/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
* \r
* This file is part of Jalview.\r
SequenceFeature sf;\r
String featureGroup = null, groupLink = null;\r
Hashtable typeLink = new Hashtable();\r
-\r
+ /**\r
+ * when true, assume GFF style features rather than Jalview style.\r
+ */\r
boolean GFFFile = true;\r
-\r
while ((line = nextLine()) != null)\r
{\r
if (line.startsWith("#"))\r
}\r
\r
st = new StringTokenizer(line, "\t");\r
+ if (st.countTokens() == 1)\r
+ {\r
+ if (line.trim().equalsIgnoreCase("GFF"))\r
+ {\r
+ // Start parsing file as if it might be GFF again.\r
+ GFFFile = true;\r
+ continue;\r
+ }\r
+ }\r
if (st.countTokens() > 1 && st.countTokens() < 4)\r
{\r
GFFFile = false;\r
{\r
Object colour = null;\r
String colscheme = st.nextToken();\r
- if (colscheme.indexOf("|") > -1)\r
+ if (colscheme.indexOf("|") > -1\r
+ || colscheme.trim().equalsIgnoreCase("label"))\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
+ // [label|][mincolour|maxcolour|[absolute|]minvalue|maxvalue|thresholdtype|thresholdvalue]\r
+ // can either provide 'label' only, first is optional, next two\r
+ // colors are required (but may be\r
+ // left blank), next is optional, nxt two min/max are required.\r
+ // first is either 'label'\r
+ // first/second and third are both hexadecimal or word equivalent\r
+ // colour.\r
+ // next 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.nextToken(), minval, maxval;\r
- if (abso.toLowerCase().indexOf("abso") != 0)\r
- {\r
- minval = abso;\r
- abso = null;\r
- }\r
- else\r
- {\r
- minval = gcol.nextToken();\r
- }\r
- maxval = gcol.nextToken();\r
+ StringTokenizer gcol = new StringTokenizer(colscheme, "|",\r
+ true);\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
- {\r
- min = new Float(minval).floatValue();\r
- }\r
- } catch (Exception e)\r
+ boolean labelCol = false;\r
+ // Parse spec line\r
+ String mincol = gcol.nextToken();\r
+ if (mincol == "|")\r
{\r
System.err\r
- .println("Couldn't parse the minimum value for graduated colour for type ("\r
- + colscheme\r
- + ") - did you misspell 'auto' for the optional automatic colour switch ?");\r
- e.printStackTrace();\r
+ .println("Expected either 'label' or a colour specification in the line: "\r
+ + line);\r
+ continue;\r
}\r
- try\r
+ String maxcol = null;\r
+ if (mincol.toLowerCase().indexOf("label") == 0)\r
+ {\r
+ labelCol = true;\r
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); // skip\r
+ // '|'\r
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);\r
+ }\r
+ String abso = null, minval, maxval;\r
+ if (mincol != null)\r
{\r
- if (maxval.length() > 0)\r
+ // at least four more tokens\r
+ if (mincol.equals("|"))\r
{\r
- max = new Float(maxval).floatValue();\r
+ mincol = "";\r
}\r
- } catch (Exception e)\r
+ else\r
+ {\r
+ gcol.nextToken(); // skip next '|'\r
+ }\r
+ // continue parsing rest of line\r
+ maxcol = gcol.nextToken();\r
+ if (maxcol.equals("|"))\r
+ {\r
+ maxcol = "";\r
+ }\r
+ else\r
+ {\r
+ gcol.nextToken(); // skip next '|'\r
+ }\r
+ abso = gcol.nextToken();\r
+ gcol.nextToken(); // skip next '|'\r
+ if (abso.toLowerCase().indexOf("abso") != 0)\r
+ {\r
+ minval = abso;\r
+ abso = null;\r
+ }\r
+ else\r
+ {\r
+ minval = gcol.nextToken();\r
+ gcol.nextToken(); // skip next '|'\r
+ }\r
+ maxval = gcol.nextToken();\r
+ if (gcol.hasMoreTokens())\r
+ {\r
+ gcol.nextToken(); // skip next '|'\r
+ }\r
+ try\r
+ {\r
+ if (minval.length() > 0)\r
+ {\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\r
+ + ") - did you misspell 'auto' for the optional automatic colour switch ?");\r
+ e.printStackTrace();\r
+ }\r
+ try\r
+ {\r
+ if (maxval.length() > 0)\r
+ {\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
+ }\r
+ else\r
{\r
- System.err\r
- .println("Couldn't parse the maximum value for graduated colour for type ("\r
- + colscheme + ")");\r
- e.printStackTrace();\r
+ // add in some dummy min/max colours for the label-only\r
+ // colourscheme.\r
+ mincol = "FFFFFF";\r
+ maxcol = "000000";\r
}\r
try\r
{\r
if (colour != null)\r
{\r
((jalview.schemes.GraduatedColor) colour)\r
+ .setColourByLabel(labelCol);\r
+ ((jalview.schemes.GraduatedColor) colour)\r
.setAutoScaled(abso == null);\r
// add in any additional parameters\r
String ttype = null, tval = null;\r
}\r
if (((GraduatedColor) colour).getThreshType() != AnnotationColourGradient.NO_THRESHOLD)\r
{\r
- tval = gcol.nextToken();\r
try\r
{\r
+ gcol.nextToken();\r
+ tval = gcol.nextToken();\r
((jalview.schemes.GraduatedColor) colour)\r
.setThresh(new Float(tval).floatValue());\r
} catch (Exception e)\r
.println("Ignoring additional tokens in parameters in graduated colour specification\n");\r
while (gcol.hasMoreTokens())\r
{\r
- System.err.println("|" + gcol);\r
+ System.err.println("|" + gcol.nextToken());\r
}\r
System.err.println("\n");\r
}\r
if (visible.get(type) instanceof GraduatedColor)\r
{\r
GraduatedColor gc = (GraduatedColor) visible.get(type);\r
- // TODO: NOW: colour by label, autoscale flags.\r
- color = Format.getHexString(gc.getMinColor()) + "|"\r
+ color = (gc.isColourByLabel() ? "label|" : "")\r
+ + Format.getHexString(gc.getMinColor()) + "|"\r
+ Format.getHexString(gc.getMaxColor())\r
+ (gc.isAutoScale() ? "|" : "|abso|") + gc.getMin() + "|"\r
+ gc.getMax() + "|";\r
\r
if (next[j].description.indexOf(href) == -1)\r
{\r
- out\r
- .append("<a href=\"" + href + "\">" + label\r
- + "</a>");\r
+ out.append("<a href=\"" + href + "\">" + label + "</a>");\r
}\r
}\r
\r
git://source.jalview.org / jalview.git / blobdiff