Java tutorial
/* BEGIN_HEADER Java TreeView * * $Author: rqluk $ * $RCSfile: GraphicsExportPanel.java,v $ * $Revision: 1.1 $ * $Date: 2006/08/16 19:13:45 $ * $Name: $ * * This file is part of Java TreeView * Copyright (C) 2001-2003 Alok Saldanha, All Rights Reserved. Modified by Alex Segal 2004/08/13. Modifications Copyright (C) Lawrence Berkeley Lab. * * This software is provided under the GNU GPL Version 2. In particular, * * 1) If you modify a source file, make a comment in it containing your name and the date. * 2) If you distribute a modified version, you must do it under the GPL 2. * 3) Developers are encouraged but not required to notify the Java TreeView maintainers at alok@genome.stanford.edu when they make a useful addition. It would be nice if significant contributions could be merged into the main distribution. * * A full copy of the license can be found in gpl.txt or online at * http://www.gnu.org/licenses/gpl.txt * * END_HEADER */ package clusterMaker.treeview.dendroview; import clusterMaker.treeview.*; import com.lowagie.text.Document; import com.lowagie.text.PageSize; import com.lowagie.text.pdf.DefaultFontMapper; import com.lowagie.text.pdf.PdfContentByte; import com.lowagie.text.pdf.PdfWriter; import cytoscape.logger.CyLogger; import org.freehep.graphicsio.ps.PSGraphics2D; import org.freehep.graphicsio.svg.SVGGraphics2D; import javax.imageio.ImageIO; import javax.swing.*; import javax.swing.event.DocumentEvent; import javax.swing.event.DocumentListener; import javax.swing.event.ListSelectionEvent; import javax.swing.event.ListSelectionListener; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.image.BufferedImage; import java.awt.image.MemoryImageSource; import java.io.BufferedOutputStream; import java.io.File; import java.io.FileOutputStream; import java.io.OutputStream; import java.util.Properties; /** * This class is a superclass which implements a GUI for selection of options relating to output. * It makes most of the relevant variables accessible to subclasses through protected methods. */ public class GraphicsExportPanel extends JPanel implements SettingsPanel { private ConfigNode root; private String[] formats = { "png", "jpg", "bmp", "pdf", "svg", "eps" }; // external links private DendroView view; private DataModel model; private CyLogger logger; private HeaderInfo arrayHeaderInfo; // allows access to array headers. private HeaderInfo geneHeaderInfo; // allows access to gene headers. private TreeSelectionI geneSelection; private TreeSelectionI arraySelection; private InvertedTreeDrawer arrayTreeDrawer; private LeftTreeDrawer geneTreeDrawer; private ArrayDrawer arrayDrawer; private MapContainer geneMap; private MapContainer arrayMap; // components private FilePanel filePanel; private InclusionPanel inclusionPanel; private HeaderSelectionPanel headerSelectionPanel; private JComboBox formatPullDown; private JCheckBox appendExt; /** * the scale of the passed in gene map and array map define the initial size. * The export panel will not actually modify the map settings for now. * <p> * To Developers- if you want to simpify the code by changing the scale * settings in the maps, make copies of them first. This might involve * implementing copyStateFrom functions in the MapContainer class. */ public GraphicsExportPanel(DendroView view) { this.view = view; logger = CyLogger.getLogger(GraphicsExportPanel.class); // Get all of the necessary information from our view model = view.getDataModel(); arrayHeaderInfo = model.getArrayHeaderInfo(); geneHeaderInfo = model.getGeneHeaderInfo(); geneSelection = view.getGeneSelection(); arraySelection = view.getArraySelection(); arrayTreeDrawer = view.getArrayTreeDrawer(); geneTreeDrawer = view.getGeneTreeDrawer(); arrayDrawer = view.getArrayDrawer(); if ((geneSelection.getNSelectedIndexes() != 0) || (arraySelection.getNSelectedIndexes() != 0)) { arrayMap = view.getZoomXmap(); geneMap = view.getZoomYmap(); } else { arrayMap = view.getGlobalXmap(); geneMap = view.getGlobalYmap(); } setupWidgets(); inclusionPanel.synchSelected(); inclusionPanel.synchEnabled(); } // accessors protected HeaderInfo getArrayHeaderInfo() { return arrayHeaderInfo; } protected HeaderInfo getGeneHeaderInfo() { return geneHeaderInfo; } protected TreeSelectionI getGeneSelection() { return geneSelection; } protected TreeSelectionI getArraySelection() { return arraySelection; } protected ArrayDrawer getArrayDrawer() { return arrayDrawer; } public void synchronizeTo() { String format = (String) formatPullDown.getSelectedItem(); if (format.equals("png") || format.equals("jpg") || format.equals("bmp")) bitmapSave(format); else if (format.equals("pdf")) pdfSave(format); else if (format.equals("eps")) epsSave(format); else if (format.equals("svg")) svgSave(format); } public void synchronizeFrom() { } // NOTE: border pixels appear on all sides. int borderPixels = 5; /** * Setter for borderPixels */ public void setBorderPixels(int border) { this.borderPixels = border; } /** * Getter for borderPixels */ public int getBorderPixels() { return borderPixels; } private static int textSpacing = 2; //pixels between boxes and text /** * for communication with subclass... (in this case PostscriptExport) */ protected boolean hasBbox() { return true; } /** * for communication with subclass... (in this case CharExport) * NOTE: better to have local, to avoid obligatory subclassing. */ boolean hasChar = false; protected boolean hasChar() { return hasChar; } // accessors for configuration information /** * returns the font for gene annotation information */ private Font geneFont = new Font("Lucida Sans Regular", 0, 12); protected Font getGeneFont() { return geneFont; } public void setGeneFont(Font f) { if (f != null) { geneFont = f; } } private Font arrayFont = new Font("Lucida Sans Regular", 0, 12); protected Font getArrayFont() { return arrayFont; } public void setArrayFont(Font f) { if (f != null) { arrayFont = f; } } /** * True if an explict bounding box should be included in the output. * Subclasses are to use this when creating output. The returned value reflects * what the user has selected in the GUI. * This is only meaningful for postscript. */ protected boolean includeBbox() { return inclusionPanel.useBbox(); } /** * This method returns the minimum correlation for the gene nodes which will be drawn. */ protected double getMinGeneCorr() { if (drawSelected()) { if (geneTreeDrawer == null) logger.error("ExportPanel.getMinGeneCorr: geneTreeDrawer null"); TreeSelectionI selection = getGeneSelection(); if (selection == null) logger.error("ExportPanel.getMinGeneCorr: selection null"); String selectedId = selection.getSelectedNode(); if (selectedId == null) logger.error("ExportPanel.getMinGeneCorr: selectedId null"); TreeDrawerNode selectedNode = geneTreeDrawer.getNodeById(selectedId); if (selectedNode == null) logger.error("ExportPanel.getMinGeneCorr: selectedNode null , id " + selectedId); return selectedNode.getCorr(); } else { return geneTreeDrawer.getCorrMin(); } } /** * This method returns the minimum correlation for the gene nodes which will be drawn. */ protected double getMinArrayCorr() { if (drawSelected()) { return arrayTreeDrawer.getNodeById(getArraySelection().getSelectedNode()).getCorr(); } else { return arrayTreeDrawer.getCorrMin(); } } /** * This method is for drawing the actual data. * <p> * It returns the offset of the first pixel of the block corresponding to the geneIndex * where the first block (index 0) always has an offset of zero. */ protected int getYmapPixel(double geneIndex) { double dp = geneMap.getPixel(geneIndex) - geneMap.getPixel(0); double ret = (int) (dp * getYscale() / geneMap.getScale()); return (int) ret; } /** * This method is for drawing the actual data. * <p> * It returns the offset of the first pixel of the block corresponding to the arrayIndex * where the first block (index 0) always has an offset of zero. */ protected int getXmapPixel(double geneIndex) { double dp = arrayMap.getPixel(geneIndex) - arrayMap.getPixel(0); int ret = (int) (dp * getXscale() / arrayMap.getScale()); return (int) ret; } protected boolean geneAnnoInside() { return headerSelectionPanel.geneAnnoInside(); } protected boolean arrayAnnoInside() { return headerSelectionPanel.arrayAnnoInside(); } protected String getGeneAnno(int i) { return headerSelectionPanel.getGeneAnno(i); } protected String getArrayAnno(int i) { return headerSelectionPanel.getArrayAnno(i); } private Color getFgColor(HeaderInfo headerInfo, int index) { int colorIndex = headerInfo.getIndex("FGCOLOR"); if (colorIndex > 0) { String[] headers = headerInfo.getHeader(index); return TreeColorer.getColor(headers[colorIndex]); } return null; } private Color getBgColor(HeaderInfo headerInfo, int index) { int colorIndex = headerInfo.getIndex("BGCOLOR"); if (colorIndex > 0) { String[] headers = headerInfo.getHeader(index); return TreeColorer.getColor(headers[colorIndex]); } return null; } protected Color getGeneFgColor(int i) { return getFgColor(geneHeaderInfo, i); } protected Color getArrayFgColor(int i) { return getFgColor(arrayHeaderInfo, i); } protected Color getGeneBgColor(int i) { return getBgColor(geneHeaderInfo, i); } protected Color getArrayBgColor(int i) { return getBgColor(arrayHeaderInfo, i); } // gene node to actually draw protected TreeDrawerNode getGeneNode() { if (inclusionPanel.drawSelected()) { return geneTreeDrawer.getNodeById(geneSelection.getSelectedNode()); } else { return getGeneRootNode(); } } // array node to actually draw protected TreeDrawerNode getArrayNode() { if (inclusionPanel.drawSelected()) { return arrayTreeDrawer.getNodeById(arraySelection.getSelectedNode()); } else { return getArrayRootNode(); } } protected File getFile() { // See if we need to add the extension if (appendExt.isSelected()) appendExtension(); return filePanel.getFile(); } public String getFilePath() { // See if we need to add the extension if (appendExt.isSelected()) appendExtension(); return filePanel.getFilePath(); } public void setFilePath(String newFile) { filePanel.setFilePath(newFile); } protected TreeDrawerNode getGeneRootNode() { if (geneTreeDrawer == null) return null; return geneTreeDrawer.getRootNode(); } protected TreeDrawerNode getArrayRootNode() { if (arrayTreeDrawer == null) return null; return arrayTreeDrawer.getRootNode(); } protected String getInitialExtension() { return ".png"; } protected String getInitialFilePath() { String defaultPath = System.getProperty("user.home"); String fileSep = System.getProperty("file.separator"); String file = model.getSource(); if (root == null) { return defaultPath + fileSep + file; } else { return root.getAttribute("file", defaultPath) + fileSep + file; } } public void setIncludedGeneHeaders(int[] newSelected) { headerSelectionPanel.geneList.setSelectedIndices(newSelected); headerSelectionPanel.setupSelected(); } public void setIncludedArrayHeaders(int[] newSelected) { headerSelectionPanel.arrayList.setSelectedIndices(newSelected); headerSelectionPanel.setupSelected(); } public void bindConfig(ConfigNode configNode) { root = configNode; } public ConfigNode createSubNode() { return root.create("File"); } private void setupWidgets() { Box upperPanel; // holds major widget panels upperPanel = new Box(BoxLayout.X_AXIS); headerSelectionPanel = new HeaderSelectionPanel(); upperPanel.add(headerSelectionPanel); inclusionPanel = new InclusionPanel(); upperPanel.add(inclusionPanel); setLayout(new BoxLayout(this, BoxLayout.Y_AXIS)); add(upperPanel); filePanel = new FilePanel(getInitialFilePath()); add(filePanel); JPanel formatPanel = new JPanel(); formatPullDown = new JComboBox(formats); appendExt = new JCheckBox("Append Extension?", true); formatPanel.add(new JLabel("Graphics Format:")); formatPanel.add(formatPullDown); formatPanel.add(appendExt); add(formatPanel); } private void appendExtension() { String fileName = filePanel.getFilePath(); int extIndex = fileName.lastIndexOf('.'); int dirIndex = fileName.lastIndexOf(File.separatorChar); if (extIndex > dirIndex) { setFilePath(fileName.substring(0, extIndex) + "." + formatPullDown.getSelectedItem()); } else { setFilePath(fileName + "." + formatPullDown.getSelectedItem()); } } //drawing specific convenience methods... protected boolean includeAtr() { return inclusionPanel.includeAtr(); } protected void includeAtr(boolean flag) { inclusionPanel.includeAtr(flag); } protected boolean includeGtr() { return inclusionPanel.includeGtr(); } protected void includeGtr(boolean flag) { inclusionPanel.includeGtr(flag); } protected boolean includeData() { return inclusionPanel.includeData(); } private boolean includeChar() { return inclusionPanel.includeChar(); } protected void includeData(boolean flag) { inclusionPanel.includeData(flag); } protected boolean drawSelected() { return inclusionPanel.drawSelected(); } protected boolean includeGeneMap() { return (includeGtr() || includeData() || (numGeneHeaders() > 0)); } protected boolean includeArrayMap() { return (includeAtr() || includeData() || (numArrayHeaders() > 0)); } public double getXmapWidth() { // HACK, doesn't account for discontinuous selection return (int) ((arrayMap.getPixel(maxArray() + 1) - arrayMap.getPixel(minArray())) * getXscale() / arrayMap.getScale()); } public double getGtrWidth() { return 200 * getXscale() / arrayMap.getScale(); } public double getXscale() { return inclusionPanel.getXscale(); } public double getYmapHeight() { // HACK, doesn't account for discontinuous selection double ret = (geneMap.getPixel(maxGene() + 1) - geneMap.getPixel(minGene())) * getYscale() / geneMap.getScale(); return ret; } public double getAtrHeight() { return 100 /* * getYscale() / geneMap.getScale()*/; } public double getYscale() { return inclusionPanel.getYscale(); } public int getBboxWidth() { return inclusionPanel.getBboxWidth(); } public int getBboxHeight() { return inclusionPanel.getBboxHeight(); } public int minGene() { if (inclusionPanel.drawSelected()) { return geneSelection.getMinIndex(); } else { return 0; } } public int minArray() { if (inclusionPanel.drawSelected()) { return arraySelection.getMinIndex(); } else { return 0; } } public int maxGene() { if (inclusionPanel.drawSelected()) { return geneSelection.getMaxIndex(); } else { return geneHeaderInfo.getNumHeaders() - 1; } } public int maxArray() { if (inclusionPanel.drawSelected()) { return arraySelection.getMaxIndex(); } else { return arrayHeaderInfo.getNumHeaders() - 1; } } public int estimateHeight() { int height = 2 * getBorderPixels(); // do we need to include the height of the map? if (includeGeneMap()) { height += (int) getYmapHeight(); } else { } // additional space for gene tree... if (includeAtr()) { height += (int) getAtrHeight(); } height += getArrayAnnoLength(); return height; } public int estimateWidth() { int width = 2 * getBorderPixels(); // do we need to include the width of the map? if (includeArrayMap()) { width += (int) getXmapWidth(); } else { } // additional space for gene tree... if (includeGtr()) { width += (int) getGtrWidth(); } width += getGeneAnnoLength(); return width; } protected int getGeneAnnoLength() { // deal with text length... if ((inclusionPanel == null) || (inclusionPanel.useBbox() == false)) { // no bounding box, have to wing it... return headerSelectionPanel.geneMaxLength() + textSpacing; } else { return getBboxWidth(); } } protected int getArrayAnnoLength() { // deal with text length... if ((inclusionPanel == null) || (inclusionPanel.useBbox() == false)) { // no bounding box, have to wing it... return headerSelectionPanel.arrayMaxLength() + textSpacing; } else { return getBboxHeight(); } } public int numArrayHeaders() { return headerSelectionPanel.numArrayHeaders(); } public int numGeneHeaders() { return headerSelectionPanel.numGeneHeaders(); } public void deselectHeaders() { headerSelectionPanel.deselectHeaders(); } /** * The following method gets the x coordiate of the data matrix, according to current settings. */ protected int getDataX() { int dataX = getBorderPixels(); if (includeGtr()) dataX += getGtrWidth(); return dataX; } /** * The following method gets the y coordiate of the data matrix, according to current settings. */ protected int getDataY() { int dataY = getBorderPixels(); if (includeAtr()) dataY += getAtrHeight(); dataY += getArrayAnnoLength(); return dataY; } /** * does the dirty work by calling methods in the superclass. */ public void drawAll(Graphics g, double scale) { int width = estimateWidth(); int height = estimateHeight(); if ((width == 0) || (height == 0)) { return; } // 5 views to worry about... first, calculate datamatrix's origin... int dataX = (int) (scale * getDataX()); int dataY = (int) (scale * getDataY()); int scaleP = (int) (scale * getBorderPixels()); drawGtr(g, scaleP, dataY, scale); if (includeAtr()) { if (arrayAnnoInside()) { drawAtr(g, dataX, scaleP, scale); drawArrayAnno(g, dataX, scaleP + (int) (scale * getAtrHeight()), scale); } else { drawArrayAnno(g, dataX, scaleP, scale); drawAtr(g, dataX, dataY - (int) (scale * getAtrHeight()), scale); } } else { drawArrayAnno(g, dataX, scaleP, scale); } drawData(g, dataX, dataY, scale); if (includeArrayMap()) { drawGeneAnno(g, dataX + (int) (getXmapWidth() * scale), dataY, scale); } else { drawGeneAnno(g, dataX, dataY, scale); } } /** * draws a scaled Gene Tree at the suggested x,y location */ protected void drawGtr(Graphics g, int x, int y, double scale) { if (includeGtr() == false) return; int width = (int) (getGtrWidth() * scale); int height = (int) (getYmapHeight() * scale); if ((height == 0) || (width == 0)) return; // clear the pallette... g.setColor(Color.black); // calculate Scaling Rectangle destRect = new Rectangle(); destRect.setBounds(x, y, width, height); double minCorr = getMinGeneCorr(); LinearTransformation xScaleEq = new LinearTransformation(minCorr, destRect.x, geneTreeDrawer.getCorrMax(), destRect.x + destRect.width); LinearTransformation yScaleEq = new LinearTransformation(minGene(), destRect.y, maxGene() + 1, destRect.y + destRect.height); // draw geneTreeDrawer.paintSubtree(g, xScaleEq, yScaleEq, destRect, getGeneNode(), false); } /** * draws a scaled Array Tree at the suggested x,y location */ protected void drawAtr(Graphics g, int x, int y, double scale) { if (includeAtr() == false) return; int width = (int) (getXmapWidth() * scale); int height = (int) (getAtrHeight() * scale); if ((height == 0) || (width == 0)) return; // clear the pallette... g.setColor(Color.black); // calculate Scaling Rectangle destRect = new Rectangle(); destRect.setBounds(x, y, width, height); LinearTransformation xScaleEq = new LinearTransformation(minArray(), destRect.x, maxArray() + 1, destRect.x + destRect.width); double minCorr = arrayTreeDrawer.getCorrMin(); if (drawSelected()) { minCorr = arrayTreeDrawer.getNodeById(getArraySelection().getSelectedNode()).getCorr(); } LinearTransformation yScaleEq = new LinearTransformation(minCorr, destRect.y, arrayTreeDrawer.getCorrMax(), destRect.y + destRect.height); // draw arrayTreeDrawer.paintSubtree(g, xScaleEq, yScaleEq, destRect, getArrayNode(), false); } /** * draws an appropriately sized box for each annotation string at the specific location */ protected void drawGeneAnnoBox(Graphics g, int x, int y, double scale) { // HACK doesn't deal with discontinuous selection right. int width = (int) (getGeneAnnoLength() * scale); int height = (int) (getYmapHeight() * scale); g.setColor(Color.black); FontMetrics fontMetrics = getFontMetrics(getGeneFont()); int geneHeight = (int) (fontMetrics.getAscent() * scale); int min = minGene(); int max = maxGene(); double spacing = (double) height / (max - min + 1); for (int i = min; i <= max; i++) { /* int geneWidth = (int) (scale * headerSelectionPanel.getLength (headerSelectionPanel.getGeneAnno(i))); */ int geneWidth = width; g.fillRect(x, y + (int) ((i - min) * spacing + (spacing - geneHeight) / 2), geneWidth, geneHeight); } } /** * draws an appropriately sized box for each annotation string at the specific location */ public void drawArrayAnnoBox(Graphics g, int x, int y, double scale) { // HACK doesn't deal with discontinuous selection right. int height = (int) (getArrayAnnoLength() * scale); int width = (int) (getXmapWidth() * scale); g.setColor(Color.black); FontMetrics fontMetrics = getFontMetrics(getArrayFont()); int arrayWidth = (int) (fontMetrics.getAscent() * scale); int min = minArray(); int max = maxArray(); double spacing = (double) width / (max - min + 1); for (int i = min; i <= max; i++) { // int arrayHeight = (int) (scale * headerSelectionPanel.getLength(headerSelectionPanel.getArrayAnno(i))); int arrayHeight = height; int thisx = x + (int) ((i - min) * spacing + (spacing - arrayWidth) / 2); int thisy = y + height - arrayHeight; if (headerSelectionPanel.arrayAnnoInside()) { thisy = y; } g.fillRect(thisx, thisy, arrayWidth, arrayHeight); } } /** * draws an annotation strings at the specific location */ protected void drawGeneAnno(Graphics g, int x, int y, double scale) { // HACK doesn't deal with discontinuous selection right. int width = (int) (getGeneAnnoLength() * scale); int height = (int) (getYmapHeight() * scale); if ((height == 0) || (width == 0)) return; int min = minGene(); int max = maxGene(); double spacing = (double) height / (max - min + 1); MapContainer tempMap = new MapContainer("Fixed"); tempMap.setScale(spacing); tempMap.setIndexRange(min, max); tempMap.setAvailablePixels(height + getBorderPixels()); TextView anv = new TextView(geneHeaderInfo); anv.setMap(tempMap); anv.setHeaderSummary(headerSelectionPanel.getGeneSummary()); // Image buf = createImage(width + getBorderPixels(), height + getBorderPixels()); anv.setFace(getGeneFont().getName()); anv.setStyle(getGeneFont().getStyle()); anv.setPoints((int) spacing); anv.updateBuffer(g, new Rectangle(x + textSpacing, y, width + getBorderPixels(), height + getBorderPixels())); // g.drawImage(buf,x+textSpacing, y, null); /* g.setColor(Color.black); g.setFont(getGeneFont()); FontMetrics fontMetrics = getFontMetrics(g.getFont()); int geneHeight = (int) (fontMetrics.getAscent() * scale); int inset = (int) (scale * getBorderPixels()); for (int i = min; i <= max; i++) { g.drawString(getGeneAnno(i), x + inset, y + (int)((i - min + 1.0) *spacing - (spacing - geneHeight) /2)); } */ } /** * draws array annotation strings at the specific location */ public void drawArrayAnno(Graphics real, int x, int y, double scale) { int height = (int) (getArrayAnnoLength() * scale); int width = (int) (getXmapWidth() * scale); if ((height == 0) || (width == 0)) return; int min = minArray(); int max = maxArray(); double spacing = (double) width / (max - min + 1); MapContainer tempMap = new MapContainer("Fixed"); tempMap.setScale(spacing); tempMap.setIndexRange(min, max); tempMap.setAvailablePixels(width + getBorderPixels()); ArrayNameView anv = new ArrayNameView(arrayHeaderInfo); anv.setFace(getArrayFont().getName()); anv.setStyle(getArrayFont().getStyle()); anv.setPoints((int) spacing); anv.setHeaderSummary(headerSelectionPanel.getArraySummary()); anv.setMapping(tempMap); // Image buf = createImage(width + getBorderPixels(), height + getBorderPixels()); // buf.getGraphics().setFont(getArrayFont()); anv.updateBuffer(real, new Rectangle(x, y - getBorderPixels() - textSpacing, width + getBorderPixels(), height + getBorderPixels())); // real.drawImage(buf,x, y-getBorderPixels()-textSpacing, null); } /** * draws the data matrix */ public void drawData(Graphics g, int x, int y, double scale) { if (includeData() == false) return; int height = (int) (getYmapHeight() * scale); int width = (int) (getXmapWidth() * scale); Rectangle sourceRect = new Rectangle(); sourceRect.setBounds(minArray(), minGene(), (maxArray() + 1 - minArray()), (maxGene() + 1 - minGene())); Rectangle destRect = new Rectangle(); // HACK does not deal with discontinuous selection... /* old version, kinda slow... destRect.setBounds(x,y, width, height); arrayDrawer.paint(g, sourceRect ,destRect); */ destRect.setBounds(0, 0, width, height); int[] pixels = new int[width * height]; arrayDrawer.paint(pixels, sourceRect, destRect, width); MemoryImageSource source = new MemoryImageSource(width, height, pixels, 0, width); Image image = createImage(source); g.drawImage(image, x, y, null); if (includeChar()) { try { Image cimage = createImage(width, height); // destRect.x += x; // destRect.y += y; cimage.getGraphics().drawImage(image, 0, 0, null); ((CharArrayDrawer) arrayDrawer).paintChars(cimage.getGraphics(), sourceRect, destRect); g.drawImage(cimage, x, y, null); } catch (Exception e) { JOptionPane.showMessageDialog(this, "Problem drawing Sequence data:" + e); logger.error("" + e); // e.printStackTrace(); g.drawImage(image, x, y, null); } } else { g.drawImage(image, x, y, null); } } JCheckBox selectionBox; public boolean getDrawSelected() { return selectionBox.isSelected(); } public void setDrawSelected(boolean bool) { selectionBox.setSelected(bool); } private void bitmapSave(String format) { try { OutputStream output = new BufferedOutputStream(new FileOutputStream(getFile())); int extraWidth = getBorderPixels(); int extraHeight = getBorderPixels(); Rectangle destRect = new Rectangle(0, 0, estimateWidth(), estimateHeight()); BufferedImage i = new BufferedImage(destRect.width + extraWidth, destRect.height + extraHeight, BufferedImage.TYPE_INT_ARGB); Graphics g = i.getGraphics(); g.setColor(Color.white); g.fillRect(0, 0, destRect.width + 1 + extraWidth, destRect.height + 1 + extraHeight); g.setColor(Color.black); g.translate(extraHeight / 2, extraWidth / 2); drawAll(g, 1.0); ImageIO.write(i, format, output); // ignore success, could keep window open on failure if save could indicate success. output.close(); } catch (Exception e) { JOptionPane.showMessageDialog(this, new JTextArea("Graphics export had problem " + e)); logger.error("Exception " + e); // e.printStackTrace(); } } private void pdfSave(String format) { com.lowagie.text.Rectangle pageSize = PageSize.LETTER; Document document = new Document(pageSize); try { OutputStream output = new BufferedOutputStream(new FileOutputStream(getFile())); PdfWriter writer = PdfWriter.getInstance(document, output); document.open(); PdfContentByte cb = writer.getDirectContent(); Graphics2D g = cb.createGraphics(pageSize.getWidth(), pageSize.getHeight(), new DefaultFontMapper()); double imageScale = Math.min(pageSize.getWidth() / ((double) estimateWidth() + getBorderPixels()), pageSize.getHeight() / ((double) estimateHeight() + getBorderPixels())); g.scale(imageScale, imageScale); drawAll(g, 1.0); g.dispose(); } catch (Exception e) { JOptionPane.showMessageDialog(this, new JTextArea("Dendrogram export had problem " + e)); logger.error("Exception " + e); // e.printStackTrace(); } document.close(); } private void epsSave(String format) { com.lowagie.text.Rectangle pageSize = PageSize.LETTER; Properties p = new Properties(); p.setProperty(PSGraphics2D.PAGE_SIZE, "Letter"); p.setProperty("org.freehep.graphicsio.AbstractVectorGraphicsIO.TEXT_AS_SHAPES", Boolean.toString(false)); try { OutputStream output = new BufferedOutputStream(new FileOutputStream(getFile())); PSGraphics2D g = new PSGraphics2D(output, view); double imageScale = Math.min(pageSize.getWidth() / ((double) estimateWidth() + getBorderPixels()), pageSize.getHeight() / ((double) estimateHeight() + getBorderPixels())); g.setMultiPage(false); g.setProperties(p); g.startExport(); g.scale(imageScale, imageScale); drawAll(g, 1.0); g.endExport(); output.close(); } catch (Exception e) { JOptionPane.showMessageDialog(this, new JTextArea("Dendrogram export had problem " + e)); logger.error("Exception " + e); // e.printStackTrace(); } } private void svgSave(String format) { com.lowagie.text.Rectangle pageSize = PageSize.LETTER; Properties p = new Properties(); p.setProperty(PSGraphics2D.PAGE_SIZE, "Letter"); p.setProperty("org.freehep.graphicsio.AbstractVectorGraphicsIO.TEXT_AS_SHAPES", Boolean.toString(false)); try { OutputStream output = new BufferedOutputStream(new FileOutputStream(getFile())); SVGGraphics2D g = new SVGGraphics2D(output, view); double imageScale = Math.min(pageSize.getWidth() / ((double) estimateWidth() + getBorderPixels()), pageSize.getHeight() / ((double) estimateHeight() + getBorderPixels())); g.setProperties(p); g.startExport(); g.scale(imageScale, imageScale); drawAll(g, 1.0); g.endExport(); output.close(); } catch (Exception e) { JOptionPane.showMessageDialog(this, new JTextArea("Dendrogram export had problem " + e)); logger.error("Exception " + e); // e.printStackTrace(); } } class InclusionPanel extends JPanel { JCheckBox gtrBox, atrBox, dataBox, bboxBox, charBox; JTextField xScaleField, yScaleField; JTextField borderField; BboxRow bboxRow; SizeRow sizeRow; public boolean useBbox() { return bboxBox.isSelected(); } public boolean includeAtr() { return atrBox.isSelected(); } public void includeAtr(boolean flag) { atrBox.setSelected(flag); } public boolean includeGtr() { return gtrBox.isSelected(); } public void includeGtr(boolean flag) { gtrBox.setSelected(flag); } public boolean includeData() { return dataBox.isSelected(); } public boolean includeChar() { if (charBox == null) return false; boolean isSelected = charBox.isSelected(); return isSelected; } public void includeData(boolean flag) { dataBox.setSelected(flag); } public double getXscale() { return extractDouble(xScaleField.getText()); } public double getYscale() { return extractDouble(yScaleField.getText()); } public int getBorderPixels() { return (int) extractDouble(borderField.getText()); } private double extractDouble(String text) { try { Double tmp = new Double(text); return tmp.doubleValue(); } catch (NumberFormatException e) { return 0; } } public int getBboxWidth() { return bboxRow.xSize(); } public int getBboxHeight() { return bboxRow.ySize(); } public boolean drawSelected() { return selectionBox.isSelected(); } public void synchEnabled() { selectionBox.setEnabled( (geneSelection.getNSelectedIndexes() != 0) || (arraySelection.getNSelectedIndexes() != 0)); bboxRow.setEnabled(bboxBox.isSelected()); // deal with array tree... if (getArrayRootNode() == null) { // no array clustering... atrBox.setSelected(false); atrBox.setEnabled(false); } else { if (selectionBox.isSelected()) { // outputting selection... if (arraySelection.getSelectedNode() == null) { // no array node selected... atrBox.setSelected(false); atrBox.setEnabled(false); } else { atrBox.setEnabled(true); } } else { // outputting global, array tree exists... atrBox.setEnabled(true); } } // deal with gene tree... if (getGeneRootNode() == null) { // no gene clustering... gtrBox.setSelected(false); gtrBox.setEnabled(false); } else { if (selectionBox.isSelected()) { // outputting selection... if (geneSelection.getSelectedNode() == null) { // no gene node selected... gtrBox.setSelected(false); gtrBox.setEnabled(false); } else { gtrBox.setEnabled(true); } } else { // outputting global, gene tree exists... gtrBox.setEnabled(true); } } if (arrayDrawer == null) { dataBox.setSelected(false); dataBox.setEnabled(false); } updateSize(); } /** * This routine selects options so that they make sense with respect to the current data * in the dendrogram. It should be called during initialization before synchEnabled() */ public void synchSelected() { // do we output selected or the whole thing? selectionBox.setSelected( (geneSelection.getNSelectedIndexes() != 0) || (arraySelection.getNSelectedIndexes() != 0)); if (selectionBox.isSelected()) { //outputting selected... atrBox.setSelected(arraySelection.getSelectedNode() != null); gtrBox.setSelected(geneSelection.getSelectedNode() != null); } else { // outputing everything atrBox.setSelected(getArrayRootNode() != null); gtrBox.setSelected(getGeneRootNode() != null); } // always inlcude the data by default... if you have the drawer, that is. dataBox.setSelected(arrayDrawer != null); // recalculateBbox(); updateSize(); } public void recalculateBbox() { if (headerSelectionPanel == null) { bboxRow.setXsize(2); bboxRow.setYsize(2); } else { bboxRow.setXsize(headerSelectionPanel.geneMaxLength()); bboxRow.setYsize(headerSelectionPanel.arrayMaxLength()); } } public void updateSize() { try { sizeRow.setXsize(estimateWidth()); sizeRow.setYsize(estimateHeight()); setBorderPixels(getBorderPixels()); } catch (Exception e) { // ignore... } } InclusionPanel() { documentListener = new DocumentListener() { public void changedUpdate(DocumentEvent e) { updateSize(); } public void insertUpdate(DocumentEvent e) { updateSize(); } public void removeUpdate(DocumentEvent e) { updateSize(); } }; setupWidgets(); recalculateBbox(); } DocumentListener documentListener = null; private void setupWidgets() { setLayout(new BoxLayout(this, BoxLayout.Y_AXIS)); ActionListener syncher = new ActionListener() { public void actionPerformed(ActionEvent e) { synchEnabled(); } }; add(new JLabel("Include")); selectionBox = new JCheckBox("Selection Only "); selectionBox.addActionListener(syncher); JPanel outputPanel = new JPanel(); outputPanel.add(selectionBox); add(outputPanel); if (!model.isSymmetrical()) gtrBox = new JCheckBox("Node Tree "); else gtrBox = new JCheckBox("Left Node Tree"); gtrBox.addActionListener(syncher); outputPanel = new JPanel(); outputPanel.add(gtrBox); add(outputPanel); if (!model.isSymmetrical()) atrBox = new JCheckBox("Attribute Tree"); else atrBox = new JCheckBox("Top Node Tree "); atrBox.addActionListener(syncher); outputPanel = new JPanel(); outputPanel.add(atrBox); add(outputPanel); dataBox = new JCheckBox("Heat Map "); dataBox.addActionListener(syncher); outputPanel = new JPanel(); outputPanel.add(dataBox); add(outputPanel); if (hasChar) { charBox = new JCheckBox("Sequence"); charBox.addActionListener(syncher); outputPanel = new JPanel(); outputPanel.add(charBox); add(outputPanel); } JPanel scalePanel = new JPanel(); scalePanel.setLayout(new BoxLayout(scalePanel, BoxLayout.Y_AXIS)); JPanel Xsub = new JPanel(); xScaleField = new JTextField(Double.toString(arrayMap.getScale())); Xsub.add(new JLabel("x scale")); Xsub.add(xScaleField); scalePanel.add(Xsub); double yScale = geneMap.getScale(); // if (yScale < 15) yScale = 15; yScaleField = new JTextField(Double.toString(yScale)); JPanel Ysub = new JPanel(); Ysub.add(new JLabel("y scale")); Ysub.add(yScaleField); scalePanel.add(Ysub); borderField = new JTextField(Double.toString(GraphicsExportPanel.this.getBorderPixels())); JPanel Bsub = new JPanel(); Bsub.add(new JLabel("Border ")); Bsub.add(borderField); scalePanel.add(Bsub); scalePanel.add(new JLabel("Use apple key to select multiple headers")); add(scalePanel); xScaleField.getDocument().addDocumentListener(documentListener); yScaleField.getDocument().addDocumentListener(documentListener); borderField.getDocument().addDocumentListener(documentListener); bboxBox = new JCheckBox("Bounding Box?", hasBbox()); bboxBox.addActionListener(syncher); outputPanel = new JPanel(); outputPanel.add(bboxBox); bboxRow = new BboxRow(); if (hasBbox()) { add(outputPanel); add(bboxRow); } sizeRow = new SizeRow(); add(sizeRow); } class BboxRow extends SizeRow { protected void setupWidgets() { DocumentListener documentListener = new DocumentListener() { public void changedUpdate(DocumentEvent e) { updateSize(); } public void insertUpdate(DocumentEvent e) { updateSize(); } public void removeUpdate(DocumentEvent e) { updateSize(); } }; add(new JLabel("BBox size:")); xSize = new JTextField("2", 4); ySize = new JTextField("2", 4); add(xSize); add(new JLabel("x")); add(ySize); add(new JLabel("(pixels)")); xSize.getDocument().addDocumentListener(documentListener); ySize.getDocument().addDocumentListener(documentListener); } } class SizeRow extends JPanel { JTextField xSize, ySize; public SizeRow() { setupWidgets(); } protected void setupWidgets() { add(new JLabel("Total Size:")); xSize = new JTextField("2", 5); ySize = new JTextField("2", 5); add(xSize); add(new JLabel("x")); add(ySize); add(new JLabel("(pixels)")); } double conversionFactor = 1; int xSize() { return (int) (extractDouble(xSize.getText()) * conversionFactor); } int ySize() { return (int) (extractDouble(ySize.getText()) * conversionFactor); } void setXsize(int points) { xSize.setText(convert(points)); } void setYsize(int points) { ySize.setText(convert(points)); } /* * makes an inch representation of the points, with 2 decimal places. */ private String convert(int points) { Double inch = new Double(Math.rint(((double) points * 100) / conversionFactor) / 100.0); return inch.toString(); } public void setEnabled(boolean flag) { super.setEnabled(flag); xSize.setEnabled(flag); ySize.setEnabled(flag); } } } class HeaderSelectionPanel extends JPanel { private JCheckBox geneAnnoInside, arrayAnnoInside; private HeaderSummary geneSummary = new HeaderSummary(); public HeaderSummary getGeneSummary() { return geneSummary; } private HeaderSummary arraySummary = new HeaderSummary(); public HeaderSummary getArraySummary() { return arraySummary; } public JList geneList, arrayList; public String getGeneAnno(int i) { return geneSummary.getSummary(geneHeaderInfo, i); // return assembleAnno(i, geneHeaderInfo, geneList.getSelectedIndices()); } public String getArrayAnno(int i) { return arraySummary.getSummary(arrayHeaderInfo, i); // return assembleAnno(i, arrayHeaderInfo, arrayList.getSelectedIndices()); } public int arrayMaxLength() { if (inclusionPanel == null) return 100; FontMetrics fontMetrics = getFontMetrics(getArrayFont()); int max = 0; boolean drawSelected = inclusionPanel.drawSelected(); for (int i = minArray(); i < maxArray(); i++) { if (drawSelected && (arraySelection.isIndexSelected(i) == false)) continue; String anno = getArrayAnno(i); if (anno == null) continue; int length = fontMetrics.stringWidth(anno); if (length > max) max = length; } return max; } public int geneMaxLength() { if (inclusionPanel == null) return 100; FontMetrics fontMetrics = getFontMetrics(getGeneFont()); int max = 0; boolean drawSelected = inclusionPanel.drawSelected(); for (int i = minGene(); i < maxGene(); i++) { // if (drawSelected && (geneSelection.isIndexSelected(i) == false)) continue; // getGeneAnno returns null in the breaks between k-means clusters if (getGeneAnno(i) == null) continue; int length = fontMetrics.stringWidth(getGeneAnno(i)); if (length > max) { max = length; } } return max; } public int getLength(String txt) { if (txt == null) return 0; // FontMetrics fontMetrics = getFontMetrics(getGraphics().getFont()); FontMetrics fontMetrics = getFontMetrics(getGeneFont()); return fontMetrics.stringWidth(txt); } public int numArrayHeaders() { return arrayList.getSelectedIndices().length; } public int numGeneHeaders() { return geneList.getSelectedIndices().length; } public void deselectHeaders() { arrayList.clearSelection(); geneList.clearSelection(); } public boolean geneAnnoInside() { return geneAnnoInside.isSelected(); } public boolean arrayAnnoInside() { return arrayAnnoInside.isSelected(); } public void addNotify() { super.addNotify(); inclusionPanel.recalculateBbox(); } HeaderSelectionPanel() { setLayout(new BoxLayout(this, BoxLayout.Y_AXIS)); add(new JLabel("Gene Headers")); String[] geneHeaders = geneHeaderInfo.getNames(); if (geneHeaders == null) { geneList = new JList(new String[0]); } else { geneList = new JList(geneHeaders); } geneList.setVisibleRowCount(5); add(new JScrollPane(geneList)); geneAnnoInside = new JCheckBox("Right of Tree?"); // add(geneAnnoInside); add(new JLabel("Array Headers")); String[] arrayHeaders = arrayHeaderInfo.getNames(); if (arrayHeaders == null) { arrayList = new JList(new String[0]); } else { arrayList = new JList(arrayHeaders); } arrayList.setVisibleRowCount(5); add(new JScrollPane(arrayList)); arrayAnnoInside = new JCheckBox("Below Tree?"); arrayAnnoInside.setSelected(true); arrayAnnoInside.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { inclusionPanel.updateSize(); } }); add(arrayAnnoInside); ListSelectionListener tmp = new ListSelectionListener() { public void valueChanged(ListSelectionEvent e) { if (inclusionPanel != null) { inclusionPanel.recalculateBbox(); inclusionPanel.updateSize(); geneSummary.setIncluded(geneList.getSelectedIndices()); arraySummary.setIncluded(arrayList.getSelectedIndices()); } } }; geneList.addListSelectionListener(tmp); arrayList.addListSelectionListener(tmp); arrayList.setSelectedIndex(0); geneList.setSelectedIndex(1); setupSelected(); } public void setupSelected() { geneSummary.setIncluded(geneList.getSelectedIndices()); arraySummary.setIncluded(arrayList.getSelectedIndices()); if (inclusionPanel != null) inclusionPanel.updateSize(); } } class FilePanel extends JPanel { private JTextField fileField; String getFilePath() { return fileField.getText(); } File getFile() { return new File(getFilePath()); } void setFilePath(String fp) { fileField.setText(fp); fileField.invalidate(); fileField.revalidate(); fileField.repaint(); } public FilePanel(String initial) { super(); add(new JLabel("Export To: ")); fileField = new JTextField(initial); add(fileField); JButton chooseButton = new JButton("Browse"); chooseButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { try { JFileChooser chooser = new JFileChooser(); int returnVal = chooser.showSaveDialog(GraphicsExportPanel.this); if (returnVal == JFileChooser.APPROVE_OPTION) { fileField.setText(chooser.getSelectedFile().getCanonicalPath()); } } catch (java.io.IOException ex) { logger.error("Got exception " + ex); } } }); add(chooseButton); } } }