X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=90438d52622454d4d5fd167e841697ac8c9c1221;hb=ad35f232acd499d9457056ca24b663866a09edd2;hp=b0027a8dab1b852d2620ee6f51b56b3c1e509863;hpb=df9b85c1cf39894039018499fe802406cc37f209;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index b0027a8..90438d5 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -49,6 +49,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, AlignmentPanel ap; int activeRow = -1; BufferedImage image; + BufferedImage fadedImage; Graphics2D gg; FontMetrics fm; int imgWidth = 0; @@ -107,7 +108,6 @@ public class AnnotationPanel extends JPanel implements MouseListener, public int adjustPanelHeight() { // setHeight of panels - image = null; AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); int height = 0; @@ -279,14 +279,13 @@ public class AnnotationPanel extends JPanel implements MouseListener, public void mousePressed(MouseEvent evt) { - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); if(aa==null) return; int height = 0; - activeRow = 0; + activeRow = -1; for (int i = 0; i < aa.length; i++) @@ -314,7 +313,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, } - if (SwingUtilities.isRightMouseButton(evt)) + if (SwingUtilities.isRightMouseButton(evt) && activeRow!=-1) { if (av.getColumnSelection() == null) { @@ -349,6 +348,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); + if(av.hasHiddenColumns) + res = av.getColumnSelection().adjustForHiddenColumns(res); + min = res; max = res; @@ -418,8 +420,8 @@ public class AnnotationPanel extends JPanel implements MouseListener, if(graphStretch>-1) { av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - evt.getY(); - if(av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight <10) - av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 10; + if(av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight <0) + av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0; graphStretchY = evt.getY(); adjustPanelHeight(); ap.repaint(); @@ -430,6 +432,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); + if(av.hasHiddenColumns) + res = av.getColumnSelection().adjustForHiddenColumns(res); + SequenceGroup sg = av.getSelectionGroup(); if (res < min) @@ -508,12 +513,17 @@ public class AnnotationPanel extends JPanel implements MouseListener, } } + if(row==-1) + return; + int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); if(av.hasHiddenColumns) res = av.getColumnSelection().adjustForHiddenColumns(res); - if (row > -1 && res -1 + && res < (int) aa[row].annotations.length) { if(aa[row].graphGroup>-1) { @@ -587,6 +597,8 @@ public class AnnotationPanel extends JPanel implements MouseListener, gg.setFont(av.getFont()); fm = gg.getFontMetrics(); + gg.setColor(Color.white); + gg.fillRect(0, 0, imgWidth, image.getHeight()); } @@ -601,9 +613,12 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public void fastPaint(int horizontal) { - if ((horizontal == 0) || gg==null || - (av.alignment.getAlignmentAnnotation() == null) || - (av.alignment.getAlignmentAnnotation().length < 1)) + if ((horizontal == 0) + || gg==null + || av.alignment.getAlignmentAnnotation()==null + || av.alignment.getAlignmentAnnotation().length < 1 + || av.updatingConsensus + || av.updatingConservation) { repaint(); return; @@ -646,16 +661,49 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public void drawComponent(Graphics g, int startRes, int endRes) { + if(av.updatingConsensus || av.updatingConservation) + { + if(image==null) + { + return; + } + //We'll keep a record of the old image, + //and draw a faded image until the calculation + //has completed + if(fadedImage==null + || fadedImage.getWidth()!=imgWidth + || fadedImage.getHeight()!=image.getHeight()) + { + fadedImage = new BufferedImage( + imgWidth, image.getHeight(), + BufferedImage.TYPE_INT_RGB); + Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics(); - g.setFont(av.getFont()); + fadedG.setColor(Color.white); + fadedG.fillRect(0, 0, imgWidth, image.getHeight()); + + fadedG.setComposite( + AlphaComposite.getInstance( + AlphaComposite.SRC_OVER, .3f)); + fadedG.drawImage(image, 0, 0, this); + + } + } + else + fadedImage = null; + + + g.setColor(Color.white); + g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight()); + + g.setFont(av.getFont()); if (fm == null) fm = g.getFontMetrics(); - g.setColor(Color.white); - g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight()); + if ( (av.alignment.getAlignmentAnnotation() == null) || (av.alignment.getAlignmentAnnotation().length < 1)) @@ -669,6 +717,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, return; } + AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); int x = 0, y = 0; @@ -691,6 +740,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, continue; } + lastSS = ' '; lastSSX = 0; @@ -708,9 +758,48 @@ public class AnnotationPanel extends JPanel implements MouseListener, } } + if (av.updatingConsensus && aa[i].label.equals("Consensus")) + { + y += av.charHeight; + + g.drawImage(fadedImage, + 0,y-row.height,imgWidth, y, + 0,y-row.height,imgWidth, y, this); + g.setColor(Color.black); + // g.drawString("Calculating Consensus....",20, y-row.height/2); + + continue; + } + else if (av.updatingConservation && aa[i].label.equals("Conservation")) + { + + y += av.charHeight; + g.drawImage(fadedImage, + 0, y - row.height, imgWidth, y, + 0, y - row.height, imgWidth, y, this); + + g.setColor(Color.black); + // g.drawString("Calculating Conservation.....",20, y-row.height/2); + + continue; + } + else if (av.updatingConservation && aa[i].label.equals("Quality")) + { + + y += av.charHeight; + g.drawImage(fadedImage, + 0, y - row.height, imgWidth, y, + 0, y - row.height, imgWidth, y, this); + g.setColor(Color.black); + /// g.drawString("Calculating Quality....",20, y-row.height/2); + + continue; + } + + if (row.hasText) { - iconOffset = av.charHeight / 2; + iconOffset = av.charHeight / 2 + 4; } else { @@ -756,7 +845,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, if (v == column) { g.fillRect(x * av.charWidth, y, - av.charWidth, row.height); + av.charWidth, av.charHeight); } } } @@ -774,8 +863,8 @@ public class AnnotationPanel extends JPanel implements MouseListener, if (column == 0 || row.graph>0) { g.drawString(row.annotations[column].displayCharacter, - x*av.charWidth+charOffset, - y + iconOffset + 3); + (x*av.charWidth)+charOffset, + y + iconOffset ); } else if ( row.annotations[column - 1] == null @@ -787,7 +876,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, { g.drawString(row.annotations[column].displayCharacter, x*av.charWidth+charOffset, - y + iconOffset + 3); + y + iconOffset ); } } @@ -799,52 +888,50 @@ public class AnnotationPanel extends JPanel implements MouseListener, switch (lastSS) { case 'H': - g.setColor(HELIX_COLOUR); - if(MAC) - { - //Off by 1 offset when drawing rects and ovals - //to offscreen image on the MAC - g.fillRoundRect(lastSSX, y + 4 + iconOffset, - x*av.charWidth - lastSSX, 7, 8, 8); - break; - } - - int sCol = (lastSSX / av.charWidth) + startRes; - int x1 = lastSSX; - int x2 = x*av.charWidth; - - if(sCol==0 || - row.annotations[sCol-1]==null || - row.annotations[sCol-1].secondaryStructure!='H') - { - g.fillArc(lastSSX, y+4+iconOffset, av.charWidth+1, 7, 90,180) ; - x1 += av.charWidth/2; - } - - if(row.annotations[column]==null || - row.annotations[column].secondaryStructure!='H') - { - g.fillArc(x*av.charWidth-av.charWidth, - y+4+iconOffset, - av.charWidth, - 7, 270,180); - x2 -= av.charWidth/2; - } - - g.fillRect(x1, y+4+iconOffset, x2-x1+1, 7); + g.setColor(HELIX_COLOUR); + if (MAC) + { + //Off by 1 offset when drawing rects and ovals + //to offscreen image on the MAC + g.fillRoundRect(lastSSX, y + 4 + iconOffset, + (x*av.charWidth) - lastSSX, 7, 8, 8); break; + } + + int sCol = (lastSSX / av.charWidth) + startRes; + int x1 = lastSSX; + int x2 = (x*av.charWidth); + + if(sCol==0 || + row.annotations[sCol-1]==null || + row.annotations[sCol-1].secondaryStructure!='H') + { + g.fillArc(lastSSX, y+4+iconOffset, av.charWidth, 8, 90,180) ; + x1 += av.charWidth/2; + } + + if(row.annotations[column]==null || + row.annotations[column].secondaryStructure!='H') + { + g.fillArc((x*av.charWidth)-av.charWidth, + y+4+iconOffset, av.charWidth, 8, 270,180); + x2 -= av.charWidth/2; + } + + g.fillRect(x1, y+4+iconOffset, x2-x1, 8); + break; case 'E': g.setColor(SHEET_COLOUR); g.fillRect(lastSSX, y + 4 + iconOffset, - x*av.charWidth - lastSSX - 4, 7); - g.fillPolygon(new int[] { x*av.charWidth - 5, - x*av.charWidth - 5, - x*av.charWidth }, + (x*av.charWidth) - lastSSX - 4, 7); + g.fillPolygon(new int[] { (x*av.charWidth) - 4, + (x*av.charWidth) - 4, + (x*av.charWidth) }, new int[] { y + iconOffset, y + 14 + iconOffset, - y + 7 + iconOffset + y + 8 + iconOffset }, 3); break; @@ -853,7 +940,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, default: g.setColor(Color.gray); g.fillRect(lastSSX, y + 6 + iconOffset, - x*av.charWidth - lastSSX, 2); + (x*av.charWidth) - lastSSX, 2); break; } @@ -867,22 +954,24 @@ public class AnnotationPanel extends JPanel implements MouseListener, lastSS = ' '; } - lastSSX = x*av.charWidth; + lastSSX = (x*av.charWidth); } } - column++; - x++; + + + column++; + x++; } if(column>=row.annotations.length) - column = row.annotations.length-1; + column = row.annotations.length-1; - x ++; + // x ++; if (row.hasIcons) { - switch (lastSS) - { + switch (lastSS) + { case 'H': g.setColor(HELIX_COLOUR); if (MAC) @@ -890,70 +979,70 @@ public class AnnotationPanel extends JPanel implements MouseListener, //Off by 1 offset when drawing rects and ovals //to offscreen image on the MAC g.fillRoundRect(lastSSX, y + 4 + iconOffset, - x*av.charWidth - lastSSX, 7, 8, 8); + (x*av.charWidth) - lastSSX, 7, 8, 8); break; } - int sCol = (lastSSX / av.charWidth) + startRes; int x1 = lastSSX; - int x2 = x; - - if(sCol==0 || - row.annotations[sCol-1]==null || - row.annotations[sCol-1].secondaryStructure!='H') - { - g.fillArc(lastSSX, y+4+iconOffset, av.charWidth+1, 7, 90,180) ; - x1 += av.charWidth/2; - } - - if(row.annotations[column]==null || - row.annotations[column].secondaryStructure!='H') + int x2 = (x*av.charWidth); + + if (sCol == 0 || + row.annotations[sCol - 1] == null || + row.annotations[sCol - 1].secondaryStructure != 'H') { - g.fillArc(x-av.charWidth, y+4+iconOffset, av.charWidth, 7, 270,180); - x2 -= av.charWidth/2; + g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, 180); + x1 += av.charWidth / 2; } - g.fillRect(x1, y+4+iconOffset, x2-x1+1, 7); + if (row.annotations[column] == null || + row.annotations[column].secondaryStructure != 'H') + { + g.fillArc((x*av.charWidth) - av.charWidth, + y + 4 + iconOffset, av.charWidth, 8, 270, + 180); + x2 -= av.charWidth / 2; + } - break; + g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8); - case 'E': - g.setColor(SHEET_COLOUR); - - if (row.annotations[endRes] ==null - || row.annotations[endRes].secondaryStructure != 'E') - { - g.fillRect(lastSSX, y + 4 + iconOffset, - x*av.charWidth - lastSSX - 4, 7); - g.fillPolygon(new int[] - {x*av.charWidth - 5, - x*av.charWidth - 5, - x*av.charWidth}, - new int[] - { - y + iconOffset, y + 14 + iconOffset, - y + 7 + iconOffset - }, 3); - } - else - g.fillRect(lastSSX, y + 4 + iconOffset, - x*av.charWidth - lastSSX, 7); + break; - break; + case 'E': + g.setColor(SHEET_COLOUR); + if (row.annotations[endRes] == null + || row.annotations[endRes].secondaryStructure != 'E') + { + g.fillRect(lastSSX, y + 4 + iconOffset, + (x*av.charWidth) - lastSSX - 4, 7); + g.fillPolygon(new int[] + {(x*av.charWidth) - 4, + (x*av.charWidth) - 4, + (x*av.charWidth)}, + new int[] + { + y + iconOffset, y + 14 + iconOffset, + y + 7 + iconOffset + }, 3); + } + else + { + g.fillRect(lastSSX, y + 4 + iconOffset, + (x+1) * av.charWidth - lastSSX, 7); + } + break; default: - g.setColor(Color.gray); - if(!av.wrapAlignment || endRes==av.endRes) - g.fillRect(lastSSX, y + 6 + iconOffset, - x*av.charWidth - lastSSX, 2); + g.setColor(Color.gray); + g.fillRect(lastSSX, y + 6 + iconOffset, + (x*av.charWidth) - lastSSX, 2); - break; - } - } + break; + } + } - if (row.graph>0) + if (row.graph>0 && row.graphHeight>0) { if(row.graph == AlignmentAnnotation.LINE_GRAPH ) { @@ -1027,8 +1116,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, if(sRes==0) { - sRes++; - x+=av.charWidth; + x++; } int y1=y, y2=y; @@ -1170,13 +1258,16 @@ public class AnnotationPanel extends JPanel implements MouseListener, for (int j = sRes; j < eRes; j++) { + if (aa.annotations[j] != null) + { g.setColor(aa.annotations[j].colour); - height = (int) ((aa.annotations[j].value / aa.graphMax) * y); - if(height>y) + height = (int) ( (aa.annotations[j].value / aa.graphMax) * y); + if (height > y) height = y; g.fillRect(x, y - height, av.charWidth, height); + } x += av.charWidth; } }