X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=75729c330775e2b93ab5067126233e926b726e18;hb=8004878db16757b62ee2c35738506bc4509428cf;hp=95a8e7cb916709f034378af8435be185f6522236;hpb=2cd1aa94f5fbcdc8a5facf3ee34447fee96ac5be;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 95a8e7c..75729c3 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) { @@ -35,22 +38,25 @@ 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); + 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); @@ -63,7 +69,6 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene Dimension d = calculateIdWidth(); d.setSize( d.width+4, d.height); idPanel.idCanvas.setPreferredSize( d ); - hscrollFillerPanel.setPreferredSize( d ); RefreshPanels(); } }); @@ -92,15 +97,19 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene 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: @@ -110,6 +119,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene alignFrame.moveSelectedSequences(true); break; case KeyEvent.VK_F: + if(evt.isControlDown()) alignFrame.findMenuItem_actionPerformed(null); break; } @@ -176,32 +186,30 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene } - public void setGraphPanelVisible(boolean b) + public void setAnnotationVisible(boolean b) { - idSpaceFillerPanel.setVisible(b); - scorePanelHolder.setVisible(b); + annotationSpaceFillerHolder.setVisible(b); + annotationScroller.setVisible(b); + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + RefreshPanels(); + } + }); - RefreshPanels(); - // bit annoying to call this twice, can you do better? - RefreshPanels(); } - 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(); @@ -232,41 +240,36 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene RefreshPanels(); } + public void RefreshPanels() { + requestFocus(); + invalidate(); + + Dimension d = idPanel.idCanvas.getPreferredSize(); + idPanelHolder.setPreferredSize(d); + hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12)); + + if (av.getWrapAlignment()) + { + int max = av.alignment.getWidth() / + (seqPanel.seqCanvas.getWidth() / av.charWidth) + 1; + vscroll.setValues(0, 1, 0, max); + } + else + { + if (overviewPanel != null) + overviewPanel.updateOverviewImage(); + setScrollValues(av.getStartRes(), av.getStartSeq()); + } - 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 - - av.getConsensus(true); - if (overviewPanel != null) - overviewPanel.updateOverviewImage(); - - validate(); - setScrollValues(av.getStartRes(), av.getStartSeq()); - repaint(); + validate(); + repaint(); } + int hextent = 0; int vextent = 0; - // return value is true if the scroll is valid public boolean scrollUp(boolean up) { @@ -274,35 +277,40 @@ 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) @@ -330,13 +338,13 @@ 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) { @@ -363,7 +371,18 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene if(overviewPanel!=null) overviewPanel.setBoxPosition(); - repaint(); + 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); + } + } public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException @@ -382,7 +401,7 @@ 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); @@ -415,10 +434,10 @@ 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; @@ -452,10 +471,18 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene } // draw main sequence panel - pg.translate(idWidth+4,0); - pg.setClip(0,0,pwidth-idWidth, pheight); + pg.translate(idWidth,0); 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; } @@ -463,7 +490,7 @@ 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; @@ -510,7 +537,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene } // draw main sequence panel - pg.translate(idWidth+4,0); + pg.translate(idWidth,0); seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth-idWidth, pheight, pi*noChunksOnPage*chunkWidth); @@ -529,6 +556,10 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene height = (av.alignment.getHeight()+1) * av.charHeight + 30; width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth; } + if(av.getShowAnnotation()) + { + height += annotationPanel.getPreferredSize().height; + } try { @@ -572,7 +603,13 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth; } + if(av.getShowAnnotation()) + { + height += annotationPanel.getPreferredSize().height; + } + +System.out.println(width +" "+height); try {