X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=f1874b161a5a82aa55297c1739c6d456e1950625;hb=7a9027c14dc5a1c3daade1f19dd5b6e87df1095e;hp=4a2e3f16a5c9afb4d2d653762d0f2d1747b5e50c;hpb=4545be0e1a91dc31383dbd6a2046d82fb2a317e9;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 4a2e3f1..f1874b1 100755 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -21,10 +21,14 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene OverviewPanel overviewPanel; SeqPanel seqPanel; IdPanel idPanel; - SecondaryStructurePanel ssPanel; + IdwidthAdjuster idwidthAdjuster; 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) { @@ -34,41 +38,30 @@ 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 iap = new IdwidthAdjuster(this); - idSpaceFillerPanel1.add(iap, 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); + + 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); - addComponentListener(new ComponentAdapter() - { - public void componentResized(ComponentEvent evt) - { - RefreshPanels(); - } - }); - - - // hscroll.setFocusable(false); - // vscroll.setFocusable(false); setFocusable(true); - addKeyListener(new KeyAdapter() { public void keyPressed(KeyEvent evt) @@ -77,18 +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: @@ -98,6 +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; } @@ -105,6 +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(); @@ -134,6 +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); } @@ -164,34 +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(); } @@ -209,50 +226,20 @@ 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; - - int h = (av.alignment.getHeight() + 2) * av.charHeight; - vextent = seqPanel.seqCanvas.getHeight() / h; - vscroll.setValues(0, vextent, 0, max); - } - else - - setScrollValues(av.getStartRes(), av.getStartSeq()); - av.getConsensus(true); - if (overviewPanel != null) - overviewPanel.updateOverviewImage(); - - validate(); - repaint(); - } + int hextent = 0; int vextent = 0; - // return value is true if the scroll is valid public boolean scrollUp(boolean up) { @@ -260,41 +247,53 @@ 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) { - hextent = 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; @@ -312,13 +311,14 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene 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) { @@ -332,7 +332,9 @@ 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 { @@ -341,11 +343,49 @@ 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 @@ -364,7 +404,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException { - int idWidth = calculateIdWidth().width; + int idWidth = calculateIdWidth().width + 4; pg.setColor(Color.white); @@ -397,10 +437,10 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene //////////////// //draw Scale - pg.translate(30,0); + pg.translate(idWidth,0); scalePanel.drawScale(pg, startRes, endRes, pwidth-idWidth); - pg.translate(-30, 30); + pg.translate(-idWidth, 30); //////////////// // Draw the ids Color currentColor=null; @@ -435,9 +475,17 @@ 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; } @@ -445,7 +493,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException { - int idWidth = calculateIdWidth().width; + int idWidth = calculateIdWidth().width+4; if( seqPanel.seqCanvas.getWidth() < pwidth-idWidth) pwidth = seqPanel.seqCanvas.getWidth() + idWidth; @@ -470,13 +518,14 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene //////////////// // Draw the ids - pg.setClip(0,0,pwidth, noChunksOnPage*chunkHeight); +// 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