X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=844c1abfaa242c082fa7ad624df27783e2bd4421;hb=9f08afb8654d8e19fddfd3c6de0e8702804ea97d;hp=0213565b98f22ce005d8521630e0a8ada21f9621;hpb=6cbc1c23947d6812cf5efa36998f237f60f4cc74;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index 0213565..844c1ab 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 @@ -24,8 +24,6 @@ import java.awt.*; import java.awt.event.*; import java.awt.image.*; -import java.util.*; - import javax.swing.*; @@ -51,6 +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; @@ -59,6 +58,11 @@ public class AnnotationPanel extends JPanel implements MouseListener, //Used For mouse Dragging and resizing graphs int graphStretch = -1; int graphStretchY = -1; + int min; //used by mouseDragged to see if user + int max; //used by mouseDragged to see if user + boolean mouseDragging = false; + + boolean MAC = false; /** * Creates a new AnnotationPanel object. @@ -67,6 +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); @@ -271,13 +279,17 @@ 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) @@ -302,7 +314,8 @@ public class AnnotationPanel extends JPanel implements MouseListener, } } - if (SwingUtilities.isRightMouseButton(evt)) + + if (SwingUtilities.isRightMouseButton(evt) && activeRow!=-1) { if (av.getColumnSelection() == null) { @@ -337,34 +350,28 @@ public class AnnotationPanel extends JPanel implements MouseListener, int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); - if (evt.isShiftDown()) - { - /*int start = Integer.parseInt(activeRes.get(activeRes.size() - - 1).toString()); - int end = res; - - if (end < start) - { - int temp = end; - end = start; - start = temp; - } + min = res; + max = res; - for (int n = start; n <= end; n++) - { - addEditableColumn(n); - } */ - } + if (av.getColumnSelection().contains(res)) + av.getColumnSelection().removeElement(res); else { - if (av.getColumnSelection().contains(res)) - av.getColumnSelection().removeElement(res); - else av.getColumnSelection().addElement(res); + SequenceGroup sg = new SequenceGroup(); - ap.repaint(); + for (int i = 0; i < av.alignment.getSequences().size(); i++) + { + sg.addSequence(av.alignment.getSequenceAt(i), false); + } + sg.setStartRes(res); + sg.setEndRes(res); + av.setSelectionGroup(sg); } + + ap.repaint(); + } /** @@ -376,6 +383,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, { graphStretch = -1; graphStretchY = -1; + mouseDragging = false; } /** @@ -385,6 +393,8 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public void mouseEntered(MouseEvent evt) { + if(mouseDragging) + ap.seqPanel.scrollCanvas(null); } /** @@ -394,8 +404,11 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public void mouseExited(MouseEvent evt) { + if(mouseDragging) + ap.seqPanel.scrollCanvas(evt); } + /** * DOCUMENT ME! * @@ -406,12 +419,62 @@ 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(); } + else + { + mouseDragging = true; + + int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); + + SequenceGroup sg = av.getSelectionGroup(); + + if (res < min) + { + min = res; + } + + if (res > max) + { + max = res; + } + + if (sg != null) + { + if (!av.getColumnSelection().contains(res)) + { + av.getColumnSelection().addElement(res); + } + + if (res > sg.getStartRes()) + { + sg.setEndRes(res); + } + else if (res < sg.getStartRes()) + { + sg.setStartRes(res); + } + + for (int i = min; i <= max; i++) + { + if ((i < sg.getStartRes()) || (i > sg.getEndRes())) + { + av.getColumnSelection().removeElement(i); + } + else + { + av.getColumnSelection().addElement(i); + } + } + + ap.repaint(); + } + + } } /** @@ -525,6 +588,8 @@ 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()); } @@ -539,9 +604,12 @@ 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; @@ -584,32 +652,65 @@ 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) + { + //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; - char[] lastSS = new char[aa.length]; - int[] lastSSX = new int[aa.length]; + int x = 0, y = 0; + int column=0; + char lastSS; + int lastSSX; int iconOffset = av.charHeight / 2; boolean validRes = false; @@ -627,6 +728,8 @@ public class AnnotationPanel extends JPanel implements MouseListener, } + lastSS = ' '; + lastSSX = 0; if (row.graph>0) { @@ -642,31 +745,68 @@ 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 { iconOffset = 0; } - int column = startRes; - int yPos = startRes; - int aaMax = row.annotations.length-1; - - while (yPos < endRes) + x = 0; + while (x < endRes-startRes) { if (av.hasHiddenColumns) { - column = av.getColumnSelection().adjustForHiddenColumns(yPos); - if (column > aaMax) + 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)) @@ -678,7 +818,6 @@ public class AnnotationPanel extends JPanel implements MouseListener, validRes = true; } - x = (yPos - startRes) * av.charWidth; if (activeRow == i) { @@ -692,14 +831,14 @@ 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)) { @@ -710,37 +849,72 @@ 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 != 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 ); } } if (row.hasIcons) { if (!validRes || - (row.annotations[column].secondaryStructure != lastSS[i])) + (row.annotations[column].secondaryStructure != lastSS)) { - switch (lastSS[i]) + switch (lastSS) { case 'H': - g.setColor(HELIX_COLOUR); - g.fillRoundRect(lastSSX[i], y + 4 + iconOffset, - x - lastSSX[i], 7, 8, 8); - + 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[i], y + 4 + iconOffset, - x - lastSSX[i] - 4, 7); - g.fillPolygon(new int[] { x - 4, x - 4, x }, + 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, @@ -752,75 +926,111 @@ public class AnnotationPanel extends JPanel implements MouseListener, default: g.setColor(Color.gray); - g.fillRect(lastSSX[i], y + 6 + iconOffset, - x - lastSSX[i], 2); + g.fillRect(lastSSX, y + 6 + iconOffset, + (x*av.charWidth) - lastSSX, 2); break; } if (validRes) { - lastSS[i] = row.annotations[column].secondaryStructure; + lastSS = row.annotations[column].secondaryStructure; } else { - lastSS[i] = ' '; + lastSS = ' '; } - lastSSX[i] = 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[i]) - { + switch (lastSS) + { case 'H': - g.setColor(HELIX_COLOUR); - g.fillRoundRect(lastSSX[i], y + 4 + iconOffset, - x - lastSSX[i], 7, 8, 8); - + 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); - case 'E': - g.setColor(SHEET_COLOUR); - - if (row.annotations[endRes] !=null - && row.annotations[endRes].secondaryStructure != 'E') - { - g.fillRect(lastSSX[i], y + 4 + iconOffset, - x - lastSSX[i] - 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[i], y + 4 + iconOffset, - x - lastSSX[i], 7); - - break; + break; - case 'C': - 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[i], y + 6 + iconOffset, x - lastSSX[i], 2); + g.setColor(Color.gray); + if(!av.wrapAlignment || endRes==av.endRes) + 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 ) { @@ -883,16 +1093,18 @@ public class AnnotationPanel extends JPanel implements MouseListener, if(sRes>aa.annotations.length) return; + int x = 0; //Adjustment for fastpaint to left 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, @@ -963,76 +1173,71 @@ public class AnnotationPanel extends JPanel implements MouseListener, if(sRes>aa.annotations.length) return; - int x=0, y1, y2; - - 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)); + eRes = Math.min(eRes, aa.annotations.length); - y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight); - g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2); - g2.setStroke(new BasicStroke()); - } + int x=0, y1=y, y2=y; - y1 = y2 = y; + float range = max - min; 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+1)*av.charWidth,y2); + 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)); @@ -1041,13 +1246,16 @@ 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; } }