import java.awt.image.*;\r
\r
import javax.swing.*;\r
+import jalview.schemes.*;\r
\r
\r
/**\r
int LABEL_WEST;\r
int LABEL_EAST;\r
\r
- boolean isOverview = false;\r
-\r
/**\r
* Creates a new SeqCanvas object.\r
*\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
// Set this to false to force a full panel paint\r
public void paintComponent(Graphics g)\r
{\r
+ super.paintComponent(g);\r
+\r
sr.renderGaps(av.renderGaps);\r
\r
- if ((img != null) &&\r
- (fastPaint || (getWidth() != g.getClipBounds().width) ||\r
- (getHeight() != g.getClipBounds().height)))\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
return;\r
}\r
\r
-\r
img = new BufferedImage(imgWidth, imgHeight, BufferedImage.TYPE_INT_RGB);\r
gg = (Graphics2D) img.getGraphics();\r
gg.setFont(av.getFont());\r
}\r
\r
g.drawImage(img, 0, 0, this);\r
+\r
+ if (pdbCanvas != null)\r
+ {\r
+ pdbCanvas.updateSeqColours();\r
+ }\r
+\r
}\r
\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
-\r
-\r
- SequenceI nextSeq;\r
-\r
- SequenceI dna = null;\r
+ Graphics2D g = (Graphics2D) g1;\r
+ g.setFont(av.getFont());\r
\r
- int aaHeight = (int)(av.getCharHeight()*aaRatio);\r
- int dnaHeight =(int)(av.getCharHeight() * (1-aaRatio));\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
- java.awt.geom.AffineTransform transform = new java.awt.geom.AffineTransform();\r
- transform.scale(1f/3f , 1);\r
- Font dnafont = new Font(av.getFont().getName(), av.getFont().getStyle(),\r
- dnaHeight);\r
- dnafont = dnafont.deriveFont(transform);\r
-\r
- Font 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
+ ColourSchemeI cs = av.getGlobalColourScheme();\r
\r
/// First draw the sequences\r
/////////////////////////////\r
{\r
nextSeq = av.alignment.getSequenceAt(i);\r
g.setFont(aafont);\r
-/*\r
- StringBuffer dnasb = new StringBuffer();\r
- for (int j = 0; j < nextSeq.getLength(); j++)\r
+ /* if(av.getShowTranslation())\r
{\r
- java.util.Vector codons = jalview.schemes.ResidueProperties.getCodons(nextSeq.getSequence(j,\r
- j + 1));\r
- if (codons != null && codons.size() > 0)\r
- dnasb.append(codons.elementAt(0).toString());\r
- }\r
-\r
- dna = new Sequence("dna", dnasb.toString());*/\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
aaHeight);\r
\r
-\r
- /* g.setFont(dnafont);\r
-\r
- sr.drawSequence(g, dna, null,\r
- x1, x2 * 3 +2, ( (x1 - startx) * av.charWidth) / 3,\r
- offset + ( (i - starty) * av.charHeight) + aaHeight, av.charWidth / 3,\r
- dnaHeight);*/\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 && !isOverview)\r
+ if (group != null)\r
{\r
do\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