X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=a8b80d2077d84b5db70343d3a508c02c746674af;hb=e7ed63f1ea56432246a6ed1553f0fe56d26f56ea;hp=cf3e3df661db8376e5320cc2eab2edc8b9273004;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index cf3e3df..a8b80d2 100755 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,98 +1,305 @@ package jalview.gui; import jalview.jbgui.GAlignmentPanel; +import jalview.schemes.*; +import jalview.analysis.*; +import jalview.datamodel.*; import java.awt.*; -import javax.swing.*; import java.awt.event.*; +import java.awt.print.*; +import java.io.*; +import java.awt.image.*; +import org.jibble.epsgraphics.*; +import javax.imageio.*; +import javax.swing.*; + -public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener + +public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable { AlignViewport av; - public SeqPanel seqPanel; - public IdPanel idPanel; + OverviewPanel overviewPanel; + SeqPanel seqPanel; + IdPanel idPanel; + IdwidthAdjuster idwidthAdjuster; public AlignFrame alignFrame; - public ScalePanel scalePanel; - public ScorePanel scorePanel; + ScalePanel scalePanel; + AnnotationPanel annotationPanel; + AnnotationLabels alabels; - public boolean groupEdit = false; + // this value is set false when selection area being dragged + boolean fastPaint = true; - public AlignmentPanel(AlignFrame af, AlignViewport av) + public AlignmentPanel(AlignFrame af, final AlignViewport av) { alignFrame = af; this.av = av; seqPanel = new SeqPanel (av, this); idPanel = new IdPanel (av, this); - scalePanel = new ScalePanel(av); - scorePanel = new ScorePanel(av); + + scalePanel = new ScalePanel(av, this); idPanelHolder.add(idPanel, BorderLayout.CENTER); + idwidthAdjuster = new IdwidthAdjuster(this); + idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER); + + annotationPanel = new AnnotationPanel(this); + alabels = new AnnotationLabels(this); + + annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize()); + annotationScroller.setPreferredSize(annotationPanel.getPreferredSize()); + annotationScroller.setViewportView(annotationPanel); + annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER); + + fontChanged(); + scalePanelHolder.add(scalePanel, BorderLayout.CENTER); - scorePanelHolder.add(scorePanel, BorderLayout.CENTER); seqPanelHolder.add(seqPanel, BorderLayout.CENTER); - setScrollValues(0,0); + + setScrollValues(0, 0); hscroll.addAdjustmentListener(this); vscroll.addAdjustmentListener(this); - selectAll(false); - addComponentListener(new ComponentAdapter() + setFocusable(true); + addKeyListener(new KeyAdapter() { - public void componentResized(ComponentEvent evt) - { RefreshPanels(); } + public void keyPressed(KeyEvent evt) + { + switch(evt.getKeyCode()) + { + case 27: // escape key + av.setSelectionGroup(null); + repaint(); + break; + case KeyEvent.VK_X: + if(evt.isControlDown()) + alignFrame.cut_actionPerformed(null); + break; + case KeyEvent.VK_C: + if(evt.isControlDown()) + alignFrame.copy_actionPerformed(null); + break; + case KeyEvent.VK_V: + if(evt.isControlDown()) + alignFrame.paste(true); + break; + case KeyEvent.VK_A: + if(evt.isControlDown()) + alignFrame.selectAllSequenceMenuItem_actionPerformed(null); + break; + case KeyEvent.VK_DOWN: + alignFrame.moveSelectedSequences(false); + break; + case KeyEvent.VK_UP: + alignFrame.moveSelectedSequences(true); + break; + case KeyEvent.VK_F: + if(evt.isControlDown()) + alignFrame.findMenuItem_actionPerformed(null); + break; + } + } }); - } - public int countSelected() + public void fontChanged() { - return av.getSelection().size(); + // set idCanvas bufferedImage to null + // to prevent drawing old image + FontMetrics fm = getFontMetrics(av.getFont()); + + scalePanelHolder.setPreferredSize(new Dimension(10, av.charHeight+fm.getDescent())); + idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av.charHeight+fm.getDescent())); + + idPanel.idCanvas.gg = null; + annotationPanel.adjustPanelHeight(); + Dimension d = calculateIdWidth(); + d.setSize(d.width + 4, d.height); + idPanel.idCanvas.setPreferredSize(d); + hscrollFillerPanel.setPreferredSize(d); + repaint(); } - public void selectAll(boolean flag) { - int i = 0; - if (flag) { - while (i < seqPanel.align.getHeight()) { - if (! av.getSelection().contains(av.getAlignment().getSequenceAt(i))) { - av.getSelection().addElement(av.getAlignment().getSequenceAt(i)); - } - i++; - } - } else { - av.getSelection().clear(); + + Dimension calculateIdWidth() + { + Graphics g = this.getGraphics(); + if(g==null) + { + javax.swing.JFrame f = new javax.swing.JFrame(); + f.addNotify(); + g = f.getGraphics(); } + + FontMetrics fm = g.getFontMetrics(av.font); + AlignmentI al = av.getAlignment(); + + int i = 0; + int idWidth = 0; + String id; + while (i < al.getHeight() && al.getSequenceAt(i) != null) + { + SequenceI s = al.getSequenceAt(i); + if(av.getShowFullId()) + id = s.getDisplayId(); + else + id = s.getName(); + + if (fm.stringWidth(id) > idWidth) + idWidth = fm.stringWidth(id); + i++; + } + + // Also check annotation label widths + i=0; + if(al.getAlignmentAnnotation()!=null) + { + fm = g.getFontMetrics(alabels.getFont()); + while (i < al.getAlignmentAnnotation().length) + { + String label = al.getAlignmentAnnotation()[i].label; + if (fm.stringWidth(label) > idWidth) + idWidth = fm.stringWidth(label); + i++; + } + } + + return new Dimension(idWidth, 12); } + public void highlightSearchResults(int [] results) + { + seqPanel.seqCanvas.highlightSearchResults( results ); + + // do we need to scroll the panel? + if(results!=null && (av.getStartSeq()>results[0] + || av.getEndSeq()results[1] + || av.getEndRes()= av.getAlignment().getHeight()) + return false; + fastPaint = false; + vscroll.setValue(vscroll.getValue() + 1); + } + fastPaint = true; + return true; + } + + public boolean scrollRight(boolean right) + { + + if (right) + { + if (hscroll.getValue() < 1) + return false; + fastPaint = false; + hscroll.setValue(hscroll.getValue() - 1); + } + else + { + if (hextent + hscroll.getValue() >= av.getAlignment().getWidth()) + return false; + fastPaint = false; + hscroll.setValue(hscroll.getValue() + 1); + } + fastPaint = true; + return true; + } + + public void setScrollValues(int x, int y) { - hextent = (int)(seqPanel.seqCanvas.getWidth()/av.getCharWidth()); - vextent = seqPanel.seqCanvas.getHeight()/av.getCharHeight(); + av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1); + + hextent = seqPanel.seqCanvas.getWidth()/av.charWidth; + vextent = seqPanel.seqCanvas.getHeight()/av.charHeight; + + if(hextent > av.alignment.getWidth()) + hextent = av.alignment.getWidth(); + if(vextent > av.alignment.getHeight()) + vextent = av.alignment.getHeight(); if(hextent+x > av.getAlignment().getWidth()) x = av.getAlignment().getWidth()- hextent; @@ -109,28 +316,386 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene hscroll.setValues(x,hextent,0,av.getAlignment().getWidth()); vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() ); + + } - public void adjustmentValueChanged(AdjustmentEvent evt) { + public void adjustmentValueChanged(AdjustmentEvent evt) + { + int oldX = av.getStartRes(); + int oldY = av.getStartSeq(); if (evt.getSource() == hscroll) { int x = hscroll.getValue(); av.setStartRes(x); - av.setEndRes(x + (int)(seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1)); + av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1); } if (evt.getSource() == vscroll) { - int offy = vscroll.getValue(); + int offy = vscroll.getValue(); + if (av.getWrapAlignment()) + { + int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()); + av.setStartRes( vscroll.getValue() * rowSize ); + av.setEndRes( (vscroll.getValue()+1) * rowSize ); + } + else + { av.setStartSeq(offy); - av.setEndSeq(offy + seqPanel.seqCanvas.getHeight()/av.getCharHeight()); + av.setEndSeq(offy + seqPanel.seqCanvas.getHeight() / av.getCharHeight()); + } } - repaint(); + if(overviewPanel!=null) + overviewPanel.setBoxPosition(); + + if(av.getWrapAlignment() || !fastPaint) + repaint(); + else + { + idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY); + seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX, + av.getStartSeq() - oldY); + + scalePanel.repaint(); + if (av.getShowAnnotation()) + annotationPanel.fastPaint(av.getStartRes() - oldX); + } + + } + + + public void paintComponent(Graphics g) + { + invalidate(); + Dimension d = idPanel.idCanvas.getPreferredSize(); + idPanelHolder.setPreferredSize(d); + hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12)); + validate(); + + if (av.getWrapAlignment()) + { + int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()); + vscroll.setMaximum(max); + vscroll.setUnitIncrement(1); + vscroll.setVisibleAmount(1); + } + else + { + setScrollValues(av.getStartRes(), av.getStartSeq()); + } + + + + } + + public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException + { + pg.translate((int)pf.getImageableX(), (int)pf.getImageableY()); + + int pwidth = (int) pf.getImageableWidth(); + int pheight = (int) pf.getImageableHeight(); + + if (av.getWrapAlignment()) + return printWrappedAlignment(pg, pwidth,pheight, pi); + else + return printUnwrapped(pg,pwidth, pheight,pi); + } + + public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException + { + + int idWidth = calculateIdWidth().width + 4; + FontMetrics fm = getFontMetrics(av.getFont()); + int scaleHeight = av.charHeight + fm.getDescent(); + + pg.setColor(Color.white); + pg.fillRect(0, 0, pwidth, pheight); + pg.setFont(av.getFont()); + + //////////////////////////////////// + /// How many sequences and residues can we fit on a printable page? + int totalRes = (pwidth - idWidth) / av.getCharWidth(); + + int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) - 1; + + int pagesWide = av.getAlignment().getWidth() / totalRes + 1; + + ///////////////////////////// + /// Only print these sequences and residues on this page + int startRes, endRes, startSeq, endSeq; + startRes = (pi % pagesWide) * totalRes; + endRes = startRes + totalRes - 1; + if (endRes > av.getAlignment().getWidth()-1) + endRes = av.getAlignment().getWidth()-1; + + startSeq = (pi / pagesWide) * totalSeq; + endSeq = startSeq + totalSeq; + if (endSeq > av.getAlignment().getHeight()) + endSeq = av.getAlignment().getHeight(); + + int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight; + + if (av.showAnnotation) + pagesHigh += annotationPanel.getHeight(); + + pagesHigh /= pheight; + + if (pi >= pagesWide * pagesHigh) + return Printable.NO_SUCH_PAGE; + + //draw Scale + pg.translate(idWidth, 0); + scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight); + pg.translate( -idWidth, scaleHeight); + //////////////// + // Draw the ids + Color currentColor = null; + Color currentTextColor = null; + for (int i = startSeq; i < endSeq; i++) + { + if (av.getSelectionGroup() != null && + av.getSelectionGroup().sequences. + contains(av.getAlignment().getSequenceAt(i))) + { + currentColor = Color.gray; + currentTextColor = Color.black; + } + else + { + currentColor = av.getAlignment().getSequenceAt(i).getColor(); + currentTextColor = Color.black; + } + + pg.setColor(currentColor); + pg.fillRect(0, + jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, + av.getCharHeight()), + idWidth, + av.getCharHeight()); + + pg.setColor(currentTextColor); + + String string = av.getAlignment().getSequenceAt(i).getName(); + if (av.getShowFullId()) + string = av.getAlignment().getSequenceAt(i).getDisplayId(); + + pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight + (startSeq, i, av.getCharHeight()) + av.getCharHeight() - + (av.getCharHeight() / 5)); + } + + // draw main sequence panel + pg.translate(idWidth, 0); + seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, + startRes, startSeq, 0); + + + if (av.showAnnotation && endSeq == av.alignment.getHeight()) + { + pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight); + alabels.drawComponent( (Graphics2D) pg); + pg.translate(idWidth, 0); + annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes+1); + } + + return Printable.PAGE_EXISTS; + } + public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException + { + int idWidth = calculateIdWidth().width + 4; + + int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth - idWidth); + int totalHeight = totalHeight = (av.alignment.getHeight() + 2) * + ( (av.alignment.getWidth() + / resWidth) + 1) * av.charHeight; + + + pg.setColor(Color.white); + pg.fillRect(0, 0, pwidth, pheight); + pg.setFont(av.getFont()); + + //////////////// + // Draw the ids + pg.setColor(Color.black); + + pg.translate(0, -pi * pheight); + + pg.setClip(0,pi*pheight,pwidth, pheight); + + int ypos = 2 * av.charHeight; + do + { + for (int i = 0; i < av.alignment.getHeight(); i++) + { + SequenceI s = av.alignment.getSequenceAt(i); + String string = s.getName(); + if (av.getShowFullId()) + string = s.getDisplayId(); + + pg.drawString(string, 0, + AlignmentUtil.getPixelHeight(0, i, av.charHeight) + + ypos + + av.charHeight - (av.charHeight / 5)); + + } + + ypos += (av.alignment.getHeight() + 2) * av.charHeight; + + } + while (ypos < totalHeight); + + pg.translate(idWidth, 0); + + seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0); + + if (pi * pheight < totalHeight) + return Printable.PAGE_EXISTS; + else + return Printable.NO_SUCH_PAGE; + + + + } + + + public void makeEPS() + { + int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight; + int width = seqPanel.getWidth() + idPanel.getWidth(); + + if (!av.getWrapAlignment()) + { + height = (av.alignment.getHeight()+1) * av.charHeight + 30; + width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth; + } + if(av.getShowAnnotation()) + { + height += annotationPanel.getPreferredSize().height; + } + + try + { + jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty( + "LAST_DIRECTORY"), new String[]{"eps"}, "Encapsulated Postscript"); + chooser.setFileView(new jalview.io.JalviewFileView()); + chooser.setDialogTitle("Create EPS file from alignment"); + chooser.setToolTipText("Save"); + + int value = chooser.showSaveDialog(this); + if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION) + return; + + jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath()); + FileOutputStream out = new FileOutputStream(chooser.getSelectedFile()); + EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width, height); + if (av.getWrapAlignment()) + printWrappedAlignment(pg, width, height, 0); + else + printUnwrapped(pg, width, height, 0); + + + pg.flush(); + pg.close(); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + + public void makePNG() + { + int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight; + int width = seqPanel.getWidth() + idPanel.getWidth(); + + if (!av.getWrapAlignment()) + { + height = (av.alignment.getHeight()+1) * av.charHeight + 30; + width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth; + } + + if(av.getShowAnnotation()) + { + height += annotationPanel.getPreferredSize().height; + } + + + + try + { + jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty( + "LAST_DIRECTORY"), new String[]{"png"}, "Portable network graphics"); + chooser.setFileView(new jalview.io.JalviewFileView()); + chooser.setDialogTitle("Create EPS file from alignment"); + chooser.setToolTipText("Save"); + + int value = chooser.showSaveDialog(this); + if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION) + return; + + jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath()); + FileOutputStream out = new FileOutputStream(chooser.getSelectedFile()); + + BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB); + Graphics2D png = (Graphics2D)bi.getGraphics(); + + png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON); + + if (av.getWrapAlignment()) + printWrappedAlignment(png, width, height, 0); + else + printUnwrapped(png, width, height, 0); + + ImageIO.write(bi, "png", out); + out.close(); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + +} + +class Preview extends JFrame +{ + + public Preview(Image image) + { + setResizable(true); + setSize(image.getWidth(this), image.getHeight(this)); + setVisible(true); + getContentPane().setLayout(new BorderLayout()); + getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER); + validate(); + repaint(); + } } + +class PreviewPanel extends JPanel +{ + Image image; + public PreviewPanel(Image image) + { + this.image = image; + } + public void paintComponent(Graphics g) + { + if(image!=null) + g.drawImage(image,0,0,this); + else + System.out.println("image is null"); + } +} + + + +