X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FContactMapRenderer.java;h=9f0cc3507590a848c250cea77f9b99419455fb38;hb=164fb77632cc3c9a3b5f5ac5290eadec920ffbc6;hp=b30206068fae574755bf851ac037310e12fa4487;hpb=306825ab43e7e4232a913f304f6d18b532213b83;p=jalview.git diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java index b302060..9f0cc35 100644 --- a/src/jalview/renderer/ContactMapRenderer.java +++ b/src/jalview/renderer/ContactMapRenderer.java @@ -1,5 +1,22 @@ -/** +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.renderer; @@ -11,6 +28,7 @@ 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 +37,97 @@ 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, @@ -35,14 +142,21 @@ public class ContactMapRenderer implements AnnotationRowRendererI } eRes = Math.min(eRes, aa_annotations.length); - int x = 0, y2 = y; + int x = 0, topY = y; - g.setColor(Color.pink); - - g.drawLine(x, y2, (eRes - sRes) * charWidth, y2); + // 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; @@ -70,42 +184,41 @@ public class ContactMapRenderer implements AnnotationRowRendererI ContactListI contacts = viewport.getContactList(_aa, column); if (contacts == null) { - return; + 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?) + + // 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 -= cgeom.pixels_step) + for (int ht = 0, botY = topY + - _aa.height; ht < _aa.graphHeight; ht += cgeom.pixels_step) { - ContactGeometry.contactInterval ci = cgeom.mapFor(y2 - ht, - y2 - ht + cgeom.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; + boolean containsHidden = false; if (columnSelection != null) { - if (_aa.sequenceRef == null) - { - rowsel = columnSelection.intersects(ci.cStart, ci.cEnd); - } - else - { - // TODO check we have correctly mapped cstart to local sequence - // numbering - int s = _aa.sequenceRef.findIndex(ci.cStart); - int e = _aa.sequenceRef.findIndex(ci.cEnd); - if (s > 0 && s < _aa.sequenceRef.getLength()) - { - rowsel = columnSelection.intersects(s, e); - } - } + rowsel = cgeom.intersects(ci, columnSelection, hiddenColumns, + maskHiddenCols); } // TODO: show selected region if (colsel || rowsel) @@ -121,20 +234,32 @@ public class ContactMapRenderer implements AnnotationRowRendererI { col = new Color(col.getBlue(), col.getBlue(), col.getBlue()); } - g.setColor(col); } else { col = getColorForRange(min, max, contacts, ci.cStart, ci.cEnd); - g.setColor(col); } + if (containsHidden) + { + col = shade.hidden; + } + if (showGroups && gpcol != null && gpcol != Color.white) + { + // todo - could overlay group as a transparent rectangle ? + col = new Color((int) ((col.getRed() + gpcol.getRed()) / 2f), + (int) ((col.getGreen() + gpcol.getGreen()) / 2f), + (int) ((col.getBlue() + gpcol.getBlue()) / 2f)); + } + g.setColor(col); if (cgeom.pixels_step > 1) { - g.fillRect(x * charWidth, ht, charWidth, 1 + cgeom.pixels_step); + 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++; @@ -142,17 +267,10 @@ public class ContactMapRenderer implements AnnotationRowRendererI } - // Shading parameters - // currently hardwired for alphafold - Color maxColor = new Color(246, 252, 243), - minColor = new Color(0, 60, 26), - selMinColor = new Color(26, 0, 60), - selMaxColor = new Color(243, 246, 252); - 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, @@ -168,8 +286,8 @@ 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, selMinColor, max, selMaxColor); + return jalview.util.ColorUtils.getGraduatedColour((float) cr.getMin(), + 0, shade.selMinColor, max, shade.selMaxColor); } }