import java.awt.image.*;\r
\r
import javax.swing.*;\r
+import jalview.schemes.*;\r
\r
\r
/**\r
AlignViewport av;\r
boolean displaySearch = false;\r
int[] searchResults = null;\r
- int chunkHeight;\r
- int chunkWidth;\r
boolean fastPaint = false;\r
int LABEL_WEST;\r
int LABEL_EAST;\r
setBackground(Color.white);\r
}\r
\r
+ MCview.PDBCanvas pdbCanvas;\r
+ public SequenceRenderer getSequenceRenderer()\r
+ {\r
+ return sr;\r
+ }\r
+\r
+ public FeatureRenderer getFeatureRenderer()\r
+ {\r
+ return fr;\r
+ }\r
+\r
+ public void setPDBCanvas(MCview.PDBCanvas pc)\r
+ {\r
+ pdbCanvas = pc;\r
+ }\r
+\r
+ public AlignViewport getViewport()\r
+ {\r
+ return av;\r
+ }\r
+\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
*/\r
public void fastPaint(int horizontal, int vertical)\r
{\r
- if (((horizontal == 0) && (vertical == 0)) || (gg == null))\r
+ if (gg == null)\r
{\r
return;\r
}\r
\r
- gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,\r
- -vertical * av.charHeight);\r
+ gg.copyArea(horizontal * av.charWidth,\r
+ vertical * av.charHeight,\r
+ imgWidth,\r
+ imgHeight,\r
+ -horizontal * av.charWidth,\r
+ -vertical * av.charHeight);\r
\r
int sr = av.startRes;\r
int er = av.endRes;\r
\r
if (horizontal > 0) // scrollbar pulled right, image to the left\r
{\r
+ er ++;\r
transX = (er - sr - horizontal) * av.charWidth;\r
sr = er - horizontal;\r
}\r
else if (horizontal < 0)\r
{\r
- er = sr - horizontal;\r
+ er = sr - horizontal-1;\r
}\r
else if (vertical > 0) // scroll down\r
{\r
}\r
\r
gg.translate(transX, transY);\r
-\r
- gg.setColor(Color.white);\r
- gg.fillRect(0, 0, (er - sr + 1) * av.charWidth,\r
- (es - ss) * av.charHeight);\r
drawPanel(gg, sr, er, ss, es, sr, ss, 0);\r
gg.translate(-transX, -transY);\r
\r
// Set this to false to force a full panel paint\r
public void paintComponent(Graphics g)\r
{\r
- if ((img != null) &&\r
- (fastPaint || (getWidth() != g.getClipBounds().width) ||\r
- (getHeight() != g.getClipBounds().height)))\r
+ super.paintComponent(g);\r
+\r
+ sr.renderGaps(av.renderGaps);\r
+\r
+ if ( img != null && (fastPaint\r
+ || (getVisibleRect().width != g.getClipBounds().width)\r
+ || (getVisibleRect().height != g.getClipBounds().height)))\r
{\r
g.drawImage(img, 0, 0, this);\r
fastPaint = false;\r
-\r
return;\r
}\r
\r
+\r
// this draws the whole of the alignment\r
imgWidth = getWidth();\r
imgHeight = getHeight();\r
gg = (Graphics2D) img.getGraphics();\r
gg.setFont(av.getFont());\r
gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
- RenderingHints.VALUE_ANTIALIAS_ON);\r
+ RenderingHints.VALUE_ANTIALIAS_ON);\r
\r
gg.setColor(Color.white);\r
gg.fillRect(0, 0, imgWidth, imgHeight);\r
\r
- chunkWidth = getWrappedCanvasWidth(getWidth());\r
- chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
-\r
- av.setChunkHeight(chunkHeight);\r
- av.setChunkWidth(chunkWidth);\r
\r
if (av.getWrapAlignment())\r
{\r
}\r
\r
g.drawImage(img, 0, 0, this);\r
+\r
+ if (pdbCanvas != null)\r
+ {\r
+ pdbCanvas.updateSeqColours();\r
+ }\r
+\r
}\r
\r
/**\r
LABEL_WEST = fm.stringWidth(getMask());\r
}\r
\r
+ int hgap = av.charHeight;\r
+ if(av.scaleAboveWrapped)\r
+ hgap += av.charHeight;\r
+\r
int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
- int cHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
+ int cHeight = av.getAlignment().getHeight() * av.charHeight;\r
+\r
+ av.setWrappedWidth(cWidth);\r
\r
av.endRes = av.startRes + cWidth;\r
\r
+\r
int endx = (startRes + cWidth) - 1;\r
- int ypos = 2 * av.charHeight;\r
+ int ypos = hgap;\r
+\r
\r
while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))\r
{\r
+ g.setFont(av.getFont());\r
g.setColor(Color.black);\r
\r
if (av.scaleLeftWrapped)\r
cWidth * av.charWidth, (int) clip.getBounds().getHeight());\r
}\r
\r
+ if (av.vconsensus!=null && av.alignment.getWidth() >= av.vconsensus.size())\r
+ {\r
+ endx = av.vconsensus.size() - 2;\r
+ }\r
+\r
+\r
drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);\r
+\r
+ if(av.showAnnotation)\r
+ {\r
+ g.translate(0, cHeight + ypos + 3);\r
+ if(annotations==null)\r
+ annotations = new AnnotationPanel(av);\r
+\r
+ annotations.drawComponent( (Graphics2D) g, startRes, endx + 1);\r
+ g.translate(0, -cHeight - ypos);\r
+ }\r
g.setClip(clip);\r
g.translate(-LABEL_WEST, 0);\r
\r
- ypos += cHeight;\r
+ ypos += cHeight+getAnnotationHeight()+hgap;\r
+ if(av.showAnnotation)\r
+ ypos -= 3;\r
+\r
startRes += cWidth;\r
endx = (startRes + cWidth) - 1;\r
\r
}\r
}\r
\r
+ AnnotationPanel annotations;\r
+ int getAnnotationHeight()\r
+ {\r
+ if(!av.showAnnotation)\r
+ return 0;\r
+\r
+ if(annotations==null)\r
+ annotations = new AnnotationPanel(av);\r
+\r
+ return annotations.adjustPanelHeight();\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
* @param starty DOCUMENT ME!\r
* @param offset DOCUMENT ME!\r
*/\r
+\r
+ float aaRatio = 2f/3f;\r
+ public void increaseAARatio()\r
+ {\r
+ aaRatio += .025;\r
+ if(aaRatio>1)\r
+ aaRatio = 1;\r
+\r
+ repaint();\r
+ }\r
+\r
+ public void decreaseAARation()\r
+ {\r
+ aaRatio -= .025;\r
+ if(aaRatio<0)\r
+ aaRatio = 0;\r
+\r
+ repaint();\r
+ }\r
+\r
+\r
synchronized public void drawPanel(Graphics g1, int x1, int x2, int y1,\r
int y2, int startx, int starty, int offset)\r
{\r
- Graphics2D g = (Graphics2D) g1;\r
- g.setFont(av.getFont());\r
- sr.renderGaps(av.renderGaps);\r
+ Graphics2D g = (Graphics2D) g1;\r
+ g.setFont(av.getFont());\r
\r
- SequenceI nextSeq;\r
+ SequenceI nextSeq, dna = null;\r
+ int aaHeight = av.charHeight, dnaHeight = av.charHeight;\r
+ Font dnafont = null, aafont = av.getFont();\r
+\r
+ /* if (av.getShowTranslation())\r
+ {\r
+ aaHeight = (int) (av.getCharHeight() * aaRatio);\r
+ dnaHeight = (int) (av.getCharHeight() * (1 - aaRatio));\r
+ java.awt.geom.AffineTransform transform = new java.awt.geom.AffineTransform();\r
+ transform.scale(1f / 3f, 1);\r
+ dnafont = new Font(av.getFont().getName(), av.getFont().getStyle(),\r
+ dnaHeight);\r
+ dnafont = dnafont.deriveFont(transform);\r
+\r
+ aafont = new Font(av.getFont().getName(), av.getFont().getStyle(),\r
+ aaHeight);\r
+ transform = new java.awt.geom.AffineTransform();\r
+ transform.scale(1 / aaRatio, 1);\r
+ aafont = aafont.deriveFont(transform);\r
+ }\r
+*/\r
+\r
+ ColourSchemeI cs = av.getGlobalColourScheme();\r
\r
/// First draw the sequences\r
/////////////////////////////\r
for (int i = y1; i < y2; i++)\r
{\r
nextSeq = av.alignment.getSequenceAt(i);\r
+ g.setFont(aafont);\r
+ /* if(av.getShowTranslation())\r
+ {\r
+ dna = nextSeq;\r
+ StringBuffer sb = new StringBuffer();\r
+ for(int r = 0; r<nextSeq.getLength(); r+=3)\r
+ {\r
+ String codon = nextSeq.getSequence(r, r+3);\r
+ codon = codon.replace('U', 'T');\r
+ String res = ResidueProperties.codonTranslate(codon);\r
+ if(res !=null )\r
+ {\r
+ if (res.equals("STOP"))\r
+ sb.append("X");\r
+ else\r
+ sb.append(res);\r
+ }\r
+ }\r
+ nextSeq = new Sequence("d", sb.toString());\r
+ }*/\r
\r
sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq),\r
- x1, x2, (x1 - startx) * av.charWidth,\r
- offset + ((i - starty) * av.charHeight), av.charWidth,\r
- av.charHeight);\r
+ x1, x2, (x1 - startx) * av.charWidth,\r
+ offset + ( (i - starty) * av.charHeight), av.charWidth,\r
+ aaHeight);\r
+\r
+ /* if(av.getShowTranslation())\r
+ {\r
+ av.setGlobalColourScheme(new NucleotideColourScheme());\r
+ g.setFont(dnafont);\r
+ sr.drawSequence(g, dna, null,\r
+ x1*3, (x2+2) * 3, ( (x1 - startx) * av.charWidth) / 3,\r
+ offset + ( (i - starty) * av.charHeight) + aaHeight,\r
+ av.charWidth / 3,\r
+ dnaHeight);\r
+ av.setGlobalColourScheme(cs);\r
+ }*/\r
\r
if (av.showSequenceFeatures)\r
{\r
- fr.drawSequence(g, nextSeq,\r
- av.alignment.findAllGroups(nextSeq), x1, x2,\r
+ fr.drawSequence(g, nextSeq, x1, x2,\r
(x1 - startx) * av.charWidth,\r
offset + ((i - starty) * av.charHeight), av.charWidth,\r
av.charHeight);\r
// Now outline any areas if necessary\r
/////////////////////////////////////\r
SequenceGroup group = av.getSelectionGroup();\r
- java.util.Vector groups = av.alignment.getGroups();\r
\r
int sx = -1;\r
int sy = -1;\r
int ex = -1;\r
int groupIndex = -1;\r
\r
- if ((group == null) && (groups.size() > 0))\r
+ if ((group == null) && (av.alignment.getGroups().size() > 0))\r
{\r
- group = (SequenceGroup) groups.elementAt(0);\r
+ group = (SequenceGroup) av.alignment.getGroups().elementAt(0);\r
groupIndex = 0;\r
}\r
\r
-\r
if (group != null)\r
{\r
do\r
ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -\r
1;\r
\r
+ if(sx+ex<0 || sx>imgWidth)\r
+ {\r
+ continue;\r
+ }\r
\r
- if ((sx < (x2-x1)*av.charWidth) &&\r
+ if ( (sx <= (x2-x1)*av.charWidth) &&\r
group.sequences.contains(av.alignment.getSequenceAt(\r
i)))\r
{\r
}\r
else\r
{\r
- if (inGroup)\r
+ if (inGroup)\r
+ {\r
+ if (sx >= 0 && sx < imgWidth)\r
+ g.drawLine(sx, oldY, sx, sy);\r
+\r
+ if (sx + ex < imgWidth)\r
+ g.drawLine(sx + ex, oldY, sx + ex, sy);\r
+\r
+ if (sx < 0)\r
{\r
- g.drawLine(sx, oldY, sx, sy);\r
- g.drawLine(sx + ex, oldY, sx + ex, sy);\r
+ ex += sx;\r
+ sx = 0;\r
+ }\r
\r
- if (top != -1)\r
- {\r
- g.drawLine(sx, top, sx + ex, top);\r
- top = -1;\r
- }\r
+ if (sx + ex > imgWidth)\r
+ ex = imgWidth;\r
\r
- if (bottom != -1)\r
- {\r
- g.drawLine(sx, bottom, sx + ex, bottom);\r
- bottom = -1;\r
- }\r
+ else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)\r
+ ex = (x2 - x1 + 1) * av.charWidth;\r
+\r
+ if (top != -1)\r
+ {\r
+ g.drawLine(sx, top, sx + ex, top);\r
+ top = -1;\r
+ }\r
+\r
+ if (bottom != -1)\r
+ {\r
+ g.drawLine(sx, bottom, sx + ex, bottom);\r
+ bottom = -1;\r
+ }\r
\r
- inGroup = false;\r
+ inGroup = false;\r
}\r
}\r
}\r
\r
-\r
if (inGroup)\r
{\r
- if (top != -1)\r
- {\r
- g.drawLine(sx, top, sx + ex, top);\r
- top = -1;\r
- }\r
-\r
- if (bottom != -1)\r
- {\r
- g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);\r
- bottom = -1;\r
- }\r
-\r
- sy = offset + ((i - starty) * av.charHeight);\r
+ sy = offset + ( (i - starty) * av.charHeight);\r
+ if (sx >= 0 && sx < imgWidth)\r
g.drawLine(sx, oldY, sx, sy);\r
+\r
+ if (sx + ex < imgWidth)\r
g.drawLine(sx + ex, oldY, sx + ex, sy);\r
+\r
+ if (sx < 0)\r
+ {\r
+ ex += sx;\r
+ sx = 0;\r
+ }\r
+\r
+ if (sx + ex > imgWidth)\r
+ ex = imgWidth;\r
+ else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)\r
+ ex = (x2 - x1 + 1) * av.charWidth;\r
+\r
+ if (top != -1)\r
+ {\r
+ g.drawLine(sx, top, sx + ex, top);\r
+ top = -1;\r
+ }\r
+\r
+ if (bottom != -1)\r
+ {\r
+ g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);\r
+ bottom = -1;\r
+ }\r
+\r
inGroup = false;\r
}\r
\r
groupIndex++;\r
\r
- if (groupIndex >= groups.size())\r
+ if (groupIndex >= av.alignment.getGroups().size())\r
{\r
break;\r
}\r
\r
- group = (SequenceGroup) groups.elementAt(groupIndex);\r
+ group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);\r
}\r
- while (groupIndex < groups.size());\r
+ while (groupIndex < av.alignment.getGroups().size());\r
}\r
\r
/// Highlight search Results once all sequences have been drawn\r
git://source.jalview.org / jalview.git / blobdiff