X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=0cbdfbe3e3fe813a9b4433e4496b14d4e8c3ead8;hb=ac07859006686a2c62bcf57b24742eb610bc46f0;hp=11c9e2b2f9a8494e6d976e0c9af471ca6a37acb9;hpb=49901c2879a03b48fafb84a251e976230459c77f;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 11c9e2b..0cbdfbe 100755 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,71 +1,193 @@ package jalview.gui; import jalview.jbgui.GAlignmentPanel; +import jalview.schemes.*; +import jalview.analysis.*; +import jalview.datamodel.*; import java.awt.*; import java.awt.event.*; +import java.awt.print.*; +import java.io.*; +import java.awt.image.*; +import org.jibble.epsgraphics.*; +import javax.imageio.*; -public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener + + +public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable { AlignViewport av; OverviewPanel overviewPanel; SeqPanel seqPanel; IdPanel idPanel; + IdwidthAdjuster idwidthAdjuster; public AlignFrame alignFrame; ScalePanel scalePanel; - ScorePanel scorePanel; + 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); - idPanel.addNotify(); + 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); + + Dimension d = calculateIdWidth(); + d.setSize( d.width+4, d.height); + idPanel.idCanvas.setPreferredSize( d ); + hscrollFillerPanel.setPreferredSize( d ); + scalePanelHolder.add(scalePanel, BorderLayout.CENTER); - scorePanelHolder.add(scorePanel, BorderLayout.CENTER); seqPanelHolder.add(seqPanel, BorderLayout.CENTER); - setScrollValues(0,0); + + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + invalidate(); + setScrollValues(0,0); + Dimension d = calculateIdWidth(); + d.setSize( d.width+4, d.height); + idPanel.idCanvas.setPreferredSize( d ); + RefreshPanels(); + } + }); + hscroll.addAdjustmentListener(this); vscroll.addAdjustmentListener(this); - selectAll(false); addComponentListener(new ComponentAdapter() { - public void componentResized(ComponentEvent evt) + public void componentResized(ComponentEvent evt) { RefreshPanels(); } }); + setFocusable(true); + addKeyListener(new KeyAdapter() + { + public void keyPressed(KeyEvent evt) + { + switch(evt.getKeyCode()) + { + case 27: // escape key + av.setSelectionGroup(null); + RefreshPanels(); + 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() + Dimension calculateIdWidth() { - return av.getSelection().size(); - } - - public void selectAll(boolean flag) { - int i = 0; - if (flag) { - while (i < av.getAlignment().getHeight()) { - if (! av.getSelection().contains(av.getAlignment().getSequenceAt(i))) { - av.getSelection().addElement(av.getAlignment().getSequenceAt(i)); - } - i++; - } - } else { - av.getSelection().clear(); + 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(); + 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; @@ -143,37 +353,319 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene hscroll.setValues(x,hextent,0,av.getAlignment().getWidth()); vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() ); - seqPanel.seqCanvas.paintFlag = true; - repaint(); } 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()); + } } if(overviewPanel!=null) overviewPanel.setBoxPosition(); + if(av.getWrapAlignment() || !fastPaint) + repaint(); + else + { + seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX, + av.getStartSeq() - oldY); + idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY); + scalePanel.repaint(); + if (av.getShowAnnotation()) + annotationPanel.fastPaint(av.getStartRes() - oldX); + } - repaint(); } + 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; + + 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 - 30)/av.getCharHeight())-1; + int pagesWide = av.getAlignment().getWidth() / totalRes +1; + int pagesHigh = av.getAlignment().getHeight() / totalSeq +1; + + if (pi >= pagesWide*pagesHigh) + return Printable.NO_SUCH_PAGE; + + ///////////////////////////// + /// 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()) + endRes = av.getAlignment().getWidth(); + + startSeq = (pi / pagesWide) * totalSeq; + endSeq = startSeq + totalSeq; + if(endSeq > av.getAlignment().getHeight()) + endSeq = av.getAlignment().getHeight(); + + + //////////////// + //draw Scale + pg.translate(idWidth,0); + scalePanel.drawScale(pg, startRes, endRes, pwidth-idWidth); + + pg.translate(-idWidth, 30); + //////////////// + // Draw the ids + Color currentColor=null; + Color currentTextColor=null; + for(int i=startSeq; i totalChunks ) + return Printable.NO_SUCH_PAGE; + + //////////////// + // Draw the ids + pg.setClip(0,0,pwidth, noChunksOnPage*chunkHeight); + + pg.setColor(Color.black); + + int rowSize = av.getEndRes() - av.getStartRes(); + // Draw the rest of the panels + + for(int ypos=2*av.charHeight, row=av.getEndRes(); row