\r
import jalview.datamodel.*;\r
import jalview.schemes.*;\r
+import jalview.util.Format;\r
\r
/**\r
* Parse and create Jalview Features files Detects GFF format features files and\r
public class FeaturesFile extends AlignFile\r
{\r
/**\r
- * work around for GFF interpretation bug where source string becomes description rather than a group\r
+ * work around for GFF interpretation bug where source string becomes\r
+ * description rather than a group\r
*/\r
private boolean doGffSource = true;\r
\r
* Creates a new FeaturesFile object.\r
* \r
* @param inFile\r
- * DOCUMENT ME!\r
+ * DOCUMENT ME!\r
* @param type\r
- * DOCUMENT ME!\r
+ * DOCUMENT ME!\r
* \r
* @throws IOException\r
- * DOCUMENT ME!\r
+ * DOCUMENT ME!\r
*/\r
public FeaturesFile(String inFile, String type) throws IOException\r
{\r
* replace links with %LINK% Both need to read links in HTML however\r
* \r
* @throws IOException\r
- * DOCUMENT ME!\r
+ * DOCUMENT ME!\r
*/\r
public boolean parse(AlignmentI align, Hashtable colours,\r
boolean removeHTML)\r
* replace links with %LINK% Both need to read links in HTML however\r
* \r
* @throws IOException\r
- * DOCUMENT ME!\r
+ * DOCUMENT ME!\r
*/\r
public boolean parse(AlignmentI align, Hashtable colours,\r
Hashtable featureLink, boolean removeHTML)\r
}\r
else\r
{\r
- UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
- colours.put(type, ucs.findColour('A'));\r
+ Object colour = null;\r
+ String colscheme = st.nextToken();\r
+ if (colscheme.indexOf("|") > -1)\r
+ {\r
+ // Parse '|' separated graduated colourscheme fields:\r
+ // mincolour|maxcolour|[absolute|]minvalue|maxvalue|thresholdtype|thresholdvalue\r
+ // first four are required.\r
+ // first two are hexadecimal or word equivalent colours.\r
+ // second two are values parsed as floats.\r
+ // fifth is either 'above','below', or 'none'.\r
+ // sixth is a float value and only required when fifth is either\r
+ // 'above' or 'below'.\r
+ StringTokenizer gcol = new StringTokenizer(colscheme, "|");\r
+ String mincol = gcol.nextToken(), maxcol = gcol.nextToken();\r
+ String abso = gcol\r
+ .nextToken(), minval, maxval;\r
+ if (abso.toLowerCase().indexOf("abso")!=0) {\r
+ minval = abso;\r
+ abso = null;\r
+ } else {\r
+ minval = gcol.nextToken();\r
+ }\r
+ maxval = gcol.nextToken();\r
+ // set defaults\r
+ int threshtype = AnnotationColourGradient.NO_THRESHOLD;\r
+ float min=Float.MIN_VALUE,max=Float.MAX_VALUE,threshval=Float.NaN;\r
+ try\r
+ {\r
+ if (minval.length()>0) { \r
+ min = new Float(minval).floatValue();\r
+ }\r
+ } catch (Exception e)\r
+ {\r
+ System.err\r
+ .println("Couldn't parse the minimum value for graduated colour for type ("\r
+ + colscheme + ") - did you misspell 'auto' for the optional automatic colour switch ?");\r
+ e.printStackTrace();\r
+ }\r
+ try\r
+ {\r
+ if (maxval.length()>0) { \r
+ max = new Float(maxval).floatValue();\r
+ }\r
+ } catch (Exception e)\r
+ {\r
+ System.err\r
+ .println("Couldn't parse the maximum value for graduated colour for type ("\r
+ + colscheme + ")");\r
+ e.printStackTrace();\r
+ }\r
+ try\r
+ {\r
+ colour = new jalview.schemes.GraduatedColor(\r
+ new UserColourScheme(mincol).findColour('A'),\r
+ new UserColourScheme(maxcol).findColour('A'),\r
+ min, max);\r
+ } catch (Exception e)\r
+ {\r
+ System.err\r
+ .println("Couldn't parse the graduated colour scheme ("\r
+ + colscheme + ")");\r
+ e.printStackTrace();\r
+ }\r
+ if (colour != null)\r
+ {\r
+ ((jalview.schemes.GraduatedColor)colour).setAutoScaled(abso==null);\r
+ // add in any additional parameters\r
+ String ttype = null, tval = null;\r
+ if (gcol.hasMoreTokens())\r
+ {\r
+ // threshold type and possibly a threshold value\r
+ ttype = gcol.nextToken();\r
+ if (ttype.toLowerCase().startsWith("below"))\r
+ {\r
+ ((jalview.schemes.GraduatedColor) colour)\r
+ .setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);\r
+ }\r
+ else if (ttype.toLowerCase().startsWith("above"))\r
+ {\r
+ ((jalview.schemes.GraduatedColor) colour)\r
+ .setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);\r
+ }\r
+ else\r
+ {\r
+ ((jalview.schemes.GraduatedColor) colour)\r
+ .setThreshType(AnnotationColourGradient.NO_THRESHOLD);\r
+ if (!ttype.toLowerCase().startsWith("no"))\r
+ {\r
+ System.err\r
+ .println("Ignoring unrecognised threshold type : "\r
+ + ttype);\r
+ }\r
+ }\r
+ }\r
+ if (((GraduatedColor)colour).getThreshType()!=AnnotationColourGradient.NO_THRESHOLD)\r
+ {\r
+ tval = gcol.nextToken();\r
+ try\r
+ {\r
+ ((jalview.schemes.GraduatedColor) colour)\r
+ .setThresh(new Float(tval).floatValue());\r
+ } catch (Exception e)\r
+ {\r
+ System.err\r
+ .println("Couldn't parse threshold value as a float: ("\r
+ + tval + ")");\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+ // parse the thresh-is-min token ?\r
+ if (gcol.hasMoreTokens())\r
+ {\r
+ System.err\r
+ .println("Ignoring additional tokens in parameters in graduated colour specification\n");\r
+ while (gcol.hasMoreTokens())\r
+ {\r
+ System.err.println("|" + gcol);\r
+ }\r
+ System.err.println("\n");\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ UserColourScheme ucs = new UserColourScheme(colscheme);\r
+ colour = ucs.findColour('A');\r
+ }\r
+ if (colour != null)\r
+ {\r
+ colours.put(type, colour);\r
+ }\r
if (st.hasMoreElements())\r
{\r
String link = st.nextToken();\r
}\r
featureLink.put(type, link);\r
}\r
-\r
}\r
continue;\r
}\r
if (seq != null)\r
{\r
desc = st.nextToken();\r
- String group=null;\r
- if (doGffSource && desc.indexOf(' ')==-1) {\r
+ String group = null;\r
+ if (doGffSource && desc.indexOf(' ') == -1)\r
+ {\r
// could also be a source term rather than description line\r
group = new String(desc);\r
}\r
try\r
{\r
String stt = st.nextToken();\r
- if (stt.length()==0 || stt.equals("-"))\r
+ if (stt.length() == 0 || stt.equals("-"))\r
{\r
start = 0;\r
- } else {\r
- start = Integer.parseInt(stt);\r
+ }\r
+ else\r
+ {\r
+ start = Integer.parseInt(stt);\r
}\r
} catch (NumberFormatException ex)\r
{\r
try\r
{\r
String stt = st.nextToken();\r
- if (stt.length()==0 || stt.equals("-"))\r
+ if (stt.length() == 0 || stt.equals("-"))\r
{\r
end = 0;\r
- } else {\r
+ }\r
+ else\r
+ {\r
end = Integer.parseInt(stt);\r
}\r
} catch (NumberFormatException ex)\r
{\r
end = 0;\r
}\r
- // TODO: decide if non positional feature assertion for input data where end==0 is generally valid\r
- if (end==0)\r
+ // TODO: decide if non positional feature assertion for input data\r
+ // where end==0 is generally valid\r
+ if (end == 0)\r
{\r
// treat as non-positional feature, regardless.\r
- start=0;\r
+ start = 0;\r
}\r
try\r
{\r
{\r
attributes.append("\t" + st.nextElement());\r
}\r
- // TODO validate and split GFF2 attributes field ? parse out ([A-Za-z][A-Za-z0-9_]*) <value> ; and add as sf.setValue(attrib, val); \r
+ // TODO validate and split GFF2 attributes field ? parse out\r
+ // ([A-Za-z][A-Za-z0-9_]*) <value> ; and add as\r
+ // sf.setValue(attrib, val);\r
sf.setValue("ATTRIBUTES", attributes.toString());\r
}\r
\r
UserColourScheme ucs = new UserColourScheme(type);\r
colours.put(type, ucs.findColour('A'));\r
}\r
-\r
sf = new SequenceFeature(type, desc, "", start, end, featureGroup);\r
-\r
+ if (st.hasMoreTokens())\r
+ {\r
+ try\r
+ {\r
+ score = new Float(st.nextToken()).floatValue();\r
+ // update colourgradient bounds if allowed to \r
+ } catch (NumberFormatException ex)\r
+ {\r
+ score = 0;\r
+ }\r
+ sf.setScore(score);\r
+ }\r
if (groupLink != null && removeHTML)\r
{\r
sf.addLink(groupLink);\r
* generate a features file for seqs\r
* \r
* @param seqs\r
- * source of sequence features\r
+ * source of sequence features\r
* @param visible\r
- * hash of feature types and colours\r
+ * hash of feature types and colours\r
* @return features file contents\r
*/\r
public String printJalviewFormat(SequenceI[] seqs, Hashtable visible)\r
* generate a features file for seqs with colours from visible (if any)\r
* \r
* @param seqs\r
- * source of features\r
+ * source of features\r
* @param visible\r
- * hash of Colours for each feature type\r
+ * hash of Colours for each feature type\r
* @param visOnly\r
- * when true only feature types in 'visible' will be output\r
+ * when true only feature types in 'visible' will be output\r
* @return features file contents\r
*/\r
public String printJalviewFormat(SequenceI[] seqs, Hashtable visible,\r
{\r
// write feature colours only if we're given them and we are generating\r
// viewed features\r
+ // TODO: decide if feature links should also be written here ?\r
Enumeration en = visible.keys();\r
- String type;\r
- int color;\r
+ String type, color;\r
while (en.hasMoreElements())\r
{\r
type = en.nextElement().toString();\r
- color = Integer.parseInt(visible.get(type).toString());\r
- out.append(type\r
- + "\t"\r
- + jalview.util.Format\r
- .getHexString(new java.awt.Color(color)) + "\n");\r
+\r
+ if (visible.get(type) instanceof GraduatedColor)\r
+ {\r
+ GraduatedColor gc = (GraduatedColor) visible.get(type);\r
+ color = Format.getHexString(gc.getMinColor()) + "|"\r
+ + Format.getHexString(gc.getMaxColor()) +\r
+ (gc.isAutoScale() ? "|" : "|abso|")+ gc.getMin() + "|" + gc.getMax() + "|";\r
+ if (gc.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)\r
+ {\r
+ if (gc.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD)\r
+ {\r
+ color += "below";\r
+ }\r
+ else\r
+ {\r
+ if (gc.getThreshType() != AnnotationColourGradient.ABOVE_THRESHOLD)\r
+ {\r
+ System.err.println("WARNING: Unsupported threshold type ("\r
+ + gc.getThreshType() + ") : Assuming 'above'");\r
+ }\r
+ color += "above";\r
+ }\r
+ // add the value\r
+ color += "|" + gc.getThresh();\r
+ }\r
+ else\r
+ {\r
+ color += "none";\r
+ }\r
+ }\r
+ else\r
+ if (visible.get(type) instanceof java.awt.Color) {\r
+ color = Format.getHexString((java.awt.Color)visible.get(type));\r
+ } else {\r
+ // legacy support for integer objects containing colour triplet values\r
+ color = Format.getHexString(new java.awt.Color(Integer\r
+ .parseInt(visible.get(type).toString())));\r
+ }\r
+ out.append(type + "\t" + color + "\n");\r
}\r
}\r
// Work out which groups are both present and visible\r
}\r
\r
out.append(seqs[i].getName() + "\t-1\t" + next[j].begin + "\t"\r
- + next[j].end + "\t" + next[j].type + "\n");\r
+ + next[j].end + "\t" + next[j].type + ((visible.get(next[j].type) instanceof GraduatedColor) ? "\t"+next[j].score+"\n" : "\n"));\r
}\r
}\r
}\r
next = seqs[i].getSequenceFeatures();\r
for (int j = 0; j < next.length; j++)\r
{\r
- if (visOnly && visible!=null && !visible.containsKey(next[j].type))\r
+ if (visOnly && visible != null\r
+ && !visible.containsKey(next[j].type))\r
{\r
continue;\r
}\r
git://source.jalview.org / jalview.git / blobdiff