X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=9180d52269a0dc660e80e4ef8639742bf384919c;hb=0ebbad305e982eeda562a1842362dc415c36cc8d;hp=55ce44a23ed71c3babeaee2d70c39d2d777ba1cf;hpb=0ccaf35f7e6a5cc62d4f433b39d574d0aa4b2d26;p=jalview.git diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index 55ce44a..9180d52 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -53,6 +53,7 @@ import javax.swing.ToolTipManager; import jalview.analysis.Conservation; import jalview.analysis.TreeModel; import jalview.api.AlignViewportI; +import jalview.bin.Console; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; import jalview.datamodel.BinaryNode; @@ -66,6 +67,7 @@ import jalview.datamodel.SequenceNode; import jalview.gui.JalviewColourChooser.ColourChooserListener; import jalview.schemes.ColourSchemeI; import jalview.structure.SelectionSource; +import jalview.util.ColorUtils; import jalview.util.Format; import jalview.util.MessageManager; import jalview.ws.datamodel.MappableContactMatrixI; @@ -143,7 +145,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, scrollPane = scroller; addMouseListener(this); addMouseMotionListener(this); - + ToolTipManager.sharedInstance().registerComponent(this); } @@ -180,6 +182,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, PaintRefresher.Refresh(tp, av.getSequenceSetId()); repaint(); } + /** * DOCUMENT ME! * @@ -221,6 +224,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, boolean has_placeholders = false; longestName = ""; + AlignmentAnnotation aa = tp.getAssocAnnotation(); + ContactMatrixI cm = (aa != null) ? av.getContactMatrix(aa) : null; + if (cm != null && cm.hasCutHeight()) + { + threshold = (float) cm.getCutHeight(); + } + for (int i = 0; i < leaves.size(); i++) { BinaryNode lf = leaves.elementAt(i); @@ -236,6 +246,18 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, longestName = TreeCanvas.PLACEHOLDER + ((Sequence) lf.element()).getName(); } + if (tp.isColumnWise() && cm != null) + { + // get color from group colours, if they are set for the matrix + try + { + Color col = cm.getGroupColorForPosition(parseColumnNode(lf)); + setColor(lf, col.brighter()); + } catch (NumberFormatException ex) + { + } + ; + } } setMarkPlaceholders(has_placeholders); @@ -259,7 +281,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * @param offy * DOCUMENT ME! */ - public void drawNode(Graphics g, BinaryNode node, float chunk, + public void drawNode(Graphics g, BinaryNode node, double chunk, double wscale, int width, int offx, int offy) { if (node == null) @@ -389,9 +411,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } int ystart = (node.left() == null ? 0 - : (int) (((BinaryNode) node.left()).ycount * chunk)) + offy; + : (int) (node.left().ycount * chunk)) + offy; int yend = (node.right() == null ? 0 - : (int) (((BinaryNode) node.right()).ycount * chunk)) + offy; + : (int) (node.right().ycount * chunk)) + offy; Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5); nodeHash.put(node, pos); @@ -774,8 +796,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (top.count == 0) { - top.count = ((BinaryNode) top.left()).count - + ((BinaryNode) top.right()).count; + top.count = top.left().count + top.right().count; } float chunk = (float) (height - (offy)) / top.count; @@ -864,7 +885,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Vector leaves = tree.findLeaves(highlightNode); if (tp.isColumnWise()) { - markColumnsFor(getAssociatedPanels(), leaves, Color.red,false); + markColumnsFor(getAssociatedPanels(), leaves, Color.red, false); } else { @@ -1025,7 +1046,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, threshold = 0f; } } - + Console.log.debug("Tree cut threshold set at:" + threshold); PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId()); repaint(); @@ -1040,8 +1061,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Map colors = new HashMap(); for (int i = 0; i < groups.size(); i++) { - Color col = new Color((int) (Math.random() * 255), - (int) (Math.random() * 255), (int) (Math.random() * 255)); + Color col = ColorUtils.getARandomColor(); + setColor(groups.get(i), col.brighter()); Vector l = tree.findLeaves(groups.get(i)); @@ -1071,41 +1092,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, cm.setColorForGroup(gp, colors.get(gp)); } } - // stash colors in linked annotation row. - // doesn't work yet. TESTS! - int sstart = aa.sequenceRef != null ? aa.sequenceRef.getStart() - 1 - : 0; - Annotation ae; - Color gpcol = null; - int[] seqpos = null; - for (BitSet gp : colors.keySet()) - { - gpcol = colors.get(gp); - for (int p = gp.nextSetBit(0); p >= 0 - && p < Integer.MAX_VALUE; p = gp.nextSetBit(p + 1)) - { - if (cm instanceof MappableContactMatrixI) - { - MappableContactMatrixI mcm = (MappableContactMatrixI) cm; - seqpos = mcm.getMappedPositionsFor(aa.sequenceRef, p); - if (seqpos == null) - { - // no mapping for this column. - continue; - } - // TODO: handle ranges... - ae = aa.getAnnotationForPosition(seqpos[0]); - } - else - { - ae = aa.getAnnotationForPosition(p + sstart); - } - if (ae != null) - { - ae.colour = gpcol.brighter().darker(); - } - } - } + cm.transferGroupColorsTo(aa); } } @@ -1124,14 +1111,19 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } } + private int parseColumnNode(BinaryNode bn) throws NumberFormatException + { + return Integer.parseInt( + bn.getName().substring(bn.getName().indexOf("c") + 1)); + } + private boolean isColumnForNodeSelected(BinaryNode bn) { SequenceI rseq = tp.assocAnnotation.sequenceRef; int colm = -1; try { - colm = Integer.parseInt( - bn.getName().substring(bn.getName().indexOf("c") + 1)); + colm = parseColumnNode(bn); } catch (Exception e) { return false; @@ -1144,16 +1136,17 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, ColumnSelection cs = av.getColumnSelection(); HiddenColumns hc = av.getAlignment().getHiddenColumns(); AlignmentAnnotation aa = tp.getAssocAnnotation(); - int offp=-1; + int offp = -1; if (aa != null) { ContactMatrixI cm = av.getContactMatrix(aa); - // generally, we assume cm has 1:1 mapping to annotation row - probably wrong + // generally, we assume cm has 1:1 mapping to annotation row - probably + // wrong // but.. if if (cm instanceof MappableContactMatrixI) { int[] pos; - // use the mappable's mapping - always the case for PAE Matrices so good + // use the mappable's mapping - always the case for PAE Matrices so good // for 2.11.3 MappableContactMatrixI mcm = (MappableContactMatrixI) cm; pos = mcm.getMappedPositionsFor(rseq, colm + 1); @@ -1162,16 +1155,18 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, { offp = rseq.findIndex(pos[0]); } - } else { + } + else + { offp = colm; } } - if (offp<=0) + if (offp <= 0) { return false; } - offp-=2; + offp -= 2; if (!av.hasHiddenColumns()) { return cs.contains(offp); @@ -1183,6 +1178,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } return false; } + private BitSet createColumnGroupFor(Vector l, Color col) { BitSet gp = new BitSet(); @@ -1198,8 +1194,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, // parse out from nodename try { - colm = Integer.parseInt( - bn.getName().substring(bn.getName().indexOf("c") + 1)); + colm = parseColumnNode(bn); } catch (Exception e) { continue; @@ -1241,17 +1236,16 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, { continue; } - if (mcm!=null) + if (mcm != null) { - int[] seqpos = mcm.getMappedPositionsFor( - tp.assocAnnotation.sequenceRef, colm); + int[] seqpos = mcm.getMappedPositionsFor(rseq, colm); if (seqpos == null) { // no mapping for this column. continue; } // TODO: handle ranges... - offp = seqpos[0]-1; + offp = rseq.findIndex(seqpos[0]) - 1; } else {