X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFeaturesFile.java;h=cfc08fbdcaebb2e8917e9fe0e0c8d0c27e342806;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=8f5e4bd1bd145759ceae74e89c82ee0b86927b0b;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 8f5e4bd..cfc08fb 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -1,5 +1,5 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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.
@@ -104,9 +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("#"))
@@ -115,6 +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;
@@ -140,58 +150,109 @@ 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)
+ 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)
+ {
+ labelCol = true;
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); // skip '|'
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
+ }
+ String abso = null, minval, maxval;
+ if (mincol != null)
{
- if (maxval.length() > 0)
+ // at least four more tokens
+ if (mincol.equals("|"))
{
- max = new Float(maxval).floatValue();
+ mincol="";
+ } else {
+ gcol.nextToken(); // skip next '|'
}
- } catch (Exception e)
+ // 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
{
@@ -209,6 +270,8 @@ public class FeaturesFile extends AlignFile
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;
@@ -240,9 +303,10 @@ public class FeaturesFile extends AlignFile
}
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)
@@ -260,7 +324,7 @@ 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");
}
@@ -616,8 +680,8 @@ public class FeaturesFile extends AlignFile
if (visible.get(type) instanceof GraduatedColor)
{
GraduatedColor gc = (GraduatedColor) visible.get(type);
- // TODO: NOW: colour by label, autoscale flags.
- color = Format.getHexString(gc.getMinColor()) + "|"
+ color = (gc.isColourByLabel() ? "label|" : "")
+ + Format.getHexString(gc.getMinColor()) + "|"
+ Format.getHexString(gc.getMaxColor())
+ (gc.isAutoScale() ? "|" : "|abso|") + gc.getMin() + "|"
+ gc.getMax() + "|";
@@ -754,9 +818,7 @@ public class FeaturesFile extends AlignFile
if (next[j].description.indexOf(href) == -1)
{
- out
- .append("" + label
- + "");
+ out.append("" + label + "");
}
}