X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFeaturesFile.java;h=6958923c2161212d66f7534fd72ab0e397ff2e44;hb=a7f8fa9c06d82efbbdbc6a0bf1054bb21610b353;hp=01cbd8a140de4d302e790875901ac38bc081fa43;hpb=7f6ab29d44b73a73192cf4382e38633eae5d95cd;p=jalview.git
diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 01cbd8a..6958923 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -1,26 +1,34 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 file is part of Jalview.
*
- * 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.
+ * 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.
*
- * 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 is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*/
package jalview.io;
import java.io.*;
import java.util.*;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.xml.sax.SAXException;
+
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+
+import jalview.analysis.SequenceIdMatcher;
import jalview.datamodel.*;
import jalview.schemes.*;
import jalview.util.Format;
@@ -59,40 +67,77 @@ public class FeaturesFile extends AlignFile
*
* @throws IOException
* DOCUMENT ME!
+ * @throws SAXException
+ * @throws ParserConfigurationException
+ * @throws ExceptionFileFormatOrSyntax
+ * @throws ExceptionLoadingFailed
+ * @throws ExceptionPermissionDenied
*/
- public FeaturesFile(String inFile, String type) throws IOException
+ public FeaturesFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
{
super(inFile, type);
}
- public FeaturesFile(FileParse source) throws IOException
+ public FeaturesFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
{
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!
+ * Parse GFF or sequence features file using case-independent matching, discarding URLs
+ * @param align - alignment/dataset containing sequences that are to be annotated
+ * @param colours - hashtable to store feature colour definitions
+ * @param removeHTML - process html strings into plain text
+ * @return true if features were added
*/
public boolean parse(AlignmentI align, Hashtable colours,
boolean removeHTML)
{
- return parse(align, colours, null, removeHTML);
+ return parse(align, colours, null, removeHTML, false);
}
/**
- * 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!
+ * Parse GFF or sequence features file optionally using case-independent matching, discarding URLs
+ * @param align - alignment/dataset containing sequences that are to be annotated
+ * @param colours - hashtable to store feature colour definitions
+ * @param removeHTML - process html strings into plain text
+ * @param relaxedIdmatching - when true, ID matches to compound sequence IDs are allowed
+ * @return true if features were added
+ */
+ public boolean parse(AlignmentI align,
+ Hashtable colours, boolean removeHTML, boolean relaxedIdMatching)
+ {
+ return parse(align, colours, null, removeHTML, relaxedIdMatching);
+ }
+
+ /**
+ * Parse GFF or sequence features file optionally using case-independent matching
+ * @param align - alignment/dataset containing sequences that are to be annotated
+ * @param colours - hashtable to store feature colour definitions
+ * @param featureLink - hashtable to store associated URLs
+ * @param removeHTML - process html strings into plain text
+ * @return true if features were added
*/
public boolean parse(AlignmentI align, Hashtable colours,
Hashtable featureLink, boolean removeHTML)
{
+ return parse(align, colours, featureLink, removeHTML, false);
+ }
+
+ /**
+ /**
+ * Parse GFF or sequence features file
+ * @param align - alignment/dataset containing sequences that are to be annotated
+ * @param colours - hashtable to store feature colour definitions
+ * @param featureLink - hashtable to store associated URLs
+ * @param removeHTML - process html strings into plain text
+ * @param relaxedIdmatching - when true, ID matches to compound sequence IDs are allowed
+ * @return true if features were added
+ */
+ public boolean parse(AlignmentI align,
+ Hashtable colours, Hashtable featureLink, boolean removeHTML, boolean relaxedIdmatching)
+ {
+
String line = null;
try
{
@@ -105,9 +150,10 @@ public class FeaturesFile extends AlignFile
SequenceFeature sf;
String featureGroup = null, groupLink = null;
Hashtable typeLink = new Hashtable();
-
+ /**
+ * when true, assume GFF style features rather than Jalview style.
+ */
boolean GFFFile = true;
-
while ((line = nextLine()) != null)
{
if (line.startsWith("#"))
@@ -116,6 +162,15 @@ public class FeaturesFile extends AlignFile
}
st = new StringTokenizer(line, "\t");
+ if (st.countTokens() == 1)
+ {
+ if (line.trim().equalsIgnoreCase("GFF"))
+ {
+ // Start parsing file as if it might be GFF again.
+ GFFFile = true;
+ continue;
+ }
+ }
if (st.countTokens() > 1 && st.countTokens() < 4)
{
GFFFile = false;
@@ -141,60 +196,124 @@ public class FeaturesFile extends AlignFile
{
Object colour = null;
String colscheme = st.nextToken();
- if (colscheme.indexOf("|") > -1)
+ if (colscheme.indexOf("|") > -1
+ || colscheme.trim().equalsIgnoreCase("label"))
{
// Parse '|' separated graduated colourscheme fields:
- // mincolour|maxcolour|[absolute|]minvalue|maxvalue|thresholdtype|thresholdvalue
- // first four are required.
- // first two are hexadecimal or word equivalent colours.
- // second two are values parsed as floats.
+ // [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, "|");
- String mincol = gcol.nextToken(), maxcol = gcol.nextToken();
- String abso = gcol
- .nextToken(), minval, maxval;
- if (abso.toLowerCase().indexOf("abso")!=0) {
- minval = abso;
- abso = null;
- } else {
- minval = gcol.nextToken();
- }
- maxval = gcol.nextToken();
+ 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;
- try
- {
- if (minval.length()>0) {
- min = new Float(minval).floatValue();
- }
- } catch (Exception e)
+ 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("Couldn't parse the minimum value for graduated colour for type ("
- + colscheme + ") - did you misspell 'auto' for the optional automatic colour switch ?");
- e.printStackTrace();
+ .println("Expected either 'label' or a colour specification in the line: "
+ + line);
+ continue;
}
- try
+ String maxcol = null;
+ if (mincol.toLowerCase().indexOf("label") == 0)
{
- if (maxval.length()>0) {
- max = new Float(maxval).floatValue();
+ labelCol = true;
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); // skip
+ // '|'
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
+ }
+ String abso = null, minval, maxval;
+ if (mincol != null)
+ {
+ // at least four more tokens
+ if (mincol.equals("|"))
+ {
+ mincol = "";
}
- } catch (Exception e)
+ 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
{
- System.err
- .println("Couldn't parse the maximum value for graduated colour for type ("
- + colscheme + ")");
- e.printStackTrace();
+ // 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);
+ new UserColourScheme(maxcol).findColour('A'), min,
+ max);
} catch (Exception e)
{
System.err
@@ -204,7 +323,10 @@ public class FeaturesFile extends AlignFile
}
if (colour != null)
{
- ((jalview.schemes.GraduatedColor)colour).setAutoScaled(abso==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())
@@ -233,11 +355,12 @@ public class FeaturesFile extends AlignFile
}
}
}
- if (((GraduatedColor)colour).getThreshType()!=AnnotationColourGradient.NO_THRESHOLD)
+ if (((GraduatedColor) colour).getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
{
- tval = gcol.nextToken();
try
{
+ gcol.nextToken();
+ tval = gcol.nextToken();
((jalview.schemes.GraduatedColor) colour)
.setThresh(new Float(tval).floatValue());
} catch (Exception e)
@@ -255,7 +378,7 @@ public class FeaturesFile extends AlignFile
.println("Ignoring additional tokens in parameters in graduated colour specification\n");
while (gcol.hasMoreTokens())
{
- System.err.println("|" + gcol);
+ System.err.println("|" + gcol.nextToken());
}
System.err.println("\n");
}
@@ -292,7 +415,7 @@ public class FeaturesFile extends AlignFile
// 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);
+ seq = findName(align, seqId, relaxedIdmatching);
if (seq != null)
{
desc = st.nextToken();
@@ -401,7 +524,7 @@ public class FeaturesFile extends AlignFile
if (!token.equals("ID_NOT_SPECIFIED"))
{
- seq = align.findName(seqId = token, true);
+ seq = findName(align, seqId = token, relaxedIdmatching);
st.nextToken();
}
else
@@ -440,7 +563,7 @@ public class FeaturesFile extends AlignFile
try
{
score = new Float(st.nextToken()).floatValue();
- // update colourgradient bounds if allowed to
+ // update colourgradient bounds if allowed to
} catch (NumberFormatException ex)
{
score = 0;
@@ -471,94 +594,70 @@ public class FeaturesFile extends AlignFile
GFFFile = false;
}
}
+ resetMatcher();
} catch (Exception ex)
{
System.out.println(line);
System.out.println("Error parsing feature file: " + ex + "\n" + line);
ex.printStackTrace(System.err);
+ resetMatcher();
return false;
}
return true;
}
- public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
+ private AlignmentI lastmatchedAl = null;
+
+ private SequenceIdMatcher matcher = null;
+
+ /**
+ * clear any temporary handles used to speed up ID matching
+ */
+ private void resetMatcher()
{
- if (sf.getDescription() == null)
+ lastmatchedAl = null;
+ matcher = null;
+ }
+
+ private SequenceI findName(AlignmentI align, String seqId,
+ boolean relaxedIdMatching)
+ {
+ SequenceI match = null;
+ if (relaxedIdMatching)
{
- return;
+ if (lastmatchedAl != align)
+ {
+ matcher = new SequenceIdMatcher(
+ (lastmatchedAl = align).getSequencesArray());
+ }
+ match = matcher.findIdMatch(seqId);
}
-
- if (removeHTML
- && sf.getDescription().toUpperCase().indexOf("") == -1)
+ else
{
- removeHTML = false;
+ match = align.findName(seqId, true);
}
+ return match;
+ }
- StringBuffer sb = new StringBuffer();
- StringTokenizer st = new StringTokenizer(sf.getDescription(), "<");
- String token, link;
- int startTag;
- String tag = null;
- while (st.hasMoreElements())
+ public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
+ {
+ if (sf.getDescription() == null)
{
- token = st.nextToken("&>");
- if (token.equalsIgnoreCase("html") || token.startsWith("/"))
- {
- continue;
- }
-
- tag = null;
- startTag = token.indexOf("<");
-
- if (startTag > -1)
- {
- tag = token.substring(startTag + 1);
- token = token.substring(0, startTag);
- }
-
- if (tag != null && tag.toUpperCase().startsWith("A HREF="))
- {
- if (token.length() > 0)
- {
- sb.append(token);
- }
- link = tag.substring(tag.indexOf("\"") + 1, tag.length() - 1);
- String label = st.nextToken("<>");
- sf.addLink(label + "|" + link);
- sb.append(label + "%LINK%");
- }
- else if (tag != null && tag.equalsIgnoreCase("br"))
- {
- sb.append("\n");
- }
- else if (token.startsWith("lt;"))
- {
- sb.append("<" + token.substring(3));
- }
- else if (token.startsWith("gt;"))
- {
- sb.append(">" + token.substring(3));
- }
- else if (token.startsWith("amp;"))
- {
- sb.append("&" + token.substring(4));
- }
- else
- {
- sb.append(token);
- }
+ return;
}
+ jalview.util.ParseHtmlBodyAndLinks parsed = new jalview.util.ParseHtmlBodyAndLinks(sf.getDescription(), removeHTML, newline);
- if (removeHTML)
+ sf.description = (removeHTML) ? parsed.getNonHtmlContent() : sf.description;
+ for (String link:parsed.getLinks())
{
- sf.description = sb.toString();
+ sf.addLink(link);
}
}
/**
- * generate a features file for seqs
+ * generate a features file for seqs includes non-pos features by default.
*
* @param seqs
* source of sequence features
@@ -568,7 +667,7 @@ public class FeaturesFile extends AlignFile
*/
public String printJalviewFormat(SequenceI[] seqs, Hashtable visible)
{
- return printJalviewFormat(seqs, visible, true);
+ return printJalviewFormat(seqs, visible, true, true);
}
/**
@@ -580,18 +679,23 @@ public class FeaturesFile extends AlignFile
* 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 visOnly, boolean nonpos)
{
StringBuffer out = new StringBuffer();
SequenceFeature[] next;
-
- if (visOnly && (visible == null || visible.size() < 1))
+ 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
@@ -606,9 +710,11 @@ public class FeaturesFile extends AlignFile
if (visible.get(type) instanceof GraduatedColor)
{
GraduatedColor gc = (GraduatedColor) visible.get(type);
- color = Format.getHexString(gc.getMinColor()) + "|"
- + Format.getHexString(gc.getMaxColor()) +
- (gc.isAutoScale() ? "|" : "|abso|")+ gc.getMin() + "|" + gc.getMax() + "|";
+ color = (gc.isColourByLabel() ? "label|" : "")
+ + Format.getHexString(gc.getMinColor()) + "|"
+ + Format.getHexString(gc.getMaxColor())
+ + (gc.isAutoScale() ? "|" : "|abso|") + gc.getMin() + "|"
+ + gc.getMax() + "|";
if (gc.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
{
if (gc.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD)
@@ -632,20 +738,26 @@ public class FeaturesFile extends AlignFile
color += "none";
}
}
+ else if (visible.get(type) instanceof java.awt.Color)
+ {
+ color = Format.getHexString((java.awt.Color) visible.get(type));
+ }
else
- if (visible.get(type) instanceof java.awt.Color) {
- color = Format.getHexString((java.awt.Color)visible.get(type));
- } else {
- // legacy support for integer objects containing colour triplet values
+ {
+ // legacy support for integer objects containing colour triplet values
color = Format.getHexString(new java.awt.Color(Integer
.parseInt(visible.get(type).toString())));
}
- out.append(type + "\t" + color + "\n");
+ out.append(type);
+ out.append("\t");
+ out.append(color);
+ out.append(newline);
}
}
// Work out which groups are both present and visible
Vector groups = new Vector();
int groupIndex = 0;
+ boolean isnonpos = false;
for (int i = 0; i < seqs.length; i++)
{
@@ -654,7 +766,10 @@ public class FeaturesFile extends AlignFile
{
for (int j = 0; j < next.length; j++)
{
- if (visOnly && !visible.containsKey(next[j].type))
+ isnonpos = next[j].begin == 0 && next[j].end == 0;
+ if ((!nonpos && isnonpos)
+ || (!isnonpos && visOnly && !visible
+ .containsKey(next[j].type)))
{
continue;
}
@@ -669,14 +784,16 @@ public class FeaturesFile extends AlignFile
}
String group = null;
-
do
{
if (groups.size() > 0 && groupIndex < groups.size())
{
group = groups.elementAt(groupIndex).toString();
- out.append("\nSTARTGROUP\t" + group + "\n");
+ out.append(newline);
+ out.append("STARTGROUP\t");
+ out.append(group);
+ out.append(newline);
}
else
{
@@ -690,8 +807,13 @@ public class FeaturesFile extends AlignFile
{
for (int j = 0; j < next.length; j++)
{
- if (visOnly && !visible.containsKey(next[j].type))
+ isnonpos = next[j].begin == 0 && next[j].end == 0;
+ if ((!nonpos && isnonpos)
+ || (!isnonpos && visOnly && !visible
+ .containsKey(next[j].type)))
{
+ // skip if feature is nonpos and we ignore them or if we only
+ // output visible and it isn't non-pos and it's not visible
continue;
}
@@ -706,7 +828,8 @@ public class FeaturesFile extends AlignFile
{
continue;
}
-
+ // we have features to output
+ featuresGen = true;
if (next[j].description == null
|| next[j].description.equals(""))
{
@@ -731,9 +854,7 @@ public class FeaturesFile extends AlignFile
if (next[j].description.indexOf(href) == -1)
{
- out
- .append("" + label
- + "");
+ out.append("" + label + "");
}
}
@@ -745,16 +866,28 @@ public class FeaturesFile extends AlignFile
out.append("\t");
}
-
- out.append(seqs[i].getName() + "\t-1\t" + next[j].begin + "\t"
- + next[j].end + "\t" + next[j].type + ((visible.get(next[j].type) instanceof GraduatedColor) ? "\t"+next[j].score+"\n" : "\n"));
+ out.append(seqs[i].getName());
+ out.append("\t-1\t");
+ out.append(next[j].begin);
+ out.append("\t");
+ out.append(next[j].end);
+ out.append("\t");
+ out.append(next[j].type);
+ if (next[j].score != Float.NaN)
+ {
+ out.append("\t");
+ out.append(next[j].score);
+ }
+ out.append(newline);
}
}
}
if (group != null)
{
- out.append("ENDGROUP\t" + group + "\n");
+ out.append("ENDGROUP\t");
+ out.append(group);
+ out.append(newline);
groupIndex++;
}
else
@@ -764,21 +897,34 @@ public class FeaturesFile extends AlignFile
} while (groupIndex < groups.size() + 1);
+ if (!featuresGen)
+ {
+ return "No Features Visible";
+ }
+
return out.toString();
}
+ /**
+ * generate a gff file for sequence features includes non-pos features by
+ * default.
+ *
+ * @param seqs
+ * @param visible
+ * @return
+ */
public String printGFFFormat(SequenceI[] seqs, Hashtable visible)
{
- return printGFFFormat(seqs, visible, true);
+ return printGFFFormat(seqs, visible, true, true);
}
public String printGFFFormat(SequenceI[] seqs, Hashtable visible,
- boolean visOnly)
+ boolean visOnly, boolean nonpos)
{
StringBuffer out = new StringBuffer();
SequenceFeature[] next;
String source;
-
+ boolean isnonpos;
for (int i = 0; i < seqs.length; i++)
{
if (seqs[i].getSequenceFeatures() != null)
@@ -786,8 +932,10 @@ public class FeaturesFile extends AlignFile
next = seqs[i].getSequenceFeatures();
for (int j = 0; j < next.length; j++)
{
- if (visOnly && visible != null
- && !visible.containsKey(next[j].type))
+ isnonpos = next[j].begin == 0 && next[j].end == 0;
+ if ((!nonpos && isnonpos)
+ || (!isnonpos && visOnly && !visible
+ .containsKey(next[j].type)))
{
continue;
}
@@ -798,13 +946,23 @@ public class FeaturesFile extends AlignFile
source = next[j].getDescription();
}
- out.append(seqs[i].getName() + "\t" + source + "\t"
- + next[j].type + "\t" + next[j].begin + "\t"
- + next[j].end + "\t" + next[j].score + "\t");
+ out.append(seqs[i].getName());
+ out.append("\t");
+ out.append(source);
+ out.append("\t");
+ out.append(next[j].type);
+ out.append("\t");
+ out.append(next[j].begin);
+ out.append("\t");
+ out.append(next[j].end);
+ out.append("\t");
+ out.append(next[j].score);
+ out.append("\t");
if (next[j].getValue("STRAND") != null)
{
- out.append(next[j].getValue("STRAND") + "\t");
+ out.append(next[j].getValue("STRAND"));
+ out.append("\t");
}
else
{
@@ -819,13 +977,15 @@ public class FeaturesFile extends AlignFile
{
out.append(".");
}
+ // TODO: verify/check GFF - should there be a /t here before attribute
+ // output ?
if (next[j].getValue("ATTRIBUTES") != null)
{
out.append(next[j].getValue("ATTRIBUTES"));
}
- out.append("\n");
+ out.append(newline);
}
}
@@ -851,4 +1011,5 @@ public class FeaturesFile extends AlignFile
{
return "USE printGFFFormat() or printJalviewFormat()";
}
+
}