6 @@
 import org.apache.log4j.Logger;
 import org.broad.igv.renderer.SequenceRenderer;
 
-import java.io.FileReader;
 import java.io.IOException;
 import java.text.DecimalFormat;
 import java.util.*;
@@ -132,7 +131,7 @@ public class Globals {
         TIMESTAMP = properties.getProperty("timestamp", "???");
         BEDtoolsPath = System.getProperty("BEDtoolsPath", BEDtoolsPath);
 
-        //Runtime property overrides compile-time property, if both exist.
+         //Runtime property overrides compile-time property, if both exist.
         //If neither exist we default to false
         final String developmentProperty = System.getProperty("development", properties.getProperty("development", "false"));
         development = Boolean.parseBoolean(developmentProperty);

src/main/java/org/broad/igv/batch/CommandListener.java

@@ -128,6 +128,7 @@ public void run() {
                     try {
                         clientSocket.close();
                         clientSocket = null;
+                        // We do NOT set isListening = false here, otherwise logout/login state change falls back to OOB
                     } catch (IOException e) {
                         log.error("Error in client socket loop", e);
                         isListening = false;
@@ -168,6 +169,7 @@ private void processClientSession(CommandExecutor cmdExe) throws IOException {
 
 
             while (!halt && (inputLine = in.readLine()) != null) {
+
                 String cmd = inputLine;
                 if (cmd.startsWith("GET")) {
 
@@ -180,11 +182,8 @@ private void processClientSession(CommandExecutor cmdExe) throws IOException {
                         if (tokens.length == 2) {
                             headers.put(tokens[0].trim(), tokens[1].trim());
                         }
-                        log.info("Tokens (as in *tokenized* headers, not oauth tokens):  "+Arrays.toString(tokens));
                     }
-
-                    log.info("Headers: "+headers);
-                    log.info("Command: "+cmd);
+                    log.info(cmd);
 
                     String command = null;
                     Map<String, String> params = null;
@@ -195,13 +194,11 @@ private void processClientSession(CommandExecutor cmdExe) throws IOException {
                     } else {
                         String[] parts = tokens[1].split("\\?");
                         command = parts[0];
-                        log.debug("Parts of the request: "+Arrays.toString(parts));
                         params = parts.length < 2 ? new HashMap() : parseParameters(parts[1]);
                     }
 
                     // Detect google oauth callback
                     if (command.equals("/oauthCallback")) {
-                        log.debug("Response parameters: " + params.toString());
                         if (params.containsKey("code")) {
                             OAuthUtils.getInstance().setAuthorizationCode(params.get("code"));
                         } else if (params.containsKey("token")) {

src/main/java/org/broad/igv/bedpe/BedPEFeature.java

@@ -15,6 +15,7 @@ public class BedPEFeature implements BedPE {
     int start2;
     int end2;
     String name;
+    String scoreString = "";
     double score;
     Color color;
     int thickness = 1;
@@ -52,12 +53,12 @@ public int getEnd() {
         return Math.max(end1, end2);
     }
 
-    public int getMidStart() {
-        return Math.min ((start1 + end1) / 2, (start2 + end2) / 2);
+    public double getMidStart() {
+        return Math.min ((start1 + end1) / 2.0, (start2 + end2) / 2.0);
     }
 
-    public int getMidEnd() {
-        return Math.max ((start1 + end1) / 2, (start2 + end2) / 2);
+    public double getMidEnd() {
+        return Math.max ((start1 + end1) / 2.0, (start2 + end2) / 2.0);
     }
 
     @Override
@@ -114,7 +115,7 @@ public String getValueString() {
         }
         buf.append(locus1);
         buf.append("<br>" + locus2);
-        buf.append("<br>Score: " + score);
+        buf.append("<br>Score: " + scoreString);
         if(attributes != null) {
             buf.append("<br><hr>");
             for (Map.Entry<String, String> entry : attributes.entrySet()) {

src/main/java/org/broad/igv/bedpe/BedPEParser.java

@@ -29,14 +29,17 @@ public static Dataset parse(ResourceLocator locator, Genome genome) throws IOExc
         int thicknessColumn = -1;
         DatasetType type = DatasetType.UNKNOWN;
         boolean parsedHeader = true;
-        String[] columns;
+
+        // Default column headers from BedPE spec.  Can be overriden
+        String[] columns = {"chrom1", "start1", "stop1", "chrom2", "start2", "stop2", "name", "score", "strand1", "strand2"};
         boolean col7isNumeric = true;   // Until proven otherwise
 
         Map<String, Color> colorCache = new HashMap<>();
         List<BedPEFeature> features = new ArrayList<>();
         BufferedReader br = null;
         br = ParsingUtils.openBufferedReader(locator.getPath());
         String nextLine;
+        boolean firstLine = true;
         while ((nextLine = br.readLine()) != null) {
 
             if (nextLine.startsWith("#columns")) {
@@ -57,11 +60,15 @@ public static Dataset parse(ResourceLocator locator, Genome genome) throws IOExc
                 } catch (NumberFormatException e) {
                     log.error("Error parsing #column line.", e);
                 }
-            } else if (nextLine.startsWith("#")) {
-                columns = Globals.tabPattern.split(nextLine);
-                if (nextLine.trim().equals("#chrom1\tstart1\tstop1\tchrom2\tstart2\tstop2\tname\tqual\tstrand1\tstrand2\tfilters\tinfo")) {
-                    type = DatasetType.TENX;
-                } else {
+            } else if (nextLine.trim().equals("#chrom1\tstart1\tstop1\tchrom2\tstart2\tstop2\tname\tqual\tstrand1\tstrand2\tfilters\tinfo")) {
+                type = DatasetType.TENX;
+            }
+
+            if (nextLine.startsWith("#") || nextLine.startsWith("chr1\tx1\tx2")) {
+
+                String[] tokens = Globals.tabPattern.split(nextLine);
+                if (tokens.length >= 6) {
+                    columns = tokens;
                     for (int i = 6; i < columns.length; i++) {
                         if (columns[i].equalsIgnoreCase("color")) {
                             colorColumn = i;
@@ -70,10 +77,16 @@ public static Dataset parse(ResourceLocator locator, Genome genome) throws IOExc
                         }
                     }
                 }
-
             } else if (nextLine.startsWith("track") || nextLine.startsWith("##track")) {
                 TrackProperties trackProperties = new TrackProperties();
                 ParsingUtils.parseTrackLine(nextLine, trackProperties);
+            } else if (firstLine && nextLine.startsWith("chromosome1\tx1\tx2") || nextLine.startsWith("chr1\tx1\tx2")) {
+                columns = Globals.tabPattern.split(nextLine);
+                for (int i = 6; i < columns.length; i++) {
+                    if (columns[i].equalsIgnoreCase("color")) {
+                        colorColumn = i;
+                    }
+                }
             } else {
                 String[] tokens = Globals.tabPattern.split(nextLine);
 
@@ -100,50 +113,68 @@ public static Dataset parse(ResourceLocator locator, Genome genome) throws IOExc
                 }
 
                 if (tokens.length > 7) {
-                    feature.score = Double.parseDouble(tokens[7]);
+                    feature.scoreString = tokens[7];
+                    try {
+                        feature.score = Double.parseDouble(tokens[7]);
+                    } catch (NumberFormatException e) {
+                        feature.score = 0;
+                    }
                 }
 
-                if (type == DatasetType.TENX) {
+                if (tokens.length > 8) {
                     Map<String, String> attributes = new LinkedHashMap<>();
-                    if (!tokens[8].equals(".")) {
-                        attributes.put("filters", tokens[8]);
-                    }
-                    String[] kvPairs = Globals.semicolonPattern.split(tokens[11]);
-                    for (String kvPair : kvPairs) {
-                        String[] kv = Globals.equalPattern.split(kvPair);
-                        attributes.put(kv[0], kv[1]);
+
+                    for (int i = 8; i < tokens.length; i++) {
+
+                        String t = tokens[i];
+                        String c = columns != null && columns.length > i ? columns[i] : String.valueOf(i);
+
+                        if (c.equals("info") && t.contains("=")) {
+                            String[] kvPairs = Globals.semicolonPattern.split(tokens[11]);
+                            for (String kvPair : kvPairs) {
+                                String[] kv = Globals.equalPattern.split(kvPair);
+                                if (kv.length > 1) {
+                                    attributes.put(kv[0], kv[1]);
+                                }
+                            }
+                        } else {
+                            attributes.put(c, t);
+                        }
                     }
                     feature.attributes = attributes;
                     feature.type = attributes.get("TYPE");
-                } else {
-                    if (colorColumn > 0) {
-                        String colorString = tokens[colorColumn];
-                        Color c = colorCache.get(colorString);
-                        if (c == null) {
-                            c = ColorUtilities.stringToColor(colorString);
-                            colorCache.put(colorString, c);
-                        }
-                        feature.color = c;
-                    }
+                }
 
-                    if (thicknessColumn > 0) {
-                        feature.thickness = Integer.parseInt(tokens[thicknessColumn]);
+                if (colorColumn > 0) {
+                    String colorString = tokens[colorColumn];
+                    Color c = colorCache.get(colorString);
+                    if (c == null) {
+                        c = ColorUtilities.stringToColor(colorString);
+                        colorCache.put(colorString, c);
                     }
+                    feature.color = c;
                 }
+
+                if (thicknessColumn > 0) {
+                    feature.thickness = Integer.parseInt(tokens[thicknessColumn]);
+                }
+
                 // Skipping remaining fields for now
 
                 features.add(feature);
             }
+            firstLine = false;
         }
 
 
         // A hack to detect "interaction" bedpe files, which are not spec compliant.  Interaction score is column 7
         if (col7isNumeric) {
             for (BedPEFeature f : features) {
                 f.score = Double.parseDouble(f.name);
+                f.scoreString = f.name;
                 f.name = null;
             }
-            if(type == DatasetType.UNKNOWN) {
+            if (type == DatasetType.UNKNOWN) {
                 type = DatasetType.CLUSTER;   // A guess
             }
         }

src/main/java/org/broad/igv/bedpe/InteractionTrack.java

@@ -41,6 +41,7 @@ public class InteractionTrack extends AbstractTrack {
     protected static Color axisLineColor = new Color(255, 180, 180);
     private JCheckBoxMenuItem autoscaleCB;
     private JMenuItem maxScoreItem;
+    private List<BedPE> wgFeatures;
 
 
     enum Direction {UP, DOWN}
@@ -101,6 +102,15 @@ public InteractionTrack(ResourceLocator locator, BedPEParser.Dataset dataset, Ge
         } else {
             direction = UP;
         }
+
+        String blockString = PreferencesManager.getPreferences().get(Constants.ARC_BLOCKS);
+        if (blockString != null) {
+            try {
+                showBlocks = Boolean.valueOf(blockString);
+            } catch (IllegalArgumentException e) {
+                log.error("Illegal arc blocks option: " + blockString, e);
+            }
+        }
     }
 
     private void init(List<BedPEFeature> featureList, Genome genome) {
@@ -116,10 +126,12 @@ private void init(List<BedPEFeature> featureList, Genome genome) {
                 newList.add(new BedPEInterFeature(f, 2));
             }
         }
-        newList.addAll(createWGFeatures(featureList, genome));
 
         featureCache = new FeatureCache<>(newList, 50);
 
+        wgFeatures = createWGFeatures(featureList, genome);
+
+
     }
 
 
@@ -160,7 +172,11 @@ public void load(ReferenceFrame frame) {
 
     private List<BedPE> getFeaturesOverlapping(String chr, double start, double end) {
 
-        return featureCache.getFeatures(chr, (int) start, (int) end);
+        if(chr.equals(Globals.CHR_ALL)) {
+            return wgFeatures;
+        } else {
+            return featureCache.getFeatures(chr, (int) start, (int) end);
+        }
     }
 
     @Override
@@ -281,6 +297,7 @@ public IGVPopupMenu getPopupMenu(TrackClickEvent te) {
         showBlocksCB.setSelected(showBlocks);
         showBlocksCB.addActionListener(e -> {
             showBlocks = showBlocksCB.isSelected();
+            PreferencesManager.getPreferences().put(Constants.ARC_BLOCKS, String.valueOf(showBlocksCB.isSelected()));
             refresh();
         });
         menu.add(showBlocksCB);

src/main/java/org/broad/igv/bedpe/PEBlockRenderer.java

@@ -8,7 +8,7 @@
 public class PEBlockRenderer implements BedPERenderer {
 
     InteractionTrack track;
-    int rowHeight = 10;
+    int rowHeight = 6;
 
     public PEBlockRenderer(InteractionTrack track) {
         this.track = track;

src/main/java/org/broad/igv/bedpe/ProportionalArcRenderer.java

@@ -49,8 +49,8 @@ public void render(List<BedPE> features, RenderContext context, Rectangle trackR
 
 
                     if (track.maxScore > 0 && bedPE.getScore() > 0) {
-                        double logMax = Math.log10(track.maxScore);
-                        h = (int) ((Math.log10(bedPE.getScore()) / logMax) * h);
+                        double logMax = Math.log10(track.maxScore + 1);
+                        h = (int) ((Math.log10(bedPE.getScore() + 1) / logMax) * h);
                     }
 
                     if (bedPE.isSameChr()) {