Java tutorial
/* * #%L * gitools-core * %% * Copyright (C) 2013 Universitat Pompeu Fabra - Biomedical Genomics group * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as * published by the Free Software Foundation, either version 3 of the * License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public * License along with this program. If not, see * <http://www.gnu.org/licenses/gpl-3.0.html>. * #L% */ package org.gitools.heatmap; import com.google.common.collect.Lists; import org.gitools.api.matrix.IAnnotations; import org.gitools.api.matrix.IMatrixDimension; import org.gitools.api.matrix.MatrixDimensionKey; import org.gitools.api.resource.ResourceReference; import org.gitools.api.resource.adapter.ResourceReferenceXmlAdapter; import org.gitools.heatmap.decorator.DetailsDecoration; import org.gitools.heatmap.header.HeatmapHeader; import org.gitools.matrix.model.matrix.AnnotationMatrix; import org.gitools.utils.xml.adapter.ColorXmlAdapter; import javax.xml.bind.annotation.*; import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter; import java.awt.*; import java.util.HashSet; import java.util.LinkedList; import java.util.List; import java.util.Set; @XmlAccessorType(XmlAccessType.FIELD) public class HeatmapDimension extends AbstractMatrixViewDimension { public static final String PROPERTY_GRID_COLOR = "gridColor"; public static final String PROPERTY_GRID_SIZE = "gridSize"; public static final String PROPERTY_CELL_SIZE = "cellSize"; public static final String PROPERTY_HEADERS = "headers"; public static final String PROPERTY_HIGHLIGHTED = "highlighted"; public static final String PROPERTY_SELECTED_HEADER = "selectedHeader"; @XmlJavaTypeAdapter(ResourceReferenceXmlAdapter.class) private ResourceReference<AnnotationMatrix> annotations; @XmlElementWrapper(name = "headers") @XmlElement(name = "header") private LinkedList<HeatmapHeader> headers; @XmlElement(name = "grid-size") private int gridSize; @XmlJavaTypeAdapter(ColorXmlAdapter.class) @XmlElement(name = "grid-color") private Color gridColor; @XmlElement(name = "cell-size") private int cellSize; @XmlTransient private Set<String> highlightedLabels; @XmlTransient private Set<String> highlightedHeaders; @XmlTransient private HeatmapHeader selectedHeader; @XmlTransient private static Color highlightingColor; public HeatmapDimension() { this(null); } public HeatmapDimension(IMatrixDimension matrixDimension) { super(); this.headers = new LinkedList<>(); this.gridSize = 1; this.gridColor = Color.WHITE; this.cellSize = 14; this.highlightedLabels = new HashSet<>(); this.highlightedHeaders = new HashSet<>(); this.selectedHeader = null; init(matrixDimension); } public void init(IMatrixDimension matrixDimension) { super.init(matrixDimension); if (matrixDimension == null) { return; } if (this.annotations == null) { this.annotations = new ResourceReference<>(matrixDimension.getId() + "-annotations", new AnnotationMatrix()); } for (HeatmapHeader header : headers) { header.init(this); } } public int getCellSize() { return cellSize; } public void setCellSize(int newValue) { int oldValue = this.cellSize; this.cellSize = newValue; firePropertyChange(PROPERTY_CELL_SIZE, oldValue, newValue); } public List<HeatmapHeader> getHeaders() { return headers; } public void updateHeaders() { firePropertyChange(PROPERTY_HEADERS, null, null); } public void addHeader(HeatmapHeader header) { if (header.getHeatmapDimension() == null) { header.setHeatmapDimension(this); } headers.addFirst(header); firePropertyChange(PROPERTY_HEADERS, null, headers); } public int getHeaderSize() { int size = 0; for (HeatmapHeader h : headers) size += h.getSize(); return size; } public int getGridSize() { return gridSize; } public void setGridSize(int gridSize) { int old = this.gridSize; this.gridSize = gridSize; firePropertyChange(PROPERTY_GRID_SIZE, old, gridSize); } public Color getGridColor() { return gridColor; } public boolean showGrid() { return getCellSize() > 4; } public int getFullCellSize() { if (showGrid()) { return getCellSize() + getGridSize(); } return getCellSize(); } public void setGridColor(Color gridColor) { Color old = this.gridColor; this.gridColor = gridColor; firePropertyChange(PROPERTY_GRID_COLOR, old, gridColor); } public ResourceReference<AnnotationMatrix> getAnnotationsReference() { return annotations; } public void setAnnotationsReference(ResourceReference<AnnotationMatrix> annotationsReference) { this.annotations = annotationsReference; } public AnnotationMatrix getAnnotations() { if (annotations == null) { return null; } return annotations.get(); } public void addAnnotations(IAnnotations annotations) { this.annotations.get().addAnnotations(annotations); } public boolean isHighlighted(String label) { return highlightedLabels.contains(label); } public void setHighlightedLabels(Set<String> highlightedLabels) { this.highlightedLabels = highlightedLabels; firePropertyChange(PROPERTY_HIGHLIGHTED, null, highlightedLabels); } public void clearHighlightedLabels() { highlightedLabels.clear(); firePropertyChange(PROPERTY_HIGHLIGHTED, null, highlightedLabels); } public Set<String> getHighlightedHeaders() { return highlightedHeaders; } public void setHighlightedHeaders(Set<String> highlightedHeaders) { this.highlightedHeaders = highlightedHeaders; firePropertyChange(PROPERTY_HIGHLIGHTED, null, highlightedLabels); } public void clearHighlightedHeaders() { this.highlightedHeaders.clear(); firePropertyChange(PROPERTY_HIGHLIGHTED, null, highlightedLabels); } public void populateDetails(List<DetailsDecoration> details) { Iterable<HeatmapHeader> itHeaders = headers; if (getId() == MatrixDimensionKey.COLUMNS) { itHeaders = Lists.reverse(headers); } for (HeatmapHeader header : itHeaders) { if (header.isVisible()) { header.populateDetails(details, getFocus(), getSelectedHeader() == header); } } } public void setHighlightingColor(Color highlightingColor) { this.highlightingColor = highlightingColor; firePropertyChange(PROPERTY_HIGHLIGHTED, null, highlightedLabels); updateHeaders(); } public Color getHighlightingColor() { if (highlightingColor == null) { return getDefaultHighlightColor(); } return highlightingColor; } private static Color getDefaultHighlightColor() { return new Color(254, 254, 0, 127); } public HeatmapHeader getSelectedHeader() { if (selectedHeader == null) { selectedHeader = headers.getFirst(); } return selectedHeader; } public void setSelectedHeader(HeatmapHeader header) { HeatmapHeader old = getSelectedHeader(); this.selectedHeader = header; firePropertyChange(PROPERTY_SELECTED_HEADER, old, header); } public void resetHighlightColor() { setHighlightingColor(getDefaultHighlightColor()); } }