X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFeaturesFile.java;h=cfc08fbdcaebb2e8917e9fe0e0c8d0c27e342806;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=42b032d361d930acc942e4f7e753fa07ef70e90c;hpb=00f52b4b20fa3077cad74e900314ded7599d0beb;p=jalview.git
diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 42b032d..cfc08fb 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -1,533 +1,960 @@
/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 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 .
+ */
package jalview.io;
-import jalview.datamodel.*;
-
import java.io.*;
import java.util.*;
-import jalview.schemes.UserColourScheme;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import jalview.util.Format;
/**
- * DOCUMENT ME!
- *
- * @author $author$
+ * 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
{
- /**
- * Creates a new FeaturesFile object.
- */
- public FeaturesFile()
- {
- }
+ /**
+ * 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);
+ }
- /**
- * 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)
+ /**
+ * 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
{
- 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)
{
- 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();
-
- boolean GFFFile = true;
+ if (line.startsWith("#"))
+ {
+ continue;
+ }
- while ( (line = nextLine()) != null)
+ st = new StringTokenizer(line, "\t");
+ if (st.countTokens() == 1)
{
- if(line.startsWith("#"))
+ if (line.trim().equalsIgnoreCase("GFF"))
+ {
+ // Start parsing file as if it might be GFF again.
+ GFFFile = true;
continue;
-
- st = new StringTokenizer(line, "\t");
- if (st.countTokens()>1 && st.countTokens() < 4 )
+ }
+ }
+ 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
{
- GFFFile = false;
- type = st.nextToken();
- if (type.equalsIgnoreCase("startgroup"))
+ Object colour = null;
+ String colscheme = st.nextToken();
+ if (colscheme.indexOf("|") > -1
+ || colscheme.trim().equalsIgnoreCase("label"))
{
- featureGroup = st.nextToken();
- if (st.hasMoreElements())
+ // 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)
{
- groupLink = st.nextToken();
- featureLink.put(featureGroup, groupLink);
+ // 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 if (type.equalsIgnoreCase("endgroup"))
+ else
{
- //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;
+ UserColourScheme ucs = new UserColourScheme(colscheme);
+ colour = ucs.findColour('A');
}
- else
+ if (colour != null)
{
- UserColourScheme ucs = new UserColourScheme(st.nextToken());
- colours.put(type, ucs.findColour("A"));
- if (st.hasMoreElements())
+ colours.put(type, colour);
+ }
+ if (st.hasMoreElements())
+ {
+ String link = st.nextToken();
+ typeLink.put(type, link);
+ if (featureLink == null)
{
- String link = st.nextToken();
- typeLink.put(type, link);
- if(featureLink==null)
- featureLink = new Hashtable();
- featureLink.put(type, link);
+ featureLink = new Hashtable();
}
-
+ featureLink.put(type, link);
}
- continue;
}
+ continue;
+ }
+ String seqId = "";
+ while (st.hasMoreElements())
+ {
- while (st.hasMoreElements())
+ if (GFFFile)
{
-
- 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)
{
- // Still possible this is an old Jalview file,
- // which does not have type colours at the beginning
- token = st.nextToken();
- seq = align.findName(token);
- if(seq != null)
+ desc = st.nextToken();
+ String group = null;
+ if (doGffSource && desc.indexOf(' ') == -1)
{
- desc = st.nextToken();
- type = st.nextToken();
- start = Integer.parseInt(st.nextToken());
- end = Integer.parseInt(st.nextToken());
- try
+ // 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("-"))
{
- score = new Float(st.nextToken()).floatValue();
+ start = 0;
}
- catch (NumberFormatException ex)
+ else
{
- score = 0;
+ start = Integer.parseInt(stt);
}
-
- sf = new SequenceFeature(type, desc, start, end, score, null);
-
- try
+ } catch (NumberFormatException ex)
+ {
+ start = 0;
+ }
+ try
+ {
+ String stt = st.nextToken();
+ if (stt.length() == 0 || stt.equals("-"))
{
- sf.setValue("STRAND", st.nextToken());
- sf.setValue("FRAME", st.nextToken());
+ end = 0;
}
- catch (Exception ex)
- {}
-
- if(st.hasMoreTokens())
+ else
{
- StringBuffer attributes = new StringBuffer();
- while (st.hasMoreTokens())
- {
- attributes.append("\t"+st.nextElement());
- }
- sf.setValue("ATTRIBUTES", attributes.toString());
+ end = Integer.parseInt(stt);
}
-
- seq.addSequenceFeature(sf);
-
- break;
+ } 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;
}
- }
-
- if(GFFFile && seq==null)
- {
- desc = token;
- }
- else
- desc = st.nextToken();
+ sf = new SequenceFeature(type, desc, start, end, score, group);
- token = st.nextToken();
- if (!token.equals("ID_NOT_SPECIFIED"))
- {
- seq = align.findName(token);
- st.nextToken();
- }
- else
- {
- try{
- index = Integer.parseInt(st.nextToken());
- seq = align.getSequenceAt(index);
+ try
+ {
+ sf.setValue("STRAND", st.nextToken());
+ sf.setValue("FRAME", st.nextToken());
+ } catch (Exception ex)
+ {
}
- catch(NumberFormatException ex)
+
+ if (st.hasMoreTokens())
{
- seq = null;
+ 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());
}
- }
- if(seq==null)
- {
- System.out.println("Sequence not found: "+line);
+ seq.addSequenceFeature(sf);
+ while ((seq = align.findName(seq, seqId, true)) != null)
+ {
+ seq.addSequenceFeature(new SequenceFeature(sf));
+ }
break;
}
+ }
- start = Integer.parseInt(st.nextToken());
- end = Integer.parseInt(st.nextToken());
+ 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;
+ }
- type = st.nextToken();
+ token = st.nextToken();
- if (!colours.containsKey(type))
+ 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)
{
- // Probably the old style groups file
- UserColourScheme ucs = new UserColourScheme(type);
- colours.put(type, ucs.findColour("A"));
+ seq = null;
}
+ }
+
+ if (seq == null)
+ {
+ System.out.println("Sequence not found: " + line);
+ break;
+ }
- sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
+ start = Integer.parseInt(st.nextToken());
+ end = Integer.parseInt(st.nextToken());
- seq.addSequenceFeature(sf);
+ type = st.nextToken();
- if(groupLink!=null && removeHTML)
+ 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
{
- sf.addLink(groupLink);
- sf.description += "%LINK%";
- }
- if(typeLink.containsKey(type) && removeHTML)
+ score = new Float(st.nextToken()).floatValue();
+ // update colourgradient bounds if allowed to
+ } catch (NumberFormatException ex)
{
- sf.addLink(typeLink.get(type).toString());
- sf.description += "%LINK%";
+ 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);
- parseDescriptionHTML(sf, removeHTML);
+ seq.addSequenceFeature(sf);
- //If we got here, its not a GFFFile
- GFFFile = false;
+ 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);
- return 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;
+ return true;
+ }
+
+ public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
+ {
+ if (sf.getDescription() == null)
+ {
+ return;
}
- public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
+ if (removeHTML
+ && sf.getDescription().toUpperCase().indexOf("") == -1)
{
- 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())
+ 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("/"))
{
- token = st.nextToken("&>");
- if(token.equalsIgnoreCase("html") || token.startsWith("/"))
- {
- continue;
- }
+ continue;
+ }
- tag = null;
- startTag = token.indexOf("<");
+ tag = null;
+ startTag = token.indexOf("<");
- if (startTag > -1)
- {
- tag = token.substring(startTag+1);
- token = token.substring(0, startTag);
- }
+ 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
+ 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();
+ if (removeHTML)
+ {
+ sf.description = sb.toString();
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
- * @param len DOCUMENT ME!
- * @param gaps DOCUMENT ME!
- * @param displayId DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String printJalviewFormat(SequenceI [] seqs,
- Hashtable visible)
- {
- StringBuffer out = new StringBuffer();
- SequenceFeature [] next;
-
- if(visible==null || visible.size()<1)
- return "No Features Visible";
+ /**
+ * 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);
+ }
- Enumeration en = visible.keys();
- String type;
- int color;
- while( en.hasMoreElements() )
- {
- type = en.nextElement().toString();
- color = Integer.parseInt( visible.get(type).toString() );
- out.append(type + "\t"
- + jalview.util.Format.getHexString(
- new java.awt.Color(color) )
- +"\n");
- }
+ /**
+ * 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";
+ }
- //Work out which groups are both present and visible
- Vector groups = new Vector();
- int groupIndex = 0;
+ 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();
- for(int i=0; i 0 && groupIndex < groups.size())
+ if (next[j].featureGroup != null
+ && !groups.contains(next[j].featureGroup))
{
- group = groups.elementAt(groupIndex).toString();
- out.append("\nSTARTGROUP\t" + group + "\n");
+ groups.addElement(next[j].featureGroup);
}
- else
- group = null;
+ }
+ }
+ }
- for (int i = 0; i < seqs.length; i++)
+ 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++)
{
- next = seqs[i].getSequenceFeatures();
- if (next != null)
+ isnonpos = next[j].begin == 0 && next[j].end == 0;
+ if ((!nonpos && isnonpos)
+ || (!isnonpos && visOnly && !visible
+ .containsKey(next[j].type)))
{
- for (int j = 0; j < next.length; j++)
- {
- if (!visible.containsKey(next[j].type))
- continue;
+ // 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 || !next[j].featureGroup
+ .equals(group)))
+ {
+ continue;
+ }
- if(group==null && next[j].featureGroup!=null)
- 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("");
+ }
- if(next[j].description==null || next[j].description.equals(""))
- out.append(next[j].type+"\t");
- else
+ out.append(next[j].description + " ");
+ if (next[j].links != null)
+ {
+ for (int l = 0; l < next[j].links.size(); l++)
{
- 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"
- + label
- + "");
- }
- }
-
- if (next[j].getDescription().indexOf("") == -1)
- out.append("");
- }
-
+ String label = next[j].links.elementAt(l).toString();
+ String href = label.substring(label.indexOf("|") + 1);
+ label = label.substring(0, label.indexOf("|"));
- out.append("\t");
+ if (next[j].description.indexOf(href) == -1)
+ {
+ out.append("" + label + "");
+ }
}
-
- out.append( seqs[i].getName() + "\t-1\t"
- + next[j].begin + "\t"
- + next[j].end + "\t"
- + next[j].type + "\n"
- );
+ if (next[j].getDescription().indexOf("") == -1)
+ {
+ out.append("");
+ }
}
- }
- }
- if(group!=null)
- {
- out.append("ENDGROUP\t"+group+"\n");
- groupIndex++;
+ 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"));
}
- else
- break;
-
}
- while(groupIndex < groups.size()+1);
+ }
+ if (group != null)
+ {
+ out.append("ENDGROUP\t" + group + "\n");
+ groupIndex++;
+ }
+ else
+ {
+ break;
+ }
- return out.toString();
- }
+ } while (groupIndex < groups.size() + 1);
- public String printGFFFormat(SequenceI [] seqs, Hashtable visible)
+ if (!featuresGen)
{
- StringBuffer out = new StringBuffer();
- SequenceFeature [] next;
- String source;
+ 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);
+ }
- for(int i=0; i