/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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 program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
+ * This file is part of Jalview.\r
* \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
* \r
- * You should have received a copy of the GNU General Public License\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
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
package jalview.io;\r
\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\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
+ StringTokenizer gcol = new StringTokenizer(colscheme, "|", 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
- min = new Float(minval).floatValue();\r
- }\r
- } catch (Exception e)\r
+ float min = Float.MIN_VALUE, max = Float.MAX_VALUE, threshval = Float.NaN;\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 + ") - 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: "+line );\r
+ continue;\r
}\r
- try\r
+ String maxcol = null;\r
+ if (mincol.toLowerCase().indexOf("label") == 0)\r
{\r
- if (maxval.length()>0) { \r
- max = new Float(maxval).floatValue();\r
+ labelCol = true;\r
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); // skip '|'\r
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);\r
+ }\r
+ String abso = null, minval, maxval;\r
+ if (mincol != null)\r
+ {\r
+ // at least four more tokens\r
+ if (mincol.equals("|"))\r
+ {\r
+ mincol="";\r
+ } else {\r
+ gcol.nextToken(); // skip next '|'\r
}\r
- } catch (Exception e)\r
+ // continue parsing rest of line\r
+ maxcol = gcol.nextToken();\r
+ if (maxcol.equals("|"))\r
+ {\r
+ maxcol="";\r
+ } else {\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
+ 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
colour = new jalview.schemes.GraduatedColor(\r
new UserColourScheme(mincol).findColour('A'),\r
- new UserColourScheme(maxcol).findColour('A'),\r
- min, max);\r
+ new UserColourScheme(maxcol).findColour('A'), min,\r
+ max);\r
} catch (Exception e)\r
{\r
System.err\r
}\r
if (colour != null)\r
{\r
- ((jalview.schemes.GraduatedColor)colour).setAutoScaled(abso==null);\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
if (gcol.hasMoreTokens())\r
}\r
}\r
}\r
- if (((GraduatedColor)colour).getThreshType()!=AnnotationColourGradient.NO_THRESHOLD)\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
try\r
{\r
score = new Float(st.nextToken()).floatValue();\r
- // update colourgradient bounds if allowed to \r
+ // update colourgradient bounds if allowed to\r
} catch (NumberFormatException ex)\r
{\r
score = 0;\r
}\r
\r
/**\r
- * generate a features file for seqs\r
+ * generate a features file for seqs includes non-pos features by default.\r
* \r
* @param seqs\r
* source of sequence features\r
*/\r
public String printJalviewFormat(SequenceI[] seqs, Hashtable visible)\r
{\r
- return printJalviewFormat(seqs, visible, true);\r
+ return printJalviewFormat(seqs, visible, true, true);\r
}\r
\r
/**\r
* hash of Colours for each feature type\r
* @param visOnly\r
* when true only feature types in 'visible' will be output\r
+ * @param nonpos\r
+ * indicates if non-positional features should be output (regardless\r
+ * of group or type)\r
* @return features file contents\r
*/\r
public String printJalviewFormat(SequenceI[] seqs, Hashtable visible,\r
- boolean visOnly)\r
+ boolean visOnly, boolean nonpos)\r
{\r
StringBuffer out = new StringBuffer();\r
SequenceFeature[] next;\r
-\r
- if (visOnly && (visible == null || visible.size() < 1))\r
+ boolean featuresGen = false;\r
+ if (visOnly && !nonpos && (visible == null || visible.size() < 1))\r
{\r
+ // no point continuing.\r
return "No Features Visible";\r
}\r
+\r
if (visible != null && visOnly)\r
{\r
// write feature colours only if we're given them and we are generating\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
+ color = (gc.isColourByLabel() ? "label|" : "")\r
+ + Format.getHexString(gc.getMinColor()) + "|"\r
+ + Format.getHexString(gc.getMaxColor())\r
+ + (gc.isAutoScale() ? "|" : "|abso|") + gc.getMin() + "|"\r
+ + gc.getMax() + "|";\r
if (gc.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)\r
{\r
if (gc.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD)\r
color += "none";\r
}\r
}\r
+ else if (visible.get(type) instanceof java.awt.Color)\r
+ {\r
+ color = Format.getHexString((java.awt.Color) visible.get(type));\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
+ {\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
// Work out which groups are both present and visible\r
Vector groups = new Vector();\r
int groupIndex = 0;\r
+ boolean isnonpos = false;\r
\r
for (int i = 0; i < seqs.length; i++)\r
{\r
{\r
for (int j = 0; j < next.length; j++)\r
{\r
- if (visOnly && !visible.containsKey(next[j].type))\r
+ isnonpos = next[j].begin == 0 && next[j].end == 0;\r
+ if ((!nonpos && isnonpos)\r
+ || (!isnonpos && visOnly && !visible\r
+ .containsKey(next[j].type)))\r
{\r
continue;\r
}\r
}\r
\r
String group = null;\r
-\r
do\r
{\r
\r
{\r
for (int j = 0; j < next.length; j++)\r
{\r
- if (visOnly && !visible.containsKey(next[j].type))\r
+ isnonpos = next[j].begin == 0 && next[j].end == 0;\r
+ if ((!nonpos && isnonpos)\r
+ || (!isnonpos && visOnly && !visible\r
+ .containsKey(next[j].type)))\r
{\r
+ // skip if feature is nonpos and we ignore them or if we only\r
+ // output visible and it isn't non-pos and it's not visible\r
continue;\r
}\r
\r
{\r
continue;\r
}\r
-\r
+ // we have features to output\r
+ featuresGen = true;\r
if (next[j].description == null\r
|| next[j].description.equals(""))\r
{\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
\r
out.append("\t");\r
}\r
-\r
- out.append(seqs[i].getName() + "\t-1\t" + next[j].begin + "\t"\r
- + next[j].end + "\t" + next[j].type + ((visible.get(next[j].type) instanceof GraduatedColor) ? "\t"+next[j].score+"\n" : "\n"));\r
+ out.append(seqs[i].getName()\r
+ + "\t-1\t"\r
+ + next[j].begin\r
+ + "\t"\r
+ + next[j].end\r
+ + "\t"\r
+ + next[j].type\r
+ + ((next[j].score != Float.NaN) ? "\t" + next[j].score\r
+ + "\n" : "\n"));\r
}\r
}\r
}\r
\r
} while (groupIndex < groups.size() + 1);\r
\r
+ if (!featuresGen)\r
+ {\r
+ return "No Features Visible";\r
+ }\r
+\r
return out.toString();\r
}\r
\r
+ /**\r
+ * generate a gff file for sequence features includes non-pos features by\r
+ * default.\r
+ * \r
+ * @param seqs\r
+ * @param visible\r
+ * @return\r
+ */\r
public String printGFFFormat(SequenceI[] seqs, Hashtable visible)\r
{\r
- return printGFFFormat(seqs, visible, true);\r
+ return printGFFFormat(seqs, visible, true, true);\r
}\r
\r
public String printGFFFormat(SequenceI[] seqs, Hashtable visible,\r
- boolean visOnly)\r
+ boolean visOnly, boolean nonpos)\r
{\r
StringBuffer out = new StringBuffer();\r
SequenceFeature[] next;\r
String source;\r
-\r
+ boolean isnonpos;\r
for (int i = 0; i < seqs.length; i++)\r
{\r
if (seqs[i].getSequenceFeatures() != null)\r
next = seqs[i].getSequenceFeatures();\r
for (int j = 0; j < next.length; j++)\r
{\r
- if (visOnly && visible != null\r
- && !visible.containsKey(next[j].type))\r
+ isnonpos = next[j].begin == 0 && next[j].end == 0;\r
+ if ((!nonpos && isnonpos)\r
+ || (!isnonpos && visOnly && !visible\r
+ .containsKey(next[j].type)))\r
{\r
continue;\r
}\r
git://source.jalview.org / jalview.git / blobdiff