package jalview.io;
import jalview.analysis.SequenceIdMatcher;
+import jalview.api.FeatureColourI;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
+import jalview.schemes.FeatureColour;
import jalview.schemes.UserColourScheme;
import jalview.util.Format;
import jalview.util.MapList;
}
/**
- * 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);
}
+ /**
+ * @param source
+ * @throws IOException
+ */
public FeaturesFile(FileParse source) throws IOException
{
super(source);
}
/**
+ * @param parseImmediately
+ * @param source
+ * @throws IOException
+ */
+ public FeaturesFile(boolean parseImmediately, FileParse source)
+ throws IOException
+ {
+ super(parseImmediately, source);
+ }
+
+ /**
+ * @param parseImmediately
+ * @param inFile
+ * @param type
+ * @throws IOException
+ */
+ public FeaturesFile(boolean parseImmediately, String inFile, String type)
+ throws IOException
+ {
+ super(parseImmediately, inFile, type);
+ }
+
+ /**
* Parse GFF or sequence features file using case-independent matching,
* discarding URLs
*
* - 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, Map colours, boolean removeHTML)
{
return parse(align, colours, null, removeHTML, false);
}
return parse(align, colours, featureLink, removeHTML, false);
}
+ @Override
+ public void addAnnotations(AlignmentI al)
+ {
+ // TODO Auto-generated method stub
+ super.addAnnotations(al);
+ }
+
+ @Override
+ public void addProperties(AlignmentI al)
+ {
+ // TODO Auto-generated method stub
+ super.addProperties(al);
+ }
+
+ @Override
+ public void addSeqGroups(AlignmentI al)
+ {
+ // TODO Auto-generated method stub
+ super.addSeqGroups(al);
+ }
+
/**
* Parse GFF or sequence features file
*
{
SequenceI seq = null;
/**
- * keep track of any sequences we try to create from the data if it is a GFF3 file
+ * keep track of any sequences we try to create from the data if it is a
+ * GFF3 file
*/
ArrayList<SequenceI> newseqs = new ArrayList<SequenceI>();
String type, desc, token = null;
}
else
{
- Object colour = null;
+ FeatureColourI colour = null;
String colscheme = st.nextToken();
if (colscheme.indexOf("|") > -1
|| colscheme.trim().equalsIgnoreCase("label"))
}
try
{
- colour = new jalview.schemes.GraduatedColor(
+ colour = new FeatureColour(
new UserColourScheme(mincol).findColour('A'),
new UserColourScheme(maxcol).findColour('A'), min,
max);
}
if (colour != null)
{
- ((jalview.schemes.GraduatedColor) colour)
- .setColourByLabel(labelCol);
- ((jalview.schemes.GraduatedColor) colour)
- .setAutoScaled(abso == null);
+ colour.setColourByLabel(labelCol);
+ colour.setAutoScaled(abso == null);
// add in any additional parameters
String ttype = null, tval = null;
if (gcol.hasMoreTokens())
ttype = gcol.nextToken();
if (ttype.toLowerCase().startsWith("below"))
{
- ((jalview.schemes.GraduatedColor) colour)
- .setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);
+ colour.setBelowThreshold(true);
}
else if (ttype.toLowerCase().startsWith("above"))
{
- ((jalview.schemes.GraduatedColor) colour)
- .setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);
+ colour.setAboveThreshold(true);
}
else
{
- ((jalview.schemes.GraduatedColor) colour)
- .setThreshType(AnnotationColourGradient.NO_THRESHOLD);
if (!ttype.toLowerCase().startsWith("no"))
{
System.err
}
}
}
- if (((GraduatedColor) colour).getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
+ if (colour.hasThreshold())
{
try
{
gcol.nextToken();
tval = gcol.nextToken();
- ((jalview.schemes.GraduatedColor) colour)
- .setThresh(new Float(tval).floatValue());
+ colour.setThreshold(new Float(tval).floatValue());
} catch (Exception e)
{
System.err
else
{
UserColourScheme ucs = new UserColourScheme(colscheme);
- colour = ucs.findColour('A');
+ colour = new FeatureColour(ucs.findColour('A'));
}
if (colour != null)
{
* @return true if sf was actually added to the sequence, false if it was
* processed in another way
*/
- public boolean processOrAddSeqFeature(AlignmentI align, List<SequenceI> newseqs, SequenceI seq, SequenceFeature sf,
+ public boolean processOrAddSeqFeature(AlignmentI align,
+ List<SequenceI> newseqs, SequenceI seq, SequenceFeature sf,
boolean gFFFile, boolean relaxedIdMatching)
{
String attr = (String) sf.getValue("ATTRIBUTES");
boolean add = true;
if (gFFFile && attr != null)
{
- int nattr=8;
+ int nattr = 8;
for (String attset : attr.split("\t"))
{
- if (attset==null || attset.trim().length()==0)
+ if (attset == null || attset.trim().length() == 0)
{
continue;
}
continue;
}
- // expect either space seperated (gff2) or '=' separated (gff3)
+ // expect either space seperated (gff2) or '=' separated (gff3)
// key/value pairs here
- int eqpos = pair.indexOf('='),sppos = pair.indexOf(' ');
+ int eqpos = pair.indexOf('='), sppos = pair.indexOf(' ');
String key = null, value = null;
if (sppos > -1 && (eqpos == -1 || sppos < eqpos))
{
key = pair.substring(0, sppos);
value = pair.substring(sppos + 1);
- } else {
+ }
+ else
+ {
if (eqpos > -1 && (sppos == -1 || eqpos < sppos))
{
key = pair.substring(0, eqpos);
value = pair.substring(eqpos + 1);
- } else
+ }
+ else
{
key = pair;
}
{
add &= processGffKey(set, nattr, seq, sf, align, newseqs,
relaxedIdMatching); // process decides if
- // feature is actually
- // added
+ // feature is actually
+ // added
} catch (InvalidGFF3FieldException ivfe)
{
System.err.println(ivfe);
{
int strand = sf.getStrand();
// exonerate cdna/protein map
- // look for fields
+ // look for fields
List<SequenceI> querySeq = findNames(align, newseqs,
- relaxedIdMatching, set.get(attr="Query"));
- if (querySeq==null || querySeq.size()!=1)
+ relaxedIdMatching, set.get(attr = "Query"));
+ if (querySeq == null || querySeq.size() != 1)
{
- throw new InvalidGFF3FieldException( attr, set,
+ throw new InvalidGFF3FieldException(attr, set,
"Expecting exactly one sequence in Query field (got "
+ set.get(attr) + ")");
}
- if (set.containsKey(attr="Align"))
+ if (set.containsKey(attr = "Align"))
{
// process the align maps and create cdna/protein maps
// ideally, the query sequences are in the alignment, but maybe not...
-
+
AlignedCodonFrame alco = new AlignedCodonFrame();
MapList codonmapping = constructCodonMappingFromAlign(set, attr,
strand);
}
private MapList constructCodonMappingFromAlign(
- Map<String, List<String>> set,
- String attr, int strand) throws InvalidGFF3FieldException
+ Map<String, List<String>> set, String attr, int strand)
+ throws InvalidGFF3FieldException
{
if (strand == 0)
{
}
}
}
-
+
}
- if (match==null && newseqs!=null)
+ if (match == null && newseqs != null)
{
match = new SequenceDummy(seqId);
if (relaxedIdMatching)
{
- matcher.addAll(Arrays.asList(new SequenceI[]
- { match }));
+ matcher.addAll(Arrays.asList(new SequenceI[] { match }));
}
// add dummy sequence to the newseqs list
newseqs.add(match);
}
return match;
}
+
public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
{
if (sf.getDescription() == null)
*
* @param seqs
* source of sequence features
- * @param visible
+ * @param map
* hash of feature types and colours
* @return features file contents
*/
- public String printJalviewFormat(SequenceI[] seqs, Map<String,Object> visible)
+ public String printJalviewFormat(SequenceI[] seqs,
+ Map<String, FeatureColourI> map)
{
- return printJalviewFormat(seqs, visible, true, true);
+ return printJalviewFormat(seqs, map, true, true);
}
/**
* generate a features file for seqs with colours from visible (if any)
*
- * @param seqs
+ * @param sequences
* source of features
* @param visible
* hash of Colours for each feature type
* of group or type)
* @return features file contents
*/
- public String printJalviewFormat(SequenceI[] seqs, Map visible,
+ public String printJalviewFormat(SequenceI[] sequences,
+ Map<String, FeatureColourI> visible,
boolean visOnly, boolean nonpos)
{
StringBuffer out = new StringBuffer();
// 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 ?
- Iterator en = visible.keySet().iterator();
- String type, color;
+ Iterator<String> en = visible.keySet().iterator();
+ String feature, color;
while (en.hasNext())
{
- type = en.next().toString();
+ feature = en.next();
- if (visible.get(type) instanceof GraduatedColor)
+ FeatureColourI gc = visible.get(feature);
+ if (!gc.isSimpleColour())
{
- GraduatedColor gc = (GraduatedColor) visible.get(type);
color = (gc.isColourByLabel() ? "label|" : "")
- + Format.getHexString(gc.getMinColor()) + "|"
- + Format.getHexString(gc.getMaxColor())
- + (gc.isAutoScale() ? "|" : "|abso|") + gc.getMin() + "|"
+ + Format.getHexString(gc.getMinColour()) + "|"
+ + Format.getHexString(gc.getMaxColour())
+ + (gc.isAutoScaled() ? "|" : "|abso|") + gc.getMin()
+ + "|"
+ gc.getMax() + "|";
- if (gc.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
+ if (gc.isBelowThreshold())
{
- 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();
+ color += "below|" + gc.getThreshold();
+ }
+ else if (gc.isAboveThreshold())
+ {
+ color += "above|" + gc.getThreshold();
}
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())));
+ color = Format.getHexString(gc.getColour());
}
- out.append(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(feature);
out.append("\t");
out.append(color);
out.append(newline);
int groupIndex = 0;
boolean isnonpos = false;
- for (int i = 0; i < seqs.length; i++)
+ for (int i = 0; i < sequences.length; i++)
{
- next = seqs[i].getSequenceFeatures();
+ next = sequences[i].getSequenceFeatures();
if (next != null)
{
for (int j = 0; j < next.length; j++)
group = null;
}
- for (int i = 0; i < seqs.length; i++)
+ for (int i = 0; i < sequences.length; i++)
{
- next = seqs[i].getSequenceFeatures();
+ next = sequences[i].getSequenceFeatures();
if (next != null)
{
for (int j = 0; j < next.length; j++)
out.append("\t");
}
- out.append(seqs[i].getName());
+ out.append(sequences[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)
+ if (!Float.isNaN(next[j].score))
{
out.append("\t");
out.append(next[j].score);
* default.
*
* @param seqs
- * @param visible
+ * @param map
* @return
*/
- public String printGFFFormat(SequenceI[] seqs, Map<String,Object> visible)
+ public String printGFFFormat(SequenceI[] seqs,
+ Map<String, FeatureColourI> map)
{
- return printGFFFormat(seqs, visible, true, true);
+ return printGFFFormat(seqs, map, true, true);
}
- public String printGFFFormat(SequenceI[] seqs, Map<String,Object> visible,
- boolean visOnly, boolean nonpos)
+ public String printGFFFormat(SequenceI[] seqs,
+ Map<String, FeatureColourI> map, boolean visOnly, boolean nonpos)
{
StringBuffer out = new StringBuffer();
SequenceFeature[] next;
{
isnonpos = next[j].begin == 0 && next[j].end == 0;
if ((!nonpos && isnonpos)
- || (!isnonpos && visOnly && !visible
+ || (!isnonpos && visOnly && !map
.containsKey(next[j].type)))
{
continue;
/**
* this is only for the benefit of object polymorphism - method does nothing.
*/
+ @Override
public void parse()
{
// IGNORED
*
* @return error message
*/
+ @Override
public String print()
{
return "USE printGFFFormat() or printJalviewFormat()";
git://source.jalview.org / jalview.git / blobdiff