X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=04b1f87c16295621a96ef3c95d632f0552f35c65;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=0fcbc131214e4bcea9e1d8cda953a9bfd73d8454;hpb=b512e41cb378d9b7fb470db08bbb4d8ddbadce6f;p=jalview.git
diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 0fcbc13..04b1f87 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -1,408 +1,583 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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 .
*/
/*
- * This extension was written by bsb at sanger.ac.uk
+ * This extension was written by Benjamin Schuster-Boeckler at sanger.ac.uk
*/
package jalview.io;
+
import java.io.*;
import java.util.*;
-import jalview.datamodel.*;
+
import com.stevesoft.pat.*;
-//import org.apache.log4j.*;
+import jalview.datamodel.*;
+
+// import org.apache.log4j.*;
/**
- * This class is supposed to parse a Stockholm format file into Jalview
+ * This class is supposed to parse a Stockholm format file into Jalview There
+ * are TODOs in this class: we do not know what the database source and version
+ * is for the file when parsing the #GS= AC tag which associates accessions with
+ * sequences. Database references are also not parsed correctly: a separate
+ * reference string parser must be added to parse the database reference form
+ * into Jalview's local representation.
+ *
* @author bsb at sanger.ac.uk
- * @version 0.3
+ * @version 0.3 + jalview mods
+ *
*/
public class StockholmFile extends AlignFile
{
- //static Logger logger = Logger.getLogger("jalview.io.StockholmFile");
-
- public StockholmFile()
+ // static Logger logger = Logger.getLogger("jalview.io.StockholmFile");
+
+ public StockholmFile()
+ {
+ }
+
+ public StockholmFile(String inFile, String type) throws IOException
+ {
+ super(inFile, type);
+ }
+
+ public StockholmFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ public void initData()
+ {
+ super.initData();
+ }
+
+ /**
+ * Parse a file in Stockholm format into Jalview's data model. The file has to
+ * be passed at construction time
+ *
+ * @throws IOException
+ * If there is an error with the input file
+ */
+ public void parse() throws IOException
+ {
+ StringBuffer treeString = new StringBuffer();
+ String treeName = null;
+ // --------------- Variable Definitions -------------------
+ String line;
+ String version;
+ // String id;
+ Hashtable seqAnn = new Hashtable(); // Sequence related annotations
+ Hashtable seqs = new Hashtable();
+ Regex p, r, rend, s, x;
+
+ // ------------------ Parsing File ----------------------
+ // First, we have to check that this file has STOCKHOLM format, i.e. the
+ // first line must match
+ r = new Regex("# STOCKHOLM ([\\d\\.]+)");
+ if (!r.search(nextLine()))
{
+ throw new IOException(
+ "This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'");
}
-
-
- public StockholmFile(String inFile, String type) throws IOException
+ else
{
- super(inFile, type);
+ version = r.stringMatched(1);
+ // logger.debug("Stockholm version: " + version);
}
- public void initData()
+ // We define some Regexes here that will be used regularily later
+ rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment
+ p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in
+ // id/from/to
+ s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype
+ r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line
+ x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence
+
+ rend.optimize();
+ p.optimize();
+ s.optimize();
+ r.optimize();
+ x.optimize();
+
+ while ((line = nextLine()) != null)
{
- super.initData();
- }
+ if (line.length() == 0)
+ {
+ continue;
+ }
+ if (rend.search(line))
+ {
+ // End of the alignment, pass stuff back
+
+ this.noSeqs = seqs.size();
+ // logger.debug("Number of sequences: " + this.noSeqs);
+ Enumeration accs = seqs.keys();
+ while (accs.hasMoreElements())
+ {
+ String acc = (String) accs.nextElement();
+ // logger.debug("Processing sequence " + acc);
+ String seq = (String) seqs.remove(acc);
+ if (maxLength < seq.length())
+ {
+ maxLength = seq.length();
+ }
+ int start = 1;
+ int end = -1;
+ String sid = acc;
+ // Retrieve hash of annotations for this accession
+ Hashtable accAnnotations = null;
+
+ if (seqAnn != null && seqAnn.containsKey(acc))
+ {
+ accAnnotations = (Hashtable) seqAnn.remove(acc);
+ }
+
+ // Split accession in id and from/to
+ if (p.search(acc))
+ {
+ sid = p.stringMatched(1);
+ start = Integer.parseInt(p.stringMatched(2));
+ end = Integer.parseInt(p.stringMatched(3));
+ }
+ // logger.debug(sid + ", " + start + ", " + end);
+
+ Sequence seqO = new Sequence(sid, seq, start, end);
+ // Add Description (if any)
+ if (accAnnotations != null && accAnnotations.containsKey("DE"))
+ {
+ String desc = (String) accAnnotations.get("DE");
+ seqO.setDescription((desc == null) ? "" : desc);
+ }
+ // Add DB References (if any)
+ if (accAnnotations != null && accAnnotations.containsKey("DR"))
+ {
+ String dbr = (String) accAnnotations.get("DR");
+ if (dbr != null && dbr.indexOf(";") > -1)
+ {
+ String src = dbr.substring(0, dbr.indexOf(";"));
+ String acn = dbr.substring(dbr.indexOf(";") + 1);
+ jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);
+ // seqO.addDBRef(dbref);
+ }
+ }
+ Hashtable features = null;
+ // We need to adjust the positions of all features to account for gaps
+ try
+ {
+ features = (Hashtable) accAnnotations.remove("features");
+ } catch (java.lang.NullPointerException e)
+ {
+ // loggerwarn("Getting Features for " + acc + ": " +
+ // e.getMessage());
+ // continue;
+ }
+ // if we have features
+ if (features != null)
+ {
+ int posmap[] = seqO.findPositionMap();
+ Enumeration i = features.keys();
+ while (i.hasMoreElements())
+ {
+ // TODO: parse out secondary structure annotation as annotation
+ // row
+ // TODO: parse out scores as annotation row
+ // TODO: map coding region to core jalview feature types
+ String type = i.nextElement().toString();
+ Hashtable content = (Hashtable) features.remove(type);
+ Enumeration j = content.keys();
+ while (j.hasMoreElements())
+ {
+ String desc = j.nextElement().toString();
+ String ns = content.get(desc).toString();
+ char[] byChar = ns.toCharArray();
+ for (int k = 0; k < byChar.length; k++)
+ {
+ char c = byChar[k];
+ if (!(c == ' ' || c == '_' || c == '-' || c == '.')) // PFAM
+ // uses
+ // '.'
+ // for
+ // feature
+ // background
+ {
+ int new_pos = posmap[k]; // look up nearest seqeunce
+ // position to this column
+ SequenceFeature feat = new SequenceFeature(type, desc,
+ new_pos, new_pos, 0f, null);
+
+ seqO.addSequenceFeature(feat);
+ }
+ }
+ }
- /**
- * Parse a file in Stockholm format into Jalview's data model. The file has
- * to be passed at construction time
- * @throws IOException If there is an error with the input file
- */
- public void parse() throws IOException
- {
- // --------------- Variable Definitions -------------------
- String line;
- String version;
- // String id;
- Hashtable alAnn = new Hashtable(); // Alignment wide annotations
- Hashtable seqAnn = new Hashtable(); // Sequence related annotations
- Hashtable seqs = new Hashtable();
- Regex p, r, rend, s, x;
-
- // ------------------ Parsing File ----------------------
- // First, we have to check that this file has STOCKHOLM format, i.e. the first line must match
- r = new Regex("# STOCKHOLM ([\\d\\.]+)");
- if(!r.search(nextLine()))
+ }
+
+ }
+ // garbage collect
+
+ // logger.debug("Adding seq " + acc + " from " + start + " to " + end
+ // + ": " + seq);
+ this.seqs.addElement(seqO);
+ }
+ return; // finished parsing this segment of source
+ }
+ else if (!r.search(line))
+ {
+ // System.err.println("Found sequence line: " + line);
+
+ // Split sequence in sequence and accession parts
+ if (!x.search(line))
{
- throw new IOException("This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'");
+ // logger.error("Could not parse sequence line: " + line);
+ throw new IOException("Could not parse sequence line: " + line);
}
- else
+ String ns = (String) seqs.get(x.stringMatched(1));
+ if (ns == null)
{
- version = r.stringMatched(1);
- //logger.debug("Stockholm version: " + version);
+ ns = "";
}
+ ns += x.stringMatched(2);
-// We define some Regexes here that will be used regularily later
- rend = new Regex("\\/\\/"); // Find the end of an alignment
- p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in id/from/to
- s = new Regex("(\\S+)\\s+(\\w{2})\\s+(.*)"); // Parses annotation subtype
- r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line
- x = new Regex("(\\S+)\\s+(\\S+)"); //split id from sequence
+ seqs.put(x.stringMatched(1), ns);
+ }
+ else
+ {
+ String annType = r.stringMatched(1);
+ String annContent = r.stringMatched(2);
- rend.optimize();
- p.optimize();
- s.optimize();
- r.optimize();
- x.optimize();
+ // System.err.println("type:" + annType + " content: " + annContent);
- while ( (line = nextLine()) != null)
+ if (annType.equals("GF"))
{
- if (line.length() == 0) continue;
- if(rend.search(line))
+ /*
+ * Generic per-File annotation, free text Magic features: #=GF NH
+ * #=GF TN Pfam descriptions: 7. DESCRIPTION OF FIELDS
+ *
+ * Compulsory fields: ------------------
+ *
+ * AC Accession number: Accession number in form PFxxxxx.version or
+ * PBxxxxxx. ID Identification: One word name for family. DE
+ * Definition: Short description of family. AU Author: Authors of the
+ * entry. SE Source of seed: The source suggesting the seed members
+ * belong to one family. GA Gathering method: Search threshold to
+ * build the full alignment. TC Trusted Cutoff: Lowest sequence score
+ * and domain score of match in the full alignment. NC Noise Cutoff:
+ * Highest sequence score and domain score of match not in full
+ * alignment. TP Type: Type of family -- presently Family, Domain,
+ * Motif or Repeat. SQ Sequence: Number of sequences in alignment. AM
+ * Alignment Method The order ls and fs hits are aligned to the model
+ * to build the full align. // End of alignment.
+ *
+ * Optional fields: ----------------
+ *
+ * DC Database Comment: Comment about database reference. DR Database
+ * Reference: Reference to external database. RC Reference Comment:
+ * Comment about literature reference. RN Reference Number: Reference
+ * Number. RM Reference Medline: Eight digit medline UI number. RT
+ * Reference Title: Reference Title. RA Reference Author: Reference
+ * Author RL Reference Location: Journal location. PI Previous
+ * identifier: Record of all previous ID lines. KW Keywords: Keywords.
+ * CC Comment: Comments. NE Pfam accession: Indicates a nested domain.
+ * NL Location: Location of nested domains - sequence ID, start and
+ * end of insert.
+ *
+ * Obsolete fields: ----------- AL Alignment method of seed: The
+ * method used to align the seed members.
+ */
+ // Let's save the annotations, maybe we'll be able to do something
+ // with them later...
+ Regex an = new Regex("(\\w+)\\s*(.*)");
+ if (an.search(annContent))
+ {
+ if (an.stringMatched(1).equals("NH"))
{
-// End of the alignment, pass stuff back
-
- this.noSeqs = seqs.size();
- //logger.debug("Number of sequences: " + this.noSeqs);
- Enumeration accs = seqs.keys();
- while (accs.hasMoreElements())
- {
- String acc = (String) accs.nextElement();
- //logger.debug("Processing sequence " + acc);
- String seq = (String) seqs.get(acc);
- if (maxLength < seq.length())
- {
- maxLength = seq.length();
- }
- int start = 1;
- int end = -1;
- String sid = acc;
- // Split accession in id and from/to
- if (p.search(acc))
- {
- sid = p.stringMatched(1);
- start = Integer.parseInt(p.stringMatched(2));
- end = Integer.parseInt(p.stringMatched(3));
- }
- //logger.debug(sid + ", " + start + ", " + end);
-
- Sequence seqO = new Sequence(sid, seq, start, end);
- Hashtable features = null;
- // We need to adjust the positions of all features to account for gaps
- try
- {
- features = (Hashtable) ((Hashtable) seqAnn.get(acc)).get("features");
- }
- catch (java.lang.NullPointerException e)
- {
- //loggerwarn("Getting Features for " + acc + ": " + e.getMessage());
- //continue;
- }
- // if we have features
- if (features != null)
- {
- Enumeration i = features.keys();
- while(i.hasMoreElements())
- {
- String type = i.nextElement().toString();
- Hashtable content = (Hashtable) features.get(type);
-
- Enumeration j = content.keys();
- while(j.hasMoreElements())
- {
- String desc = j.nextElement().toString();
- String ns = content.get(desc).toString();
- char[] byChar = ns.toCharArray();
- for (int k = 0; k < byChar.length; k++)
- {
- char c = byChar[k];
- if (! (c == ' ' || c == '_' ||
- c == '-'))
- {
- int new_pos = seqO.findPosition(k);
- SequenceFeature feat =
- new SequenceFeature(type,
- desc, new_pos, new_pos, 0f, null);
-
- seqO.addSequenceFeature(feat);
- }
- }
- }
-
- }
-
- }
- //logger.debug("Adding seq " + acc + " from " + start + " to " + end + ": " + seq);
- this.seqs.addElement(seqO);
- }
+ treeString.append(an.stringMatched(2));
}
- else if (!r.search(line))
+ else if (an.stringMatched(1).equals("TN"))
{
- //System.err.println("Found sequence line: " + line);
-
- // Split sequence in sequence and accession parts
- if(!x.search(line))
+ if (treeString.length() > 0)
+ {
+ if (treeName == null)
{
- //logger.error("Could not parse sequence line: " + line);
- throw new IOException("Could not parse sequence line: " + line);
+ treeName = "Tree " + (getTreeCount() + 1);
}
- String ns = (String) seqs.get(x.stringMatched(1));
- if (ns == null) ns = "";
- ns += x.stringMatched(2);
+ addNewickTree(treeName, treeString.toString());
+ }
+ treeName = an.stringMatched(2);
+ treeString = new StringBuffer();
+ }
+ setAlignmentProperty(an.stringMatched(1), an.stringMatched(2));
+ }
+ }
+ else if (annType.equals("GS"))
+ {
+ // Generic per-Sequence annotation, free text
+ /*
+ * Pfam uses these features: Feature Description ---------------------
+ * ----------- AC ACcession number DE
+ * DEscription DR ; ; Database Reference OS
+ * OrganiSm (species) OC Organism Classification (clade, etc.)
+ * LO Look (Color, etc.)
+ */
+ if (s.search(annContent))
+ {
+ String acc = s.stringMatched(1);
+ String type = s.stringMatched(2);
+ String content = s.stringMatched(3);
+ // TODO: store DR in a vector.
+ // TODO: store AC according to generic file db annotation.
+ Hashtable ann;
+ if (seqAnn.containsKey(acc))
+ {
+ ann = (Hashtable) seqAnn.get(acc);
+ }
+ else
+ {
+ ann = new Hashtable();
+ }
+ ann.put(type, content);
+ seqAnn.put(acc, ann);
+ }
+ else
+ {
+ throw new IOException("Error parsing " + line);
+ }
+ }
+ else if (annType.equals("GC"))
+ {
+ // Generic per-Column annotation, exactly 1 char per column
+ // always need a label.
+ if (x.search(annContent))
+ {
+ // parse out and create alignment annotation directly.
+ parseAnnotationRow(annotations, x.stringMatched(1), x
+ .stringMatched(2));
+ }
+ }
+ else if (annType.equals("GR"))
+ {
+ // Generic per-Sequence AND per-Column markup, exactly 1 char per
+ // column
+ /*
+ * Feature Description Markup letters ------- -----------
+ * -------------- SS Secondary Structure [HGIEBTSCX] SA Surface
+ * Accessibility [0-9X] (0=0%-10%; ...; 9=90%-100%) TM TransMembrane
+ * [Mio] PP Posterior Probability [0-9*] (0=0.00-0.05; 1=0.05-0.15;
+ * *=0.95-1.00) LI LIgand binding [*] AS Active Site [*] IN INtron (in
+ * or after) [0-2]
+ */
+ if (s.search(annContent))
+ {
+ String acc = s.stringMatched(1);
+ String type = s.stringMatched(2);
+ String seq = new String(s.stringMatched(3));
+ String description = null;
+ // Check for additional information about the current annotation
+ // We use a simple string tokenizer here for speed
+ StringTokenizer sep = new StringTokenizer(seq, " \t");
+ description = sep.nextToken();
+ if (sep.hasMoreTokens())
+ {
+ seq = sep.nextToken();
+ }
+ else
+ {
+ seq = description;
+ description = new String();
+ }
+ // sequence id with from-to fields
- seqs.put(x.stringMatched(1), ns);
+ Hashtable ann;
+ // Get an object with all the annotations for this sequence
+ if (seqAnn.containsKey(acc))
+ {
+ // logger.debug("Found annotations for " + acc);
+ ann = (Hashtable) seqAnn.get(acc);
}
else
{
- String annType = r.stringMatched(1);
- String annContent = r.stringMatched(2);
+ // logger.debug("Creating new annotations holder for " + acc);
+ ann = new Hashtable();
+ seqAnn.put(acc, ann);
+ }
- //System.err.println("type:" + annType + " content: " + annContent);
+ Hashtable features;
+ // Get an object with all the content for an annotation
+ if (ann.containsKey("features"))
+ {
+ // logger.debug("Found features for " + acc);
+ features = (Hashtable) ann.get("features");
+ }
+ else
+ {
+ // logger.debug("Creating new features holder for " + acc);
+ features = new Hashtable();
+ ann.put("features", features);
+ }
- if (annType.equals("GF"))
- {
- /* Generic per-File annotation, free text
- * Magic features:
- * #=GF NH
- * #=GF TN
- * Pfam descriptions:
- 7. DESCRIPTION OF FIELDS
-
- Compulsory fields:
- ------------------
-
- AC Accession number: Accession number in form PFxxxxx.version or PBxxxxxx.
- ID Identification: One word name for family.
- DE Definition: Short description of family.
- AU Author: Authors of the entry.
- SE Source of seed: The source suggesting the seed members belong to one family.
- GA Gathering method: Search threshold to build the full alignment.
- TC Trusted Cutoff: Lowest sequence score and domain score of match in the full alignment.
- NC Noise Cutoff: Highest sequence score and domain score of match not in full alignment.
- TP Type: Type of family -- presently Family, Domain, Motif or Repeat.
- SQ Sequence: Number of sequences in alignment.
- AM Alignment Method The order ls and fs hits are aligned to the model to build the full align.
- // End of alignment.
-
- Optional fields:
- ----------------
-
- DC Database Comment: Comment about database reference.
- DR Database Reference: Reference to external database.
- RC Reference Comment: Comment about literature reference.
- RN Reference Number: Reference Number.
- RM Reference Medline: Eight digit medline UI number.
- RT Reference Title: Reference Title.
- RA Reference Author: Reference Author
- RL Reference Location: Journal location.
- PI Previous identifier: Record of all previous ID lines.
- KW Keywords: Keywords.
- CC Comment: Comments.
- NE Pfam accession: Indicates a nested domain.
- NL Location: Location of nested domains - sequence ID, start and end of insert.
-
- Obsolete fields:
- -----------
- AL Alignment method of seed: The method used to align the seed members.
- */
- // Let's save the annotations, maybe we'll be able to do something with them later...
- Regex an = new Regex("(\\w+)\\s*(.*)");
- if (an.search(annContent)) alAnn.put(an.stringMatched(1), an.stringMatched(2));
- }
- else if(annType.equals("GS"))
- {
- // Generic per-Sequence annotation, free text
- /* Pfam uses these features:
- Feature Description
- --------------------- -----------
- AC ACcession number
- DE DEscription
- DR ; ; Database Reference
- OS OrganiSm (species)
- OC Organism Classification (clade, etc.)
- LO Look (Color, etc.)
- */
- if (s.search(annContent))
- {
- String acc = s.stringMatched(1);
- String type = s.stringMatched(2);
- String content = s.stringMatched(3);
-
- Hashtable ann;
- if (seqAnn.containsKey(acc))
- {
- ann = (Hashtable) seqAnn.get(acc);
- }
- else
- {
- ann = new Hashtable();
- }
- ann.put(type, content);
- seqAnn.put(acc, ann);
- }
- else
- {
- throw new IOException("Error parsing " + line);
- }
- }
- else if(annType.equals("GC"))
- {
- // Generic per-Column annotation, exactly 1 char per column
- }
- else if(annType.equals("GR"))
- {
- // Generic per-Sequence AND per-Column markup, exactly 1 char per column
- /*
- Feature Description Markup letters
- ------- ----------- --------------
- SS Secondary Structure [HGIEBTSCX]
- SA Surface Accessibility [0-9X]
- (0=0%-10%; ...; 9=90%-100%)
- TM TransMembrane [Mio]
- PP Posterior Probability [0-9*]
- (0=0.00-0.05; 1=0.05-0.15; *=0.95-1.00)
- LI LIgand binding [*]
- AS Active Site [*]
- IN INtron (in or after) [0-2]
- */
- if (s.search(annContent))
- {
- String acc = s.stringMatched(1);
- String type = s.stringMatched(2);
- String seq = s.stringMatched(3);
- String description = new String();
-
- // Check for additional information about the current annotation
- if (x.search(seq))
- {
- description = x.stringMatched(1);
- seq = x.stringMatched(2);
- }
- // sequence id with from-to fields
-
- Hashtable ann;
- // Get an object with all the annotations for this sequence
- if (seqAnn.containsKey(acc))
- {
- //logger.debug("Found annotations for " + acc);
- ann = (Hashtable) seqAnn.get(acc);
- }
- else
- {
- //logger.debug("Creating new annotations holder for " + acc);
- ann = new Hashtable();
- seqAnn.put(acc, ann);
- }
-
- Hashtable features;
- // Get an object with all the content for an annotation
- if (ann.containsKey("features"))
- {
- //logger.debug("Found features for " + acc);
- features = (Hashtable) ann.get("features");
- }
- else
- {
- //logger.debug("Creating new features holder for " + acc);
- features = new Hashtable();
- ann.put("features", features);
- }
-
- Hashtable content;
- if (features.containsKey(this.id2type(type)))
- {
- //logger.debug("Found content for " + this.id2type(type));
- content = (Hashtable) features.get(this.id2type(type));
- }
- else
- {
- //logger.debug("Creating new content holder for " + this.id2type(type));
- content = new Hashtable();
- features.put(this.id2type(type), content);
- }
- String ns = (String) content.get(description);
- if (ns == null) ns = "";
- ns += seq;
- content.put(description, seq);
- }
- else
- {
- throw new IOException("Error parsing " + line);
- }
- }
- else
- {
- throw new IOException("Unknown annotation detected: " + annType + " " + annContent);
- }
+ Hashtable content;
+ if (features.containsKey(this.id2type(type)))
+ {
+ // logger.debug("Found content for " + this.id2type(type));
+ content = (Hashtable) features.get(this.id2type(type));
+ }
+ else
+ {
+ // logger.debug("Creating new content holder for " +
+ // this.id2type(type));
+ content = new Hashtable();
+ features.put(this.id2type(type), content);
+ }
+ String ns = (String) content.get(description);
+ if (ns == null)
+ {
+ ns = "";
}
+ ns += seq;
+ content.put(description, seq);
+ }
+ else
+ {
+ System.err
+ .println("Warning - couldn't parse sequence annotation row line:\n"
+ + line);
+ // throw new IOException("Error parsing " + line);
+ }
+ }
+ else
+ {
+ throw new IOException("Unknown annotation detected: " + annType
+ + " " + annContent);
}
+ }
}
-
- public static String print(SequenceI[] s)
+ if (treeString.length() > 0)
{
- return "not yet implemented";
+ if (treeName == null)
+ {
+ treeName = "Tree " + (1 + getTreeCount());
+ }
+ addNewickTree(treeName, treeString.toString());
}
+ }
+
+ private AlignmentAnnotation parseAnnotationRow(Vector annotation,
+ String label, String annots)
+ {
+ String type = (label.indexOf("_cons") == label.length() - 5) ? label
+ .substring(0, label.length() - 5) : label;
+ boolean ss = false;
+ type = id2type(type);
+ if (type.equals("secondary structure"))
+ {
+ ss = true;
+ }
+ // decide on secondary structure or not.
+ Annotation[] els = new Annotation[annots.length()];
+ for (int i = 0; i < annots.length(); i++)
+ {
+ String pos = annots.substring(i, i + 1);
+ Annotation ann;
+ ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not
+ // be written out
+ if (ss)
+ {
+ ann.secondaryStructure = jalview.schemes.ResidueProperties
+ .getDssp3state(pos).charAt(0);
+ if (ann.secondaryStructure == pos.charAt(0) || pos.charAt(0) == 'C')
+ {
+ ann.displayCharacter = ""; // null; // " ";
+ }
+ else
+ {
+ ann.displayCharacter = " " + ann.displayCharacter;
+ }
+ }
- public String print()
+ els[i] = ann;
+ }
+ AlignmentAnnotation annot = null;
+ Enumeration e = annotation.elements();
+ while (e.hasMoreElements())
+ {
+ annot = (AlignmentAnnotation) e.nextElement();
+ if (annot.label.equals(type))
+ break;
+ annot = null;
+ }
+ if (annot == null)
{
- return print(getSeqsAsArray());
+ annot = new AlignmentAnnotation(type, type, els);
+ annotation.addElement(annot);
+ }
+ else
+ {
+ Annotation[] anns = new Annotation[annot.annotations.length
+ + els.length];
+ System.arraycopy(annot.annotations, 0, anns, 0,
+ annot.annotations.length);
+ System.arraycopy(els, 0, anns, annot.annotations.length, els.length);
+ annot.annotations = anns;
+ }
+ return annot;
+ }
+
+ public static String print(SequenceI[] s)
+ {
+ return "not yet implemented";
+ }
+
+ public String print()
+ {
+ return print(getSeqsAsArray());
+ }
+
+ private static Hashtable typeIds = null;
+ static
+ {
+ if (typeIds == null)
+ {
+ typeIds = new Hashtable();
+ typeIds.put("SS", "secondary structure");
+ typeIds.put("SA", "surface accessibility");
+ typeIds.put("TM", "transmembrane");
+ typeIds.put("PP", "posterior probability");
+ typeIds.put("LI", "ligand binding");
+ typeIds.put("AS", "active site");
+ typeIds.put("IN", "intron");
+ typeIds.put("IR", "interacting residue");
+ typeIds.put("AC", "accession");
+ typeIds.put("OS", "organism");
+ typeIds.put("CL", "class");
+ typeIds.put("DE", "description");
+ typeIds.put("DR", "reference");
+ typeIds.put("LO", "look");
+ typeIds.put("RF", "reference positions");
+
}
+ }
- private String id2type(String id)
+ private String id2type(String id)
+ {
+ if (typeIds.containsKey(id))
{
- // GR ids
- if (id.equals("SS")) return "secondary structure";
- else if (id.equals("SA")) return "surface accessibility";
- else if (id.equals("TM")) return "transmembrane";
- else if (id.equals("PP")) return "posterior probability";
- else if (id.equals("LI")) return "ligand binding";
- else if (id.equals("AS")) return "active site";
- else if (id.equals("IN")) return "intron";
- else if (id.equals("IR")) return "interacting residue";
- // GS ids
- else if (id.equals("AC")) return "accession";
- else if (id.equals("OS")) return "organism";
- else if (id.equals("CL")) return "class";
- else if (id.equals("DE")) return "description";
- else if (id.equals("DR")) return "reference";
- else if (id.equals("LO")) return "look";
- else return null;
+ return (String) typeIds.get(id);
}
+ System.err.println("Warning : Unknown Stockholm annotation type code "
+ + id);
+ return id;
+ }
}