-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.io;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import java.io.*;\r
-import java.util.*;\r
-import jalview.schemes.UserColourScheme;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class FeaturesFile extends AlignFile\r
-{\r
- /**\r
- * Creates a new FeaturesFile object.\r
- */\r
- public FeaturesFile()\r
- {\r
- }\r
-\r
-\r
- /**\r
- * Creates a new FeaturesFile object.\r
- *\r
- * @param inFile DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- *\r
- * @throws IOException DOCUMENT ME!\r
- */\r
- public FeaturesFile(String inFile, String type)\r
- throws IOException\r
- {\r
- super(inFile, type);\r
- }\r
-\r
- /**\r
- * The Application can render HTML, but the applet will\r
- * remove HTML tags and replace links with %LINK%\r
- * Both need to read links in HTML however\r
- *\r
- * @throws IOException DOCUMENT ME!\r
- */\r
- public boolean parse(AlignmentI align,\r
- Hashtable colours,\r
- boolean removeHTML)\r
- {\r
- return parse(align, colours, null, removeHTML);\r
- }\r
- /**\r
- * The Application can render HTML, but the applet will\r
- * remove HTML tags and replace links with %LINK%\r
- * Both need to read links in HTML however\r
- *\r
- * @throws IOException DOCUMENT ME!\r
- */\r
- public boolean parse(AlignmentI align,\r
- Hashtable colours,\r
- Hashtable featureLink,\r
- 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
- boolean GFFFile = true;\r
-\r
- while ( (line = nextLine()) != null)\r
- {\r
- if(line.startsWith("#"))\r
- continue;\r
-\r
- st = new StringTokenizer(line, "\t");\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
- UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
- colours.put(type, ucs.findColour("A"));\r
- if (st.hasMoreElements())\r
- {\r
- String link = st.nextToken();\r
- typeLink.put(type, link);\r
- if(featureLink==null)\r
- featureLink = new Hashtable();\r
- featureLink.put(type, link);\r
- }\r
-\r
- }\r
- continue;\r
- }\r
-\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
- token = st.nextToken();\r
- seq = align.findName(token);\r
- if(seq != null)\r
- {\r
- desc = st.nextToken();\r
- type = st.nextToken();\r
- start = Integer.parseInt(st.nextToken());\r
- end = Integer.parseInt(st.nextToken());\r
- try\r
- {\r
- score = new Float(st.nextToken()).floatValue();\r
- }\r
- catch (NumberFormatException ex)\r
- {\r
- score = 0;\r
- }\r
-\r
- sf = new SequenceFeature(type, desc, start, end, score, null);\r
-\r
- try\r
- {\r
- sf.setValue("STRAND", st.nextToken());\r
- sf.setValue("FRAME", st.nextToken());\r
- }\r
- catch (Exception ex)\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
- sf.setValue("ATTRIBUTES", attributes.toString());\r
- }\r
-\r
- seq.addSequenceFeature(sf);\r
-\r
- break;\r
- }\r
- }\r
-\r
- if(GFFFile && seq==null)\r
- {\r
- desc = token;\r
- }\r
- else\r
- desc = st.nextToken();\r
-\r
-\r
- token = st.nextToken();\r
- if (!token.equals("ID_NOT_SPECIFIED"))\r
- {\r
- seq = align.findName(token);\r
- st.nextToken();\r
- }\r
- else\r
- {\r
- try{\r
- index = Integer.parseInt(st.nextToken());\r
- seq = align.getSequenceAt(index);\r
- }\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
-\r
- sf = new SequenceFeature(type, desc, "", start, end, featureGroup);\r
-\r
- seq.addSequenceFeature(sf);\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
- //If we got here, its not a GFFFile\r
- GFFFile = false;\r
- }\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- System.out.println(line);\r
- ex.printStackTrace();\r
- System.out.println("Error parsing feature file: " + ex +"\n"+line);\r
- return false;\r
- }\r
-\r
- return true;\r
- }\r
-\r
- void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)\r
- {\r
- StringBuffer sb = new StringBuffer();\r
- StringTokenizer st = new StringTokenizer(sf.getDescription(), "<");\r
- String token, link;\r
- while(st.hasMoreElements())\r
- {\r
- token = st.nextToken("<>");\r
- if(token.equalsIgnoreCase("html") || token.startsWith("/"))\r
- continue;\r
-\r
- if(token.startsWith("a href="))\r
- {\r
- link = token.substring(token.indexOf("\"")+1, token.length()-1);\r
- String label = st.nextToken("<>");\r
- sf.addLink(label+"|"+link);\r
- sb.append(label+"%LINK%");\r
- }\r
- else if(token.equalsIgnoreCase("br"))\r
- sb.append("\n");\r
- else\r
- sb.append(token);\r
- }\r
-\r
- if(removeHTML)\r
- sf.description = sb.toString();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s DOCUMENT ME!\r
- * @param len DOCUMENT ME!\r
- * @param gaps DOCUMENT ME!\r
- * @param displayId DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String printJalviewFormat(SequenceI [] seqs,\r
- Hashtable visible)\r
- {\r
- StringBuffer out = new StringBuffer();\r
- SequenceFeature [] next;\r
-\r
- if(visible==null || visible.size()<1)\r
- return "No Features Visible";\r
-\r
- Enumeration en = visible.keys();\r
- String type;\r
- int color;\r
- while( en.hasMoreElements() )\r
- {\r
- type = en.nextElement().toString();\r
- color = Integer.parseInt( visible.get(type).toString() );\r
- out.append(type + "\t"\r
- + jalview.util.Format.getHexString(\r
- new java.awt.Color(color) )\r
- +"\n");\r
- }\r
-\r
- //Work out which groups are both present and visible\r
- Vector groups = new Vector();\r
- int groupIndex = 0;\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
- if (!visible.containsKey(next[j].type))\r
- continue;\r
-\r
- if ( next[j].featureGroup != null\r
- && !groups.contains(next[j].featureGroup))\r
- groups.addElement(next[j].featureGroup);\r
- }\r
- }\r
- }\r
-\r
- String group = null;\r
-\r
- do\r
- {\r
-\r
-\r
- if (groups.size() > 0 && groupIndex < groups.size())\r
- {\r
- group = groups.elementAt(groupIndex).toString();\r
- out.append("\nSTARTGROUP\t" + group + "\n");\r
- }\r
- else\r
- group = null;\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
- if (!visible.containsKey(next[j].type))\r
- continue;\r
-\r
- if (group != null\r
- && (next[j].featureGroup==null\r
- || !next[j].featureGroup.equals(group))\r
- )\r
- continue;\r
-\r
- if(group==null && next[j].featureGroup!=null)\r
- continue;\r
-\r
- if(next[j].description==null || next[j].description.equals(""))\r
- out.append(next[j].type+"\t");\r
- else\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=\""\r
- + href\r
- + "\">"\r
- + label\r
- + "</a>");\r
- }\r
- }\r
- }\r
- out.append("\t");\r
- }\r
-\r
-\r
- out.append( seqs[i].getName() + "\t-1\t"\r
- + next[j].begin + "\t"\r
- + next[j].end + "\t"\r
- + next[j].type + "\n"\r
- );\r
- }\r
- }\r
- }\r
-\r
- if(group!=null)\r
- {\r
- out.append("ENDGROUP\t"+group+"\n");\r
- groupIndex++;\r
- }\r
- else\r
- break;\r
-\r
- }\r
- while(groupIndex < groups.size()+1);\r
-\r
-\r
- return out.toString();\r
- }\r
-\r
- public String printGFFFormat(SequenceI [] seqs, Hashtable visible)\r
- {\r
- StringBuffer out = new StringBuffer();\r
- SequenceFeature [] next;\r
- String source;\r
-\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
- if(!visible.containsKey(next[j].type))\r
- continue;\r
-\r
- source = next[j].featureGroup;\r
- if(source==null)\r
- source = next[j].getDescription();\r
-\r
- out.append(seqs[i].getName() + "\t"\r
- + source + "\t"\r
- + next[j].type + "\t"\r
- + next[j].begin + "\t"\r
- + next[j].end + "\t"\r
- + next[j].score + "\t"\r
- );\r
-\r
- if(next[j].getValue("STRAND")!=null)\r
- out.append(next[j].getValue("STRAND")+"\t");\r
- else\r
- out.append(".\t");\r
-\r
- if(next[j].getValue("FRAME")!=null)\r
- out.append(next[j].getValue("FRAME"));\r
- else\r
- out.append(".");\r
-\r
- if(next[j].getValue("ATTRIBUTES")!=null)\r
- out.append(next[j].getValue("ATTRIBUTES"));\r
-\r
- out.append("\n");\r
-\r
- }\r
- }\r
- }\r
-\r
- return out.toString();\r
- }\r
-\r
- public void parse()\r
- {\r
- //IGNORED\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\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 jalview.analysis.AlignmentUtils;
+import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignViewportI;
+import jalview.api.FeatureColourI;
+import jalview.api.FeaturesSourceI;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceDummy;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.gff.GffHelperBase;
+import jalview.io.gff.GffHelperFactory;
+import jalview.io.gff.GffHelperI;
+import jalview.schemes.FeatureColour;
+import jalview.schemes.UserColourScheme;
+import jalview.util.MapList;
+import jalview.util.ParseHtmlBodyAndLinks;
+import jalview.util.StringUtils;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+
+/**
+ * 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 ID_NOT_SPECIFIED = "ID_NOT_SPECIFIED";
+
+ private static final String NOTE = "Note";
+
+ protected static final String TAB = "\t";
+
+ 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 inFile
+ * @param type
+ * @throws IOException
+ */
+ public FeaturesFile(String inFile, String type) throws IOException
+ {
+ super(false, inFile, type);
+ }
+
+ /**
+ * @param source
+ * @throws IOException
+ */
+ public FeaturesFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ /**
+ * Constructor that optionally parses the file immediately
+ *
+ * @param parseImmediately
+ * @param inFile
+ * @param type
+ * @throws IOException
+ */
+ public FeaturesFile(boolean parseImmediately, String inFile, String type)
+ throws IOException
+ {
+ super(parseImmediately, inFile, 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
+ * - 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<String, FeatureColourI> colours, boolean removeHTML,
+ boolean relaxedIdmatching)
+ {
+ Map<String, String> gffProps = new HashMap<String, String>();
+ /*
+ * keep track of any sequences we try to create from the data
+ */
+ List<SequenceI> newseqs = new ArrayList<SequenceI>();
+
+ 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().startsWith("##"))
+ {
+ processGffPragma(line, gffProps, align, newseqs);
+ }
+ continue;
+ }
+
+ gffColumns = line.split("\\t"); // tab as 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 > 1 && 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("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.getSequenceFeatures() != null)
+ {
+ align.addSequence(newseq);
+ }
+ }
+ return true;
+ }
+
+ /**
+ * 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
+ */
+ UserColourScheme ucs = new UserColourScheme(ft);
+ featureColours.put(ft, new FeatureColour(ucs.findColour('A')));
+ }
+ SequenceFeature sf = new SequenceFeature(ft, desc, "", startPos,
+ endPos, featureGroup);
+ if (gffColumns.length > 6)
+ {
+ float score = Float.NaN;
+ try
+ {
+ score = new Float(gffColumns[6]).floatValue();
+ // update colourgradient bounds if allowed to
+ } catch (NumberFormatException ex)
+ {
+ // leave as NaN
+ }
+ sf.setScore(score);
+ }
+
+ 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);
+
+ 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 sequences
+ * source of sequence features
+ * @param visible
+ * hash of feature types and colours
+ * @return features file contents
+ */
+ public String printJalviewFormat(SequenceI[] sequences,
+ Map<String, FeatureColourI> visible)
+ {
+ return printJalviewFormat(sequences, visible, true, true);
+ }
+
+ /**
+ * generate a features file for seqs with colours from visible (if any)
+ *
+ * @param sequences
+ * 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[] sequences,
+ Map<String, FeatureColourI> visible, boolean visOnly,
+ boolean nonpos)
+ {
+ StringBuilder out = new StringBuilder(256);
+ 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 ?
+ Iterator<String> en = visible.keySet().iterator();
+ while (en.hasNext())
+ {
+ String featureType = en.next().toString();
+ FeatureColourI colour = visible.get(featureType);
+ out.append(colour.toJalviewFormat(featureType)).append(newline);
+ }
+ }
+
+ // Work out which groups are both present and visible
+ List<String> groups = new ArrayList<String>();
+ int groupIndex = 0;
+ boolean isnonpos = false;
+
+ SequenceFeature[] features;
+ for (int i = 0; i < sequences.length; i++)
+ {
+ features = sequences[i].getSequenceFeatures();
+ if (features != null)
+ {
+ for (int j = 0; j < features.length; j++)
+ {
+ isnonpos = features[j].begin == 0 && features[j].end == 0;
+ if ((!nonpos && isnonpos)
+ || (!isnonpos && visOnly && !visible
+ .containsKey(features[j].type)))
+ {
+ continue;
+ }
+
+ if (features[j].featureGroup != null
+ && !groups.contains(features[j].featureGroup))
+ {
+ groups.add(features[j].featureGroup);
+ }
+ }
+ }
+ }
+
+ String group = null;
+ do
+ {
+ if (groups.size() > 0 && groupIndex < groups.size())
+ {
+ group = groups.get(groupIndex);
+ out.append(newline);
+ out.append("STARTGROUP").append(TAB);
+ out.append(group);
+ out.append(newline);
+ }
+ else
+ {
+ group = null;
+ }
+
+ for (int i = 0; i < sequences.length; i++)
+ {
+ features = sequences[i].getSequenceFeatures();
+ if (features != null)
+ {
+ for (SequenceFeature sequenceFeature : features)
+ {
+ isnonpos = sequenceFeature.begin == 0
+ && sequenceFeature.end == 0;
+ if ((!nonpos && isnonpos)
+ || (!isnonpos && visOnly && !visible
+ .containsKey(sequenceFeature.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
+ && (sequenceFeature.featureGroup == null || !sequenceFeature.featureGroup
+ .equals(group)))
+ {
+ continue;
+ }
+
+ if (group == null && sequenceFeature.featureGroup != null)
+ {
+ continue;
+ }
+ // we have features to output
+ featuresGen = true;
+ 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=\"" + href + "\">" + label
+ + "</a>");
+ }
+ }
+
+ if (sequenceFeature.getDescription().indexOf("</html>") == -1)
+ {
+ out.append("</html>");
+ }
+ }
+
+ out.append(TAB);
+ }
+ out.append(sequences[i].getName());
+ 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);
+ }
+ }
+ }
+
+ if (group != null)
+ {
+ out.append("ENDGROUP").append(TAB);
+ out.append(group);
+ out.append(newline);
+ groupIndex++;
+ }
+ else
+ {
+ break;
+ }
+
+ } while (groupIndex < groups.size() + 1);
+
+ if (!featuresGen)
+ {
+ return "No Features Visible";
+ }
+
+ return out.toString();
+ }
+
+ /**
+ * 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[] {});
+ }
+
+ boolean parseResult = parse(dataset, null, 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()
+ {
+ return "Use printGffFormat() or printJalviewFormat()";
+ }
+
+ /**
+ * Returns features output in GFF2 format, including hidden and non-positional
+ * features
+ *
+ * @param sequences
+ * the sequences whose features are to be output
+ * @param visible
+ * a map whose keys are the type names of visible features
+ * @return
+ */
+ public String printGffFormat(SequenceI[] sequences,
+ Map<String, FeatureColourI> visible)
+ {
+ return printGffFormat(sequences, visible, true, true);
+ }
+
+ /**
+ * 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 outputVisibleOnly
+ * @param includeNonPositionalFeatures
+ * @return
+ */
+ public String printGffFormat(SequenceI[] sequences,
+ Map<String, FeatureColourI> visible, boolean outputVisibleOnly,
+ boolean includeNonPositionalFeatures)
+ {
+ StringBuilder out = new StringBuilder(256);
+ int version = gffVersion == 0 ? 2 : gffVersion;
+ out.append(String.format("%s %d\n", GFF_VERSION, version));
+ String source;
+ boolean isnonpos;
+ for (SequenceI seq : sequences)
+ {
+ SequenceFeature[] features = seq.getSequenceFeatures();
+ if (features != null)
+ {
+ for (SequenceFeature sf : features)
+ {
+ isnonpos = sf.begin == 0 && sf.end == 0;
+ if (!includeNonPositionalFeatures && isnonpos)
+ {
+ /*
+ * ignore non-positional features if not wanted
+ */
+ continue;
+ }
+ // TODO why the test !isnonpos here?
+ // what about not visible non-positional features?
+ if (!isnonpos && outputVisibleOnly
+ && !visible.containsKey(sf.type))
+ {
+ /*
+ * ignore not visible features if not wanted
+ */
+ continue;
+ }
+
+ 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);
+
+ // miscellaneous key-values (GFF column 9)
+ String attributes = sf.getAttributes();
+ if (attributes != null)
+ {
+ out.append(TAB).append(attributes);
+ }
+
+ out.append(newline);
+ }
+ }
+ }
+
+ return out.toString();
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * Process the 'column 9' data of the GFF file. This is less formally defined,
+ * and its interpretation will vary depending on the tool that has generated
+ * it.
+ *
+ * @param attributes
+ * @param sf
+ */
+ protected void processGffColumnNine(String attributes, SequenceFeature sf)
+ {
+ sf.setAttributes(attributes);
+
+ /*
+ * Parse attributes in column 9 and add them to the sequence feature's
+ * 'otherData' table; use Note as a best proxy for description
+ */
+ char nameValueSeparator = gffVersion == 3 ? '=' : ' ';
+ // TODO check we don't break GFF2 values which include commas here
+ Map<String, List<String>> nameValues = GffHelperBase
+ .parseNameValuePairs(attributes, ";", nameValueSeparator, ",");
+ for (Entry<String, List<String>> attr : nameValues.entrySet())
+ {
+ String values = StringUtils.listToDelimitedString(attr.getValue(),
+ "; ");
+ sf.setValue(attr.getKey(), values);
+ if (NOTE.equals(attr.getKey()))
+ {
+ sf.setDescription(values);
+ }
+ }
+ }
+
+ /**
+ * 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) ?
+ SequenceFeature[] sfs = seq.getSequenceFeatures();
+ if (sfs != null)
+ {
+ String newName = (String) sfs[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