X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=71f51eaa1c165af833eab70fa4428d47383b1bb2;hb=e30c8f0736f711e2dc7c32680ac57a28c77d567d;hp=cb638dda875a1e6ef53157f53921785fb50051e2;hpb=be8ed26b63eec2546c415d23e58fce77d3e14f2c;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java index cb638dd..71f51ea 100755 --- a/src/jalview/appletgui/AnnotationPanel.java +++ b/src/jalview/appletgui/AnnotationPanel.java @@ -51,11 +51,16 @@ public class AnnotationPanel public static int GRAPH_HEIGHT = 40; + boolean MAC = false; + public AnnotationPanel(AlignmentPanel ap) { + if (System.getProperty("os.name").startsWith("Mac")) + MAC = true; + this.ap = ap; av = ap.av; - this.setLayout(null); + setLayout(null); adjustPanelHeight(); addMouseMotionListener(new MouseMotionAdapter() @@ -126,9 +131,6 @@ public class AnnotationPanel } this.setSize(getSize().width, height); - if(ap!=null) - ap.annotationScroller.setSize(getSize().width, height); - repaint(); @@ -206,6 +208,8 @@ public class AnnotationPanel public void paint(Graphics g) { + + imgWidth = (av.endRes - av.startRes + 1) * av.charWidth; if (image == null || imgWidth != image.getWidth(this)) @@ -225,6 +229,8 @@ public class AnnotationPanel } drawComponent(gg, av.startRes, av.endRes + 1); + g.setColor(Color.white); + g.fillRect(0, 0, getSize().width, getSize().height); g.drawImage(image, 0, 0, this); } @@ -286,18 +292,18 @@ public class AnnotationPanel g.setColor(Color.white); g.fillRect(0, 0, getSize().width, getSize().height); 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 j; int x = 0; int y = 0; - char[] lastSS = new char[aa.length]; - int[] lastSSX = new int[aa.length]; + char lastSS; + int lastSSX; int iconOffset = av.charHeight / 2; boolean validRes = false; @@ -314,7 +320,8 @@ public class AnnotationPanel continue; } - + lastSS = ' '; + lastSSX = 0; if (row.graph>0) { @@ -339,10 +346,11 @@ public class AnnotationPanel iconOffset = 0; } - for (j = startRes; j < endRes; j++) + int column = startRes; + while(column < endRes) { - if ((row.annotations.length <= j) || - (row.annotations[j] == null)) + if ((row.annotations.length <= column) || + (row.annotations[column] == null)) { validRes = false; } @@ -351,68 +359,79 @@ public class AnnotationPanel validRes = true; } - x = (j - startRes) * av.charWidth; - - if (activeRow == i) - { - g.setColor(Color.red); - - if (activeRes != null) - { - for (int n = 0; n < activeRes.size(); n++) - { - int v = Integer.parseInt(activeRes.elementAt(n).toString()); + x = (column - startRes) * av.charWidth; - if (v == j) - { - g.fillRect((j - startRes) * av.charWidth, y, - av.charWidth, row.height); - } - } - } - } - if (validRes && - (row.annotations[j].displayCharacter.length() > 0)) + if (av.validCharWidth && validRes && + (row.annotations[column].displayCharacter.length() > 0)) { - - int charOffset = (av.charWidth - - fm.charWidth(row.annotations[j].displayCharacter.charAt( - 0))) / 2; - g.setColor(row.annotations[j].colour); - - if (j == 0 || row.graph>0) - { - g.drawString(row.annotations[j].displayCharacter, x+charOffset, - y + iconOffset + 3); - } - else if (((row.annotations[j - 1] == null) || - (!row.annotations[j].displayCharacter.equals( - row.annotations[j - 1].displayCharacter)))) - { - g.drawString(row.annotations[j].displayCharacter, x+charOffset, - y + iconOffset + 3); - } + int charOffset = (av.charWidth - + fm.charWidth(row.annotations[column].displayCharacter.charAt( + 0))) / 2; + g.setColor(row.annotations[column].colour); + + if (column == 0 || row.graph>0) + { + g.drawString(row.annotations[column].displayCharacter, x+charOffset, + y + iconOffset + 3); + } + 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); + } } if (row.hasIcons) { if (!validRes || - (row.annotations[j].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 - 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, 8, 90,180) ; + x1 += av.charWidth/2; + } + + if(row.annotations[column]==null || + row.annotations[column].secondaryStructure!='H') + { + g.fillArc(x-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.fillRect(lastSSX, y + 4 + iconOffset, + x - lastSSX - 4, 7); g.fillPolygon(new int[] { x - 4, x - 4, x }, new int[] { @@ -425,38 +444,69 @@ public class AnnotationPanel default: g.setColor(Color.gray); - g.fillRect(lastSSX[i], y + 6 + iconOffset, - x - lastSSX[i], 2); + g.fillRect(lastSSX, y + 6 + iconOffset, + x - lastSSX, 2); break; } if (validRes) { - lastSS[i] = row.annotations[j].secondaryStructure; + lastSS = row.annotations[column].secondaryStructure; } else { - lastSS[i] = ' '; + lastSS = ' '; } - lastSSX[i] = x; + lastSSX = x; } } + + + column++; } x += av.charWidth; 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 - 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, 8, 90,180) ; + x1 += av.charWidth/2; + } + + if(row.annotations[column]==null || + row.annotations[column].secondaryStructure!='H') + { + g.fillArc(x-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); @@ -464,8 +514,8 @@ public class AnnotationPanel if (row.annotations.length > endRes && row.annotations[endRes].secondaryStructure != 'E') { - g.fillRect(lastSSX[i], y + 4 + iconOffset, - x - lastSSX[i] - 4, 7); + g.fillRect(lastSSX, y + 4 + iconOffset, + x - lastSSX - 4, 7); g.fillPolygon(new int[] {x - 4, x - 4, x}, new int[] @@ -475,17 +525,15 @@ public class AnnotationPanel }, 3); } else - g.fillRect(lastSSX[i], y + 4 + iconOffset, - x - lastSSX[i], 7); + g.fillRect(lastSSX, y + 4 + iconOffset, + x - lastSSX, 7); break; - case 'C': - break; default: g.setColor(Color.gray); - g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2); + g.fillRect(lastSSX, y + 6 + iconOffset, x - lastSSX, 2); break; } @@ -555,7 +603,6 @@ public class AnnotationPanel return; - eRes = Math.min(eRes, aa.annotations.length); int x = 0; @@ -563,6 +610,9 @@ public class AnnotationPanel if(eRes