X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=dbc1c926f8343cdbee711700eecdf9a9c87109b4;hb=52c2c3879d5dc5e7b4ba7916f1ea964f83551f95;hp=1b4a230a526f78d0d50d6dfe7a7d906372bc5fd0;hpb=b27f973bd368619235ff19f706afb28b81c731e7;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index 1b4a230..dbc1c92 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 @@ -61,6 +61,8 @@ 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 +70,10 @@ 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); @@ -272,13 +278,17 @@ 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) @@ -303,7 +313,8 @@ public class AnnotationPanel extends JPanel implements MouseListener, } } - if (SwingUtilities.isRightMouseButton(evt)) + + if (SwingUtilities.isRightMouseButton(evt) && activeRow!=-1) { if (av.getColumnSelection() == null) { @@ -407,8 +418,8 @@ 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(); @@ -644,21 +655,23 @@ public class AnnotationPanel extends JPanel implements MouseListener, 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 +690,10 @@ public class AnnotationPanel extends JPanel implements MouseListener, continue; } + lastSS = ' '; lastSSX = 0; - if (row.graph>0) { if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] ) @@ -695,30 +708,51 @@ public class AnnotationPanel extends JPanel implements MouseListener, } } + if (av.updatingConsensus && aa[i].label.equals("Consensus")) + { + g.setColor(Color.darkGray); + g.drawString("Recalculating Consensus....", 20, y - 5); + y += av.charHeight; + continue; + } + else if (av.updatingConservation && aa[i].label.equals("Conservation")) + { + g.setColor(Color.darkGray); + g.drawString("Recalculating Conservation.....", 20, y - 5); + y += av.charHeight; + continue; + } + else if (av.updatingConservation && aa[i].label.equals("Quality")) + { + g.setColor(Color.darkGray); + g.drawString("Recalculating Quality....", 20, y - 5); + 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 +764,6 @@ public class AnnotationPanel extends JPanel implements MouseListener, validRes = true; } - x = (yPos - startRes) * av.charWidth; if (activeRow == i) { @@ -744,14 +777,14 @@ 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 +795,21 @@ 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 +821,46 @@ 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 +873,7 @@ 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 +887,96 @@ 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); + 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 ) { @@ -934,7 +1039,6 @@ 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 +1046,11 @@ 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); @@ -1016,55 +1121,49 @@ 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; - 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) { @@ -1084,6 +1183,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, // 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));