X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=b4fd7465772d65d18cc40c69eaafbbce8d2016a4;hb=eacce9627f059fc2f9e880c81d8d1bdfbe7fe5b3;hp=d8ed3eeba55acdb6635868e15c22f167f30fc949;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index d8ed3ee..b4fd746 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -50,13 +50,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, JScrollPane scrollPane; AlignViewport av; Font font; - int fontSize = 12; + FontMetrics fm; boolean fitToWindow = true; boolean showDistances = false; boolean showBootstrap = false; boolean markPlaceholders = false; int offx = 20; - int offy = 20; + int offy; float threshold; String longestName; int labelLength = -1; @@ -74,19 +74,16 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * @param scroller DOCUMENT ME! * @param label DOCUMENT ME! */ - public TreeCanvas(AlignViewport av, NJTree tree, JScrollPane scroller, - String label) + public TreeCanvas(AlignViewport av, JScrollPane scroller) { this.av = av; - this.tree = tree; + font = av.getFont(); scrollPane = scroller; addMouseListener(this); - tree.findHeight(tree.getTopNode()); - longestName = label; - PaintRefresher.Register(this, av.alignment); } + /** * DOCUMENT ME! * @@ -102,7 +99,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, av.setSelectionGroup(selected); } - selected.setEndRes(av.alignment.getWidth()); + selected.setEndRes(av.alignment.getWidth()-1); selected.addOrRemove(sequence, true); PaintRefresher.Refresh(this, av.alignment); @@ -118,6 +115,30 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, { this.tree = tree; tree.findHeight(tree.getTopNode()); + + // Now have to calculate longest name based on the leaves + Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector()); + boolean has_placeholders = false; + longestName = ""; + + for (int i = 0; i < leaves.size(); i++) + { + SequenceNode lf = (SequenceNode) leaves.elementAt(i); + + if (lf.isPlaceholder()) + { + has_placeholders = true; + } + + if (longestName.length() < ( (Sequence) lf.element()).getName() + .length()) + { + longestName = TreeCanvas.PLACEHOLDER + + ( (Sequence) lf.element()).getName(); + } + } + + setMarkPlaceholders(has_placeholders); } /** @@ -174,7 +195,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (showDistances && (node.dist > 0)) { - nodeLabel = new Format("%5.2f").form(node.dist); + nodeLabel = new Format("%-.2f").form(node.dist); } if (showBootstrap) @@ -189,16 +210,16 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (!nodeLabel.equals("")) { - g.drawString(nodeLabel, xstart, ypos - 10); + g.drawString(nodeLabel, xstart+2, ypos - 2); } String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node.getName()) : node.getName(); - FontMetrics fm = g.getFontMetrics(font); + int charWidth = fm.stringWidth(name) + 3; - int charHeight = fm.getHeight(); + int charHeight = font.getSize(); - Rectangle rect = new Rectangle(xend + 20, ypos - charHeight, + Rectangle rect = new Rectangle(xend+10, ypos-charHeight/2, charWidth, charHeight); nameHash.put((SequenceI) node.element(), rect); @@ -211,12 +232,12 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, { g.setColor(Color.gray); - g.fillRect(xend + 10, ypos - charHeight + 3, charWidth, + g.fillRect(xend + 10, ypos-charHeight/2, charWidth, charHeight); g.setColor(Color.white); } - g.drawString(name, xend + 10, ypos); + g.drawString(name, xend + 10, ypos+fm.getDescent()); g.setColor(Color.black); } else @@ -252,8 +273,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (showDistances && (node.dist > 0)) { - g.drawString(new Format("%5.2f").form(node.dist), xstart, - ypos - 5); + g.drawString(new Format("%-.2f").form(node.dist).trim(), xstart+2, + ypos - 2); } } } @@ -319,7 +340,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, ((SequenceNode) top.right()).count; } - float chunk = (float) (height - (offy * 2)) / top.count; + float chunk = (float) (height - (offy)) / top.count; pickNode(pickBox, top, chunk, wscale, width, offx, offy); } @@ -503,52 +524,49 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, public void paintComponent(Graphics g) { super.paintComponent(g); - font = new Font("Verdana", Font.PLAIN, fontSize); g.setFont(font); - FontMetrics fm = g.getFontMetrics(font); - - if (nameHash.size() == 0) + if(tree==null) { - repaint(); + g.drawString("Calculating tree....", 20, getHeight()/2); } - - if (fitToWindow || - (!fitToWindow && - (scrollPane.getHeight() > ((fm.getHeight() * nameHash.size()) + - offy)))) + else { + fm = g.getFontMetrics(font); + + if (nameHash.size() == 0) + { + repaint(); + } + + if (fitToWindow || + (!fitToWindow && + (scrollPane.getHeight() > ( (fm.getHeight() * nameHash.size()) + + offy)))) + { draw(g, scrollPane.getWidth(), scrollPane.getHeight()); setPreferredSize(null); - } - else - { + } + else + { setPreferredSize(new Dimension(scrollPane.getWidth(), - fm.getHeight() * nameHash.size())); + fm.getHeight() * nameHash.size())); draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size()); - } + } - scrollPane.revalidate(); + scrollPane.revalidate(); + } } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getFontSize() - { - return fontSize; - } /** * DOCUMENT ME! * * @param fontSize DOCUMENT ME! */ - public void setFontSize(int fontSize) + public void setFont(Font font) { - this.fontSize = fontSize; + this.font = font; repaint(); } @@ -567,7 +585,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, g2.setColor(Color.white); g2.fillRect(0, 0, width, height); - labelLength = g2.getFontMetrics(font).stringWidth(longestName) + 20; //20 allows for scrollbar + g2.setFont(font); + + offy = font.getSize()+10; + + fm = g2.getFontMetrics(font); + + labelLength = fm.stringWidth(longestName) + 20; //20 allows for scrollbar float wscale = (float) (width - labelLength - (offx * 2)) / tree.getMaxHeight(); @@ -579,7 +603,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, ((SequenceNode) top.right()).count; } - float chunk = (float) (height - (offy * 2)) / top.count; + float chunk = (float) (height - (offy)) / top.count; drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy); @@ -704,32 +728,42 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } } - ColourSchemeI cs = ColourSchemeProperty.getColour(sequences, - av.alignment.getWidth(), - ColourSchemeProperty.getColourName( - av.getGlobalColourScheme())); + ColourSchemeI cs = null; + + if (av.getGlobalColourScheme() != null) + { + if (av.getGlobalColourScheme() instanceof UserColourScheme) + { + cs = new UserColourScheme( + ( (UserColourScheme) av.getGlobalColourScheme()).getColours()); + + } + else + cs = ColourSchemeProperty.getColour(sequences, + av.alignment.getWidth(), + ColourSchemeProperty.getColourName( + av.getGlobalColourScheme())); + + cs.setThreshold(av.getGlobalColourScheme().getThreshold(), + av.getIgnoreGapsConsensus()); + } + SequenceGroup sg = new SequenceGroup(sequences, "TreeGroup", cs, true, true, false, 0, av.alignment.getWidth()); - if (sg.cs != null) - { - ((ResidueColourScheme) sg.cs).setThreshold(25); - } - if (av.getGlobalColourScheme() instanceof ConservationColourScheme) + if ( av.getGlobalColourScheme()!=null + && av.getGlobalColourScheme().conservationApplied()) { - ConservationColourScheme ccs = (ConservationColourScheme) av.getGlobalColourScheme(); Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, sg.sequences, sg.getStartRes(), sg.getEndRes()); c.calculate(); c.verdict(false, av.ConsPercGaps); - ccs = new ConservationColourScheme(c, ccs.cs); - - sg.cs = ccs; + sg.cs.setConservation(c); } av.alignment.addGroup(sg);