X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=02330a58e5b492cc99630abb98539d6ef7152d1e;hb=1a6fbadeec90e7524075ed6e37bbe4b7bba97a94;hp=d8131b4706c170a857f2e98f8848c79c0ea2990e;hpb=416b11342497ccc6f86cabfd5ae2a608f402ce9c;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index d8131b4..02330a5 100755 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -22,10 +22,13 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene SeqPanel seqPanel; IdPanel idPanel; IdwidthAdjuster idwidthAdjuster; - SecondaryStructurePanel ssPanel; public AlignFrame alignFrame; ScalePanel scalePanel; - ScorePanel scorePanel; + AnnotationPanel annotationPanel; + AnnotationLabels alabels; + + // this value is set false when selection area being dragged + boolean fastPaint = true; public AlignmentPanel(AlignFrame af, final AlignViewport av) { @@ -35,51 +38,29 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene idPanel = new IdPanel (av, this); scalePanel = new ScalePanel(av, this); - scorePanel = new ScorePanel(av); - ssPanel = new SecondaryStructurePanel(av); - - secondaryPanelHolder.add(ssPanel, BorderLayout.CENTER); idPanelHolder.add(idPanel, BorderLayout.CENTER); idwidthAdjuster = new IdwidthAdjuster(this); idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER); - Dimension d = calculateIdWidth(); - d.setSize( d.width+4, d.height); - idPanel.idCanvas.setPreferredSize( d ); - hscrollFillerPanel.setPreferredSize( d ); + annotationPanel = new AnnotationPanel(this); + alabels = new AnnotationLabels(this); - scalePanelHolder.add(scalePanel, BorderLayout.CENTER); - scorePanelHolder.add(scorePanel, BorderLayout.CENTER); - seqPanelHolder.add(seqPanel, BorderLayout.CENTER); + annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize()); + annotationScroller.setPreferredSize(annotationPanel.getPreferredSize()); + annotationScroller.setViewportView(annotationPanel); + annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER); + fontChanged(); - if(seqPanel.seqCanvas.getWidth()==0) - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - public void run() - { - setScrollValues(0,0); - Dimension d = calculateIdWidth(); - d.setSize( d.width+4, d.height); - idPanel.idCanvas.setPreferredSize( d ); - hscrollFillerPanel.setPreferredSize( d ); - RefreshPanels(); - } - }); + scalePanelHolder.add(scalePanel, BorderLayout.CENTER); + seqPanelHolder.add(seqPanel, BorderLayout.CENTER); + setScrollValues(0, 0); hscroll.addAdjustmentListener(this); vscroll.addAdjustmentListener(this); - addComponentListener(new ComponentAdapter() - { - public void componentResized(ComponentEvent evt) - { - RefreshPanels(); - } - }); - setFocusable(true); addKeyListener(new KeyAdapter() { @@ -89,18 +70,22 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene { case 27: // escape key av.setSelectionGroup(null); - RefreshPanels(); + 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: @@ -110,6 +95,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene alignFrame.moveSelectedSequences(true); break; case KeyEvent.VK_F: + if(evt.isControlDown()) alignFrame.findMenuItem_actionPerformed(null); break; } @@ -117,6 +103,20 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene }); } + public void fontChanged() + { + // set idCanvas bufferedImage to null + // to prevent drawing old image + idPanel.idCanvas.gg = null; + annotationPanel.adjustPanelHeight(); + Dimension d = calculateIdWidth(); + d.setSize(d.width + 4, d.height); + idPanel.idCanvas.setPreferredSize(d); + hscrollFillerPanel.setPreferredSize(d); + repaint(); + } + + Dimension calculateIdWidth() { Graphics g = this.getGraphics(); @@ -146,6 +146,20 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene 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); } @@ -176,35 +190,25 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene } - public void setGraphPanelVisible(boolean b) + public void setAnnotationVisible(boolean b) { - idSpaceFillerPanel.setVisible(b); - scorePanelHolder.setVisible(b); - - RefreshPanels(); - // bit annoying to call this twice, can you do better? - RefreshPanels(); + annotationSpaceFillerHolder.setVisible(b); + annotationScroller.setVisible(b); } - public void setSecondaryStructureVisible(boolean b) - { - secondaryPanelHolder.setVisible(b); - RefreshPanels(); - } public void setWrapAlignment(boolean wrap) { - scorePanelHolder.setVisible(!wrap); scalePanelHolder.setVisible(!wrap); - secondaryPanelHolder.setVisible(!wrap); - hscroll.setVisible(!wrap); - idwidthAdjuster.setVisible(!wrap); - idSpaceFillerPanel.setVisible(!wrap); + + av.setShowAnnotation(!wrap); + annotationScroller.setVisible(!wrap); + annotationSpaceFillerHolder.setVisible(!wrap); idSpaceFillerPanel1.setVisible(!wrap); - RefreshPanels(); + repaint(); } @@ -222,46 +226,16 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene al.getWidth() ); c.calculate(); - c.verdict(false, 100); + c.verdict(false, av.ConsPercGaps); ConservationColourScheme ccs = new ConservationColourScheme(c, cs); av.setGlobalColourScheme( ccs ); } - RefreshPanels(); + repaint(); } - public void RefreshPanels() - { - - requestFocus(); - invalidate(); - idPanelHolder.setPreferredSize(idPanel.idCanvas.getPreferredSize()); - if(idPanel.idCanvas.getPreferredSize()!=null) - hscrollFillerPanel.setPreferredSize(new Dimension(idPanel.idCanvas.getPreferredSize().width, 12)); - idSpaceFillerPanel1.setPreferredSize(new Dimension(500, - av.charHeight / 2 + 12)); - scalePanelHolder.setPreferredSize(new Dimension(500, - av.charHeight / 2 + 12)); - - if (av.getWrapAlignment()) - { - int max = av.alignment.getWidth() / - (seqPanel.seqCanvas.getWidth() / av.charWidth)+1 ; - - vscroll.setValues(0, 1, 0, max); - } - else - { - av.getConsensus(true); - if (overviewPanel != null) - overviewPanel.updateOverviewImage(); - setScrollValues(av.getStartRes(), av.getStartSeq()); - } - - repaint(); - } int hextent = 0; int vextent = 0; @@ -273,35 +247,40 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene { if(vscroll.getValue()<1) return false; + fastPaint = false; vscroll.setValue(vscroll.getValue() - 1); } else { if(vextent+vscroll.getValue() >= 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; - hscroll.setValue(hscroll.getValue() - 1); - } - else - { - if(hextent+hscroll.getValue() >= av.getAlignment().getWidth()) - return false; - hscroll.setValue(hscroll.getValue() + 1); - } - return true; - } + 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) @@ -329,13 +308,13 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene hscroll.setValues(x,hextent,0,av.getAlignment().getWidth()); vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() ); - repaint(); - } public void adjustmentValueChanged(AdjustmentEvent evt) { + int oldX = av.getStartRes(); + int oldY = av.getStartSeq(); if (evt.getSource() == hscroll) { @@ -349,7 +328,9 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene int offy = vscroll.getValue(); if (av.getWrapAlignment()) { - av.setStartRes( vscroll.getValue() * av.getChunkWidth()); + int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()); + av.setStartRes( vscroll.getValue() * rowSize ); + av.setEndRes( (vscroll.getValue()+1) * rowSize ); } else { @@ -362,7 +343,46 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene if(overviewPanel!=null) overviewPanel.setBoxPosition(); - repaint(); + 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 + { + if (overviewPanel != null) + overviewPanel.updateOverviewImage(); + setScrollValues(av.getStartRes(), av.getStartSeq()); + } + + + } public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException @@ -452,9 +472,17 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene // draw main sequence panel pg.translate(idWidth,0); - pg.setClip(0,0,pwidth-idWidth, pheight); seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0); + + if(av.getShowAnnotation()) + { + 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; } @@ -489,11 +517,13 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene // Draw the ids pg.setClip(0,0,pwidth, noChunksOnPage*chunkHeight); - int row = pi*noChunksOnPage; pg.setColor(Color.black); - for(int ypos=2*av.charHeight; - ypos <= pheight && row*chunkWidth