X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=0f6901d018a510e3ae4909f71daa407de87f297a;hb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;hp=497fc2a2e26cbd1eb552be9b772faad77c6abef4;hpb=ae282720c1bba85d9b52ebc2e85c6a9857b2c6db;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index 497fc2a..0f6901d 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -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; @@ -167,6 +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++) @@ -279,7 +288,6 @@ public class AnnotationPanel extends JPanel implements MouseListener, public void mousePressed(MouseEvent evt) { - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); if(aa==null) return; @@ -314,7 +322,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, } - if (SwingUtilities.isRightMouseButton(evt)) + if (SwingUtilities.isRightMouseButton(evt) && activeRow!=-1) { if (av.getColumnSelection() == null) { @@ -349,6 +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; @@ -430,6 +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) @@ -487,6 +501,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, if (aa == null) { + this.setToolTipText(null); return; } @@ -508,12 +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) { @@ -529,18 +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); } /** @@ -587,6 +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()); } @@ -601,9 +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; @@ -646,14 +679,49 @@ 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) || (av.alignment.getAlignmentAnnotation().length < 1)) @@ -667,6 +735,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, return; } + AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); int x = 0, y = 0; @@ -689,6 +758,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, continue; } + lastSS = ' '; lastSSX = 0; @@ -706,6 +776,45 @@ 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 + 4; @@ -944,7 +1053,6 @@ public class AnnotationPanel extends JPanel implements MouseListener, default: g.setColor(Color.gray); - if(!av.wrapAlignment || endRes==av.endRes) g.fillRect(lastSSX, y + 6 + iconOffset, (x*av.charWidth) - lastSSX, 2); @@ -1168,13 +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; } }