X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFeaturesFile.java;h=cfc08fbdcaebb2e8917e9fe0e0c8d0c27e342806;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=462ee22dd65d8260f500437db9f2b22d4abc7bfe;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 462ee22..cfc08fb 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -1,20 +1,19 @@
/*
- * 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 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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;
@@ -23,6 +22,7 @@ import java.util.*;
import jalview.datamodel.*;
import jalview.schemes.*;
+import jalview.util.Format;
/**
* Parse and create Jalview Features files Detects GFF format features files and
@@ -36,6 +36,12 @@ import jalview.schemes.*;
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()
@@ -46,12 +52,12 @@ public class FeaturesFile extends AlignFile
* Creates a new FeaturesFile object.
*
* @param inFile
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param type
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @throws IOException
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public FeaturesFile(String inFile, String type) throws IOException
{
@@ -68,7 +74,7 @@ public class FeaturesFile extends AlignFile
* replace links with %LINK% Both need to read links in HTML however
*
* @throws IOException
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public boolean parse(AlignmentI align, Hashtable colours,
boolean removeHTML)
@@ -81,7 +87,7 @@ public class FeaturesFile extends AlignFile
* replace links with %LINK% Both need to read links in HTML however
*
* @throws IOException
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public boolean parse(AlignmentI align, Hashtable colours,
Hashtable featureLink, boolean removeHTML)
@@ -98,9 +104,10 @@ 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("#"))
@@ -109,6 +116,15 @@ 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;
@@ -132,8 +148,197 @@ public class FeaturesFile extends AlignFile
}
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();
@@ -144,7 +349,6 @@ public class FeaturesFile extends AlignFile
}
featureLink.put(type, link);
}
-
}
continue;
}
@@ -161,20 +365,49 @@ public class FeaturesFile extends AlignFile
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());
+ String stt = st.nextToken();
+ if (stt.length() == 0 || stt.equals("-"))
+ {
+ start = 0;
+ }
+ else
+ {
+ start = Integer.parseInt(stt);
+ }
} catch (NumberFormatException ex)
{
start = 0;
}
try
{
- end = Integer.parseInt(st.nextToken());
+ String stt = st.nextToken();
+ if (stt.length() == 0 || stt.equals("-"))
+ {
+ end = 0;
+ }
+ else
+ {
+ end = Integer.parseInt(stt);
+ }
} catch (NumberFormatException ex)
{
- end = -1;
+ 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
{
@@ -184,7 +417,7 @@ public class FeaturesFile extends AlignFile
score = 0;
}
- sf = new SequenceFeature(type, desc, start, end, score, null);
+ sf = new SequenceFeature(type, desc, start, end, score, group);
try
{
@@ -201,6 +434,9 @@ public class FeaturesFile extends AlignFile
{
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());
}
@@ -267,9 +503,19 @@ public class FeaturesFile extends AlignFile
UserColourScheme ucs = new UserColourScheme(type);
colours.put(type, ucs.findColour('A'));
}
-
sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
-
+ 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);
@@ -381,60 +627,104 @@ public class FeaturesFile extends AlignFile
}
/**
- * generate a features file for seqs
+ * generate a features file for seqs includes non-pos features by default.
*
* @param seqs
- * source of sequence features
+ * source of sequence features
* @param visible
- * hash of feature types and colours
+ * hash of feature types and colours
* @return features file contents
*/
public String printJalviewFormat(SequenceI[] seqs, Hashtable visible)
{
- return printJalviewFormat(seqs, visible, true);
+ return printJalviewFormat(seqs, visible, true, true);
}
/**
* generate a features file for seqs with colours from visible (if any)
*
* @param seqs
- * source of features
+ * source of features
* @param visible
- * hash of Colours for each feature type
+ * hash of Colours for each feature type
* @param visOnly
- * when true only feature types in 'visible' will be output
+ * 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
// viewed features
+ // TODO: decide if feature links should also be written here ?
Enumeration en = visible.keys();
- String type;
- int color;
+ String type, 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");
+
+ 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 + "\t" + color + "\n");
}
}
// 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++)
{
@@ -443,7 +733,10 @@ 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;
}
@@ -458,7 +751,6 @@ public class FeaturesFile extends AlignFile
}
String group = null;
-
do
{
@@ -479,8 +771,13 @@ 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;
}
@@ -495,7 +792,8 @@ public class FeaturesFile extends AlignFile
{
continue;
}
-
+ // we have features to output
+ featuresGen = true;
if (next[j].description == null
|| next[j].description.equals(""))
{
@@ -520,9 +818,7 @@ public class FeaturesFile extends AlignFile
if (next[j].description.indexOf(href) == -1)
{
- out
- .append("" + label
- + "");
+ out.append("" + label + "");
}
}
@@ -534,9 +830,15 @@ 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 + "\n");
+ 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"));
}
}
}
@@ -553,21 +855,34 @@ 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)
@@ -575,7 +890,10 @@ public class FeaturesFile extends AlignFile
next = seqs[i].getSequenceFeatures();
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;
}