X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFeaturesFile.java;h=11135b7dac9f376d6d61440f951b3fa9df4cfb7d;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=cfc08fbdcaebb2e8917e9fe0e0c8d0c27e342806;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git
diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index cfc08fb..11135b7 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -1,960 +1,1028 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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 .
- */
-package jalview.io;
-
-import java.io.*;
-import java.util.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.util.Format;
-
-/**
- * Parse and create Jalview Features files Detects GFF format features files and
- * parses. Does not implement standard print() - call specific printFeatures or
- * printGFF. Uses AlignmentI.findSequence(String id) to find the sequence object
- * for the features annotation - this normally works on an exact match.
- *
- * @author AMW
- * @version $Revision$
- */
-public class FeaturesFile extends AlignFile
-{
- /**
- * work around for GFF interpretation bug where source string becomes
- * description rather than a group
- */
- private boolean doGffSource = true;
-
- /**
- * Creates a new FeaturesFile object.
- */
- public FeaturesFile()
- {
- }
-
- /**
- * Creates a new FeaturesFile object.
- *
- * @param inFile
- * DOCUMENT ME!
- * @param type
- * DOCUMENT ME!
- *
- * @throws IOException
- * DOCUMENT ME!
- */
- public FeaturesFile(String inFile, String type) throws IOException
- {
- super(inFile, type);
- }
-
- public FeaturesFile(FileParse source) throws IOException
- {
- super(source);
- }
-
- /**
- * The Application can render HTML, but the applet will remove HTML tags and
- * replace links with %LINK% Both need to read links in HTML however
- *
- * @throws IOException
- * DOCUMENT ME!
- */
- public boolean parse(AlignmentI align, Hashtable colours,
- boolean removeHTML)
- {
- return parse(align, colours, null, removeHTML);
- }
-
- /**
- * The Application can render HTML, but the applet will remove HTML tags and
- * replace links with %LINK% Both need to read links in HTML however
- *
- * @throws IOException
- * DOCUMENT ME!
- */
- public boolean parse(AlignmentI align, Hashtable colours,
- Hashtable featureLink, boolean removeHTML)
- {
- String line = null;
- try
- {
- SequenceI seq = null;
- String type, desc, token = null;
-
- int index, start, end;
- float score;
- StringTokenizer st;
- SequenceFeature sf;
- String featureGroup = null, groupLink = null;
- Hashtable typeLink = new Hashtable();
- /**
- * when true, assume GFF style features rather than Jalview style.
- */
- boolean GFFFile = true;
- while ((line = nextLine()) != null)
- {
- if (line.startsWith("#"))
- {
- continue;
- }
-
- st = new StringTokenizer(line, "\t");
- if (st.countTokens() == 1)
- {
- if (line.trim().equalsIgnoreCase("GFF"))
- {
- // Start parsing file as if it might be GFF again.
- GFFFile = true;
- continue;
- }
- }
- if (st.countTokens() > 1 && st.countTokens() < 4)
- {
- GFFFile = false;
- type = st.nextToken();
- if (type.equalsIgnoreCase("startgroup"))
- {
- featureGroup = st.nextToken();
- if (st.hasMoreElements())
- {
- groupLink = st.nextToken();
- featureLink.put(featureGroup, groupLink);
- }
- }
- else if (type.equalsIgnoreCase("endgroup"))
- {
- // We should check whether this is the current group,
- // but at present theres no way of showing more than 1 group
- st.nextToken();
- featureGroup = null;
- groupLink = null;
- }
- else
- {
- Object colour = null;
- String colscheme = st.nextToken();
- if (colscheme.indexOf("|") > -1
- || colscheme.trim().equalsIgnoreCase("label"))
- {
- // Parse '|' separated graduated colourscheme fields:
- // [label|][mincolour|maxcolour|[absolute|]minvalue|maxvalue|thresholdtype|thresholdvalue]
- // can either provide 'label' only, first is optional, next two
- // colors are required (but may be
- // left blank), next is optional, nxt two min/max are required.
- // first is either 'label'
- // first/second and third are both hexadecimal or word equivalent
- // colour.
- // next two are values parsed as floats.
- // fifth is either 'above','below', or 'none'.
- // sixth is a float value and only required when fifth is either
- // 'above' or 'below'.
- StringTokenizer gcol = new StringTokenizer(colscheme, "|", true);
- // set defaults
- int threshtype = AnnotationColourGradient.NO_THRESHOLD;
- float min = Float.MIN_VALUE, max = Float.MAX_VALUE, threshval = Float.NaN;
- boolean labelCol = false;
- // Parse spec line
- String mincol = gcol.nextToken();
- if (mincol=="|")
- {
- System.err
- .println("Expected either 'label' or a colour specification in the line: "+line );
- continue;
- }
- String maxcol = null;
- if (mincol.toLowerCase().indexOf("label") == 0)
- {
- labelCol = true;
- mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); // skip '|'
- mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
- }
- String abso = null, minval, maxval;
- if (mincol != null)
- {
- // at least four more tokens
- if (mincol.equals("|"))
- {
- mincol="";
- } else {
- gcol.nextToken(); // skip next '|'
- }
- // continue parsing rest of line
- maxcol = gcol.nextToken();
- if (maxcol.equals("|"))
- {
- maxcol="";
- } else {
- gcol.nextToken(); // skip next '|'
- }
- abso = gcol.nextToken();
- gcol.nextToken(); // skip next '|'
- if (abso.toLowerCase().indexOf("abso") != 0)
- {
- minval = abso;
- abso = null;
- }
- else
- {
- minval = gcol.nextToken();
- gcol.nextToken(); // skip next '|'
- }
- maxval = gcol.nextToken();
- if (gcol.hasMoreTokens()) {
- gcol.nextToken(); // skip next '|'
- }
- try
- {
- if (minval.length() > 0)
- {
- min = new Float(minval).floatValue();
- }
- } catch (Exception e)
- {
- System.err
- .println("Couldn't parse the minimum value for graduated colour for type ("
- + colscheme
- + ") - did you misspell 'auto' for the optional automatic colour switch ?");
- e.printStackTrace();
- }
- try
- {
- if (maxval.length() > 0)
- {
- max = new Float(maxval).floatValue();
- }
- } catch (Exception e)
- {
- System.err
- .println("Couldn't parse the maximum value for graduated colour for type ("
- + colscheme + ")");
- e.printStackTrace();
- }
- }
- else
- {
- // add in some dummy min/max colours for the label-only
- // colourscheme.
- mincol = "FFFFFF";
- maxcol = "000000";
- }
- try
- {
- colour = new jalview.schemes.GraduatedColor(
- new UserColourScheme(mincol).findColour('A'),
- new UserColourScheme(maxcol).findColour('A'), min,
- max);
- } catch (Exception e)
- {
- System.err
- .println("Couldn't parse the graduated colour scheme ("
- + colscheme + ")");
- e.printStackTrace();
- }
- if (colour != null)
- {
- ((jalview.schemes.GraduatedColor) colour)
- .setColourByLabel(labelCol);
- ((jalview.schemes.GraduatedColor) colour)
- .setAutoScaled(abso == null);
- // add in any additional parameters
- String ttype = null, tval = null;
- if (gcol.hasMoreTokens())
- {
- // threshold type and possibly a threshold value
- ttype = gcol.nextToken();
- if (ttype.toLowerCase().startsWith("below"))
- {
- ((jalview.schemes.GraduatedColor) colour)
- .setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);
- }
- else if (ttype.toLowerCase().startsWith("above"))
- {
- ((jalview.schemes.GraduatedColor) colour)
- .setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);
- }
- else
- {
- ((jalview.schemes.GraduatedColor) colour)
- .setThreshType(AnnotationColourGradient.NO_THRESHOLD);
- if (!ttype.toLowerCase().startsWith("no"))
- {
- System.err
- .println("Ignoring unrecognised threshold type : "
- + ttype);
- }
- }
- }
- if (((GraduatedColor) colour).getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
- {
- try
- {
- gcol.nextToken();
- tval = gcol.nextToken();
- ((jalview.schemes.GraduatedColor) colour)
- .setThresh(new Float(tval).floatValue());
- } catch (Exception e)
- {
- System.err
- .println("Couldn't parse threshold value as a float: ("
- + tval + ")");
- e.printStackTrace();
- }
- }
- // parse the thresh-is-min token ?
- if (gcol.hasMoreTokens())
- {
- System.err
- .println("Ignoring additional tokens in parameters in graduated colour specification\n");
- while (gcol.hasMoreTokens())
- {
- System.err.println("|" + gcol.nextToken());
- }
- System.err.println("\n");
- }
- }
- }
- else
- {
- UserColourScheme ucs = new UserColourScheme(colscheme);
- colour = ucs.findColour('A');
- }
- if (colour != null)
- {
- colours.put(type, colour);
- }
- if (st.hasMoreElements())
- {
- String link = st.nextToken();
- typeLink.put(type, link);
- if (featureLink == null)
- {
- featureLink = new Hashtable();
- }
- featureLink.put(type, link);
- }
- }
- continue;
- }
- String seqId = "";
- while (st.hasMoreElements())
- {
-
- if (GFFFile)
- {
- // Still possible this is an old Jalview file,
- // which does not have type colours at the beginning
- seqId = token = st.nextToken();
- seq = align.findName(seqId, true);
- if (seq != null)
- {
- desc = st.nextToken();
- String group = null;
- if (doGffSource && desc.indexOf(' ') == -1)
- {
- // could also be a source term rather than description line
- group = new String(desc);
- }
- type = st.nextToken();
- try
- {
- String stt = st.nextToken();
- if (stt.length() == 0 || stt.equals("-"))
- {
- start = 0;
- }
- else
- {
- start = Integer.parseInt(stt);
- }
- } catch (NumberFormatException ex)
- {
- start = 0;
- }
- try
- {
- String stt = st.nextToken();
- if (stt.length() == 0 || stt.equals("-"))
- {
- end = 0;
- }
- else
- {
- end = Integer.parseInt(stt);
- }
- } catch (NumberFormatException ex)
- {
- end = 0;
- }
- // TODO: decide if non positional feature assertion for input data
- // where end==0 is generally valid
- if (end == 0)
- {
- // treat as non-positional feature, regardless.
- start = 0;
- }
- try
- {
- score = new Float(st.nextToken()).floatValue();
- } catch (NumberFormatException ex)
- {
- score = 0;
- }
-
- sf = new SequenceFeature(type, desc, start, end, score, group);
-
- try
- {
- sf.setValue("STRAND", st.nextToken());
- sf.setValue("FRAME", st.nextToken());
- } catch (Exception ex)
- {
- }
-
- if (st.hasMoreTokens())
- {
- StringBuffer attributes = new StringBuffer();
- while (st.hasMoreTokens())
- {
- attributes.append("\t" + st.nextElement());
- }
- // TODO validate and split GFF2 attributes field ? parse out
- // ([A-Za-z][A-Za-z0-9_]*) ; and add as
- // sf.setValue(attrib, val);
- sf.setValue("ATTRIBUTES", attributes.toString());
- }
-
- seq.addSequenceFeature(sf);
- while ((seq = align.findName(seq, seqId, true)) != null)
- {
- seq.addSequenceFeature(new SequenceFeature(sf));
- }
- break;
- }
- }
-
- if (GFFFile && seq == null)
- {
- desc = token;
- }
- else
- {
- desc = st.nextToken();
- }
- if (!st.hasMoreTokens())
- {
- System.err
- .println("DEBUG: Run out of tokens when trying to identify the destination for the feature.. giving up.");
- // in all probability, this isn't a file we understand, so bail
- // quietly.
- return false;
- }
-
- token = st.nextToken();
-
- if (!token.equals("ID_NOT_SPECIFIED"))
- {
- seq = align.findName(seqId = token, true);
- st.nextToken();
- }
- else
- {
- seqId = null;
- try
- {
- index = Integer.parseInt(st.nextToken());
- seq = align.getSequenceAt(index);
- } catch (NumberFormatException ex)
- {
- seq = null;
- }
- }
-
- if (seq == null)
- {
- System.out.println("Sequence not found: " + line);
- break;
- }
-
- start = Integer.parseInt(st.nextToken());
- end = Integer.parseInt(st.nextToken());
-
- type = st.nextToken();
-
- if (!colours.containsKey(type))
- {
- // Probably the old style groups file
- UserColourScheme ucs = new UserColourScheme(type);
- colours.put(type, ucs.findColour('A'));
- }
- sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
- if (st.hasMoreTokens())
- {
- try
- {
- score = new Float(st.nextToken()).floatValue();
- // update colourgradient bounds if allowed to
- } catch (NumberFormatException ex)
- {
- score = 0;
- }
- sf.setScore(score);
- }
- if (groupLink != null && removeHTML)
- {
- sf.addLink(groupLink);
- sf.description += "%LINK%";
- }
- if (typeLink.containsKey(type) && removeHTML)
- {
- sf.addLink(typeLink.get(type).toString());
- sf.description += "%LINK%";
- }
-
- parseDescriptionHTML(sf, removeHTML);
-
- seq.addSequenceFeature(sf);
-
- while (seqId != null
- && (seq = align.findName(seq, seqId, false)) != null)
- {
- seq.addSequenceFeature(new SequenceFeature(sf));
- }
- // If we got here, its not a GFFFile
- GFFFile = false;
- }
- }
- } catch (Exception ex)
- {
- System.out.println(line);
- System.out.println("Error parsing feature file: " + ex + "\n" + line);
- ex.printStackTrace(System.err);
- return false;
- }
-
- return true;
- }
-
- public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
- {
- if (sf.getDescription() == null)
- {
- return;
- }
-
- if (removeHTML
- && sf.getDescription().toUpperCase().indexOf("") == -1)
- {
- removeHTML = false;
- }
-
- StringBuffer sb = new StringBuffer();
- StringTokenizer st = new StringTokenizer(sf.getDescription(), "<");
- String token, link;
- int startTag;
- String tag = null;
- while (st.hasMoreElements())
- {
- token = st.nextToken("&>");
- if (token.equalsIgnoreCase("html") || token.startsWith("/"))
- {
- continue;
- }
-
- tag = null;
- startTag = token.indexOf("<");
-
- if (startTag > -1)
- {
- tag = token.substring(startTag + 1);
- token = token.substring(0, startTag);
- }
-
- if (tag != null && tag.toUpperCase().startsWith("A HREF="))
- {
- if (token.length() > 0)
- {
- sb.append(token);
- }
- link = tag.substring(tag.indexOf("\"") + 1, tag.length() - 1);
- String label = st.nextToken("<>");
- sf.addLink(label + "|" + link);
- sb.append(label + "%LINK%");
- }
- else if (tag != null && tag.equalsIgnoreCase("br"))
- {
- sb.append("\n");
- }
- else if (token.startsWith("lt;"))
- {
- sb.append("<" + token.substring(3));
- }
- else if (token.startsWith("gt;"))
- {
- sb.append(">" + token.substring(3));
- }
- else if (token.startsWith("amp;"))
- {
- sb.append("&" + token.substring(4));
- }
- else
- {
- sb.append(token);
- }
- }
-
- if (removeHTML)
- {
- sf.description = sb.toString();
- }
-
- }
-
- /**
- * generate a features file for seqs includes non-pos features by default.
- *
- * @param seqs
- * source of sequence features
- * @param visible
- * hash of feature types and colours
- * @return features file contents
- */
- public String printJalviewFormat(SequenceI[] seqs, Hashtable visible)
- {
- return printJalviewFormat(seqs, visible, true, true);
- }
-
- /**
- * generate a features file for seqs with colours from visible (if any)
- *
- * @param seqs
- * source of features
- * @param visible
- * hash of Colours for each feature type
- * @param visOnly
- * when true only feature types in 'visible' will be output
- * @param nonpos
- * indicates if non-positional features should be output (regardless
- * of group or type)
- * @return features file contents
- */
- public String printJalviewFormat(SequenceI[] seqs, Hashtable visible,
- boolean visOnly, boolean nonpos)
- {
- StringBuffer out = new StringBuffer();
- SequenceFeature[] next;
- boolean featuresGen = false;
- if (visOnly && !nonpos && (visible == null || visible.size() < 1))
- {
- // no point continuing.
- return "No Features Visible";
- }
-
- if (visible != null && visOnly)
- {
- // write feature colours only if we're given them and we are generating
- // viewed features
- // TODO: decide if feature links should also be written here ?
- Enumeration en = visible.keys();
- String type, color;
- while (en.hasMoreElements())
- {
- type = en.nextElement().toString();
-
- if (visible.get(type) instanceof GraduatedColor)
- {
- GraduatedColor gc = (GraduatedColor) visible.get(type);
- color = (gc.isColourByLabel() ? "label|" : "")
- + Format.getHexString(gc.getMinColor()) + "|"
- + Format.getHexString(gc.getMaxColor())
- + (gc.isAutoScale() ? "|" : "|abso|") + gc.getMin() + "|"
- + gc.getMax() + "|";
- if (gc.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
- {
- if (gc.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD)
- {
- color += "below";
- }
- else
- {
- if (gc.getThreshType() != AnnotationColourGradient.ABOVE_THRESHOLD)
- {
- System.err.println("WARNING: Unsupported threshold type ("
- + gc.getThreshType() + ") : Assuming 'above'");
- }
- color += "above";
- }
- // add the value
- color += "|" + gc.getThresh();
- }
- else
- {
- color += "none";
- }
- }
- else if (visible.get(type) instanceof java.awt.Color)
- {
- color = Format.getHexString((java.awt.Color) visible.get(type));
- }
- else
- {
- // legacy support for integer objects containing colour triplet values
- color = Format.getHexString(new java.awt.Color(Integer
- .parseInt(visible.get(type).toString())));
- }
- out.append(type + "\t" + color + "\n");
- }
- }
- // Work out which groups are both present and visible
- Vector groups = new Vector();
- int groupIndex = 0;
- boolean isnonpos = false;
-
- for (int i = 0; i < seqs.length; i++)
- {
- next = seqs[i].getSequenceFeatures();
- if (next != null)
- {
- for (int j = 0; j < next.length; j++)
- {
- isnonpos = next[j].begin == 0 && next[j].end == 0;
- if ((!nonpos && isnonpos)
- || (!isnonpos && visOnly && !visible
- .containsKey(next[j].type)))
- {
- continue;
- }
-
- if (next[j].featureGroup != null
- && !groups.contains(next[j].featureGroup))
- {
- groups.addElement(next[j].featureGroup);
- }
- }
- }
- }
-
- String group = null;
- do
- {
-
- if (groups.size() > 0 && groupIndex < groups.size())
- {
- group = groups.elementAt(groupIndex).toString();
- out.append("\nSTARTGROUP\t" + group + "\n");
- }
- else
- {
- group = null;
- }
-
- for (int i = 0; i < seqs.length; i++)
- {
- next = seqs[i].getSequenceFeatures();
- if (next != null)
- {
- for (int j = 0; j < next.length; j++)
- {
- isnonpos = next[j].begin == 0 && next[j].end == 0;
- if ((!nonpos && isnonpos)
- || (!isnonpos && visOnly && !visible
- .containsKey(next[j].type)))
- {
- // skip if feature is nonpos and we ignore them or if we only
- // output visible and it isn't non-pos and it's not visible
- continue;
- }
-
- if (group != null
- && (next[j].featureGroup == null || !next[j].featureGroup
- .equals(group)))
- {
- continue;
- }
-
- if (group == null && next[j].featureGroup != null)
- {
- continue;
- }
- // we have features to output
- featuresGen = true;
- if (next[j].description == null
- || next[j].description.equals(""))
- {
- out.append(next[j].type + "\t");
- }
- else
- {
- if (next[j].links != null
- && next[j].getDescription().indexOf("") == -1)
- {
- out.append("");
- }
-
- out.append(next[j].description + " ");
- if (next[j].links != null)
- {
- for (int l = 0; l < next[j].links.size(); l++)
- {
- String label = next[j].links.elementAt(l).toString();
- String href = label.substring(label.indexOf("|") + 1);
- label = label.substring(0, label.indexOf("|"));
-
- if (next[j].description.indexOf(href) == -1)
- {
- out.append("" + label + "");
- }
- }
-
- if (next[j].getDescription().indexOf("") == -1)
- {
- out.append("");
- }
- }
-
- out.append("\t");
- }
- out.append(seqs[i].getName()
- + "\t-1\t"
- + next[j].begin
- + "\t"
- + next[j].end
- + "\t"
- + next[j].type
- + ((next[j].score != Float.NaN) ? "\t" + next[j].score
- + "\n" : "\n"));
- }
- }
- }
-
- if (group != null)
- {
- out.append("ENDGROUP\t" + group + "\n");
- groupIndex++;
- }
- else
- {
- break;
- }
-
- } while (groupIndex < groups.size() + 1);
-
- if (!featuresGen)
- {
- return "No Features Visible";
- }
-
- return out.toString();
- }
-
- /**
- * generate a gff file for sequence features includes non-pos features by
- * default.
- *
- * @param seqs
- * @param visible
- * @return
- */
- public String printGFFFormat(SequenceI[] seqs, Hashtable visible)
- {
- return printGFFFormat(seqs, visible, true, true);
- }
-
- public String printGFFFormat(SequenceI[] seqs, Hashtable visible,
- boolean visOnly, boolean nonpos)
- {
- StringBuffer out = new StringBuffer();
- SequenceFeature[] next;
- String source;
- boolean isnonpos;
- for (int i = 0; i < seqs.length; i++)
- {
- if (seqs[i].getSequenceFeatures() != null)
- {
- next = seqs[i].getSequenceFeatures();
- for (int j = 0; j < next.length; j++)
- {
- isnonpos = next[j].begin == 0 && next[j].end == 0;
- if ((!nonpos && isnonpos)
- || (!isnonpos && visOnly && !visible
- .containsKey(next[j].type)))
- {
- continue;
- }
-
- source = next[j].featureGroup;
- if (source == null)
- {
- source = next[j].getDescription();
- }
-
- out.append(seqs[i].getName() + "\t" + source + "\t"
- + next[j].type + "\t" + next[j].begin + "\t"
- + next[j].end + "\t" + next[j].score + "\t");
-
- if (next[j].getValue("STRAND") != null)
- {
- out.append(next[j].getValue("STRAND") + "\t");
- }
- else
- {
- out.append(".\t");
- }
-
- if (next[j].getValue("FRAME") != null)
- {
- out.append(next[j].getValue("FRAME"));
- }
- else
- {
- out.append(".");
- }
-
- if (next[j].getValue("ATTRIBUTES") != null)
- {
- out.append(next[j].getValue("ATTRIBUTES"));
- }
-
- out.append("\n");
-
- }
- }
- }
-
- return out.toString();
- }
-
- /**
- * this is only for the benefit of object polymorphism - method does nothing.
- */
- public void parse()
- {
- // IGNORED
- }
-
- /**
- * this is only for the benefit of object polymorphism - method does nothing.
- *
- * @return error message
- */
- public String print()
- {
- return "USE printGFFFormat() or printJalviewFormat()";
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import java.io.*;
+import java.util.*;
+
+import jalview.analysis.SequenceIdMatcher;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import jalview.util.Format;
+
+/**
+ * Parse and create Jalview Features files Detects GFF format features files and
+ * parses. Does not implement standard print() - call specific printFeatures or
+ * printGFF. Uses AlignmentI.findSequence(String id) to find the sequence object
+ * for the features annotation - this normally works on an exact match.
+ *
+ * @author AMW
+ * @version $Revision$
+ */
+public class FeaturesFile extends AlignFile
+{
+ /**
+ * work around for GFF interpretation bug where source string becomes
+ * description rather than a group
+ */
+ private boolean doGffSource = true;
+
+ /**
+ * Creates a new FeaturesFile object.
+ */
+ public FeaturesFile()
+ {
+ }
+
+ /**
+ * Creates a new FeaturesFile object.
+ *
+ * @param inFile
+ * DOCUMENT ME!
+ * @param type
+ * DOCUMENT ME!
+ *
+ * @throws IOException
+ * DOCUMENT ME!
+ */
+ public FeaturesFile(String inFile, String type) throws IOException
+ {
+ super(inFile, type);
+ }
+
+ public FeaturesFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ /**
+ * 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, Hashtable colours,
+ boolean removeHTML)
+ {
+ return parse(align, colours, null, removeHTML, false);
+ }
+
+ /**
+ * Parse GFF or sequence features file optionally 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
+ * @param relaxedIdmatching
+ * - when true, ID matches to compound sequence IDs are allowed
+ * @return true if features were added
+ */
+ public boolean parse(AlignmentI align, Map colours, boolean removeHTML,
+ boolean relaxedIdMatching)
+ {
+ return parse(align, colours, null, removeHTML, relaxedIdMatching);
+ }
+
+ /**
+ * Parse GFF or sequence features file optionally using case-independent
+ * matching
+ *
+ * @param align
+ * - alignment/dataset containing sequences that are to be annotated
+ * @param colours
+ * - hashtable to store feature colour definitions
+ * @param featureLink
+ * - hashtable to store associated URLs
+ * @param removeHTML
+ * - process html strings into plain text
+ * @return true if features were added
+ */
+ public boolean parse(AlignmentI align, Map colours, Map featureLink,
+ boolean removeHTML)
+ {
+ return parse(align, colours, featureLink, removeHTML, false);
+ }
+
+ /**
+ * Parse GFF or sequence features file
+ *
+ * @param align
+ * - alignment/dataset containing sequences that are to be annotated
+ * @param colours
+ * - hashtable to store feature colour definitions
+ * @param featureLink
+ * - hashtable to store associated URLs
+ * @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 colours, Map featureLink,
+ boolean removeHTML, boolean relaxedIdmatching)
+ {
+
+ String line = null;
+ try
+ {
+ SequenceI seq = null;
+ String type, desc, token = null;
+
+ int index, start, end;
+ float score;
+ StringTokenizer st;
+ SequenceFeature sf;
+ String featureGroup = null, groupLink = null;
+ Map typeLink = new Hashtable();
+ /**
+ * when true, assume GFF style features rather than Jalview style.
+ */
+ boolean GFFFile = true;
+ while ((line = nextLine()) != null)
+ {
+ if (line.startsWith("#"))
+ {
+ continue;
+ }
+
+ st = new StringTokenizer(line, "\t");
+ if (st.countTokens() == 1)
+ {
+ if (line.trim().equalsIgnoreCase("GFF"))
+ {
+ // Start parsing file as if it might be GFF again.
+ GFFFile = true;
+ continue;
+ }
+ }
+ if (st.countTokens() > 1 && st.countTokens() < 4)
+ {
+ GFFFile = false;
+ type = st.nextToken();
+ if (type.equalsIgnoreCase("startgroup"))
+ {
+ featureGroup = st.nextToken();
+ if (st.hasMoreElements())
+ {
+ groupLink = st.nextToken();
+ featureLink.put(featureGroup, groupLink);
+ }
+ }
+ else if (type.equalsIgnoreCase("endgroup"))
+ {
+ // We should check whether this is the current group,
+ // but at present theres no way of showing more than 1 group
+ st.nextToken();
+ featureGroup = null;
+ groupLink = null;
+ }
+ else
+ {
+ Object colour = null;
+ String colscheme = st.nextToken();
+ if (colscheme.indexOf("|") > -1
+ || colscheme.trim().equalsIgnoreCase("label"))
+ {
+ // Parse '|' separated graduated colourscheme fields:
+ // [label|][mincolour|maxcolour|[absolute|]minvalue|maxvalue|thresholdtype|thresholdvalue]
+ // can either provide 'label' only, first is optional, next two
+ // colors are required (but may be
+ // left blank), next is optional, nxt two min/max are required.
+ // first is either 'label'
+ // first/second and third are both hexadecimal or word equivalent
+ // colour.
+ // next two are values parsed as floats.
+ // fifth is either 'above','below', or 'none'.
+ // sixth is a float value and only required when fifth is either
+ // 'above' or 'below'.
+ StringTokenizer gcol = new StringTokenizer(colscheme, "|",
+ true);
+ // set defaults
+ int threshtype = AnnotationColourGradient.NO_THRESHOLD;
+ float min = Float.MIN_VALUE, max = Float.MAX_VALUE, threshval = Float.NaN;
+ boolean labelCol = false;
+ // Parse spec line
+ String mincol = gcol.nextToken();
+ if (mincol == "|")
+ {
+ System.err
+ .println("Expected either 'label' or a colour specification in the line: "
+ + line);
+ continue;
+ }
+ String maxcol = null;
+ if (mincol.toLowerCase().indexOf("label") == 0)
+ {
+ labelCol = true;
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); // skip
+ // '|'
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
+ }
+ String abso = null, minval, maxval;
+ if (mincol != null)
+ {
+ // at least four more tokens
+ if (mincol.equals("|"))
+ {
+ mincol = "";
+ }
+ else
+ {
+ gcol.nextToken(); // skip next '|'
+ }
+ // continue parsing rest of line
+ maxcol = gcol.nextToken();
+ if (maxcol.equals("|"))
+ {
+ maxcol = "";
+ }
+ else
+ {
+ gcol.nextToken(); // skip next '|'
+ }
+ abso = gcol.nextToken();
+ gcol.nextToken(); // skip next '|'
+ if (abso.toLowerCase().indexOf("abso") != 0)
+ {
+ minval = abso;
+ abso = null;
+ }
+ else
+ {
+ minval = gcol.nextToken();
+ gcol.nextToken(); // skip next '|'
+ }
+ maxval = gcol.nextToken();
+ if (gcol.hasMoreTokens())
+ {
+ gcol.nextToken(); // skip next '|'
+ }
+ try
+ {
+ if (minval.length() > 0)
+ {
+ min = new Float(minval).floatValue();
+ }
+ } catch (Exception e)
+ {
+ System.err
+ .println("Couldn't parse the minimum value for graduated colour for type ("
+ + colscheme
+ + ") - did you misspell 'auto' for the optional automatic colour switch ?");
+ e.printStackTrace();
+ }
+ try
+ {
+ if (maxval.length() > 0)
+ {
+ max = new Float(maxval).floatValue();
+ }
+ } catch (Exception e)
+ {
+ System.err
+ .println("Couldn't parse the maximum value for graduated colour for type ("
+ + colscheme + ")");
+ e.printStackTrace();
+ }
+ }
+ else
+ {
+ // add in some dummy min/max colours for the label-only
+ // colourscheme.
+ mincol = "FFFFFF";
+ maxcol = "000000";
+ }
+ try
+ {
+ colour = new jalview.schemes.GraduatedColor(
+ new UserColourScheme(mincol).findColour('A'),
+ new UserColourScheme(maxcol).findColour('A'), min,
+ max);
+ } catch (Exception e)
+ {
+ System.err
+ .println("Couldn't parse the graduated colour scheme ("
+ + colscheme + ")");
+ e.printStackTrace();
+ }
+ if (colour != null)
+ {
+ ((jalview.schemes.GraduatedColor) colour)
+ .setColourByLabel(labelCol);
+ ((jalview.schemes.GraduatedColor) colour)
+ .setAutoScaled(abso == null);
+ // add in any additional parameters
+ String ttype = null, tval = null;
+ if (gcol.hasMoreTokens())
+ {
+ // threshold type and possibly a threshold value
+ ttype = gcol.nextToken();
+ if (ttype.toLowerCase().startsWith("below"))
+ {
+ ((jalview.schemes.GraduatedColor) colour)
+ .setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);
+ }
+ else if (ttype.toLowerCase().startsWith("above"))
+ {
+ ((jalview.schemes.GraduatedColor) colour)
+ .setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);
+ }
+ else
+ {
+ ((jalview.schemes.GraduatedColor) colour)
+ .setThreshType(AnnotationColourGradient.NO_THRESHOLD);
+ if (!ttype.toLowerCase().startsWith("no"))
+ {
+ System.err
+ .println("Ignoring unrecognised threshold type : "
+ + ttype);
+ }
+ }
+ }
+ if (((GraduatedColor) colour).getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
+ {
+ try
+ {
+ gcol.nextToken();
+ tval = gcol.nextToken();
+ ((jalview.schemes.GraduatedColor) colour)
+ .setThresh(new Float(tval).floatValue());
+ } catch (Exception e)
+ {
+ System.err
+ .println("Couldn't parse threshold value as a float: ("
+ + tval + ")");
+ e.printStackTrace();
+ }
+ }
+ // parse the thresh-is-min token ?
+ if (gcol.hasMoreTokens())
+ {
+ System.err
+ .println("Ignoring additional tokens in parameters in graduated colour specification\n");
+ while (gcol.hasMoreTokens())
+ {
+ System.err.println("|" + gcol.nextToken());
+ }
+ System.err.println("\n");
+ }
+ }
+ }
+ else
+ {
+ UserColourScheme ucs = new UserColourScheme(colscheme);
+ colour = ucs.findColour('A');
+ }
+ if (colour != null)
+ {
+ colours.put(type, colour);
+ }
+ if (st.hasMoreElements())
+ {
+ String link = st.nextToken();
+ typeLink.put(type, link);
+ if (featureLink == null)
+ {
+ featureLink = new Hashtable();
+ }
+ featureLink.put(type, link);
+ }
+ }
+ continue;
+ }
+ String seqId = "";
+ while (st.hasMoreElements())
+ {
+
+ if (GFFFile)
+ {
+ // Still possible this is an old Jalview file,
+ // which does not have type colours at the beginning
+ seqId = token = st.nextToken();
+ seq = findName(align, seqId, relaxedIdmatching);
+ if (seq != null)
+ {
+ desc = st.nextToken();
+ String group = null;
+ if (doGffSource && desc.indexOf(' ') == -1)
+ {
+ // could also be a source term rather than description line
+ group = new String(desc);
+ }
+ type = st.nextToken();
+ try
+ {
+ String stt = st.nextToken();
+ if (stt.length() == 0 || stt.equals("-"))
+ {
+ start = 0;
+ }
+ else
+ {
+ start = Integer.parseInt(stt);
+ }
+ } catch (NumberFormatException ex)
+ {
+ start = 0;
+ }
+ try
+ {
+ String stt = st.nextToken();
+ if (stt.length() == 0 || stt.equals("-"))
+ {
+ end = 0;
+ }
+ else
+ {
+ end = Integer.parseInt(stt);
+ }
+ } catch (NumberFormatException ex)
+ {
+ end = 0;
+ }
+ // TODO: decide if non positional feature assertion for input data
+ // where end==0 is generally valid
+ if (end == 0)
+ {
+ // treat as non-positional feature, regardless.
+ start = 0;
+ }
+ try
+ {
+ score = new Float(st.nextToken()).floatValue();
+ } catch (NumberFormatException ex)
+ {
+ score = 0;
+ }
+
+ sf = new SequenceFeature(type, desc, start, end, score, group);
+
+ try
+ {
+ sf.setValue("STRAND", st.nextToken());
+ sf.setValue("FRAME", st.nextToken());
+ } catch (Exception ex)
+ {
+ }
+
+ if (st.hasMoreTokens())
+ {
+ StringBuffer attributes = new StringBuffer();
+ while (st.hasMoreTokens())
+ {
+ attributes.append("\t" + st.nextElement());
+ }
+ // TODO validate and split GFF2 attributes field ? parse out
+ // ([A-Za-z][A-Za-z0-9_]*) ; and add as
+ // sf.setValue(attrib, val);
+ sf.setValue("ATTRIBUTES", attributes.toString());
+ }
+
+ seq.addSequenceFeature(sf);
+ while ((seq = align.findName(seq, seqId, true)) != null)
+ {
+ seq.addSequenceFeature(new SequenceFeature(sf));
+ }
+ break;
+ }
+ }
+
+ if (GFFFile && seq == null)
+ {
+ desc = token;
+ }
+ else
+ {
+ desc = st.nextToken();
+ }
+ if (!st.hasMoreTokens())
+ {
+ System.err
+ .println("DEBUG: Run out of tokens when trying to identify the destination for the feature.. giving up.");
+ // in all probability, this isn't a file we understand, so bail
+ // quietly.
+ return false;
+ }
+
+ token = st.nextToken();
+
+ if (!token.equals("ID_NOT_SPECIFIED"))
+ {
+ seq = findName(align, seqId = token, relaxedIdmatching);
+ st.nextToken();
+ }
+ else
+ {
+ seqId = null;
+ try
+ {
+ index = Integer.parseInt(st.nextToken());
+ seq = align.getSequenceAt(index);
+ } catch (NumberFormatException ex)
+ {
+ seq = null;
+ }
+ }
+
+ if (seq == null)
+ {
+ System.out.println("Sequence not found: " + line);
+ break;
+ }
+
+ start = Integer.parseInt(st.nextToken());
+ end = Integer.parseInt(st.nextToken());
+
+ type = st.nextToken();
+
+ if (!colours.containsKey(type))
+ {
+ // Probably the old style groups file
+ UserColourScheme ucs = new UserColourScheme(type);
+ colours.put(type, ucs.findColour('A'));
+ }
+ sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
+ if (st.hasMoreTokens())
+ {
+ try
+ {
+ score = new Float(st.nextToken()).floatValue();
+ // update colourgradient bounds if allowed to
+ } catch (NumberFormatException ex)
+ {
+ score = 0;
+ }
+ sf.setScore(score);
+ }
+ if (groupLink != null && removeHTML)
+ {
+ sf.addLink(groupLink);
+ sf.description += "%LINK%";
+ }
+ if (typeLink.containsKey(type) && removeHTML)
+ {
+ sf.addLink(typeLink.get(type).toString());
+ sf.description += "%LINK%";
+ }
+
+ parseDescriptionHTML(sf, removeHTML);
+
+ seq.addSequenceFeature(sf);
+
+ while (seqId != null
+ && (seq = align.findName(seq, seqId, false)) != null)
+ {
+ seq.addSequenceFeature(new SequenceFeature(sf));
+ }
+ // If we got here, its not a GFFFile
+ GFFFile = false;
+ }
+ }
+ resetMatcher();
+ } catch (Exception ex)
+ {
+ System.out.println("Error parsing feature file: " + ex + "\n" + line);
+ ex.printStackTrace(System.err);
+ resetMatcher();
+ return false;
+ }
+
+ return true;
+ }
+
+ private AlignmentI lastmatchedAl = null;
+
+ private SequenceIdMatcher matcher = null;
+
+ /**
+ * clear any temporary handles used to speed up ID matching
+ */
+ private void resetMatcher()
+ {
+ lastmatchedAl = null;
+ matcher = null;
+ }
+
+ private SequenceI findName(AlignmentI align, String seqId,
+ boolean relaxedIdMatching)
+ {
+ SequenceI match = null;
+ if (relaxedIdMatching)
+ {
+ if (lastmatchedAl != align)
+ {
+ matcher = new SequenceIdMatcher(
+ (lastmatchedAl = align).getSequencesArray());
+ }
+ match = matcher.findIdMatch(seqId);
+ }
+ else
+ {
+ match = align.findName(seqId, true);
+ }
+ return match;
+ }
+
+ public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
+ {
+ if (sf.getDescription() == null)
+ {
+ return;
+ }
+ jalview.util.ParseHtmlBodyAndLinks parsed = new jalview.util.ParseHtmlBodyAndLinks(
+ sf.getDescription(), removeHTML, newline);
+
+ sf.description = (removeHTML) ? parsed.getNonHtmlContent()
+ : sf.description;
+ for (String link : parsed.getLinks())
+ {
+ sf.addLink(link);
+ }
+
+ }
+
+ /**
+ * generate a features file for seqs includes non-pos features by default.
+ *
+ * @param seqs
+ * source of sequence features
+ * @param visible
+ * hash of feature types and colours
+ * @return features file contents
+ */
+ public String printJalviewFormat(SequenceI[] seqs, Hashtable visible)
+ {
+ return printJalviewFormat(seqs, visible, true, true);
+ }
+
+ /**
+ * generate a features file for seqs with colours from visible (if any)
+ *
+ * @param seqs
+ * source of features
+ * @param visible
+ * hash of Colours for each feature type
+ * @param visOnly
+ * when true only feature types in 'visible' will be output
+ * @param nonpos
+ * indicates if non-positional features should be output (regardless
+ * of group or type)
+ * @return features file contents
+ */
+ public String printJalviewFormat(SequenceI[] seqs, Hashtable visible,
+ boolean visOnly, boolean nonpos)
+ {
+ StringBuffer out = new StringBuffer();
+ SequenceFeature[] next;
+ boolean featuresGen = false;
+ if (visOnly && !nonpos && (visible == null || visible.size() < 1))
+ {
+ // no point continuing.
+ return "No Features Visible";
+ }
+
+ if (visible != null && visOnly)
+ {
+ // write feature colours only if we're given them and we are generating
+ // viewed features
+ // TODO: decide if feature links should also be written here ?
+ Enumeration en = visible.keys();
+ String type, color;
+ while (en.hasMoreElements())
+ {
+ type = en.nextElement().toString();
+
+ if (visible.get(type) instanceof GraduatedColor)
+ {
+ GraduatedColor gc = (GraduatedColor) visible.get(type);
+ color = (gc.isColourByLabel() ? "label|" : "")
+ + Format.getHexString(gc.getMinColor()) + "|"
+ + Format.getHexString(gc.getMaxColor())
+ + (gc.isAutoScale() ? "|" : "|abso|") + gc.getMin() + "|"
+ + gc.getMax() + "|";
+ if (gc.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
+ {
+ if (gc.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD)
+ {
+ color += "below";
+ }
+ else
+ {
+ if (gc.getThreshType() != AnnotationColourGradient.ABOVE_THRESHOLD)
+ {
+ System.err.println("WARNING: Unsupported threshold type ("
+ + gc.getThreshType() + ") : Assuming 'above'");
+ }
+ color += "above";
+ }
+ // add the value
+ color += "|" + gc.getThresh();
+ }
+ else
+ {
+ color += "none";
+ }
+ }
+ else if (visible.get(type) instanceof java.awt.Color)
+ {
+ color = Format.getHexString((java.awt.Color) visible.get(type));
+ }
+ else
+ {
+ // legacy support for integer objects containing colour triplet values
+ color = Format.getHexString(new java.awt.Color(Integer
+ .parseInt(visible.get(type).toString())));
+ }
+ out.append(type);
+ out.append("\t");
+ out.append(color);
+ out.append(newline);
+ }
+ }
+ // Work out which groups are both present and visible
+ Vector groups = new Vector();
+ int groupIndex = 0;
+ boolean isnonpos = false;
+
+ for (int i = 0; i < seqs.length; i++)
+ {
+ next = seqs[i].getSequenceFeatures();
+ if (next != null)
+ {
+ for (int j = 0; j < next.length; j++)
+ {
+ isnonpos = next[j].begin == 0 && next[j].end == 0;
+ if ((!nonpos && isnonpos)
+ || (!isnonpos && visOnly && !visible
+ .containsKey(next[j].type)))
+ {
+ continue;
+ }
+
+ if (next[j].featureGroup != null
+ && !groups.contains(next[j].featureGroup))
+ {
+ groups.addElement(next[j].featureGroup);
+ }
+ }
+ }
+ }
+
+ String group = null;
+ do
+ {
+
+ if (groups.size() > 0 && groupIndex < groups.size())
+ {
+ group = groups.elementAt(groupIndex).toString();
+ out.append(newline);
+ out.append("STARTGROUP\t");
+ out.append(group);
+ out.append(newline);
+ }
+ else
+ {
+ group = null;
+ }
+
+ for (int i = 0; i < seqs.length; i++)
+ {
+ next = seqs[i].getSequenceFeatures();
+ if (next != null)
+ {
+ for (int j = 0; j < next.length; j++)
+ {
+ isnonpos = next[j].begin == 0 && next[j].end == 0;
+ if ((!nonpos && isnonpos)
+ || (!isnonpos && visOnly && !visible
+ .containsKey(next[j].type)))
+ {
+ // skip if feature is nonpos and we ignore them or if we only
+ // output visible and it isn't non-pos and it's not visible
+ continue;
+ }
+
+ if (group != null
+ && (next[j].featureGroup == null || !next[j].featureGroup
+ .equals(group)))
+ {
+ continue;
+ }
+
+ if (group == null && next[j].featureGroup != null)
+ {
+ continue;
+ }
+ // we have features to output
+ featuresGen = true;
+ if (next[j].description == null
+ || next[j].description.equals(""))
+ {
+ out.append(next[j].type + "\t");
+ }
+ else
+ {
+ if (next[j].links != null
+ && next[j].getDescription().indexOf("") == -1)
+ {
+ out.append("");
+ }
+
+ out.append(next[j].description + " ");
+ if (next[j].links != null)
+ {
+ for (int l = 0; l < next[j].links.size(); l++)
+ {
+ String label = next[j].links.elementAt(l).toString();
+ String href = label.substring(label.indexOf("|") + 1);
+ label = label.substring(0, label.indexOf("|"));
+
+ if (next[j].description.indexOf(href) == -1)
+ {
+ out.append("" + label + "");
+ }
+ }
+
+ if (next[j].getDescription().indexOf("") == -1)
+ {
+ out.append("");
+ }
+ }
+
+ out.append("\t");
+ }
+ out.append(seqs[i].getName());
+ out.append("\t-1\t");
+ out.append(next[j].begin);
+ out.append("\t");
+ out.append(next[j].end);
+ out.append("\t");
+ out.append(next[j].type);
+ if (next[j].score != Float.NaN)
+ {
+ out.append("\t");
+ out.append(next[j].score);
+ }
+ out.append(newline);
+ }
+ }
+ }
+
+ if (group != null)
+ {
+ out.append("ENDGROUP\t");
+ out.append(group);
+ out.append(newline);
+ groupIndex++;
+ }
+ else
+ {
+ break;
+ }
+
+ } while (groupIndex < groups.size() + 1);
+
+ if (!featuresGen)
+ {
+ return "No Features Visible";
+ }
+
+ return out.toString();
+ }
+
+ /**
+ * generate a gff file for sequence features includes non-pos features by
+ * default.
+ *
+ * @param seqs
+ * @param visible
+ * @return
+ */
+ public String printGFFFormat(SequenceI[] seqs, Hashtable visible)
+ {
+ return printGFFFormat(seqs, visible, true, true);
+ }
+
+ public String printGFFFormat(SequenceI[] seqs, Hashtable visible,
+ boolean visOnly, boolean nonpos)
+ {
+ StringBuffer out = new StringBuffer();
+ SequenceFeature[] next;
+ String source;
+ boolean isnonpos;
+ for (int i = 0; i < seqs.length; i++)
+ {
+ if (seqs[i].getSequenceFeatures() != null)
+ {
+ next = seqs[i].getSequenceFeatures();
+ for (int j = 0; j < next.length; j++)
+ {
+ isnonpos = next[j].begin == 0 && next[j].end == 0;
+ if ((!nonpos && isnonpos)
+ || (!isnonpos && visOnly && !visible
+ .containsKey(next[j].type)))
+ {
+ continue;
+ }
+
+ source = next[j].featureGroup;
+ if (source == null)
+ {
+ source = next[j].getDescription();
+ }
+
+ out.append(seqs[i].getName());
+ out.append("\t");
+ out.append(source);
+ out.append("\t");
+ out.append(next[j].type);
+ out.append("\t");
+ out.append(next[j].begin);
+ out.append("\t");
+ out.append(next[j].end);
+ out.append("\t");
+ out.append(next[j].score);
+ out.append("\t");
+
+ if (next[j].getValue("STRAND") != null)
+ {
+ out.append(next[j].getValue("STRAND"));
+ out.append("\t");
+ }
+ else
+ {
+ out.append(".\t");
+ }
+
+ if (next[j].getValue("FRAME") != null)
+ {
+ out.append(next[j].getValue("FRAME"));
+ }
+ else
+ {
+ out.append(".");
+ }
+ // TODO: verify/check GFF - should there be a /t here before attribute
+ // output ?
+
+ if (next[j].getValue("ATTRIBUTES") != null)
+ {
+ out.append(next[j].getValue("ATTRIBUTES"));
+ }
+
+ out.append(newline);
+
+ }
+ }
+ }
+
+ return out.toString();
+ }
+
+ /**
+ * this is only for the benefit of object polymorphism - method does nothing.
+ */
+ public void parse()
+ {
+ // IGNORED
+ }
+
+ /**
+ * this is only for the benefit of object polymorphism - method does nothing.
+ *
+ * @return error message
+ */
+ public String print()
+ {
+ return "USE printGFFFormat() or printJalviewFormat()";
+ }
+
+}