import java.util.*;\r
import java.io.InputStreamReader;\r
import java.io.BufferedReader;\r
-import java.io.FileReader;\r
+import java.net.URL;\r
\r
public class AlignFrame\r
extends GAlignFrame\r
* @param String DOCUMENT ME!\r
*/\r
\r
- public void parseGroupsFile(String file)\r
+ public void parseFeaturesFile(String file)\r
{\r
try\r
{\r
- BufferedReader in = new BufferedReader(new FileReader(file));\r
+ URL url = new URL(file);\r
+\r
+ BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));\r
SequenceI seq = null;\r
- String line, text, token;\r
- UserColourScheme ucs;\r
+ String line, type, desc, token;\r
+\r
int index, start, end;\r
StringTokenizer st;\r
- SequenceGroup sg;\r
+ SequenceFeature sf;\r
+ FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
int lineNo = 0;\r
while ( (line = in.readLine()) != null)\r
{\r
lineNo++;\r
st = new StringTokenizer(line, "\t");\r
- if (st.countTokens() != 6)\r
+ if (st.countTokens() == 2)\r
{\r
- System.out.println("Groups file " + file +\r
- " is invalid. Read help file.\nLine: \n"\r
- +lineNo +": "+line);\r
- break;\r
+ type = st.nextToken();\r
+ UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
+ fr.setColour(type, ucs.findColour("A"));\r
+ continue;\r
}\r
\r
while (st.hasMoreElements())\r
{\r
- text = st.nextToken();\r
+ desc = st.nextToken();\r
token = st.nextToken();\r
if (!token.equals("ID_NOT_SPECIFIED"))\r
{\r
\r
start = Integer.parseInt(st.nextToken());\r
end = Integer.parseInt(st.nextToken());\r
- ucs = new UserColourScheme(st.nextToken());\r
\r
seq = viewport.alignment.getSequenceAt(index);\r
start = seq.findIndex(start) - 1;\r
end = seq.findIndex(end) - 1;\r
\r
- sg = new SequenceGroup(text, ucs, true, true, false, start, end);\r
- sg.addSequence(seq, false);\r
+ type = st.nextToken();\r
+\r
+ if(fr.getColour(type)==null)\r
+ {\r
+ // Probably the old style groups file\r
+ UserColourScheme ucs = new UserColourScheme(type);\r
+ fr.setColour(type, ucs.findColour("A"));\r
+ }\r
\r
- viewport.alignment.addGroup(sg);\r
+ sf = new SequenceFeature(type, desc, "", start, end);\r
\r
+ seq.addSequenceFeature(sf);\r
}\r
}\r
\r
+ viewport.showSequenceFeatures = true;\r
+ ((Alignment)viewport.alignment).featuresAdded = true;\r
+\r
alignPanel.repaint();\r
\r
}\r
\r
protected void documentation_actionPerformed(ActionEvent e)\r
{\r
- jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");\r
+ showURL("http://www.jalview.org/help.html");\r
}\r
\r
protected void about_actionPerformed(ActionEvent e)\r
jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
\r
}\r
+\r
+ /**\r
+ * Displays the given URL in a new browser window\r
+ *\r
+ * @param url URL to display in browser window.\r
+ * <br>New window will be named "HELP_WINDOW"\r
+ */\r
+ public void showURL(String url)\r
+ {\r
+ showURL(url, "HELP");\r
+ }\r
+\r
+ public void showURL(String url, String target)\r
+ {\r
+ if (applet == null)\r
+ {\r
+ System.out.println("Not running as applet - no browser available.");\r
+ }\r
+ else\r
+ {\r
+ try\r
+ {\r
+ applet.getAppletContext().showDocument(new java.net.URL(url),\r
+ target);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+\r
}\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.appletgui;\r
\r
-import java.util.*;\r
+import jalview.datamodel.*;\r
\r
import java.awt.*;\r
\r
-import jalview.datamodel.*;\r
+import java.util.*;\r
+\r
+import java.awt.image.*;\r
\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
public class FeatureRenderer\r
{\r
- AlignViewport av;\r
-\r
- SequenceGroup currentSequenceGroup = null;\r
- SequenceGroup[] allGroups = null;\r
- Color resBoxColour;\r
- Graphics graphics;\r
-\r
- public FeatureRenderer(AlignViewport av)\r
- {\r
- this.av = av;\r
- }\r
-\r
- public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,\r
- int start, int end, int x1, int y1, int width,\r
- int height)\r
- {\r
- Vector features = seq.getSequenceFeatures();\r
- Enumeration e = features.elements();\r
- while (e.hasMoreElements())\r
+ AlignViewport av;\r
+ SequenceGroup currentSequenceGroup = null;\r
+ SequenceGroup[] allGroups = null;\r
+ Color resBoxColour;\r
+ Graphics graphics;\r
+ float transparency = .4f;\r
+\r
+ // The following vector holds the features which are\r
+ // to be added, in the correct order or rendering\r
+ Vector featuresDisplayed;\r
+\r
+ /**\r
+ * Creates a new FeatureRenderer object.\r
+ *\r
+ * @param av DOCUMENT ME!\r
+ */\r
+ public FeatureRenderer(AlignViewport av)\r
{\r
- SequenceFeature sf = (SequenceFeature) e.nextElement();\r
- if (sf.getBegin() > seq.getEnd())\r
- {\r
- continue;\r
- }\r
+ this.av = av;\r
+ initColours();\r
+ String version = System.getProperty("java.version");\r
+ if (version.indexOf("1.1") == 0)\r
+ highlightTransparent = false;\r
\r
- int fstart = seq.findIndex(sf.getBegin()) - 1;\r
- int fend = seq.findIndex(sf.getEnd()) - 1;\r
+ }\r
\r
- if ( (fstart <= end && fend >= start))\r
- {\r
- if (fstart < 0) // fix for if the feature we have starts before the sequence start,\r
+boolean highlightTransparent = true;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ * @param seq DOCUMENT ME!\r
+ * @param sg DOCUMENT ME!\r
+ * @param start DOCUMENT ME!\r
+ * @param end DOCUMENT ME!\r
+ * @param x1 DOCUMENT ME!\r
+ * @param y1 DOCUMENT ME!\r
+ * @param width DOCUMENT ME!\r
+ * @param height DOCUMENT ME!\r
+ */\r
+ public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,\r
+ int start, int end, int x1, int y1, int width, int height)\r
+ {\r
+\r
+ if(seq.getSequenceFeatures()==null)\r
+ return;\r
+\r
+ Enumeration e = null, e2;\r
+ String type;\r
+ if(featuresDisplayed!=null)\r
+ e = featuresDisplayed.elements();\r
+ else\r
+ e = seq.getSequenceFeatures().elements();\r
+\r
+ if(highlightTransparent)\r
{\r
- fstart = 0; // but the feature end is still valid!!\r
+ // MyGraphics.SetTransparency(g, transparency);\r
}\r
\r
- if (fstart == fend)\r
- {\r
- g.setColor(Color.red);\r
- g.fillRoundRect( (fstart - start) * width, y1, width, height, 4, 4);\r
- g.setColor(Color.white);\r
-\r
- char s = seq.getSequence().charAt(fstart);\r
- FontMetrics fm = g.getFontMetrics();\r
- int charOffset = (width - fm.charWidth(s)) / 2;\r
- int pady = height / 5;\r
- g.drawString(String.valueOf(s),\r
- charOffset + x1 + width * (fstart - start),\r
- y1 + height - pady);\r
\r
- }\r
- else\r
+ while (e.hasMoreElements())\r
{\r
- for (int i = fstart; i <= fend; i++)\r
- {\r
- char s = seq.getSequence().charAt(i);\r
- if (jalview.util.Comparison.isGap(s))\r
+ SequenceFeature sf=null;\r
+ if(featuresDisplayed!=null)\r
{\r
+ e2 = seq.getSequenceFeatures().elements();\r
+ type = e.nextElement().toString();\r
+ while(e2.hasMoreElements())\r
+ {\r
+ sf = (SequenceFeature) e2.nextElement();\r
+ if(sf.getType().equals(type))\r
+ break;\r
+ else\r
+ sf = null;\r
+ }\r
+ }\r
+ else\r
+ {\r
+ sf = (SequenceFeature) e.nextElement();\r
+ type = sf.getType();\r
+ }\r
+\r
+ if(sf==null)\r
continue;\r
+\r
+\r
+ if (sf.getBegin() > seq.getEnd())\r
+ {\r
+ continue;\r
}\r
\r
- g.setColor(Color.blue);\r
- g.fillRect( (i - start) * width, y1, width, height);\r
+ int fstart = seq.findIndex(sf.getBegin()) - 1;\r
+ int fend = seq.findIndex(sf.getEnd()) - 1;\r
+\r
+ if (((fstart <= end) && (fend >= start)))\r
+ {\r
+ if (fstart < start)\r
+ { // fix for if the feature we have starts before the sequence start,\r
+ fstart = start; // but the feature end is still valid!!\r
+ }\r
+\r
+ if (fend >= end)\r
+ {\r
+ fend = end;\r
+ }\r
+\r
+ if (fstart == fend)\r
+ {\r
+ g.setColor(getColour(type));\r
+ g.fillRoundRect((fstart - start) * width, y1, width,\r
+ height, 4, 4);\r
+ g.setColor(Color.white);\r
+\r
+ char s = seq.getSequence().charAt(fstart);\r
+ FontMetrics fm = g.getFontMetrics();\r
+ int charOffset = (width - fm.charWidth(s)) / 2;\r
+ int pady = height / 5;\r
+ g.drawString(String.valueOf(s),\r
+ charOffset + x1 + (width * (fstart - start)),\r
+ (y1 + height) - pady);\r
+ }\r
+ else\r
+ {\r
+ for (int i = fstart; i <= fend; i++)\r
+ {\r
+ char s = seq.getSequence().charAt(i);\r
\r
- g.setColor(Color.white);\r
+ if (jalview.util.Comparison.isGap(s))\r
+ {\r
+ continue;\r
+ }\r
\r
- FontMetrics fm = g.getFontMetrics();\r
- int charOffset = (width - fm.charWidth(s)) / 2;\r
- int pady = height / 5;\r
- g.drawString(String.valueOf(s),\r
- charOffset + x1 + width * (i - start),\r
- y1 + height - pady);\r
+ g.setColor(getColour(type));\r
+ g.fillRect((i - start) * width, y1, width, height);\r
+\r
+ g.setColor(Color.white);\r
+\r
+ FontMetrics fm = g.getFontMetrics();\r
+ int charOffset = (width - fm.charWidth(s)) / 2;\r
+ int pady = height / 5;\r
+ g.drawString(String.valueOf(s),\r
+ charOffset + x1 + (width * (i - start)),\r
+ (y1 + height) - pady);\r
+ }\r
+ }\r
+ }\r
}\r
- }\r
+\r
+ if (highlightTransparent)\r
+ {\r
+ // MyGraphics.SetTransparency(g, 1.0f);\r
+ }\r
+ }\r
+\r
+ public Color getColour(String featureType)\r
+ {\r
+ return (Color)featureColours.get(featureType);\r
+ }\r
+\r
+ public void setColour(String featureType, Color col)\r
+ {\r
+ featureColours.put(featureType, col);\r
+ }\r
+\r
+ public void setTransparency(float value)\r
+ {\r
+ transparency = value;\r
+ }\r
+\r
+ public float getTransparency()\r
+ {\r
+ return transparency;\r
+ }\r
+\r
+ public void setFeaturePriority(Object [][] data)\r
+ {\r
+ // The feature table will display high priority\r
+ // features at the top, but theses are the ones\r
+ // we need to render last, so invert the data\r
+ featuresDisplayed = new Vector();\r
+ for(int i=data.length-1; i>-1; i--)\r
+ {\r
+ String type = data[i][0].toString();\r
+ setColour(type, (Color)data[i][1]);\r
+ if( ((Boolean)data[i][2]).booleanValue() )\r
+ featuresDisplayed.addElement(type);\r
}\r
+ }\r
\r
+ Hashtable featureColours = new Hashtable();\r
+ void initColours()\r
+ {\r
+ featureColours.put("active site", new Color(255, 75, 0));\r
+ featureColours.put("binding site", new Color(245, 85, 0));\r
+ featureColours.put("calcium-binding region", new Color(235, 95, 0));\r
+ featureColours.put("chain", new Color(225, 105, 0));\r
+ featureColours.put("coiled-coil region", new Color(215, 115, 0));\r
+ featureColours.put("compositionally biased region", new Color(205, 125, 0));\r
+ featureColours.put("cross-link", new Color(195, 135, 0));\r
+ featureColours.put("disulfide bond", new Color(185, 145, 0));\r
+ featureColours.put("DNA-binding region", new Color(175, 155, 0));\r
+ featureColours.put("domain", new Color(165, 165, 0));\r
+ featureColours.put("glycosylation site", new Color(155, 175, 0));\r
+ featureColours.put("helix", new Color(145, 185, 0));\r
+ featureColours.put("initiator methionine", new Color(135, 195, 5));\r
+ featureColours.put("lipid moiety-binding region", new Color(125, 205, 15));\r
+ featureColours.put("metal ion-binding site", new Color(115, 215, 25));\r
+ featureColours.put("modified residue", new Color(105, 225, 35));\r
+ featureColours.put("mutagenesis site", new Color(95, 235, 45));\r
+ featureColours.put("non-consecutive residues", new Color(85, 245, 55));\r
+ featureColours.put("non-terminal residue", new Color(75, 255, 65));\r
+ featureColours.put("nucleotide phosphate-binding region",\r
+ new Color(65, 245, 75));\r
+ featureColours.put("peptide", new Color(55, 235, 85));\r
+ featureColours.put("propeptide", new Color(45, 225, 95));\r
+ featureColours.put("region of interest", new Color(35, 215, 105));\r
+ featureColours.put("repeat", new Color(25, 205, 115));\r
+ featureColours.put("selenocysteine", new Color(15, 195, 125));\r
+ featureColours.put("sequence conflict", new Color(5, 185, 135));\r
+ featureColours.put("sequence variant", new Color(0, 175, 145));\r
+ featureColours.put("short sequence motif", new Color(0, 165, 155));\r
+ featureColours.put("signal peptide", new Color(0, 155, 165));\r
+ featureColours.put("site", new Color(0, 145, 175));\r
+ featureColours.put("splice variant", new Color(0, 135, 185));\r
+ featureColours.put("strand", new Color(0, 125, 195));\r
+ featureColours.put("topological domain", new Color(0, 115, 205));\r
+ featureColours.put("transit peptide", new Color(0, 105, 215));\r
+ featureColours.put("transmembrane region", new Color(0, 95, 225));\r
+ featureColours.put("turn", new Color(0, 85, 235));\r
+ featureColours.put("unsure residue", new Color(0, 75, 245));\r
+ featureColours.put("zinc finger region", new Color(0, 65, 255));\r
}\r
- }\r
\r
}\r
+\r
+\r
+\r
git://source.jalview.org / jalview.git / commitdiff