-/*\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
- * \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
- * 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
-import java.io.*;\r
-import java.util.*;\r
-\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
- * parses. Does not implement standard print() - call specific printFeatures or\r
- * printGFF. Uses AlignmentI.findSequence(String id) to find the sequence object\r
- * for the features annotation - this normally works on an exact match.\r
- * \r
- * @author AMW\r
- * @version $Revision$\r
- */\r
-public class FeaturesFile extends AlignFile\r
-{\r
- /**\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
- /**\r
- * Creates a new FeaturesFile object.\r
- */\r
- public FeaturesFile()\r
- {\r
- }\r
-\r
- /**\r
- * Creates a new FeaturesFile object.\r
- * \r
- * @param inFile\r
- * DOCUMENT ME!\r
- * @param type\r
- * DOCUMENT ME!\r
- * \r
- * @throws IOException\r
- * DOCUMENT ME!\r
- */\r
- public FeaturesFile(String inFile, String type) throws IOException\r
- {\r
- super(inFile, type);\r
- }\r
-\r
- public FeaturesFile(FileParse source) throws IOException\r
- {\r
- super(source);\r
- }\r
-\r
- /**\r
- * The Application can render HTML, but the applet will remove HTML tags and\r
- * replace links with %LINK% Both need to read links in HTML however\r
- * \r
- * @throws IOException\r
- * DOCUMENT ME!\r
- */\r
- public boolean parse(AlignmentI align, Hashtable colours,\r
- boolean removeHTML)\r
- {\r
- return parse(align, colours, null, removeHTML);\r
- }\r
-\r
- /**\r
- * The Application can render HTML, but the applet will remove HTML tags and\r
- * replace links with %LINK% Both need to read links in HTML however\r
- * \r
- * @throws IOException\r
- * DOCUMENT ME!\r
- */\r
- public boolean parse(AlignmentI align, Hashtable colours,\r
- Hashtable featureLink, boolean removeHTML)\r
- {\r
- String line = null;\r
- try\r
- {\r
- SequenceI seq = null;\r
- String type, desc, token = null;\r
-\r
- int index, start, end;\r
- float score;\r
- StringTokenizer st;\r
- SequenceFeature sf;\r
- String featureGroup = null, groupLink = null;\r
- Hashtable typeLink = new Hashtable();\r
- /**\r
- * when true, assume GFF style features rather than Jalview style.\r
- */\r
- boolean GFFFile = true;\r
- while ((line = nextLine()) != null)\r
- {\r
- if (line.startsWith("#"))\r
- {\r
- continue;\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
- type = st.nextToken();\r
- if (type.equalsIgnoreCase("startgroup"))\r
- {\r
- featureGroup = st.nextToken();\r
- if (st.hasMoreElements())\r
- {\r
- groupLink = st.nextToken();\r
- featureLink.put(featureGroup, groupLink);\r
- }\r
- }\r
- else if (type.equalsIgnoreCase("endgroup"))\r
- {\r
- // We should check whether this is the current group,\r
- // but at present theres no way of showing more than 1 group\r
- st.nextToken();\r
- featureGroup = null;\r
- groupLink = null;\r
- }\r
- else\r
- {\r
- Object colour = null;\r
- String colscheme = st.nextToken();\r
- if (colscheme.indexOf("|") > -1\r
- || colscheme.trim().equalsIgnoreCase("label"))\r
- {\r
- // Parse '|' separated graduated colourscheme fields:\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
- true);\r
- // set defaults\r
- int threshtype = AnnotationColourGradient.NO_THRESHOLD;\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("Expected either 'label' or a colour specification in the line: "\r
- + line);\r
- continue;\r
- }\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
- // at least four more tokens\r
- if (mincol.equals("|"))\r
- {\r
- mincol = "";\r
- }\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
- // 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'), min,\r
- 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)\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
- // 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
- 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
- {\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.nextToken());\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
- typeLink.put(type, link);\r
- if (featureLink == null)\r
- {\r
- featureLink = new Hashtable();\r
- }\r
- featureLink.put(type, link);\r
- }\r
- }\r
- continue;\r
- }\r
- String seqId = "";\r
- while (st.hasMoreElements())\r
- {\r
-\r
- if (GFFFile)\r
- {\r
- // Still possible this is an old Jalview file,\r
- // which does not have type colours at the beginning\r
- seqId = token = st.nextToken();\r
- seq = align.findName(seqId, true);\r
- if (seq != null)\r
- {\r
- desc = st.nextToken();\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
- type = st.nextToken();\r
- try\r
- {\r
- String stt = st.nextToken();\r
- if (stt.length() == 0 || stt.equals("-"))\r
- {\r
- start = 0;\r
- }\r
- else\r
- {\r
- start = Integer.parseInt(stt);\r
- }\r
- } catch (NumberFormatException ex)\r
- {\r
- start = 0;\r
- }\r
- try\r
- {\r
- String stt = st.nextToken();\r
- if (stt.length() == 0 || stt.equals("-"))\r
- {\r
- end = 0;\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\r
- // where end==0 is generally valid\r
- if (end == 0)\r
- {\r
- // treat as non-positional feature, regardless.\r
- start = 0;\r
- }\r
- try\r
- {\r
- score = new Float(st.nextToken()).floatValue();\r
- } catch (NumberFormatException ex)\r
- {\r
- score = 0;\r
- }\r
-\r
- sf = new SequenceFeature(type, desc, start, end, score, group);\r
-\r
- try\r
- {\r
- sf.setValue("STRAND", st.nextToken());\r
- sf.setValue("FRAME", st.nextToken());\r
- } catch (Exception ex)\r
- {\r
- }\r
-\r
- if (st.hasMoreTokens())\r
- {\r
- StringBuffer attributes = new StringBuffer();\r
- while (st.hasMoreTokens())\r
- {\r
- attributes.append("\t" + st.nextElement());\r
- }\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
- seq.addSequenceFeature(sf);\r
- while ((seq = align.findName(seq, seqId, true)) != null)\r
- {\r
- seq.addSequenceFeature(new SequenceFeature(sf));\r
- }\r
- break;\r
- }\r
- }\r
-\r
- if (GFFFile && seq == null)\r
- {\r
- desc = token;\r
- }\r
- else\r
- {\r
- desc = st.nextToken();\r
- }\r
- if (!st.hasMoreTokens())\r
- {\r
- System.err\r
- .println("DEBUG: Run out of tokens when trying to identify the destination for the feature.. giving up.");\r
- // in all probability, this isn't a file we understand, so bail\r
- // quietly.\r
- return false;\r
- }\r
-\r
- token = st.nextToken();\r
-\r
- if (!token.equals("ID_NOT_SPECIFIED"))\r
- {\r
- seq = align.findName(seqId = token, true);\r
- st.nextToken();\r
- }\r
- else\r
- {\r
- seqId = null;\r
- try\r
- {\r
- index = Integer.parseInt(st.nextToken());\r
- seq = align.getSequenceAt(index);\r
- } catch (NumberFormatException ex)\r
- {\r
- seq = null;\r
- }\r
- }\r
-\r
- if (seq == null)\r
- {\r
- System.out.println("Sequence not found: " + line);\r
- break;\r
- }\r
-\r
- start = Integer.parseInt(st.nextToken());\r
- end = Integer.parseInt(st.nextToken());\r
-\r
- type = st.nextToken();\r
-\r
- if (!colours.containsKey(type))\r
- {\r
- // Probably the old style groups file\r
- UserColourScheme ucs = new UserColourScheme(type);\r
- colours.put(type, ucs.findColour('A'));\r
- }\r
- sf = new SequenceFeature(type, desc, "", start, end, featureGroup);\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
- sf.description += "%LINK%";\r
- }\r
- if (typeLink.containsKey(type) && removeHTML)\r
- {\r
- sf.addLink(typeLink.get(type).toString());\r
- sf.description += "%LINK%";\r
- }\r
-\r
- parseDescriptionHTML(sf, removeHTML);\r
-\r
- seq.addSequenceFeature(sf);\r
-\r
- while (seqId != null\r
- && (seq = align.findName(seq, seqId, false)) != null)\r
- {\r
- seq.addSequenceFeature(new SequenceFeature(sf));\r
- }\r
- // If we got here, its not a GFFFile\r
- GFFFile = false;\r
- }\r
- }\r
- } catch (Exception ex)\r
- {\r
- System.out.println(line);\r
- System.out.println("Error parsing feature file: " + ex + "\n" + line);\r
- ex.printStackTrace(System.err);\r
- return false;\r
- }\r
-\r
- return true;\r
- }\r
-\r
- public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)\r
- {\r
- if (sf.getDescription() == null)\r
- {\r
- return;\r
- }\r
-\r
- if (removeHTML\r
- && sf.getDescription().toUpperCase().indexOf("<HTML>") == -1)\r
- {\r
- removeHTML = false;\r
- }\r
-\r
- StringBuffer sb = new StringBuffer();\r
- StringTokenizer st = new StringTokenizer(sf.getDescription(), "<");\r
- String token, link;\r
- int startTag;\r
- String tag = null;\r
- while (st.hasMoreElements())\r
- {\r
- token = st.nextToken("&>");\r
- if (token.equalsIgnoreCase("html") || token.startsWith("/"))\r
- {\r
- continue;\r
- }\r
-\r
- tag = null;\r
- startTag = token.indexOf("<");\r
-\r
- if (startTag > -1)\r
- {\r
- tag = token.substring(startTag + 1);\r
- token = token.substring(0, startTag);\r
- }\r
-\r
- if (tag != null && tag.toUpperCase().startsWith("A HREF="))\r
- {\r
- if (token.length() > 0)\r
- {\r
- sb.append(token);\r
- }\r
- link = tag.substring(tag.indexOf("\"") + 1, tag.length() - 1);\r
- String label = st.nextToken("<>");\r
- sf.addLink(label + "|" + link);\r
- sb.append(label + "%LINK%");\r
- }\r
- else if (tag != null && tag.equalsIgnoreCase("br"))\r
- {\r
- sb.append(newline);\r
- }\r
- else if (token.startsWith("lt;"))\r
- {\r
- sb.append("<" + token.substring(3));\r
- }\r
- else if (token.startsWith("gt;"))\r
- {\r
- sb.append(">" + token.substring(3));\r
- }\r
- else if (token.startsWith("amp;"))\r
- {\r
- sb.append("&" + token.substring(4));\r
- }\r
- else\r
- {\r
- sb.append(token);\r
- }\r
- }\r
-\r
- if (removeHTML)\r
- {\r
- sf.description = sb.toString();\r
- }\r
-\r
- }\r
-\r
- /**\r
- * generate a features file for seqs includes non-pos features by default.\r
- * \r
- * @param seqs\r
- * source of sequence features\r
- * @param visible\r
- * hash of feature types and colours\r
- * @return features file contents\r
- */\r
- public String printJalviewFormat(SequenceI[] seqs, Hashtable visible)\r
- {\r
- return printJalviewFormat(seqs, visible, true, true);\r
- }\r
-\r
- /**\r
- * generate a features file for seqs with colours from visible (if any)\r
- * \r
- * @param seqs\r
- * source of features\r
- * @param visible\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, boolean nonpos)\r
- {\r
- StringBuffer out = new StringBuffer();\r
- SequenceFeature[] next;\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
- // viewed features\r
- // TODO: decide if feature links should also be written here ?\r
- Enumeration en = visible.keys();\r
- String type, color;\r
- while (en.hasMoreElements())\r
- {\r
- type = en.nextElement().toString();\r
-\r
- if (visible.get(type) instanceof GraduatedColor)\r
- {\r
- GraduatedColor gc = (GraduatedColor) visible.get(type);\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
- {\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 if (visible.get(type) instanceof java.awt.Color)\r
- {\r
- color = Format.getHexString((java.awt.Color) visible.get(type));\r
- }\r
- else\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
- out.append(type);\r
- out.append("\t");\r
- out.append(color);\r
- out.append(newline);\r
- }\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
- next = seqs[i].getSequenceFeatures();\r
- if (next != null)\r
- {\r
- for (int j = 0; j < next.length; j++)\r
- {\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
- if (next[j].featureGroup != null\r
- && !groups.contains(next[j].featureGroup))\r
- {\r
- groups.addElement(next[j].featureGroup);\r
- }\r
- }\r
- }\r
- }\r
-\r
- String group = null;\r
- do\r
- {\r
-\r
- if (groups.size() > 0 && groupIndex < groups.size())\r
- {\r
- group = groups.elementAt(groupIndex).toString();\r
- out.append(newline);\r
- out.append("STARTGROUP\t");\r
- out.append(group);\r
- out.append(newline);\r
- }\r
- else\r
- {\r
- group = null;\r
- }\r
-\r
- for (int i = 0; i < seqs.length; i++)\r
- {\r
- next = seqs[i].getSequenceFeatures();\r
- if (next != null)\r
- {\r
- for (int j = 0; j < next.length; j++)\r
- {\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
- if (group != null\r
- && (next[j].featureGroup == null || !next[j].featureGroup\r
- .equals(group)))\r
- {\r
- continue;\r
- }\r
-\r
- if (group == null && next[j].featureGroup != null)\r
- {\r
- continue;\r
- }\r
- // we have features to output\r
- featuresGen = true;\r
- if (next[j].description == null\r
- || next[j].description.equals(""))\r
- {\r
- out.append(next[j].type + "\t");\r
- }\r
- else\r
- {\r
- if (next[j].links != null\r
- && next[j].getDescription().indexOf("<html>") == -1)\r
- {\r
- out.append("<html>");\r
- }\r
-\r
- out.append(next[j].description + " ");\r
- if (next[j].links != null)\r
- {\r
- for (int l = 0; l < next[j].links.size(); l++)\r
- {\r
- String label = next[j].links.elementAt(l).toString();\r
- String href = label.substring(label.indexOf("|") + 1);\r
- label = label.substring(0, label.indexOf("|"));\r
-\r
- if (next[j].description.indexOf(href) == -1)\r
- {\r
- out.append("<a href=\"" + href + "\">" + label + "</a>");\r
- }\r
- }\r
-\r
- if (next[j].getDescription().indexOf("</html>") == -1)\r
- {\r
- out.append("</html>");\r
- }\r
- }\r
-\r
- out.append("\t");\r
- }\r
- out.append(seqs[i].getName());\r
- out.append("\t-1\t");\r
- out.append(next[j].begin);\r
- out.append("\t");\r
- out.append(next[j].end);\r
- out.append("\t");\r
- out.append(next[j].type);\r
- if (next[j].score != Float.NaN)\r
- {\r
- out.append("\t");\r
- out.append(next[j].score);\r
- }\r
- out.append(newline);\r
- }\r
- }\r
- }\r
-\r
- if (group != null)\r
- {\r
- out.append("ENDGROUP\t");\r
- out.append(group);\r
- out.append(newline);\r
- groupIndex++;\r
- }\r
- else\r
- {\r
- break;\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, true);\r
- }\r
-\r
- public String printGFFFormat(SequenceI[] seqs, Hashtable visible,\r
- boolean visOnly, boolean nonpos)\r
- {\r
- StringBuffer out = new StringBuffer();\r
- SequenceFeature[] next;\r
- String source;\r
- boolean isnonpos;\r
- for (int i = 0; i < seqs.length; i++)\r
- {\r
- if (seqs[i].getSequenceFeatures() != null)\r
- {\r
- next = seqs[i].getSequenceFeatures();\r
- for (int j = 0; j < next.length; j++)\r
- {\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
- source = next[j].featureGroup;\r
- if (source == null)\r
- {\r
- source = next[j].getDescription();\r
- }\r
-\r
- out.append(seqs[i].getName());\r
- out.append("\t");\r
- out.append(source);\r
- out.append("\t");\r
- out.append(next[j].type);\r
- out.append( "\t");\r
- out.append( next[j].begin );\r
- out.append("\t");\r
- out.append(\r
- next[j].end);\r
- out.append( "\t");\r
- out.append( next[j].score);\r
- out.append( "\t");\r
-\r
- if (next[j].getValue("STRAND") != null)\r
- {\r
- out.append(next[j].getValue("STRAND"));\r
- out.append( "\t");\r
- }\r
- else\r
- {\r
- out.append(".\t");\r
- }\r
-\r
- if (next[j].getValue("FRAME") != null)\r
- {\r
- out.append(next[j].getValue("FRAME"));\r
- }\r
- else\r
- {\r
- out.append(".");\r
- }\r
- // TODO: verify/check GFF - should there be a /t here before attribute output ?\r
-\r
- if (next[j].getValue("ATTRIBUTES") != null)\r
- {\r
- out.append(next[j].getValue("ATTRIBUTES"));\r
- }\r
-\r
- out.append(newline);\r
-\r
- }\r
- }\r
- }\r
-\r
- return out.toString();\r
- }\r
-\r
- /**\r
- * this is only for the benefit of object polymorphism - method does nothing.\r
- */\r
- public void parse()\r
- {\r
- // IGNORED\r
- }\r
-\r
- /**\r
- * this is only for the benefit of object polymorphism - method does nothing.\r
- * \r
- * @return error message\r
- */\r
- public String print()\r
- {\r
- return "USE printGFFFormat() or printJalviewFormat()";\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import java.util.Locale;
+
+import java.awt.Color;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.TreeMap;
+
+import jalview.analysis.AlignmentUtils;
+import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignViewportI;
+import jalview.api.FeatureColourI;
+import jalview.api.FeatureRenderer;
+import jalview.api.FeaturesSourceI;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.MappedFeatures;
+import jalview.datamodel.SequenceDummy;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcherSet;
+import jalview.datamodel.features.FeatureMatcherSetI;
+import jalview.gui.Desktop;
+import jalview.io.gff.GffHelperFactory;
+import jalview.io.gff.GffHelperI;
+import jalview.schemes.FeatureColour;
+import jalview.util.ColorUtils;
+import jalview.util.MapList;
+import jalview.util.ParseHtmlBodyAndLinks;
+import jalview.util.StringUtils;
+
+/**
+ * Parses and writes features files, which may be in Jalview, GFF2 or GFF3
+ * format. These are tab-delimited formats but with differences in the use of
+ * columns.
+ *
+ * A Jalview feature file may define feature colours and then declare that the
+ * remainder of the file is in GFF format with the line 'GFF'.
+ *
+ * GFF3 files may include alignment mappings for features, which Jalview will
+ * attempt to model, and may include sequence data following a ##FASTA line.
+ *
+ *
+ * @author AMW
+ * @author jbprocter
+ * @author gmcarstairs
+ */
+public class FeaturesFile extends AlignFile implements FeaturesSourceI
+{
+ private static final String EQUALS = "=";
+
+ private static final String TAB_REGEX = "\\t";
+
+ private static final String STARTGROUP = "STARTGROUP";
+
+ private static final String ENDGROUP = "ENDGROUP";
+
+ private static final String STARTFILTERS = "STARTFILTERS";
+
+ private static final String ENDFILTERS = "ENDFILTERS";
+
+ private static final String ID_NOT_SPECIFIED = "ID_NOT_SPECIFIED";
+
+ protected static final String GFF_VERSION = "##gff-version";
+
+ private AlignmentI lastmatchedAl = null;
+
+ private SequenceIdMatcher matcher = null;
+
+ protected AlignmentI dataset;
+
+ protected int gffVersion;
+
+ /**
+ * Creates a new FeaturesFile object.
+ */
+ public FeaturesFile()
+ {
+ }
+
+ /**
+ * Constructor which does not parse the file immediately
+ *
+ * @param file File or String filename
+ * @param paste
+ * @throws IOException
+ */
+ public FeaturesFile(Object file, DataSourceType paste)
+ throws IOException
+ {
+ super(false, file, paste);
+ }
+
+ /**
+ * @param source
+ * @throws IOException
+ */
+ public FeaturesFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ /**
+ * Constructor that optionally parses the file immediately
+ *
+ * @param parseImmediately
+ * @param file
+ * @param type
+ * @throws IOException
+ */
+ public FeaturesFile(boolean parseImmediately, Object file,
+ DataSourceType type) throws IOException
+ {
+ super(parseImmediately, file, type);
+ }
+
+ /**
+ * Parse GFF or sequence features file using case-independent matching,
+ * discarding URLs
+ *
+ * @param align
+ * - alignment/dataset containing sequences that are to be annotated
+ * @param colours
+ * - hashtable to store feature colour definitions
+ * @param removeHTML
+ * - process html strings into plain text
+ * @return true if features were added
+ */
+ public boolean parse(AlignmentI align,
+ Map<String, FeatureColourI> colours, boolean removeHTML)
+ {
+ return parse(align, colours, removeHTML, false);
+ }
+
+ /**
+ * Extends the default addProperties by also adding peptide-to-cDNA mappings
+ * (if any) derived while parsing a GFF file
+ */
+ @Override
+ public void addProperties(AlignmentI al)
+ {
+ super.addProperties(al);
+ if (dataset != null && dataset.getCodonFrames() != null)
+ {
+ AlignmentI ds = (al.getDataset() == null) ? al : al.getDataset();
+ for (AlignedCodonFrame codons : dataset.getCodonFrames())
+ {
+ ds.addCodonFrame(codons);
+ }
+ }
+ }
+
+ /**
+ * Parse GFF or Jalview format sequence features file
+ *
+ * @param align
+ * - alignment/dataset containing sequences that are to be annotated
+ * @param colours
+ * - map to store feature colour definitions
+ * @param removeHTML
+ * - process html strings into plain text
+ * @param relaxedIdmatching
+ * - when true, ID matches to compound sequence IDs are allowed
+ * @return true if features were added
+ */
+ public boolean parse(AlignmentI align,
+ Map<String, FeatureColourI> colours, boolean removeHTML,
+ boolean relaxedIdmatching)
+ {
+ return parse(align, colours, null, removeHTML, relaxedIdmatching);
+ }
+
+ /**
+ * Parse GFF or Jalview format sequence features file
+ *
+ * @param align
+ * - alignment/dataset containing sequences that are to be annotated
+ * @param colours
+ * - map to store feature colour definitions
+ * @param filters
+ * - map to store feature filter definitions
+ * @param removeHTML
+ * - process html strings into plain text
+ * @param relaxedIdmatching
+ * - when true, ID matches to compound sequence IDs are allowed
+ * @return true if features were added
+ */
+ public boolean parse(AlignmentI align,
+ Map<String, FeatureColourI> colours,
+ Map<String, FeatureMatcherSetI> filters, boolean removeHTML,
+ boolean relaxedIdmatching)
+ {
+ Map<String, String> gffProps = new HashMap<>();
+ /*
+ * keep track of any sequences we try to create from the data
+ */
+ List<SequenceI> newseqs = new ArrayList<>();
+
+ String line = null;
+ try
+ {
+ String[] gffColumns;
+ String featureGroup = null;
+
+ while ((line = nextLine()) != null)
+ {
+ // skip comments/process pragmas
+ if (line.length() == 0 || line.startsWith("#"))
+ {
+ if (line.toLowerCase(Locale.ROOT).startsWith("##"))
+ {
+ processGffPragma(line, gffProps, align, newseqs);
+ }
+ continue;
+ }
+
+ gffColumns = line.split(TAB_REGEX);
+ if (gffColumns.length == 1)
+ {
+ if (line.trim().equalsIgnoreCase("GFF"))
+ {
+ /*
+ * Jalview features file with appended GFF
+ * assume GFF2 (though it may declare ##gff-version 3)
+ */
+ gffVersion = 2;
+ continue;
+ }
+ }
+
+ if (gffColumns.length > 0 && gffColumns.length < 4)
+ {
+ /*
+ * if 2 or 3 tokens, we anticipate either 'startgroup', 'endgroup' or
+ * a feature type colour specification
+ */
+ String ft = gffColumns[0];
+ if (ft.equalsIgnoreCase(STARTFILTERS))
+ {
+ parseFilters(filters);
+ continue;
+ }
+ if (ft.equalsIgnoreCase(STARTGROUP))
+ {
+ featureGroup = gffColumns[1];
+ }
+ else if (ft.equalsIgnoreCase(ENDGROUP))
+ {
+ // We should check whether this is the current group,
+ // but at present there's no way of showing more than 1 group
+ featureGroup = null;
+ }
+ else
+ {
+ String colscheme = gffColumns[1];
+ FeatureColourI colour = FeatureColour
+ .parseJalviewFeatureColour(colscheme);
+ if (colour != null)
+ {
+ colours.put(ft, colour);
+ }
+ }
+ continue;
+ }
+
+ /*
+ * if not a comment, GFF pragma, startgroup, endgroup or feature
+ * colour specification, that just leaves a feature details line
+ * in either Jalview or GFF format
+ */
+ if (gffVersion == 0)
+ {
+ parseJalviewFeature(line, gffColumns, align, colours, removeHTML,
+ relaxedIdmatching, featureGroup);
+ }
+ else
+ {
+ parseGff(gffColumns, align, relaxedIdmatching, newseqs);
+ }
+ }
+ resetMatcher();
+ } catch (Exception ex)
+ {
+ // should report somewhere useful for UI if necessary
+ warningMessage = ((warningMessage == null) ? "" : warningMessage)
+ + "Parsing error at\n" + line;
+ System.out.println("Error parsing feature file: " + ex + "\n" + line);
+ ex.printStackTrace(System.err);
+ resetMatcher();
+ return false;
+ }
+
+ /*
+ * experimental - add any dummy sequences with features to the alignment
+ * - we need them for Ensembl feature extraction - though maybe not otherwise
+ */
+ for (SequenceI newseq : newseqs)
+ {
+ if (newseq.getFeatures().hasFeatures())
+ {
+ align.addSequence(newseq);
+ }
+ }
+ return true;
+ }
+
+ /**
+ * Reads input lines from STARTFILTERS to ENDFILTERS and adds a feature type
+ * filter to the map for each line parsed. After exit from this method,
+ * nextLine() should return the line after ENDFILTERS (or we are already at
+ * end of file if ENDFILTERS was missing).
+ *
+ * @param filters
+ * @throws IOException
+ */
+ protected void parseFilters(Map<String, FeatureMatcherSetI> filters)
+ throws IOException
+ {
+ String line;
+ while ((line = nextLine()) != null)
+ {
+ if (line.toUpperCase(Locale.ROOT).startsWith(ENDFILTERS))
+ {
+ return;
+ }
+ String[] tokens = line.split(TAB_REGEX);
+ if (tokens.length != 2)
+ {
+ System.err.println(String.format("Invalid token count %d for %d",
+ tokens.length, line));
+ }
+ else
+ {
+ String featureType = tokens[0];
+ FeatureMatcherSetI fm = FeatureMatcherSet.fromString(tokens[1]);
+ if (fm != null && filters != null)
+ {
+ filters.put(featureType, fm);
+ }
+ }
+ }
+ }
+
+ /**
+ * Try to parse a Jalview format feature specification and add it as a
+ * sequence feature to any matching sequences in the alignment. Returns true
+ * if successful (a feature was added), or false if not.
+ *
+ * @param line
+ * @param gffColumns
+ * @param alignment
+ * @param featureColours
+ * @param removeHTML
+ * @param relaxedIdmatching
+ * @param featureGroup
+ */
+ protected boolean parseJalviewFeature(String line, String[] gffColumns,
+ AlignmentI alignment, Map<String, FeatureColourI> featureColours,
+ boolean removeHTML, boolean relaxedIdMatching,
+ String featureGroup)
+ {
+ /*
+ * tokens: description seqid seqIndex start end type [score]
+ */
+ if (gffColumns.length < 6)
+ {
+ System.err.println("Ignoring feature line '" + line
+ + "' with too few columns (" + gffColumns.length + ")");
+ return false;
+ }
+ String desc = gffColumns[0];
+ String seqId = gffColumns[1];
+ SequenceI seq = findSequence(seqId, alignment, null, relaxedIdMatching);
+
+ if (!ID_NOT_SPECIFIED.equals(seqId))
+ {
+ seq = findSequence(seqId, alignment, null, relaxedIdMatching);
+ }
+ else
+ {
+ seqId = null;
+ seq = null;
+ String seqIndex = gffColumns[2];
+ try
+ {
+ int idx = Integer.parseInt(seqIndex);
+ seq = alignment.getSequenceAt(idx);
+ } catch (NumberFormatException ex)
+ {
+ System.err.println("Invalid sequence index: " + seqIndex);
+ }
+ }
+
+ if (seq == null)
+ {
+ System.out.println("Sequence not found: " + line);
+ return false;
+ }
+
+ int startPos = Integer.parseInt(gffColumns[3]);
+ int endPos = Integer.parseInt(gffColumns[4]);
+
+ String ft = gffColumns[5];
+
+ if (!featureColours.containsKey(ft))
+ {
+ /*
+ * Perhaps an old style groups file with no colours -
+ * synthesize a colour from the feature type
+ */
+ Color colour = ColorUtils.createColourFromName(ft);
+ featureColours.put(ft, new FeatureColour(colour));
+ }
+ SequenceFeature sf = null;
+ if (gffColumns.length > 6)
+ {
+ float score = Float.NaN;
+ try
+ {
+ score = Float.valueOf(gffColumns[6]).floatValue();
+ } catch (NumberFormatException ex)
+ {
+ sf = new SequenceFeature(ft, desc, startPos, endPos, featureGroup);
+ }
+ sf = new SequenceFeature(ft, desc, startPos, endPos, score,
+ featureGroup);
+ }
+ else
+ {
+ sf = new SequenceFeature(ft, desc, startPos, endPos, featureGroup);
+ }
+
+ parseDescriptionHTML(sf, removeHTML);
+
+ seq.addSequenceFeature(sf);
+
+ while (seqId != null
+ && (seq = alignment.findName(seq, seqId, false)) != null)
+ {
+ seq.addSequenceFeature(new SequenceFeature(sf));
+ }
+ return true;
+ }
+
+ /**
+ * clear any temporary handles used to speed up ID matching
+ */
+ protected void resetMatcher()
+ {
+ lastmatchedAl = null;
+ matcher = null;
+ }
+
+ /**
+ * Returns a sequence matching the given id, as follows
+ * <ul>
+ * <li>strict matching is on exact sequence name</li>
+ * <li>relaxed matching allows matching on a token within the sequence name,
+ * or a dbxref</li>
+ * <li>first tries to find a match in the alignment sequences</li>
+ * <li>else tries to find a match in the new sequences already generated while
+ * parsing the features file</li>
+ * <li>else creates a new placeholder sequence, adds it to the new sequences
+ * list, and returns it</li>
+ * </ul>
+ *
+ * @param seqId
+ * @param align
+ * @param newseqs
+ * @param relaxedIdMatching
+ *
+ * @return
+ */
+ protected SequenceI findSequence(String seqId, AlignmentI align,
+ List<SequenceI> newseqs, boolean relaxedIdMatching)
+ {
+ // TODO encapsulate in SequenceIdMatcher, share the matcher
+ // with the GffHelper (removing code duplication)
+ SequenceI match = null;
+ if (relaxedIdMatching)
+ {
+ if (lastmatchedAl != align)
+ {
+ lastmatchedAl = align;
+ matcher = new SequenceIdMatcher(align.getSequencesArray());
+ if (newseqs != null)
+ {
+ matcher.addAll(newseqs);
+ }
+ }
+ match = matcher.findIdMatch(seqId);
+ }
+ else
+ {
+ match = align.findName(seqId, true);
+ if (match == null && newseqs != null)
+ {
+ for (SequenceI m : newseqs)
+ {
+ if (seqId.equals(m.getName()))
+ {
+ return m;
+ }
+ }
+ }
+
+ }
+ if (match == null && newseqs != null)
+ {
+ match = new SequenceDummy(seqId);
+ if (relaxedIdMatching)
+ {
+ matcher.addAll(Arrays.asList(new SequenceI[] { match }));
+ }
+ // add dummy sequence to the newseqs list
+ newseqs.add(match);
+ }
+ return match;
+ }
+
+ public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
+ {
+ if (sf.getDescription() == null)
+ {
+ return;
+ }
+ ParseHtmlBodyAndLinks parsed = new ParseHtmlBodyAndLinks(
+ sf.getDescription(), removeHTML, newline);
+
+ if (removeHTML)
+ {
+ sf.setDescription(parsed.getNonHtmlContent());
+ }
+
+ for (String link : parsed.getLinks())
+ {
+ sf.addLink(link);
+ }
+ }
+
+ /**
+ * Returns contents of a Jalview format features file, for visible features, as
+ * filtered by type and group. Features with a null group are displayed if their
+ * feature type is visible. Non-positional features may optionally be included
+ * (with no check on type or group).
+ *
+ * @param sequences
+ * @param fr
+ * @param includeNonPositional
+ * if true, include non-positional features
+ * (regardless of group or type)
+ * @param includeComplement
+ * if true, include visible complementary
+ * (CDS/protein) positional features, with
+ * locations converted to local sequence
+ * coordinates
+ * @return
+ */
+ public String printJalviewFormat(SequenceI[] sequences,
+ FeatureRenderer fr, boolean includeNonPositional,
+ boolean includeComplement)
+ {
+ Map<String, FeatureColourI> visibleColours = fr
+ .getDisplayedFeatureCols();
+ Map<String, FeatureMatcherSetI> featureFilters = fr.getFeatureFilters();
+
+ /*
+ * write out feature colours (if we know them)
+ */
+ // TODO: decide if feature links should also be written here ?
+ StringBuilder out = new StringBuilder(256);
+ if (visibleColours != null)
+ {
+ for (Entry<String, FeatureColourI> featureColour : visibleColours
+ .entrySet())
+ {
+ FeatureColourI colour = featureColour.getValue();
+ out.append(colour.toJalviewFormat(featureColour.getKey())).append(
+ newline);
+ }
+ }
+
+ String[] types = visibleColours == null ? new String[0]
+ : visibleColours.keySet()
+ .toArray(new String[visibleColours.keySet().size()]);
+
+ /*
+ * feature filters if any
+ */
+ outputFeatureFilters(out, visibleColours, featureFilters);
+
+ /*
+ * output features within groups
+ */
+ int count = outputFeaturesByGroup(out, fr, types, sequences,
+ includeNonPositional);
+
+ if (includeComplement)
+ {
+ count += outputComplementFeatures(out, fr, sequences);
+ }
+
+ return count > 0 ? out.toString() : "No Features Visible";
+ }
+
+ /**
+ * Outputs any visible complementary (CDS/peptide) positional features as
+ * Jalview format, within feature group. The coordinates of the linked features
+ * are converted to the corresponding positions of the local sequences.
+ *
+ * @param out
+ * @param fr
+ * @param sequences
+ * @return
+ */
+ private int outputComplementFeatures(StringBuilder out,
+ FeatureRenderer fr, SequenceI[] sequences)
+ {
+ AlignViewportI comp = fr.getViewport().getCodingComplement();
+ FeatureRenderer fr2 = Desktop.getAlignFrameFor(comp)
+ .getFeatureRenderer();
+
+ /*
+ * bin features by feature group and sequence
+ */
+ Map<String, Map<String, List<SequenceFeature>>> map = new TreeMap<>(
+ String.CASE_INSENSITIVE_ORDER);
+ int count = 0;
+
+ for (SequenceI seq : sequences)
+ {
+ /*
+ * find complementary features
+ */
+ List<SequenceFeature> complementary = findComplementaryFeatures(seq,
+ fr2);
+ String seqName = seq.getName();
+
+ for (SequenceFeature sf : complementary)
+ {
+ String group = sf.getFeatureGroup();
+ if (!map.containsKey(group))
+ {
+ map.put(group, new LinkedHashMap<>()); // preserves sequence order
+ }
+ Map<String, List<SequenceFeature>> groupFeatures = map.get(group);
+ if (!groupFeatures.containsKey(seqName))
+ {
+ groupFeatures.put(seqName, new ArrayList<>());
+ }
+ List<SequenceFeature> foundFeatures = groupFeatures.get(seqName);
+ foundFeatures.add(sf);
+ count++;
+ }
+ }
+
+ /*
+ * output features by group
+ */
+ for (Entry<String, Map<String, List<SequenceFeature>>> groupFeatures : map.entrySet())
+ {
+ out.append(newline);
+ String group = groupFeatures.getKey();
+ if (!"".equals(group))
+ {
+ out.append(STARTGROUP).append(TAB).append(group).append(newline);
+ }
+ Map<String, List<SequenceFeature>> seqFeaturesMap = groupFeatures
+ .getValue();
+ for (Entry<String, List<SequenceFeature>> seqFeatures : seqFeaturesMap
+ .entrySet())
+ {
+ String sequenceName = seqFeatures.getKey();
+ for (SequenceFeature sf : seqFeatures.getValue())
+ {
+ formatJalviewFeature(out, sequenceName, sf);
+ }
+ }
+ if (!"".equals(group))
+ {
+ out.append(ENDGROUP).append(TAB).append(group).append(newline);
+ }
+ }
+
+ return count;
+ }
+
+ /**
+ * Answers a list of mapped features visible in the (CDS/protein) complement,
+ * with feature positions translated to local sequence coordinates
+ *
+ * @param seq
+ * @param fr2
+ * @return
+ */
+ protected List<SequenceFeature> findComplementaryFeatures(SequenceI seq,
+ FeatureRenderer fr2)
+ {
+ /*
+ * avoid duplication of features (e.g. peptide feature
+ * at all 3 mapped codon positions)
+ */
+ List<SequenceFeature> found = new ArrayList<>();
+ List<SequenceFeature> complementary = new ArrayList<>();
+
+ for (int pos = seq.getStart(); pos <= seq.getEnd(); pos++)
+ {
+ MappedFeatures mf = fr2.findComplementFeaturesAtResidue(seq, pos);
+
+ if (mf != null)
+ {
+ for (SequenceFeature sf : mf.features)
+ {
+ /*
+ * make a virtual feature with local coordinates
+ */
+ if (!found.contains(sf))
+ {
+ String group = sf.getFeatureGroup();
+ if (group == null)
+ {
+ group = "";
+ }
+ found.add(sf);
+ int begin = sf.getBegin();
+ int end = sf.getEnd();
+ int[] range = mf.getMappedPositions(begin, end);
+ SequenceFeature sf2 = new SequenceFeature(sf, range[0],
+ range[1], group, sf.getScore());
+ complementary.add(sf2);
+ }
+ }
+ }
+ }
+
+ return complementary;
+ }
+
+ /**
+ * Outputs any feature filters defined for visible feature types, sandwiched by
+ * STARTFILTERS and ENDFILTERS lines
+ *
+ * @param out
+ * @param visible
+ * @param featureFilters
+ */
+ void outputFeatureFilters(StringBuilder out,
+ Map<String, FeatureColourI> visible,
+ Map<String, FeatureMatcherSetI> featureFilters)
+ {
+ if (visible == null || featureFilters == null
+ || featureFilters.isEmpty())
+ {
+ return;
+ }
+
+ boolean first = true;
+ for (String featureType : visible.keySet())
+ {
+ FeatureMatcherSetI filter = featureFilters.get(featureType);
+ if (filter != null)
+ {
+ if (first)
+ {
+ first = false;
+ out.append(newline).append(STARTFILTERS).append(newline);
+ }
+ out.append(featureType).append(TAB).append(filter.toStableString())
+ .append(newline);
+ }
+ }
+ if (!first)
+ {
+ out.append(ENDFILTERS).append(newline);
+ }
+
+ }
+
+ /**
+ * Appends output of visible sequence features within feature groups to the
+ * output buffer. Groups other than the null or empty group are sandwiched by
+ * STARTGROUP and ENDGROUP lines. Answers the number of features written.
+ *
+ * @param out
+ * @param fr
+ * @param featureTypes
+ * @param sequences
+ * @param includeNonPositional
+ * @return
+ */
+ private int outputFeaturesByGroup(StringBuilder out,
+ FeatureRenderer fr, String[] featureTypes,
+ SequenceI[] sequences, boolean includeNonPositional)
+ {
+ List<String> featureGroups = fr.getFeatureGroups();
+
+ /*
+ * sort groups alphabetically, and ensure that features with a
+ * null or empty group are output after those in named groups
+ */
+ List<String> sortedGroups = new ArrayList<>(featureGroups);
+ sortedGroups.remove(null);
+ sortedGroups.remove("");
+ Collections.sort(sortedGroups);
+ sortedGroups.add(null);
+ sortedGroups.add("");
+
+ int count = 0;
+ List<String> visibleGroups = fr.getDisplayedFeatureGroups();
+
+ /*
+ * loop over all groups (may be visible or not);
+ * non-positional features are output even if group is not visible
+ */
+ for (String group : sortedGroups)
+ {
+ boolean firstInGroup = true;
+ boolean isNullGroup = group == null || "".equals(group);
+
+ for (int i = 0; i < sequences.length; i++)
+ {
+ String sequenceName = sequences[i].getName();
+ List<SequenceFeature> features = new ArrayList<>();
+
+ /*
+ * get any non-positional features in this group, if wanted
+ * (for any feature type, whether visible or not)
+ */
+ if (includeNonPositional)
+ {
+ features.addAll(sequences[i].getFeatures()
+ .getFeaturesForGroup(false, group));
+ }
+
+ /*
+ * add positional features for visible feature types, but
+ * (for named groups) only if feature group is visible
+ */
+ if (featureTypes.length > 0
+ && (isNullGroup || visibleGroups.contains(group)))
+ {
+ features.addAll(sequences[i].getFeatures().getFeaturesForGroup(
+ true, group, featureTypes));
+ }
+
+ for (SequenceFeature sf : features)
+ {
+ if (sf.isNonPositional() || fr.isVisible(sf))
+ {
+ count++;
+ if (firstInGroup)
+ {
+ out.append(newline);
+ if (!isNullGroup)
+ {
+ out.append(STARTGROUP).append(TAB).append(group)
+ .append(newline);
+ }
+ }
+ firstInGroup = false;
+ formatJalviewFeature(out, sequenceName, sf);
+ }
+ }
+ }
+
+ if (!isNullGroup && !firstInGroup)
+ {
+ out.append(ENDGROUP).append(TAB).append(group).append(newline);
+ }
+ }
+ return count;
+ }
+
+ /**
+ * Formats one feature in Jalview format and appends to the string buffer
+ *
+ * @param out
+ * @param sequenceName
+ * @param sequenceFeature
+ */
+ protected void formatJalviewFeature(
+ StringBuilder out, String sequenceName,
+ SequenceFeature sequenceFeature)
+ {
+ if (sequenceFeature.description == null
+ || sequenceFeature.description.equals(""))
+ {
+ out.append(sequenceFeature.type).append(TAB);
+ }
+ else
+ {
+ if (sequenceFeature.links != null
+ && sequenceFeature.getDescription().indexOf("<html>") == -1)
+ {
+ out.append("<html>");
+ }
+
+ out.append(sequenceFeature.description);
+ if (sequenceFeature.links != null)
+ {
+ for (int l = 0; l < sequenceFeature.links.size(); l++)
+ {
+ String label = sequenceFeature.links.elementAt(l);
+ String href = label.substring(label.indexOf("|") + 1);
+ label = label.substring(0, label.indexOf("|"));
+
+ if (sequenceFeature.description.indexOf(href) == -1)
+ {
+ out.append(" <a href=\"").append(href).append("\">")
+ .append(label).append("</a>");
+ }
+ }
+
+ if (sequenceFeature.getDescription().indexOf("</html>") == -1)
+ {
+ out.append("</html>");
+ }
+ }
+
+ out.append(TAB);
+ }
+ out.append(sequenceName);
+ out.append("\t-1\t");
+ out.append(sequenceFeature.begin);
+ out.append(TAB);
+ out.append(sequenceFeature.end);
+ out.append(TAB);
+ out.append(sequenceFeature.type);
+ if (!Float.isNaN(sequenceFeature.score))
+ {
+ out.append(TAB);
+ out.append(sequenceFeature.score);
+ }
+ out.append(newline);
+ }
+
+ /**
+ * Parse method that is called when a GFF file is dragged to the desktop
+ */
+ @Override
+ public void parse()
+ {
+ AlignViewportI av = getViewport();
+ if (av != null)
+ {
+ if (av.getAlignment() != null)
+ {
+ dataset = av.getAlignment().getDataset();
+ }
+ if (dataset == null)
+ {
+ // working in the applet context ?
+ dataset = av.getAlignment();
+ }
+ }
+ else
+ {
+ dataset = new Alignment(new SequenceI[] {});
+ }
+
+ Map<String, FeatureColourI> featureColours = new HashMap<>();
+ boolean parseResult = parse(dataset, featureColours, false, true);
+ if (!parseResult)
+ {
+ // pass error up somehow
+ }
+ if (av != null)
+ {
+ // update viewport with the dataset data ?
+ }
+ else
+ {
+ setSeqs(dataset.getSequencesArray());
+ }
+ }
+
+ /**
+ * Implementation of unused abstract method
+ *
+ * @return error message
+ */
+ @Override
+ public String print(SequenceI[] sqs, boolean jvsuffix)
+ {
+ System.out.println("Use printGffFormat() or printJalviewFormat()");
+ return null;
+ }
+
+ /**
+ * Returns features output in GFF2 format
+ *
+ * @param sequences
+ * the sequences whose features are to be
+ * output
+ * @param visible
+ * a map whose keys are the type names of
+ * visible features
+ * @param visibleFeatureGroups
+ * @param includeNonPositionalFeatures
+ * @param includeComplement
+ * @return
+ */
+ public String printGffFormat(SequenceI[] sequences,
+ FeatureRenderer fr, boolean includeNonPositionalFeatures,
+ boolean includeComplement)
+ {
+ FeatureRenderer fr2 = null;
+ if (includeComplement)
+ {
+ AlignViewportI comp = fr.getViewport().getCodingComplement();
+ fr2 = Desktop.getAlignFrameFor(comp).getFeatureRenderer();
+ }
+
+ Map<String, FeatureColourI> visibleColours = fr.getDisplayedFeatureCols();
+
+ StringBuilder out = new StringBuilder(256);
+
+ out.append(String.format("%s %d\n", GFF_VERSION, gffVersion == 0 ? 2 : gffVersion));
+
+ String[] types = visibleColours == null ? new String[0]
+ : visibleColours.keySet()
+ .toArray(new String[visibleColours.keySet().size()]);
+
+ for (SequenceI seq : sequences)
+ {
+ List<SequenceFeature> seqFeatures = new ArrayList<>();
+ List<SequenceFeature> features = new ArrayList<>();
+ if (includeNonPositionalFeatures)
+ {
+ features.addAll(seq.getFeatures().getNonPositionalFeatures());
+ }
+ if (visibleColours != null && !visibleColours.isEmpty())
+ {
+ features.addAll(seq.getFeatures().getPositionalFeatures(types));
+ }
+ for (SequenceFeature sf : features)
+ {
+ if (sf.isNonPositional() || fr.isVisible(sf))
+ {
+ /*
+ * drop features hidden by group visibility, colour threshold,
+ * or feature filter condition
+ */
+ seqFeatures.add(sf);
+ }
+ }
+
+ if (includeComplement)
+ {
+ seqFeatures.addAll(findComplementaryFeatures(seq, fr2));
+ }
+
+ /*
+ * sort features here if wanted
+ */
+ for (SequenceFeature sf : seqFeatures)
+ {
+ formatGffFeature(out, seq, sf);
+ out.append(newline);
+ }
+ }
+
+ return out.toString();
+ }
+
+ /**
+ * Formats one feature as GFF and appends to the string buffer
+ */
+ private void formatGffFeature(StringBuilder out, SequenceI seq,
+ SequenceFeature sf)
+ {
+ String source = sf.featureGroup;
+ if (source == null)
+ {
+ source = sf.getDescription();
+ }
+
+ out.append(seq.getName());
+ out.append(TAB);
+ out.append(source);
+ out.append(TAB);
+ out.append(sf.type);
+ out.append(TAB);
+ out.append(sf.begin);
+ out.append(TAB);
+ out.append(sf.end);
+ out.append(TAB);
+ out.append(sf.score);
+ out.append(TAB);
+
+ int strand = sf.getStrand();
+ out.append(strand == 1 ? "+" : (strand == -1 ? "-" : "."));
+ out.append(TAB);
+
+ String phase = sf.getPhase();
+ out.append(phase == null ? "." : phase);
+
+ if (sf.otherDetails != null && !sf.otherDetails.isEmpty())
+ {
+ Map<String, Object> map = sf.otherDetails;
+ formatAttributes(out, map);
+ }
+ }
+
+ /**
+ * A helper method that outputs attributes stored in the map as
+ * semicolon-delimited values e.g.
+ *
+ * <pre>
+ * AC_Male=0;AF_NFE=0.00000e 00;Hom_FIN=0;GQ_MEDIAN=9
+ * </pre>
+ *
+ * A map-valued attribute is formatted as a comma-delimited list within braces,
+ * for example
+ *
+ * <pre>
+ * jvmap_CSQ={ALLELE_NUM=1,UNIPARC=UPI0002841053,Feature=ENST00000585561}
+ * </pre>
+ *
+ * The {@code jvmap_} prefix designates a values map and is removed if the value
+ * is parsed when read in. (The GFF3 specification allows 'semi-structured data'
+ * to be represented provided the attribute name begins with a lower case
+ * letter.)
+ *
+ * @param sb
+ * @param map
+ * @see http://gmod.org/wiki/GFF3#GFF3_Format
+ */
+ void formatAttributes(StringBuilder sb, Map<String, Object> map)
+ {
+ sb.append(TAB);
+ boolean first = true;
+ for (String key : map.keySet())
+ {
+ if (SequenceFeature.STRAND.equals(key)
+ || SequenceFeature.PHASE.equals(key))
+ {
+ /*
+ * values stashed in map but output to their own columns
+ */
+ continue;
+ }
+ {
+ if (!first)
+ {
+ sb.append(";");
+ }
+ }
+ first = false;
+ Object value = map.get(key);
+ if (value instanceof Map<?, ?>)
+ {
+ formatMapAttribute(sb, key, (Map<?, ?>) value);
+ }
+ else
+ {
+ String formatted = StringUtils.urlEncode(value.toString(),
+ GffHelperI.GFF_ENCODABLE);
+ sb.append(key).append(EQUALS).append(formatted);
+ }
+ }
+ }
+
+ /**
+ * Formats the map entries as
+ *
+ * <pre>
+ * key=key1=value1,key2=value2,...
+ * </pre>
+ *
+ * and appends this to the string buffer
+ *
+ * @param sb
+ * @param key
+ * @param map
+ */
+ private void formatMapAttribute(StringBuilder sb, String key,
+ Map<?, ?> map)
+ {
+ if (map == null || map.isEmpty())
+ {
+ return;
+ }
+
+ /*
+ * AbstractMap.toString would be a shortcut here, but more reliable
+ * to code the required format in case toString changes in future
+ */
+ sb.append(key).append(EQUALS);
+ boolean first = true;
+ for (Entry<?, ?> entry : map.entrySet())
+ {
+ if (!first)
+ {
+ sb.append(",");
+ }
+ first = false;
+ sb.append(entry.getKey().toString()).append(EQUALS);
+ String formatted = StringUtils.urlEncode(entry.getValue().toString(),
+ GffHelperI.GFF_ENCODABLE);
+ sb.append(formatted);
+ }
+ }
+
+ /**
+ * Returns a mapping given list of one or more Align descriptors (exonerate
+ * format)
+ *
+ * @param alignedRegions
+ * a list of "Align fromStart toStart fromCount"
+ * @param mapIsFromCdna
+ * if true, 'from' is dna, else 'from' is protein
+ * @param strand
+ * either 1 (forward) or -1 (reverse)
+ * @return
+ * @throws IOException
+ */
+ protected MapList constructCodonMappingFromAlign(
+ List<String> alignedRegions, boolean mapIsFromCdna, int strand)
+ throws IOException
+ {
+ if (strand == 0)
+ {
+ throw new IOException(
+ "Invalid strand for a codon mapping (cannot be 0)");
+ }
+ int regions = alignedRegions.size();
+ // arrays to hold [start, end] for each aligned region
+ int[] fromRanges = new int[regions * 2]; // from dna
+ int[] toRanges = new int[regions * 2]; // to protein
+ int fromRangesIndex = 0;
+ int toRangesIndex = 0;
+
+ for (String range : alignedRegions)
+ {
+ /*
+ * Align mapFromStart mapToStart mapFromCount
+ * e.g. if mapIsFromCdna
+ * Align 11270 143 120
+ * means:
+ * 120 bases from pos 11270 align to pos 143 in peptide
+ * if !mapIsFromCdna this would instead be
+ * Align 143 11270 40
+ */
+ String[] tokens = range.split(" ");
+ if (tokens.length != 3)
+ {
+ throw new IOException("Wrong number of fields for Align");
+ }
+ int fromStart = 0;
+ int toStart = 0;
+ int fromCount = 0;
+ try
+ {
+ fromStart = Integer.parseInt(tokens[0]);
+ toStart = Integer.parseInt(tokens[1]);
+ fromCount = Integer.parseInt(tokens[2]);
+ } catch (NumberFormatException nfe)
+ {
+ throw new IOException(
+ "Invalid number in Align field: " + nfe.getMessage());
+ }
+
+ /*
+ * Jalview always models from dna to protein, so adjust values if the
+ * GFF mapping is from protein to dna
+ */
+ if (!mapIsFromCdna)
+ {
+ fromCount *= 3;
+ int temp = fromStart;
+ fromStart = toStart;
+ toStart = temp;
+ }
+ fromRanges[fromRangesIndex++] = fromStart;
+ fromRanges[fromRangesIndex++] = fromStart + strand * (fromCount - 1);
+
+ /*
+ * If a codon has an intron gap, there will be contiguous 'toRanges';
+ * this is handled for us by the MapList constructor.
+ * (It is not clear that exonerate ever generates this case)
+ */
+ toRanges[toRangesIndex++] = toStart;
+ toRanges[toRangesIndex++] = toStart + (fromCount - 1) / 3;
+ }
+
+ return new MapList(fromRanges, toRanges, 3, 1);
+ }
+
+ /**
+ * Parse a GFF format feature. This may include creating a 'dummy' sequence to
+ * hold the feature, or for its mapped sequence, or both, to be resolved
+ * either later in the GFF file (##FASTA section), or when the user loads
+ * additional sequences.
+ *
+ * @param gffColumns
+ * @param alignment
+ * @param relaxedIdMatching
+ * @param newseqs
+ * @return
+ */
+ protected SequenceI parseGff(String[] gffColumns, AlignmentI alignment,
+ boolean relaxedIdMatching, List<SequenceI> newseqs)
+ {
+ /*
+ * GFF: seqid source type start end score strand phase [attributes]
+ */
+ if (gffColumns.length < 5)
+ {
+ System.err.println("Ignoring GFF feature line with too few columns ("
+ + gffColumns.length + ")");
+ return null;
+ }
+
+ /*
+ * locate referenced sequence in alignment _or_
+ * as a forward or external reference (SequenceDummy)
+ */
+ String seqId = gffColumns[0];
+ SequenceI seq = findSequence(seqId, alignment, newseqs,
+ relaxedIdMatching);
+
+ SequenceFeature sf = null;
+ GffHelperI helper = GffHelperFactory.getHelper(gffColumns);
+ if (helper != null)
+ {
+ try
+ {
+ sf = helper.processGff(seq, gffColumns, alignment, newseqs,
+ relaxedIdMatching);
+ if (sf != null)
+ {
+ seq.addSequenceFeature(sf);
+ while ((seq = alignment.findName(seq, seqId, true)) != null)
+ {
+ seq.addSequenceFeature(new SequenceFeature(sf));
+ }
+ }
+ } catch (IOException e)
+ {
+ System.err.println("GFF parsing failed with: " + e.getMessage());
+ return null;
+ }
+ }
+
+ return seq;
+ }
+
+ /**
+ * After encountering ##fasta in a GFF3 file, process the remainder of the
+ * file as FAST sequence data. Any placeholder sequences created during
+ * feature parsing are updated with the actual sequences.
+ *
+ * @param align
+ * @param newseqs
+ * @throws IOException
+ */
+ protected void processAsFasta(AlignmentI align, List<SequenceI> newseqs)
+ throws IOException
+ {
+ try
+ {
+ mark();
+ } catch (IOException q)
+ {
+ }
+ FastaFile parser = new FastaFile(this);
+ List<SequenceI> includedseqs = parser.getSeqs();
+
+ SequenceIdMatcher smatcher = new SequenceIdMatcher(newseqs);
+
+ /*
+ * iterate over includedseqs, and replacing matching ones with newseqs
+ * sequences. Generic iterator not used here because we modify
+ * includedseqs as we go
+ */
+ for (int p = 0, pSize = includedseqs.size(); p < pSize; p++)
+ {
+ // search for any dummy seqs that this sequence can be used to update
+ SequenceI includedSeq = includedseqs.get(p);
+ SequenceI dummyseq = smatcher.findIdMatch(includedSeq);
+ if (dummyseq != null && dummyseq instanceof SequenceDummy)
+ {
+ // probably have the pattern wrong
+ // idea is that a flyweight proxy for a sequence ID can be created for
+ // 1. stable reference creation
+ // 2. addition of annotation
+ // 3. future replacement by a real sequence
+ // current pattern is to create SequenceDummy objects - a convenience
+ // constructor for a Sequence.
+ // problem is that when promoted to a real sequence, all references
+ // need to be updated somehow. We avoid that by keeping the same object.
+ ((SequenceDummy) dummyseq).become(includedSeq);
+ dummyseq.createDatasetSequence();
+
+ /*
+ * Update mappings so they are now to the dataset sequence
+ */
+ for (AlignedCodonFrame mapping : align.getCodonFrames())
+ {
+ mapping.updateToDataset(dummyseq);
+ }
+
+ /*
+ * replace parsed sequence with the realised forward reference
+ */
+ includedseqs.set(p, dummyseq);
+
+ /*
+ * and remove from the newseqs list
+ */
+ newseqs.remove(dummyseq);
+ }
+ }
+
+ /*
+ * finally add sequences to the dataset
+ */
+ for (SequenceI seq : includedseqs)
+ {
+ // experimental: mapping-based 'alignment' to query sequence
+ AlignmentUtils.alignSequenceAs(seq, align,
+ String.valueOf(align.getGapCharacter()), false, true);
+
+ // rename sequences if GFF handler requested this
+ // TODO a more elegant way e.g. gffHelper.postProcess(newseqs) ?
+ List<SequenceFeature> sfs = seq.getFeatures().getPositionalFeatures();
+ if (!sfs.isEmpty())
+ {
+ String newName = (String) sfs.get(0).getValue(
+ GffHelperI.RENAME_TOKEN);
+ if (newName != null)
+ {
+ seq.setName(newName);
+ }
+ }
+ align.addSequence(seq);
+ }
+ }
+
+ /**
+ * Process a ## directive
+ *
+ * @param line
+ * @param gffProps
+ * @param align
+ * @param newseqs
+ * @throws IOException
+ */
+ protected void processGffPragma(String line, Map<String, String> gffProps,
+ AlignmentI align, List<SequenceI> newseqs) throws IOException
+ {
+ line = line.trim();
+ if ("###".equals(line))
+ {
+ // close off any open 'forward references'
+ return;
+ }
+
+ String[] tokens = line.substring(2).split(" ");
+ String pragma = tokens[0];
+ String value = tokens.length == 1 ? null : tokens[1];
+
+ if ("gff-version".equalsIgnoreCase(pragma))
+ {
+ if (value != null)
+ {
+ try
+ {
+ // value may be e.g. "3.1.2"
+ gffVersion = Integer.parseInt(value.split("\\.")[0]);
+ } catch (NumberFormatException e)
+ {
+ // ignore
+ }
+ }
+ }
+ else if ("sequence-region".equalsIgnoreCase(pragma))
+ {
+ // could capture <seqid start end> if wanted here
+ }
+ else if ("feature-ontology".equalsIgnoreCase(pragma))
+ {
+ // should resolve against the specified feature ontology URI
+ }
+ else if ("attribute-ontology".equalsIgnoreCase(pragma))
+ {
+ // URI of attribute ontology - not currently used in GFF3
+ }
+ else if ("source-ontology".equalsIgnoreCase(pragma))
+ {
+ // URI of source ontology - not currently used in GFF3
+ }
+ else if ("species-build".equalsIgnoreCase(pragma))
+ {
+ // save URI of specific NCBI taxon version of annotations
+ gffProps.put("species-build", value);
+ }
+ else if ("fasta".equalsIgnoreCase(pragma))
+ {
+ // process the rest of the file as a fasta file and replace any dummy
+ // sequence IDs
+ processAsFasta(align, newseqs);
+ }
+ else
+ {
+ System.err.println("Ignoring unknown pragma: " + line);
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff