Java tutorial
/* * To change this license header, choose License Headers in Project Properties. * To change this template file, choose Tools | Templates * and open the template in the editor. */ package org.mskcc.shenkers.control.track.rest; import org.mskcc.shenkers.control.track.gene.*; import com.google.common.collect.Range; import org.mskcc.shenkers.control.track.bigwig.*; import org.mskcc.shenkers.control.track.bam.*; import htsjdk.samtools.Cigar; import htsjdk.samtools.CigarElement; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.SAMRecordIterator; import htsjdk.samtools.SamReader; import java.util.ArrayList; import java.util.Arrays; import java.util.HashMap; import java.util.List; import java.util.Map; import java.util.Optional; import java.util.concurrent.Semaphore; import java.util.concurrent.locks.LockSupport; import javafx.beans.InvalidationListener; import javafx.beans.Observable; import javafx.beans.binding.Bindings; import javafx.beans.binding.BooleanBinding; import javafx.beans.binding.DoubleBinding; import javafx.beans.property.Property; import javafx.beans.property.SimpleBooleanProperty; import javafx.beans.property.SimpleDoubleProperty; import javafx.concurrent.Task; import javafx.geometry.Insets; import javafx.geometry.Orientation; import javafx.scene.Node; import javafx.scene.control.Label; import javafx.scene.control.ScrollBar; import javafx.scene.control.ScrollPane; import javafx.scene.layout.Background; import javafx.scene.layout.BackgroundFill; import javafx.scene.layout.BorderPane; import javafx.scene.layout.CornerRadii; import javafx.scene.layout.Pane; import javafx.scene.paint.Color; import javafx.util.Pair; import org.apache.commons.lang3.ArrayUtils; import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; import org.broad.igv.bbfile.BBFileReader; import org.broad.igv.bbfile.BigWigIterator; import org.broad.igv.bbfile.WigItem; import org.controlsfx.control.HiddenSidesPane; import org.fxmisc.easybind.EasyBind; import org.mskcc.shenkers.control.track.DomainFlippable; import org.mskcc.shenkers.control.track.View; import static org.mskcc.shenkers.control.track.bam.BamView1.coverage; import org.mskcc.shenkers.model.datatypes.GenomeSpan; import org.mskcc.shenkers.view.GeneViewBuilder; import org.mskcc.shenkers.view.GenericIntervalView; import org.mskcc.shenkers.view.GenericStackedIntervalView; import org.mskcc.shenkers.view.LineHistogramView; import org.mskcc.shenkers.view.RectangleIntervalNode; import org.mskcc.shenkers.view.SparseLineHistogramView; /** * * @author sol */ public class RestIntervalView implements View<RestIntervalContext> { private final Logger logger = LogManager.getLogger(); @Override public Task<Pane> getContent(RestIntervalContext context) { return context.spanProperty().getValue().map(i -> { String chr = i.getChr(); int start = i.getStart(); int end = i.getEnd(); Task<Pane> task = new PaneTask(context, chr, start, end); logger.info("returning task"); return task; }).orElse(new Task<Pane>() { @Override protected Pane call() throws Exception { return new BorderPane(new Label("coordinates not set")); } } // new BorderPane(new Label("bamview1: span not set")) // new Pane() ); } public class PaneTask<T extends Pane & DomainFlippable> extends Task<Pane> { RestIntervalContext context; RestIntervalProvider modelProvider; String chr; int start; int end; BooleanBinding flipBinding; Semaphore semaphore; public PaneTask(RestIntervalContext context, String chr, int start, int end) { super(); this.context = context; this.modelProvider = context.readerProperty().getValue(); this.chr = chr; this.start = start; this.end = end; } @Override protected Pane call() throws Exception { synchronized (context) { try { logger.info("calculating coverage for region {}:{}-{}", chr, start, end); logger.info("acquiring semaphore for gene model provider"); context.acquireReader(); logger.info("querying gene models"); List<Pair<Integer, Integer>> modelSpans = modelProvider.query(chr, start, end); List<T> modelPanes = new ArrayList<>(); for (Pair<Integer, Integer> span : modelSpans) { GenericIntervalView<T> view = new GenericIntervalView<T>(span.getKey(), span.getValue()); view.setData(Arrays.asList(new Pair(span.getKey(), span.getValue())), Arrays.asList((T) new RectangleIntervalNode())); modelPanes.add((T) view); } GenericStackedIntervalView stackedIntervalView = new GenericStackedIntervalView(start, end); stackedIntervalView.getStyleClass().add("track"); stackedIntervalView.setData(modelSpans, modelPanes); class FlipBinding extends BooleanBinding { private final Property<Optional<GenomeSpan>> span; private FlipBinding(Property<Optional<GenomeSpan>> spanProperty) { this.span = spanProperty; } protected boolean computeValue() { if (span.getValue().isPresent()) { return span.getValue().get().isNegativeStrand(); } else { return false; } } } flipBinding = new FlipBinding(context.spanProperty()); ScrollPane scrollWrapper = new ScrollPane(stackedIntervalView); HiddenSidesPane hsp = new HiddenSidesPane(); BorderPane pane = new BorderPane(scrollWrapper); // pane.getStyleClass().add("track"); // scrollWrapper.setBackground(new Background(new BackgroundFill(Color.WHITE, CornerRadii.EMPTY, Insets.EMPTY))); // stackedIntervalView.setBackground(new Background(new BackgroundFill(Color.WHITE, CornerRadii.EMPTY, Insets.EMPTY))); scrollWrapper.setPadding(Insets.EMPTY); int tile_height = 20; int gap_pixels = 10; stackedIntervalView.flipDomainProperty().bind(flipBinding); stackedIntervalView.setOrientation(Orientation.VERTICAL); stackedIntervalView.setPrefTileHeight(tile_height); stackedIntervalView.prefHeightProperty() .bind(Bindings.max(new SimpleDoubleProperty(tile_height + gap_pixels) .multiply(Bindings.size(stackedIntervalView.getChildren())) .subtract(gap_pixels), 100)); stackedIntervalView.prefTileWidthProperty().bind(pane.widthProperty()); stackedIntervalView.prefWidthProperty().bind(pane.widthProperty()); stackedIntervalView.setVgap(gap_pixels); ScrollBar scrollBar = new ScrollBar(); scrollBar.maxProperty().bind(scrollWrapper.vmaxProperty()); scrollBar.minProperty().bind(scrollWrapper.vminProperty()); scrollBar.visibleAmountProperty() .bind(scrollWrapper.heightProperty().divide(stackedIntervalView.prefHeightProperty())); scrollBar.setOrientation(Orientation.VERTICAL); scrollWrapper.vvalueProperty().bindBidirectional(scrollBar.valueProperty()); // hsp.setContent(scrollWrapper); // hsp.setRight(scrollBar); scrollWrapper.setVbarPolicy(ScrollPane.ScrollBarPolicy.NEVER); scrollWrapper.setHbarPolicy(ScrollPane.ScrollBarPolicy.NEVER); return pane; } catch (Throwable t) { logger.info("task {} threw exception {}", this, t.getMessage()); logger.info("exception: ", t); throw t; } finally { logger.info("{} releasing semaphore for task {}", Thread.currentThread().getName(), this); context.releaseReader(); logger.info("released semaphore"); } } } @Override protected void cancelled() { super.cancelled(); logger.info("Cancelling task"); } } }