return s.hashCode() + getBegin() + getEnd() + (int) getScore()
+ getStrand();
}
+
+ /**
+ * Answers true if the feature's start/end values represent two related
+ * positions, rather than ends of a range. Such features may be visualised or
+ * reported differently to features on a range.
+ */
+ public boolean isContactFeature()
+ {
+ // TODO abstract one day to a FeatureType class
+ if ("disulfide bond".equalsIgnoreCase(type)
+ || "disulphide bond".equalsIgnoreCase(type))
+ {
+ return true;
+ }
+ return false;
+ }
}
if (onscreen
|| (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
{
- return (getIdPanel().getWidth() > 0 ? getIdPanel().getWidth()
- : calculateIdWidth().width + 4);
+ int w = getIdPanel().getWidth();
+ return (w > 0 ? w : calculateIdWidth().width + 4);
}
return idwidth.intValue() + 4;
}
public void makePNGImageMap(File imgMapFile, String imageName)
{
- // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
+ // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
// ////////////////////////////////////////////
int idWidth = getVisibleIdWidth(false);
FontMetrics fm = getFontMetrics(av.getFont());
{
int s, sSize = av.getAlignment().getHeight(), res, alwidth = av
.getAlignment().getWidth(), g, gSize, f, fSize, sy;
- StringBuffer text = new StringBuffer();
PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
out.println(jalview.io.HTMLOutput.getImageMapHTML());
out.println("<img src=\"" + imageName
SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
for (res = 0; res < alwidth; res++)
{
- text = new StringBuffer();
+ StringBuilder text = new StringBuilder();
String triplet = null;
if (av.getAlignment().isNucleotide())
{
{
if (text.length() < 1)
{
- text.append("<area shape=\"rect\" coords=\""
- + (idWidth + res * av.getCharWidth()) + "," + sy
- + "," + (idWidth + (res + 1) * av.getCharWidth())
- + "," + (av.getCharHeight() + sy) + "\""
- + " onMouseOver=\"toolTip('" + alIndex + " "
- + triplet);
+ text.append("<area shape=\"rect\" coords=\"")
+ .append((idWidth + res * av.getCharWidth()))
+ .append(",").append(sy).append(",")
+ .append((idWidth + (res + 1) * av.getCharWidth()))
+ .append(",").append((av.getCharHeight() + sy))
+ .append("\"").append(" onMouseOver=\"toolTip('")
+ .append(alIndex).append(" ").append(triplet);
}
if (groups[g].getStartRes() < res
&& groups[g].getEndRes() > res)
{
- text.append("<br><em>" + groups[g].getName() + "</em>");
+ text.append("<br><em>").append(groups[g].getName())
+ .append("</em>");
}
}
{
if (text.length() < 1)
{
- text.append("<area shape=\"rect\" coords=\""
- + (idWidth + res * av.getCharWidth()) + "," + sy
- + "," + (idWidth + (res + 1) * av.getCharWidth())
- + "," + (av.getCharHeight() + sy) + "\""
- + " onMouseOver=\"toolTip('" + alIndex + " "
- + triplet);
+ text.append("<area shape=\"rect\" coords=\"")
+ .append((idWidth + res * av.getCharWidth()))
+ .append(",").append(sy).append(",")
+ .append((idWidth + (res + 1) * av.getCharWidth()))
+ .append(",").append((av.getCharHeight() + sy))
+ .append("\"").append(" onMouseOver=\"toolTip('")
+ .append(alIndex).append(" ").append(triplet);
}
fSize = features.length;
for (f = 0; f < fSize; f++)
if ((features[f].getBegin() <= seq.findPosition(res))
&& (features[f].getEnd() >= seq.findPosition(res)))
{
- if (features[f].getType().equals("disulfide bond"))
+ if (features[f].isContactFeature())
{
if (features[f].getBegin() == seq.findPosition(res)
|| features[f].getEnd() == seq
.findPosition(res))
{
- text.append("<br>disulfide bond "
- + features[f].getBegin() + ":"
- + features[f].getEnd());
+ text.append("<br>").append(features[f].getType())
+ .append(" ").append(features[f].getBegin())
+ .append(":").append(features[f].getEnd());
}
}
else
&& !features[f].getType().equals(
features[f].getDescription()))
{
- text.append(" " + features[f].getDescription());
+ text.append(" ").append(features[f].getDescription());
}
if (features[f].getValue("status") != null)
{
- text.append(" (" + features[f].getValue("status")
- + ")");
+ text.append(" (").append(features[f].getValue("status"))
+ .append(")");
}
}
}
void appendFeature(final StringBuilder sb, int rpos,
Map<String, float[][]> minmax, SequenceFeature feature)
{
- String tmpString;
- if (feature.getType().equals("disulfide bond"))
+ if (feature.isContactFeature())
{
if (feature.getBegin() == rpos || feature.getEnd() == rpos)
{
{
sb.append("<br>");
}
- sb.append("disulfide bond ").append(feature.getBegin()).append(":")
+ sb.append(feature.getType()).append(" ").append(feature.getBegin())
+ .append(":")
.append(feature.getEnd());
}
}
if (feature.getDescription() != null
&& !feature.description.equals(feature.getType()))
{
- tmpString = feature.getDescription();
+ String tmpString = feature.getDescription();
String tmp2up = tmpString.toUpperCase();
int startTag = tmp2up.indexOf("<HTML>");
if (startTag > -1)
// check score should be shown
if (!Float.isNaN(feature.getScore()))
{
- float[][] rng = (minmax == null) ? null : ((float[][]) minmax
- .get(feature.getType()));
+ float[][] rng = (minmax == null) ? null : minmax.get(feature
+ .getType());
if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
{
- sb.append(" Score=" + feature.getScore());
+ sb.append(" Score=").append(String.valueOf(feature.getScore()));
}
}
String status = (String) feature.getValue("status");
}
/**
- * This is used by the Molecule Viewer and Overview to get the accurate colour
- * of the rendered sequence
+ * This is used by Structure Viewers and the Overview Window to get the
+ * feature colour of the rendered sequence, returned as an RGB value
+ *
+ * @param defaultColour
+ * @param seq
+ * @param column
+ * @return
*/
- public synchronized int findFeatureColour(int initialCol,
+ public synchronized int findFeatureColour(int defaultColour,
final SequenceI seq, int column)
{
if (!av.isShowSequenceFeatures())
{
- return initialCol;
+ return defaultColour;
}
SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
if (lastSequenceFeatures == null || sfSize == 0)
{
- return initialCol;
+ return defaultColour;
}
if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
if (offscreenImage != null)
{
- offscreenImage.setRGB(0, 0, initialCol);
+ offscreenImage.setRGB(0, 0, defaultColour);
drawSequence(offscreenImage.getGraphics(), lastSeq, column, column, 0);
return offscreenImage.getRGB(0, 0);
if (currentColour == null)
{
- return initialCol;
+ return defaultColour;
}
else
{
int epos;
+ /**
+ * Draws the sequence on the graphics context, or just determines the colour
+ * that would be drawn (if flag offscreenrender is true).
+ *
+ * @param g
+ * @param seq
+ * @param start
+ * start column (or sequence position in offscreenrender mode)
+ * @param end
+ * end column (not used in offscreenrender mode)
+ * @param y1
+ * vertical offset at which to draw on the graphics
+ */
public synchronized void drawSequence(Graphics g, final SequenceI seq,
int start, int end, int y1)
{
}
sfSize = lastSequenceFeatures.length;
- String type;
for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
{
- type = renderOrder[renderIndex];
-
- if (type == null || !showFeatureOfType(type))
+ String type = renderOrder[renderIndex];
+ if (!showFeatureOfType(type))
{
continue;
}
continue;
}
- if (featureGroups != null
- && sequenceFeature.featureGroup != null
- && sequenceFeature.featureGroup.length() != 0
- && featureGroups.containsKey(sequenceFeature.featureGroup)
- && !featureGroups.get(sequenceFeature.featureGroup)
- .booleanValue())
+ if (featureGroupNotShown(sequenceFeature))
{
continue;
}
+ /*
+ * check feature overlaps the visible part of the alignment,
+ * unless doing offscreenRender (to the Overview window or a
+ * structure viewer) which is not limited
+ */
if (!offscreenRender
&& (sequenceFeature.getBegin() > epos || sequenceFeature
.getEnd() < spos))
continue;
}
+ Color featureColour = getColour(sequenceFeature);
+ boolean isContactFeature = sequenceFeature.isContactFeature();
+
if (offscreenRender && offscreenImage == null)
{
- if (sequenceFeature.begin <= start
- && sequenceFeature.end >= start)
+ /*
+ * offscreen mode with no image (image is only needed if transparency
+ * is applied to feature colours) - just check feature is rendered at
+ * the requested position (start == sequence position in this mode)
+ */
+ boolean featureIsAtPosition = sequenceFeature.begin <= start
+ && sequenceFeature.end >= start;
+ if (isContactFeature)
+ {
+ featureIsAtPosition = sequenceFeature.begin == start
+ || sequenceFeature.end == start;
+ }
+ if (featureIsAtPosition)
{
// this is passed out to the overview and other sequence renderers
// (e.g. molecule viewer) to get displayed colour for rendered
// sequence
- currentColour = new Integer(getColour(sequenceFeature).getRGB());
+ currentColour = new Integer(featureColour.getRGB());
// used to be retreived from av.featuresDisplayed
// currentColour = av.featuresDisplayed
// .get(sequenceFeatures[sfindex].type);
}
}
- else if (sequenceFeature.type.equals("disulfide bond"))
+ else if (isContactFeature)
{
renderFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1,
- seq.findIndex(sequenceFeature.begin) - 1,
- getColour(sequenceFeature)
- // new Color(((Integer) av.featuresDisplayed
- // .get(sequenceFeatures[sfindex].type)).intValue())
- , start, end, y1);
+ seq.findIndex(sequenceFeature.begin) - 1, featureColour,
+ start, end, y1);
renderFeature(g, seq, seq.findIndex(sequenceFeature.end) - 1,
- seq.findIndex(sequenceFeature.end) - 1,
- getColour(sequenceFeature)
- // new Color(((Integer) av.featuresDisplayed
- // .get(sequenceFeatures[sfindex].type)).intValue())
- , start, end, y1);
+ seq.findIndex(sequenceFeature.end) - 1, featureColour,
+ start, end, y1);
}
else if (showFeature(sequenceFeature))
renderScoreFeature(g, seq,
seq.findIndex(sequenceFeature.begin) - 1,
seq.findIndex(sequenceFeature.end) - 1,
- getColour(sequenceFeature), start, end, y1,
+ featureColour, start, end, y1,
normaliseScore(sequenceFeature));
}
else
{
renderFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1,
seq.findIndex(sequenceFeature.end) - 1,
- getColour(sequenceFeature), start, end, y1);
+ featureColour, start, end, y1);
}
}
-
}
-
}
if (transparency != 1.0f && g != null)
}
/**
+ * Answers true if the feature belongs to a feature group which is not
+ * currently displayed, else false
+ *
+ * @param sequenceFeature
+ * @return
+ */
+ protected boolean featureGroupNotShown(
+ final SequenceFeature sequenceFeature)
+ {
+ return featureGroups != null
+ && sequenceFeature.featureGroup != null
+ && sequenceFeature.featureGroup.length() != 0
+ && featureGroups.containsKey(sequenceFeature.featureGroup)
+ && !featureGroups.get(sequenceFeature.featureGroup)
+ .booleanValue();
+ }
+
+ /**
* Called when alignment in associated view has new/modified features to
* discover and display.
*
return fc.isColored(sequenceFeature);
}
+ /**
+ * Answers true if the feature type is currently selected to be displayed,
+ * else false
+ *
+ * @param type
+ * @return
+ */
protected boolean showFeatureOfType(String type)
{
- return av.getFeaturesDisplayed().isVisible(type);
+ return type == null ? false : av.getFeaturesDisplayed().isVisible(type);
}
@Override
sf1.setStatus("new");
assertTrue(sf1.equals(sf2));
}
+
+ @Test(groups = { "Functional" })
+ public void testIsContactFeature()
+ {
+ SequenceFeature sf = new SequenceFeature("type", "desc", 22, 33, 12.5f,
+ "group");
+ assertFalse(sf.isContactFeature());
+ sf.setType("");
+ assertFalse(sf.isContactFeature());
+ sf.setType(null);
+ assertFalse(sf.isContactFeature());
+ sf.setType("Disulfide Bond");
+ assertTrue(sf.isContactFeature());
+ sf.setType("disulfide bond");
+ assertTrue(sf.isContactFeature());
+ sf.setType("Disulphide Bond");
+ assertTrue(sf.isContactFeature());
+ sf.setType("disulphide bond");
+ assertTrue(sf.isContactFeature());
+ }
}
git://source.jalview.org / jalview.git / commitdiff