X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFeaturesFile.java;h=2ac0e13458f32eb1076948cc6a5332bee5191504;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=3c8ad21b2978de6d84dd414bfc3375bc520771ad;hpb=336b270e68fe281a9a881f751fe850e8a92e05c9;p=jalview.git
diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 3c8ad21..2ac0e13 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -1,41 +1,48 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*/
package jalview.io;
import java.io.*;
import java.util.*;
+import jalview.analysis.SequenceIdMatcher;
import jalview.datamodel.*;
import jalview.schemes.*;
+import jalview.util.Format;
/**
- * Parse and create Jalview Features files
- * Detects GFF format features files and parses.
- * Does not implement standard print() - call specific printFeatures or printGFF.
- * Uses AlignmentI.findSequence(String id) to find the sequence object for the features annotation - this normally works on an exact match.
+ * 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
+public class FeaturesFile extends AlignFile
{
/**
+ * work around for GFF interpretation bug where source string becomes
+ * description rather than a group
+ */
+ private boolean doGffSource = true;
+
+ /**
* Creates a new FeaturesFile object.
*/
public FeaturesFile()
@@ -44,44 +51,80 @@ public class FeaturesFile
/**
* Creates a new FeaturesFile object.
- *
- * @param inFile DOCUMENT ME!
- * @param type DOCUMENT ME!
- *
- * @throws IOException DOCUMENT ME!
+ *
+ * @param inFile
+ * DOCUMENT ME!
+ * @param type
+ * DOCUMENT ME!
+ *
+ * @throws IOException
+ * DOCUMENT ME!
*/
- public FeaturesFile(String inFile, String type)
- throws IOException
+ 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!
+ * 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)
+ public boolean parse(AlignmentI align, Hashtable colours,
+ boolean removeHTML)
+ {
+ return parse(align, colours, null, removeHTML, false);
+ }
+
+ /**
+ * Parse GFF or sequence features file optionally using case-independent matching, discarding URLs
+ * @param align - alignment/dataset containing sequences that are to be annotated
+ * @param colours - hashtable to store feature colour definitions
+ * @param removeHTML - process html strings into plain text
+ * @param relaxedIdmatching - when true, ID matches to compound sequence IDs are allowed
+ * @return true if features were added
+ */
+ public boolean parse(AlignmentI align,
+ 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, null, removeHTML);
+ return parse(align, colours, featureLink, 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
+ * @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)
+ Hashtable colours, Hashtable featureLink, boolean removeHTML, boolean relaxedIdmatching)
{
+
String line = null;
try
{
@@ -94,10 +137,11 @@ public class FeaturesFile
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)
+ while ((line = nextLine()) != null)
{
if (line.startsWith("#"))
{
@@ -105,6 +149,15 @@ public class FeaturesFile
}
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;
@@ -120,16 +173,213 @@ public class FeaturesFile
}
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
+ // 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
{
- UserColourScheme ucs = new UserColourScheme(st.nextToken());
- colours.put(type, ucs.findColour('A'));
+ Object colour = null;
+ String colscheme = st.nextToken();
+ if (colscheme.indexOf("|") > -1
+ || colscheme.trim().equalsIgnoreCase("label"))
+ {
+ // Parse '|' separated graduated colourscheme fields:
+ // [label|][mincolour|maxcolour|[absolute|]minvalue|maxvalue|thresholdtype|thresholdvalue]
+ // can either provide 'label' only, first is optional, next two
+ // colors are required (but may be
+ // left blank), next is optional, nxt two min/max are required.
+ // first is either 'label'
+ // first/second and third are both hexadecimal or word equivalent
+ // colour.
+ // next two are values parsed as floats.
+ // fifth is either 'above','below', or 'none'.
+ // sixth is a float value and only required when fifth is either
+ // 'above' or 'below'.
+ StringTokenizer gcol = new StringTokenizer(colscheme, "|",
+ true);
+ // set defaults
+ int threshtype = AnnotationColourGradient.NO_THRESHOLD;
+ float min = Float.MIN_VALUE, max = Float.MAX_VALUE, threshval = Float.NaN;
+ boolean labelCol = false;
+ // Parse spec line
+ String mincol = gcol.nextToken();
+ if (mincol == "|")
+ {
+ System.err
+ .println("Expected either 'label' or a colour specification in the line: "
+ + line);
+ continue;
+ }
+ String maxcol = null;
+ if (mincol.toLowerCase().indexOf("label") == 0)
+ {
+ labelCol = true;
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); // skip
+ // '|'
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
+ }
+ String abso = null, minval, maxval;
+ if (mincol != null)
+ {
+ // at least four more tokens
+ if (mincol.equals("|"))
+ {
+ mincol = "";
+ }
+ else
+ {
+ gcol.nextToken(); // skip next '|'
+ }
+ // continue parsing rest of line
+ maxcol = gcol.nextToken();
+ if (maxcol.equals("|"))
+ {
+ maxcol = "";
+ }
+ else
+ {
+ gcol.nextToken(); // skip next '|'
+ }
+ abso = gcol.nextToken();
+ gcol.nextToken(); // skip next '|'
+ if (abso.toLowerCase().indexOf("abso") != 0)
+ {
+ minval = abso;
+ abso = null;
+ }
+ else
+ {
+ minval = gcol.nextToken();
+ gcol.nextToken(); // skip next '|'
+ }
+ maxval = gcol.nextToken();
+ if (gcol.hasMoreTokens())
+ {
+ gcol.nextToken(); // skip next '|'
+ }
+ try
+ {
+ if (minval.length() > 0)
+ {
+ min = new Float(minval).floatValue();
+ }
+ } catch (Exception e)
+ {
+ System.err
+ .println("Couldn't parse the minimum value for graduated colour for type ("
+ + colscheme
+ + ") - did you misspell 'auto' for the optional automatic colour switch ?");
+ e.printStackTrace();
+ }
+ try
+ {
+ if (maxval.length() > 0)
+ {
+ max = new Float(maxval).floatValue();
+ }
+ } catch (Exception e)
+ {
+ System.err
+ .println("Couldn't parse the maximum value for graduated colour for type ("
+ + colscheme + ")");
+ e.printStackTrace();
+ }
+ }
+ else
+ {
+ // add in some dummy min/max colours for the label-only
+ // colourscheme.
+ mincol = "FFFFFF";
+ maxcol = "000000";
+ }
+ try
+ {
+ colour = new jalview.schemes.GraduatedColor(
+ new UserColourScheme(mincol).findColour('A'),
+ new UserColourScheme(maxcol).findColour('A'), min,
+ max);
+ } catch (Exception e)
+ {
+ System.err
+ .println("Couldn't parse the graduated colour scheme ("
+ + colscheme + ")");
+ e.printStackTrace();
+ }
+ if (colour != null)
+ {
+ ((jalview.schemes.GraduatedColor) colour)
+ .setColourByLabel(labelCol);
+ ((jalview.schemes.GraduatedColor) colour)
+ .setAutoScaled(abso == null);
+ // add in any additional parameters
+ String ttype = null, tval = null;
+ if (gcol.hasMoreTokens())
+ {
+ // threshold type and possibly a threshold value
+ ttype = gcol.nextToken();
+ if (ttype.toLowerCase().startsWith("below"))
+ {
+ ((jalview.schemes.GraduatedColor) colour)
+ .setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);
+ }
+ else if (ttype.toLowerCase().startsWith("above"))
+ {
+ ((jalview.schemes.GraduatedColor) colour)
+ .setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);
+ }
+ else
+ {
+ ((jalview.schemes.GraduatedColor) colour)
+ .setThreshType(AnnotationColourGradient.NO_THRESHOLD);
+ if (!ttype.toLowerCase().startsWith("no"))
+ {
+ System.err
+ .println("Ignoring unrecognised threshold type : "
+ + ttype);
+ }
+ }
+ }
+ if (((GraduatedColor) colour).getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
+ {
+ try
+ {
+ gcol.nextToken();
+ tval = gcol.nextToken();
+ ((jalview.schemes.GraduatedColor) colour)
+ .setThresh(new Float(tval).floatValue());
+ } catch (Exception e)
+ {
+ System.err
+ .println("Couldn't parse threshold value as a float: ("
+ + tval + ")");
+ e.printStackTrace();
+ }
+ }
+ // parse the thresh-is-min token ?
+ if (gcol.hasMoreTokens())
+ {
+ System.err
+ .println("Ignoring additional tokens in parameters in graduated colour specification\n");
+ while (gcol.hasMoreTokens())
+ {
+ System.err.println("|" + gcol.nextToken());
+ }
+ System.err.println("\n");
+ }
+ }
+ }
+ else
+ {
+ UserColourScheme ucs = new UserColourScheme(colscheme);
+ colour = ucs.findColour('A');
+ }
+ if (colour != null)
+ {
+ colours.put(type, colour);
+ }
if (st.hasMoreElements())
{
String link = st.nextToken();
@@ -140,11 +390,10 @@ public class FeaturesFile
}
featureLink.put(type, link);
}
-
}
continue;
}
-
+ String seqId = "";
while (st.hasMoreElements())
{
@@ -152,43 +401,72 @@ public class FeaturesFile
{
// Still possible this is an old Jalview file,
// which does not have type colours at the beginning
- token = st.nextToken();
- seq = align.findName(token);
+ seqId = token = st.nextToken();
+ seq = findName(align, seqId, relaxedIdmatching);
if (seq != null)
{
desc = st.nextToken();
+ String group = null;
+ if (doGffSource && desc.indexOf(' ') == -1)
+ {
+ // could also be a source term rather than description line
+ group = new String(desc);
+ }
type = st.nextToken();
- try {
- start = Integer.parseInt(st.nextToken());
+ try
+ {
+ String stt = st.nextToken();
+ if (stt.length() == 0 || stt.equals("-"))
+ {
+ start = 0;
+ }
+ else
+ {
+ start = Integer.parseInt(stt);
+ }
} catch (NumberFormatException ex)
{
- start=0;
+ start = 0;
}
- try {
- end = Integer.parseInt(st.nextToken());
+ try
+ {
+ String stt = st.nextToken();
+ if (stt.length() == 0 || stt.equals("-"))
+ {
+ end = 0;
+ }
+ else
+ {
+ end = Integer.parseInt(stt);
+ }
+ } catch (NumberFormatException ex)
+ {
+ end = 0;
}
- catch (NumberFormatException ex)
+ // TODO: decide if non positional feature assertion for input data
+ // where end==0 is generally valid
+ if (end == 0)
{
- end=-1;
- }
+ // treat as non-positional feature, regardless.
+ start = 0;
+ }
try
{
score = new Float(st.nextToken()).floatValue();
- }
- catch (NumberFormatException ex)
+ } catch (NumberFormatException ex)
{
score = 0;
}
- sf = new SequenceFeature(type, desc, start, end, score, null);
+ sf = new SequenceFeature(type, desc, start, end, score, group);
try
{
sf.setValue("STRAND", st.nextToken());
sf.setValue("FRAME", st.nextToken());
+ } catch (Exception ex)
+ {
}
- catch (Exception ex)
- {}
if (st.hasMoreTokens())
{
@@ -197,11 +475,17 @@ public class FeaturesFile
{
attributes.append("\t" + st.nextElement());
}
+ // TODO validate and split GFF2 attributes field ? parse out
+ // ([A-Za-z][A-Za-z0-9_]*) ; and add as
+ // sf.setValue(attrib, val);
sf.setValue("ATTRIBUTES", attributes.toString());
}
seq.addSequenceFeature(sf);
-
+ while ((seq = align.findName(seq, seqId, true)) != null)
+ {
+ seq.addSequenceFeature(new SequenceFeature(sf));
+ }
break;
}
}
@@ -216,26 +500,28 @@ public class FeaturesFile
}
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.
+ System.err
+ .println("DEBUG: Run out of tokens when trying to identify the destination for the feature.. giving up.");
+ // in all probability, this isn't a file we understand, so bail
+ // quietly.
return false;
}
-
+
token = st.nextToken();
-
+
if (!token.equals("ID_NOT_SPECIFIED"))
{
- seq = align.findName(token);
+ seq = findName(align, seqId = token, relaxedIdmatching);
st.nextToken();
}
else
{
+ seqId = null;
try
{
index = Integer.parseInt(st.nextToken());
seq = align.getSequenceAt(index);
- }
- catch (NumberFormatException ex)
+ } catch (NumberFormatException ex)
{
seq = null;
}
@@ -258,11 +544,19 @@ public class FeaturesFile
UserColourScheme ucs = new UserColourScheme(type);
colours.put(type, ucs.findColour('A'));
}
-
sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
-
- seq.addSequenceFeature(sf);
-
+ if (st.hasMoreTokens())
+ {
+ try
+ {
+ score = new Float(st.nextToken()).floatValue();
+ // update colourgradient bounds if allowed to
+ } catch (NumberFormatException ex)
+ {
+ score = 0;
+ }
+ sf.setScore(score);
+ }
if (groupLink != null && removeHTML)
{
sf.addLink(groupLink);
@@ -276,133 +570,181 @@ public class FeaturesFile
parseDescriptionHTML(sf, removeHTML);
- //If we got here, its not a GFFFile
+ seq.addSequenceFeature(sf);
+
+ while (seqId != null
+ && (seq = align.findName(seq, seqId, false)) != null)
+ {
+ seq.addSequenceFeature(new SequenceFeature(sf));
+ }
+ // If we got here, its not a GFFFile
GFFFile = false;
}
}
- }
- catch (Exception ex)
+ 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);
}
}
/**
- * DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
- * @param len DOCUMENT ME!
- * @param gaps DOCUMENT ME!
- * @param displayId DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * 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)
+ public String printJalviewFormat(SequenceI[] seqs, Hashtable visible)
+ {
+ return printJalviewFormat(seqs, visible, true, true);
+ }
+
+ /**
+ * generate a features file for seqs with colours from visible (if any)
+ *
+ * @param seqs
+ * source of features
+ * @param visible
+ * hash of Colours for each feature type
+ * @param visOnly
+ * when true only feature types in 'visible' will be output
+ * @param nonpos
+ * indicates if non-positional features should be output (regardless
+ * of group or type)
+ * @return features file contents
+ */
+ public String printJalviewFormat(SequenceI[] seqs, Hashtable visible,
+ boolean visOnly, boolean nonpos)
{
StringBuffer out = new StringBuffer();
SequenceFeature[] next;
-
- if (visible == null || visible.size() < 1)
+ boolean featuresGen = false;
+ if (visOnly && !nonpos && (visible == null || visible.size() < 1))
{
+ // no point continuing.
return "No Features Visible";
}
- Enumeration en = visible.keys();
- String type;
- int color;
- while (en.hasMoreElements())
+ if (visible != null && visOnly)
{
- 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");
- }
+ // 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();
- //Work out which groups are both present and visible
+ if (visible.get(type) instanceof GraduatedColor)
+ {
+ GraduatedColor gc = (GraduatedColor) visible.get(type);
+ color = (gc.isColourByLabel() ? "label|" : "")
+ + Format.getHexString(gc.getMinColor()) + "|"
+ + Format.getHexString(gc.getMaxColor())
+ + (gc.isAutoScale() ? "|" : "|abso|") + gc.getMin() + "|"
+ + gc.getMax() + "|";
+ if (gc.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
+ {
+ if (gc.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD)
+ {
+ color += "below";
+ }
+ else
+ {
+ if (gc.getThreshType() != AnnotationColourGradient.ABOVE_THRESHOLD)
+ {
+ System.err.println("WARNING: Unsupported threshold type ("
+ + gc.getThreshType() + ") : Assuming 'above'");
+ }
+ color += "above";
+ }
+ // add the value
+ color += "|" + gc.getThresh();
+ }
+ else
+ {
+ color += "none";
+ }
+ }
+ else if (visible.get(type) instanceof java.awt.Color)
+ {
+ color = Format.getHexString((java.awt.Color) visible.get(type));
+ }
+ else
+ {
+ // legacy support for integer objects containing colour triplet values
+ color = Format.getHexString(new java.awt.Color(Integer
+ .parseInt(visible.get(type).toString())));
+ }
+ out.append(type);
+ out.append("\t");
+ out.append(color);
+ out.append(newline);
+ }
+ }
+ // Work out which groups are both present and visible
Vector groups = new Vector();
int groupIndex = 0;
+ boolean isnonpos = false;
for (int i = 0; i < seqs.length; i++)
{
@@ -411,13 +753,16 @@ public class FeaturesFile
{
for (int j = 0; j < next.length; j++)
{
- if (!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;
}
if (next[j].featureGroup != null
- && !groups.contains(next[j].featureGroup))
+ && !groups.contains(next[j].featureGroup))
{
groups.addElement(next[j].featureGroup);
}
@@ -426,14 +771,16 @@ public class FeaturesFile
}
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
{
@@ -447,15 +794,19 @@ public class FeaturesFile
{
for (int j = 0; j < next.length; j++)
{
- if (!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;
}
if (group != null
- && (next[j].featureGroup == null
- || !next[j].featureGroup.equals(group))
- )
+ && (next[j].featureGroup == null || !next[j].featureGroup
+ .equals(group)))
{
continue;
}
@@ -464,15 +815,17 @@ public class FeaturesFile
{
continue;
}
-
- if (next[j].description == null || next[j].description.equals(""))
+ // 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)
+ && next[j].getDescription().indexOf("") == -1)
{
out.append("");
}
@@ -488,11 +841,7 @@ public class FeaturesFile
if (next[j].description.indexOf(href) == -1)
{
- out.append(""
- + label
- + "");
+ out.append("" + label + "");
}
}
@@ -504,19 +853,28 @@ public class FeaturesFile
out.append("\t");
}
-
- out.append(seqs[i].getName() + "\t-1\t"
- + next[j].begin + "\t"
- + next[j].end + "\t"
- + next[j].type + "\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
@@ -524,18 +882,36 @@ public class FeaturesFile
break;
}
+ } while (groupIndex < groups.size() + 1);
+
+ if (!featuresGen)
+ {
+ return "No Features Visible";
}
- while (groupIndex < groups.size() + 1);
return out.toString();
}
+ /**
+ * generate a gff file for sequence features includes non-pos features by
+ * default.
+ *
+ * @param seqs
+ * @param visible
+ * @return
+ */
public String printGFFFormat(SequenceI[] seqs, Hashtable visible)
{
+ return printGFFFormat(seqs, visible, true, true);
+ }
+
+ public String printGFFFormat(SequenceI[] seqs, Hashtable visible,
+ boolean visOnly, boolean nonpos)
+ {
StringBuffer out = new StringBuffer();
SequenceFeature[] next;
String source;
-
+ boolean isnonpos;
for (int i = 0; i < seqs.length; i++)
{
if (seqs[i].getSequenceFeatures() != null)
@@ -543,7 +919,10 @@ public class FeaturesFile
next = seqs[i].getSequenceFeatures();
for (int j = 0; j < next.length; j++)
{
- if (!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;
}
@@ -554,17 +933,23 @@ public class FeaturesFile
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
{
@@ -579,13 +964,15 @@ public class FeaturesFile
{
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);
}
}
@@ -594,18 +981,22 @@ public class FeaturesFile
return out.toString();
}
+ /**
+ * this is only for the benefit of object polymorphism - method does nothing.
+ */
public void parse()
{
- //IGNORED
+ // IGNORED
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * this is only for the benefit of object polymorphism - method does nothing.
+ *
+ * @return error message
*/
public String print()
{
return "USE printGFFFormat() or printJalviewFormat()";
}
+
}