X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fschemes%2FFeatureColour.java;h=bdc70c94718da9e0b5bb0f861c7895c8b339d14e;hb=73fd64da56448bcb2a7771cc174d9d9c62da87ad;hp=ce382c3af84267a67a7884241a3020e8beecd530;hpb=0b1c761dfaa8242f122cf868e8897a06ec6eb727;p=jalview.git
diff --git a/src/jalview/schemes/FeatureColour.java b/src/jalview/schemes/FeatureColour.java
index ce382c3..bdc70c9 100644
--- a/src/jalview/schemes/FeatureColour.java
+++ b/src/jalview/schemes/FeatureColour.java
@@ -2,14 +2,18 @@ package jalview.schemes;
import jalview.api.FeatureColourI;
import jalview.datamodel.SequenceFeature;
+import jalview.util.Format;
import java.awt.Color;
+import java.util.StringTokenizer;
/**
* A class that wraps either a simple colour or a graduated colour
*/
public class FeatureColour implements FeatureColourI
{
+ private static final String BAR = "|";
+
final private Color colour;
final private Color minColour;
@@ -49,6 +53,204 @@ public class FeatureColour implements FeatureColourI
final private float deltaBlue;
/**
+ * Parses a Jalview features file format colour descriptor
+ * [label|][mincolour|maxcolour
+ * |[absolute|]minvalue|maxvalue|thresholdtype|thresholdvalue] Examples:
+ *
+ * - red
+ * - a28bbb
+ * - 25,125,213
+ * - label
+ * - label|||0.0|0.0|above|12.5
+ * - label|||0.0|0.0|below|12.5
+ * - red|green|12.0|26.0|none
+ * - a28bbb|3eb555|12.0|26.0|above|12.5
+ * - a28bbb|3eb555|abso|12.0|26.0|below|12.5
+ *
+ *
+ * @param descriptor
+ * @return
+ * @throws IllegalArgumentException
+ * if not parseable
+ */
+ public static FeatureColour parseJalviewFeatureColour(String descriptor)
+ {
+ StringTokenizer gcol = new StringTokenizer(descriptor, "|", true);
+ float min = Float.MIN_VALUE;
+ float max = Float.MAX_VALUE;
+ boolean labelColour = false;
+
+ String mincol = gcol.nextToken();
+ if (mincol == "|")
+ {
+ throw new IllegalArgumentException(
+ "Expected either 'label' or a colour specification in the line: "
+ + descriptor);
+ }
+ String maxcol = null;
+ if (mincol.toLowerCase().indexOf("label") == 0)
+ {
+ labelColour = true;
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
+ // skip '|'
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
+ }
+
+ if (!labelColour && !gcol.hasMoreTokens())
+ {
+ /*
+ * only a simple colour specification - parse it
+ */
+ Color colour = UserColourScheme.getColourFromString(descriptor);
+ if (colour == null)
+ {
+ throw new IllegalArgumentException("Invalid colour descriptor: "
+ + descriptor);
+ }
+ return new FeatureColour(colour);
+ }
+
+ /*
+ * autoScaled == true: colours range over actual score range
+ * autoScaled == false ('abso'): colours range over min/max range
+ */
+ boolean autoScaled = true;
+ String tok = null, minval, maxval;
+ if (mincol != null)
+ {
+ // at least four more tokens
+ if (mincol.equals("|"))
+ {
+ mincol = "";
+ }
+ else
+ {
+ gcol.nextToken(); // skip next '|'
+ }
+ maxcol = gcol.nextToken();
+ if (maxcol.equals("|"))
+ {
+ maxcol = "";
+ }
+ else
+ {
+ gcol.nextToken(); // skip next '|'
+ }
+ tok = gcol.nextToken();
+ gcol.nextToken(); // skip next '|'
+ if (tok.toLowerCase().startsWith("abso"))
+ {
+ minval = gcol.nextToken();
+ gcol.nextToken(); // skip next '|'
+ autoScaled = false;
+ }
+ else
+ {
+ minval = tok;
+ }
+ maxval = gcol.nextToken();
+ if (gcol.hasMoreTokens())
+ {
+ gcol.nextToken(); // skip next '|'
+ }
+ try
+ {
+ if (minval.length() > 0)
+ {
+ min = new Float(minval).floatValue();
+ }
+ } catch (Exception e)
+ {
+ throw new IllegalArgumentException(
+ "Couldn't parse the minimum value for graduated colour ("
+ + descriptor + ")");
+ }
+ try
+ {
+ if (maxval.length() > 0)
+ {
+ max = new Float(maxval).floatValue();
+ }
+ } catch (Exception e)
+ {
+ throw new IllegalArgumentException(
+ "Couldn't parse the maximum value for graduated colour ("
+ + descriptor + ")");
+ }
+ }
+ else
+ {
+ // add in some dummy min/max colours for the label-only
+ // colourscheme.
+ mincol = "FFFFFF";
+ maxcol = "000000";
+ }
+
+ /*
+ * construct the FeatureColour
+ */
+ FeatureColour featureColour;
+ try
+ {
+ featureColour = new FeatureColour(
+ new UserColourScheme(mincol).findColour('A'),
+ new UserColourScheme(maxcol).findColour('A'), min, max);
+ featureColour.setColourByLabel(labelColour);
+ featureColour.setAutoScaled(autoScaled);
+ // 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"))
+ {
+ featureColour.setBelowThreshold(true);
+ }
+ else if (ttype.toLowerCase().startsWith("above"))
+ {
+ featureColour.setAboveThreshold(true);
+ }
+ else
+ {
+ if (!ttype.toLowerCase().startsWith("no"))
+ {
+ System.err.println("Ignoring unrecognised threshold type : "
+ + ttype);
+ }
+ }
+ }
+ if (featureColour.hasThreshold())
+ {
+ try
+ {
+ gcol.nextToken();
+ tval = gcol.nextToken();
+ featureColour.setThreshold(new Float(tval).floatValue());
+ } catch (Exception e)
+ {
+ System.err.println("Couldn't parse threshold value as a float: ("
+ + tval + ")");
+ }
+ }
+ 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");
+ }
+ return featureColour;
+ } catch (Exception e)
+ {
+ throw new IllegalArgumentException(e.getMessage());
+ }
+ }
+
+ /**
* Default constructor
*/
public FeatureColour()
@@ -63,8 +265,8 @@ public class FeatureColour implements FeatureColourI
*/
public FeatureColour(Color c)
{
- minColour = null;
- maxColour = null;
+ minColour = Color.WHITE;
+ maxColour = Color.BLACK;
minRed = 0f;
minGreen = 0f;
minBlue = 0f;
@@ -115,6 +317,7 @@ public class FeatureColour implements FeatureColourI
*/
public FeatureColour(FeatureColour fc)
{
+ graduatedColour = fc.graduatedColour;
colour = fc.colour;
minColour = fc.minColour;
maxColour = fc.maxColour;
@@ -157,8 +360,7 @@ public class FeatureColour implements FeatureColourI
* Sets the 'graduated colour' flag. If true, also sets 'colour by label' to
* false.
*/
- @Override
- public void setGraduatedColour(boolean b)
+ void setGraduatedColour(boolean b)
{
graduatedColour = b;
if (b)
@@ -418,4 +620,54 @@ public class FeatureColour implements FeatureColourI
return isAboveThreshold() || isBelowThreshold();
}
+ @Override
+ public String toJalviewFormat(String featureType)
+ {
+ String colourString = null;
+ if (isSimpleColour())
+ {
+ colourString = Format.getHexString(getColour());
+ }
+ else
+ {
+ StringBuilder sb = new StringBuilder(32);
+ if (isColourByLabel())
+ {
+ sb.append("label");
+ if (hasThreshold())
+ {
+ sb.append(BAR).append(BAR).append(BAR);
+ }
+ }
+ if (isGraduatedColour())
+ {
+ sb.append(Format.getHexString(getMinColour())).append(BAR);
+ sb.append(Format.getHexString(getMaxColour())).append(BAR);
+ if (!isAutoScaled())
+ {
+ sb.append("abso").append(BAR);
+ }
+ }
+ if (hasThreshold() || isGraduatedColour())
+ {
+ sb.append(getMin()).append(BAR);
+ sb.append(getMax()).append(BAR);
+ if (isBelowThreshold())
+ {
+ sb.append("below").append(BAR).append(getThreshold());
+ }
+ else if (isAboveThreshold())
+ {
+ sb.append("above").append(BAR).append(getThreshold());
+ }
+ else
+ {
+ sb.append("none");
+ }
+ }
+ colourString = sb.toString();
+ }
+ return String.format("%s\t%s", featureType, colourString);
+ }
+
}