X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=75729c330775e2b93ab5067126233e926b726e18;hb=24efbd38f2c3dceaf6d3e305eef41ba0b0c9ebdc;hp=76fc8d5cc86f61268a43dbeb586c0616e30bfea6;hpb=2b9c6a8948800edf58dd055631920654729fd675;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 76fc8d5..75729c3 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) { @@ -34,14 +38,18 @@ 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); + + 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); @@ -49,9 +57,22 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene hscrollFillerPanel.setPreferredSize( d ); scalePanelHolder.add(scalePanel, BorderLayout.CENTER); - scorePanelHolder.add(scorePanel, BorderLayout.CENTER); seqPanelHolder.add(seqPanel, BorderLayout.CENTER); - setScrollValues(0,0); + + + 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 ); + RefreshPanels(); + } + }); + hscroll.addAdjustmentListener(this); vscroll.addAdjustmentListener(this); @@ -64,11 +85,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene } }); - - // hscroll.setFocusable(false); - // vscroll.setFocusable(false); setFocusable(true); - addKeyListener(new KeyAdapter() { public void keyPressed(KeyEvent evt) @@ -80,15 +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: @@ -98,6 +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; } @@ -164,31 +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(); @@ -219,40 +240,36 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene RefreshPanels(); } + 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(); + 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()); + } + + validate(); + repaint(); } + int hextent = 0; int vextent = 0; - // return value is true if the scroll is valid public boolean scrollUp(boolean up) { @@ -260,41 +277,51 @@ 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(); + 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; @@ -311,14 +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) { @@ -345,7 +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 @@ -364,7 +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); @@ -397,10 +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; @@ -434,10 +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; } @@ -445,7 +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; @@ -492,7 +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); @@ -511,6 +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 { @@ -554,7 +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 {