X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=0f6901d018a510e3ae4909f71daa407de87f297a;hb=ca26cdb914e0a8885bb0a3986750481bde71383a;hp=c5708ee155338244482c5ff4d034ac40eda02919;hpb=14bad6b2390493bb6ad030c6f3ea7cde4cba1b53;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index c5708ee..0f6901d 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; @@ -61,6 +62,8 @@ public class AnnotationPanel extends JPanel implements MouseListener, int max; //used by mouseDragged to see if user boolean mouseDragging = false; + boolean MAC = false; + /** * Creates a new AnnotationPanel object. * @@ -68,6 +71,10 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public AnnotationPanel(AlignmentPanel ap) { + + if(System.getProperty("os.name").startsWith("Mac")) + MAC = true; + ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); @@ -101,7 +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; @@ -161,6 +167,15 @@ public class AnnotationPanel extends JPanel implements MouseListener, AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); Annotation[] anot = aa[activeRow].annotations; + if (anot.length < av.getColumnSelection().getMax()) + { + Annotation[] temp = new Annotation[av.getColumnSelection().getMax()+2 ]; + System.arraycopy(anot, 0, temp, 0, anot.length); + anot = temp; + aa[activeRow].annotations = anot; + } + + if (evt.getActionCommand().equals(REMOVE)) { for (int i = 0; i < av.getColumnSelection().size(); i++) @@ -272,13 +287,16 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public void mousePressed(MouseEvent evt) { - int height = 0; - activeRow = -1; AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); if(aa==null) return; + + int height = 0; + activeRow = -1; + + for (int i = 0; i < aa.length; i++) { if (aa[i].visible) @@ -303,7 +321,8 @@ public class AnnotationPanel extends JPanel implements MouseListener, } } - if (SwingUtilities.isRightMouseButton(evt)) + + if (SwingUtilities.isRightMouseButton(evt) && activeRow!=-1) { if (av.getColumnSelection() == null) { @@ -338,6 +357,9 @@ 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; @@ -407,8 +429,8 @@ 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(); @@ -419,6 +441,9 @@ 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) @@ -476,6 +501,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, if (aa == null) { + this.setToolTipText(null); return; } @@ -497,12 +523,20 @@ public class AnnotationPanel extends JPanel implements MouseListener, } } + if(row==-1) + { + this.setToolTipText(null); + 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) { @@ -518,18 +552,23 @@ public class AnnotationPanel extends JPanel implements MouseListener, this.setToolTipText(tip.toString() + ""); } } - else if(aa[row].annotations[res] != null) + else if(aa[row].annotations[res] != null + && aa[row].annotations[res].description!=null) this.setToolTipText(aa[row].annotations[res].description); if(aa[row].annotations[res]!=null) { StringBuffer text = new StringBuffer("Sequence position " + - (res + 1) + " " + - aa[row].annotations[res].description); + (res + 1)); + + if (aa[row].annotations[res].description != null) + text.append(" " + aa[row].annotations[res].description); ap.alignFrame.statusBar.setText(text.toString()); } } + else + this.setToolTipText(null); } /** @@ -576,6 +615,8 @@ 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()); } @@ -590,9 +631,12 @@ 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; @@ -635,30 +679,67 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public void drawComponent(Graphics g, int startRes, int endRes) { - g.setFont(av.getFont()); + 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(); + + 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) || + + if ( (av.alignment.getAlignmentAnnotation() == null) || (av.alignment.getAlignmentAnnotation().length < 1)) { g.setColor(Color.white); g.fillRect(0, 0, getWidth(), getHeight()); g.setColor(Color.black); - g.drawString("Alignment has no annotations", 20, 15); + if(av.validCharWidth) + g.drawString("Alignment has no annotations", 20, 15); return; } + AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - int x = 0; - int y = 0; + int x = 0, y = 0; + int column=0; char lastSS; int lastSSX; int iconOffset = av.charHeight / 2; @@ -677,10 +758,10 @@ public class AnnotationPanel extends JPanel implements MouseListener, continue; } + lastSS = ' '; lastSSX = 0; - if (row.graph>0) { if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] ) @@ -695,30 +776,68 @@ public class AnnotationPanel extends JPanel implements MouseListener, } } + if (av.updatingConsensus && aa[i]==av.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 { iconOffset = 0; } - int column = startRes; - int yPos = startRes; - - while (yPos < endRes) + x = 0; + while (x < endRes-startRes) { if (av.hasHiddenColumns) { - column = av.getColumnSelection().adjustForHiddenColumns(yPos); + column = av.getColumnSelection().adjustForHiddenColumns(startRes+x); if (column > row.annotations.length-1) { break; } } else - column = yPos; + column = startRes+x; + if ((row.annotations.length <= column) || (row.annotations[column] == null)) @@ -730,7 +849,6 @@ public class AnnotationPanel extends JPanel implements MouseListener, validRes = true; } - x = (yPos - startRes) * av.charWidth; if (activeRow == i) { @@ -744,14 +862,14 @@ public class AnnotationPanel extends JPanel implements MouseListener, if (v == column) { - g.fillRect((column - startRes) * av.charWidth, y, - av.charWidth, row.height); + g.fillRect(x * av.charWidth, y, + av.charWidth, av.charHeight); } } } } - if (validRes && + if (av.validCharWidth && validRes && (row.annotations[column].displayCharacter.length() > 0)) { @@ -762,16 +880,21 @@ public class AnnotationPanel extends JPanel implements MouseListener, if (column == 0 || row.graph>0) { - g.drawString(row.annotations[column].displayCharacter, x+charOffset, - y + iconOffset + 3); + g.drawString(row.annotations[column].displayCharacter, + (x*av.charWidth)+charOffset, + y + iconOffset ); } - else if (((row.annotations[column - 1] == null) - || - (!row.annotations[column].displayCharacter.equals( - row.annotations[column - 1].displayCharacter)))) + else if ( + row.annotations[column - 1] == null + ||(!row.annotations[column].displayCharacter.equals( + row.annotations[column - 1].displayCharacter) + || + (row.annotations[column].displayCharacter.length() <2 && + row.annotations[column].secondaryStructure==' '))) { - g.drawString(row.annotations[column].displayCharacter, x+charOffset, - y + iconOffset + 3); + g.drawString(row.annotations[column].displayCharacter, + x*av.charWidth+charOffset, + y + iconOffset ); } } @@ -783,17 +906,46 @@ public class AnnotationPanel extends JPanel implements MouseListener, switch (lastSS) { case 'H': - g.setColor(HELIX_COLOUR); + 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 - lastSSX, 7, 8, 8); - + (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 - lastSSX - 4, 7); - g.fillPolygon(new int[] { x - 4, x - 4, x }, + (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, @@ -806,7 +958,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, default: g.setColor(Color.gray); g.fillRect(lastSSX, y + 6 + iconOffset, - x - lastSSX, 2); + (x*av.charWidth) - lastSSX, 2); break; } @@ -820,58 +972,95 @@ public class AnnotationPanel extends JPanel implements MouseListener, lastSS = ' '; } - lastSSX = x; + lastSSX = (x*av.charWidth); } } - yPos++; + + column++; + x++; } - x += av.charWidth; + if(column>=row.annotations.length) + column = row.annotations.length-1; + + // x ++; if (row.hasIcons) { - switch (lastSS) - { + switch (lastSS) + { case 'H': - g.setColor(HELIX_COLOUR); + 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 - lastSSX, 7, 8, 8); - + (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); - case 'E': - g.setColor(SHEET_COLOUR); - - if (row.annotations[endRes] !=null - && row.annotations[endRes].secondaryStructure != 'E') - { - g.fillRect(lastSSX, y + 4 + iconOffset, - x - lastSSX - 4, 7); - g.fillPolygon(new int[] - {x - 4, x - 4, x}, - new int[] - { - y + iconOffset, y + 14 + iconOffset, - y + 7 + iconOffset - }, 3); - } - else - g.fillRect(lastSSX, y + 4 + iconOffset, - x - 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); - g.fillRect(lastSSX, y + 6 + iconOffset, x - 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 ) { @@ -934,7 +1123,6 @@ public class AnnotationPanel extends JPanel implements MouseListener, if(sRes>aa.annotations.length) return; - eRes = Math.min(eRes, aa.annotations.length); int x = 0; @@ -942,10 +1130,11 @@ public class AnnotationPanel extends JPanel implements MouseListener, if(eRes aaMax) - { - break; - } + column = av.getColumnSelection().adjustForHiddenColumns(column); } - else - column = yPos; - yPos ++; + if (column > aaMax) + { + break; + } if(aa.annotations[column]==null || aa.annotations[column-1]==null) { - x+=av.charWidth; + x++; continue; } + g.setColor(aa.annotations[column].colour); y1 = y - (int) (((aa.annotations[column-1].value-min) / range) * graphHeight); y2 = y - (int) (((aa.annotations[column].value-min) / range) * graphHeight); - g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2); - x += av.charWidth; + + g.drawLine(x*av.charWidth-av.charWidth/2, y1, x*av.charWidth+av.charWidth/2, y2); + x ++; } + + if(aa.threshold!=null) + { + g.setColor(aa.threshold.colour); + Graphics2D g2 = (Graphics2D)g; + g2.setStroke(new BasicStroke(1, + BasicStroke.CAP_SQUARE, + BasicStroke.JOIN_ROUND, 3f, + new float[] { 5f, 3f }, 0f)); + + y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight); + g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2); + g2.setStroke(new BasicStroke()); + } } public void drawBarGraph(Graphics g, AlignmentAnnotation aa, @@ -1018,76 +1205,69 @@ public class AnnotationPanel extends JPanel implements MouseListener, eRes = Math.min(eRes, aa.annotations.length); - int x=0, y1, y2; + int x=0, y1=y, y2=y; float range = max - min; - if(aa.threshold!=null) - { - g.setColor(aa.threshold.colour); - Graphics2D g2 = (Graphics2D)g; - g2.setStroke(new BasicStroke(1, - BasicStroke.CAP_SQUARE, - BasicStroke.JOIN_ROUND, 3f, - new float[] { 5f, 3f }, 0f)); - - y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight); - g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2); - g2.setStroke(new BasicStroke()); - } - - y1 = y2 = y; - if(min<0) - y2 = (int)(y - (0-min / (range))*aa.graphHeight); + y2 = y - (int)((0-min / (range))*aa.graphHeight); g.setColor(Color.gray); g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2); - - int column = sRes; - int yPos = sRes; + int column; int aaMax = aa.annotations.length-1; - while( yPos < eRes ) + while( x < eRes-sRes ) { + column = sRes + x; if(av.hasHiddenColumns) { - column = av.getColumnSelection().adjustForHiddenColumns(yPos); - if(column > aaMax) - { - break; - } + column = av.getColumnSelection().adjustForHiddenColumns(column); } - else - column = yPos; - yPos ++; + if(column > aaMax) + { + break; + } if (aa.annotations[column] == null) { - x += av.charWidth; + x ++; continue; } - g.setColor(aa.annotations[column].colour); y1 = y - (int) (((aa.annotations[column].value-min) / (range)) * aa.graphHeight); if(y1-y2>0) - g.fillRect(x, y2, av.charWidth, y1-y2 ); + g.fillRect(x*av.charWidth, y2, av.charWidth, y1-y2 ); else - g.fillRect(x, y1, av.charWidth, y2-y1 ); + g.fillRect(x*av.charWidth, y1, av.charWidth, y2-y1 ); + + x ++ ; - x += av.charWidth; } + if(aa.threshold!=null) + { + g.setColor(aa.threshold.colour); + Graphics2D g2 = (Graphics2D)g; + g2.setStroke(new BasicStroke(1, + BasicStroke.CAP_SQUARE, + BasicStroke.JOIN_ROUND, 3f, + new float[] { 5f, 3f }, 0f)); + y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight); + g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2); + g2.setStroke(new BasicStroke()); + } } // used by overview window public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes) { + eRes = Math.min(eRes, aa.annotations.length); g.setColor(Color.white); g.fillRect(0, 0, width, y); g.setColor(new Color(0, 0, 180)); @@ -1096,13 +1276,16 @@ 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; } }