X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FContactMapRenderer.java;h=edf3ca2100011415f6159f898623b959e41878d6;hb=0b5e12b6e86604263fe6b45814b50d7ccc60d1ee;hp=f5c4c311f207f4e4b70f30543ab6cedb773ff257;hpb=47a6e772d30202cfb73fe296fea6c8474bc2b8bb;p=jalview.git diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java index f5c4c31..edf3ca2 100644 --- a/src/jalview/renderer/ContactMapRenderer.java +++ b/src/jalview/renderer/ContactMapRenderer.java @@ -5,12 +5,14 @@ package jalview.renderer; import java.awt.Color; import java.awt.Graphics; +import java.util.Iterator; import jalview.api.AlignViewportI; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; import jalview.datamodel.ColumnSelection; import jalview.datamodel.ContactListI; +import jalview.datamodel.ContactMatrixI; import jalview.datamodel.ContactRange; import jalview.datamodel.HiddenColumns; import jalview.renderer.api.AnnotationRowRendererI; @@ -19,8 +21,89 @@ import jalview.renderer.api.AnnotationRowRendererI; * @author jprocter * */ -public class ContactMapRenderer implements AnnotationRowRendererI +public abstract class ContactMapRenderer implements AnnotationRowRendererI { + /** + * bean holding colours for shading + * + * @author jprocter + * + */ + public class Shading + { + /** + * shown when no data available from map + */ + Color no_data; + /** + * shown for region not currently visible - should normally not see this + */ + Color hidden; + /** + * linear shading scheme min/max + */ + Color maxColor, minColor; + + /** + * linear shading scheme min/max for selected region + */ + Color selMinColor, selMaxColor; + + /** + * + * @param no_data - colour when no data available + * @param hidden - colour if this row is hidden + * @param maxColor - colour for maximum value of contact + * @param minColor - colour for minimum value of contact + * @param selMinColor - min colour if the contact has been selected + * @param selMaxColor - max colour if contact is selected + */ + public Shading(Color no_data, Color hidden, Color maxColor, + Color minColor, Color selMinColor, Color selMaxColor) + { + super(); + this.no_data = no_data; + this.hidden = hidden; + this.maxColor = maxColor; + this.minColor = minColor; + this.selMinColor = selMinColor; + this.selMaxColor = selMaxColor; + } + + } + + final Shading shade; + + /** + * build an EBI-AlphaFold style renderer of PAE matrices + * + * @return + */ + public static ContactMapRenderer newPAERenderer() + { + return new ContactMapRenderer() + { + @Override + public Shading getShade() + { + return new Shading(Color.pink, Color.red, + + new Color(247, 252, 245), new Color(0, 68, 28), + new Color(28, 0, 68), new Color(245,247,252)); + } + }; + } + + /** + * + * @return instance of Shading used to initialise the renderer + */ + public abstract Shading getShade(); + + public ContactMapRenderer() + { + this.shade = getShade(); + } @Override public void renderRow(Graphics g, int charWidth, int charHeight, @@ -28,21 +111,27 @@ public class ContactMapRenderer implements AnnotationRowRendererI HiddenColumns hiddenColumns, ColumnSelection columnSelection, AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes, int eRes, float min, float max, int y) - { + { if (sRes > aa_annotations.length) { return; } eRes = Math.min(eRes, aa_annotations.length); - int x = 0, y2 = y; - - g.setColor(Color.pink); - - g.drawLine(x, y2, (eRes - sRes) * charWidth, y2); + int x = 0, topY = y; + // uncomment below to render whole area of matrix as pink + // g.setColor(shade.no_data); + // g.fillRect(x, topY-_aa.height, (eRes - sRes) * charWidth, _aa.graphHeight); + + boolean showGroups = _aa.isShowGroupsForContactMatrix(); int column; int aaMax = aa_annotations.length - 1; + ContactMatrixI cm = viewport.getContactMatrix(_aa); + if (cm==null) + { + return; + } while (x < eRes - sRes) { column = sRes + x; @@ -67,85 +156,85 @@ public class ContactMapRenderer implements AnnotationRowRendererI x++; continue; } - if (_aa.sequenceRef != null) - { - // get the sequence position for the column - column = _aa.sequenceRef.findPosition(column) - 1; - } ContactListI contacts = viewport.getContactList(_aa, column); if (contacts == null) { - return; - } - int contact_height = contacts.getContactHeight(); - // fractional number of contacts covering each pixel - double contacts_per_pixel = ((double) contact_height) - / ((double) _aa.graphHeight); - - int pixels_step; - - if (contacts_per_pixel >= 1) - { - // many contacts rendered per pixel - pixels_step = 1; - } - else - { - // pixel height for each contact - pixels_step = (int) Math - .ceil(((double) _aa.graphHeight) / (double) contact_height); + x++; + continue; } + // ContactListI from viewport can map column -> group + Color gpcol = (cm == null) ? Color.white + : contacts.getColourForGroup(); // cm.getColourForGroup(cm.getGroupsFor(column)); + // feature still in development - highlight or omit regions hidden in + // the alignment - currently marks them as red rows + boolean maskHiddenCols = false; + // TODO: optionally pass visible column mask to the ContactGeometry object + // so it maps + // only visible contacts to geometry + // Bean holding mapping from contact list to pixels + // TODO: allow bracketing/limiting of range on contacts to render (like + // visible column mask but more flexible?) - int cstart = 0, cend; + // COntactListI provides mapping for column -> cm-groupmapping + final ContactGeometry cgeom = new ContactGeometry(contacts, + _aa.graphHeight); - for (int ht = y2, - eht = y2 - _aa.graphHeight; ht >= eht; ht -= pixels_step) + for (int ht = 0, botY = topY + - _aa.height; ht < _aa.graphHeight; ht += cgeom.pixels_step) { - cstart = (int) Math.floor(((double) y2 - ht) * contacts_per_pixel); - cend = (int) Math.min(contact_height, - Math.ceil(cstart + contacts_per_pixel * pixels_step)); + ContactGeometry.contactInterval ci = cgeom.mapFor(ht); + // cstart = (int) Math.floor(((double) y2 - ht) * contacts_per_pixel); + // cend = (int) Math.min(contact_height, + // Math.ceil(cstart + contacts_per_pixel * pixels_step)); - // TODO show maximum colour for range - sort of done - // also need a 'getMaxPosForRange(start,end)' to accurately render Color col; boolean rowsel = false; - if (!colsel && columnSelection != null) + boolean containsHidden = false; + if (columnSelection != null) + { + rowsel = cgeom.intersects(ci, columnSelection, hiddenColumns, + maskHiddenCols); + } + // TODO: show selected region + if (colsel || rowsel) { - if (_aa.sequenceRef == null) + + col = getSelectedColorForRange(min, max, contacts, ci.cStart, + ci.cEnd); + if (colsel && rowsel) { - rowsel = columnSelection.intersects(cstart, cend); + col = new Color(col.getBlue(), col.getGreen(), col.getRed()); } else { - // TODO check we have correctly mapped cstart to local sequence - // numbering - int s = _aa.sequenceRef.findIndex(cstart); - int e = _aa.sequenceRef.findIndex(cend); - if (s > 0 && s < _aa.sequenceRef.getLength()) - { - rowsel = columnSelection.intersects(s, e); - } + col = new Color(col.getBlue(), col.getBlue(), col.getBlue()); } } - // TODO: show selected region - if (colsel || rowsel) + else { - - col = getSelectedColorForRange(min, max, contacts, cstart, cend); - g.setColor(col); + col = getColorForRange(min, max, contacts, ci.cStart, ci.cEnd); } - else + if (containsHidden) { - col = getColorForRange(min, max, contacts, cstart, cend); - g.setColor(col); + col = shade.hidden; } - if (pixels_step > 1) + if (showGroups && gpcol != null && gpcol != Color.white) { - g.fillRect(x * charWidth, ht, charWidth, 1 + pixels_step); + // todo - could overlay group as a transparent rectangle ? + col = new Color( + (int) (((float) (col.getRed() + gpcol.getRed())) / 2f), + (int) (((float) (col.getGreen() + gpcol.getGreen())) + / 2f), + (int) (((float) (col.getBlue() + gpcol.getBlue())) / 2f)); + } + g.setColor(col); + if (cgeom.pixels_step > 1) + { + g.fillRect(x * charWidth, botY+ht, charWidth, cgeom.pixels_step); } else { - g.drawLine(x * charWidth, ht, (x + 1) * charWidth, ht); + g.drawLine(x * charWidth, botY+ht, (x + 1) * charWidth, botY+ht); } } x++; @@ -153,14 +242,10 @@ public class ContactMapRenderer implements AnnotationRowRendererI } - // Shading parameters - Color minColor = Color.white, maxColor = Color.green.darker().darker(), - selMaxColor = Color.magenta.darker(); - Color shadeFor(float min, float max, float value) { - return jalview.util.ColorUtils.getGraduatedColour(value, 0, minColor, - max, maxColor); + return jalview.util.ColorUtils.getGraduatedColour(value, 0, + shade.minColor, max, shade.maxColor); } public Color getColorForRange(float min, float max, ContactListI cl, @@ -176,8 +261,8 @@ public class ContactMapRenderer implements AnnotationRowRendererI { ContactRange cr = cl.getRangeFor(i, j); // average for moment - probably more interested in maxIntProj though - return jalview.util.ColorUtils.getGraduatedColour((float) cr.getMean(), - 0, minColor, max, selMaxColor); + return jalview.util.ColorUtils.getGraduatedColour((float) cr.getMin(), + 0, shade.selMinColor, max, shade.selMaxColor); } }